gnu: rust-cargo-c: Update to 0.10.21.

* gnu/packages/rust-apps.scm (rust-cargo-c): Update to 0.10.21.
* gnu/packages/rust-crates.scm (lookup-cargo-inputs): Update entry for
rust-cargo-c.

Change-Id: Id2c5d0cc1568d0787257ad44e1865adac7c9377e

.dir-locals.el

@@ -141,7 +141,6 @@
    (eval . (put 'substitute* 'scheme-indent-function 1))
    (eval . (put 'match-record 'scheme-indent-function 3))
    (eval . (put 'match-record-lambda 'scheme-indent-function 2))
-   (eval . (put 'with-fluids 'scheme-indent-function 2))
 
    ;; TODO: Contribute these to Emacs' scheme-mode.
    (eval . (put 'let-keywords 'scheme-indent-function 3))

.forgejo/pull_request_template.md

@@ -28,13 +28,7 @@ Tick a box by changing it from [ ] to [x].
   - [ ] i586-gnu
 
 - Package **update**
-  - Closure size increase.
+  - Closure size increase after update (`./pre-inst-env guix size PACKAGE`).
-```console
-$ guix size PACKAGE | tail -n1 # before
-total: ...
-$ ./pre-inst-env guix size PACKAGE | tail -n1 # after
-total: ...
-```
   - Build status of direct dependents (`./pre-inst-env guix build -k -P1 PACKAGE ...`):
 ```text
 

.guix-authorizations

@@ -23,8 +23,6 @@
    (name "cbaines"))
   ("3CE4 6455 8A84 FDC6 9DB4  0CFB 090B 1199 3D9A EBB5"
    (name "civodul"))
-  ("838A FE0D 55DC 074E 360F  943A 84B6 9CE6 F3F6 B767"
-   (name "cnx"))
   ("CCB8 1842 F9D7 058E CD67  377A BF5C DF4D F6BF 6682"
    (name "csantosb"))
   ("510A 8628 E2A7 7678 8F8C  709C 4BC0 2592 5FF8 F4D3"

CODEOWNERS

@@ -68,7 +68,6 @@ guix/discovery\.scm                                @guix/core
 guix/docker\.scm                                   @guix/core
 guix/download\.scm                                 @guix/core
 guix/elf\.scm                                      @guix/core
-guix/fossil-download\.scm                          @guix/core
 guix/ftp-client\.scm                               @guix/core
 guix/gexp\.scm                                     @guix/core
 guix/git-authenticate\.scm                         @guix/core
@@ -240,7 +239,6 @@ tests/guix-home\.sh                                @guix/home
 tests/home-import\.scm                             @guix/home
 tests/home-services\.scm                           @guix/home
 
-gnu/packages/fabric-management\.scm                @guix/hpc
 gnu/packages/mpi\.scm                              @guix/hpc
 gnu/packages/oneapi\.scm                           @guix/hpc
 gnu/packages/opencl\.scm                           @guix/hpc
@@ -334,7 +332,6 @@ guix/build-system/rakudo\.scm                      @guix/perl
 guix/import/cpan\.scm                              @guix/perl
 guix/scripts/import/cpan\.scm                      @guix/perl
 
-gnu/packages/aux-files/python/.*\.py$              @guix/python
 gnu/packages/django\.scm                           @guix/python
 gnu/packages/jupyter\.scm                          @guix/python
 gnu/packages/python(-.+|)\.scm$                    @guix/python
@@ -350,6 +347,7 @@ guix/scripts/import/pypi\.scm                      @guix/python
 tests/import/pypi\.scm                             @guix/python
 tests/toml\.scm                                    @guix/python
 
+gnu/ci\.scm                                        @guix/qa-packages
 gnu/packages/benchmark\.scm                        @guix/qa-packages
 gnu/packages/check\.scm                            @guix/qa-packages
 gnu/packages/ci\.scm                               @guix/qa-packages
@@ -486,7 +484,6 @@ gnu/services/version-control\.scm                  @guix/vcs
 gnu/tests/version-control\.scm                     @guix/vcs
 guix/build/bzr\.scm                                @guix/vcs
 guix/build/cvs\.scm                                @guix/vcs
-guix/build/fossil\.scm                             @guix/vcs
 guix/build/git\.scm                                @guix/vcs
 guix/build/hg\.scm                                 @guix/vcs
 guix/build/svn\.scm                                @guix/vcs

Makefile.am

@@ -104,7 +104,6 @@ MODULES =					\
   guix/discovery.scm				\
   guix/android-repo-download.scm		\
   guix/bzr-download.scm            		\
-  guix/fossil-download.scm			\
   guix/git-download.scm				\
   guix/hg-download.scm				\
   guix/hash.scm					\
@@ -237,7 +236,6 @@ MODULES =					\
   guix/build/asdf-build-system.scm		\
   guix/build/bzr.scm				\
   guix/build/copy-build-system.scm		\
-  guix/build/fossil.scm				\
   guix/build/git.scm				\
   guix/build/hg.scm				\
   guix/build/glib-or-gtk-build-system.scm	\
@@ -486,7 +484,6 @@ AUX_FILES =						\
   gnu/packages/aux-files/linux-libre/5.10-x86_64.conf	\
   gnu/packages/aux-files/ovmf/51-edk2-ovmf-2m-raw-x64-nosb.json	\
   gnu/packages/aux-files/pack-audit.c			\
-  gnu/packages/aux-files/python/pytest_guix.py		\
   gnu/packages/aux-files/python/sanity-check.py		\
   gnu/packages/aux-files/python/sitecustomize.py	\
   gnu/packages/aux-files/renpy/renpy.in	\
@@ -805,17 +802,17 @@ EXTRA_DIST +=						\
   etc/manifests/upgrade.scm				\
   scripts/guix.in					\
   tests/cve-sample.json					\
-  tests/keys/openpgp/civodul.pub			\
+  tests/keys/civodul.pub				\
-  tests/keys/openpgp/dsa.pub				\
+  tests/keys/dsa.pub					\
-  tests/keys/openpgp/ed25519-2.pub			\
+  tests/keys/ed25519-2.pub				\
-  tests/keys/openpgp/ed25519-2.sec			\
+  tests/keys/ed25519-2.sec				\
-  tests/keys/openpgp/ed25519-3.pub			\
+  tests/keys/ed25519-3.pub				\
-  tests/keys/openpgp/ed25519-3.sec			\
+  tests/keys/ed25519-3.sec				\
-  tests/keys/openpgp/ed25519.pub			\
+  tests/keys/ed25519.pub				\
-  tests/keys/openpgp/ed25519.sec			\
+  tests/keys/ed25519.sec				\
-  tests/keys/openpgp/rsa.pub				\
+  tests/keys/rsa.pub					\
-  tests/keys/openpgp/signing-key.pub			\
+  tests/keys/signing-key.pub				\
-  tests/keys/openpgp/signing-key.sec			\
+  tests/keys/signing-key.sec				\
   tests/test.drv					\
   $(TESTS)
 

NEWS

@@ -17,11 +17,6 @@ Please send Guix bug reports to bug-guix@gnu.org.
 * Changes in 1.6.0 (since 1.5.0)
 ** Distribution
 *** GNOME updated to version 48
-*** New service for Fossil SCM
-*** TeX Live updated to 2026.1
-
-** Programming interfaces
-*** New (guix fossil-download) module, for fetching Fossil repositories
 
 * Changes in 1.5.0 (since 1.4.0)
 ** Package management

build-aux/test-env.in

@@ -73,8 +73,8 @@ then
 	# Copy the keys so that the secret key has the right permissions (the
 	# daemon errors out when this is not the case.)
 	mkdir -p "$GUIX_CONFIGURATION_DIRECTORY"
-	cp "@abs_top_srcdir@/tests/keys/openpgp/signing-key.sec"	\
+	cp "@abs_top_srcdir@/tests/keys/signing-key.sec"	\
-	   "@abs_top_srcdir@/tests/keys/openpgp/signing-key.pub"	\
+	   "@abs_top_srcdir@/tests/keys/signing-key.pub"	\
 	   "$GUIX_CONFIGURATION_DIRECTORY"
 	chmod 400 "$GUIX_CONFIGURATION_DIRECTORY/signing-key.sec"
     fi

doc/guix.texi

@@ -2658,11 +2658,9 @@ bootloaders.
 
 Once you are done partitioning the target hard disk drive, you have to
 create a file system on the relevant partition(s)@footnote{Currently
-Guix System supports only ext4, btrfs, bcachefs, JFS, F2FS, and XFS
+Guix System only supports ext4, btrfs, JFS, F2FS, and XFS file systems.  In
-file systems.  In particular, code that reads file system UUIDs and
+particular, code that reads file system UUIDs and labels only works for these
-labels works only for these file system types.  For bcachefs, also add
+file system types.}.  For the ESP, if you have one and assuming it is
-the @code{bcachefs-linux-module} to your @code{operating-system}'s
-@code{initrd-modules}.}.  For the ESP, if you have one and assuming it is
 @file{/dev/sda1}, run:
 
 @example
@@ -8737,52 +8735,6 @@ The example below denotes a version of gnu-standards to fetch:
 
 @end deftp
 
-For Fossil repositories, the module @code{(guix fossil-download)} defines
-the @code{fossil-fetch} origin method and @code{fossil-reference} data type
-for support of the Fossil @abbr{SCM, software configuration management} system.
-
-@deffn {Procedure} fossil-fetch ref hash-algo hash [name]
-Return a fixed-output derivation that fetches @var{ref}, a
-@code{<fossil-reference>} object.  The output is expected to have recursive
-hash @var{hash} of type @var{hash-algo} (a symbol).  Use @var{name} as
-the file name, or a generic name if @code{#f}.
-@end deffn
-
-@deftp {Data Type} fossil-reference
-This data type represents a Fossil reference
-for @code{fossil-fetch} to retrieve.
-
-@table @asis
-@item @code{uri} (type: string)
-The URI of a Fossil repository to clone, in one of the following forms,
-in which @code{[...]} denotes optional elements:
-
-@table @code
-@item http[s]://[userid[:password]@@]host[:port][/path]
-A HTTP/HTTPS URL.
-@item [file://]path/to/repo.fossil
-A file URI, where the path must have an extra leading @code{/}
-to use an absolute path (without the URI scheme, the repository
-is opened directly without cloning).
-@end table
-
-@item @code{check-in} (type: string)
-A @url{https://fossil-scm.org/home/doc/trunk/www/checkin_names.wiki,
-name of the check-in} to fetch, e.g.@: its canonical hexadecimal identifier,
-associated tag and/or timestamp.
-@end table
-
-The example below denotes the @code{version-3.51.1} tag
-of the SQLite repository:
-
-@lisp
-(fossil-reference
- (uri "https://sqlite.org/src")
- (check-in "version-3.51.1"))
-@end lisp
-
-@end deftp
-
 @node Defining Package Variants
 @section Defining Package Variants
 
@@ -19194,10 +19146,6 @@ swap file is encrypted because the entire device is encrypted.
 @xref{Swap Space}, or @xref{Preparing for Installation,,Disk
 Partitioning}, for an example.
 
-When using GRUB as the bootloader, the LUKS password is only requested
-once: GRUB passes the master key to the initial RAM disk automatically.
-@xref{Bootloader Configuration, Automatic LUKS Master Key Passing}, for
-details.
 
 @end defvar
 
@@ -27067,32 +27015,6 @@ Deprecated option.
 @end deftp
 
 
-@c %end of fragment
-
-@defvar gardenhostd-service-type
-Type for the service that runs gardenhostd, a partial implementation of
-the systemd-hostnamed daemon.  It provides the org.freedesktop.hostname1
-D-Bus interface, which helps applications like gnome-control-center
-retrieve and modify the system’s hostname, as well as set a pretty
-hostname for display.
-
-The value for this service is a @code{<gardenhostd-configuration>} object.
-@end defvar
-
-@c %start of fragment
-
-@deftp {Data Type} gardenhostd-configuration
-Available @code{gardenhostd-configuration} fields are:
-
-@table @asis
-@item @code{gardenhostd} (default: @code{gardenhostd}) (type: package)
-The gardenhostd package to use.
-
-@end table
-
-@end deftp
-
-
 @c %end of fragment
 
 @defvar accountsservice-service-type
@@ -36639,14 +36561,13 @@ in @code{Nginx}.  It is used to generate cat avatar from a seed, for instance
 the hash of a user's email address.
 
 @deffn {Procedure} cat-avatar-generator-service @
-       [#:cache-dir "/var/cache/cat-avatar-generator/"] @
+       [#:cache-dir "/var/cache/cat-avatar-generator"] @
        [#:package cat-avatar-generator] @
        [#:configuration (nginx-server-configuration)]
 Returns an nginx-server-configuration that inherits @code{configuration}.  It
 extends the nginx configuration to add a server block that serves @code{package},
 a version of cat-avatar-generator.  During execution, cat-avatar-generator will
-be able to use @code{cache-dir} as its cache directory, which must end
+be able to use @code{cache-dir} as its cache directory.
-with a slash, be created manually, and be writable by php-fpm.
 @end deffn
 
 A simple setup for cat-avatar-generator can look like this:
@@ -44322,11 +44243,10 @@ behind a reverse proxy and serve repositories from a custom location.
 (service fossil-service-type
          (fossil-configuration
           (repository "/srv/museum")
-          (list-repositories? #t)
+          (repo-list? #t)
           (base-url "https://museum.example")
-          (compress? #f)
+          (socket-file "/var/run/fossil.sock")
-          (https? #t)
+          (compress? #f)))
-          (socket-file "/var/run/fossil.sock")))
 @end lisp
 
 @deftp {Data Type} fossil-configuration
@@ -48472,10 +48392,9 @@ A string denoting the name service (@pxref{Services in the NSS
 configuration,,, libc, The GNU C Library Reference Manual}).
 
 Note that name services listed here must be visible to nscd.  This is
-achieved by providing the list of packages implementing the needed
+achieved by passing the @code{#:name-services} argument to
-services via the @code{name-services} field of the
+@code{nscd-service} the list of packages providing the needed name
-@code{nscd-configuration} record to be used with the @code{nscd-service-type}
+services (@pxref{Base Services, @code{nscd-service}}).
-service (@pxref{Base Services, @code{nscd-configuration}}).
 
 @item reaction
 An action specified using the @code{lookup-specification} macro
@@ -48918,56 +48837,49 @@ This option in enabled by default.  In some cases involving the
 in RAM, it can be handy to disable the option by setting it to
 @code{#f}.
 
-@subsubheading Automatic LUKS Master Key Passing
-
-When booting from a LUKS-encrypted device using GRUB, the password is
-normally requested twice: once by GRUB to access @file{/boot}, and a
-second time by the initial RAM disk to mount the root file system.
-
-When GRUB's @code{cryptomount} command unlocks a LUKS device, GRUB
-retains the volume's master key in memory.  The @code{cryptodisk}
-module exposes these master keys via a GRUB-internal virtual file
-system called @dfn{procfs}, accessible as @code{(proc)/luks_script}.
-Each line of this virtual file has the form:
-
-@example
-luks_mount @var{uuid} @var{offset} @var{sector-size} @var{cipher-mode-iv} @var{hex-master-key}
-@end example
-
-@noindent
-(or @code{luks2_mount} for LUKS2 volumes).
-
-When the store resides on an encrypted device, the generated GRUB
-configuration automatically injects this virtual file into the initial
-RAM disk using GRUB's @code{newc:} initrd prefix---a documented
-mechanism for synthesizing a CPIO archive on the fly
-(@pxref{GNU/Linux,,, grub, GNU GRUB manual}).  The resulting initrd
-line is equivalent to:
-
-@example
-initrd newc:etc/luks_script:(proc)/luks_script @dots{} /boot/initrd
-@end example
-
-@noindent
-The initial RAM disk then reads @file{/etc/luks_script}, looks up the
-matching UUID, and calls @command{cryptsetup open --volume-key-file} to
-unlock the device without prompting for a password a second time.  If
-the master key is missing or does not match, the system falls back to
-an interactive password prompt, so this mechanism is transparent to the
-user.
-
-No configuration is required: GRUB's @code{procfs} and @code{luks}
-modules are loaded automatically when encrypted devices are declared
-via @code{luks-device-mapping} (@pxref{Mapped Devices}).
-
 @item @code{extra-initrd} (default: @code{#f})
 File name of an additional initrd to load during the boot.  It may or
 may not point to a file in the store, but the main use case is for
 out-of-store files containing secrets.
 
+In order to be able to provide decryption keys for LUKS devices, they
+need to be available in the initial RAM disk.  However they cannot be
+stored inside the usual initrd, since it is stored in the store and
+being world-readable (as files in the store are) is not a desired
+property for an initrd containing decryption keys.  You can therefore
+use this field to instruct GRUB to also load a manually created initrd
+not stored in the store.
+
 For any use case not involving secrets, you should use regular initrd
 (@pxref{operating-system Reference, @code{initrd}}) instead.
 
+Suitable image can be created for example like this:
+
+@example
+echo /key-file.bin | cpio -oH newc >/key-file.cpio
+chmod 0000 /key-file.cpio
+@end example
+
+After it is created, you can use it in this manner:
+
+@lisp
+;; Operating system with encrypted boot partition
+(operating-system
+  @dots{}
+  (bootloader (bootloader-configuration
+               (bootloader grub-efi-bootloader)
+               (targets '("/boot/efi"))
+               ;; Load the initrd with a key file...
+               (extra-initrd "/key-file.cpio")))
+  (mapped-devices
+   (list (mapped-device
+          (source (uuid "12345678-1234-1234-1234-123456789abc"))
+          (target "my-root")
+          (type luks-device-mapping)
+          ;; ... and use it to unlock the root device.
+          (arguments '(#:key-file "/key-file.bin"))))))
+@end lisp
+
 Be careful when using this option, since pointing to a file that is not
 readable by the grub while booting will cause the boot to fail and
 require a manual edit of the initrd line in the grub menu.
@@ -51709,63 +51621,6 @@ phone-number = 0
 is-married = true
 @end example
 
-@subsubsection Serializing to environment variables
-@cindex environment variables, serialization of configuration records
-
-There are services which expect their configuration as environment variables.
-The @code{(gnu services configuration environment-variables)} module provides
-facilities to serialize configuration records from
-@code{(gnu services configuration)} to list of pairs representing environment
-variables.
-
-For example this configuration record:
-
-@lisp
-(define-configuration/no-serialization server
-  (ssh-port
-   (number 22)
-   "The public SSH port of the server.")
-  (fqdn
-   (maybe-string)
-   "The fully qualified domain name of the server.")
-  (active?
-   (boolean #f)
-   "Whether or not the server should be activated."))
-
-(define my-server
- (server
-  (ssh-port 20022)
-  (active? #t)))
-@end lisp
-
-with this call:
-
-@lisp
-(serialize-environment-variables my-server server-fields
-                                 #:true-value "1"
-                                 #:false-value "0")
-@end lisp
-
-would yield:
-
-@lisp
-'(("SSH_PORT" . "20022")
-  ("ACTIVE" . "1"))
-@end lisp
-
-@anchor{serialize-environment-variables-procedure}
-@deffn {Procedure} serialize-environment-variables @var{config} @var{fields} @
-         [@var{selection} #f] [@var{negate?} #f] [#:prefix #f] @
-         [#:true-value "true"] [#:false-value "false"]
-Serializes the fields whose name is included in SELECTION from CONFIG, a
-configuration from @code{(gnu services configuration)}, and FIELDS, the
-list of its field records, to a list of pairs.  When NEGATE? is #t all services
-not included in SELECTION will be serialized.  Each  pair represents an
-environment variable.  The first element of each pair is the variable name, the
-second is the value.  When PREFIX is a string it is prepended to the variable
-name.  TRUE-VALUE and FALSE-VALUE will be used as a representation for
-respectfully @code{#t} and @code{#f}.
-@end deffn
 
 @c *********************************************************************
 @cindex troubleshooting, Guix System

etc/news.scm

@@ -46,8 +46,7 @@
  (entry (commit "a7c8e68dc51144a6d3981b770aca9c4897fc7c0c")
         (title
          (en "Records can refer to inherited values of thunked fields")
-         (de "Vererbung in Verbundsobjekten erlaubt Verweise auf geerbte Werte verzögert ausgewerteter Felder")
+         (de "Vererbung in Verbundsobjekten erlaubt Verweise auf geerbte Werte verzögert ausgewerteter Felder"))
-         (pt "Registros podem referir-se a valores herdados de campos ainda não evaluados (thunks)"))
         (body
          (en "A new feature has been added to records—the facility used when
 defining packages, services, operating systems, and many other things—that,
@@ -115,42 +114,7 @@ Verbundstypen aus, die mit @code{define-record-type*} erstellt wurden:
 und so weiter.
 
 Hinweis: das ist eine inkompatible Änderung. Die neu eingeführte Bindung –
-@code{inputs} im obigen Beispiel – kann gleichnamige Bindungen überschatten.")
+@code{inputs} im obigen Beispiel – kann gleichnamige Bindungen überschatten.")))
-         (pt "Um novo recurso foi adicionado aos registros - a ferramenta
-usada quando se definem pacotes, serviços, sistemas operacionais, e muitas
-outras coisas - que, quando herdados de outro registro, te permitem referir
-aos valores de campos herdados.  Durante a definição de variantes de pacotes,
-você pode encontrar este padrão:
-
-@lisp
-(package
-  (inherit gdb)
-  (inputs (modify-inputs (package-inputs gdb)
-            (delete \"guile\"))))
-@end lisp
-
-Agora isto pode ser escrito desta forma:
-
-@lisp
-(package
-  (inherit gdb)
-  (inputs (modify-inputs inputs ;<- Note a modificação
-            (delete \"guile\"))))
-@end lisp
-
-Dentro do corpo de @code{inputs}, o identificador @code{inputs} agora está
-atrelado ao @dfn{valor herdado} - id est, ap valor que este campo herda de
-@code{gdb}.  O mesmo mecanismo pode ser empregado ao modificar outros campos
-da entrada ou ao campo @code{arguments}.  É menos verboso mas também
-@uref{https://issues.guix.gnu.org/50335, é mais preciso}.
-
-Esta mudança se aplica aos campos \"thunk-ados\" de todos os tipos de registro
-produzidos por @code{define-record-type*}: @code{package}, @code{origin},
-@code{operating-system}, @code{home-environment}, e assim por diante.
-
-Note que esta é uma modificação incompatível: as ligações introduzidas
-recentemente - @code{inputs} no exemplo acima - podem sombrear ligações de
-mesmo nome.")))
 
  (entry (commit "b52ce9041ad58aeababd2d50d3e72bc23dffff60")
         (title

etc/teams.scm

@@ -565,7 +565,6 @@ challenges"))
               "guix/docker.scm"
               "guix/download.scm"
               "guix/elf.scm"
-              "guix/fossil-download.scm"
               "guix/ftp-client.scm"
               "guix/gexp.scm"
               "guix/git-authenticate.scm"
@@ -787,8 +786,7 @@ the haskell-build-system."
   (team 'hpc
         #:name "High-performance computing team"
         #:description "High-performance computing (HPC) related packages."
-        #:scope (list "gnu/packages/fabric-management.scm"
+        #:scope (list "gnu/packages/mpi.scm"
-                      "gnu/packages/mpi.scm"
                       "gnu/packages/oneapi.scm"
                       "gnu/packages/opencl.scm"
                       "gnu/packages/parallel.scm"
@@ -972,8 +970,7 @@ perl-build-system as well as the rakudo-build-system."
         #:description
         "Python, Python packages, the \"pypi\" importer, and the python-build-system."
         #:scope
-        (list (make-regexp* "^gnu/packages/aux-files/python/.*\\.py$")
+        (list "gnu/packages/django.scm"
-              "gnu/packages/django.scm"
               "gnu/packages/jupyter.scm"
               (make-regexp* "^gnu/packages/python(-.+|)\\.scm$")
               "gnu/packages/sphinx.scm"
@@ -994,7 +991,8 @@ perl-build-system as well as the rakudo-build-system."
         #:description
         "Quality assurance software (CI/CD, testing, analysis;
 no direct relation to Guix's QA)."
-        #:scope (list "gnu/packages/benchmark.scm"
+        #:scope (list "gnu/ci.scm"
+                      "gnu/packages/benchmark.scm"
                       "gnu/packages/check.scm"
                       "gnu/packages/ci.scm"
                       "gnu/packages/code.scm"
@@ -1216,7 +1214,6 @@ the \"texlive\" importer."
                       "gnu/tests/version-control.scm"
                       "guix/build/bzr.scm"
                       "guix/build/cvs.scm"
-                      "guix/build/fossil.scm"
                       "guix/build/git.scm"
                       "guix/build/hg.scm"
                       "guix/build/svn.scm")))

etc/teams/hpc/mpi-manifest.scm

@@ -1,44 +0,0 @@
-;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2026 Ludovic Courtès <ludo@gnu.org>
-;;;
-;;; This file is part of GNU Guix.
-;;;
-;;; GNU Guix is free software; you can redistribute it and/or modify it
-;;; under the terms of the GNU General Public License as published by
-;;; the Free Software Foundation; either version 3 of the License, or (at
-;;; your option) any later version.
-;;;
-;;; GNU Guix is distributed in the hope that it will be useful, but
-;;; WITHOUT ANY WARRANTY; without even the implied warranty of
-;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-;;; GNU General Public License for more details.
-;;;
-;;; You should have received a copy of the GNU General Public License
-;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
-
-;; This manifest lists all MPI-related packages: useful for 'guix refresh',
-;; 'guix build', etc.
-
-(use-modules (guix)
-             (gnu packages fabric-management)
-             (gnu packages linux)
-             (gnu packages mpi)
-             (gnu packages parallel))
-
-;; The packages below are what constitutes the MPI stack: helper libraries,
-;; interconnect drivers, and MPI implementations.
-(packages->manifest
- (list cassini-headers
-       cxi-driver
-       hwloc
-       libcxi
-       libfabric
-       mpich
-       openmpi-5
-       openpmix
-       opensm
-       prrte
-       psm
-       psm2
-       rdma-core
-       ucx))

etc/teams/tex/tex-manifest.scm

@@ -26,6 +26,7 @@
 
 (define %sundry-texlive-packages
   (list bibtool
+        dvisvgm
         rubber
         texmaker
         texstudio

gnu/bootloader/grub.scm

@@ -404,10 +404,7 @@ when booting a root file system on a Btrfs subvolume."
               (initrd (normalize-file (menu-entry-initrd entry)
                                       device-mount-point
                                       store-directory-prefix))
-              (extra-initrd (bootloader-configuration-extra-initrd config))
+              (extra-initrd (bootloader-configuration-extra-initrd config)))
-              (luks-script-initrd
-               (and (pair? store-crypto-devices)
-                    "newc:etc/luks_script:(proc)/luks_script")))
           ;; Here DEVICE is the store and DEVICE-MOUNT-POINT is its mount point.
           ;; Use the right file names for LINUX and INITRD in case
           ;; DEVICE-MOUNT-POINT is not "/", meaning that the store is on a
@@ -415,20 +412,14 @@ when booting a root file system on a Btrfs subvolume."
 
           ;; When STORE-DIRECTORY-PREFIX is defined, prepend it the linux and
           ;; initrd paths, to allow booting from a Btrfs subvolume.
-
-          ;; When the store is on an encrypted device, inject GRUB's
-          ;; (proc)/luks_script into the initrd as /etc/luks_script so the
-          ;; initrd can use the already-decrypted master key to open LUKS
-          ;; volumes without prompting for the password a second time.
           #~(format port "menuentry ~s {
   ~a
   linux ~a ~a
-  initrd ~a ~a ~a
+  initrd ~a ~a
 }~%"
                     #$label
                     #$(grub-root-search device linux)
                     #$linux (string-join (list #$@arguments))
-                    (or #$luks-script-initrd "")
                     (or #$extra-initrd "")
                     #$initrd)))
        (multiboot-kernel
@@ -473,7 +464,7 @@ menuentry ~s {
           ;; Other type of devices aren't implemented.
           #~()))
     (let ((devices (map crypto-device->cryptomount store-crypto-devices))
-          (modules #~(format port "insmod procfs~%insmod luks~%insmod luks2~%")))
+          (modules #~(format port "insmod luks~%insmod luks2~%")))
       (if (null? devices)
           devices
           (cons modules devices))))

gnu/build/file-systems.scm

@@ -1,5 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2014-2018, 2020-2022, 2026 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2014-2018, 2020-2022 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2016, 2017 David Craven <david@craven.ch>
 ;;; Copyright © 2017 Mathieu Othacehe <m.othacehe@gmail.com>
 ;;; Copyright © 2019 Guillaume Le Vaillant <glv@posteo.net>
@@ -1455,14 +1455,9 @@ corresponds to the symbols listed in FLAGS."
                (raise c)))
             ((system-error? c)
              (format (current-error-port)
-                     "could not mount partition '~a': ~a~%"
+                     "could not mount partition ~a: ~a~%"
                      (file-system-device fs)
-                     (string-trim-both
+                     (exception-message c))
-                      (call-with-output-string
-                        (lambda (port)
-                          (print-exception port #f
-                                           (exception-kind c)
-                                           (exception-args c))))))
              (unless (file-system-mount-may-fail? fs)
                (raise c))))
       (let* ((type    (file-system-type fs))

gnu/home/services/niri.scm

@@ -19,7 +19,6 @@
 (define-module (gnu home services niri)
   #:use-module (gnu home services)
   #:use-module (gnu home services shepherd)
-  #:use-module (gnu home services desktop)
   #:use-module (gnu packages bash)
   #:use-module (gnu packages freedesktop)
   #:use-module (gnu packages glib)
@@ -41,15 +40,14 @@
 
 (define (home-niri-shepherd-service config)
   "Return a shepherd service that runs Niri, a scrollable tiling Wayland
-compositor.  The service starts Niri with appropriate environment variables
+compositor.  The service starts Niri in a DBus session with appropriate
-set for a Wayland desktop session."
+environment variables set for a Wayland desktop session."
   (list (shepherd-service
           (documentation "Run Niri scrollable tiling Wayland compositor.")
           (provision '(niri))
-          (requirement '(dbus))
           (start #~(make-forkexec-constructor
                     (list #$(file-append bash "/bin/bash") "-l"
-                          "-c" "exec niri --session")
+                          "-c" "exec dbus-run-session niri --session")
                     #:environment-variables
                     (append (list #$@(niri-configuration-environment-variables config))
                             '("DESKTOP_SESSION=niri"
@@ -68,8 +66,6 @@ set for a Wayland desktop session."
    (extensions
     (list (service-extension home-shepherd-service-type
                              home-niri-shepherd-service)
-          (service-extension home-dbus-service-type
-                             (const '()))
           (service-extension home-profile-service-type
                              (lambda (config)
                                (list dbus

gnu/local.mk

@@ -56,7 +56,6 @@
 # Copyright © 2022 Alex Griffin <a@ajgrf.com>
 # Copyright © 2022 ( <paren@disroot.org>
 # Copyright © 2022, 2026 jgart <jgart@dismail.de>
-# Copyright © 2022-2023, 2025-2026 Denis 'GNUtoo' Carikli <GNUtoo@cyberdimension.org>
 # Copyright © 2023-2025 Zheng Junjie <z572@z572.online>
 # Copyright © 2023 Ivana Drazovic <iv.dra@hotmail.com>
 # Copyright © 2023 Andy Tai <atai@atai.org>
@@ -217,7 +216,6 @@ GNU_SYSTEM_MODULES =				\
   %D%/packages/convmv.scm			\
   %D%/packages/codex.scm				\
   %D%/packages/coq.scm				\
-  %D%/packages/coreboot.scm			\
   %D%/packages/cpio.scm				\
   %D%/packages/cpp.scm 				\
   %D%/packages/cppi.scm				\
@@ -425,7 +423,6 @@ GNU_SYSTEM_MODULES =				\
   %D%/packages/kde-utils.scm			\
   %D%/packages/kerberos.scm			\
   %D%/packages/kodi.scm				\
-  %D%/packages/kubernetes.scm	        	\
   %D%/packages/language.scm			\
   %D%/packages/lc0.scm			\
   %D%/packages/lean.scm				\
@@ -740,8 +737,6 @@ GNU_SYSTEM_MODULES =				\
   %D%/services/cgit.scm			\
   %D%/services/ci.scm				\
   %D%/services/configuration.scm		\
-  %D%/services/configuration/environment-variables.scm		\
-  %D%/services/configuration/utils.scm		\
   %D%/services/containers.scm   		\
   %D%/services/cuirass.scm			\
   %D%/services/cups.scm				\
@@ -1039,7 +1034,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/azr3.patch				\
   %D%/packages/patches/azr3-remove-lash.patch			\
   %D%/packages/patches/barony-fix-textures.patch		\
-  %D%/packages/patches/bam-python3-compat.patch		\
   %D%/packages/patches/bash-completion-directories.patch	\
   %D%/packages/patches/bash-linux-pgrp-pipe.patch		\
   %D%/packages/patches/basis-universal-unbundle-libs.patch	\
@@ -1175,7 +1169,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/curlftpfs-fix-memory-leak.patch		\
   %D%/packages/patches/curlftpfs-fix-no_verify_hostname.patch	\
   %D%/packages/patches/cursynth-wave-rand.patch			\
-  %D%/packages/patches/cvc5-reproducible-build.patch		\
   %D%/packages/patches/cvs-CVE-2017-12836.patch		\
   %D%/packages/patches/cyrus-sasl-fix-time-h.patch              \
   %D%/packages/patches/d-feet-drop-unused-meson-argument.patch	\
@@ -1185,7 +1178,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/date-output-pkg-config-files.patch	\
   %D%/packages/patches/dbacl-include-locale.h.patch		\
   %D%/packages/patches/dbacl-icheck-multiple-definitions.patch	\
-  %D%/packages/patches/dblatex-importlib.patch		\
   %D%/packages/patches/dblatex-inkscape-1.0.patch		\
   %D%/packages/patches/dbus-helper-search-path.patch		\
   %D%/packages/patches/ddd-build.patch				\
@@ -1586,9 +1578,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/gtk3-respect-GUIX_GTK3_PATH.patch	\
   %D%/packages/patches/gtk3-respect-GUIX_GTK3_IM_MODULE_FILE.patch \
   %D%/packages/patches/gtk-doc-respect-xml-catalog.patch	\
-  %D%/packages/patches/gtk-doc-mkhtml-test-fix.patch	        \
+  %D%/packages/patches/gtk-doc-mkhtml-test-fix.patch	\
-  %D%/packages/patches/gtk4-demo-reproducible.patch             \
-  %D%/packages/patches/gtk4-needs-udmabuf.patch                 \
   %D%/packages/patches/gtk4-respect-GUIX_GTK4_PATH.patch    	\
   %D%/packages/patches/gtkglext-disable-disable-deprecated.patch \
   %D%/packages/patches/gtksourceview-2-add-default-directory.patch \
@@ -1660,6 +1650,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/inkscape-libxml2.patch		\
   %D%/packages/patches/instead-use-games-path.patch		\
   %D%/packages/patches/intltool-perl-compatibility.patch	\
+  %D%/packages/patches/inetutils-hurd64.patch			\
   %D%/packages/patches/insight-toolkit-fix-build.patch			\
   %D%/packages/patches/irrlicht-use-system-libs.patch		\
   %D%/packages/patches/irrlicht-link-against-needed-libs.patch	\
@@ -1691,6 +1682,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/jfsutils-gcc-compat.patch		\
   %D%/packages/patches/jfsutils-include-systypes.patch		\
   %D%/packages/patches/john-the-ripper-jumbo-with-gcc-11.patch	\
+  %D%/packages/patches/json-c-0.12-CVE-2020-12762.patch		\
   %D%/packages/patches/json-c-0.13-CVE-2020-12762.patch		\
   %D%/packages/patches/jsonnet-include-cstdint-for-gcc-13-builds.patch	\
   %D%/packages/patches/julia-SOURCE_DATE_EPOCH-mtime.patch	\
@@ -1701,7 +1693,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/libcss-check-format.patch		\
   %D%/packages/patches/libeb-gcc-14.patch			\
   %D%/packages/patches/libextractor-tidy-support.patch		\
-  %D%/packages/patches/libfossil-skip-amalgamation.patch	\
   %D%/packages/patches/libftdi-fix-paths-when-FTDIPP-set.patch	\
   %D%/packages/patches/libgeotiff-fix-tests-with-proj-9.1.1.patch	\
   %D%/packages/patches/libgeotiff-fix-tests-with-proj-9.3.0.patch	\
@@ -1763,7 +1754,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/kwin-unwrap-executable-name-for-dot-desktop-search.patch\
   %D%/packages/patches/laby-make-install.patch			\
   %D%/packages/patches/laby-use-tmpdir-from-runtime.patch	\
-  %D%/packages/patches/ldc-i686-int128-alignment.patch 		\
   %D%/packages/patches/ldns-drill-examples.patch		\
   %D%/packages/patches/leela-zero-gtest.patch			\
   %D%/packages/patches/less-hurd-path-max.patch			\
@@ -1817,6 +1807,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/libqalculate-3.8.0-libcurl-ssl-fix.patch	\
   %D%/packages/patches/libquicktime-ffmpeg.patch 		\
   %D%/packages/patches/libsepol-versioned-docbook.patch		\
+  %D%/packages/patches/libskk-fix-invalid-escape.patch		\
   %D%/packages/patches/libsoup-auth-digest-fix-crash.patch      \
   %D%/packages/patches/libsoup-deadlock-in-add_listener_in_thread.patch \
   %D%/packages/patches/libsoup-fix-merge-of-ranges.patch        \
@@ -1984,10 +1975,8 @@ dist_patch_DATA =						\
   %D%/packages/patches/netsurf-y2038-tests.patch		\
   %D%/packages/patches/netsurf-longer-test-timeout.patch	\
   %D%/packages/patches/nhc98-c-update.patch			\
-  %D%/packages/patches/nheko-0-12-1-fix-rendering-replies.patch	\
   %D%/packages/patches/nix-dont-build-html-doc.diff		\
   %D%/packages/patches/nfs4-acl-tools-0.3.7-fixpaths.patch	\
-  %D%/packages/patches/neovim-tree-sitter-grammar-path.patch	\
   %D%/packages/patches/network-manager-plugin-ownership.patch	\
   %D%/packages/patches/network-manager-plugin-path.patch	\
   %D%/packages/patches/newlib-getentropy.patch			\
@@ -2118,12 +2107,10 @@ dist_patch_DATA =						\
   %D%/packages/patches/python-random2-getrandbits-test.patch		\
   %D%/packages/patches/python-pillow-use-zlib-1.3.patch	\
   %D%/packages/patches/python-pydocstyle-add-support-for-pep701.patch	\
-  %D%/packages/patches/python-pynvim-fix-test-command-error.patch	\
   %D%/packages/patches/python-pypytools-python-3-fixes.patch	\
   %D%/packages/patches/python-pyreadstat-link-libiconv.patch	\
   %D%/packages/patches/python-sip-include-dirs.patch	\
   %D%/packages/patches/python-scikit-build-setuptools-compat.patch	\
-  %D%/packages/patches/python-scikit-image-fix-python-pillow.patch	\
   %D%/packages/patches/python-sgmllib3k-assertions.patch	\
   %D%/packages/patches/python-sphobjinv-defer-ssl-import.patch	\
   %D%/packages/patches/python-sphinx-prompt-docutils-0.19.patch	\
@@ -2346,6 +2333,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/rapidcheck-fix-libs.patch		\
   %D%/packages/patches/ratpoison-shell.patch			\
   %D%/packages/patches/retroarch-unbundle-spirv-cross.patch	\
+  %D%/packages/patches/rct-add-missing-headers.patch		\
   %D%/packages/patches/readline-link-ncurses.patch		\
   %D%/packages/patches/renpy-python-3.11-compat.patch			\
   %D%/packages/patches/renpy-fix-integer-slots.patch			\
@@ -2355,6 +2343,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/r-sapa-lapack.patch			\
   %D%/packages/patches/ripperx-missing-file.patch		\
   %D%/packages/patches/rpcbind-CVE-2017-8779.patch		\
+  %D%/packages/patches/rtags-separate-rct.patch			\
   %D%/packages/patches/rtosc-0.3.1-fix-invalid-comparison-operator.patch	\
   %D%/packages/patches/racket-chez-scheme-bin-sh.patch		\
   %D%/packages/patches/racket-launcher-config-dir.patch		\
@@ -2387,12 +2376,12 @@ dist_patch_DATA =						\
   %D%/packages/patches/ruby-flores-fix-deprecations.patch	\
   %D%/packages/patches/ruby-latex-decode-fix-test.patch		\
   %D%/packages/patches/ruby-mustache-1.1.1-fix-race-condition-tests.patch \
+  %D%/packages/patches/ruby-pg-fix-connect-timeout.patch	\
   %D%/packages/patches/ruby-x25519-automatic-fallback-non-x86_64.patch \
   %D%/packages/patches/rust-1.64-fix-riscv64-bootstrap.patch	\
   %D%/packages/patches/rust-1.70-fix-rustix-build.patch	\
   %D%/packages/patches/rust-1.78-unwinding-fix.patch		\
   %D%/packages/patches/rust-1.81-fix-riscv64-bootstrap.patch	\
-  %D%/packages/patches/rust-candle-0.9.1-add-candle-onnx-to-workspace.patch	\
   %D%/packages/patches/rust-codex-0.98.0-core-remove-self-dep.patch	\
   %D%/packages/patches/rust-codex-0.98.0-test-shebangs.patch	\
   %D%/packages/patches/rust-codex-0.98.0-test-timeout.patch	\
@@ -2478,7 +2467,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/t4k-common-libpng16.patch		\
   %D%/packages/patches/tao-add-missing-headers.patch		\
   %D%/packages/patches/tao-fix-parser-types.patch		\
-  %D%/packages/patches/tao-synth-include-string-you-use.patch		\
   %D%/packages/patches/tar-remove-wholesparse-check.patch	\
   %D%/packages/patches/tar-skip-unreliable-tests.patch		\
   %D%/packages/patches/taskwarrior-link-taskchampion-cpp-with-sqlite3.patch \
@@ -2502,6 +2490,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/texmacs-wayland-hidpi.patch	\
   %D%/packages/patches/tflite-micro_disable_download.patch 	\
   %D%/packages/patches/thefuck-test-environ.patch		\
+  %D%/packages/patches/thefuck-remove-broken-tests.patch	\
   %D%/packages/patches/tidy-CVE-2015-5522+5523.patch		\
   %D%/packages/patches/timewarrior-time-sensitive-tests.patch	\
   %D%/packages/patches/tinydir-fix-cbehave-test.patch		\
@@ -2526,11 +2515,10 @@ dist_patch_DATA =						\
   %D%/packages/patches/ultrastar-deluxe-no-freesans.patch		\
   %D%/packages/patches/unity-test-set-subdir-correctly.patch		\
   %D%/packages/patches/unity-test-support-int64.patch		\
-  %D%/packages/patches/ungoogled-chromium-custom-compiler.patch 	\
-  %D%/packages/patches/ungoogled-chromium-empty-parsed-rustc-args.patch	\
   %D%/packages/patches/ungoogled-chromium-extension-search-path.patch	\
   %D%/packages/patches/ungoogled-chromium-RUNPATH.patch		\
   %D%/packages/patches/ungoogled-chromium-system-nspr.patch	\
+  %D%/packages/patches/ungoogled-chromium-unbundle-icu-target.patch     \
   %D%/packages/patches/unknown-horizons-python-3.8-distro.patch	\
   %D%/packages/patches/unknown-horizons-python-3.9.patch	\
   %D%/packages/patches/unknown-horizons-python-3.10.patch	\
@@ -2631,17 +2619,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/yggdrasil-extra-config.patch	\
   %D%/packages/patches/ypsilon-Use-GNU-toolchain-as-default.patch	\
   %D%/packages/patches/zabbix-agent2-test-timezone-fix.patch	\
-  %D%/packages/patches/zed-0.225.10-add-message-notification-action.patch \
-  %D%/packages/patches/zed-0.225.10-add-guix-container-support.patch	\
-  %D%/packages/patches/zed-0.225.10-collapse-multiline-git-deps.patch	\
-  %D%/packages/patches/zed-0.225.10-exclude-libwebrtc-from-audio.patch		\
-  %D%/packages/patches/zed-0.225.10-disable-dlopen.patch	\
-  %D%/packages/patches/zed-0.225.10-fix-sqlite-memory-mode.patch	\
-  %D%/packages/patches/zed-0.225.10-fix-test-db-isolation.patch	\
-  %D%/packages/patches/zed-0.225.10-fix-workspace-race.patch	\
-  %D%/packages/patches/zed-0.225.10-keep-regular-file-workspaces.patch	\
-  %D%/packages/patches/zed-0.225.10-remove-patch-crates-io.patch	\
-  %D%/packages/patches/zed-0.225.10-use-mock-livekit-on-linux.patch	\
   %D%/packages/patches/zig-0.9-build-respect-PKG_CONFIG-env-var.patch	\
   %D%/packages/patches/zig-0.9-fix-runpath.patch		\
   %D%/packages/patches/zig-0.9-riscv-support.patch		\

gnu/packages.scm

@@ -518,9 +518,8 @@ return its return value."
                 (location->string (package-location pkg))))
      (match (package-superseded pkg)
        ((? package? new)
-        (unless (assoc-ref (package-properties pkg) 'supress-supersession-info?)
+        (info (G_ "package '~a' has been superseded by '~a'~%")
-          (info (G_ "package '~a' has been superseded by '~a'~%")
+              (package-name pkg) (package-name new))
-                (package-name pkg) (package-name new)))
         new)
        (#f
         pkg)))

gnu/packages/acl.scm

@@ -37,6 +37,7 @@
   #:use-module (gnu packages)
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system pyproject)
+  #:use-module (guix build-system python)
   #:use-module (guix utils))
 
 (define-public acl

gnu/packages/admin.scm

@@ -109,6 +109,7 @@
   #:use-module (guix build-system go)
   #:use-module (guix build-system meson)
   #:use-module (guix build-system perl)
+  #:use-module (guix build-system python)
   #:use-module (guix build-system pyproject)
   #:use-module (guix build-system qt)
   #:use-module (guix build-system ruby)
@@ -1301,14 +1302,14 @@ re-executing them as necessary.")
 (define-public inetutils
   (package
     (name "inetutils")
-    (version "2.7")
+    (version "2.5")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://gnu/inetutils/inetutils-"
                                   version ".tar.gz"))
               (sha256
                (base32
-                "11n01vsd51r7qraaaylhhx04hq4s6vcq0896zkz0yp1wvqfbwmm1"))))
+                "0q1257ci22g2jbdiqs00mharc1lqkbibdlkhj23f3si6qjxkn17s"))))
     (build-system gnu-build-system)
     (arguments
      (list
@@ -1339,7 +1340,17 @@ re-executing them as necessary.")
                              "\\\""))
       ;; On some systems, 'libls.sh' may fail with an error such as:
       ;; "Failed to tell switch -a apart from -A".
-      #:parallel-tests? #f))
+      #:parallel-tests? #f
+      #:phases (if (target-hurd64?)
+                   #~(modify-phases %standard-phases
+                       (add-after 'unpack 'apply-hurd64-patch
+                         (lambda _
+                           (let ((patch
+                                  #$(local-file
+                                     (search-patch
+                                      "inetutils-hurd64.patch"))))
+                             (invoke "patch" "--force" "-p1" "-i" patch)))))
+                   #~%standard-phases)))
     (inputs
      (list coreutils
            shadow                     ;for login (used in telnetd and rlogind)
@@ -1362,7 +1373,7 @@ hostname.")
 (define-public shadow
   (package
     (name "shadow")
-    (version "4.19.0")
+    (version "4.13")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -1370,7 +1381,7 @@ hostname.")
                     "download/" version "/shadow-" version ".tar.xz"))
               (sha256
                (base32
-                "0crbcfdp7ayyii33srinwd0yr27dkx9mbzglx1d0mvhr1z28xclw"))))
+                "0b6xz415b4y3y5nk3pw9xibv05kln4cjbmhybyncmrx2g5fj9zls"))))
     (build-system gnu-build-system)
     (arguments
      `(;; Assume System V `setpgrp (void)', which is the default on GNU
@@ -1379,9 +1390,7 @@ hostname.")
        '(,@(if (target-hurd?)
              '()
              '("--with-libpam"))
-         "--disable-logind" ;; no systemd
+          "shadow_cv_logdir=/var/log"
-         "--without-libbsd" ;; no libbsd
-         "shadow_cv_logdir=/var/log"
           "ac_cv_func_setpgrp_void=yes")
        #:phases
        (modify-phases %standard-phases
@@ -1417,8 +1426,15 @@ hostname.")
              ;; The top-level Makefile.am wrongfully has "SUBDIRS += man"
              ;; under "if ENABLE_REGENERATE_MAN", even though prebuilt man
              ;; pages are available.  Thus, install them manually.
-             (invoke "make" "-C" "man" "install"))))))
+             (invoke "make" "-C" "man" "install")))
-    (native-inputs (list pkg-config))
+         (add-after 'install-man-pages 'remove-groups
+           (lambda* (#:key outputs #:allow-other-keys)
+             ;; Remove `groups', which is already provided by Coreutils.
+             (let* ((out (assoc-ref outputs "out"))
+                    (bin (string-append out "/bin"))
+                    (man (string-append out "/share/man")))
+               (delete-file (string-append bin "/groups"))
+               (for-each delete-file (find-files man "^groups\\."))))))))
     (inputs
      (append (if (target-hurd?)
                  '()
@@ -3140,7 +3156,7 @@ track changes in important system configuration files.")
 (define-public libcap-ng
   (package
     (name "libcap-ng")
-    (version "0.9.3")
+    (version "0.9")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -3149,20 +3165,12 @@ track changes in important system configuration files.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "13iy7dddcslpmmdhybgvfcgznsvpaa4r3fp9ldlpkq592lw8yyva"))))
+                "0izrrh2kmhi6dcy5iqcccmx90nwlaqcglhc60sl8n5ds8il14pi8"))))
     (build-system gnu-build-system)
     (arguments
-     (list
+     `(#:configure-flags
-      #:configure-flags
+       (list "--disable-static"
-      #~(list "--disable-static"
+             "--without-python")))
-              "--without-python")
-      #:phases
-      #~(modify-phases %standard-phases
-          (add-after 'unpack 'patch-configure-ac
-            (lambda _
-              (substitute* "configure.ac"
-                (("linux/sock_diag.h" all)
-                 (string-append all " \\"))))))))
     (inputs
      (list libbpf))
     (native-inputs
@@ -3916,18 +3924,6 @@ rules is done with the @code{auditctl} utility.")
                 (wrap-program (string-append ndiff "/bin/ndiff")
                   `("GUIX_PYTHONPATH" prefix
                     (,(python-path ndiff)))))))
-          (add-before 'check 'fix-tests-for-python-3.12
-            (lambda _
-              (substitute* "ndiff/ndifftest.py"
-                (("import imp")
-                 "import importlib.util")
-                (("ndiff = imp\\.load_source\\(\"ndiff\", \"ndiff\\.py\"\\)")
-                 (string-join
-                  '("spec = \
-importlib.util.spec_from_file_location(\"ndiff\", \"ndiff.py\")"
-                    "ndiff = importlib.util.module_from_spec(spec)"
-                    "spec.loader.exec_module(ndiff)")
-                  "\n")))))
           ;; These are the tests that do not require network access.
           (replace 'check
             (lambda* (#:key tests? #:allow-other-keys)
@@ -4057,59 +4053,51 @@ plug-in architecture to allow monitoring other system metrics.")
     (license license:gpl2+)))
 
 (define-public thefuck
-  ;; Latest release, 3.32, is not compatible with Python 3.12.
+  (package
-  (let ((revision "0")
+    (name "thefuck")
-        (commit "c7e7e1d884d3bb241ea6448f72a989434c2a35ec"))
+    (version "3.32")
-    (package
+    (source
-      (name "thefuck")
+     (origin
-      (version (git-version "3.32" revision commit))
+       (method git-fetch)
-      (source
+       (uri (git-reference
-       (origin
+             (url "https://github.com/nvbn/thefuck")
-         (method git-fetch)
+             (commit version)))
-         (uri (git-reference
+       (file-name (git-file-name name version))
-                (url "https://github.com/nvbn/thefuck")
+       (sha256
-                (commit commit)))
+        (base32 "18ipa1bm6q1n5drbi8i65726hhqhl1g41390lfqrc11hkbvv443d"))
-         (file-name (git-file-name name version))
+       (patches (search-patches "thefuck-test-environ.patch"
-         (sha256
+                                "thefuck-remove-broken-tests.patch"))))
-          (base32 "1l3i2cpdf3vznpbzqw7b18l23xikqs7andx6yzqvm5415snaqg06"))
+    (build-system pyproject-build-system)
-         (patches (search-patches "thefuck-test-environ.patch"))))
+    (arguments
-      (build-system pyproject-build-system)
+     (list
-      (arguments
+      #:phases
-       (list
+      #~(modify-phases %standard-phases
-        #:test-flags
+          (add-before 'check 'pre-check
-        #~(list
+            (lambda _
-           "--deselect=tests/test_utils.py::TestGetValidHistoryWithoutCurrent"
+              ;; Tests look for installed package
-           "--ignore=tests/functional/conftest.py")
+              ;; Some tests need write access to $HOME.
-        #:phases
+              (setenv "HOME" "/tmp")
-        #~(modify-phases %standard-phases
+              ;; Even with that, this function tries to mkdir /.config.
-            (add-before 'check 'pre-check
+              (substitute* "tests/test_utils.py"
-              (lambda _
+                (("settings\\.init\\(\\)") "")))))))
-                ;; ModuleNotFoundError: No module named 'pytest_docker_pexpect'
+    (native-inputs
-                (delete-file "tests/functional/conftest.py")
+     (list go
-                ;; Tests look for installed package
+           python-mock
-                ;; Some tests need write access to $HOME.
+           python-pytest-8
-                (setenv "HOME" "/tmp")
+           python-pytest-mock
-                ;; Even with that, this function tries to mkdir /.config.
+           python-setuptools
-                (substitute* "tests/test_utils.py"
+           python-wheel))
-                  (("settings\\.init\\(\\)") "")))))))
+    (inputs
-      (native-inputs
+     (list python-colorama
-       (list go
+           python-decorator
-             python-mock
+           python-psutil
-             ;; Uses test markers that are incompatible with pytest 9.
+           python-pyte))
-             python-pytest-8
+    (home-page "https://github.com/nvbn/thefuck")
-             python-pytest-mock
+    (synopsis "Correct mistyped console command")
-             python-setuptools))
+    (description
-      (inputs
+     "The Fuck tries to match a rule for a previous, mistyped command, creates
-       (list python-colorama
-             python-decorator
-             python-psutil
-             python-pyte))
-      (home-page "https://github.com/nvbn/thefuck")
-      (synopsis "Correct mistyped console command")
-      (description
-       "The Fuck tries to match a rule for a previous, mistyped command, creates
 a new command using the matched rule, and runs it.")
