Merge remote-tracking branch 'origin/python-team'

Change-Id: I08cf47c4ee8c4019615ba45cef4cca1bd362d31b

gnu/local.mk

@@ -1927,7 +1927,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/ocaml-4.09-multiple-definitions.patch	\
   %D%/packages/patches/omake-fix-non-determinism.patch	\
   %D%/packages/patches/oneko-remove-nonfree-characters.patch	\
-  %D%/packages/patches/onionshare-cli-async-mode.patch		\
   %D%/packages/patches/online-judge-tools.patch		\
   %D%/packages/patches/onnx-optimizer-system-library.patch	\
   %D%/packages/patches/onnx-1.13.1-use-system-googletest.patch	\
@@ -2006,9 +2005,11 @@ dist_patch_DATA =						\
   %D%/packages/patches/prusa-slicer-fix-tests.patch		\
   %D%/packages/patches/prusa-wxwidgets-makefile-fix.patch	\
   %D%/packages/patches/pthreadpool-system-libraries.patch	\
+  %D%/packages/patches/python-3.11-fix-tests.patch		\
   %D%/packages/patches/python-3.12-fix-tests.patch		\
   %D%/packages/patches/python-accupy-use-matplotx.patch		\
   %D%/packages/patches/python-accupy-fix-use-of-perfplot.patch	\
+  %D%/packages/patches/python-bed-reader-use-store-samples.patch	\
   %D%/packages/patches/python-chai-drop-python2.patch		\
   %D%/packages/patches/python-clarabel-blas.patch		\
   %D%/packages/patches/python-docrepr-fix-tests.patch		\
@@ -2023,7 +2024,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/python-sgmllib3k-assertions.patch	\
   %D%/packages/patches/python-sphobjinv-defer-ssl-import.patch	\
   %D%/packages/patches/python-sphinx-prompt-docutils-0.19.patch	\
-  %D%/packages/patches/python-wxwidgets-type-errors.patch	\
   %D%/packages/patches/qcodeeditor-qt6.patch			\
   %D%/packages/patches/qtdeclarative-5-disable-qmlcache.patch	\
   %D%/packages/patches/qtdeclarative-disable-qmlcache.patch	\
@@ -2130,6 +2130,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/python-memcached-syntax-warnings.patch	\
   %D%/packages/patches/python-mox3-python3.6-compat.patch	\
   %D%/packages/patches/python-packaging-test-arch.patch		\
+  %D%/packages/patches/python-property-cached-asyncio-3_11.patch	\
   %D%/packages/patches/python-pyan3-fix-absolute-path-bug.patch \
   %D%/packages/patches/python-pyan3-fix-positional-arguments.patch \
   %D%/packages/patches/python-pytorch-fix-codegen.patch		\
@@ -2143,6 +2144,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/python-robotframework-sshlibrary-rf5-compat.patch \
   %D%/packages/patches/python-unittest2-python3-compat.patch	\
   %D%/packages/patches/python-unittest2-remove-argparse.patch	\
+  %D%/packages/patches/python-vaex-core-fix-tsl-use.patch	\
   %D%/packages/patches/python-vega-datasets-remove-la-riots-code.patch	\
   %D%/packages/patches/python-versioneer-guix-support.patch	\
   %D%/packages/patches/python-werkzeug-tests.patch		\
@@ -2329,7 +2331,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/tpetra-remove-duplicate-using.patch	\
   %D%/packages/patches/transcode-ffmpeg.patch	\
   %D%/packages/patches/transmission-4.0.6-fix-build.patch	\
-  %D%/packages/patches/trytond-add-egg-modules-to-path.patch	\
   %D%/packages/patches/trytond-add-guix_trytond_path.patch	\
   %D%/packages/patches/ttf2eot-cstddef.patch			\
   %D%/packages/patches/tup-unbundle-dependencies.patch		\

gnu/packages/admin.scm

@@ -1065,25 +1065,29 @@ memory, disks, network and processes.")
        (uri (pypi-uri "bpytop" version))
        (sha256
         (base32 "1clvajbv7pzlya9s1xs6dvjic8rv3kx7aqiwnjxapiypx246gdjk"))))
-    (build-system python-build-system)
+    (build-system pyproject-build-system)
-    (inputs
-     (list python-psutil))
     (arguments
-     `(#:phases
+     (list
-       (modify-phases %standard-phases
+      #:tests? #f ; No tests in Pypi archive.
-         ;; sanity-check phase fail, but the application seems to be working
+      #:phases
-         (delete 'sanity-check)
+      #~(modify-phases %standard-phases
+          (add-after 'unpack 'use-poetry-core
+            (lambda _
+              ;; Patch to use the core poetry API.
+              (substitute* "pyproject.toml"
+                (("poetry.masonry.api")
+                 "poetry.core.masonry.api"))))
           (add-after 'install 'install-themes
-           (lambda* (#:key outputs #:allow-other-keys)
+            (lambda* (#:key inputs outputs #:allow-other-keys)
-             (let ((themes (string-append (assoc-ref outputs "out")
+              (let ((themes (string-append (site-packages inputs outputs)
-                                          "/lib/python"
+                                           "/bpytop-themes")))
-                                          ,(version-major+minor
-                                            (package-version python))
-                                          "/site-packages/bpytop-themes")))
                 (mkdir-p themes)
                 (copy-recursively "themes" themes)))))))
-    (home-page
+    (inputs
-     "https://github.com/aristocratos/bpytop")
+     (list python-psutil))
+    (native-inputs
+     (list python-poetry-core))
+    (home-page "https://github.com/aristocratos/bpytop")
     (synopsis "Resource monitor")
     (description "Resource monitor that shows usage and stats for processor,
 memory, disks, network and processes.  It's a Python port and continuation of
@@ -3280,7 +3284,7 @@ provides the following commands:
      ;; variable in the tests/cpan.scm test.
      (list (search-path-specification
             (variable "GUIX_PYTHONPATH")
-            (files (list "lib/python3.10/site-packages")))))
+            (files (list "lib/python3.11/site-packages")))))
     (home-page "https://www.ansible.com/")
     (synopsis "Radically simple IT automation")
     (description "Ansible aims to be a radically simple IT automation system.

