gnu: sweeper: Update to 26.04.1.

* gnu/packages/kde-utils.scm (sweeper): Update to 26.04.1.

Change-Id: Ia3bf8408390716188d4e877f31f0f5ef163b466c

CODEOWNERS

@@ -341,7 +341,6 @@ guix/build-system/rakudo\.scm                      @guix/perl
 guix/import/cpan\.scm                              @guix/perl
 guix/scripts/import/cpan\.scm                      @guix/perl
 
-gnu/packages/aux-files/python/.*\.py$              @guix/python
 gnu/packages/django\.scm                           @guix/python
 gnu/packages/jupyter\.scm                          @guix/python
 gnu/packages/python(-.+|)\.scm$                    @guix/python

Makefile.am

@@ -488,7 +488,6 @@ AUX_FILES =						\
   gnu/packages/aux-files/linux-libre/5.10-x86_64.conf	\
   gnu/packages/aux-files/ovmf/51-edk2-ovmf-2m-raw-x64-nosb.json	\
   gnu/packages/aux-files/pack-audit.c			\
-  gnu/packages/aux-files/python/pytest_guix.py		\
   gnu/packages/aux-files/python/sanity-check.py		\
   gnu/packages/aux-files/python/sitecustomize.py	\
   gnu/packages/aux-files/renpy/renpy.in	\

etc/teams.scm

@@ -984,8 +984,7 @@ perl-build-system as well as the rakudo-build-system."
         #:description
         "Python, Python packages, the \"pypi\" importer, and the python-build-system."
         #:scope
-        (list (make-regexp* "^gnu/packages/aux-files/python/.*\\.py$")
-              "gnu/packages/django.scm"
+        (list "gnu/packages/django.scm"
               "gnu/packages/jupyter.scm"
               (make-regexp* "^gnu/packages/python(-.+|)\\.scm$")
               "gnu/packages/sphinx.scm"

gnu/home/services/gnupg.scm

@@ -125,18 +125,16 @@ entry will be expired even if it has been accessed recently.")
                  (requirement shepherd-requirement)
                  (modules '((shepherd support)))  ;for '%user-runtime-dir'
                  (start
-                  #~(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)))
+                  #~(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)))
                  (stop #~(make-systemd-destructor))
                  (documentation "Start 'gpg-agent', the GnuPG passphrase
 agent, with support for handling OpenSSH material."))))

gnu/local.mk

@@ -76,7 +76,6 @@
 # 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.
 #
@@ -344,7 +343,6 @@ 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	        	\
@@ -1001,7 +999,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/agg-am_c_prototype.patch			\
   %D%/packages/patches/agg-2.5-gcc8.patch			\
   %D%/packages/patches/akonadi-paths.patch		\
-  %D%/packages/patches/akonadi-not-relocatable.patch		\
   %D%/packages/patches/akonadi-timestamps.patch		\
   %D%/packages/patches/alure-dumb-2.patch			\
   %D%/packages/patches/amd-smi-newer-libdrm.patch		\
@@ -1022,7 +1019,6 @@ 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	\
@@ -1105,6 +1101,7 @@ 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			\
@@ -1137,8 +1134,11 @@ 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	\
@@ -1189,7 +1189,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/date-output-pkg-config-files.patch	\
   %D%/packages/patches/dbacl-include-locale.h.patch		\
   %D%/packages/patches/dbacl-icheck-multiple-definitions.patch	\
-  %D%/packages/patches/dblatex-importlib.patch		\
   %D%/packages/patches/dblatex-inkscape-1.0.patch		\
   %D%/packages/patches/dbus-helper-search-path.patch		\
   %D%/packages/patches/ddd-build.patch				\
@@ -1508,7 +1507,6 @@ 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		\
@@ -1526,7 +1524,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/gnumach-version.patch			\
   %D%/packages/patches/gnupg-default-pinentry.patch		\
   %D%/packages/patches/gnupg-1-build-with-gcc10.patch		\
-  %D%/packages/patches/gnutls-no-which.patch			\
   %D%/packages/patches/gobject-introspection-absolute-shlib-path.patch \
   %D%/packages/patches/gobject-introspection-cc.patch		\
   %D%/packages/patches/gobject-introspection-girepository.patch	\
@@ -1584,9 +1581,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/gtk3-respect-GUIX_GTK3_PATH.patch	\
   %D%/packages/patches/gtk3-respect-GUIX_GTK3_IM_MODULE_FILE.patch \
   %D%/packages/patches/gtk-doc-respect-xml-catalog.patch	\
-  %D%/packages/patches/gtk-doc-mkhtml-test-fix.patch	        \
-  %D%/packages/patches/gtk4-demo-reproducible.patch             \
-  %D%/packages/patches/gtk4-needs-udmabuf.patch                 \
+  %D%/packages/patches/gtk-doc-mkhtml-test-fix.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 \
@@ -2109,13 +2104,11 @@ 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		\
   %D%/packages/patches/python-daemon-relax-lockfile.patch	\
   %D%/packages/patches/python-docrepr-fix-tests.patch		\
-  %D%/packages/patches/python-gpg-setup-72.patch                \
   %D%/packages/patches/python-hdmedians-replace-nose.patch	\
   %D%/packages/patches/python-jinja2-fragments-modify-conftest-py.patch	\
   %D%/packages/patches/python-louvain-fix-test.patch		\
@@ -2132,20 +2125,16 @@ 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	\
@@ -2255,7 +2244,6 @@ 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		\
@@ -2271,7 +2259,6 @@ 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	\
@@ -2416,8 +2403,13 @@ 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	\
@@ -2432,6 +2424,7 @@ 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	\
@@ -2526,6 +2519,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/texmacs-wayland-hidpi.patch	\
   %D%/packages/patches/tflite-micro_disable_download.patch 	\
   %D%/packages/patches/thefuck-test-environ.patch		\
+  %D%/packages/patches/thefuck-remove-broken-tests.patch	\
   %D%/packages/patches/tidy-CVE-2015-5522+5523.patch		\
   %D%/packages/patches/timewarrior-time-sensitive-tests.patch	\
   %D%/packages/patches/tinydir-fix-cbehave-test.patch		\
@@ -2541,7 +2535,6 @@ 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			\

gnu/packages/accessibility.scm

@@ -51,7 +51,6 @@
   #: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)
@@ -186,9 +185,7 @@ terminals.")
     (native-inputs
      (append
        (list clisp
-             ;; See: <https://bugzilla.redhat.com/show_bug.cgi?id=2231865>.
-             python-cython-0
-             python-setuptools  ;remove with next update
+             python-cython-0 ;; See https://bugzilla.redhat.com/show_bug.cgi?id=2231865
              doxygen
              gettext-minimal)
        ;; icedtea doesn't build reliably on all architectures.

gnu/packages/acl.scm

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

gnu/packages/admin.scm

@@ -109,6 +109,7 @@
   #:use-module (guix build-system go)
   #:use-module (guix build-system meson)
   #:use-module (guix build-system perl)
+  #:use-module (guix build-system python)
   #:use-module (guix build-system pyproject)
   #:use-module (guix build-system qt)
   #:use-module (guix build-system ruby)
@@ -743,7 +744,7 @@ manager.")
 (define-public swineherd
   (package
     (name "swineherd")
-    (version "0.0.5")
+    (version "0.0.4")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -752,7 +753,7 @@ manager.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "1w3fvkdmqvbzqfx3xindm8qgam54wja46isgwasaiqmmhnla7p52"))))
+                "0iij1pl0y410k1dk1ifa56dxmjb1blv0y3k5rxy794gwg6w6c480"))))
     (build-system gnu-build-system)
     (arguments
      '(#:configure-flags '("--localstatedir=/var")
@@ -766,7 +767,7 @@ manager.")
            guile-netlink
            guile-3.0
            guix
-           shepherd-1.0))
+           shepherd-0.10))
     (home-page "https://github.com/BIMSBbioinfo/swineherd")
     (synopsis "System container manager")
     (description
@@ -3405,7 +3406,7 @@ provides the following commands:
      ;; variable in the tests/import/cpan.scm test.
      (list (search-path-specification
             (variable "GUIX_PYTHONPATH")
-            (files (list "lib/python3.12/site-packages")))))
+            (files (list "lib/python3.11/site-packages")))))
     (home-page "https://www.ansible.com/")
     (synopsis "Radically simple IT automation")
     (description "Ansible aims to be a radically simple IT automation system.
@@ -3423,7 +3424,7 @@ modules and plugins that extend Ansible.")
 (define-public debops
   (package
     (name "debops")
-    (version "3.3.0")
+    (version "3.2.5")
     (source
      (origin
        (method git-fetch)
@@ -3432,7 +3433,7 @@ modules and plugins that extend Ansible.")
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "0z6wck5kax5h2bjv1vw8pbd7fdcdhx87bj9fakh3h0rar9d2qksj"))
+        (base32 "15wfhha2b315i15l40j3sylyvs3mdrfw5awzq4cix51l5jppx8z5"))
        (patches
         (search-patches "debops-setup-py-avoid-git.patch"))))
     (build-system pyproject-build-system)
@@ -3454,8 +3455,8 @@ modules and plugins that extend Ansible.")
            python-future
            python-gitpython
            python-jinja2
-           python-pyxdg
            python-pyyaml
+           python-pyxdg
            python-toml))
     (arguments
      (list
@@ -3470,7 +3471,7 @@ modules and plugins that extend Ansible.")
                          `("PATH" ":" prefix
                            ,(map dirname
                                  (map (cut search-input-file inputs <>)
-                                      (list ;; "bin/ansible"    ;see above
+                                      (list "bin/ansible"
                                             "bin/gpg"
                                             "bin/git"
                                             "bin/git-crypt"
@@ -3926,18 +3927,6 @@ rules is done with the @code{auditctl} utility.")
                 (wrap-program (string-append ndiff "/bin/ndiff")
                   `("GUIX_PYTHONPATH" prefix
                     (,(python-path ndiff)))))))
-          (add-before 'check 'fix-tests-for-python-3.12
-            (lambda _
-              (substitute* "ndiff/ndifftest.py"
-                (("import imp")
-                 "import importlib.util")
-                (("ndiff = imp\\.load_source\\(\"ndiff\", \"ndiff\\.py\"\\)")
-                 (string-join
-                  '("spec = \
-importlib.util.spec_from_file_location(\"ndiff\", \"ndiff.py\")"
-                    "ndiff = importlib.util.module_from_spec(spec)"
-                    "spec.loader.exec_module(ndiff)")
-                  "\n")))))
           ;; These are the tests that do not require network access.
           (replace 'check
             (lambda* (#:key tests? #:allow-other-keys)
@@ -4067,59 +4056,51 @@ plug-in architecture to allow monitoring other system metrics.")
     (license license:gpl2+)))
 
 (define-public thefuck
-  ;; Latest release, 3.32, is not compatible with Python 3.12.
-  (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
+  (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
 a new command using the matched rule, and runs it.")
-      (license license:x11))))
+    (license license:x11)))
 
 (define-public di
   (package

gnu/packages/aidc.scm

@@ -117,7 +117,7 @@ Features:
 (define-public python-zbarlight
   (package
     (name "python-zbarlight")
-    (version "4.0")
+    (version "3.0")
     (source
      (origin
        (method git-fetch)
@@ -126,7 +126,7 @@ Features:
              (commit version)))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "1q1nfc7g7bl9y63fwvnq1fcgqk79inc2hhw3ilvyw0nk0g74v8cm"))))
+        (base32 "1radfpfhfhkx3xnz01bqr5l9pl2zv70zis6l2kw1gwqbfw65r6w6"))))
     (build-system pyproject-build-system)
     (propagated-inputs (list python-pillow))
     (inputs (list zbar))

gnu/packages/algebra.scm

@@ -88,6 +88,7 @@
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system cmake)
   #:use-module (guix build-system pyproject)
+  #:use-module ((guix build-system python) #:select (pypi-uri))
   #:use-module (guix build-system r)
   #:use-module (guix download)
   #:use-module (guix gexp)

gnu/packages/android.scm

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

gnu/packages/apparmor.scm

@@ -180,7 +180,7 @@ supported by Canonical since 2009.")
        (list libapparmor))
       ;; Python module `readline' needed
       (native-inputs
-       (list bison flex gettext-minimal perl python python-setuptools which))
+       (list bison flex gettext-minimal perl python which))
       (license license:gpl2))))
 
 (define-public pam-apparmor

gnu/packages/astronomy.scm

@@ -37,6 +37,7 @@
 
 (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)
@@ -1991,22 +1992,12 @@ 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-setuptools
+           python-wheel))
     (propagated-inputs
      (list python-mock
            python-requests
@@ -3862,6 +3853,10 @@ 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"))))))
@@ -4663,6 +4658,7 @@ Cesium.")
     (native-inputs
      (list python-pydot
            python-pytest
+           python-pytest-cov
            python-pytest-asdf-plugin
            python-pytest-doctestplus
            python-pytest-filter-subpackage
@@ -5187,6 +5183,7 @@ files.")
     (build-system pyproject-build-system)
     (native-inputs
      (list python-pytest
+           python-pytest-cov
            python-setuptools
            python-setuptools-scm
            python-wheel))
@@ -5781,6 +5778,7 @@ across many files.")
      (list python-mock
            python-objgraph
            python-pytest
+           python-pytest-cov
            ;; python-pytest-faulthandler
            python-setuptools
            python-wheel
@@ -6627,6 +6625,19 @@ 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"))))))
@@ -6684,7 +6695,7 @@ astronomical tables
     (build-system pyproject-build-system)
     (arguments
      (list
-      ;; tests: 1508 passed, 43621 warnings
+      ;; tests: 1509 passed, 55331 warnings
       #:test-flags
       #~(list "--numprocesses" (number->string (min 8 (parallel-job-count)))
               ;; TypeError: SparseSolverBase.__init__() got an unexpected
@@ -6701,12 +6712,7 @@ astronomical tables
               (string-append "--deselect=test/test_Sampling/test_Likelihoods/"
                              "test_position_likelihood.py"
                              "::TestPositionLikelihood"
-                             "::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"))
+                             "::test_multiplane_position_likelihood"))
       #:phases
       #~(modify-phases %standard-phases
           (add-before 'check 'pre-check
@@ -11663,6 +11669,7 @@ 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))

gnu/packages/audio.scm

@@ -146,7 +146,6 @@
   #: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)
@@ -182,6 +181,7 @@
   #:use-module (guix build-system glib-or-gtk)
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system meson)
+  #:use-module (guix build-system python)
   #:use-module (guix build-system pyproject)
   #:use-module (guix build-system qt)
   #:use-module (guix build-system trivial)
@@ -821,8 +821,7 @@ Filter) modules follow the convention of 1V / Octave.")
                    "https://aubio.org/pub/aubio-" version ".tar.bz2"))
              (sha256
               (base32
-               "1npks71ljc48w6858l9bq30kaf5nph8z0v61jkfb70xb9np850nl"))
-             (patches (search-patches "aubio-waflib-python312-compat.patch"))))
+               "1npks71ljc48w6858l9bq30kaf5nph8z0v61jkfb70xb9np850nl"))))
     (build-system waf-build-system)
     (arguments
      (list
@@ -3280,27 +3279,30 @@ synchronous execution of all clients, and low latency operation.")
   (package
     (inherit jack-1)
     (name "jack2")
-    ;; 1.9.22 does not compile with Python 3.12, use the latest commit instead.
-    (properties '((commit . "17959465a722225a36a8b612aed26764036f258e")
-                  (revision . "0")))
-    (version (git-version "1.9.22"
-                          (assoc-ref properties 'revision)
-                          (assoc-ref properties 'commit)))
+    (version "1.9.21")
     (source (origin
               (method git-fetch)
               (uri (git-reference
-                     (url "https://github.com/jackaudio/jack2")
-                     (commit (assoc-ref properties 'commit))))
+                    (url "https://github.com/jackaudio/jack2")
+                    (commit (string-append "v" version))))
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "18dbjq9y8mcp27j9aaqdlg4976hrisr7b88lk84ck09gmzlwqalp"))))
+                "0sbrffmdbajvrk7iqvsvrnwnpvmicvbjyq3f52r6ashdsznsz03b"))))
     (build-system waf-build-system)
     (arguments
      `(#:tests? #f                      ; no check target
        #:configure-flags '("--dbus" "--alsa")
        #:phases
        (modify-phases %standard-phases
+         ;; Python 3.11 has removed the 'U' (universal newline) mode.  It has
+         ;; been the default since Python 3.3.
+         (add-after 'unpack 'python-compatibility
+           (lambda _
+             (substitute* '("waflib/Context.py"
+                            "waflib/ConfigSet.py")
+               (("m='rU'") "m='r'")
+               (("read\\('rU'") "read('r'"))))
          (add-before 'configure 'set-linkflags
            (lambda _
              ;; Ensure -lstdc++ is the tail of LDFLAGS or the simdtests.cpp
@@ -3326,7 +3328,7 @@ synchronous execution of all clients, and low latency operation.")
            expat
            libsamplerate
            opus
-           python-dbus
+           python-dbus-1.2
            readline))
     (native-inputs
      (list pkg-config))
@@ -4204,7 +4206,9 @@ one-dimensional sample-rate conversion library.")
                  (string-append "'" #$(this-package-input "libsndfile")
                                 "/lib/libsndfile"))))))))
     (native-inputs
-     (list python-pytest python-setuptools))
+     (list python-pytest
+           python-pytest-cov
+           python-setuptools))
     (inputs
      (list libsndfile
            portaudio))
@@ -7982,59 +7986,60 @@ Rate} 3600x2250 bit/s vocoder used in various radio systems.")
                   (delete-file-recursively "third_party")
                   (delete-file-recursively "modules")))))
     (build-system cmake-build-system)
-    (arguments
-     (list
-      #:configure-flags
-      #~(list "-DLINK_BUILD_QT_EXAMPLES=ON"
-              "-DLINK_BUILD_JACK=ON")
-      #:phases
-      #~(modify-phases %standard-phases
-          (replace 'check
-            (lambda* (#:key inputs tests? #:allow-other-keys)
-              (when tests?
-                (let* ((python (search-input-file inputs "/bin/python3"))
-                       (run-tests "../source/ci/run-tests.py"))
-                  (invoke python run-tests "--target" "LinkCoreTest")
-                  (invoke python run-tests "--target" "LinkDiscoveryTest")))))
-          (add-before 'install 'patch-cmake
-            (lambda* (#:key inputs #:allow-other-keys)
-              (let* ((source "../source/"))
-                (substitute* (string-append source
-                                            "cmake_include/AsioStandaloneConfig.cmake")
-                  (((string-append "\\$\\{CMAKE_CURRENT_LIST_DIR\\}/\\.\\./"
-                                   "modules/asio-standalone/asio/include"))
-                   (dirname (search-input-file inputs "include/asio.hpp"))))
-                (substitute* (string-append source "AbletonLinkConfig.cmake")
-                  (("\\$\\{CMAKE_CURRENT_LIST_DIR\\}/include")
-                   "${CMAKE_CURRENT_LIST_DIR}/../../../include")
-                  (("\\$\\{CMAKE_CURRENT_LIST_DIR\\}/include/ableton/Link\\.hpp")
-                   "${CMAKE_CURRENT_LIST_DIR}/../../../include/ableton/Link.hpp")))))
-          (replace 'install
-            (lambda _
-              (let* ((out #$output)
-                     (lib-cmake (string-append out "/lib/cmake/ableton-link"))
-                     (source "../source"))
-                (for-each delete-file
-                          '("bin/LinkDiscoveryTest" "bin/LinkCoreTest"))
-                (copy-recursively "bin" (string-append out "/bin"))
-                (copy-recursively (string-append source "/include/ableton")
-                                  (string-append out "/include/ableton"))
-                (install-file (string-append source "/AbletonLinkConfig.cmake")
-                              lib-cmake)
-                (install-file (string-append source
-                                             "/cmake_include/AsioStandaloneConfig.cmake")
-                              (string-append lib-cmake "/cmake_include"))))))))
     (native-inputs
      (list catch-framework
-           portaudio                    ;for portaudio examples
-           python                       ;for running tests
-           python-setuptools))          ;for running tests
+           python ;for running tests
+           portaudio)) ;for portaudio examples
     (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
@@ -8230,7 +8235,7 @@ as sample rate, determining whether an audio file is silent, and much more.")
     (propagated-inputs
      (list python-numba python-numpy python-scipy python-six))
     (native-inputs
-     (list python-pytest python-setuptools python-wheel))
+     (list python-pytest python-pytest-cov python-setuptools python-wheel))
     (home-page "https://github.com/bmcfee/resampy")
     (synopsis "Efficient signal resampling")
     (description
@@ -8248,10 +8253,10 @@ Home Page}.")
      (origin
        (method git-fetch)
        (uri (git-reference
-              (url "https://github.com/librosa/librosa/")
-              (commit version)
-              ;; TODO: Package test data.
-              (recursive? #true)))
+             (url "https://github.com/librosa/librosa/")
+             (commit version)
+             ;; For test files.
+             (recursive? #true)))
        (file-name (git-file-name name version))
        (sha256
         (base32 "065x43hx670rjrclxi4hiqxscllb16v9s7myjvg7rd5pd3y0k7sg"))))
@@ -8259,13 +8264,15 @@ Home Page}.")
     (arguments
      (list
       #:test-flags
-      #~(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"))))
+      ;; 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"))))
     (propagated-inputs
      (list python-audioread
            python-decorator
@@ -8284,9 +8291,10 @@ Home Page}.")
      (list python-matplotlib
            python-packaging
            python-pytest
-           python-pytest-mpl
+           python-pytest-cov
            python-resampy
-           python-setuptools))
+           python-setuptools
+           python-wheel))
     (home-page "https://librosa.org")
     (synopsis "Python module for audio and music processing")
     (description