-      (license license:x11))))
+    (license license:x11)))
 
 (define-public di
   (package
@@ -5000,16 +4988,16 @@ Python loading in HPC environments.")
   (let ((real-name "inxi"))
     (package
       (name "inxi-minimal")
-      (version "3.3.40-1")
+      (version "3.3.31-2")
       (source
        (origin
          (method git-fetch)
          (uri (git-reference
-               (url "https://codeberg.org/smxi/inxi")
+               (url "https://github.com/smxi/inxi")
                (commit version)))
          (file-name (git-file-name real-name version))
          (sha256
-          (base32 "0ivj0dcx7d2hmmkhyql156sb08385rzw640z9kyq4cv1n8ndz58s"))))
+          (base32 "1fca5minalpmizbxh5kmjiv8xrl7k6g91zn8d84fxmbhsk8vn3kk"))))
       (build-system trivial-build-system)
       (inputs
        (list bash-minimal
@@ -5035,8 +5023,8 @@ Python loading in HPC environments.")
            (copy-recursively (assoc-ref %build-inputs "source")
                              ,(string-append real-name "-" version))
            (with-directory-excursion ,(string-append real-name "-" version)
-             (patch-shebang "inxi" (list (dirname (search-input-file
+             (with-fluids ((%default-port-encoding #f))
-                                                    %build-inputs "bin/perl"))))
+               (substitute* "inxi" (("/usr/bin/env perl") (which "perl"))))
              (let ((bin (string-append %output "/bin")))
                (install-file "inxi" bin)
                (wrap-program (string-append bin "/inxi")
@@ -5051,8 +5039,7 @@ Python loading in HPC environments.")
                                    ((member name '("util-linux"))
                                     (string-append (store-append "/bin") ":"
                                                    (store-append "/sbin")))
-                                   ((member name '("dmidecode" "iproute2" "lvm2"
+                                   ((member name '("dmidecode" "iproute2"))
-                                                   "mdadm"))
                                     (store-append "/sbin"))
                                    (else (store-append "/bin")))))))
                            %build-inputs)))
@@ -5080,7 +5067,6 @@ support forum.  It runs with the @code{/exec} command in most IRC clients.")
     (name "inxi")
     (inputs
      `(("dmidecode" ,dmidecode)
-       ("eudev" ,eudev)
        ("file" ,file)
        ("bind:utils" ,isc-bind "utils") ; dig
        ("gzip" ,gzip)
@@ -5106,14 +5092,11 @@ support forum.  It runs with the @code{/exec} command in most IRC clients.")
        ("perl-time-hires" ,perl-time-hires)
        ("lvm2" ,lvm2)                   ; lvs
        ("mdadm" ,mdadm)
-       ("wayland-utils" ,wayland-utils)
        ;; TODO: Add more inputs:
        ;; ipmi-sensors
        ;; hddtemp
        ;; perl-xml-dumper
        ;; ipmitool
-       ;; wlr-randr
-       ;; vulkan-tools
        ,@(package-inputs inxi-minimal)))))
 
 (define-public pscircle
@@ -5619,61 +5602,69 @@ representation to stdout.")
 (define-public hosts
   (package
     (name "hosts")
-    (version "3.6.5")
+    (version "3.6.3")
-    (source
+    (source (origin
-     (origin
+              (method git-fetch)
-       (method git-fetch)
+              (uri (git-reference
-       (uri (git-reference
+                    (url "https://github.com/xwmx/hosts")
-              (url "https://github.com/xwmx/hosts")
+                    (commit version)))
-              (commit version)))
+              (file-name (git-file-name name version))
-       (file-name (git-file-name name version))
+              (sha256
-       (sha256
+               (base32
-        (base32 "1kzd4lxlflam87dhbx1jx7bj6v6sa4f2024mfxj2768kp9qapraj"))))
+                "1ni4z89kxzgwm26hhx908g04f2h0fypy7lgfa0rvsz8d0wslgcsn"))))
-    (build-system copy-build-system)
+    (build-system trivial-build-system)
-    (native-inputs
-     (list bats)) ;for tests
     (inputs
-     (list gawk
+     `(("bats" ,bats) ;for test
-           bash-minimal
+       ("awk" ,gawk)
-           coreutils
+       ("bash" ,bash)
-           diffutils
+       ("coreutils" ,coreutils)
-           grep
+       ("diffutils" ,diffutils)
-           ncurses ;for tput
+       ("grep" ,grep)
-           sed))
+       ("ncurses" ,ncurses) ;tput
+       ("sed" ,sed)))
     (arguments
-     (list
+     `(#:modules ((guix build utils))
-      #:install-plan
+       #:builder
-      #~'(("hosts" "bin/hosts")
+       (begin
-          ("etc/hosts-completion.bash" "/etc/bash_completion.d/hosts")
+         (use-modules (guix build utils))
-          ("etc/hosts-completion.zsh" "/share/zsh/site-functions/_hosts")
+         ;; copy source
-          ("README.md"
+         (copy-recursively (assoc-ref %build-inputs "source") ".")
-           #$(string-append "/share/doc/" name "-" version "/README.md")))
+         ;; patch-shebang phase
-      #:phases
+         (setenv "PATH"
-      #~(modify-phases %standard-phases
+                 (string-append (assoc-ref %build-inputs "bash") "/bin"
-          (add-after 'unpack 'patch-hosts
+                                ":" (assoc-ref %build-inputs "awk") "/bin"
-            (lambda* (#:key inputs #:allow-other-keys)
+                                ":" (assoc-ref %build-inputs "coreutils") "/bin"
-              (substitute* "test/test_helper.bash"
+                                ":" (assoc-ref %build-inputs "diffutils") "/bin"
-                (("export _HOSTS=.*")
+                                ":" (assoc-ref %build-inputs "grep") "/bin"
-                 (string-append "export _HOSTS=" #$output "/bin/hosts")))
+                                ":" (assoc-ref %build-inputs "ncurses") "/bin"
-              (substitute* (cons* "hosts"
+                                ":" (assoc-ref %build-inputs "sed") "/bin"
-                            ;; *.bash and *.bats.
+                                ":" "/run/privileged/bin"
-                            (find-files "test" "\\.bat?sh?.*$"))
+                                ":" (getenv "PATH")))
-                (("\\btput\\b") (search-input-file inputs "bin/tput"))
+         (substitute* "hosts"
-                (("\\bsed\\b") (search-input-file inputs "bin/sed"))
+           (("#!/usr/bin/env bash")
-                (("\\bawk\\b") (search-input-file inputs "bin/awk"))
+            (string-append "#!" (which "bash")
-                (("\\bgrep\\b") (search-input-file inputs "bin/grep"))
+                           "\nPATH=" (getenv "PATH"))))
-                (("\\bdiff\\b") (search-input-file inputs "bin/diff"))
+         ;; check phase
-                (("\\bcp\\b") (search-input-file inputs "bin/cp"))
+         (setenv "TERM" "linux") ;set to tty for test
-                (("\\bchmod\\b") (search-input-file inputs "bin/chmod")))))
+         (invoke (search-input-file %build-inputs "/bin/bats")
-          (add-after 'install 'check
+                 "test")
-            (lambda* (#:key tests? inputs #:allow-other-keys)
+         ;; install phase
-              (if tests?
+         (install-file "hosts" (string-append %output "/bin"))
-                  (begin
+         (let ((bash-completion
-                    (delete-file "hosts") ;Ensure installed hosts is checked.
+                (string-append %output "/etc/bash_completion.d")))
-                    (setenv "PATH" "") ;Ensure substitutions were correct.
+           (mkdir-p bash-completion)
-                    (setenv "TERM" "linux") ;Set to tty for test.
+           (copy-file "etc/hosts-completion.bash"
-                    (invoke (search-input-file inputs "/bin/bats")
+                      (string-append bash-completion "/hosts")))
-                            "test"))))))))
+         (let ((zsh-completion
+                (string-append %output "/share/zsh/site-functions")))
+           (mkdir-p zsh-completion)
+           (copy-file "etc/hosts-completion.zsh"
+                      (string-append zsh-completion "/_hosts")))
+         (let ((doc (string-append %output "/share/doc/" ,name "-" ,version)))
+           (mkdir-p doc)
+           (install-file "LICENSE" doc)
+           (install-file "README.md" doc))
+         #t)))
     (home-page "https://github.com/xwmx/hosts/")
     (synopsis "Script for editing a foreign distro's @file{/etc/hosts} file")
     (description "Hosts is a command line program for managing

gnu/packages/adns.scm

@@ -1,5 +1,9 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2026 Anderson Torres <anderson.torres.8519@gmail.com>
+;;; Copyright © 2014 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2015, 2016, 2018, 2020 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2018 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2019, 2021 Marius Bakke <marius@gnu.org>
+;;; Copyright © 2023 Janneke Nieuwenhuizen <janneke@gnu.org>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -17,20 +21,160 @@
 ;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
 
 (define-module (gnu packages adns)
-  #:use-module (gnu packages dns)
+  #:use-module (guix gexp)
-  #:use-module (guix deprecation))
+  #:use-module (guix licenses)
+  #:use-module (guix packages)
+  #:use-module (guix download)
+  #:use-module (guix utils)
+  #:use-module (guix build-system cmake)
+  #:use-module (guix build-system gnu)
+  #:use-module (gnu packages m4)
+  #:use-module (gnu packages pkg-config))
 
-(define-deprecated/public-alias adns
+(define-public adns
-  (@ (gnu packages dns) adns))
+  (package
+    (name "adns")
+    (version "1.6.1")
+    (source (origin
+              (method url-fetch)
+              (uri (list (string-append "mirror://gnu/adns/adns-"
+                                        version ".tar.gz")
+                         (string-append
+                           "https://www.chiark.greenend.org.uk/~ian/adns/ftp/adns-"
+                           version ".tar.gz")))
+              (sha256
+               (base32
+                "1k81sjf0yzv6xj35vcxp0ccajxrhhmyly7a57xlbs1kmkdwb6f3i"))))
+    (build-system gnu-build-system)
+    (arguments
+     ;; Make sure the programs under bin/ fine libadns.so.
+     '(#:configure-flags (list (string-append "LDFLAGS=-Wl,-rpath -Wl,"
+                                              (assoc-ref %outputs "out")
+                                              "/lib"))
 
-(define-deprecated/public-alias c-ares
+       ;; XXX: Tests expect real name resolution to work.
-  (@ (gnu packages dns) c-ares))
+       #:tests? #f))
+    (native-inputs
+     (list m4))
+    (home-page "https://www.gnu.org/software/adns/")
+    (synopsis "Asynchronous DNS client library and utilities")
+    (description
+     "GNU adns is a C library that provides easy-to-use DNS resolution
+functionality.  The library is asynchronous, allowing several concurrent
+calls.  The package also includes several command-line utilities for use in
+scripts.")
+    (license gpl3+)))
 
-(define-deprecated/public-alias c-ares-for-node-lts
+(define-public c-ares
-  (@ (gnu packages dns) c-ares-for-node-lts))
+  (package
+    (name "c-ares")
+    (version "1.34.4")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append
+                    "https://github.com/c-ares/c-ares/releases/download/v"
+                    version "/" name "-" version ".tar.gz"))
+              (sha256
+               (base32
+                "0br2msk3bpl5myhjp9vr5j2scpspvbg2fpnz69dcrr4ycpnxnf7s"))))
+    (build-system gnu-build-system)
+    (arguments
+     (list
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-before 'check 'filter-live-tests
+            (lambda _
+              ;; Filter tests that require internet access.
+              (setenv "GTEST_FILTER" "-*.Live*:*.FamilyV4*")))
+          #$@(if (system-hurd?)
+                 #~((add-after 'unpack 'skip-tests
+                      (lambda _
+                        (substitute* "test/ares-test-main.cc"
+                          (("(^| )main *\\(.*" all)
+                           (string-append all "  exit (77);\n")))))
+                    (add-after 'filter-live-tests 'filter-hurd-tests
+                      (lambda _
+                        (setenv "GTEST_FILTER"
+                                (string-append
+                                 (getenv "GTEST_FILTER")
+                                 ":.*Basic/2"
+                                 ":.*CancelImmediate/2"
+                                 ":.*CancelImmediateGetHostByAddr/2"
+                                 ":.*CancelLater/1"
+                                 ":.*FamilyUnspecified/2"
+                                 ":.*FamilyV6/2"
+                                 ":.*GetAddrInfoParallelLookups/1"
+                                 ":.*GetHostByAddrDestroy/2"
+                                 ":.*GetHostByNameCNAMENoData/2"
+                                 ":.*GetHostByNameDestroyAbsolute/2"
+                                 ":.*GetHostByNameDestroyRelative/2"
+                                 ":.*GetHostByNameParallelLookups/1"
+                                 ":.*HostAlias/2"
+                                 ":.*HostAliasMissing/2"
+                                 ":.*HostAliasMissingFile/2"
+                                 ":.*NotImplResponse/2"
+                                 ":.*RefusedResponse/2"
+                                 ":.*Resend/1"
+                                 ":.*RetryWithoutEDNS/2"
+                                 ":.*SearchDomains/2"
+                                 ":.*SearchDomainsBare/2"
+                                 ":.*SearchDomainsServFailOnAAAA/2"
+                                 ":.*SearchDomainsWithResentReply/1"
+                                 ":.*SearchHighNdots/2"
+                                 ":.*SearchNoDataThenFail/2"
+                                 ":.*SearchNoDataThenNoDataBare/2"
+                                 ":.*SearchNoDataThenSuccess/2"
+                                 ":.*ServFailResponse/2"
+                                 ":.*SimpleQuery/2"
+                                 ":.*SockCallback/2"
+                                 ":.*SockConfigureCallback/2"
+                                 ":.*SortListV4/2"
+                                 ":.*SortListV6/2"
+                                 ":.*ThirdServer/2"
+                                 ":.*TruncationRetry/1"
+                                 ":.*UnspecifiedFamilyCname6A4/2"
+                                 ":.*UnspecifiedFamilyV4/2"
+                                 ":.*UnspecifiedFamilyV6/2")))))
+                 #~()))))
+    (native-inputs
+     (list pkg-config))
+    (home-page "https://c-ares.haxx.se/")
+    (synopsis "C library for asynchronous DNS requests")
+    (description
+     "C-ares is a C library that performs DNS requests and name resolution
+asynchronously.  It is intended for applications which need to perform DNS
+queries without blocking, or need to perform multiple DNS queries in parallel.
+The primary examples of such applications are servers which communicate with
+multiple clients and programs with graphical user interfaces.")
+    (license (x11-style "https://c-ares.haxx.se/license.html"))))
 
-(define-deprecated/public-alias c-ares-for-node-bootstrap
+(define-public c-ares-for-node-lts
-  (@ (gnu packages dns) c-ares-for-node-bootstrap))
+  (hidden-package c-ares))
 
-(define-deprecated/public-alias c-ares/cmake
+(define-public c-ares-for-node-bootstrap
-  (@ (gnu packages dns) c-ares/cmake))
+  (hidden-package
+   (package
+     (inherit c-ares)
+     (version "1.18.1")
+     (source (origin
+               (method url-fetch)
+               (uri (string-append
+                     "https://c-ares.haxx.se/download/c-ares-" version
+                     ".tar.gz"))
+               (sha256
+                (base32
+                 "1kxviskwsaa7dcgscvssxa8ps88pdq7kq4z93gxvz7sam2l54z8s")))))))
+
+;; gRPC requires a c-ares built with CMake in order to get the .cmake modules.
+;; We can not build c-ares itself with CMake because that would introduce a
+;; circular dependency through nghttp2.
+;; XXX: It would be nice if we could extract the modules somehow and make them
+;; work with the "normal" c-ares package instead of building a whole new library.
+(define-public c-ares/cmake
+  (hidden-package
+   (package
+     (inherit c-ares)
+     (build-system cmake-build-system)
+     (arguments
+      `(;; XXX: Tests require name resolution (the normal variant runs no tests).
+        #:tests? #f)))))

gnu/packages/aidc.scm

@@ -370,7 +370,7 @@ This package includes the following programs:
            libjpeg-turbo
            perl
            python
-           v4l-utils))
+           v4l-utils-minimal))
     (propagated-inputs
      ;; These are in 'requires' field of .pc files.
      (list glib gtk+))

gnu/packages/algebra.scm

@@ -1,7 +1,7 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2012, 2013, 2014, 2015, 2016, 2017, 2018, 2019, 2022, 2023, 2024, 2025 Andreas Enge <andreas@enge.fr>
 ;;; Copyright © 2013, 2015, 2017, 2018, 2021 Ludovic Courtès <ludo@gnu.org>
-;;; Copyright © 2016-2026 Nicolas Goaziou <mail@nicolasgoaziou.fr>
+;;; Copyright © 2016-2025 Nicolas Goaziou <mail@nicolasgoaziou.fr>
 ;;; Copyright © 2014, 2018 Mark H Weaver <mhw@netris.org>
 ;;; Copyright © 2016, 2018, 2019, 2021, 2023 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2017, 2020-2022 Efraim Flashner <efraim@flashner.co.il>
@@ -88,6 +88,7 @@
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system cmake)
   #:use-module (guix build-system pyproject)
+  #:use-module ((guix build-system python) #:select (pypi-uri))
   #:use-module (guix build-system r)
   #:use-module (guix download)
   #:use-module (guix gexp)
@@ -405,7 +406,7 @@ precision.")
 (define-public giac
   (package
     (name "giac")
-    (version "2.0.0-21")
+    (version "2.0.0-10")
     (source
      (origin
        (method url-fetch)
@@ -417,7 +418,7 @@ precision.")
               "https://www-fourier.ujf-grenoble.fr/~parisse/debian/dists/"
               "stable/main/source/giac_" version ".tar.gz"))
        (sha256
-        (base32 "1j6bip76hhqvycapf7xy26y0b8g5zzx4gwkfsr7bf6m2h71a2zry"))))
+        (base32 "1lzb0jjmkg5ml1qfl0m00qqng4sxgfqwrbq10gpkp4b301k2ckv1"))))
     (build-system gnu-build-system)
     (arguments
      (list

gnu/packages/android.scm

@@ -41,6 +41,7 @@
   #:use-module (guix build-system emacs)
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system go)
+  #:use-module (guix build-system python)
   #:use-module (guix build-system pyproject)
   #:use-module (guix build-system qt)
   #:use-module (guix build-system trivial)
@@ -764,7 +765,7 @@ file system.")
        (sha256
         (base32 "0r3xwk8xsfxvmxyw3d57sy2i9by24g0l1jl40735jiac9mypcg7n"))))
     (build-system pyproject-build-system)
-    (propagated-inputs (list python-requests python-argcomplete python-urllib3
+    (inputs (list python-requests python-argcomplete python-urllib3
                   python-looseversion gnupg))
     (native-inputs (list python-setuptools python-wheel python-requests-cache
                          python-defusedxml))
@@ -772,7 +773,8 @@ file system.")
      (list $SSL_CERT_FILE))
     (arguments
      (list
-      #:test-backend #~'unittest
+      #:test-flags
+      #~(list "-k" "test_*")
       #:phases
       #~(modify-phases %standard-phases
           (add-after 'unpack 'patch-tests
@@ -791,7 +793,11 @@ file system.")
             (lambda _
               (substitute* "sdkmanager.py"
                 (("gpgv")
-                 (string-append #$(this-package-input "gnupg") "/bin/gpgv"))))))))
+                 (string-append #$(this-package-input "gnupg") "/bin/gpgv")))))
+          (replace 'check
+            (lambda* (#:key tests? test-flags #:allow-other-keys)
+              (when tests?
+                (apply invoke "python" "-m" "unittest" test-flags)))))))
     (home-page "https://gitlab.com/fdroid/sdkmanager")
     (synopsis "Replacement for Android sdkmanager written in Python")
     (description
@@ -1176,16 +1182,14 @@ for communicating with Xiaomi smart appliances over miIO and MIoT protocols.")
 (define-public fdroidserver
   (package
     (name "fdroidserver")
-    (version "2.4.3")
+    (version "2.4.2")
     (source
      (origin
-       (method git-fetch)
+       (method url-fetch)
-       (uri (git-reference
+       (uri (pypi-uri "fdroidserver" version))
-              (url "https://gitlab.com/fdroid/fdroidserver")
-              (commit version)))
-       (file-name (git-file-name name version))
        (sha256
-        (base32 "1745fqxr2qfrls4wr6x9w1262b9pxmw9yvzd9b71ya2qmj74q17n"))))
+        (base32
+         "06xybginrwi5c7bw000wz5s5hzi0aqrxskzwh8qc6wv463w2djax"))))
     (build-system pyproject-build-system)
     (arguments
      (list
@@ -1196,17 +1200,22 @@ for communicating with Xiaomi smart appliances over miIO and MIoT protocols.")
             (lambda _
               (setenv "HOME" "/tmp"))))))
     (propagated-inputs
-     (list python-platformdirs
+     (list python-androguard
-           python-androguard
            python-apache-libcloud
+           python-argcomplete
            python-asn1crypto
            python-clint
            python-defusedxml
+           python-docker
            python-gitpython
+           python-mwclient
            python-oscrypto
            python-paramiko
            python-pillow
+           python-platformdirs
            python-puremagic
+           python-pyasn1
+           python-pyasn1-modules
            python-pyyaml
            python-qrcode
            python-requests
@@ -1378,7 +1387,6 @@ mounted via FUSE.")
        (uri (git-reference
              (url "https://github.com/anestisb/android-simg2img")
              (commit version)))
-       (file-name (git-file-name name version))
        (sha256
         (base32
          "0drwvqxbhajka580j93z8ldckhjlpr0i84nh20krdpxcp54xvldh"))))

gnu/packages/anthy.scm

@@ -33,8 +33,9 @@
        ;; The URI does not appear to be easily guessable.  For
        ;; example, you cannot download version "9100g" simply
        ;; by replacing "9100h" in the URI.
-       (uri (string-append "https://ftp.jaist.ac.jp/pub/Linux/Gentoo/"
+       (uri (list (string-append "https://ftp.jaist.ac.jp/pub/Linux/Gentoo/"
-                           "distfiles/31/anthy-9100h.tar.gz"))
+                                 "distfiles/31/anthy-9100h.tar.gz")
+                  "https://osdn.dl.osdn.net/anthy/37536/anthy-9100h.tar.gz"))
        (sha256
         (base32 "0ism4zibcsa5nl77wwi12vdsfjys3waxcphn1p5s7d0qy1sz0mnj"))))
     (build-system gnu-build-system)

gnu/packages/apl.scm

@@ -30,26 +30,20 @@
   #:use-module (guix packages)
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system trivial)
-  #:use-module (gnu packages algebra)
-  #:use-module (gnu packages base)
   #:use-module (gnu packages bash)
   #:use-module (gnu packages compression)
   #:use-module (gnu packages gettext)
-  #:use-module (gnu packages gtk)
-  #:use-module (gnu packages image)
   #:use-module (gnu packages java)
   #:use-module (gnu packages maths)
   #:use-module (gnu packages pcre)
-  #:use-module (gnu packages pkg-config)
   #:use-module (gnu packages readline)
-  #:use-module (gnu packages sqlite)
+  #:use-module (gnu packages sqlite))
-  #:use-module (gnu packages xorg))
 
 (define-public apl
-  (let ((revision 1977))
+  (let ((revision 1550))
     (package
       (name "apl")
-      (version (string-append "2.0.1-r" (number->string revision)))
+      (version (string-append "1.8-r" (number->string revision)))
       (source
        (origin
          (method svn-fetch)
@@ -58,18 +52,12 @@
                (revision revision)))
          (file-name (git-file-name name version))
          (sha256
-          (base32 "1llm1hqpfd71jrhd4pizhmvvca5wr18v8zqfajwmvjjxcmzfkvv1"))))
+          (base32 "1bgc3a09f35zrqq2irhm1hspppnxjqas0fmcw14hkc7910br9ip3"))))
       (build-system gnu-build-system)
       (home-page "https://www.gnu.org/software/apl/")
-      (native-inputs (list gettext-minimal which pkg-config))
       (inputs
        (list gettext-minimal
-             libxcb
-             fftw
              openblas
-             gsl
-             libpng
-             gtk+
              pcre2
              readline
              sqlite))
@@ -81,11 +69,15 @@
              #~(modify-phases %standard-phases
                  (add-before 'configure 'fix-configure
                    (lambda _
-                     (substitute* "configure"
+                     (substitute* "buildtag.sh"
-                       ;; Manually set the SVN revision, since the directory
+                       ;; Don't exit on failed SVN-related calls.
-                       ;; is unversioned and we know it anyway.
+                       (("^ +return 0\n") "")
-                       (("\\$apl_ARCHIVE_SVNINFO")
+                       ;; Manually set the SVN revision, since the directory is
-                        #$(number->string revision))))))))
+                       ;; unversioned and we know it anyway.
+                       (("^SVNINFO=.*")
+                        (string-append "SVNINFO=" #$(number->string revision) "\n"))
+                       ;; Requires running ‘svn info’ on a versioned directory.
+                       (("\\\\\"\\$ARCHIVE_SVNINFO\\\\\"") "\\\"\\\"")))))))
       (synopsis "APL interpreter")
       (description
        "GNU APL is a free interpreter for the programming language APL.  It is

gnu/packages/appimage.scm

@@ -19,11 +19,9 @@
 (define-module (gnu packages appimage)
   #:use-module ((guix licenses) #:prefix license:)
   #:use-module (gnu packages base)
-  #:use-module (gnu packages c)
   #:use-module (gnu packages compression)
   #:use-module (gnu packages file-systems)
   #:use-module (gnu packages linux)
-  #:use-module (gnu packages pkg-config)
   #:use-module (gnu packages)
   #:use-module (guix build-system gnu)
   #:use-module (guix gexp)
@@ -32,9 +30,9 @@
   #:use-module (guix utils))
 
 (define-public appimage-type2-runtime
-  (let ((revision "1")
+  (let ((revision "0")
         ;; No releases, just the latest commit.
-        (commit "caf24f9f712084686bfc24a70b75e50df0aefb9c"))
+        (commit "47b665594856b4e8928f8932adcf6d13061d8c30"))
     (package
       (name "appimage-type2-runtime")
       (version (git-version "continuous" revision commit))
@@ -46,16 +44,16 @@
                 (commit commit)))
          (file-name (git-file-name name version))
          (sha256
-          (base32 "17z0byws3dp375wcyq5xwy5npqy7hslqw21n677dp38z4f940nzv"))))
+          (base32 "0954crhlbapxis96g1s0vfpf78ybr64zvjalak387ksxj560g44x"))))
       (build-system gnu-build-system)
       (arguments
        (list
         #:tests? #f                     ; No tests
         #:make-flags
-        #~(list "-Csrc/runtime" "runtime"
+        #~(list "-Csrc/runtime" "runtime-fuse3"
                 (string-append "CC=" #$(cc-for-target))
                 (string-append
-                 "CFLAGS=" "-I" #$(this-package-input "fuse") "/include/fuse3/"
+                 "CFLAGS=" "-I" #$(this-package-input "fuse") "/include/fuse/"
                  " -DGIT_COMMIT='\"" "guix-" #$version "\"'"
                  " -D_FILE_OFFSET_BITS=64"
                  " -static"
@@ -66,22 +64,17 @@
           (ice-9 binary-ports))
         #:phases
         #~(modify-phases %standard-phases
-            (add-after 'unpack 'use-pkgconfig-flags
-              (lambda _
-                (substitute* "src/runtime/Makefile"
-                  (("-lmimalloc")
-                   "$(pkg-config --cflags mimalloc)"))))
             (delete 'configure)
             (replace 'install
               (lambda _
-                (install-file "src/runtime/runtime"
+                (install-file "src/runtime/runtime-fuse3"
                               (string-append #$output "/bin"))))
             ;; Must be after all elf reliant phases.  Used to identify the
             ;; executable as an AppImage as per the specification.
             (add-after 'make-dynamic-linker-cache 'set-magic-bytes
               (lambda _
                 (let ((port (open (string-append #$output
-                                                 "/bin/runtime")
+                                                 "/bin/runtime-fuse3")
                                   (logior O_WRONLY))))
                   (seek port 8 SEEK_SET)
                   (put-bytevector port #vu8(#x41 #x49 #x02))
@@ -91,12 +84,9 @@
               (this-package-input "fuse")
               (gexp-input (this-package-input "zstd") "static")
               (gexp-input (this-package-input "zlib") "static"))))
-      (native-inputs (list pkg-config))
       ;; Only needed at build time.
-      (inputs (list `(,fuse "out")
+      (inputs (list squashfuse-for-appimage
-                    `(,fuse "static")
+                    fuse-for-appimage
-                    mimalloc
-                    squashfuse-for-appimage
                     `(,zstd "static")
                     `(,zlib "static")))
       (synopsis "Runtime for executing AppImages")

gnu/packages/apr.scm

@@ -34,14 +34,14 @@
 (define-public apr
   (package
     (name "apr")
-    (version "1.7.6")
+    (version "1.7.4")
     (source (origin
              (method url-fetch)
              (uri (string-append "mirror://apache/apr/apr-"
                                  version ".tar.bz2"))
              (sha256
               (base32
-               "0cpbbmng9ir8rjl9nxwljkzmrkpk4b1nsj8vg4ssfpapsa90s0s9"))
+               "0xsmqgjiyw3s6va5dm86djnjzg9r0qc1zsldwz4sd8pkhglqsr7w"))
              (patches
               (search-patches "apr-skip-getservbyname-test.patch"))
              (patch-flags '("-p0"))))

gnu/packages/audio.scm

@@ -42,7 +42,7 @@
 ;;; Copyright © 2022 Andy Tai <atai@atai.org>
 ;;; Copyright © 2023 Sergiu Ivanov <sivanov@colimite.fr>
 ;;; Copyright © 2023 David Thompson <dthompson2@worcester.edu>
-;;; Copyright © 2023, 2025-2026 Sharlatan Hellseher <sharlatanus@gmail.com>
+;;; Copyright © 2023 Sharlatan Hellseher <sharlatanus@gmail.com>
 ;;; Copyright © 2023 Gabriel Wicki <gabriel@erlikon.ch>
 ;;; Copyright © 2023 Zheng Junjie <873216071@qq.com>
 ;;; Copyright © 2023 Parnikkapore <poomklao@yahoo.com>
@@ -62,7 +62,6 @@
 ;;; Copyright © 2026 Luis Guilherme Coelho <lgcoelho@disroot.org>
 ;;; Copyright © 2026 Noé Lopez <noelopez@free.fr>
 ;;; Copyright © 2026 Carlos Durán Domínguez <wurt@wurt.eu>
-;;; Copyright © 2026 Daniel Martins <email@danielfm.me>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -179,6 +178,7 @@
   #:use-module (guix build-system glib-or-gtk)
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system meson)
+  #:use-module (guix build-system python)
   #:use-module (guix build-system pyproject)
   #:use-module (guix build-system qt)
   #:use-module (guix build-system trivial)
@@ -2316,13 +2316,13 @@ object library.")
                 (file-name (git-file-name name version))
                 (sha256
                  (base32
-                  "1jds2l3cb96b02jxd7lmrjjl9s7mylnrvg6fpw0j8c141bk8vyg3"))
+                  "1jds2l3cb96b02jxd7lmrjjl9s7mylnrvg6fpw0j8c141bk8vyg3"))))
-                (patches
-                 (search-patches "tao-synth-include-string-you-use.patch"))))
       (build-system cmake-build-system)
       (arguments (list #:tests? #false))  ;there are no tests
       (inputs
        (list glfw freeglut))
+      (native-inputs
+       (list gcc-7))
       (home-page "https://github.com/lucasw/tao_synth")
       (synopsis "Sound synthesis with physical models")
       (description "Tao is a software package for sound synthesis using physical
@@ -3237,27 +3237,30 @@ synchronous execution of all clients, and low latency operation.")
   (package
     (inherit jack-1)
     (name "jack2")
-    ;; 1.9.22 does not compile with Python 3.12, use the latest commit instead.
+    (version "1.9.21")
-    (properties '((commit . "17959465a722225a36a8b612aed26764036f258e")
-                  (revision . "0")))
-    (version (git-version "1.9.22"
-                          (assoc-ref properties 'revision)
-                          (assoc-ref properties 'commit)))
     (source (origin
               (method git-fetch)
               (uri (git-reference
-                     (url "https://github.com/jackaudio/jack2")
+                    (url "https://github.com/jackaudio/jack2")
-                     (commit (assoc-ref properties 'commit))))
+                    (commit (string-append "v" version))))
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "18dbjq9y8mcp27j9aaqdlg4976hrisr7b88lk84ck09gmzlwqalp"))))
+                "0sbrffmdbajvrk7iqvsvrnwnpvmicvbjyq3f52r6ashdsznsz03b"))))
     (build-system waf-build-system)
     (arguments
      `(#:tests? #f                      ; no check target
        #:configure-flags '("--dbus" "--alsa")
        #:phases
        (modify-phases %standard-phases
+         ;; Python 3.11 has removed the 'U' (universal newline) mode.  It has
+         ;; been the default since Python 3.3.
+         (add-after 'unpack 'python-compatibility
+           (lambda _
+             (substitute* '("waflib/Context.py"
+                            "waflib/ConfigSet.py")
+               (("m='rU'") "m='r'")
+               (("read\\('rU'") "read('r'"))))
          (add-before 'configure 'set-linkflags
            (lambda _
              ;; Ensure -lstdc++ is the tail of LDFLAGS or the simdtests.cpp
@@ -3283,7 +3286,7 @@ synchronous execution of all clients, and low latency operation.")
            expat
            libsamplerate
            opus
-           python-dbus
+           python-dbus-1.2
            readline))
     (native-inputs
      (list pkg-config))
@@ -3435,7 +3438,7 @@ from being able to mix multiple JACK audio streams.")
             (commit (string-append "v" version))))
       (file-name (git-file-name name version))
       (sha256
-       (base32 "0fvnvr74q5khxlj5sylfnkblydmwgdbvj04mhdqw0zzmfqwignhd"))))
+       (base32 "08ji4lg24flzi6g3yaavfq8hz3kr98q2ripk5m4qk9z172qxbbc9"))))
     (build-system meson-build-system)
     (arguments
      (list
@@ -3700,44 +3703,6 @@ compensation, (de)interleaving, and byte-swapping
     ;; original developer.
     (license license:expat)))
 
-(define-public rtcqs
-  (package
-    (name "rtcqs")
-    (version "0.6.7")
-    (source
-     (origin
-       (method git-fetch)
-       (uri (git-reference
-             (url "https://codeberg.org/rtcqs/rtcqs")
-             (commit (string-append "v" version))))
-       (file-name (git-file-name name version))
-       (sha256
-        (base32 "1kc3niyaq4m8di68832pgfb1b0m54q5gm68dwlzwwilgxi61ifzc"))))
-    (build-system pyproject-build-system)
-    (arguments
-     (list
-      #:tests? #f ;no test suite
-      #:phases
-      #~(modify-phases %standard-phases
-          (add-after 'unpack 'remove-gui
-            (lambda _
-              (substitute* "pyproject.toml"
-                (("\"FreeSimpleGUI\",?")
-                 "")
-                (("rtcqs_gui = \"rtcqs\\.rtcqs_gui:main\"")
-                 ""))
-              (delete-file "src/rtcqs/rtcqs_gui.py")
-              (delete-file "src/rtcqs/rtcqs_qt_gui.py"))))))
-    (native-inputs (list python-setuptools))
-    (home-page "https://codeberg.org/rtcqs/rtcqs")
-    (synopsis "Linux audio real-time performance analyzer")
-    (description
-     "rtcqs analyzes a Linux system to detect possible bottlenecks that could
-have a negative impact on real-time audio performance.  It checks kernel
-configuration, IRQ priorities, CPU governor, swappiness, and other settings
-relevant to low-latency audio work.")
-    (license license:expat)))
-
 (define-public rtosc
   (package
     (name "rtosc")
@@ -4086,7 +4051,9 @@ one-dimensional sample-rate conversion library.")
                  (string-append "'" #$(this-package-input "libsndfile")
                                 "/lib/libsndfile"))))))))
     (native-inputs
-     (list python-pytest python-setuptools))
+     (list python-pytest
+           python-pytest-cov
+           python-setuptools))
     (inputs
      (list libsndfile
            portaudio))
@@ -6391,59 +6358,6 @@ It is currently fairly complete for PCM devices, and has some support for
 mixers.")
     (license license:psfl)))
 
-(define-public python-pyo
-  (package
-    (name "python-pyo")
-    (version "1.0.6")
-    (source
-     (origin
-       (method git-fetch)
-       (uri (git-reference
-              (url "https://github.com/belangeo/pyo")
-              (commit version)))
-       (file-name (git-file-name name version))
-       (sha256
-        (base32 "1igz75kv94dav28rzz19gckgfgdli05q5ghadlvm03ia7xd9l5zm"))))
-    (build-system pyproject-build-system)
-    (arguments
-     (list
-     ;; TODO: collecting ... Fatal Python error: Segmentation fault
-      #:tests? #f
-      #:phases
-      #~(modify-phases %standard-phases
-          (add-before 'sanity-check 'set-HOME
-            (lambda _
-              (setenv "HOME" "/tmp"))))))
-    (native-inputs
-     (list python-pytest
-           python-setuptools))
-    (inputs
-     (list liblo
-           libsndfile
-           portaudio
-           portmidi))
-    (propagated-inputs
-     (list python-wxpython))
-    (home-page "https://github.com/belangeo/pyo")
-    (synopsis "Python module to build digital signal processing program")
-    (description
-     "pyo is a Python module containing classes for a wide variety of audio
-signal processing types.
-
-With pyo, user will be able to include signal processing chains directly in
-Python scripts or projects, and to manipulate them in real time through the
-interpreter.  Tools in pyo module offer primitives, like mathematical
-operations on audio signal, basic signal processing (filters, delays,
-synthesis generators, etc.), but also complex algorithms to create sound
-granulation and others creative audio manipulations.
-
-pyo supports OSC protocol (Open Sound Control), to ease communications between
-softwares, and MIDI protocol, for generating sound events and controlling
-process parameters.  pyo allows creation of sophisticated signal processing
-chains with all the benefits of a mature, and widely used, general programming
-language.")
-    (license license:lgpl3+)))
-
 (define-public ldacbt
   (package
     (name "ldacbt")
@@ -7815,59 +7729,60 @@ Rate} 3600x2250 bit/s vocoder used in various radio systems.")
                   (delete-file-recursively "third_party")
                   (delete-file-recursively "modules")))))
     (build-system cmake-build-system)
-    (arguments
-     (list
-      #:configure-flags
-      #~(list "-DLINK_BUILD_QT_EXAMPLES=ON"
-              "-DLINK_BUILD_JACK=ON")
-      #:phases
-      #~(modify-phases %standard-phases
-          (replace 'check
-            (lambda* (#:key inputs tests? #:allow-other-keys)
-              (when tests?
-                (let* ((python (search-input-file inputs "/bin/python3"))
-                       (run-tests "../source/ci/run-tests.py"))
-                  (invoke python run-tests "--target" "LinkCoreTest")
-                  (invoke python run-tests "--target" "LinkDiscoveryTest")))))
-          (add-before 'install 'patch-cmake
-            (lambda* (#:key inputs #:allow-other-keys)
-              (let* ((source "../source/"))
-                (substitute* (string-append source
-                                            "cmake_include/AsioStandaloneConfig.cmake")
-                  (((string-append "\\$\\{CMAKE_CURRENT_LIST_DIR\\}/\\.\\./"
-                                   "modules/asio-standalone/asio/include"))
-                   (dirname (search-input-file inputs "include/asio.hpp"))))
-                (substitute* (string-append source "AbletonLinkConfig.cmake")
-                  (("\\$\\{CMAKE_CURRENT_LIST_DIR\\}/include")
-                   "${CMAKE_CURRENT_LIST_DIR}/../../../include")
-                  (("\\$\\{CMAKE_CURRENT_LIST_DIR\\}/include/ableton/Link\\.hpp")
-                   "${CMAKE_CURRENT_LIST_DIR}/../../../include/ableton/Link.hpp")))))
-          (replace 'install
-            (lambda _
-              (let* ((out #$output)
-                     (lib-cmake (string-append out "/lib/cmake/ableton-link"))
-                     (source "../source"))
-                (for-each delete-file
-                          '("bin/LinkDiscoveryTest" "bin/LinkCoreTest"))
-                (copy-recursively "bin" (string-append out "/bin"))
-                (copy-recursively (string-append source "/include/ableton")
-                                  (string-append out "/include/ableton"))
-                (install-file (string-append source "/AbletonLinkConfig.cmake")
-                              lib-cmake)
-                (install-file (string-append source
-                                             "/cmake_include/AsioStandaloneConfig.cmake")
-                              (string-append lib-cmake "/cmake_include"))))))))
     (native-inputs
      (list catch-framework
-           portaudio                    ;for portaudio examples
+           python ;for running tests
-           python                       ;for running tests
+           portaudio)) ;for portaudio examples
-           python-setuptools))          ;for running tests
     (inputs
      (list jack-1)) ;for JACK examples
     (propagated-inputs
      ;; This is because include/ableton/platforms/asio/AsioWrapper.hpp
      ;; contains '#include <asio.hpp>'.
      (list asio-1.28))
+    (arguments
+     `(#:configure-flags
+       '("-DLINK_BUILD_QT_EXAMPLES=ON"
+         "-DLINK_BUILD_JACK=ON")
+       #:phases
+       (modify-phases %standard-phases
+         (replace 'check
+           (lambda* (#:key inputs tests? #:allow-other-keys)
+             (when tests?
+               (let* ((python (search-input-file inputs "/bin/python3"))
+                      (run-tests "../source/ci/run-tests.py"))
+                 (invoke python run-tests "--target" "LinkCoreTest")
+                 (invoke python run-tests "--target" "LinkDiscoveryTest")))))
+         (add-before 'install 'patch-cmake
+           (lambda* (#:key inputs #:allow-other-keys)
+             (let* ((source "../source/"))
+               (substitute* (string-append source
+                                           "cmake_include/AsioStandaloneConfig.cmake")
+                 (((string-append "\\$\\{CMAKE_CURRENT_LIST_DIR\\}/\\.\\./"
+                                  "modules/asio-standalone/asio/include"))
+                  (string-append (assoc-ref inputs "asio")
+                                 "/include")))
+               (substitute* (string-append source "AbletonLinkConfig.cmake")
+                 (("\\$\\{CMAKE_CURRENT_LIST_DIR\\}/include")
+                  "${CMAKE_CURRENT_LIST_DIR}/../../../include")
+                 (("\\$\\{CMAKE_CURRENT_LIST_DIR\\}/include/ableton/Link\\.hpp")
+                  "${CMAKE_CURRENT_LIST_DIR}/../../../include/ableton/Link.hpp")))))
+         (replace 'install
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let* ((out (assoc-ref outputs "out"))
+                    (bin (string-append out "/bin"))
+                    (lib-cmake (string-append out "/lib/cmake/ableton-link"))
+                    (source "../source"))
+               (for-each (lambda (test-file)
+                           (delete-file test-file))
+                         '("bin/LinkDiscoveryTest" "bin/LinkCoreTest"))
+               (copy-recursively "bin" bin)
+               (copy-recursively (string-append source "/include/ableton")
+                                 (string-append out "/include/ableton"))
+               (install-file (string-append source "/AbletonLinkConfig.cmake")
+                             lib-cmake)
+               (install-file (string-append source
+                                            "/cmake_include/AsioStandaloneConfig.cmake")
+                             (string-append lib-cmake "/cmake_include"))))))))
     (home-page "https://github.com/Ableton/link")
     (synopsis "Synchronize musical beat, tempo, and phase across multiple applications")
     (description
@@ -8053,7 +7968,7 @@ as sample rate, determining whether an audio file is silent, and much more.")
     (propagated-inputs
      (list python-numba python-numpy python-scipy python-six))
     (native-inputs
-     (list python-pytest python-setuptools python-wheel))
+     (list python-pytest python-pytest-cov python-setuptools python-wheel))
     (home-page "https://github.com/bmcfee/resampy")
     (synopsis "Efficient signal resampling")
     (description
@@ -8075,7 +7990,6 @@ Home Page}.")
              (commit version)
              ;; For test files.
              (recursive? #true)))
-       (file-name (git-file-name name version))
        (sha256
         (base32 "065x43hx670rjrclxi4hiqxscllb16v9s7myjvg7rd5pd3y0k7sg"))))
     (build-system pyproject-build-system)
@@ -8083,7 +7997,8 @@ Home Page}.")
      (list
       #:test-flags
       ;; Ignore --mpl flag.
-      '(list "-k" (string-append
+      '(list "-c" "/dev/null"
+             "-k" (string-append
                    ;; Resampling tests require python-samplerate.
                    "not resample"
                    ;; These tests use Pooch and download data files.
@@ -8108,6 +8023,7 @@ Home Page}.")
      (list python-matplotlib
            python-packaging
            python-pytest
+           python-pytest-cov
            python-resampy
            python-setuptools
            python-wheel))
@@ -8204,7 +8120,7 @@ and DSD streams.")
 (define-public qpwgraph
   (package
     (name "qpwgraph")
-    (version "1.0.0")
+    (version "0.9.9")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -8213,7 +8129,7 @@ and DSD streams.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "0l3fflfpwkqy4iif8ifzzr3yy39ahzqdixx5g3rhj3zzbaysj73h"))))
+                "03001pvcbvr206k00751232gm50x1icf086z8c5hiakl2ym79gwl"))))
     (build-system cmake-build-system)
     (arguments
      (list #:tests? #f))                ; no tests

gnu/packages/aux-files/python/pytest_guix.py

@@ -1,58 +0,0 @@
-# GNU Guix --- Functional package management for GNU
-# Copyright © 2025 Nicolas Graves <ngraves@ngraves.fr>
-#
-# This file is part of GNU Guix.
-#
-# GNU Guix is free software; you can redistribute it and/or modify it
-# under the terms of the GNU General Public License as published by
-# the Free Software Foundation; either version 3 of the License, or (at
-# your option) any later version.
-#
-# GNU Guix is distributed in the hope that it will be useful, but
-# WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-# GNU General Public License for more details.
-#
-# You should have received a copy of the GNU General Public License
-# along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
-
-import importlib.util
-import json
-
-
-def pytest_addoption(parser):
-    """Add stub options to be ignored by pytest.
-
-    More precisely, inject all options provided in .pytest_guix_options.json,
-    except options whose plugin is indeed installed.
-
-    For example, if the json file records --cov:
-      if the pytest_cov module is installed, its --cov will be used.
-      otherwise, --cov is ignored (read by this parser, but nothing is done
-      with it).
-
-    Flags can be given with additional keyword arguments in a json object.
-    If the json object is not given, fallback to the default
-    {"action": "append", "nargs": "?"}.  In practice, these arguments are only
-    mandatory for the store_true and store_const actions to avoid eating other
-    arguments.
-
-    This allows to remove development packages, which are not required at build
-    time while at the same time avoiding the need to adjust test options in
-    pyproject.toml or other configuration files.
-    """
-    with open(".pytest_guix_options.json", "r") as options_file:
-        plugin_options = json.load(options_file)
-        group = parser.getgroup(
-            "guix", "Options ignored by the Guix pyproject-build-system"
-        )
-
-        # Only add options for plugins that are not present.
-        for key, options in plugin_options.items():
-            if importlib.util.find_spec(f"pytest_{key}") is None:
-                # Plugin not found, add stub options
-                for option, kwargs in options.items():
-                    if kwargs:
-                        group.addoption(option, **kwargs)
-                    else:
-                        group.addoption(option, action="append", nargs="?")

gnu/packages/backup.scm

@@ -50,6 +50,7 @@
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system go)
   #:use-module (guix build-system pyproject)
+  #:use-module (guix build-system python)
   #:use-module (guix build-system qt)
   #:use-module (guix download)
   #:use-module (guix gexp)
@@ -106,7 +107,6 @@
   #:use-module (gnu packages rsync)
   #:use-module (gnu packages ruby-xyz)
   #:use-module (gnu packages serialization)
-  #:use-module (gnu packages sphinx)
   #:use-module (gnu packages ssh)
   #:use-module (gnu packages time)
   #:use-module (gnu packages tls)
@@ -137,6 +137,7 @@
            python-paramiko
            python-pexpect
            python-pytest
+           python-pytest-runner
            python-setuptools-scm
            tzdata-for-tests
            python-mock))
@@ -546,7 +547,7 @@ remain fully idle, saving power and producing less noise.")
          "0miklk4bqblpyzh1bni4x6lqn88fa8fjn15x1k1n8bxkx60nlymd"))))
     (build-system gnu-build-system)
     (inputs
-     (list librsync))
+     (list librsync-0.9))
     (arguments
      `(#:make-flags `("CFLAGS=-fcommon"
                       ,(string-append "PREFIX=" (assoc-ref %outputs "out"))
@@ -631,26 +632,41 @@ rsnapshot uses hard links to deduplicate identical files.")
 (define-public borg
   (package
     (name "borg")
-    (version "1.4.4")
+    (version "1.4.3")
     (source
      (origin
-       (method git-fetch)
+       (method url-fetch)
-       (uri (git-reference
+       (uri (pypi-uri "borgbackup" version))
-              (url "https://github.com/borgbackup/borg")
-              (commit version)))
-       (file-name (git-file-name name version))
        (sha256
-        (base32 "0bk302lbjjz1y8dg78wqqys80bm7mzkj5yf6wgyqdwvbqpsnpim4"))))
+        (base32 "07s4jqcv03s98hi6lvqpvmnnhl532qnvv11mjy2xc08rbmsgmfvr"))
+       (snippet
+        #~(begin
+            ;; Delete files generated by Cython.  We used to have a regex that
+            ;; created the list of generated files but Borg has added new
+            ;; non-generated C files that cause the regex to generate the
+            ;; wrong list.
+            (for-each delete-file
+                      '("src/borg/algorithms/checksums.c"
+                        "src/borg/chunker.c"
+                        "src/borg/compress.c"
+                        "src/borg/crypto/low_level.c"
+                        "src/borg/hashindex.c"
+                        "src/borg/item.c"
+                        "src/borg/platform/darwin.c"
+                        "src/borg/platform/freebsd.c"
+                        "src/borg/platform/linux.c"
+                        "src/borg/platform/posix.c"
+                        "src/borg/platform/syncfilerange.c"
+                        "src/borg/platform/windows.c"))))))
     (build-system pyproject-build-system)
     (arguments
      (list
       #:modules '((srfi srfi-26)        ; for cut
                   (guix build utils)
                   (guix build pyproject-build-system))
-      ;; tests: 1318 passed, 293 skipped
       #:test-flags
       #~(list "--benchmark-skip"
-              "--numprocesses" (number->string (min 8 (parallel-job-count)))
+              "--numprocesses" (number->string (parallel-job-count))
               "--pyargs" "borg.testsuite"
               "-k" (string-join
                     ;; These tests need to write to '/var'.
@@ -671,15 +687,7 @@ rsnapshot uses hard links to deduplicate identical files.")
                           "test_mount_hardlinks "
                           "test_readonly_mount "
                           "test_fuse_versions_view "
-                          "test_migrate_lock_alive"
+                          "test_migrate_lock_alive")
-                          ;; Test files are not in /gnu/store
-                          "test_convert_all[False]"
-                          "test_convert_all[True]"
-                          "test_convert_segments[False]"
-                          "test_convert_segments[True]"
-                          "test_detect_attic_repo"
-                          "test_key_export_qr"
-                          "test_keys")
                     " and not "))
       #:phases
       #~(modify-phases %standard-phases
@@ -695,58 +703,46 @@ rsnapshot uses hard links to deduplicate identical files.")
                 (setenv "BORG_LIBLZ4_PREFIX" lz4)
                 (setenv "BORG_LIBXXHASH_PREFIX" xxhash)
                 (setenv "BORG_LIBZSTD_PREFIX" zstd))))
-          (add-before 'build 'fix-testsuite-setuid-mode
+          (add-after 'install 'install-doc
             (lambda _
-              (substitute* "src/borg/testsuite/archiver.py"
+              (let ((man (string-append #$output "/share/man/man1"))
-                (("0o4755") "0o0755"))))
+                    (misc (string-append #$output "/share/doc/borg-"
-          (add-after 'install 'build-and-install-docs
+                                         #$(package-version this-package))))
-            (lambda _
-              (let* ((doc (string-append #$output "/share/doc/borg-" #$version))
-                     (html (string-append doc "/html"))
-                     (txt (string-append doc "/txt"))
-                     (misc (string-append doc "/misc"))
-                     (man (string-append #$output "/share/man/man1")))
-                (with-directory-excursion "docs"
-                  (invoke "make" "text" "man" "singlehtml"))
                 (for-each (cut install-file <> misc)
                           '("docs/misc/create_chunker-params.txt"
                             "docs/misc/borg-data-flow.png"
                             "docs/misc/internals-picture.txt"
                             "docs/misc/prune-example.txt"))
-                (copy-recursively "docs/_build/man" man)
+                (copy-recursively "docs/man" man))))
-                (copy-recursively "docs/_build/singlehtml" html)
+          (add-after 'install-doc 'install-shell-completions
-                (copy-recursively "docs/_build/text" txt))))
-          (add-after 'build-and-install-docs 'install-shell-completions
             (lambda _
-              (let* ((etc (string-append #$output "/etc"))
+              (let ((etc (string-append #$output "/etc"))
-                     (share (string-append #$output "/share"))
+                    (share (string-append #$output "/share")))
-                     (bash (string-append etc "/bash_completion.d"))
-                     (zsh (string-append share "/zsh/site-functions"))
-                     (fish (string-append share "/fish/vendor_completions.d")))
                 (with-directory-excursion "scripts/shell_completions"
-                  (install-file "bash/borg" bash)
+                  (install-file "bash/borg"
-                  (install-file "zsh/_borg" zsh)
+                                (string-append etc "/bash_completion.d"))
-                  (install-file "fish/borg.fish" fish))))))))
+                  (install-file "zsh/_borg"
+                                (string-append share "/zsh/site-functions"))
+                  (install-file "fish/borg.fish"
+                                (string-append share "/fish/vendor_completions.d")))))))))
     (native-inputs
      (list python-cython
-           python-guzzle-sphinx-theme
+           python-dateutil
-           python-pkgconfig
            python-pytest
            python-pytest-benchmark
            python-pytest-xdist
            python-setuptools
            python-setuptools-scm
-           python-sphinx
+           python-wheel))
-           python-sphinxcontrib-jquery))
     (inputs
      (list acl
            lz4
            openssl
-           python-msgpack
+           ;; This is the latest version of msgpack accepted by 'setup.py'.
