gnu: linux-libre: Update default version to 7.0.

* gnu/packages/linux.scm (linux-libre-version, linux-libre-gnu-revision, linux-libre-pristine-source, linux-libre-source, linux-libre, linux-libre-arm64-mnt-reform): Update to 7.0.
gnu: evince: Update to 48.4.
2026-07-11 10:54:07 +02:00 · 2026-05-27 12:30:54 -07:00 · 2026-05-27 20:27:45 +02:00 · 2026-05-27 20:25:43 +02:00 · 2026-05-27 20:04:12 +02:00 · 2026-05-27 19:42:06 +02:00
288 changed files with 22202 additions and 16886 deletions
@@ -341,6 +341,7 @@ 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
@@ -488,6 +488,7 @@ 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	\
@@ -120,6 +120,7 @@ running 'guix-daemon $extra_options'" >&2
    "@abs_top_builddir@/pre-inst-env"				\
 	"@abs_top_builddir@/guix-daemon"			\
        $extra_options						\
+        --allow-aslr                                            \
 	--substitute-urls="$GUIX_BINARY_SUBSTITUTE_URL" &

    daemon_pid=$!
@@ -618,6 +618,33 @@ enhance @code{scheme-mode} and Geiser.  @xref{Introduction,,,
 emacs-guix, Emacs-Guix Reference Manual}, to make sure you don't miss
 out!

+@unnumberedsubsubsec Submitting Pull Requests Following the AGit Workflow
+
+@cindex AGit workflow, for pull requests (Emacs).
+@url{https://codeberg.org/halvin/agitjo, Agitjo} is a helper to ease
+AGit workflow based patch submission (@pxref{Submitting Patches}).
+Install it with:
+
+@example
+guix install emacs-agitjo
+@end example
+
+Assuming your local checkout is on the branch containing the changes you
+would like to submit for inclusion in the @code{master} branch, use
+@command{M-x agitjo-push} then:
+
+@itemize
+@item
+Set options like the title @option{-t} and the session identifier
+@option{-s}.
+@item
+Invoke one of the push commands to execute a @command{git push} operation.
+@end itemize
+
+When creating a new pull request, a dedicated buffer will open for
+drafting a description. The force-push option @option{-f} is enabled to
+push changes to the existing pull request.
+
@unnumberedsubsubsec Taming Boilerplate with Templates

@cindex code snippets
@@ -152,6 +152,7 @@ Copyright @copyright{} 2026 David Elsing@*
 Copyright @copyright{} 2026 Nguyễn Gia Phong@*
 Copyright @copyright{} 2026 Yarl Baudig@*
 Copyright @copyright{} 2026 Joan Vilardaga Castro@*
+Copyright @copyright{} 2026 Nemin@*

 Permission is granted to copy, distribute and/or modify this document
 under the terms of the GNU Free Documentation License, Version 1.3 or
@@ -305,6 +306,7 @@ Package Management
 Substitutes

 * Official Substitute Servers::  One particular source of substitutes.
+* Volunteer Run Mirrors::        Additional, regional sources of substitutes.
 * Substitute Server Authorization::  How to enable or disable substitutes.
 * Getting Substitutes from Other Servers::  Substitute diversity.
 * Substitute Authentication::   How Guix verifies substitutes.
@@ -1779,6 +1781,21 @@ user namespaces is missing (@pxref{Build Environment Setup}).  Use at
 your own risk!
@end quotation

+@cindex ASLR (address space layout randomization), for builds
+@cindex address space layout randomization (ASLR), for builds
+@cindex Docker, running @command{guix-daemon}
+@cindex @command{guix-daemon}, running under Docker
+@item --allow-aslr
+Allow builds to start even if @acronym{ASLR, Address Space Layout
+Randomization} cannot be disabled on Linux systems.  This is normally
+done so as to increase reproducibility, but some environments, such as
+those affected by Docker's default seccomp policy, don't permit
+disabling ASLR.  Passing this option will allow builds to start with
+reduced reproducibility regardless.
+
+Note that passing this option doesn't ensure that ASLR is enabled, it
+only allows builds to start even when disabling it is blocked.
+
@item --isolate-host-loopback
 Prevent fixed-output chroot builds from accessing the host loopback.
 When this is used, fixed-output builds will have their own loopback
@@ -3936,6 +3953,7 @@ also result from derivation builds, can be available as substitutes.

@menu
 * Official Substitute Servers::  One particular source of substitutes.
+* Volunteer Run Mirrors::  Additional, regional sources of substitutes.
 * Substitute Server Authorization::  How to enable or disable substitutes.
 * Getting Substitutes from Other Servers::  Substitute diversity.
 * Substitute Authentication::   How Guix verifies substitutes.
@@ -3966,13 +3984,54 @@ could use the information gathered to determine, for instance, whether
 your system has unpatched security vulnerabilities.

 Substitutes from the official build farms are enabled by default when
-using Guix System (@pxref{GNU Distribution}).  However,
-they are disabled by default when using Guix on a foreign distribution,
-unless you have explicitly enabled them via one of the recommended
-installation steps (@pxref{Installation}).  The following paragraphs
-describe how to enable or disable substitutes for the official build
-farm; the same procedure can also be used to enable substitutes for any
-other substitute server.
+using Guix System (@pxref{GNU Distribution}).  However, they are
+disabled by default when using Guix on a foreign distribution, unless
+you have explicitly enabled them via one of the recommended installation
+steps (@pxref{Installation}).  Please @pxref{Substitute Server
+Authorization} on how to enable or disable substitutes for the official
+build farm; the same procedure can also be used to enable substitutes
+for any other substitute server.
+
+@node Volunteer Run Mirrors
+@subsection Volunteer Run Mirrors
+
+@cindex substitutes
+@cindex mirrors
+Beyond the two official substitute servers, there are additionally
+volunteer run mirrors.  These mirrors do not build their own
+substitutes, but rather copy them from the official build farm and
+distribute them to users.  Enabling a mirror may be beneficial in case
+the official servers are temporarily unavailable or provide inadequate
+bandwidth at the user's location.
+
+@quotation Note
+Mirrored substitutes are signed by the original builder, not the mirror.
+This means that mirror operators @strong{cannot} add or modify binaries,
+as long as you trust only the official substitute servers,
+@pxref{Substitute Server Authorization}.
+@end quotation
+
+List of volunteer run mirrors, grouped by location (with the build farm
+they mirror in parentheses):
+
+@table @asis
+@item Germany
+@itemize
+@item @code{https://hydra-guix-129.guix.gnu.org} (bordeaux.guix.gnu.org)
+@end itemize
+@item People's Republic of China
+@itemize
+@item @code{https://mirrors.sjtug.sjtu.edu.cn/guix} (ci.guix.gnu.org)
+@item @code{https://mirrors.sjtug.sjtu.edu.cn/guix-bordeaux} (bordeaux.guix.gnu.org)
+@end itemize
+@item Russia
+@itemize
+@item @code{https://mirror.yandex.ru/mirrors/guix/} (bordeaux.guix.gnu.org)
+@end itemize
+@end table
+
+To enable receiving substitutions from these mirrors, please @pxref{Getting
+Substitutes from Other Servers}.

@node Substitute Server Authorization
@subsection Substitute Server Authorization
@@ -36234,6 +36293,10 @@ Launch the app as this group (it must be an existing group).
 A list of sockets (as path strings) which gunicorn will be listening
 on.  This list must contain at least one socket.

+@item @code{control-socket} (default: #f) (type: string)
+If set, creates a gunicorn control-socket at the given path.  Note that,
+the control socket should refer to a path listed in @code{mappings}.
+
@item @code{socket-user} (default: @code{user}) (type: string)
 Owner of the directory containing the socket (must be an existing user).

@@ -38069,6 +38132,21 @@ This is the type of the dnsmasq service, whose value should be a
           (servers '("192.168.1.1"))))
@end lisp

+The following example shows a slightly more complex configuration that
+defines an authoritative DNS server on a given subdomain.
+@lisp
+(service dnsmasq-service-type
+         (dnsmasq-configuration
+           (listen-addresses '("10.1.1.1"))
+           (no-resolv? #t)
+           (no-hosts? #t)
+           (authoritative-servers '("vpn.example.com")) ;self
+           (authoritative-zones '("vpn.example.com"))
+           (host-records '("some-service.vpn.example.com,10.1.1.1"))))
+@end lisp
+
+For more examples, refer to @samp{man 8 dnsmasq.}
+
@code{dnsmasq-service-type} provides two actions:

@table @code
@@ -38158,12 +38236,33 @@ ie a subnet for which an interface exists on the server.
@item @code{listen-addresses} (default: @code{'()})
 Listen on the given IP addresses.

+@item @code{ipv4?} (default: @code{#t})
+Whether to include A records in answers.
+
+@item @code{ipv6?} (default: @code{#t})
+Whether to include AAAA records in answers.
+
@item @code{resolv-file} (default: @code{"/etc/resolv.conf"})
 The file to read the IP address of the upstream nameservers from.

@item @code{no-resolv?} (default: @code{#f})
 When true, don't read @var{resolv-file}.

+@item @code{authoritative-servers} (default: @code{'()})
+A list of strings corresponding to valid @option{--auth-server} values,
+such as a domain name.  This is useful to make @command{dnsmasq}
+authoritative for a given domain name or interface.
+
+@item @code{authoritative-zones} (default: @code{'()})
+A list of strings corresponding to valid @option{--auth-zone} values,
+such as a domain name.  This is useful to make @command{dnsmasq}
+authoritative for a given domain name.  Note that this must be used in
+conjunction with the @code{authoritative-servers} option.
+
+@item @code{host-records} (default: @code{'()})
+A list of strings corresponding to valid @option{--host-record} values,
+for example @code{'("some-service.example.com,10.1.1.1")}.
+
@item @code{forward-private-reverse-lookup?} (default: @code{#t})
 When false, all reverse lookups for private IP ranges are answered with
 "no such domain" rather than being forwarded upstream.
@@ -38172,6 +38271,12 @@ When false, all reverse lookups for private IP ranges are answered with
 When true, dnsmasq queries the servers in the same order as they appear
 in @var{servers}.

+@item @code{locals} (default: @code{'()})
+Specify domain name @emph{patterns} which should be treated as local,
+that is, for which there should be no delegation to upstream servers.
+Provided pattern values should be of the form
+@code{'("/vpn.example.com/")}.
+
@item @code{servers} (default: @code{'()})
 Specify IP address of upstream servers directly.

@@ -984,7 +984,8 @@ perl-build-system as well as the rakudo-build-system."
        #:description
        "Python, Python packages, the \"pypi\" importer, and the python-build-system."
        #:scope
-        (list "gnu/packages/django.scm"
+        (list (make-regexp* "^gnu/packages/aux-files/python/.*\\.py$")
+              "gnu/packages/django.scm"
              "gnu/packages/jupyter.scm"
              (make-regexp* "^gnu/packages/python(-.+|)\\.scm$")
              "gnu/packages/sphinx.scm"
@@ -1576,7 +1577,7 @@ the \"texlive\" importer."
 (define-member (person "Nguyễn Gia Phong"
                       "cnx@loang.net"
                       "cnx")
-  build-tools python qa-packages sysadmin vcs)
+  build-tools lua qa-packages sysadmin vcs)

 (define-member (person "Lilah Tascheter"
                       "lilah@lunabee.space"
@@ -173,7 +173,16 @@ SYSTEM."
 (define (core-packages system)
  "Return the 'core' package set suitable for SYSTEM, which might be a system
 type or a GNU triplet."
-  (cond ((target-linux? system) (append %core-packages %linux-packages))
+  (cond ((target-linux? system)
+         (append %core-packages
+                 %linux-packages
+                 (cond ((target-arm32? system)
+                        (list linux-libre-arm-generic))
+                       ((target-aarch64? system)
+                        (list linux-libre-arm64-generic))
+                       ((target-riscv64? system)
+                        (list linux-libre-riscv64-generic))
+                       (else '()))))
        ((target-hurd? system) (append %core-packages %hurd-packages))
        ((target-mingw? system) %core-packages-for-mingw)
        (else '())))
@@ -125,16 +125,18 @@ entry will be expired even if it has been accessed recently.")
                 (requirement shepherd-requirement)
                 (modules '((shepherd support)))  ;for '%user-runtime-dir'
                 (start
-                  #~(make-systemd-constructor
-                     (list #$(file-append gnupg "/bin/gpg-agent")
-                           "--supervised" "--enable-ssh-support")
-                     (list #$(endpoint "ssh" "S.gpg-agent.ssh")
-                           #$(endpoint "browser" "S.gpg-agent.browser")
-                           #$(endpoint "extra" "S.gpg-agent.extra")
-                           ;; #$(endpoint "scdaemon" "S.scdaemon")
-                           #$(endpoint "std" "S.gpg-agent"))
-                     ;; Inherit graphical session environment.
-                     #:environment-variables (environ)))
+                  #~(lambda args
+                      ((make-systemd-constructor
+                        (list #$(file-append gnupg "/bin/gpg-agent")
+                              "--supervised" "--enable-ssh-support")
+                        (list #$(endpoint "ssh" "S.gpg-agent.ssh")
+                              #$(endpoint "browser" "S.gpg-agent.browser")
+                              #$(endpoint "extra" "S.gpg-agent.extra")
+                              ;; #$(endpoint "scdaemon" "S.scdaemon")
+                              #$(endpoint "std" "S.gpg-agent"))
+                        ;; Inherit graphical session environment.
+                        #:environment-variables (environ))
+                       args)))
                 (stop #~(make-systemd-destructor))
                 (documentation "Start 'gpg-agent', the GnuPG passphrase
 agent, with support for handling OpenSSH material."))))
@@ -76,6 +76,7 @@
 # Copyright © 2025 Nigko Yerden <nigko.yerden@gmail.com>
 # Copyright © 2025 Cayetano Santos <csantosb@inventati.org>
 # Copyright © 2025 bdunahu <bdunahu@operationnull.com>
+# Copyright © 2026 Simen Endsjø <contact@simendsjo.me>
 #
 # This file is part of GNU Guix.
 #
@@ -343,6 +344,7 @@ GNU_SYSTEM_MODULES =				\
  %D%/packages/golang-check.scm		\
  %D%/packages/golang-compression.scm		\
  %D%/packages/golang-crypto.scm	      	\
+  %D%/packages/golang-graphics.scm	\
  %D%/packages/golang-maths.scm		\
  %D%/packages/golang-vcs.scm	        	\
  %D%/packages/golang-web.scm	        	\
@@ -1004,6 +1006,7 @@ dist_patch_DATA =						\
  %D%/packages/patches/alure-dumb-2.patch			\
  %D%/packages/patches/amd-smi-newer-libdrm.patch		\
  %D%/packages/patches/amd-smi-python.patch			\
+  %D%/packages/patches/angband-remove-nonfree-tile-options.patch	\
  %D%/packages/patches/ibus-anthy-fix-tests.patch		\
  %D%/packages/patches/ibus-table-paths.patch			\
  %D%/packages/patches/antiword-CVE-2014-8123.patch			\
@@ -1020,6 +1023,7 @@ dist_patch_DATA =						\
  %D%/packages/patches/ath9k-htc-firmware-gcc.patch		\
  %D%/packages/patches/ath9k-htc-firmware-gcc-compat.patch	\
  %D%/packages/patches/atlas-gfortran-compat.patch		\
+  %D%/packages/patches/aubio-waflib-python312-compat.patch	\
  %D%/packages/patches/audacity-ffmpeg-fallback.patch		\
  %D%/packages/patches/audiofile-fix-datatypes-in-tests.patch	\
  %D%/packages/patches/audiofile-fix-sign-conversion.patch	\
@@ -1102,7 +1106,6 @@ dist_patch_DATA =						\
  %D%/packages/patches/cdparanoia-fpic.patch			\
  %D%/packages/patches/cdrkit-libre-cross-compile.patch	\
  %D%/packages/patches/cdrtools-3.01-mkisofs-isoinfo.patch 	\
-  %D%/packages/patches/ceph-fix-cmake.patch                     \
  %D%/packages/patches/cf-tool-add-languages.patch		\
  %D%/packages/patches/chmlib-inttypes.patch			\
  %D%/packages/patches/cl-ana-pr-49.patch			\
@@ -1135,11 +1138,8 @@ dist_patch_DATA =						\
  %D%/packages/patches/clog-fix-shared-build.patch		\
  %D%/packages/patches/clucene-gcc-14.patch			\
  %D%/packages/patches/clucene-pkgconfig.patch			\
-  %D%/packages/patches/coda-use-system-libs.patch		\
  %D%/packages/patches/codex-acp-0.11.1-disable-code-mode.patch \
  %D%/packages/patches/codex-acp-0.11.1-remove-patch-sections.patch \
-  %D%/packages/patches/codex-0.98.0-remove-patch-sections.patch    \
-  %D%/packages/patches/rust-codex-0.117.0-remove-patch-sections.patch    \
  %D%/packages/patches/cogl-fix-double-free.patch		\
  %D%/packages/patches/collada-dom-boost.patch			\
  %D%/packages/patches/collectd-5.11.0-noinstallvar.patch	\
@@ -1190,6 +1190,7 @@ 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				\
@@ -1508,6 +1509,7 @@ dist_patch_DATA =						\
  %D%/packages/patches/glibc-reinstate-prlimit64-fallback.patch	\
  %D%/packages/patches/glibc-supported-locales.patch     	\
  %D%/packages/patches/glibc-versioned-locpath.patch		\
+  %D%/packages/patches/glog-windows-h-nonwindows.patch		\
  %D%/packages/patches/glycin-sandbox-Adapt-bwrap-invocation.patch	\
  %D%/packages/patches/gmime-disable-tests.patch		\
  %D%/packages/patches/gmp-arm-asm-nothumb.patch		\
@@ -1583,7 +1585,9 @@ 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 \
@@ -1877,6 +1881,7 @@ dist_patch_DATA =						\
  %D%/packages/patches/lua-5.4-pkgconfig.patch			\
  %D%/packages/patches/lua-5.4-liblua-so.patch			\
  %D%/packages/patches/lua-5.4-search-paths.patch		\
+  %D%/packages/patches/lua-5.5-search-paths.patch		\
  %D%/packages/patches/lua-5.x-search-path-helpers.patch	\
  %D%/packages/patches/lua-lgi-fix-pango.patch			\
  %D%/packages/patches/lua-lgi-fix-ref.patch			\
@@ -2106,6 +2111,7 @@ dist_patch_DATA =						\
  %D%/packages/patches/python-3.11-fix-tests.patch		\
  %D%/packages/patches/python-3.12-fix-tests.patch		\
  %D%/packages/patches/python-anyio-unuse-exceptiongroup-in-test.patch	\
+  %D%/packages/patches/python-beangulp-click-8.2-compat.patch	\
  %D%/packages/patches/python-bed-reader-use-store-samples.patch	\
  %D%/packages/patches/python-chai-drop-python2.patch		\
  %D%/packages/patches/python-clarabel-blas.patch		\
@@ -2128,16 +2134,20 @@ dist_patch_DATA =						\
  %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	\
  %D%/packages/patches/python-sshtunnel-pep518.patch	\
  %D%/packages/patches/python-zeroc-ice-3.6.5-python-3.11-support.patch	\
+  %D%/packages/patches/python-zeroc-ice-3.6.5-python-3.12-support.patch	\
+  %D%/packages/patches/python-zipfile2-python-3.12-support.patch	\
  %D%/packages/patches/qcodeeditor-qt6.patch			\
  %D%/packages/patches/qtdeclarative-5-disable-qmlcache.patch	\
  %D%/packages/patches/qtdeclarative-disable-qmlcache.patch	\
  %D%/packages/patches/qtlocation-5.15.8-mapboxgl-gcc13.patch	\
  %D%/packages/patches/qtwebengine-revert-egl.patch		\
+  %D%/packages/patches/qtwebengine5-python312-six-compat.patch	\
  %D%/packages/patches/quodlibet-disable-bundled-packages.patch	\
  %D%/packages/patches/qxlsx-fix-include-directory.patch	\
  %D%/packages/patches/schiffbruch-fix-build-for-gcc-13.patch	\
@@ -2247,6 +2257,7 @@ dist_patch_DATA =						\
  %D%/packages/patches/python-piexif-fix-tests-with-pillow-7.2.patch	\
  %D%/packages/patches/python-pillow-CVE-2022-45199.patch	\
  %D%/packages/patches/python-libxml2-utf8.patch		\
+  %D%/packages/patches/python-lsp-server-python-3.13-compatibility.patch	\
  %D%/packages/patches/python-memcached-syntax-warnings.patch	\
  %D%/packages/patches/python-mslice-matplotlib-3.6-compatibility.patch	\
  %D%/packages/patches/python-packaging-test-arch.patch		\
@@ -2262,6 +2273,7 @@ dist_patch_DATA =						\
  %D%/packages/patches/python-pytorch-system-libraries.patch	\
  %D%/packages/patches/python-pytorch-without-kineto.patch	\
  %D%/packages/patches/python-robotframework-sshlibrary-rf5-compat.patch \
+  %D%/packages/patches/python-py-ubjson-recursion-test.patch	\
  %D%/packages/patches/python-vaex-core-fix-tsl-use.patch	\
  %D%/packages/patches/python-vega-datasets-remove-la-riots-code.patch	\
  %D%/packages/patches/python-versioneer-guix-support.patch	\
@@ -2406,13 +2418,8 @@ dist_patch_DATA =						\
  %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	\
-  %D%/packages/patches/rust-codex-0.98.0-windows-sandbox-protocol-version.patch	\
  %D%/packages/patches/rust-codex-0.117.0-core-remove-self-dep.patch	\
-  %D%/packages/patches/rust-codex-0.120.0-core-remove-self-dep.patch	\
-  %D%/packages/patches/rust-codex-0.120.0-connectors-cache-test-race.patch	\
  %D%/packages/patches/rust-codex-0.120.0-remove-libwebrtc.patch	\
  %D%/packages/patches/rust-codex-0.120.0-test-timeout.patch	\
  %D%/packages/patches/rust-codex-0.124.0-code-mode-stub-toolname.patch	\
@@ -2427,7 +2434,6 @@ dist_patch_DATA =						\
  %D%/packages/patches/sajson-build-with-gcc10.patch		\
  %D%/packages/patches/sane-look-for-plugins-in-SANE_BACKEND_LIB_PATH.patch	\
  %D%/packages/patches/sbc-fix-build-non-x86.patch		\
-  %D%/packages/patches/sbcl-fix-arm64-shared-lib.patch		\
  %D%/packages/patches/sbcl-aserve-add-HTML-5-elements.patch	\
  %D%/packages/patches/sbcl-aserve-fix-rfe12668.patch	\
  %D%/packages/patches/sbcl-burgled-batteries3-fix-signals.patch	\
@@ -2522,7 +2528,6 @@ 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		\
@@ -2538,6 +2543,7 @@ dist_patch_DATA =						\
  %D%/packages/patches/transcode-ffmpeg.patch	\
  %D%/packages/patches/trytond-add-guix_trytond_path.patch	\
  %D%/packages/patches/ttf2eot-cstddef.patch			\
+  %D%/packages/patches/tuir-python-3.12-support.patch	\
  %D%/packages/patches/tuxpaint-stamps-path.patch		\
  %D%/packages/patches/tvm_fix_cpptest_build.patch              \
  %D%/packages/patches/twinkle-bcg729.patch			\
@@ -51,6 +51,7 @@
  #:use-module (gnu packages libusb)
  #:use-module (gnu packages java)
  #:use-module (gnu packages python)
+  #:use-module (gnu packages python-build)
  #:use-module (gnu packages python-xyz)
  #:use-module (gnu packages tcl)
  #:use-module (gnu packages xml)
@@ -185,7 +186,9 @@ terminals.")
    (native-inputs
     (append
       (list clisp
-             python-cython-0 ;; See https://bugzilla.redhat.com/show_bug.cgi?id=2231865
+             ;; See: <https://bugzilla.redhat.com/show_bug.cgi?id=2231865>.
+             python-cython-0
+             python-setuptools  ;remove with next update
             doxygen
             gettext-minimal)
       ;; icedtea doesn't build reliably on all architectures.
@@ -37,7 +37,6 @@
  #: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
@@ -109,7 +109,6 @@
  #: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)
@@ -744,7 +743,7 @@ manager.")
 (define-public swineherd
  (package
    (name "swineherd")
-    (version "0.0.4")
+    (version "0.0.5")
    (source (origin
              (method git-fetch)
              (uri (git-reference
@@ -753,7 +752,7 @@ manager.")
              (file-name (git-file-name name version))
              (sha256
               (base32
-                "0iij1pl0y410k1dk1ifa56dxmjb1blv0y3k5rxy794gwg6w6c480"))))
+                "1w3fvkdmqvbzqfx3xindm8qgam54wja46isgwasaiqmmhnla7p52"))))
    (build-system gnu-build-system)
    (arguments
     '(#:configure-flags '("--localstatedir=/var")
@@ -767,7 +766,7 @@ manager.")
           guile-netlink
           guile-3.0
           guix
-           shepherd-0.10))
+           shepherd-1.0))
    (home-page "https://github.com/BIMSBbioinfo/swineherd")
    (synopsis "System container manager")
    (description
@@ -1085,7 +1084,7 @@ console.")
 (define-public btop
  (package
    (name "btop")
-    (version "1.4.6")
+    (version "1.4.7")
    (source (origin
              (method git-fetch)
              (uri (git-reference
@@ -1094,7 +1093,7 @@ console.")
              (file-name (git-file-name name version))
              (sha256
               (base32
-                "1nj58dbv3c0rj8fngldkyrmdmacmjnbg8ch1c07ik97kqnnzd3l7"))))
+                "0d3cr5l6gpcwhxgnrizny5b5kg6fys2hy9a58bc68w4n2hc040fy"))))
    (build-system gnu-build-system)
    (native-inputs (list lowdown))
    (arguments
@@ -3406,7 +3405,7 @@ provides the following commands:
     ;; variable in the tests/import/cpan.scm test.
     (list (search-path-specification
            (variable "GUIX_PYTHONPATH")
-            (files (list "lib/python3.11/site-packages")))))
+            (files (list "lib/python3.12/site-packages")))))
    (home-page "https://www.ansible.com/")
    (synopsis "Radically simple IT automation")
    (description "Ansible aims to be a radically simple IT automation system.
@@ -3424,7 +3423,7 @@ modules and plugins that extend Ansible.")
 (define-public debops
  (package
    (name "debops")
-    (version "3.2.5")
+    (version "3.3.0")
    (source
     (origin
       (method git-fetch)
@@ -3433,7 +3432,7 @@ modules and plugins that extend Ansible.")
             (commit (string-append "v" version))))
       (file-name (git-file-name name version))
       (sha256
-        (base32 "15wfhha2b315i15l40j3sylyvs3mdrfw5awzq4cix51l5jppx8z5"))
+        (base32 "0z6wck5kax5h2bjv1vw8pbd7fdcdhx87bj9fakh3h0rar9d2qksj"))
       (patches
        (search-patches "debops-setup-py-avoid-git.patch"))))
    (build-system pyproject-build-system)
@@ -3455,8 +3454,8 @@ modules and plugins that extend Ansible.")
           python-future
           python-gitpython
           python-jinja2
-           python-pyyaml
           python-pyxdg
+           python-pyyaml
           python-toml))
    (arguments
     (list
@@ -3471,7 +3470,7 @@ modules and plugins that extend Ansible.")
                         `("PATH" ":" prefix
                           ,(map dirname
                                 (map (cut search-input-file inputs <>)
-                                      (list "bin/ansible"
+                                      (list ;; "bin/ansible"    ;see above
                                            "bin/gpg"
                                            "bin/git"
                                            "bin/git-crypt"
@@ -3927,6 +3926,18 @@ 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)
@@ -4056,51 +4067,59 @@ plug-in architecture to allow monitoring other system metrics.")
    (license license:gpl2+)))

 (define-public thefuck
-  (package
-    (name "thefuck")
-    (version "3.32")
-    (source
-     (origin
-       (method git-fetch)
-       (uri (git-reference
-             (url "https://github.com/nvbn/thefuck")
-             (commit version)))
-       (file-name (git-file-name name version))
-       (sha256
-        (base32 "18ipa1bm6q1n5drbi8i65726hhqhl1g41390lfqrc11hkbvv443d"))
-       (patches (search-patches "thefuck-test-environ.patch"
-                                "thefuck-remove-broken-tests.patch"))))
-    (build-system pyproject-build-system)
-    (arguments
-     (list
-      #:phases
-      #~(modify-phases %standard-phases
-          (add-before 'check 'pre-check
-            (lambda _
-              ;; Tests look for installed package
-              ;; Some tests need write access to $HOME.
-              (setenv "HOME" "/tmp")
-              ;; Even with that, this function tries to mkdir /.config.
-              (substitute* "tests/test_utils.py"
-                (("settings\\.init\\(\\)") "")))))))
-    (native-inputs
-     (list go
-           python-mock
-           python-pytest-8
-           python-pytest-mock
-           python-setuptools
-           python-wheel))
-    (inputs
-     (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
+  ;; Latest release, 3.32, is not compatible with Python 3.12.
+  (let ((revision "0")
+        (commit "c7e7e1d884d3bb241ea6448f72a989434c2a35ec"))
+    (package
+      (name "thefuck")
+      (version (git-version "3.32" revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+                (url "https://github.com/nvbn/thefuck")
+                (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32 "1l3i2cpdf3vznpbzqw7b18l23xikqs7andx6yzqvm5415snaqg06"))
+         (patches (search-patches "thefuck-test-environ.patch"))))
+      (build-system pyproject-build-system)
+      (arguments
+       (list
+        #:test-flags
+        #~(list
+           "--deselect=tests/test_utils.py::TestGetValidHistoryWithoutCurrent"
+           "--ignore=tests/functional/conftest.py")
+        #:phases
+        #~(modify-phases %standard-phases
+            (add-before 'check 'pre-check
+              (lambda _
+                ;; ModuleNotFoundError: No module named 'pytest_docker_pexpect'
+                (delete-file "tests/functional/conftest.py")
+                ;; Tests look for installed package
+                ;; Some tests need write access to $HOME.
+                (setenv "HOME" "/tmp")
+                ;; Even with that, this function tries to mkdir /.config.
+                (substitute* "tests/test_utils.py"
+                  (("settings\\.init\\(\\)") "")))))))
+      (native-inputs
+       (list go
+             python-mock
+             ;; Uses test markers that are incompatible with pytest 9.
+             python-pytest-8
+             python-pytest-mock
+             python-setuptools))
+      (inputs
+       (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
@@ -117,7 +117,7 @@ Features:
 (define-public python-zbarlight
  (package
    (name "python-zbarlight")
-    (version "3.0")
+    (version "4.0")
    (source
     (origin
       (method git-fetch)
@@ -126,7 +126,7 @@ Features:
             (commit version)))
       (file-name (git-file-name name version))
       (sha256
-        (base32 "1radfpfhfhkx3xnz01bqr5l9pl2zv70zis6l2kw1gwqbfw65r6w6"))))
+        (base32 "1q1nfc7g7bl9y63fwvnq1fcgqk79inc2hhw3ilvyw0nk0g74v8cm"))))
    (build-system pyproject-build-system)
    (propagated-inputs (list python-pillow))
    (inputs (list zbar))
@@ -88,7 +88,6 @@
  #: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)
@@ -41,7 +41,6 @@
  #: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)
@@ -180,7 +180,7 @@ supported by Canonical since 2009.")
       (list libapparmor))
      ;; Python module `readline' needed
      (native-inputs
-       (list bison flex gettext-minimal perl python which))
+       (list bison flex gettext-minimal perl python python-setuptools which))
      (license license:gpl2))))

