gnu: python-geventhttpclient: Update to 2.3.9.

* gnu/packages/python-web.scm (python-geventhttpclient): Update to 2.3.9.

Change-Id: I83ff865b8ae052d24f9920b3d5c029e7c91373cc

CODEOWNERS

@@ -334,7 +334,6 @@ 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

@@ -486,7 +486,6 @@ 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

@@ -972,8 +972,7 @@ 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/local.mk

@@ -1185,7 +1185,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/date-output-pkg-config-files.patch	\
   %D%/packages/patches/dbacl-include-locale.h.patch		\
   %D%/packages/patches/dbacl-icheck-multiple-definitions.patch	\
-  %D%/packages/patches/dblatex-importlib.patch		\
   %D%/packages/patches/dblatex-inkscape-1.0.patch		\
   %D%/packages/patches/dbus-helper-search-path.patch		\
   %D%/packages/patches/ddd-build.patch				\
@@ -1586,9 +1585,7 @@ 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 \
@@ -2123,7 +2120,6 @@ 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	\
@@ -2502,6 +2498,7 @@ 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		\

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)
@@ -3916,18 +3917,6 @@ rules is done with the @code{auditctl} utility.")
                 (wrap-program (string-append ndiff "/bin/ndiff")
                   `("GUIX_PYTHONPATH" prefix
                     (,(python-path ndiff)))))))
-          (add-before 'check 'fix-tests-for-python-3.12
-            (lambda _
-              (substitute* "ndiff/ndifftest.py"
-                (("import imp")
-                 "import importlib.util")
-                (("ndiff = imp\\.load_source\\(\"ndiff\", \"ndiff\\.py\"\\)")
-                 (string-join
-                  '("spec = \
-importlib.util.spec_from_file_location(\"ndiff\", \"ndiff.py\")"
-                    "ndiff = importlib.util.module_from_spec(spec)"
-                    "spec.loader.exec_module(ndiff)")
-                  "\n")))))
           ;; These are the tests that do not require network access.
           (replace 'check
             (lambda* (#:key tests? #:allow-other-keys)
@@ -4057,59 +4046,51 @@ 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/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)
@@ -764,7 +765,7 @@ file system.")
        (sha256
         (base32 "0r3xwk8xsfxvmxyw3d57sy2i9by24g0l1jl40735jiac9mypcg7n"))))
     (build-system pyproject-build-system)
-    (propagated-inputs (list python-requests python-argcomplete python-urllib3
+    (inputs (list python-requests python-argcomplete python-urllib3
                   python-looseversion gnupg))
     (native-inputs (list python-setuptools python-wheel python-requests-cache
                          python-defusedxml))
@@ -772,7 +773,8 @@ file system.")
      (list $SSL_CERT_FILE))
     (arguments
      (list
-      #:test-backend #~'unittest
+      #:test-flags
+      #~(list "-k" "test_*")
       #:phases
       #~(modify-phases %standard-phases
           (add-after 'unpack 'patch-tests
@@ -791,7 +793,11 @@ file system.")
             (lambda _
               (substitute* "sdkmanager.py"
                 (("gpgv")
-                 (string-append #$(this-package-input "gnupg") "/bin/gpgv"))))))))
+                 (string-append #$(this-package-input "gnupg") "/bin/gpgv")))))
+          (replace 'check
+            (lambda* (#:key tests? test-flags #:allow-other-keys)
+              (when tests?
+                (apply invoke "python" "-m" "unittest" test-flags)))))))
     (home-page "https://gitlab.com/fdroid/sdkmanager")
     (synopsis "Replacement for Android sdkmanager written in Python")
     (description
@@ -1176,16 +1182,14 @@ for communicating with Xiaomi smart appliances over miIO and MIoT protocols.")
 (define-public fdroidserver
   (package
     (name "fdroidserver")
-    (version "2.4.3")
+    (version "2.4.2")
     (source
      (origin
-       (method git-fetch)
-       (uri (git-reference
-              (url "https://gitlab.com/fdroid/fdroidserver")
-              (commit version)))
-       (file-name (git-file-name name version))
+       (method url-fetch)
+       (uri (pypi-uri "fdroidserver" version))
        (sha256
-        (base32 "1745fqxr2qfrls4wr6x9w1262b9pxmw9yvzd9b71ya2qmj74q17n"))))
+        (base32
+         "06xybginrwi5c7bw000wz5s5hzi0aqrxskzwh8qc6wv463w2djax"))))
     (build-system pyproject-build-system)
     (arguments
      (list
@@ -1196,17 +1200,22 @@ for communicating with Xiaomi smart appliances over miIO and MIoT protocols.")
             (lambda _
               (setenv "HOME" "/tmp"))))))
     (propagated-inputs
-     (list python-platformdirs
-           python-androguard
+     (list python-androguard
            python-apache-libcloud
+           python-argcomplete
            python-asn1crypto
            python-clint
            python-defusedxml
+           python-docker
            python-gitpython
+           python-mwclient
            python-oscrypto
            python-paramiko
            python-pillow
+           python-platformdirs
            python-puremagic
+           python-pyasn1
+           python-pyasn1-modules
            python-pyyaml
            python-qrcode
            python-requests

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)
@@ -3789,6 +3790,10 @@ bad pixel tracking throughout the reduction process.")
       #~(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-env
             (lambda _
               (setenv "HOME" (getcwd)))))))
@@ -4420,6 +4425,7 @@ Cesium.")
     (native-inputs
      (list python-pydot
            python-pytest
+           python-pytest-cov
            python-pytest-asdf-plugin
            python-pytest-doctestplus
            python-pytest-filter-subpackage
@@ -4944,6 +4950,7 @@ files.")
     (build-system pyproject-build-system)
     (native-inputs
      (list python-pytest
+           python-pytest-cov
            python-setuptools
            python-setuptools-scm
            python-wheel))
@@ -5505,6 +5512,7 @@ across many files.")
      (list python-mock
            python-objgraph
            python-pytest
+           python-pytest-cov
            ;; python-pytest-faulthandler
            python-setuptools
            python-wheel
@@ -6318,6 +6326,19 @@ 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"
+                      #$(version-major+minor+point version))))
           (add-before 'check 'prepare-test-environment
             (lambda _
               (setenv "HOME" "/tmp"))))))
@@ -9902,7 +9923,13 @@ implemented in the @acronym{JWST, James Webb Space Telescope} and
                             "test_step.py::test_build_config_pipe_kwarg"
                             "test_step.py::test_build_config_step_config_file"
                             "test_step.py::test_build_config_step_kwarg"
-                            "test_step.py::test_step_list_args")))))
+                            "test_step.py::test_step_list_args")))
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-after 'unpack 'set-version
+            (lambda _
+              (setenv "SETUPTOOLS_SCM_PRETEND_VERSION"
+                      #$(version-major+minor+point version)))))))
     (native-inputs
      (list python-pytest
            python-pytest-doctestplus
@@ -10910,6 +10937,7 @@ cosmological simulations.")
     (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