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

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

gnu/packages/backup.scm

@@ -50,6 +50,7 @@
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system go)
   #:use-module (guix build-system pyproject)
+  #:use-module (guix build-system python)
   #:use-module (guix build-system qt)
   #:use-module (guix download)
   #:use-module (guix gexp)
@@ -106,7 +107,6 @@
   #:use-module (gnu packages rsync)
   #:use-module (gnu packages ruby-xyz)
   #:use-module (gnu packages serialization)
-  #:use-module (gnu packages sphinx)
   #:use-module (gnu packages ssh)
   #:use-module (gnu packages time)
   #:use-module (gnu packages tls)
@@ -137,6 +137,7 @@
            python-paramiko
            python-pexpect
            python-pytest
+           python-pytest-runner
            python-setuptools-scm
            tzdata-for-tests
            python-mock))
@@ -631,26 +632,41 @@ rsnapshot uses hard links to deduplicate identical files.")
 (define-public borg
   (package
     (name "borg")
-    (version "1.4.4")
+    (version "1.4.3")
     (source
      (origin
-       (method git-fetch)
-       (uri (git-reference
-              (url "https://github.com/borgbackup/borg")
-              (commit version)))
-       (file-name (git-file-name name version))
+       (method url-fetch)
+       (uri (pypi-uri "borgbackup" version))
        (sha256
-        (base32 "0bk302lbjjz1y8dg78wqqys80bm7mzkj5yf6wgyqdwvbqpsnpim4"))))
+        (base32 "07s4jqcv03s98hi6lvqpvmnnhl532qnvv11mjy2xc08rbmsgmfvr"))
+       (snippet
+        #~(begin
+            ;; Delete files generated by Cython.  We used to have a regex that
+            ;; created the list of generated files but Borg has added new
+            ;; non-generated C files that cause the regex to generate the
+            ;; wrong list.
+            (for-each delete-file
+                      '("src/borg/algorithms/checksums.c"
+                        "src/borg/chunker.c"
+                        "src/borg/compress.c"
+                        "src/borg/crypto/low_level.c"
+                        "src/borg/hashindex.c"
+                        "src/borg/item.c"
+                        "src/borg/platform/darwin.c"
+                        "src/borg/platform/freebsd.c"
+                        "src/borg/platform/linux.c"
+                        "src/borg/platform/posix.c"
+                        "src/borg/platform/syncfilerange.c"
+                        "src/borg/platform/windows.c"))))))
     (build-system pyproject-build-system)
     (arguments
      (list
       #:modules '((srfi srfi-26)        ; for cut
                   (guix build utils)
                   (guix build pyproject-build-system))
-      ;; tests: 1318 passed, 293 skipped
       #:test-flags
       #~(list "--benchmark-skip"
-              "--numprocesses" (number->string (min 8 (parallel-job-count)))
+              "--numprocesses" (number->string (parallel-job-count))
               "--pyargs" "borg.testsuite"
               "-k" (string-join
                     ;; These tests need to write to '/var'.
@@ -671,15 +687,7 @@ rsnapshot uses hard links to deduplicate identical files.")
                           "test_mount_hardlinks "
                           "test_readonly_mount "
                           "test_fuse_versions_view "
-                          "test_migrate_lock_alive"
-                          ;; Test 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")
+                          "test_migrate_lock_alive")
                     " and not "))
       #:phases
       #~(modify-phases %standard-phases
@@ -695,58 +703,46 @@ rsnapshot uses hard links to deduplicate identical files.")
                 (setenv "BORG_LIBLZ4_PREFIX" lz4)
                 (setenv "BORG_LIBXXHASH_PREFIX" xxhash)
                 (setenv "BORG_LIBZSTD_PREFIX" zstd))))
-          (add-before 'build 'fix-testsuite-setuid-mode
+          (add-after 'install 'install-doc
             (lambda _
-              (substitute* "src/borg/testsuite/archiver.py"
-                (("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 #$output "/share/man/man1")))
-                (with-directory-excursion "docs"
-                  (invoke "make" "text" "man" "singlehtml"))
+              (let ((man (string-append #$output "/share/man/man1"))
+                    (misc (string-append #$output "/share/doc/borg-"
+                                         #$(package-version this-package))))
                 (for-each (cut install-file <> misc)
                           '("docs/misc/create_chunker-params.txt"
                             "docs/misc/borg-data-flow.png"
                             "docs/misc/internals-picture.txt"
                             "docs/misc/prune-example.txt"))
-                (copy-recursively "docs/_build/man" man)
-                (copy-recursively "docs/_build/singlehtml" html)
-                (copy-recursively "docs/_build/text" txt))))
-          (add-after 'build-and-install-docs 'install-shell-completions
+                (copy-recursively "docs/man" man))))
+          (add-after 'install-doc 'install-shell-completions
             (lambda _
-              (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")))
+              (let ((etc (string-append #$output "/etc"))
+                    (share (string-append #$output "/share")))
                 (with-directory-excursion "scripts/shell_completions"
-                  (install-file "bash/borg" bash)
-                  (install-file "zsh/_borg" zsh)
-                  (install-file "fish/borg.fish" fish))))))))
+                  (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")))))))))
     (native-inputs
      (list python-cython
-           python-guzzle-sphinx-theme
-           python-pkgconfig
+           python-dateutil
            python-pytest
            python-pytest-benchmark
            python-pytest-xdist
            python-setuptools
            python-setuptools-scm
-           python-sphinx
-           python-sphinxcontrib-jquery))
+           python-wheel))
     (inputs
      (list acl
            lz4
            openssl
-           python-msgpack
+           ;; This is the latest version of msgpack accepted by 'setup.py'.
+           python-msgpack-for-borg
            ;; FUSE 3 isn't working well, so we stick with FUSE 2 for now:
            ;; <https://issues.guix.gnu.org/53407>
            python-llfuse
-           python-packaging
            xxhash
            `(,zstd "lib")))
     (synopsis "Deduplicated, encrypted, authenticated and compressed backups")
@@ -1268,9 +1264,10 @@ compression parameters used by Gzip.")
 (define-public borgmatic
   (package
     (name "borgmatic")
-    (version "2.1.5")
+    (version "2.1.2")
     (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")
@@ -1278,11 +1275,10 @@ compression parameters used by Gzip.")
        (file-name (git-file-name name version))
        (sha256
         (base32
-         "17i15ysg0wbcnfvki8wz2z9gx3zx99czv3czjh83y2m1xppvqbl5"))))
+         "0vrpl21n6hf3pj0di4n7s36jq64sx24c93j48cmbdgczs8jiwi36"))))
     (build-system pyproject-build-system)
     (arguments
      (list
-      ;; tests: 2609 passed
       #:phases
       #~(modify-phases %standard-phases
           (add-after 'unpack 'configure
@@ -1297,12 +1293,19 @@ 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-timeout
-           python-setuptools))
+           python-pytest-cov
+           python-setuptools
+           python-wheel))
     (inputs
      (list borg
            python-apprise
@@ -1364,9 +1367,9 @@ borgmatic is powered by borg.")
             (assoc-ref qt:%standard-phases 'qt-wrap)))))
     (native-inputs
      (list python-platformdirs
-           python-pytest
            python-pytest-mock
            python-pytest-qt
+           python-pytest-runner
            python-setuptools
            python-setuptools-git))
     (inputs

gnu/packages/benchmark.scm

@@ -44,6 +44,7 @@
   #: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)

gnu/packages/bioinformatics.scm

@@ -65,6 +65,7 @@
   #:use-module (guix build-system meson)
   #:use-module (guix build-system perl)
   #:use-module (guix build-system pyproject)
+  #:use-module (guix build-system python)
   #:use-module (guix build-system qt)
   #:use-module (guix build-system r)
   #:use-module (guix build-system ruby)
@@ -2289,10 +2290,10 @@ 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))
@@ -3323,17 +3324,7 @@ trees, synthetic data generation, or just phylogenetic tree simulation.")
               (commit (assoc-ref properties 'commit))))
        (file-name (git-file-name name version))
        (sha256
-        (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")))))))
+        (base32 "1x0c1zhlfplhm4n07vibvh4jprjsdlypnlig87a8r07d26d4qphh"))))
     (build-system pyproject-build-system)
     (arguments
      (list
@@ -3358,29 +3349,25 @@ defined rule on an input file.")
 (define-public python-pdbfixer
   (package
     (name "python-pdbfixer")
-    (version "1.12")
+    (version "1.9")
     (source
      (origin
        (method git-fetch)
        (uri (git-reference
              (url "https://github.com/openmm/pdbfixer")
-             (commit (string-append "v" version))))
+             (commit version)))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "0jj724fkvk7bk47izk92ss8nz9ymfvj0f1fkypc0ig4xd5qzjqsz"))))
+        (base32 "1zjhb19q5dclkwvzh8n29p31n1vzkhlmmzwqllimi89jsis1cx35"))))
     (build-system pyproject-build-system)
     (arguments
      (list
       #:test-flags
-      ;; These tests fail because they require internet access or test data.
       '(list "-k"
-             (string-join (list "not test_build_and_simulate"
-                                "test_charge_and_solvate"
-                                "test_cli"
-                                "test_leaving_atoms"
-                                "test_mutate"
-                                "test_nonstandard")
-                          " and not "))))
+             ;; 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"))))
     (propagated-inputs (list openmm python-numpy))
     (native-inputs (list python-pytest python-setuptools python-wheel))
     (home-page "https://github.com/openmm/pdbfixer")
@@ -3394,36 +3381,35 @@ encountered in PDB files prior to simulation tasks.")
 (define-public python-peaks2utr
   (package
     (name "python-peaks2utr")
-    (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"))))
+    (version "1.4.1")
+    (source (origin
+              (method url-fetch)
+              (uri (pypi-uri "peaks2utr" version))
+              (sha256
+               (base32
+                "104il0kk61q07b58g9xrss7xflwlbx4kzsmw9iih99lhfsii0wzg"))))
     (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"
-                (("==") ">=")
-                ;; 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))
+      '(modify-phases %standard-phases
+         (add-after 'unpack 'relax-requirements
+           (lambda _
+             (substitute* "setup.cfg"
+               (("==") ">=")))))))
     (propagated-inputs
      (list python-asgiref
            python-gffutils
            python-importlib-resources
-           macs-3
-           python-numpy
+           macs
+           python-numpy-1
            python-psutil
            python-pybedtools
            python-pysam
@@ -3431,6 +3417,7 @@ encountered in PDB files prior to simulation tasks.")
            python-tqdm
            python-typing-extensions
            python-zipp))
+    (native-inputs (list python-setuptools python-wheel))
     (home-page "https://github.com/haessar/peaks2utr")
     (synopsis "Python CLI for annotating three prime UTR")
     (description
@@ -3879,6 +3866,7 @@ raw/ed14e050b2b75e7f4ddb73d512fbe928bbdb2b85")
            python-scipy))
     (native-inputs
      (list python-pytest
+           python-pytest-cov
            python-pytest-datadir
            python-pytest-doctestplus
            python-setuptools
@@ -4051,16 +4039,7 @@ counts.")
                      "test_scatter_rotate_mp4"
                      "test_sparse_svd"
                      "test_to_array_or_spmatrix_list_of_strings"
-                     "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_unzip_no_destination)")
                "|")
               "test")
       #:phases
@@ -4313,6 +4292,7 @@ e.g. microbiome samples, genomes, metagenomes.")
     (native-inputs
      (list python-cython
            python-pytest
+           python-pytest-cov
            python-setuptools
            python-wheel))
     (propagated-inputs
@@ -6988,6 +6968,7 @@ and v1.1 to v1.2.")
      (list python-mypy-extensions
            python-pytest
            python-pytest-mock
+           python-pytest-runner
            python-setuptools
            python-wheel))
     (propagated-inputs
@@ -7905,7 +7886,7 @@ software to answer ad hoc questions.")
            r-tidyr
            r-upsetr
            r-yaml
-           snakemake))
+           snakemake-7))
     (native-inputs (list python-cython python-pyfakefs python-pytest))
     (home-page "https://github.com/dieterich-lab/Baltica")
     (synopsis "Integrated splice junction usage analysis")
@@ -8795,8 +8776,7 @@ high-throughput sequencing (HTS) assays")
          ;; Needed by tests
          (add-after 'unpack 'set-HOME
            (lambda _ (setenv "HOME" "/tmp"))))))
-    (propagated-inputs (list mysql-connector-python
-                             python-appdirs
+    (propagated-inputs (list python-appdirs
                              python-biopython
                              python-click
                              python-colorama
@@ -8804,6 +8784,7 @@ high-throughput sequencing (HTS) assays")
                              python-filelock
                              python-loguru
                              python-mygene
+                             python-mysql-connector-python
                              python-norns
                              python-numpy
                              python-pandas
@@ -9769,39 +9750,29 @@ sequencing tag position and orientation.")
 (define-public macs-3
   (package
     (name "macs")
-    (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"))))
+    (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"))))
     (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
@@ -12360,9 +12331,15 @@ 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))))))))
+                (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)))))))
     (native-inputs
-     (list python-pytest python-setuptools))
+     (list python-setuptools python-wheel))
     (propagated-inputs
      (list python-biopython
            python-decorator
@@ -14268,7 +14245,11 @@ quality control are provided.")
             (lambda _
               (substitute* "setup.cfg"
                 (("intervaltree~=3.0.2") "intervaltree")
-                (("termcolor~=1.1.0") "termcolor")))))))
+                (("termcolor~=1.1.0") "termcolor"))))
+          (add-after 'unpack 'fix-pytest-config
+            (lambda _
+              (substitute* "pyproject.toml"
+                ((" --cov=gdc_client --cov-report term") "")))))))
     (native-inputs
      (list python-flask
            python-httmock
@@ -14558,7 +14539,7 @@ data.  It also generates basic statistics for your sequences.")
 (define-public shorah
   (package
     (name "shorah")
-    (version "1.99.3")
+    (version "1.99.2")
     (source
      (origin
        (method url-fetch)
@@ -14567,7 +14548,7 @@ data.  It also generates basic statistics for your sequences.")
                            "/shorah-" version ".tar.xz"))
        (sha256
         (base32
-         "0zclbvdvbbfv3qpln3f47qa1yn77wf68z2b30vcxrzq3vsla4kgb"))))
+         "158dir9qcqspknlnyfr9zwk41x48nrh5wcg10k2grh9cidp9daiq"))))
     (build-system gnu-build-system)
     (arguments
      `(#:phases
@@ -14602,7 +14583,6 @@ data.  It also generates basic statistics for your sequences.")
            python
            python-biopython
            python-numpy
-           python-setuptools
            zlib))
     (native-inputs
      (list pkg-config))
@@ -18072,8 +18052,6 @@ 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
@@ -19890,8 +19868,8 @@ set.")
     (name "instrain")
     ;; Git repository does not tag releases, use the latest commit from master
     ;; branch.
-    (properties '((commit . "f172367e599851a6cb90048ae890d1bb6569063f")
-                  (revision . "1")))
+    (properties '((commit . "6180be7b49a61b7e1ffe9f1489da5c6aa2ff9ac3")
+                  (revision . "0")))
     (version (git-version "1.10.0"
                           (assoc-ref properties 'revision)
                           (assoc-ref properties 'commit)))
@@ -19903,32 +19881,18 @@ set.")
               (commit (assoc-ref properties 'commit))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "12rrkcckna7k095clir9100cz6i5dn77anih6aq1blbsg4yhprnr"))))
+        (base32 "1njsxjf3248121yw3q1ig6asf6b3wa5fgjfyc6dkgk6nd4ih8wni"))))
     (build-system pyproject-build-system)
     (arguments
      (list
-      ;; 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")))
+      ;; 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
       #: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")
@@ -19941,10 +19905,9 @@ set.")
          (add-after 'unpack 'relax-requirements
            (lambda _
              (substitute* "setup.py"
-               (("biopython<=1.74") "biopython")
                ((".*pytest.*") "")))))))
     (propagated-inputs
-     (list python-biopython
+     (list python-biopython-1.73
            python-h5py
            python-lmfit
            python-matplotlib
@@ -19956,9 +19919,7 @@ set.")
            python-seaborn
            python-tqdm))
     (native-inputs
-     (list python-boto3
-           python-pytest
-           python-setuptools))
+     (list python-setuptools))
     (home-page "https://github.com/MrOlm/inStrain")
     (synopsis "Calculation of strain-level metrics")
     (description
@@ -20189,32 +20150,33 @@ fasta subsequences.")
 (define-public python-cooler
   (package
     (name "python-cooler")
-    ;; 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)))
+    (version "0.10.4")
     (source
      (origin
-       (method git-fetch)
-       (uri (git-reference
-              (url "https://github.com/open2c/cooler")
-              (commit (assoc-ref properties 'commit))))
-       (file-name (git-file-name name version))
+       (method url-fetch)
+       (uri (pypi-uri "cooler" version))
        (sha256
-        (base32 "0xdb7lvyzj3wwv6jhkrxlj7gk830wkac4lwq5rjwk1r5qshjbn3n"))))
+        (base32
+         "1fh5wjffbl5j8fdkc3c3lybscwvhv4v6r5jiyqgxvkkhb5nn498w"))))
     (build-system pyproject-build-system)
     (arguments
      (list
-      ;; tests: 141 passed, 4 skipped, 2 deselected, 270 warnings
+      ;; tests: 141 passed, 4 skipped, 2 deselected, 268 warnings
       #:test-flags
-      ;; 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")))
+      '(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.*") "")))))))
     (native-inputs
      (list python-hatchling
            python-pytest))
@@ -20616,8 +20578,8 @@ 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 "109e437280436d1ec27e5a5b7a34ffb752176390")
-        (revision "2"))
+  (let ((commit "289d5dca4a5fc327f97b3f8cecb68ecaf1014861")
+        (revision "1"))
     (package
       (name "porechop")
       (version (git-version "0.2.3" revision commit))
@@ -20625,28 +20587,13 @@ 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 "0m7bsgvknv0cbkrpc0qi7b39jaws38dcdih4hi2ppg6z7byxip0k"))))
+          (base32 "05ps43gig0d3ia9x5lj84lb00hbsl6ba9n7y7jz927npxbr2ym23"))))
       (build-system pyproject-build-system)
-      (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))
+      (native-inputs (list python-setuptools python-wheel python-pytest))
       (home-page "https://github.com/rrwick/porechop")
       (synopsis
        "Finding, trimming or splitting adapters, in Oxford Nanopore reads")
@@ -21931,10 +21878,6 @@ 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"
@@ -23148,7 +23091,7 @@ genomes known to contain a given k-mer.")
     (inputs
      (list htslib python-wrapper zlib))
     (native-inputs
-     (list autoconf automake python-setuptools which))
+     (list autoconf automake 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

gnu/packages/bittorrent.scm

@@ -86,6 +86,7 @@
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system meson)
   #:use-module (guix build-system pyproject)
+  #:use-module (guix build-system python)
   #:use-module (guix build-system qt)
   #:use-module (guix download)
   #:use-module (guix gexp)
@@ -533,9 +534,8 @@ and will take advantage of multiple processor cores where possible.")
     (inputs (list boost-1.83 openssl))
     (native-inputs
      (list libfaketime
-           pkg-config
-           python-setuptools
-           python-wrapper))
+           python-wrapper
+           pkg-config))
     (home-page "https://www.libtorrent.org/")
     (synopsis "Feature-complete BitTorrent implementation")
     (description

gnu/packages/boost.scm

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

gnu/packages/build-tools.scm

@@ -94,6 +94,7 @@
   #: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)
@@ -431,8 +432,9 @@ files and generates build instructions for the Ninja build system.")
     (arguments
      (list
       #:tests? #f                       ;disabled to avoid extra dependencies
-      ;; Custom build steps to prevent using pyproject-build-system which
-      ;; allows to edit the latter without a C++ world rebuild.
+      ;; 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.
       #:phases
       #~(modify-phases %standard-phases
           (delete 'bootstrap)

gnu/packages/c.scm

@@ -55,6 +55,7 @@
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system meson)
   #:use-module (guix build-system pyproject)
+  #:use-module (guix build-system python)
   #:use-module (guix store)
   #:use-module (gnu packages)
   #:use-module (gnu packages bash)

gnu/packages/calendar.scm

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

gnu/packages/check.scm

@@ -131,6 +131,7 @@
   #:use-module (guix build-system meson)
   #:use-module (guix build-system perl)
   #:use-module (guix build-system pyproject)
+  #:use-module (guix build-system python)
   #:use-module (guix build-system trivial)
   #:use-module (ice-9 match)
   #:use-module (srfi srfi-1))
@@ -1881,6 +1882,7 @@ http server.")
     (arguments (list #:tests? #false)) ;no tests included
     (native-inputs
      (list python-pytest
+           python-pytest-cov
            python-setuptools
            python-wheel
            python-xmlschema))
@@ -1913,6 +1915,42 @@ XML output")
 decorators from external files.")
     (license license:expat)))
 