 (define-public pam-apparmor
@@ -37,7 +37,6 @@

 (define-module (gnu packages astronomy)
  #:use-module ((guix licenses) #:prefix license:)
-  #:use-module ((guix build-system python) #:select (pypi-uri)) ;to be removed soon
  #:use-module (guix build-system ant)
  #:use-module (guix build-system cmake)
  #:use-module (guix build-system copy)
@@ -1992,12 +1991,22 @@ model-fitting photometry or morphological analyses.")
       (sha256
        (base32 "156y3zp0nm77976rwsxjjdh7yvggas8s6m0nm523khvn4lq8f9n0"))))
    (build-system pyproject-build-system)
+    (arguments
+     (list
+      #:test-flags
+      ;; Assertion errors:
+      ;;
+      ;; You are lazy loading attributes via 'bibtex', and so are making
+      ;; multiple calls to the API. This will impact your overall rate
+      ;; limits. bibtex should be queried with ads.ExportQuery(); You will hit
+      ;; API ratelimits very quickly otherwise.
+      #~(list (string-append "--deselect=ads/tests/test_search.py"
+                             "::TestArticle::test_get_field_bibtex"))))
    (native-inputs
     (list nss-certs-for-test
           python-httpretty
           python-pytest
-           python-setuptools
-           python-wheel))
+           python-setuptools))
    (propagated-inputs
     (list python-mock
           python-requests
@@ -3853,10 +3862,6 @@ find,download, and read the data files.")
      #~(list "-m" "not remote_data")
      #:phases
      #~(modify-phases %standard-phases
-          (add-after 'unpack 'fix-pytest-config
-            (lambda _
-              (substitute* "pyproject.toml"
-                ((" --cov=cdflib --cov-report=xml") ""))))
          (add-before 'check 'set-HOME
            (lambda _
              (setenv "HOME" "/tmp"))))))
@@ -4658,7 +4663,6 @@ Cesium.")
    (native-inputs
     (list python-pydot
           python-pytest
-           python-pytest-cov
           python-pytest-asdf-plugin
           python-pytest-doctestplus
           python-pytest-filter-subpackage
@@ -5183,7 +5187,6 @@ files.")
    (build-system pyproject-build-system)
    (native-inputs
     (list python-pytest
-           python-pytest-cov
           python-setuptools
           python-setuptools-scm
           python-wheel))
@@ -5778,7 +5781,6 @@ across many files.")
     (list python-mock
           python-objgraph
           python-pytest
-           python-pytest-cov
           ;; python-pytest-faulthandler
           python-setuptools
           python-wheel
@@ -6625,19 +6627,6 @@ files.")
                 (string-append
                  "from astropy.units.core import Unit, UnitBase\n"
                  "from astropy.units.errors import UnitTypeError\n")))))
-          (add-after 'unpack 'relax-requirements
-            (lambda _
-              (substitute* "pyproject.toml"
-                ;; RuntimeError: Unable to detect version control
-                ;; system. Checked: Git. Not installed: Mercurial, Darcs,
-                ;; Subversion, Bazaar, Fossil, Pijul.  See
-                ;; <https://github.com/blacklanternsecurity/bbot/issues/1257>.
-                (("enable = true") "enable = false"))))
-          (add-before 'build 'set-version
-            (lambda _
-              ;; TODO: Include in pyproject-build-system.
-              (setenv "POETRY_DYNAMIC_VERSIONING_BYPASS"
-                      #$(version-major+minor+point version))))
          (add-before 'check 'prepare-test-environment
            (lambda _
              (setenv "HOME" "/tmp"))))))
@@ -6695,7 +6684,7 @@ astronomical tables
    (build-system pyproject-build-system)
    (arguments
     (list
-      ;; tests: 1509 passed, 55331 warnings
+      ;; tests: 1508 passed, 43621 warnings
      #:test-flags
      #~(list "--numprocesses" (number->string (min 8 (parallel-job-count)))
              ;; TypeError: SparseSolverBase.__init__() got an unexpected
@@ -6712,7 +6701,12 @@ astronomical tables
              (string-append "--deselect=test/test_Sampling/test_Likelihoods/"
                             "test_position_likelihood.py"
                             "::TestPositionLikelihood"
-                             "::test_multiplane_position_likelihood"))
+                             "::test_multiplane_position_likelihood")
+              ;; XXX: AttributeError: 'FileFinder' object has no attribute
+              ;; 'find_module'.
+              ;; See: <https://github.com/lenstronomy/lenstronomy/issues/845>.
+              (string-append "--deselect=test/test_Util/test_package_util.py"
+                             "::test_short_and_laconic"))
      #:phases
      #~(modify-phases %standard-phases
          (add-before 'check 'pre-check
@@ -11669,7 +11663,6 @@ for dealing with particle data and a few related utility functions.")
    (build-system pyproject-build-system)
    (propagated-inputs (list python-numpy python-scipy))
    (native-inputs (list python-pytest
-                         python-pytest-cov
                         python-pytest-doctestplus
                         python-setuptools-scm
                         python-wheel))
@@ -137,7 +137,6 @@
  #:use-module (gnu packages music)
  #:use-module (gnu packages ncurses)
  #:use-module (gnu packages networking)
-  #:use-module (gnu packages ninja)
  #:use-module (gnu packages onc-rpc)
  #:use-module (gnu packages oneapi)
  #:use-module (gnu packages perl)
@@ -146,6 +145,7 @@
  #:use-module (gnu packages pretty-print)
  #:use-module (gnu packages python)
  #:use-module (gnu packages python-build)
+  #:use-module (gnu packages python-check)
  #:use-module (gnu packages python-crypto)
  #:use-module (gnu packages python-science)
  #:use-module (gnu packages python-web)
@@ -181,7 +181,6 @@
  #: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)
@@ -821,7 +820,8 @@ Filter) modules follow the convention of 1V / Octave.")
                   "https://aubio.org/pub/aubio-" version ".tar.bz2"))
             (sha256
              (base32
-               "1npks71ljc48w6858l9bq30kaf5nph8z0v61jkfb70xb9np850nl"))))
+               "1npks71ljc48w6858l9bq30kaf5nph8z0v61jkfb70xb9np850nl"))
+             (patches (search-patches "aubio-waflib-python312-compat.patch"))))
    (build-system waf-build-system)
    (arguments
     (list
@@ -3279,30 +3279,27 @@ synchronous execution of all clients, and low latency operation.")
  (package
    (inherit jack-1)
    (name "jack2")
-    (version "1.9.21")
+    ;; 1.9.22 does not compile with Python 3.12, use the latest commit instead.
+    (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")
-                    (commit (string-append "v" version))))
+                     (url "https://github.com/jackaudio/jack2")
+                     (commit (assoc-ref properties 'commit))))
              (file-name (git-file-name name version))
              (sha256
               (base32
-                "0sbrffmdbajvrk7iqvsvrnwnpvmicvbjyq3f52r6ashdsznsz03b"))))
+                "18dbjq9y8mcp27j9aaqdlg4976hrisr7b88lk84ck09gmzlwqalp"))))
    (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
@@ -3328,7 +3325,7 @@ synchronous execution of all clients, and low latency operation.")
           expat
           libsamplerate
           opus
-           python-dbus-1.2
+           python-dbus
           readline))
    (native-inputs
     (list pkg-config))
@@ -4206,9 +4203,7 @@ one-dimensional sample-rate conversion library.")
                 (string-append "'" #$(this-package-input "libsndfile")
                                "/lib/libsndfile"))))))))
    (native-inputs
-     (list python-pytest
-           python-pytest-cov
-           python-setuptools))
+     (list python-pytest python-setuptools))
    (inputs
     (list libsndfile
           portaudio))
@@ -7986,60 +7981,59 @@ 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
-           python ;for running tests
-           portaudio)) ;for portaudio examples
+           portaudio                    ;for portaudio examples
+           python                       ;for running tests
+           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
@@ -8235,7 +8229,7 @@ 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-pytest-cov python-setuptools python-wheel))
+     (list python-pytest python-setuptools python-wheel))
    (home-page "https://github.com/bmcfee/resampy")
    (synopsis "Efficient signal resampling")
    (description
@@ -8253,10 +8247,10 @@ Home Page}.")
     (origin
       (method git-fetch)
       (uri (git-reference
-             (url "https://github.com/librosa/librosa/")
-             (commit version)
-             ;; For test files.
-             (recursive? #true)))
+              (url "https://github.com/librosa/librosa/")
+              (commit version)
+              ;; TODO: Package test data.
+              (recursive? #true)))
       (file-name (git-file-name name version))
       (sha256
        (base32 "065x43hx670rjrclxi4hiqxscllb16v9s7myjvg7rd5pd3y0k7sg"))))
@@ -8264,15 +8258,13 @@ Home Page}.")
    (arguments
     (list
      #:test-flags
-      ;; Ignore --mpl flag.
-      '(list "-c" "/dev/null"
-             "-k" (string-append
-                   ;; Resampling tests require python-samplerate.
-                   "not resample"
-                   ;; These tests use Pooch and download data files.
-                   " and not example and not test_cite"
-                   ;; XXX assert 22050 == 31744
-                   " and not test_stream"))))
+      #~(list "-k" (string-append
+                    ;; Resampling tests require python-samplerate.
+                    "not resample"
+                    ;; These tests use Pooch and download data files.
+                    " and not example and not test_cite"
+                    ;; XXX assert 22050 == 31744
+                    " and not test_stream"))))
    (propagated-inputs
     (list python-audioread
           python-decorator
@@ -8291,10 +8283,9 @@ Home Page}.")
     (list python-matplotlib
           python-packaging
           python-pytest
-           python-pytest-cov
+           python-pytest-mpl
           python-resampy
-           python-setuptools
-           python-wheel))
+           python-setuptools))
    (home-page "https://librosa.org")
    (synopsis "Python module for audio and music processing")
    (description
@@ -0,0 +1,58 @@
+# 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="?")
@@ -50,7 +50,6 @@
  #: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)
@@ -107,6 +106,7 @@
  #: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)
@@ -137,7 +137,6 @@
           python-paramiko
           python-pexpect
           python-pytest
-           python-pytest-runner
           python-setuptools-scm
           tzdata-for-tests
           python-mock))
@@ -632,41 +631,26 @@ rsnapshot uses hard links to deduplicate identical files.")
 (define-public borg
  (package
    (name "borg")
-    (version "1.4.3")
+    (version "1.4.4")
    (source
     (origin
-       (method url-fetch)
-       (uri (pypi-uri "borgbackup" version))
+       (method git-fetch)
+       (uri (git-reference
+              (url "https://github.com/borgbackup/borg")
+              (commit version)))
+       (file-name (git-file-name name version))
       (sha256
-        (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"))))))
+        (base32 "0bk302lbjjz1y8dg78wqqys80bm7mzkj5yf6wgyqdwvbqpsnpim4"))))
    (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 (parallel-job-count))
+              "--numprocesses" (number->string (min 8 (parallel-job-count)))
              "--pyargs" "borg.testsuite"
              "-k" (string-join
                    ;; These tests need to write to '/var'.
@@ -687,7 +671,15 @@ 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
@@ -703,46 +695,58 @@ rsnapshot uses hard links to deduplicate identical files.")
                (setenv "BORG_LIBLZ4_PREFIX" lz4)
                (setenv "BORG_LIBXXHASH_PREFIX" xxhash)
                (setenv "BORG_LIBZSTD_PREFIX" zstd))))
-          (add-after 'install 'install-doc
+          (add-before 'build 'fix-testsuite-setuid-mode
            (lambda _
-              (let ((man (string-append #$output "/share/man/man1"))
-                    (misc (string-append #$output "/share/doc/borg-"
-                                         #$(package-version this-package))))
+              (substitute* "src/borg/testsuite/archiver.py"
+                (("0o4755") "0o0755"))))
+          (add-after 'install 'build-and-install-docs
+            (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 #$output "/share/man/man1")))
+                (with-directory-excursion "docs"
+                  (invoke "make" "text" "man" "singlehtml"))
                (for-each (cut install-file <> misc)
                          '("docs/misc/create_chunker-params.txt"
                            "docs/misc/borg-data-flow.png"
                            "docs/misc/internals-picture.txt"
                            "docs/misc/prune-example.txt"))
-                (copy-recursively "docs/man" man))))
-          (add-after 'install-doc 'install-shell-completions
+                (copy-recursively "docs/_build/man" man)
+                (copy-recursively "docs/_build/singlehtml" html)
+                (copy-recursively "docs/_build/text" txt))))
+          (add-after 'build-and-install-docs 'install-shell-completions
            (lambda _
-              (let ((etc (string-append #$output "/etc"))
-                    (share (string-append #$output "/share")))
+              (let* ((etc (string-append #$output "/etc"))
+                     (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"
-                                (string-append etc "/bash_completion.d"))
-                  (install-file "zsh/_borg"
-                                (string-append share "/zsh/site-functions"))
-                  (install-file "fish/borg.fish"
-                                (string-append share "/fish/vendor_completions.d")))))))))
+                  (install-file "bash/borg" bash)
+                  (install-file "zsh/_borg" zsh)
+                  (install-file "fish/borg.fish" fish))))))))
    (native-inputs
     (list python-cython
-           python-dateutil
+           python-guzzle-sphinx-theme
+           python-pkgconfig
           python-pytest
           python-pytest-benchmark
           python-pytest-xdist
           python-setuptools
           python-setuptools-scm
-           python-wheel))
+           python-sphinx
+           python-sphinxcontrib-jquery))
    (inputs
     (list acl
           lz4
           openssl
-           ;; This is the latest version of msgpack accepted by 'setup.py'.
-           python-msgpack-for-borg
+           python-msgpack
           ;; 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")
@@ -1264,10 +1268,9 @@ compression parameters used by Gzip.")
 (define-public borgmatic
  (package
    (name "borgmatic")
-    (version "2.1.2")
+    (version "2.1.5")
    (source
     (origin
-       ;; PyPI archive does not contain NEWS file needed for one test.
       (method git-fetch)
       (uri (git-reference
              (url "https://projects.torsion.org/borgmatic-collective/borgmatic")
@@ -1275,10 +1278,11 @@ compression parameters used by Gzip.")
       (file-name (git-file-name name version))
       (sha256
        (base32
-         "0vrpl21n6hf3pj0di4n7s36jq64sx24c93j48cmbdgczs8jiwi36"))))
+         "17i15ysg0wbcnfvki8wz2z9gx3zx99czv3czjh83y2m1xppvqbl5"))))
    (build-system pyproject-build-system)
    (arguments
     (list
+      ;; tests: 2609 passed
      #:phases
      #~(modify-phases %standard-phases
          (add-after 'unpack 'configure
@@ -1293,19 +1297,12 @@ compression parameters used by Gzip.")
                (("(module.get_local_path.+ == )'borg'" all start)
                 (string-append start "'"
                                (search-input-file inputs "bin/borg")
-                                "'")))))
-          (add-before 'check 'set-path
-            (lambda _
-              ;; Tests require the installed executable.
-              (setenv "PATH"
-                      (string-append #$output "/bin" ":"
-                                     (getenv "PATH"))))))))
+                                "'"))))))))
    (native-inputs
     (list python-flexmock
           python-pytest
-           python-pytest-cov
-           python-setuptools
-           python-wheel))
+           python-pytest-timeout
+           python-setuptools))
    (inputs
     (list borg
           python-apprise
@@ -1367,9 +1364,9 @@ 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
@@ -44,7 +44,6 @@
  #:use-module (guix build-system cmake)
  #:use-module (guix build-system qt)
  #: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)
@@ -65,7 +65,6 @@
  #: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)
@@ -2290,10 +2289,10 @@ 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
+                         python-setuptools
                         python-sphinx))
    (inputs (cons python-wrapper (cargo-inputs 'python-bed-reader)))
    (propagated-inputs (list python-numpy python-pandas python-scipy))
@@ -3324,7 +3323,17 @@ trees, synthetic data generation, or just phylogenetic tree simulation.")
              (commit (assoc-ref properties 'commit))))
       (file-name (git-file-name name version))
       (sha256
-        (base32 "1x0c1zhlfplhm4n07vibvh4jprjsdlypnlig87a8r07d26d4qphh"))))
+        (base32 "1x0c1zhlfplhm4n07vibvh4jprjsdlypnlig87a8r07d26d4qphh"))
+       (patches
+        (list
+         (origin
+           (method url-fetch)
+           (uri
+            (string-append "https://github.com/cancerit/parabam/commit/"
+                           "477246d7a13b227841bf49521181235c76afe75f.patch"))
+           (file-name (string-append name "-" version "-pull-16.patch"))
+           (sha256
+            (base32 "0znmyvrmwbscqymhsx60pnp9jhzpz94diyv409jygjm58hj5454z")))))))
    (build-system pyproject-build-system)
    (arguments
     (list
@@ -3349,25 +3358,29 @@ defined rule on an input file.")
 (define-public python-pdbfixer
  (package
    (name "python-pdbfixer")
-    (version "1.9")
+    (version "1.12")
    (source
     (origin
       (method git-fetch)
       (uri (git-reference
             (url "https://github.com/openmm/pdbfixer")
-             (commit version)))
+             (commit (string-append "v" version))))
       (file-name (git-file-name name version))
       (sha256
-        (base32 "1zjhb19q5dclkwvzh8n29p31n1vzkhlmmzwqllimi89jsis1cx35"))))
+        (base32 "0jj724fkvk7bk47izk92ss8nz9ymfvj0f1fkypc0ig4xd5qzjqsz"))))
    (build-system pyproject-build-system)
    (arguments
     (list
      #:test-flags
+      ;; These tests fail because they require internet access or test data.
      '(list "-k"
-             ;; These tests fail because they require internet access.
-             (string-append "not test_build_and_simulate.py"
-                            " and not test_cli.py"
-                            " and not test_mutate.py"))))
+             (string-join (list "not test_build_and_simulate"
+                                "test_charge_and_solvate"
+                                "test_cli"
+                                "test_leaving_atoms"
+                                "test_mutate"
+                                "test_nonstandard")
+                          " and not "))))
    (propagated-inputs (list openmm python-numpy))
    (native-inputs (list python-pytest python-setuptools python-wheel))
    (home-page "https://github.com/openmm/pdbfixer")
@@ -3381,35 +3394,36 @@ encountered in PDB files prior to simulation tasks.")
 (define-public python-peaks2utr
  (package
    (name "python-peaks2utr")
-    (version "1.4.1")
-    (source (origin
-              (method url-fetch)
-              (uri (pypi-uri "peaks2utr" version))
-              (sha256
-               (base32
-                "104il0kk61q07b58g9xrss7xflwlbx4kzsmw9iih99lhfsii0wzg"))))
+    (version "1.5.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+              (url "https://github.com/haessar/peaks2utr")
+              (commit (string-append "v" version))))
+       (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
-         (add-after 'unpack 'relax-requirements
-           (lambda _
-             (substitute* "setup.cfg"
-               (("==") ">=")))))))
+      #~(modify-phases %standard-phases
+          (add-after 'unpack 'relax-requirements
+            (lambda _
+              (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
-           python-numpy-1
+           macs-3
+           python-numpy
           python-psutil
           python-pybedtools
           python-pysam
@@ -3417,7 +3431,6 @@ 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
@@ -3866,7 +3879,6 @@ raw/ed14e050b2b75e7f4ddb73d512fbe928bbdb2b85")
           python-scipy))
    (native-inputs
     (list python-pytest
-           python-pytest-cov
           python-pytest-datadir
           python-pytest-doctestplus
           python-setuptools
@@ -4039,7 +4051,16 @@ counts.")
                     "test_scatter_rotate_mp4"
                     "test_sparse_svd"
                     "test_to_array_or_spmatrix_list_of_strings"
-                     "test_unzip_no_destination)")
+                     "test_unzip_no_destination"
+                     ;; AttributeError: module 'rpy2' has no attribute
+                     ;; '__version__'
+                     "test_verbose"
+                     "test_conversion_list"
+                     "test_conversion_dict"
+                     "test_conversion_array"
+                     "test_conversion_dataframe"
+                     "test_conversion_anndata_missing"
+                     "test_r_traceback)")
               "|")
              "test")
      #:phases
@@ -4292,7 +4313,6 @@ e.g. microbiome samples, genomes, metagenomes.")
    (native-inputs
     (list python-cython
           python-pytest
-           python-pytest-cov
           python-setuptools
           python-wheel))
    (propagated-inputs
@@ -6968,7 +6988,6 @@ and v1.1 to v1.2.")
     (list python-mypy-extensions
           python-pytest
           python-pytest-mock
-           python-pytest-runner
           python-setuptools
           python-wheel))
    (propagated-inputs
@@ -7886,7 +7905,7 @@ software to answer ad hoc questions.")
           r-tidyr
           r-upsetr
           r-yaml
-           snakemake-7))
+           snakemake))
    (native-inputs (list python-cython python-pyfakefs python-pytest))
    (home-page "https://github.com/dieterich-lab/Baltica")
    (synopsis "Integrated splice junction usage analysis")
@@ -8776,7 +8795,8 @@ high-throughput sequencing (HTS) assays")
         ;; Needed by tests
         (add-after 'unpack 'set-HOME
           (lambda _ (setenv "HOME" "/tmp"))))))
-    (propagated-inputs (list python-appdirs
+    (propagated-inputs (list mysql-connector-python
+                             python-appdirs
                             python-biopython
                             python-click
                             python-colorama
@@ -8784,7 +8804,6 @@ high-throughput sequencing (HTS) assays")
                             python-filelock
                             python-loguru
                             python-mygene
-                             python-mysql-connector-python
                             python-norns
                             python-numpy
                             python-pandas
@@ -9750,29 +9769,39 @@ sequencing tag position and orientation.")
 (define-public macs-3
  (package
    (name "macs")
-    (version "3.0.3")
-    (source (origin
-              (method git-fetch)
-              (uri (git-reference
-                    (url "https://github.com/macs3-project/MACS")
-                    (commit (string-append "v" version))
-                    (recursive? #true)))
-              (file-name (git-file-name name version))
-              (sha256
-               (base32
-                "08hi0a2a0md9gfg7jc75wxv69rggv2yqfd1hyrg4mi5bhi712m0v"))))
+    (version "3.0.4")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+              (url "https://github.com/macs3-project/MACS")
+              (commit (string-append "v" version))
+              (recursive? #true)))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "16cv6bvvppi0z69r5l357ai8x4jg61rx8xrvcapk1wz6mh9naf5s"))))
    (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
@@ -12331,15 +12360,9 @@ Cuffdiff or Ballgown programs.")
              ;; This version file is expected to be created with git describe.
              (mkdir-p "taxtastic/data")
              (with-output-to-file "taxtastic/data/ver"
-                (lambda () (display #$version)))))
-          (replace 'check
-            ;; Note, this fails to run with "-v" as it tries to write to a
-            ;; closed output stream.
-            (lambda* (#:key tests? test-flags #:allow-other-keys)
-              (when tests?
-                (apply invoke "python" "-m" "unittest" test-flags)))))))
+                (lambda () (display #$version))))))))
    (native-inputs
-     (list python-setuptools python-wheel))
+     (list python-pytest python-setuptools))
    (propagated-inputs
     (list python-biopython
           python-decorator
@@ -14245,11 +14268,7 @@ quality control are provided.")
            (lambda _
              (substitute* "setup.cfg"
                (("intervaltree~=3.0.2") "intervaltree")
-                (("termcolor~=1.1.0") "termcolor"))))
-          (add-after 'unpack 'fix-pytest-config
-            (lambda _
-              (substitute* "pyproject.toml"
-                ((" --cov=gdc_client --cov-report term") "")))))))
+                (("termcolor~=1.1.0") "termcolor")))))))
    (native-inputs
     (list python-flask
           python-httmock
@@ -14539,7 +14558,7 @@ data.  It also generates basic statistics for your sequences.")
 (define-public shorah
  (package
    (name "shorah")
-    (version "1.99.2")
+    (version "1.99.3")
    (source
     (origin
       (method url-fetch)
@@ -14548,7 +14567,7 @@ data.  It also generates basic statistics for your sequences.")
                           "/shorah-" version ".tar.xz"))
       (sha256
        (base32
-         "158dir9qcqspknlnyfr9zwk41x48nrh5wcg10k2grh9cidp9daiq"))))
+         "0zclbvdvbbfv3qpln3f47qa1yn77wf68z2b30vcxrzq3vsla4kgb"))))
    (build-system gnu-build-system)
    (arguments
     `(#:phases
@@ -14583,6 +14602,7 @@ data.  It also generates basic statistics for your sequences.")
           python
           python-biopython
           python-numpy
+           python-setuptools
           zlib))
    (native-inputs
     (list pkg-config))
@@ -18052,6 +18072,8 @@ methylation and segmentation.")
             (setenv "NUMBA_CACHE_DIR" "/tmp")
             ;; Needed to capture environment
             (setenv "PYTHONPATH" (getenv "GUIX_PYTHONPATH")))))))
+    (native-inputs
+     (list python-setuptools))
    (inputs
     (list coreutils
           perl
@@ -19868,8 +19890,8 @@ set.")
    (name "instrain")
    ;; Git repository does not tag releases, use the latest commit from master
    ;; branch.
-    (properties '((commit . "6180be7b49a61b7e1ffe9f1489da5c6aa2ff9ac3")
-                  (revision . "0")))
+    (properties '((commit . "f172367e599851a6cb90048ae890d1bb6569063f")
+                  (revision . "1")))
    (version (git-version "1.10.0"
                          (assoc-ref properties 'revision)
                          (assoc-ref properties 'commit)))
@@ -19881,18 +19903,32 @@ set.")
              (commit (assoc-ref properties 'commit))))
       (file-name (git-file-name name version))
       (sha256
-        (base32 "1njsxjf3248121yw3q1ig6asf6b3wa5fgjfyc6dkgk6nd4ih8wni"))))
+        (base32 "12rrkcckna7k095clir9100cz6i5dn77anih6aq1blbsg4yhprnr"))))
    (build-system pyproject-build-system)
    (arguments
     (list
-      ;; Tests assume that test files exist (they don't) and are located in
-      ;; the developer's home directory, see:
-      ;; <https://github.com/MrOlm/inStrain/issues/218>.
-      #:tests? #false
+      ;; tests: 10 failed, 86 passed, 15 skipped, 220 warnings
+      #:test-flags
+      #~(list #$@(map (lambda (test)
+                        (string-append "--deselect=test/tests/" test))
+                      ;; Mixture of "FileNotFoundError" and "AssertionError"
+                      ;; errors.
+                      (list "test_genes.py::test_genes_0"
+                            "test_genes.py::test_genes_1"
+                            "test_genes.py::test_genes_2"
+                            "test_genes.py::test_genes_3"
+                            "test_parse_gene_annotations.py::test_PA_2"
+                            "test_polymorpher.py::test_polymorpher_unit_0"
+                            "test_polymorpher.py::test_polymorpher_unit_3"
+                            "test_quick_profile.py::test_quick_profile_0"
+                            "test_quick_profile.py::test_quick_profile_1"
+                            "test_quick_profile.py::test_quick_profile_2")))
      #:phases
      #~(modify-phases %standard-phases
         (add-after 'unpack 'patch-relative-imports
           (lambda _
+             ;; See: <https://github.com/MrOlm/inStrain/issues/218>.
+             (mkdir "test/test_backend/")
             (substitute* (find-files "test/tests" "test_.*\\.py")
               (("from test_utils import BTO")
                "from .test_utils import BTO")
@@ -19905,9 +19941,10 @@ set.")
         (add-after 'unpack 'relax-requirements
           (lambda _
             (substitute* "setup.py"
+               (("biopython<=1.74") "biopython")
               ((".*pytest.*") "")))))))
    (propagated-inputs
-     (list python-biopython-1.73
+     (list python-biopython
           python-h5py
           python-lmfit
           python-matplotlib
@@ -19919,7 +19956,9 @@ set.")
           python-seaborn
           python-tqdm))
    (native-inputs
-     (list python-setuptools))
+     (list python-boto3
+           python-pytest
+           python-setuptools))
    (home-page "https://github.com/MrOlm/inStrain")
    (synopsis "Calculation of strain-level metrics")
    (description
@@ -20150,33 +20189,32 @@ fasta subsequences.")
 (define-public python-cooler
  (package
    (name "python-cooler")
-    (version "0.10.4")
+    ;; 0.10.4 (2025-07-21), the latest changes provide support for Python
+    ;; 3.12+; move back to git tag when released.
+    (properties '((commit . "6c2d65b1420a636193b7f05100a96410ea252147")
+                  (revision . "0")))
+    (version (git-version "0.10.4"
+                          (assoc-ref properties 'revision)
+                          (assoc-ref properties 'commit)))
    (source
     (origin
-       (method url-fetch)
-       (uri (pypi-uri "cooler" version))
+       (method git-fetch)
+       (uri (git-reference
+              (url "https://github.com/open2c/cooler")
+              (commit (assoc-ref properties 'commit))))
+       (file-name (git-file-name name version))
       (sha256
-        (base32
-         "1fh5wjffbl5j8fdkc3c3lybscwvhv4v6r5jiyqgxvkkhb5nn498w"))))
+        (base32 "0xdb7lvyzj3wwv6jhkrxlj7gk830wkac4lwq5rjwk1r5qshjbn3n"))))
    (build-system pyproject-build-system)
    (arguments
     (list
-      ;; tests: 141 passed, 4 skipped, 2 deselected, 268 warnings
+      ;; tests: 141 passed, 4 skipped, 2 deselected, 270 warnings
      #:test-flags
-      '(list "-k"
-             (string-append
-              ;; These tests download files from the internet.
-              "not test_fetch_chromsizes"
-              " and not test_roundtrip"
-              ;; This test depends on ipytree, which contains a lot of
-              ;; minified JavaScript.
-              " and not test_print_trees"))
-      #:phases
-      #~(modify-phases %standard-phases
-          (add-after 'unpack 'fix-pytest-config
-            (lambda _
-              (substitute* "pyproject.toml"
-                ((".*--cov.*") "")))))))
+      ;; This test depends on ipytree, which contains a lot of minified
+      ;; JavaScript.
+      #~(list "--deselect=tests/test_fileops.py::test_print_trees"
+              ;; Network access is required.
+              "--deselect=tests/test_create.py::test_roundtrip")))
    (native-inputs
     (list python-hatchling
           python-pytest))
@@ -20578,8 +20616,8 @@ and intra-cell population structure.\" Baron et al. Cell Systems (2016)
 (define-public porechop
  ;; The recommended way to install is to clone the git repository
  ;; https://github.com/rrwick/Porechop#installation
-  (let ((commit "289d5dca4a5fc327f97b3f8cecb68ecaf1014861")
-        (revision "1"))
+  (let ((commit "109e437280436d1ec27e5a5b7a34ffb752176390")
+        (revision "2"))
    (package
      (name "porechop")
      (version (git-version "0.2.3" revision commit))
@@ -20587,13 +20625,28 @@ and intra-cell population structure.\" Baron et al. Cell Systems (2016)
       (origin
         (method git-fetch)
         (uri (git-reference
-               (url "https://github.com/rrwick/Porechop")
-               (commit commit)))
+                (url "https://github.com/rrwick/Porechop")
+                (commit commit)))
         (file-name (git-file-name name version))
         (sha256
-          (base32 "05ps43gig0d3ia9x5lj84lb00hbsl6ba9n7y7jz927npxbr2ym23"))))
+          (base32 "0m7bsgvknv0cbkrpc0qi7b39jaws38dcdih4hi2ppg6z7byxip0k"))))
      (build-system pyproject-build-system)
-      (native-inputs (list python-setuptools python-wheel python-pytest))
+      (arguments
+       (list
+        #:test-flags
+        ;; Tests fail with errors: "SyntaxWarning: invalid escape sequence"
+        ;; and "AssertionError: Lists differ".
+        #~(list "-k" (string-join
+                      (list "not test_albacore_directory_all"
+                            "test_albacore_directory_unclassified"
+                            "test_verbosity_0_output"
+                            "test_albacore_directory_3"
+                            "test_verbosity_1_output"
+                            "test_verbosity_2_output")
+                      " and not "))))
+      (native-inputs
+       (list python-pytest
+             python-setuptools))
      (home-page "https://github.com/rrwick/porechop")
      (synopsis
       "Finding, trimming or splitting adapters, in Oxford Nanopore reads")
@@ -21878,6 +21931,10 @@ pycisTarget and SCENIC.")
      #:test-backend #~'unittest
      #:phases
      #~(modify-phases %standard-phases
+          (add-after 'unpack 'python-3.12-compatibility
+            (lambda _
+              (substitute* (find-files "tests" "\\.py")
+                (("assertEquals") "assertEqual"))))
          (add-after 'unpack 'disable-failing-tests
            (lambda _
              (substitute* "tests/test_algo.py"
@@ -23091,7 +23148,7 @@ genomes known to contain a given k-mer.")
    (inputs
     (list htslib python-wrapper zlib))
    (native-inputs
-     (list autoconf automake which))
+     (list autoconf automake python-setuptools which))
    (home-page "https://csb5.github.io/lofreq/")
    (synopsis "Sensitive variant calling from sequencing data")
    (description "LoFreq is a fast and sensitive variant-caller for inferring
@@ -86,7 +86,6 @@
  #: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)
@@ -534,8 +533,9 @@ and will take advantage of multiple processor cores where possible.")
    (inputs (list boost-1.83 openssl))
    (native-inputs
     (list libfaketime
-           python-wrapper
-           pkg-config))
+           pkg-config
+           python-setuptools
+           python-wrapper))
    (home-page "https://www.libtorrent.org/")
    (synopsis "Feature-complete BitTorrent implementation")
    (description
@@ -83,9 +83,6 @@
    (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
@@ -94,17 +91,26 @@
           ;; Auto-detection looks for ICU only in traditional
           ;; install locations.
           (string-append "--with-icu=" icu)
-           ;; Ditto for Python.
-           #$@(if (%current-target-system)
-                  #~()
-                  #~((let ((python (dirname (dirname (search-input-file
-                                                      %build-inputs
-                                                      "bin/python")))))
-                       (string-append "--with-python-root=" python)
-                       (string-append "--with-python=" python
-                                      "/bin/python")
-                       (string-append "--with-python-version="
-                                      (python-version python)))))
+           ;; Ditto for Python.  The Gexp can't be evaluated if python is not
+           ;; in the inputs (e.g. boost-for-mysql), so delay its evaluation
+           ;; after checking for python, rather than concurrently.
+           #$@(force
+               (if (or (%current-target-system)
+                       (not (this-package-input "python-minimal-wrapper")))
+                   (delay
+                     #~())
+                   (delay
+                     #~((let ((python (dirname (dirname (search-input-file
+                                                         %build-inputs
+                                                         "bin/python")))))
+                          (string-append "--with-python-root=" python)
+                          (string-append "--with-python=" python
+                                         "/bin/python")
+                          (string-append "--with-python-version="
+                                         #$(version-major+minor
+                                            (package-version
+                                             (this-package-input
+                                              "python-minimal-wrapper")))))))))
           "--with-toolset=gcc"))
      #:make-flags
      #~(list "threading=multi" "link=shared"
@@ -200,29 +206,39 @@
          (replace 'install
            (lambda* (#:key make-flags #:allow-other-keys)
              (apply invoke "./b2" "install" make-flags)))
-          #$@(if (%current-target-system)
-                 #~()
-                 #~((add-after 'install 'provide-libboost_python
-                      (lambda* (#:key make-flags inputs outputs #:allow-other-keys)
-                        (let* ((static? (member "link=static" make-flags))
-                               (libext (if static? ".a" ".so"))
-                               (python (dirname (dirname (search-input-file
-                                                          inputs "bin/python"))))
-                               (python-version (python-version python))
-                               (libboost_pythonNN
-                                (string-append "libboost_python"
-                                               (string-join (string-split
-                                                             python-version #\.)
-                                                            "")
-                                               libext)))
-                          (with-directory-excursion (string-append #$output "/lib")
-                            (symlink libboost_pythonNN
-                                     (string-append "libboost_python" libext))
-                            ;; Some packages only look for the major version.
-                            (symlink libboost_pythonNN
-                                     (string-append "libboost_python"
-                                                    (string-take python-version 1)
-                                                    libext)))))))))))
+          #$@(force  ; See above for why the force is necessary.
+              (if (or (%current-target-system)
+                      (not (this-package-input "python-minimal-wrapper")))
+                  (delay
+                    #~())
+                  (delay
+                    #~((add-after 'install 'provide-libboost_python
+                         (lambda* (#:key make-flags inputs outputs
+                                   #:allow-other-keys)
+                           (let* ((static? (member "link=static" make-flags))
+                                  (ext (if static? ".a" ".so"))
+                                  (python (dirname
+                                           (dirname (search-input-file
+                                                     inputs "bin/python"))))
+                                  (python-version
+                                   #$(version-major+minor
+                                      (package-version
+                                       (this-package-input
+                                        "python-minimal-wrapper"))))
+                                  (NN (string-join (string-split
+                                                    python-version #\.)
+                                                   ""))
+                                  (libboost_pythonNN
+                                   (string-append "libboost_python" NN ext))
+                                  (major (string-take python-version 1)))
+                             (with-directory-excursion
+                                 (string-append #$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)
@@ -48,6 +48,7 @@
  #:use-module (gnu packages base)
  #:use-module (gnu packages disk)
  #:use-module (gnu packages bison)
+  #:use-module (gnu packages build-tools)
  #:use-module (gnu packages cdrom)
  #:use-module (gnu packages check)
  #:use-module (gnu packages compression)
@@ -65,7 +66,6 @@
  #:use-module (gnu packages man)
  #:use-module (gnu packages mtools)
  #:use-module (gnu packages ncurses)
-  #:use-module (gnu packages ninja)
  #:use-module (gnu packages package-management)
  #:use-module (gnu packages perl)
  #:use-module (gnu packages pkg-config)
@@ -1815,63 +1815,68 @@ For more information, refer to
 (define-public os-prober
  (package
    (name "os-prober")
-    (version "1.81")
+    (version "1.84")
    (source
     (origin
-       (method url-fetch)
-       (uri (string-append "mirror://debian/pool/main/o/os-prober/os-prober_"
-                           version ".tar.xz"))
+       (method git-fetch)
+       (uri (git-reference
+              (url "https://salsa.debian.org/installer-team/os-prober.git")
+              (commit version)))
+       (file-name (git-file-name name version))
       (sha256
-        (base32 "10w8jz6mqhp0skdcam9mpgv79vx1sv7lkpra3rqjg0jkhvn2in9g"))))
+        (base32 "1bji3w6nbqaz8zqrbmy8b1j5dph9xn7bdh1cd2z8ia1q125i6mgp"))))
    (build-system gnu-build-system)
    (arguments
-     `(#:modules ((guix build gnu-build-system)
+     (list
+      #:tests? #f                       ; No tests.
+      #:modules '((guix build gnu-build-system)
                  (guix build utils)
-                  (ice-9 regex)         ; for string-match
-                  (srfi srfi-26))       ; for cut
-       #:make-flags
-       (list ,(string-append "CC=" (cc-for-target)))
-       #:tests? #f                      ; no tests
-       #:phases
-       (modify-phases %standard-phases
-         (replace 'configure
-           (lambda* (#:key outputs #:allow-other-keys)
-             (substitute* (find-files ".")
-               (("/usr") (assoc-ref outputs "out")))
-             (substitute* (find-files "." "50mounted-tests$")
-               (("mkdir") "mkdir -p"))))
-         (replace 'install
-           (lambda* (#:key outputs #:allow-other-keys)
-             (define (find-files-non-recursive directory)
-               (find-files directory
-                           (lambda (file stat)
-                             (string-match (string-append "^" directory "/[^/]*$")
-                                           file))
-                           #:directories? #t))
+                  (ice-9 regex)         ; string-match
+                  (srfi srfi-26))       ; cut
+      #:make-flags
+      #~(list (string-append "CC=" #$(cc-for-target)))
+      #:phases
+      #~(modify-phases %standard-phases
+          (replace 'configure
+            (lambda _
+              (substitute* (find-files ".")
+                (("/usr") #$output))
+              (substitute* (find-files "." "50mounted-tests$")
+                (("mkdir") "mkdir -p -v"))))
+          (replace 'install
+            (lambda _
+              (define (find-files-non-recursive directory)
+                (find-files directory
+                            (lambda (file stat)
+                              (string-match (string-append "^" directory "/[^/]*$")
+                                            file))
+                            #:directories? #t))