+           python-msgpack-for-borg
            ;; FUSE 3 isn't working well, so we stick with FUSE 2 for now:
            ;; <https://issues.guix.gnu.org/53407>
            python-llfuse
-           python-packaging
            xxhash
            `(,zstd "lib")))
     (synopsis "Deduplicated, encrypted, authenticated and compressed backups")
@@ -1303,6 +1299,7 @@ compression parameters used by Gzip.")
     (native-inputs
      (list python-flexmock
            python-pytest
+           python-pytest-cov
            python-setuptools
            python-wheel))
     (inputs
@@ -1366,9 +1363,9 @@ borgmatic is powered by borg.")
             (assoc-ref qt:%standard-phases 'qt-wrap)))))
     (native-inputs
      (list python-platformdirs
-           python-pytest
            python-pytest-mock
            python-pytest-qt
+           python-pytest-runner
            python-setuptools
            python-setuptools-git))
     (inputs

gnu/packages/benchmark.scm

@@ -42,6 +42,7 @@
   #:use-module (guix search-paths)
   #:use-module (guix build-system cmake)
   #:use-module (guix build-system gnu)
+  #:use-module (guix build-system python)
   #:use-module (guix build-system pyproject)
   #:use-module (guix build-system meson)
   #:use-module (gnu packages)
@@ -943,20 +944,7 @@ configurable through a set of options.")
       #~(list (string-append
                "CC=" #$(this-package-input "openmpi") "/bin/mpicc")
               (string-append
-               "CXX=" #$(this-package-input "openmpi") "/bin/mpicxx"))
+               "CXX=" #$(this-package-input "openmpi") "/bin/mpicxx"))))
-      #:phases
-      #~(modify-phases %standard-phases
-          ;; OSU installs its binaries to /libexec. Have a symlink in /bin to
-          ;; improve user experience.
-          (add-after 'install 'symlink-binaries-in-bin
-            (lambda _
-              (mkdir-p (string-append #$output "/bin"))
-              (for-each (lambda (file)
-                          (symlink file
-                                   (string-append #$output "/bin/"
-                                                  (basename file))))
-                        (find-files (string-append #$output
-                                                   "/libexec"))))))))
     (home-page "https://mvapich.cse.ohio-state.edu/benchmarks/")
     (synopsis "Benchmarking suite from the MVAPICH project")
     (description

gnu/packages/bioconductor.scm

@@ -3436,14 +3436,14 @@ the @code{HorvathMethylChip40} (Mammal40) array.")
 (define-public r-systempiperdata
   (package
     (name "r-systempiperdata")
-    (version "2.14.6")
+    (version "2.14.5")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "systemPipeRdata" version
                               'experiment))
        (sha256
-        (base32 "1j7h40hcm0gyahmlilvlb83ddmwrarqn319qwpnrgwcji8fm92jd"))))
+        (base32 "1yrq1vyc0pmp3iv621cvdsavlarcca3z4bbxfzbg0ny3fyqp67pb"))))
     (properties `((upstream-name . "systemPipeRdata")))
     (build-system r-build-system)
     (propagated-inputs (list r-biocgenerics r-biostrings r-jsonlite r-remotes))
@@ -4552,9 +4552,15 @@ these biases and construct statistically consistent estimators.")
     (build-system r-build-system)
     (arguments
      (list
-      #:skipped-tests
+      #:phases
-      ;; This test needs Internet access.
+      '(modify-phases %standard-phases
-      '(("test-examples.R" ".*find_taxonomy\\(\\) is working.*"))))
+         (add-after 'unpack 'skip-bad-tests
+           (lambda _
+             ;; This test needs Internet access.
+             (with-directory-excursion "tests/testthat"
+               (substitute* "test-examples.R"
+                 ((".*find_taxonomy\\(\\) is working.*" m)
+                  (string-append m "skip('guix')\n")))))))))
     (propagated-inputs
      (list r-ape
            r-assertthat
@@ -4605,13 +4611,13 @@ to understand their data better and discover new insights.")
 (define-public r-anndatar
   (package
     (name "r-anndatar")
-    (version "1.0.2")
+    (version "1.0.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "anndataR" version))
        (sha256
-        (base32 "1gn1yyfs08a77zrl4cidahxim3kgcvpbsrgfxxnhhrka57xcylld"))))
+        (base32 "1vi9aqgdjy0nlbsk7628sz12jsxd9bfb79yxhh0ngijpxj9sxd4p"))))
     (properties `((upstream-name . "anndataR")))
     (build-system r-build-system)
     (arguments
@@ -4664,13 +4670,14 @@ directly access various slots (e.g. X, obs, var), or convert the data into
     (build-system r-build-system)
     (arguments
      (list
-      #:test-directory "inst/unitTests"
-      ;; These tests require internet access.
-      #:skipped-tests
-      '("test_recipe.R"
-        "test_webAccessFunctions.R")
       #:phases
       '(modify-phases %standard-phases
+         (add-after 'unpack 'delete-bad-tests
+           (lambda _
+             ;; These tests require internet access.
+             (for-each delete-file
+                       '("inst/unitTests/test_recipe.R"
+                         "inst/unitTests/test_webAccessFunctions.R"))))
          (add-before 'install 'set-home
            (lambda _ (setenv "HOME" "/tmp"))))))
     (propagated-inputs
@@ -5237,13 +5244,13 @@ structures: @code{ExpressionSet}, @code{AffyBatch}, @code{NChannelSet}.")
 (define-public r-arrayqualitymetrics
   (package
     (name "r-arrayqualitymetrics")
-    (version "3.66.0")
+    (version "3.64.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "arrayQualityMetrics" version))
               (sha256
                (base32
-                "0y9k81vwqq74zfdrc2hvx7mg0l7572hvrsby00m20z034j7f9pmi"))))
+                "1kz2d40wx2ksy9dz1z3wylcj7y7ad9z8xphsnz39j02m4g5mbvlp"))))
     (properties
      '((upstream-name . "arrayQualityMetrics")
        ;; We don't need these.
@@ -5265,7 +5272,7 @@ structures: @code{ExpressionSet}, @code{AffyBatch}, @code{NChannelSet}.")
                              r-svglite
                              r-vsn
                              r-xml))
-    (native-inputs (list r-biocstyle r-knitr))
+    (native-inputs (list r-knitr))
     (home-page "https://bioconductor.org/packages/arrayQualityMetrics")
     (synopsis "Quality metrics report for microarray data sets")
     (description
@@ -6103,8 +6110,10 @@ retrieval analyses, or similar technologies.")
     (build-system r-build-system)
     (arguments
      (list
-      ;; This requires internet access.
+      #:phases
-      #:skipped-tests '("test-download.R")))
+      '(modify-phases %standard-phases
+         (add-after 'unpack 'disable-bad-tests
+           (lambda _ (delete-file "tests/testthat/test-download.R"))))))
     (propagated-inputs (list cmake r-dir-expiry))
     (native-inputs (list r-knitr r-testthat))
     (home-page "https://github.com/LTLA/biocmake")
@@ -6412,6 +6421,17 @@ objects.")
         (base32 "189akh4lpbp0dzgflb3nb3vi94bhmsj7qkcl597dnnzxqz00hsb2"))))
     (properties `((upstream-name . "CoreGx")))
     (build-system r-build-system)
+    (arguments
+     (list
+      #:phases
+      '(modify-phases %standard-phases
+         (add-after 'unpack 'disable-bad-tests
+           (lambda _
+             ;; It is unclear why 3 tests fail.
+             (with-directory-excursion "tests/testthat"
+               (substitute* "test-LongTable-utils.R"
+                 ((".*doesn't miss assay observations.*" m)
+                  (string-append m "skip('guix')\n")))))))))
     (propagated-inputs
      (list r-bench
            r-biobase
@@ -7880,13 +7900,13 @@ Kallisto, Salmon, StringTie, Cufflinks/Cuffdiff etc.")
 (define-public r-isva
   (package
     (name "r-isva")
-    (version "1.10")
+    (version "1.9")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "isva" version))
               (sha256
                (base32
-                "1im1bwbf6l88m4bwwwr0z2x8bvw927s3fqbwc06s5240wc8syjpl"))))
+                "05qx9q0kg4ma23v4abhihw0vz017nq6hv2jzsiqx4d20ngh1dl4z"))))
     (properties `((upstream-name . "isva")))
     (build-system r-build-system)
     (propagated-inputs (list r-fastica r-jade r-qvalue))
@@ -8653,13 +8673,13 @@ on Bioconductor or which replace R functions.")
 (define-public r-biomart
   (package
     (name "r-biomart")
-    (version "2.66.2")
+    (version "2.66.1")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "biomaRt" version))
               (sha256
                (base32
-                "1awsfklcs35vrmjkc12bk5ys9w7ib0799i3d0k138y44a0837pph"))))
+                "1cmzay4z9s183dc001rxfa81ql67la9y8m0p0wsn2iwzxzx94n8g"))))
     (properties
      `((upstream-name . "biomaRt")))
     (build-system r-build-system)
@@ -10317,13 +10337,13 @@ Enrichment Analysis} (GSEA).")
 (define-public r-gsva
   (package
     (name "r-gsva")
-    (version "2.4.8")
+    (version "2.4.6")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "GSVA" version))
               (sha256
                (base32
-                "0p9awi85dbmmyplhdfz0in4nhaavb58gpf48kqyp30rcc3v5a8h0"))))
+                "08i2s5zlm75mr7zl357cic2zxcy7aqqfv67xb0w67n48cw016ri6"))))
     (properties `((upstream-name . "GSVA")))
     (build-system r-build-system)
     (propagated-inputs (list r-biobase
@@ -10718,54 +10738,6 @@ nucleotide sequence analysis.  The package is primarily useful to developers
 of other R packages who wish to make use of HTSlib.")
     (license license:lgpl2.0+)))
 
-(define-public r-rliger
-  (package
-    (name "r-rliger")
-    (version "2.2.1")
-    (source
-     (origin
-       (method git-fetch)
-       (uri (git-reference
-              (url "https://github.com/welch-lab/liger")
-              (commit (string-append "v" version))))
-       (file-name (git-file-name name version))
-       (sha256
-        (base32 "1w849km9b347m56qwr5lr6ymdk7wv22hr224riscm0zrnx402yb3"))))
-    (properties `((upstream-name . "rliger")))
-    (build-system r-build-system)
-    (propagated-inputs (list r-cli
-                             r-delayedarray
-                             r-dplyr
-                             r-ggplot2
-                             r-hdf5array
-                             r-hdf5r
-                             r-leidenalg
-                             r-lifecycle
-                             r-magrittr
-                             r-matrix
-                             r-patchwork
-                             r-rann
-                             r-rcpp
-                             r-rcpparmadillo
-                             r-rcppplanc
-                             r-rcppprogress
-                             r-rlang
-                             r-s4vectors
-                             r-scales
-                             r-uwot))
-    (native-inputs
-     (list r-circlize r-complexheatmap r-knitr r-testthat r-viridis))
-    (home-page "https://github.com/welch-lab/liger")
-    (synopsis "Linked inference of genomic experimental relationships")
-    (description
-     "LIGER is a package for integrating and analyzing multiple single-cell
-datasets. It relies on integrative non-negative matrix factorization to
-identify shared and dataset-specific factors.")
-    (license license:gpl3)))
-
-(define-deprecated-package r-liger
-  r-rliger)
-
 (define-public r-rnbeads
   (package
     (name "r-rnbeads")
@@ -11145,13 +11117,13 @@ different technologies, including microarrays, RNA-seq, and quantitative PCR.")
 (define-public r-maaslin2
   (package
     (name "r-maaslin2")
-    (version "1.24.1")
+    (version "1.22.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "Maaslin2" version))
        (sha256
-        (base32 "0z8vfx6db6xfvqdhg6n8jx3fmgwvq22facsacq6ym867kw2jafiz"))))
+        (base32 "10hdjhi1ykk513hzvs0bi6avzghqmkqns8knhz3ycv7bj3ynp70x"))))
     (properties `((upstream-name . "Maaslin2")))
     (build-system r-build-system)
     (propagated-inputs
@@ -11339,6 +11311,17 @@ high distances can be flagged as potentially low-quality.")
        ;; Avoid dependency cycle.
        (updater-ignored-native-inputs . ("r-spectra"))))
     (build-system r-build-system)
+    (arguments
+     (list
+      #:phases
+      '(modify-phases %standard-phases
+         ;; This test uses a deprecated procedure that has since been removed
+         ;; from testthat.
+         (add-after 'unpack 'testthat-compatibility
+           (lambda _
+             (substitute* "tests/testthat/test_zzz.R"
+               ((".*.onLoad works.*" m)
+                (string-append m "skip('guix')\n"))))))))
     (propagated-inputs (list r-biocparallel r-mscoreutils))
     (native-inputs (list r-callr r-knitr r-microbenchmark r-robustbase
                          r-testthat))
@@ -11545,13 +11528,13 @@ time-series data (including a graphical user interface).")
 (define-public r-mmuphin
   (package
     (name "r-mmuphin")
-    (version "1.24.0")
+    (version "1.22.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "MMUPHin" version))
        (sha256
-        (base32 "1zdk9ffa996w4acnhbs7grbji5s3plwhcl6m21yajrlck2i9y3cw"))
+        (base32 "0d8i9b6pjwz409jd46fm1n9h21hzg8zgzpvchywpyc1k896fvz4l"))
        ;; Delete generated files.
        (snippet
         '(for-each delete-file
@@ -14315,13 +14298,13 @@ level.")
 (define-public r-tcgautils
   (package
     (name "r-tcgautils")
-    (version "1.30.3")
+    (version "1.30.2")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "TCGAutils" version))
               (sha256
                (base32
-                "1nppp70675y3ds76jf61rhfis2lgkxqjhz48b367qa55g3q2ah61"))))
+                "1zwzx7mfp4s0v1rdjsyxj4l9w360g4qm3am8yf5lsd0biciqqh93"))))
     (properties `((upstream-name . "TCGAutils")))
     (build-system r-build-system)
     (arguments
@@ -15041,14 +15024,14 @@ unmodeled, or latent sources of noise.")
 (define-public r-systempiper
   (package
     (name "r-systempiper")
-    (version "2.16.4")
+    (version "2.16.3")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "systemPipeR" version))
        (sha256
         (base32
-         "1zrk6ky58f30wvaxph5dc2wr418qfpwc7d8pkxpl5dhb5g7vgn8r"))))
+         "0maixi0hwqzkpiq60hf60x4q3gv3hkvmrqh3ygv0fk63g1k9f6cj"))))
     (properties `((upstream-name . "systemPipeR")))
     (build-system r-build-system)
     ;; Tests fail because genWorkenvir fails to set up the environment.
@@ -15415,13 +15398,13 @@ molecular functions, respectively, and produces intuitive graphical outputs.")
 (define-public r-xllim
   (package
     (name "r-xllim")
-    (version "2.3.1")
+    (version "2.3")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "xLLiM" version))
        (sha256
-        (base32 "1h2z6a3j3yi7rj5lyk7gb1iyp2vf516fgmk7wr333gfkvk522n2r"))))
+        (base32 "08v6acn6vpn8asn61ldqdryjz0xk5zyd2v63aqrc5xximpqwrp7d"))))
     (properties `((upstream-name . "xLLiM")))
     (build-system r-build-system)
     (propagated-inputs (list r-abind
@@ -16321,14 +16304,14 @@ signals directly in the Bruker format.")
 (define-public r-codedepends
   (package
     (name "r-codedepends")
-    (version "0.6.7")
+    (version "0.6.6")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "CodeDepends" version))
        (sha256
         (base32
-         "02sj40qxq5vywgqay9q9vpv3s6j3jjr46kc8q3v1yw2vbsmlvrz0"))))
+         "0msq5ksjqp2pjzl6f1vizw53gdf5lz520bpdr5dbjwz5mc1mp0bz"))))
     (properties `((upstream-name . "CodeDepends")))
     (build-system r-build-system)
     (propagated-inputs
@@ -17399,14 +17382,14 @@ data.")
 (define-public r-ggtree
   (package
     (name "r-ggtree")
-    (version "4.0.5")
+    (version "4.0.4")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "ggtree" version))
        (sha256
         (base32
-         "0w9hqc3m35mrdqy5iwcm201pzpbl8jw6rd3wyzwp6f53wbbm2lbh"))))
+         "1qi5nispv0cirfayijybnn1nr8l6sb2adnic3y37qm3yv91w6s6z"))))
     (properties `((upstream-name . "ggtree")))
     (build-system r-build-system)
     (propagated-inputs
@@ -18720,13 +18703,13 @@ standardization of the analyses and the development of best practices.")
 (define-public r-microbiomestat
   (package
     (name "r-microbiomestat")
-    (version "1.4")
+    (version "1.3")
     (source (origin
               (method url-fetch)
               (uri (cran-uri "MicrobiomeStat" version))
               (sha256
                (base32
-                "0in28lzds3sv1xa25vs8q5mmm1ax78s2axhq7mi23njqip5xmsr1"))))
+                "02xg8l4d0z5wrdrm5dj5a0q51vsbhf3f6z2lk8294c4d85s09dhl"))))
     (properties
      '((upstream-name . "MicrobiomeStat")
        (updater-extra-inputs . ("nlopt"))
@@ -18734,21 +18717,23 @@ standardization of the analyses and the development of best practices.")
     (build-system r-build-system)
     (inputs (list nlopt))
     (native-inputs (list pkg-config))
-    (propagated-inputs (list r-bbotk
+    (propagated-inputs (list r-bbmisc
                              r-dplyr
                              r-foreach
                              r-ggplot2
                              r-ggrepel
+                             r-lhs
                              r-lmertest
                              r-mass
                              r-matrix
                              r-matrixstats
-                             r-mlr3
+                             r-mlr
-                             r-mlr3mbo
+                             r-mlrmbo
                              r-modeest
-                             r-paradox
+                             r-paramhelpers
                              r-rcpp
                              r-rcpparmadillo
+                             r-smoof
                              r-statmod))
     (home-page "https://cran.r-project.org/package=MicrobiomeStat")
     (synopsis "Statistical methods for microbiome compositional data")
@@ -19652,14 +19637,14 @@ correspondence between different data sources.")
 (define-public r-enrichplot
   (package
     (name "r-enrichplot")
-    (version "1.30.5")
+    (version "1.30.4")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "enrichplot" version))
        (sha256
         (base32
-         "12c6xwp29mmalvxp3asliv2hlha5vv8l37prmmcgpdi4nghfic3b"))))
+         "080q91ll8rvqf93hcmxc7kjbmmihyh0vrpxck2pqrwglbqxm4xll"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-aplot
@@ -22904,14 +22889,14 @@ expression space.")
 (define-public r-cicero
   (package
     (name "r-cicero")
-    (version "1.28.3")
+    (version "1.28.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "cicero" version))
        (sha256
         (base32
-         "016wpficnbricf4f7sgq8j53cl178f1332fh9zvlx7q560489zf1"))))
+         "1ibxynw77a8mqv9av7z828wcazjpm4sfp83hd412f2rmgkls895x"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-assertthat
@@ -23543,14 +23528,14 @@ populations, splice site strength, conservation, etc.")
 (define-public r-variancepartition
   (package
     (name "r-variancepartition")
-    (version "1.40.2")
+    (version "1.40.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "variancePartition" version))
        (sha256
         (base32
-         "0k2rcgg4ll06b9j7999d4l60wpmi3vnjaqiy5ay8ppd1z0m38ygf"))))
+         "1xqy4jl8im7i4kd4iwn8hvhy172fzsadyn90kprihmvccmpd5cr3"))))
     (properties
      '((upstream-name . "variancePartition")
        (updater-extra-native-inputs . ("r-rfast"))))
@@ -23891,26 +23876,30 @@ rate} (FDR).")
 (define-public r-activedriverwgs
   (package
     (name "r-activedriverwgs")
-    (version "1.2.1")
+    (version "1.2.0")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "ActiveDriverWGS" version))
        (sha256
         (base32
-         "1v6lnzbaksqpc33q3bp4mwij6rrfbqhi5wk1qx32h2wr2hr4208y"))))
+         "0xnplgwxd197a4d422bsxg753q158i12ils16awd1cw30wafdxkk"))))
     (properties
      `((upstream-name . "ActiveDriverWGS")))
     (build-system r-build-system)
     (propagated-inputs
      (list r-biostrings
            r-bsgenome
+           r-bsgenome-hsapiens-ucsc-hg19
+           r-bsgenome-hsapiens-ucsc-hg38
+           r-bsgenome-mmusculus-ucsc-mm9
+           r-bsgenome-mmusculus-ucsc-mm10
            r-genomeinfodb
            r-genomicranges
            r-iranges
            r-s4vectors))
     (native-inputs
-     (list r-bsgenome-hsapiens-ucsc-hg19 r-knitr r-testthat))
+     (list r-knitr r-testthat))
     (home-page "https://cran.r-project.org/web/packages/ActiveDriverWGS/")
     (synopsis "Driver discovery tool for cancer whole genomes")
     (description
@@ -24770,13 +24759,13 @@ functionality.")
 (define-public r-biocviews
   (package
     (name "r-biocviews")
-    (version "1.78.1")
+    (version "1.78.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "biocViews" version))
               (sha256
                (base32
-                "1qw3xwsffdqfwpmwrpzg8rnjwv9l45lkjz8bf5272hkhgjc7b1a8"))))
+                "1dfsfj4dm9wnh4qr1sqdrwzccl3pgw58j17vr3i1bvxkrq31p1ws"))))
     (properties
      `((upstream-name . "biocViews")))
     (build-system r-build-system)
@@ -24889,14 +24878,14 @@ db and resource files to AWS S3 buckets.")
 (define-public r-multiassayexperiment
   (package
     (name "r-multiassayexperiment")
-    (version "1.36.2")
+    (version "1.36.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "MultiAssayExperiment" version))
        (sha256
         (base32
-         "0bhr51c58vdfvly0bh3hgr397qkq45yw8221rpr38cah7dbzvrba"))))
+         "09jwnwiq4vx7cmzq5va3rh7npjyhi1p5p344c4n0h9nr55mxzjiw"))))
     (properties
      '((upstream-name . "MultiAssayExperiment")
        (updater-extra-native-inputs
@@ -25965,13 +25954,13 @@ provided for direct creation of an in-memory tatami matrix from a HDF5 file.")
 (define-public r-beadarray
   (package
     (name "r-beadarray")
-    (version "2.60.1")
+    (version "2.58.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "beadarray" version))
               (sha256
                (base32
-                "1bcirbg10ai6jpa8a5ppq4450r5h2bwizb98qn0z0hmm1mm4ww9r"))))
+                "0m9hmy4xn7q2v4ra95b9h08d0qh5qmjgqmg96vabyv46gn5i7qp4"))))
     (properties `((upstream-name . "beadarray")))
     (build-system r-build-system)
     (propagated-inputs (list r-annotationdbi
@@ -26401,13 +26390,13 @@ of other packages.")
 (define-public r-scater
   (package
     (name "r-scater")
-    (version "1.38.1")
+    (version "1.38.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "scater" version))
               (sha256
                (base32
-                "1p8dzjphrcqai1f8wh56jfv377dqzdfnx2sl9sn73axbsr41swa7"))))
+                "1qwygk8fg8nharrkmjs65fcl3lsdi232f2383s5j8vm1qil5gghd"))))
     (build-system r-build-system)
     (properties
      '((updater-extra-native-inputs
@@ -26512,13 +26501,13 @@ variable and significantly correlated genes.")
 (define-public r-sparsearray
   (package
     (name "r-sparsearray")
-    (version "1.10.10")
+    (version "1.10.8")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "SparseArray" version))
        (sha256
-        (base32 "19c1dfa5wizq7k53a43i5dwwaqs44prclxbf1k0i3awx5wz6qlbw"))))
+        (base32 "1bjxljwfrv787ikp61xl29wx3k6624qz75gl1kzfif62vys7vgf0"))))
     (properties `((upstream-name . "SparseArray")))
     (build-system r-build-system)
     (propagated-inputs (list r-biocgenerics
@@ -27172,14 +27161,14 @@ with your data.")
 (define-public r-gwascat
   (package
     (name "r-gwascat")
-    (version "2.42.1")
+    (version "2.42.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "gwascat" version))
        (sha256
         (base32
-         "0djrd63nsqpy46acblg5k8pq6ldqccr35r6h0sf4xridpkqm78b1"))))
+         "1v5z4fmwgs3swvpa09y986sracz0nsggq8s9hp1nmwb9a9grw8px"))))
     (build-system r-build-system)
     (propagated-inputs
      (list r-annotationdbi
@@ -27194,6 +27183,7 @@ with your data.")
            r-readr
            r-s4vectors
            r-seqinfo
+           r-snpstats
            r-tibble
            r-variantannotation))
     (native-inputs
@@ -27654,6 +27644,16 @@ visualizations for publication-quality multi-panel figures.")
          "1c7vy10ga3cswsqwxljbgqlsjg0d2lx9srfknbjy4fkbyrjci15k"))))
     (properties `((upstream-name . "ballgown")))
     (build-system r-build-system)
+    (arguments
+     (list
+      #:phases
+      '(modify-phases %standard-phases
+         ;; These deprecated procedures have been removed in testthat.
+         (add-after 'unpack 'testthat-compatibility
+           (lambda _
+             (substitute* "tests/testthat/test-annotation.R"
+               (("is_true\\(\\)") "expect_true")
+               (("is_false\\(\\)") "expect_false")))))))
     (propagated-inputs
      (list r-biobase
            r-genomicranges
@@ -28409,18 +28409,28 @@ separate published packages.")
 (define-public r-biomformat
   (package
     (name "r-biomformat")
-    (version "1.38.3")
+    (version "1.38.0")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "biomformat" version))
        (sha256
         (base32
-         "0b0w0mfx448ph8fla3nb4i50mvpnv498kxip7rnh14xwas9rhdd7"))))
+         "1ydcgifdrgg48y7qxg0gw30h332y3yk3k3n17fajkv58mlvyx1yc"))))
     (properties `((upstream-name . "biomformat")))
     (build-system r-build-system)
+    (arguments
+     (list
+      #:phases
+      '(modify-phases %standard-phases
+         ;; These deprecated procedures have been removed in testthat.
+         (add-after 'unpack 'testthat-compatibility
+           (lambda _
+             (substitute* "tests/testthat/test-IO.R"
+               (("is_true\\(\\)") "expect_true")
+               (("is_false\\(\\)") "expect_false")))))))
     (propagated-inputs
-     (list r-jsonlite r-matrix r-rhdf5))
+     (list r-jsonlite r-matrix r-plyr r-rhdf5))
     (native-inputs (list r-knitr r-testthat))
     (home-page "https://github.com/joey711/biomformat/")
     (synopsis "Interface package for the BIOM file format")
@@ -29178,15 +29188,25 @@ reproducibility.")
 (define-public r-phyloseq
   (package
     (name "r-phyloseq")
-    (version "1.54.2")
+    (version "1.54.1")
     (source
      (origin
        (method url-fetch)
        (uri (bioconductor-uri "phyloseq" version))
        (sha256
-        (base32 "106zwzzwzvb5x0lz9i68wshh2nsa2rf5rmkqjqsvr4smxq6hknlj"))))
+        (base32 "1zivxag6b2bjh32k1mpn7hlvalap97rp90x3cbfynqrk6933f4bq"))))
     (properties `((upstream-name . "phyloseq")))
     (build-system r-build-system)
+    (arguments
+     (list
+      #:phases
+      '(modify-phases %standard-phases
+         ;; These deprecated procedures have been removed in testthat.
+         (add-after 'unpack 'testthat-compatibility
+           (lambda _
+             (substitute* (find-files "tests/testthat" "\\.R$")
+               (("is_true\\(\\)") "expect_true")
+               (("is_false\\(\\)") "expect_false")))))))
     (propagated-inputs
      (list r-ade4
            r-ape

gnu/packages/bioinformatics.scm

@@ -65,6 +65,7 @@
   #:use-module (guix build-system meson)
   #:use-module (guix build-system perl)
   #:use-module (guix build-system pyproject)
+  #:use-module (guix build-system python)
   #:use-module (guix build-system qt)
   #:use-module (guix build-system r)
   #:use-module (guix build-system ruby)
@@ -921,10 +922,7 @@ suite native in R.")
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "12h1di45fg06nhsliii7v0h1z567pkpis1xm4ar1qr8ns1n8iljw"))
+        (base32 "12h1di45fg06nhsliii7v0h1z567pkpis1xm4ar1qr8ns1n8iljw"))))
-       (modules '((guix build utils)))
-       (snippet
-        '(delete-file-recursively "r/src/vendor/highway"))))
     (properties `((upstream-name . "BPCells")))
     (build-system r-build-system)
     (arguments
@@ -932,11 +930,7 @@ suite native in R.")
       #:phases
       '(modify-phases %standard-phases
          (add-after 'unpack 'chdir
-           (lambda _
+           (lambda _ (chdir "r"))))))
-             (substitute* "r/configure"
-               (("tools/hwy-test.cpp" m)
-                (string-append m " $HWY_LIBS $HWY_CFLAGS")))
-             (chdir "r"))))))
     (propagated-inputs
      (list r-dplyr
            r-ggplot2
@@ -963,7 +957,7 @@ suite native in R.")
            r-igraph
            r-iranges
            r-matrixstats))
-    (inputs (list hdf5 google-highway zlib))
+    (inputs (list hdf5 zlib))
     (native-inputs (list pkg-config))
     (home-page "https://github.com/bnprks/BPCells")
     (synopsis "Single cell counts matrices to PCA")
@@ -2287,6 +2281,7 @@ version = ~s
                   (delete-file-recursively
                    (string-append #$output "/.pytest_cache")))))))))
     (native-inputs (list python-pytest
+                         python-pytest-cov
                          python-pytest-datadir
                          python-pytest-doctestplus
                          python-recommonmark
@@ -3377,36 +3372,35 @@ encountered in PDB files prior to simulation tasks.")
 (define-public python-peaks2utr
   (package
     (name "python-peaks2utr")
-    (version "1.5.0")
+    (version "1.4.1")
-    (source
+    (source (origin
-     (origin
+              (method url-fetch)
-       (method git-fetch)
+              (uri (pypi-uri "peaks2utr" version))
-       (uri (git-reference
+              (sha256
-              (url "https://github.com/haessar/peaks2utr")
+               (base32
-              (commit (string-append "v" version))))
+                "104il0kk61q07b58g9xrss7xflwlbx4kzsmw9iih99lhfsii0wzg"))))
-       (file-name (git-file-name name version))
-       (sha256
-        (base32 "1b4qiccp5j394pzqd1d4ss3k90zv3kdr84lykl6p8izn3k85b2bl"))))
     (build-system pyproject-build-system)
     (arguments
      (list
+      #:test-flags
+      ;; These tests fail because file names are not URLs.
+      '(list "-k" (string-join
+                   (list "not test_forward_strand_annotations"
+                         "test_matching_chr"
+                         "test_reverse_strand_annotations")
+                   " and not "))
       #:phases
-      #~(modify-phases %standard-phases
+      '(modify-phases %standard-phases
-          (add-after 'unpack 'relax-requirements
+         (add-after 'unpack 'relax-requirements
-            (lambda _
+           (lambda _
-              (substitute* "setup.cfg"
+             (substitute* "setup.cfg"
-                (("==") ">=")
+               (("==") ">=")))))))
-                ;; See: <https://github.com/haessar/peaks2utr/issues/47>.
-                (("numpy >= 1.21.4, <= 1.26.4") "numpy >= 1.21.4")))))))
-    (native-inputs
-     (list python-pytest
-           python-setuptools))
     (propagated-inputs
      (list python-asgiref
            python-gffutils
            python-importlib-resources
-           macs-3
+           macs
-           python-numpy
+           python-numpy-1
            python-psutil
            python-pybedtools
            python-pysam
@@ -3414,6 +3408,7 @@ encountered in PDB files prior to simulation tasks.")
            python-tqdm
            python-typing-extensions
            python-zipp))
+    (native-inputs (list python-setuptools python-wheel))
     (home-page "https://github.com/haessar/peaks2utr")
     (synopsis "Python CLI for annotating three prime UTR")
     (description
@@ -3862,6 +3857,7 @@ raw/ed14e050b2b75e7f4ddb73d512fbe928bbdb2b85")
            python-scipy))
     (native-inputs
      (list python-pytest
+           python-pytest-cov
            python-pytest-datadir
            python-pytest-doctestplus
            python-setuptools
@@ -4287,6 +4283,7 @@ e.g. microbiome samples, genomes, metagenomes.")
     (native-inputs
      (list python-cython
            python-pytest
+           python-pytest-cov
            python-setuptools
            python-wheel))
     (propagated-inputs
@@ -4893,29 +4890,26 @@ relying on a complex dependency tree.")
 (define-public biosoup
   (package
     (name "biosoup")
-    (version "0.11.0")
+    (version "0.10.0")
     (source
      (origin
        (method git-fetch)
        (uri (git-reference
              (url "https://github.com/rvaser/biosoup")
-             (commit version)))
+             ;; Corresponds to version 0.10.0
+             (commit "38181f09854ff42cbd9632200a2ec9fb37a4b7b6")))
        (file-name (git-file-name name version))
        (sha256
         (base32
-         "0vn1hj3h152iwahnrzghqll34qaphchi07klb3j70vgc248micbz"))))
+         "02hvyka703zagx0nvv2yx3dkc748zc8g6qbrpya7r8kfkcl7y8hw"))))
     (build-system cmake-build-system)
     (arguments
-     (list
+     `(#:phases
-      #:phases
+       (modify-phases %standard-phases
-      #~(modify-phases %standard-phases
+         (replace 'check
-          (add-after 'unpack 'enable-testing
+           (lambda* (#:key tests? #:allow-other-keys)
-            (lambda _
+             (when tests?
-              (substitute* "CMakeLists.txt"
+               (invoke "./bin/biosoup_test")))))))
-                (("target_link_libraries\\(biosoup_test")
-                 "enable_testing()
-  add_test(NAME biosoup-test COMMAND biosoup_test)
-  target_link_libraries(biosoup_test")))))))
     (native-inputs
      (list googletest))
     (home-page "https://github.com/rvaser/biosoup")
@@ -4927,29 +4921,26 @@ used for storage and logging in bioinformatics tools.")
 (define-public bioparser
   (package
     (name "bioparser")
-    (version "3.1.0")
+    (version "3.0.13")
     (source
      (origin
        (method git-fetch)
        (uri (git-reference
              (url "https://github.com/rvaser/bioparser")
-             (commit version)))
+             ;; Corresponds to tag 3.0.13
+             (commit "13341e6e0855c6b358ffcea6dad216e1009e1287")))
        (file-name (git-file-name name version))
        (sha256
         (base32
-         "057zb3g8qyvbkbfzgkygrf0iphz3v4icm13pchxzrafiy7zkbmrq"))))
+         "0c5p2dl8jb12ci9f427jzrmmm9cgvc1k4fxsn2ggkfsin6r1r82i"))))
     (build-system cmake-build-system)
     (arguments
-     (list
+     `(#:phases
-      #:phases
+       (modify-phases %standard-phases
-      #~(modify-phases %standard-phases
+         (replace 'check
-          (add-after 'unpack 'enable-testing
+           (lambda* (#:key tests? #:allow-other-keys)
-            (lambda _
+             (when tests?
-              (substitute* "CMakeLists.txt"
+               (invoke "./bin/bioparser_test")))))))
-                (("target_link_libraries\\(bioparser_test")
-                 "enable_testing()
-  add_test(NAME bioparser-test COMMAND bioparser_test)
-  target_link_libraries(bioparser_test")))))))
     (inputs
      (list biosoup))
     (propagated-inputs
@@ -4963,6 +4954,113 @@ bioinformatics formats (FASTA/Q, MHAP/PAF/SAM), with support for zlib
 compressed files.")
     (license license:expat)))
 
+(define-public circtools
+  (package
+    (name "circtools")
+    (version "1.0.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/Kevinzjy/circtools")
+             ;; Corresponds to tag v1.0.0
+             (commit "79380de59013601021ca3b1352d6f64d2fb89646")
+             (recursive? #t)))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32
+         "0wg1s927g32k25j967kfr8l30nmr4c0p4zvy5igvy7cs6chd60lh"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:tests? #f
+       #:install-source? #f
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'make-writable
+           (lambda _
+             (for-each make-file-writable (find-files "."))))
+         (add-after 'unpack 'prepare-spoa-dependencies
+           (lambda* (#:key inputs #:allow-other-keys)
+             (substitute* "vendor/spoa/CMakeLists.txt"
+               (("find_package\\(bioparser 3.0.13 QUIET\\)")
+                "find_package(bioparser 3.0.13 CONFIG)")
+               (("find_package\\(biosoup 0.10.0 QUIET\\)")
+                "find_package(biosoup 0.10.0 CONFIG)")
+               (("GTest_FOUND") "TRUE")))))))
+    (inputs
+     (cons* bioparser biosoup (cargo-inputs 'circtools)))
+    (native-inputs
+     (list cmake-minimal pkg-config googletest))
+    (home-page "https://github.com/Kevinzjy/circtools")
+    (synopsis "Accelerating functions in CIRI toolkit")
+    (description "This package provides accelerated functions for the CIRI
+toolkit.  It also provides the @code{ccs} executable to scan for circular
+consensus sequences.")
+    (license license:expat)))
+
+(define-public ciri-long
+  (package
+    (name "ciri-long")
+    (version "1.0.2")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/bioinfo-biols/CIRI-long")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "10k88i1fcqchrrjv82rmylwvbwqfba0n51palhig9hsg71xs0dbi"))
+       ;; Delete bundled binary
+       (snippet '(delete-file "libs/ccs"))))
+    (build-system pyproject-build-system)
+    (arguments
+     (list
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-after 'unpack 'relax-requirements
+            (lambda _
+              (substitute* "setup.py"
+                (("'argparse[^']*',")
+                 "") ;only for python2
+                (("==")
+                 ">=")
+                ;; This package changed names.
+                (("python-Levenshtein")
+                 "levenshtein"))))
+          (add-before 'build 'build-libssw
+            (lambda _
+              (with-directory-excursion "libs/striped_smith_waterman"
+                (invoke "make" "libssw.so"))))
+          (add-before 'build 'fix-reference-to-ccs
+            (lambda* (#:key inputs #:allow-other-keys)
+              (substitute* "CIRI_long/pipeline.py"
+                (("'ccs -i")
+                 (string-append "'"
+                                (assoc-ref inputs "circtools") "/bin/ccs"
+                                " -i")))
+              ;; yuck!
+              (substitute* "CIRI_long/main.py"
+                (("os.chmod\\(lib_path.*")
+                 "")))))))
+    (inputs (list circtools
+                  python-biopython
+                  python-bwapy
+                  python-levenshtein
+                  python-mappy
+                  python-numpy
+                  python-pandas
+                  python-pysam
+                  python-pyspoa
+                  python-scikit-learn
+                  python-scipy))
+    (native-inputs (list python-cython python-pynose python-setuptools))
+    (home-page "https://ciri-cookbook.readthedocs.io/")
+    (synopsis "Circular RNA identification for Nanopore sequencing")
+    (description "CIRI-long is a package for circular RNA identification using
+long-read sequencing data.")
+    (license license:expat)))
+
 (define-public python-circe
   (package
     (name "python-circe")
@@ -6962,6 +7060,7 @@ and v1.1 to v1.2.")
      (list python-mypy-extensions
            python-pytest
            python-pytest-mock
+           python-pytest-runner
            python-setuptools
            python-wheel))
     (propagated-inputs
@@ -7069,16 +7168,14 @@ CWL descriptions.")
   (package
     (name "ravanan")
     (version "0.2.0")
-    (source
+    (source (origin
-     (origin
+              (method url-fetch)
-       (method git-fetch)
+              (uri (string-append
-       (uri (git-reference
+                    "https://github.com/arunisaac/ravanan/releases/download/v"
-              (url "https://github.com/arunisaac/ravanan")
+                    version "/ravanan-" version ".tar.lz"))
-              (commit (string-append "v" version))))
+              (sha256
-       (file-name (git-file-name name version))
+               (base32
-       (sha256
+                "00ayvxsgvma3231ja1759f5fr99a4nw3j23i8qz616wfxa54745s"))))
-        (base32
-         "1ap9h2d92wjvnn8914baqkx6xn8zdanxmpjfg81v3qx35pn938al"))))
     (arguments
      (list #:make-flags
            #~(list (string-append "prefix=" #$output)
@@ -7112,7 +7209,7 @@ CWL descriptions.")
     (inputs
      (list bash-minimal
            node
-           (lookup-package-input guix "guile")
+           guile-3.0
            guile-filesystem
            guile-gcrypt
            guile-json-4
@@ -7231,7 +7328,7 @@ genome- and pangenome-scale queries using a laptop.")
 (define-public delly
   (package
     (name "delly")
-    (version "1.7.3")
+    (version "0.8.3")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -7239,7 +7336,7 @@ genome- and pangenome-scale queries using a laptop.")
                     (commit (string-append "v" version))))
               (file-name (git-file-name name version))
               (sha256
-               (base32 "1ri7m7iv3wakm7zdwqdzm5m71y0swad9n78dzrzr9gs3j7j5yxjs"))
+               (base32 "1ibnplgfzj96w8glkx17v7sld3pm402fr5ybmf3h0rlcryabxrqy"))
               (modules '((guix build utils)))
               (snippet
                '(delete-file-recursively "src/htslib"))))
@@ -8841,8 +8938,7 @@ high-throughput sequencing (HTS) assays")
          ;; Needed by tests
          (add-after 'unpack 'set-HOME
            (lambda _ (setenv "HOME" "/tmp"))))))
-    (propagated-inputs (list mysql-connector-python
+    (propagated-inputs (list python-appdirs
-                             python-appdirs
                              python-biopython
                              python-click
                              python-colorama
@@ -8850,6 +8946,7 @@ high-throughput sequencing (HTS) assays")
                              python-filelock
                              python-loguru
                              python-mygene
+                             python-mysql-connector-python
                              python-norns
                              python-numpy
                              python-pandas
@@ -9805,39 +9902,29 @@ sequencing tag position and orientation.")
 (define-public macs-3
   (package
     (name "macs")
-    (version "3.0.4")
+    (version "3.0.3")
-    (source
+    (source (origin
-     (origin
+              (method git-fetch)
-       (method git-fetch)
+              (uri (git-reference
-       (uri (git-reference
+                    (url "https://github.com/macs3-project/MACS")
-              (url "https://github.com/macs3-project/MACS")
+                    (commit (string-append "v" version))
-              (commit (string-append "v" version))
+                    (recursive? #true)))
-              (recursive? #true)))
+              (file-name (git-file-name name version))
-       (file-name (git-file-name name version))
+              (sha256
-       (sha256
+               (base32
-        (base32 "16cv6bvvppi0z69r5l357ai8x4jg61rx8xrvcapk1wz6mh9naf5s"))))
+                "08hi0a2a0md9gfg7jc75wxv69rggv2yqfd1hyrg4mi5bhi712m0v"))))
     (build-system pyproject-build-system)
-    (arguments
-     (list
-      #:test-flags
-      ;; AssertionError: np.float32(1.0) != np.float64(-1.0)
-      ;; calculated step by step:
-      ;;  6.559423e-18
-      ;; expected:
-      ;;  -2.98155597e-18
-      #~(list (string-append "--deselect=test/test_SignalProcessing.py::"
-                             "Test_maxima::test_implement_smooth_here"))))
-    (native-inputs
-     (list python-cython
-           python-pytest
-           python-setuptools
-           zlib))
     (propagated-inputs
      (list python-cykhash
            python-hmmlearn
            python-numpy
            python-scikit-learn
            python-scipy))
+    (native-inputs
+     (list python-cython
+           python-pytest
+           python-setuptools
+           zlib))
     (home-page "https://github.com/macs3-project/MACS")
     (synopsis "Model based analysis for ChIP-Seq data")
     (description
@@ -13121,22 +13208,28 @@ differently labelled data.")
 (define-public r-pando
   (package
     (name "r-pando")
-    (version "1.1.1")
+    (version "1.0.5")
     (source
      (origin
        (method git-fetch)
        (uri (git-reference
-              (url "https://github.com/quadbio/Pando")
+             (url "https://github.com/quadbiolab/Pando")
-              (commit (string-append "v" version))))
+             (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "1zcsg3my1ka2wprvlx8p08cdz3dqphga54d5rp418zfhcyjy4fkp"))))
+        (base32 "04kr1b28p5j7h48g32cldkg87xcmxnmd4kspygkfs7a4amihpi66"))))
     (properties `((upstream-name . "Pando")))
     (build-system r-build-system)
     (arguments
      (list
       ;; The test file data/test_seurat.rds is not included.
-      #:tests? #false))
+      #:tests? #false
+      #:phases
+      '(modify-phases %standard-phases
+         (add-after 'unpack 'loosen-requirements
+           (lambda _
+             (substitute* "DESCRIPTION"
+               ((" \\(==.*,") ",")))))))
     (propagated-inputs
      (list r-bayestestr
            r-foreach
@@ -14310,7 +14403,11 @@ quality control are provided.")
             (lambda _
               (substitute* "setup.cfg"
                 (("intervaltree~=3.0.2") "intervaltree")
-                (("termcolor~=1.1.0") "termcolor")))))))
+                (("termcolor~=1.1.0") "termcolor"))))
+          (add-after 'unpack 'fix-pytest-config
+            (lambda _
+              (substitute* "pyproject.toml"
+                ((" --cov=gdc_client --cov-report term") "")))))))
     (native-inputs
      (list python-flask
            python-httmock
@@ -18336,6 +18433,44 @@ following the assay and produces a file detailing peaks of significant
 enrichment.")
     (license license:expat)))
 
+(define-public mantis
+  ;; This is an arbitrary commit as a year has passed since 0.1 was tagged.
+  (let ((commit "b6979a269172a45201c8366680d8b889f889432b")
+        (revision "2"))
+    (package
+      (name "mantis")
+      (version (git-version "0.1" revision commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "https://github.com/splatlab/mantis")
+                      (commit commit)))
+                (file-name (git-file-name name version))
+                (sha256
+                 (base32
+                  "0dq8a785hnaxx5kq757m5czs8xpcjpcph1inq2nm8h6zfvqyj8xs"))))
+      (build-system cmake-build-system)
+      (arguments
+       '(#:tests? #f ; there are none
+         #:configure-flags (list "-DNH=ON"))) ; do not use SSE4.2 instructions
+      (inputs
+       (list sdsl-lite openssl zlib))
+      (native-inputs
+       (list gcc-7))
+      (home-page "https://github.com/splatlab/mantis")
+      (synopsis "Large-scale sequence-search index data structure")
+      (description "Mantis is a space-efficient data structure that can be
+used to index thousands of raw-read genomics experiments and facilitate
+large-scale sequence searches on those experiments.  Mantis uses counting
+quotient filters instead of Bloom filters, enabling rapid index builds and
+queries, small indexes, and exact results, i.e., no false positives or
+negatives.  Furthermore, Mantis is also a colored de Bruijn graph
+representation, so it supports fast graph traversal and other topological
+analyses in addition to large-scale sequence-level searches.")
+      ;; uses __uint128_t and inline assembly
+      (supported-systems '("x86_64-linux"))
+      (license license:bsd-3))))
+
 (define-public sjcount
   ;; There is no tag for version 3.2, nor is there a release archive.
   (let ((commit "292d3917cadb3f6834c81e509c30e61cd7ead6e5")
@@ -20231,7 +20366,13 @@ fasta subsequences.")
               " and not test_roundtrip"
               ;; This test depends on ipytree, which contains a lot of
               ;; minified JavaScript.
-              " and not test_print_trees"))))
+              " and not test_print_trees"))
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-after 'unpack 'fix-pytest-config
+            (lambda _
+              (substitute* "pyproject.toml"
+                ((".*--cov.*") "")))))))
     (native-inputs
      (list python-hatchling
            python-pytest))

gnu/packages/bittorrent.scm

@@ -41,16 +41,32 @@
 ;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
 
 (define-module (gnu packages bittorrent)
+  #:use-module (guix packages)
+  #:use-module (guix download)
+  #:use-module (guix git-download)
+  #:use-module (guix build-system cmake)
+  #:use-module (guix build-system gnu)
+  #:use-module (guix build-system meson)
+  #:use-module (guix build-system pyproject)
+  #:use-module (guix build-system python)
+  #:use-module (guix build-system qt)
+  #:use-module (guix build-system glib-or-gtk)
+  #:use-module ((guix licenses) #:prefix l:)
+  #:use-module (guix gexp)
+  #:use-module (guix utils)
+  #:use-module ((guix search-paths) #:select ($SSL_CERT_DIR $SSL_CERT_FILE))
+  #:use-module (gnu packages)
+  #:use-module (gnu packages adns)
   #:use-module (gnu packages autotools)
   #:use-module (gnu packages bash)
   #:use-module (gnu packages boost)
+  #:use-module (gnu packages nss)
   #:use-module (gnu packages check)
   #:use-module (gnu packages cmake)
   #:use-module (gnu packages compression)
   #:use-module (gnu packages crypto)
   #:use-module (gnu packages curl)
   #:use-module (gnu packages cyrus-sasl)
-  #:use-module (gnu packages dns)
   #:use-module (gnu packages freedesktop)
   #:use-module (gnu packages gettext)
   #:use-module (gnu packages glib)
@@ -60,9 +76,8 @@
   #:use-module (gnu packages gtk)
   #:use-module (gnu packages libevent)
   #:use-module (gnu packages multiprecision)
-  #:use-module (gnu packages ncurses)
   #:use-module (gnu packages nettle)
-  #:use-module (gnu packages nss)
+  #:use-module (gnu packages ncurses)
   #:use-module (gnu packages perl)
   #:use-module (gnu packages pkg-config)
   #:use-module (gnu packages python)
@@ -71,29 +86,15 @@
   #:use-module (gnu packages python-crypto)
   #:use-module (gnu packages python-web)
   #:use-module (gnu packages python-xyz)
-  #:use-module (gnu packages qt)
   #:use-module (gnu packages serialization)
+  #:use-module (gnu packages qt)
   #:use-module (gnu packages sqlite)
   #:use-module (gnu packages ssh)
   #:use-module (gnu packages tls)
   #:use-module (gnu packages version-control)
   #:use-module (gnu packages web)
   #:use-module (gnu packages xml)
-  #:use-module (gnu packages xorg)
+  #:use-module (gnu packages xorg))
-  #:use-module (gnu packages)
-  #:use-module (guix build-system cmake)
-  #:use-module (guix build-system glib-or-gtk)
-  #:use-module (guix build-system gnu)
-  #:use-module (guix build-system meson)
-  #:use-module (guix build-system pyproject)
-  #:use-module (guix build-system qt)
-  #:use-module (guix download)
-  #:use-module (guix gexp)
-  #:use-module (guix git-download)
-  #:use-module ((guix licenses) #:prefix license:)
-  #:use-module (guix packages)
-  #:use-module ((guix search-paths) #:select ($SSL_CERT_DIR $SSL_CERT_FILE))
-  #:use-module (guix utils))
 
 (define-public transmission
   (package
@@ -193,7 +194,7 @@ DHT, µTP, PEX and Magnet Links.")
     ;; or any future license endorsed by Mnemosyne LLC.
     ;;
     ;; A few files files carry an MIT/X11 license header.
-    (license (list license:gpl2 license:gpl3))))
+    (license (list l:gpl2 l:gpl3))))
 
 (define-public transmission-remote-gtk
   (package
@@ -223,7 +224,7 @@ DHT, µTP, PEX and Magnet Links.")
     (description "transmission-remote-gtk is a GTK client for remote management
 of the Transmission BitTorrent client, using its HTTP RPC protocol.")
     (home-page "https://github.com/transmission-remote-gtk/transmission-remote-gtk")
-    (license license:gpl2+)))
+    (license l:gpl2+)))
 
 (define-public stig
   (package
@@ -266,7 +267,7 @@ of the Transmission BitTorrent client, using its HTTP RPC protocol.")
      "Stig is a @acronym{TUI, Text User Interface} and @acronym{CLI, Command
 Line Interface} client for the BitTorrent client Transmission.")
     (home-page "https://github.com/rndusr/stig")
-    (license license:gpl3)))
+    (license l:gpl3)))
 
 (define-public libtorrent
   (package
@@ -290,7 +291,7 @@ Line Interface} client for the BitTorrent client Transmission.")
 with the BitTorrent client rtorrent.  It is written in C++ with emphasis on
 speed and efficiency.")
     (home-page "https://github.com/rakshasa/libtorrent")
-    (license license:gpl2+)))
+    (license l:gpl2+)))
 
 (define-public rtorrent
   (package
@@ -319,7 +320,7 @@ speed and efficiency.")
 full encryption, DHT, PEX, and Magnet Links.  It can also be controlled via
 XML-RPC over SCGI.")
     (home-page "https://github.com/rakshasa/rtorrent")
-    (license license:gpl2+)))
+    (license l:gpl2+)))
 
 (define-public tremc
   (let ((commit "d8deaa5ac25bb45a2ca3a930309d6ecc74836a54")
@@ -353,7 +354,7 @@ XML-RPC over SCGI.")
     (description "Tremc is a console client, with a curses interface, for the
 Transmission BitTorrent daemon.")
     (home-page "https://github.com/tremc/tremc")
-    (license license:gpl3+))))
+    (license l:gpl3+))))
 
 (define-public aria2
   (package
@@ -418,7 +419,7 @@ download utility.  It supports HTTP/HTTPS, FTP, SFTP, BitTorrent and Metalink.
 Aria2 can be manipulated via built-in JSON-RPC and XML-RPC interfaces.")
     (properties
      '((release-monitoring-url . "https://github.com/aria2/aria2/releases")))
-    (license license:gpl2+)))
+    (license l:gpl2+)))
 
 (define-public uget
   (package
@@ -452,7 +453,7 @@ Aria2 can be manipulated via built-in JSON-RPC and XML-RPC interfaces.")
      "uGet is portable download manager with GTK+ interface supporting
 HTTP, HTTPS, BitTorrent and Metalink, supporting multi-connection
 downloads, download scheduling, download rate limiting.")
-    (license license:lgpl2.1+)))
+    (license l:lgpl2.1+)))
 
 (define-public mktorrent
   (package
@@ -487,8 +488,8 @@ files and whole directories.  It can add multiple trackers and web seed URLs,
 and set the @code{private} flag to disallow advertisement through the
 distributed hash table (@dfn{DHT}) and Peer Exchange.  Hashing is multi-threaded
 and will take advantage of multiple processor cores where possible.")
-    (license (list license:public-domain ; sha1.*, used to build without OpenSSL
+    (license (list l:public-domain      ; sha1.*, used to build without OpenSSL
-                   license:gpl2+))))     ; with permission to link with OpenSSL
+                   l:gpl2+))))          ; with permission to link with OpenSSL
 
 (define-public libtorrent-rasterbar
   (package
@@ -532,16 +533,15 @@ and will take advantage of multiple processor cores where possible.")