@@ -179,6 +179,7 @@
   #: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)
@@ -3237,27 +3238,30 @@ 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
@@ -3283,7 +3287,7 @@ synchronous execution of all clients, and low latency operation.")
            expat
            libsamplerate
            opus
-           python-dbus
+           python-dbus-1.2
            readline))
     (native-inputs
      (list pkg-config))
@@ -4086,7 +4090,9 @@ one-dimensional sample-rate conversion library.")
                  (string-append "'" #$(this-package-input "libsndfile")
                                 "/lib/libsndfile"))))))))
     (native-inputs
-     (list python-pytest python-setuptools))
+     (list python-pytest
+           python-pytest-cov
+           python-setuptools))
     (inputs
      (list libsndfile
            portaudio))
@@ -7815,59 +7821,60 @@ Rate} 3600x2250 bit/s vocoder used in various radio systems.")
                   (delete-file-recursively "third_party")
                   (delete-file-recursively "modules")))))
     (build-system cmake-build-system)
-    (arguments
-     (list
-      #:configure-flags
-      #~(list "-DLINK_BUILD_QT_EXAMPLES=ON"
-              "-DLINK_BUILD_JACK=ON")
-      #:phases
-      #~(modify-phases %standard-phases
-          (replace 'check
-            (lambda* (#:key inputs tests? #:allow-other-keys)
-              (when tests?
-                (let* ((python (search-input-file inputs "/bin/python3"))
-                       (run-tests "../source/ci/run-tests.py"))
-                  (invoke python run-tests "--target" "LinkCoreTest")
-                  (invoke python run-tests "--target" "LinkDiscoveryTest")))))
-          (add-before 'install 'patch-cmake
-            (lambda* (#:key inputs #:allow-other-keys)
-              (let* ((source "../source/"))
-                (substitute* (string-append source
-                                            "cmake_include/AsioStandaloneConfig.cmake")
-                  (((string-append "\\$\\{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
@@ -8053,7 +8060,7 @@ 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
@@ -8083,7 +8090,8 @@ Home Page}.")
      (list
       #:test-flags
       ;; Ignore --mpl flag.
-      '(list "-k" (string-append
+      '(list "-c" "/dev/null"
+             "-k" (string-append
                    ;; Resampling tests require python-samplerate.
                    "not resample"
                    ;; These tests use Pooch and download data files.
@@ -8108,6 +8116,7 @@ Home Page}.")
      (list python-matplotlib
            python-packaging
            python-pytest
+           python-pytest-cov
            python-resampy
            python-setuptools
            python-wheel))

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")
@@ -1303,6 +1299,7 @@ compression parameters used by Gzip.")
     (native-inputs
      (list python-flexmock
            python-pytest
+           python-pytest-cov
            python-setuptools
            python-wheel))
     (inputs
@@ -1366,9 +1363,9 @@ borgmatic is powered by borg.")
             (assoc-ref qt:%standard-phases 'qt-wrap)))))
     (native-inputs
      (list python-platformdirs
-           python-pytest
            python-pytest-mock
            python-pytest-qt
+           python-pytest-runner
            python-setuptools
            python-setuptools-git))
     (inputs

gnu/packages/benchmark.scm

@@ -42,6 +42,7 @@
   #:use-module (guix search-paths)
   #:use-module (guix build-system cmake)
   #:use-module (guix build-system gnu)
+  #:use-module (guix build-system python)
   #:use-module (guix build-system pyproject)
   #:use-module (guix build-system meson)
   #:use-module (gnu packages)

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)
@@ -2287,6 +2288,7 @@ version = ~s
                   (delete-file-recursively
                    (string-append #$output "/.pytest_cache")))))))))
     (native-inputs (list python-pytest
+                         python-pytest-cov
                          python-pytest-datadir
                          python-pytest-doctestplus
                          python-recommonmark
@@ -3377,36 +3379,35 @@ 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
@@ -3414,6 +3415,7 @@ encountered in PDB files prior to simulation tasks.")
            python-tqdm
            python-typing-extensions
            python-zipp))
+    (native-inputs (list python-setuptools python-wheel))
     (home-page "https://github.com/haessar/peaks2utr")
     (synopsis "Python CLI for annotating three prime UTR")
     (description
@@ -3862,6 +3864,7 @@ raw/ed14e050b2b75e7f4ddb73d512fbe928bbdb2b85")
            python-scipy))
     (native-inputs
      (list python-pytest
+           python-pytest-cov
            python-pytest-datadir
            python-pytest-doctestplus
            python-setuptools
@@ -4287,6 +4290,7 @@ e.g. microbiome samples, genomes, metagenomes.")
     (native-inputs
      (list python-cython
            python-pytest
+           python-pytest-cov
            python-setuptools
            python-wheel))
     (propagated-inputs
@@ -6962,6 +6966,7 @@ and v1.1 to v1.2.")
      (list python-mypy-extensions
            python-pytest
            python-pytest-mock
+           python-pytest-runner
            python-setuptools
            python-wheel))
     (propagated-inputs
@@ -8841,8 +8846,7 @@ 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
@@ -8850,6 +8854,7 @@ high-throughput sequencing (HTS) assays")
                              python-filelock
                              python-loguru
                              python-mygene
+                             python-mysql-connector-python
                              python-norns
                              python-numpy
                              python-pandas
@@ -9805,39 +9810,29 @@ 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
@@ -14310,7 +14305,11 @@ 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
@@ -20231,7 +20230,13 @@ fasta subsequences.")
               " and not test_roundtrip"
               ;; This test depends on ipytree, which contains a lot of
               ;; minified JavaScript.
-              " and not test_print_trees"))))
+              " and not test_print_trees"))
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-after 'unpack 'fix-pytest-config
+            (lambda _
+              (substitute* "pyproject.toml"
+                ((".*--cov.*") "")))))))
     (native-inputs
      (list python-hatchling
            python-pytest))

gnu/packages/bittorrent.scm

@@ -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)
@@ -532,9 +533,8 @@ 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

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

gnu/packages/calendar.scm

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

gnu/packages/check.scm

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

gnu/packages/chemistry.scm

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

gnu/packages/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/cpp.scm

@@ -78,6 +78,7 @@
   #:use-module (guix build-system copy)
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system meson)
+  #:use-module (guix build-system python)
   #:use-module (guix build-system pyproject)
   #:use-module (guix build-system scons)
   #:use-module (guix modules)
@@ -1903,7 +1904,8 @@ 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)
@@ -275,18 +276,17 @@ Ed448-Goldilocks and Curve448, using the Decaf encoding.")
 (define-public libsodium
   (package
     (name "libsodium")
-    (version "1.0.18")
-    (source (origin
-            (method url-fetch)
-            (uri (list (string-append
-                        "https://download.libsodium.org/libsodium/"
-                        "releases/libsodium-" version ".tar.gz")
-                       (string-append
-                        "https://download.libsodium.org/libsodium/"
-                        "releases/old/libsodium-" version ".tar.gz")))
-            (sha256
-             (base32
-              "1h9ncvj23qbbni958knzsli8dvybcswcjbx0qjjgi922nf848l3g"))))
+    (version "1.0.21")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+              (url "https://github.com/jedisct1/libsodium")
+              (commit (string-append version "-RELEASE"))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32
+         "1l6pc3m8zl1sip9ib91bjsb2z2zr7xa7bhblwwmyn9x4nkwqj17n"))))
     (build-system gnu-build-system)
     (synopsis "Portable NaCl-based crypto library")
     (description

gnu/packages/cups.scm

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

gnu/packages/cybersecurity.scm

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

gnu/packages/databases.scm

@@ -200,6 +200,7 @@
   #:use-module (guix build-system meson)
   #:use-module (guix build-system perl)
   #:use-module (guix build-system pyproject)
+  #:use-module (guix build-system python)
   #:use-module (guix build-system qt)
   #:use-module (guix build-system ruby)
   #:use-module (guix build-system cmake)
@@ -1251,98 +1252,6 @@ management system that supports the standardized Structured Query
 Language.")
     (license license:gpl2)))
 