-             (let* ((out (assoc-ref outputs "out"))
-                    (bin (string-append out "/bin"))
-                    (lib (string-append out "/lib"))
-                    (share (string-append out "/share")))
-               (for-each (cut install-file <> bin)
-                         (list "linux-boot-prober" "os-prober"))
-               (install-file "newns" (string-append lib "/os-prober"))
-               (install-file "common.sh" (string-append share "/os-prober"))
-               (install-file "os-probes/mounted/powerpc/20macosx"
-                             (string-append lib "/os-probes/mounted"))
-               (for-each
-                (lambda (directory)
-                  (for-each
-                   (lambda (file)
-                     (let ((destination (string-append lib "/" directory
-                                                       "/" (basename file))))
-                       (mkdir-p (dirname destination))
-                       (copy-recursively file destination)))
-                   (append (find-files-non-recursive (string-append directory "/common"))
-                           (find-files-non-recursive (string-append directory "/x86")))))
-                (list "os-probes" "os-probes/mounted" "os-probes/init"
-                      "linux-boot-probes" "linux-boot-probes/mounted"))))))))
-    (home-page "https://joeyh.name/code/os-prober")
+              (let ((bin (string-append #$output "/bin"))
+                     (lib (string-append #$output "/lib"))
+                     (share (string-append #$output "/share")))
+                (for-each (cut install-file <> bin)
+                          (list "linux-boot-prober" "os-prober"))
+                (install-file "newns" (string-append lib "/os-prober"))
+                (install-file "common.sh" (string-append share "/os-prober"))
+                (install-file "os-probes/mounted/powerpc/20macosx"
+                              (string-append lib "/os-probes/mounted"))
+                (for-each
+                 (lambda (directory)
+                   (for-each
+                    (lambda (file)
+                      (let ((destination (string-append lib "/" directory
+                                                        "/" (basename file))))
+                        (mkdir-p (dirname destination))
+                        (copy-recursively file destination)))
+                    (append (find-files-non-recursive (string-append directory "/common"))
+                            (find-files-non-recursive (string-append directory "/x86")))))
+                 (list "linux-boot-probes"
+                       "linux-boot-probes/mounted"
+                       "os-probes"
+                       "os-probes/init"
+                       "os-probes/mounted"))))))))
+    (home-page "https://joeyh.name/code/os-prober/")
    (synopsis "Detect other operating systems")
    (description "os-prober probes disks on the system for other operating
 systems so that they can be added to the bootloader.  It also works out how to
@@ -64,7 +64,6 @@
  #:use-module (gnu packages logging)
  #:use-module (gnu packages lua)
  #:use-module (gnu packages man)
-  #:use-module (gnu packages ninja)
  #:use-module (gnu packages package-management)
  #:use-module (gnu packages pcre)
  #:use-module (gnu packages perl)
@@ -77,6 +76,7 @@
  #:use-module (gnu packages python-crypto)
  #:use-module (gnu packages python-web)
  #:use-module (gnu packages python-xyz)
+  #:use-module (gnu packages re2c)
  #:use-module (gnu packages regex)
  #:use-module (gnu packages rpc)
  #:use-module (gnu packages serialization)
@@ -94,7 +94,6 @@
  #: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)
@@ -105,7 +104,8 @@
  #:use-module (guix packages)
  #:use-module (guix search-paths)
  #:use-module (guix utils)
-  #:use-module (ice-9 optargs))
+  #:use-module (ice-9 optargs)
+  #:use-module (srfi srfi-1))

 (define-public acr
  (package
@@ -432,9 +432,8 @@ files and generates build instructions for the Ninja build system.")
    (arguments
     (list
      #:tests? #f                       ;disabled to avoid extra dependencies
-      ;; Essentially a lighter copy of the former python-build-system.
-      ;; Using it rather than pyproject-build-system allows to edit the latter
-      ;; without a C++ world rebuild.
+      ;; Custom build steps to prevent using pyproject-build-system which
+      ;; allows to edit the latter without a C++ world rebuild.
      #:phases
      #~(modify-phases %standard-phases
          (delete 'bootstrap)
@@ -1485,3 +1484,114 @@ Features:
@item Support for languages outside C/C++ (e.g. Go, Rust, Zig).
@end itemize")
   (license license:asl2.0)))
+
+(define-public ninja/pinned
+  (hidden-package
+   (package
+     (name "ninja")
+     (version "1.13.2")
+     (source (origin
+               (method git-fetch)
+               (uri (git-reference
+                     (url "https://github.com/ninja-build/ninja")
+                     (commit (string-append "v" version))))
+               (file-name (git-file-name name version))
+               (sha256
+                (base32
+                 "0lp9dmxbjyjwv089i8mgq3nvnhpbnsn01ifm05m9s47w7cifrl8g"))))
+     (build-system gnu-build-system)
+     (inputs (list python-wrapper re2c))
+     (arguments
+      '(; Tests now require googletest, which is a circular dependency.
+        #:tests? #f
+        #:phases
+        (modify-phases %standard-phases
+          (replace 'configure
+            (lambda _
+              (substitute* "src/subprocess-posix.cc"
+                (("/bin/sh") (which "sh")))
+              (substitute* "src/subprocess_test.cc"
+                (("/bin/echo") (which "echo")))))
+          (replace 'build
+            (lambda _
+              (invoke "./configure.py" "--bootstrap")))
+          (replace 'check
+            (lambda* (#:key tests? #:allow-other-keys)
+              (when tests?
+                (invoke "./configure.py")
+                (invoke "./ninja" "ninja_test")
+                (invoke "./ninja_test"))))
+          (replace 'install
+            (lambda* (#:key outputs #:allow-other-keys)
+              (let* ((out (assoc-ref outputs "out"))
+                     (bin (string-append out "/bin"))
+                     (doc (string-append out "/share/doc/ninja")))
+                (install-file "ninja" bin)
+                (install-file "doc/manual.asciidoc" doc)))))))
+     (home-page "https://ninja-build.org/")
+     (synopsis "Small build system")
+     (description
+      "Ninja is a small build system with a focus on speed.  It differs from
+other build systems in two major respects: it is designed to have its input
+files generated by a higher-level build system, and it is designed to run
+builds as fast as possible.")
+    (license license:asl2.0))))
+
+(define-public ninja
+  (package/inherit ninja/pinned
+    (properties (alist-delete 'hidden? (package-properties ninja/pinned)))))
+
+(define-public samurai
+  (package
+    (name "samurai")
+    (version "1.2")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/michaelforney/samurai")
+                    (commit version)))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "04iw18hgkm72yrl83a2xh1jc47w9rilpb95kwick0j37b4q3gxj4"))))
+    (build-system gnu-build-system)
+    (arguments
+     (list #:tests? #f                  ;no test suite
+           #:make-flags #~(list (string-append "CC=" #$(cc-for-target))
+                                (string-append "PREFIX=" #$output))
+           #:phases #~(modify-phases %standard-phases
+                        (add-after 'unpack 'patch-/bin/sh
+                          (lambda* (#:key inputs #:allow-other-keys)
+                            (substitute* "build.c"
+                              (("/bin/sh")
+                               (search-input-file inputs "bin/sh")))))
+                        (delete 'configure))))
+    (inputs (list bash-minimal))
+    (home-page "https://github.com/michaelforney/samurai")
+    (synopsis "Ninja-compatible build tool written in C")
+    (description "@code{samurai} is a ninja-compatible build tool written in
+C99 with a focus on simplicity, speed, and portability.  It is
+feature-complete and supports most of the same options as ninja.  This package
+provides the command @command{samu}.  For a @command{ninja} command
+replacement, use the @code{samu-as-ninja-wrapper} package.")
+    (license (list license:asl2.0               ;for the most part
+                   license:expat))))            ;htab.h, htab.c and tree.c
+
+(define-public samu-as-ninja-wrapper
+  (package/inherit samurai
+    (name "samu-as-ninja-wrapper")
+    (build-system trivial-build-system)
+    (arguments
+     (list #:builder
+           (with-imported-modules '((guix build utils))
+             #~(begin
+                 (use-modules (guix build utils))
+                 (let ((bindir (string-append #$output "/bin"))
+                       (samu (string-append #$(this-package-input "samurai")
+                                            "/bin/samu")))
+                   (mkdir-p bindir)
+                   (symlink samu (string-append bindir "/ninja")))))))
+    (inputs (list samurai))
+    (description "This package provides the @command{ninja} command,
+implemented as a symbolic link to the @command{samu} command of @code{samurai}
+package.")))
@@ -55,7 +55,6 @@
  #: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)
@@ -45,7 +45,6 @@
  #: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)
@@ -131,7 +131,6 @@
  #: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))
@@ -1882,7 +1881,6 @@ http server.")
    (arguments (list #:tests? #false)) ;no tests included
    (native-inputs
     (list python-pytest
-           python-pytest-cov
           python-setuptools
           python-wheel
           python-xmlschema))
@@ -1915,42 +1913,6 @@ 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")
@@ -2733,7 +2695,11 @@ failures and errors instantly.")
                     "test_is_not_identity"
                     "test_resolves_builtin_types[object]"
                     "test_resolves_forwardrefs_to_builtin_types[object]"
-                     "test_timezone_lookup[tzinfo]")
+                     "test_timezone_lookup[tzinfo]"
+                     ;; hypothesis.errors.FailedHealthCheck: Input generation is slow
+                     #$@(if (target-riscv64?)
+                            '("test_can_run_with_no_db")
+                            '()))
               " and not "))
      #:phases
      #~(modify-phases %standard-phases
@@ -2956,12 +2922,8 @@ 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
@@ -3068,21 +3030,28 @@ possible to write plugins to add your own checks.")
 (define-public behave
  (package
    (name "behave")
-    (version "1.3.3")
+    ;; 1.3.3 (2025-09-04), the latest changes provide support for Python
+    ;; 3.12+; move back to git tag when released.
+    (properties '((commit . "43d0a93240c0b25b0cbf59bdc196b74fb8a2353e")
+                  (revision . "0")))
+    (version (git-version "1.3.3"
+                          (assoc-ref properties 'revision)
+                          (assoc-ref properties 'commit)))
    (source
     (origin
       (method git-fetch)
       (uri (git-reference
              (url "https://github.com/behave/behave")
-              (commit (string-append "v" version))))
+              (commit (assoc-ref properties 'commit))))
       (file-name (git-file-name name version))
       (sha256
-        (base32 "1fxj51kailsdakqi7qbw700k258n7r3lv75mgxs45ld5xh2jfyxh"))))
+        (base32 "05671jf7scpgqr8chzgs9bxidvf12nlkqqiqxa5qwmykqfvc8nk4"))))
    (build-system pyproject-build-system)
+    ;; tests: 1638 passed, 3 skipped, 2 xfailed
    (native-inputs
-     (list python-assertpy
-           python-chardet
-           python-mock
+     (list python-chardet
+           python-freezegun
+           python-charset-normalizer
           python-path
           python-pyhamcrest
           python-pytest
@@ -28,7 +28,6 @@
  #: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)
@@ -53,7 +53,6 @@
  #:use-module (gnu packages llvm)
  #:use-module (gnu packages kerberos)
  #:use-module (gnu packages maths)
-  #:use-module (gnu packages ninja)
  #:use-module (gnu packages node)
  #:use-module (gnu packages nss)
  #:use-module (gnu packages pciutils)
@@ -30,7 +30,6 @@
  #: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)
@@ -47,7 +47,6 @@
  #: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)
@@ -49,7 +49,6 @@
  #: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)
@@ -1475,7 +1475,7 @@ for most inputs, but the resulting compressed files are anywhere from 20% to
 (define-public 7zip
  (package
    (name "7zip")
-    (version "26.00")
+    (version "26.01")
    (source
     (origin
       (method git-fetch)
@@ -1483,7 +1483,7 @@ for most inputs, but the resulting compressed files are anywhere from 20% to
              (url "https://github.com/ip7z/7zip")
              (commit version)))
       (sha256
-        (base32 "1fvgl9qp2pl5c0jmvgbdx6qig3qd80mhxvml42yby8y412x65sh7"))
+        (base32 "0qwzn9pz1m6f8q20cqgmfqp1qx6s7959xnyikpr60n1v8c1mj98q"))
       (file-name (git-file-name name version))
       (modules '((guix build utils)
                  (ice-9 regex)))
@@ -127,6 +127,76 @@ formats:
 It also comes with example files generated by bincfg.")
    (license license:gpl3+)))

+(define-public bucts
+  (package
+    (name "bucts")
+    (version %coreboot-version)
+    (source %coreboot-origin)
+    (build-system gnu-build-system)
+    (arguments
+     (list
+      #:tests? #f ;no tests
+      #:make-flags #~(list (string-append "CC=" #$(cc-for-target)))
+      #:phases #~(modify-phases %standard-phases
+                   (delete 'configure) ;no configure script
+                   (add-after 'unpack 'enter-source
+                     (lambda _
+                       (chdir "util/bucts")))
+                   (add-after 'enter-source 'set-version
+                     (lambda _
+                       (substitute* "Makefile"
+                         (("^VERSION:=*")
+                          #$(string-append "VERSION:=" version)))))
+                   ;; no install target
+                   (replace 'install
+                     (lambda _
+                       (let ((bin (string-append #$output "/bin"))
+                             (doc (string-append #$output "/share/doc/bucts/"))
+                             (licenses (string-append #$output
+                                        "/share/licenses/bucts/")))
+                         (install-file "bucts" bin)
+                         (install-file "readme.md" doc)
+                         (install-file "../../COPYING" licenses)))))))
+    (inputs (list pciutils))
+    (home-page "https://coreboot.org")
+    (synopsis "Tool to swap the BIOS bootblock and backup bootblock on the
+Intel I945 chipsets")
+    (description
+     "The @command{bucts} command can flip a bit in the BUC.TS register of the
+Intel I945 chipsets and show the register status.  When the bit is set, it
+swaps the bootblock location.  Because the bootblock region is often set
+read-only by the default BIOS, this enables to bypass that restriction and is
+used as part of a procedure to replace the nonfree BIOS with free software on
+various computers (Lenovo X60, X60s, X60T, T60, probably more).")
+    (license license:gpl2)))
+
+(define-public ectool
+  (package
+    (name "ectool")
+    (version %coreboot-version)
+    (source %coreboot-origin)
+    (build-system gnu-build-system)
+    (arguments
+     (list
+      #:tests? #f ; no test suite
+      #:make-flags
+      #~(list (string-append "CC=" #$(cc-for-target))
+              "INSTALL=install"
+              (string-append "PREFIX=" #$output))
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-after 'unpack 'chdir
+            (lambda _
+              (chdir "util/ectool")))
+          (delete 'configure)))) ; no configure script
+    (home-page "https://doc.coreboot.org/util.html")
+    (synopsis "Tool to dump and modify @acronym{EC, Embedded Controller} RAM
+on computers such as laptops")
+    (description "This package provides @command{ectool}, a program to dump
+and modify the contents of @acronym{EC, Embedded Controller} RAM
+on mobile computers.")
+    (license license:gpl2)))
+
 (define-public ifdtool
  (package
    (name "ifdtool")
@@ -79,7 +79,6 @@
  #: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)
@@ -2017,8 +2016,7 @@ using the string similarity calculations from FuzzyWuzzy.")
          (add-after 'unpack 'fix-pytest-config
            (lambda _
              (substitute* "pyproject.toml"
-                ((" \"pytest-cov\", ") "")
-                ((" --cov-fail-under=90 --cov=cpplint") "")))))))
+                (("\"pytest-cov\", ") "")))))))
    (native-inputs
     (list python-pytest
           python-pytest-timeout
@@ -105,7 +105,6 @@
  #: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)
@@ -62,7 +62,6 @@
  #: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)
@@ -31,7 +31,6 @@
  #: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)
@@ -112,7 +111,7 @@ Refresh}in-DRAM mitigations effectively and as such can trigger bit flips.")
 (define-public gallia
  (package
    (name "gallia")
-    (version "2.0.2")
+    (version "2.1.1")
    (source
     (origin
       (method git-fetch)
@@ -121,7 +120,7 @@ Refresh}in-DRAM mitigations effectively and as such can trigger bit flips.")
              (commit (string-append "v" version))))
       (file-name (git-file-name name version))
       (sha256
-        (base32 "1yvjpwpqq6r6glfm4qzb8j91d2gsfy4lvygd9z9pg2j6jvcq6f6s"))))
+        (base32 "04xzh5fi18wrkjs7sqwlv344jf54njvnly042rhxq3x5jrvpvkdw"))))
    (build-system pyproject-build-system)
    (arguments
     (list
@@ -133,25 +132,16 @@ Refresh}in-DRAM mitigations effectively and as such can trigger bit flips.")
      #:test-flags #~(list "tests/pytest")))
    (native-inputs
     (list python-poetry-core
-           python-pygit2
           python-pytest
           python-pytest-asyncio))
    (inputs
-     (list python-aiofiles
-           python-aiosqlite
+     (list python-aiosqlite
           python-argcomplete
           python-boltons
-           python-can
-           python-construct
-           python-exitcode
-           python-httpx
-           python-more-itertools
-           python-msgspec
           python-platformdirs
-           python-psutil
           python-pydantic
-           python-pygit2
           python-tabulate
+           python-wcwidth
           python-zstandard))
    (home-page "https://github.com/Fraunhofer-AISEC/gallia")
    (synopsis "Extendable Pentesting Framework")
@@ -205,7 +205,6 @@
  #: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)
@@ -1279,6 +1278,98 @@ 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")
@@ -4738,33 +4829,24 @@ PickleShare.")
 (define-public python-apsw
  (package
    (name "python-apsw")
-    (version "3.46.0.0")
-    ;; The compressed release has fetching functionality disabled.
+    (version "3.50.4.0")
    (source
     (origin
-       (method url-fetch)
-       (uri (string-append
-             "https://github.com/rogerbinns/apsw/releases/download/"
-             version "/apsw-" version ".zip"))
+       (method git-fetch)
+       (uri (git-reference
+              (url "https://github.com/rogerbinns/apsw")
+              (commit version)))
+       (file-name (git-file-name name version))
       (sha256
-        (base32
-         "10yfbasi4mq63g0svyl1h49ylwn9znjylq78id16dzxzk9q9ipdx"))))
+        (base32 "0r9awjgpl9cmqz5xd4zbqrpiv0rv5c36a18jkqnsfky6n6sgr424"))))
    (build-system pyproject-build-system)
-    (native-inputs
-     (list unzip python-setuptools python-wheel))
-    (inputs (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"))))))
+     (list #:test-backend #~'custom
+           #:test-flags #~(list "-m" "apsw.tests")))
+    (native-inputs
+     (list python-setuptools))
+    (inputs
+     (list sqlite-next))         ;SQLite 3.45.1 required.
    (home-page "https://github.com/rogerbinns/apsw/")
    (synopsis "Another Python SQLite Wrapper")
    (description
@@ -5741,7 +5823,6 @@ __version_tuple__ = version_tuple = (~a)~%" version version-tuple))))))
           pkg-config
           python-cython
           python-pytest
-           python-pytest-runner
           python-setuptools-scm
           python-setuptools))
    (outputs '("out"))
@@ -6338,7 +6419,7 @@ mechanism of @code{dogpile}.")
 (define-public datasette
  (package
    (name "datasette")
-    (version "1.0a19")
+    (version "1.0a26")
    (source
     (origin
       (method git-fetch)
@@ -6347,23 +6428,20 @@ mechanism of @code{dogpile}.")
              (commit version)))
       (file-name (git-file-name name version))
       (sha256
-        (base32 "0wb73iksrc5vg2lnq3q4vr7yhlzxwr711jfmjdndd0s77996zsfh"))))
+        (base32 "1ra0yfrz9w3jx7ix3dmcsg0g8hjxkz37586g7ijmqshxpzczxfm7"))))
    (build-system pyproject-build-system)
    (arguments
     (list
+      ;; tests: 1720 passed, 9 skipped, 8 xfailed, 13 xpassed, 3 warnings, 120
+      ;; subtests passed
      #:test-flags
-      ;; See https://github.com/simonw/datasette/issues/2048
-      #~(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)))
+      #~(list "--numprocesses" (number->string (min 8 (parallel-job-count)))
+              "--ignore=tests/test_black.py")
      #:phases
      #~(modify-phases %standard-phases
          (add-after 'unpack 'relax-requirements
            (lambda _
-              (substitute* "setup.py"
+              (substitute* "pyproject.toml"
                (("\"pip\",") "")))))))
    (propagated-inputs
     (list python-aiofiles
@@ -6378,7 +6456,6 @@ mechanism of @code{dogpile}.")
           python-janus
           python-jinja2
           python-mergedeep
-           python-pint
           python-pluggy
           python-pyyaml
           python-sqlite-utils
@@ -6387,9 +6464,9 @@ mechanism of @code{dogpile}.")
     (list nss-certs-for-test
           python-beautifulsoup4
           python-cogapp
+           python-multipart-form-data-conformance
           python-pytest
-           python-pytest-asyncio-0.26
-           python-pytest-runner
+           python-pytest-asyncio
           python-pytest-timeout
           python-pytest-xdist
           python-setuptools
@@ -27,7 +27,6 @@
 (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)
@@ -143,9 +142,6 @@ 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))
@@ -244,7 +240,6 @@ efficient syncing
     (list python-aioresponses
           python-pytest
           python-pytest-asyncio
-           python-pytest-cov
           python-pytest-httpserver
           python-setuptools
           python-setuptools-scm
@@ -77,7 +77,6 @@
  #:use-module (gnu packages mail)
  #:use-module (gnu packages multiprecision)
  #:use-module (gnu packages ncurses)
-  #:use-module (gnu packages ninja)
  #:use-module (gnu packages perl)
  #:use-module (gnu packages pkg-config)
  #:use-module (gnu packages pretty-print)
@@ -263,7 +262,7 @@ simple way to add custom protocol messages.")
 (define-public c-vise
  (package
    (name "c-vise")
-    (version "2.4.0")
+    (version "2.8.0")
    (source
     (origin
       (method git-fetch)
@@ -271,37 +270,53 @@ simple way to add custom protocol messages.")
             (url "https://github.com/marxin/cvise")
             (commit (string-append "v" version))))
       (sha256
-        (base32 "1i2z5q2pcwh1gpdqc24x1a2q5vzwhblzzq021nzwf304di7m18vl"))
+        (base32 "1ynhm1d56r25apgvv0wqbdrhjbwigkwrgw92g2czz4nfx77rjxz2"))
       (file-name (git-file-name name version))))
    (build-system cmake-build-system)
-    (native-inputs
-     (list flex python-pytest python-pytest-flake8))
-    (inputs
-     (list bash-minimal clang llvm unifdef
-           python python-pebble python-psutil python-chardet))
    (arguments
-     `(#:phases
-       (modify-phases %standard-phases
-         (add-after 'unpack 'fix-linkage
-           (lambda _
-            (substitute* "clang_delta/CMakeLists.txt"
-              (("\\$\\{LLVM_LINK_LLVM_DYLIB\\}") "True")
-              (("  LLVM") "  LLVMSupport"))))
-         (add-before 'build 'hardcode-paths
-           (lambda _
-            (substitute* "cvise.py"
-              (("/bin/bash") (which "bash"))
-              (("(.*)# Special case for clang-format" & >)
-               (string-append > "# Special case for unifdef\n"
-                              > "programs['unifdef'] = '" (which "unifdef") "'\n"
-                              &)))))
-         (add-after 'install 'wrap
-           (lambda* (#:key outputs #:allow-other-keys)
-             (let ((out (assoc-ref outputs "out"))
-                   (python-path (getenv "GUIX_PYTHONPATH")))
-               (wrap-program (string-append out "/bin/cvise")
-                 `("PYTHONPATH" ":" prefix (,python-path)))
-               #t))))))
+     (list
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-after 'unpack 'fix-linkage
+            (lambda _
+              (substitute* "clang_delta/CMakeLists.txt"
+                (("\\$\\{LLVM_LINK_LLVM_DYLIB\\}")
+                 "True")
+                (("  LLVM")
+                 "  LLVMSupport"))))
+          (add-before 'build 'hardcode-paths
+            (lambda _
+              (substitute* "cvise.py"
+                (("/bin/bash")
+                 (which "bash"))
+                (("(.*)# Special case for clang-format" all blank)
+                 (format #f "~a# Special case for unifdef
+~aprograms['unifdef'] = ~s
+~a"
+                         blank blank (which "unifdef") all)))))
+          (add-after 'install 'wrap
+            (lambda _
+              (let ((python-path (getenv "GUIX_PYTHONPATH")))
+                (wrap-program (string-append #$output "/bin/cvise")
+                  `("PYTHONPATH" ":" prefix
+                    (,(string-join
+                       (filter (lambda (cand)
+                                 (not (string-contains cand "pytest")))
+                               (string-split python-path #\:))
+                       ":"))))))))))
+    (native-inputs
+     (list flex
+           python-pytest
+           python-pytest-flake8))
+    (inputs
+     (list bash-minimal
+           clang
+           llvm
+           unifdef
+           python
+           python-pebble
+           python-psutil
+           python-chardet))
    (home-page "https://github.com/marxin/cvise")
    (synopsis "Reducer for interesting code")
    (description
@@ -1214,7 +1229,7 @@ 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))      ; for tests
+    (native-inputs (list python python-setuptools)) ; for tests
    (synopsis "Fault injector in userspace")
    (description "Fiu provides CLI utilities and a C library
 to mark points of failure inside your code
@@ -41,7 +41,6 @@
  #: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)
@@ -49,6 +48,7 @@
  #:use-module (gnu packages base)
  #:use-module (gnu packages bash)
  #:use-module (gnu packages bison)
+  #:use-module (gnu packages build-tools)
  #:use-module (gnu packages check)
  #:use-module (gnu packages compression)
  #:use-module (gnu packages cpp)
@@ -122,58 +122,83 @@ Carnegie Mellon University.")
              "https://github.com/cmusphinx/cmudict/blob/master/LICENSE"))))

 (define-public dico
-  (package
-    (name "dico")
-    (version "2.12")
-    (source (origin
-              (method url-fetch)
-              (uri (string-append "mirror://gnu/dico/dico-"
-                                  version ".tar.xz"))
-              (sha256
-               (base32
-                "1xvahrav8aml90qcj4cj3a33y0n7nm1k0ywgks1zy2q91v2qk2vj"))))
-    (build-system gnu-build-system)
-    (arguments
-     (list
-      #:configure-flags #~(list "--disable-static")
-      #:phases
-      #~(modify-phases %standard-phases
-          (add-before 'build 'set-shell-file-name
-            (lambda* (#:key inputs #:allow-other-keys)
-              ;; This code invokes "/bin/sh -c 'm4 -s ...'".
-              (substitute* "grecs/src/grecs-lex.c"
-                (("\"/bin/sh\"")
-                 (string-append "\""
-                                (search-input-file inputs "/bin/sh")
-                                "\"")))))
-          (add-before 'check 'silence-guile
-            (lambda _
-              ;; Guile is too talkative, which disturbs the test
-              ;; infrastructure.  Gag it.
-              (setenv "GUILE_AUTO_COMPILE" "0")
-              (setenv "GUILE_WARN_DEPRECATED" "no"))))))
-    (native-inputs (list groff))
-    (inputs
-     (list m4                           ;used at run time
-           bash-minimal                 ;likewise
-           pcre
-           python-wrapper
-           guile-3.0
-           gsasl
-           readline
-           zlib
-           wordnet
-           libxcrypt                    ;for 'crypt'
-           libltdl))
-    (home-page "https://www.gnu.org.ua/software/dico/")
-    (synopsis "Implementation of DICT server (RFC 2229)")
-    (description
-     "GNU Dico implements a flexible dictionary server and client according to
-RFC 2229 (DICT Server).  It is able to access any database available,
+  (let ((commit "05da4bc9e613834fdb065e38c7181044d8889575")
+        (revision "0"))
+    (package
+      (name "dico")
+      (version (git-version "2.12" revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+                (url "https://git.gnu.org.ua/dico.git")
+                (commit commit)
+                (recursive? #t)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32 "1fmr01gpvvb1p6p9ylr67nqx8ymmmkqjhsi9y5zvp2nc32cgxvah"))))
+      (build-system gnu-build-system)
+      (arguments
+       (list
+        #:configure-flags #~(list "--disable-static")
+        #:phases
+        #~(modify-phases %standard-phases
+            (replace 'bootstrap
+              (lambda* (#:key inputs #:allow-other-keys)
+                (substitute* "grecs/bootstrap"
+                  (("/bin/sh")
+                   (which "bash"))
+                  ((" GRECS_GIT_ID=.*")
+                   " GRECS_GIT_ID=v1.0-25-g51b12be\n"))
+                (invoke "perl" "./bootstrap" "--force" "--skip-po")))
+            (add-before 'build 'post-configure
+              (lambda* (#:key inputs #:allow-other-keys)
+                ;; For some reason, this file is missing.
+                (install-file "gnulib/lib/getopt.c"
+                              "xdico/gnu")
+                ;; This code invokes "/bin/sh -c 'm4 -s ...'".
+                (substitute* "grecs/src/grecs-lex.l"
+                  (("\"/bin/sh")
+                   (string-append "\""
+                                  (search-input-file inputs "/bin/sh"))))))
+
+            (add-before 'check 'silence-guile
+              (lambda _
+                ;; Guile is too talkative, which disturbs the test
+                ;; infrastructure.  Gag it.
+                (setenv "GUILE_AUTO_COMPILE" "0")
+                (setenv "GUILE_WARN_DEPRECATED" "no"))))))
+      (native-inputs
+       (list autoconf-2.71
+             automake
+             bison
+             flex
+             gettext-minimal
+             groff
+             libtool
+             perl
+             texinfo))
+      (inputs
+       (list m4                           ;used at run time
+             bash-minimal                 ;likewise
+             pcre
+             python-wrapper
+             guile-3.0
+             gsasl
+             readline
+             zlib
+             wordnet
+             libxcrypt                    ;for 'crypt'
+             libltdl))
+      (home-page "https://www.gnu.org.ua/software/dico/")
+      (synopsis "Implementation of DICT server (RFC 2229)")
+      (description
+       "GNU Dico implements a flexible dictionary server and client according
+to RFC 2229 (DICT Server).  It is able to access any database available,
 regardless of format, thanks to its modular structure.  New modules may be
 written in C, Guile or Python.  Dico also includes a command-line client,
 which may be used to query remote dictionary databases.")
-    (license license:gpl3+)))
+      (license license:gpl3+))))