+(define-public python-pytest-random-order
+  (package
+    (name "python-pytest-random-order")
+    (version "1.1.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "pytest-random-order" version))
+       (sha256
+        (base32 "104hww3b86jchk41kjhyycr541pd2dfgqkww6lx5y70z9z9xfwj4"))))
+    (build-system pyproject-build-system)
+    (arguments
+     (list
+      #:test-flags
+      ;; AttributeError: module 'py' has no attribute 'code'.
+      #~(list "-k" (string-append "not test_it_works_with_actual_tests"
+                                  " and not test_failed_first"
+                                  " and not test_doctests"))))
+    (native-inputs
+     (list python-pytest-xdist
+           python-setuptools
+           python-py
+           python-wheel))
+    (propagated-inputs
+     (list python-pytest))
+    (home-page "https://github.com/jbasko/pytest-random-order")
+    (synopsis "Pytest plugin to randomize the order of tests")
+    (description "@code{pytest-random-order} is a Pytest plugin that
+randomizes the order of tests.  This can be useful to detect a test that
+passes just because it happens to run after an unrelated test that leaves the
+system in a favourable state.  The plugin allows user to control the level of
+randomness they want to introduce and to disable reordering on subsets of
+tests.  Tests can be rerun in a specific order by passing a seed value
+reported in a previous test run.")
+    (license license:expat)))
+
 (define-public python-pytest-runner
   (package
     (name "python-pytest-runner")
@@ -2695,11 +2733,7 @@ failures and errors instantly.")
                      "test_is_not_identity"
                      "test_resolves_builtin_types[object]"
                      "test_resolves_forwardrefs_to_builtin_types[object]"
-                     "test_timezone_lookup[tzinfo]"
-                     ;; hypothesis.errors.FailedHealthCheck: Input generation is slow
-                     #$@(if (target-riscv64?)
-                            '("test_can_run_with_no_db")
-                            '()))
+                     "test_timezone_lookup[tzinfo]")
                " and not "))
       #:phases
       #~(modify-phases %standard-phases
@@ -2922,8 +2956,12 @@ mypy plugins.")
                            "and not upstream_url"))))
     (native-inputs
      (list python-pytest
+           python-pytest-black
            python-pytest-checkdocs
+           python-pytest-cov
            python-pytest-enabler
+           python-pytest-flake8
+           python-pytest-mypy
            python-setuptools
            python-wheel))
     (propagated-inputs
@@ -3030,28 +3068,21 @@ possible to write plugins to add your own checks.")
 (define-public behave
   (package
     (name "behave")
-    ;; 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)))
+    (version "1.3.3")
     (source
      (origin
        (method git-fetch)
        (uri (git-reference
               (url "https://github.com/behave/behave")
-              (commit (assoc-ref properties 'commit))))
+              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "05671jf7scpgqr8chzgs9bxidvf12nlkqqiqxa5qwmykqfvc8nk4"))))
+        (base32 "1fxj51kailsdakqi7qbw700k258n7r3lv75mgxs45ld5xh2jfyxh"))))
     (build-system pyproject-build-system)
-    ;; tests: 1638 passed, 3 skipped, 2 xfailed
     (native-inputs
-     (list python-chardet
-           python-freezegun
-           python-charset-normalizer
+     (list python-assertpy
+           python-chardet
+           python-mock
            python-path
            python-pyhamcrest
            python-pytest

gnu/packages/chemistry.scm

@@ -28,6 +28,7 @@
   #:use-module (guix build-system cmake)
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system pyproject)
+  #:use-module (guix build-system python)
   #:use-module (guix download)
   #:use-module (guix gexp)
   #:use-module (guix git-download)

gnu/packages/cinnamon.scm

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

gnu/packages/cmake.scm

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

gnu/packages/code.scm

@@ -49,6 +49,7 @@
   #:use-module (guix git-download)
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system cmake)
+  #:use-module ((guix build-system python) #:select (pypi-uri))
   #:use-module (guix build-system pyproject)
   #:use-module (guix build-system trivial)
   #:use-module (guix build-system go)

gnu/packages/compression.scm

@@ -34,7 +34,7 @@
 ;;; Copyright © 2021 Vincent Legoll <vincent.legoll@gmail.com>
 ;;; Copyright © 2021 Simon Tournier <zimon.toutoune@gmail.com>
 ;;; Copyright © 2021, 2024-2025 Maxim Cournoyer <maxim@guixotic.coop>
-;;; Copyright © 2021 Ahmad Jarara <git@ajarara.io>
+;;; Copyright © 2021, 2026 Ahmad Jarara <ajarara@fastmail.com>
 ;;; Copyright © 2022 Greg Hogan <code@greghogan.com>
 ;;; Copyright © 2022 Zhu Zihao <all_but_last@163.com>
 ;;; Copyright © 2021 Foo Chuan Wei <chuanwei.foo@hotmail.com>
@@ -3005,17 +3005,13 @@ can append files to the end of such compressed archives.")
           "00ibddiy62kbs9wl52c35j0hbqanx6pi7lvzkpzmbsizkj8mhp1p"))))
     (build-system cmake-build-system)
     (arguments
-     '(#:tests? #f
-       #:configure-flags
-       (let* ((out (assoc-ref %outputs "out"))
-              (lib (string-append out "/lib")))
-         (list
-          "-DCMAKE_BUILD_TYPE=Release"
-          "-DBUILD_SHARED_LIBS=ON"
-          "-DCBOR_CUSTOM_ALLOC=ON"
-          (string-append "-DCMAKE_INSTALL_LIBDIR=" lib)
-          (string-append "-DCMAKE_INSTALL_RPATH=" lib)))))
+     (list
+      #:configure-flags
+      #~'("-DWITH_TESTS=ON"
+          "-DBUILD_SHARED_LIBS=ON")))
     (synopsis "The C library for parsing and generating CBOR")
+    (native-inputs
+     (list cmocka))
     (description
      "@acronym{CBOR, The Concise Binary Object Representation} is a data format
 whose design goals include the possibility of extremely small code size, fairly

gnu/packages/cpp.scm

@@ -79,6 +79,7 @@
   #:use-module (guix build-system copy)
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system meson)
+  #:use-module (guix build-system python)
   #:use-module (guix build-system pyproject)
   #:use-module (guix build-system scons)
   #:use-module (guix modules)
@@ -2016,7 +2017,8 @@ using the string similarity calculations from FuzzyWuzzy.")
           (add-after 'unpack 'fix-pytest-config
             (lambda _
               (substitute* "pyproject.toml"
-                (("\"pytest-cov\", ") "")))))))
+                ((" \"pytest-cov\", ") "")
+                ((" --cov-fail-under=90 --cov=cpplint") "")))))))
     (native-inputs
      (list python-pytest
            python-pytest-timeout

gnu/packages/crypto.scm

@@ -105,6 +105,7 @@
   #:use-module (guix build-system copy)
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system perl)
+  #:use-module (guix build-system python)
   #:use-module (guix build-system pyproject)
   #:use-module (guix utils)
   #:use-module (srfi srfi-1)
@@ -1009,7 +1010,7 @@ SHA-1, SHA-2, and SHA-3, yet is at least as secure as SHA-3.")
 (define-public rhash
   (package
     (name "rhash")
-    (version "1.4.3")
+    (version "1.4.6")
     (source
      (origin
        (method url-fetch)
@@ -1018,7 +1019,7 @@ SHA-1, SHA-2, and SHA-3, yet is at least as secure as SHA-3.")
        (file-name (string-append "rhash-" version ".tar.gz"))
        (sha256
         (base32
-         "0glaghjvwh9ziiqf599v0fdr6jrgc7lcnriq0h7r41k3jrkglh0y"))))
+         "0ylkxhkj4nzmb0iampn2lv7v4yw59x7dl8mdcxqcx2mfxv7ijq4z"))))
     (build-system gnu-build-system)
     (arguments
      (list #:configure-flags

gnu/packages/cups.scm

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

gnu/packages/cybersecurity.scm

@@ -31,6 +31,7 @@
   #:use-module ((guix licenses) #:prefix license:)
   #:use-module (guix build-system cmake)
   #:use-module (guix build-system pyproject)
+  #:use-module (guix build-system python)
   #:use-module (gnu packages databases)
   #:use-module (gnu packages check)
   #:use-module (gnu packages cpp)
@@ -111,7 +112,7 @@ Refresh}in-DRAM mitigations effectively and as such can trigger bit flips.")
 (define-public gallia
   (package
     (name "gallia")
-    (version "2.1.1")
+    (version "2.0.2")
     (source
      (origin
        (method git-fetch)
@@ -120,7 +121,7 @@ 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 "04xzh5fi18wrkjs7sqwlv344jf54njvnly042rhxq3x5jrvpvkdw"))))
+        (base32 "1yvjpwpqq6r6glfm4qzb8j91d2gsfy4lvygd9z9pg2j6jvcq6f6s"))))
     (build-system pyproject-build-system)
     (arguments
      (list
@@ -132,16 +133,25 @@ 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-aiosqlite
+     (list python-aiofiles
+           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")

gnu/packages/databases.scm

@@ -205,6 +205,7 @@
   #:use-module (guix build-system meson)
   #:use-module (guix build-system perl)
   #:use-module (guix build-system pyproject)
+  #:use-module (guix build-system python)
   #:use-module (guix build-system qt)
   #:use-module (guix build-system ruby)
   #:use-module (guix build-system cmake)
@@ -1278,98 +1279,6 @@ management system that supports the standardized Structured Query
 Language.")
     (license license:gpl2)))
 
-(define-public mysql-connector-python
-  (package
-    (name "mysql-connector-python")
-    (version "8.3.0")
-    (source
-     (origin
-       (method git-fetch)
-       (uri (git-reference
-              (url "https://github.com/mysql/mysql-connector-python")
-              (commit version)))
-       (file-name (git-file-name name version))
-       (sha256
-        (base32 "18jvpnnwmfrn961rvqmsygp7dw3spf3swhxhal4hhj5hqddckj5f"))))
-    (build-system pyproject-build-system)
-    (arguments
-     (list
-      ;; tests: 1371 passed
-      #:phases
-      #~(modify-phases %standard-phases
-          (add-after 'unpack 'compatibility
-            (lambda _
-              (substitute* "src/mysql_capi.c"
-                (("res = mysql_options\\(&self->session, MYSQL_OPT_LOAD_DATA_LOCAL_DIR.*")
-                 "res = 0;")
-                (("mysql_options\\(&self->session, MYSQL_OPT_LOAD_DATA_LOCAL_DIR.*")
-                 "")
-                (("mysql_options\\(&self->session, MYSQL_OPT_TLS_CIPHERSUITES.*")
-                 "")
-                ;; The C API does not have mysql_bind_param, so we produce an
-                ;; error here.
-                (("status = mysql_bind_param.*") "status = 1;")
-                (("#include \"mysql_capi_conversion\\.h\"" all)
-                 (string-append all "\n" "#include <stdbool.h>")))))
-          (add-after 'unpack 'chdir
-            (lambda _
-              (chdir "mysql-connector-python")))
-          (add-before 'build 'prepare-build
-            (lambda _
-              (setenv "MYSQL_CAPI" #$(this-package-input "mysql"))))
-          (replace 'check
-            (lambda* (#:key tests? #:allow-other-keys)
-              (when tests?
-                ;; Some of these tests might be failing due to the build
-                ;; container's restrictions, others are due to the version
-                ;; mismatch.
-                (substitute* "tests/cext/test_cext_api.py"
-                  (("def test_change_user") "def _do_not_test_change_user")
-                  (("def test_get_character_set_info")
-                   "def _do_not_test_get_character_set_info"))
-                (substitute* "tests/test_bugs.py"
-                  (("def test_change_user") "def _do_not_test_change_user")
-                  (("def test_lost_connection") "def _do_not_test_lost_connection")
-                  (("def test_kill_query") "def _do_not_test_kill_query")
-                  ;; These all fail because of expired certificates.
-                  (("def test_cext_verify_server_certificate")
-                   "def _do_not_test_cext_verify_server_certificate")
-                  (("def test_pure_verify_server_certificate")
-                   "def _do_not_test_pure_verify_server_certificate")
-                  (("def test_verify_server_name_cext_cnx")
-                   "def _do_not_test_verify_server_name_cext_cnx")
-                  (("def test_verify_server_name_pure_cnx")
-                   "def _do_not_test_verify_server_name_pure_cnx"))
-                (substitute* '("tests/test_connection.py"
-                               "tests/test_aio_connection.py")
-                  (("def test_allow_local_infile_in_path")
-                   "def _do_not_test_allow_local_infile_in_path")
-                  ;; This fails because of expired certificates.
-                  (("def test_connect_with_unix_socket")
-                   "def _do_not_test_connect_with_unix_socket"))
-                (substitute* "tests/test_constants.py"
-                  (("def test_deprecated")
-                   "def _do_not_test_deprecated"))
-                (mkdir-p "/tmp/datadir")
-                (invoke "python3" "unittests.py"
-                        "--verbosity=3"
-                        (string-append "--with-mysql=" #$(this-package-input "mysql"))
-                        "--keep"
-                        "--mysql-topdir=/tmp/datadir"
-                        "--unix-socket=/tmp/datadir")))))))
-    (propagated-inputs (list python-protobuf))
-    (inputs (list mysql protobuf-3.20 openssl-1.1 zlib))
-    (native-inputs (list python-setuptools))
-    (home-page "https://dev.mysql.com/doc/connector-python/en/index.html")
-    (synopsis "MySQL driver written in Python")
-    (description "MySQL Connector/Python enables Python programs to access
-MySQL databases, using an API that is compliant with the Python Database API
-Specification v2.0 (PEP 249).")
-    (license license:gpl2)))
-
-(define-deprecated-package python-mysql-connector-python
-  mysql-connector-python)
-
 (define-public mariadb
   (package
     (name "mariadb")
@@ -4829,24 +4738,33 @@ PickleShare.")
 (define-public python-apsw
   (package
     (name "python-apsw")
-    (version "3.50.4.0")
+    (version "3.46.0.0")
+    ;; The compressed release has fetching functionality disabled.
     (source
      (origin
-       (method git-fetch)
-       (uri (git-reference
-              (url "https://github.com/rogerbinns/apsw")
-              (commit version)))
-       (file-name (git-file-name name version))
+       (method url-fetch)
+       (uri (string-append
+             "https://github.com/rogerbinns/apsw/releases/download/"
+             version "/apsw-" version ".zip"))
        (sha256
-        (base32 "0r9awjgpl9cmqz5xd4zbqrpiv0rv5c36a18jkqnsfky6n6sgr424"))))
+        (base32
+         "10yfbasi4mq63g0svyl1h49ylwn9znjylq78id16dzxzk9q9ipdx"))))
     (build-system pyproject-build-system)
-    (arguments
-     (list #:test-backend #~'custom
-           #:test-flags #~(list "-m" "apsw.tests")))
     (native-inputs
-     (list python-setuptools))
-    (inputs
-     (list sqlite-next))         ;SQLite 3.45.1 required.
+     (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"))))))
     (home-page "https://github.com/rogerbinns/apsw/")
     (synopsis "Another Python SQLite Wrapper")
     (description
@@ -5823,6 +5741,7 @@ __version_tuple__ = version_tuple = (~a)~%" version version-tuple))))))
            pkg-config
            python-cython
            python-pytest
+           python-pytest-runner
            python-setuptools-scm
            python-setuptools))
     (outputs '("out"))
@@ -6419,7 +6338,7 @@ mechanism of @code{dogpile}.")
 (define-public datasette
   (package
     (name "datasette")
-    (version "1.0a26")
+    (version "1.0a19")
     (source
      (origin
        (method git-fetch)
@@ -6428,20 +6347,23 @@ mechanism of @code{dogpile}.")
               (commit version)))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "1ra0yfrz9w3jx7ix3dmcsg0g8hjxkz37586g7ijmqshxpzczxfm7"))))
+        (base32 "0wb73iksrc5vg2lnq3q4vr7yhlzxwr711jfmjdndd0s77996zsfh"))))
     (build-system pyproject-build-system)
     (arguments
      (list
-      ;; tests: 1720 passed, 9 skipped, 8 xfailed, 13 xpassed, 3 warnings, 120
-      ;; subtests passed
       #:test-flags
-      #~(list "--numprocesses" (number->string (min 8 (parallel-job-count)))
-              "--ignore=tests/test_black.py")
+      ;; 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)))
       #:phases
       #~(modify-phases %standard-phases
           (add-after 'unpack 'relax-requirements
             (lambda _
-              (substitute* "pyproject.toml"
+              (substitute* "setup.py"
                 (("\"pip\",") "")))))))
     (propagated-inputs
      (list python-aiofiles
@@ -6456,6 +6378,7 @@ mechanism of @code{dogpile}.")
            python-janus
            python-jinja2
            python-mergedeep
+           python-pint
            python-pluggy
            python-pyyaml
            python-sqlite-utils
@@ -6464,9 +6387,9 @@ mechanism of @code{dogpile}.")
      (list nss-certs-for-test
            python-beautifulsoup4
            python-cogapp
-           python-multipart-form-data-conformance
            python-pytest
-           python-pytest-asyncio
+           python-pytest-asyncio-0.26
+           python-pytest-runner
            python-pytest-timeout
            python-pytest-xdist
            python-setuptools

gnu/packages/dav.scm

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

gnu/packages/debug.scm

@@ -263,7 +263,7 @@ simple way to add custom protocol messages.")
 (define-public c-vise
   (package
     (name "c-vise")
-    (version "2.8.0")
+    (version "2.4.0")
     (source
      (origin
        (method git-fetch)
@@ -271,53 +271,37 @@ simple way to add custom protocol messages.")
              (url "https://github.com/marxin/cvise")
              (commit (string-append "v" version))))
        (sha256
-        (base32 "1ynhm1d56r25apgvv0wqbdrhjbwigkwrgw92g2czz4nfx77rjxz2"))
+        (base32 "1i2z5q2pcwh1gpdqc24x1a2q5vzwhblzzq021nzwf304di7m18vl"))
        (file-name (git-file-name name version))))
     (build-system cmake-build-system)
-    (arguments
-     (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 #$output "/bin/cvise")
-                  `("PYTHONPATH" ":" prefix
-                    (,(string-join
-                       (filter (lambda (cand)
-                                 (not (string-contains cand "pytest")))
-                               (string-split python-path #\:))
-                       ":"))))))))))
     (native-inputs
-     (list flex
-           python-pytest
-           python-pytest-flake8))
+     (list flex python-pytest python-pytest-flake8))
     (inputs
-     (list bash-minimal
-           clang
-           llvm
-           unifdef
-           python
-           python-pebble
-           python-psutil
-           python-chardet))
+     (list bash-minimal clang llvm unifdef
+           python python-pebble python-psutil python-chardet))
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'fix-linkage
+           (lambda _
+            (substitute* "clang_delta/CMakeLists.txt"
+              (("\\$\\{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))))))
     (home-page "https://github.com/marxin/cvise")
     (synopsis "Reducer for interesting code")
     (description
@@ -1230,7 +1214,7 @@ and input distributions can also be expressed in Fandango.")
                           ;; Shorten paths to sockets in tests.
                           (lambda _ (setenv "TMPDIR" "/tmp"))))
            #:test-target "test"))
-    (native-inputs (list python python-setuptools)) ; for tests
+    (native-inputs (list python))      ; for tests
     (synopsis "Fault injector in userspace")
     (description "Fiu provides CLI utilities and a C library
 to mark points of failure inside your code

gnu/packages/dictionaries.scm

@@ -41,6 +41,7 @@
   #:use-module (guix build-system copy)
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system pyproject)
+  #:use-module (guix build-system python)
   #:use-module (guix build-system qt)
   #:use-module (guix build-system trivial)
   #:use-module (gnu packages)
@@ -48,7 +49,6 @@
   #: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)
@@ -122,83 +122,58 @@ Carnegie Mellon University.")
               "https://github.com/cmusphinx/cmudict/blob/master/LICENSE"))))
 
 (define-public dico
-  (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,
+  (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,
 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

gnu/packages/diffoscope.scm

@@ -67,6 +67,7 @@
   #:use-module (gnu packages vim)
   #:use-module (gnu packages web)
   #:use-module (gnu packages xml)
+  #:use-module (guix build-system python)
   #:use-module (guix build-system pyproject)
   #:use-module (guix gexp)
   #:use-module (guix git-download)
@@ -289,6 +290,14 @@ install.")
               (for-each (lambda (file)
                           (chmod file #o755))
                         (find-files #$output "autopkgtest-virt-.*"))))
+          ;; Adjust use of importlib.resources to use python 3.10 compatible
+          ;; syntax, which requires an argument.
+          ;; Drop when switching to python 3.12+.
+          (add-after 'unpack 'adjust-importlib-resources-for-old-python
+            (lambda _
+              (substitute* "reprotest/__init__.py"
+                (("importlib.resources.files\\(\\)")
+                  "importlib.resources.files(package='reprotest')"))))
           (add-after 'unpack 'skip-most-tests
             ;; These tests require functionality not available in the guix
             ;; build environment

gnu/packages/digest.scm

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

gnu/packages/disk.scm

@@ -59,6 +59,7 @@
   #:use-module (guix build-system meson)
   #:use-module (guix build-system perl)
   #:use-module (guix build-system pyproject)
+  #:use-module (guix build-system python)
   #:use-module (guix build-system qt)
   #:use-module (guix build-system scons)
   #:use-module (guix build-system trivial)
@@ -1225,25 +1226,16 @@ and its highly optimized now for efficient performance.")
   (package
     (name "volume-key")
     (version "0.3.12")
-    (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"))))
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "https://releases.pagure.org/volume_key/volume_key-"
+                                  version ".tar.xz"))
+              (sha256
+               (base32
+                "16rhfz6sjwxlmss1plb2wv2i3jq6wza02rmz1d2jrlnsq67p98vc"))))
     (build-system gnu-build-system)
     (native-inputs
-     (list autoconf
-           automake
-           gettext-minimal
-           libtool
-           pkg-config
-           python       ; used to generate the Python bindings
-           python-setuptools
-           swig))
+     (list pkg-config swig-4.0 python-3))           ; used to generate the Python bindings
     (inputs
      (append
       (cons cryptsetup-minimal (libcryptsetup-propagated-inputs))
@@ -1253,21 +1245,15 @@ and its highly optimized now for efficient performance.")
             glib
             gpgme)))
     (arguments
-     (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"))))))))
+     `(#: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))))))
     (home-page "https://pagure.io/volume_key")
     (synopsis "Manipulate storage volume encryption keys")
     (description

gnu/packages/distributed.scm

@@ -46,7 +46,6 @@
   #: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
@@ -109,11 +108,7 @@ resources).  It supports virtualized, parallel, and GPU-based applications.")
                                      "--with-gtk"
                                      "--with-auth")))
     (native-inputs
-     (list autoconf
-           automake
-           pkg-config
-           python-setuptools
-           which))
+     (list pkg-config autoconf automake which))
     (inputs
      (list avahi
            gtk+