     (inputs (list boost-1.83 openssl))
     (native-inputs
      (list libfaketime
-           pkg-config
+           python-wrapper
-           python-setuptools
+           pkg-config))
-           python-wrapper))
     (home-page "https://www.libtorrent.org/")
     (synopsis "Feature-complete BitTorrent implementation")
     (description
      "libtorrent-rasterbar is a feature-complete C++ BitTorrent implementation
 focusing on efficiency and scalability.  It runs on embedded devices as well as
 desktops.")
-    (license license:bsd-2)))
+    (license l:bsd-2)))
 
 (define-public qbittorrent
   (package
@@ -585,7 +585,7 @@ libtorrent (sometimes called libtorrent-rasterbar) by Arvid Norberg.
 It aims to be a good alternative to all other BitTorrent clients out there.
 qBittorrent is fast, stable and provides unicode support as well as many
 features.")
-    (license license:gpl2+)))
+    (license l:gpl2+)))
 
 (define-public qbittorrent-no-x
   (let ((base qbittorrent))
@@ -727,4 +727,4 @@ Protocol Encryption, DHT, Local Peer Discovery (LSD), Peer Exchange
 speed limits.  Deluge heavily utilises the ​libtorrent library.  It is
 designed to run as both a normal standalone desktop application and as a
 ​client-server.")
-    (license license:gpl3+)))
+    (license l:gpl3+)))

gnu/packages/boost.scm

@@ -83,6 +83,9 @@
     (build-system gnu-build-system)
     (arguments
      (list
+      #:imported-modules %pyproject-build-system-modules
+      #:modules `(((guix build pyproject-build-system) #:select (python-version))
+                  ,@%default-gnu-modules)
       #:tests? #f
       #:configure-flags
       #~(let ((icu (dirname (dirname (search-input-file
@@ -91,26 +94,17 @@
            ;; Auto-detection looks for ICU only in traditional
            ;; install locations.
            (string-append "--with-icu=" icu)
-           ;; Ditto for Python.  The Gexp can't be evaluated if python is not
+           ;; Ditto for Python.
-           ;; in the inputs (e.g. boost-for-mysql), so delay its evaluation
+           #$@(if (%current-target-system)
-           ;; after checking for python, rather than concurrently.
+                  #~()
-           #$@(force
+                  #~((let ((python (dirname (dirname (search-input-file
-               (if (or (%current-target-system)
+                                                      %build-inputs
-                       (not (this-package-input "python-minimal-wrapper")))
+                                                      "bin/python")))))
-                   (delay
+                       (string-append "--with-python-root=" python)
-                     #~())
+                       (string-append "--with-python=" python
-                   (delay
+                                      "/bin/python")
-                     #~((let ((python (dirname (dirname (search-input-file
+                       (string-append "--with-python-version="
-                                                         %build-inputs
+                                      (python-version python)))))
-                                                         "bin/python")))))
-                          (string-append "--with-python-root=" python)
-                          (string-append "--with-python=" python
-                                         "/bin/python")
-                          (string-append "--with-python-version="
-                                         #$(version-major+minor
-                                            (package-version
-                                             (this-package-input
-                                              "python-minimal-wrapper")))))))))
            "--with-toolset=gcc"))
       #:make-flags
       #~(list "threading=multi" "link=shared"
@@ -206,39 +200,29 @@
           (replace 'install
             (lambda* (#:key make-flags #:allow-other-keys)
               (apply invoke "./b2" "install" make-flags)))
-          #$@(force  ; See above for why the force is necessary.
+          #$@(if (%current-target-system)
-              (if (or (%current-target-system)
+                 #~()
-                      (not (this-package-input "python-minimal-wrapper")))
+                 #~((add-after 'install 'provide-libboost_python
-                  (delay
+                      (lambda* (#:key make-flags inputs outputs #:allow-other-keys)
-                    #~())
+                        (let* ((static? (member "link=static" make-flags))
-                  (delay
+                               (libext (if static? ".a" ".so"))
-                    #~((add-after 'install 'provide-libboost_python
+                               (python (dirname (dirname (search-input-file
-                         (lambda* (#:key make-flags inputs outputs
+                                                          inputs "bin/python"))))
-                                   #:allow-other-keys)
+                               (python-version (python-version python))
-                           (let* ((static? (member "link=static" make-flags))
+                               (libboost_pythonNN
-                                  (ext (if static? ".a" ".so"))
+                                (string-append "libboost_python"
-                                  (python (dirname
+                                               (string-join (string-split
-                                           (dirname (search-input-file
+                                                             python-version #\.)
-                                                     inputs "bin/python"))))
+                                                            "")
-                                  (python-version
+                                               libext)))
-                                   #$(version-major+minor
+                          (with-directory-excursion (string-append #$output "/lib")
-                                      (package-version
+                            (symlink libboost_pythonNN
-                                       (this-package-input
+                                     (string-append "libboost_python" libext))
-                                        "python-minimal-wrapper"))))
+                            ;; Some packages only look for the major version.
-                                  (NN (string-join (string-split
+                            (symlink libboost_pythonNN
-                                                    python-version #\.)
+                                     (string-append "libboost_python"
-                                                   ""))
+                                                    (string-take python-version 1)
-                                  (libboost_pythonNN
+                                                    libext)))))))))))
-                                   (string-append "libboost_python" NN ext))
-                                  (major (string-take python-version 1)))
-                             (with-directory-excursion
-                                 (string-append #$output "/lib")
-                               (symlink libboost_pythonNN
-                                        (string-append "libboost_python" ext))
-                               ;; Some packages only look for the major version.
-                               (symlink libboost_pythonNN
-                                        (string-append "libboost_python"
-                                                       major ext)))))))))))))
     (inputs
      (append
       (list icu4c zlib)

gnu/packages/browser-extensions.scm

@@ -95,8 +95,8 @@ supported content to the Kodi media center.")
   ;; Arbitrary commit of branch master,
   ;; Update when updating uBlockOrigin.
   (let* ((name "ublock-main-assets")
-         (commit "004af606e6a0efc22bc65ab1016b553441cacb71")
+         (commit "011eef4a5b36a7ebf4adedc486d96b77cfa25c54")
-         (revision "6")
+         (revision "5")
          (version (git-version "0" revision commit)))
     (origin
       (method git-fetch)
@@ -105,14 +105,14 @@ supported content to the Kodi media center.")
             (commit commit)))
       (file-name (git-file-name name version))
       (sha256
-       (base32 "1bfd2d53flrkgvjcr1kj9nbxj4y9a4pcr7m3dycccdhd21x6k0ln")))))
+       (base32 "0ng8a88zdvrxg30fz83gswjy27b3hfx9q11n2i715id7az7kqf9x")))))
 
 (define ublock-prod-assets
   ;; Arbitrary commit of branch gh-pages,
   ;; Update when updating uBlockOrigin.
   (let* ((name "ublock-prod-assets")
-         (commit "6c15e4ef91888c610caf73829dc78ae9549ed24a")
+         (commit "6844322800de647da0c4fe06dd6a0b212a3942e4")
-         (revision "6")
+         (revision "5")
          (version (git-version "0" revision commit)))
     (origin
       (method git-fetch)
@@ -121,12 +121,12 @@ supported content to the Kodi media center.")
             (commit commit)))
       (file-name (git-file-name name version))
       (sha256
-       (base32 "0n2h6drqh44b1zgl729bfr70n08mkm536a2vqgivw7dm5dmi8zd3")))))
+       (base32 "13vxq4z1wxivz5xklncxd2sj5aqkyhq919vzbbfp0fgh0imhikib")))))
 
 (define ublock-origin
   (package
     (name "ublock-origin")
-    (version "1.70.0")
+    (version "1.66.2")
     (home-page "https://github.com/gorhill/uBlock")
     (source (origin
               (method git-fetch)
@@ -136,7 +136,7 @@ supported content to the Kodi media center.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "0j1m80nz86yc69c42hv5di5zza0vkycqmjaydb9jgx0abcvi19x5"))))
+                "16ph031hb8bf4rxyxvm6jr0bxmy0snza11jfrbjgfb390gax9r63"))))
     (build-system gnu-build-system)
     (outputs '("xpi" "firefox" "chromium"))
     (properties '((addon-id . "uBlock0@raymondhill.net")))

gnu/packages/build-tools.scm

@@ -26,7 +26,6 @@
 ;;; Copyright © 2025 Josep Bigorra <jjbigorra@gmail.com>
 ;;; Copyright © 2025 John Kehayias <john.kehayias@protonmail.com>
 ;;; Copyright © 2026 Nemin <bergengocia@protonmail.com>
-;;; Copyright © 2026 Nguyễn Gia Phong <cnx@loang.net>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -44,17 +43,37 @@
 ;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
 
 (define-module (gnu packages build-tools)
+  #:use-module (ice-9 optargs)
+  #:use-module ((guix licenses) #:prefix license:)
+  #:use-module (gnu packages c)
+  #:use-module (guix build-system cmake)
+  #:use-module (guix build-system copy)
+  #:use-module (guix build-system gnu)
+  #:use-module (guix build-system guile)
+  #:use-module (guix build-system hare)
+  #:use-module (guix build-system meson)
+  #:use-module (guix build-system pyproject)
+  #:use-module (guix build-system python)
+  #:use-module (guix build-system trivial)
+  #:use-module (guix deprecation)
+  #:use-module (guix download)
+  #:use-module (guix gexp)
+  #:use-module (guix git-download)
+  #:use-module (guix modules)
+  #:use-module (guix packages)
+  #:use-module (guix search-paths)
+  #:use-module (guix utils)
+  #:use-module (gnu packages)
+  #:use-module (gnu packages adns)
   #:use-module (gnu packages algebra)
   #:use-module (gnu packages autotools)
   #:use-module (gnu packages base)
   #:use-module (gnu packages bash)
-  #:use-module (gnu packages c)
   #:use-module (gnu packages check)
   #:use-module (gnu packages code)
   #:use-module (gnu packages compression)
   #:use-module (gnu packages cpp)
   #:use-module (gnu packages cppi)
-  #:use-module (gnu packages dns)
   #:use-module (gnu packages elf)
   #:use-module (gnu packages gcc)
   #:use-module (gnu packages guile)
@@ -81,30 +100,10 @@
   #:use-module (gnu packages rpc)
   #:use-module (gnu packages serialization)
   #:use-module (gnu packages sqlite)
-  #:use-module (gnu packages tcl)
   #:use-module (gnu packages tls)
   #:use-module (gnu packages unicode)
   #:use-module (gnu packages version-control)
-  #:use-module (gnu packages xml)
+  #:use-module (gnu packages xml))
-  #:use-module (gnu packages)
-  #:use-module (guix build-system cmake)
-  #:use-module (guix build-system copy)
-  #:use-module (guix build-system gnu)
-  #:use-module (guix build-system guile)
-  #:use-module (guix build-system hare)
-  #:use-module (guix build-system meson)
-  #:use-module (guix build-system pyproject)
-  #:use-module (guix build-system trivial)
-  #:use-module (guix deprecation)
-  #:use-module (guix download)
-  #:use-module (guix gexp)
-  #:use-module (guix git-download)
-  #:use-module ((guix licenses) #:prefix license:)
-  #:use-module (guix modules)
-  #:use-module (guix packages)
-  #:use-module (guix search-paths)
-  #:use-module (guix utils)
-  #:use-module (ice-9 optargs))
 
 (define-public acr
   (package
@@ -140,48 +139,6 @@ Bourne shell script instead of m4.")
     (home-page "https://github.com/radareorg/acr")
     (license license:gpl2)))
 
-(define-public autosetup
-  (package
-    (name "autosetup")
-    (version "0.7.2")
-    (source
-     (origin
-       (method git-fetch)
-       (uri (git-reference
-             (url "https://github.com/msteveb/autosetup")
-             (commit (string-append "v" version))))
-       (file-name (git-file-name name version))
-       (sha256 (base32 "002b380073cpxlqziia2gvngywrb37b08p9k0zk9vlxn2p174hc6"))
-       (modules '((guix build utils)))
-       (snippet
-        #~(begin
-            (delete-file "jimsh0.c")
-            (substitute* "Makefile"
-              (("^.*tclsh8\\..*")       ;tests run with specific Tcl versions
-               ""))))))
-    (build-system gnu-build-system)
-    (arguments
-     (list #:test-target "test"
-           #:phases
-           #~(modify-phases %standard-phases
-               (delete 'configure)
-               (delete 'build)
-               (replace 'install
-                 (lambda* (#:key inputs #:allow-other-keys)
-                   (substitute* "sys-find-tclsh"
-                     (("jimsh tclsh")
-                      (search-input-file inputs "bin/tclsh")))
-                   (invoke "tclsh" "autosetup"
-                           (string-append "--sysinstall=" #$output)))))))
-    (inputs (list tcl))
-    (home-page "https://msteveb.github.io/autosetup/")
-    (synopsis "Build environment auto-configurator")
-    (description
-     "@command{autosetup} is a tool, similar to @command{autoconf},
-to configure a build system for the appropriate environment,
-according to the system capabilities and the user-selected options.")
-    (license license:bsd-2)))
-
 (define-public bam
   (package
     (name "bam")
@@ -195,8 +152,7 @@ according to the system capabilities and the user-selected options.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "13br735ig7lygvzyfd15fc2rdygrqm503j6xj5xkrl1r7w2wipq6"))
+                "13br735ig7lygvzyfd15fc2rdygrqm503j6xj5xkrl1r7w2wipq6"))))
-              (patches (search-patches "bam-python3-compat.patch"))))
     (build-system gnu-build-system)
     (arguments
      `(#:make-flags `(,(string-append "CC=" ,(cc-for-target))
@@ -207,7 +163,7 @@ according to the system capabilities and the user-selected options.")
        (modify-phases %standard-phases
          (delete 'configure))))
     (native-inputs
-     (list python-minimal-wrapper))
+     `(("python" ,python-2)))
     (inputs
      (list lua))
     (home-page "https://matricks.github.io/bam/")
@@ -344,8 +300,8 @@ programs and other files depend.")
     (license license:bsd-3)))
 
 (define-public gn
-  (let ((commit "6e8dcdebbadf4f8aa75e6a4b6e0bdf89dce1513a")
+  (let ((commit "ee5b7e32b961a9da1933e9f46a018ba6cac8ef60")
-        (revision "2354"))            ;as returned by `git describe`, used below
+        (revision "2277"))            ;as returned by `git describe`, used below
     (package
       (name "gn")
       (version (git-version "0.0" revision commit))
@@ -355,7 +311,7 @@ programs and other files depend.")
                 (uri (git-reference (url home-page) (commit commit)))
                 (sha256
                  (base32
-                  "0yz38czmbc72q1hkiv3cwxqh2i8ji2vkkvvk5ws2cjplmn2vj0x9"))
+                  "19kkvwxl66vlzlfppbq03fmi59i5g8a1yc71fsfgwqqmx4wywd6w"))
                 (file-name (git-file-name name version))))
       (build-system gnu-build-system)
       (arguments
@@ -365,8 +321,7 @@ programs and other files depend.")
                    (lambda _
                      (setenv "CC" "gcc")
                      (setenv "CXX" "g++")
-                     (setenv "CXXFLAGS"
+                     (setenv "CXXFLAGS" "-g -O2 -Wno-error=redundant-move")
-                             "-g -O2 -Wno-error=redundant-move -Wno-error=comment")
                      (setenv "AR" "ar")))
                  (replace 'configure
                    (lambda _
@@ -431,8 +386,9 @@ files and generates build instructions for the Ninja build system.")
     (arguments
      (list
       #:tests? #f                       ;disabled to avoid extra dependencies
-      ;; Custom build steps to prevent using pyproject-build-system which
+      ;; Essentially a lighter copy of the former python-build-system.
-      ;; allows to edit the latter without a C++ world rebuild.
+      ;; Using it rather than pyproject-build-system allows to edit the latter
+      ;; without a C++ world rebuild.
       #:phases
       #~(modify-phases %standard-phases
           (delete 'bootstrap)

gnu/packages/c.scm

@@ -54,6 +54,7 @@
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system meson)
   #:use-module (guix build-system pyproject)
+  #:use-module (guix build-system python)
   #:use-module (guix store)
   #:use-module (gnu packages)
   #:use-module (gnu packages bash)

gnu/packages/calendar.scm

@@ -45,6 +45,7 @@
   #:use-module (guix build-system go)
   #:use-module (guix build-system cmake)
   #:use-module (guix build-system pyproject)
+  #:use-module ((guix build-system python) #:select (pypi-uri))
   #:use-module (gnu packages admin)
   #:use-module (gnu packages autotools)
   #:use-module (gnu packages base)

gnu/packages/cdrom.scm

@@ -595,11 +595,7 @@ capacity is user-selectable.")
                             version "/DVDStyler-" version ".tar.bz2"))
        (sha256
         (base32
-         "0n3mfjsazvlzk9hl23q3iz7bmxjq7b5lx0ab8nbk1jgl763k9cqb"))
+         "0n3mfjsazvlzk9hl23q3iz7bmxjq7b5lx0ab8nbk1jgl763k9cqb"))))
-       (snippet
-        #~(begin (delete-file "src/dvdvml.c")
-                 (delete-file "src/dvdvmy.c")
-                 (delete-file "src/dvdvmy.h")))))
     (build-system gnu-build-system)
     (arguments
      `(#:configure-flags
@@ -629,28 +625,27 @@ capacity is user-selectable.")
              #t)))
        #:tests? #f)) ; No tests.
     (inputs ; TODO package bundled wxvillalib
-     (list bash-minimal ; for wrap-program
+     `(("wxwidgets" ,wxwidgets)
-           cdrtools
+       ("wssvg" ,wxsvg)
-           dbus
+       ("bash" ,bash-minimal) ; for wrap-program
-           dvd+rw-tools
+       ("dbus" ,dbus)
-           dvdauthor
+       ("cdrtools" ,cdrtools)
-           eudev
+       ("dvd+rw-tools" ,dvd+rw-tools)
-           ffmpeg-4
+       ("dvdauthor" ,dvdauthor)
-           fontconfig
+       ("eudev" ,eudev)
-           libexif
+       ("fontconfig" ,fontconfig)
-           libjpeg-turbo
+       ("libexif" ,libexif)
-           wxsvg
+       ("libjpeg" ,libjpeg-turbo)
-           wxwidgets))
+       ("ffmpeg" ,ffmpeg-4)))
     (native-inputs
-     (list bison
+     `(("pkg-config" ,pkg-config)
-           docbook-xml
+       ("flex" ,flex)
-           docbook-xsl
+       ("python" ,python-2)
-           flex
+       ("xmlto" ,xmlto)
-           gettext-minimal
+       ("gettext" ,gettext-minimal)
-           pkg-config
+       ("docbook-xml" ,docbook-xml)
-           python-minimal-wrapper
+       ("docbook-xsl" ,docbook-xsl)
-           xmlto
+       ("zip" ,zip)))
-           zip))
     (synopsis "DVD authoring application")
     (description "DVDStyler is a DVD authoring application which allows users
 to burn video files in many formats to DVD discs, complete with individually

gnu/packages/check.scm

@@ -131,6 +131,7 @@
   #:use-module (guix build-system meson)
   #:use-module (guix build-system perl)
   #:use-module (guix build-system pyproject)
+  #:use-module (guix build-system python)
   #:use-module (guix build-system trivial)
   #:use-module (ice-9 match)
   #:use-module (srfi srfi-1))
@@ -1881,6 +1882,7 @@ http server.")
     (arguments (list #:tests? #false)) ;no tests included
     (native-inputs
      (list python-pytest
+           python-pytest-cov
            python-setuptools
            python-wheel
            python-xmlschema))
@@ -1913,6 +1915,42 @@ XML output")
 decorators from external files.")
     (license license:expat)))
 
+(define-public python-pytest-random-order
+  (package
+    (name "python-pytest-random-order")
+    (version "1.1.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "pytest-random-order" version))
+       (sha256
+        (base32 "104hww3b86jchk41kjhyycr541pd2dfgqkww6lx5y70z9z9xfwj4"))))
+    (build-system pyproject-build-system)
+    (arguments
+     (list
+      #:test-flags
+      ;; AttributeError: module 'py' has no attribute 'code'.
+      #~(list "-k" (string-append "not test_it_works_with_actual_tests"
+                                  " and not test_failed_first"
+                                  " and not test_doctests"))))
+    (native-inputs
+     (list python-pytest-xdist
+           python-setuptools
+           python-py
+           python-wheel))
+    (propagated-inputs
+     (list python-pytest))
+    (home-page "https://github.com/jbasko/pytest-random-order")
+    (synopsis "Pytest plugin to randomize the order of tests")
+    (description "@code{pytest-random-order} is a Pytest plugin that
+randomizes the order of tests.  This can be useful to detect a test that
+passes just because it happens to run after an unrelated test that leaves the
+system in a favourable state.  The plugin allows user to control the level of
+randomness they want to introduce and to disable reordering on subsets of
+tests.  Tests can be rerun in a specific order by passing a seed value
+reported in a previous test run.")
+    (license license:expat)))
+
 (define-public python-pytest-runner
   (package
     (name "python-pytest-runner")
@@ -2918,8 +2956,12 @@ mypy plugins.")
                            "and not upstream_url"))))
     (native-inputs
      (list python-pytest
+           python-pytest-black
            python-pytest-checkdocs
+           python-pytest-cov
            python-pytest-enabler
+           python-pytest-flake8
+           python-pytest-mypy
            python-setuptools
            python-wheel))
     (propagated-inputs
@@ -3044,6 +3086,7 @@ possible to write plugins to add your own checks.")
            python-path
            python-pyhamcrest
            python-pytest
+           python-pytest-html
            python-setuptools))
     (propagated-inputs
      (list python-colorama

gnu/packages/chemistry.scm

@@ -28,6 +28,7 @@
   #:use-module (guix build-system cmake)
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system pyproject)
+  #:use-module (guix build-system python)
   #:use-module (guix download)
   #:use-module (guix gexp)
   #:use-module (guix git-download)
@@ -825,7 +826,7 @@ colleagues, or to generate pre-rendered animations.")
 (define-public python-pyscf
   (package
     (name "python-pyscf")
-    (version "2.12.1")
+    (version "2.9.0")
     (source
      (origin
        (method git-fetch)
@@ -834,10 +835,14 @@ colleagues, or to generate pre-rendered animations.")
               (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "00q5c0r5yzp05m65679164s7jzm9678b63msm8g7953vh8v9g25y"))))
+        (base32 "1lj48c749aqf9zd5xbshjsfr0y972r2nsm8lf3760jbfadg9jdsi"))))
     (build-system pyproject-build-system)
     (arguments
      (list
+      #:modules
+      '((guix build pyproject-build-system)
+        (guix build utils)
+        (ice-9 textual-ports))
       ;; Some tests take a very long time and libxc support is not enabled.
       #:tests? #f
       #:phases
@@ -863,8 +868,16 @@ colleagues, or to generate pre-rendered animations.")
                          "-DBUILD_XCFUN=OFF"
                          "-DBUILD_LIBCINT=OFF"))))))))
     (native-inputs
-     (list cmake-minimal
+     (list
-           python-setuptools))
+      cmake-minimal
+      ;; HACK: Add gcc, make tune work.
+      ;; build-system-with-tuning-compiler on guix/transformations.scm
+      ;; want to find compiler on the build-inputs, but gcc is on the
+      ;; python-build-system's host-inputs, so when tune it , will report:
+      ;; "failed to determine which compiler is used"
+      (canonical-package gcc)
+      python-setuptools
+      python-wheel))
     (inputs
      (list
       ;; Use qcint when tuning for x86_64.

gnu/packages/chromium.scm

@@ -79,13 +79,11 @@
   '("base/third_party/cityhash" ;Expat
     "base/third_party/double_conversion" ;BSD-3
     "base/third_party/icu" ;Unicode, X11-style
-    "base/third_party/nspr" ;MPL-2.0
     "base/third_party/superfasthash" ;BSD-3
     "base/third_party/symbolize" ;BSD-3
     "base/third_party/xdg_user_dirs" ;Expat
-    "buildtools/third_party/libc++" ;BSD
-    "buildtools/third_party/libc++abi" ;BSD
     "net/third_party/mozilla_security_manager" ;MPL-1.1/GPL2+/LGPL2.1+
+    "net/third_party/nss" ;MPL-2.0
     "net/third_party/quiche" ;BSD-3
     "net/third_party/uri_template" ;ASL2.0
     "third_party/abseil-cpp" ;ASL2.0
@@ -106,11 +104,8 @@
     "third_party/catapult" ;BSD-3
     "third_party/catapult/common/py_vulcanize/third_party/rcssmin" ;ASL2.0
     "third_party/catapult/common/py_vulcanize/third_party/rjsmin" ;ASL2.0
-    "third_party/catapult/third_party/beautifulsoup4-4.9.3" ;Expat
-    "third_party/catapult/third_party/html5lib-1.1" ;Expat
     "third_party/catapult/third_party/polymer" ;BSD-3
     "third_party/catapult/third_party/six" ;Expat
-    "third_party/catapult/third_party/typ" ;ASL2.0
     ;; XXX: This is a minified version of <https://d3js.org/>.
     "third_party/catapult/tracing/third_party/d3" ;BSD-3
     "third_party/catapult/tracing/third_party/gl-matrix" ;Expat
@@ -125,12 +120,19 @@
     "third_party/cld_3" ;ASL2.0
     "third_party/closure_compiler" ;ASL2.0
     "third_party/compiler-rt" ;ASL2.0
+    "third_party/compiler-rt/src/lib" ;ASL2.0
+    "third_party/compiler-rt/src/lib/builtins" ;ASL2.0
     "third_party/content_analysis_sdk" ;BSD-3
     "third_party/cpuinfo" ;BSD-2
     "third_party/crabbyavif" ;ASL2.0
+    "third_party/crabbyavif/src/sys/dav1d-sys" ;ASL2.0
+    "third_party/crabbyavif/src/sys/aom-sys" ;ASL2.0
+    "third_party/crabbyavif/src/sys/libgav1-sys" ;ASL2.0
+    "third_party/crabbyavif/src/sys/libyuv-sys" ;ASL2.0
+    "third_party/crabbyavif/src/sys/ndk-sys" ;ASL2.0
     "third_party/crashpad" ;ASL2.0
     "third_party/crashpad/crashpad/third_party/lss" ;ASL2.0
-    "third_party/crashpad/crashpad/third_party/zlib" ;Zlib
+    "third_party/crashpad/crashpad/third_party/zlib/zlib_crashpad.h" ;Zlib
     "third_party/crc32c" ;BSD-3
     "third_party/cros_system_api" ;BSD-3
     "third_party/dav1d" ;BSD-2
@@ -138,25 +140,19 @@
     ;; TODO: can likely be unbundled when Vulkan is updated.
     "third_party/dawn/third_party/khronos" ;ASL2.0
     "third_party/dawn/third_party/gn/webgpu-cts" ;BSD-3
-    "third_party/dawn/third_party/renderdoc" ;Expat
-    "third_party/dawn/third_party/webgpu-headers" ;BSD-3
-    "third_party/depot_tools" ;BSD-3
-    "third_party/devscripts" ;GPL2.0
     "third_party/devtools-frontend" ;BSD-3
     "third_party/devtools-frontend/src/front_end"
     "third_party/devtools-frontend/src/front_end/third_party"
     "third_party/devtools-frontend/src/front_end/third_party/acorn" ;Expat
     "third_party/devtools-frontend/src/front_end/third_party\
 /additional_readme_paths.json" ;no explicit license; trivial
+    "third_party/devtools-frontend/src/front_end/third_party/json5" ;Expat
     "third_party/devtools-frontend/src/front_end/third_party/axe-core" ;MPL2.0
     "third_party/devtools-frontend/src/front_end/third_party/chromium" ;BSD-3
     "third_party/devtools-frontend/src/front_end/third_party/codemirror" ;Expat
-    "third_party/devtools-frontend/src/front_end/third_party/csp_evaluator" ;BSD-3
     "third_party/devtools-frontend/src/front_end/third_party/diff" ;ASL2.0
     "third_party/devtools-frontend/src/front_end/third_party/i18n" ;ASL2.0
     "third_party/devtools-frontend/src/front_end/third_party/intl-messageformat" ;BSD-3
-    "third_party/devtools-frontend/src/front_end/third_party/json5" ;Expat
-    "third_party/devtools-frontend/src/front_end/third_party/legacy-javascript" ;ASL-2.0
     "third_party/devtools-frontend/src/front_end/third_party/lighthouse" ;ASL2.0
     "third_party/devtools-frontend/src/front_end/third_party/lit" ;BSD-3
     "third_party/devtools-frontend/src/front_end/third_party/marked" ;Expat, BSD-3
@@ -168,12 +164,10 @@
     "third_party/devtools-frontend/src/front_end/third_party/puppeteer/third_party/parsel" ; Expat
     "third_party/devtools-frontend/src/front_end/third_party/puppeteer/third_party/rxjs" ; ASL2.0
     "third_party/devtools-frontend/src/front_end/third_party/puppeteer-replay" ;ASL2.0
-    "third_party/devtools-frontend/src/front_end/third_party/source-map-scopes-codec" ;BSD-3
     "third_party/devtools-frontend/src/front_end/third_party\
 /vscode.web-custom-data" ;Expat
     "third_party/devtools-frontend/src/front_end/third_party/third-party-web" ;Expat
     "third_party/devtools-frontend/src/front_end/third_party/wasmparser" ;ASL2.0
-    "third_party/devtools-frontend/src/front_end/third_party/web-vitals" ;Expat
     "third_party/devtools-frontend/src/third_party/i18n" ;ASL2.0
     "third_party/devtools-frontend/src/third_party/pyjson5" ;ASL2.0
 
@@ -185,7 +179,6 @@
     "third_party/farmhash" ;Expat
     "third_party/fast_float" ;ASL2.0, Boost1.0, Expat
     "third_party/fdlibm" ;non-copyleft
-    "third_party/federated_compute/chromium/fcp/confidentialcompute" ;ASL2.0
     "third_party/federated_compute/src/fcp/base" ;ASL2.0
     "third_party/federated_compute/src/fcp/confidentialcompute" ;ASL2.0
     "third_party/federated_compute/src/fcp/protos/confidentialcompute" ;ASL2.0
@@ -194,9 +187,7 @@
     "third_party/fft2d" ;non-copyleft
     "third_party/flatbuffers" ;ASL2.0
     "third_party/fp16" ;Expat
-    "third_party/freetype" ;GPL2.0
     "third_party/fusejs" ;ASL2.0
-    "third_party/fxdiv" ;Expat
     "third_party/gemmlowp" ;ASL2.0
     "third_party/google_input_tools" ;ASL2.0
     "third_party/google_input_tools/third_party/closure_library" ;ASL2.0
@@ -205,9 +196,6 @@
     "third_party/harfbuzz-ng" ;Expat
     "third_party/highway" ;ASL2.0
     "third_party/hunspell" ;MPL1.1/GPL2+/LGPL2.1+
-    "third_party/hyphenation-patterns" ;Expat
-    ;; FIXME: Our icu does not have some headers such as udatamem.h.
-    "third_party/icu" ;Unicode3.0
     "third_party/ink" ;ASL2.0
     "third_party/ink_stroke_modeler" ;ASL2.0
     "third_party/inspector_protocol" ;BSD-3
@@ -220,14 +208,12 @@
     "third_party/libaddressinput" ;ASL2.0
     "third_party/libaom" ;BSD-2 or "Alliance for Open Media Patent License 1.0"
     "third_party/libaom/source/libaom/third_party/fastfeat" ;BSD-3
+    "third_party/libaom/source/libaom/third_party/SVT-AV1" ;BSD-3
     "third_party/libaom/source/libaom/third_party/vector" ;Expat
     "third_party/libaom/source/libaom/third_party/x86inc" ;ISC
-    "third_party/libc++" ;Expat
     "third_party/libdrm" ; Expat
     "third_party/libgav1" ;ASL2.0
     "third_party/libjingle_xmpp" ;BSD-3
-    "third_party/libpfm4" ;BSD
-    "third_party/libpng" ;PNG2.0
     "third_party/libphonenumber" ;ASL2.0
     "third_party/libsecret" ;LGPL2.1+
     "third_party/libsrtp" ;BSD-3
@@ -241,15 +227,11 @@
     "third_party/libvpx/source/libvpx/third_party/x86inc" ;Expat
 
     "third_party/libwebm" ;BSD-3
-    "third_party/libx11" ;BSD
-    "third_party/libxcb-keysyms" ;BSD
     "third_party/libxml/chromium" ;BSD-3
     "third_party/libyuv" ;BSD-3
     "third_party/libzip" ;BSD-3
     "third_party/lit" ;BSD-3
     "third_party/lit/v3_0" ;BSD-3
-    "third_party/llvm-libc" ;ASL2.0
-    "third_party/llvm-libc/src/shared" ;ASL2.0
     "third_party/lottie" ;Expat
     "third_party/lss" ;BSD-3
     "third_party/lzma_sdk" ;public domain
@@ -262,7 +244,6 @@
     "third_party/modp_b64" ;BSD-3
     "third_party/nasm" ;BSD-2
     "third_party/nearby" ;ASL2.0
-    "third_party/neon_2_sse" ;BSD-2
     "third_party/node" ;Expat
     "third_party/oak/chromium/proto" ;ASL2.0
     "third_party/oak/chromium/proto/attestation" ;ASL2.0
@@ -270,20 +251,14 @@
     "third_party/one_euro_filter" ;BSD-3
     "third_party/openscreen" ;BSD-3
     "third_party/openscreen/src/third_party/tinycbor" ;Expat
-    "third_party/opus" ;BSD-3
     "third_party/ots" ;BSD-3
     "third_party/pdfium" ;BSD-3
     "third_party/pdfium/third_party/agg23" ;Expat
     "third_party/pdfium/third_party/bigint" ;Public domain, BSD-3
-    "third_party/pdfium/third_party/lcms" ;Expat
-    "third_party/pdfium/third_party/libopenjpeg" ;BDS-2
     "third_party/pdfium/third_party/libtiff" ;non-copyleft
     "third_party/pdfium/third_party/freetype/include/pstables.h" ;FreeType
     "third_party/perfetto" ;ASL2.0
     "third_party/perfetto/protos/third_party/chromium" ;BSD-3
-    "third_party/perfetto/protos/third_party/pprof" ;ASL2.0
-    "third_party/perfetto/protos/third_party/primes" ;ASL2.0
-    "third_party/perfetto/protos/third_party/simpleperf" ;ASL2.0
     "third_party/pffft" ;the "FFTPACK" license
     "third_party/ply" ;BSD-3
     "third_party/polymer" ;BSD-3
@@ -293,7 +268,6 @@
     "third_party/protobuf/third_party/utf8_range" ; Expat
     "third_party/pthreadpool" ;BSD-2
     "third_party/puffin" ;Non-copyleft
-    "third_party/pyyaml" ;Expat
     "third_party/pyjson5" ;ASL2.0
     "third_party/rapidhash" ;BSD-2
     "third_party/readability" ;ASL2.0
@@ -305,14 +279,11 @@
     "third_party/search_engines_data" ;BSD-3
     "third_party/securemessage" ;ASL2.0
     "third_party/selenium-atoms" ;ASL2.0
-    "third_party/sentencepiece" ;ASL2.0
-    "third_party/sentencepiece/src/third_party/darts_clone" ;BSD-3
     "third_party/shell-encryption" ;ASL2.0
     "third_party/simdutf" ;Non-copyleft
     "third_party/simplejson" ; Non-copyleft
-    "third_party/six" ;Expat
     "third_party/skia" ;BSD-3
-    "third_party/skia/include/third_party/vulkan" ;BSD-3
+    "third_party/skia/third_party/vulkanmemoryallocator" ;BSD-3, Expat
     "third_party/smhasher" ;Expat, public domain
 
     ;; FIXME: the snappy "replacement" shim (see replace_gn_files.py below) does
@@ -367,6 +338,7 @@
     "third_party/webrtc/modules/third_party/fft" ;Non-copyleft
     "third_party/webrtc/modules/third_party/g711" ;Public domain
     "third_party/webrtc/modules/third_party/g722" ;Public domain
+    "third_party/webrtc/rtc_base/third_party/sigslot" ;Public domain
     "third_party/widevine/cdm/widevine_cdm_common.h" ;BSD-3
     "third_party/woff2" ;ASL2.0
     "third_party/wuffs" ;ASL2.0
@@ -400,7 +372,7 @@
   ;; run the Blink performance tests, just remove everything to save ~70MiB.
   '("third_party/blink/perf_tests"))
 
-(define %chromium-version "147.0.7727.55")
+(define %chromium-version "141.0.7390.65")
 (define %ungoogled-revision (string-append %chromium-version "-1"))
 (define %debian-revision (string-append "debian/" %ungoogled-revision))
 
@@ -412,7 +384,7 @@
     (file-name (git-file-name "ungoogled-chromium" %ungoogled-revision))
     (sha256
      (base32
-      "0l6v4wf16067igawjlh90f3d287mkw0cq4j5lvrxxy17y1skynzc"))))
+      "1hk4rww2gccly1qv0xnswd77haj02rlza82403dxdjm8fkdfndy6"))))
 
 (define %debian-origin
   (origin
@@ -425,7 +397,7 @@
                                 ((_ version) version))))
     (sha256
      (base32
-      "0gqarll08i7rcs1amapciv263xvzglc8p44ikavq3xd12yyvcd98"))))
+      "06s3kvwb3490xb28n6r3q5n1c0ylsvchiw6s4h1rrp8jqzwjbmc6"))))
 
 (define (origin-file origin file)
   (computed-file
@@ -438,38 +410,26 @@
 
 (define %debian-patches
   (map debian-patch
-       '("bookworm/foreach.patch"
+       '("bookworm/clang19.patch"
-         "debianization/safe-libcxx.patch"
+         "bookworm/foreach.patch"
-         "disable/enterprise-tests.patch"
          "disable/node-version-ck.patch"
-         "disable/rustc-allow-features.patch"
-         "fixes/bytemuck.patch"
          "fixes/gentoo-stylesheet.patch"
          "fixes/libcpp-headers.patch"
-         "fixes/libpng-testonly.patch"
          "fixes/rust-clanglib.patch"
-         "llvm-19/clang19.patch"
-         "llvm-19/clone-traits.patch"
-         "llvm-19/keyfactory.patch"
-         "llvm-19/value-or.patch"
-         "llvm-22/ignore-for-ubsan.patch"
          "system/openjpeg.patch"
-         "trixie/cookie-string-view.patch"
+         ;; Remove after rust is past
-         "trixie/nodejs-main.patch")))
+         ;; <https://github.com/rust-lang/rust/pull/141061>.
+         "trixie/rust-no-alloc-shim.patch")))
 
 (define %guix-patches
   (list (local-file
-         (assume-valid-file-name
-          (search-patch
-           "ungoogled-chromium-custom-compiler.patch")))
-        (local-file
-         (assume-valid-file-name
-          (search-patch
-           "ungoogled-chromium-empty-parsed-rustc-args.patch")))
-        (local-file
          (assume-valid-file-name
           (search-patch
            "ungoogled-chromium-extension-search-path.patch")))
+        (local-file
+         (assume-valid-file-name
+          (search-patch
+           "ungoogled-chromium-unbundle-icu-target.patch")))
         (local-file
          (assume-valid-file-name
           (search-patch
@@ -540,8 +500,9 @@
              "#if 0"))
           (invoke "python" "build/linux/unbundle/replace_gn_files.py"
                   "--system-libraries" "flac" "fontconfig" "freetype"
-                  "harfbuzz-ng" "libjpeg" "libpng" "libwebp" "libxml"
+                  "harfbuzz-ng" "icu" "libjpeg"
-                  "libxslt" "openh264" "opus" "zlib")))))
+                  "libpng" "libwebp" "libxml" "libxslt" "openh264" "opus"
+                  "zlib")))))
 
 (define opus+custom
   (package/inherit opus
@@ -570,7 +531,7 @@
                                   %chromium-version "-lite.tar.xz"))
               (sha256
                (base32
-                "1salvlw5sykx3zmsbp7cgmf7y8yy6jlgb4b4zswzsbjrprk4jnap"))
+                "09iwglswnr6d45zz3zsjw7jpm1xlwwkxlz9h5nlhqxyd933a04fq"))
               (modules '((guix build utils)))
               (snippet (force ungoogled-chromium-snippet))))
     (build-system gnu-build-system)
@@ -587,7 +548,6 @@
       ;; directory for an exhaustive list of supported flags.
       ;; (Note: The 'configure' phase will do that for you.)
       #~(list "is_debug=false"
-              "is_component_build=false"
               ;; Use the "official" release optimizations, as opposed to
               ;; a developer build.
               "is_official_build=true"
@@ -595,7 +555,6 @@
               "use_clang_modules=false"
               "use_custom_libcxx=false" ; support for this is deprecated and to be removed.
               "optimize_webui=false"
-              "webnn_use_tflite=false"
               "safe_browsing_use_unrar=false"
               "chrome_pgo_phase=0"
               "use_sysroot=false"
@@ -613,10 +572,12 @@
               "enable_service_discovery=false"
               "enable_vr=false"
               "enable_enterprise_companion=false"
+              "enable_glic=false"
               "enable_iterator_debugging=false"
               "enable_hangout_services_extension=false"
               "enable_widevine=false"
-              "fatal_linker_warnings=false"
+              ;; Disable type-checking for the Web UI to avoid a Java dependency.
+              "enable_js_type_check=false"
               ;; Disable code using TensorFlow until it has been scrutinized
               ;; by the ungoogled project.
               "build_with_tflite_lib=false"
@@ -628,11 +589,6 @@
               "angle_has_histograms=false"
               "angle_build_tests=false"
               "build_angle_perftests=false"
-              "enable_perfetto_unittests=false"
-              "skia_enable_skshapper_tests=false"
-              "tint_build_unittests=false"
-              "enable_nocompile_tests=false"
-              "enable_screen_ai_browsertests=false"
 
               "clang_warning_suppression_file=\"\""
 
@@ -641,8 +597,6 @@
               "is_cfi=false"
 
               "symbol_level=0"
-              "blink_symbol_level=0"
-              "v8_symbol_level=0"
               "v8_enable_backtrace=false"
 
               ;; Define a custom toolchain that simply looks up CC, AR and
@@ -674,10 +628,26 @@
                              ;; invokation and fails if it's just the version number.
                              " (f6e511eec 2024-10-15) (built from a source tarball)\"")
 
+              ;; Chromium's build/rust/std/BUILD.gn has a hardcoded
+              ;; list of stdlib rlibs (stdlib_files) that GN uses to
+              ;; declare build outputs.  GN requires static output
+              ;; declarations, so the list must exactly match what
+              ;; rlibs exist in the Rust sysroot.  Chromium's list
+              ;; includes unicode_width because their bundled
+              ;; toolchain (Rust 1.89) ships it as a dependency of
+              ;; getopts 0.2.23.  Our Rust 1.93 has getopts 0.2.24
+              ;; which dropped that dependency, so unicode_width is
+              ;; not in our sysroot.  This GN arg removes it from
+              ;; the list.  (Chromium's own use of unicode_width via
+              ;; codespan-reporting is a separate vendored copy under
+              ;; third_party/rust/chromium_crates_io/ and is
+              ;; unaffected.)
+              "removed_rust_stdlib_libs=[\"unicode_width\"]"
+
               ;; Prefer system libraries.
               "use_system_freetype=true"
               "use_system_harfbuzz=true"
-              "use_system_icu=false"
+              "use_system_icu=true"
               "use_system_lcms2=true"
               "use_system_libffi=true"
               "use_system_libjpeg=true"
@@ -743,9 +713,9 @@
 
                 ;; Many files try to include ICU headers from "third_party/icu/...".
                 ;; Remove the "third_party/" prefix to use system headers instead.
-                ;(substitute* (find-files "chrome" "\\.cc$")
+                (substitute* (find-files "chrome" "\\.cc$")
-                ;  (("third_party/icu/source/(common|i18n)/")
+                  (("third_party/icu/source/(common|i18n)/")
-                ;   ""))
+                   ""))
 
                 ;; XXX: Should be unnecessary when use_system_lcms2=true.
                 (substitute* "third_party/pdfium/core/fxcodec/icc/icc_transform.h"
@@ -762,19 +732,16 @@
                   (("include \"third_party/curl")
                    "include \"curl"))
 
-                ;; Our clang libs and rustfmt are not under bindgen root directory.
+                ;; Unknown flags as of clang-19, can be removed when building with
-                (substitute* '("build/rust/rust_bindgen_generator.gni"
+                ;; newer clang.
-                               "build/rust/rust_bindgen.gni")
+                (substitute* "build/config/compiler/BUILD.gn"
+                  (("-gsimple-template-names") ""))
+
+                ;; Clang libs are not under bindgen root directory.
+                (substitute* "build/rust/rust_bindgen_generator.gni"
                   (("(_libclang_path = )rust_bindgen_root" _ libclang)
-                   (string-append libclang "clang_base_path"))
+                   (string-append libclang "clang_base_path"))))))
-                  (("(_rustfmt_path = \")\\$\\{rust_bindgen_root\\}" _ rustfmt)
+          (add-after 'patch-stuff 'add-absolute-references
-                   (string-append rustfmt "${rust_sysroot_absolute}"))))))
-          (add-after 'patch-stuff 'include-pthreadpool
-            ;; FIXME: Somehow the build system cannot locate this header.
-            (lambda _
-              (copy-file "third_party/pthreadpool/src/include/pthreadpool.h"
-                         "pthreadpool.h")))
-          (add-after 'include-pthreadpool 'add-absolute-references
             (lambda* (#:key inputs #:allow-other-keys)
               (let ((cups-config (search-input-file inputs "/bin/cups-config"))
                     (libnssckbi.so (search-input-file inputs
@@ -796,22 +763,13 @@
           (add-after 'add-absolute-references 'adjust-CPLUS_INCLUDE_PATH
             ;; The libcxx include/c++/v1 directory is not exposed via
             ;; CPLUS_INCLUDE_PATH by default, causing errors like
-            ;; "fatal error: 'format' file not found".  Also clang is
+            ;; "fatal error: 'format' file not found".
-            ;; unable to find gcc's bits/c++config.h which is machine
-            ;; dependent.
             (lambda* (#:key native-inputs inputs #:allow-other-keys)
-              (let* ((libcxx-v1 (search-input-directory inputs
+              (setenv "CPLUS_INCLUDE_PATH"
-                                                        "include/c++/v1"))
+                      (string-append
-                     (target-system  #$(nix-system->gnu-triplet
+                       (search-input-directory inputs
-                                         (or (%current-target-system)
+                                               "/include/c++/v1")
-                                             (%current-system))))
+                       ":" (getenv "CPLUS_INCLUDE_PATH")))))
-                     (target-include (string-append "include/c++/"
-                                                    target-system))
-                     (gcc-bits  (search-input-directory inputs
-                                                        target-include)))
-                (setenv "CPLUS_INCLUDE_PATH"
-                        (string-append libcxx-v1 ":" gcc-bits ":"
-                         (getenv "CPLUS_INCLUDE_PATH"))))))
           (add-before 'configure 'prepare-build-environment
             (lambda* (#:key native-inputs inputs #:allow-other-keys)
               (let ((node (search-input-file (or native-inputs inputs)
@@ -997,7 +955,7 @@
            glib
            gtk+
            harfbuzz
-           icu4c-77
+           icu4c
            lcms
            libcxx
            libffi

gnu/packages/cinnamon.scm

@@ -30,6 +30,7 @@
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system meson)
   #:use-module (guix build-system pyproject)
+  #:use-module (guix build-system python)
   #:use-module (gnu packages)
   #:use-module (gnu packages admin)
   #:use-module (gnu packages autotools)
@@ -252,7 +253,7 @@ as well as some desktop-wide documents.")
            pkg-config
            xorg-server-for-tests))
     (inputs
-     (list at-spi2-core
+     (list atk
            cinnamon-desktop
            exempi
            gsettings-desktop-schemas

gnu/packages/cmake.scm

@@ -47,6 +47,7 @@
   #:use-module (guix build-system copy)
   #:use-module (guix build-system emacs)
   #:use-module (guix build-system pyproject)
+  #:use-module (guix build-system python)
   #:use-module ((guix search-paths) #:select ($SSL_CERT_DIR $SSL_CERT_FILE))
   #:use-module (gnu packages)
   #:use-module (gnu packages backup)

gnu/packages/code.scm

@@ -49,6 +49,7 @@
   #:use-module (guix git-download)
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system cmake)
+  #:use-module ((guix build-system python) #:select (pypi-uri))
   #:use-module (guix build-system pyproject)
   #:use-module (guix build-system trivial)
   #:use-module (guix build-system go)
@@ -694,6 +695,57 @@ Kcov uses DWARF debugging information for compiled programs to make it
 possible to collect coverage information without special compiler switches.")
     (license license:gpl2+)))
 
+(define-public rtags
+  (package
+    (name "rtags")
+    (version "2.18")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/Andersbakken/rtags")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (patches (search-patches "rtags-separate-rct.patch"))
+       (modules '((guix build utils)))
+       (snippet
+        ;; Part of spliting rct with rtags.
+        ;; Substitute #include "rct/header.h" with #include <rct/header.h>.
+        '(with-directory-excursion "src"
+           (delete-file-recursively "rct")        ;remove bundled copy
+           (let ((files (find-files "." ".*\\.cpp|.*\\.h")))
+             (substitute* files
+               (("#include ?\"rct/(.*.h)\"" all header)
+                (string-append "#include <rct/" header ">")))
+             #t)))
+       (sha256
+        (base32
+         "0raqjbkl1ykga4ahgl9xw49cgh3cyqcf42z36z7d6fz1fw192kg0"))))
+    (build-system cmake-build-system)
+    (arguments
+     '(#:build-type "RelWithDebInfo"
+       #:configure-flags
+       '("-DRTAGS_NO_ELISP_FILES=1")
+       #:tests? #f))
+    (native-inputs
+     (list pkg-config))
+    (inputs
+     (list bash-completion
+           clang
+           llvm
+           lua
+           rct
+           selene))
+    (home-page "https://github.com/Andersbakken/rtags")
+    (synopsis "Indexer for the C language family with Emacs integration")
+    (description
+     "RTags is a client/server application that indexes C/C++ code and keeps a
+persistent file-based database of references, declarations, definitions,
+symbolnames etc.  There’s also limited support for ObjC/ObjC++.  It allows you
+to find symbols by name (including nested class and namespace scope).  Most
+importantly we give you proper follow-symbol and find-references support.")
+    (license license:gpl3+)))
+
 (define-public colormake
   (package
     (name "colormake")

gnu/packages/containers.scm

@@ -375,7 +375,7 @@ contents, and discovering ways to shrink the size of Docker/OCI image.")
 (define-public guix-compose
   (package
     (name "guix-compose")
-    (version "0.2.0")
+    (version "0.1.1")
     (source
      (origin
        (method git-fetch)
@@ -384,7 +384,7 @@ contents, and discovering ways to shrink the size of Docker/OCI image.")
               (commit version)))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "1dy48qkz3ifxagijpvwg7rmq7hz3pikhdcfral6djyc9ppmz8mbm"))))
+        (base32 "1ij6rfs5pfykk8c53q029sl2qx3k572dqdfb6pn5s569l6697ci1"))))
     (build-system guile-build-system)
     (arguments
      (list
@@ -426,7 +426,7 @@ contents, and discovering ways to shrink the size of Docker/OCI image.")
                  "guile" "-L" "./modules" "-s" "tests/test-compose.scm")))))))
     (native-inputs (list guile-3.0))
     ;; Avoid setting propagated so that we use the user’s profile.
-    (inputs (list guix guile-dotenv guile-yamlpp))
+    (inputs (list guix guile-yamlpp))
     (native-search-paths
      (list $GUIX_EXTENSIONS_PATH))
     (synopsis "Guix' docker compose compatibility layer")
@@ -714,7 +714,7 @@ Its main purpose is to support the key usage by @code{docker-init}:
 (define-public podman
   (package
     (name "podman")
-    (version "5.8.2")
+    (version "5.8.1")
     (outputs '("out" "docker"))
     (properties
      `((output-synopsis "docker" "docker alias for podman")
@@ -727,7 +727,7 @@ Its main purpose is to support the key usage by @code{docker-init}:
              (url "https://github.com/containers/podman")
              (commit (string-append "v" version))))
        (sha256
-        (base32 "12bmzbfyjsf0mwnam38cw9ib54wj1znh5b7lxzdyll9cvvkhqisr"))
+        (base32 "1wdsdc0nj4m1v8mn95dhavi87ad0adqmld70da59gvp2abff5f0f"))
        (file-name (git-file-name name version))))
     (build-system gnu-build-system)
     (arguments

gnu/packages/coreboot.scm

@@ -1,226 +0,0 @@
-;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2018 Danny Milosavljevic <dannym@scratchpost.org>
-;;; Copyright © 2018 Ludovic Courtès <ludo@gnu.org>
-;;; Copyright © 2019 Tobias Geerinckx-Rice <me@tobias.gr>
-;;; Copyright © 2025 Cayetano Santos <csantosb@inventati.org>
-;;; Copyright © 2026 Denis 'GNUtoo' Carikli <GNUtoo@cyberdimension.org>
-;;;
-;;; This file is part of GNU Guix.
-;;;
-;;; GNU Guix is free software; you can redistribute it and/or modify it
-;;; under the terms of the GNU General Public License as published by
-;;; the Free Software Foundation; either version 3 of the License, or (at
-;;; your option) any later version.
-;;;
-;;; GNU Guix is distributed in the hope that it will be useful, but
-;;; WITHOUT ANY WARRANTY; without even the implied warranty of
-;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-;;; GNU General Public License for more details.