 (define-public libmaa
  (package
@@ -67,7 +67,6 @@
  #: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)
@@ -290,14 +289,6 @@ 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
@@ -27,7 +27,6 @@
  #: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)
@@ -59,7 +59,6 @@
  #: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)
@@ -106,7 +105,6 @@
  #:use-module (gnu packages libbsd)
  #:use-module (gnu packages linux)
  #:use-module (gnu packages ncurses)
-  #:use-module (gnu packages ninja)
  #:use-module (gnu packages nss)
  #:use-module (gnu packages perl)
  #:use-module (gnu packages perl-web)
@@ -1226,16 +1224,25 @@ and its highly optimized now for efficient performance.")
  (package
    (name "volume-key")
    (version "0.3.12")
-    (source (origin
-              (method url-fetch)
-              (uri (string-append "https://releases.pagure.org/volume_key/volume_key-"
-                                  version ".tar.xz"))
-              (sha256
-               (base32
-                "16rhfz6sjwxlmss1plb2wv2i3jq6wza02rmz1d2jrlnsq67p98vc"))))
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+              (url "https://pagure.io/volume_key")
+              (commit (string-append "volume_key-" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "0zadzbh26ckk263w02d02r2x3mry2kxbybkhwwaxwpv6jsrm7xr6"))))
    (build-system gnu-build-system)
    (native-inputs
-     (list pkg-config swig-4.0 python-3))           ; used to generate the Python bindings
+     (list autoconf
+           automake
+           gettext-minimal
+           libtool
+           pkg-config
+           python       ; used to generate the Python bindings
+           python-setuptools
+           swig))
    (inputs
     (append
      (cons cryptsetup-minimal (libcryptsetup-propagated-inputs))
@@ -1245,15 +1252,21 @@ and its highly optimized now for efficient performance.")
            glib
            gpgme)))
    (arguments
-     `(#:tests? #f ; not sure how tests are supposed to pass, even when run manually
-       #:phases
-       (modify-phases %standard-phases
-         (add-before 'configure 'patch-python.h-path
-           (lambda* (#:key inputs #:allow-other-keys)
-             (let ((python (assoc-ref inputs "python")))
-               (substitute* "Makefile.in"
-                 (("/usr/include/python") (string-append python "/include/python")))
-               #t))))))
+     (list
+      #:tests? #f ; not sure how tests are supposed to pass, even when run manually
+      #:configure-flags
+      #~(list "--without-python"
+              (string-append "--with-gpgme-prefix="
+                             #$(this-package-input "gpgme")))
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-before 'configure 'set-python-paths
+            (lambda* (#:key inputs #:allow-other-keys)
+              (let ((python #$(this-package-native-input "python")))
+                (setenv "PYTHON3"
+                        (string-append python "/bin/python3"))
+                (setenv "PYTHON3_CONFIG"
+                        (string-append python "/bin/python3-config"))))))))
    (home-page "https://pagure.io/volume_key")
    (synopsis "Manipulate storage volume encryption keys")
    (description
@@ -46,6 +46,7 @@
  #:use-module (gnu packages perl)
  #:use-module (gnu packages sqlite)
  #:use-module (gnu packages python)
+  #:use-module (gnu packages python-build)
  #:use-module (gnu packages python-xyz))

 (define-public boinc-client
@@ -108,7 +109,11 @@ resources).  It supports virtualized, parallel, and GPU-based applications.")
                                     "--with-gtk"
                                     "--with-auth")))
    (native-inputs
-     (list pkg-config autoconf automake which))
+     (list autoconf
+           automake
+           pkg-config
+           python-setuptools
+           which))
    (inputs
     (list avahi
           gtk+
@@ -37,7 +37,6 @@
  #: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)
@@ -313,7 +312,7 @@ to the @dfn{don't repeat yourself} (DRY) principle.")
        (base32 "1a5vd07wrnfbclvf6pz9p8ag9kdd1453lsl9q0bkyc45hq2xqd2a"))))
    (build-system pyproject-build-system)
    (native-inputs
-     (list python-django python-pytest python-pytest-cov python-setuptools))
+     (list python-django python-pytest python-setuptools))
    (home-page "https://github.com/epicserve/django-cache-url")
    (synopsis "Configure Django cache settings from URLs")
    (description
@@ -404,7 +403,6 @@ 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
@@ -1313,7 +1311,6 @@ 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
@@ -2170,7 +2167,6 @@ 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))
@@ -29,7 +29,6 @@
  #: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)
@@ -41,6 +41,7 @@
  #:use-module (gnu packages)
  #:use-module (gnu packages base)
  #:use-module (gnu packages bash)
+  #:use-module (gnu packages build-tools)
  #:use-module (gnu packages check)
  #:use-module (gnu packages compression)
  #:use-module (gnu packages curl)
@@ -48,10 +49,10 @@
  #:use-module (gnu packages gdb)
  #:use-module (gnu packages libedit)
  #:use-module (gnu packages llvm)
-  #:use-module (gnu packages ninja)
  #:use-module (gnu packages perl)
  #:use-module (gnu packages pkg-config)
  #:use-module (gnu packages python)
+  #:use-module (gnu packages python-build)
  #:use-module (gnu packages python-xyz)
  #:use-module (gnu packages textutils)
  #:use-module (gnu packages xorg)
@@ -116,6 +117,7 @@
       ("ldc" ,gdmd)
       ("ninja" ,ninja)
       ("python-wrapper" ,python-wrapper)
+       ("python-setuptools" ,python-setuptools)
       ("tzdata" ,tzdata-for-tests)
       ("unzip" ,unzip)))
    (home-page "http://wiki.dlang.org/LDC")
@@ -53,7 +53,6 @@
  #: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
@@ -666,7 +665,8 @@ the in DocBook SGML DTDs.")
               (base32
                "0yd09nypswy3q4scri1dg7dr99d7gd6r2dwx0xm81l9f4y32gs0n"))
              (patches
-               (search-patches "dblatex-inkscape-1.0.patch"))))
+               (search-patches "dblatex-importlib.patch"
+                               "dblatex-inkscape-1.0.patch"))))
    (outputs '("out" "doc"))
    (build-system pyproject-build-system)
    (arguments
@@ -39,7 +39,6 @@
  #: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)
@@ -41,7 +41,6 @@
  #: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)
@@ -490,9 +489,8 @@ inspired by Dash.")
    (build-system gnu-build-system)
    (arguments
     (list
-      ;; Essentially a lighter copy of the former python-build-system.
-      ;; Using it rather than pyproject-build-system allows to edit the latter
-      ;; without a texlive + haskell world rebuild.
+      ;; Custom build steps to prevent using pyproject-build-system which
+      ;; allows to edit the latter without a texlive + haskell world rebuild.
      #:phases
      #~(modify-phases %standard-phases
          (delete 'bootstrap)
@@ -62,7 +62,6 @@
  #: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
@@ -25,7 +25,6 @@
  #: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)
@@ -40,7 +40,6 @@
  #: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)
@@ -207,7 +206,7 @@ with Microsoft Compiled HTML (CHM) files.")
           python-css-parser
           python-cssselect
           python-dateutil
-           python-dnspython-1.16
+           python-dnspython
           python-feedparser
           python-fonttools
           python-html2text
@@ -283,7 +282,9 @@ tags = [\"WS_X11\"]")
                 (string-append "[tool.sip.project]
 sip-include-dirs = [\""
                   #$(this-package-input "python-pyqt")
-                   "/lib/python3.11/site-packages/PyQt6/bindings\"]")))
+                   "/lib/python"
+                   #$(version-major+minor (package-version python))
+                   "/site-packages/PyQt6/bindings\"]")))
              (substitute* "src/calibre/ebooks/pdf/pdftohtml.py"
                (("PDFTOHTML = 'pdftohtml'")
                 (string-append "PDFTOHTML = \""
@@ -91,7 +91,6 @@
  #: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))
@@ -64,7 +64,6 @@
  #: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)
@@ -196,6 +195,10 @@
            (add-after 'unpack 'generate-gdk-pixbuf-loaders-cache-file
              (assoc-ref glib-or-gtk:%standard-phases
                         'generate-gdk-pixbuf-loaders-cache-file))
+            (add-after 'unpack 'fix-python-incompatibilities
+              (lambda _
+                (substitute* (find-files "." "\\.py$")
+                  (("assertEquals") "assertEqual"))))
            (add-before 'build 'set-home-env
              (lambda _
                (setenv "HOME" "/tmp")))
@@ -579,8 +582,10 @@ individual low-level driver modules.")
    (build-system gnu-build-system)
    (arguments
     (list
-      #:imported-modules (append %default-gnu-imported-modules
-                                 %python-build-system-modules)
+      #:imported-modules %pyproject-build-system-modules
+      #:modules '((guix build gnu-build-system)
+                  ((guix build pyproject-build-system) #:prefix py:)
+                  (guix build utils))
      #:make-flags
      #~(list (string-append "PREFIX=" #$output))
      #:phases
@@ -607,7 +612,7 @@ individual low-level driver modules.")
                (invoke "make" "-C" "examples/spm")
                (invoke "make" "-C" "examples/simple"))))
          (add-after 'install 'python:wrap
-            (@@ (guix build python-build-system) wrap)))))
+            (assoc-ref py:%standard-phases 'wrap)))))
    (native-inputs
     (list clang python-minimal-wrapper python-sphinx texinfo yosys))
    (inputs
@@ -1672,6 +1677,10 @@ an embedded event driven algorithm.")
     (list
      #:phases
      #~(modify-phases %standard-phases
+          (add-after 'unpack 'relax-requirements
+            (lambda _
+              (substitute* "pyproject.toml"
+                (("click>=8,<8.3") "click>=8"))))
          (add-after 'compress-documentation 'wrap-program
            (lambda _
              (wrap-program (string-append #$output "/bin/librelane")
@@ -2252,7 +2261,10 @@ versus schematic} tests and can assist with automatic routing.")
     (list
      #:tests? #f                       ;there are no tests
      #:imported-modules (append %qt-build-system-modules
-                                 %python-build-system-modules)
+                                 %pyproject-build-system-modules)
+      #:modules '((guix build qt-build-system)
+                  ((guix build pyproject-build-system) #:prefix py:)
+                  (guix build utils))
      #:phases
      #~(modify-phases %standard-phases
          (add-after 'unpack 'build-info-documentation
@@ -2281,7 +2293,7 @@ versus schematic} tests and can assist with automatic routing.")
              (install-it "mcy")
              (install-it "mcy-dash")))
          (add-after 'make-install 'python:wrap
-            (@@ (guix build python-build-system) wrap)))))
+            (assoc-ref py:%standard-phases 'wrap)))))
    (native-inputs
     (list pkg-config
           python-sphinx
@@ -2509,7 +2521,7 @@ Automation}, portable and vendor neutral FPGA place and route tool.")
 (define-public nvc
  (package
    (name "nvc")
-    (version "1.20.1")
+    (version "1.21.0")
    (source (origin
              (method git-fetch)
              (uri (git-reference
@@ -2518,7 +2530,7 @@ Automation}, portable and vendor neutral FPGA place and route tool.")
              (file-name (git-file-name name version))
              (sha256
               (base32
-                "1b38x2ch468s4p6mrq6c8s0d95vb84p6w4v8in79l4w7sfy8jnr0"))))
+                "00hnrzk9dw88srfmjxxb9xkgnd5n26pmqlcw1bff1y0bckblsr38"))))
    (build-system gnu-build-system)
    (arguments
     (list #:out-of-source? #t
@@ -3248,7 +3260,6 @@ Numpy arrays for convenience.")
              (setenv "PDM_BUILD_SCM_VERSION" #$version))))))
    (native-inputs
     (list python-pdm-backend
-           python-pytest-cov
           python-setuptools
           python-setuptools-scm
           sby
@@ -3427,8 +3438,12 @@ SystemVerilog, and SystemC, with conversion between languages and to JSON.")
                                          inputs "include/antlr4-runtime"))
                     (antlr4cpp-lib (search-input-file
                                      inputs "lib/libantlr4-runtime.so"))
-                     (python-include (search-input-directory
-                                       inputs "include/python3.11")))
+                     (python-include
+                      (search-input-directory
+                       inputs
+                       (string-append
+                        "include/python"
+                        #$(version-major+minor (package-version python))))))
                ;; Patch CMake to use our paths directly.
                (substitute* "src/CMake_antlr4.txt"
                  (("set\\(ANTLR_CLASSPATH \"\"\\)")
@@ -3593,15 +3608,16 @@ Standard} data mode.")
    (version "0.4.1")
    (source
     (origin
-       (method url-fetch)
-       (uri (pypi-uri "pyvcd" version))
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/SanDisk-Open-Source/pyvcd")
+             (commit version)))
+       (file-name (git-file-name name version))
       (sha256
-        (base32 "15nnydvr1a4ykh8cagi484sfgvdg0dnjxaw6c0ivhjbrbblpaqnw"))))
+        (base32 "1a1fsgxmpy6gbrs7lp3a56b7d4g6srlp42y5azb1ywjx3w8fiwc6"))))
    (build-system pyproject-build-system)
    (native-inputs
-     (list python-pytest-cov
-           python-setuptools
-           python-setuptools-scm))
+     (list python-pytest python-setuptools python-setuptools-scm))
    (home-page "http://pyvcd.readthedocs.io/")
    (synopsis "Library to manipulate digital wave files")
    (description
@@ -3878,10 +3894,7 @@ Automation}.")
                         #$output "/share/info/hdlmake-figures")))))
      #:test-flags #~(list "test_all.py")))
    (native-inputs
-     (list python-pytest-cov
-           python-setuptools
-           python-sphinx
-           texinfo))
+     (list python-pytest 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")
@@ -4044,18 +4057,9 @@ 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))))
-      #:phases
-      #~(modify-phases %standard-phases
-          (add-after 'unpack 'pathch-pytest-options
-            (lambda _
-              (substitute* "pyproject.toml"
-                ((".*--cov=.*") "")
-                ((".*--self-contained-html.*") "")
-                ((".*-n.*auto.*") "")))))))
+         "--numprocesses" (number->string (min 8 (parallel-job-count))))))
    (native-inputs
-     (list python-pytest-cov
-           python-pytest-html
+     (list python-pytest
           python-pytest-xdist
           python-setuptools))
    (propagated-inputs
@@ -4619,11 +4623,10 @@ them usable as simple logic analyzer and/or oscilloscope hardware.")
     (list
      #:parallel-tests? #f
      #:test-target "test"
+      #:imported-modules %pyproject-build-system-modules
      #:modules `((guix build gnu-build-system)
-                  ((guix build python-build-system) #:prefix python:)
+                  ((guix build pyproject-build-system) #:prefix python:)
                  (guix build utils))
-      #:imported-modules `(,@%default-gnu-imported-modules
-                           (guix build python-build-system))
      #:make-flags #~(list (string-append "PREFIX=" #$output))
      #:phases
      #~(modify-phases %standard-phases
@@ -242,6 +242,7 @@
  #:use-module (gnu packages networking)
  #:use-module (gnu packages ocr)
  #:use-module (gnu packages python)
+  #:use-module (gnu packages python-build)
  #:use-module (gnu packages python-xyz)
  #:use-module (gnu packages python-check)
  #:use-module (gnu packages telephony)
@@ -14050,46 +14051,54 @@ libraries from Swagger specs.")
      #:imported-modules (append %emacs-build-system-modules
                                 %pyproject-build-system-modules)
      #:modules '((guix build emacs-build-system)
-                  ((guix build python-build-system) #:prefix py:)
+                  ((guix build pyproject-build-system) #:prefix py:)
                  (guix build emacs-utils)
                  (guix build utils))
      #:phases
-      #~(modify-phases %standard-phases
-          (add-after 'unpack 'avoid-server-installation-for-tests
-            (lambda _
-              (substitute* "Makefile"
-                ;; Disable tox since it's only configured for python 3.8 and
-                ;; python 3.9 by the project--that's ancient.
-                (("tox")
-                 "echo tox")
-                (("env: .*$")
-                 (string-append "env: " #$output "/bin/jediepcserver\n")))))
-          (add-after 'unpack 'ensure-no-mtimes-pre-1980
-            (assoc-ref py:%standard-phases 'ensure-no-mtimes-pre-1980))
-          (add-before 'check 'setenv
-            (lambda _
-              (setenv "HOME" "/tmp")))
-          (add-after 'ensure-no-mtimes-pre-1980 'relax-python-requirements
-            (lambda _
-              ;; Argparse should only be required for Python < 3.2
-              ;; (see: https://github.com/tkf/emacs-jedi/issues/365).
-              (substitute* "setup.py"
-                ((".*argparse.*") ""))))
-          (add-after 'relax-python-requirements 'python:add-install-to-pythonpath
-            (assoc-ref py:%standard-phases 'add-install-to-pythonpath))
-          (add-after 'python:add-install-to-pythonpath 'python:install
-            (assoc-ref py:%standard-phases 'install))
-          (add-after 'python:install 'python:wrap
-            (assoc-ref py:%standard-phases 'wrap))
-          (add-after 'python:wrap 'patch-jedi:server-command
-            (lambda* (#:key outputs #:allow-other-keys)
-              (emacs-substitute-variables "jedi-core.el"
-                ("jedi:server-command"
-                 `(list ,(search-input-file outputs "bin/jediepcserver")))))))))
+      (with-extensions (list (pyproject-guile-json))
+        #~(modify-phases %standard-phases
+            (add-after 'unpack 'avoid-server-installation-for-tests
+              (lambda _
+                (substitute* "Makefile"
+                  ;; Disable tox since it's only configured for python 3.8 and
+                  ;; python 3.9 by the project--that's ancient.
+                  (("tox")
+                   "echo tox")
+                  (("env: .*$")
+                   (string-append "env: " #$output "/bin/jediepcserver\n")))))
+            (add-after 'unpack 'ensure-no-mtimes-pre-1980
+              (assoc-ref py:%standard-phases 'ensure-no-mtimes-pre-1980))
+            (add-before 'check 'setenv
+              (lambda _
+                (setenv "HOME" "/tmp")))
+            (add-after 'ensure-no-mtimes-pre-1980 'relax-python-requirements
+              (lambda _
+                ;; Argparse should only be required for Python < 3.2
+                ;; (see: https://github.com/tkf/emacs-jedi/issues/365).
+                (substitute* "setup.py"
+                  ((".*argparse.*") ""))))
+            (add-after 'relax-python-requirements 'python:build
+              (assoc-ref py:%standard-phases 'build))
+            (add-after 'python:build 'python:add-install-to-pythonpath
+              (assoc-ref py:%standard-phases 'add-install-to-pythonpath))
+            (add-after 'python:add-install-to-pythonpath 'python:install
+              (assoc-ref py:%standard-phases 'install))
+            (add-after 'python:install 'python:create-entrypoints
+              (assoc-ref py:%standard-phases 'create-entrypoints))
+            (add-after 'python:create-entrypoints 'python:wrap
+              (assoc-ref py:%standard-phases 'wrap))
+            (add-after 'python:wrap 'patch-jedi:server-command
+              (lambda* (#:key outputs #:allow-other-keys)
+                (emacs-substitute-variables "jedi-core.el"
+                  ("jedi:server-command"
+                   `(list ,(search-input-file outputs "bin/jediepcserver"))))))))))
    (native-inputs (list emacs-mocker python-wrapper))
    (inputs (list python-wrapper python-epc python-jedi)) ;wrapped
    (propagated-inputs
-     (list emacs-auto-complete emacs-python-environment emacs-epc))
+     (list emacs-auto-complete
+           emacs-python-environment
+           emacs-epc
+           python-setuptools))
    (home-page "https://github.com/tkf/emacs-jedi")
    (synopsis "Provides Python completion in Emacs")
    (description
@@ -15517,34 +15526,6 @@ underlying library functionality for performing various activities related to
 the game of chess.")
    (license license:gpl3+)))

-(define-public emacs-4clojure
-  ;; There is no release.  Base version is extracted from Version keyword in
-  ;; the main file.
-  (let ((commit "4eccf8c7d4341a36c269451838114b27836699f9")
-        (revision "1"))
-    (package
-      (name "emacs-4clojure")
-      (version (git-version "0.2.1" revision commit))
-      (source
-       (origin
-         (method git-fetch)
-         (uri (git-reference
-               (url "https://github.com/emacsorphanage/4clojure")
-               (commit commit)))
-         (file-name (git-file-name name version))
-         (sha256
-          (base32 "19x653lzc1dxil4ix257hciidbdmbhaxhs6qhlkwi9ygjrlrgvnk"))))
-      (build-system emacs-build-system)
-      (propagated-inputs
-       (list emacs-request))
-      (home-page "https://github.com/emacsorphanage/4clojure/")
-      (synopsis "Open and evaluate 4clojure questions in Emacs")
-      (description "Emacs 4clojure interacts with
-@url{http://www.4clojure.com, 4clojure} problems.  You can open a specific
-question and move to the next or previous one.  You can also verify your
-answers.")
-      (license license:gpl3+))))
-
 (define-public emacs-base16-theme
  (package
    (name "emacs-base16-theme")
@@ -45,7 +45,6 @@
  #: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)
@@ -2037,13 +2036,7 @@ 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")
-      #:phases
-      #~(modify-phases %standard-phases
-          (add-after 'unpack 'fix-pytest-config
-            (lambda _
-              (substitute* "pytest.ini"
-                (("addopts = .*") "")))))))
+      #~(list "--ignore=tests/ci_scripts/test_sync_board_db.py")))
    (native-inputs
     (list python-factory-boy
           python-pytest
@@ -68,6 +68,7 @@
  #: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 cdrom)
  #:use-module (gnu packages check)
  #:use-module (gnu packages cmake)
@@ -107,7 +108,6 @@
  #:use-module (gnu packages music)
  #:use-module (gnu packages ncurses)
  #:use-module (gnu packages networking)
-  #:use-module (gnu packages ninja)
  #:use-module (gnu packages parallel)
  #:use-module (gnu packages pkg-config)
  #:use-module (gnu packages pretty-print)
@@ -140,7 +140,6 @@
  #: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))
@@ -41,7 +41,6 @@
  #: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))

@@ -77,7 +77,6 @@
  #: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)
@@ -1673,7 +1672,7 @@ multiple services and devices with hundreds of supported integrations.")
 (define-public python-esptool
  (package
    (name "python-esptool")
-    (version "5.0.2")
+    (version "5.2.0")
    (source
     (origin
       (method git-fetch)
@@ -1682,7 +1681,7 @@ multiple services and devices with hundreds of supported integrations.")
              (commit (string-append "v" version))))
       (file-name (git-file-name name version))
       (sha256
-        (base32 "1wl75j6ncm5lahy9pzc38qivhaf9p42a2bijishdkwkw388fs6x1"))))
+        (base32 "0rgwa7mimznwkn8ql17yxwxsfp0is3i75y7bf62mgsxjyx7zawcd"))))
    (build-system pyproject-build-system)
    (arguments
     (list
@@ -1931,21 +1930,55 @@ r2ghidra.")
 (define-public rayforge
  (package
    (name "rayforge")
-    (version "1.0.2")
+    (version "1.7.7")   ;newer version requires python-raygeo (Rust)
    (source
     (origin
       (method git-fetch)
       (uri (git-reference
-             (url "https://github.com/barebaric/rayforge")
-             (commit version)))
+              (url "https://github.com/barebaric/rayforge")
+              (commit version)))
       (file-name (git-file-name name version))
       (sha256
-        (base32 "1c6dl0x3pafmh4p533jbk2cj73q90vz1797jya3hzzxdv0h383yc"))))
+        (base32 "1w44qw51nynf1rk61y0d0wj6xl66ciswpcsp38dnwrpfwsqgafxw"))))
    (build-system pyproject-build-system)
+    (arguments
+     (list
+      ;; tests: 1626 passed
+      #:test-flags
+      ;; XXX: Tests fail to pick exact version of cairo: E gi.RepositoryError:
+      ;; Typelib file for namespace 'cairo', version '1.0' not found
+      #~(list "--ignore=tests/core/geo/test_font_config.py"
+              "--ignore=tests/core/geo/test_geo_text.py"
+              "--ignore=tests/core/geo/test_geometry.py"
+              "--ignore=tests/core/geo/test_text.py"
+              "--ignore=tests/core/geo/test_transform.py"
+              ;; XXX: Projects ships a huge test suite which the majority
+              ;; fail, run bare minimal core tests.
+              "tests/core")
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-after 'unpack 'relax-requirements
+            (lambda _
+              ;; All of the dependencies are pined to exact version.
+              (substitute* "requirements.txt"
+                (("[=~]=.*") "\n")
+                ;; XXX: Guix's opencv package does not provide Python's
+                ;; version metadata.
+                (("opencv_python") ""))))
+          (add-before  'sanity-check 'set-home
+            (lambda _
+              (setenv "HOME" "/tmp")))
+          (add-before 'check 'remove-local-source
+            (lambda _
+              (delete-file-recursively "rayforge")))
+          (add-after 'wrap 'wrap-rayforge
+            (lambda _
+              (wrap-program (string-append #$output "/bin/rayforge")
+                `("GI_TYPELIB_PATH" ":" prefix
+                  (,(getenv "GI_TYPELIB_PATH")))))))))
    (native-inputs (list python-gitpython
                         python-pytest
                         python-pytest-asyncio
-                         python-pytest-cov
                         python-pytest-mock
                         python-setuptools))
    (inputs (list bash-minimal
@@ -1955,54 +1988,27 @@ r2ghidra.")
                  python-asyncudp
                  python-blinker
                  python-ezdxf
+                  python-gitpython
                  python-numpy
                  python-platformdirs
+                  python-pluggy
                  python-pycairo
                  python-pyclipper
                  python-pygobject
+                  python-pymupdf
                  python-pyopengl
                  python-pyopengl-accelerate
                  python-pypdf
-                  python-pyserial-asyncio
+                  python-pyserial
                  python-pyvips
                  python-pyyaml
                  python-scipy
                  python-semver
                  python-svgelements
+                  python-trimesh
                  python-websockets
                  vtracer))
-    (arguments
-     (list
-      #:phases
-      #~(modify-phases %standard-phases
-          (add-after 'unpack 'write-version-file
-            (lambda _
-              (call-with-output-file "rayforge/version.txt"
-                (lambda (port)
-                  (display #$version port)))
-              (let ((port (open-file "MANIFEST.in" "a")))
-                (display "include rayforge/version.txt\n" port)
-                (close-port port))))
-          (add-after 'unpack 'fix-tests
-            (lambda _
-              (mkdir "tmp-home")
-              (setenv "HOME"
-                      (string-append (getcwd) "/tmp-home"))
-              ;; Fix abstract class test for older Python error message format
-              (substitute* "tests/pipeline/stage/test_base_stage.py"
-                (("without an implementation for abstract method 'reconcile'")
-                 "abstract method '?reconcile'?"))
-              ;; Fix arc fitting test: add looser tolerance for floating point comparison
-              (substitute* "tests/core/geo/test_fitting.py"
-                (("(assert np\\.allclose\\(.*, \\(-10\\.0, 0\\.0\\))" match)
-                 (string-append match ", atol=1e-3")))))
-          (delete 'sanity-check) ; Tests against python package version of rayforge
-          (add-after 'wrap 'wrap-rayforge
-            (lambda _
-              (wrap-program (string-append #$output "/bin/rayforge")
-                `("GI_TYPELIB_PATH" ":" prefix
-                  (,(getenv "GI_TYPELIB_PATH")))))))))
-    (home-page "https://github.com/barebaric/rayforge")
+    (home-page "https://rayforge.org/")
    (synopsis "Desktop application for laser cutting and engraving")
    (description
     "Rayforge is a cross-platform 2D CAD and G-code control software designed
@@ -2484,7 +2490,6 @@ 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
@@ -3019,20 +3024,22 @@ interpolation toolkit.")
 (define-public python-motulator
  (package
    (name "python-motulator")
-    (version "0.5.0")
+    (version "0.6.2")
    (source
     (origin
-       (method url-fetch)
-       (uri (pypi-uri "motulator" version))
+       (method git-fetch)
+       (uri (git-reference
+              (url "https://github.com/Aalto-Electric-Drives/motulator/")
+              (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
       (sha256
-        (base32 "1kh13zfa4w73q04pny2w2zgym47fp8xy7glwfx82fdx4fihk7dv7"))))
+        (base32 "1di2r1i19jl751v0hj426zkwk48w5yf8zpw2bl6qzk0vq4z2vpbw"))))
    (build-system pyproject-build-system)
    (arguments
     (list #:tests? #f)) ; there are no tests
-    (propagated-inputs (list python-matplotlib python-numpy python-scipy))
-    (native-inputs (list python-hatchling
-                         python-ipykernel
-                         python-toml))
+    (propagated-inputs
+     (list python-numpy python-matplotlib python-scipy python-tqdm))
+    (native-inputs (list python-hatchling))
    (home-page "https://aalto-electric-drives.github.io/motulator/")
    (synopsis "Motor Drive Simulator in Python")
    (description "This package includes simulation models for an induction
@@ -4176,10 +4183,6 @@ BOM creation and has a lot of extra features.")
       (sha256
        (base32 "19fi0y0lk45cyampczgh3kz2swai4zcgzkffp0xf5h55rxxrdpvk"))))
    (build-system cmake-build-system)
-    (inputs
-     (list protobuf
-           python
-           python-sip-4))
    (arguments
     `(#:tests? #f
       #:configure-flags '("-DBUILD_EXAMPLES=OFF")
@@ -4200,6 +4203,11 @@ BOM creation and has a lot of extra features.")
                                 (package-version python))
                               "/site-packages"
                               " Python3_SITEARCH"))))))))
+    (inputs
+     (list protobuf
+           python
+           python-sip-4))
+    (native-inputs (list python-setuptools))
    (home-page "https://github.com/Ultimaker/libArcus")
    (synopsis "Communication library for Ultimaker software components")
    (description "This library contains C++ code and Python3 bindings for
@@ -4418,15 +4426,6 @@ problem.  It was inspired from the SVGNest Javascript library.")
       (sha256
        (base32 "0jhqfylg6vzlbz9rqs981bg6y8s18iklw1p8hmax72xq2c7561s1"))))
    (build-system cmake-build-system)
-    (native-inputs
-     (list pkg-config))
-    (inputs
-     (list boost
-           clipper
-           libnest2d-for-cura
-           nlopt
-           python
-           python-sip-4))
    (arguments
     `(#:tests? #f
       #:phases
@@ -4446,6 +4445,16 @@ problem.  It was inspired from the SVGNest Javascript library.")
                  (string-append path " Python3_SITEARCH"))
                 (("\\$\\{_process_output\\} Python3_SITELIB")
                  (string-append path " Python3_SITELIB")))))))))
+    (native-inputs
+     (list pkg-config
+           python-setuptools))
+    (inputs
+     (list boost
+           clipper
+           libnest2d-for-cura
+           nlopt
+           python
+           python-sip-4))
    (home-page "https://github.com/Ultimaker/pynest2d")
    (synopsis "Python bindings for libnest2d")
    (description
@@ -4490,8 +4499,6 @@ belongs to the Cura project from Ultimaker.")
       (sha256
        (base32 "1cq85x0xizsjwf9nl7v7x4i9vl335mgv2lda3q2c9fcwrndsc3wk"))))
    (build-system cmake-build-system)
-    (inputs
-     (list python python-sip-4))
    (arguments
     `(#:tests? #f ; No test suite.
       #:phases
@@ -4508,6 +4515,8 @@ belongs to the Cura project from Ultimaker.")
                  (string-append path " Python3_SITEARCH"))
                 (("\\$\\{_process_output\\} Python3_SITELIB")
                  (string-append path " Python3_SITELIB")))))))))
+    (inputs (list python python-sip-4))
+    (native-inputs (list python-setuptools))
    (home-page "https://github.com/Ultimaker/libSavitar")
    (synopsis "C++ implementation of 3mf loading with SIP python bindings")
    (description "LibSavitar is a C++ implementation of 3mf loading with SIP
@@ -4950,7 +4959,9 @@ and mogan.")
               (("'\" [+] python_path [+]")
                (string-append "'\" + std::string(\""
                               (assoc-ref outputs "out")
-                               "/lib/python3.11/site-packages"
+                               "/lib/python"
+                               #$(version-major+minor (package-version python))
+                               "/site-packages"
                               "\") +")))))
          (add-before 'check 'prepare-checks
            (lambda _
@@ -30,7 +30,6 @@
  #: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)
@@ -29,7 +29,6 @@
  #: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)
@@ -245,7 +244,6 @@ 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
@@ -52,7 +52,6 @@
  #: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)
@@ -1508,158 +1507,6 @@ can create and compare snapshots, revert differences between them, and
 supports automatic snapshots timelines.")
    (license license:gpl2)))