gnu/packages/django.scm

@@ -37,6 +37,7 @@
   #:use-module (guix git-download)
   #:use-module (guix gexp)
   #:use-module (guix build-system pyproject)
+  #:use-module (guix build-system python)
   #:use-module (guix deprecation)
   #:use-module (guix search-paths)
   #:use-module (guix utils)
@@ -312,7 +313,7 @@ to the @dfn{don't repeat yourself} (DRY) principle.")
         (base32 "1a5vd07wrnfbclvf6pz9p8ag9kdd1453lsl9q0bkyc45hq2xqd2a"))))
     (build-system pyproject-build-system)
     (native-inputs
-     (list python-django python-pytest python-setuptools))
+     (list python-django python-pytest python-pytest-cov python-setuptools))
     (home-page "https://github.com/epicserve/django-cache-url")
     (synopsis "Configure Django cache settings from URLs")
     (description
@@ -403,6 +404,7 @@ and adapters that are useful for non-trivial configuration scenarios.")
            python-factory-boy
            python-pygments
            python-pytest
+           python-pytest-cov ; runs by default
            python-pytest-django
            python-setuptools
            python-shortuuid
@@ -1311,6 +1313,7 @@ server headers required for Cross-Origin Resource Sharing (CORS).")
            python-mock
            python-msgpack
            python-pytest
+           python-pytest-cov
            python-pytest-django
            python-pytest-mock
            python-setuptools
@@ -2167,6 +2170,7 @@ templates and not in python-level form definitions.")
     (build-system pyproject-build-system)
     (native-inputs
      (list python-pytest
+           python-pytest-cov ; runs by default
            python-pytest-django
            python-setuptools
            python-wheel))

gnu/packages/djvu.scm

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

gnu/packages/dlang.scm

@@ -52,7 +52,6 @@
   #: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)
@@ -117,7 +116,6 @@
        ("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")

gnu/packages/dns.scm

@@ -1425,7 +1425,7 @@ and TCP-capable recursive DNS server for finding domains on the internet.")
 (define-public openresolv
   (package
     (name "openresolv")
-    (version "3.17.4")
+    (version "3.13.2")
     (source
      (origin
        (method git-fetch)
@@ -1435,7 +1435,7 @@ and TCP-capable recursive DNS server for finding domains on the internet.")
        (file-name (git-file-name name version))
        (sha256
         (base32
-         "1lawj50qhr2yj7fy3p8x4m3kqz4lbvghnjc4jlqnxp484hg83ki3"))
+         "03m8n0j0kxxm5kpl66gz4lxr1qqgrp8zlkaq9j8fz27fih0g75xf"))
        (patches
         (search-patches "openresolv-restartcmd-guix.patch"))))
     (build-system gnu-build-system)

gnu/packages/docbook.scm

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

gnu/packages/docker.scm

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

gnu/packages/documentation.scm

@@ -41,6 +41,7 @@
   #:use-module (guix build-system cmake)
   #:use-module (guix build-system copy)
   #:use-module (guix build-system perl)
+  #:use-module (guix build-system python)
   #:use-module (guix build-system pyproject)
   #:use-module (guix build-system qt)
   #:use-module (guix deprecation)
@@ -489,8 +490,9 @@ inspired by Dash.")
     (build-system gnu-build-system)
     (arguments
      (list
-      ;; Custom build steps to prevent using pyproject-build-system which
-      ;; allows to edit the latter without a texlive + haskell world rebuild.
+      ;; 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.
       #:phases
       #~(modify-phases %standard-phases
           (delete 'bootstrap)

gnu/packages/dotnet.scm

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

gnu/packages/duckdb.scm

@@ -25,6 +25,7 @@
   #:use-module ((guix licenses) #:prefix license:)
   #:use-module (guix build-system cmake)
   #:use-module (guix build-system pyproject)
+  #:use-module ((guix build-system python) #:select (pypi-uri))
   #:use-module (guix build-system r)
   #:use-module (guix download)
   #:use-module (guix gexp)

gnu/packages/ebook.scm

@@ -40,6 +40,7 @@
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system meson)
   #:use-module (guix build-system pyproject)
+  #:use-module (guix build-system python)
   #:use-module (guix build-system qt)
   #:use-module (gnu packages)
   #:use-module (gnu packages autotools)
@@ -206,7 +207,7 @@ with Microsoft Compiled HTML (CHM) files.")
            python-css-parser
            python-cssselect
            python-dateutil
-           python-dnspython
+           python-dnspython-1.16
            python-feedparser
            python-fonttools
            python-html2text
@@ -282,9 +283,7 @@ tags = [\"WS_X11\"]")
                  (string-append "[tool.sip.project]
 sip-include-dirs = [\""
                    #$(this-package-input "python-pyqt")
-                   "/lib/python"
-                   #$(version-major+minor (package-version python))
-                   "/site-packages/PyQt6/bindings\"]")))
+                   "/lib/python3.11/site-packages/PyQt6/bindings\"]")))
               (substitute* "src/calibre/ebooks/pdf/pdftohtml.py"
                 (("PDFTOHTML = 'pdftohtml'")
                  (string-append "PDFTOHTML = \""

gnu/packages/education.scm

@@ -91,6 +91,7 @@
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system go)
   #:use-module (guix build-system pyproject)
+  #:use-module (guix build-system python)
   #:use-module (guix build-system qt)
   #:use-module (guix build-system trivial)
   #:use-module (srfi srfi-1))

gnu/packages/electronics.scm

@@ -64,6 +64,7 @@
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system meson)
   #:use-module (guix build-system pyproject)
+  #:use-module (guix build-system python)
   #:use-module (guix build-system qt)
   #:use-module (guix deprecation)
   #:use-module (guix download)
@@ -195,10 +196,6 @@
             (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$")
-                  (("assertEquals") "assertEqual"))))
             (add-before 'build 'set-home-env
               (lambda _
                 (setenv "HOME" "/tmp")))
@@ -582,10 +579,8 @@ individual low-level driver modules.")
     (build-system gnu-build-system)
     (arguments
      (list
-      #:imported-modules %pyproject-build-system-modules
-      #:modules '((guix build gnu-build-system)
-                  ((guix build pyproject-build-system) #:prefix py:)
-                  (guix build utils))
+      #:imported-modules (append %default-gnu-imported-modules
+                                 %python-build-system-modules)
       #:make-flags
       #~(list (string-append "PREFIX=" #$output))
       #:phases
@@ -612,7 +607,7 @@ individual low-level driver modules.")
                 (invoke "make" "-C" "examples/spm")
                 (invoke "make" "-C" "examples/simple"))))
           (add-after 'install 'python:wrap
-            (assoc-ref py:%standard-phases 'wrap)))))
+            (@@ (guix build python-build-system) wrap)))))
     (native-inputs
      (list clang python-minimal-wrapper python-sphinx texinfo yosys))
     (inputs
@@ -1677,10 +1672,6 @@ 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 #$output "/bin/librelane")
@@ -2261,10 +2252,7 @@ versus schematic} tests and can assist with automatic routing.")
      (list
       #:tests? #f                       ;there are no tests
       #:imported-modules (append %qt-build-system-modules
-                                 %pyproject-build-system-modules)
-      #:modules '((guix build qt-build-system)
-                  ((guix build pyproject-build-system) #:prefix py:)
-                  (guix build utils))
+                                 %python-build-system-modules)
       #:phases
       #~(modify-phases %standard-phases
           (add-after 'unpack 'build-info-documentation
@@ -2293,7 +2281,7 @@ versus schematic} tests and can assist with automatic routing.")
               (install-it "mcy")
               (install-it "mcy-dash")))
           (add-after 'make-install 'python:wrap
-            (assoc-ref py:%standard-phases 'wrap)))))
+            (@@ (guix build python-build-system) wrap)))))
     (native-inputs
      (list pkg-config
            python-sphinx
@@ -3260,6 +3248,7 @@ Numpy arrays for convenience.")
               (setenv "PDM_BUILD_SCM_VERSION" #$version))))))
     (native-inputs
      (list python-pdm-backend
+           python-pytest-cov
            python-setuptools
            python-setuptools-scm
            sby
@@ -3438,12 +3427,8 @@ 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
-                       (string-append
-                        "include/python"
-                        #$(version-major+minor (package-version python))))))
+                     (python-include (search-input-directory
+                                       inputs "include/python3.11")))
                 ;; Patch CMake to use our paths directly.
                 (substitute* "src/CMake_antlr4.txt"
                   (("set\\(ANTLR_CLASSPATH \"\"\\)")
@@ -3608,16 +3593,15 @@ Standard} data mode.")
     (version "0.4.1")
     (source
      (origin
-       (method git-fetch)
-       (uri (git-reference
-             (url "https://github.com/SanDisk-Open-Source/pyvcd")
-             (commit version)))
-       (file-name (git-file-name name version))
+       (method url-fetch)
+       (uri (pypi-uri "pyvcd" version))
        (sha256
-        (base32 "1a1fsgxmpy6gbrs7lp3a56b7d4g6srlp42y5azb1ywjx3w8fiwc6"))))
+        (base32 "15nnydvr1a4ykh8cagi484sfgvdg0dnjxaw6c0ivhjbrbblpaqnw"))))
     (build-system pyproject-build-system)
     (native-inputs
-     (list python-pytest python-setuptools python-setuptools-scm))
+     (list python-pytest-cov
+           python-setuptools
+           python-setuptools-scm))
     (home-page "http://pyvcd.readthedocs.io/")
     (synopsis "Library to manipulate digital wave files")
     (description
@@ -3894,7 +3878,10 @@ Automation}.")
                          #$output "/share/info/hdlmake-figures")))))
       #:test-flags #~(list "test_all.py")))
     (native-inputs
-     (list python-pytest python-setuptools python-sphinx texinfo))
+     (list python-pytest-cov
+           python-setuptools
+           python-sphinx
+           texinfo))
     (propagated-inputs (list python-networkx))
     (home-page "https://ohwr.gitlab.io/project/hdl-make/")
     (synopsis "Generate multi-purpose makefiles for HDL projects")
@@ -4057,9 +4044,18 @@ design.")
       ;; Tests are expensive and may introduce race condition on systems with
       ;; high (more than 16) threads count; limit parallel jobs to 8x.
       #~(list
-         "--numprocesses" (number->string (min 8 (parallel-job-count))))))
+         "--numprocesses" (number->string (min 8 (parallel-job-count))))
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-after 'unpack 'pathch-pytest-options
+            (lambda _
+              (substitute* "pyproject.toml"
+                ((".*--cov=.*") "")
+                ((".*--self-contained-html.*") "")
+                ((".*-n.*auto.*") "")))))))
     (native-inputs
-     (list python-pytest
+     (list python-pytest-cov
+           python-pytest-html
            python-pytest-xdist
            python-setuptools))
     (propagated-inputs
@@ -4623,10 +4619,11 @@ 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 pyproject-build-system) #:prefix python:)
+                  ((guix build python-build-system) #:prefix python:)
                   (guix build utils))
+      #:imported-modules `(,@%default-gnu-imported-modules
+                           (guix build python-build-system))
       #:make-flags #~(list (string-append "PREFIX=" #$output))
       #:phases
       #~(modify-phases %standard-phases

gnu/packages/emacs-xyz.scm

@@ -242,7 +242,6 @@
   #: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)
@@ -14051,54 +14050,46 @@ libraries from Swagger specs.")
       #:imported-modules (append %emacs-build-system-modules
                                  %pyproject-build-system-modules)
       #:modules '((guix build emacs-build-system)
-                  ((guix build pyproject-build-system) #:prefix py:)
+                  ((guix build python-build-system) #:prefix py:)
                   (guix build emacs-utils)
                   (guix build utils))
       #:phases
-      (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"))))))))))
+      #~(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")))))))))
     (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
-           python-setuptools))
+     (list emacs-auto-complete emacs-python-environment emacs-epc))
     (home-page "https://github.com/tkf/emacs-jedi")
     (synopsis "Provides Python completion in Emacs")
     (description

gnu/packages/embedded.scm

@@ -45,6 +45,7 @@
   #:use-module (guix build-system cmake)
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system pyproject)
+  #:use-module (guix build-system python)
   #:use-module (guix build-system trivial)
   #:use-module ((guix build utils) #:select (alist-replace delete-file-recursively))
   #:use-module (gnu packages)
@@ -2036,7 +2037,13 @@ whereas kdmx creates pseudo-ttys.")
       ;; tests: 631 passed, 27 skipped, 1 warning
       #:test-flags
       ;; E   ModuleNotFoundError: No module named 'mbed_tools_ci_scripts'
-      #~(list "--ignore=tests/ci_scripts/test_sync_board_db.py")))
+      #~(list "--ignore=tests/ci_scripts/test_sync_board_db.py")
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-after 'unpack 'fix-pytest-config
+            (lambda _
+              (substitute* "pytest.ini"
+                (("addopts = .*") "")))))))
     (native-inputs
      (list python-factory-boy
            python-pytest

gnu/packages/emulators.scm

@@ -140,6 +140,7 @@
   #:use-module (guix build-system glib-or-gtk)
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system meson)
+  #:use-module (guix build-system python)
   #:use-module (guix build-system pyproject)
   #:use-module (guix build-system qt)
   #:use-module (guix build-system trivial))

gnu/packages/enchant.scm

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

gnu/packages/engineering.scm

@@ -77,6 +77,7 @@
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system meson)
   #:use-module (guix build-system pyproject)
+  #:use-module (guix build-system python)
   #:use-module (guix build-system qt)
   #:use-module (guix download)
   #:use-module (guix gexp)
@@ -1672,7 +1673,7 @@ multiple services and devices with hundreds of supported integrations.")
 (define-public python-esptool
   (package
     (name "python-esptool")
-    (version "5.2.0")
+    (version "5.0.2")
     (source
      (origin
        (method git-fetch)
@@ -1681,7 +1682,7 @@ multiple services and devices with hundreds of supported integrations.")
               (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "0rgwa7mimznwkn8ql17yxwxsfp0is3i75y7bf62mgsxjyx7zawcd"))))
+        (base32 "1wl75j6ncm5lahy9pzc38qivhaf9p42a2bijishdkwkw388fs6x1"))))
     (build-system pyproject-build-system)
     (arguments
      (list
@@ -1930,55 +1931,21 @@ r2ghidra.")
 (define-public rayforge
   (package
     (name "rayforge")
-    (version "1.7.7")   ;newer version requires python-raygeo (Rust)
+    (version "1.0.2")
     (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 "1w44qw51nynf1rk61y0d0wj6xl66ciswpcsp38dnwrpfwsqgafxw"))))
+        (base32 "1c6dl0x3pafmh4p533jbk2cj73q90vz1797jya3hzzxdv0h383yc"))))
     (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 #$output "/bin/rayforge")
-                `("GI_TYPELIB_PATH" ":" prefix
-                  (,(getenv "GI_TYPELIB_PATH")))))))))
     (native-inputs (list python-gitpython
                          python-pytest
                          python-pytest-asyncio
+                         python-pytest-cov
                          python-pytest-mock
                          python-setuptools))
     (inputs (list bash-minimal
@@ -1988,27 +1955,54 @@ r2ghidra.")
                   python-asyncudp
                   python-blinker
                   python-ezdxf
-                  python-gitpython
                   python-numpy
                   python-platformdirs
-                  python-pluggy
                   python-pycairo
                   python-pyclipper
                   python-pygobject
-                  python-pymupdf
                   python-pyopengl
                   python-pyopengl-accelerate
                   python-pypdf
-                  python-pyserial
+                  python-pyserial-asyncio
                   python-pyvips
                   python-pyyaml
                   python-scipy
                   python-semver
                   python-svgelements
-                  python-trimesh
                   python-websockets
                   vtracer))
-    (home-page "https://rayforge.org/")
+    (arguments
+     (list
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-after 'unpack 'write-version-file
+            (lambda _
+              (call-with-output-file "rayforge/version.txt"
+                (lambda (port)
+                  (display #$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")
     (synopsis "Desktop application for laser cutting and engraving")
     (description
      "Rayforge is a cross-platform 2D CAD and G-code control software designed
@@ -2490,6 +2484,7 @@ Newton-Raphson power flow solvers in the C++ library lightsim2grid, and the
                          python-networkx
                          python-openpyxl
                          python-pytest
+                         python-pytest-cov ; --cov runs by default on skrf
                          python-pytest-mock
                          python-pyvisa
                          python-setuptools
@@ -3024,22 +3019,20 @@ interpolation toolkit.")
 (define-public python-motulator
   (package
     (name "python-motulator")
-    (version "0.6.2")
+    (version "0.5.0")
     (source
      (origin
-       (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))
+       (method url-fetch)
+       (uri (pypi-uri "motulator" version))
        (sha256
-        (base32 "1di2r1i19jl751v0hj426zkwk48w5yf8zpw2bl6qzk0vq4z2vpbw"))))
+        (base32 "1kh13zfa4w73q04pny2w2zgym47fp8xy7glwfx82fdx4fihk7dv7"))))
     (build-system pyproject-build-system)
     (arguments
      (list #:tests? #f)) ; there are no tests
-    (propagated-inputs
-     (list python-numpy python-matplotlib python-scipy python-tqdm))
-    (native-inputs (list python-hatchling))
+    (propagated-inputs (list python-matplotlib python-numpy python-scipy))
+    (native-inputs (list python-hatchling
+                         python-ipykernel
+                         python-toml))
     (home-page "https://aalto-electric-drives.github.io/motulator/")
     (synopsis "Motor Drive Simulator in Python")
     (description "This package includes simulation models for an induction
@@ -4183,6 +4176,10 @@ 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")
@@ -4203,11 +4200,6 @@ 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
@@ -4426,6 +4418,15 @@ 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
@@ -4445,16 +4446,6 @@ 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
@@ -4499,6 +4490,8 @@ 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
@@ -4515,8 +4508,6 @@ 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
@@ -4959,9 +4950,7 @@ and mogan.")
                (("'\" [+] python_path [+]")
                 (string-append "'\" + std::string(\""
                                (assoc-ref outputs "out")
-                               "/lib/python"
-                               #$(version-major+minor (package-version python))
-                               "/site-packages"
+                               "/lib/python3.11/site-packages"
                                "\") +")))))
           (add-before 'check 'prepare-checks
             (lambda _

gnu/packages/enlightenment.scm

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

gnu/packages/fediverse.scm

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

gnu/packages/file-systems.scm

@@ -52,6 +52,7 @@
   #:use-module (guix build-system go)
   #:use-module (guix build-system linux-module)
   #:use-module (guix build-system pyproject)
+  #:use-module (guix build-system python)
   #:use-module (guix build-system qt)
   #:use-module (guix build-system trivial)
   #:use-module (guix utils)
@@ -1507,6 +1508,158 @@ 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")
@@ -1919,10 +2072,6 @@ 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))

gnu/packages/finance.scm

@@ -71,6 +71,7 @@
   #:use-module (guix build-system copy)
   #:use-module (guix build-system emacs)
   #:use-module (guix build-system haskell)
+  #:use-module (guix build-system python)
   #:use-module (guix build-system pyproject)
   #:use-module (guix build-system glib-or-gtk)
   #:use-module (guix build-system go)
@@ -650,6 +651,49 @@ 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")
@@ -1284,7 +1328,7 @@ Ledger Blue/Nano S.")
 (define-public python-trezor
   (package
     (name "python-trezor")
-    (version "0.20.0")
+    (version "0.13.7")
     (source
      (origin
        (method git-fetch)
@@ -1293,7 +1337,7 @@ Ledger Blue/Nano S.")
              (commit (string-append "python/v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "06d4mw8iydgv2c3qxa47482k7dqpg89a2b6wd8f4g15ydn3gsfmn"))
+        (base32 "13wyl9b15c8iscfakprwfvh2akw180hfqdjww79b78ywz51y7hdh"))
        (modules
         '((guix build utils)
           (srfi srfi-26)
@@ -1331,32 +1375,26 @@ Ledger Blue/Nano S.")
                           "test_legacy_basic"
                           "test_unsigned"
                           "test_vendor_header")
-                    " and not "))
-      #:phases
-      #~(modify-phases %standard-phases
-          (add-after 'unpack 'relax-requirements
-            (lambda _
-              (substitute* "pyproject.toml"
-                (("platformdirs>=4.4.0") "platformdirs")))))))
+                    " and not "))))
     (propagated-inputs
-     (list python-click
-           python-construct
+     (list python-attrs
+           python-click
            python-construct-classes
-           python-cryptography
-           python-keyring
+           python-ecdsa
+           python-hidapi
            python-libusb1
            python-mnemonic
-           python-noiseprotocol
-           python-platformdirs
            python-requests
-           python-shamir-mnemonic
-           python-slip10
            python-typing-extensions))
-    (native-inputs
+    (native-inputs ; Only needed for running the tests
      (list nss-certs-for-test
-           python-hatchling
-           python-setuptools
-           python-pytest))
+           protobuf
+           python-pytest
+           python-pillow
+           python-protobuf
+           python-pyqt
+           python-pytest
+           python-simple-rlp))
     (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
@@ -1583,7 +1621,10 @@ features:
        (sha256
         (base32 "0yir8hka3vmpk0qhiaffagkdjg3mjgai808s0razsggbd5cn80bb"))))
     (build-system pyproject-build-system)
-    (native-inputs (list python-pytest python-setuptools))
+    (native-inputs
+     (list python-pytest
+           python-pytest-cov
+           python-setuptools))
     (home-page "https://arthurdejong.org/python-stdnum/")
     (synopsis "Python module to handle standardized number and code formats")
     (description
@@ -1675,26 +1716,19 @@ main features are:
 (define-public silkaj
   (package
     (name "silkaj")
-    ;; 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)))
+    (version "0.12.1")
     (source
      (origin
        (method git-fetch)
        (uri (git-reference
              (url "https://git.duniter.org/clients/python/silkaj")
-              (commit (assoc-ref properties 'commit))))
+             (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "08wg4q3y747apj5phq4ghjgg9cdr8mnyzjspjvd8v9qz08v5zg6b"))))
+        (base32 "0prglgwvzi676h4lyw9266sqiqbfs2l0mv0bmjvplvdxzzcs63bv"))))
     (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/"
@@ -2113,10 +2147,7 @@ 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"))
-       ;; TODO: Remove in the next release:
-       ;; https://github.com/beancount/beangulp/commit/254bfb38ffed
-       (patches (search-patches "python-beangulp-click-8.2-compat.patch"))))
+        (base32 "0zlanw88dq7czgsdvqwz2fgxamyrfnx15ymv4d7fnjrj04glpg47"))))
     (build-system pyproject-build-system)
     (propagated-inputs
      (list beancount
@@ -2184,18 +2215,12 @@ 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.  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.")
+    (description "Envelope budgeting for Fava/Beancount with stats, scheduled
+transactions, and color-coded UI.")
     (license license:expat)))
 