-;;;
-;;; You should have received a copy of the GNU General Public License
-;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
-
-(define-module (gnu packages coreboot)
-  #:use-module (gnu packages bison)
-  #:use-module (gnu packages compression)
-  #:use-module (gnu packages flex)
-  #:use-module (gnu packages pciutils)
-  #:use-module ((guix licenses) #:prefix license:)
-  #:use-module (guix build-system cargo)
-  #:use-module (guix build-system cmake)
-  #:use-module (guix build-system copy)
-  #:use-module (guix build-system gnu)
-  #:use-module (guix build-system go)
-  #:use-module (guix build-system meson)
-  #:use-module (guix build-system pyproject)
-  #:use-module (guix build-system python)
-  #:use-module (guix build-system qt)
-  #:use-module (guix download)
-  #:use-module (guix gexp)
-  #:use-module (guix git-download)
-  #:use-module (guix packages)
-  #:use-module (guix utils)
-  #:use-module (srfi srfi-26))
-
-(define %coreboot-version "26.03")
-
-(define %coreboot-origin
-  (origin
-    (method git-fetch)
-    (uri (git-reference
-           (url "https://review.coreboot.org/coreboot")
-           (commit %coreboot-version)))
-    (file-name (git-file-name "coreboot" %coreboot-version))
-    (sha256
-     (base32
-      "0436rr0vibh35phvkxrc939njvrmnfq9xw87y1b0nlllglvq07kk"))))
-
-(define-public bincfg
-  (package
-    (name "bincfg")
-    (version %coreboot-version)
-    (source %coreboot-origin)
-    (build-system gnu-build-system)
-    (arguments
-     (list
-      #:tests? #f ; no test suite
-      #:make-flags
-      #~(list
-         (string-append "CC=" #$(cc-for-target)))
-      #:phases
-      #~(modify-phases %standard-phases
-          (delete 'configure) ; no configure script
-          (add-after 'unpack 'chdir
-            (lambda _
-              (chdir "util/bincfg")))
-          (add-after 'build 'build-binaries
-            (lambda* (#:key make-flags #:allow-other-keys)
-              (for-each
-               (lambda (target result)
-                 (apply invoke "make" (string-append "gen-" target) make-flags)
-                 (rename-file result
-                              (string-append target ".bin")))
-               (list
-                ;; generate GbE for X200
-                "gbe-ich9m"
-                ;; generate GbE for X220/x230
-                "gbe-82579LM"
-                ;; generate IFD for X200
-                "ifd-x200")
-               (list
-                "flashregion_3_gbe.bin"
-                "flashregion_3_gbe.bin"
-                "flashregion_0_fd.bin"))))
-          ;; The Makefile has no install target.
-          (replace 'install
-            (lambda _
-              (let ((bin (string-append #$output "/bin"))
-                    (lib (string-append #$output "/lib/bincfg"))
-                    (data (string-append #$output "/share/bincfg")))
-                ;; Install the program
-                (install-file "bincfg" bin)
-                ;; And its data
-                (for-each
-                 (lambda (path)
-                   (install-file path data))
-                 (append (find-files "." ".*\\.set")
-                         (find-files "." ".*\\.spec")))
-                ;; And the files generated with the data
-                (for-each
-                 (lambda (path)
-                   (install-file path lib))
-                 (find-files "." ".*\\.bin"))))))))
-    (native-inputs (list bison flex))
-    (home-page "https://coreboot.org")
-    (synopsis "Encoder/decoder for binary formats described in text files")
-    (description "
-The bincfg program comes with specifications files for the following binary
-formats:
-@itemize
-@item Various DDR3 and DDR4 SPD
-@item Configuration data for the Intel 82579LM Gigabit Ethernet PHY
-@item Configuration data for the Intel Gigabit Ethernet controller present in
-      the Intel ICH9-M chipset.
-@item Intel Firmware Descriptor data for the Lenovo ThinkPad X200
-@item Configuration data for the ITE IT8718F SuperIO
-@end itemize
-It also comes with example files generated by bincfg.")
-    (license license:gpl3+)))
-
-(define-public ifdtool
-  (package
-    (name "ifdtool")
-    (version %coreboot-version)
-    (source %coreboot-origin)
-    (build-system gnu-build-system)
-    (arguments
-     (list
-      #:make-flags
-      #~(list (string-append "CC=" #$(cc-for-target))
-              "INSTALL=install"
-              (string-append "PREFIX=" #$output))
-      #:phases
-      #~(modify-phases %standard-phases
-          (add-after 'unpack 'chdir
-            (lambda _
-              (chdir "util/ifdtool")))
-          (delete 'configure))           ; no configure script
-      #:tests? #f))                    ; no test suite
-    (home-page "https://doc.coreboot.org/util/ifdtool/")
-    (synopsis "Intel Firmware Descriptor dumper")
-    (description "This package provides @command{ifdtool}, a program to
-dump Intel Firmware Descriptor data of an image file.")
-    (license license:gpl2)))
-
-(define-public intelmetool
-  (package
-    (name "intelmetool")
-    (version %coreboot-version)
-    (source %coreboot-origin)
-    (build-system gnu-build-system)
-    (arguments
-     (list
-      #:tests? #f                       ;no test suite
-      #:make-flags
-      #~(list (string-append "CC=" #$(cc-for-target))
-              "INSTALL=install"
-              (string-append "PREFIX=" #$output))
-      #:phases
-      #~(modify-phases %standard-phases
-          (add-after 'unpack 'chdir
-            (lambda _
-              (chdir "util/intelmetool")))
-          (delete 'configure) ;no configure script
-          (delete 'check))))
-    (inputs (list pciutils zlib))
-    (home-page
-     "https://github.com/coreboot/coreboot/tree/main/util/intelmetool/")
-    (synopsis "Intel Management Engine tools")
-    (description "This package provides tools for working with Intel
-Management Engine (ME).  You need to @code{sudo rmmod mei_me} and
-@code{sudo rmmod mei} before using this tool.  Also pass
-@code{iomem=relaxed} to the Linux kernel command line.")
-    (license license:gpl2)
-
-    ;; This is obviously an Intel thing, plus it requires <cpuid.h>.
-    (supported-systems '("x86_64-linux" "i686-linux"))))
-
-(define-public nvramtool
-  (package
-    (name "nvramtool")
-    (version %coreboot-version)
-    (source %coreboot-origin)
-    (build-system gnu-build-system)
-    (arguments
-     (list
-      #:tests? #f ; no test suite
-      #:make-flags
-      #~(list (string-append "CC=" #$(cc-for-target))
-              "INSTALL=install"
-              (string-append "PREFIX=" #$output))
-      #:phases
-      #~(modify-phases %standard-phases
-          (add-after 'unpack 'chdir
-            (lambda _
-              (chdir "util/nvramtool")))
-          (delete 'configure)))) ; no configure script
-    (home-page "https://coreboot.org")
-    (synopsis "Command line tool that can edit Coreboot settings")
-    (description "@command{nvramtool} can see and/or modify Coreboot settings
-like the serial port speed, log level, etc.  It requires Coreboot to be compiled
-with CONFIG_USE_OPTION_TABLE and some options require the iomem=relaxed kernel
-command line to work.  Features:
-@itemize
-@item If Coreboot was compiled without CONFIG_STATIC_OPTION_TABLE, it can change
-      its settings, which are applied after a reboot.
-@item It can modify Coreboot images  default settings with
-      @command{nvramtool -C coreboot.rom [...]}.
-@item It has various options related to the file format used to store these
-      settings.
-@item It can also read/write the CMOS memory where the Coreboot settings can be
-      located.
-@end itemize")
-    ;; Some files are "GPL-2.0-only or BSD-3-Clause", other are GPL-2.0-only
-    ;; and anyway there is. There is also a license declaration in
-    ;; cli/nvramtool.8 that applies to "This program" which uses the GPLv2.
-    (license license:gpl2)))

gnu/packages/cpp.scm

@@ -78,6 +78,7 @@
   #:use-module (guix build-system copy)
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system meson)
+  #:use-module (guix build-system python)
   #:use-module (guix build-system pyproject)
   #:use-module (guix build-system scons)
   #:use-module (guix modules)
@@ -682,6 +683,38 @@ computer program to introspect and modify an object at runtime.  It is also
 the name of the library itself, which is written in C++.")
     (license license:expat)))
 
+(define-public rct
+  (let* ((commit "b3e6f41d9844ef64420e628e0c65ed98278a843a")
+         (revision "2"))
+    (package
+      (name "rct")
+      (version (git-version "0.0.0" revision commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "https://github.com/Andersbakken/rct")
+                      (commit commit)))
+                (sha256
+                 (base32
+                  "1m2931jacka27ghnpgf1z1plkkr64z0pga4r4zdrfpp2d7xnrdvb"))
+                (patches (search-patches "rct-add-missing-headers.patch"))
+                (file-name (git-file-name name version))))
+      (build-system cmake-build-system)
+      (arguments
+       '(#:configure-flags
+         '("-DWITH_TESTS=ON"            ; To run the test suite
+           "-DRCT_RTTI_ENABLED=ON")))
+      (native-inputs
+       (list cppunit pkg-config))
+      (inputs
+       (list openssl zlib))
+      (home-page "https://github.com/Andersbakken/rct")
+      (synopsis "C++ library providing Qt-like APIs on top of the STL")
+      (description "Rct is a set of C++ tools that provide nicer (more Qt-like)
+ APIs on top of Standard Template Library (@dfn{STL}) classes.")
+      (license (list license:expat        ; cJSON
+                     license:bsd-4)))))   ; everything else (LICENSE.txt)
+
 (define-public plutovg
   (package
     (name "plutovg")
@@ -1903,7 +1936,8 @@ using the string similarity calculations from FuzzyWuzzy.")
           (add-after 'unpack 'fix-pytest-config
             (lambda _
               (substitute* "pyproject.toml"
-                (("\"pytest-cov\", ") "")))))))
+                ((" \"pytest-cov\", ") "")
+                ((" --cov-fail-under=90 --cov=cpplint") "")))))))
     (native-inputs
      (list python-pytest
            python-pytest-timeout

gnu/packages/cross-base.scm

@@ -135,10 +135,20 @@
                                         (search-patches
                                          "ath9k-htc-firmware-binutils.patch")))
                  ((target-mingw? target)
-                  (package-with-extra-patches binutils
+                  (package-with-extra-patches
-                                              (search-patches
+                   (package-with-extra-configure-variable
-                                               "binutils-cross-windres.patch"
+                    ;; mingw binutils does not work correctly when configured
-                                               "binutils-mingw-w64-deterministic.patch")))
+                    ;; with `--enable-compressed-debug-sections`. An error
+                    ;; like the following will occur whenever you try to link:
+                    ;;
+                    ;;   x86_64-w64-mingw32-ld: final link failed: bad value
+                    ;;
+                    ;; TODO: This seems like a deeper problem that warrants
+                    ;; deeper investigation.
+                    binutils "--enable-compressed-debug-sections" "no")
+                   (search-patches
+                    "binutils-cross-windres.patch"
+                    "binutils-mingw-w64-deterministic.patch")))
                  (else binutils))
            target)))
 

gnu/packages/crypto.scm

@@ -105,6 +105,7 @@
   #:use-module (guix build-system copy)
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system perl)
+  #:use-module (guix build-system python)
   #:use-module (guix build-system pyproject)
   #:use-module (guix utils)
   #:use-module (srfi srfi-1)
@@ -1687,14 +1688,14 @@ structure.  However CryFS is not considered stable yet by the developers.")
 (define-public b3sum
   (package
     (name "b3sum")
-    (version "1.8.4")
+    (version "1.8.2")
     (source
       (origin
         (method url-fetch)
         (uri (crate-uri "b3sum" version))
         (file-name (string-append name "-" version ".tar.gz"))
         (sha256
-         (base32 "0pkra5zh680cl9q92hpzmg9flz99b06bhpg7jyhymg1nkm0anw7a"))))
+         (base32 "06qc6iv574km4j1ja4qhxyai680jkll58qzpz4mb79c0rk750dpd"))))
     (build-system cargo-build-system)
     (arguments
      (list

gnu/packages/cups.scm

@@ -62,6 +62,7 @@
   #:use-module (guix build-system cmake)
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system meson)
+  #:use-module (guix build-system python)
   #:use-module (guix build-system pyproject)
   #:use-module (guix download)
   #:use-module (guix git-download)

gnu/packages/cybersecurity.scm

@@ -31,6 +31,7 @@
   #:use-module ((guix licenses) #:prefix license:)
   #:use-module (guix build-system cmake)
   #:use-module (guix build-system pyproject)
+  #:use-module (guix build-system python)
   #:use-module (gnu packages databases)
   #:use-module (gnu packages check)
   #:use-module (gnu packages cpp)

gnu/packages/databases.scm

@@ -200,6 +200,7 @@
   #:use-module (guix build-system meson)
   #:use-module (guix build-system perl)
   #:use-module (guix build-system pyproject)
+  #:use-module (guix build-system python)
   #:use-module (guix build-system qt)
   #:use-module (guix build-system ruby)
   #:use-module (guix build-system cmake)
@@ -1251,98 +1252,6 @@ management system that supports the standardized Structured Query
 Language.")
     (license license:gpl2)))
 
-(define-public mysql-connector-python
-  (package
-    (name "mysql-connector-python")
-    (version "8.3.0")
-    (source
-     (origin
-       (method git-fetch)
-       (uri (git-reference
-              (url "https://github.com/mysql/mysql-connector-python")
-              (commit version)))
-       (file-name (git-file-name name version))
-       (sha256
-        (base32 "18jvpnnwmfrn961rvqmsygp7dw3spf3swhxhal4hhj5hqddckj5f"))))
-    (build-system pyproject-build-system)
-    (arguments
-     (list
-      ;; tests: 1371 passed
-      #:phases
-      #~(modify-phases %standard-phases
-          (add-after 'unpack 'compatibility
-            (lambda _
-              (substitute* "src/mysql_capi.c"
-                (("res = mysql_options\\(&self->session, MYSQL_OPT_LOAD_DATA_LOCAL_DIR.*")
-                 "res = 0;")
-                (("mysql_options\\(&self->session, MYSQL_OPT_LOAD_DATA_LOCAL_DIR.*")
-                 "")
-                (("mysql_options\\(&self->session, MYSQL_OPT_TLS_CIPHERSUITES.*")
-                 "")
-                ;; The C API does not have mysql_bind_param, so we produce an
-                ;; error here.
-                (("status = mysql_bind_param.*") "status = 1;")
-                (("#include \"mysql_capi_conversion\\.h\"" all)
-                 (string-append all "\n" "#include <stdbool.h>")))))
-          (add-after 'unpack 'chdir
-            (lambda _
-              (chdir "mysql-connector-python")))
-          (add-before 'build 'prepare-build
-            (lambda _
-              (setenv "MYSQL_CAPI" #$(this-package-input "mysql"))))
-          (replace 'check
-            (lambda* (#:key tests? #:allow-other-keys)
-              (when tests?
-                ;; Some of these tests might be failing due to the build
-                ;; container's restrictions, others are due to the version
-                ;; mismatch.
-                (substitute* "tests/cext/test_cext_api.py"
-                  (("def test_change_user") "def _do_not_test_change_user")
-                  (("def test_get_character_set_info")
-                   "def _do_not_test_get_character_set_info"))
-                (substitute* "tests/test_bugs.py"
-                  (("def test_change_user") "def _do_not_test_change_user")
-                  (("def test_lost_connection") "def _do_not_test_lost_connection")
-                  (("def test_kill_query") "def _do_not_test_kill_query")
-                  ;; These all fail because of expired certificates.
-                  (("def test_cext_verify_server_certificate")
-                   "def _do_not_test_cext_verify_server_certificate")
-                  (("def test_pure_verify_server_certificate")
-                   "def _do_not_test_pure_verify_server_certificate")
-                  (("def test_verify_server_name_cext_cnx")
-                   "def _do_not_test_verify_server_name_cext_cnx")
-                  (("def test_verify_server_name_pure_cnx")
-                   "def _do_not_test_verify_server_name_pure_cnx"))
-                (substitute* '("tests/test_connection.py"
-                               "tests/test_aio_connection.py")
-                  (("def test_allow_local_infile_in_path")
-                   "def _do_not_test_allow_local_infile_in_path")
-                  ;; This fails because of expired certificates.
-                  (("def test_connect_with_unix_socket")
-                   "def _do_not_test_connect_with_unix_socket"))
-                (substitute* "tests/test_constants.py"
-                  (("def test_deprecated")
-                   "def _do_not_test_deprecated"))
-                (mkdir-p "/tmp/datadir")
-                (invoke "python3" "unittests.py"
-                        "--verbosity=3"
-                        (string-append "--with-mysql=" #$(this-package-input "mysql"))
-                        "--keep"
-                        "--mysql-topdir=/tmp/datadir"
-                        "--unix-socket=/tmp/datadir")))))))
-    (propagated-inputs (list python-protobuf))
-    (inputs (list mysql protobuf-3.20 openssl-1.1 zlib))
-    (native-inputs (list python-setuptools))
-    (home-page "https://dev.mysql.com/doc/connector-python/en/index.html")
-    (synopsis "MySQL driver written in Python")
-    (description "MySQL Connector/Python enables Python programs to access
-MySQL databases, using an API that is compliant with the Python Database API
-Specification v2.0 (PEP 249).")
-    (license license:gpl2)))
-
-(define-deprecated-package python-mysql-connector-python
-  mysql-connector-python)
-
 (define-public mariadb
   (package
     (name "mariadb")
@@ -1636,17 +1545,17 @@ and high-availability (HA).")
     (license license:gpl2)))                  ;'COPYING' says "version 2" only
 
 ;; Don't forget to update the other postgresql packages when upgrading this one.
-(define-public postgresql-17
+(define-public postgresql-16
   (package
     (name "postgresql")
-    (version "17.7")
+    (version "16.4")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://ftp.postgresql.org/pub/source/v"
                                   version "/postgresql-" version ".tar.bz2"))
               (sha256
                (base32
-                "1dg9labqgph2idaypb8khdvbag29pr3h4bqv5w8k7kgc08rk97pg"))
+                "0vvd73rzj0sl294v15bh8yslakqv412bxqzlkqxyjwxa8pb6c5wp"))
               (patches (search-patches
                         "postgresql-disable-normalize_exec_path.patch"))))
     (build-system gnu-build-system)
@@ -1676,22 +1585,18 @@ and high-availability (HA).")
           (add-after 'build 'build-contrib
             (lambda _
               (invoke "make" "-C" "contrib")))
-          ;; FIXME: Install manpages too.
-          ;; The 'install-mangpages phase in postgresql-16 fails silently here.
           (add-after 'install 'install-contrib
             (lambda _
-              (invoke "make" "-C" "contrib" "install"))))))
+              (invoke "make" "-C" "contrib" "install")))
+          (add-after 'install 'install-manuals
+            (lambda _
+              (with-directory-excursion "doc/src/sgml"
+                (invoke "make" "install-man")
+                (invoke "make" "postgres.info")
+                (install-file "postgres.info"
+                              (string-append #$output "/share/info"))))))))
     (native-inputs
-     (list bison
+     (list docbook-xml-4.5 docbook2x libxml2 perl pkg-config texinfo))
-           docbook-xml-4.5
-           docbook-xsl
-           docbook2x
-           flex
-           libxml2
-           libxslt
-           perl
-           pkg-config
-           texinfo))
     (inputs
      (list icu4c readline `(,util-linux "lib") openssl zlib))
     (home-page "https://www.postgresql.org/")
@@ -1705,49 +1610,18 @@ TIMESTAMP.  It also supports storage of binary large objects, including
 pictures, sounds, or video.")
     (license (license:x11-style "file://COPYRIGHT"))))
 
-(define-public postgresql-16
-  (package
-    (inherit postgresql-17)
-    (name "postgresql")
-    (version "16.10")
-    (source (origin
-              (method url-fetch)
-              (uri (string-append "https://ftp.postgresql.org/pub/source/v"
-                                  version "/postgresql-" version ".tar.bz2"))
-              (sha256
-               (base32
-                "0hib575m9x3z8c71gkcv9jsyq77d3qk7q2zgzvfy6clwrvs8b16y"))
-              (patches (search-patches
-                        "postgresql-disable-normalize_exec_path.patch"))))
-    (arguments
-     (substitute-keyword-arguments (package-arguments postgresql-17)
-       ((#:phases phases #~%standard-phases)
-        #~(modify-phases #$phases
-            (add-after 'install 'install-manuals
-              (lambda _
-                (with-directory-excursion "doc/src/sgml"
-                  (invoke "make" "install-man")
-                  (invoke "make" "postgres.info")
-                  (install-file "postgres.info"
-                                (string-append #$output "/share/info")))))))))
-    (native-inputs (modify-inputs (package-native-inputs postgresql-17)
-                     (delete "bison")
-                     (delete "docbook-xsl")
-                     (delete "flex")
-                     (delete "libxslt")))))
-
 (define-public postgresql-15
   (package
     (inherit postgresql-16)
     (name "postgresql")
-    (version "15.15")
+    (version "15.8")
     (source (origin
-              (method url-fetch)
+              (inherit (package-source postgresql-16))
               (uri (string-append "https://ftp.postgresql.org/pub/source/v"
                                   version "/postgresql-" version ".tar.bz2"))
               (sha256
                (base32
-                "1ais46b2ij38y75i1w336as03pybyndsd2pp2q8gdjq9igmsllsp"))
+                "0snbxmlygf7m4cxjpscmz3yjn4lnqsw313y9xgpv7vk9k9gm20s4"))
               (patches (search-patches
                         "postgresql-disable-resolve_symlinks.patch"))))
     (native-inputs (modify-inputs native-inputs
@@ -1759,26 +1633,26 @@ pictures, sounds, or video.")
   (package
     (inherit postgresql-15)
     (name "postgresql")
-    (version "14.20")
+    (version "14.13")
     (source (origin
               (inherit (package-source postgresql-15))
               (uri (string-append "https://ftp.postgresql.org/pub/source/v"
                                   version "/postgresql-" version ".tar.bz2"))
               (sha256
                (base32
-                "0sv45dsmyplfys6dfdjdwmrczl46s82x35xdh311nxj02q7z29vm"))))))
+                "0misc5yiklflz96n7wxcdzzg0lcc4ahd0flzqsg6mcjs955krajr"))))))
 
-(define-deprecated/public postgresql-13 #f
+(define-public postgresql-13
   (package
     (inherit postgresql-14)
-    (version "13.23")
+    (version "13.16")
     (source (origin
               (inherit (package-source postgresql-14))
               (uri (string-append "https://ftp.postgresql.org/pub/source/v"
                                   version "/postgresql-" version ".tar.bz2"))
               (sha256
                (base32
-                "1mhz0h7b3dmc0nnxz1wp46j95jhyi3girykkr3gbg4mg4qkwihvf"))))))
+                "0rc8rpsw2lwa5af35zd8iifah02wg2rnn1i890h2h8zh55hvpjy9"))))))
 
 (define-public postgresql postgresql-14)
 
@@ -1817,7 +1691,7 @@ pictures, sounds, or video.")
 (define-public timescaledb
   (package
     (name "timescaledb")
-    (version "2.26.1")
+    (version "2.16.1")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -1826,7 +1700,7 @@ pictures, sounds, or video.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "0zfm224jyz874pk4r9qlz5c2mn1xjvairhxh6widlbh3mn62m3j8"))
+                "1v17x00a15il4r3rbr0waqjv1nwzy6rcqxgfi2hdk1x235s5dg5h"))
               (modules '((guix build utils)))
               (snippet
                ;; Remove files carrying the proprietary TIMESCALE license.
@@ -1836,7 +1710,8 @@ pictures, sounds, or video.")
                             '("scripts/c_license_header-timescale.h"
                               "scripts/license_tsl.spec"
                               "scripts/sql_license_tsl.sql"
-                              "test/t/001_replication_telemetry.pl"
+                              "test/perl/AccessNode.pm"
+                              "test/perl/DataNode.pm"
                               "test/perl/TimescaleNode.pm"))))))
     (build-system cmake-build-system)
     (arguments
@@ -1920,7 +1795,7 @@ pictures, sounds, or video.")
                  (lambda* (#:rest args)
                    (apply (assoc-ref gnu:%standard-phases 'check)
                           #:test-target "regresschecklocal" args))))))
-    (inputs (list openssl postgresql-17))
+    (inputs (list openssl postgresql))
     (home-page "https://www.timescale.com/")
     (synopsis "Time-series extension for PostgreSQL")
     (description
@@ -3169,7 +3044,7 @@ temporary directory, and destroys it when the perl script exits.")
 (define-public unixodbc
   (package
    (name "unixodbc")
-   (version "2.3.14")
+   (version "2.3.9")
    (source (origin
             (method url-fetch)
             (uri
@@ -3177,7 +3052,7 @@ temporary directory, and destroys it when the perl script exits.")
               "ftp://ftp.unixodbc.org/pub/unixODBC/unixODBC-"
               version ".tar.gz"))
             (sha256
-             (base32 "0wa7a82h5dsba23155gfhh1sp4dsbaxq6pppp6q31z017vg18a2f"))))
+             (base32 "01xj65d02i3yjy7p9z08y9jakcs5szmz4rask868n7387nn3x0sj"))))
    (build-system gnu-build-system)
    (synopsis "Data source abstraction library")
    (description "Unixodbc is a library providing an API with which to access
@@ -4744,24 +4619,33 @@ PickleShare.")
 (define-public python-apsw
   (package
     (name "python-apsw")
-    (version "3.50.4.0")
+    (version "3.46.0.0")
+    ;; The compressed release has fetching functionality disabled.
     (source
      (origin
-       (method git-fetch)
+       (method url-fetch)
-       (uri (git-reference
+       (uri (string-append
-              (url "https://github.com/rogerbinns/apsw")
+             "https://github.com/rogerbinns/apsw/releases/download/"
-              (commit version)))
+             version "/apsw-" version ".zip"))
-       (file-name (git-file-name name version))
        (sha256
-        (base32 "0r9awjgpl9cmqz5xd4zbqrpiv0rv5c36a18jkqnsfky6n6sgr424"))))
+        (base32
+         "10yfbasi4mq63g0svyl1h49ylwn9znjylq78id16dzxzk9q9ipdx"))))
     (build-system pyproject-build-system)
-    (arguments
-     (list #:test-backend #~'custom
-           #:test-flags #~(list "-m" "apsw.tests")))
     (native-inputs
-     (list python-setuptools))
+     (list unzip python-setuptools python-wheel))
-    (inputs
+    (inputs (list sqlite-next))         ;SQLite 3.45.1 required.
-     (list sqlite-next))         ;SQLite 3.45.1 required.
+    (arguments
+     (list
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-before 'build 'build-extensions
+            (lambda _
+              (invoke "python" "setup.py" "build" "--enable-all-extensions"
+                      "--enable=load_extension")))
+          (add-after 'build 'build-test-helper
+            (lambda _
+              (invoke "gcc" "-fPIC" "-shared" "-o" "./testextension.sqlext"
+                      "-I." "-Isqlite3" "src/testextension.c"))))))
     (home-page "https://github.com/rogerbinns/apsw/")
     (synopsis "Another Python SQLite Wrapper")
     (description
@@ -5690,6 +5574,7 @@ __version_tuple__ = version_tuple = (~a)~%" version version-tuple))))))
            pkg-config
            python-cython
            python-pytest
+           python-pytest-runner
            python-setuptools-scm
            python-setuptools))
     (outputs '("out"))
@@ -6286,7 +6171,7 @@ mechanism of @code{dogpile}.")
 (define-public datasette
   (package
     (name "datasette")
-    (version "1.0a26")
+    (version "1.0a19")
     (source
      (origin
        (method git-fetch)
@@ -6295,20 +6180,23 @@ mechanism of @code{dogpile}.")
               (commit version)))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "1ra0yfrz9w3jx7ix3dmcsg0g8hjxkz37586g7ijmqshxpzczxfm7"))))
+        (base32 "0wb73iksrc5vg2lnq3q4vr7yhlzxwr711jfmjdndd0s77996zsfh"))))
     (build-system pyproject-build-system)
     (arguments
      (list
-      ;; tests: 1720 passed, 9 skipped, 8 xfailed, 13 xpassed, 3 warnings, 120
-      ;; subtests passed
       #:test-flags
-      #~(list "--numprocesses" (number->string (min 8 (parallel-job-count)))
+      ;; See https://github.com/simonw/datasette/issues/2048
-              "--ignore=tests/test_black.py")
+      #~(list "-k" (string-append
+                    ;; These contain two unexpected extra items.
+                    "not test_searchable"
+                    " and not test_searchmode")
+              "--ignore=tests/test_black.py"
+              "-n" (number->string (parallel-job-count)))
       #:phases
       #~(modify-phases %standard-phases
           (add-after 'unpack 'relax-requirements
             (lambda _
-              (substitute* "pyproject.toml"
+              (substitute* "setup.py"
                 (("\"pip\",") "")))))))
     (propagated-inputs
      (list python-aiofiles
@@ -6323,6 +6211,7 @@ mechanism of @code{dogpile}.")
            python-janus
            python-jinja2
            python-mergedeep
+           python-pint
            python-pluggy
            python-pyyaml
            python-sqlite-utils
@@ -6331,9 +6220,9 @@ mechanism of @code{dogpile}.")
      (list nss-certs-for-test
            python-beautifulsoup4
            python-cogapp
-           python-multipart-form-data-conformance
            python-pytest
-           python-pytest-asyncio
+           python-pytest-asyncio-0.26
+           python-pytest-runner
            python-pytest-timeout
            python-pytest-xdist
            python-setuptools

gnu/packages/dav.scm

@@ -27,6 +27,7 @@
 (define-module (gnu packages dav)
   #:use-module (guix build-system cargo)
   #:use-module (guix build-system gnu)
+  #:use-module (guix build-system python)
   #:use-module (guix build-system pyproject)
   #:use-module (guix download)
   #:use-module (guix gexp)
@@ -142,6 +143,9 @@ CardDAV server with a local folder or file.")
     (build-system pyproject-build-system)
     (native-inputs
      (list python-pytest
+           python-pytest-cov
+           python-pytest-flake8
+           python-pytest-isort
            python-setuptools
            python-waitress
            python-wheel))
@@ -240,6 +244,7 @@ efficient syncing
      (list python-aioresponses
            python-pytest
            python-pytest-asyncio
+           python-pytest-cov
            python-pytest-httpserver
            python-setuptools
            python-setuptools-scm

gnu/packages/debian.scm

@@ -20,6 +20,18 @@
 ;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
 
 (define-module (gnu packages debian)
+  #:use-module ((guix licenses) #:prefix license:)
+  #:use-module (guix download)
+  #:use-module (guix git-download)
+  #:use-module (guix gexp)
+  #:use-module (guix packages)
+  #:use-module (guix utils)
+  #:use-module (guix build-system cmake)
+  #:use-module (guix build-system copy)
+  #:use-module (guix build-system gnu)
+  #:use-module (guix build-system perl)
+  #:use-module (guix build-system trivial)
+  #:use-module (gnu packages adns)
   #:use-module (gnu packages autotools)
   #:use-module (gnu packages backup)
   #:use-module (gnu packages base)
@@ -28,7 +40,6 @@
   #:use-module (gnu packages crypto)
   #:use-module (gnu packages databases)
   #:use-module (gnu packages dbm)
-  #:use-module (gnu packages dns)
   #:use-module (gnu packages gettext)
   #:use-module (gnu packages gnupg)
   #:use-module (gnu packages guile)
@@ -42,17 +53,6 @@
   #:use-module (gnu packages tls)
   #:use-module (gnu packages web)
   #:use-module (gnu packages wget)
-  #:use-module (guix build-system cmake)
-  #:use-module (guix build-system copy)
-  #:use-module (guix build-system gnu)
-  #:use-module (guix build-system perl)
-  #:use-module (guix build-system trivial)
-  #:use-module (guix download)
-  #:use-module (guix gexp)
-  #:use-module (guix git-download)
-  #:use-module ((guix licenses) #:prefix license:)
-  #:use-module (guix packages)
-  #:use-module (guix utils)
   #:use-module (srfi srfi-1)
   #:use-module (srfi srfi-26))
 

gnu/packages/debug.scm

@@ -275,7 +275,7 @@ simple way to add custom protocol messages.")
        (file-name (git-file-name name version))))
     (build-system cmake-build-system)
     (native-inputs
-     (list flex python-pytest))
+     (list flex python-pytest python-pytest-flake8))
     (inputs
      (list bash-minimal clang llvm unifdef
            python python-pebble python-psutil python-chardet))
@@ -1213,7 +1213,7 @@ and input distributions can also be expressed in Fandango.")
                           ;; Shorten paths to sockets in tests.
                           (lambda _ (setenv "TMPDIR" "/tmp"))))
            #:test-target "test"))
-    (native-inputs (list python python-setuptools)) ; for tests
+    (native-inputs (list python))      ; for tests
     (synopsis "Fault injector in userspace")
     (description "Fiu provides CLI utilities and a C library
 to mark points of failure inside your code

gnu/packages/dictionaries.scm

@@ -41,6 +41,7 @@
   #:use-module (guix build-system copy)
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system pyproject)
+  #:use-module (guix build-system python)
   #:use-module (guix build-system qt)
   #:use-module (guix build-system trivial)
   #:use-module (gnu packages)

gnu/packages/diffoscope.scm

@@ -67,6 +67,7 @@
   #:use-module (gnu packages vim)
   #:use-module (gnu packages web)
   #:use-module (gnu packages xml)
+  #:use-module (guix build-system python)
   #:use-module (guix build-system pyproject)
   #:use-module (guix gexp)
   #:use-module (guix git-download)
@@ -78,7 +79,7 @@
 (define-public diffoscope
   (package
     (name "diffoscope")
-    (version "317")
+    (version "315")
     (source
      (origin
        (method git-fetch)
@@ -87,7 +88,7 @@
              (commit version)))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "13r96c49wrpx0xa8bbkki832w58gjdgqb4khjsaawk5mb5yv4c39"))))
+        (base32 "1q2q60hw36d1capqdrg6gp2220dg87bmxgmk52m7yml4xw13zi2p"))))
     (build-system pyproject-build-system)
     (arguments
      (list
@@ -289,6 +290,14 @@ install.")
               (for-each (lambda (file)
                           (chmod file #o755))
                         (find-files #$output "autopkgtest-virt-.*"))))
+          ;; Adjust use of importlib.resources to use python 3.10 compatible
+          ;; syntax, which requires an argument.
+          ;; Drop when switching to python 3.12+.
+          (add-after 'unpack 'adjust-importlib-resources-for-old-python
+            (lambda _
+              (substitute* "reprotest/__init__.py"
+                (("importlib.resources.files\\(\\)")
+                  "importlib.resources.files(package='reprotest')"))))
           (add-after 'unpack 'skip-most-tests
             ;; These tests require functionality not available in the guix
             ;; build environment

gnu/packages/digest.scm

@@ -27,6 +27,7 @@
   #:use-module (guix git-download)
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system pyproject)
+  #:use-module (guix build-system python)
   #:use-module (guix build-system trivial)
   #:use-module (guix utils)
   #:use-module (gnu packages check)

gnu/packages/disk.scm

@@ -59,6 +59,7 @@
   #:use-module (guix build-system meson)
   #:use-module (guix build-system perl)
   #:use-module (guix build-system pyproject)
+  #:use-module (guix build-system python)
   #:use-module (guix build-system qt)
   #:use-module (guix build-system scons)
   #:use-module (guix build-system trivial)
@@ -1230,7 +1231,7 @@ passphrases.")
 (define-public ndctl
   (package
     (name "ndctl")
-    (version "84")
+    (version "78")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -1239,7 +1240,7 @@ passphrases.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "0jal7w4mk5l5j0qfays27kya8n1h2qwkncl0s317rfxp56bkjp6y"))))
+                "0rhmxjajxxslsikixlf9cdg5vcn42h7zzqkqj5p5pshxch368kn0"))))
     (build-system meson-build-system)
     (arguments
      ;; The test suite runs but SKIPs all tests: do not consider this tested!

gnu/packages/distributed.scm

@@ -51,7 +51,7 @@
 (define-public boinc-client
   (package
     (name "boinc-client")
-    (version "8.2.9")
+    (version "8.2.8")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -62,7 +62,7 @@
               (file-name (git-file-name "boinc" version))
               (sha256
                (base32
-                "0ik9423ii6kal29jdn907pxy8w86zpi8n158qx1gcsh8lsaif1v5"))))
+                "1ppcf57p6dkv9dv5k90fj3xhbv9di2d3yjkg2flfv5d45s82lay8"))))
     (build-system gnu-build-system)
     (arguments
      (list

gnu/packages/django.scm

@@ -37,6 +37,7 @@
   #:use-module (guix git-download)
   #:use-module (guix gexp)
   #:use-module (guix build-system pyproject)
+  #:use-module (guix build-system python)
   #:use-module (guix deprecation)
   #:use-module (guix search-paths)
   #:use-module (guix utils)
@@ -328,7 +329,7 @@ to the @dfn{don't repeat yourself} (DRY) principle.")
         (base32 "1a5vd07wrnfbclvf6pz9p8ag9kdd1453lsl9q0bkyc45hq2xqd2a"))))
     (build-system pyproject-build-system)
     (native-inputs
-     (list python-django python-pytest python-setuptools))
+     (list python-django python-pytest python-pytest-cov python-setuptools))
     (home-page "https://github.com/epicserve/django-cache-url")
     (synopsis "Configure Django cache settings from URLs")
     (description
@@ -419,6 +420,7 @@ and adapters that are useful for non-trivial configuration scenarios.")
            python-factory-boy
            python-pygments
            python-pytest
+           python-pytest-cov ; runs by default
            python-pytest-django
            python-setuptools
            python-shortuuid
@@ -547,7 +549,6 @@ when coding custom template tags.")
        (uri (git-reference
              (url "https://github.com/jazzband/django-taggit")
              (commit version)))
-       (file-name (git-file-name name version))
        (sha256
         (base32
          "1i8an3wcl7nygl5f565jcpyhyws9gabawazggxpf6m3vklxn3cj0"))))
@@ -708,13 +709,13 @@ your code.")
 (define-public python-django-filter
   (package
     (name "python-django-filter")
-    (version "25.2")
+    (version "25.1")
     (source (origin
               (method url-fetch)
               (uri (pypi-uri "django_filter" version))
               (sha256
                (base32
-                "08wgzqirabxzcdhh0wvv45hqr6dqxy3ifm7mjv86hi0zjd59h3kn"))))
+                "0lvi82f3dnj89ip8hry8fq8w7x632r5p84dlr451rnm8izsfxj8y"))))
     (build-system pyproject-build-system)
     (arguments
      '(#:phases
@@ -1327,6 +1328,7 @@ server headers required for Cross-Origin Resource Sharing (CORS).")
            python-mock
            python-msgpack
            python-pytest
+           python-pytest-cov
            python-pytest-django
            python-pytest-mock
            python-setuptools
@@ -2183,6 +2185,7 @@ templates and not in python-level form definitions.")
     (build-system pyproject-build-system)
     (native-inputs
      (list python-pytest
+           python-pytest-cov ; runs by default
            python-pytest-django
            python-setuptools
            python-wheel))

gnu/packages/djvu.scm

@@ -29,6 +29,7 @@
   #:use-module (guix git-download)
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system pyproject)
+  #:use-module (guix build-system python)
   #:use-module (gnu packages autotools)
   #:use-module (gnu packages base)
   #:use-module (gnu packages bash)

gnu/packages/dlang.scm

@@ -75,8 +75,7 @@
        (uri (string-append "https://github.com/ldc-developers/ldc/releases"
                            "/download/v" version "/ldc-" version "-src.tar.gz"))
        (sha256
-        (base32 "13pkg69wjj4ali4ikijicccpg8y6f2hghhb70z9lrqr2w3pkhqna"))
+        (base32 "13pkg69wjj4ali4ikijicccpg8y6f2hghhb70z9lrqr2w3pkhqna"))))
-       (patches (search-patches "ldc-i686-int128-alignment.patch"))))
     (build-system cmake-build-system)
     (arguments
      `(#:disallowed-references (,tzdata-for-tests)
@@ -108,7 +107,9 @@
            (lambda _
              (invoke "cmake" "--install" "."))))))
     (inputs
-     `(("zlib" ,zlib)))
+     `(("libconfig" ,libconfig)
+       ("libedit" ,libedit)
+       ("zlib" ,zlib)))
     (native-inputs
      `(("lld-wrapper" ,(make-lld-wrapper lld-17 #:lld-as-ld? #t))
        ("llvm" ,llvm-17)
@@ -371,7 +372,6 @@ integration tests...\n")
               ;; Do not build the shared libphobos2.so library, to avoid
               ;; retaining a reference to gcc:lib.
               "SHARED=0"
-              "DIFFABLE=1"              ;constant timestamp
               "VERBOSE=1")
       #:modules
       `(,@%default-gnu-modules
@@ -476,15 +476,6 @@ integration tests...\n")
               (phase-in-sub-dir 'build "dmd"))
             (add-after 'build 'build-phobos
               (phase-in-sub-dir 'build "phobos"))
-            (add-after 'build-phobos 'build-man
-              (lambda* (#:key make-flags #:allow-other-keys)
-                (with-directory-excursion "dmd/compiler/docs"
-                  (let ((dmd (or (which "gdmd")
-                                 (which "dmd"))))
-                    ((assoc-ref %standard-phases 'build)
-                     #:make-flags (cons
-                                   (string-append "DMD=" dmd)
-                                   make-flags))))))
             (replace 'check
               (phase-in-sub-dir 'check "dmd"))
             (add-after 'check 'check-phobos
@@ -510,7 +501,7 @@ integration tests...\n")
                       (for-each (cut install-file <> lib-lib)
                                 (find-files "." "^libdruntime\\.so[.0-9]*$")))
                     (copy-recursively "druntime/import" out-include)
-                    (copy-recursively "generated/docs/man" out-man))
+                    (copy-recursively "compiler/docs/man" out-man))
                   (with-directory-excursion "phobos"
                     (with-directory-excursion build-sub-dir
                       (install-file "libphobos2.a" out-lib)
@@ -685,7 +676,6 @@ needed.")
                  (lambda* (#:key tests? #:allow-other-keys)
                    (when tests?
                      (invoke "bin/rdmd" "rdmd_test.d" "bin/rdmd"
-                             "-m" (if #$(target-64bit?) "64" "32")
                              "--rdmd-default-compiler" "ldmd2"))))
                (replace 'install
                  (lambda* (#:key outputs #:allow-other-keys)

gnu/packages/dns.scm

@@ -1,13 +1,12 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2014 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2015 Taylan Ulrich Bayırlı/Kammer <taylanbayirli@gmail.com>
 ;;; Copyright © 2016 Mark H Weaver <mhw@netris.org>
-;;; Copyright © 2016, 2018 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2016 Ricardo Wurmus <rekado@elephly.net>
-;;; Copyright © 2015-2018, 2020 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2016, 2017 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2016 John Darrington <jmd@gnu.org>
 ;;; Copyright © 2016 Nikita <nikita@n0.is>
 ;;; Copyright © 2016–2022 Tobias Geerinckx-Rice <me@tobias.gr>
-;;; Copyright © 2016, 2019-2021 Marius Bakke <mbakke@fastmail.com>
+;;; Copyright © 2016, 2020 Marius Bakke <mbakke@fastmail.com>
 ;;; Copyright © 2017 Vasile Dumitrascu <va511e@yahoo.com>
 ;;; Copyright © 2017 Gregor Giesen <giesen@zaehlwerk.net>
 ;;; Copyright © 2022 Oleg Pykhalov <go.wigust@gmail.com>
@@ -22,11 +21,9 @@
 ;;; Copyright © 2021, 2024 Zheng Junjie <873216071@qq.com>
 ;;; Copyright © 2023 Bruno Victal <mirai@makinata.eu>
 ;;; Copyright © 2023 Hilton Chain <hako@ultrarare.space>
-;;; Copyright © 2023 Janneke Nieuwenhuizen <janneke@gnu.org>
 ;;; Copyright © 2024 John Kehayias <john.kehayias@protonmail.com>
 ;;; Copyright © 2024, 2025 Ashish SHUKLA <ashish.is@lostca.se>
 ;;; Copyright © 2025 Artyom V. Poptsov <poptsov.artyom@gmail.com>
-;;; Copyright © 2026 Anderson Torres <anderson.torres.8519@gmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -49,12 +46,12 @@
   #:use-module (gnu packages base)
   #:use-module (gnu packages bash)
   #:use-module (gnu packages check)
-  #:use-module (gnu packages compression)
-  #:use-module (gnu packages crypto)
   #:use-module (gnu packages curl)
   #:use-module (gnu packages databases)
-  #:use-module (gnu packages datastructures)
   #:use-module (gnu packages documentation)
+  #:use-module (gnu packages compression)
+  #:use-module (gnu packages crypto)
+  #:use-module (gnu packages datastructures)
   #:use-module (gnu packages elf)
   #:use-module (gnu packages flex)
   #:use-module (gnu packages freedesktop)
@@ -68,7 +65,6 @@
   #:use-module (gnu packages libidn)
   #:use-module (gnu packages linux)
   #:use-module (gnu packages lua)
-  #:use-module (gnu packages m4)
   #:use-module (gnu packages ncurses)
   #:use-module (gnu packages nettle)
   #:use-module (gnu packages networking)
@@ -88,173 +84,17 @@
   #:use-module (gnu packages web)
   #:use-module (gnu packages xml)
   #:use-module (gnu packages)
-  #:use-module (guix build-system cmake)
-  #:use-module (guix build-system copy)
-  #:use-module (guix build-system glib-or-gtk)
-  #:use-module (guix build-system gnu)
-  #:use-module (guix build-system meson)
-  #:use-module (guix download)
   #:use-module (guix gexp)
-  #:use-module (guix git-download)
   #:use-module ((guix licenses) #:prefix license:)
   #:use-module (guix packages)
   #:use-module ((guix search-paths) #:select ($SSL_CERT_DIR $SSL_CERT_FILE))
-  #:use-module (guix utils))
+  #:use-module (guix download)
-
+  #:use-module (guix git-download)
-(define-public adns
+  #:use-module (guix utils)
-  (package
+  #:use-module (guix build-system copy)
-    (name "adns")
+  #:use-module (guix build-system glib-or-gtk)
-    (version "1.6.1")
+  #:use-module (guix build-system gnu)
-    (source
+  #:use-module (guix build-system meson))
-     (origin
-       (method git-fetch)
-       (uri (git-reference
-              (url "git://git.chiark.greenend.org.uk/~ianmdlvl/adns.git")
-              (commit (string-append "adns-" version))))
-       (sha256
-        (base32
-         "0ln3l5j7wb1xazrzl76p9xar52p6l2k1cwy7jazxw1acl71k9h5n"))))
-    (build-system gnu-build-system)
-    (arguments
-     (list
-      ;; INFO: Tests expect real name resolution to work.
-      #:tests? #f
-      #:configure-flags
-      #~(list
-         ;; Make sure the programs under bin/ find libadns.so.
-         (string-append "LDFLAGS=-Wl,-rpath -Wl,"
-                        #$output:out
-                        "/lib"))))
-    (native-inputs
-     (list m4))
-    (home-page "https://www.gnu.org/software/adns/")
-    (synopsis "Asynchronous DNS client library and utilities")
-    (description
-     "GNU adns is a C library that provides easy-to-use @acronym{DNS, Domain
-Name System} resolution functionality.  The library is asynchronous, allowing
-several concurrent calls.  The package also includes several command-line
-utilities for use in scripts.")
-    (license license:gpl3+)))
-
-(define-public c-ares
-  (package
-    (name "c-ares")
-    (version "1.34.4")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (string-append
-             "https://github.com/c-ares/c-ares/releases/download/v"
-             version "/" name "-" version ".tar.gz"))
-       (sha256
-        (base32
-         "0br2msk3bpl5myhjp9vr5j2scpspvbg2fpnz69dcrr4ycpnxnf7s"))))
-    (build-system gnu-build-system)
-    (arguments
-     (list
-      #:phases
-      #~(modify-phases %standard-phases
-          (add-before 'check 'filter-live-tests
-            (lambda _
-              ;; Filter tests that require internet access.
-              (setenv "GTEST_FILTER" "-*.Live*:*.FamilyV4*")))
-          #$@(if (system-hurd?)
-                 #~((add-after 'unpack 'skip-tests
-                      (lambda _
-                        (substitute* "test/ares-test-main.cc"
-                          (("(^| )main *\\(.*" all)
-                           (string-append all "  exit (77);\n")))))
-                    (add-after 'filter-live-tests 'filter-hurd-tests
-                      (lambda _
-                        (setenv "GTEST_FILTER"
-                                (string-append
-                                 (getenv "GTEST_FILTER")
-                                 ":.*Basic/2"
-                                 ":.*CancelImmediate/2"
-                                 ":.*CancelImmediateGetHostByAddr/2"
-                                 ":.*CancelLater/1"
-                                 ":.*FamilyUnspecified/2"
-                                 ":.*FamilyV6/2"
-                                 ":.*GetAddrInfoParallelLookups/1"
-                                 ":.*GetHostByAddrDestroy/2"
-                                 ":.*GetHostByNameCNAMENoData/2"
-                                 ":.*GetHostByNameDestroyAbsolute/2"
-                                 ":.*GetHostByNameDestroyRelative/2"
-                                 ":.*GetHostByNameParallelLookups/1"
-                                 ":.*HostAlias/2"
-                                 ":.*HostAliasMissing/2"
-                                 ":.*HostAliasMissingFile/2"
-                                 ":.*NotImplResponse/2"
-                                 ":.*RefusedResponse/2"
-                                 ":.*Resend/1"
-                                 ":.*RetryWithoutEDNS/2"
-                                 ":.*SearchDomains/2"
-                                 ":.*SearchDomainsBare/2"
-                                 ":.*SearchDomainsServFailOnAAAA/2"
-                                 ":.*SearchDomainsWithResentReply/1"
-                                 ":.*SearchHighNdots/2"
-                                 ":.*SearchNoDataThenFail/2"
-                                 ":.*SearchNoDataThenNoDataBare/2"
-                                 ":.*SearchNoDataThenSuccess/2"
-                                 ":.*ServFailResponse/2"
-                                 ":.*SimpleQuery/2"
-                                 ":.*SockCallback/2"
-                                 ":.*SockConfigureCallback/2"
-                                 ":.*SortListV4/2"
-                                 ":.*SortListV6/2"
-                                 ":.*ThirdServer/2"
-                                 ":.*TruncationRetry/1"
-                                 ":.*UnspecifiedFamilyCname6A4/2"
-                                 ":.*UnspecifiedFamilyV4/2"
-                                 ":.*UnspecifiedFamilyV6/2")))))
-                 #~()))))
-    (native-inputs
-     (list pkg-config))
-    (home-page "https://c-ares.haxx.se/")
-    (synopsis "C library for asynchronous DNS requests")
-    (description
-     "C-ares is a C library that performs DNS requests and name resolution
-asynchronously.  It is intended for applications which need to perform DNS
-queries without blocking, or need to perform multiple DNS queries in parallel.
-The primary examples of such applications are servers which communicate with
-multiple clients and programs with graphical user interfaces.")
-    (license (license:x11-style "https://c-ares.haxx.se/license.html"))))
-
-(define-public c-ares-for-node-lts
-  (hidden-package c-ares))
-
-(define-public c-ares-for-node-bootstrap
-  (hidden-package
-   (package
-     (inherit c-ares)
-     (version "1.18.1")
-     (source
-      (origin
-        (method url-fetch)
-        (uri (string-append
-              "https://c-ares.haxx.se/download/c-ares-" version
-              ".tar.gz"))
-        (sha256
-         (base32
-          "1kxviskwsaa7dcgscvssxa8ps88pdq7kq4z93gxvz7sam2l54z8s")))))))
-
-;; INFO: gRPC requires a c-ares built with CMake in order to get the .cmake
-;; modules.  We can not build c-ares itself with CMake because that would
-;; introduce a circular dependency through nghttp2.
-;;
-;; TODO: It would be nice if we could extract the modules somehow and make
-;; them work with the "normal" c-ares package instead of building a whole new
-;; library.
-(define-public c-ares/cmake
-  (hidden-package
-   (package
-     (inherit c-ares)
-     (build-system cmake-build-system)
-     (arguments
-      (list
-       ;; INFO: Tests require name resolution (the normal variant runs no
-       ;; tests).
-       #:tests? #f)))))
 
 (define-public cloudflare-cli
   (let ((commit "2d986d3ec1b0e3158c4bd40e8918947cb74aa392")
@@ -455,37 +295,35 @@ prompt the user with the option to go with insecure DNS only.")
 (define-public dnsmasq
   (package
     (name "dnsmasq")
-    (version "2.92")
+    (version "2.90")
-    (source
+    (source (origin
-     (origin
+              (method url-fetch)
-       (method git-fetch)
+              (uri (string-append
-       (uri (git-reference
+                    "http://www.thekelleys.org.uk/dnsmasq/dnsmasq-"
-              (url "http://thekelleys.org.uk/git/dnsmasq.git")
+                    version ".tar.xz"))
-              (commit (string-append "v" version))))
+              (sha256
-       (file-name (git-file-name name version))
+               (base32
-       (sha256
+                "1r09l537vi867hlpv6vl7nvqhscvq1kf04m896bfrgrpv2dk0l4f"))))
-        (base32 "055gn5kigz0m9y09vig97s1g257hnlkhw4wv9d9wdficnsxcbwwm"))))
     (build-system gnu-build-system)
-    (arguments
-     (list
-      #:tests? #f ;no tests
-      #:make-flags
-      #~(list (string-append "PREFIX=" #$output)
-              (string-append "CC=" #$(cc-for-target))
-              (string-append "PKG_CONFIG=" #$(pkg-config-for-target))
-              "COPTS=\"-DHAVE_DBUS\"")
-      #:phases
-      #~(modify-phases %standard-phases
-          (delete 'configure) ;no configure
-          (add-after 'install 'install-dbus
-            (lambda _
-              (install-file "dbus/dnsmasq.conf"
-                            (string-append #$output "/etc/dbus-1/system.d")))))))
     (native-inputs
      (list pkg-config))
     (inputs
      (list dbus))
-    (home-page "https://thekelleys.org.uk/dnsmasq/doc.html")
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (delete 'configure)
+         (add-after 'install 'install-dbus
+           (lambda _
+             (install-file "dbus/dnsmasq.conf"
+                           (string-append %output "/etc/dbus-1/system.d")))))
+
+       #:make-flags (list (string-append "PREFIX=" (assoc-ref %outputs "out"))
+                          (string-append "CC=" ,(cc-for-target))
+                          (string-append "PKG_CONFIG=" ,(pkg-config-for-target))
+                          "COPTS=\"-DHAVE_DBUS\"")
+       #:tests? #f))                    ; no ‘check’ target
+    (home-page "https://www.thekelleys.org.uk/dnsmasq/doc.html")
     (synopsis "Small caching DNS proxy and DHCP/TFTP server")
     (description
      "Dnsmasq is a light-weight DNS forwarder and DHCP server.  It is designed

gnu/packages/docbook.scm

@@ -53,6 +53,7 @@
   #:use-module (guix build-system copy)
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system pyproject)
+  #:use-module (guix build-system python)
   #:use-module (srfi srfi-26))
 
 ;; The fetch-plan, install-plan and phases for docbook-xml tend to vary
@@ -665,8 +666,7 @@ the in DocBook SGML DTDs.")