-(define-public xfstests
-  ;; The last release (1.1.0) is from 2011.
-  (let ((revision "3")
-        (commit "8de535c53887bb49adae74a1b2e83e77d7e8457d"))
-    (package
-      (name "xfstests")
-      (version (git-version "1.1.0" revision commit))
-      (source
-       (origin
-         (method git-fetch)
-         (uri (git-reference
-               (url "git://git.kernel.org/pub/scm/fs/xfs/xfstests-dev.git")
-               (commit commit)))
-         (file-name (git-file-name name version))
-         (sha256
-          (base32 "1sbkryl04xflrk6jb4fsl3h2whilj5m3vpdkpwwb26idp7ckjjv6"))))
-      (build-system gnu-build-system)
-      (arguments
-       (list
-        #:configure-flags
-        #~'("CFLAGS=-Wno-error=implicit-int")
-        #:phases
-        #~(modify-phases %standard-phases
-            (add-after 'unpack 'patch-tool-locations
-              (lambda* (#:key inputs #:allow-other-keys)
-                (substitute* "common/config"
-                  ;; Make absolute file names relative.
-                  (("(MKFS_PROG=\").*(\")" _ pre post)
-                   (string-append pre "mkfs" post)))
-                (for-each (lambda (file)
-                            (substitute* file
-                              (("( -s|#.|[= ])(/bin/sh|/bin/bash)" _ pre match)
-                               (string-append pre
-                                              (search-input-file inputs match)))
-                              (("/bin/(rm|true)" match)
-                               (search-input-file inputs match))
-                              (("/usr(/bin/time)" _ match)
-                               (search-input-file inputs match))))
-                          (append (find-files "common" ".*")
-                                  (find-files "tests" ".*")
-                                  (find-files "tools" ".*")
-                                  (find-files "src" "\\.(c|sh)$")))))
-            (replace 'bootstrap
-              (lambda* (#:key make-flags #:allow-other-keys)
-                (substitute* "Makefile"
-                  ;; Avoid a mysterious (to me) ‘permission denied’ error.
-                  (("cp ") "cp -f "))
-                (substitute* "m4/package_utilies.m4"
-                  ;; Fix the bogus hard-coded paths for every single binary.
-                  (("(AC_PATH_PROG\\(.*, ).*(\\))" _ pre post)
-                   (string-append pre (getenv "PATH") post)))
-                (apply invoke "make" "configure" make-flags)))
-            (add-after 'install 'wrap-xfstests/check
-              ;; Keep wrapping distinct from 'create-helper-script below: users
-              ;; must be able to invoke xfstests/check directly if they prefer.
-              (lambda* (#:key inputs #:allow-other-keys)
-                (wrap-program (string-append #$output "/xfstests/check")
-                  ;; Prefix the user's PATH with the minimum required tools.
-                  ;; The suite has many other optional dependencies and will
-                  ;; automatically select tests based on the original PATH.
-                  `("PATH" ":" prefix
-                    ,(map (lambda (file)
-                            (dirname (search-input-file inputs file)))
-                          (list "bin/setfacl"         ; acl
-                                "bin/attr"            ; attr
-                                "bin/bc"              ; bc
-                                "bin/df"              ; coreutils
-                                "bin/hostname"        ; inetutils
-                                "bin/perl"            ; perl
-                                "sbin/mkfs.xfs")))))) ; xfsprogs
-            (add-after 'install 'create-helper
-              ;; Upstream installs only a ‘check’ script that's not in $PATH and
-              ;; would try to write to the store without explaining how to change
-              ;; that.  Install a simple helper script to make it discoverable.
-              (lambda* (#:key inputs #:allow-other-keys)
-                (let* ((check  (string-append #$output "/xfstests/check"))
-                       (bin    (string-append #$output "/bin"))
-                       (helper (string-append bin "/xfstests-check")))
-                  (mkdir-p bin)
-                  (with-output-to-file helper
-                    (lambda _
-                      (format #t "#!~a --no-auto-compile\n!#\n"
-                              (search-input-file inputs "/bin/guile"))
-                      (write
-                       `(begin
-                          (define (try proc dir)
-                            "Try to PROC DIR.  Return DIR on success, else #f."
-                            (with-exception-handler (const #f)
-                              (lambda _ (proc dir) dir)
-                              #:unwind? #t))
-
-                          (define args
-                            (cdr (command-line)))
-
-                          (when (or (member "--help" args)
-                                    (member "-h" args))
-                            (format #t "Usage: ~a [OPTION]...
-This Guix helper sets up a new writable RESULT_BASE if it's unset, then executes
-xfstest's \"~a\" command (with any OPTIONs) as documented below.\n\n"
-                                    ,(basename helper)
-                                    ,(basename check)))
-
-                          (let* ((gotenv-base (getenv "RESULT_BASE"))
-                                 (base (or gotenv-base
-                                           (let loop ((count 0))
-                                             (or (try mkdir
-                                                      (format #f "xfstests.~a"
-                                                              count))
-                                                 (loop (+ 1 count))))))
-                                 (result-base (if (string-prefix? "/" base)
-                                                  base
-                                                  (string-append (getcwd) "/"
-                                                                 base))))
-                            (setenv "RESULT_BASE" result-base)
-                            ;; CHECK must run in its own directory or will fail.
-                            (chdir ,(dirname check))
-                            (let ((status
-                                   (status:exit-val (apply system* ,check args))))
-                              (unless gotenv-base
-                                (try rmdir result-base))
-                              status))))))
-                  (chmod helper #o755)))))))
-      (native-inputs
-       (list autoconf automake libtool))
-      (inputs
-       (list acl
-             attr
-             bash-minimal
-             bc
-             guile-3.0                  ; for our xfstests-check helper script
-             inetutils
-             `(,util-linux "lib")
-             perl
-             time
-             xfsprogs))
-      (home-page "https://git.kernel.org/pub/scm/fs/xfs/xfstests-dev.git")
-      (synopsis "File system @acronym{QA, Quality Assurance} test suite")
-      (description
-       "The @acronym{FSQA, File System Quality Assurance} regression test suite,
-more commonly known as xfstests, comprises over 1,500 tests that exercise
-(@dfn{torture}) both the user- and kernel-space parts of many different file
-systems.
-
-As the package's name subtly implies, it was originally developed to test the
-XFS file system.  Today, xfstests is the primary test suite for all major file
-systems supported by the kernel Linux including XFS, ext4, and Btrfs, but also
-virtual and network file systems such as NFS, 9P, and the overlay file system.
-
-The packaged @command{check} script is not in @env{PATH} but can be invoked
-with the included @command{xfstests-check} helper.")
-      (license license:gpl2))))
-
 (define-public zfs
  (package
    (name "zfs")
@@ -2072,6 +1919,10 @@ local file system using FUSE.")
       (sha256
        (base32 "09409sjncz7n9m2ia5nfzy10q7c23dvpgjdkc3j9bjs4f5hvc9aq"))))
    (build-system pyproject-build-system)
+    (arguments
+     (list
+      #:test-backend #~'custom
+      #:test-flags #~(list "bitmasklist_test.py")))
    (native-inputs
     (list python-setuptools
           python-setuptools-scm))
@@ -71,7 +71,6 @@
  #: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)
@@ -130,7 +129,6 @@
  #:use-module (gnu packages multiprecision)
  #:use-module (gnu packages ncurses)
  #:use-module (gnu packages networking)
-  #:use-module (gnu packages ninja)
  #:use-module (gnu packages nss)
  #:use-module (gnu packages perl)
  #:use-module (gnu packages pdf)
@@ -651,49 +649,6 @@ It's not clear at the moment whether one day it will be possible to
 do so.")
    (license license:agpl3+)))

-(define-public libbwt-jni
-  (package
-    (name "libbwt-jni")
-    (version "0.2.4")
-    (source (origin
-              (method git-fetch)
-              (uri (git-reference
-                     (url "https://github.com/bwt-dev/libbwt-jni")
-                     (commit (string-append "v" version))))
-              (file-name (git-file-name name version))
-              (sha256
-               (base32
-                "1xbb8ad6rlpg972rnf7fipgzz6ry7yzbnxacgisqpkcjnw768zy5"))
-              (snippet
-               '(begin
-                  (use-modules (guix build utils))
-                  (delete-file-recursively "bwt")
-                  (substitute* "Cargo.toml"
-                    (("path = \"./bwt\"")
-                     "version = \"0.2.4\""))))))
-    (build-system cargo-build-system)
-    (arguments
-     (list
-      #:install-source? #f
-      #:phases
-      #~(modify-phases %standard-phases
-          (add-after 'install 'install-lib
-            (lambda _
-              (install-file "target/release/libbwt_jni.so"
-                            (string-append #$output "/lib")))))))
-    (inputs (cons (package-source bwt)
-                  (cargo-inputs 'libbwt-jni)))
-    (home-page "https://github.com/bwt-dev/libbwt-jni")
-    (synopsis "Java Native Interface bindings for Bitcoin Wallet Tracker")
-    (description "Libbwt-jni is Java Native Interface bindings for Bitcoin
-Wallet Tracker, a lightweight personal indexer for Bitcoin wallets.
-Libbwt-jni allows you to programmatically manage bwt's Electrum RPC and HTTP
-API servers.  It can be used as a compatibility layer for easily upgrading
-Electrum-backed wallets to support a Bitcoin Core full node backend (by
-running the Electrum server in the wallet), or for shipping software that
-integrates bwt's HTTP API as an all-in-one package.")
-    (license license:expat)))
-
 (define-public python-electrum-ecc
  (package
    (name "python-electrum-ecc")
@@ -1328,7 +1283,7 @@ Ledger Blue/Nano S.")
 (define-public python-trezor
  (package
    (name "python-trezor")
-    (version "0.13.7")
+    (version "0.20.0")
    (source
     (origin
       (method git-fetch)
@@ -1337,7 +1292,7 @@ Ledger Blue/Nano S.")
             (commit (string-append "python/v" version))))
       (file-name (git-file-name name version))
       (sha256
-        (base32 "13wyl9b15c8iscfakprwfvh2akw180hfqdjww79b78ywz51y7hdh"))
+        (base32 "06d4mw8iydgv2c3qxa47482k7dqpg89a2b6wd8f4g15ydn3gsfmn"))
       (modules
        '((guix build utils)
          (srfi srfi-26)
@@ -1375,26 +1330,32 @@ Ledger Blue/Nano S.")
                          "test_legacy_basic"
                          "test_unsigned"
                          "test_vendor_header")
-                    " and not "))))
+                    " and not "))
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-after 'unpack 'relax-requirements
+            (lambda _
+              (substitute* "pyproject.toml"
+                (("platformdirs>=4.4.0") "platformdirs")))))))
    (propagated-inputs
-     (list python-attrs
-           python-click
+     (list python-click
+           python-construct
           python-construct-classes
-           python-ecdsa
-           python-hidapi
+           python-cryptography
+           python-keyring
           python-libusb1
           python-mnemonic
+           python-noiseprotocol
+           python-platformdirs
           python-requests
+           python-shamir-mnemonic
+           python-slip10
           python-typing-extensions))
-    (native-inputs ; Only needed for running the tests
+    (native-inputs
     (list nss-certs-for-test
-           protobuf
-           python-pytest
-           python-pillow
-           python-protobuf
-           python-pyqt
-           python-pytest
-           python-simple-rlp))
+           python-hatchling
+           python-setuptools
+           python-pytest))
    (home-page "https://github.com/trezor/python-trezor")
    (synopsis "Python library for communicating with TREZOR Hardware Wallet")
    (description "@code{trezor} is a Python library for communicating with
@@ -1621,10 +1582,7 @@ features:
       (sha256
        (base32 "0yir8hka3vmpk0qhiaffagkdjg3mjgai808s0razsggbd5cn80bb"))))
    (build-system pyproject-build-system)
-    (native-inputs
-     (list python-pytest
-           python-pytest-cov
-           python-setuptools))
+    (native-inputs (list python-pytest python-setuptools))
    (home-page "https://arthurdejong.org/python-stdnum/")
    (synopsis "Python module to handle standardized number and code formats")
    (description
@@ -1716,19 +1674,26 @@ main features are:
 (define-public silkaj
  (package
    (name "silkaj")
-    (version "0.12.1")
+    ;; 0.12.1 (2025-07-08), all tests passed on the latest commit, revert back
+    ;; to git tag when released.
+    (properties '((commit . "dabe484ba1871030be33a1473ee473004e102763")
+                  (revision . "0")))
+    (version (git-version "0.12.1"
+                          (assoc-ref properties 'revision)
+                          (assoc-ref properties 'commit)))
    (source
     (origin
       (method git-fetch)
       (uri (git-reference
             (url "https://git.duniter.org/clients/python/silkaj")
-             (commit (string-append "v" version))))
+              (commit (assoc-ref properties 'commit))))
       (file-name (git-file-name name version))
       (sha256
-        (base32 "0prglgwvzi676h4lyw9266sqiqbfs2l0mv0bmjvplvdxzzcs63bv"))))
+        (base32 "08wg4q3y747apj5phq4ghjgg9cdr8mnyzjspjvd8v9qz08v5zg6b"))))
    (build-system pyproject-build-system)
    (arguments
     (list
+      ;; tests: 224 passed, 4 skipped, 2 deselected
      #:test-flags
      ;; They require Poetry in the PATH.
      #~(list "--ignore=tests/integration/"
@@ -2147,7 +2112,10 @@ it can easily generate custom reports specific to accounting purposes.")
             (commit (string-append "v" version))))
       (file-name (git-file-name name version))
       (sha256
-        (base32 "0zlanw88dq7czgsdvqwz2fgxamyrfnx15ymv4d7fnjrj04glpg47"))))
+        (base32 "0zlanw88dq7czgsdvqwz2fgxamyrfnx15ymv4d7fnjrj04glpg47"))
+       ;; TODO: Remove in the next release:
+       ;; https://github.com/beancount/beangulp/commit/254bfb38ffed
+       (patches (search-patches "python-beangulp-click-8.2-compat.patch"))))
    (build-system pyproject-build-system)
    (propagated-inputs
     (list beancount
@@ -2215,12 +2183,18 @@ software Beancount with a focus on features and usability.")
       (sha256
        (base32 "18kdic6rg9qizam6cgd2ljpapwiqh2dc3s6wsaz46kjc1yhhwjqy"))))
    (build-system pyproject-build-system)
+    (arguments
+     (list #:tests? #f))        ;no tests
    (propagated-inputs (list fava))
    (native-inputs (list python-pdm-backend))
    (home-page "https://github.com/stenius/fava-envelope-airmail")
    (synopsis "Envelope budgeting for Fava/Beancount")
-    (description "Envelope budgeting for Fava/Beancount with stats, scheduled
-transactions, and color-coded UI.")
+    (description
+     "Envelope budgeting for Fava/Beancount with stats, scheduled
+transactions, and color-coded UI.  It's a fork of
+@url{https://github.com/memst/fava-envelope} (itself a fork of
+@url{https://github.com/polarmutex/fava-envelope}) that adds several
+enhancements for envelope budgeting.")
    (license license:expat)))

 (define-public emacs-beancount
@@ -2507,10 +2481,6 @@ 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")
@@ -47,7 +47,6 @@
  #: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)
@@ -49,7 +49,6 @@
  #: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)
@@ -74,6 +74,7 @@
 ;;; Copyright © 2026 Carlos Durán Domínguez <wurt@wurt.eu>
 ;;; Copyright © 2026 Joan Vilardaga Castro <codeberg-hn80@joanvc.cat>
 ;;; Copyright © 2026 Sughosha <sughosha@disroot.org>
+;;; Copyright © 2026 bdunahu <bdunahu@operationnull.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -2817,6 +2818,32 @@ family.")
 (define-deprecated-package font-adobe-source-serif-pro
  font-adobe-source-serif)

+(define-public font-medieval-sharp
+  ;; No releases, use newest commit.
+  (let ((commit "ee7510b6b13854fd340e7d2e44c218780f672cd1")
+        (revision "1"))
+    (package
+      (name "font-medieval-sharp")
+      ;; From FONTLOG.txt.
+      (version (git-version "3.1.0" revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+                (url "https://github.com/wmk69/Medieval-Sharp")
+                (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32
+           "1r300591pra4nxpm5kppl5q3ihsp01wk2zh24f9pvv0jgf1ik87x"))))
+      (build-system font-build-system)
+      (home-page "https://github.com/wmk69/Medieval-Sharp")
+      (synopsis "Font based on gothic letters")
+      (description
+       "Medieval Sharp is a font created for inscriptions on stone, based on
+gothic letters.")
+      (license license:silofl1.1))))
+
 (define-public font-microsoft-cascadia
  (package
    (name "font-microsoft-cascadia")
@@ -47,6 +47,7 @@
  #:use-module (gnu packages autotools)
  #:use-module (gnu packages bash)
  #:use-module (gnu packages bison)
+  #:use-module (gnu packages build-tools)
  #:use-module (gnu packages check)
  #:use-module (gnu packages compression)
  #:use-module (gnu packages datastructures)
@@ -69,7 +70,6 @@
  #:use-module (gnu packages linux)
  #:use-module (gnu packages man)
  #:use-module (gnu packages mc)
-  #:use-module (gnu packages ninja)
  #:use-module (gnu packages perl)
  #:use-module (gnu packages pkg-config)
  #:use-module (gnu packages python)
@@ -96,7 +96,6 @@
  #: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))

@@ -473,6 +472,53 @@ 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")
@@ -574,7 +620,6 @@ for fontTools.")
     (list python-cython
           python-defcon
           python-pytest
-           python-pytest-runner
           python-setuptools
           python-setuptools-scm
           python-wheel
@@ -701,8 +746,7 @@ implementing the pen protocol for manipulating glyphs.")
      (modify-inputs native-inputs
        (append python-fontparts-bootstrap
                python-fontpens-bootstrap
-                python-pytest
-                python-pytest-runner))))))
+                python-pytest))))))

 ;;; A variant used to break a cycle with python-fontpens.
 (define-public python-fontparts-bootstrap
@@ -983,7 +1027,6 @@ 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
@@ -1827,6 +1870,10 @@ 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
@@ -75,7 +75,6 @@
  #: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)
@@ -1379,41 +1378,43 @@ For information about libevdev, see:
    (license license:expat)))

 (define-public python-pyxdg
-  (package
-    (name "python-pyxdg")
-    (version "0.28")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (pypi-uri "pyxdg" version))
-       (sha256
-        (base32
-         "1d48bqwkbnpid80cpwz6h62i112laxl0ivpj58hdyd79fhqbnrrj"))))
-    (build-system pyproject-build-system)
-    (arguments
-     (list
-      #:test-flags
-      ;; Tests failing with error: AssertionError: 'image' != 'inode'
-      #~(list "--deselect=test/test_mime.py::MimeTest::test_get_type"
-              "--deselect=test/test_mime.py::MimeTest::test_get_type2")
-      #:phases
-      #~(modify-phases %standard-phases
-          (add-before 'check 'pre-check
-            (lambda _
-              (setenv "XDG_DATA_DIRS"
-                      (string-append #$(this-package-native-input "shared-mime-info")
-                                     "/share/")))))))
-    (native-inputs
-     (list shared-mime-info
-           hicolor-icon-theme
-           python-pytest
-           python-setuptools))
-    (home-page "https://www.freedesktop.org/wiki/Software/pyxdg")
-    (synopsis "Implementations of freedesktop.org standards in Python")
-    (description
-     "PyXDG is a collection of implementations of freedesktop.org standards in
+  ;; Latest unreleased commits add Python 3.12, 3.14 and 3.15 support.
+  (let ((commit "63033ac306aa26d32e1439417e59ae8f8a4c9820")
+        (revision "0"))
+    (package
+      (name "python-pyxdg")
+      (version "0.28")
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+                (url "https://gitlab.freedesktop.org/xdg/pyxdg")
+                (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32
+           "10wk95rmcr2fglmvmv1a6ad9hkw9587r0rlww0gq6kbfz85whgmd"))))
+      (build-system pyproject-build-system)
+      (arguments
+       (list
+        #:phases
+        #~(modify-phases %standard-phases
+            (add-before 'check 'pre-check
+              (lambda _
+                (setenv "XDG_DATA_DIRS"
+                        (string-append #$(this-package-native-input "shared-mime-info")
+                                       "/share/")))))))
+      (native-inputs
+       (list shared-mime-info
+             hicolor-icon-theme
+             python-pytest
+             python-setuptools))
+      (home-page "https://www.freedesktop.org/wiki/Software/pyxdg")
+      (synopsis "Implementations of freedesktop.org standards in Python")
+      (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
@@ -1971,6 +1972,10 @@ message bus.")
         "-Dsystemdsystemunitdir=/tmp/empty")
       #:phases
       (modify-phases %standard-phases
+         (add-after 'unpack 'fix-python-incompatibilities
+           (lambda _
+             (substitute* (find-files "tests" "\\.py$")
+               (("assertEquals") "assertEqual"))))
         (add-after 'unpack 'patch-paths
           (lambda* (#:key inputs #:allow-other-keys)
             (substitute* "meson_post_install.py"
@@ -2178,7 +2183,7 @@ which speak the Qualcomm MSM Interface (QMI) protocol.")
           libxslt                      ;for xsltproc
           pkg-config
           python-minimal
-           python-dbus-1.2              ;for test
+           python-dbus                  ;for test
           python-pygobject             ;for test
           vala))
    (propagated-inputs
@@ -2372,7 +2377,7 @@ 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-1.2))
+      (inputs (list libxslt python-wrapper python-dbus))
      (propagated-inputs (list telepathy-glib))
      (home-page "https://telepathy.freedesktop.org/")
      (synopsis "Telepathy IRC connection manager")
@@ -70,7 +70,6 @@
  #: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)
@@ -1751,13 +1750,16 @@ color switches, and many more, with multiple options to customize.")
 (define-public python-pygame-ce
  (package
    (name "python-pygame-ce")
-    (version "2.5.5")
+    (version "2.5.7")
    (source
     (origin
-       (method url-fetch)
-       (uri (pypi-uri "pygame_ce" version))
+       (method git-fetch)
+       (uri (git-reference
+              (url "https://github.com/pygame-community/pygame-ce")
+              (commit version)))
+       (file-name (git-file-name name version))
       (sha256
-        (base32 "0sxfchimdg606z65qychgvm66mq0aybs2isxsqb5zqy64g19gwm7"))))
+        (base32 "1awvs4wa9fgm8xldsxzdx1knijjpzz560lzj3rjvks3gcw8szhzx"))))
    (build-system pyproject-build-system)
    (arguments
     (list
@@ -98,6 +98,7 @@
 ;;; Copyright © 2026 Cayetano Santos <csantosb@inventati.org>
 ;;; Copyright © 2026 Carlos Durán Domínguez <wurt@wurt.eu>
 ;;; Copyright © 2026 Nikita Alkhovik <forgoty13@gmail.com>
+;;; Copyright © 2026 bdunahu <bdunahu@operationnull.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -200,7 +201,6 @@
  #:use-module (gnu packages ncurses)
  #:use-module (gnu packages netpbm)
  #:use-module (gnu packages networking)
-  #:use-module (gnu packages ninja)
  #:use-module (gnu packages ocaml)
  #:use-module (gnu packages oneapi)
  #:use-module (gnu packages opencl)
@@ -1957,7 +1957,7 @@ real-time combat.")
 (define-public golly
  (package
    (name "golly")
-    (version "4.2")
+    (version "5.0")
    (source (origin
              (method url-fetch)
              (uri (string-append "mirror://sourceforge/golly/golly/golly-"
@@ -1965,47 +1965,53 @@ real-time combat.")
                                  "-src.tar.gz"))
              (sha256
               (base32
-                "0pg9cp83nxc354lizgza5bqdy7z5wh36863203zw6r6s4flji4an"))))
+                "049n634abxfpgh4imh3s5qqfn9nbwmcl6jm91f29ngqm53jcsdaq"))))
    (build-system gnu-build-system)
    (arguments
-     '(#:make-flags (list "CC=gcc"
-                          (string-append "GOLLYDIR="
-                                         (assoc-ref %outputs "out")
-                                         "/share/golly"))
-       #:tests? #f ; no check target
-       #:phases
-       (modify-phases %standard-phases
-         (delete 'configure)
-         (replace 'build
-           (lambda* (#:key make-flags outputs #:allow-other-keys)
-             (with-directory-excursion "gui-wx"
-               (apply invoke `("make" ,@make-flags "-f" "makefile-gtk")))))
-         (replace 'install
-           (lambda* (#:key outputs #:allow-other-keys)
-             (let* ((out (assoc-ref outputs "out"))
-                    (bin (string-append out "/bin"))
-                    (doc (string-append out "/share/doc/golly"))
-                    (pixmaps (string-append out "/share/pixmaps"))
-                    (share (string-append out "/share/golly")))
-               (for-each (lambda (binary)
-                           (install-file binary bin))
-                         '("bgolly" "golly"))
-               (for-each (lambda (document)
-                           (install-file
-                            (string-append "docs/" document ".html")
-                            doc))
-                         '("License" "ReadMe" "ToDo"))
-               (install-file "gui-wx/icons/appicon.xpm" pixmaps)
-               (for-each (lambda (folder)
-                           (copy-recursively
-                            folder
-                            (string-append share "/" folder)))
-                         '("Help" "Patterns" "Rules" "Scripts")))
-             #t)))))
+     (list
+      #:make-flags
+      #~(list "CC=gcc"
+              (string-append "GOLLYDIR="
+                             #$output
+                             "/share/golly"))
+      #:tests? #f ; no check target
+      #:phases
+      #~(modify-phases %standard-phases
+          (delete 'configure)
+          (replace 'build
+            (lambda* (#:key make-flags #:allow-other-keys)
+              (with-directory-excursion "gui-wx"
+                (apply invoke `("make" ,@make-flags "-f" "makefile-gtk")))))
+          (replace 'install
+            (lambda _
+                (let* ((bin (string-append #$output "/bin"))
+                     (doc (string-append #$output "/share/doc/golly"))
+                     (pixmaps (string-append #$output "/share/pixmaps"))
+                     (share (string-append #$output "/share/golly")))
+                (for-each (lambda (binary)
+                            (install-file binary bin))
+                          (list "bgolly" "golly"))
+                (for-each (lambda (document)
+                            (install-file
+                             (string-append "docs/" document ".html")
+                             doc))
+                          (list "License" "ReadMe" "ToDo"))
+                (install-file "gui-wx/icons/appicon.xpm" pixmaps)
+                (for-each (lambda (folder)
+                            (copy-recursively
+                             folder
+                             (string-append share "/" folder)))
+                          (list "Help" "Patterns" "Rules" "Scripts"))))))))
    (native-inputs
-     (list lua))
+     (list lua
+           python-setuptools))
    (inputs
-     (list glu mesa python sdl2 wxwidgets zlib))
+     (list glu
+           mesa
+           python
+           sdl2
+           wxwidgets
+           zlib))
    (home-page "https://golly.sourceforge.net/")
    (synopsis "Software for exploring cellular automata")
    (description
@@ -3982,27 +3988,26 @@ that beneath its ruins lay buried an ancient evil.")
        (base32 "0hgzdvlh0j42w4q9kch9xvhnbvcrypac01xhpksw35gj9my887cp"))
       (modules '((guix build utils)))
       (snippet
-        ;; So, some of the sounds/graphics/tilesets are under different
-        ;; licenses... some of them even nonfree!  This is a console-only
-        ;; version of this package so we just remove them.
-        ;; In the future, if someone tries to make a graphical variant of
-        ;; this package, they can deal with that mess themselves. :)
        '(begin
-           (for-each (lambda (subdir)
-                       (let ((lib-subdir (string-append "lib/" subdir)))
-                         (delete-file-recursively lib-subdir)))
-                     '("fonts" "icons" "sounds" "tiles"))
-           (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"))
-           ;; Remove nonfree .dll files too.
-           (delete-file-recursively "src/win")))))
+           (for-each delete-file-recursively
+                     '("lib/tiles/shockbolt" ;nonfree
+                       "src/win"))      ;contains .dlls!
+           ;; Don't build the shockbolt directory either.
+           (substitute* "lib/tiles/Makefile"
+             (("shockbolt") ""))))
+       (patches (search-patches "angband-remove-nonfree-tile-options.patch"))))
    (build-system gnu-build-system)
    (arguments
-     `(#:configure-flags (list (string-append "--bindir=" %output "/bin"))
+     `(#:configure-flags (list (string-append "--bindir=" %output "/bin")
+                               "--disable-x11")
       #:phases
       (modify-phases %standard-phases
+         (add-after 'unpack 'disable-graphics-and-sounds
+           (lambda _
+             (substitute* "lib/Makefile"
+               ;; Do not build any graphics for this version.
+               (("gamedata customize help screens fonts tiles sounds icons user")
+                "gamedata customize help screens user"))))
         (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
@@ -4052,6 +4057,59 @@ the depths below Angband, seeking riches, fighting monsters, and preparing to
 fight Morgoth, the Lord of Darkness.")
    (license license:gpl2)))

+(define-public angband-sdl2
+  (package
+    (inherit angband)
+    (name "angband-sdl2")
+    (arguments
+     (substitute-keyword-arguments
+         (package-arguments angband)
+       ((#:configure-flags flags)
+        #~(cons* "--enable-sdl2" #$flags))
+       ((#:phases phases)
+        #~(modify-phases #$phases
+            (delete 'disable-graphics-and-sounds)
+            (add-after 'unpack 'patch-sdl-wrapper-headers
+              (lambda _
+                (with-directory-excursion "src"
+                  (substitute* '("snd-sdl.c"
+                                 "main-sdl2.c"
+                                 "sdl2/pui-win.h")
+                    (("\"SDL_image.h\"") "\"SDL2/SDL_image.h\"")
+                    (("\"SDL_mixer.h\"") "\"SDL2/SDL_mixer.h\"")
+                    (("\"SDL_ttf.h\"") "\"SDL2/SDL_ttf.h\"")))))
+            (add-after 'unpack 'patch-desktop-file
+              (lambda* (#:key outputs #:allow-other-keys)
+                 (let ((out (assoc-ref outputs "out")))
+                   (substitute* "lib/icons/angband-sdl2.desktop"
+                     (("Exec=angband" _)
+                      (string-append "Exec=" #$output "/bin/angband-sdl2"))))))
+            (add-after 'install 'rename-binary
+              (lambda _
+                (with-directory-excursion #$output
+                  ;; allows parallel installation with angband
+                  (rename-file "bin/angband"
+                               "bin/angband-sdl2"))))))))
+    (inputs
+     (modify-inputs inputs
+       (prepend sdl2
+                sdl2-image
+                sdl2-mixer
+                sdl2-ttf)))
+    (description "Angband is a Classic dungeon exploration roguelike.  Explore
+the depths below Angband, seeking riches, fighting monsters, and preparing to
+fight Morgoth, the Lord of Darkness.
+
+This version includes the SDL2 frontend, providing tilesets and sounds which
+can be enabled through in-game options.")
+    ;; XXX: fonts and adam bolt tileset are free but being clarified:
+    ;; https://github.com/angband/angband/issues/6608
+    ;; For the rest, see:
+    ;; https://github.com/angband/angband/blob/master/docs/copying.rst
+    (license (list license:gpl2            ;code, nomad+old tilesets
+                   license:cc-by-sa3.0     ;david gervais tileset
+                   license:cc-by-sa4.0)))) ;sounds
+
 (define-public pingus
  ;; Latest release is from 2021-12-24.
  (let ((commit "7d65221e1cd1026053c8a5a08ad911fbdd13d3ed")
@@ -80,14 +80,14 @@
 (define-public gdb-17
  (package
    (name "gdb")
-    (version "17.1")
+    (version "17.2")
    (source (origin
              (method url-fetch)
              (uri (string-append "mirror://gnu/gdb/gdb-"
                                  version ".tar.xz"))
              (sha256
               (base32
-                "0xnqqv3j463r5rnfmblj3zwhf0l0lyy4bp1zaid8zxn9fignz68l"))))
+                "1312lccryan1jfkjwkbw9mpxgyfnmlr8dj4lbkxx3cz4f86nq0qw"))))
    (build-system gnu-build-system)
    (outputs '("out" "debug"))
    (arguments
@@ -1,6 +1,7 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2019 Guillaume Le Vaillant <glv@posteo.net>
 ;;; Copyright © 2020, 2021 Tobias Geerinckx-Rice <me@tobias.gr>
+;;; Copyright © 2026 Sharlatan Hellseher <sharlatanus@gmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -18,13 +19,15 @@
 ;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.