-(define-public mysql-connector-python
-  (package
-    (name "mysql-connector-python")
-    (version "8.3.0")
-    (source
-     (origin
-       (method git-fetch)
-       (uri (git-reference
-              (url "https://github.com/mysql/mysql-connector-python")
-              (commit version)))
-       (file-name (git-file-name name version))
-       (sha256
-        (base32 "18jvpnnwmfrn961rvqmsygp7dw3spf3swhxhal4hhj5hqddckj5f"))))
-    (build-system pyproject-build-system)
-    (arguments
-     (list
-      ;; tests: 1371 passed
-      #:phases
-      #~(modify-phases %standard-phases
-          (add-after 'unpack 'compatibility
-            (lambda _
-              (substitute* "src/mysql_capi.c"
-                (("res = mysql_options\\(&self->session, MYSQL_OPT_LOAD_DATA_LOCAL_DIR.*")
-                 "res = 0;")
-                (("mysql_options\\(&self->session, MYSQL_OPT_LOAD_DATA_LOCAL_DIR.*")
-                 "")
-                (("mysql_options\\(&self->session, MYSQL_OPT_TLS_CIPHERSUITES.*")
-                 "")
-                ;; The C API does not have mysql_bind_param, so we produce an
-                ;; error here.
-                (("status = mysql_bind_param.*") "status = 1;")
-                (("#include \"mysql_capi_conversion\\.h\"" all)
-                 (string-append all "\n" "#include <stdbool.h>")))))
-          (add-after 'unpack 'chdir
-            (lambda _
-              (chdir "mysql-connector-python")))
-          (add-before 'build 'prepare-build
-            (lambda _
-              (setenv "MYSQL_CAPI" #$(this-package-input "mysql"))))
-          (replace 'check
-            (lambda* (#:key tests? #:allow-other-keys)
-              (when tests?
-                ;; Some of these tests might be failing due to the build
-                ;; container's restrictions, others are due to the version
-                ;; mismatch.
-                (substitute* "tests/cext/test_cext_api.py"
-                  (("def test_change_user") "def _do_not_test_change_user")
-                  (("def test_get_character_set_info")
-                   "def _do_not_test_get_character_set_info"))
-                (substitute* "tests/test_bugs.py"
-                  (("def test_change_user") "def _do_not_test_change_user")
-                  (("def test_lost_connection") "def _do_not_test_lost_connection")
-                  (("def test_kill_query") "def _do_not_test_kill_query")
-                  ;; These all fail because of expired certificates.
-                  (("def test_cext_verify_server_certificate")
-                   "def _do_not_test_cext_verify_server_certificate")
-                  (("def test_pure_verify_server_certificate")
-                   "def _do_not_test_pure_verify_server_certificate")
-                  (("def test_verify_server_name_cext_cnx")
-                   "def _do_not_test_verify_server_name_cext_cnx")
-                  (("def test_verify_server_name_pure_cnx")
-                   "def _do_not_test_verify_server_name_pure_cnx"))
-                (substitute* '("tests/test_connection.py"
-                               "tests/test_aio_connection.py")
-                  (("def test_allow_local_infile_in_path")
-                   "def _do_not_test_allow_local_infile_in_path")
-                  ;; This fails because of expired certificates.
-                  (("def test_connect_with_unix_socket")
-                   "def _do_not_test_connect_with_unix_socket"))
-                (substitute* "tests/test_constants.py"
-                  (("def test_deprecated")
-                   "def _do_not_test_deprecated"))
-                (mkdir-p "/tmp/datadir")
-                (invoke "python3" "unittests.py"
-                        "--verbosity=3"
-                        (string-append "--with-mysql=" #$(this-package-input "mysql"))
-                        "--keep"
-                        "--mysql-topdir=/tmp/datadir"
-                        "--unix-socket=/tmp/datadir")))))))
-    (propagated-inputs (list python-protobuf))
-    (inputs (list mysql protobuf-3.20 openssl-1.1 zlib))
-    (native-inputs (list python-setuptools))
-    (home-page "https://dev.mysql.com/doc/connector-python/en/index.html")
-    (synopsis "MySQL driver written in Python")
-    (description "MySQL Connector/Python enables Python programs to access
-MySQL databases, using an API that is compliant with the Python Database API
-Specification v2.0 (PEP 249).")
-    (license license:gpl2)))
-
-(define-deprecated-package python-mysql-connector-python
-  mysql-connector-python)
-
 (define-public mariadb
   (package
     (name "mariadb")
@@ -4744,24 +4653,33 @@ 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
@@ -5690,6 +5608,7 @@ __version_tuple__ = version_tuple = (~a)~%" version version-tuple))))))
            pkg-config
            python-cython
            python-pytest
+           python-pytest-runner
            python-setuptools-scm
            python-setuptools))
     (outputs '("out"))
@@ -6286,7 +6205,7 @@ mechanism of @code{dogpile}.")
 (define-public datasette
   (package
     (name "datasette")
-    (version "1.0a26")
+    (version "1.0a19")
     (source
      (origin
        (method git-fetch)
@@ -6295,20 +6214,23 @@ 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
@@ -6323,6 +6245,7 @@ mechanism of @code{dogpile}.")
            python-janus
            python-jinja2
            python-mergedeep
+           python-pint
            python-pluggy
            python-pyyaml
            python-sqlite-utils
@@ -6331,9 +6254,9 @@ 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

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

gnu/packages/dictionaries.scm

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

gnu/packages/diffoscope.scm

@@ -67,6 +67,7 @@
   #:use-module (gnu packages vim)
   #:use-module (gnu packages web)
   #:use-module (gnu packages xml)
+  #:use-module (guix build-system python)
   #:use-module (guix build-system pyproject)
   #:use-module (guix gexp)
   #:use-module (guix git-download)
@@ -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)

gnu/packages/django.scm

@@ -37,6 +37,7 @@
   #:use-module (guix git-download)
   #:use-module (guix gexp)
   #:use-module (guix build-system pyproject)
+  #:use-module (guix build-system python)
   #:use-module (guix deprecation)
   #:use-module (guix search-paths)
   #:use-module (guix utils)
@@ -328,7 +329,7 @@ to the @dfn{don't repeat yourself} (DRY) principle.")
         (base32 "1a5vd07wrnfbclvf6pz9p8ag9kdd1453lsl9q0bkyc45hq2xqd2a"))))
     (build-system pyproject-build-system)
     (native-inputs
-     (list python-django python-pytest python-setuptools))
+     (list python-django python-pytest python-pytest-cov python-setuptools))
     (home-page "https://github.com/epicserve/django-cache-url")
     (synopsis "Configure Django cache settings from URLs")
     (description
@@ -419,6 +420,7 @@ and adapters that are useful for non-trivial configuration scenarios.")
            python-factory-boy
            python-pygments
            python-pytest
+           python-pytest-cov ; runs by default
            python-pytest-django
            python-setuptools
            python-shortuuid
@@ -1327,6 +1329,7 @@ server headers required for Cross-Origin Resource Sharing (CORS).")
            python-mock
            python-msgpack
            python-pytest
+           python-pytest-cov
            python-pytest-django
            python-pytest-mock
            python-setuptools
@@ -2183,6 +2186,7 @@ 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/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)
@@ -471,8 +472,9 @@ 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)