 (define-public emacs-beancount
@@ -2482,6 +2507,10 @@ analysis of financial market data.")
         (base32 "13g5338aa8vgkx8g94vz5d8ynfq3jndvyh1nz6dlhw4axwr4x8dp"))))
     (properties '(("upstream-name" #{.}# "mt-940")))
     (build-system pyproject-build-system)
+    (arguments
+     (list
+      #:test-flags
+      #~(list "-c" "/dev/null")))       ; Remove custom --cov flags.
     (native-inputs (list python-pytest python-pyyaml python-setuptools))
     (home-page "https://mt940.readthedocs.io/")
     (synopsis "Python parser for MT940-encoded SWIFT data")

gnu/packages/firmware.scm

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

gnu/packages/flashing-tools.scm

@@ -49,6 +49,7 @@
   #:use-module (guix build-system go)
   #:use-module (guix build-system meson)
   #:use-module (guix build-system pyproject)
+  #:use-module (guix build-system python)
   #:use-module (guix build-system qt)
   #:use-module (guix download)
   #:use-module (guix gexp)

gnu/packages/fontutils.scm

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

gnu/packages/freedesktop.scm

@@ -75,6 +75,7 @@
   #:use-module (guix build-system meson)
   #:use-module (guix build-system perl)
   #:use-module (guix build-system pyproject)
+  #:use-module (guix build-system python)
   #:use-module (guix build-system glib-or-gtk)
   #:use-module (guix build-system qt)
   #:use-module (guix search-paths)
@@ -1378,43 +1379,41 @@ For information about libevdev, see:
     (license license:expat)))
 
 (define-public python-pyxdg
-  ;; Latest unreleased commits add Python 3.12, 3.14 and 3.15 support.
-  (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 #$(this-package-native-input "shared-mime-info")
-                                       "/share/")))))))
-      (native-inputs
-       (list shared-mime-info
-             hicolor-icon-theme
-             python-pytest
-             python-setuptools))
-      (home-page "https://www.freedesktop.org/wiki/Software/pyxdg")
-      (synopsis "Implementations of freedesktop.org standards in Python")
-      (description
-       "PyXDG is a collection of implementations of freedesktop.org standards in
+  (package
+    (name "python-pyxdg")
+    (version "0.28")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "pyxdg" version))
+       (sha256
+        (base32
+         "1d48bqwkbnpid80cpwz6h62i112laxl0ivpj58hdyd79fhqbnrrj"))))
+    (build-system pyproject-build-system)
+    (arguments
+     (list
+      #:test-flags
+      ;; Tests failing with error: AssertionError: 'image' != 'inode'
+      #~(list "--deselect=test/test_mime.py::MimeTest::test_get_type"
+              "--deselect=test/test_mime.py::MimeTest::test_get_type2")
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-before 'check 'pre-check
+            (lambda _
+              (setenv "XDG_DATA_DIRS"
+                      (string-append #$(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
 Python.")
-      (license license:lgpl2.0))))
+    (license license:lgpl2.0)))
 
 (define-public hyprland-protocols
   (package
@@ -1972,10 +1971,6 @@ 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"
@@ -2183,7 +2178,7 @@ which speak the Qualcomm MSM Interface (QMI) protocol.")
            libxslt                      ;for xsltproc
            pkg-config
            python-minimal
-           python-dbus                  ;for test
+           python-dbus-1.2              ;for test
            python-pygobject             ;for test
            vala))
     (propagated-inputs
@@ -2377,7 +2372,7 @@ different sorts of messages in different formats.")
           (base32 "02wb61h2k3hhis5y2xi5rhc6pmikd13x722hk620sqb9b3m5pn3s"))))
       (build-system gnu-build-system)
       (native-inputs (list autoconf automake libtool pkg-config))
-      (inputs (list libxslt python-wrapper python-dbus))
+      (inputs (list libxslt python-wrapper python-dbus-1.2))
       (propagated-inputs (list telepathy-glib))
       (home-page "https://telepathy.freedesktop.org/")
       (synopsis "Telepathy IRC connection manager")

gnu/packages/game-development.scm

@@ -70,6 +70,7 @@
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system go)
   #:use-module (guix build-system pyproject)
+  #:use-module (guix build-system python)
   #:use-module (guix build-system renpy)
   #:use-module (guix build-system scons)
   #:use-module (gnu packages)
@@ -1750,16 +1751,13 @@ color switches, and many more, with multiple options to customize.")
 (define-public python-pygame-ce
   (package
     (name "python-pygame-ce")
-    (version "2.5.7")
+    (version "2.5.5")
     (source
      (origin
-       (method git-fetch)
-       (uri (git-reference
-              (url "https://github.com/pygame-community/pygame-ce")
-              (commit version)))
-       (file-name (git-file-name name version))
+       (method url-fetch)
+       (uri (pypi-uri "pygame_ce" version))
        (sha256
-        (base32 "1awvs4wa9fgm8xldsxzdx1knijjpzz560lzj3rjvks3gcw8szhzx"))))
+        (base32 "0sxfchimdg606z65qychgvm66mq0aybs2isxsqb5zqy64g19gwm7"))))
     (build-system pyproject-build-system)
     (arguments
      (list

gnu/packages/games.scm

@@ -1957,7 +1957,7 @@ real-time combat.")
 (define-public golly
   (package
     (name "golly")
-    (version "5.0")
+    (version "4.2")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://sourceforge/golly/golly/golly-"
@@ -1965,53 +1965,47 @@ real-time combat.")
                                   "-src.tar.gz"))
               (sha256
                (base32
-                "049n634abxfpgh4imh3s5qqfn9nbwmcl6jm91f29ngqm53jcsdaq"))))
+                "0pg9cp83nxc354lizgza5bqdy7z5wh36863203zw6r6s4flji4an"))))
     (build-system gnu-build-system)
     (arguments
-     (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"))))))))
+     '(#: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)))))
     (native-inputs
-     (list lua
-           python-setuptools))
+     (list lua))
     (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

gnu/packages/genealogy.scm

@@ -1,7 +1,6 @@
 ;;; 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.
 ;;;
@@ -19,15 +18,13 @@
 ;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
 
 (define-module (gnu packages genealogy)
-  #: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 licenses) #:prefix license:)
+  #:use-module (guix gexp)
   #: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)
@@ -37,7 +34,6 @@
   #: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)
@@ -61,42 +57,15 @@
     (build-system pyproject-build-system)
     (arguments
      (list
-      #:imported-modules (append %glib-or-gtk-build-system-modules
-                                 %pyproject-build-system-modules)
+      #:imported-modules
+      `((guix build glib-or-gtk-build-system)
+        ,@%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.
-              #$@(map (lambda (ls) (string-append "--deselect=gramps/"
-                                                  (string-join ls "::")))
-                      '(("gen/proxy/test/proxies_test.py"
-                         "LivingProxyTest" "test_person_count")
-                        ("gen/proxy/test/proxies_test.py"
-                         "LivingPrivateProxyTest" "test_person_count")
-                        ("plugins/test/reports_test.py"
-                         "TestDynamic" "test_export_gedcom")
-                        ("plugins/test/reports_test.py"
-                         "TestDynamic" "test_export_gpkg")
-                        ("plugins/test/reports_test.py"
-                         "TestDynamic" "test_indiv_complete")
-                        ("plugins/test/reports_test.py"
-                         "TestDynamic" "test_navwebpage")
-                        ("plugins/test/reports_test.py"
-                         "TestDynamic" "test_tool_check")
-                        ("plugins/test/tools_test.py"
-                         "ToolControl" "test_tcg_and_check_and_repair")
-                        ("plugins/test/db_undo_and_signals_test.py"
-                         "TestSQLite" "test_one"))))
       #:phases
       #~(modify-phases %standard-phases
           (add-before 'build 'fix-gexiv2-dependency
@@ -104,19 +73,15 @@
               ;; Use our own version
               (substitute* (find-files "." ".*\\.py$")
                 (("\"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 "GDK_BACKEND" "-")
-              (setenv "HOME" "/tmp")
+              (setenv "HOME" (getenv "TMPDIR"))
               ;; Presence of .git directory is used to determine whether this
               ;; is a final installation.  Without it, tests fail to determine
               ;; resource path.
-              (mkdir ".git")))
+              (mkdir ".git")
+              ;; Test is failing
+              (delete-file "gramps/gen/utils/test/file_test.py")))
           (add-before 'wrap 'wrap-with-GI_TYPELIB_PATH
             (lambda* (#:key inputs #:allow-other-keys)
               (wrap-program (string-append #$output "/bin/gramps")
@@ -133,11 +98,8 @@
           (add-after 'wrap 'glib-or-gtk-wrap
             (assoc-ref glib-or-gtk:%standard-phases 'glib-or-gtk-wrap)))))
     (native-inputs
-     (list gettext-minimal
-           intltool
-           python-jsonschema
-           python-mock
-           python-pytest
+     (list gettext-minimal intltool
+           glibc-utf8-locales ;for one test
            python-setuptools))
     (inputs
      (list bash-minimal
@@ -153,12 +115,12 @@
            (librsvg-for-system)
            osm-gps-map
            pango
-           python-berkeleydb
-           python-imagesize
+           python-bsddb3
+           python-jsonschema
+           python-lxml
            python-orjson
            python-pillow
            python-pycairo
-           python-pycountry
            python-pygobject
            python-pyicu
            rcs

gnu/packages/geo.scm

@@ -55,6 +55,7 @@
   #:use-module (guix build-system go)
   #:use-module (guix build-system meson)
   #:use-module (guix build-system pyproject)
+  #:use-module (guix build-system python)
   #:use-module (guix build-system qt)
   #:use-module (guix build-system r)
   #:use-module (guix build-system zig)
@@ -297,7 +298,7 @@ than 600 operators available.")
 (define-public h3
   (package
     (name "h3")
-    (version "4.4.1")
+    (version "4.1.0")
     (source
      (origin
        (method git-fetch)
@@ -306,7 +307,7 @@ than 600 operators available.")
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "1ijnbr4a54ph7bkn8waqwgnxmxlylv9yly9mwjdj69lkmdfjgaml"))))
+        (base32 "0x764xzna8ka6yhgv2y4hb158a61y3g9a6835qckqp7wfkpqvb7f"))))
     (build-system cmake-build-system)
     (arguments
      (list #:configure-flags #~(list "-DBUILD_SHARED_LIBS=ON")))
@@ -318,25 +319,48 @@ combining the benefits of a hexagonal grid with S2's hierarchical
 subdivisions.")
     (license license:asl2.0)))
 
-(define-public python-h3
+;; For python-timezonefinder, remove it when it starts supporting newer
+;; version.
+(define-public h3-3
   (package
-    (name "python-h3")
-    (version "4.4.2")
+    (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")
+    (source
+     (origin
+       (method git-fetch) ; no tests data in PyPi package
        (uri (git-reference
              (url "https://github.com/uber/h3-py")
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "02gry51hn8x2bl80y1ipcyrg0ghcif4vjch26qil215wdzz1yrzv"))
+        (base32 "1k1n256hhlh05gjcj64pqh08zlaz6962jkb6nk1aazsgg8p41zs0"))
        (modules '((guix build utils)))
        ;; Remove bundled H3 lib.
        (snippet #~(begin (delete-file-recursively "src/h3lib")))))
     (build-system pyproject-build-system)
     (arguments
      (list
+      ;; FIXME: Check why these tests are failing.
+      ;; test_versions - assert (4, 1) == (4, 0)
+      ;; test_resolution - h3._cy.error_system.H3Failed
+      #:test-flags #~(list "-k" (string-append
+                                 "not test_versions"
+                                 " and not test_resolution"))
       #:phases
       #~(modify-phases %standard-phases
           ;; Use packaged in Guix h3 source.
@@ -357,7 +381,10 @@ subdivisions.")
            python-cython
            python-numpy
            python-pytest
-           python-scikit-build-core))
+           python-scikit-build
+           python-setuptools
+           python-setuptools-scm
+           python-wheel))
     (inputs (list h3))
     (home-page "https://uber.github.io/h3-py")
     (synopsis "Python bindings for H3")
@@ -365,6 +392,26 @@ subdivisions.")
 hierarchical hexagonal geospatial indexing system")
     (license license:asl2.0)))
 
+;; For python-timezonefinder, remove it when it starts supporting newer
+;; version.
+(define-public python-h3-3
+  (package
+    (inherit python-h3)
+    (name "python-h3")
+    (version "3.7.6")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/uber/h3-py")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "16gxa1sivghxw179rik87r918mjasars2qkzidlwq83qfa4axn20"))))
+    (inputs
+     (modify-inputs inputs
+       (replace "h3" h3-3)))))
+
 (define-public geos
   (package
     (name "geos")
@@ -1077,6 +1124,7 @@ for seismology.")
     (inputs (list gdal))
     (native-inputs (list python-cython
                          python-pytest
+                         python-pytest-cov
                          python-setuptools
                          python-tomli
                          python-versioneer
@@ -1176,7 +1224,7 @@ projections and coordinate transformations library.")
 (define-public python-fiona
   (package
     (name "python-fiona")
-    (version "1.10.1")
+    (version "1.9.6")
     (source
      (origin
        (method git-fetch)
@@ -1185,38 +1233,24 @@ projections and coordinate transformations library.")
               (commit version)))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "0xribbcy5wvrm5y3bq281dry86vhjcnphg9772yp9s3y30y7mlz4"))))
+        (base32 "08whhjrspp194qasjhr9kf70fl342ms47k78rwpcf5q6ikf0rfii"))))
     (build-system pyproject-build-system)
     (arguments
      (list
-      ;; tests: 757 passed, 161 skipped, 24 deselected, 1 xfailed, 6 xpassed
       #:test-flags
       #~(list "-m" "not network and not wheel"
-              #$@(map (lambda (test) (string-append "--deselect=tests/" test))
-                      ;; 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")))
+              ;; FIXME: Find why the
+              ;; test_no_append_driver_cannot_append[PCIDSK] test is failing.
+              "-k" "not test_no_append_driver_cannot_append")
       #:phases
       #~(modify-phases %standard-phases
-          (add-before 'check 'remove-local-source
+          (add-before 'build 'set-configure-flags
             (lambda _
+              (setenv "CFLAGS" "-Wno-error=incompatible-pointer-types")))
+          (add-before 'check 'remove-local-fiona
+            (lambda _
+              ;; This would otherwise interfere with finding the installed
+              ;; fiona when running tests.
               (delete-file-recursively "fiona"))))))
     (inputs
      (list gdal))
@@ -1224,19 +1258,19 @@ projections and coordinate transformations library.")
      (list python-attrs
            python-certifi
            python-click
-           python-click-plugins
+           python-click-plugins-1
            python-cligj))
     (native-inputs
      (list gdal ; for gdal-config
            python-boto3
            python-cython
-           python-fsspec
            python-pytest
+           python-pytest-cov
            python-pytz
-           python-setuptools
-           python-shapely))
+           python-setuptools))
     (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
@@ -1499,6 +1533,7 @@ street bearings/orientations, and speed/travel time.")
            python-pyproj
            python-pyyaml
            python-pytest
+           python-pytest-cov
            python-pytest-httpserver
            python-pytz
            python-requests
@@ -1830,7 +1865,10 @@ utilities for data translation and processing.")
       ;; This test requires internet access.
       '(list "--deselect" "test_shapefile.py::test_reader_url")))
     (native-inputs
-     (list python-pytest python-setuptools python-wheel))
+     (list python-pytest
+           python-pytest-runner
+           python-setuptools
+           python-wheel))
     (home-page "https://github.com/GeospatialPython/pyshp")
     (synopsis "Read/write support for ESRI Shapefile format")
     (description
@@ -3540,9 +3578,10 @@ orienteering sport.")
        (list
         #:tests? #f                    ; No tests
         #:modules `((guix build gnu-build-system)
-                    ((guix build pyproject-build-system) #:prefix python:)
+                    ((guix build python-build-system) #:prefix python:)
                     (guix build utils))
-        #:imported-modules %pyproject-build-system-modules
+        #:imported-modules `(,@%default-gnu-imported-modules
+                             (guix build python-build-system))
         #:configure-flags
         #~(list "--with-blas"
                 "--with-bzlib"
@@ -3714,13 +3753,13 @@ growing set of geoscientific methods.")
     (build-system cmake-build-system)
     (arguments
      (list
-      #:imported-modules (append %cmake-build-system-modules
-                                 %pyproject-build-system-modules
-                                 '((guix build qt-utils)))
       #:modules '((guix build cmake-build-system)
-                  ((guix build pyproject-build-system) #:prefix py:)
+                  ((guix build python-build-system) #:prefix python:)
                   (guix build qt-utils)
                   (guix build utils))
+      #:imported-modules `(,@%cmake-build-system-modules
+                           (guix build python-build-system)
+                           (guix build qt-utils))
       #:configure-flags
       #~(list "-DWITH_QTWEBKIT=NO")
       #:phases
@@ -3881,10 +3920,11 @@ growing set of geoscientific methods.")
             ;; Configure correct path to PyQt5 SIP directory
             (add-after 'unpack 'configure-pyqt5-sip-path
               (lambda* (#:key inputs #:allow-other-keys)
-                (let* ((pyqt (assoc-ref inputs "python-pyqt+qscintilla"))
-                       (sip-dir (string-append
-                                 (py:site-packages inputs `(("out" . ,pyqt)))
-                                 "/PyQt5/bindings")))
+                (let ((sip-dir (string-append
+                                (assoc-ref inputs "python-pyqt+qscintilla")
+                                "/lib/python"
+                                (python:python-version (assoc-ref inputs "python"))
+                                "/site-packages/PyQt5/bindings")))
                   (substitute* "cmake/FindPyQt5.py"
                     (("sip_dir = cfg.default_sip_dir")
                      (string-append "sip_dir = \"" sip-dir "\"")))
@@ -3914,7 +3954,7 @@ SET\\(PYQT5_SIP_DIR \"\\$\\{Python_SITEARCH\\}/PyQt5/bindings\"\\)")
                               "-E" (string-join ignored-tests "|")))
                     (format #t "test suite not run~%"))))
             (add-after 'install 'wrap-python
-              (assoc-ref py:%standard-phases 'wrap))
+              (assoc-ref python:%standard-phases 'wrap))
             (add-after 'wrap-python 'wrap-qt
               (lambda* (#:key inputs #:allow-other-keys)
                 (wrap-qt-program "qgis" #:output #$output #:inputs inputs)))

gnu/packages/gimp.scm

@@ -476,31 +476,17 @@ inverse fourier transform.")
   (package
     (name "libmypaint")
     (version "1.6.1")
-    (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"))))
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "https://github.com/mypaint/libmypaint/"
+                                  "releases/download/v" version "/libmypaint-"
+                                  version ".tar.xz"))
+              (sha256
+               (base32
+                "0priwpmc7dizccqvn21ig6d649bprl3xl1hmjj7nddznjgr585vl"))))
     (build-system gnu-build-system)
-    (arguments
-     (list
-      #:phases
-      #~(modify-phases %standard-phases
-          (add-before 'bootstrap 'overwrite-automake-and-aclocal-versions
-            (lambda _
-              (setenv "AUTOMAKE" "automake")
-              (setenv "ACLOCAL" "aclocal"))))))
     (native-inputs
-     (list autoconf
-           automake
-           intltool
-           libtool
-           pkg-config
-           python))
+     (list intltool pkg-config))
     ;; As needed by 'libmypaint.pc'.
     (propagated-inputs
      (list json-c gobject-introspection))
@@ -512,26 +498,6 @@ brushstrokes which is used by MyPaint and GIMP.")
     (home-page "http://mypaint.org")
     (license license:isc)))
 