 (define-module (gnu packages genealogy)
-  #:use-module (guix build-system pyproject)
-  #:use-module (guix git-download)
  #:use-module ((guix licenses) #:prefix license:)
+  #:use-module (guix build-system glib-or-gtk)
+  #:use-module (guix build-system pyproject)
  #:use-module (guix gexp)
+  #:use-module (guix git-download)
  #:use-module (guix packages)
  #:use-module (gnu packages base)
  #:use-module (gnu packages bash)
+  #:use-module (gnu packages check)
  #:use-module (gnu packages fonts)
  #:use-module (gnu packages freedesktop)
  #:use-module (gnu packages geo)
@@ -34,6 +37,7 @@
  #:use-module (gnu packages gnome)
  #:use-module (gnu packages graphviz)
  #:use-module (gnu packages gtk)
+  #:use-module (gnu packages iso-codes)
  #:use-module (gnu packages python)
  #:use-module (gnu packages python-build)
  #:use-module (gnu packages python-xyz)
@@ -57,15 +61,42 @@
    (build-system pyproject-build-system)
    (arguments
     (list
-      #:imported-modules
-      `((guix build glib-or-gtk-build-system)
-        ,@%pyproject-build-system-modules)
+      #:imported-modules (append %glib-or-gtk-build-system-modules
+                                 %pyproject-build-system-modules)
      #:modules
      `((ice-9 match)
        (srfi srfi-1)
        (guix build pyproject-build-system)
        ((guix build glib-or-gtk-build-system) #:prefix glib-or-gtk:)
        (guix build utils))
+      ;; tests: 32408 passed, 44 skipped, 9 deselected, 1 warning, 65730 subtests passed
+      #:test-flags
+      ;; Tests failing during collection.
+      #~(list "--ignore=gramps/gen/merge/test/merge_ref_test.py"
+              "--ignore=po/test/po_test.py"
+              "--ignore=test/LosHawlos_db_test.py"
+              "--ignore=test/blob_to_json_test.py"
+              ;; Assertions are not equal for these tests.
+              #$@(map (lambda (ls) (string-append "--deselect=gramps/"
+                                                  (string-join ls "::")))
+                      '(("gen/proxy/test/proxies_test.py"
+                         "LivingProxyTest" "test_person_count")
+                        ("gen/proxy/test/proxies_test.py"
+                         "LivingPrivateProxyTest" "test_person_count")
+                        ("plugins/test/reports_test.py"
+                         "TestDynamic" "test_export_gedcom")
+                        ("plugins/test/reports_test.py"
+                         "TestDynamic" "test_export_gpkg")
+                        ("plugins/test/reports_test.py"
+                         "TestDynamic" "test_indiv_complete")
+                        ("plugins/test/reports_test.py"
+                         "TestDynamic" "test_navwebpage")
+                        ("plugins/test/reports_test.py"
+                         "TestDynamic" "test_tool_check")
+                        ("plugins/test/tools_test.py"
+                         "ToolControl" "test_tcg_and_check_and_repair")
+                        ("plugins/test/db_undo_and_signals_test.py"
+                         "TestSQLite" "test_one"))))
      #:phases
      #~(modify-phases %standard-phases
          (add-before 'build 'fix-gexiv2-dependency
@@ -73,15 +104,19 @@
              ;; Use our own version
              (substitute* (find-files "." ".*\\.py$")
                (("\"GExiv2\", \"0.10\"") "\"GExiv2\", \"0.16\""))))
+          (add-after 'unpack 'swap-bsddb3-with-berkeleydb
+            ;; bsddb3 was renamed upstream to berkeleydb.
+            (lambda _
+              (substitute* (find-files "." ".*\\.py")
+                (("bsddb3") "berkeleydb"))))
          (add-before 'check 'prepare-tests
            (lambda _
-              (setenv "HOME" (getenv "TMPDIR"))
+              (setenv "GDK_BACKEND" "-")
+              (setenv "HOME" "/tmp")
              ;; Presence of .git directory is used to determine whether this
              ;; is a final installation.  Without it, tests fail to determine
              ;; resource path.
-              (mkdir ".git")
-              ;; Test is failing
-              (delete-file "gramps/gen/utils/test/file_test.py")))
+              (mkdir ".git")))
          (add-before 'wrap 'wrap-with-GI_TYPELIB_PATH
            (lambda* (#:key inputs #:allow-other-keys)
              (wrap-program (string-append #$output "/bin/gramps")
@@ -98,8 +133,11 @@
          (add-after 'wrap 'glib-or-gtk-wrap
            (assoc-ref glib-or-gtk:%standard-phases 'glib-or-gtk-wrap)))))
    (native-inputs
-     (list gettext-minimal intltool
-           glibc-utf8-locales ;for one test
+     (list gettext-minimal
+           intltool
+           python-jsonschema
+           python-mock
+           python-pytest
           python-setuptools))
    (inputs
     (list bash-minimal
@@ -115,12 +153,12 @@
           (librsvg-for-system)
           osm-gps-map
           pango
-           python-bsddb3
-           python-jsonschema
-           python-lxml
+           python-berkeleydb
+           python-imagesize
           python-orjson
           python-pillow
           python-pycairo
+           python-pycountry
           python-pygobject
           python-pyicu
           rcs
@@ -55,7 +55,6 @@
  #: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)
@@ -129,7 +128,6 @@
  #:use-module (gnu packages mpi)
  #:use-module (gnu packages multiprecision)
  #:use-module (gnu packages ncurses)
-  #:use-module (gnu packages ninja)
  #:use-module (gnu packages pcre)
  #:use-module (gnu packages pdf)
  #:use-module (gnu packages perl)
@@ -298,7 +296,7 @@ than 600 operators available.")
 (define-public h3
  (package
    (name "h3")
-    (version "4.1.0")
+    (version "4.4.1")
    (source
     (origin
       (method git-fetch)
@@ -307,7 +305,7 @@ than 600 operators available.")
             (commit (string-append "v" version))))
       (file-name (git-file-name name version))
       (sha256
-        (base32 "0x764xzna8ka6yhgv2y4hb158a61y3g9a6835qckqp7wfkpqvb7f"))))
+        (base32 "1ijnbr4a54ph7bkn8waqwgnxmxlylv9yly9mwjdj69lkmdfjgaml"))))
    (build-system cmake-build-system)
    (arguments
     (list #:configure-flags #~(list "-DBUILD_SHARED_LIBS=ON")))
@@ -319,48 +317,25 @@ combining the benefits of a hexagonal grid with S2's hierarchical
 subdivisions.")
    (license license:asl2.0)))

-;; For python-timezonefinder, remove it when it starts supporting newer
-;; version.
-(define-public h3-3
-  (package
-    (inherit h3)
-    (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")
+    (version "4.4.2")
    (source
     (origin
-       (method git-fetch) ; no tests data in PyPi package
+       (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 "1k1n256hhlh05gjcj64pqh08zlaz6962jkb6nk1aazsgg8p41zs0"))
+        (base32 "02gry51hn8x2bl80y1ipcyrg0ghcif4vjch26qil215wdzz1yrzv"))
       (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.
@@ -381,10 +356,7 @@ subdivisions.")
           python-cython
           python-numpy
           python-pytest
-           python-scikit-build
-           python-setuptools
-           python-setuptools-scm
-           python-wheel))
+           python-scikit-build-core))
    (inputs (list h3))
    (home-page "https://uber.github.io/h3-py")
    (synopsis "Python bindings for H3")
@@ -392,26 +364,6 @@ 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")
@@ -1124,7 +1076,6 @@ for seismology.")
    (inputs (list gdal))
    (native-inputs (list python-cython
                         python-pytest
-                         python-pytest-cov
                         python-setuptools
                         python-tomli
                         python-versioneer
@@ -1224,7 +1175,7 @@ projections and coordinate transformations library.")
 (define-public python-fiona
  (package
    (name "python-fiona")
-    (version "1.9.6")
+    (version "1.10.1")
    (source
     (origin
       (method git-fetch)
@@ -1233,24 +1184,38 @@ projections and coordinate transformations library.")
              (commit version)))
       (file-name (git-file-name name version))
       (sha256
-        (base32 "08whhjrspp194qasjhr9kf70fl342ms47k78rwpcf5q6ikf0rfii"))))
+        (base32 "0xribbcy5wvrm5y3bq281dry86vhjcnphg9772yp9s3y30y7mlz4"))))
    (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"
-              ;; FIXME: Find why the
-              ;; test_no_append_driver_cannot_append[PCIDSK] test is failing.
-              "-k" "not test_no_append_driver_cannot_append")
+              #$@(map (lambda (test) (string-append "--deselect=tests/" test))
+                      ;; UserWarning: The parameter --where is used more than
+                      ;; once. Remove its duplicate as parameters should be
+                      ;; 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 'build 'set-configure-flags
+          (add-before 'check 'remove-local-source
            (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))
@@ -1258,19 +1223,19 @@ projections and coordinate transformations library.")
     (list python-attrs
           python-certifi
           python-click
-           python-click-plugins-1
+           python-click-plugins
           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
@@ -1533,7 +1498,6 @@ street bearings/orientations, and speed/travel time.")
           python-pyproj
           python-pyyaml
           python-pytest
-           python-pytest-cov
           python-pytest-httpserver
           python-pytz
           python-requests
@@ -1865,10 +1829,7 @@ 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-pytest-runner
-           python-setuptools
-           python-wheel))
+     (list python-pytest python-setuptools python-wheel))
    (home-page "https://github.com/GeospatialPython/pyshp")
    (synopsis "Read/write support for ESRI Shapefile format")
    (description
@@ -3578,10 +3539,9 @@ orienteering sport.")
       (list
        #:tests? #f                    ; No tests
        #:modules `((guix build gnu-build-system)
-                    ((guix build python-build-system) #:prefix python:)
+                    ((guix build pyproject-build-system) #:prefix python:)
                    (guix build utils))
-        #:imported-modules `(,@%default-gnu-imported-modules
-                             (guix build python-build-system))
+        #:imported-modules %pyproject-build-system-modules
        #:configure-flags
        #~(list "--with-blas"
                "--with-bzlib"
@@ -3753,13 +3713,13 @@ 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 python-build-system) #:prefix python:)
+                  ((guix build pyproject-build-system) #:prefix py:)
                  (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
@@ -3920,11 +3880,10 @@ 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 ((sip-dir (string-append
-                                (assoc-ref inputs "python-pyqt+qscintilla")
-                                "/lib/python"
-                                (python:python-version (assoc-ref inputs "python"))
-                                "/site-packages/PyQt5/bindings")))
+                (let* ((pyqt (assoc-ref inputs "python-pyqt+qscintilla"))
+                       (sip-dir (string-append
+                                 (py:site-packages inputs `(("out" . ,pyqt)))
+                                 "/PyQt5/bindings")))
                  (substitute* "cmake/FindPyQt5.py"
                    (("sip_dir = cfg.default_sip_dir")
                     (string-append "sip_dir = \"" sip-dir "\"")))
@@ -3954,7 +3913,7 @@ 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 python:%standard-phases 'wrap))
+              (assoc-ref py:%standard-phases 'wrap))
            (add-after 'wrap-python 'wrap-qt
              (lambda* (#:key inputs #:allow-other-keys)
                (wrap-qt-program "qgis" #:output #$output #:inputs inputs)))
@@ -476,17 +476,31 @@ inverse fourier transform.")
  (package
    (name "libmypaint")
    (version "1.6.1")
-    (source (origin
-              (method url-fetch)
-              (uri (string-append "https://github.com/mypaint/libmypaint/"
-                                  "releases/download/v" version "/libmypaint-"
-                                  version ".tar.xz"))
-              (sha256
-               (base32
-                "0priwpmc7dizccqvn21ig6d649bprl3xl1hmjj7nddznjgr585vl"))))
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+              (url "https://github.com/mypaint/libmypaint")
+              (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (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 intltool pkg-config))
+     (list autoconf
+           automake
+           intltool
+           libtool
+           pkg-config
+           python))
    ;; As needed by 'libmypaint.pc'.
    (propagated-inputs
     (list json-c gobject-introspection))
@@ -498,6 +512,26 @@ 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")
@@ -79,7 +79,6 @@
  #: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)
@@ -1420,8 +1419,8 @@ original glmark benchmark by Ben Smith.")
    (license license:bsd-2)))

 (define-public piglit
-  (let ((revision "1")
-        (commit "814046fe6942eac660ee4a6cc5fcc54011a49945"))
+  (let ((revision "2")
+        (commit "040ed91f234abb6a502d3a6910f1b0e54bd239a7"))
    (package
     (name "piglit")
     (version (git-version "0.0.0" revision commit))
@@ -1432,7 +1431,7 @@ original glmark benchmark by Ben Smith.")
                    (commit commit)))
              (file-name (git-file-name name version))
              (sha256
-               (base32 "1bzaalcxskckfnwprw77sbbmfqi59by2j8imaq8ghnlzhlxv7mk7"))))
+               (base32 "1j5dmkym1mmz410xgwygimnjk2aswsqmcpjwz4s98pgmymh1yjvf"))))
     (build-system cmake-build-system)
     (arguments
      (list #:configure-flags #~(list "-DPIGLIT_SSE2=OFF")
@@ -1451,16 +1450,21 @@ original glmark benchmark by Ben Smith.")
                                      "'")))))
                (add-after 'install 'wrap
                  (lambda* (#:key outputs #:allow-other-keys)
-                    (wrap-script (string-append (assoc-ref outputs "out")
-                                                "/bin/piglit")
+                    (wrap-script (string-append #$output "/bin/piglit")
                      `("GUIX_PYTHONPATH" prefix
                        (,(getenv "GUIX_PYTHONPATH")))))))))
-     (inputs (list guile-3.0            ; for wrap-script
+     (inputs (list glslang
+                   guile-3.0            ; for wrap-script
                   libxkbcommon
-                   python python-lxml python-mako python-numpy-1
-                   glslang vulkan-headers vulkan-loader
+                   python
+                   wayland-protocols
+                   vulkan-headers
+                   vulkan-loader
                   waffle))
-     (native-inputs (list pkg-config))
+     (native-inputs (list pkg-config
+                          python-lxml
+                          python-mako
+                          python-numpy))
     (home-page "https://piglit.freedesktop.org/")
     (synopsis "Test OpenGL implementations")
     (description "Piglit is a collection of automated tests for OpenGL and
@@ -320,7 +320,11 @@ You can also use it to fall asleep in a noisy environment.")
            (lambda* (#:key inputs #:allow-other-keys)
              (wrap-program (string-append #$output "/bin/cartridges")
                `("GUIX_PYTHONPATH" =
-                  (,(string-append #$output "/lib/python3.11/site-packages:"
+                  (,(string-append #$output
+                                   "/lib/python"
+                                   #$(version-major+minor
+                                      (package-version python))
+                                   "/site-packages:"
                                   (getenv "GUIX_PYTHONPATH"))))
                `("GI_TYPELIB_PATH" = (,(getenv "GI_TYPELIB_PATH")))
                `("GDK_PIXBUF_MODULE_FILE" =
@@ -682,17 +686,17 @@ and a high score table.")
 (define-public komikku
  (package
    (name "komikku")
-    (version "50.3.0")
+    (version "50.4.0")
    (source
     (origin
       (method git-fetch)
       (uri (git-reference
-             (url "https://codeberg.org/valos/Komikku/")
-             (commit (string-append "v" version))))
+              (url "https://codeberg.org/valos/Komikku/")
+              (commit (string-append "v" version))))
       (file-name (git-file-name name version))
       (sha256
        (base32
-         "0hm1infvdsms193g2yp7qw7lrsxjsx5zziib8hgch34y6dbhfhf1"))))
+         "0skkb1b6jgfzy3v1bhbgxkgxmjvnxdi442asp5gdm7j8j9cv5wxv"))))
    (build-system meson-build-system)
    (arguments
     (list
@@ -738,21 +742,18 @@ and a high score table.")
           python
           python-beautifulsoup4
           python-brotli
-           python-cloudscraper
           python-colorthief
+           ;; python-curl-cffi          ;not packaged yet in Guix
           python-dateparser
           python-ebooklib
           python-emoji
-           python-keyring
           python-jxlpy
+           python-keyring
           python-lxml
           python-magic
           python-natsort
           python-piexif
           python-pillow
-           python-pillow-heif-0.22
-           python-pure-protobuf
-           python-pycairo
           python-pygobject
           python-pyjwt
           python-pypdf
@@ -774,8 +775,8 @@ and a high score table.")
 developed with the aim of being used with the Librem 5 phone.")
    (license license:gpl3+)
    (native-search-paths (list (search-path-specification
-                                (variable "KOMIKKU_SERVERS_PATH")
-                                (files '("lib/komikku/servers")))))))
+                                 (variable "KOMIKKU_SERVERS_PATH")
+                                 (files '("lib/komikku/servers")))))))

 (define-public komikku-servers
  (package
@@ -51,7 +51,6 @@
  #:use-module (guix build-system copy)
  #:use-module (guix build-system meson)
  #:use-module (guix build-system pyproject)
-  #:use-module (guix build-system python)
  #:use-module (guix gexp)
  #:use-module (guix git-download)
  #:use-module (guix packages)
@@ -851,7 +850,7 @@ intellihide and multimonitor support.")
 (define-public gnome-shell-extension-gsconnect
  (package
    (name "gnome-shell-extension-gsconnect")
-    (version "71")
+    (version "72")
    (source (origin
              (method git-fetch)
              (uri (git-reference
@@ -861,7 +860,7 @@ intellihide and multimonitor support.")
              (file-name (git-file-name name version))
              (sha256
               (base32
-                "0i6zrvb40h0af96md7jb4y3f2c1g37h5qp649xk68gp6gwn1401s"))))
+                "06ps946q53jfqi4ycapjb9755763z8p0dvd7jssw6l8h8ma11ly3"))))
    (build-system meson-build-system)
    (arguments
     (list
@@ -936,7 +935,6 @@ intellihide and multimonitor support.")
     (list
      at-spi2-core
      bash-minimal
-      caribou
      evolution-data-server
      gjs
      glib
@@ -250,7 +250,6 @@
  #: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 trivial)
  #:use-module ((guix config) #:select (%storedir))
  #:use-module (guix deprecation)
@@ -2530,7 +2529,7 @@ forgotten when the session ends.")
 (define-public evince
  (package
    (name "evince")
-    (version "48.1")
+    (version "48.4")
    (source
     (origin
       (method url-fetch)
@@ -2538,7 +2537,7 @@ forgotten when the session ends.")
                           (version-major version) "/"
                           "evince-" version ".tar.xz"))
       (sha256
-        (base32 "047s8d4qh9jijk1kp4kfzy4afwwcd0kr11a8j1dkypd0ldprm2vx"))))
+        (base32 "0s46prlb55ghnz136ra8whmrirydmz08lzjrrpa3arl8cb3cb5pj"))))
    (build-system meson-build-system)
    (arguments
     `(#:glib-or-gtk? #t
@@ -2759,7 +2758,7 @@ schemas for settings shared by various components of the GNOME desktop.")
                (invoke "./run-tests")))))))
    (native-inputs (list python-pytest python-setuptools xorg-server-for-tests))
    (inputs (list gtk+))
-    (propagated-inputs (list python-pygobject))
+    (propagated-inputs (list python-pygobject-3.50))
    (home-page "https://getting-things-gnome.github.io/liblarch")
    (synopsis "Library to easily handle complex data structures")
    (description
@@ -2818,7 +2817,7 @@ and how they are displayed (View).")
           gtksourceview-4
           pango
           python
-           python-dbus-1.2
+           python-dbus
           python-liblarch
           python-lxml
           python-pycairo
@@ -2986,7 +2985,7 @@ guidelines.")
           python
           cups
           gtk+
-           python-dbus-1.2
+           python-dbus
           python-pygobject
           python-pycups
           python-requests
@@ -5000,6 +4999,7 @@ as OpenStreetMap, OpenCycleMap, OpenAerialMap and Maps.")
    (arguments
     (list
      #:configure-flags #~(list "-Ddocs=disabled")
+      #:parallel-tests? #f              ;hsts-db-test might hang otherwise.
      #:phases
      #~(modify-phases %standard-phases
          (add-after 'unpack 'adjust-tests
@@ -5041,7 +5041,7 @@ as OpenStreetMap, OpenCycleMap, OpenAerialMap and Maps.")
           zlib))
    (inputs
     (list samba/pinned))               ; For ntlm_auth support
-    (home-page "https://wiki.gnome.org/Projects/libsoup")
+    (home-page "https://libsoup.gnome.org")
    (synopsis "GLib-based HTTP Library")
    (description
     "LibSoup is an HTTP client/server library for GNOME.  It uses GObjects
@@ -5157,7 +5157,7 @@ and the GLib main loop, to integrate well with GNOME applications.")
           libxslt
           pkg-config
           python
-           python-dbus-1.2
+           python-dbus
           python-pygobject-3.50
           vala))
    (propagated-inputs
@@ -8158,12 +8158,6 @@ to display dialog boxes from the commandline and shell scripts.")
    (build-system meson-build-system)
    (arguments
     (list
-      #:modules '((guix build meson-build-system)
-                  ((guix build python-build-system) #:prefix python:)
-                  (guix build utils)
-                  (ice-9 match))
-      #:imported-modules `(,@%meson-build-system-modules
-                           (guix build python-build-system))
      #:glib-or-gtk? #t
      #:configure-flags
      #~(list
@@ -8510,67 +8504,78 @@ Evolution (hence the name), but is now used by other packages as well.")
    (license license:lgpl2.0)))

 (define-public caribou
-  (package
-    (name "caribou")
-    (version "0.4.21")
-    (source (origin
-              (method url-fetch)
-              (uri (string-append "mirror://gnome/sources/" name "/"
-                                  (version-major+minor version) "/"
-                                  name "-" version ".tar.xz"))
-              (sha256
-               (base32
-                "0mfychh1q3dx0b96pjz9a9y112bm9yqyim40yykzxx1hppsdjhww"))))
-    (build-system glib-or-gtk-build-system)
-    (arguments
-     (list
-      #:configure-flags
-      ;; Relax gcc-14's strictness.
-      #~(list "CFLAGS=-g -O2 -Wno-error=incompatible-pointer-types")
-      #:phases
-       #~(modify-phases %standard-phases
-           (add-before
-               'build 'pre-build
-             (lambda _
-               ;; Use absolute shared library path in Caribou-1.0.typelib.
-               (substitute* "libcaribou/Makefile"
-                 (("--shared-library=libcaribou.so")
-                  (string-append "--shared-library="
-                                 #$output "/lib/libcaribou.so")))))
-         (add-after 'install 'wrap-programs
-          (lambda* (#:key outputs #:allow-other-keys)
-            (let ((python-path (getenv "GUIX_PYTHONPATH"))
-                  (gi-typelib-path (getenv "GI_TYPELIB_PATH")))
-              (for-each
-               (lambda (prog)
-                 (wrap-program prog
-                   `("GUIX_PYTHONPATH"      ":" prefix (,python-path))
-                   `("GI_TYPELIB_PATH" ":" prefix (,gi-typelib-path))))
-               (list (string-append #$output "/bin/caribou-preferences")
-                     (string-append #$output "/libexec/antler-keyboard")))))))))
-    (native-inputs
-     `(("glib:bin" ,glib "bin") ; for glib-compile-schemas, etc.
-       ("gobject-introspection" ,gobject-introspection)
-       ("intltool" ,intltool)
-       ("pkg-config" ,pkg-config)
-       ("python" ,python)
-       ("vala" ,vala)
-       ("xsltproc" ,libxslt)))
-    (propagated-inputs
-     ;; caribou-1.0.pc refers to all these.
-     (list libgee libxklavier libxtst gtk+))
-    (inputs
-     `(("bash" ,bash-minimal) ; for wrap-program
-       ("clutter" ,clutter)
-       ("dconf" ,dconf)
-       ("gtk+-2" ,gtk+-2)
-       ("python-pygobject" ,python-pygobject)))
-    (synopsis "Text entry and UI navigation application")
-    (home-page "https://wiki.gnome.org/Projects/Caribou")
-    (description
-     "Caribou is an input assistive technology intended for switch and pointer
+  ;; Latest tag does not work with recent vala versions.
+  (let ((commit "9c900f0139af225bb35bf34bb2aee83f47495ba5")
+        (revision "0"))
+    (package
+      (name "caribou")
+      (version (git-version "0.4.21" revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+                (url "https://gitlab.gnome.org/Archive/caribou")
+                (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32
+           "066z098gfqyrjscbchbjlwkd5sakrrmwm4k2s76vjl5ir62w0mxg"))))
+      (build-system glib-or-gtk-build-system)
+      (arguments
+       (list
+        #:configure-flags
+        ;; Relax gcc-14's strictness.
+        #~(list "CFLAGS=-g -O2 -Wno-error=incompatible-pointer-types")
+        #:phases
+        #~(modify-phases %standard-phases
+            (add-before
+                'build 'pre-build
+              (lambda _
+                ;; Use absolute shared library path in Caribou-1.0.typelib.
+                (substitute* "libcaribou/Makefile"
+                  (("--shared-library=libcaribou.so")
+                   (string-append "--shared-library="
+                                  #$output "/lib/libcaribou.so")))))
+            (add-after 'install 'wrap-programs
+              (lambda* (#:key outputs #:allow-other-keys)
+                (let ((python-path (getenv "GUIX_PYTHONPATH"))
+                      (gi-typelib-path (getenv "GI_TYPELIB_PATH")))
+                  (for-each
+                   (lambda (prog)
+                     (wrap-program prog
+                       `("GUIX_PYTHONPATH" ":" prefix (,python-path))
+                       `("GI_TYPELIB_PATH" ":" prefix (,gi-typelib-path))))
+                   (list
+                    (string-append #$output "/bin/caribou-preferences")
+                    (string-append #$output "/libexec/antler-keyboard")))))))))
+      (native-inputs
+       (list autoconf
+             automake
+             `(,glib "bin") ;for glib-compile-schemas, etc.
+             gobject-introspection
+             gnome-common ;for gnome-autogen.sh
+             intltool
+             libtool
+             libxslt
+             pkg-config
+             python
+             vala
+             which))
+      (propagated-inputs
+       ;; caribou-1.0.pc refers to all these.
+       (list libgee libxklavier libxtst gtk+))
+      (inputs
+       (list bash-minimal ; for wrap-program
+             clutter
+             dconf
+             gtk+-2
+             python-pygobject))
+      (synopsis "Text entry and UI navigation application")
+      (home-page "https://wiki.gnome.org/Projects/Caribou")
+      (description
+       "Caribou is an input assistive technology intended for switch and pointer
 users.")
-    (license license:lgpl2.1)))
+      (license license:lgpl2.1))))

 (define-public network-manager
  (package
@@ -8686,7 +8691,7 @@ users.")
           libxslt
           perl
           pkg-config
-           python-dbus-1.2
+           python-dbus
           python-pygobject-3.50
           python-wrapper
           vala))
@@ -12402,7 +12407,6 @@ advanced image management tool")
           intltool
           pkg-config
           python-psutil
-           python-pytest-runner
           python-pytest))
    (inputs
     (list bash-minimal ;for wrap-program
@@ -12411,7 +12415,7 @@ advanced image management tool")
           gsettings-desktop-schemas
           gtk+
           python-wrapper
-           python-dbus-1.2
+           python-dbus
           python-notify2
           python-pycairo
           python-pygobject
@@ -13696,59 +13700,71 @@ useful to navigate and edit translation messages and comments.")
  (package
    (name "ocrfeeder")
    (version "0.8.5")
-    (source (origin
-              (method url-fetch)
-              (uri (string-append "mirror://gnome/sources/ocrfeeder/"
-                                  (version-major+minor version) "/"
-                                  "ocrfeeder-" version ".tar.xz"))
-              (sha256
-               (base32
-                "1vaaphzk6zn7pp2x9scphdzlbsma910wnbhd9xry50nx95cjlgdh"))))
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+              (url "https://gitlab.gnome.org/GNOME/ocrfeeder")
+              (commit version)))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "11xj5vidvppfd34hrvadz8fljsasljrgq7smfjx7asf88hv79d60"))))
    (build-system gnu-build-system)
    (arguments
-     `(#:phases
-       (modify-phases %standard-phases
-         (add-after
-          'install 'wrap-program
-          (lambda* (#:key outputs #:allow-other-keys)
-            (let ((prog (string-append (assoc-ref outputs "out")
-                                       "/bin/" "ocrfeeder"))
-                  (pylib (string-append (assoc-ref outputs "out")
-                                        "/lib/python"
-                                        ,(version-major+minor
-                                          (package-version python))
-                                        "/site-packages")))
-              (wrap-program prog
-                `("PYTHONPATH" = (,(getenv "GUIX_PYTHONPATH") ,pylib))
-                `("GI_TYPELIB_PATH" = (,(getenv "GI_TYPELIB_PATH"))))))))))
+     (list
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-after 'unpack 'fix-configure-on-python-3.12
+            (lambda _
+              (substitute* "m4/m4_ax_python_module.m4"
+                (("import imp; imp\\.find_module\\((.*)\\)" all target)
+                 (format #f "import importlib.util; \
+exit(0 if importlib.util.find_spec(~a) else 1)"
+                         target)))))
+          (add-after 'install 'wrap-program
+            (lambda _
+              (wrap-program (string-append #$output "/bin/ocrfeeder")
+                `("PYTHONPATH" =
+                  (,(getenv "GUIX_PYTHONPATH")
+                   ,(string-append #$output "/lib/python"
+                                   #$(version-major+minor
+                                      (package-version python))
+                                   "/site-packages")))
+                `("GI_TYPELIB_PATH" =
+                  (,(getenv "GI_TYPELIB_PATH")))))))))
    (native-inputs
-     `(("glib:bin" ,glib "bin")                   ; for glib-compile-resources
-       ("gobject-introspection" ,gobject-introspection)
-       ("gtk+:bin" ,gtk+ "bin")                   ; for gtk-update-icon-cache
-       ("intltool" ,intltool)
-       ("itstool" ,itstool)
-       ("pkg-config" ,pkg-config)
-       ("xmllint" ,libxml2)))
+     (list autoconf
+           automake
+           `(,glib "bin")               ;for glib-compile-resources
+           gobject-introspection
+           `(,gtk+ "bin")               ;for gtk-update-icon-cache
+           intltool
+           itstool
+           gnome-common
+           libxml2
+           pkg-config
+           which
+           yelp-tools))
    (inputs
-     `(("bash" ,bash-minimal) ; for wrap-program
-       ("enchant" ,enchant)
-       ("glib" ,glib)
-       ("goocanvas" ,goocanvas)
-       ("gtk" ,gtk+)
-       ("gtkspell3" ,gtkspell3)
-       ("libjpeg" ,libjpeg-turbo)
-       ("libtiff" ,libtiff)
-       ("libraw" ,libraw)
-       ("ocrad" ,ocrad)
-       ("python" ,python-wrapper)
-       ("python-pygobject" ,python-pygobject)
-       ("python-odfpy" ,python-odfpy)
-       ("python-pillow" ,python-pillow)
-       ("python-pyenchant" ,python-pyenchant)
-       ("python-reportlab" ,python-reportlab)
-       ("python-sane" ,python-sane)
-       ("sane" ,sane)
-       ("tesseract-ocr" ,tesseract-ocr)))
+     (list bash-minimal                 ;for wrap-program
+           enchant
+           glib
+           goocanvas
+           gtk+
+           gtkspell3
+           libjpeg-turbo
+           libtiff
+           libraw
+           ocrad
+           python-wrapper
+           python-pygobject
+           python-odfpy
+           python-pillow
+           python-pyenchant
+           python-reportlab
+           python-sane
+           sane
+           tesseract-ocr))
    (home-page "https://wiki.gnome.org/Apps/OCRFeeder")
    (synopsis "Complete OCR Suite")
    (description "OCRFeeder is a complete Optical Character Recognition and
@@ -87,7 +87,6 @@
  #: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 download)
  #:use-module (guix gexp)
@@ -2,8 +2,9 @@
 ;;; Copyright © 2023 JOULAUD François <Francois.JOULAUD@radiofrance.com>
 ;;; Copyright © 2025 Maxim Cournoyer <maxim@guixotic.coop>
 ;;; Copyright © 2025 Tomas Volf <~@wolfsden.cz>
-;;; Copyright © 2025 Sharlatan Hellseher <sharlatanus@gmail.com>
+;;; Copyright © 2025-2026 Sharlatan Hellseher <sharlatanus@gmail.com>
 ;;; Copyright © 2025 jgart <jgart@dismail.de>
+;;; Copyright © 2026 Ankit Gadiya <git@argp.in>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -48,7 +49,7 @@
 (define-public go-chroma
  (package
    (name "go-chroma")
-    (version "2.20.0")
+    (version "2.24.1")
    (source
     (origin
       (method git-fetch)
@@ -57,7 +58,7 @@
              (commit (string-append "v" version ))))
       (file-name (git-file-name name version))
       (sha256
-        (base32 "05w4hnfcxqdlsz7mkc0m3jbp1aj67wzyhq5jh8ldfgnyjnlafia3"))))
+        (base32 "0kww0yhwqzzgl8n3alislf0136rk7kh507bbvr32a30wmk5dzi81"))))
    (build-system go-build-system)
    (arguments
     (list
@@ -83,17 +84,16 @@ translators for Pygments lexers and styles.")
 (define-public go-fxlint
  (package
    (name "go-fxlint")
-    (version "0.0.0-20251227140935-d5da5b04ac90")
+    (version "1.24.0")
    (source
     (origin
       (method git-fetch)
       (uri (git-reference
              (url "https://github.com/uber-go/fx")
-              (commit (go-version->git-ref version
-                                           #:subdir "tools"))))
+              (commit (string-append "v" version ))))
       (file-name (git-file-name name version))
       (sha256
-        (base32 "0yw9x95v82dcxh0zf13inz8c3q7p2hmzqzgja360b1yifi01rvrc"))))
+        (base32 "0iifq4gjd873l444qh32x2zzsz2yinrvpjsdfphxsfk1h0cyk4q9"))))
    (build-system go-build-system)
    (arguments
     (list
@@ -115,7 +115,7 @@ that handle none of the event types.")
 (define-public go-jsonnet
  (package
    (name "go-jsonnet")
-    (version "0.21.0")
+    (version "0.22.0")
    (source
     (origin
       (method git-fetch)
@@ -124,7 +124,7 @@ that handle none of the event types.")
              (commit (string-append "v" version))))
       (file-name (git-file-name name version))
       (sha256
-        (base32 "0d05f16qxabfhaj0l3da3x7zl5g8jbvkcyn39bidd2a278sb3p97"))))
+        (base32 "1c7h14rvavgadvbsyfa9j4rchsgxb5j363f53rhcvghvmblzddiv"))))
    (build-system go-build-system)
    (arguments
     (list
@@ -276,19 +276,20 @@ import of a 3rd party package at runtime).")
    (name "gopls")
    ;; XXX: Starting from 0.14.0 gppls needs golang.org/x/telemetry, which
    ;; needs to be discussed if it may be included in Guix.
-    (version "0.19.1")
+    (version "0.22.0")
    (source
     (origin
       (method git-fetch)
       (uri (git-reference
-             (url "https://go.googlesource.com/tools")
-             (commit (go-version->git-ref version #:subdir "gopls"))))
+              (url "https://go.googlesource.com/tools")
+              (commit (go-version->git-ref version #:subdir "gopls"))))
       (file-name (git-file-name name version))
       (sha256
-        (base32 "1dihdw4nzp21hlbwxf6qyhyfgavi1a55lmlyk36czd85v0jcp6a0"))))
+        (base32 "0n5ixvk6c8hww5z9lvf74dx6p4j573bq3ssvp77n6033l0fcbv94"))))
    (build-system go-build-system)
    (arguments
     (list
+      #:go go-1.26
      #:install-source? #f
      #:import-path "golang.org/x/tools/gopls"
      #:unpack-path "golang.org/x/tools"
@@ -311,11 +312,13 @@ import of a 3rd party package at runtime).")
              (setenv "GODEBUG" "gotypesalias=1"))))))
    (native-inputs
     (list go-github-com-fatih-gomodifytags
+           go-github-com-fsnotify-fsnotify
           go-github-com-google-go-cmp
+           go-github-com-google-jsonschema-go
           go-github-com-jba-templatecheck
+           go-github-com-modelcontextprotocol-go-sdk
           go-golang-org-x-mod
           go-golang-org-x-sync
-           go-golang-org-x-sys
           go-golang-org-x-telemetry
           go-golang-org-x-text
           go-golang-org-x-tools
@@ -150,6 +150,31 @@ the @code{c2go} tool at
@url{https://github.com/andybalholm/c2go,https://github.com/andybalholm/c2go}.")
    (license license:expat)))