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)
@@ -479,10 +480,8 @@ 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=" #$output))
       #:phases
@@ -508,7 +507,8 @@ individual low-level driver modules.")
                 ;; https://github.com/YosysHQ/eqy/actions/runs/18767539188/job/53545383858
                 (invoke "make" "-C" "examples/spm")
                 (invoke "make" "-C" "examples/simple"))))
-          (add-after 'install 'python:wrap py:wrap))))
+          (add-after 'install 'python:wrap
+            (@@ (guix build python-build-system) wrap)))))
     (native-inputs
      (list clang python-minimal-wrapper python-sphinx texinfo yosys))
     (inputs
@@ -2072,10 +2072,7 @@ versus schematic} tests and can assist with automatic routing.")
      (list
       #:tests? #f                       ;there are no tests
       #:imported-modules (append %qt-build-system-modules
-                                 %pyproject-build-system-modules)
-      #:modules '((guix build qt-build-system)
-                  ((guix build pyproject-build-system) #:prefix py:)
-                  (guix build utils))
+                                 %python-build-system-modules)
       #:phases
       #~(modify-phases %standard-phases
           (add-after 'unpack 'build-info-documentation
@@ -2103,7 +2100,8 @@ versus schematic} tests and can assist with automatic routing.")
                   (chmod bin_ #o755)))
               (install-it "mcy")
               (install-it "mcy-dash")))
-          (add-after 'make-install 'python:wrap py:wrap))))
+          (add-after 'make-install 'python:wrap
+            (@@ (guix build python-build-system) wrap)))))
     (native-inputs
      (list pkg-config
            python-sphinx
@@ -3010,6 +3008,7 @@ Numpy arrays for convenience.")
               (setenv "PDM_BUILD_SCM_VERSION" #$version))))))
     (native-inputs
      (list python-pdm-backend
+           python-pytest-cov
            python-setuptools
            python-setuptools-scm
            sby
@@ -3322,7 +3321,9 @@ Standard} data mode.")
         (base32 "15nnydvr1a4ykh8cagi484sfgvdg0dnjxaw6c0ivhjbrbblpaqnw"))))
     (build-system pyproject-build-system)
     (native-inputs
-     (list python-setuptools python-setuptools-scm))
+     (list python-pytest-cov
+           python-setuptools
+           python-setuptools-scm))
     (home-page "http://pyvcd.readthedocs.io/")
     (synopsis "Library to manipulate digital wave files")
     (description
@@ -3599,7 +3600,10 @@ Automation}.")
                          #$output "/share/info/hdlmake-figures")))))
       #:test-flags #~(list "test_all.py")))
     (native-inputs
-     (list python-setuptools python-sphinx texinfo))
+     (list python-pytest-cov
+           python-setuptools
+           python-sphinx
+           texinfo))
     (propagated-inputs (list python-networkx))
     (home-page "https://ohwr.gitlab.io/project/hdl-make/")
     (synopsis "Generate multi-purpose makefiles for HDL projects")
@@ -3762,9 +3766,18 @@ design.")
       ;; Tests are expensive and may introduce race condition on systems with
       ;; high (more than 16) threads count; limit parallel jobs to 8x.
       #~(list
-         "--numprocesses" (number->string (min 8 (parallel-job-count))))))
+         "--numprocesses" (number->string (min 8 (parallel-job-count))))
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-after 'unpack 'pathch-pytest-options
+            (lambda _
+              (substitute* "pyproject.toml"
+                ((".*--cov=.*") "")
+                ((".*--self-contained-html.*") "")
+                ((".*-n.*auto.*") "")))))))
     (native-inputs
-     (list python-pytest
+     (list python-pytest-cov
+           python-pytest-html
            python-pytest-xdist
            python-setuptools))
     (propagated-inputs
@@ -4233,10 +4246,11 @@ them usable as simple logic analyzer and/or oscilloscope hardware.")
      (list
       #:parallel-tests? #f
       #:test-target "test"
-      #:imported-modules %pyproject-build-system-modules
       #:modules `((guix build gnu-build-system)
-                  ((guix build pyproject-build-system) #:prefix python:)
+                  ((guix build python-build-system) #:prefix python:)
                   (guix build utils))
+      #:imported-modules `(,@%default-gnu-imported-modules
+                           (guix build python-build-system))
       #:make-flags #~(list (string-append "PREFIX=" #$output))
       #:phases
       #~(modify-phases %standard-phases

gnu/packages/emacs-xyz.scm

@@ -13826,7 +13826,7 @@ generates it as a string.  Please see the homepage for usage examples.")
       #:imported-modules (append %emacs-build-system-modules
                                  %pyproject-build-system-modules)
       #:modules '((guix build emacs-build-system)
-                  ((guix build pyproject-build-system) #:prefix py:)
+                  ((guix build python-build-system) #:prefix py:)
                   (guix build emacs-utils)
                   (guix build utils))
       #:phases

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)
@@ -2032,7 +2033,13 @@ 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)
@@ -1827,6 +1828,7 @@ it suitable for security research and analysis.")
     (native-inputs (list python-gitpython
                          python-pytest
                          python-pytest-asyncio
+                         python-pytest-cov
                          python-pytest-mock
                          python-setuptools))
     (inputs (list bash-minimal
@@ -2365,6 +2367,7 @@ 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
@@ -2898,22 +2901,20 @@ 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

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

@@ -50,6 +50,7 @@
   #:use-module (guix build-system go)
   #:use-module (guix build-system linux-module)
   #:use-module (guix build-system pyproject)
+  #:use-module (guix build-system python)
   #:use-module (guix build-system qt)
   #:use-module (guix build-system trivial)
   #:use-module (guix utils)

gnu/packages/finance.scm

@@ -70,6 +70,7 @@
   #:use-module (guix build-system copy)
   #:use-module (guix build-system emacs)
   #:use-module (guix build-system haskell)
+  #:use-module (guix build-system python)
   #:use-module (guix build-system pyproject)
   #:use-module (guix build-system glib-or-gtk)
   #:use-module (guix build-system go)
@@ -1622,7 +1623,10 @@ features:
        (sha256
         (base32 "0yir8hka3vmpk0qhiaffagkdjg3mjgai808s0razsggbd5cn80bb"))))
     (build-system pyproject-build-system)
-    (native-inputs (list python-pytest python-setuptools))
+    (native-inputs
+     (list python-pytest
+           python-pytest-cov
+           python-setuptools))
     (home-page "https://arthurdejong.org/python-stdnum/")
     (synopsis "Python module to handle standardized number and code formats")
     (description
@@ -2505,6 +2509,10 @@ analysis of financial market data.")
         (base32 "13g5338aa8vgkx8g94vz5d8ynfq3jndvyh1nz6dlhw4axwr4x8dp"))))
     (properties '(("upstream-name" #{.}# "mt-940")))
     (build-system pyproject-build-system)
+    (arguments
+     (list
+      #:test-flags
+      #~(list "-c" "/dev/null")))       ; Remove custom --cov flags.
     (native-inputs (list python-pytest python-pyyaml python-setuptools))
     (home-page "https://mt940.readthedocs.io/")
     (synopsis "Python parser for MT940-encoded SWIFT data")

gnu/packages/firmware.scm

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

gnu/packages/flashing-tools.scm

@@ -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

@@ -73,6 +73,7 @@
   #:use-module (guix build-system meson)
   #:use-module (guix build-system perl)
   #:use-module (guix build-system pyproject)
+  #:use-module (guix build-system python)
   #:use-module (guix build-system glib-or-gtk)
   #:use-module (guix build-system qt)
   #:use-module (guix search-paths)
@@ -1377,43 +1378,41 @@ 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
@@ -2178,7 +2177,7 @@ which speak the Qualcomm MSM Interface (QMI) protocol.")
            libxslt                      ;for xsltproc
            pkg-config
            python-minimal
-           python-dbus                  ;for test
+           python-dbus-1.2              ;for test
            python-pygobject             ;for test
            vala))
     (propagated-inputs
@@ -2372,7 +2371,7 @@ 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)