-;; To update mypaint, remove when a fresh version is released.
-(define-public libmypaint-next
-  (package
-    (inherit libmypaint)
-    (name "libmypaint")
-    (properties '((commit . "551dfb9ca5d2b82f2361a5a8a9e7f386f35fd320")
-                  (revision . "0")))
-    (version (git-version "1.6.1"
-                          (assoc-ref properties 'revision)
-                          (assoc-ref properties 'commit)))
-    (source
-     (origin
-       (method git-fetch)
-       (uri (git-reference
-              (url "https://github.com/mypaint/libmypaint")
-              (commit (assoc-ref properties 'commit))))
-       (file-name (git-file-name name version))
-       (sha256
-        (base32 "0pl8cma6gfkrqx364fs1xw7f491f7y6pzxqjq1cdqlrf9r8gg0sk"))))))
-
 (define-public mypaint-brushes
   (package
     (name "mypaint-brushes")

gnu/packages/gl.scm

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

gnu/packages/gnome-circle.scm

@@ -320,11 +320,7 @@ 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/python"
-                                   #$(version-major+minor
-                                      (package-version python))
-                                   "/site-packages:"
+                  (,(string-append #$output "/lib/python3.11/site-packages:"
                                    (getenv "GUIX_PYTHONPATH"))))
                 `("GI_TYPELIB_PATH" = (,(getenv "GI_TYPELIB_PATH")))
                 `("GDK_PIXBUF_MODULE_FILE" =
@@ -686,17 +682,17 @@ and a high score table.")
 (define-public komikku
   (package
     (name "komikku")
-    (version "50.4.0")
+    (version "50.3.0")
     (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
-         "0skkb1b6jgfzy3v1bhbgxkgxmjvnxdi442asp5gdm7j8j9cv5wxv"))))
+         "0hm1infvdsms193g2yp7qw7lrsxjsx5zziib8hgch34y6dbhfhf1"))))
     (build-system meson-build-system)
     (arguments
      (list
@@ -742,18 +738,21 @@ 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-jxlpy
            python-keyring
+           python-jxlpy
            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
@@ -775,8 +774,8 @@ 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

gnu/packages/gnome-xyz.scm

@@ -51,6 +51,7 @@
   #: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)
@@ -850,7 +851,7 @@ intellihide and multimonitor support.")
 (define-public gnome-shell-extension-gsconnect
   (package
     (name "gnome-shell-extension-gsconnect")
-    (version "72")
+    (version "71")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -860,7 +861,7 @@ intellihide and multimonitor support.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "06ps946q53jfqi4ycapjb9755763z8p0dvd7jssw6l8h8ma11ly3"))))
+                "0i6zrvb40h0af96md7jb4y3f2c1g37h5qp649xk68gp6gwn1401s"))))
     (build-system meson-build-system)
     (arguments
      (list
@@ -935,6 +936,7 @@ intellihide and multimonitor support.")
      (list
       at-spi2-core
       bash-minimal
+      caribou
       evolution-data-server
       gjs
       glib

gnu/packages/gnome.scm

@@ -250,6 +250,7 @@
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system meson)
   #:use-module (guix build-system pyproject)
+  #:use-module (guix build-system python)
   #:use-module (guix build-system trivial)
   #:use-module ((guix config) #:select (%storedir))
   #:use-module (guix deprecation)
@@ -2758,7 +2759,7 @@ 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-3.50))
+    (propagated-inputs (list python-pygobject))
     (home-page "https://getting-things-gnome.github.io/liblarch")
     (synopsis "Library to easily handle complex data structures")
     (description
@@ -2817,7 +2818,7 @@ and how they are displayed (View).")
            gtksourceview-4
            pango
            python
-           python-dbus
+           python-dbus-1.2
            python-liblarch
            python-lxml
            python-pycairo
@@ -2985,7 +2986,7 @@ guidelines.")
            python
            cups
            gtk+
-           python-dbus
+           python-dbus-1.2
            python-pygobject
            python-pycups
            python-requests
@@ -4999,7 +5000,6 @@ 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://libsoup.gnome.org")
+    (home-page "https://wiki.gnome.org/Projects/libsoup")
     (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
+           python-dbus-1.2
            python-pygobject-3.50
            vala))
     (propagated-inputs
@@ -8158,6 +8158,12 @@ 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
@@ -8504,78 +8510,67 @@ Evolution (hence the name), but is now used by other packages as well.")
     (license license:lgpl2.0)))
 
 (define-public caribou
-  ;; 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 #$output "/libexec/antler-keyboard")))))))))
-      (native-inputs
-       (list autoconf
-             automake
-             `(,glib "bin") ;for glib-compile-schemas, etc.
-             gobject-introspection
-             gnome-common ;for gnome-autogen.sh
-             intltool
-             libtool
-             libxslt
-             pkg-config
-             python
-             vala
-             which))
-      (propagated-inputs
-       ;; caribou-1.0.pc refers to all these.
-       (list libgee libxklavier libxtst gtk+))
-      (inputs
-       (list bash-minimal ; for wrap-program
-             clutter
-             dconf
-             gtk+-2
-             python-pygobject))
-      (synopsis "Text entry and UI navigation application")
-      (home-page "https://wiki.gnome.org/Projects/Caribou")
-      (description
-       "Caribou is an input assistive technology intended for switch and pointer
+  (package
+    (name "caribou")
+    (version "0.4.21")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "mirror://gnome/sources/" name "/"
+                                  (version-major+minor version) "/"
+                                  name "-" version ".tar.xz"))
+              (sha256
+               (base32
+                "0mfychh1q3dx0b96pjz9a9y112bm9yqyim40yykzxx1hppsdjhww"))))
+    (build-system glib-or-gtk-build-system)
+    (arguments
+     (list
+      #:configure-flags
+      ;; Relax gcc-14's strictness.
+      #~(list "CFLAGS=-g -O2 -Wno-error=incompatible-pointer-types")
+      #:phases
+       #~(modify-phases %standard-phases
+           (add-before
+               'build 'pre-build
+             (lambda _
+               ;; Use absolute shared library path in Caribou-1.0.typelib.
+               (substitute* "libcaribou/Makefile"
+                 (("--shared-library=libcaribou.so")
+                  (string-append "--shared-library="
+                                 #$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
 users.")
-      (license license:lgpl2.1))))
+    (license license:lgpl2.1)))
 
 (define-public network-manager
   (package
@@ -8691,7 +8686,7 @@ users.")
            libxslt
            perl
            pkg-config
-           python-dbus
+           python-dbus-1.2
            python-pygobject-3.50
            python-wrapper
            vala))
@@ -12407,6 +12402,7 @@ advanced image management tool")
            intltool
            pkg-config
            python-psutil
+           python-pytest-runner
            python-pytest))
     (inputs
      (list bash-minimal ;for wrap-program
@@ -12415,7 +12411,7 @@ advanced image management tool")
            gsettings-desktop-schemas
            gtk+
            python-wrapper
-           python-dbus
+           python-dbus-1.2
            python-notify2
            python-pycairo
            python-pygobject
@@ -13700,71 +13696,59 @@ useful to navigate and edit translation messages and comments.")
   (package
     (name "ocrfeeder")
     (version "0.8.5")
-    (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"))))
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "mirror://gnome/sources/ocrfeeder/"
+                                  (version-major+minor version) "/"
+                                  "ocrfeeder-" version ".tar.xz"))
+              (sha256
+               (base32
+                "1vaaphzk6zn7pp2x9scphdzlbsma910wnbhd9xry50nx95cjlgdh"))))
     (build-system gnu-build-system)
     (arguments
-     (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")))))))))
+     `(#: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"))))))))))
     (native-inputs
-     (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))
+     `(("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)))
     (inputs
-     (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))
+     `(("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)))
     (home-page "https://wiki.gnome.org/Apps/OCRFeeder")
     (synopsis "Complete OCR Suite")
     (description "OCRFeeder is a complete Optical Character Recognition and

gnu/packages/gnupg.scm

@@ -82,11 +82,13 @@
   #:use-module (gnu packages xml)
   #:use-module (gnu packages xorg)
   #:use-module (gnu packages)
+  #:use-module (guix build-system cmake)
   #:use-module (guix build-system copy)
   #:use-module (guix build-system gnu)
   #: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)
@@ -434,16 +436,16 @@ libskba (working with X.509 certificates and CMS data).")
                (substitute* "checks/Makefile.in"
                  (("/bin/sh") (which "sh"))))))))))
 
-(define-public gpgme
+(define-public gpgme-2
   (package
     (name "gpgme")
-    (version "1.24.1")
+    (version "2.0.1")
     (source
      (origin
       (method url-fetch)
       (uri (string-append "mirror://gnupg/gpgme/gpgme-" version ".tar.bz2"))
       (sha256
-       (base32 "0px87fbp90xp8vf1wms02flk14zmrqsfr135f5his1kiiqjx01ga"))))
+       (base32 "0rj9g0kablnmj7vh6hfhmmz0qhdhj869i09afm8snbl4bilv06l2"))))
     (build-system gnu-build-system)
     (arguments
      (list
@@ -455,7 +457,7 @@ libskba (working with X.509 certificates and CMS data).")
     (propagated-inputs
      ;; As required by the pkg-config's Requires.private.
      (list libgpg-error libassuan))
-    (home-page "https://www.gnupg.org/related_software/gpgme/")
+    (home-page "https://gnupg.org/software/gpgme/index.html")
     (synopsis "Library providing simplified access to GnuPG functionality")
     (description
      "GnuPG Made Easy (GPGME) is a library designed to make access to GnuPG
@@ -469,57 +471,107 @@ instead.  This way bug fixes or improvements can be done at a central place
 and every application benefits from this.")
     (license license:lgpl2.1+)))
 
+(define-public gpgme-1
+  (package
+    (inherit gpgme-2)
+    (version "1.24.1")
+    (source
+     (origin
+      (method url-fetch)
+      (uri (string-append "mirror://gnupg/gpgme/gpgme-" version ".tar.bz2"))
+      (sha256
+       (base32 "0px87fbp90xp8vf1wms02flk14zmrqsfr135f5his1kiiqjx01ga"))))))
+
+(define-public gpgme gpgme-1)
+
+(define-public gpgmepp
+  (package
+    (name "gpgmepp")
+    (version "2.0.0")
+    (source
+     (origin
+      (method url-fetch)
+      (uri (string-append "mirror://gnupg/gpgmepp/gpgmepp-" version ".tar.xz"))
+      (sha256
+       (base32 "10jkaqzjr5gy04bmcw75q6iy2isk17plixwn61ps4237q14n0yfl"))))
+    (build-system cmake-build-system)
+    (arguments
+     (list
+      ;; FIXME: BUILD_TESTING variable is enabled by deault, but still no tests
+      ;; are found.
+      #:tests? #f))
+    (propagated-inputs
+     ;; As required by the pkg-config's Requires.private.
+     (list gpgme-2 libgpg-error))
+    (home-page "https://gnupg.org/software/gpgme/index.html")
+    (synopsis "C++ bindings/wrapper for GPGME")
+    (description
+     "GPGME++ is a C++ wrapper (or C++ bindings) for the GnuPG project's
+@acronym{GPGME, GnuPG Made Easy} library.")
+    (license license:lgpl2.1+)))
+
 (define-public qgpgme-qt5
   (package
-    (inherit gpgme)
     (name "qgpgme-qt5")
+    (version "2.0.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "mirror://gnupg/qgpgme/qgpgme-" version ".tar.xz"))
+       (sha256
+        (base32 "1bb198dk49bd7yx4cf4w07acjhllilx1nczdna7139ncflj5nr0m"))))
+    (build-system qt-build-system)
     (arguments
-     `(#:phases
-       (modify-phases %standard-phases
-         (add-before 'build 'chdir-and-symlink
-           (lambda* (#:key inputs #:allow-other-keys)
-             (let ((gpgme (assoc-ref inputs "gpgme")))
-               (symlink (string-append gpgme "/lib/libgpgmepp.la")
-                        "lang/cpp/src/libgpgmepp.la")
-               (symlink (string-append gpgme "/lib/libgpgme.la")
-                        "src/libgpgme.la"))
-             (chdir "lang/qt"))))))
-    (propagated-inputs (list gpgme))    ;required by QGpgmeConfig.cmake
+     (list
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-before 'check 'check-setup
+            (lambda _
+              (setenv "HOME" (getcwd))
+              (invoke "gpg-agent" "--daemon"))))))
+    (propagated-inputs
+     (list gpgme-2        ;for FindGpgme.cmake and QGpgmeQt6Config.cmake
+           gpgmepp        ;for QGpgmeQt6Config.cmake
+           libgpg-error)) ;for FindLibGpgError.cmake and QGpgmeQt6Config.cmake
     (native-inputs
-     (modify-inputs native-inputs
-       (prepend pkg-config)))
-    (inputs
-     (modify-inputs inputs
-       (prepend qtbase-5)))
+     (list gnupg        ;for tests
+           pkg-config))
+    (home-page "https://gnupg.org/software/gpgme/index.html")
     (synopsis "Qt API bindings for gpgme")
     (description "QGpgme provides a very high level Qt API around GpgMEpp.
 
 QGpgME was originally developed as part of libkleo and incorporated into
 gpgpme starting with version 1.7.")
-    (license license:gpl2+))) ;; Note: this differs from gpgme
+    (license license:gpl2+)))
 
 (define-public qgpgme
   (package
-    (inherit gpgme)
     (name "qgpgme")
+    (version "2.0.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "mirror://gnupg/qgpgme/qgpgme-" version ".tar.xz"))
+       (sha256
+        (base32 "1bb198dk49bd7yx4cf4w07acjhllilx1nczdna7139ncflj5nr0m"))))
+    (build-system qt-build-system)
     (arguments
-     `(#:phases
-       (modify-phases %standard-phases
-         (add-before 'build 'chdir-and-symlink
-           (lambda* (#:key inputs #:allow-other-keys)
-             (let ((gpgme (assoc-ref inputs "gpgme")))
-               (symlink (string-append gpgme "/lib/libgpgmepp.la")
-                        "lang/cpp/src/libgpgmepp.la")
-               (symlink (string-append gpgme "/lib/libgpgme.la")
-                        "src/libgpgme.la"))
-             (chdir "lang/qt"))))))
-    (propagated-inputs (list gpgme))    ;required by QGpgmeConfig.cmake
+     (list
+      #:qtbase qtbase
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-before 'check 'check-setup
+            (lambda _
+              (setenv "HOME" (getcwd))
+              (invoke "gpg-agent" "--daemon"))))))
+    (propagated-inputs
+     (list gpgme-2        ;for FindGpgme.cmake and QGpgmeQt6Config.cmake
+           gpgmepp        ;for QGpgmeQt6Config.cmake
+           libgpg-error)) ;for FindLibGpgError.cmake and QGpgmeQt6Config.cmake
     (native-inputs
-     (modify-inputs native-inputs
-       (prepend pkg-config)))
-    (inputs
-     (modify-inputs inputs
-       (prepend qtbase)))
+     (list gnupg        ;for tests
+           pkg-config))
+    (home-page "https://gnupg.org/software/gpgme/index.html")
     (synopsis "Qt API bindings for gpgme")
     (description "QGpgme provides a very high level Qt API around GpgMEpp.")
     (license license:gpl2+)))
@@ -583,21 +635,20 @@ interface (FFI) of Guile.")
 (define-public python-gpg
   (package
     (name "python-gpg")
-    (version "1.10.0")
+    (version "2.0.0")
     (source (origin
               (method url-fetch)
               (uri (pypi-uri "gpg" version))
-              (patches (search-patches "python-gpg-setup-72.patch"))
               (sha256
                (base32
-                "1ji3ynhp36m1ccx7bmaq75dhij9frpn19v9mpi4aajn8csl194il"))))
+                "0f2l0iyc8gp49i604c5wpliaa1dsyj0i0p9xc9zfj4z7fwaavdsf"))))
     (build-system pyproject-build-system)
     (arguments
      (list
       #:tests? #f ; No test suite.
       #:phases
       #~(modify-phases %standard-phases
-          (add-before 'build 'set-environment
+          (add-before 'build 'patch-setup.py
             (lambda _
               ;; GPGME is built with large file support, so we need to set
               ;; _FILE_OFFSET_BITS to 64 in all users of the GPGME library.
@@ -607,9 +658,16 @@ interface (FFI) of Guile.")
                            "extra_macros = { \"_FILE_OFFSET_BITS\": 64 }")))
                      #~())
               (substitute* "setup.py"
-                (("cc") (which "gcc"))))))))
+                (("cc") (which "gcc"))
+                (("\\/usr\\/lib\\/x86_64-linux-gnu( -lgpg-error)" _ keep)
+                 (string-append #$(this-package-input "libgpg-error") "/lib"
+                                keep))
+                (("\\/usr\\/lib\\/x86_64-linux-gnu( -lgpgme)" _ keep)
+                 (string-append #$(this-package-input "gpgme") "/lib" keep))
+                (("\\/usr\\/local(', 'include', 'gpgme\\.h')" _ keep)
+                 (string-append #$(this-package-input "gpgme") keep))))))))
     (inputs
-     (list gpgme))
+     (list gpgme-2 libgpg-error))
     (native-inputs
      (list swig-4.0 python-setuptools))
     (home-page (package-home-page gpgme))

gnu/packages/golang-graphics.scm

@@ -1,251 +0,0 @@
-;;; 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)))

gnu/packages/golang-xyz.scm

@@ -77,7 +77,6 @@
 ;;; 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.
 ;;;
@@ -1789,32 +1788,6 @@ 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")
@@ -4072,6 +4045,38 @@ 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")
@@ -15778,67 +15783,6 @@ 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"))
@@ -16197,32 +16141,6 @@ 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")
@@ -30956,33 +30874,6 @@ 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"))

gnu/packages/gpodder.scm

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

gnu/packages/graph.scm

@@ -36,6 +36,7 @@
   #:use-module (guix build-system cmake)
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system pyproject)
+  #:use-module (guix build-system python)
   #:use-module (guix build-system r)
   #:use-module (guix download)
   #:use-module (guix gexp)
@@ -666,7 +667,7 @@ contains supporting code for evaluation and parameter tuning.")
                                                 (not (member file ignored))))))))
                     (format #t "test suite not run~%"))))))))
     (native-inputs
-     (list python-scipy python-setuptools))
+     (list python-scipy))
     (inputs
      (list faiss openblas python-wrapper swig-4.0))
     (propagated-inputs

gnu/packages/graphics.scm

@@ -43,7 +43,6 @@
 ;;; 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.
 ;;;
@@ -147,6 +146,7 @@
   #:use-module (guix build-system cmake)
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system meson)
+  #:use-module (guix build-system python)
   #:use-module (guix build-system pyproject)
   #:use-module (guix build-system qt)
   #:use-module (guix download)
@@ -700,40 +700,17 @@ 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 "4.5.10")                   ;5.1.x+ requires Python >= 3.13
+    (version "3.6.23")                   ;4.2.x+ requires Python >= 3.12
     (source (origin
               (method url-fetch)
               (uri (string-append "https://download.blender.org/source/"
                                   "blender-" version ".tar.xz"))
               (sha256
                (base32
-                "1z4sq4rmg5lx0502i2kgalmdyw3a4kc3lw70kwnwkih5wkjnrbyx"))))
+                "16ah70kqznxz60n39d4hnlnwh1vi7xn9kx37di708n03l5bn6mmw"))))
     (build-system cmake-build-system)
     (arguments
      (list
@@ -760,50 +737,37 @@ typically encountered in feature film production.")
                 "-DWITH_SYSTEM_GLOG=ON"
                 "-DWITH_SYSTEM_LZO=ON"
                 (string-append "-DPYTHON_LIBRARY=python" #$python-version)
-                (string-append "-DPYTHON_LIBPATH=" #$python "/lib")
-                (string-append "-DPYTHON_INCLUDE_DIR=" #$python
+                (string-append "-DPYTHON_LIBPATH="
+                               (assoc-ref %build-inputs "python")
+                               "/lib")
+                (string-append "-DPYTHON_INCLUDE_DIR="
+                               (assoc-ref %build-inputs "python")
                                "/include/python" #$python-version)
                 (string-append "-DPYTHON_VERSION=" #$python-version)
                 (string-append "-DPYTHON_NUMPY_INCLUDE_DIRS="
-                               #$(this-package-input "python-numpy")
+                               (assoc-ref %build-inputs "python-numpy")
                                "/lib/python" #$python-version
                                "/site-packages/numpy/core/include/")
                 (string-append "-DPYTHON_NUMPY_PATH="
-                               #$(this-package-input "python-numpy")
+                               (assoc-ref %build-inputs "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 #$(this-package-input "python")
-                         blender-python-dir))))
           (add-after 'install 'wrap-bin
-            (lambda _
-              (let ((python-path (getenv "GUIX_PYTHONPATH")))
-                (when python-path
-                  (wrap-program (string-append #$output "/bin/blender")
-                    `("GUIX_PYTHONPATH" ":" prefix (,python-path))))))))))
-    (native-inputs
-     (list pkg-config))
+            (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)))))))))
     (inputs
      (list bash-minimal
-           blender-assets
            boost
            bullet
            eigen
            embree
            ffmpeg-6
            fftw
-           fftwf
            freetype-with-brotli
            glew
            glog
@@ -831,9 +795,6 @@ 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/")
@@ -1251,7 +1212,7 @@ quaternions and other useful 2D and 3D math functions.  Iex is an
 exception-handling library.")
     (license license:bsd-3)))
 
-(define-public lib2geom/pinned
+(define-public lib2geom
   (package
     (name "lib2geom")
     (version "1.3")
@@ -1329,25 +1290,52 @@ 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+)
-    (properties '((hidden? . #t)))))
+    (license license:gpl3+)))
 
-(define-public lib2geom
+(define-public python-booleanoperations
   (package
-    (inherit lib2geom/pinned)
-    (name "lib2geom")
-    (version "1.4")
+    (name "python-booleanoperations")
+    (version "0.9.0")
     (source
      (origin
-       (inherit (package-source lib2geom/pinned))
        (method git-fetch)
        (uri (git-reference
-              (url "https://gitlab.com/inkscape/lib2geom")
+              (url "https://github.com/typemytype/booleanOperations")
               (commit version)))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "0gfgzwm5s50caj5s6l7irgmlifpmypd0fnm6ckzli1fdziwjgdwi"))))
-    (properties '((hidden? . #f)))))
+        (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 "))))
+    (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)))
 