+(define-public go-github-com-blakesmith-ar
+  (package
+    (name "go-github-com-blakesmith-ar")
+    (version "0.0.0-20190502131153-809d4375e1fb")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+              (url "https://github.com/blakesmith/ar")
+              (commit (go-version->git-ref version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "00fxkc04b9cb53xxzw5gdqqpwlqv9n5kk0yn2lb5w4rgj5gm8ph1"))))
+    (build-system go-build-system)
+    (arguments
+     (list
+      #:import-path "github.com/blakesmith/ar"
+      #:test-flags #~(list "-vet=off")))
+    (home-page "https://github.com/blakesmith/ar")
+    (synopsis "Golang archive file reader")
+    (description
+     "This package provides a Golang file reader for archive files generated
+with @code{ar}.")
+    (license license:expat)))
+
 (define-public go-github-com-bodgit-sevenzip
  (package
    (name "go-github-com-bodgit-sevenzip")
@@ -221,6 +246,31 @@ blocks allowing it to only read the compressed blocks required.")
    (license (list license:bsd-3
                   license:expat))))

+(define-public go-github-com-cavaliergopher-cpio
+  (package
+    (name "go-github-com-cavaliergopher-cpio")
+    (version "1.0.1")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/cavaliergopher/cpio")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "0b1ix8z9kwfpwqi0q08ivcfcimlqk781jbzbfw7qbqavh702w3m2"))))
+    (build-system go-build-system)
+    (arguments
+     (list
+      #:import-path "github.com/cavaliergopher/cpio"))
+    (home-page "https://github.com/cavaliergopher/cpio")
+    (synopsis "Readers and writers for CPIO archives")
+    (description
+     "This package provides readers and writers for CPIO archives.  Currently,
+only the SVR4 (New ASCII) format is supported, both with and without
+checksums.")
+    (license license:bsd-3)))
+
 (define-public go-github-com-containerd-stargz-snapshotter-estargz
  (package
    (name "go-github-com-containerd-stargz-snapshotter-estargz")
@@ -385,6 +435,37 @@ Implements the XFLATE format, an random-access extension to DEFLATE.
 compression format.")
    (license license:bsd-3)))

+(define-public go-github-com-google-rpmpack
+  (package
+    (name "go-github-com-google-rpmpack")
+    (version "0.7.1")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+              (url "https://github.com/google/rpmpack")
+              (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "17h2s1g191cvbs16fnclkpb42d9mx6mdmhd04kxzv8bss7m59pr4"))))
+    (build-system go-build-system)
+    (arguments
+     (list
+      #:import-path "github.com/google/rpmpack"))
+    (native-inputs
+     (list go-github-com-google-go-cmp))
+    (propagated-inputs
+     (list go-github-com-cavaliergopher-cpio
+           go-github-com-klauspost-compress
+           go-github-com-klauspost-pgzip
+           go-github-com-ulikunitz-xz))
+    (home-page "https://github.com/google/rpmpack")
+    (synopsis "Pack files to rpm files")
+    (description
+     "Package rpmpack packs files to rpm files.  It is designed to be simple
+to use and deploy, not requiring any filesystem access to create rpm files.")
+    (license license:asl2.0)))
+
 (define-public go-github-com-hhrutter-lzw
  (package
    (name "go-github-com-hhrutter-lzw")
@@ -884,6 +965,40 @@ format's \"Extra Fields\".  The intention is to eventually support and provide
 a low-level API for the majority of PKWARE's and Info-ZIP's extra fields.")
    (license license:expat)))

+(define-public go-github-com-sassoftware-go-rpmutils
+  (package
+    (name "go-github-com-sassoftware-go-rpmutils")
+    (version "0.4.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+              (url "https://github.com/sassoftware/go-rpmutils")
+              (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "06ymwjn6xvc4cpxcsh5achwgma4i075ikbzq8jm143m0pck4pmfi"))))
+    (build-system go-build-system)
+    (arguments
+     (list
+      #:import-path "github.com/sassoftware/go-rpmutils"))
+    (native-inputs
+     (list go-github-com-stretchr-testify
+           go-go-uber-org-goleak))
+    (propagated-inputs
+     (list go-github-com-datadog-zstd
+           go-github-com-klauspost-compress
+           go-github-com-protonmail-go-crypto
+           go-github-com-ulikunitz-xz
+           go-github-com-xi2-xz
+           go-golang-org-x-sys))
+    (home-page "https://github.com/sassoftware/go-rpmutils")
+    (synopsis "Parse RPM packages in Golang")
+    (description
+     "This package provides some Golang interfaces for handling RPM packages,
+such extracting RPM header and CPIO content.")
+    (license license:asl2.0)))
+
 (define-public go-github-com-sorairolake-lzip-go
  (package
    (name "go-github-com-sorairolake-lzip-go")
@@ -0,0 +1,251 @@
+;;; GNU Guix --- Functional package management for GNU
+;;; Copyright © 2026 Sughosha <sughosha@disroot.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 golang-graphics)
+  #:use-module (guix build-system go)
+  #:use-module (guix gexp)
+  #:use-module (guix git-download)
+  #:use-module ((guix licenses) #:prefix license:)
+  #:use-module (guix packages)
+  #:use-module (gnu packages)
+  #:use-module (gnu packages glib)
+  #:use-module (gnu packages golang-build)
+  #:use-module (gnu packages golang-check)
+  #:use-module (gnu packages golang-xyz)
+  #:use-module (gnu packages gtk)
+  #:use-module (gnu packages pkg-config)
+  #:use-module (gnu packages xorg))
+
+;;; Commentary:
+;;;
+;;; Please: Try to add new module packages in alphabetic order.
+;;;
+;;; Code:
+
+;;;
+;;; Libraries:
+;;;
+
+(define-public go-github-com-diamondburned-gotk4
+  (package
+    (name "go-github-com-diamondburned-gotk4")
+    ;; 0.3.1 (2024-08-03); the latest commit includes fixes for tests, revert
+    ;; back to git tag when released.
+    (properties '((commit . "d44ab4b5b24e200c90c6a9ffb6632ada7e166a79")
+                  (revision . "0")))
+    (version (git-version "0.3.1"
+                          (assoc-ref properties 'revision)
+                          (assoc-ref properties 'commit)))
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/diamondburned/gotk4")
+              (commit (assoc-ref properties 'commit))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "0xwsl5n3hksrbyap11zhm4jp2hx1v8zqk796bh87qplw7468pn51"))))
+    (build-system go-build-system)
+    (arguments
+     (list
+      #:import-path "github.com/diamondburned/gotk4"
+      #:test-flags #~(list "-vet=off")
+      ;; XXX: Code is generated with "go generate", but the atemp to
+      ;; re-generate it before build/test fails, see:
+      ;; <https://github.com/diamondburned/gotk4/issues/174>.
+      ;; #:phases
+      #;
+      #~(modify-phases %standard-phases
+        (add-before 'build 'go-generate
+          (lambda* (#:key import-path #:allow-other-keys)
+            (with-directory-excursion (string-append "src/" import-path)
+              (invoke "go" "generate" "-v" "-n")))))))
+    (native-inputs
+     (list at-spi2-core
+           cairo
+           gdk-pixbuf
+           glib
+           go-github-com-alecthomas-assert-v2
+           gobject-introspection
+           graphene
+           gtk
+           gtk+
+           pango
+           pkg-config))
+    (propagated-inputs
+     (list go-github-com-davecgh-go-spew
+           go-github-com-fatih-color
+           go-github-com-karpeleslab-weak               ;for gotk4/pkg/go.mod
+           go-go4-org-unsafe-assume-no-moving-gc        ;for gotk4/pkg/go.mod
+           go-golang-org-x-sync))
+    (home-page "https://github.com/diamondburned/gotk4")
+    (synopsis "GTK4 bindings generator for Go")
+    (description
+     "gotk4 is a GTK4 bindings generator for Go.  It also provides generated
+bindings for ATK, Cairo, GdkPixbuf, GLib, Graphene, GTK4, GTK+3 and Pango.")
+    (license (list license:agpl3+    ;used by gotk4/gir
+                   license:mpl2.0    ;used by gotk4/pkg
+                   license:expat)))) ;used by gotk4/pkg/cairo
+
+(define-public go-github-com-diamondburned-gotk4-layer-shell
+  ;; There are no tags or releases upstream.
+  (let ((commit "6efa9f6dc438e10869f9ef0b8f7b5197e585bac1")
+        (revision "0"))
+    (package
+      (name "go-github-com-diamondburned-gotk4-layer-shell")
+      (version (git-version "0.0.0" revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+                (url "https://github.com/diamondburned/gotk4-layer-shell")
+                (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32 "03kch2g9fzgbd7q2lnp7xhdbi9rsh1fd997nw1phdvw80xshsvlr"))))
+      (build-system go-build-system)
+      (arguments
+       (list
+        #:import-path "github.com/diamondburned/gotk4-layer-shell"
+        #:embed-files #~(list "capitalized.txt" "replaced.txt")
+        #:phases
+        #~(modify-phases %standard-phases
+            (add-before 'build 'go-generate
+              (lambda* (#:key import-path #:allow-other-keys)
+                (with-directory-excursion (string-append "src/" import-path)
+                  (invoke "go" "generate" "-v" "-n")))))))
+      (native-inputs
+       (list at-spi2-core
+             cairo
+             gdk-pixbuf
+             glib
+             go-github-com-davecgh-go-spew
+             gobject-introspection
+             graphene
+             gtk
+             gtk+
+             gtk-layer-shell
+             gtk4-layer-shell
+             pango
+             pkg-config))
+      (propagated-inputs
+       (list go-github-com-diamondburned-gotk4
+             go-github-com-fatih-color
+             go-github-com-mattn-go-colorable
+             go-github-com-mattn-go-isatty
+             go-github-com-pkg-errors
+             go-golang-org-x-sync
+             go-golang-org-x-sys))
+      (home-page "https://github.com/diamondburned/gotk4-layer-shell")
+      (synopsis "Layer Shell bindings generator for Go and gotk4")
+      (description
+       "gotk4-layer-shell is a GTK Layer Shell and GTK4 Layer Shell bindings
+ generator for Go and gotk4.  It also provides generated bindings.")
+      (license (list license:agpl3       ;used by the generator
+                     license:mpl2.0))))) ;used by the generated code
+
+(define-public go-github-com-dlasky-gotk3-layershell
+  ;; There are no tags or releases upstream.
+  (let ((commit "5c5115f0d77479c452ef686e3d7f327f2a341b3c")
+        (revision "0"))
+    (package
+      (name "go-github-com-dlasky-gotk3-layershell")
+      (version (git-version "0.0.0" revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+                (url "https://github.com/dlasky/gotk3-layershell")
+                (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32 "0k7flgwmkwfq3lki4fjwx0868nxv2wa2igbqxjgqfm6150mnhmp8"))))
+      (build-system go-build-system)
+      (arguments
+       (list
+        #:import-path "github.com/dlasky/gotk3-layershell"))
+      (native-inputs
+       (list cairo
+             gdk-pixbuf
+             glib
+             gtk+
+             gtk-layer-shell
+             pango
+             pkg-config))
+      (propagated-inputs
+       (list go-github-com-gotk3-gotk3))
+      (home-page "https://github.com/dlasky/gotk3-layershell")
+      (synopsis "gotk3 addon module for GTK Layer Shell compatibility")
+      (description
+       "gotk3-layershell is a simple golang library to provide bindings for
+GTK Layer Shell library which can also be consumed in the gotk3 library.")
+      (license license:expat))))
+
+(define-public go-github-com-gotk3-gotk3
+  (package
+    (name "go-github-com-gotk3-gotk3")
+    (version "0.6.4.2")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+              (url "https://github.com/gotk3/gotk3")
+              (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "1hbqy4skn56xi69wqbys9rc1g46cx9sazj5n8ckq9638wphnp202"))))
+    (build-system go-build-system)
+    (arguments
+     (list
+      #:skip-build? #t
+      #:import-path "github.com/gotk3/gotk3"
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-before 'check 'start-xorg-server
+            (lambda* (#:key inputs #:allow-other-keys)
+              ;; The test suite requires opening a display server.
+              (system "Xvfb :1 &")
+              (setenv "DISPLAY" ":1"))))))
+    (native-inputs
+     (list cairo
+           gdk-pixbuf
+           glib
+           gtk+
+           pango
+           pkg-config
+           xorg-server))
+    (home-page "https://github.com/gotk3/gotk3")
+    (synopsis "Go bindings for GTK+3")
+    (description
+     "gotk3 provides Go bindings for GTK+3 and dependent projects.
+
+Partial binding support for the following libraries is currently implemented:
+
+@itemize
+@item GTK 3 (3.12 and later)
+@item GDK 3 (3.12 and later)
+@item GLib 2 (2.36 and later)
+@item Cairo (1.10 and later)
+@end itemize
+
+Functions use the same names as the native C function calls, but use
+CamelCase.  In cases where native GTK uses pointers to values to simulate
+multiple return values, Go's native multiple return values are used instead.
+Whenever a native GTK call could return an unexpected NULL pointer, an
+additional error is returned in the Go binding.")
+    (license license:isc)))
@@ -607,6 +607,30 @@ Actions} locally.")
 It's a static checker for GitHub Actions workflow files.")
    (license license:expat)))

+(define-public go-gitlab-com-digitalxero-go-conventional-commit
+  (package
+    (name "go-gitlab-com-digitalxero-go-conventional-commit")
+    (version "1.0.7")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+              (url "https://gitlab.com/digitalxero/go-conventional-commit.git")
+              (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "1191j3k9ma5sv8w2zsw8gb1407561zll0ca8hwy0dja6s0b3z0xy"))))
+    (build-system go-build-system)
+    (arguments
+     (list
+      #:import-path "gitlab.com/digitalxero/go-conventional-commit"))
+    (home-page "https://gitlab.com/digitalxero/go-conventional-commit")
+    (synopsis "Go parser for conventional commits")
+    (description
+     "This package provides a Go parser for conventional-commit messages
+@url{https://www.conventionalcommits.org/}.")
+    (license license:expat)))
+
 (define-public go-github-com-xanzy-go-gitlab
  (package
    (name "go-github-com-xanzy-go-gitlab")
@@ -10796,6 +10796,33 @@ dhcpv6 and dhcpv4
@end itemize")
    (license license:bsd-3)))

+(define-public go-github-com-invopop-jsonschema
+  (package
+    (name "go-github-com-invopop-jsonschema")
+    (version "0.14.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+              (url "https://github.com/invopop/jsonschema")
+              (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "0y881agfaycn5l5qn2y2jmiskchi0cvn5v602hna4ljy9rv5jxw2"))))
+    (build-system go-build-system)
+    (arguments
+     (list
+      #:import-path "github.com/invopop/jsonschema"))
+    (native-inputs
+     (list go-github-com-stretchr-testify))
+    (propagated-inputs
+     (list go-github-com-pb33f-ordered-map-v2))
+    (home-page "https://github.com/invopop/jsonschema")
+    (synopsis "Go JSON Schema Reflection")
+    (description
+     "Package jsonschema uses reflection to generate JSON Schemas from Go types.")
+    (license license:expat)))
+
 (define-public go-github-com-ipfs-go-cid
  (package
    (name "go-github-com-ipfs-go-cid")
@@ -16985,9 +17012,11 @@ kinds of referrer URLs (search, social, ...).")
     (list
      #:skip-build? #t
      #:import-path "github.com/sigstore/rekor"
-      ;; XXX: Remove when all inputs are packaged.
+      #:embed-files #~(list ".*\\.json")
+      ;; ;; XXX: Remove when all inputs are packaged.
      #:test-subdirs
-      #~(list "pkg/events/newentry"
+      #~(list "pkg/client"
+              "pkg/events/newentry"
              "pkg/indexstorage/mysql"
              "pkg/pki/minisign"
              "pkg/pki/pgp"
@@ -16995,7 +17024,10 @@ kinds of referrer URLs (search, social, ...).")
              "pkg/pki/tuf"
              "pkg/pki/x509"
              "pkg/pubsub/gcp"
-              "pkg/util")))
+              "pkg/tle"
+              "pkg/types"
+              "pkg/util"
+              "pkg/verify")))
    (native-inputs
     (list go-github-com-asaskevich-govalidator
           go-github-com-data-dog-go-sqlmock
@@ -17023,6 +17055,7 @@ kinds of referrer URLs (search, social, ...).")
           go-github-com-go-openapi-validate
           go-github-com-go-sql-driver-mysql
           go-github-com-go-viper-mapstructure-v2
+           go-github-com-google-rpmpack
           go-github-com-google-trillian
           go-github-com-grpc-ecosystem-go-grpc-middleware
           go-github-com-hashicorp-go-cleanhttp
@@ -17066,7 +17099,6 @@ kinds of referrer URLs (search, social, ...).")
           ;; go-github-com-adamkorcz-go-fuzz-headers-1
           ;; go-github-com-cavaliercoder-go-rpm
           ;; go-github-com-go-redis-redismock-v9
-           ;; go-github-com-google-rpmpack
           ;; go-github-com-sassoftware-relic
           ;; go-github-com-sassoftware-relic-v7
           ;; go-go-step-sm-crypto
@@ -18549,6 +18581,31 @@ Tailscale for access control.")
 Tailscale.")
    (license license:bsd-3)))

+(define-public go-github-com-tcnksm-go-httpstat
+  (package
+    (name "go-github-com-tcnksm-go-httpstat")
+    (version "0.2.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+              (url "https://github.com/tcnksm/go-httpstat")
+              (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "18jn40ra97waxx1mf23pkh6rq46y0nqd7vi3zcx9cwc39zqaf9bc"))))
+    (build-system go-build-system)
+    (arguments
+     (list
+      #:tests? #f ;Tests require network connection
+      #:import-path "github.com/tcnksm/go-httpstat"))
+    (home-page "https://github.com/tcnksm/go-httpstat")
+    (synopsis "Trace HTTP latency information in Go")
+    (description
+     "Package httpstat traces HTTP latency infomation, such as DNSLookup and
+TCP Connection, on any Golang HTTP request with no big code modification.")
+    (license license:expat)))
+
 (define-public go-github-com-tdewolff-minify-v2
  (package
    (name "go-github-com-tdewolff-minify-v2")
@@ -19080,6 +19137,30 @@ caching protocol.  It provides support to programmatically store and retrieve
 build caches, instead of relying on the standard actions/cache YAML step.")
    (license license:expat)))

+(define-public go-github-com-toqueteos-webbrowser
+  (package
+    (name "go-github-com-toqueteos-webbrowser")
+    (version "1.2.1")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+              (url "https://github.com/toqueteos/webbrowser")
+              (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "0bnn02zcfc9xkxc2qvv4q6wy5sipcwc0hwmx7hdhvv3lsw177flw"))))
+    (build-system go-build-system)
+    (arguments
+     (list
+      #:import-path "github.com/toqueteos/webbrowser"))
+    (home-page "https://github.com/toqueteos/webbrowser")
+    (synopsis "Simple API for opening web pages")
+    (description
+     "This package provides a simple API for opening web pages on your default
+browser.")
+    (license license:expat)))
+
 (define-public go-github-com-transparency-dev-tessera
  (package
    (name "go-github-com-transparency-dev-tessera")
@@ -77,6 +77,7 @@
 ;;; Copyright © 2026 Evgeny Pisemsky <mail@pisemsky.site>
 ;;; Copyright © 2026 Vinicius Monego <monego@posteo.net>
 ;;; Copyright © 2026 Daniel Littlewood <dan@danielittlewood.xyz>
+;;; Copyright © 2026 Sughosha <sughosha@disroot.org>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -113,6 +114,7 @@
  #:use-module (gnu packages golang-compression)
  #:use-module (gnu packages golang-crypto)
  #:use-module (gnu packages golang-maths)
+  #:use-module (gnu packages golang-vcs)
  #:use-module (gnu packages golang-web)
  #:use-module (gnu packages graph)
  #:use-module (gnu packages imagemagick)
@@ -1760,6 +1762,30 @@ strings for a safe use as command line arguments in the most common POSIX
 shells.")
    (license license:expat)))

+(define-public go-github-com-aleksi-pointer
+  (package
+    (name "go-github-com-aleksi-pointer")
+    (version "1.2.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+              (url "https://github.com/AlekSi/pointer")
+              (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "0rncmanv62wwy7ihvjhvb695mkvy4kdzhgnn90zygs9yrfzzk0wk"))))
+    (build-system go-build-system)
+    (arguments
+     (list
+      #:import-path "github.com/AlekSi/pointer"))
+    (home-page "https://github.com/AlekSi/pointer")
+    (synopsis "Helper Go library to convert between pointers and values")
+    (description
+     "This package provides helpers to convert between pointers and values of
+built-in and, with generics, of any types.")
+    (license license:expat)))
+
 (define-public go-github-com-alexflint-go-filemutex
  (package
    (name "go-github-com-alexflint-go-filemutex")
@@ -1788,6 +1814,32 @@ shells.")
 synchronizes across processes.")
    (license license:expat)))

+(define-public go-github-com-allan-simon-go-singleinstance
+  (package
+    (name "go-github-com-allan-simon-go-singleinstance")
+    (version "1.0.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+              (url "https://github.com/allan-simon/go-singleinstance")
+              (commit version)))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "1q0s03cmp488d4pyxjysfingzisj4r5n8vy4cffapr6rcr9rfj1h"))))
+    (build-system go-build-system)
+    (arguments
+     (list
+      #:import-path "github.com/allan-simon/go-singleinstance"
+      #:test-flags #~(list "-vet=off")))
+    (home-page "https://github.com/allan-simon/go-singleinstance")
+    (synopsis "Go library to have only one instance of a software")
+    (description
+     "@code{go-singleinstance} is a Go library to have only one instance of a
+software (based on Python's
+@uref{https://github.com/pycontribs/tendo, tendo}).")
+    (license license:expat)))
+
 (define-public go-github-com-alsm-ioprogress
  (package
    (name "go-github-com-alsm-ioprogress")
@@ -4045,38 +4097,6 @@ Supported Barcode Types:
     "This is a memcache client library for the Go programming language.")
    (license license:asl2.0)))

-(define-public go-github-com-bradfitz-iter
-  ;; XXX Report to the users of this package, note from maintainer:
-  ;;
-  ;; This package was intended to be an educational joke when it was released
-  ;; in 2014. People didn't get the joke part and started depending on
-  ;; it. That's fine, I guess. (This is the Internet.) But it's kinda
-  ;; weird. It's one line, and not even idiomatic Go style. I encourage you
-  ;; not to depend on this or write code like this, but I do encourage you to
-  ;; read the code and think about the representation of Go slices and why it
-  ;; doesn't allocate.
-  (package
-    (name "go-github-com-bradfitz-iter")
-    (version "0.0.0-20191230175014-e8f45d346db8")
-    (source
-     (origin
-       (method git-fetch)
-       (uri (git-reference
-              (url "https://github.com/bradfitz/iter")
-              (commit (go-version->git-ref version))))
-       (file-name (git-file-name name version))
-       (sha256
-        (base32 "1qqy1fhmlrsfz6l1arsxmkpfj30s090j1a3ij0lap6h45pc1z509"))))
-    (build-system go-build-system)
-    (arguments
-     (list
-      #:import-path "github.com/bradfitz/iter"))
-    (home-page "https://github.com/bradfitz/iter")
-    (synopsis "Syntactically different way to iterate over integers")
-    (description
-     "This package provides a syntactically different way to iterate over integers.")
-    (license license:bsd-3)))
-
 (define-public go-github-com-bradfitz-parentdeath
  (package
    (name "go-github-com-bradfitz-parentdeath")
@@ -4414,6 +4434,29 @@ information for Golang.")
 variables into structs.")
    (license license:expat)))

+(define-public go-github-com-caarlos0-go-version
+  (package
+    (name "go-github-com-caarlos0-go-version")
+    (version "0.2.2")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+              (url "https://github.com/caarlos0/go-version")
+              (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "0kp78am3yzffz8r70f1skq0m2vms0wk37f76hqbfg1r29hay1ban"))))
+    (build-system go-build-system)
+    (arguments
+     (list
+      #:import-path "github.com/caarlos0/go-version"))
+    (home-page "https://github.com/caarlos0/go-version")
+    (synopsis "Fetch Go module version")
+    (description
+     "Package goversion provides utilities to get the Go module version information.")
+    (license license:expat)))
+
 (define-public go-github-com-calebcase-tmpfile
  (package
    (name "go-github-com-calebcase-tmpfile")
@@ -4466,6 +4509,36 @@ color palette} for Go applications.  Catppuccin is a community-driven pastel
 theme with four flavors: Latte, Frappe, Macchiato, and Mocha.")
    (license license:expat)))

+(define-public go-github-com-ccojocar-zxcvbn-go
+  (package
+    (name "go-github-com-ccojocar-zxcvbn-go")
+    (version "1.0.4")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+              (url "https://github.com/ccojocar/zxcvbn-go")
+              (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "0dlrd6afpfwnpj6cbbvjhwbf33ldr0nzffl8p43jrmn62mwf7cn7"))))
+    (build-system go-build-system)
+    (arguments
+     (list
+      #:import-path "github.com/ccojocar/zxcvbn-go"))
+    (native-inputs
+     (list go-github-com-stretchr-testify))
+    (home-page "https://github.com/ccojocar/zxcvbn-go")
+    (synopsis "Password-strength generator in Go")
+    (description
+     "This package provides a password strength generators written in Golang.
+It attempts to give sound password advice through pattern matching and
+conservative entropy calculations.  It finds 10k common passwords, common
+American names and surnames, common English words, and common patterns like
+dates, repeats (aaa), sequences (abcd), and QWERTY patterns. It's an active
+fork of @url{https://github.com/nbutton23/zxcvbn-go}.")
+    (license license:expat)))
+
 (define-public go-github-com-cention-sany-utf7
  (package
    (name "go-github-com-cention-sany-utf7")
@@ -11731,6 +11804,33 @@ native Go structure.")
    (description "Package yaml implements YAML support for the Go language.")
    (license license:asl2.0)))

+(define-public go-github-com-gobuffalo-flect
+  (package
+    (name "go-github-com-gobuffalo-flect")
+    (version "1.0.3")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+              (url "https://github.com/gobuffalo/flect")
+              (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "0lyb1876byv9q52y6dlq17aahwl108mhp67cmxykckjpxxykb442"))))
+    (build-system go-build-system)
+    (arguments
+     (list
+      #:import-path "github.com/gobuffalo/flect"))
+    (native-inputs
+     (list go-github-com-stretchr-testify))
+    (home-page "https://github.com/gobuffalo/flect")
+    (synopsis "Inflection engine for Golang")
+    (description
+     "This package provides a new inflection engine to replace
+@url{https://github.com/markbates/inflect,} designed to be more modular,
+readable, and easier to fix issues on than the original.")
+    (license license:expat)))
+
 (define-public go-github-com-gobwas-glob
  (package
    (name "go-github-com-gobwas-glob")
@@ -12574,6 +12674,41 @@ color (24-bit, RGB)
@end itemize")
    (license license:expat)))

+(define-public go-github-com-goreleaser-chglog
+  (package
+    (name "go-github-com-goreleaser-chglog")
+    (version "0.7.4")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+              (url "https://github.com/goreleaser/chglog")
+              (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "09ni4y644zhp3bf9nwy9qc9wkxrn2hla6nczg3zpn0ls8qaxjd40"))))
+    (build-system go-build-system)
+    (arguments
+     (list
+      #:import-path "github.com/goreleaser/chglog"))
+    (native-inputs
+     (list go-github-com-go-git-go-billy-v5
+	   go-github-com-google-go-cmp
+           go-github-com-smartystreets-goconvey
+	   go-github-com-spf13-cobra
+           go-github-com-spf13-viper))
+    (propagated-inputs
+     (list go-github-com-go-git-go-git-v5
+           go-github-com-masterminds-semver-v3
+           go-github-com-masterminds-sprig-v3
+           go-gitlab-com-digitalxero-go-conventional-commit
+           go-go-yaml-in-yaml-v3))
+    (home-page "https://github.com/goreleaser/chglog")
+    (synopsis "Changelog management Go library")
+    (description
+     "This package provides Go functions to manage changelogs.")
+    (license license:expat)))
+
 (define-public go-github-com-goreleaser-fileglob
  (package
    (name "go-github-com-goreleaser-fileglob")
@@ -12604,6 +12739,66 @@ underneath and returns only matching files or directories, depending on the
 configuration.")
    (license license:expat)))

+(define-public go-github-com-goreleaser-nfpm-v2
+  (package
+    (name "go-github-com-goreleaser-nfpm-v2")
+    (version "2.44.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+              (url "https://github.com/goreleaser/nfpm")
+              (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "17dmzkvy3ihjjaxi10l9xc1mcg9vmlr2v1xc4a361fa22aqigz0v"))))
+    (build-system go-build-system)
+    (arguments
+     (list
+      #:go go-1.25
+      #:import-path "github.com/goreleaser/nfpm/v2"
+      #:unpack-path "github.com/goreleaser/nfpm/v2"
+      ;; Tests fail due to read-only filesystem when trying to manipulate mode
+      ;; of the files.
+      #:test-flags
+      #~(list "-skip" "TestPrepareForPackager|TestDeepPathsWithGlobAndUmask")
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-after 'unpack 'fix-tests
+            (lambda* (#:key unpack-path #:allow-other-keys)
+              (with-directory-excursion (string-append "src/" unpack-path)
+                (substitute*  "rpm/rpm_test.go"
+                  (("/bin/bash") (which "bash")))))))))
+    (native-inputs
+     (list go-github-com-caarlos0-go-version
+           go-github-com-invopop-jsonschema
+           go-github-com-muesli-mango-cobra
+           go-github-com-muesli-roff
+           go-github-com-sassoftware-go-rpmutils
+           go-github-com-stretchr-testify))
+    (propagated-inputs
+     (list go-dario-cat-mergo
+           go-github-com-aleksi-pointer
+           go-github-com-blakesmith-ar
+           go-github-com-google-rpmpack
+           go-github-com-goreleaser-chglog
+           go-github-com-goreleaser-fileglob
+           go-github-com-klauspost-compress
+           go-github-com-klauspost-pgzip
+           go-github-com-masterminds-semver-v3
+           go-github-com-protonmail-go-crypto
+           go-github-com-protonmail-gopenpgp-v2
+           go-github-com-spf13-cobra
+           go-github-com-ulikunitz-xz
+           go-gopkg-in-yaml-v3))
+    (home-page "https://github.com/goreleaser/nfpm")
+    (synopsis "Go library to package programs in various Linux formats")
+    (description
+     "nFPM is Not FPM -- provides ways to package programs in popular Linux
+packaging formats, such as @code{deb}, @code{rpm}, @code{apk}, @code{ipk} and
+Arch.")
+    (license license:expat)))
+
 (define-public go-github-com-gorhill-cronexpr
  (package
    (name "go-github-com-gorhill-cronexpr")
@@ -15783,6 +15978,67 @@ called concurrently with themselves and each other.")
     "This package provides an easy access to native byte order.")
    (license license:expat)))

+(define-public go-github-com-joshuarubin-go-sway
+  (package
+    (name "go-github-com-joshuarubin-go-sway")
+    (version "1.2.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+              (url "https://github.com/joshuarubin/go-sway")
+              (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "1a4h34m5l2fjxp4s5ps66rjwpkvccvbqk4hr86cd2ajh127icvyv"))))
+    (build-system go-build-system)
+    (arguments
+     (list
+      #:tests? #f       ;require sway running
+      #:import-path "github.com/joshuarubin/go-sway"))
+    (propagated-inputs
+     (list go-github-com-joshuarubin-lifecycle
+           go-go-uber-org-multierr))
+    (home-page "https://github.com/joshuarubin/go-sway")
+    (synopsis "Sway client for Go")
+    (description
+     "This package simplifies working with the sway IPC from Go.
+
+The @env{SWAYSOCK} environment variable must be set properly and
+@command{sway} must be running with the same byteorder as the client.")
+    (license license:expat)))
+
+(define-public go-github-com-joshuarubin-lifecycle
+  (package
+    (name "go-github-com-joshuarubin-lifecycle")
+    (version "1.2.1")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+              (url "https://github.com/joshuarubin/lifecycle")
+              (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "0k2siagdyh1v99hlnykd0ldi9icfsaq19rjfz0npvjczza52dg3z"))))
+    (build-system go-build-system)
+    (arguments
+     (list
+      #:import-path "github.com/joshuarubin/lifecycle"))
+    (propagated-inputs
+     (list go-golang-org-x-sync))
+    (home-page "https://github.com/joshuarubin/lifecycle")
+    (synopsis "Goroutines management helper for Golang applications")
+    (description
+     "@code{lifecycle} helps manage goroutines at the application
+level.  @code{context.Context} has been great for propagating cancellation
+signals, but not for getting any feedback about when goroutines actually
+finish.
+
+This package works with @code{context.Context} to ensure that applications
+don't quit before their goroutines do.")
+    (license license:expat)))
+
 (define-public go-github-com-jpillora-backoff
  (let ((commit "fab01a9d9810a410d2d95a0a697f0afb604658f9")
        (revision "1"))
@@ -16141,6 +16397,32 @@ resources located relative to the executable file.")
 using reflink operations on compatible filesystems such as btrfs and xfs.")
    (license license:expat)))