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")
@@ -1012,6 +1059,7 @@ for seismology.")
     (inputs (list gdal))
     (native-inputs (list python-cython
                          python-pytest
+                         python-pytest-cov
                          python-setuptools
                          python-tomli
                          python-versioneer
@@ -1111,7 +1159,7 @@ projections and coordinate transformations library.")
 (define-public python-fiona
   (package
     (name "python-fiona")
-    (version "1.10.1")
+    (version "1.9.6")
     (source
      (origin
        (method git-fetch)
@@ -1120,38 +1168,24 @@ projections and coordinate transformations library.")
               (commit version)))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "0xribbcy5wvrm5y3bq281dry86vhjcnphg9772yp9s3y30y7mlz4"))))
+        (base32 "08whhjrspp194qasjhr9kf70fl342ms47k78rwpcf5q6ikf0rfii"))))
     (build-system pyproject-build-system)
     (arguments
      (list
-      ;; tests: 757 passed, 161 skipped, 24 deselected, 1 xfailed, 6 xpassed
       #:test-flags
       #~(list "-m" "not network and not wheel"
-              #$@(map (lambda (test) (string-append "--deselect=tests/" test))
-                      ;; 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))
@@ -1159,19 +1193,19 @@ projections and coordinate transformations library.")
      (list python-attrs
            python-certifi
            python-click
-           python-click-plugins
+           python-click-plugins-1
            python-cligj))
     (native-inputs
      (list gdal ; for gdal-config
            python-boto3
            python-cython
-           python-fsspec
            python-pytest
+           python-pytest-cov
            python-pytz
-           python-setuptools
-           python-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
@@ -1431,6 +1465,7 @@ street bearings/orientations, and speed/travel time.")
            python-pyproj
            python-pyyaml
            python-pytest
+           python-pytest-cov
            python-pytest-httpserver
            python-pytz
            python-requests
@@ -1762,7 +1797,10 @@ utilities for data translation and processing.")
       ;; This test requires internet access.
       '(list "--deselect" "test_shapefile.py::test_reader_url")))
     (native-inputs
-     (list python-pytest python-setuptools python-wheel))
+     (list python-pytest
+           python-pytest-runner
+           python-setuptools
+           python-wheel))
     (home-page "https://github.com/GeospatialPython/pyshp")
     (synopsis "Read/write support for ESRI Shapefile format")
     (description
@@ -3492,9 +3530,10 @@ orienteering sport.")
        (list
         #:tests? #f                    ; No tests
         #:modules `((guix build gnu-build-system)
-                    ((guix build pyproject-build-system) #:prefix python:)
+                    ((guix build python-build-system) #:prefix python:)
                     (guix build utils))
-        #:imported-modules %pyproject-build-system-modules
+        #:imported-modules `(,@%default-gnu-imported-modules
+                             (guix build python-build-system))
         #:configure-flags
         #~(list "--with-blas"
                 "--with-bzlib"
@@ -3666,13 +3705,13 @@ growing set of geoscientific methods.")
     (build-system cmake-build-system)
     (arguments
      (list
-      #:imported-modules (append %cmake-build-system-modules
-                                 %pyproject-build-system-modules
-                                 '((guix build qt-utils)))
       #:modules '((guix build cmake-build-system)
-                  ((guix build pyproject-build-system) #:prefix py:)
+                  ((guix build python-build-system) #:prefix python:)
                   (guix build qt-utils)
                   (guix build utils))
+      #:imported-modules `(,@%cmake-build-system-modules
+                           (guix build python-build-system)
+                           (guix build qt-utils))
       #:configure-flags
       #~(list "-DWITH_QTWEBKIT=NO")
       #:phases
@@ -3833,10 +3872,11 @@ growing set of geoscientific methods.")
             ;; Configure correct path to PyQt5 SIP directory
             (add-after 'unpack 'configure-pyqt5-sip-path
               (lambda* (#:key inputs #:allow-other-keys)
-                (let* ((pyqt (assoc-ref inputs "python-pyqt+qscintilla"))
-                       (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 "\"")))
@@ -3866,7 +3906,7 @@ SET\\(PYQT5_SIP_DIR \"\\$\\{Python_SITEARCH\\}/PyQt5/bindings\"\\)")
                               "-E" (string-join ignored-tests "|")))
                     (format #t "test suite not run~%"))))
             (add-after 'install 'wrap-python
-              (assoc-ref py:%standard-phases 'wrap))
+              (assoc-ref python:%standard-phases 'wrap))
             (add-after 'wrap-python 'wrap-qt
               (lambda* (#:key inputs #:allow-other-keys)
                 (wrap-qt-program "qgis" #:output #$output #:inputs inputs)))

gnu/packages/gimp.scm

@@ -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-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)

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
@@ -8680,7 +8686,7 @@ users.")
            libxslt
            perl
            pkg-config
-           python-dbus
+           python-dbus-1.2
            python-pygobject-3.50
            python-wrapper
            vala))
@@ -12331,6 +12337,7 @@ advanced image management tool")
            intltool
            pkg-config
            python-psutil
+           python-pytest-runner
            python-pytest))
     (inputs
      (list bash-minimal ;for wrap-program
@@ -12339,7 +12346,7 @@ advanced image management tool")
            gsettings-desktop-schemas
            gtk+
            python-wrapper
-           python-dbus
+           python-dbus-1.2
            python-notify2
            python-pycairo
            python-pygobject

gnu/packages/gnupg.scm

@@ -86,6 +86,7 @@
   #: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/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)

gnu/packages/graphics.scm

@@ -146,6 +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)
@@ -1264,6 +1265,51 @@ basic geometries.")
     ;; https://gitlab.com/inkscape/inkscape/issues/784).
     (license license:gpl3+)))
 
+(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 "))))
+    (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
     (name "pstoedit")

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)
@@ -1122,7 +1123,7 @@ application suites.")
 (define-public gtk
   (package
     (name "gtk")
-    (version "4.22.1")
+    (version "4.20.3")
     (source
      (origin
        (method url-fetch)
@@ -1130,11 +1131,9 @@ 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"))
@@ -1258,10 +1257,8 @@ 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))
@@ -1304,7 +1301,6 @@ 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
@@ -1372,8 +1368,8 @@ 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")

gnu/packages/hardware.scm

@@ -117,6 +117,7 @@
   #: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

@@ -66,6 +66,7 @@
   #: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)

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.
 ;;;
@@ -129,6 +128,7 @@
   #: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)
@@ -2967,89 +2967,77 @@ 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/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)

gnu/packages/irc.scm

@@ -47,6 +47,7 @@
   #: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

@@ -8941,12 +8941,6 @@ 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/jupyter.scm

@@ -46,6 +46,7 @@
   #: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)
@@ -173,7 +174,8 @@ 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")
@@ -375,7 +377,7 @@ 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
@@ -391,12 +393,6 @@ 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
@@ -441,12 +437,15 @@ 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
@@ -985,6 +984,7 @@ 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
@@ -1236,6 +1236,7 @@ are interactive HTML widgets for Jupyter notebooks and the IPython kernel.")
     (native-inputs (list python-ansi2html
                          python-hatchling
                          python-pytest-console-scripts
+                         python-pytest-cov
                          python-pytest-xdist
                          python-tornado))
     (home-page "https://github.com/jupyterlite/jupyterlite")
@@ -1341,6 +1342,7 @@ 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")
@@ -1643,6 +1645,7 @@ 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")
@@ -1654,7 +1657,7 @@ datasets across widgets.")
 (define-public python-papermill
   (package
     (name "python-papermill")
-    (version "2.7.0")
+    (version "2.6.0")
     (source
      (origin
        (method git-fetch)
@@ -1663,25 +1666,26 @@ 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

gnu/packages/libffi.scm

@@ -45,6 +45,7 @@
   #:use-module (gnu packages sphinx)
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system pyproject)
+  #:use-module ((guix build-system python) #:select (pypi-uri))
   #:use-module (guix build-system ruby))
 
 (define-public libffi

gnu/packages/libftdi.scm

@@ -33,7 +33,6 @@
   #:use-module (gnu packages libusb)
   #:use-module (gnu packages pkg-config)
   #:use-module (gnu packages python)
-  #:use-module (gnu packages python-build)
   #:use-module (gnu packages swig)
   #:use-module (gnu packages textutils))
 