 (define-public pstoedit
   (package

gnu/packages/graphviz.scm

@@ -35,6 +35,7 @@
   #: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)
@@ -151,46 +152,32 @@ interfaces for other technical domains.")
 (define-public python-graphviz
   (package
     (name "python-graphviz")
-    (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"))))
+    (version "0.20.3")
+    (source (origin
+              (method url-fetch)
+              (uri (pypi-uri "graphviz" version ".zip"))
+              (sha256
+               (base32
+                "0pcjnnhprs1hb4r9jr7r4qjxc7lzsjlka8d5gcp3kym9ws0vrmh9"))))
     (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* "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
+              (substitute* "setup.cfg"
+                ((".*doctest.*") "")
+                (("--cov.*") ""))))
+          (replace 'check
+            (lambda* (#:key tests? test-flags #:allow-other-keys)
               (when tests?
-                (invoke "pytest" "-v" "tests/backend/")))))))
+                (setenv "HOME" "/tmp")
+                  (apply invoke "python" "run-tests.py" test-flags)))))))
     (native-inputs
-     (list graphviz
+     (list unzip
+           ;; For tests.
+           graphviz
            python-mock
            python-pytest
            python-pytest-mock
@@ -259,6 +246,7 @@ layout algorithms.")
      (list graphviz
            python-defusedxml
            python-pytest
+           python-pytest-cov
            python-setuptools
            python-typing-extensions))
     (propagated-inputs

gnu/packages/gtk.scm

@@ -71,6 +71,7 @@
   #: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)
@@ -1119,7 +1120,7 @@ application suites.")
 (define-public gtk
   (package
     (name "gtk")
-    (version "4.22.1")
+    (version "4.20.3")
     (source
      (origin
        (method url-fetch)
@@ -1127,11 +1128,9 @@ application suites.")
                            (version-major+minor version)  "/"
                            name "-" version ".tar.xz"))
        (sha256
-        (base32 "1z2mkmazc2d51jbg3qwwdycycqiwswm88nhw6bxscz8j86f5lyyd"))
+        (base32 "0ly1gqc6ybxv5f2a9hvjp5k6l9mfzy2yv8iy2xqnr9l8628g4wr8"))
        (patches
-        (search-patches "gtk4-demo-reproducible.patch"
-                        "gtk4-needs-udmabuf.patch"
-                        "gtk4-respect-GUIX_GTK4_PATH.patch"))
+        (search-patches "gtk4-respect-GUIX_GTK4_PATH.patch"))
        (modules '((guix build utils)))))
     (build-system meson-build-system)
     (outputs '("out" "bin" "doc"))
@@ -1255,10 +1254,8 @@ application suites.")
               (setenv "XDG_CACHE_HOME" (getcwd))))
           (add-before 'check 'pre-check
             (lambda* (#:key inputs #:allow-other-keys)
-              ;; 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 &")
+              ;; Tests require a running X server.
+              (system "Xvfb :1 +extension GLX &")
               (setenv "DISPLAY" ":1")
               ;; Tests write to $HOME.
               (setenv "HOME" (getcwd))
@@ -1301,7 +1298,6 @@ 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
@@ -1369,8 +1365,8 @@ 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")
@@ -2807,7 +2803,7 @@ to rename these directories if the locale changes.")
 (define-public goocanvas
   (package
     (name "goocanvas")
-    (version "3.0.0")
+    (version "2.0.4")
     (source
      (origin
        (method url-fetch)
@@ -2815,7 +2811,7 @@ to rename these directories if the locale changes.")
                            (version-major+minor version)
                            "/goocanvas-" version ".tar.xz"))
        (sha256
-        (base32 "06j05g2lmwvklmv51xsb7gm7rszcarhm01sal41jfp0qzrbpa2k7"))))
+        (base32 "141fm7mbqib0011zmkv3g8vxcjwa7hypmq71ahdyhnj2sjvy4a67"))))
     (build-system gnu-build-system)
     (native-inputs
      (list gettext-minimal

gnu/packages/guile-xyz.scm

@@ -155,7 +155,6 @@
   #: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)
@@ -2934,7 +2933,7 @@ user which package sets would they like to install from it.")
 (define-public guile-wisp
   (package
     (name "guile-wisp")
-    (version "1.0.13")
+    (version "1.0.12")
     (source (origin
               (method hg-fetch)
               (uri (hg-reference
@@ -2943,7 +2942,7 @@ user which package sets would they like to install from it.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "0fb4l0ww4rnkrsh4x46301j5xrqniny9b7yh7i6lp4wprwx0a7fs"))))
+                "0m5ssl4ngk2jl1zk0fnsss0asyvwanjaa5rrcksldqnh2ikcr4bm"))))
     (build-system gnu-build-system)
     (arguments
      `(#:modules ((guix build gnu-build-system)
@@ -2952,7 +2951,9 @@ user which package sets would they like to install from it.")
                   (guix build emacs-utils)
                   (ice-9 rdelim)
                   (ice-9 popen))
-       #:imported-modules ,%emacs-build-system-modules
+       #:imported-modules (,@%default-gnu-imported-modules
+                           (guix build emacs-build-system)
+                           (guix build emacs-utils))
        #:phases
        (modify-phases %standard-phases
          (replace 'bootstrap
@@ -2996,11 +2997,11 @@ user which package sets would they like to install from it.")
     (inputs
      (list guile-3.0))
     (native-inputs
-     (list autoconf
-           automake
-           emacs-minimal
-           pkg-config
-           python))
+     `(("autoconf" ,autoconf)
+       ("automake" ,automake)
+       ("emacs" ,emacs-minimal)
+       ("python" ,python)
+       ("pkg-config" ,pkg-config)))
     (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
@@ -7813,8 +7814,8 @@ is an attempt to combine both into something useful.")
       (license license:asl2.0))))
 
 (define-public guile-knots
-  (let ((commit "d1cecc06fb96a193bb4bdbef159e4c3a83895436")
-        (revision "36"))
+  (let ((commit "49996c432a4616e03ecaf01cb42afc5fd78eafd5")
+        (revision "35"))
     (package
     (name "guile-knots")
     (version (git-version "0.1" revision commit))
@@ -7825,7 +7826,7 @@ is an attempt to combine both into something useful.")
                     (commit commit)))
               (sha256
                (base32
-                "1ssgkbnxfjvnvyrmyva40yywi5dybyqds1q9v9i674d6i435zlbl"))
+                "0i6vk432shy7qmsq1hli71a9kmgf8yy9hx3bck0r9qzsldv1m3m9"))
               (file-name (git-file-name name version))))
     (build-system gnu-build-system)
     (arguments

gnu/packages/hardware.scm

@@ -119,6 +119,7 @@
   #:use-module (guix build-system meson)
   #:use-module (guix build-system perl)
   #:use-module (guix build-system pyproject)
+  #:use-module (guix build-system python)
   #:use-module (guix build-system qt)
   #:use-module (guix download)
   #:use-module (guix gexp)

gnu/packages/ibus.scm

@@ -43,6 +43,7 @@
   #: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)

gnu/packages/image-processing.scm

@@ -58,6 +58,7 @@
   #:use-module (guix build-system cmake)
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system meson)
+  #:use-module (guix build-system python)
   #:use-module (guix build-system pyproject)
   #:use-module (gnu packages)
   #:use-module (gnu packages algebra)

gnu/packages/image-viewers.scm

@@ -67,6 +67,7 @@
   #:use-module (guix build-system copy)
   #:use-module (guix build-system go)
   #: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 (gnu packages autotools)
@@ -742,7 +743,7 @@ For PDF support, install the @emph{mupdf} package.")
 (define-public qpageview
   (package
     (name "qpageview")
-    (version "1.0.4")
+    (version "1.0.1")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -751,10 +752,8 @@ For PDF support, install the @emph{mupdf} package.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "1g1lslc3aljhcl4nbwd81clmzbdl89n6dkaxn7nizc8f4v2iiaiy"))))
+                "0h3b7qhmjk1bz7ws7jwa9012wh2yvmk45j21ciyzj28mcjx9ygz4"))))
     (build-system pyproject-build-system)
-    (arguments
-     (list #:tests? #f))                ;no tests in repository.
     (home-page "https://qpageview.org/")
     (synopsis "Page based document viewer widget for Qt/PyQt")
     (inputs

gnu/packages/image.scm

@@ -29,7 +29,7 @@
 ;;; Copyright © 2020, 2025 Janneke Nieuwenhuizen <janneke@gnu.org>
 ;;; Copyright © 2020 Zhu Zihao <all_but_last@163.com>
 ;;; Copyright © 2020, 2021, 2022, 2023, 2024 Vinicius Monego <monego@posteo.net>
-;;; Copyright © 2021, 2026 Sharlatan Hellseher <sharlatanus@gmail.com>
+;;; Copyright © 2021 Sharlatan Hellseher <sharlatanus@gmail.com>
 ;;; Copyright © 2021 Nicolò Balzarotti <nicolo@nixo.xyz>
 ;;; Copyright © 2021 Alexandr Vityazev <avityazev@posteo.org>
 ;;; Copyright © 2022 Jai Vetrivelan <jaivetrivelan@gmail.com>
@@ -42,9 +42,8 @@
 ;;; Copyright © 2025 Josep Bigorra <jjbigorra@gmail.com>
 ;;; Copyright © 2025 Jake Forster <jakecameron.forster@gmail.com>
 ;;; Copyright © 2025 Ghislain Vaillant <ghislain.vaillant@inria.fr>
-;;; Copyright © 2025 Junker <dk@junkeria.club>
-;;; Copyright © 2025 Hugo Buddelmeijer <hugo@buddelmeijer.nl>
 ;;; Copyright © 2026 Carlos Durán Domínguez <wurt@wurt.eu>
+;;; Copyright © 2025 Junker <dk@junkeria.club>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -130,6 +129,7 @@
   #:use-module (guix build-system guile)
   #: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 scons)
   #:use-module (guix deprecation)
@@ -3044,89 +3044,77 @@ GIF, TIFF, WEBP, BMP, PNG, XPM formats.")
 (define-public mypaint
   (package
     (name "mypaint")
-    ;; The latest changes contains support for Python 3.12+.
-    (properties '((commit . "35aa9d33cd3deba6cafea6d8fc901b5a1d161ceb")
-                  (revision . "0")))
-    (version (git-version "2.0.1"
-                          (assoc-ref properties 'revision)
-                          (assoc-ref properties 'commit)))
-    (source
-     (origin
-       (method git-fetch)
-       (uri (git-reference
-              (url "https://github.com/mypaint/mypaint")
-              (commit (assoc-ref properties 'commit))))
-       (file-name (git-file-name name version))
-       (sha256
-        (base32 "1p1i799dzpx0zr7chkz0pjdq9l32ahckgyagbiw82c27mwxqabfh"))))
-    (build-system pyproject-build-system)
+    (version "2.0.1")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "https://github.com/mypaint/mypaint/"
+                                  "releases/download/v" version "/mypaint-"
+                                  version ".tar.xz"))
+              (sha256
+               (base32
+                "05mvay73vb9d2sh1ckv4vny45n059dmsps1jcppjizfmrpbkgr7k"))))
+    (build-system python-build-system)
     (arguments
-     (list
-      #:imported-modules `(,@%pyproject-build-system-modules
-                           (guix build glib-or-gtk-build-system))
-      #:modules '((guix build pyproject-build-system)
+     `(#:imported-modules ((guix build glib-or-gtk-build-system)
+                           ,@%python-build-system-modules)
+       #:modules ((guix build python-build-system)
                   ((guix build glib-or-gtk-build-system) #:prefix glib-or-gtk:)
                   (guix build utils))
-      #:phases
-      #~(modify-phases %standard-phases
-          (add-after 'install 'move-assets-to-data
-            ;; XXX: Check why.
-            ;;
-            ;; ERROR: gui.application: Missing icon 'org.mypaint.MyPaint':
-            ;; check that mypaint icons have been installed into
-            ;; /gnu/store/<...>/data/icons
-            ;;
-            ;; gi.repository.GLib.GError: g-file-error-quark: Failed to open
-            ;; file
-            ;; “/gnu/store/<...>/data/mypaint/pixmaps/cursor_color_picker.png”:
-            ;; No such file or directory (4)
-            (lambda _
-              (let* ((data (string-append #$output "/data"))
-                     (data-icons (string-append data "/icons"))
-                     (data-mypaint (string-append data "/mypaint"))
-                     (icons (string-append #$output "/icons"))
-                     (mypaint (string-append #$output "/mypaint")))
-                (mkdir-p data-icons)
-                (mkdir-p data-mypaint)
-                (copy-recursively icons data-icons)
-                (copy-recursively mypaint data-mypaint)
-                (delete-file-recursively icons)
-                (delete-file-recursively mypaint))))
-          (add-after 'install 'glib-or-gtk-wrap
-            (assoc-ref glib-or-gtk:%standard-phases 'glib-or-gtk-wrap))
-          (add-after 'install 'wrap-program
-            (lambda* (#:key outputs inputs #:allow-other-keys)
-              (wrap-program (string-append #$output "/bin/mypaint")
-                `("GI_TYPELIB_PATH" ":" prefix
-                  (,(getenv "GI_TYPELIB_PATH"))))))
-          (add-before 'check 'pre-check
-            (lambda _
-              ;; Need to get the 'lib' in 'build/'.
-              (delete-file-recursively "lib")
-              ;; Tests need writing access
-              (setenv "HOME" "/tmp"))))))
+       ;; XXX: Tests are not discovered.
+       #:tests? #false
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'python3.11-compatibility
+           (lambda _
+             (substitute* "setup.py"
+               (("\"rU\"") "\"r\"")
+               (("test_suite='tests'.*") ""))
+             (substitute* "setup.cfg"
+               (("install-") "install_"))
+             ;; This file makes Python confuse it for a module, so we rename
+             ;; it.
+             (rename-file "lib/xml.py" "lib/xmlo.py")
+             (substitute* (find-files "." "\\.py$")
+               (("lib.xml") "lib.xmlo"))
+             ;; This procedure has been removed.
+             (substitute* "lib/gettext_setup.py"
+               (("c = gettext.bind_textdomain_codeset.*") "c = True\n"))))
+         (add-after 'install 'glib-or-gtk-wrap
+           (assoc-ref glib-or-gtk:%standard-phases 'glib-or-gtk-wrap))
+         (add-after 'install 'wrap-program
+           (lambda* (#:key outputs inputs #:allow-other-keys)
+             (let* ((out (assoc-ref outputs "out"))
+                    (gdk-pixbuf (assoc-ref inputs "gdk-pixbuf"))
+                    (gtk+ (assoc-ref inputs "gtk+")))
+               ;; This is replaced with an invalid shebang.
+               (substitute* (string-append out "/bin/mypaint")
+                 (("#!python")
+                  (string-append "#!" (which "python3"))))
+               (wrap-program (string-append out "/bin/mypaint")
+                 `("GI_TYPELIB_PATH" ":" prefix
+                   (,(getenv "GI_TYPELIB_PATH")))))))
+         (add-before 'check 'pre-check
+           (lambda _
+             ;; Tests need writing access
+             (setenv "HOME" "/tmp"))))))
     (native-inputs
-     (list gettext-minimal
+     (list pkg-config
            gobject-introspection
-           pkg-config
-           python-pytest
-           python-setuptools
-           swig))
+           swig-4.0
+           gettext-minimal))
     (inputs
      (list bash-minimal
-           gdk-pixbuf
            gtk+
+           (librsvg-for-system)
            hicolor-icon-theme
+           libmypaint
+           mypaint-brushes
            json-c
            lcms
-           libmypaint-next
-           libpng
-           (librsvg-for-system)
-           mypaint-brushes
            python-numpy
            python-pycairo
            python-pygobject))
-    (home-page "https://mypaint.org/")
+    (home-page "http://mypaint.org/")
     (synopsis "Fast and simple painting app for artists")
     (description
      "MyPaint is a simple drawing and painting program that works well with

gnu/packages/inkscape.scm

@@ -296,7 +296,7 @@ endif()~%~%"
             gtk+
             gtkmm-3
             lcms
-            lib2geom/pinned
+            lib2geom
             libcdr
             libgc
             libjpeg-turbo
@@ -342,12 +342,12 @@ as the native format.")
 
 ;;; The Inkscape release year used in the about dialog.  Please keep it sync
 ;;; when updating the package!
-(define %inkscape-release-year 2025)
+(define %inkscape-release-year 2023)
 (define-public inkscape
   (package
     (inherit inkscape/pinned)
     (name "inkscape")
-    (version "1.4.3")
+    (version "1.3.2")
     (source
      (origin
        (inherit (package-source inkscape/pinned))
@@ -355,9 +355,8 @@ as the native format.")
        (uri (string-append "https://media.inkscape.org/dl/"
                            "resources/file/"
                            "inkscape-" version ".tar.xz"))
-       (patches '())
        (sha256
-        (base32 "1lfi1rqr32kwjdkka4sbsxmkyyw3k1qgxk0gzyhwbdkhnlyjqfp8"))))
+        (base32 "0sq81smxwypgnp7r3wgza8w25dsz9qa8ga79sc85xzj3qi6q9lfv"))))
     (build-system cmake-build-system)
     (arguments
      (substitute-keyword-arguments (package-arguments inkscape/pinned)
@@ -390,9 +389,7 @@ as the native format.")
                   `("GDK_PIXBUF_MODULE_FILE" =
                     (,(getenv "GDK_PIXBUF_MODULE_FILE"))))))))))
     (inputs (modify-inputs (package-inputs inkscape/pinned)
-              (replace "lib2geom" lib2geom)
-              (append imagemagick       ;for libMagickCore and libMagickWand
-                      python-tinycss2)))
+              (append imagemagick)))    ;for libMagickCore and libMagickWand
     (native-inputs
      (modify-inputs (package-native-inputs inkscape/pinned)
                     ;; Only use 1 imagemagick across the package build.

gnu/packages/installers.scm

@@ -18,14 +18,13 @@
 ;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
 
 (define-module (gnu packages installers)
+  #:use-module ((guix licenses) #:prefix license:)
   #:use-module (gnu packages)
   #:use-module (gnu packages build-tools)
   #:use-module (gnu packages compression)
   #:use-module (gnu packages cross-base)
-  #:use-module (guix download)
-  #:use-module (guix gexp)
-  #:use-module ((guix licenses) #:prefix license:)
   #:use-module (guix packages)
+  #:use-module (guix download)
   #:use-module (guix build-system scons)
   #:use-module (guix utils))
 
@@ -51,75 +50,65 @@
                        ("mingw-w64" ,xlibc)))
       (inputs (list zlib))
       (arguments
-       (list
-        #:modules `((srfi srfi-1)
+       `(#:scons ,scons-3
+         #:modules ((srfi srfi-1)
                     (srfi srfi-26)
                     (guix build utils)
                     (guix build scons-build-system))
-        #:tests? #f
-        #:scons-flags
-        #~(list "UNICODE=yes"
-                "SKIPUTILS=MakeLangId,Makensisw,NSIS Menu,SubStart,zip2exe"
-                "SKIPDOC=COPYING"
-                "STRIP_CP=no"
-                (string-append "PREFIX=" #$output)
-                (string-append "TARGET_ARCH=" #$target-arch)
-                (string-append "XGCC_W32_PREFIX=" #$triplet "-")
-                (string-append "PREFIX_PLUGINAPI_INC="
-                               (assoc-ref %build-inputs "mingw-w64")
-                               "/include/")
-                (string-append "PREFIX_PLUGINAPI_LIB="
-                               (assoc-ref %build-inputs "mingw-w64")
-                               "/lib/"))
-        #:build-targets #~(list "makensis" "stubs" "plugins" "utils")
-        #:install-targets
-        #~(list "install-stubs"
-                "install-plugins"
-                "install-data"
-                "install-utils"
-                "install-compiler"
-                "install-conf")
-        #:phases
-        #~(modify-phases %standard-phases
-            (add-before 'build 'fix-env
-              (lambda _
-                (define* (filter-delimited-string delimited-string predicate
-                                                  #:optional (delimiter #\:))
-                  ;; Given a DELIMITED-STRING delimited by DELIMITER,
-                  ;; only keep items that satisfy PREDICATE
-                  (string-join
-                   (filter predicate (string-split delimited-string delimiter))
-                   (string delimiter)))
-                (define (mingw-path? path)
-                  (string-prefix? (assoc-ref %build-inputs "mingw-w64") path))
-                (define (xgcc-path? path)
-                  (string-prefix? (assoc-ref %build-inputs "xgcc") path))
-                (define (cross-toolchain-path? path)
-                  (or (xgcc-path? path) (mingw-path? path)))
+         #:tests? #f
+         #:scons-flags `("UNICODE=yes"
+                         "SKIPUTILS=MakeLangId,Makensisw,NSIS Menu,SubStart,zip2exe"
+                         "SKIPDOC=COPYING"
+                         "STRIP_CP=no"
+                         ,(string-append "PREFIX=" %output)
+                         ,(string-append "TARGET_ARCH=" ,target-arch)
+                         ,(string-append "XGCC_W32_PREFIX=" ,triplet "-")
+                         ,(string-append "PREFIX_PLUGINAPI_INC=" (assoc-ref %build-inputs "mingw-w64") "/include/")
+                         ,(string-append "PREFIX_PLUGINAPI_LIB=" (assoc-ref %build-inputs "mingw-w64") "/lib/"))
+         #:build-targets '("makensis"
+                           "stubs"
+                           "plugins"
+                           "utils")
+         #:install-targets '("install-stubs"
+                             "install-plugins"
+                             "install-data"
+                             "install-utils"
+                             "install-compiler"
+                             "install-conf")
+         #:phases (modify-phases %standard-phases
+                    (add-before 'build 'fix-env
+                      (lambda _
+                        (define* (filter-delimited-string delimited-string predicate #:optional (delimiter #\:))
+                          ;; Given a DELIMITED-STRING delimited by DELIMITER,
+                          ;; only keep items that satisfy PREDICATE
+                          (string-join
+                           (filter predicate (string-split delimited-string delimiter))
+                           (string delimiter)))
+                        (define (mingw-path? path)
+                          (string-prefix? (assoc-ref %build-inputs "mingw-w64") path))
+                        (define (xgcc-path? path)
+                          (string-prefix? (assoc-ref %build-inputs "xgcc") path))
+                        (define (cross-toolchain-path? path)
+                          (or (xgcc-path? path) (mingw-path? path)))
 