                (base32
                 "0yd09nypswy3q4scri1dg7dr99d7gd6r2dwx0xm81l9f4y32gs0n"))
               (patches
-               (search-patches "dblatex-importlib.patch"
+               (search-patches "dblatex-inkscape-1.0.patch"))))
-                               "dblatex-inkscape-1.0.patch"))))
     (outputs '("out" "doc"))
     (build-system pyproject-build-system)
     (arguments

gnu/packages/docker.scm

@@ -39,6 +39,7 @@
   #:use-module (guix build-system cmake)
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system go)
+  #:use-module (guix build-system python)
   #:use-module (guix build-system pyproject)
   #:use-module (guix utils)
   #:use-module (gnu packages autotools)

gnu/packages/documentation.scm

@@ -41,6 +41,7 @@
   #:use-module (guix build-system cmake)
   #:use-module (guix build-system copy)
   #:use-module (guix build-system perl)
+  #:use-module (guix build-system python)
   #:use-module (guix build-system pyproject)
   #:use-module (guix build-system qt)
   #:use-module (guix deprecation)
@@ -69,7 +70,6 @@
   #:use-module (gnu packages qt)
   #:use-module (gnu packages sqlite)
   #:use-module (gnu packages sphinx)
-  #:use-module (gnu packages tex)
   #:use-module (gnu packages uglifyjs)
   #:use-module (gnu packages xml)
   #:use-module (gnu packages xorg))
@@ -108,13 +108,10 @@
                           #$output)
                          (("\\$cfg\\{'TMPSPACE'\\} = q'[^']*'")
                           "$cfg{'TMPSPACE'} = q'/tmp'")))))))
-    (propagated-inputs (list texlive-preview texlive-xcolor texlive-dvips))
     (inputs (list perl netpbm ghostscript))
     (synopsis "LaTeX documents to HTML")
     (description "LaTeX2HTML is a utility that converts LaTeX documents to web
-pages in HTML.  Since there are many different latex packages, it is expected
+pages in HTML.")
-that the user has their latex installation set up correctly when invoking
-@code{latex2html}.")
     (home-page "https://www.latex2html.org/")
     (license license:gpl2+)))
 
@@ -471,8 +468,9 @@ inspired by Dash.")
     (build-system gnu-build-system)
     (arguments
      (list
-      ;; Custom build steps to prevent using pyproject-build-system which
+      ;; Essentially a lighter copy of the former python-build-system.
-      ;; allows to edit the latter without a texlive + haskell world rebuild.
+      ;; Using it rather than pyproject-build-system allows to edit the latter
+      ;; without a texlive + haskell world rebuild.
       #:phases
       #~(modify-phases %standard-phases
           (delete 'bootstrap)

gnu/packages/dotnet.scm

@@ -62,6 +62,7 @@
   #:use-module (guix utils)
   #:use-module (guix build-system cmake)
   #:use-module (guix build-system gnu)
+  #:use-module (guix build-system python)
   #:use-module (ice-9 match))
 
 (define-public treecc

gnu/packages/duckdb.scm

@@ -25,6 +25,7 @@
   #:use-module ((guix licenses) #:prefix license:)
   #:use-module (guix build-system cmake)
   #:use-module (guix build-system pyproject)
+  #:use-module ((guix build-system python) #:select (pypi-uri))
   #:use-module (guix build-system r)
   #:use-module (guix download)
   #:use-module (guix gexp)
@@ -147,13 +148,13 @@ system.")
 (define-public r-duckdb
   (package
     (name "r-duckdb")
-    (version "1.5.1")
+    (version "1.4.4")
     (source
      (origin
        (method url-fetch)
        (uri (cran-uri "duckdb" version))
        (sha256
-        (base32 "177621m08whqqk4yhj3zrr08l3d9hhlqh3gm9jzhi5cplg47cksq"))
+        (base32 "1hch36v3lsymnx30lv3cjy12gs3v3mhd44ha97l7w9mwp9wbzmxl"))
        ;; This package bundles the duckdb sources and builds a custom variant
        ;; of duckdb.  I'd be happy to link it with our duckdb library instead,
        ;; but it does not seem possible to do that.
@@ -178,12 +179,10 @@ system.")
                          r-dplyr
                          r-remotes
                          r-rlang
-                         r-sf
                          r-testthat
                          r-tibble
                          r-vctrs
                          r-withr
-                         r-wk
                          tzdata-for-tests))
     (home-page "https://r.duckdb.org/")
     (synopsis "DBI package for the DuckDB database management system")

gnu/packages/ebook.scm

@@ -40,6 +40,7 @@
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system meson)
   #:use-module (guix build-system pyproject)
+  #:use-module (guix build-system python)
   #:use-module (guix build-system qt)
   #:use-module (gnu packages)
   #:use-module (gnu packages autotools)

gnu/packages/education.scm

@@ -4,7 +4,7 @@
 ;;; Copyright © 2016 Hartmut Goebel <h.goebel@crazy-compilers.com>
 ;;; Copyright © 2017-2023 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2018–2021 Tobias Geerinckx-Rice <me@tobias.gr>
-;;; Copyright © 2018-2026 Nicolas Goaziou <mail@nicolasgoaziou.fr>
+;;; Copyright © 2018-2025 Nicolas Goaziou <mail@nicolasgoaziou.fr>
 ;;; Copyright © 2020 Robert Smith <robertsmith@posteo.net>
 ;;; Copyright © 2020 Guy Fleury Iteriteka <gfleury@disroot.org>
 ;;; Copyright © 2020 Jakub Kądziołka <kuba@kadziolka.net>
@@ -91,6 +91,7 @@
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system go)
   #:use-module (guix build-system pyproject)
+  #:use-module (guix build-system python)
   #:use-module (guix build-system qt)
   #:use-module (guix build-system trivial)
   #:use-module (srfi srfi-1))
@@ -384,7 +385,7 @@ not have any other specialized device.")
 (define-public openboard
   (package
     (name "openboard")
-    (version "1.7.7")
+    (version "1.7.3")
     (source
      (origin
        (method git-fetch)
@@ -393,7 +394,7 @@ not have any other specialized device.")
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "1i27h84p77pl1chw791fjs3vyzsjvsqc9ky2mbw7g8xpzxz1nd9j"))))
+        (base32 "1098pys5p82sx97xrhw54vlkn6jly0rhq8b09grmmx2h4mcpj2i2"))))
     (build-system qt-build-system)
     (arguments
      (list

gnu/packages/electronics.scm

@@ -64,6 +64,7 @@
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system meson)
   #:use-module (guix build-system pyproject)
+  #:use-module (guix build-system python)
   #:use-module (guix build-system qt)
   #:use-module (guix deprecation)
   #:use-module (guix download)
@@ -239,8 +240,8 @@ are also taken from the original.")
       (license license:gpl3+))))
 
 (define-public abc
-  (let ((commit "80c8a9a1928ef8148a6b504e9590ec07c55c8bcf")
+  (let ((commit "c18b9a24de46d3b0209afa416511b7a1127344f9")
-        (revision "10"))
+        (revision "9"))
     (package
       (name "abc")
       (version (git-version "0.0" revision commit))
@@ -252,7 +253,7 @@ are also taken from the original.")
                 (file-name (git-file-name name version))
                 (sha256
                  (base32
-                  "1fbnwsd841z86vfv45443qfpx0l199vf08sgms8wyz19jw7m5ds6"))))
+                  "12fjhlr9r34l6kw2jyaalh53fs783r1h2zx0ldzaxxrbcslb0bxh"))))
       (build-system gnu-build-system)
       (inputs
        (list readline))
@@ -277,7 +278,7 @@ formal verification.")
   (package
     (inherit abc)
     (name "abc-yosyshq")
-    (version "0.64")
+    (version "0.63")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -286,7 +287,7 @@ formal verification.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "1jk74yq7dnrnai8r9hqc10jcjmgj50jxj6hsflmvc61acm1r3f8r"))))
+                "1nwj4zhjqjgvb7fh877j51kfccwzrc591ag25qm9jirycgq1cqx6"))))
     (home-page "https://github.com/YosysHQ/abc/")
     (description "ABC is a program for sequential logic synthesis and
 formal verification.  This is the Yosyshq fork of ABC.")
@@ -295,7 +296,7 @@ formal verification.  This is the Yosyshq fork of ABC.")
 (define-public apycula
   (package
     (name "apycula")
-    (version "0.32")
+    (version "0.31")
     ;; The pypi tar.gz file includes the necessary .pickle files, not available
     ;; in the home-page repository.
     (source
@@ -303,7 +304,7 @@ formal verification.  This is the Yosyshq fork of ABC.")
        (method url-fetch)
        (uri (pypi-uri "apycula" version))
        (sha256
-        (base32 "0zz6mz1s7razbqsysaji7qwfsjj19av4mg7zclxaigz4hmq9ar0d"))))
+        (base32 "0pf43cd071kv5ann78hl5qrcj9vhndr46ds2g12sgnfjfvh6pfpg"))))
     (build-system pyproject-build-system)
     (arguments
      (list #:tests? #f ;requires Gowin EDA tools
@@ -466,7 +467,7 @@ individual low-level driver modules.")
 (define-public eqy
   (package
     (name "eqy")
-    (version "0.64")
+    (version "0.63")
     (source
      (origin
        (method git-fetch)
@@ -475,14 +476,12 @@ individual low-level driver modules.")
               (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "1lsf8wm10wq67lmwz1ck30inl3byfy27ya39fj93gym5ys815ma6"))))
+        (base32 "05rk6gy0xnaksxqdkpm08i3ngh0adavfyfjyscw5l1b7d7yhfavh"))))
     (build-system gnu-build-system)
     (arguments
      (list
-      #:imported-modules %pyproject-build-system-modules
+      #:imported-modules (append %default-gnu-imported-modules
-      #:modules '((guix build gnu-build-system)
+                                 %python-build-system-modules)
-                  ((guix build pyproject-build-system) #:prefix py:)
-                  (guix build utils))
       #:make-flags
       #~(list (string-append "PREFIX=" #$output))
       #:phases
@@ -508,7 +507,8 @@ individual low-level driver modules.")
                 ;; https://github.com/YosysHQ/eqy/actions/runs/18767539188/job/53545383858
                 (invoke "make" "-C" "examples/spm")
                 (invoke "make" "-C" "examples/simple"))))
-          (add-after 'install 'python:wrap py:wrap))))
+          (add-after 'install 'python:wrap
+            (@@ (guix build python-build-system) wrap)))))
     (native-inputs
      (list clang python-minimal-wrapper python-sphinx texinfo yosys))
     (inputs
@@ -1502,7 +1502,7 @@ an embedded event driven algorithm.")
 (define-public librelane
   (package
     (name "librelane")
-    (version "3.0.2")
+    (version "3.0.0")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -1511,7 +1511,7 @@ an embedded event driven algorithm.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "1v43adkw5c624nd06g11cb609v8pj3prfyyawbq3i4k1w1law597"))))
+                "01zi2v5qi26h09hwjafsq9k0anrc5g5fc6q5vg87k9lcwyfsi685"))))
     (build-system pyproject-build-system)
     (arguments
      (list
@@ -2018,7 +2018,7 @@ which allows one to install the M8 firmware on any Teensy.")
 (define-public magic
   (package
     (name "magic")
-    (version "8.3.633")
+    (version "8.3.625")
     (source
      (origin
        (method git-fetch)
@@ -2027,7 +2027,7 @@ which allows one to install the M8 firmware on any Teensy.")
              (commit version)))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "1rwrhb0q99rpv4lbiw1sqykwzf9gj1my2wkh6mp8g36rab2vhii3"))))
+        (base32 "0ld238cdq8mzzcx7vgk67aqim0ypbfyks486z59q19yzxpr6c42s"))))
     (build-system gnu-build-system)
     (arguments
      (list
@@ -2057,7 +2057,7 @@ versus schematic} tests and can assist with automatic routing.")
 (define-public mcy
   (package
     (name "mcy")
-    (version "0.64")
+    (version "0.63")
     (source
      (origin
        (method git-fetch)
@@ -2072,10 +2072,7 @@ versus schematic} tests and can assist with automatic routing.")
      (list
       #:tests? #f                       ;there are no tests
       #:imported-modules (append %qt-build-system-modules
-                                 %pyproject-build-system-modules)
+                                 %python-build-system-modules)
-      #:modules '((guix build qt-build-system)
-                  ((guix build pyproject-build-system) #:prefix py:)
-                  (guix build utils))
       #:phases
       #~(modify-phases %standard-phases
           (add-after 'unpack 'build-info-documentation
@@ -2103,7 +2100,8 @@ versus schematic} tests and can assist with automatic routing.")
                   (chmod bin_ #o755)))
               (install-it "mcy")
               (install-it "mcy-dash")))
-          (add-after 'make-install 'python:wrap py:wrap))))
+          (add-after 'make-install 'python:wrap
+            (@@ (guix build python-build-system) wrap)))))
     (native-inputs
      (list pkg-config
            python-sphinx
@@ -2122,7 +2120,7 @@ coverage.")
 (define-public netgen
   (package
     (name "netgen")
-    (version "1.5.318")
+    (version "1.5.316")
     (source
      (origin
        (method git-fetch)
@@ -2131,7 +2129,7 @@ coverage.")
              (commit version)))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "19rd8y2pspycr2296nhm60fhsgnzlyzb09wx2kgqzg6s7h6cmrr5"))))
+        (base32 "1923mynqw1wjhlcij639gdqrkifyb5lcks1x11gwpgp4gijwj3qb"))))
     (build-system gnu-build-system)
     (arguments
      (list
@@ -2692,20 +2690,20 @@ formats.")
 (define-public openroad
   (package
     (name "openroad")
-    (version "26Q2")
+    (version "26Q1")
     (source
      (origin
        (method git-fetch)
        (uri (git-reference
               (url "https://github.com/The-OpenROAD-Project/OpenROAD")
-              (commit version)
+              (commit "e06ca0f5f2e641cd7b138a4d9b4fdd290359eca8")
               ;; 26Q1 Uses:
-              ;; - forked, custom opensta: v2.2.0-1952-g43177bba
+              ;; - forked, custom opensta: v2.2.0-1579-g9c9b5659
-              ;; - forked, custom (berkeley) abc: 20260301.0445-g17cadca08
+              ;; - forked, custom (berkeley) abc: 20260104.1628-g4c756ffb8
               (recursive? #t)))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "152j78c47wyq4sw42bwlxdhvs5g47a8jqz1qz5yzdsk9z5y4y7vl"))))
+        (base32 "13x4kqi4j489k4sz56ws4aqhp60nff1i18z6hjd6xx8y7flaik0c"))))
     (build-system qt-build-system)
     (arguments
      (list
@@ -2739,7 +2737,7 @@ formats.")
            flex
            googletest
            pkg-config
-           swig-4.4))
+           swig-4.0))
     (inputs
      (list abseil-cpp
            boost
@@ -2778,6 +2776,7 @@ clock tree synthesis, routing, parasitic extraction, and timing analysis.")
   (package
     (inherit openroad)
     (name "openroad-cli")
+    (build-system cmake-build-system)
     (arguments
      (delkw
       #:qtbase
@@ -3010,6 +3009,7 @@ Numpy arrays for convenience.")
               (setenv "PDM_BUILD_SCM_VERSION" #$version))))))
     (native-inputs
      (list python-pdm-backend
+           python-pytest-cov
            python-setuptools
            python-setuptools-scm
            sby
@@ -3322,7 +3322,9 @@ Standard} data mode.")
         (base32 "15nnydvr1a4ykh8cagi484sfgvdg0dnjxaw6c0ivhjbrbblpaqnw"))))
     (build-system pyproject-build-system)
     (native-inputs
-     (list python-setuptools python-setuptools-scm))
+     (list python-pytest-cov
+           python-setuptools
+           python-setuptools-scm))
     (home-page "http://pyvcd.readthedocs.io/")
     (synopsis "Library to manipulate digital wave files")
     (description
@@ -3458,7 +3460,7 @@ form of AXI, AXI lite, and AXI stream modules.")
 (define-public python-edalize
   (package
     (name "python-edalize")
-    (version "0.6.6")
+    (version "0.6.5")
     (source
      (origin
        (method git-fetch)
@@ -3467,7 +3469,7 @@ form of AXI, AXI lite, and AXI stream modules.")
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "115nc15n2cx4x9irjim07zkg0287418djqd6ja7rm8jrnyldvln9"))))
+        (base32 "1drmc126a12zlynx8ps9iwghaqs058pqj2xpdysxnrj26hg3sp15"))))
     (build-system pyproject-build-system)
     (arguments
      (list
@@ -3494,17 +3496,17 @@ form of AXI, AXI lite, and AXI stream modules.")
     (native-inputs
      (list python-pytest python-setuptools python-setuptools-scm))
     (propagated-inputs
-     (list python-importlib-metadata python-jinja2 python-pandas))
+     (list python-importlib-metadata python-jinja2))
     (home-page "https://github.com/olofk/edalize/")
     (synopsis "Python Library for interacting with EDA tools")
     (description
-     "This package can create project files for supported tools and run them in
+     "This package implements a functionality to create project files for
-batch or GUI mode.  All EDA tools such as Icarus, Yosys, ModelSim, Vivado,
+supported tools and run them in batch or GUI mode.  All EDA tools such as
-Verilator, GHDL, Quartus etc get input HDL files (Verilog and VHDL) and some
+Icarus, Yosys, ModelSim, Vivado, Verilator, GHDL, Quartus etc get input HDL
-tool-specific files (constraint files,memory initialization files, IP
+files (Verilog and VHDL) and some tool-specific files (constraint files,memory
-description files etc).  Together with the files, perhaps a couple of Verilog
+initialization files, IP description files etc).  Together with the files,
-`defines, some top-level parameters/generics or some tool-specific options are
+perhaps a couple of Verilog `defines, some top-level parameters/generics or
-set.")
+some tool-specific options are set.")
     (license license:bsd-2)))
 
 (define-public fusesoc
@@ -3599,7 +3601,10 @@ Automation}.")
                          #$output "/share/info/hdlmake-figures")))))
       #:test-flags #~(list "test_all.py")))
     (native-inputs
-     (list python-setuptools python-sphinx texinfo))
+     (list python-pytest-cov
+           python-setuptools
+           python-sphinx
+           texinfo))
     (propagated-inputs (list python-networkx))
     (home-page "https://ohwr.gitlab.io/project/hdl-make/")
     (synopsis "Generate multi-purpose makefiles for HDL projects")
@@ -3762,9 +3767,18 @@ design.")
       ;; Tests are expensive and may introduce race condition on systems with
       ;; high (more than 16) threads count; limit parallel jobs to 8x.
       #~(list
-         "--numprocesses" (number->string (min 8 (parallel-job-count))))))
+         "--numprocesses" (number->string (min 8 (parallel-job-count))))
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-after 'unpack 'pathch-pytest-options
+            (lambda _
+              (substitute* "pyproject.toml"
+                ((".*--cov=.*") "")
+                ((".*--self-contained-html.*") "")
+                ((".*-n.*auto.*") "")))))))
     (native-inputs
-     (list python-pytest
+     (list python-pytest-cov
+           python-pytest-html
            python-pytest-xdist
            python-setuptools))
     (propagated-inputs
@@ -3779,7 +3793,7 @@ to enforce it.")
 (define-public python-vunit
   (package
     (name "python-vunit")
-    (version "5.0.0-dev.10") ;v4.7.0 dates back from 2 years ago.
+    (version "5.0.0-dev.9") ;v4.7.0 dates back from 2 years ago.
     (source
      (origin
        (method git-fetch)
@@ -3788,7 +3802,7 @@ to enforce it.")
               (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "1gr9ghwgqly9zf0sf15ai20sac520rs84b9i5qjxdqpj26ayyl1q"))))
+        (base32 "1j9rvlshzi4mdy7wah1j8ri63drkjb47xly22q40wvl2xp2ghqgs"))))
     (build-system pyproject-build-system)
     (arguments
      (list
@@ -3986,7 +4000,7 @@ input and outputs an XML dataset.")
 (define-public qucs-s
   (package
     (name "qucs-s")
-    (version "26.1.0")                  ;update qucsator-rf accordingly
+    (version "25.2.0")                  ;update qucsator-rf accordingly
     (source
      (origin
        (method git-fetch)
@@ -3996,7 +4010,7 @@ input and outputs an XML dataset.")
        (file-name (git-file-name name version))
        (sha256
         (base32
-         "0aiyrcrxln4v6qm2dmigb54wl0mj499q3g18pz87m1s2lfgicpb1"))))
+         "0328irynm8vy4xjdip5286fd8nag1zdp0p6rcbhdhp4fca6wp5ak"))))
     (build-system qt-build-system)
     (arguments
      (list
@@ -4218,7 +4232,7 @@ them usable as simple logic analyzer and/or oscilloscope hardware.")
 (define-public sby
   (package
     (name "sby")
-    (version "0.64")
+    (version "0.63")
     (source
      (origin
        (method git-fetch)
@@ -4227,16 +4241,17 @@ them usable as simple logic analyzer and/or oscilloscope hardware.")
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "0jksspdgq2grk4a80i5yfc9bazfij37wpmrlkvygpz9ys5ny1432"))))
+        (base32 "1p23w9jd95b86n7f94zpqdaz19fn2b2lyww1p8dcy9p3zrcn7750"))))
     (build-system gnu-build-system)
     (arguments
      (list
       #:parallel-tests? #f
       #:test-target "test"
-      #:imported-modules %pyproject-build-system-modules
       #:modules `((guix build gnu-build-system)
-                  ((guix build pyproject-build-system) #:prefix python:)
+                  ((guix build python-build-system) #:prefix python:)
                   (guix build utils))
+      #:imported-modules `(,@%default-gnu-imported-modules
+                           (guix build python-build-system))
       #:make-flags #~(list (string-append "PREFIX=" #$output))
       #:phases
       #~(modify-phases %standard-phases
@@ -4275,8 +4290,8 @@ front-end program for Yosys-based formal hardware verification flows.")
     (license license:isc)))
 
 (define-public sby-gui
-  (let ((commit "0a89301bf347c9f42932186e49ba2c0014ff3661")
+  (let ((commit "6c977084c17c4842c504829c6d455a07d67e119c")
-        (revision "1"))
+        (revision "0"))
     (package
       (name "sby-gui")
       (version (git-version "0" revision commit))
@@ -4288,13 +4303,10 @@ front-end program for Yosys-based formal hardware verification flows.")
                 (commit commit)))
          (file-name (git-file-name name version))
          (sha256
-          (base32 "1zp2c7zqclsfvl5xhb8zlc1dclp2s36w2nd0x80fazsxp7ksw5gr"))))
+          (base32 "137x3s5mwbzlcv2p6671ijvbafzwhxpvszzfi9wifq0wcli6cxxg"))))
       (build-system qt-build-system)
       (arguments
-       (list
+       (list #:tests? #f))               ;no tests
-        #:qtbase qtbase                 ;for Qt 6
-        #:tests? #f))                   ;no tests
-      (native-inputs (list python-minimal-wrapper))
       (propagated-inputs (list sby))
       (home-page "https://github.com/YosysHQ/sby-gui/")
       (synopsis "Graphical user interface for code{sby}")
@@ -4649,7 +4661,7 @@ parallel computing platforms.  It also supports serial execution.")
 (define-public yosys
   (package
     (name "yosys")
-    (version "0.64")
+    (version "0.63")
     (source
      (origin
        (method git-fetch)
@@ -4657,7 +4669,7 @@ parallel computing platforms.  It also supports serial execution.")
               (url "https://github.com/YosysHQ/yosys")
               (commit (string-append "v" version))))
        (sha256
-        (base32 "13gw5msk1kv05jkb330nybvx2s0ixm6l6mdpyapnqmv3lkhby1mj"))
+        (base32 "1iaafzsc0pbd61m5hh12nzr2z4rn4n7i68l6ij9vli4m5zsxw39k"))
        (file-name (git-file-name name version))))
     (build-system gnu-build-system)
     (outputs '("out" "doc"))
@@ -4770,12 +4782,12 @@ parallel computing platforms.  It also supports serial execution.")
               (git-reference
                 (url "https://github.com/povik/yosys-slang")
                 ;; No tags, nor releases.
-                (commit "4e53d772996184b07e9bfe784060f96e6cb0a267")
+                (commit "d82b0b163a725fc1a401fbb6b465cd862517ec1f")
                 (recursive? #t)))  ;requires slang and fmt
              (file-name "yosys-slang")
              (sha256
               (base32
-               "1jjr1b6xd1sr9fkyfyl4y2wkzl51m7g10bw97mnw81v2mzssrs2q")))))
+               "07h4qssphggd4mbn376vldqwzj1i16y1ix455xzr4lgx6s2q9ryg")))))
     ;; Optional dependencies increase considerably package closure.
     ;; - gtkwave: required only for vcd2fst binary, used by ‘sim’ command.
     ;; - graphviz, xdot: used by ‘show’ command to display schematics.

gnu/packages/emacs-xyz.scm

@@ -784,7 +784,7 @@ reading the extensive documentation about BookmarkPlus on the Emacs Wiki.")
   (package
     (name "emacs-bqn-mode")
     ;; Upstream releases are tagged by date.
-    (version "2026-02-08")
+    (version "2025-07-06")
     (source
      (origin
        (method git-fetch)
@@ -793,7 +793,7 @@ reading the extensive documentation about BookmarkPlus on the Emacs Wiki.")
              (commit version)))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "1m9l4if3a9i6r76v370gh6azgj2lwqcnpavfv2bkvm9ad56f3pa8"))))
+        (base32 "1b25k66nn4qa4ryhm8mzc53qvsvhgjzdngisw28cpdh109627iz3"))))
     (build-system emacs-build-system)
     (arguments
      (list #:tests? #f)) ;No tests found in source.
@@ -2809,56 +2809,6 @@ versions of a topic branch.")
 diffs.")
       (license license:expat))))
 
-(define-public emacs-majutsu
-  (package
-    (name "emacs-majutsu")
-    (version "0.6.0")
-    (source (origin
-              (method git-fetch)
-              (uri (git-reference
-                     (url "https://github.com/0WD0/majutsu")
-                     (commit (string-append "v" version))))
-              (file-name (git-file-name name version))
-              (sha256
-               (base32
-                "1b840z3p10jyh8d6kmj7syad7308qr9p09gsci4gmha0iw3adnx5"))))
-    (build-system emacs-build-system)
-    (arguments
-     (list
-      ;; XXX: Test fails with `void-function transient--set-layout' when using
-      ;; wrapped ert-runner.
-      #:test-command
-      #~'(".ert-runner-real")
-      #:phases
-      #~(modify-phases %standard-phases
-          (add-after 'unpack 'patch-references
-            (lambda* (#:key inputs #:allow-other-keys)
-              (emacs-substitute-variables "majutsu-jj.el"
-                ("majutsu-jj-executable"
-                 (search-input-file inputs "bin/jj")))))
-          (add-after 'install 'install-docs
-            (lambda _
-              (with-directory-excursion "docs"
-                (invoke "make" "majutsu.info")
-                (install-file "majutsu.info"
-                              (in-vicinity #$output "share/info"))))))))
-    (native-inputs
-     ;; Use unwrapped ert-runner in test, adding its inputs here.
-     (modify-inputs (package-inputs emacs-ert-runner)
-       (delete "bash-minimal")
-       (prepend emacs-ert-runner texinfo)))
-    (inputs (list jujutsu))
-    (propagated-inputs (list emacs-magit))
-    (home-page "https://github.com/0WD0/majutsu")
-    (synopsis "Emacs interface for Jujutsu version control system")
-    (description
-     "Majutsu provides a @code{emacs-magit}-style interface for
-@code{jujutsu}, offering an efficient way to interact with Jujutsu repositories
-from within Emacs.")
-    (license
-     (list license:gpl3+
-           license:expat))))
-
 (define-public emacs-conflict-buttons
   ;; No releases
   (let ((commit "22af851d6a0cdd226ef7ba0db54fa096c8ddf235")
@@ -9485,40 +9435,35 @@ column by drawing a thin line down the length of the editing window.")
     (license license:gpl3+)))
 
 (define-public emacs-greader
-  (package
+  (let ((commit "b25974aeae49f11b91bb78d94ab51913fdfcdc05")) ;version bump
-    (name "emacs-greader")
+    (package
-    (version "0.19.0")
+      (name "emacs-greader")
-    (source
+      (version "0.13.1")
-     (origin
+      (source
-       (uri (git-reference
+       (origin
-              (url "https://gitlab.com/michelangelo-rodriguez/greader")
+         (uri (git-reference
-              (commit (string-append "v" version))))
+                (url "https://gitlab.com/michelangelo-rodriguez/greader")
-       (method git-fetch)
+                (commit commit)))
-       (file-name (git-file-name name version))
+         (method git-fetch)
-       (sha256
+         (file-name (git-file-name name version))
-        (base32 "08c4i5qbr0ndbbps6y5kpp0lzfmxnwifrxssqkd9qdzj068k69k3"))))
+         (sha256
-    (build-system emacs-build-system)
+          (base32 "1qkszb4yrfnzb2rqkf6vmzca53w68p78zb58frcxslxn7s5l7ih1"))))
-    (arguments
+      (build-system emacs-build-system)
-     (list #:tests? #f ;no tests
+      (arguments
-           #:phases
+       (list #:tests? #f))              ;no tests
-           #~(modify-phases %standard-phases
+      (inputs (list emacs-compat espeak-ng))
-               (add-after 'unpack 'make-info
+      (home-page "https://gitlab.com/michelangelo-rodriguez/greader")
-                 (lambda _
+      (synopsis
-                   (invoke "makeinfo" "--no-split" "greader.texi"))))))
+       "Gnamù Reader, or Greader, sends buffer contents to a speech engine")
-    (inputs (list emacs-compat espeak-ng))
+      (description
-    (native-inputs (list texinfo))
+       "Greader is a module that sends any Emacs buffer to a @acronym{TTS,
-    (home-page "https://gitlab.com/michelangelo-rodriguez/greader")
-    (synopsis
-     "Gnamù Reader, or Greader, sends buffer contents to a speech engine")
-    (description
-     "Greader is a module that sends any Emacs buffer to a @acronym{TTS,
 Text To Speech} engine, such as Espeak-NG or Speech Dispatcher.
 
 The mode supports timer reading, automatic scrolling of buffers in modes like
 Info mode, and repeating reading of regions or the whole buffer.  It also
 includes a feature to facilitate the compilation of Espeak-NG
 pronunciations.")
-    (license license:gpl3+)))
+      (license license:gpl3+))))
 
 (define-public emacs-grep-a-lot
   (package
@@ -13826,7 +13771,7 @@ generates it as a string.  Please see the homepage for usage examples.")
       #:imported-modules (append %emacs-build-system-modules
                                  %pyproject-build-system-modules)
       #:modules '((guix build emacs-build-system)
-                  ((guix build pyproject-build-system) #:prefix py:)
+                  ((guix build python-build-system) #:prefix py:)
                   (guix build emacs-utils)
                   (guix build utils))
       #:phases
@@ -15208,27 +15153,6 @@ exporter already existing in Org mode.  It supports the Github flavored
 markdown features.")
     (license license:gpl3+)))
 
-(define-public emacs-grip-mode
-  (package
-    (name "emacs-grip-mode")
-    (version "2.5.0")
-    (source
-     (origin
-       (method git-fetch)
-       (uri (git-reference
-             (url "https://github.com/seagle0128/grip-mode")
-             (commit (string-append "v" version))))
-       (file-name (git-file-name name version))
-       (sha256
-        (base32 "1mrpmzcxgc9hkv55d6kv79f8y6ldqrf5b48f0a4fy30qlgby2wyz"))))
-    (arguments (list #:tests? #f)) ;no tests
-    (build-system emacs-build-system)
-    (home-page "https://github.com/seagle0128/grip-mode")
-    (synopsis "Instant GitHub-flavored Markdown/Org preview")
-    (description "Instant GitHub-flavored Markdown/Org preview using
-@code{grip}, @code{mdopen} or @code{go-grip}.")
-    (license license:gpl3)))
-
 (define-public emacs-2048-game
   (package
     (name "emacs-2048-game")
@@ -15372,33 +15296,35 @@ them easier to distinguish from other, less important buffers.")
     (license license:expat)))
 
 (define-public emacs-embark
-  (package
+  (let ((commit "0bdfd38d281d6375e6e675ce6f1bd597a9e3b136")
-    (name "emacs-embark")
+        (revision "1"))
-    (version "1.2")
+    (package
-    (source
+      (name "emacs-embark")
-     (origin
+      (version (git-version "1.1" revision commit))
-       (method git-fetch)
+      (source
-       (uri (git-reference
+       (origin
-              (url "https://github.com/oantolin/embark")
+         (method git-fetch)
-              (commit version)))
+         (uri (git-reference
-       (sha256
+                (url "https://github.com/oantolin/embark")
-        (base32 "1y97kibzz36wrzcjv997qp5pliikda0dhsm9461pin3q5gv8y6kq"))
+                (commit commit)))
-       (file-name (git-file-name name version))))
+         (sha256
-    (build-system emacs-build-system)
+          (base32 "0m9y2wraapi744fg7y6cgz6y2gx0xzaglnxqalynz44ca9z6m6y4"))
-    (arguments
+         (file-name (git-file-name name version))))
-     (list
+      (build-system emacs-build-system)
-      #:tests? #false                 ;no tests
+      (arguments
-      #:phases
+       (list
-      #~(modify-phases %standard-phases
+        #:tests? #false                 ;no tests
-          (add-before 'install 'makeinfo
+        #:phases
-            (lambda _ (emacs-makeinfo))))))
+        #~(modify-phases %standard-phases
-    (native-inputs (list texinfo))
+            (add-before 'install 'makeinfo
-    (propagated-inputs
+              (lambda _ (emacs-makeinfo))))))
-     (list emacs-avy emacs-consult))
+      (native-inputs (list texinfo))
-    (home-page "https://github.com/oantolin/embark")
+      (propagated-inputs
-    (synopsis "Emacs mini-buffer actions rooted in keymaps")
+       (list emacs-avy emacs-consult))
-    (description
+      (home-page "https://github.com/oantolin/embark")
-     "This package provides a sort of right-click contextual menu for Emacs
+      (synopsis "Emacs mini-buffer actions rooted in keymaps")
+      (description
+       "This package provides a sort of right-click contextual menu for Emacs
 offering you relevant @emph{actions} to use on a @emph{target} determined by
 the context.
 
@@ -15412,7 +15338,7 @@ get offered actions like deleting, copying, renaming, visiting in another
 window, running a shell command on the file, etc.  For buffers the actions
 include switching to or killing the buffer.  For package names the actions
 include installing, removing or visiting the homepage.")
-    (license license:gpl3+)))
+      (license license:gpl3+))))
 
 (define-public emacs-prescient
   (package
@@ -17049,35 +16975,6 @@ called.  If there are more, each window will have its first character
 highlighted.  Pressing that character will switch to that window.")
     (license license:gpl3+)))
 
-(define-public emacs-spatial-window
-  (package
-    (name "emacs-spatial-window")
-    (version "0.9.2")
-    (source
-     (origin
-       (method git-fetch)
-       (uri (git-reference
-             (url "https://github.com/lewang/spatial-window")
-             (commit (string-append "v" version))))
-       (file-name (git-file-name name version))
-       (sha256
-        (base32 "19whlw6p2q6ma20ifkr6iyrhj5l99vj1hv06s7j6j6pvgah27lm4"))))
-    (build-system emacs-build-system)
-    (arguments
-     (list
-      #:test-command
-      #~(list "emacs" "-Q" "-batch" "-L"  "."
-              "-l" "spatial-window-geometry-test.el"
-              "-l" "spatial-window-test.el"
-              "-f" "ert-run-tests-batch-and-exit")))
-    (propagated-inputs (list emacs-posframe))
-    (home-page "https://github.com/lewang/spatial-window")
-    (synopsis "Jump to windows by spatial position")
-    (description
-     "Jump to Emacs windows by pressing keys that match their spatial position
-on your keyboard.")
-    (license license:gpl3+)))
-
 (define-public emacs-windsize
   ;; There is no proper release.  The base version is extracted from the
   ;; "Version" keyword in the main file.
@@ -17422,11 +17319,11 @@ accessing slash commands.")
 
 (define-public emacs-claude-code-ide
   ;; Upstream does not make versioned releases.
-  (let ((commit "56db02ee386d009ddb8b1482310f1f9beeefb810")
+  (let ((commit "5f12e60c6d2d1802c8c1b7944bbdf935d5db1364")
-        (revision "2"))
+        (revision "1"))
     (package
       (name "emacs-claude-code-ide")
-      (version (git-version "0.2.7" revision commit))
+      (version (git-version "0.2.6" revision commit))
       (source
        (origin
          (method git-fetch)
@@ -17435,7 +17332,7 @@ accessing slash commands.")
                 (commit commit)))
          (file-name (git-file-name name version))
          (sha256
-          (base32 "060n6alwgnxqpqcl74c1ixjm0am1pfj2kx7v3wi4bys6dsf50zd8"))))
+          (base32 "148xcrqff6khpwf8nnadcyvz8h6mk45xz1498k0wbzy80yzd2axn"))))
       (build-system emacs-build-system)
       (arguments
        (list
@@ -17824,29 +17721,6 @@ etc), but also compiling languages (C, C++, Go, Java etc) and markup
 languages.")
     (license license:gpl3+)))
 
-(define-public emacs-quotable
-  (package
-    (name "emacs-quotable")
-    (version "1.1.0")
-    (source
-     (origin
-       (method git-fetch)
-       (uri (git-reference
-             (url "https://codeberg.org/coopi/emacs-quotable")
-             (commit (string-append "v" version))))
-       (file-name (git-file-name name version))
-       (sha256
-        (base32 "00359yljynmk6bqifvfrrradm4na9ap76isibi2d6s4i810szixh"))))
-    (build-system emacs-build-system)
-    (home-page "https://codeberg.org/coopi/emacs-quotable")
-    (synopsis "Emacs Lisp client for the Quotable API")
-    (description
-     "This package provides a programmatic interface for the
-@uref{https://github.com/lukePeavey/quotable, Quotable @acronym{API,
-Application Programming Interface}}, a free and open-source quotations
-@acronym{API}.")
-    (license license:agpl3+)))
-
 (define-public emacs-pkg-info
   (package
     (name "emacs-pkg-info")
@@ -22429,7 +22303,7 @@ are common in Chromium-derived projects.")
 (define-public emacs-gnosis
   (package
     (name "emacs-gnosis")
-    (version "0.10.3")
+    (version "0.8.0")
     (source
      (origin
        (method git-fetch)
@@ -22438,7 +22312,7 @@ are common in Chromium-derived projects.")
               (commit version)))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "0kpzc2jw51sklz15v0d0vzm5ck05n3d90l02la4nxn8r85jb1f53"))))
+        (base32 "003pmd0ahpcss5ydk3wbx5j45225ypa85zrgljz5qajijiybvxpi"))))
     (build-system emacs-build-system)
     (arguments
      (list
@@ -22451,21 +22325,20 @@ are common in Chromium-derived projects.")
             (lambda _
               (setenv "HOME"
                       (getenv "TMPDIR"))
-              (mkdir-p (string-append
+              (mkdir-p (string-append (getenv "HOME") "/.emacs.d"))))
-                        (getenv "HOME")
-                        "/.emacs.d"))))
           (add-before 'install 'make-info
             (lambda _
               (invoke "make" "doc" "GUIX_SHELL="))))))
     (native-inputs (list texinfo))
-    (propagated-inputs (list emacs-transient))
+    (propagated-inputs (list emacs-compat emacs-emacsql emacs-org-gnosis
+                             emacs-transient))
     (home-page "https://thanosapollo.org/projects/gnosis/")
-    (synopsis "Personal knowledge system for GNU Emacs")
+    (synopsis "Spaced repetition system for GNU Emacs")
     (description
-     "Gnosis is a personal knowledge system for GNU Emacs that
+     "Gnosis is a spaced repetition system for note-taking and self-testing
-integrates note-taking with spaced repetition.  It combines
+where notes are formatted as Question/Answer/Explanation.  Notes are reviewed
-Zettelkasten-style linked notes with self-testing review,
+at spaced intervals based on the success or failure in recalling the answer to
-all stored in a single SQLite database.")
+each question.")
     (license license:gpl3+)))
 
 (define-public emacs-drag-stuff
@@ -24533,27 +24406,6 @@ key-bindings, avoiding most if not all the hassle introduced by key-binding
 conflicts.")
     (license license:gpl3+)))
 
-(define-public emacs-meow-tree-sitter
-  (package
-    (name "emacs-meow-tree-sitter")
-    (version "2.0.2")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (string-append
-             "https://stable.melpa.org/packages/meow-tree-sitter-" version
-             ".tar"))
-       (sha256
-        (base32 "1sxa1flngzsj3hh3sp3kccwgsxq6d40wsn8vzgv0ahrxkz2s6fxg"))))
-    (build-system emacs-build-system)
-    (propagated-inputs (list emacs-meow))
-    (home-page "https://github.com/skissue/meow-tree-sitter")
-    (synopsis "Tree-sitter powered motions for Meow")
-    (description
-     "This package integrates the treesitter library in modern Emacs with
-Meow’s motions.")
-    (license (list license:gpl3+ license:mpl2.0))))
-
 (define-public emacs-xelb
   (package
     (name "emacs-xelb")
@@ -24580,21 +24432,15 @@ Meow’s motions.")
       #:tests? #f                       ; no test suite
       #:phases
       #~(modify-phases %standard-phases
-          (add-before 'patch-el-files 'patch-xauth-path
-            ;; Uses xauth directly at runtime to authenticate with the X server.
-            (lambda* (#:key inputs #:allow-other-keys)
-              (substitute* "xcb.el"
-                (("xauth list")
-                 (string-append (search-input-file inputs "/bin/xauth")
-                                " list")))))
           (add-after 'expand-load-path 'regenerate-el-files
             (lambda* (#:key inputs native-inputs #:allow-other-keys)
               (substitute* "xelb-gen"
                 (("/usr/bin/env") (which "env")))
-              (invoke "make"
+              (let ((xcb-proto #$(this-package-native-input "xcb-proto"))
-                      (format #f "PROTO_PATH=~a/share/xcb"
+                    (emacs (search-input-file (or native-inputs inputs)
-                              #$(this-package-native-input "xcb-proto"))))))))
+                                              "/bin/emacs")))
-    (inputs (list xauth))
+                (invoke "make"
+                        (format #f "PROTO_PATH=~a/share/xcb" xcb-proto))))))))
     (native-inputs (list xcb-proto))
     (propagated-inputs (list emacs-compat))
     (home-page "https://github.com/emacs-exwm/xelb")
@@ -24691,8 +24537,7 @@ of XELB.")
     (name "emacs-exwm-no-x-toolkit")
     (synopsis "Emacs X window manager (without an X toolkit)")
     (propagated-inputs
-     (modify-inputs propagated-inputs
+     (list emacs-xelb-no-x-toolkit))
-       (replace "emacs-xelb" emacs-xelb-no-x-toolkit)))
     (arguments
      (substitute-keyword-arguments arguments
        ((#:emacs emacs) `,emacs-no-x-toolkit)))))
@@ -25058,91 +24903,36 @@ with Eglot.")
 (define-public emacs-jabber
   (package
     (name "emacs-jabber")
-    (version "0.10.3")
+    (version "0.9.0")
     (source (origin
               (method git-fetch)
               (uri (git-reference
-                    (url "https://git.thanosapollo.org/emacs-jabber")
+                    (url "https://codeberg.org/emacs-jabber/emacs-jabber")
-                    (commit version)))
+                    (commit (string-append "v" version))))
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "1v1a09h6ndqhkwyn44cnx1b0l4p155a09mfjrfmg62li50hvw1zm"))))
+                "0ain52p79sxll0bnsb4llfp1h4pqcqx3l6im4ibia06lg2aiqhpv"))))
     (build-system emacs-build-system)
     (arguments
      (list
       #:lisp-directory "lisp"
-      #:include #~(cons "^[^/]*\\.so$"
-                        %default-include)
       #:emacs emacs                   ;requires gnutls
-      #:test-command #~(list "make" "-C" ".." "test")
+      #:test-command #~(list "ert-runner" "../tests")
       #:phases
       #~(modify-phases %standard-phases
-          (add-after 'unpack 'build-native-module
+          (add-after 'unpack 'make-info
             (lambda _
-              (invoke "make" "-C" "../src")))
+              (invoke "makeinfo" "../jabber.texi"))))))
-          (add-before 'build-native-module 'unpack-picomemo
+    (native-inputs (list emacs-ert-runner texinfo))
-            (lambda _
+    (propagated-inputs (list emacs-fsm emacs-srv gnutls))
-              (copy-recursively
+    (home-page "https://codeberg.org/emacs-jabber/emacs-jabber")
-               #$(this-package-native-input
-                  "emacs-jabber-picomemo")
-               "../src/picomemo")
-              (invoke "chmod" "--recursive" "u+w"
-                      "../src/picomemo")))
-          (add-after 'unpack 'fix-test-runner
-            (lambda _
-              ;; Replace grep -oP (Perl regex) with a
-              ;; POSIX-compatible alternative so the test
-              ;; runner counts results correctly.
-              (substitute* "../Makefile"
-                (("grep -oP '\\^Ran \\\\K\\[0-9\\]\\+'")
-                 (string-append
-                  "grep -o 'Ran [0-9]*'"
-                  " | grep -o '[0-9]*'")))))
-          (add-after 'unpack 'disable-failing-tests
-            (lambda _
-              ;; These 4 tests pass outside the build
-              ;; environment but fail inside it.
-              (define skip "\n  (skip-unless nil)")
-              (substitute*
-                  "../tests/jabber-disco-tests.el"
-                ((".*query-if-needed-cache-miss \\(\\)"
-                  all)
-                 (string-append all skip))
-                ((".*process-caps-modern.*queries \\(\\)"
-                  all)
-                 (string-append all skip)))
-              (substitute*
-                  (string-append
-                   "../tests/"
-                   "jabber-message-correct-tests.el")
-                ((".*correct-last-uses-original-id \\(\\)"
-                  all)
-                 (string-append all skip))
-                ((".*mam-syncing-skipped.*dispatch \\(\\)"
-                  all)
-                 (string-append all skip))))))))
-    (native-inputs
-     (list pkg-config
-           (origin
-             (method git-fetch)
-             (uri (git-reference
-                    (url "https://github.com/mierenhoop/picomemo")
-                    (commit "1.1.0")))
-             (file-name "emacs-jabber-picomemo")
-             (sha256
-              (base32
-               "044xd1gn9lpd5yrb3c1lmvqsc1chbkhd3vnh7800hxn23a0hxbzj")))))
-    (inputs (list mbedtls))
-    (propagated-inputs (list emacs-fsm))
-    (home-page "https://thanosapollo.org/projects/jabber/")
     (synopsis "XMPP (Jabber) client for Emacs")
     (description
      "@code{jabber.el} is an XMPP client for Emacs.  XMPP (also known as
 \"Jabber\") is an instant messaging system; see @url{https://xmpp.org} for
-more information.  It supports OMEMO end-to-end encryption via picomemo.")
+more information.")
-    (license (list license:gpl3+    ;gpl2+ elisp, gpl3+ C
+    (license license:gpl2+)))
-                   license:isc))))  ;picomemo
 
 (define-public emacs-jarchive
   (package
@@ -28281,7 +28071,7 @@ match and total match information in the mode-line in various search modes.")
 (define-public emacs-pg
   (package
     (name "emacs-pg")
-    (version "0.6.4")
+    (version "0.62")
     (source (origin
               (method git-fetch)
               (uri (git-reference (url "https://github.com/emarsden/pg-el")
@@ -28289,7 +28079,7 @@ match and total match information in the mode-line in various search modes.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "0w9a8y3s2dbmpqbbnxycxd38niqq2slzr26bfl4v1pfcm0w7skfz"))))
+                "0fjzrn5b4s00km71ya98vwwfyvd4rvcywxdxqzy5xfrv8crm92w6"))))
     (build-system emacs-build-system)
     (propagated-inputs (list emacs-peg))
     (home-page "https://github.com/emarsden/pg-el")
@@ -28305,7 +28095,7 @@ end users.")
 (define-public emacs-pgmacs
   (package
     (name "emacs-pgmacs")
-    (version "0.30")
+    (version "0.42")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -28314,7 +28104,7 @@ end users.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "0f4mbamk2n9l7qwhi2n1kwvng6wa9yp6k2w1qn6yc07pri2mb6yc"))))
+                "0pf8y64hka1fl47dphmh4xgxiwfsd0g4q2fazq5yc48zwr9nsf02"))))
     (build-system emacs-build-system)
     (propagated-inputs
      (list emacs-pg))
@@ -28323,12 +28113,6 @@ end users.")
     (home-page "https://github.com/emarsden/pgmacs")
     (license license:gpl3+)))
 
-(define-public emacs-pgmacs-0.42
-  (package
-    (inherit emacs-pgmacs)
-    (version "0.42")
-    (properties `((superseded . ,emacs-pgmacs)))))
-
 (define-public emacs-finalize
   (package
   (name "emacs-finalize")
@@ -35420,199 +35204,12 @@ files are easily readable and they work nicely with version control systems.")
       (build-system emacs-build-system)
       (arguments
        (list #:include #~(cons "^data\\/" %default-include)
-             #:tests? #f              ; no tests
+             #:tests? #f))              ; no tests
-             #:phases
-             #~(modify-phases %standard-phases
-                 ;; The nerd-icons-install-fonts function would otherwise
-                 ;; download fonts from the network.  Replace it with a stub
-                 ;; that instructs the user to install the font via Guix.
-                 (add-after 'unpack 'disable-font-installer
-                   (lambda _
-                     (emacs-batch-edit-file "nerd-icons.el"
-                       '(progn
-                         (search-forward "(defun nerd-icons-install-fonts")
-                         (beginning-of-line)
-                         (kill-sexp)
-                         (insert "\
-(defun nerd-icons-install-fonts (&optional pfx)
-  (interactive \"P\")
-  (message \"To use nerd-icons fonts, install `font-nerd-symbols' using
-`guix package -i font-nerd-symbols' or add it to your manifest or home config.
-Remember, that you may have to run `fc-cache -rv' to refresh the font cache.\
-\"))")
-                         (basic-save-buffer))))))))
       (synopsis "Library for easily using nerd font icons inside Emacs")
       (description "Nerd-icons an alternative to all-the-icons.  It works on both
 GUI and terminal, and requires a nerd font installed on your system.")
       (license license:gpl3+))))
 
-(define-public emacs-nerd-icons-dired
-  ;; No tags provided upstream
-  (let ((commit "adf9a2bb5f3f13be7a676923639337f3fcc5d8c3")
-        (revision "0"))
-    (package
-      (name "emacs-nerd-icons-dired")
-      (version (git-version "0.0.1" revision commit))
-      (source
-       (origin
-         (method git-fetch)
-         (uri (git-reference
-                (url "https://github.com/rainstormstudio/nerd-icons-dired")
-                (commit commit)))
-         (file-name (git-file-name name version))
-         (sha256
-          (base32 "0x1xmwlfjgbk5kk4bxvgz4ykwwgiwmdbzhgsw49kpzz678a3qzrp"))))
-      (build-system emacs-build-system)
-      (arguments
-       (list
-        #:tests? #f))                   ;no tests
-      (propagated-inputs (list emacs-nerd-icons))
-      (home-page "https://github.com/rainstormstudio/nerd-icons-dired")
-      (synopsis "Icons for Dired via Nerd Icons")
-      (description
-       "This package adds icons to Dired, using the @code{nerd-icons} package.")
-      (license license:gpl3+))))
-
-(define-public emacs-nerd-icons-ivy-rich
-  ;; Tagged release is not up-to-date, according to the "Version:" keyword in
-  ;; main file.
-  (let ((commit "5006f91b49e86e232cdc1a628501b76124c41dac")
-        (revision "0"))
-    (package
-      (name "emacs-nerd-icons-ivy-rich")
-      (version (git-version "1.0.1" revision commit))
-      (source
-       (origin
-         (method git-fetch)
-         (uri (git-reference
-                (url "https://github.com/seagle0128/nerd-icons-ivy-rich")
-                (commit commit)))
-         (file-name (git-file-name name version))
-         (sha256
-          (base32 "0m62l4cl9j3ssd25rz40vgrv99bmwn6l4ig2sf8zzi0fpzm8axgh"))))
-      (build-system emacs-build-system)
-      (arguments
-       (list
-        #:tests? #f))                   ;tests require Cask
-      (propagated-inputs
-       (list emacs-ivy-rich
-             emacs-nerd-icons))
-      (home-page "https://github.com/seagle0128/nerd-icons-ivy-rich")
-      (synopsis "Icons for Ivy via Nerd Icons")
-      (description
-       "This package adds icons to Ivy, using the @code{ivy-rich} and
-@code{nerd-icons} packages.")
-      (license license:gpl3+))))
-
-(define-public emacs-nerd-icons-ibuffer
-  (package
-    (name "emacs-nerd-icons-ibuffer")
-    (version "1.0.0")
-    (source
-     (origin
-       (method git-fetch)
-       (uri (git-reference
-              (url "https://github.com/seagle0128/nerd-icons-ibuffer")
-              (commit (string-append "v" version))))
-       (file-name (git-file-name name version))
-       (sha256
-        (base32 "1wj6kcgvh700maj9i5pmgzc48lbj0dbxx849a8w519m4anr7b23s"))))
-    (build-system emacs-build-system)
-    (arguments
-     (list
-      #:tests? #f))                   ;tests require Cask
-    (propagated-inputs
-     (list emacs-nerd-icons))
-    (home-page "https://github.com/seagle0128/nerd-icons-ibuffer")
-    (synopsis "Icons for Ibuffer via Nerd Icons")
-    (description
-     "This package adds icons to ibuffer in Emacs, using the @code{nerd-icons}
-package.")
-    (license license:gpl3+)))
-
-(define-public emacs-nerd-icons-completion
-  ;; No tags provided upstream
-  (let ((commit "63a6b3f1eb98bb381c86a1658ac401c8967079b8")
-        (revision "0"))
-    (package
-      (name "emacs-nerd-icons-completion")
-      (version (git-version "0.0.1" revision commit))
-      (source
-       (origin
-         (method git-fetch)
-         (uri (git-reference
-                (url "https://github.com/rainstormstudio/nerd-icons-completion")
-                (commit commit)))
-         (file-name (git-file-name name version))
-         (sha256
-          (base32 "08p361rh5mv3ng10av1381kzl9s4msdjyca96hsgsh05qwq5pdrf"))))
-      (build-system emacs-build-system)
-      (arguments
-       (list
-        #:tests? #f))                   ;no tests
-      (propagated-inputs (list emacs-nerd-icons))
-      (home-page "https://github.com/rainstormstudio/nerd-icons-completion")
-      (synopsis "Icons for Emacs minibuffer completion via Nerd Icons")
-      (description
-       "This package adds icons to minibuffer completion in Emacs, using the
-@code{nerd-icons} package.  It supports @code{vertico} and @code{marginalia}.")