@@ -96,7 +95,7 @@
                                                  "/html"))))))
       #:tests? #f))                     ; tests fail without access to USB
     (native-inputs
-     (list doxygen graphviz pkg-config python python-setuptools swig))
+     (list doxygen graphviz pkg-config python swig-4.0))
     (inputs
      (list boost libconfuse))
     (propagated-inputs

gnu/packages/libreoffice.scm

@@ -35,6 +35,7 @@
   #:use-module (guix build-system cmake)
   #:use-module (guix build-system glib-or-gtk)
   #:use-module (guix build-system gnu)
+  #:use-module (guix build-system python)
   #:use-module (guix build-system pyproject)
   #:use-module (guix gexp)
   #:use-module (guix download)

gnu/packages/libusb.scm

@@ -43,6 +43,7 @@
   #: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 download)
   #:use-module (guix gexp)
   #:use-module (guix git-download)
@@ -531,8 +532,7 @@ broken iOS devices.")
     (inputs
      (list python))
     (native-inputs
-     (list autoconf automake libtool pkg-config
-           python-cython-0 python-setuptools)) ; to build Python bindings
+     (list autoconf automake libtool pkg-config python-cython-0)) ; to build Python bindings
     (home-page "https://libimobiledevice.org/")
     (synopsis "C library to handle Apple Property List files")
     (description "This package provides a small portable C library to handle
@@ -585,7 +585,7 @@ connections from and to iOS devices by connecting to a socket provided by a
     (inputs
      (list python))
     (native-inputs
-     (list pkg-config python-cython-0 python-setuptools))
+     (list pkg-config python-cython-0))
     (home-page "https://libimobiledevice.org/")
     (synopsis "Protocol library and tools to communicate with Apple devices")
     (description "libimobiledevice is a software library that talks the

gnu/packages/license.scm

@@ -37,6 +37,7 @@
   #:use-module (gnu packages version-control)
   #:use-module (gnu packages web)
   #:use-module (guix build-system perl)
+  #:use-module (guix build-system python)
   #:use-module (guix build-system pyproject)
   #:use-module (guix download)
   #:use-module (guix gexp)

gnu/packages/linux.scm

@@ -218,6 +218,7 @@
   #:use-module (guix build-system linux-module)
   #: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 trivial)
   #:use-module (guix deprecation)    ;for libcap/next
@@ -6827,7 +6828,10 @@ isolation or root privileges.")
     (inputs
      (list singularity))
     (native-inputs
-     (list python-pytest python-setuptools python-wheel))
+     (list python-pytest
+           python-pytest-runner
+           python-setuptools
+           python-wheel))
     (home-page "https://github.com/singularityhub/singularity-cli")
     (synopsis "Singularity Python client")
     (description "@code{python-spython} is a Python library to interact with

gnu/packages/lirc.scm

@@ -24,6 +24,7 @@
   #:use-module (guix download)
   #:use-module (guix git-download)
   #:use-module (guix build-system gnu)
+  #:use-module (guix build-system python)
   #:use-module ((guix licenses) #:prefix license:)
   #:use-module (gnu packages)
   #:use-module (gnu packages pkg-config)

gnu/packages/lisp-xyz.scm

@@ -82,10 +82,9 @@
   #:use-module (guix hg-download)
   #:use-module (guix utils)
   #:use-module (guix build-system asdf)
-  #:use-module (guix build-system emacs)
   #:use-module (guix build-system gnu)
-  #:use-module (guix build-system pyproject)
   #:use-module (guix build-system trivial)
+  #:use-module (guix build-system emacs)
   #:use-module (gnu packages audio)
   #:use-module (gnu packages autotools)
   #:use-module (gnu packages base)
@@ -2895,37 +2894,37 @@ cartesian product.")
           (search-patches "sbcl-burgled-batteries3-fix-signals.patch"))))
       (build-system asdf-build-system/sbcl)
       (arguments
-       (list
-        #:tests? #f
-        #:imported-modules (append %asdf-build-system-modules
-                                   %pyproject-build-system-modules)
-        #:modules `(((guix build pyproject-build-system) #:prefix py:)
+       `(#:tests? #f
+         #:modules (((guix build python-build-system) #:select (python-version))
                     ,@%asdf-build-system-modules)
-        #:phases
-        #~(modify-phases (@ (guix build asdf-build-system) %standard-phases)
-            (add-after 'unpack 'set-*cpython-include-dir*-var
-              (lambda* (#:key inputs #:allow-other-keys)
-                (let* ((lib (search-input-file inputs "/lib/libpython3.so"))
-                       (base (dirname (dirname lib))))
-                  (setenv "BB_PYTHON3_DYLIB" lib)
-                  (setenv "BB_PYTHON3_INCLUDE_DIR"
-                          (string-append base "/include/python"
-                                         (py:python-version base))))))
-            (add-after 'unpack 'adjust-for-python-3.10
-              (lambda _
-                ;; These methods are no longer part of the public API.
-                (substitute* "ffi-interface.lisp"
-                  ((".*PyEval_ReInitThreads.*") "")
-                  ((".*\"PyErr_Warn\".*") "")
-                  ((".*\"PyFloat_ClearFreeList\".*") "")
-                  ((".*\"PyParser_SimpleParseString\".*") "")
-                  ((".*\"PyParser_SimpleParseStringFlags\".*") "")
-                  ((".*\"PyParser_SimpleParseStringFlagsFilename\".*") "")
-                  ((".*\"PyParser_SimpleParseFile\".*") "")
-                  ((".*\"PyParser_SimpleParseFileFlags\".*") "")
-                  ((".*\"PyLong_FromUnicode\".*") "")
-                  ((".*\"PyUnicodeEncodeError_Create\".*") "")
-                  ((".*\"PyUnicodeTranslateError_Create\".*") "")))))))
+         #:imported-modules ((guix build python-build-system)
+                             ,@%asdf-build-system-modules)
+         #:phases
+         (modify-phases (@ (guix build asdf-build-system) %standard-phases)
+           (add-after 'unpack 'set-*cpython-include-dir*-var
+             (lambda* (#:key inputs #:allow-other-keys)
+               (let ((python (assoc-ref inputs "python")))
+                 (setenv "BB_PYTHON3_INCLUDE_DIR"
+                         (string-append python "/include/python"
+                                        (python-version python)))
+                 (setenv "BB_PYTHON3_DYLIB"
+                         (string-append python "/lib/libpython3.so"))
+                 #t)))
+           (add-after 'unpack 'adjust-for-python-3.10
+             (lambda _
+               ;; These methods are no longer part of the public API.
+               (substitute* "ffi-interface.lisp"
+                 ((".*PyEval_ReInitThreads.*") "")
+                 ((".*\"PyErr_Warn\".*") "")
+                 ((".*\"PyFloat_ClearFreeList\".*") "")
+                 ((".*\"PyParser_SimpleParseString\".*") "")
+                 ((".*\"PyParser_SimpleParseStringFlags\".*") "")
+                 ((".*\"PyParser_SimpleParseStringFlagsFilename\".*") "")
+                 ((".*\"PyParser_SimpleParseFile\".*") "")
+                 ((".*\"PyParser_SimpleParseFileFlags\".*") "")
+                 ((".*\"PyLong_FromUnicode\".*") "")
+                 ((".*\"PyUnicodeEncodeError_Create\".*") "")
+                 ((".*\"PyUnicodeTranslateError_Create\".*") "")))))))
       (native-inputs
        (list sbcl-cl-fad sbcl-lift sbcl-cl-quickcheck))
       (inputs

gnu/packages/llvm.scm

@@ -61,6 +61,7 @@
   #:use-module (guix build-system cmake)
   #:use-module (guix build-system emacs)
   #:use-module (guix build-system gnu)
+  #:use-module (guix build-system python)
   #:use-module (guix build-system pyproject)
   #:use-module (guix build-system trivial)
   #:use-module (gnu packages)
@@ -2085,7 +2086,6 @@ generator targetting AMD hardware.")
                                                           "/lib/libclang.so")))
                          (substitute* "clang/cindex.py"
                            (("libclang\\.so") libclang))))))))
-    (native-inputs (list python-setuptools))
     (inputs (list clang))
     (native-inputs (modify-inputs (package-native-inputs clang)
                      (append python-setuptools)))