+(define-public go-github-com-karpeleslab-weak
+  (package
+    (name "go-github-com-karpeleslab-weak")
+    (version "0.1.1")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+              (url "https://github.com/KarpelesLab/weak")
+              (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "1jjyd04iqwhk1mjjw7fbxn91qvf8z2a370gpkm3wg6caym4s99sm"))))
+    (build-system go-build-system)
+    (arguments
+     (list #:import-path "github.com/KarpelesLab/weak"))
+    (home-page "https://github.com/KarpelesLab/weak")
+    (synopsis "Weak reference map for Go 1.18+")
+    (description
+     "This is a weakref map for Go 1.18, with some inspiration from
+@uref{https://github.com/xeus2001/go-weak, xeus2001's weakref implementation}.
+
+This provides both a @code{weak.Ref} object to store weak references, and a
+@code{weak.Map} object for maps.")
+    (license license:expat)))
+
 (define-public go-github-com-karrick-godirwalk
  (package
    (name "go-github-com-karrick-godirwalk")
@@ -20438,6 +20720,90 @@ for any given struct and a set of its potential member values.  This can be
 used to generate extensive test matrixes among other things.")
    (license license:expat)))

+(define-public go-github-com-muesli-mango
+  (package
+    (name "go-github-com-muesli-mango")
+    (version "0.2.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+              (url "https://github.com/muesli/mango")
+              (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "16d0sga6cbdxzlqkibcgw0civkw11fpkcjpgv21i0q5j9mjbsjw4"))))
+    (build-system go-build-system)
+    (arguments
+     (list
+      #:import-path "github.com/muesli/mango"))
+    (propagated-inputs
+     (list go-github-com-muesli-roff))
+    (home-page "https://github.com/muesli/mango")
+    (synopsis "Golang man-page generator")
+    (description
+     "This package provides a man-page generator for the Go flag, pflag, cobra, coral,
+and kong packages.  It extracts commands, flags, and arguments from the target
+program and enables it to self-document.")
+    (license license:expat)))
+
+(define-public go-github-com-muesli-mango-cobra
+  (package
+    (name "go-github-com-muesli-mango-cobra")
+    (version "1.3.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+              (url "https://github.com/muesli/mango-cobra")
+              (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "11vvm3f2mq8yaqbfrjbzdcyvkn9f75rp4kygxyvqwc5jsw1kdwal"))))
+    (build-system go-build-system)
+    (arguments
+     (list
+      #:import-path "github.com/muesli/mango-cobra"))
+    (propagated-inputs
+     (list go-github-com-muesli-mango
+           go-github-com-muesli-mango-pflag
+           go-github-com-muesli-roff
+           go-github-com-spf13-cobra))
+    (home-page "https://github.com/muesli/mango-cobra")
+    (synopsis "Cobra adapter for mango")
+    (description
+     "This package provides a cobra adapter for the
+@url{https://github.com/muesli/mango,mango} man-page generator.")
+    (license license:expat)))
+
+(define-public go-github-com-muesli-mango-pflag
+  (package
+    (name "go-github-com-muesli-mango-pflag")
+    (version "0.2.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+              (url "https://github.com/muesli/mango-pflag")
+              (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "1k4m88i9shs36a8n86k3a1vlxmdf5vwavkih2f2j3xj718hnhpw0"))))
+    (build-system go-build-system)
+    (arguments
+     (list
+      #:import-path "github.com/muesli/mango-pflag"))
+    (propagated-inputs
+     (list go-github-com-muesli-mango
+           go-github-com-muesli-roff
+           go-github-com-spf13-pflag))
+    (home-page "https://github.com/muesli/mango-pflag")
+    (synopsis "Pflag adapter for mango")
+    (description
+     "This package provides a pflag adapter for the
+@url{https://github.com/muesli/mango, mango} man-page generator.")
+    (license license:expat)))
+
 (define-public go-github-com-muesli-reflow
  (package
    (name "go-github-com-muesli-reflow")
@@ -20465,6 +20831,32 @@ used to generate extensive test matrixes among other things.")
 helping you to transform blocks of text.")
    (license license:expat)))

+(define-public go-github-com-muesli-roff
+  (package
+    (name "go-github-com-muesli-roff")
+    (version "0.1.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+              (url "https://github.com/muesli/roff")
+              (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "0l263rqwq2ccr1lpamsvs48dddsr70xim8mv6rsj2x9y3prcq3yh"))))
+    (build-system go-build-system)
+    (arguments
+     (list
+      #:import-path "github.com/muesli/roff"
+      ;; Expected title heading, got:
+      ;; .TH TITLE 1 "2026-05-22" "Title" "A short description"
+      #:test-flags #~(list "-skip" "TestTitleHeading")))
+    (home-page "https://github.com/muesli/roff")
+    (synopsis "Write roff documents in Go")
+    (description "This package provides tools to write @code{roff}
+documents in Golang.")
+    (license license:expat)))
+
 (define-public go-github-com-muesli-termenv
  (package
    (name "go-github-com-muesli-termenv")
@@ -22424,6 +22816,36 @@ expiration times, it doesn't need to serialize or transmit its contents over
 the network.")
    (license license:expat)))

+(define-public go-github-com-pb33f-ordered-map-v2
+  (package
+    (name "go-github-com-pb33f-ordered-map-v2")
+    (version "2.3.1")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+              (url "https://github.com/pb33f/ordered-map")
+              (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "1k4r1rvlziddaszm1jvgz27nkrk1jfka0zik16f4b3gmhdnmd9vc"))))
+    (build-system go-build-system)
+    (arguments
+     (list
+      #:import-path "github.com/pb33f/ordered-map/v2"))
+    (native-inputs
+     (list go-github-com-stretchr-testify))
+    (propagated-inputs
+     (list go-github-com-bahlo-generic-list-go
+           go-github-com-buger-jsonparser
+           go-go-yaml-in-yaml-v4))
+    (home-page "https://github.com/pb33f/ordered-map")
+    (synopsis "Ordered maps in Golang")
+    (description
+     "This package provides a Golang implementation of an ordered map, which
+is a map that also keeps track of the order in which keys were inserted.")
+    (license license:asl2.0)))
+
 (define-public go-github-com-pbnjay-memory
  (let ((commit "7b4eea64cf580186c0eceb10dc94ba3a098af46c")
        (revision "2"))
@@ -30874,6 +31296,33 @@ for locating directories
 pass & access either a read-only @code{[]byte} or a @code{string}.")
    (license license:asl2.0)))

+(define-public go-go4-org-unsafe-assume-no-moving-gc
+  ;; XXX: No release and not published in <https://pkg.go.dev/>.
+  (let ((commit "b99613f794b6b2f6d80da53bb131c5c98ea2fdd2")
+        (revision "0"))
+    (package
+      (name "go-go4-org-unsafe-assume-no-moving-gc")
+      (version (git-version "0.0.0" revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+                (url "https://github.com/go4org/unsafe-assume-no-moving-gc")
+                (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32 "00ny3qha8k9nnx37ryvls2n5r7lw3bnldz6kwdmjxk8s19mxqim7"))))
+      (build-system go-build-system)
+      (arguments
+       (list
+        #:import-path "go4.org/unsafe/assume-no-moving-gc"))
+      (home-page "https://github.com/go4org/unsafe-assume-no-moving-gc")
+      (synopsis "Declare that Go package plays @code{unsafe} games")
+      (description
+       "This package provides a Go library which helps to declare that which
+of imported modules uses @code{unsafe} and report back as error trace.")
+      (license license:bsd-3))))
+
 (define-public go-golang-org-rainycape-unidecode
  (let ((commit "cb7f23ec59bec0d61b19c56cd88cee3d0cc1870c")
        (revision "1"))
@@ -33528,6 +33977,22 @@ library.")
 ;;; Executables:
 ;;;

+(define-public chglog
+  (package/inherit go-github-com-goreleaser-chglog
+    (name "chglog")
+    (arguments
+     (substitute-keyword-arguments arguments
+       ((#:tests? _ #t) #f)
+       ((#:install-source? _ #t) #f)
+       ((#:import-path _) "github.com/goreleaser/chglog/cmd/chglog")
+       ((#:unpack-path _ "") "github.com/goreleaser/chglog")))
+    (native-inputs
+     (append
+      (package-native-inputs go-github-com-goreleaser-chglog)
+      (package-propagated-inputs go-github-com-goreleaser-chglog)))
+    (inputs '())
+    (propagated-inputs '())))
+
 (define-public containers-storage
  (package/inherit go-github-com-containers-storage
    (name "containers-storage")
@@ -34068,6 +34533,22 @@ various modes for analyzing and transforming YAML data.")))
    (propagated-inputs '())
    (inputs '())))

+(define-public nfpm
+  (package/inherit go-github-com-goreleaser-nfpm-v2
+    (name "nfpm")
+    (arguments
+     (substitute-keyword-arguments arguments
+       ((#:import-path _) "github.com/goreleaser/nfpm/v2/cmd/nfpm")
+       ((#:install-source? _ #t) #f)
+       ((#:tests? _ #t) #f)
+       ((#:unpack-path _ "") "github.com/goreleaser/nfpm/v2")))
+    (native-inputs
+     (append
+      (package-native-inputs go-github-com-goreleaser-nfpm-v2)
+      (package-propagated-inputs go-github-com-goreleaser-nfpm-v2)))
+    (inputs '())
+    (propagated-inputs '())))
+
 (define-public oci-runtime-tool
  (package/inherit go-github-com-opencontainers-runtime-tools
    (name "oci-runtime-tool")
@@ -29,7 +29,6 @@
  #: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 (gnu packages)
  #:use-module (gnu packages autotools)
  #:use-module (gnu packages base)
@@ -36,7 +36,6 @@
  #: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 r)
  #:use-module (guix download)
  #:use-module (guix gexp)
@@ -667,7 +666,7 @@ contains supporting code for evaluation and parameter tuning.")
                                                (not (member file ignored))))))))
                    (format #t "test suite not run~%"))))))))
    (native-inputs
-     (list python-scipy))
+     (list python-scipy python-setuptools))
    (inputs
     (list faiss openblas python-wrapper swig-4.0))
    (propagated-inputs
@@ -43,6 +43,7 @@
 ;;; Copyright © 2024 Janneke Nieuwenhuizen <janneke@gnu.org>
 ;;; Copyright © 2025 James Smith <jsubuntuxp@disroot.org>
 ;;; Copyright © 2026 Cayetano Santos <csantosb@inventati.org>
+;;; Copyright © 2026 Jan Wielkiewicz <tona_kosmicznego_smiecia@interia.pl>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -110,7 +111,6 @@
  #:use-module (gnu packages maths)
  #:use-module (gnu packages mp3)
  #:use-module (gnu packages multiprecision)
-  #:use-module (gnu packages ninja)
  #:use-module (gnu packages opencl)
  #:use-module (gnu packages oneapi)
  #:use-module (gnu packages pciutils)
@@ -146,7 +146,6 @@
  #: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 qt)
  #:use-module (guix download)
@@ -700,17 +699,40 @@ It was developed by DreamWorks Animation for use in volumetric applications
 typically encountered in feature film production.")
    (license license:mpl2.0)))

+(define-public blender-assets
+  (package
+    (name "blender-assets")
+    (version "4.4.3")
+    (source
+     (origin
+       (method git-fetch/lfs) ;Needs LFS because .blender files are dummies
+       (uri (git-reference
+              (url "https://projects.blender.org/blender/blender-assets.git")
+              (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (modules '((guix build utils)))
+       (snippet '(begin
+                   (delete-file-recursively "working")))
+       (sha256
+        (base32 "1011zn4g1f5hs4dqar4sa7mh02kl4jnrwkpl6gfsi6sc0qhrxxdz"))))
+    (build-system copy-build-system)
+    (home-page "https://www.blender.org/")
+    (synopsis "Bundled assets for Blender")
+    (description
+     "Assets bundled with Blender releases in the Essentials assets library.")
+    (license license:cc0)))
+
 (define-public blender
  (package
    (name "blender")
-    (version "3.6.23")                   ;4.2.x+ requires Python >= 3.12
+    (version "4.5.10")                   ;5.1.x+ requires Python >= 3.13
    (source (origin
              (method url-fetch)
              (uri (string-append "https://download.blender.org/source/"
                                  "blender-" version ".tar.xz"))
              (sha256
               (base32
-                "16ah70kqznxz60n39d4hnlnwh1vi7xn9kx37di708n03l5bn6mmw"))))
+                "1z4sq4rmg5lx0502i2kgalmdyw3a4kc3lw70kwnwkih5wkjnrbyx"))))
    (build-system cmake-build-system)
    (arguments
     (list
@@ -737,37 +759,50 @@ typically encountered in feature film production.")
                "-DWITH_SYSTEM_GLOG=ON"
                "-DWITH_SYSTEM_LZO=ON"
                (string-append "-DPYTHON_LIBRARY=python" #$python-version)
-                (string-append "-DPYTHON_LIBPATH="
-                               (assoc-ref %build-inputs "python")
-                               "/lib")
-                (string-append "-DPYTHON_INCLUDE_DIR="
-                               (assoc-ref %build-inputs "python")
+                (string-append "-DPYTHON_LIBPATH=" #$python "/lib")
+                (string-append "-DPYTHON_INCLUDE_DIR=" #$python
                               "/include/python" #$python-version)
                (string-append "-DPYTHON_VERSION=" #$python-version)
                (string-append "-DPYTHON_NUMPY_INCLUDE_DIRS="
-                               (assoc-ref %build-inputs "python-numpy")
+                               #$(this-package-input "python-numpy")
                               "/lib/python" #$python-version
                               "/site-packages/numpy/core/include/")
                (string-append "-DPYTHON_NUMPY_PATH="
-                               (assoc-ref %build-inputs "python-numpy")
+                               #$(this-package-input "python-numpy")
                               "/lib/python" #$python-version
                               "/site-packages/")))
      #:phases
      #~(modify-phases %standard-phases
+          (add-after 'unpack 'install-assets
+            (lambda _
+              (copy-recursively #$(this-package-input "blender-assets")
+                                "./release/datafiles/assets")))
+          (add-after 'install 'link-python-binary
+            (lambda _
+              (let* ((blender-dir (string-append #$output "/share/blender/"
+                                                 #$(version-major+minor version)))
+                     (blender-python-dir (string-append blender-dir "/python")))
+                (mkdir-p blender-dir)
+                (symlink #$(this-package-input "python")
+                         blender-python-dir))))
          (add-after 'install 'wrap-bin
-            (lambda* (#:key outputs #:allow-other-keys)
-              (let* ((out (assoc-ref outputs "out"))
-                     (python-path (getenv "GUIX_PYTHONPATH")))
-                (wrap-program (string-append out "/bin/blender")
-                  `("GUIX_PYTHONPATH" ":" prefix (,python-path)))))))))
+            (lambda _
+              (let ((python-path (getenv "GUIX_PYTHONPATH")))
+                (when python-path
+                  (wrap-program (string-append #$output "/bin/blender")
+                    `("GUIX_PYTHONPATH" ":" prefix (,python-path))))))))))
+    (native-inputs
+     (list pkg-config))
    (inputs
     (list bash-minimal
+           blender-assets
           boost
           bullet
           eigen
           embree
           ffmpeg-6
           fftw
+           fftwf
           freetype-with-brotli
           glew
           glog
@@ -795,6 +830,9 @@ typically encountered in feature film production.")
           pugixml
           python
           python-numpy-1
+           shaderc
+           vulkan-headers
+           vulkan-loader
           zlib
           `(,zstd "lib")))
    (home-page "https://www.blender.org/")
@@ -959,24 +997,17 @@ baking tools to produce normal maps.")
                   (string-append "-DLLVM_BC_GENERATOR="
                                  #$(this-package-native-input "clang")
                                  "/bin/clang++"))
-           #:phases
-           #~(modify-phases %standard-phases
-               (replace 'check
-                 (lambda* (#:key tests? #:allow-other-keys)
-                   (when tests?
-                     (invoke
-                      "ctest" "--exclude-regex"
-                      (string-join
-                       (list
-                        "osl-imageio" ; file does not exist
-                        "osl-imageio.opt" ; file does not exist
-                        "osl-imageio.opt.rs_bitcode" ; file does not exist
-                        "texture-udim"    ; file does not exist
-                        "texture-udim.opt" ; file does not exist
-                        "texture-udim.opt.rs_bitcode" ; file does not exist
-                        "example-deformer" ; could not find OSLConfig
-                        "python-oslquery") ; no module oslquery
-                       "|"))))))))
+           #:test-exclude (string-join
+                           (list
+                            "osl-imageio" ; file does not exist
+                            "osl-imageio.opt" ; file does not exist
+                            "osl-imageio.opt.rs_bitcode" ; file does not exist
+                            "texture-udim"    ; file does not exist
+                            "texture-udim.opt" ; file does not exist
+                            "texture-udim.opt.rs_bitcode" ; file does not exist
+                            "example-deformer" ; could not find OSLConfig
+                            "python-oslquery") ; no module oslquery
+                           "|")))
    (native-inputs
     (list bison
           clang
@@ -1212,7 +1243,7 @@ quaternions and other useful 2D and 3D math functions.  Iex is an
 exception-handling library.")
    (license license:bsd-3)))

-(define-public lib2geom
+(define-public lib2geom/pinned
  (package
    (name "lib2geom")
    (version "1.3")
@@ -1290,52 +1321,38 @@ basic geometries.")
    ;; Because the library is linked with the GNU Scientific Library
    ;; (GPLv3+), the combined work must be licensed as GPLv3+ (see:
    ;; https://gitlab.com/inkscape/inkscape/issues/784).
-    (license license:gpl3+)))
+    (license license:gpl3+)
+    (properties '((hidden? . #t)))))

-(define-public python-booleanoperations
+(define-public lib2geom
  (package
-    (name "python-booleanoperations")
-    (version "0.9.0")
+    (inherit lib2geom/pinned)
+    (name "lib2geom")
+    (version "1.4")
    (source
     (origin
+       (inherit (package-source lib2geom/pinned))
       (method git-fetch)
       (uri (git-reference
-              (url "https://github.com/typemytype/booleanOperations")
+              (url "https://gitlab.com/inkscape/lib2geom")
              (commit version)))
       (file-name (git-file-name name version))
       (sha256
-        (base32 "0ahfgamyq1ndwbr9n8sdx8qhqc2195xnbahylgjpk877hbr2gxav"))))
-    (build-system pyproject-build-system)
+        (base32 "0gfgzwm5s50caj5s6l7irgmlifpmypd0fnm6ckzli1fdziwjgdwi"))))
    (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 "))))
-    (propagated-inputs (list python-fonttools-minimal python-pyclipper))
-    (native-inputs
-     (list python-defcon-bootstrap
-           python-fontpens-bootstrap
-           python-pytest
-           python-setuptools
-           python-setuptools-scm))
-    (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)))
+     ;; https://gitlab.com/inkscape/lib2geom/-/work_items/82
+     (if (or (target-aarch64?)
+             (target-riscv64?)
+             (target-ppc64le?))
+         (substitute-keyword-arguments arguments
+           ((#:phases phases #~%standard-phases)
+            #~(modify-phases #$phases
+                (add-after 'unpack 'disable-polynomial-test
+                  (lambda _
+                    (substitute* "tests/CMakeLists.txt"
+                      (("polynomial-test") "")))))))
+         arguments))
+    (properties '((hidden? . #f)))))

 (define-public pstoedit
  (package
@@ -2380,6 +2397,71 @@ and engineering community.")
 (define-deprecated coin3D-4 coin3d)
 (export coin3D-4)

+(define-public skcms
+  ;; No tags are available.
+  (let ((commit "a7a3b15f06355692d86a3b8373c579a521598f4c")
+        (revision "0"))
+    (package
+      (name "skcms")
+      (version (git-version "0" revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://skia.googlesource.com/skcms")
+               (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32 "0ylrsm7cinw59ilgbffazbgifax81kkya5cxq8q8wybnxx6z6ps6"))))
+      (build-system gnu-build-system)
+      (arguments
+       (list
+        #:phases
+        #~(modify-phases %standard-phases
+            (add-after 'unpack 'patch-includes
+              (lambda _
+                (substitute* "skcms.h"
+                  (("src\\/skcms_public\\.h") "skcms/skcms_public.h"))))
+            (delete 'configure)
+            (replace 'build
+              (lambda _
+                ;; Some CPUs may not support these features.
+                (let ((cflags (append '("-DSKCMS_DISABLE_HSW=1"
+                                        "-DSKCMS_DISABLE_SKX=1")
+                                      (if #$(target-mingw?)
+                                          '("-DSKCMS_HAS_MUSTTAIL=0")
+                                          '())))
+                      (ldflags '("-lstdc++")))
+                  (apply invoke #$(cc-for-target)
+                         `("-O2" "-g" "-fPIC" ,@cflags
+                           "skcms.cc"
+                           "src/skcms_TransformBaseline.cc"
+                           "src/skcms_TransformHsw.cc"
+                           "src/skcms_TransformSkx.cc"
+                           "-shared" ,@ldflags
+                           "-o" "libskcms.so"))
+                  (apply invoke #$(cc-for-target)
+                         `(,@cflags
+                           "tests.c" "test_only.c"
+                           "-Wl,-rpath=." "-L." "-lskcms" ,@ldflags
+                           "-o" "tests")))))
+            (replace 'check
+              (lambda* (#:key tests? #:allow-other-keys)
+                (when tests?
+                  (invoke "./tests"))))
+            (replace 'install
+              (lambda _
+                (install-file "libskcms.so" (string-append #$output "/lib"))
+                (install-file "skcms.h" (string-append #$output "/include"))
+                (install-file "src/skcms_public.h"
+                              (string-append #$output "/include/skcms")))))))
+      (native-inputs (list ninja))
+      (home-page "https://skia.org/")
+      (synopsis "Color management engine")
+      (description
+       "skcms is the color management engine.  It is a part of @code{skia}.")
+      (license license:bsd-3))))
+
 (define-public skia
  ;; Releases follow those of Chromium, about every 6 weeks.  The release
  ;; version can be found on this page:
@@ -35,7 +35,6 @@
  #:use-module (guix packages)
  #: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 git-download)
  #:use-module (guix utils)
@@ -152,32 +151,46 @@ interfaces for other technical domains.")
 (define-public python-graphviz
  (package
    (name "python-graphviz")
-    (version "0.20.3")
-    (source (origin
-              (method url-fetch)
-              (uri (pypi-uri "graphviz" version ".zip"))
-              (sha256
-               (base32
-                "0pcjnnhprs1hb4r9jr7r4qjxc7lzsjlka8d5gcp3kym9ws0vrmh9"))))
+    (version "0.21")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+              (url "https://github.com/xflr6/graphviz")
+              (commit version)))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "00hgh1ab54h2jhqnwn5vrggg0hqbwmjn0cx2a9nw4vi1wmijib53"))))
    (build-system pyproject-build-system)
    (arguments
     (list
+      #:test-flags
+      #~(list "--ignore=tests/backend/")
      #:phases
      #~(modify-phases %standard-phases
          (add-after 'unpack 'patch-pytest-options
            (lambda _
-              (substitute* "setup.cfg"
-                ((".*doctest.*") "")
-                (("--cov.*") ""))))
-          (replace 'check
-            (lambda* (#:key tests? test-flags #:allow-other-keys)
+              (substitute* "pyproject.toml"
+                ((".*--cov-report=term.*") ""))))
+          (add-before 'check 'pre-check
+            (lambda _
+              (setenv "HOME" "/tmp")))
+          (add-after 'check 'test-backend
+            (lambda* (#:key tests? #:allow-other-keys)
+              ;; Running tests together fails with error:
+              ;;
+              ;; import file mismatch:
+              ;; imported module 'conftest' has this __file__ attribute:
+              ;;   /<...>/source/tests/backend/conftest.py
+              ;; which is not the same as the test file we want to collect:
+              ;;   /<...>/source/tests/conftest.py
+              ;;
+              ;; HINT: remove __pycache__ / .pyc files and/or use a unique
+              ;; basename for your test file modules
              (when tests?
-                (setenv "HOME" "/tmp")
-                  (apply invoke "python" "run-tests.py" test-flags)))))))
+                (invoke "pytest" "-v" "tests/backend/")))))))
    (native-inputs
-     (list unzip
-           ;; For tests.
-           graphviz
+     (list graphviz
           python-mock
           python-pytest
           python-pytest-mock
@@ -246,7 +259,6 @@ layout algorithms.")
     (list graphviz
           python-defusedxml
           python-pytest
-           python-pytest-cov
           python-setuptools
           python-typing-extensions))
    (propagated-inputs
@@ -329,7 +341,7 @@ $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CFLAGS) $(CFLAGS) $(srcdir)/predicates_init.c \
 (define-public xdot
  (package
    (name "xdot")
-    (version "1.4")
+    (version "1.6")
    (source
     (origin
       ;; PyPI tarball is missing some test files.
@@ -339,7 +351,7 @@ $(AM_CPPFLAGS) $(CPPFLAGS) $(AM_CFLAGS) $(CFLAGS) $(srcdir)/predicates_init.c \
             (commit version)))
       (file-name (git-file-name name version))
       (sha256
-        (base32 "1l34ahvcz90j3j7aspp9wqvxpq10mzgq7l0sanrj142ihdnbahvy"))))
+        (base32 "0gg54k6zhdviz17aa3harc82f7bx4mpwnj292q066dzamvr87svq"))))
    (build-system pyproject-build-system)
    (arguments
     (list
@@ -71,7 +71,6 @@
  #:use-module (guix build-system gnu)
  #: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 waf)
  #:use-module (gnu packages)
@@ -1120,7 +1119,7 @@ application suites.")
 (define-public gtk
  (package
    (name "gtk")
-    (version "4.20.3")
+    (version "4.22.1")
    (source
     (origin
       (method url-fetch)
@@ -1128,9 +1127,11 @@ application suites.")
                           (version-major+minor version)  "/"
                           name "-" version ".tar.xz"))
       (sha256
-        (base32 "0ly1gqc6ybxv5f2a9hvjp5k6l9mfzy2yv8iy2xqnr9l8628g4wr8"))
+        (base32 "1z2mkmazc2d51jbg3qwwdycycqiwswm88nhw6bxscz8j86f5lyyd"))
       (patches
-        (search-patches "gtk4-respect-GUIX_GTK4_PATH.patch"))
+        (search-patches "gtk4-demo-reproducible.patch"
+                        "gtk4-needs-udmabuf.patch"
+                        "gtk4-respect-GUIX_GTK4_PATH.patch"))
       (modules '((guix build utils)))))
    (build-system meson-build-system)
    (outputs '("out" "bin" "doc"))
@@ -1172,7 +1173,8 @@ application suites.")
                     '("--no-suite=gsk-compare-gl"
                       "--no-suite=gsk-compare-cairo"
                       "--no-suite=gsk-compare-ngl"
-                       "--no-suite=gsk-compare-vulkan")
+                       "--no-suite=gsk-compare-vulkan"
+                       "--no-suite=svg")
                     '()))
      #:phases
      #~(modify-phases %standard-phases
@@ -1254,8 +1256,10 @@ application suites.")
              (setenv "XDG_CACHE_HOME" (getcwd))))
          (add-before 'check 'pre-check
            (lambda* (#:key inputs #:allow-other-keys)
-              ;; Tests require a running X server.
-              (system "Xvfb :1 +extension GLX &")
+              ;; Tests require a running X server.  The '-noreset' option is
+              ;; necessary to avoid spurious "Failed to open display" test
+              ;; errors.
+              (system "Xvfb :1 +extension GLX -screen 0 1024x768x24 -noreset &")
              (setenv "DISPLAY" ":1")
              ;; Tests write to $HOME.
              (setenv "HOME" (getcwd))
@@ -1298,6 +1302,7 @@ application suites.")
           docbook-xsl
           gettext-minimal
           `(,glib "bin")
+           glibc-utf8-locales           ;some tests require en_US.UTF-8
           gobject-introspection        ;for building introspection data
           graphene
           gtk-doc/stable               ;for building documentation
@@ -1365,8 +1370,8 @@ application suites.")
    (native-search-paths
     (list
      (search-path-specification
-       (variable "GUIX_GTK4_PATH")
-       (files '("lib/gtk-4.0")))))
+        (variable "GUIX_GTK4_PATH")
+        (files '("lib/gtk-4.0")))))
    (search-paths native-search-paths)
    (home-page "https://www.gtk.org/")
    (synopsis "Cross-platform widget toolkit")
@@ -2803,7 +2808,7 @@ to rename these directories if the locale changes.")
 (define-public goocanvas
  (package
    (name "goocanvas")
-    (version "2.0.4")
+    (version "3.0.0")
    (source
     (origin
       (method url-fetch)
@@ -2811,7 +2816,7 @@ to rename these directories if the locale changes.")
                           (version-major+minor version)
                           "/goocanvas-" version ".tar.xz"))
       (sha256
-        (base32 "141fm7mbqib0011zmkv3g8vxcjwa7hypmq71ahdyhnj2sjvy4a67"))))
+        (base32 "06j05g2lmwvklmv51xsb7gm7rszcarhm01sal41jfp0qzrbpa2k7"))))
    (build-system gnu-build-system)
    (native-inputs
     (list gettext-minimal
@@ -155,6 +155,7 @@
  #:use-module (guix git-download)
  #:use-module (guix hg-download)
  #:use-module (guix build-system cmake)
+  #:use-module (guix build-system emacs)
  #:use-module (guix build-system glib-or-gtk)
  #:use-module (guix build-system gnu)
  #:use-module (guix build-system guile)
@@ -2933,7 +2934,7 @@ user which package sets would they like to install from it.")
 (define-public guile-wisp
  (package
    (name "guile-wisp")
-    (version "1.0.12")
+    (version "1.0.13")
    (source (origin
              (method hg-fetch)
              (uri (hg-reference
@@ -2942,7 +2943,7 @@ user which package sets would they like to install from it.")
              (file-name (git-file-name name version))
              (sha256
               (base32
-                "0m5ssl4ngk2jl1zk0fnsss0asyvwanjaa5rrcksldqnh2ikcr4bm"))))
+                "0fb4l0ww4rnkrsh4x46301j5xrqniny9b7yh7i6lp4wprwx0a7fs"))))
    (build-system gnu-build-system)
    (arguments
     `(#:modules ((guix build gnu-build-system)
@@ -2951,9 +2952,7 @@ user which package sets would they like to install from it.")
                  (guix build emacs-utils)
                  (ice-9 rdelim)
                  (ice-9 popen))
-       #:imported-modules (,@%default-gnu-imported-modules
-                           (guix build emacs-build-system)
-                           (guix build emacs-utils))
+       #:imported-modules ,%emacs-build-system-modules
       #:phases
       (modify-phases %standard-phases
         (replace 'bootstrap
@@ -2997,11 +2996,11 @@ user which package sets would they like to install from it.")
    (inputs
     (list guile-3.0))
    (native-inputs
-     `(("autoconf" ,autoconf)
-       ("automake" ,automake)
-       ("emacs" ,emacs-minimal)
-       ("python" ,python)
-       ("pkg-config" ,pkg-config)))
+     (list autoconf
+           automake
+           emacs-minimal
+           pkg-config
+           python))
    (synopsis "Whitespace to lisp syntax for Guile")
    (description "Wisp is a syntax for Guile which provides a Python-like
 whitespace-significant language.  It may be easier on the eyes for some
@@ -7814,8 +7813,8 @@ is an attempt to combine both into something useful.")
      (license license:asl2.0))))

 (define-public guile-knots
-  (let ((commit "49996c432a4616e03ecaf01cb42afc5fd78eafd5")
-        (revision "35"))
+  (let ((commit "d1cecc06fb96a193bb4bdbef159e4c3a83895436")
+        (revision "36"))
    (package
    (name "guile-knots")
    (version (git-version "0.1" revision commit))
@@ -7826,7 +7825,7 @@ is an attempt to combine both into something useful.")
                    (commit commit)))
              (sha256
               (base32
-                "0i6vk432shy7qmsq1hli71a9kmgf8yy9hx3bck0r9qzsldv1m3m9"))
+                "1ssgkbnxfjvnvyrmyva40yywi5dybyqds1q9v9i674d6i435zlbl"))
              (file-name (git-file-name name version))))
    (build-system gnu-build-system)
    (arguments
@@ -529,6 +529,17 @@ without requiring the source code to be rewritten.")
 ;;; (security or else) and this deprecation could be removed.
 (define-deprecated/public-alias guile-3.0/fixed guile-3.0/pinned)

+(define-public guile-with-gmp
+  (package/inherit guile-3.0-latest
+    (name "guile-with-gmp")
+    (propagated-inputs
+      (modify-inputs propagated-inputs
+        (append gmp)))
+    (arguments
+     (substitute-keyword-arguments arguments
+       ((#:configure-flags flags #~'())
+        #~(delete "--enable-mini-gmp" #$flags))))))
+
 (define-public guile-3.0/pinned
  ;; A package of Guile that's rarely changed.  It is the one used in the
  ;; `base' module, and thus changing it entails a full rebuild.
@@ -119,7 +119,6 @@
  #: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 download)
  #:use-module (guix gexp)
@@ -43,7 +43,6 @@
  #:use-module (guix build-system glib-or-gtk)
  #:use-module (guix build-system meson)
  #:use-module (guix build-system pyproject)
-  #:use-module (guix build-system python)
  #:use-module (guix utils)
  #:use-module (gnu packages)
  #:use-module (gnu packages anthy)
--- a/Show More
+++ b/Show More