-      (license license:gpl3+))))
-
-(define-public emacs-nerd-icons-corfu
-  (package
-    (name "emacs-nerd-icons-corfu")
-    (version "1.0.0")
-    (source
-     (origin
-       (method git-fetch)
-       (uri (git-reference
-              (url "https://github.com/LuigiPiucco/nerd-icons-corfu")
-              (commit (string-append "v" version))))
-       (file-name (git-file-name name version))
-       (sha256
-        (base32 "036p45wqwrqhn5xv5sn3gsm2mb79gj6fk24zpkfa7wrv45qqgb21"))))
-    (build-system emacs-build-system)
-    (arguments
-     (list
-      #:tests? #f))                   ;no tests
-    (propagated-inputs
-     (list emacs-corfu
-           emacs-nerd-icons))
-    (home-page "https://github.com/LuigiPiucco/nerd-icons-corfu")
-    (synopsis "Icons for Corfu via Nerd Icons")
-    (description
-     "This package adds icons to @code{corfu}, using the @code{nerd-icons}
-package.")
-    (license license:gpl3+)))
-
-(define-public emacs-nerd-icons-mode-line
-  ;; No tags provided upstream
-  (let ((commit "23eca8e16799524889d661f4140355e81b8f929c")
-        (revision "0"))
-    (package
-      (name "emacs-nerd-icons-mode-line")
-      (version (git-version "0.0.1" revision commit))
-      (source
-       (origin
-         (method git-fetch)
-         (uri (git-reference
-                (url "https://github.com/grolongo/nerd-icons-mode-line")
-                (commit commit)))
-         (file-name (git-file-name name version))
-         (sha256
-          (base32 "0l2bg22cllab9wz5wxd6zhrywavqrlvv1a6y49ij63qhlsfncy6s"))))
-      (build-system emacs-build-system)
-      (arguments
-       (list
-        #:tests? #f))                   ;no tests
-      (propagated-inputs (list emacs-nerd-icons))
-      (home-page "https://github.com/grolongo/nerd-icons-mode-line")
-      (synopsis "Icons for the Emacs modeline via Nerd Icons")
-      (description
-       "This package adds icons to the modeline in Emacs, using the
-@code{nerd-icons} package.")
-      (license license:gpl3+))))
-
 (define-public emacs-all-the-icons
   ;; The latest release was on 3 June 2021.
   (let ((commit "4778632b29c8c8d2b7cd9ce69535d0be01d846f9")
@@ -39686,16 +39283,10 @@ user interfaces for various built-in modes.")
               (make-file-writable "calibredb-core.el")
               (let ((calibredb (search-input-file inputs "/bin/calibredb"))
                     (fetch-ebook-metadata
-                     (search-input-file inputs "/bin/fetch-ebook-metadata"))
+                     (search-input-file inputs "/bin/fetch-ebook-metadata")))
-                    (ebook-convert
-                     (search-input-file inputs "/bin/ebook-convert"))
-                    (calibre-debug
-                     (search-input-file inputs "/bin/calibre-debug")))
                 (emacs-substitute-variables "calibredb-core.el"
                   ("calibredb-fetch-metadata-program" fetch-ebook-metadata)
-                  ("calibredb-program" calibredb)
+                  ("calibredb-program" calibredb))))))))
-                  ("calibredb-convert-program" ebook-convert)
-                  ("calibredb-debug-program" calibre-debug))))))))
     (inputs
      (list calibre))
     (propagated-inputs
@@ -41395,7 +40986,7 @@ Lisp's (relatively new) EIEIO object oriented libraries.")
 (define-public emacs-fj
   (package
     (name "emacs-fj")
-    (version "0.34")
+    (version "0.33")
     (source
      (origin
        (method git-fetch)
@@ -41404,10 +40995,10 @@ Lisp's (relatively new) EIEIO object oriented libraries.")
               (commit version)))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "1y3k82q5iii7ddm6yj7397x2jscbcnvapd04zc5wjkqdr50cay3l"))))
+        (base32 "0cfzw9shd6jjir9zqcqbsz8vidsvs609a58aakh54dylngp52qmh"))))
     (build-system emacs-build-system)
     (arguments (list #:tests? #f))      ;depends on exemplify-ert
-    (propagated-inputs (list emacs-fedi emacs-magit emacs-tp emacs-transient))
+    (propagated-inputs (list emacs-fedi emacs-magit emacs-tp))
     (home-page "https://codeberg.org/martianh/fj.el")
     (synopsis "Client for Forgejo instances")
     (description
@@ -42468,10 +42059,10 @@ service, and connect it with Emacs via inter-process communication.")
       (license license:gpl3+))))
 
 (define-public emacs-telega
-  (let ((commit "8078beccf88c132d504ba9031062a6a2c65a1c8b"))
+  (let ((commit "805819bf81dffe2922e9e06ae02d58429d03aa1a"))
     (package
       (name "emacs-telega")
-      (version "0.8.620")               ; see telega-version in telega.el
+      (version "0.8.601")               ; see telega-version in telega.el
       (source
        (origin
          (method git-fetch)
@@ -42479,7 +42070,7 @@ service, and connect it with Emacs via inter-process communication.")
                (url "https://github.com/zevlg/telega.el")
                (commit commit)))
          (sha256
-          (base32 "1m7gs90hrmmwm7pvf5iz3y4v39psp6kbnw1d97q6v55hhgq3isxz"))
+          (base32 "0d02ymr5fw6fknzf9ikaky48swd9yfp5zn846zlwb5083p6bpmis"))
          (file-name (git-file-name "emacs-telega" version))
          (patches
           (search-patches "emacs-telega-test-env.patch"))))
@@ -46934,7 +46525,7 @@ Fennel code within Emacs.")
 (define-public emacs-org-modern
   (package
     (name "emacs-org-modern")
-    (version "1.13")
+    (version "1.12")
     (source
      (origin
        (method git-fetch)
@@ -46942,18 +46533,10 @@ Fennel code within Emacs.")
              (url "https://github.com/minad/org-modern")
              (commit version)))
        (sha256
-        (base32 "16i1nwdilhpjlphpbwi8vjfwfb721gm0mm37hjx570wx4sskvg30"))
+        (base32 "01p5k85hj677x2vk7j7a88gchp51ybiaj6iqmdhxivmcw3lb6ibi"))
        (file-name (git-file-name name version))))
     (build-system emacs-build-system)
-    (arguments
-     (list
-      #:tests? #f                       ;no tests
-      #:phases
-      #~(modify-phases %standard-phases
-          (add-before 'install 'makeinfo
-            (lambda _ (emacs-makeinfo))))))
     (propagated-inputs (list emacs-compat))
-    (native-inputs (list texinfo))
     (home-page "https://github.com/minad/org-modern")
     (synopsis "Modern Org style")
     (description

gnu/packages/emacs.scm

@@ -644,6 +644,32 @@ editor (console only)")
     (description "This Emacs build implements graphical UI purely in terms
 of GTK.")))
 
+(define-public emacs-xwidgets
+  (package/inherit emacs
+    (name "emacs-xwidgets")
+    (synopsis "The extensible, customizable, self-documenting text
+editor (with xwidgets support)")
+    (arguments
+     (substitute-keyword-arguments arguments
+       ((#:configure-flags flags #~'())
+        #~(cons "--with-xwidgets" #$flags))))
+    (inputs
+     (modify-inputs inputs
+       (prepend webkitgtk-with-libsoup2 libxcomposite)))))
+
+(define-public emacs-pgtk-xwidgets
+  (package
+    (inherit emacs-pgtk)
+    (name "emacs-pgtk-xwidgets")
+    (synopsis "Emacs text editor with @code{xwidgets} and @code{pgtk} support")
+    (arguments
+     (substitute-keyword-arguments arguments
+       ((#:configure-flags flags #~'())
+        #~(cons "--with-xwidgets" #$flags))))
+    (inputs
+     (modify-inputs inputs
+       (prepend gsettings-desktop-schemas webkitgtk-with-libsoup2)))))
+
 (define-public emacs-lucid
   (package/inherit emacs-no-x
     (name "emacs-lucid")
@@ -748,6 +774,7 @@ editor (with wide ints)" )
 
 (define-public emacs-next (emacs->emacs-next emacs))
 (define-public emacs-next-pgtk (emacs->emacs-next emacs-pgtk))
+(define-public emacs-next-pgtk-xwidgets (emacs->emacs-next emacs-pgtk-xwidgets))
 (define-deprecated-package emacs-next-tree-sitter
   emacs-next)
 

gnu/packages/embedded.scm

@@ -45,6 +45,7 @@
   #:use-module (guix build-system cmake)
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system pyproject)
+  #:use-module (guix build-system python)
   #:use-module (guix build-system trivial)
   #:use-module ((guix build utils) #:select (alist-replace delete-file-recursively))
   #:use-module (gnu packages)
@@ -64,7 +65,6 @@
   #:use-module (gnu packages libffi)
   #:use-module (gnu packages libftdi)
   #:use-module (gnu packages libusb)
-  #:use-module (gnu packages linux)
   #:use-module (gnu packages messaging)
   #:use-module (gnu packages ncurses)
   #:use-module (gnu packages perl)
@@ -1505,8 +1505,7 @@ hardware.  The utility support USB and UART as serial link.")
                  (apply (assoc-ref cargo:%standard-phases phase)
                         #:cargo-target #$(cargo-triplet)
                         args))
-               '(prepare-rust-crates
+               '(unpack-rust-crates
-                 unpack-rust-crates
                  configure
                  check-for-pregenerated-files
                  patch-cargo-checksums)))))))
@@ -1901,7 +1900,7 @@ PicoBlaze; and Zilog Z80 families, plus many of their variants.")
     (inputs
      (list readline ucsim))
     (native-inputs
-     (list bison boost flex python-minimal-wrapper texinfo zlib))
+     (list bison boost flex python-2 texinfo zlib))
     (home-page "https://sdcc.sourceforge.net/")
     (synopsis "C compiler suite for 8-bit microcontrollers")
     (description "SDCC is a retargetable, optimizing Standard C compiler suite
@@ -2032,7 +2031,13 @@ whereas kdmx creates pseudo-ttys.")
       ;; tests: 631 passed, 27 skipped, 1 warning
       #:test-flags
       ;; E   ModuleNotFoundError: No module named 'mbed_tools_ci_scripts'
-      #~(list "--ignore=tests/ci_scripts/test_sync_board_db.py")))
+      #~(list "--ignore=tests/ci_scripts/test_sync_board_db.py")
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-after 'unpack 'fix-pytest-config
+            (lambda _
+              (substitute* "pytest.ini"
+                (("addopts = .*") "")))))))
     (native-inputs
      (list python-factory-boy
            python-pytest
@@ -2061,27 +2066,26 @@ operations.")
     (license license:asl2.0)))
 
 (define-public ts4900-utils
-  (package
+  ;; There are no proper release nor tag; use the latest commit.
-    (name "ts4900-utils")
+  (let ((revision "0")
-    (version "3.0.0")
+        (commit "e10a12f8050d1d1229e711c7cfab8a0d5d93ee58"))
-    (source (origin
+    (package
-              (method git-fetch)
+      (name "ts4900-utils")
-              (uri (git-reference
+      (version (git-version "0.0.0" revision commit))
-                     (url "https://github.com/embeddedTS/ts4900-utils")
+      (source (origin
-                     (commit (string-append "v" version))))
+                (method git-fetch)
-              (file-name (git-file-name name version))
+                (uri (git-reference
-              (sha256
+                      (url "https://github.com/embeddedTS/ts4900-utils")
-               (base32
+                      (commit commit)))
-                "08x40ii56v4cmnz9hk6rvjrc500k1bij5ns52360vczznc8lx8bx"))))
+                (file-name (git-file-name name version))
-    (build-system gnu-build-system)
+                (sha256
-    (native-inputs
+                 (base32
-     (list autoconf
+                  "1vr8i425qijbwgbc10av3wr35p3x11wy6y442w0ja0yny7si8wp8"))))
-           automake
+      (build-system gnu-build-system)
-           libgpiod
+      (native-inputs (list autoconf automake))
-           pkg-config))
+      (home-page "https://github.com/embeddedTS/ts4900-utils")
-    (home-page "https://github.com/embeddedTS/ts4900-utils")
+      (synopsis "Utilities for the TS-4900 board family")
-    (synopsis "Utilities for the TS-4900 board family")
+      (description "This package contains utilities useful for boards of the
-    (description "This package contains utilities useful for boards of the
 TS-4900 family.  The included commands are:
 @itemize @code
 @item adc8390
@@ -2094,7 +2098,7 @@ TS-4900 family.  The included commands are:
 @item tsmicroupdate
 @item tssilomon
 @end itemize")
-    (license license:bsd-2)))
+      (license license:bsd-2))))
 
 (define-public cc-tool
   (package

gnu/packages/emulators.scm

@@ -6,7 +6,7 @@
 ;;; Copyright © 2015, 2018, 2023 David Thompson <dthompson2@worcester.edu>
 ;;; Copyright © 2016 Manolis Fragkiskos Ragkousis <manolis837@gmail.com>
 ;;; Copyright © 2016, 2017, 2018, 2020 Efraim Flashner <efraim@flashner.co.il>
-;;; Copyright © 2017-2024, 2026 Nicolas Goaziou <mail@nicolasgoaziou.fr>
+;;; Copyright © 2017-2024 Nicolas Goaziou <mail@nicolasgoaziou.fr>
 ;;; Copyright © 2017, 2020, 2021 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2017, 2018, 2019 Rutger Helling <rhelling@mykolab.com>
 ;;; Copyright © 2019 Pierre Neidhardt <mail@ambrevar.xyz>
@@ -140,6 +140,7 @@
   #:use-module (guix build-system glib-or-gtk)
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system meson)
+  #:use-module (guix build-system python)
   #:use-module (guix build-system pyproject)
   #:use-module (guix build-system qt)
   #:use-module (guix build-system trivial))
@@ -3246,14 +3247,14 @@ that compiles to WebAssembly.")
 (define-public scummvm
   (package
     (name "scummvm")
-    (version "2026.2.0")
+    (version "2.9.1")
     (source
      (origin
        (method url-fetch)
        (uri (string-append "https://downloads.scummvm.org/frs/scummvm/" version
                            "/scummvm-" version ".tar.xz"))
        (sha256
-        (base32 "1wv0z9c4dnjywgla9zhbkgnzahj829ybvcx9jw67hdmagnbys42f"))))
+        (base32 "1qspqawdazsxisxm1lxzgi0i4gx54qd10xyk3nmmirwxz9mg70ka"))))
     (build-system gnu-build-system)
     (arguments
      (list

gnu/packages/enchant.scm

@@ -41,6 +41,7 @@
   #:use-module (guix build-system cmake)
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system pyproject)
+  #:use-module (guix build-system python)
   #:use-module (guix licenses)
   #:use-module (srfi srfi-1))
 

gnu/packages/engineering.scm

@@ -50,7 +50,6 @@
 ;;; Copyright © 2026 Cayetano Santos <csantosb@inventati.org>
 ;;; Copyright © 2026 Daniel Khodabakhsh <d@niel.khodabakh.sh>
 ;;; Copyright © 2026 Spencer King <spencer.king@wustl.edu>
-;;; Copyright © 2026 Brent Wedderburn <mb@bean.za.net>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -77,6 +76,7 @@
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system meson)
   #:use-module (guix build-system pyproject)
+  #:use-module (guix build-system python)
   #:use-module (guix build-system qt)
   #:use-module (guix download)
   #:use-module (guix gexp)
@@ -135,7 +135,6 @@
   #:use-module (gnu packages imagemagick)
   #:use-module (gnu packages javascript)
   #:use-module (gnu packages jupyter)
-  #:use-module (gnu packages icu4c)
   #:use-module (gnu packages kde-frameworks)
   #:use-module (gnu packages libcanberra)
   #:use-module (gnu packages libevent)
@@ -253,21 +252,13 @@ their devices.")
           (replace 'build (assoc-ref gnu:%standard-phases 'build))
           (replace 'check (assoc-ref gnu:%standard-phases 'check))
           (replace 'install
-            (lambda _
+            (lambda* (#:key outputs #:allow-other-keys)
-              (let* ((bin (string-append #$output "/bin"))
+              (let ((bin   (string-append #$output "/bin"))
-                     (share (string-append #$output "/share"))
+                    (share (string-append #$output "/share/librecad")))
-                     (apps (string-append share "/applications"))
-                     (icons (string-append share "/icons/hicolor/128x128/apps")))
                 (mkdir-p bin)
                 (install-file "unix/librecad" bin)
                 (mkdir-p share)
-                (copy-recursively "unix/resources"
+                (copy-recursively "unix/resources" share)))))))
-                                  (string-append share "/librecad"))
-                (mkdir-p apps)
-                (install-file "desktop/librecad.desktop" apps)
-                (mkdir-p icons)
-                (copy-file "librecad/res/main/librecad.png"
-                           (string-append icons "/librecad.png"))))))))
     (inputs
      (list bash-minimal boost muparser freetype qtbase-5 qtsvg-5))
     (native-inputs
@@ -1827,6 +1818,7 @@ it suitable for security research and analysis.")
     (native-inputs (list python-gitpython
                          python-pytest
                          python-pytest-asyncio
+                         python-pytest-cov
                          python-pytest-mock
                          python-setuptools))
     (inputs (list bash-minimal
@@ -2365,6 +2357,7 @@ Newton-Raphson power flow solvers in the C++ library lightsim2grid, and the
                          python-networkx
                          python-openpyxl
                          python-pytest
+                         python-pytest-cov ; --cov runs by default on skrf
                          python-pytest-mock
                          python-pyvisa
                          python-setuptools
@@ -2727,17 +2720,16 @@ dynamics is used by FreeCAD 1.0.0 for its new Assembly workbench.")
 (define-public freecad
   (package
     (name "freecad")
-    (version "1.1.0")
+    (version "1.0.2")
     (source
      (origin
        (method git-fetch)
        (uri (git-reference
              (url "https://github.com/FreeCAD/FreeCAD")
-             (commit version)
+             (commit version)))
-             (recursive? #t)))          ;needed for the AddonManager
        (file-name (git-file-name name version))
        (sha256
-        (base32 "029ndw1dypx0xhs4fyiinf7gpk8am0vm9b24idvdsx9x7ghrqz4j"))
+        (base32 "1zyz473fzrz9h073wp4k65qq4bkhqsp245nsv6nv186sl78l99xa"))
        (snippet
         #~(begin
             (use-modules (guix build utils))
@@ -2754,7 +2746,7 @@ dynamics is used by FreeCAD 1.0.0 for its new Assembly workbench.")
       #:configure-flags
       #~(list
          "-DBUILD_FLAT_MESH:BOOL=ON"
-         "-DBUILD_ENABLE_CXX_STD:STRING=C++20"  ; FreeCAD 1.1 requires C++20
+         "-DBUILD_ENABLE_CXX_STD:STRING=C++17"
          "-DENABLE_DEVELOPER_TESTS=OFF"  ;; see the above: #:tests? comment
          "-DFREECAD_QT_VERSION=6"  ;; Build with Qt6
          "-DFREECAD_USE_EXTERNAL_ONDSELSOLVER=ON"  ;; unbundle ondsel-solver
@@ -2776,13 +2768,12 @@ dynamics is used by FreeCAD 1.0.0 for its new Assembly workbench.")
      (list c++-gsl
            doxygen
            graphviz
-           pybind11
            qttools
            pkg-config
-           swig-4.4))
+           swig-4.0))
     (inputs
      (list bash-minimal
-           boost
+           boost-1.83
            coin3d
            double-conversion
            eigen
@@ -2792,7 +2783,6 @@ dynamics is used by FreeCAD 1.0.0 for its new Assembly workbench.")
            gl2ps
            glew
            hdf5-1.10
-           icu4c
            jsoncpp
            libarea
            libjpeg-turbo
@@ -2815,11 +2805,13 @@ dynamics is used by FreeCAD 1.0.0 for its new Assembly workbench.")
            python-ply
            python-pyside-6
            python-pyyaml
+           python-shiboken-6
            python-wrapper
            qtsvg
            qtwebchannel
            qtwebengine
            qtwayland
+           qtx11extras
            sqlite
            onetbb                       ;same version as opencascade-occt
            vtk-9.5
@@ -2898,22 +2890,20 @@ interpolation toolkit.")
 (define-public python-motulator
   (package
     (name "python-motulator")
-    (version "0.6.2")
+    (version "0.5.0")
     (source
      (origin
-       (method git-fetch)
+       (method url-fetch)
-       (uri (git-reference
+       (uri (pypi-uri "motulator" version))
-              (url "https://github.com/Aalto-Electric-Drives/motulator/")
-              (commit (string-append "v" version))))
-       (file-name (git-file-name name version))
        (sha256
-        (base32 "1di2r1i19jl751v0hj426zkwk48w5yf8zpw2bl6qzk0vq4z2vpbw"))))
+        (base32 "1kh13zfa4w73q04pny2w2zgym47fp8xy7glwfx82fdx4fihk7dv7"))))
     (build-system pyproject-build-system)
     (arguments
      (list #:tests? #f)) ; there are no tests
-    (propagated-inputs
+    (propagated-inputs (list python-matplotlib python-numpy python-scipy))
-     (list python-numpy python-matplotlib python-scipy python-tqdm))
+    (native-inputs (list python-hatchling
-    (native-inputs (list python-hatchling))
+                         python-ipykernel
+                         python-toml))
     (home-page "https://aalto-electric-drives.github.io/motulator/")
     (synopsis "Motor Drive Simulator in Python")
     (description "This package includes simulation models for an induction

gnu/packages/enlightenment.scm

@@ -30,6 +30,7 @@
   #:use-module (guix gexp)
   #:use-module (guix utils)
   #:use-module (guix build-system meson)
+  #:use-module (guix build-system python)
   #:use-module (guix build-system pyproject)
   #:use-module (gnu packages)
   #:use-module (gnu packages algebra)

gnu/packages/fabric-management.scm

@@ -186,7 +186,7 @@ testing InfiniBand networks.")
 (define-public ucx
   (package
     (name "ucx")
-    (version "1.20.0")
+    (version "1.19.0")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -196,7 +196,7 @@ testing InfiniBand networks.")
               (patches (search-patches "ucx-tcp-iface-ioctl.patch"))
               (sha256
                (base32
-                "12w1mxacml1w8zvl1hpn786cs77y056b9hxv7q1kq482bgc2si0v"))
+                "12j9200iyg6d0yr84r25hcpq8qqzfaa08klbhvgrqpflpfcljz4z"))
               (snippet
                ;; As seen in commit b0a275a5492125a13020cd095fe9934e0b5e7c6a.
                #~(begin (use-modules (guix build utils))

gnu/packages/fcitx5.scm

@@ -34,7 +34,6 @@
   #:use-module (gnu packages anthy)
   #:use-module (gnu packages boost)
   #:use-module (gnu packages compression)
-  #:use-module (gnu packages cpp)
   #:use-module (gnu packages curl)
   #:use-module (gnu packages datastructures)
   #:use-module (gnu packages dictionaries)
@@ -96,7 +95,7 @@ client.")
 (define-public fcitx5
   (package
     (name "fcitx5")
-    (version "5.1.19")
+    (version "5.1.16")
     (source
      (origin
        (method url-fetch)
@@ -104,14 +103,9 @@ client.")
              "https://download.fcitx-im.org/fcitx5/fcitx5/fcitx5-"
              version "_dict.tar.zst"))
        (sha256
-        (base32 "1ngsadqdrwy99w63dmk493gg56j7r991v6pq1nwkx6apib9ykpc0"))
+        (base32 "0lwp90wjrkiws121rqn9kzdz6p1ncsk18dkmbv0zi37yqx2mv180"))))
-       (snippet
-        #~(begin
-            (use-modules (guix build utils))
-            (delete-file-recursively "third_party")))))
     (arguments
-     (list #:configure-flags #~(list "-DUSE_SYSTEMD=OFF"
+     (list #:configure-flags #~(list "-DUSE_SYSTEMD=OFF")))
-                                     "-DUSE_SYSTEM_YOGA=ON")))
     (build-system cmake-build-system)
     (inputs
      (list cairo
@@ -124,12 +118,12 @@ client.")
            gettext-minimal
            glib
            iso-codes/pinned
+           json-c
            libevent
            libuv
            libxcb
            libxkbcommon
            libxkbfile
-           nlohmann-json
            pango
            `(,util-linux "lib")         ;For libuuid.
            wayland
@@ -138,8 +132,7 @@ client.")
            xcb-util
            xcb-util-keysyms
            xcb-util-wm
-           xkeyboard-config
+           xkeyboard-config))
-           yoga))
     (native-inputs
      (list extra-cmake-modules
            zstd
@@ -161,7 +154,7 @@ client.")
 (define-public fcitx5-lua
   (package
     (name "fcitx5-lua")
-    (version "5.0.16")
+    (version "5.0.15")
     (source
      (origin
        (method url-fetch)
@@ -169,7 +162,7 @@ client.")
              "https://download.fcitx-im.org/fcitx5/fcitx5-lua/fcitx5-lua-"
              version ".tar.zst"))
        (sha256
-        (base32 "1zjiyadhqq8hijjv09khyj2shaw3ri4jgmb1ql67w9366wd0ykj2"))))
+        (base32 "1yp5z97m8n7fwvxps1gn8pflg69j3yawgabz36bpd4wl43zkgchg"))))
     (build-system cmake-build-system)
     (arguments
      (list
@@ -178,7 +171,7 @@ client.")
     (inputs
      (list fcitx5 lua gettext-minimal))
     (native-inputs
-     (list extra-cmake-modules pkg-config))
+     (list extra-cmake-modules))
     (home-page "https://github.com/fcitx/fcitx5-lua")
     (synopsis "Lua support for Fcitx 5")
     (description "Fcitx5-lua allows writing Fcitx5 extension in Lua.")
@@ -187,14 +180,14 @@ client.")
 (define-public libime
   (package
     (name "libime")
-    (version "1.1.14")
+    (version "1.1.12")
     (source
      (origin
        (method url-fetch)
        (uri (string-append "https://download.fcitx-im.org/fcitx5/libime/libime-"
                            version "_dict.tar.zst"))
        (sha256
-        (base32 "17r54fd6whvcxn389k4ah9mj1fc61zgama5nhiv1ilx40n1hnnpv"))))
+        (base32 "02n6xbbxfckzx5sqrclnh4cvqlnj9c5rpys07kd8r8m51paqzigq"))))
     (build-system cmake-build-system)
     (inputs
      (list fcitx5 boost (list zstd "lib")))
@@ -209,7 +202,7 @@ editors.")
 (define-public fcitx5-gtk
   (package
     (name "fcitx5-gtk")
-    (version "5.1.6")
+    (version "5.1.4")
     (source
      (origin
        (method url-fetch)
@@ -217,7 +210,7 @@ editors.")
                            "/fcitx5-gtk/fcitx5-gtk-"
                            version ".tar.zst"))
        (sha256
-        (base32 "0qj5gjdnrxcyz6a455b4379iwnzazw5a6c6dyk6wz0d2bgainc75"))))
+        (base32 "0lwl17mbfm3pxpd3y7h4sxf77npr16hyzygrc7a6v26bx6ycbkqx"))))
     (build-system cmake-build-system)
     (arguments
      (list
@@ -331,7 +324,7 @@ IM module for GTK+3 applications.
 (define-public fcitx5-qt
   (package
     (name "fcitx5-qt")
-    (version "5.1.13")
+    (version "5.1.11")
     (source
      (origin
        (method url-fetch)
@@ -339,7 +332,7 @@ IM module for GTK+3 applications.
                            "/fcitx5-qt/fcitx5-qt-"
                            version ".tar.zst"))
        (sha256
-        (base32 "1yawhwnycrqp1flik3hc2vskvsyjfm6rkcdhsqnawix22r2n1wl0"))))
+        (base32 "0mc396zfafs34jraj9fdk0wyzvdzg4xi605rhrd492xcpf25b59v"))))
     (build-system cmake-build-system)
     (arguments
      (list #:configure-flags
@@ -370,7 +363,7 @@ for Qt based application.")
 (define-public fcitx5-anthy
   (package
     (name "fcitx5-anthy")
-    (version "5.1.10")
+    (version "5.1.8")
     (source
      (origin
        (method url-fetch)
@@ -378,7 +371,7 @@ for Qt based application.")
                            "/fcitx5-anthy/fcitx5-anthy-"
                            version ".tar.zst"))
        (sha256
-        (base32 "11h7b687xj2k1hp7dqj6wh5y6i55cm8m5pqbi5vbflgg0cy5v1mp"))))
+        (base32 "1kv930nxz6q8ijb319fnnkzdyigbi36f2cwijnv4sy3rd0nykxrv"))))
     (build-system cmake-build-system)
     (arguments
      `(#:tests? #f)) ;; no tests
@@ -394,7 +387,7 @@ the Anthy input method.")
 (define-public fcitx5-skk
   (package
     (name "fcitx5-skk")
-    (version "5.1.10")
+    (version "5.1.8")
     (source
      (origin
        (method git-fetch)
@@ -403,14 +396,14 @@ the Anthy input method.")
              (commit version)))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "1fjiyx6dyiqxlypr1k4024lnc077xsnx4qwrwx9hj3yjdni5f2p0"))))
+        (base32 "11h6y7rv6yppp7iy8csy7r2pi2mlnjgl8h4h8ghfwab1gm7v32fn"))))
     (build-system cmake-build-system)
     (arguments
      (list #:tests? #f      ; no tests
            #:configure-flags
-           #~(list (string-append "-DSKK_PATH="
+           #~(list (string-append "-DSKK_DEFAULT_PATH="
                                   #$(this-package-input "skk-jisyo")
-                                  "/share/skk"))))
+                                  "/share/skk/SKK-JISYO.L"))))
     (native-inputs
      (list extra-cmake-modules gobject-introspection
            pkg-config gettext-minimal))
@@ -430,14 +423,14 @@ backend.")
 (define-public fcitx5-unikey
   (package
     (name "fcitx5-unikey")
-    (version "5.1.10")
+    (version "5.1.8")
     (source (origin
               (method git-fetch)
               (uri (git-reference
                     (url "https://github.com/fcitx/fcitx5-unikey")
                     (commit version)))
               (sha256
-               (base32 "1ddg5648r8jbdr8khawfhl26020snvrlgjwppw5rlh4iw3a4m143"))
+               (base32 "1nai5v6r367iwj8yxg4flv41my57l88l9vy0id9wr3hvrvls9v31"))
               (file-name (git-file-name name version))))
     (build-system qt-build-system)
     (arguments
@@ -457,14 +450,14 @@ backend.")
 (define-public fcitx5-chewing
   (package
     (name "fcitx5-chewing")
-    (version "5.1.11")
+    (version "5.1.9")
     (source (origin
               (method git-fetch)
               (uri (git-reference
                     (url "https://github.com/fcitx/fcitx5-chewing")
                     (commit version)))
               (sha256
-               (base32 "1x4a4vcb7vg9dx0f2bjrb2v6dcr8cwxnm8gdd47fkxqn890rgrnc"))
+               (base32 "1mgpxvmxfbqy8gymdsdmspgknh0pc751dm5rsrvdvfbd5lsa6pn6"))
               (file-name (git-file-name name version))))
     (build-system cmake-build-system)
     (arguments
@@ -486,7 +479,7 @@ backend.")
 (define-public fcitx5-chinese-addons
   (package
     (name "fcitx5-chinese-addons")
-    (version "5.1.12")
+    (version "5.1.10")
     (source
      (origin
        (method url-fetch)
@@ -494,7 +487,7 @@ backend.")
                            "/fcitx5-chinese-addons/fcitx5-chinese-addons-"
                            version "_dict.tar.zst"))
        (sha256
-        (base32 "09kk8r6pcxjhivwv4z5cdv2pqy0ry8ngnfbrcmwagzyq2jq9p2cr"))))
+        (base32 "11gnywigqys3gndb175nxk10k1ld3xvwd6kggqnxs95imc2004dd"))))
     (build-system cmake-build-system)
     (arguments
      (list #:configure-flags
@@ -547,7 +540,7 @@ including input methods previous bundled inside Fcitx 4:
 (define-public fcitx5-configtool
   (package
     (name "fcitx5-configtool")
-    (version "5.1.13")
+    (version "5.1.11")
     (source
      (origin
        (method url-fetch)
@@ -555,7 +548,7 @@ including input methods previous bundled inside Fcitx 4:
              "https://download.fcitx-im.org/fcitx5"
              "/fcitx5-configtool/fcitx5-configtool-" version ".tar.zst"))
        (sha256
-        (base32 "1sr8ri68qbkgvnj9pr5yw680zq506h26ymfmyz7ihw5ri14a6klr"))))
+        (base32 "1c5pw6p33z7lyk16jr1w72snazdc4q83ywn0gsk68qgmmfql5qr1"))))
     (build-system qt-build-system)
     (arguments
      (list #:qtbase qtbase
@@ -668,7 +661,7 @@ for Fcitx 5 with following color variants:
 (define-public fcitx5-rime
   (package
     (name "fcitx5-rime")
-    (version "5.1.13")
+    (version "5.1.12")
     (source (origin
               (method url-fetch)
               (uri (string-append "https://download.fcitx-im.org/fcitx5"
@@ -676,7 +669,7 @@ for Fcitx 5 with following color variants:
                                   ".tar.zst"))
               (sha256
                (base32
-                "03wcdgdhkvw5341vjv3idyksykm65y0873vkcrsi16dsp8w0h7i8"))))
+                "1blqfk8zpzd5v2r7gwjy12jbnsh26pcvad8q4mmhlg5j10yppg03"))))
     (build-system cmake-build-system)
     (arguments
      '(#:tests? #f ;no tests
@@ -707,7 +700,7 @@ output.")
 (define-public fcitx5-hangul
   (package
     (name "fcitx5-hangul")
-    (version "5.1.9")
+    (version "5.1.7")
     (source
      (origin
        (method git-fetch)
@@ -716,7 +709,7 @@ output.")
              (commit version)))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "0ja5faara4xz8waccpa5gbi3prh02hh3gpf915czhbkihffby6ng"))))
+        (base32 "02lkbwg25jr4hazjyxcy69midfsmxc0ksbdrfwbmqcfa3kz5d9gb"))))
     (build-system cmake-build-system)
     (native-inputs (list extra-cmake-modules pkg-config gettext-minimal))
     (inputs (list fcitx5 libhangul))

gnu/packages/fediverse.scm

@@ -29,6 +29,7 @@
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system meson)
   #:use-module (guix build-system pyproject)
+  #:use-module (guix build-system python)
   #:use-module ((guix licenses) #:prefix license:)
   #:use-module (guix utils)
   #:use-module (gnu packages)
@@ -244,6 +245,7 @@ seamlessly with your desktop environment.")
     (native-inputs
      (list nss-certs-for-test
            python-pytest
+           python-pytest-cov
            python-pytest-mock
            python-pytest-recording
            python-pytest-retry

gnu/packages/file-systems.scm

@@ -50,6 +50,7 @@
   #:use-module (guix build-system go)
   #:use-module (guix build-system linux-module)
   #:use-module (guix build-system pyproject)
+  #:use-module (guix build-system python)
   #:use-module (guix build-system qt)
   #:use-module (guix build-system trivial)
   #:use-module (guix utils)
@@ -87,7 +88,6 @@
   #:use-module (gnu packages golang-build)
   #:use-module (gnu packages golang-check)
   #:use-module (gnu packages golang-crypto)
-  #:use-module (gnu packages golang-web)
   #:use-module (gnu packages golang-xyz)
   #:use-module (gnu packages guile)
   #:use-module (gnu packages haskell-xyz)
@@ -761,7 +761,7 @@ from a mounted file system.")
   ;; completions by running a native bcachefs binary at build time.
   (package
     (name "bcachefs-tools-minimal")
-    (version "1.37.4")
+    (version "1.35.1")
     (source
      (origin
        (method git-fetch)
@@ -770,7 +770,7 @@ from a mounted file system.")
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "17041jphzbg0ppxlc1acr3d73zyn02spjvi5my30wak8xh9n6nan"))))
+        (base32 "1jn7fqlvhr0iazfx31wamvmf3qmgrzlf9ghvz8qazk8b6ipv77fn"))))
     (build-system cargo-build-system)
     (arguments
      (list
@@ -968,13 +968,20 @@ minimal bcachefs-tools package.  It is meant to be used in initrds.")
 (define-public bcachefs-linux-module
   (package
     (name "bcachefs-linux-module")
-    (version (package-version bcachefs-tools-minimal))
+    (version "1.35.1")
-    (source (package-source bcachefs-tools-minimal))
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://evilpiepirate.org/git/bcachefs-tools.git")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "1jn7fqlvhr0iazfx31wamvmf3qmgrzlf9ghvz8qazk8b6ipv77fn"))))
     (build-system linux-module-build-system)
     (arguments
      (list
-      #:make-flags #~(list "BCACHEFS_DKMS=1")
+      #:tests? #f ;no 'check' target
-      #:tests? #f                       ;no 'check' target
       #:source-directory "build/src/fs/bcachefs"
       #:phases
       #~(modify-phases %standard-phases
@@ -983,14 +990,18 @@ minimal bcachefs-tools package.  It is meant to be used in initrds.")
               (with-output-to-file ".version"
                 (lambda ()
                   (display #$version)))))
-          (add-before 'configure 'prepare-build-directory
+          (add-after 'unpack 'patch-source
-            (lambda* (#:key make-flags #:allow-other-keys)
+            (lambda _
-              (apply invoke "make" "install_dkms"
+              (substitute* "Makefile"
-                     (string-append "DESTDIR="
+                ;; Remove unnecessary dependencies
-                                    (getcwd) "/")
+                (("^.*PKG_CONFIG.*$")
-                     "DKMSDIR=build/"
+                 ""))))
-                     make-flags))))))
+          (add-before 'configure 'prepare-build-dir
-    (home-page (package-home-page bcachefs-tools-minimal))
+            (lambda _
+              (invoke "make" "install_dkms"
+                      (string-append "DESTDIR="
+                                     (getcwd) "/") "DKMSDIR=build/"))))))
+    (home-page (package-home-page bcachefs-tools-minimal/static))
     (synopsis "Bcachefs Linux kernel module")
     (description
      "This package provides the Linux kernel module for Bcachefs.
@@ -2129,79 +2140,10 @@ the XDG directory specification from @file{~/.@var{name}} to
 @file{~/.config/@var{name}}.")
       (license license:gpl2+))))
 
-(define-public s5cmd
-  (package
-    (name "s5cmd")
-    (version "2.3.0")
-    (source
-     (origin
-       (method git-fetch)
-       (uri (git-reference
-              (url "https://github.com/peak/s5cmd")
-              (commit (string-append "v" version))))
-       (file-name (git-file-name name version))
-       (sha256
-        (base32 "1y1bwma6f68j00jfdjxvw5flp9l4cdys7dgkrr0yvfz68lk9a17v"))
-       (snippet
-        #~(begin (use-modules (guix build utils))
-                 (delete-file-recursively "vendor")))))
-    (build-system go-build-system)
-    (arguments
-     (list
-      #:install-source? #f
-      #:import-path "github.com/peak/s5cmd/v2"
-      #:test-flags
-      #~(list "-vet=off"
-              ;; cp_test.go:74: assertion failed: text/plain; charset=utf-8
-              ;; (tc.expectedContentType string) != text/html; charset=utf-8
-              ;; (string)
-              "-skip" "TestGuessContentType")
-      #:test-subdirs
-      ;; build flag -mod=vendor only valid when using modules
-      ;; /<...>/peak/s5cmd/v2/e2e/util_test.go:417 +0x3b9
-      ;; /<...>/peak/s5cmd/v2/e2e/main_test.go:12 +0x65
-      #~(list "command/..."
-              "orderedwriter/..."
-              "progressbar/..."
-              "storage/..."
-              "storage/url/..."
-              "strutil/...")
-      #:phases
-      #~(modify-phases %standard-phases
-	  (add-after 'install 'rename-binaries
-	    (lambda _
-	      (rename-file
-	       (string-append #$output "/bin/v2")
-	       (string-append #$output "/bin/s5cmd")))))))
-    (native-inputs
-     (list go-github-com-aws-aws-sdk-go
-           go-github-com-cheggaaa-pb-v3
-           go-github-com-google-go-cmp
-           go-github-com-hashicorp-go-multierror
-           go-github-com-iancoleman-strcase
-           go-github-com-igungor-gofakes3
-           go-github-com-karrick-godirwalk
-           go-github-com-kballard-go-shellquote
-           go-github-com-lanrat-extsort-1.0.2
-           go-github-com-termie-go-shutil
-           go-github-com-urfave-cli-v2
-           go-go-uber-org-mock
-           go-gotest-tools-v3
-           go-honnef-co-go-tools
-           go-mvdan-cc-unparam))
-    (home-page "https://github.com/peak/s5cmd")
-    (synopsis "Parallel S3 and local filesystem execution tool")
-    (description
-     "@code{s5cmd} is a fast S3 and local filesystem execution tool.  It comes
-with support for a multitude of operations including tab completion and
-wildcard support for files, which can be handy for object storage workflow
-while working with large number of files.")
-    (license license:expat)))
-
 (define-public squashfuse
   (package
     (name "squashfuse")
-    (version "0.6.1")
+    (version "0.1.105")
     (source
      (origin
        (method git-fetch)
@@ -2210,7 +2152,7 @@ while working with large number of files.")
              (commit version)))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "16ds2xlk6hb5cggi6di8s0aalir3mrx7rk24rw5daad1xw4dbq0y"))))
+        (base32 "03aw8pw8694jyrzpnbry05rk9718sqw66kiyq878bbb679gl7224"))))
     (build-system gnu-build-system)
     (arguments
      (list
@@ -2248,8 +2190,7 @@ memory-efficient.")
                  (install-file "fuseprivate.h"
                                (string-append #$output
                                               "/include/squashfuse/")))))))))
-    (inputs (list `(,fuse "out")
+    (inputs (list fuse-for-appimage
-                  `(,fuse "static")
                   `(,zstd "lib")
                   `(,zstd "static")
                   `(,zlib "out")

gnu/packages/finance.scm

@@ -70,6 +70,7 @@
   #:use-module (guix build-system copy)
   #:use-module (guix build-system emacs)
   #:use-module (guix build-system haskell)
+  #:use-module (guix build-system python)
   #:use-module (guix build-system pyproject)
   #:use-module (guix build-system glib-or-gtk)
   #:use-module (guix build-system go)
@@ -765,7 +766,7 @@ require Coincurve.")
 (define-public electrum
   (package
     (name "electrum")
-    (version "4.7.2")
+    (version "4.7.1")
     (source
      (origin
        (method git-fetch)
@@ -774,7 +775,7 @@ require Coincurve.")
               (commit version)))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "05y3w9jhpfxd7frzlilqvsfggrgfzcml2spc2qb5xx9j4q62hnmx"))))
+        (base32 "171jbap3khzwkyxg730sasfj01qiip396sgyiwr1i6yq5fxd23pi"))))
     (build-system pyproject-build-system)
     (arguments
      (list
@@ -1622,7 +1623,10 @@ features:
        (sha256
         (base32 "0yir8hka3vmpk0qhiaffagkdjg3mjgai808s0razsggbd5cn80bb"))))
     (build-system pyproject-build-system)
-    (native-inputs (list python-pytest python-setuptools))
+    (native-inputs
+     (list python-pytest
+           python-pytest-cov
+           python-setuptools))
     (home-page "https://arthurdejong.org/python-stdnum/")
     (synopsis "Python module to handle standardized number and code formats")
     (description
@@ -2505,6 +2509,10 @@ analysis of financial market data.")
         (base32 "13g5338aa8vgkx8g94vz5d8ynfq3jndvyh1nz6dlhw4axwr4x8dp"))))
     (properties '(("upstream-name" #{.}# "mt-940")))
     (build-system pyproject-build-system)
+    (arguments
+     (list
+      #:test-flags
+      #~(list "-c" "/dev/null")))       ; Remove custom --cov flags.
     (native-inputs (list python-pytest python-pyyaml python-setuptools))
     (home-page "https://mt940.readthedocs.io/")
     (synopsis "Python parser for MT940-encoded SWIFT data")

gnu/packages/firmware.scm

@@ -47,6 +47,7 @@
   #:use-module (guix build-system cmake)
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system meson)
+  #:use-module (guix build-system python)
   #:use-module (guix build-system pyproject)
   #:use-module (guix build-system trivial)
   #:use-module (gnu packages)

gnu/packages/flashing-tools.scm

@@ -2,7 +2,7 @@
 ;;; Copyright © 2014 Mark H Weaver <mhw@netris.org>
 ;;; Copyright © 2014 Manolis Fragkiskos Ragkousis <manolis837@gmail.com>
 ;;; Copyright © 2016 Hartmut Goebel <h.goebel@crazy-compilers.com>
-;;; Copyright © 2016, 2021 Ludovic Courtès <ludo@gnu.org>
+;;; Copyright © 2016, 2018, 2021 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2016, 2019 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2017 Jonathan Brielmaier <jonathan.brielmaier@web.de>
 ;;; Copyright © 2017 Julien Lepiller <julien@lepiller.eu>
@@ -49,6 +49,7 @@
   #:use-module (guix build-system go)
   #:use-module (guix build-system meson)
   #:use-module (guix build-system pyproject)
+  #:use-module (guix build-system python)
   #:use-module (guix build-system qt)
   #:use-module (guix download)
   #:use-module (guix gexp)
@@ -83,6 +84,7 @@
   #:use-module (gnu packages linux)
   #:use-module (gnu packages mtools)
   #:use-module (gnu packages pciutils)
+  #:use-module (gnu packages pciutils)
   #:use-module (gnu packages perl)
   #:use-module (gnu packages pkg-config)
   #:use-module (gnu packages python)
@@ -522,6 +524,162 @@ Loke and Heimdall communicate via the custom Samsung-developed protocol typicall
 referred to as the \"Odin 3 protocol\".")
     (license license:expat)))
 
+(define-public ifdtool
+  (package
+    (name "ifdtool")
+    (version "25.09")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+              (url "https://review.coreboot.org/coreboot")
+              (commit version)))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32
+         "1a1n64dwr5fzdnaj45bjci85ap5yra5gwz4x056zn6481xwvbsmv"))))
+    (build-system gnu-build-system)
+    (arguments
+     (list
+      #:make-flags
+      #~(list (string-append "CC=" #$(cc-for-target))
+              "INSTALL=install"
+              (string-append "PREFIX=" #$output))
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-after 'unpack 'chdir
+            (lambda _
+              (chdir "util/ifdtool")))
+          (delete 'configure))           ; no configure script
+      #:tests? #f))                    ; no test suite
+    (home-page "https://doc.coreboot.org/util/ifdtool/")
+    (synopsis "Intel Firmware Descriptor dumper")
+    (description "This package provides @command{ifdtool}, a program to
+dump Intel Firmware Descriptor data of an image file.")
+    (license license:gpl2)))
+
+(define-public bincfg
+  (package
+    (name "bincfg")
+    (version "25.09")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+              (url "https://review.coreboot.org/coreboot")
+              (commit version)))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32
+         "1a1n64dwr5fzdnaj45bjci85ap5yra5gwz4x056zn6481xwvbsmv"))))
+    (build-system gnu-build-system)
+    (arguments
+     (list
+      #:tests? #f ; no test suite
+      #:make-flags
+      #~(list
+         (string-append "CC=" #$(cc-for-target)))
+      #:phases
+      #~(modify-phases %standard-phases
+          (delete 'configure) ; no configure script
+          (add-after 'unpack 'chdir
+            (lambda _
+              (chdir "util/bincfg")))
+          (add-after 'build 'build-binaries
+            (lambda* (#:key make-flags #:allow-other-keys)
+              (for-each
+               (lambda (target result)
+                 (apply invoke "make" (string-append "gen-" target) make-flags)
+                 (rename-file result
+                              (string-append target ".bin")))
+               (list
+                ;; generate GbE for X200
+                "gbe-ich9m"
+                ;; generate GbE for X220/x230
+                "gbe-82579LM"
+                ;; generate IFD for X200
+                "ifd-x200")
+               (list
+                "flashregion_3_gbe.bin"
+                "flashregion_3_gbe.bin"
+                "flashregion_0_fd.bin"))))
+          ;; The Makefile has no install target.
+          (replace 'install
+            (lambda _
+              (let ((bin (string-append #$output "/bin"))
+                    (lib (string-append #$output "/lib/bincfg"))
+                    (data (string-append #$output "/share/bincfg")))
+                ;; Install the program
+                (install-file "bincfg" bin)
+                ;; And its data
+                (for-each
+                 (lambda (path)
+                   (install-file path data))
+                 (append (find-files "." ".*\\.set")
+                         (find-files "." ".*\\.spec")))
+                ;; And the files generated with the data
+                (for-each
+                 (lambda (path)
+                   (install-file path lib))
+                 (find-files "." ".*\\.bin"))))))))
+    (native-inputs (list bison flex))
+    (home-page "https://coreboot.org")
+    (synopsis "Encoder/decoder for binary formats described in text files")
+    (description "
+The bincfg program comes with specifications files for the following binary
+formats:
+@itemize
+@item Various DDR3 and DDR4 SPD
+@item Configuration data for the Intel 82579LM Gigabit Ethernet PHY
+@item Configuration data for the Intel Gigabit Ethernet controller present in
+      the Intel ICH9-M chipset.
+@item Intel Firmware Descriptor data for the Lenovo ThinkPad X200
+@item Configuration data for the ITE IT8718F SuperIO
+@end itemize
+It also comes with example files generated by bincfg.")
+    (license license:gpl3+)))
+
+(define-public intelmetool
+  (package
+    (name "intelmetool")
+    (version "25.09")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://review.coreboot.org/coreboot")
+                    (commit version)))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "1a1n64dwr5fzdnaj45bjci85ap5yra5gwz4x056zn6481xwvbsmv"))))
+    (build-system gnu-build-system)
+    (arguments
+     (list
+      #:tests? #f                       ;no test suite
+      #:make-flags
+      #~(list (string-append "CC=" #$(cc-for-target))
+              "INSTALL=install"
+              (string-append "PREFIX=" #$output))
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-after 'unpack 'chdir
+            (lambda _
+              (chdir "util/intelmetool")))
+          (delete 'configure) ;no configure script
+          (delete 'check))))
+    (inputs (list pciutils zlib))
+    (home-page
+     "https://github.com/coreboot/coreboot/tree/main/util/intelmetool/")
+    (synopsis "Intel Management Engine tools")
+    (description "This package provides tools for working with Intel
+Management Engine (ME).  You need to @code{sudo rmmod mei_me} and
+@code{sudo rmmod mei} before using this tool.  Also pass
+@code{iomem=relaxed} to the Linux kernel command line.")
+    (license license:gpl2)
+
+    ;; This is obviously an Intel thing, plus it requires <cpuid.h>.
+    (supported-systems '("x86_64-linux" "i686-linux"))))
+
 (define-public me-cleaner
   (package
     (name "me-cleaner")

gnu/packages/fltk.scm

@@ -52,7 +52,6 @@
       (uri (git-reference
               (url "https://github.com/fltk/fltk")
               (commit (string-append "release-" version))))
-      (file-name (git-file-name name version))
       (sha256
        (base32 "0pnifyhhvcqfjd6iaa4m14kvfyqhjjdw0aqbcizcdhhqrl6q4pjg"))))
    (build-system gnu-build-system)

gnu/packages/fontutils.scm

@@ -96,6 +96,7 @@
   #:use-module (guix build-system go)
   #:use-module (guix build-system meson)
   #:use-module (guix build-system pyproject)
+  #:use-module (guix build-system python)
   #:use-module (guix utils)
   #:use-module (srfi srfi-1))
 
@@ -472,53 +473,6 @@ font design software, it allows you to join, split, offset, and perform many
 other operations on paths.")
     (license license:expat)))
 
-(define-public python-booleanoperations
-  (package
-    (name "python-booleanoperations")
-    (version "0.9.0")
-    (source
-     (origin
-       (method git-fetch)
-       (uri (git-reference
-              (url "https://github.com/typemytype/booleanOperations")
-              (commit version)))
-       (file-name (git-file-name name version))
-       (sha256
-        (base32 "0ahfgamyq1ndwbr9n8sdx8qhqc2195xnbahylgjpk877hbr2gxav"))))
-    (build-system pyproject-build-system)
-    (arguments
-     (list
-      ;; Some tests fail due to small differences in the expected result (see:
-      ;; <https://github.com/typemytype/booleanOperations/issues/69>).
-      #:test-flags
-      #~(list "-k"
-              (string-join
-               (list "not test_QTail_reversed_difference"
-                     "test_QTail_reversed_intersection"
-                     "test_QTail_reversed_union"
-                     "test_QTail_reversed_xor"
-                     "test_Q_difference"
-                     "test_Q_intersection"
-                     "test_Q_union"
-                     "test_Q_xor")
-               " and not "))))
-    (native-inputs
-     (list python-defcon-bootstrap
-           python-fontpens-bootstrap
-           python-pytest
-           python-setuptools
-           python-setuptools-scm))
-    (propagated-inputs
-     (list python-fonttools-minimal
-           python-pyclipper))
-    (home-page "https://github.com/typemytype/booleanOperations")
-    (synopsis "Boolean operations on paths")
-    (description
-     "Boolean operations on paths which uses a super fast
-@url{http://www.angusj.com/delphi/clipper.php, polygon clipper library by
-Angus Johnson}.")
-    (license license:expat)))
-
 (define-public python-cffsubr
   (package
     (name "python-cffsubr")
@@ -620,6 +574,7 @@ for fontTools.")
      (list python-cython
            python-defcon
            python-pytest
+           python-pytest-runner
            python-setuptools
            python-setuptools-scm
            python-wheel
@@ -746,7 +701,8 @@ implementing the pen protocol for manipulating glyphs.")
       (modify-inputs native-inputs
         (append python-fontparts-bootstrap
                 python-fontpens-bootstrap
-                python-pytest))))))
+                python-pytest
+                python-pytest-runner))))))
 
 ;;; A variant used to break a cycle with python-fontpens.
 (define-public python-fontparts-bootstrap
@@ -1027,6 +983,7 @@ suite of the @code{psautohint} package.")
     (native-inputs
      (list psautohint-font-data
            python-pytest
+           python-pytest-cov
            python-pytest-xdist
            python-setuptools-scm
            python-setuptools
@@ -1870,10 +1827,6 @@ definitions.")
            pango
            potrace
            python
-           ;; XXX: Python 3.12 lacks distutils:
-           ;; ModuleNotFoundError: No module named 'distutils'
-           ;; Remove when package is updated.
-           python-setuptools-bootstrap
            zlib))
     (arguments
      (append

gnu/packages/fortran-xyz.scm

@@ -28,8 +28,7 @@
   #:use-module (gnu packages libffi)
   #:use-module (gnu packages maths)
   #:use-module (gnu packages pkg-config)
-  #:use-module (gnu packages python)
+  #:use-module (gnu packages python))
-  #:use-module (gnu packages python-build))
 
 ;;; Please: Try to add new module packages in alphabetic order.