gnu/packages/logging.scm

@@ -35,6 +35,7 @@
   #:use-module (guix git-download)
   #:use-module (guix build-system cmake)
   #:use-module (guix build-system gnu)
+  #:use-module (guix build-system python)
   #:use-module (gnu packages)
   #:use-module (gnu packages apr)
   #:use-module (gnu packages autotools)

gnu/packages/machine-learning.scm

@@ -144,6 +144,7 @@
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system ocaml)
   #:use-module (guix build-system pyproject)
+  #:use-module (guix build-system python)
   #:use-module (guix build-system r)
   #:use-module (guix build-system trivial)
   #:use-module (guix download)
@@ -850,12 +851,6 @@ NumPy @code{dtype} extensions used in machine learning libraries, including:
       (build-system cmake-build-system)
       (arguments
        (list
-        #:imported-modules (append %cmake-build-system-modules
-                                   %pyproject-build-system-modules)
-        #:modules '((ice-9 textual-ports)
-                    (guix build utils)
-                    ((guix build pyproject-build-system) #:prefix python:)
-                    (guix build cmake-build-system))
         #:configure-flags
         #~(list "-DBUILD_SHARED_LIBS=ON"
                 "-DLLAMA_USE_SYSTEM_GGML=ON")
@@ -1076,7 +1071,7 @@ algorithm.")
 (define-public openmm
   (package
     (name "openmm")
-    (version "8.5.0")
+    (version "8.4.0")
     (source
      (origin
        (method git-fetch)
@@ -1086,7 +1081,7 @@ algorithm.")
        (file-name (git-file-name name version))
        (sha256
         (base32
-         "081yxldinf5ldrag4f50a7kx13fi9wzynq1zc1m619ap14y6nzrl"))))
+         "0lb1idyaas550fp6j8ykiy37lykkm7wzz5na70z27hj4m1m1sgdw"))))
     (build-system cmake-build-system)
     (arguments
      (list
@@ -1097,13 +1092,13 @@ algorithm.")
              "-DOPENMM_BUILD_CUDA_LIB=FALSE")
       #:phases
       #~(modify-phases %standard-phases
-          (add-after 'unpack 'patch-wrappers-python-install
+          (add-after 'unpack 'patch-python-build-system
             (lambda _
               (substitute* "wrappers/python/CMakeLists.txt"
                 (("install --root=\\\\\\$ENV\\{DESTDIR\\}/")
                  (string-append "install --prefix=" #$output
                                 " --root=/ --single-version-externally-managed")))))
-          (add-after 'unpack 'remove-shaky-tests
+          (add-after 'patch-python-build-system 'remove-shaky-tests
             (lambda _
               ;; These tests may unpredictably fail in CI, even passing
               ;; locally.
@@ -1122,18 +1117,15 @@ algorithm.")
     (propagated-inputs
      (list python-numpy))
     (native-inputs
-     (list doxygen gfortran opencl-headers python-cython swig))
+     (list doxygen gfortran opencl-headers python-cython swig-4.0))
     (home-page "https://github.com/openmm/openmm/")
     (synopsis "Toolkit for molecular simulation")
     (description
      "OpenMM is a toolkit for molecular simulation.  It can be used either as
 a stand-alone application for running simulations, or as a library you call
 from your own code.")
-    ;; All licenses are listed in  <docs-source/licenses/Licenses.txt>.
-    (license (list license:cc-by3.0  ;PdbxReader
-                   license:expat     ;API, Reference Platform, CPU Platform, VkFFT
-                   license:gpl3      ;Hilbert Curve
-                   license:lgpl3)))) ;CUDA and OpenCL Platforms
+    ;; See https://github.com/openmm/openmm/issues/4278#issuecomment-1772982471
+    (license license:expat)))
 
 (define-public randomjungle
   (package
@@ -1541,6 +1533,7 @@ learning.")
     (native-inputs (list python-autograd
                          python-matplotlib
                          python-pytest
+                         python-pytest-cov
                          python-setuptools
                          python-setuptools-scm
                          python-wheel))
@@ -2033,6 +2026,7 @@ parts of speech and entities, do syntactic analysis, and more.")
             python-fb-re2
             python-parameterized
             python-pytest
+            python-pytest-runner
             python-setuptools
             python-wheel)
       (filter
@@ -2939,7 +2933,10 @@ Covariance Matrix Adaptation Evolution Strategy (CMA-ES) for Python.")
        (file-name (git-file-name name version))))
     (build-system pyproject-build-system)
     (native-inputs
-     (list python-hatchling python-pytest python-pytest-xdist))
+     (list python-hatchling
+           python-pytest
+           python-pytest-cov
+           python-pytest-xdist))
     (propagated-inputs
      (list python-future
            python-numpy))
@@ -4206,7 +4203,7 @@ These include a barrier, broadcast, and allreduce.")
          ;; nor is examples/plot_quantum.py
          " and not test_file_is_generated"))))
     (propagated-inputs (list python-jsmin python-numpy python-scipy))
-    (native-inputs (list python-pytest python-sphinx
+    (native-inputs (list python-pytest python-pytest-cov python-sphinx
                          python-setuptools python-wheel))
     (home-page "https://github.com/tensorly/tensorly")
     (synopsis "Tensor learning in Python")
@@ -4690,9 +4687,10 @@ different backends")
     (arguments
      (list
       #:tests? #f                       ;no tests
-      #:imported-modules %pyproject-build-system-modules
+      #:imported-modules `(,@%default-gnu-imported-modules
+                           (guix build python-build-system))
       #:modules '((guix build gnu-build-system)
-                  ((guix build pyproject-build-system) #:prefix python:)
+                  ((guix build python-build-system) #:prefix python:)
                   (guix build utils))
       #:make-flags
       #~(list (string-append "CC=" #$(cc-for-target))
@@ -5400,7 +5398,7 @@ in the audio domain.")
     (name "python-pytorch")
     (version %python-pytorch-for-r-torch-version)
     (source %python-pytorch-for-r-torch-src)
-    (build-system pyproject-build-system)
+    (build-system python-build-system)
     (inputs
      (modify-inputs inputs
        (replace "gloo" gloo-for-r-torch)))
@@ -5559,7 +5557,10 @@ in the audio domain.")
              python-tqdm
              python-xxhash))
       (native-inputs
-       (list openssl python-flit-core python-pytest))
+       (list openssl
+             python-flit-core
+             python-pytest
+             python-pytest-cov))
       (home-page "https://pyg.org")
       (synopsis "Graph Neural Network library for PyTorch")
       (description
@@ -5694,7 +5695,9 @@ as torchvision, torchtext, and others.")
          "16ypci664l54ka6ickwkpaa2id14h9h00y7z24z0bv0szld4mrxg"))))
     (build-system pyproject-build-system)
     (native-inputs
-     (list python-pytest-8 python-setuptools))
+     (list python-pytest-8
+           python-pytest-cov
+           python-setuptools))
     (home-page "https://github.com/magmax/python-readchar")
     (synopsis "Library to easily read single chars and key strokes")
     (description "This package provides a Python library to easily read single
@@ -5856,6 +5859,7 @@ PyTorch code to decouple the science from the engineering.")
            python-pandas
            python-psutil
            python-pytest
+           python-pytest-cov
            python-pytest-doctestplus
            python-pytest-rerunfailures
            python-pytest-timeout
@@ -6405,35 +6409,43 @@ powered by the Argos Translate library.")
     (version "0.3.3")
     (source
      (origin
-       (method git-fetch)
-       (uri (git-reference
-              (url "https://github.com/hmmlearn/hmmlearn")
-              (commit version)))
-       (file-name (git-file-name name version))
+       (method url-fetch)
+       (uri (pypi-uri "hmmlearn" version))
        (sha256
-        (base32 "1d1gcw2xb1i7zvkcz2vmrk4c2iqsfy71pgrc0r5p65r51w9p97n1"))))
+        (base32
+         "1v24rkqjjf67w2rys25qxa3vk30bf23m7zn1ilihqzi5qp25sg0x"))))
+    (properties
+     '((updater-extra-native-inputs . ("pybind11" "python-setuptools-scm"))))
     (build-system pyproject-build-system)
     (arguments
      (list
       #:test-flags
-      #~(list "--pyargs" "hmmlearn")
+      ;; _flapack.error: (liwork>=max(1,10*n)||liwork==-1) failed for 10th
+      ;; keyword liwork: dsyevr:liwork=1
+      #~(list "-k" (string-join
+                    (list "not test_fit_mcgrory_titterington1d"
+                          "test_common_initialization"
+                          "test_initialization")
+                    " and not "))
       #:phases
-      #~(modify-phases %standard-phases
-          (add-after 'unpack 'set-core-count
-            (lambda _
-              ;; "Could not find the number of physical cores", so we tell it
-              ;; how many cores to use.
-              (setenv "LOKY_MAX_CPU_COUNT" "1"))))))
+      '(modify-phases %standard-phases
+         (add-after 'unpack 'set-core-count
+           (lambda _
+             ;; "Could not find the number of physical cores", so we tell it
+             ;; how many cores to use.
+             (setenv "LOKY_MAX_CPU_COUNT" "1")))
+         (add-before 'check 'build-extensions
+           (lambda _
+             (invoke "python" "setup.py" "build_ext" "--inplace"))))))
+    (propagated-inputs
+     (list python-numpy python-scikit-learn python-scipy))
     (native-inputs
-     (list pybind11
+     (list pybind11-2
            python-pytest
            python-setuptools
            python-setuptools-scm
+           python-wheel
            util-linux)) ;for lscpu
-    (propagated-inputs
-     (list python-numpy
-           python-scikit-learn
-           python-scipy))
     (home-page "https://github.com/hmmlearn/hmmlearn")
     (synopsis "Hidden Markov Models with scikit-learn like API")
     (description
@@ -6736,7 +6748,14 @@ linear algebra routines needed for structured matrices (or operators).")
                    ;; PyTorch 2.10 rejects passing a torch.Size plus extra args to `view'.
                    (substitute* "botorch/utils/multi_objective/hypervolume.py"
                      (("self\\._batch_sample_shape, *\\*obj\\.shape\\[-2:\\]")
-                      "self._batch_sample_shape")))))))
+                      "self._batch_sample_shape"))))
+               (add-before 'build 'pretend-version
+                 ;; The version string is usually derived via setuptools-scm,
+                 ;; but without the git metadata available, the version string
+                 ;; is set to '0.0.0'.
+                 (lambda _
+                   (setenv "SETUPTOOLS_SCM_PRETEND_VERSION"
+                           #$(package-version this-package)))))))
     (propagated-inputs (list python-gpytorch
                              python-linear-operator
                              python-multipledispatch