-                (for-each
-                 (lambda (env-name)
-                   (let ((env-val (getenv env-name)))
-                     ;; Remove all mingw-w64 and xgcc paths from env vars meant
-                     ;; for native toolchain
-                     (setenv env-name
-                             (filter-delimited-string
-                              env-val (negate cross-toolchain-path?)))
-                     ;; Add the removed paths back into CROSS_-prefixed
-                     ;; version of env vars
-                     (setenv (string-append "CROSS_" env-name)
-                             (filter-delimited-string
-                              env-val cross-toolchain-path?))))
-                          '("C_INCLUDE_PATH"
-                            "CPLUS_INCLUDE_PATH"
-                            "LIBRARY_PATH"))))
-            (add-before 'build 'fix-target-detection
-              (lambda _
-                ;; NSIS target detection is screwed up, manually change
-                ;; it ourselves
-                (substitute* "Source/build.cpp"
-                  (("m_target_type=TARGET_X86UNICODE")
-                   (string-append "m_target_type=" #$nsis-target-type))))))))
+                        (for-each
+                         (lambda (env-name)
+                           (let ((env-val (getenv env-name)))
+                             ;; Remove all mingw-w64 and xgcc paths from env vars meant
+                             ;; for native toolchain
+                             (setenv env-name
+                                     (filter-delimited-string env-val (negate cross-toolchain-path?)))
+                             ;; Add the removed paths back into CROSS_-prefixed
+                             ;; version of env vars
+                             (setenv (string-append "CROSS_" env-name)
+                                     (filter-delimited-string env-val cross-toolchain-path?))))
+                         '("C_INCLUDE_PATH" "CPLUS_INCLUDE_PATH" "LIBRARY_PATH"))))
+                    (add-before 'build 'fix-target-detection
+                      (lambda _
+                        ;; NSIS target detection is screwed up, manually change
+                        ;; it ourselves
+                        (substitute* "Source/build.cpp" (("m_target_type=TARGET_X86UNICODE")
+                                                         (string-append "m_target_type=" ,nsis-target-type))))))))
       (home-page "https://nsis.sourceforge.io/Main_Page")
       (synopsis "System to create Windows installers")
       (description

gnu/packages/instrumentation.scm

@@ -63,6 +63,7 @@
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system linux-module)
   #: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)
@@ -108,7 +109,6 @@
            flex
            pkg-config
            python-3
-           python-setuptools
            python-sphinx
            swig-4.0
            xmltoman))
@@ -489,7 +489,7 @@ ftrace.")
 (define-public systemtap
   (package
     (name "systemtap")
-    (version "5.4")
+    (version "4.9")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -497,9 +497,20 @@ ftrace.")
                     version ".tar.gz"))
               (sha256
                (base32
-                "0vibrp5chf3q0n7byg6bdv3bl6z4354dqavhywjv0xbpf5rk5yfa"))))
+                "161smpv4ajqfncmgylvs89bbix1id60nf0g7clmga2lxxax3646h"))))
     (build-system gnu-build-system)
-    (native-inputs (list boost cpio python python-setuptools))
+    (arguments
+     (list
+      #:configure-flags
+      #~(list "CXXFLAGS=-g -O2 -Wno-error=calloc-transposed-args"
+              "CFLAGS=-g -O2 -Wno-error=calloc-transposed-args")
+      #:phases #~(modify-phases %standard-phases
+                   (add-after 'unpack 'patch-source
+                     (lambda _
+                         (substitute* "language-server/jsonrpc.h"
+                           (("#include <unistd.h>")
+                            "#include <unistd.h>\n#include<stdint.h>")))))))
+    (native-inputs (list cpio python))
     (inputs (list elfutils))
 
     (home-page "https://sourceware.org/systemtap/")

gnu/packages/irc.scm

@@ -48,6 +48,7 @@
   #:use-module (guix build-system guile)
   #:use-module (guix build-system haskell)
   #: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 (gnu packages)

gnu/packages/iso-codes.scm

@@ -231,6 +231,8 @@ concerned with representation of names for languages and language groups.")
           (add-after 'unpack 'fix-pytest-config
             (lambda _  ; Removes the need for python-pytest-cov.
               (substitute* "pyproject.toml"
+                (("--cov --cov-report=html --cov-report=term-missing")
+                 "")
                 (("^required_plugins =.*")
                  "")))))))
     (native-inputs (list python-poetry-core python-pytest))

gnu/packages/java.scm

@@ -9732,12 +9732,6 @@ generated sources by ANTLR.")))
           (add-after 'unpack 'chdir
             (lambda _
               (chdir "runtime/Python3")))
-          ;; TODO: Remove when updating ANTLR4:
-          ;; https://github.com/antlr/antlr4/pull/4593
-          (add-after 'chdir 'fix-python-3.12-compatibility
-            (lambda _
-              (substitute* "tests/TestIntervalSet.py"
-                (("assertEquals") "assertEqual"))))
           (add-after 'chdir 'regenerate-parsers
             (lambda _
               (invoke "antlr4" "-no-listener" "-Dlanguage=Python3"

gnu/packages/julia-xyz.scm

@@ -30,7 +30,6 @@
   #:use-module (guix packages)
   #:use-module (guix git-download)
   #:use-module (guix build-system julia)
-  #:use-module (guix build-system pyproject)
   #:use-module (gnu packages gcc)
   #:use-module (gnu packages julia-jll)
   #:use-module (gnu packages python)
@@ -5446,8 +5445,8 @@ This can help users track the progress of long-running tasks.")
     (build-system julia-build-system)
     (arguments
      (list
-      #:imported-modules (append %julia-build-system-modules
-                                 %pyproject-build-system-modules)
+      #:imported-modules `((guix build pyproject-build-system)
+                           ,@%julia-build-system-modules)
       #:modules '((guix build julia-build-system)
                   (guix build utils)
                   ((guix build pyproject-build-system) #:prefix py:))
@@ -5505,7 +5504,7 @@ share large data structures between Julia and Python without copying them.")
 (define-public julia-pyplot
   (package
     (name "julia-pyplot")
-    (version "2.11.6")
+    (version "2.10.0")
     (source
       (origin
         (method git-fetch)
@@ -5514,7 +5513,7 @@ share large data structures between Julia and Python without copying them.")
                (commit (string-append "v" version))))
         (file-name (git-file-name name version))
         (sha256
-         (base32 "15yjx0b6maw1frnpjk4llnj62l16swah3vnql07310kybrd5fyj7"))))
+         (base32 "007zs0imfgs69f30pp2a3rc93kl0qiq7qjx6ig35z4wzkmps4skd"))))
     (build-system julia-build-system)
     (propagated-inputs
      (list julia-colors

gnu/packages/jupyter.scm

@@ -47,6 +47,7 @@
   #:use-module (guix git-download)
   #:use-module (guix build-system cmake)
   #:use-module (guix build-system pyproject)
+  #:use-module (guix build-system python)
   #:use-module (guix utils)
   #:use-module (gnu packages algebra)
   #:use-module (gnu packages bash)
@@ -176,7 +177,8 @@ simulation, statistical modeling, machine learning and much more.")
            python-hatchling
            python-ipyparallel-bootstrap
            python-pytest
-           python-pytest-asyncio-0.26
+           python-pytest-asyncio-0.26  ;some tests fail with v1
+           python-pytest-cov
            python-pytest-timeout))
     (home-page "https://ipython.org")
     (synopsis "IPython Kernel for Jupyter")
@@ -378,7 +380,7 @@ the namespace @code{/nbclassic/}.")
     (build-system pyproject-build-system)
     (arguments
      (list
-      ;; tests: 305 passed, 7 skipped, 18 deselected, 2696 warning
+      ;; tests: 307 passed, 7 skipped, 16 deselected, 9 warnings
       #:test-flags
       '(list "-k" (string-append
                    ;; TODO: This tests fails because nbconvert does not
@@ -394,12 +396,6 @@ the namespace @code{/nbclassic/}.")
                    ;; tornado.simple_httpclient.HTTPTimeoutError: Timeout
                    ;; during request
                    " and not test_connections")
-        ;; AttributeError: 'TestContentsManager' object has no attribute
-        ;; 'assertDictContainsSubset'
-        (string-append "--deselect=notebook/services/contents/tests/"
-                       "test_manager.py::TestContentsManager::test_get")
-        (string-append "--deselect=notebook/services/contents/tests/"
-                       "test_manager.py::TestContentsManagerNoAtomic::test_get")
         ;; These tests require a browser.
         "--ignore=notebook/tests/selenium")
       #:phases
@@ -444,12 +440,15 @@ the namespace @code{/nbclassic/}.")
            python-tornado
            python-traitlets))
     (native-inputs
-     (list python-jupyter-server
+     (list python-coverage
+           python-jupyter-server
            python-nbval
            python-pytest
+           python-pytest-cov
            python-requests
            python-requests-unixsocket2
-           python-setuptools))
+           python-setuptools
+           python-wheel))
     (home-page "https://jupyter.org/")
     (synopsis "Web-based notebook environment for interactive computing")
     (description
@@ -988,6 +987,7 @@ the JupyterLab CSS variables.")
            python-openapi-spec-validator
            python-pytest
            python-pytest-console-scripts
+           python-pytest-cov
            python-pytest-jupyter
            python-pytest-timeout
            python-requests-mock
@@ -1006,37 +1006,32 @@ JupyterLab-like applications from a more limited scope.")
 (define-public python-jupyter-events
   (package
     (name "python-jupyter-events")
-    (version "0.12.1")
+    (version "0.10.0")
     (source
      (origin
-       (method git-fetch)
-       (uri (git-reference
-              (url "https://github.com/jupyter/jupyter_events")
-              (commit (string-append "v" version))))
-       (file-name (git-file-name name version))
+       (method url-fetch)
+       (uri (pypi-uri "jupyter_events" version))
        (sha256
-        (base32 "1n0jgk49kjiv6j6xnwnqfzw88zba7alh6m5gzq78gjvr1kf5cdir"))))
+        (base32 "08jyhj16drl3hg594gr677bc5q991lpd4khlhb3jx26csclq42v7"))))
     (build-system pyproject-build-system)
     (arguments
      ;; This passes the whole command line to shutil.which, instead of just
      ;; the executable.
      (list #:test-flags '(list "--ignore=tests/test_cli.py")))
-    (native-inputs
-     (list python-click
-           python-hatchling
-           python-pytest
-           python-rich
-           python-pytest-asyncio
-           python-pytest-console-scripts))
-    (propagated-inputs
-     (list python-jsonschema
-           python-json-logger
-           python-pyyaml
-           python-referencing
-           python-rfc3339-validator
-           python-rfc3986-validator
-           python-traitlets))
-    (home-page "https://github.com/jupyter/jupyter_events")
+    (propagated-inputs (list python-jsonschema
+                             python-json-logger
+                             python-pyyaml
+                             python-referencing
+                             python-rich
+                             python-rfc3339-validator
+                             python-rfc3986-validator
+                             python-traitlets))
+    (native-inputs (list python-click
+                         python-hatchling
+                         python-pytest
+                         python-pytest-asyncio
+                         python-pytest-console-scripts))
+    (home-page "https://pypi.org/project/jupyter-events/")
     (synopsis "Jupyter Event System library")
     (description "Jupyter Events enables Jupyter Python
 Applications (e.g. Jupyter Server, JupyterLab Server, JupyterHub, etc.) to
@@ -1113,14 +1108,14 @@ JavaScript build steps.")
 (define-public python-jupyter-server
   (package
     (name "python-jupyter-server")
-    (version "2.17.0")
+    (version "2.14.0")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "jupyter_server" version))
        (sha256
         (base32
-         "1mcrgqgzhwfiqk7x4lc2x294ba7cb3ny2akpnj4chr39ascai3n3"))))
+         "0xz69anflhib514lgpdrs0ppmbwp13zbg4vwzls3820jlp7594b5"))))
     (build-system pyproject-build-system)
     (arguments
      (list
@@ -1173,7 +1168,6 @@ JavaScript build steps.")
            python-hatch-jupyter-builder
            python-ipykernel
            python-pytest
-           python-pytest-asyncio
            python-pytest-console-scripts
            python-pytest-jupyter
            python-pytest-timeout
@@ -1188,13 +1182,13 @@ endpoints—to Jupyter web applications.")
 (define-public python-jupyter-server-terminals
   (package
     (name "python-jupyter-server-terminals")
-    (version "0.5.4")
+    (version "0.5.3")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "jupyter_server_terminals" version))
        (sha256
-        (base32 "1xc7zdhlfy8r2jgsrxfm7skm56dblkrg3ya90c1fj2qxsj715nmv"))))
+        (base32 "0sajiadhwncrr0inzzkrs7l1xc6jmw9b5zfw1v79l3i2cx8jkq2s"))))
     (build-system pyproject-build-system)
     ;; The tests require python-jupyter-server, but python-jupyter-server
     ;; needs this package.
@@ -1244,8 +1238,8 @@ are interactive HTML widgets for Jupyter notebooks and the IPython kernel.")
     (propagated-inputs (list python-doit python-jupyter-core))
     (native-inputs (list python-ansi2html
                          python-hatchling
-                         python-pytest
                          python-pytest-console-scripts
+                         python-pytest-cov
                          python-pytest-xdist
                          python-tornado))
     (home-page "https://github.com/jupyterlite/jupyterlite")
@@ -1351,6 +1345,7 @@ and a default CommManager that can be used.")
            python-flaky
            python-pytest
            python-pytest-asyncio
+           python-pytest-cov
            python-testpath
            python-xmltodict))
     (home-page "https://jupyter.org")
@@ -1653,6 +1648,7 @@ Docker registry.")
      (list python-jupyter-packaging
            python-nbval
            python-pytest
+           python-pytest-cov
            python-setuptools))
     (home-page "https://github.com/vidartf/ipydatawidgets")
     (synopsis "Widgets to help facilitate reuse of large datasets across widgets")
@@ -1664,7 +1660,7 @@ datasets across widgets.")
 (define-public python-papermill
   (package
     (name "python-papermill")
-    (version "2.7.0")
+    (version "2.6.0")
     (source
      (origin
        (method git-fetch)
@@ -1673,25 +1669,26 @@ datasets across widgets.")
               (commit version)))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "0lafh4lazx4rc3ly746bjflmihkzf9rhp788bni1l4vq12ks6a49"))))
+        (base32 "1i5zikvl9inficryqfz0v885v24pcs78cj5nzyjw0x232kxbj41p"))))
     (build-system pyproject-build-system)
     (arguments
      (list
-      ;; tests: 503 passed, 2 deselected, 226 warnings
+      ;; tests: 500 passed, 3 skipped, 2 deselected, 29 warnings
       #:test-flags
       ;; Do not bother testing Azure, AWS, and Google Cloud features.
       #~(list "--ignore=papermill/tests/test_abs.py"
               "--ignore=papermill/tests/test_adl.py"
               "--ignore=papermill/tests/test_gcs.py"
               "--ignore=papermill/tests/test_s3.py"
-              #$@(map (lambda (ls)
-                        (string-append "--deselect=papermill/tests/"
-                                       (string-join ls "::")))
-                      ;; AssertionError: 'error' != 'display_data'
-                      '(("test_execute.py" "TestBrokenNotebook2" "test")
-                        ;; NameError: name 'FileSelector' is not defined
-                        ("test_hdfs.py" "HDFSTest" "test_hdfs_listdir"))))))
+              ;; AssertionError
+              #$@(map (lambda (test) (string-append "--deselect="
+                                                    "papermill/tests/"
+                                                    "test_execute.py::"
+                                                    test))
+                      (list "TestBrokenNotebook2::test"
+                            "TestOutputFormatting::test_output_formatting")))))
     (propagated-inputs (list python-aiohttp
+                             python-ansicolors
                              python-click
                              python-entrypoints
                              python-nbclient
@@ -1727,8 +1724,15 @@ analyzing Jupyter Notebooks.")
     (arguments
      (list
       #:test-flags
-      ;; See: <https://github.com/spyder-ide/qtconsole/issues/582>.
-      #~(list "--ignore=qtconsole/tests/test_jupyter_widget.py")
+      ;; All tests fail with error: This plugin does not support
+      ;; propagateSizeHints()
+      #~(list "--ignore=qtconsole/tests/test_00_console_widget.py"
+              ;; AssertionError: '<!DO[261 chars]size:12pt; font-weight:400;
+              ;; font-style:normal;[1218 chars]tml>' != '<!DO[261
+              ;; chars]size:9pt; font-weight:400; font-style:normal;"[1217
+              ;; chars]tml>'Diff is 1756 characters long. Set self.maxDiff to
+              ;; None to see it.
+              "-k" "not test_other_output")
       #:phases
       #~(modify-phases %standard-phases
           (add-before 'check 'pre-check

gnu/packages/kde-education.scm

@@ -65,14 +65,14 @@
 (define-public kqtquickcharts
   (package
     (name "kqtquickcharts")
-    (version "25.12.3")
+    (version "26.04.1")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://kde/stable/release-service/"
                                   version "/src/kqtquickcharts-" version ".tar.xz"))
               (sha256
                (base32
-                "0jywd5s5l9bj4bv1jvbjghgdmiac4q1infxr1mfs7z4fd6408nbc"))))
+                "0d4i7l41wrhgn8m408y8fj50w0s9y0v1lv2v8dyqssqbimdxgk8l"))))
     (build-system qt-build-system)
     (native-inputs (list extra-cmake-modules))
     (inputs (list qtdeclarative))
@@ -89,14 +89,14 @@ charts.")
 (define-public analitza
   (package
     (name "analitza")
-    (version "25.12.3")
+    (version "26.04.1")
     (source
      (origin
        (method url-fetch)
        (uri (string-append "mirror://kde/stable/release-service/"
                            version "/src/analitza-" version ".tar.xz"))
        (sha256
-        (base32 "1dzx7ff4bx1ma3am7928y3qp99lxxd1zk4czfpcm66fn2q8w02sg"))))
+        (base32 "1rn1w6spz776zl23ri5fdk499f7ihldkh3iv03cimda1l26h6v61"))))
     (native-inputs (list extra-cmake-modules qttools))
     (inputs (list eigen qtbase qtdeclarative qtsvg))
     (build-system qt-build-system)
@@ -111,7 +111,7 @@ expressions and let you evaluate and draw them.")
 (define-public gcompris-qt
   (package
     (name "gcompris-qt")
-    (version "26.0")
+    (version "26.1")
     (source
      (origin
        (method url-fetch)
@@ -119,7 +119,7 @@ expressions and let you evaluate and draw them.")
              "mirror://kde//stable/gcompris/qt/src/gcompris-qt-"
              version ".tar.xz"))
        (sha256
-        (base32 "0czk3srhx7g370mhx8yk13ak004h6y8lzqdbj0wqhvnxjszghgbx"))))
+        (base32 "0f8kycj62ipfjwrk8bisq5a7cv7zh84p9vry3g62q0czn9ivi2f3"))))
     (build-system qt-build-system)
     (arguments
      (list #:qtbase qtbase
@@ -179,14 +179,14 @@ Currently available boards include:
 (define-public kalgebra
   (package
     (name "kalgebra")
-    (version "25.12.3")
+    (version "26.04.1")
     (source
      (origin
        (method url-fetch)
        (uri (string-append "mirror://kde/stable/release-service/"
                            version "/src/kalgebra-" version ".tar.xz"))
        (sha256
-        (base32 "05chl85zvcvlkdn657awx93n0zpk6lzpq5cgx27rfl0wjyy5mbbm"))))
+        (base32 "0br2ffh50p7l7w3ym5393vjcw8pzr3z9snqk9j99qdm1kpslxhck"))))
     (build-system qt-build-system)
     (arguments
      (list
@@ -231,14 +231,14 @@ such as addition, trigonometric functions or derivatives.")
 (define-public ktouch
   (package
     (name "ktouch")
-    (version "25.12.3")
+    (version "26.04.1")
     (source
      (origin
        (method url-fetch)
        (uri (string-append "mirror://kde/stable/release-service/"
                            version "/src/ktouch-" version ".tar.xz"))
        (sha256
-        (base32 "1467905b8l5dnml5bdm0zg9agi3knprkmg16r7k1ncljqkq5xvc8"))))
+        (base32 "0hd2vp8yj24aa8wa3hh2lhnsjqh4i7p65i5036h0272ciyhzp4zy"))))
     (build-system qt-build-system)
     (native-inputs
      (list extra-cmake-modules kdoctools pkg-config))
@@ -369,30 +369,44 @@ to perform data analysis.")
 (define-public marble
   (package
     (name "marble")
-    (version "25.12.3")
+    (version "26.04.1")
     (source
      (origin
        (method url-fetch)
        (uri (string-append "mirror://kde/stable/release-service/"
                            version "/src/marble-" version ".tar.xz"))
        (sha256
-        (base32 "1m1x1imcibyq6z38l9wk6qk9b9w8lyz0gk69lavy9qqsyrq4wi3g"))))
+        (base32 "04gz0ivzs385c87myh1pwiy92c8j9ycm6i979bw3k2al0jxfnjqp"))))
     (build-system qt-build-system)
     (arguments
-     ;; FIXME: libmarblewidget-qt5.so.28 not found.  Also enable the
-     ;; corresponding configure flag to build tests.
      (list
-      #:tests? #f
+      #:test-exclude
+      (string-append "("
+                     (string-join '("MarbleRunnerManagerTest"
+                                    "MarbleMapTest"
+                                    "MarbleWidgetTest"
+                                    "RenderPluginTest"
+                                    "AbstractDataPluginModelTest"
+                                    "AbstractDataPluginTest"
+                                    "AbstractFloatItemTest")
+                                  "|")
+                     ")")
       #:qtbase qtbase
-      #:configure-flags #~(list "-DBUILD_MARBLE_TOOLS=YES" ;file conversion tools
-                                "-DBUILD_TOUCH=YES")
-      #:phases #~(modify-phases %standard-phases
-                   (add-after 'unpack 'alter-osmctools-lookup
-                     (lambda _
-                       (substitute* "tools/vectorosm-tilecreator/autotests/CMakeLists.txt"
-                         (("\\$<TARGET_FILE:osmconvert>")
-                          (which "osmconvert"))))))))
-    (native-inputs (list abseil-cpp extra-cmake-modules kdoctools osmctools
+      #:configure-flags
+      #~(list "-DBUILD_MARBLE_TOOLS=YES" ;file conversion tools
+              "-DBUILD_TOUCH=YES")
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-after 'unpack 'alter-osmctools-lookup
+            (lambda _
+              (substitute* "tools/vectorosm-tilecreator/autotests/CMakeLists.txt"
+                (("\\$<TARGET_FILE:osmconvert>")
+                 (which "osmconvert"))))))))
+    (native-inputs (list abseil-cpp
+                         extra-cmake-modules
+                         kdoctools
+                         osmctools
+                         python-minimal
                          qttools))
     ;; One optional dependency missing: libwlocate.
     (inputs (list gpsd