 ;;;
@@ -145,7 +144,7 @@ a.s.o.
 (define-public fortran-mctc-lib
   (package
     (name "fortran-mctc-lib")
-    (version "0.5.1")
+    (version "0.3.2")
     (source
      (origin
        (method git-fetch)
@@ -155,7 +154,7 @@ a.s.o.
        (file-name (git-file-name name version))
        (sha256
         (base32
-         "1wp8apv0psl2hkhlrd5pgnhbxk8zpxa0ijkhcnb09klbxcsi8p5f"))))
+         "1gabdxllx2pcw1mbv4gw9zpn6817ikz9ql8xs9w86wswd6f0m5kl"))))
     (build-system meson-build-system)
     (arguments
      (list
@@ -244,7 +243,7 @@ calculate partial charges used in the DFT-D4 model.")
 (define-public fortran-simple-dftd3
   (package
     (name "fortran-simple-dftd3")
-    (version "1.3.0")
+    (version "1.2.1")
     (source
      (origin
        (method git-fetch)
@@ -253,7 +252,7 @@ calculate partial charges used in the DFT-D4 model.")
               (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "1602pwmxa8qjllgj7k9hq2bm4s838f6qzr7mpc0rbh28gm00c1fw"))))
+        (base32 "0aygmnax3vwz2x3ad7syksfjca4zc85nyslsibs0wg8wqfsmr33k"))))
     (build-system meson-build-system)
     (arguments
      (list
@@ -266,8 +265,7 @@ calculate partial charges used in the DFT-D4 model.")
      (list gfortran
            pkg-config
            python-minimal
-           python-cffi
+           python-cffi))
-           python-setuptools))
     (inputs
      (list fortran-mctc-lib
            fortran-mstore

gnu/packages/freedesktop.scm

@@ -73,6 +73,7 @@
   #:use-module (guix build-system meson)
   #:use-module (guix build-system perl)
   #:use-module (guix build-system pyproject)
+  #:use-module (guix build-system python)
   #:use-module (guix build-system glib-or-gtk)
   #:use-module (guix build-system qt)
   #:use-module (guix search-paths)
@@ -1149,60 +1150,6 @@ GNOME Shell.  The @command{localectl} command-line tool allows you to interact
 with localed.  This package is extracted from the broader systemd package.")
     (license license:lgpl2.1+)))
 
-(define-public gardenhostd
-  (package
-   (name "gardenhostd")
-   (version "1.1")
-   (source (origin
-            (method git-fetch)
-            (uri (git-reference
-                  (url "https://codeberg.org/axtlos/gardenhostd.git")
-                  (commit (string-append "v" version))))
-            (file-name (git-file-name name version))
-            (sha256
-             (base32
-              "1q0pdh0imc2ggb26cddl62hx6fmz6z4hqj2352a4k9wxyn5kfiam"))))
-   (build-system meson-build-system)
-   (arguments
-    (list
-     #:imported-modules `(,@%meson-build-system-modules
-                          ,@%pyproject-build-system-modules)
-     #:modules '(((guix build pyproject-build-system) #:prefix pyproject:)
-                 (guix build meson-build-system)
-                 (guix build utils))
-     #:phases
-     #~(modify-phases %standard-phases
-         (add-after 'install 'remove-extra-files
-           (lambda _
-             (with-directory-excursion #$output
-               (delete-file-recursively "etc/init.d")
-               (rmdir "etc"))))
-         ;; See <https://codeberg.org/guix/guix/issues/7579>.
-         (add-after 'install 'wrap-search-paths
-           (lambda _
-             (wrap-program (string-append #$output "/libexec/gardenhostd")
-               `("GUIX_PYTHONPATH" prefix
-                 ,(map
-                   (lambda (package)
-                     (string-append
-                      package "/lib/python"
-                      (pyproject:python-version #$(this-package-input "python"))
-                      "/site-packages"))
-                   ;; Avoids references to meson’s libraries.
-                   (list #$(this-package-input "python")
-                         #$(this-package-input "python-pygobject"))))))))))
-   (inputs
-    (list bash-minimal
-          python
-          python-pygobject))
-   (home-page "https://codeberg.org/axtlos/gardenhostd")
-   (synopsis "Minimal Python implementation of systemd-hostnamed")
-   (description "This package is a partial implementation of the
-systemd-hostnamed daemon.  It provides the @code{org.freedesktop.hostname1}
-D-Bus interface, which helps applications like GNOME Settings retrieve and
-modify the system’s hostname, as well as set a pretty hostname for display.")
-   (license license:gpl3+)))
-
 (define-public packagekit
   (package
     (name "packagekit")
@@ -1377,43 +1324,41 @@ For information about libevdev, see:
     (license license:expat)))
 
 (define-public python-pyxdg
-  ;; Latest unreleased commits add Python 3.12, 3.14 and 3.15 support.
+  (package
-  (let ((commit "63033ac306aa26d32e1439417e59ae8f8a4c9820")
+    (name "python-pyxdg")
-        (revision "0"))
+    (version "0.28")
-    (package
+    (source
-      (name "python-pyxdg")
+     (origin
-      (version "0.28")
+       (method url-fetch)
-      (source
+       (uri (pypi-uri "pyxdg" version))
-       (origin
+       (sha256
-         (method git-fetch)
+        (base32
-         (uri (git-reference
+         "1d48bqwkbnpid80cpwz6h62i112laxl0ivpj58hdyd79fhqbnrrj"))))
-                (url "https://gitlab.freedesktop.org/xdg/pyxdg")
+    (build-system pyproject-build-system)
-                (commit commit)))
+    (arguments
-         (file-name (git-file-name name version))
+     (list
-         (sha256
+      #:test-flags
-          (base32
+      ;; Tests failing with error: AssertionError: 'image' != 'inode'
-           "10wk95rmcr2fglmvmv1a6ad9hkw9587r0rlww0gq6kbfz85whgmd"))))
+      #~(list "--deselect=test/test_mime.py::MimeTest::test_get_type"
-      (build-system pyproject-build-system)
+              "--deselect=test/test_mime.py::MimeTest::test_get_type2")
-      (arguments
+      #:phases
-       (list
+      #~(modify-phases %standard-phases
-        #:phases
+          (add-before 'check 'pre-check
-        #~(modify-phases %standard-phases
+            (lambda _
-            (add-before 'check 'pre-check
+              (setenv "XDG_DATA_DIRS"
-              (lambda _
+                      (string-append #$(this-package-native-input "shared-mime-info")
-                (setenv "XDG_DATA_DIRS"
+                                     "/share/")))))))
-                        (string-append #$(this-package-native-input "shared-mime-info")
+    (native-inputs
-                                       "/share/")))))))
+     (list shared-mime-info
-      (native-inputs
+           hicolor-icon-theme
-       (list shared-mime-info
+           python-pytest
-             hicolor-icon-theme
+           python-setuptools))
-             python-pytest
+    (home-page "https://www.freedesktop.org/wiki/Software/pyxdg")
-             python-setuptools))
+    (synopsis "Implementations of freedesktop.org standards in Python")
-      (home-page "https://www.freedesktop.org/wiki/Software/pyxdg")
+    (description
-      (synopsis "Implementations of freedesktop.org standards in Python")
+     "PyXDG is a collection of implementations of freedesktop.org standards in
-      (description
-       "PyXDG is a collection of implementations of freedesktop.org standards in
 Python.")
-      (license license:lgpl2.0))))
+    (license license:lgpl2.0)))
 
 (define-public hyprland-protocols
   (package
@@ -2178,7 +2123,7 @@ which speak the Qualcomm MSM Interface (QMI) protocol.")
            libxslt                      ;for xsltproc
            pkg-config
            python-minimal
-           python-dbus                  ;for test
+           python-dbus-1.2              ;for test
            python-pygobject             ;for test
            vala))
     (propagated-inputs
@@ -2372,7 +2317,7 @@ different sorts of messages in different formats.")
           (base32 "02wb61h2k3hhis5y2xi5rhc6pmikd13x722hk620sqb9b3m5pn3s"))))
       (build-system gnu-build-system)
       (native-inputs (list autoconf automake libtool pkg-config))
-      (inputs (list libxslt python-wrapper python-dbus))
+      (inputs (list libxslt python-wrapper python-dbus-1.2))
       (propagated-inputs (list telepathy-glib))
       (home-page "https://telepathy.freedesktop.org/")
       (synopsis "Telepathy IRC connection manager")
@@ -2917,7 +2862,7 @@ to the C library @code{uchardet} to increase performance.")
 (define-public udiskie
   (package
     (name "udiskie")
-    (version "2.6.2")
+    (version "2.6.1")
     (source
      (origin
        (method git-fetch)
@@ -2926,7 +2871,7 @@ to the C library @code{uchardet} to increase performance.")
               (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "0zc23yf2sw1m21xkfbpfjzbp7xykqjwq56fr2nxzlc02n7g6iqgk"))))
+        (base32 "0ngr8sdzd32mxamzfh82ar8m40z52lx91339b7dq3in0cr5r1ynp"))))
     (build-system pyproject-build-system)
     (arguments
      (list

gnu/packages/game-development.scm

@@ -70,6 +70,7 @@
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system go)
   #:use-module (guix build-system pyproject)
+  #:use-module (guix build-system python)
   #:use-module (guix build-system renpy)
   #:use-module (guix build-system scons)
   #:use-module (gnu packages)

gnu/packages/games.scm

@@ -30,7 +30,7 @@
 ;;; Copyright © 2017, 2019, 2020 Marius Bakke <mbakke@fastmail.com>
 ;;; Copyright © 2017, 2018 Rutger Helling <rhelling@mykolab.com>
 ;;; Copyright © 2017 Roel Janssen <roel@gnu.org>
-;;; Copyright © 2017-2026 Nicolas Goaziou <mail@nicolasgoaziou.fr>
+;;; Copyright © 2017-2025 Nicolas Goaziou <mail@nicolasgoaziou.fr>
 ;;; Copyright © 2018 okapi <okapi@firemail.cc>
 ;;; Copyright © 2018 Tim Gesthuizen <tim.gesthuizen@yahoo.de>
 ;;; Copyright © 2018 Madalin Ionel-Patrascu <madalinionel.patrascu@mdc-berlin.de>
@@ -97,7 +97,6 @@
 ;;; Copyright © 2025 Aiden Isik <aidenisik+git@member.fsf.org>
 ;;; Copyright © 2026 Cayetano Santos <csantosb@inventati.org>
 ;;; Copyright © 2026 Carlos Durán Domínguez <wurt@wurt.eu>
-;;; Copyright © 2026 Nikita Alkhovik <forgoty13@gmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -115,32 +114,40 @@
 ;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
 
 (define-module (gnu packages games)
-  #:autoload (gnu packages pascal) (fpc)
+  #:use-module (ice-9 match)
+  #:use-module ((guix licenses) #:prefix license:)
+  #:use-module (guix utils)
+  #:use-module (guix packages)
+  #:use-module (guix download)
+  #:use-module (guix git-download)
+  #:use-module (guix svn-download)
+  #:use-module (guix gexp)
+  #:use-module (gnu packages)
   #:use-module (gnu packages acl)
-  #:use-module (gnu packages admin)
+  #:use-module (gnu packages adns)
   #:use-module (gnu packages algebra)
-  #:use-module (gnu packages assembly)
-  #:use-module (gnu packages audio)
   #:use-module (gnu packages autotools)
-  #:use-module (gnu packages avahi)
   #:use-module (gnu packages backup)
   #:use-module (gnu packages base)
+  #:use-module (gnu packages build-tools)
+  #:use-module (gnu packages admin)
+  #:use-module (gnu packages audio)
+  #:use-module (gnu packages avahi)
+  #:use-module (gnu packages assembly)
   #:use-module (gnu packages bash)
   #:use-module (gnu packages bison)
   #:use-module (gnu packages boost)
-  #:use-module (gnu packages build-tools)
   #:use-module (gnu packages c)
   #:use-module (gnu packages check)
   #:use-module (gnu packages cmake)
-  #:use-module (gnu packages code)
   #:use-module (gnu packages compression)
+  #:use-module (gnu packages code)
   #:use-module (gnu packages cpp)
-  #:use-module (gnu packages crypto)
   #:use-module (gnu packages curl)
+  #:use-module (gnu packages crypto)
   #:use-module (gnu packages cyrus-sasl)
-  #:use-module (gnu packages dns)
-  #:use-module (gnu packages docbook)
   #:use-module (gnu packages documentation)
+  #:use-module (gnu packages docbook)
   #:use-module (gnu packages emacs)
   #:use-module (gnu packages emulators)
   #:use-module (gnu packages flex)
@@ -195,8 +202,8 @@
   #:use-module (gnu packages maths)
   #:use-module (gnu packages messaging)
   #:use-module (gnu packages mp3)
-  #:use-module (gnu packages multiprecision)
   #:use-module (gnu packages music)
+  #:use-module (gnu packages multiprecision)
   #:use-module (gnu packages ncurses)
   #:use-module (gnu packages netpbm)
   #:use-module (gnu packages networking)
@@ -205,6 +212,7 @@
   #:use-module (gnu packages oneapi)
   #:use-module (gnu packages opencl)
   #:use-module (gnu packages pcre)
+  #:autoload (gnu packages pascal) (fpc)
   #:use-module (gnu packages perl)
   #:use-module (gnu packages perl-check)
   #:use-module (gnu packages perl-compression)
@@ -222,9 +230,9 @@
   #:use-module (gnu packages readline)
   #:use-module (gnu packages regex)
   #:use-module (gnu packages ruby-xyz)
+  #:use-module (gnu packages shells)
   #:use-module (gnu packages sdl)
   #:use-module (gnu packages serialization)
-  #:use-module (gnu packages shells)
   #:use-module (gnu packages sqlite)
   #:use-module (gnu packages squirrel)
   #:use-module (gnu packages swig)
@@ -241,31 +249,22 @@
   #:use-module (gnu packages wget)
   #:use-module (gnu packages wxwidgets)
   #:use-module (gnu packages xdisorg)
+  #:use-module (gnu packages xorg)
   #:use-module (gnu packages xiph)
   #:use-module (gnu packages xml)
-  #:use-module (gnu packages xorg)
-  #:use-module (gnu packages)
-  #:use-module (guix build-system cmake)
   #:use-module (guix build-system copy)
+  #:use-module (guix build-system cmake)
   #:use-module (guix build-system glib-or-gtk)
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system go)
   #:use-module (guix build-system haskell)
   #:use-module (guix build-system meson)
   #:use-module (guix build-system perl)
-  #:use-module (guix build-system pyproject)
   #:use-module (guix build-system python)
+  #:use-module (guix build-system pyproject)
   #:use-module (guix build-system qt)
   #:use-module (guix build-system scons)
   #:use-module (guix build-system trivial)
-  #:use-module (guix download)
-  #:use-module (guix gexp)
-  #:use-module (guix git-download)
-  #:use-module ((guix licenses) #:prefix license:)
-  #:use-module (guix packages)
-  #:use-module (guix svn-download)
-  #:use-module (guix utils)
-  #:use-module (ice-9 match)
   #:use-module ((srfi srfi-1) #:hide (zip))
   #:use-module (srfi srfi-26))
 
@@ -484,7 +483,7 @@ mouse and joystick control, and original music.")
       (source (origin
                 (method git-fetch)
                 (uri (git-reference
-                      (url "https://gitlab.com/drummyfish/anarch")
+                      (url "https://git.sr.ht/~drummyfish/Anarch")
                       (commit commit)))
                 (file-name (git-file-name name version))
                 (sha256
@@ -3965,7 +3964,7 @@ that beneath its ruins lay buried an ancient evil.")
 (define-public angband
   (package
     (name "angband")
-    (version "4.2.6")
+    (version "4.2.5")
     (source
      (origin
        (method git-fetch)
@@ -3974,7 +3973,7 @@ that beneath its ruins lay buried an ancient evil.")
              (commit version)))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "0hgzdvlh0j42w4q9kch9xvhnbvcrypac01xhpksw35gj9my887cp"))
+        (base32 "0kg6npbfy42mhggsqvs04khc8198i980z52xm59pws29698qazaw"))
        (modules '((guix build utils)))
        (snippet
         ;; So, some of the sounds/graphics/tilesets are under different
@@ -3990,55 +3989,12 @@ that beneath its ruins lay buried an ancient evil.")
            (substitute* "lib/Makefile"
              ;; And don't try to invoke makefiles in the directories we removed.
              (("gamedata customize help screens fonts tiles sounds icons user")
-              "gamedata customize help screens user"))
+              "gamedata customize help screens user"))))))
-           ;; Remove nonfree .dll files too.
-           (delete-file-recursively "src/win")))))
     (build-system gnu-build-system)
     (arguments
-     `(#:configure-flags (list (string-append "--bindir=" %output "/bin"))
+     `(#:tests? #f                      ; no check target
-       #:phases
+       #:configure-flags (list (string-append "--bindir=" %output "/bin"))))
-       (modify-phases %standard-phases
+    (native-inputs (list autoconf automake))
-         (add-before 'build 'fix-infinite-loop-on-sighup
-           ;; XXX Release 4.2.6 has a major bug where sending the process a
-           ;; SIGHUP when closing the terminal causes it to infinite loop
-           ;; waiting for input: https://github.com/angband/angband/issues/6558
-           ;; Reevaluate for future versions.
-           (lambda _
-             (substitute* "src/ui-signals.c"
-               (("(SIGHUP, )SIG_IGN" _ first)
-                (string-append first "handle_signal_abort")))))
-         (add-before 'check 'skip-failing-tests
-           (lambda _
-             (let ((to-skip '(;; some of these may be fixable, but most try to
-                              ;; create a directory in the user's home directory.
-                              ;; Rather than reading environment variables, they
-                              ;; lookup the username using getpwnam(3) and manually
-                              ;; construct the string.
-                              ;; Generic "Suite died":
-                              "game/basic"
-                              "game/mage"
-                              ;; "Cannot create '//.angband/Angband'":
-                              "effects/chain"
-                              "effects/destruction"
-                              "effects/earthquake"
-                              "object/info"
-                              "object/slays"
-                              "player/calc-inventory"
-                              "player/combine-pack"
-                              "player/digging"
-                              "player/inven-carry-num"
-                              "player/inven-wield"
-                              "player/timed"
-                              ;; This file likes to read /etc/passwd
-                              "z-file/path-normalize")))
-               (substitute* "src/tests/Makefile"
-                 (("include \\$\\(SUITES\\)" all)
-                  (string-append all "\nTESTPROGS := $(filter-out "
-                                 (string-join to-skip " ")
-                                 ", $(TESTPROGS))")))))))))
-    (native-inputs (list autoconf
-                         automake
-                         perl)) ;for tests
     (inputs (list ncurses))
     (home-page "https://rephial.org/")
     (synopsis "Dungeon exploration roguelike")
@@ -4277,11 +4233,11 @@ interface or via an external visual interface such as GNU XBoard.")
                (("TestIOTouchDragAnywhere (test_integration)" all _) _))))
          (add-before 'bootstrap 'autoreconf
            (lambda _
-             ;; automake is out of date in the source
+	     ;; automake is out of date in the source
-             ;; autoreconf updates the automake scripts
+	     ;; autoreconf updates the automake scripts
-             (invoke "autoreconf")
+	     (invoke "autoreconf")
-             ;; Build fails when autom4te.cache exists.
+	     ;; Build fails when autom4te.cache exists.
-             (delete-file-recursively "autom4te.cache")
+	     (delete-file-recursively "autom4te.cache")
              #t))
          (add-after 'install 'delete-freedinkedit-desktop
            (lambda* (#:key outputs #:allow-other-keys)
@@ -4611,105 +4567,6 @@ for common mesh file formats, and collision detection.")
     (home-page "https://irrlicht.sourceforge.io/")
     (license license:zlib)))
 
-(define-public pegasus-frontend
-  (let ((commit "c3462e68bf3a178420b44f356998255f8d82a113")
-        (revision "weekly_2024w38"))
-    (package
-      (name "pegasus-frontend")
-      (version (git-version "0.0" revision commit))
-      (source
-       (origin
-         (method git-fetch)
-         (uri (git-reference
-               (url "https://github.com/mmatyas/pegasus-frontend")
-               (commit commit)))
-         (sha256
-          (base32 "1p350nlbif33mw5cbqxwli5yf47dxpransxlj2wp8xvh4w1rb3jx"))
-         (file-name (git-file-name name version))))
-      (build-system qt-build-system)
-      (arguments
-       (list
-        #:qtbase qtbase-5
-        #:make-flags
-        #~(list (string-append "INSTALL_DESKTOPDIR="
-                               #$output "/share/applications")
-                (string-append "INSTALL_ICONDIR="
-                               #$output "/share/icons/hicolor"))
-        #:phases
-        #~(modify-phases %standard-phases
-            (add-after 'unpack 'copy-modules
-              (lambda* (#:key inputs #:allow-other-keys)
-                (copy-recursively #$(this-package-native-input
-                                     "SortFilterProxyModel")
-                                  "./thirdparty/SortFilterProxyModel")
-                (copy-recursively #$(this-package-native-input
-                                     "pegasus-theme-grid")
-                                  "./src/themes/pegasus-theme-grid")
-                (copy-recursively #$(this-package-native-input
-                                     "pegasus-frontend-translations") "./lang")))
-            (add-before 'check 'prepare-test-env
-              (lambda* (#:key tests? #:allow-other-keys)
-                (when tests?
-                  (setenv "QT_QPA_PLATFORM" "offscreen")
-                  (setenv "QT_QUICK_BACKEND" "software"))))
-            (add-after 'qt-wrap 'gst-wrap
-              (lambda* (#:key inputs #:allow-other-keys)
-                (wrap-program (string-append #$output "/bin/pegasus-fe")
-                  `("GST_PLUGIN_PATH" suffix
-                    ,(search-path-as-list '("lib/gstreamer-1.0")
-                                          (map cdr inputs)))))))))
-      (inputs (list sdl2
-                    bash-minimal
-                    qtbase-5
-                    qtsvg-5
-                    qtdeclarative-5
-                    qtgraphicaleffects
-                    qtmultimedia-5
-                    qtgamepad-5
-                    gst-plugins-base
-                    gst-plugins-bad
-                    gst-plugins-good))
-      (native-inputs (list qttools-5
-                           (origin
-                             (method git-fetch)
-                             (uri (git-reference
-                                   (url
-                                    "https://github.com/mmatyas/pegasus-frontend-translations")
-                                   (commit
-                                    "46c7cecec745bdd4c61bfc7ecb967156ad208642")))
-                             (file-name "pegasus-frontend-translations")
-                             (sha256 (base32
-                                      "0rvlx199wdrjxr8pgibga556zf4njq4w2n31fdirqgb631rgyqxd")))
-                           (origin
-                             (method git-fetch)
-                             (uri (git-reference
-                                   (url
-                                    "https://github.com/mmatyas/pegasus-theme-grid")
-                                   (commit
-                                    "5951db6f2a4fe0db6a4fd6f00da1f280cadfa536")))
-                             (file-name "pegasus-theme-grid")
-                             (sha256 (base32
-                                      "1nfnq6lppdm9ni6jk48l1i7hk90m8w2p13swl5nr4zwczln8dbz1")))
-                           (origin
-                             (method git-fetch)
-                             (uri (git-reference
-                                   (url
-                                    "https://github.com/mmatyas/SortFilterProxyModel")
-                                   (commit
-                                    "2061f8136ba372fd06c1928a610258b7d88cb144")))
-                             (file-name "SortFilterProxyModel")
-                             (sha256 (base32
-                                      "16va8fcf7v6kfm8r9zym0516qrk4vlsy5wmpd3r3002wpz8q39h2")))))
-      (synopsis
-       "Graphical frontend for launching and managing game collection")
-      (description
-       "Pegasus is a graphical frontend for browsing your game library and
-  launching all kinds of games from the same place. It's focusing on
-  customizability, cross platform support (including embedded)
-  and high performance.")
-      (home-page "https://pegasus-frontend.org")
-      (license license:gpl3+))))
-
 (define-public mars
   ;; No official release since 2013: use the latest commit.
   (let ((commit   "84664cda094efe6e49d9b1550e4f4f98c33eefa2")
@@ -5048,7 +4905,7 @@ Protocol).")
 (define-public extremetuxracer
   (package
     (name "extremetuxracer")
-    (version "0.8.4")
+    (version "0.8.2")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -5056,7 +4913,7 @@ Protocol).")
                     version "/etr-" version ".tar.xz"))
               (sha256
                (base32
-                "1rbk8zqfzzk90znf3f5lqqa12j0n6pm2qgwzabzmlnkm1k68acps"))))
+                "0knd22lzhzqih1w92y6m7yxha376c6ydl22wy4xm6jg2x5jlk1qw"))))
     (build-system gnu-build-system)
     (native-inputs
      (list pkg-config))
@@ -5521,7 +5378,7 @@ falling, themeable graphics and sounds, and replays.")
     (name "wesnoth")
     ;; Even-numbered minor versions indicate stable versions:
     ;; https://wiki.wesnoth.org/ReleasingWesnoth#Version_numbering
-    (version "1.18.7")
+    (version "1.18.6")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -5530,7 +5387,7 @@ falling, themeable graphics and sounds, and replays.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "0hdrp4xm9d8kj8id2g5q0wwdwykx4a0f1cs8a7fghmv0czryfv7f"))))
+                "0cdlczxczqgzdaqwydb9gfgi7d9jc39li72p2rb5nk1rlgfff79s"))))
     (build-system cmake-build-system)
     (arguments
      (list #:tests? #f                  ;no test target
@@ -6749,7 +6606,7 @@ in-window at 640x480 resolution or fullscreen.")
 (define-public warzone2100
   (package
     (name "warzone2100")
-    (version "4.6.3")
+    (version "4.6.1")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://sourceforge/warzone2100/releases/"
@@ -6765,7 +6622,7 @@ in-window at 640x480 resolution or fullscreen.")
                                  "inih" "re2" "utf8proc" "utfcpp")))))
               (sha256
                 (base32
-                  "0fmiy0pm56yy69c0nhynjdiaslwlfg8cdvfl5s78g5pzdi1y47s3"))))
+                  "02x5ihkpfkpjxwvh00d8yqzd796af7d684nk96hzhhq28qw5bb16"))))
     (build-system cmake-build-system)
     (arguments (list #:configure-flags #~'("-GNinja"
                                            "-DWZ_DISTRIBUTOR=Guix"
@@ -6802,7 +6659,7 @@ in-window at 640x480 resolution or fullscreen.")
                   opusfile
                   physfs
                   re2
-                  sdl3
+                  sdl2
                   sqlite
                   utf8proc
                   utfcpp
@@ -8291,7 +8148,7 @@ fish.  The whole game is accompanied by quiet, comforting music.")
 (define-public crawl
   (package
     (name "crawl")
-    (version "0.34.1")
+    (version "0.34.0")
     (source
      (origin
        (method git-fetch)
@@ -8300,7 +8157,7 @@ fish.  The whole game is accompanied by quiet, comforting music.")
              (commit version)))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "09x4n4w3rw8sldwprb03yg1igwh4m09iw00g2iq30466jryys6bv"))
+        (base32 "16fsvrzcndrplw8zcn6nh8459x8zl5xdnf9r9hzh4ll2a4w9dkcr"))
        (patches (search-patches "crawl-upgrade-saves.patch"))))
     (build-system gnu-build-system)
     (inputs
@@ -9243,7 +9100,7 @@ elements to achieve a simple goal in the most complex way possible.")
 (define-public the-powder-toy
   (package
     (name "the-powder-toy")
-    (version "99.5.394")
+    (version "99.3.384")
     (source
      (origin
        (method git-fetch)
@@ -9252,7 +9109,7 @@ elements to achieve a simple goal in the most complex way possible.")
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "0wd0sg3lpl9xafyj76syvpdjh574cxjmxaf9kssfjjxs20y3hjn8"))
+        (base32 "0l067j0bbzvr0i2prxrgb0af4xdpl648x741jgnyp4bjzdbm61x7"))
        (snippet
         #~(begin (use-modules (guix build utils))
                  (substitute* "meson.build"
@@ -10243,7 +10100,7 @@ your score gets higher, you level up and the blocks fall faster.")
                                      "-DES_USE_SYSTEM_LIBRARIES=1")
            #:make-flags #~(list (string-append "PREFIX=" #$output))
            #:build-type "Release"
-           #:tests? (not (target-x86-32?))
+	   #:tests? (not (target-x86-32?))
            #:phases
            #~(modify-phases %standard-phases
                (add-after 'unpack 'fix-paths
@@ -11227,7 +11084,7 @@ levels to unlock.")
 (define-public simgear
   (package
     (name "simgear")
-    (version "2024.1.5")
+    (version "2024.1.4")
     (source
      (origin
        (method git-fetch)
@@ -11239,7 +11096,7 @@ levels to unlock.")
               (commit version)))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "1ygdc8xkrj7qzm9zklibb1v5w3jp718707zmiwl8fn63sxanbqsq"))
+        (base32 "1k855yxq06gv42f83c3k9hrsz05xxj6vi1c60227zm0dx3jkb4jq"))
        (modules '((guix build utils)))
        (snippet
         '(begin
@@ -11291,7 +11148,7 @@ and also provides the base for the FlightGear Flight Simulator.")
               (commit version)))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "0hpfvacnba2kcyjwm01lkrqkz0gccvljjil8b0ai42l38hxn5r5h"))
+        (base32 "0xlpry1g5xci4qmj37rjk4sdhg9zada0vw6a047gsm7cq5p7pkxk"))
        (modules '((guix build utils)))
        (snippet
         '(begin
@@ -11375,12 +11232,12 @@ and also provides the base for the FlightGear Flight Simulator.")
        ("flightgear-data"
         ,(origin
            (method url-fetch)
-           (uri (string-append "https://mirrors.ibiblio.org/flightgear/ftp/release-"
+           (uri (string-append "mirror://sourceforge/flightgear/release-"
                                (version-major+minor version) "/"
                                "FlightGear-" version "-data.txz"))
            (sha256
             (base32
-             "0d81yz9jqmg2jzw5rm769pl1j18pvh2mjkx61l13kw76ja8p6159"))))))
+             "0pgwxpm5cdm0y6klrmpqspmhmqsfxshz4jljw2kd4wy18fqzd1s6"))))))
     (home-page "https://www.flightgear.org/")
     (synopsis "Flight simulator")
     (description "The goal of the FlightGear project is to create a
@@ -11455,33 +11312,46 @@ to remap axis and buttons and a way to calibrate joysticks.")
 (define-public jumpnbump
   (package
     (name "jumpnbump")
-    (version "1.70")
+    (version "1.61")
     (source (origin
               (method git-fetch)
               (uri (git-reference
-                     (url "https://gitlab.com/LibreGames/jumpnbump.git")
+                    (url "https://gitlab.com/LibreGames/jumpnbump.git")
-                     (commit version)))
+                    (commit version)))
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "1irpssijxrfrjm023v642dl3aw4ldlv95fh073jlpdpl1mwqz71a"))))
+                "12lwl5sl5n009nb83r8l4lakb9286csqdf1ynpmwwydy17giqsdp"))))
     (build-system gnu-build-system)
     (arguments
-     (list
+     `(#:make-flags
-      #:make-flags
+       (list "CC=gcc"
-      #~(list (string-append "CC=" #$(cc-for-target))
+             (string-append "PREFIX=" (assoc-ref %outputs "out")))
-              (string-append "PREFIX=" #$output)
+       #:tests? #f                      ;no test
-              "SYSINSTALL=1")
+       #:phases
-      #:tests? #f                       ;no test
+       (modify-phases %standard-phases
-      #:phases
+         ;; There is no configure script
-      #~(modify-phases %standard-phases
+         (replace 'configure
-          (delete 'configure))))        ;no configure script
+           (lambda _
+             (substitute* "Makefile"
+               (("-funroll-loops")
+                "-funroll-loops -fcommon")
+               (("SDL_CFLAGS =")
+                "SDL_CFLAGS = -fcommon"))))
+         (add-after 'unpack 'fix-sdl-path
+           ;; XXX: For some reason, `sdl2-config' reports stand-alone SDL
+           ;; directory, not SDL-union provided as an input to the package.
+           ;; We force the latter with "--prefix=" option.
+           (lambda* (#:key inputs #:allow-other-keys)
+             (substitute* "Makefile"
+               (("sdl2-config" command)
+                (string-append command " --prefix=" (assoc-ref inputs "sdl")))))))))
     (inputs
-     (list bzip2
+     `(("bzip2" ,bzip2)
-           (sdl-union (list sdl2 sdl2-mixer sdl2-net))
+       ("sdl" ,(sdl-union (list sdl2 sdl2-mixer sdl2-net)))
-           zlib))
+       ("zlib" ,zlib)))
     (native-inputs
-     (list gettext-minimal))            ;for msgfmt
+     `(("gettext" ,gettext-minimal)))   ;for msgfmt
     (home-page "https://gitlab.com/LibreGames/jumpnbump")
     (synopsis "Multiplayer platform game with bunnies")
     (description "You, as a bunny, have to jump on your opponents to make them
@@ -11617,7 +11487,7 @@ player adaptability for character progression.")
 (define-public li-ri
   (package
     (name "li-ri")
-    (version "3.1.6")
+    (version "3.1.5")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -11626,7 +11496,7 @@ player adaptability for character progression.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "09r6l0sbxp3q750kpbrx513yrafmg7a2769j4wgx812lsk92n3hg"))))
+                "1fd5hl9qhgvyix51la8sl34jzk4mcin8sai05gidy2r2grb1dy4s"))))
     (build-system cmake-build-system)
     (arguments
      (list #:tests? #false              ;no tests
@@ -12284,7 +12154,7 @@ for using any UCI engine and also to connect UCI engines to Lichess and IRC.")
         (base32 "1kkcnpkzgybm7rqg7nafd7sqd5m4alns6l4j5zcf3p41jdc9s3iv"))))
     (build-system glib-or-gtk-build-system)
     (inputs (list automake autoconf pkg-config intltool
-                  gettext-minimal libtool glib gtk+-2 boost))
+		  gettext-minimal libtool glib gtk+-2 boost))
     (arguments (list #:tests? #f))  ; No tests in source.
     (home-page "http://nine-mens-morris.net/downloads.html")
     (synopsis "Implementation of the board game Nine Men's Morris")
@@ -13508,8 +13378,8 @@ rules to solve permissions issues.")
 
 (define-public steam-devices-udev-rules
   ;; Last release from 2019-04-10
-  (let ((commit "7dde9ecb3c386363ecd9bd0a3b77e4756d200704")
+  (let ((commit "13443480a64fe8f10676606bd57da6de89f8ccb1")
-        (revision "2"))
+        (revision "1"))
     (package
       (name "steam-devices-udev-rules")
       (version (git-version "1.0.0.61" revision commit))
@@ -13521,7 +13391,7 @@ rules to solve permissions issues.")
                 (file-name (git-file-name name version))
                 (sha256
                  (base32
-                  "0w0xkgi9fpvdbpl57f8fy2nwy2icm6iag39b8ifpkijlxgclx1p3"))))
+                  "0i086gmnk93q76sw1laa9br6b7zj2r6nrrw7d64y4q9wcrlxw2bi"))))
       (build-system copy-build-system)
       (arguments
        '(#:install-plan '(("./" "lib/udev/rules.d"

gnu/packages/geo.scm

@@ -55,6 +55,7 @@
   #:use-module (guix build-system go)
   #:use-module (guix build-system meson)
   #:use-module (guix build-system pyproject)
+  #:use-module (guix build-system python)
   #:use-module (guix build-system qt)
   #:use-module (guix build-system r)
   #:use-module (guix build-system zig)
@@ -297,7 +298,7 @@ than 600 operators available.")
 (define-public h3
   (package
     (name "h3")
-    (version "4.4.1")
+    (version "4.1.0")
     (source
      (origin
        (method git-fetch)
@@ -306,7 +307,7 @@ than 600 operators available.")
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "1ijnbr4a54ph7bkn8waqwgnxmxlylv9yly9mwjdj69lkmdfjgaml"))))
+        (base32 "0x764xzna8ka6yhgv2y4hb158a61y3g9a6835qckqp7wfkpqvb7f"))))
     (build-system cmake-build-system)
     (arguments
      (list #:configure-flags #~(list "-DBUILD_SHARED_LIBS=ON")))
@@ -318,25 +319,48 @@ combining the benefits of a hexagonal grid with S2's hierarchical
 subdivisions.")
     (license license:asl2.0)))
 
-(define-public python-h3
+;; For python-timezonefinder, remove it when it starts supporting newer
+;; version.
+(define-public h3-3
   (package
-    (name "python-h3")
+    (inherit h3)
-    (version "4.4.2")
+    (name "h3")
+    (version "3.7.2")
     (source
      (origin
        (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/uber/h3")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "0bvsljfxmjvl23v9gxykc4aynjzh5xfy3wg02bxad7cknr1amx9j"))))))
+
+(define-public python-h3
+  (package
+    (name "python-h3")
+    (version "4.0.0b2")
+    (source
+     (origin
+       (method git-fetch) ; no tests data in PyPi package
        (uri (git-reference
              (url "https://github.com/uber/h3-py")
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "02gry51hn8x2bl80y1ipcyrg0ghcif4vjch26qil215wdzz1yrzv"))
+        (base32 "1k1n256hhlh05gjcj64pqh08zlaz6962jkb6nk1aazsgg8p41zs0"))
        (modules '((guix build utils)))
        ;; Remove bundled H3 lib.
        (snippet #~(begin (delete-file-recursively "src/h3lib")))))
     (build-system pyproject-build-system)
     (arguments
      (list
+      ;; FIXME: Check why these tests are failing.
+      ;; test_versions - assert (4, 1) == (4, 0)
+      ;; test_resolution - h3._cy.error_system.H3Failed
+      #:test-flags #~(list "-k" (string-append
+                                 "not test_versions"
+                                 " and not test_resolution"))
       #:phases
       #~(modify-phases %standard-phases
           ;; Use packaged in Guix h3 source.
@@ -357,7 +381,10 @@ subdivisions.")
            python-cython
            python-numpy
            python-pytest
-           python-scikit-build-core))
+           python-scikit-build
+           python-setuptools
+           python-setuptools-scm
+           python-wheel))
     (inputs (list h3))
     (home-page "https://uber.github.io/h3-py")
     (synopsis "Python bindings for H3")
@@ -365,6 +392,26 @@ subdivisions.")
 hierarchical hexagonal geospatial indexing system")
     (license license:asl2.0)))
 
+;; For python-timezonefinder, remove it when it starts supporting newer
+;; version.
+(define-public python-h3-3
+  (package
+    (inherit python-h3)
+    (name "python-h3")
+    (version "3.7.6")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/uber/h3-py")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "16gxa1sivghxw179rik87r918mjasars2qkzidlwq83qfa4axn20"))))
+    (inputs
+     (modify-inputs inputs
+       (replace "h3" h3-3)))))
+
 (define-public geos
   (package
     (name "geos")
@@ -1012,6 +1059,7 @@ for seismology.")
     (inputs (list gdal))
     (native-inputs (list python-cython
                          python-pytest
+                         python-pytest-cov
                          python-setuptools
                          python-tomli
                          python-versioneer
@@ -1111,7 +1159,7 @@ projections and coordinate transformations library.")
 (define-public python-fiona
   (package
     (name "python-fiona")
-    (version "1.10.1")
+    (version "1.9.6")
     (source
      (origin
        (method git-fetch)
@@ -1120,38 +1168,24 @@ projections and coordinate transformations library.")
               (commit version)))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "0xribbcy5wvrm5y3bq281dry86vhjcnphg9772yp9s3y30y7mlz4"))))
+        (base32 "08whhjrspp194qasjhr9kf70fl342ms47k78rwpcf5q6ikf0rfii"))))
     (build-system pyproject-build-system)
     (arguments
      (list
-      ;; tests: 757 passed, 161 skipped, 24 deselected, 1 xfailed, 6 xpassed
       #:test-flags
       #~(list "-m" "not network and not wheel"
-              #$@(map (lambda (test) (string-append "--deselect=tests/" test))
+              ;; FIXME: Find why the
-                      ;; UserWarning: The parameter --where is used more than
+              ;; test_no_append_driver_cannot_append[PCIDSK] test is failing.
-                      ;; once. Remove its duplicate as parameters should be
+              "-k" "not test_no_append_driver_cannot_append")
-                      ;; unique.
-                      (list "test_fio_cat.py::test_bbox_json_yes"
-                            "test_fio_cat.py::test_bbox_no"
-                            "test_fio_cat.py::test_bbox_where"
-                            "test_fio_cat.py::test_bbox_yes"
-                            "test_fio_cat.py::test_bbox_yes_two_files"
-                            "test_fio_cat.py::test_dst_crs_epsg3857"
-                            "test_fio_cat.py::test_multi_layer"
-                            "test_fio_cat.py::test_one"
-                            "test_fio_cat.py::test_two"
-                            "test_fio_cat.py::test_vfs"
-                            "test_fio_cat.py::test_where_no"
-                            "test_fio_cat.py::test_where_yes"
-                            "test_fio_cat.py::test_where_yes_two_files"
-                            ;; FileNotFoundError:
-                            ;; https://github.com/Toblerity/Fiona/files/\
-                            ;; 11151652/coutwildrnp.zip
-                            "test_pyopener.py::test_opener_fsspec_zip_http_fs")))
       #:phases
       #~(modify-phases %standard-phases
-          (add-before 'check 'remove-local-source
+          (add-before 'build 'set-configure-flags
             (lambda _
+              (setenv "CFLAGS" "-Wno-error=incompatible-pointer-types")))
+          (add-before 'check 'remove-local-fiona
+            (lambda _
+              ;; This would otherwise interfere with finding the installed
+              ;; fiona when running tests.
               (delete-file-recursively "fiona"))))))
     (inputs
      (list gdal))
@@ -1159,19 +1193,19 @@ projections and coordinate transformations library.")
      (list python-attrs
            python-certifi
            python-click
-           python-click-plugins
+           python-click-plugins-1
            python-cligj))
     (native-inputs
      (list gdal ; for gdal-config
            python-boto3
            python-cython
-           python-fsspec
            python-pytest
+           python-pytest-cov
            python-pytz
-           python-setuptools
+           python-setuptools))
-           python-shapely))
     (home-page "https://github.com/Toblerity/Fiona")
-    (synopsis "Fiona reads and writes spatial data files")
+    (synopsis
+     "Fiona reads and writes spatial data files")
     (description
      "Fiona is GDAL’s neat and nimble vector API for Python programmers. Fiona
 is designed to be simple and dependable.  It focuses on reading and writing
@@ -1431,6 +1465,7 @@ street bearings/orientations, and speed/travel time.")
            python-pyproj
            python-pyyaml
            python-pytest
+           python-pytest-cov
            python-pytest-httpserver
            python-pytz
            python-requests
@@ -1762,7 +1797,10 @@ utilities for data translation and processing.")
       ;; This test requires internet access.
       '(list "--deselect" "test_shapefile.py::test_reader_url")))
     (native-inputs
-     (list python-pytest python-setuptools python-wheel))
+     (list python-pytest
+           python-pytest-runner
+           python-setuptools
+           python-wheel))
     (home-page "https://github.com/GeospatialPython/pyshp")
     (synopsis "Read/write support for ESRI Shapefile format")
     (description
@@ -2898,7 +2936,7 @@ to the OSM opening hours specification.")
 (define-public josm
   (package
     (name "josm")
-    (version "19555")
+    (version "19539")
     (source (origin
               (method svn-fetch)
               (uri (svn-reference
@@ -2907,7 +2945,7 @@ to the OSM opening hours specification.")
                      (recursive? #f)))
               (sha256
                (base32
-                "0kpshdj8kf9ag7h1qqrh9jqc6c9iv8v369mk60a8g7cbzf0xpblw"))
+                "05kslpvdwl4fldjzl6m2kmqvbmjv5yvipfavg01l30ywhw2c7v7v"))
               (file-name (string-append name "-" version "-checkout"))
               (modules '((guix build utils)))
             (snippet
@@ -3492,9 +3530,10 @@ orienteering sport.")
        (list
         #:tests? #f                    ; No tests
         #:modules `((guix build gnu-build-system)
-                    ((guix build pyproject-build-system) #:prefix python:)
+                    ((guix build python-build-system) #:prefix python:)
                     (guix build utils))
-        #:imported-modules %pyproject-build-system-modules
+        #:imported-modules `(,@%default-gnu-imported-modules
+                             (guix build python-build-system))
         #:configure-flags
         #~(list "--with-blas"
                 "--with-bzlib"
@@ -3666,13 +3705,13 @@ growing set of geoscientific methods.")
     (build-system cmake-build-system)
     (arguments
      (list
-      #:imported-modules (append %cmake-build-system-modules
-                                 %pyproject-build-system-modules
-                                 '((guix build qt-utils)))
       #:modules '((guix build cmake-build-system)
-                  ((guix build pyproject-build-system) #:prefix py:)
+                  ((guix build python-build-system) #:prefix python:)
                   (guix build qt-utils)
                   (guix build utils))
+      #:imported-modules `(,@%cmake-build-system-modules
+                           (guix build python-build-system)
+                           (guix build qt-utils))
       #:configure-flags
       #~(list "-DWITH_QTWEBKIT=NO")
       #:phases
@@ -3833,10 +3872,11 @@ growing set of geoscientific methods.")
             ;; Configure correct path to PyQt5 SIP directory
             (add-after 'unpack 'configure-pyqt5-sip-path
               (lambda* (#:key inputs #:allow-other-keys)
-                (let* ((pyqt (assoc-ref inputs "python-pyqt+qscintilla"))
+                (let ((sip-dir (string-append
-                       (sip-dir (string-append
+                                (assoc-ref inputs "python-pyqt+qscintilla")
-                                 (py:site-packages inputs `(("out" . ,pyqt)))
+                                "/lib/python"
-                                 "/PyQt5/bindings")))
+                                (python:python-version (assoc-ref inputs "python"))
+                                "/site-packages/PyQt5/bindings")))
                   (substitute* "cmake/FindPyQt5.py"
                     (("sip_dir = cfg.default_sip_dir")
                      (string-append "sip_dir = \"" sip-dir "\"")))
@@ -3866,7 +3906,7 @@ SET\\(PYQT5_SIP_DIR \"\\$\\{Python_SITEARCH\\}/PyQt5/bindings\"\\)")
                               "-E" (string-join ignored-tests "|")))
                     (format #t "test suite not run~%"))))
             (add-after 'install 'wrap-python
-              (assoc-ref py:%standard-phases 'wrap))
+              (assoc-ref python:%standard-phases 'wrap))
             (add-after 'wrap-python 'wrap-qt
               (lambda* (#:key inputs #:allow-other-keys)
                 (wrap-qt-program "qgis" #:output #$output #:inputs inputs)))

gnu/packages/gimp.scm

@@ -398,8 +398,7 @@ that is extensible via a plugin system.")
                         ;; environment, as it could cause Gimp to crash (see
                         ;; bug#77921).
                         `("GI_TYPELIB_PATH" prefix
-                          (,(getenv "GI_TYPELIB_PATH")
+                          (,(getenv "GI_TYPELIB_PATH")))
-                           ,(string-append #$output "/lib/girepository-1.0")))
                         `("GUIX_PYTHONPATH" prefix
                           (,(getenv "GUIX_PYTHONPATH")))
                         `("GDK_PIXBUF_MODULE_FILE" =
@@ -476,31 +475,17 @@ inverse fourier transform.")
   (package
     (name "libmypaint")
     (version "1.6.1")
-    (source
+    (source (origin
-     (origin
+              (method url-fetch)
-       (method git-fetch)
+              (uri (string-append "https://github.com/mypaint/libmypaint/"
-       (uri (git-reference
+                                  "releases/download/v" version "/libmypaint-"
-              (url "https://github.com/mypaint/libmypaint")
+                                  version ".tar.xz"))
-              (commit (string-append "v" version))))
+              (sha256
-       (file-name (git-file-name name version))
+               (base32
-       (sha256
+                "0priwpmc7dizccqvn21ig6d649bprl3xl1hmjj7nddznjgr585vl"))))
-        (base32 "1ppgpmnhph9h8ayx9776f79a0bxbdszfw9c6bw7c3ffy2yk40178"))))
     (build-system gnu-build-system)
-    (arguments
-     (list
-      #:phases
-      #~(modify-phases %standard-phases
-          (add-before 'bootstrap 'overwrite-automake-and-aclocal-versions
-            (lambda _
-              (setenv "AUTOMAKE" "automake")
-              (setenv "ACLOCAL" "aclocal"))))))
     (native-inputs
-     (list autoconf
+     (list intltool pkg-config))
-           automake
-           intltool
-           libtool
-           pkg-config
-           python))
     ;; As needed by 'libmypaint.pc'.
     (propagated-inputs
      (list json-c gobject-introspection))
@@ -512,26 +497,6 @@ brushstrokes which is used by MyPaint and GIMP.")
     (home-page "http://mypaint.org")
     (license license:isc)))
 
-;; To update mypaint, remove when a fresh version is released.
-(define-public libmypaint-next
-  (package
-    (inherit libmypaint)
-    (name "libmypaint")
-    (properties '((commit . "551dfb9ca5d2b82f2361a5a8a9e7f386f35fd320")
-                  (revision . "0")))
-    (version (git-version "1.6.1"
-                          (assoc-ref properties 'revision)
-                          (assoc-ref properties 'commit)))
-    (source
-     (origin
-       (method git-fetch)
-       (uri (git-reference
-              (url "https://github.com/mypaint/libmypaint")
-              (commit (assoc-ref properties 'commit))))
-       (file-name (git-file-name name version))
-       (sha256
-        (base32 "0pl8cma6gfkrqx364fs1xw7f491f7y6pzxqjq1cdqlrf9r8gg0sk"))))))
-
 (define-public mypaint-brushes
   (package
     (name "mypaint-brushes")

gnu/packages/gkrellm.scm

@@ -19,12 +19,10 @@
 ;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
 
 (define-module (gnu packages gkrellm)
-  #:use-module (guix build-system gnu)
-  #:use-module (guix download)
-  #:use-module (guix gexp)
   #:use-module ((guix licenses) #:prefix license:)
   #:use-module (guix packages)
-  #:use-module (guix utils)
+  #:use-module (guix download)
+  #:use-module (guix build-system gnu)
   #:use-module (gnu packages gettext)
   #:use-module (gnu packages gtk)
   #:use-module (gnu packages pkg-config)
@@ -33,27 +31,32 @@
 (define-public gkrellm
   (package
     (name "gkrellm")
-    (version "2.5.1")
+    (version "2.3.11")
     (source
      (origin
-       (method url-fetch)
+      (method url-fetch)
-       (uri (string-append "https://gkrellm.srcbox.net/releases/gkrellm-"
+      (uri (string-append "http://gkrellm.srcbox.net/releases/gkrellm-"
-                           version ".tar.bz2"))
+                          version ".tar.bz2"))
-       (sha256
+      (sha256
-        (base32 "0qvy2xmwmfy5f0g09yn9lr262shnx82ba04r5il2wj4qscg3r7h8"))))
+       (base32 "01lccz4fga40isv09j8rjgr0qy10rff9vj042n6gi6gdv4z69q0y"))))
     (build-system gnu-build-system)
-    (inputs (list gtk+-2 libsm))
+    (inputs
-    (native-inputs (list gettext-minimal pkg-config))
+     `(("gettext" ,gettext-minimal)
+       ("gtk+" ,gtk+-2)
+       ("libice" ,libice)
+       ("libsm" ,libsm)))
+    (native-inputs
+     (list pkg-config))
     (arguments
-     (list
+     `(#:tests? #f                      ; there is no check target
-      #:tests? #f ;there is no check target
+       #:phases
-      #:phases
+       (modify-phases %standard-phases
-      #~(modify-phases %standard-phases
+         (delete 'configure))           ; no configure script
-          (delete 'configure)) ;no configure script
+       #:make-flags
-      #:make-flags
+       (let ((out (assoc-ref %outputs "out")))
-      #~(list (string-append "INSTALLROOT=" #$output)
+         (list (string-append "INSTALLROOT=" out)
-              (string-append "CC=" #$(cc-for-target)))))
+               "CC=gcc"))))
-    (home-page "https://gkrellm.srcbox.net/")
+    (home-page "http://gkrellm.srcbox.net/")
     (synopsis "System monitors")
     (description
      "GKrellM is a single process stack of system monitors which supports

gnu/packages/gl.scm

@@ -79,6 +79,7 @@
   #:use-module (guix build-system cargo)
   #:use-module (guix build-system cmake)
   #:use-module (guix build-system meson)
+  #:use-module (guix build-system python)
   #:use-module (guix build-system pyproject)
   #:use-module ((guix licenses) #:prefix license:)
   #:use-module (guix packages)
@@ -1419,8 +1420,8 @@ original glmark benchmark by Ben Smith.")
     (license license:bsd-2)))
 
 (define-public piglit
-  (let ((revision "2")
+  (let ((revision "1")
-        (commit "040ed91f234abb6a502d3a6910f1b0e54bd239a7"))
+        (commit "814046fe6942eac660ee4a6cc5fcc54011a49945"))
     (package
      (name "piglit")
      (version (git-version "0.0.0" revision commit))
@@ -1431,7 +1432,7 @@ original glmark benchmark by Ben Smith.")
                     (commit commit)))
               (file-name (git-file-name name version))
               (sha256
-               (base32 "1j5dmkym1mmz410xgwygimnjk2aswsqmcpjwz4s98pgmymh1yjvf"))))
+               (base32 "1bzaalcxskckfnwprw77sbbmfqi59by2j8imaq8ghnlzhlxv7mk7"))))
      (build-system cmake-build-system)
      (arguments
       (list #:configure-flags #~(list "-DPIGLIT_SSE2=OFF")
@@ -1450,21 +1451,16 @@ original glmark benchmark by Ben Smith.")
                                       "'")))))
                 (add-after 'install 'wrap
                   (lambda* (#:key outputs #:allow-other-keys)
-                    (wrap-script (string-append #$output "/bin/piglit")
+                    (wrap-script (string-append (assoc-ref outputs "out")
+                                                "/bin/piglit")
                       `("GUIX_PYTHONPATH" prefix
                         (,(getenv "GUIX_PYTHONPATH")))))))))
-     (inputs (list glslang
+     (inputs (list guile-3.0            ; for wrap-script
-                   guile-3.0            ; for wrap-script
                    libxkbcommon
-                   python
+                   python python-lxml python-mako python-numpy-1
-                   wayland-protocols
+                   glslang vulkan-headers vulkan-loader
-                   vulkan-headers
-                   vulkan-loader
                    waffle))
-     (native-inputs (list pkg-config
+     (native-inputs (list pkg-config))
-                          python-lxml
-                          python-mako
-                          python-numpy))
      (home-page "https://piglit.freedesktop.org/")
      (synopsis "Test OpenGL implementations")
      (description "Piglit is a collection of automated tests for OpenGL and