gnu/packages/magic-wormhole.scm

@@ -25,6 +25,7 @@
 (define-module (gnu packages magic-wormhole)
   #:use-module ((guix licenses) #:prefix license:)
   #:use-module (guix build-system pyproject)
+  #:use-module ((guix build-system python) #:select (pypi-uri))
   #:use-module (guix download)
   #:use-module (guix gexp)
   #:use-module (guix packages)

gnu/packages/mail.scm

@@ -207,6 +207,7 @@
   #: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 trivial)
   #:use-module (guix deprecation)
@@ -1730,6 +1731,8 @@ and search library.")
           ;; tree, so chdir into it before building.
           (add-after 'unpack 'enter-python-dir
             (lambda _ (chdir "bindings/python-cffi")))
+          ;; python-build-system does not invoke the configure script
+          ;; so _notmuch_config.py is missing
           (add-after 'enter-python-dir 'create-notmuch-config
             (lambda* (#:key inputs #:allow-other-keys)
               (with-output-to-file "_notmuch_config.py"
@@ -1749,7 +1752,7 @@ and search library.")
                 (("version=VERSION,")
                  (string-append "version='" #$version "',"))))))))
     (propagated-inputs (list python-cffi))
-    (native-inputs (list python-pytest python-setuptools))
+    (native-inputs (list python-pytest python-pytest-cov python-setuptools))
     (synopsis "Pythonic bindings for the notmuch mail database using CFFI")
     (license license:gpl3+)))
 
@@ -4701,7 +4704,10 @@ DKIM and ARC sign messages and output the corresponding signature headers.")
        ;; This QA test requires git.
        (list #:test-flags ''("-k" "not test_ge_master")))
       (native-inputs
-       (list python-pytest python-pytest-mock python-setuptools))
+       (list python-pytest
+             python-pytest-cov
+             python-pytest-mock
+             python-setuptools))
       (propagated-inputs
        (list python-atpublic
              python-attrs))

gnu/packages/markup.scm

@@ -44,6 +44,7 @@
   #:use-module (guix build-system trivial)
   #:use-module (guix build-system cmake)
   #:use-module (guix build-system perl)
+  #:use-module (guix build-system python)
   #:use-module (guix build-system pyproject)
   #:use-module (guix utils)
   #:use-module (guix gexp)

gnu/packages/maths.scm

@@ -112,6 +112,7 @@
   #:use-module (guix build-system ocaml)
   #: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 (gnu packages algebra)
@@ -4608,6 +4609,7 @@ savings are consistently > 5x.")
                          python-mock
                          python-mpi4py
                          python-pytest
+                         python-pytest-cov
                          python-pytest-timeout
                          python-setuptools
                          python-wheel))

gnu/packages/medical.scm

@@ -24,6 +24,7 @@
   #: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 qt)
   #:use-module (guix download)
   #:use-module (guix gexp)

gnu/packages/messaging.scm

@@ -167,6 +167,7 @@
   #: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 rebar)
   #:use-module (guix build-system qt)
@@ -3166,6 +3167,11 @@ share/zulip/integrations or in lib/<...>/site-packages/integrations:
                     " and not "))
       #:phases
       #~(modify-phases %standard-phases
+          (add-after 'unpack 'fix-pytest-config
+            (lambda _
+              (substitute* "pyproject.toml"
+                ((" --cov=zulipterminal --no-cov-on-fail")
+                 ""))))
           (add-after 'unpack 'relax-requirements
             (lambda _
               (substitute* "setup.py"

gnu/packages/monitoring.scm

@@ -47,6 +47,7 @@
   #:use-module (guix build-system cargo)
   #:use-module (guix build-system cmake)
   #:use-module (guix build-system pyproject)
+  #:use-module (guix build-system python)
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system go)
   #:use-module (guix utils)

gnu/packages/mp3.scm

@@ -70,6 +70,7 @@
   #:use-module (guix utils)
   #:use-module (guix build-system copy)
   #:use-module (guix build-system gnu)
+  #:use-module (guix build-system python)
   #:use-module (guix build-system pyproject)
   #:use-module (guix build-system cmake)
   #:use-module (guix build-system meson))

gnu/packages/mpd.scm

@@ -41,6 +41,7 @@
   #: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 algebra)
   #:use-module (gnu packages audio)
@@ -501,6 +502,7 @@ other MPD frontends.")
                (base32
                 "17ys8ccr3h6vix0agvhz859slz0phhk7lwqn5bg4az8s7zgqm3nm"))))
     (build-system gnu-build-system)
+    ;; Manually wrap the binary, because we’re not using python-build-system.
     (arguments
      (list
       #:phases