gnu/packages/aidc.scm

@@ -179,7 +179,7 @@ C/C++ programs to use its capabilities without restrictions or overhead.")
 (define-public zbar
   (package
     (name "zbar")
-    (version "0.23.92")
+    (version "0.23.93")
     (source
      (origin
        (method git-fetch)
@@ -189,7 +189,7 @@ C/C++ programs to use its capabilities without restrictions or overhead.")
          (commit version)))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "0k3g0ql2m4dnflppp9r3k804d927g7zslczblzcrbvhp02g6n5an"))))
+        (base32 "0x71clkkm4w765c2d5h3svr29w08dj03r6785f9jwqx5r4ral0za"))))
     (build-system glib-or-gtk-build-system)
     (arguments
      (list

gnu/packages/android.scm

@@ -738,7 +738,10 @@ file system.")
                (base32
                 "11as7n2mj3nbqsqb3ivyv9985n73i022s748qvjg36cs8ig50afx"))))
     (build-system pyproject-build-system)
-    (inputs (list python-requests python-argcomplete python-urllib3 gnupg))
+    (inputs (list python-requests
+                  python-argcomplete
+                  python-urllib3-1.26
+                  gnupg))
     (native-inputs (list python-setuptools python-wheel))
     (arguments
      (list #:phases #~(modify-phases %standard-phases

gnu/packages/astronomy.scm

@@ -2059,7 +2059,10 @@ simulated Astronomical data in Python.")
         "--ignore=astroML/density_estimation/tests/test_bayesian_blocks.py"
         "--ignore=astroML/density_estimation/tests/test_bayesian_blocks.py"
         "--ignore=astroML/density_estimation/tests/test_hist_binwidth.py"
-        "--ignore=astroML/density_estimation/tests/test_hist_binwidth.py")
+        "--ignore=astroML/density_estimation/tests/test_hist_binwidth.py"
+        ;; Disalbe tests with NumPy, see
+        ;; <https://github.com/astroML/astroML/issues/281>.
+        "--ignore=astroML/tests/test_resample.py")
       #:phases
       '(modify-phases %standard-phases
          (add-after 'unpack 'patch-build-system
@@ -2085,11 +2088,18 @@ simulated Astronomical data in Python.")
            ;; Some tests need this
            (lambda _
              (setenv "HOME" "/tmp"))))))
-    (propagated-inputs (list python-astropy python-matplotlib python-numpy
+    (native-inputs
-                             python-scikit-learn python-scipy))
+     (list python-pytest-astropy-header
-    (native-inputs (list python-pytest-astropy-header python-pytest-cov
+           python-pytest-cov
-                         python-pytest-doctestplus python-pytest-remotedata
+           python-pytest-doctestplus
+           python-pytest-remotedata
            python-wheel))
+    (propagated-inputs
+     (list python-astropy
+           python-matplotlib
+           python-numpy
+           python-scikit-learn
+           python-scipy))
     (home-page "https://astroml.org")
     (synopsis "Tools for machine learning and data mining in astronomy")
     (description "This package provides tools for machine learning and data
@@ -2136,7 +2146,9 @@ mining in astronomy.")
                           "test_table_comp[t16-t26]"
                           ;; UnboundLocalError: local variable 'ihd'
                           ;; referenced before assignment
-                          "test_delay_doc_updates")
+                          "test_delay_doc_updates"
+                          ;; assert 13 == 1
+                          "test_skip_meta")
                     " and not "))
       #:phases
       #~(modify-phases %standard-phases
@@ -2488,6 +2500,46 @@ attempting to maintain ISTP compliance
      "This package contains a helper functionality to test ROMAN and JWST.")
     (license license:bsd-3)))
 
+(define-public python-cesium
+  (package
+    (name "python-cesium")
+    (version "0.12.1")
+    (source (origin
+              (method url-fetch)
+              (uri (pypi-uri "cesium" version))
+              (sha256
+               (base32
+                "0jr0ycqz9ns6mcskm4sxx92k40fj3v0x9knjaw5ac9f3mpqxsfbv"))))
+    (build-system pyproject-build-system)
+    (arguments
+     (list
+      #:phases
+      #~(modify-phases %standard-phases
+          ;; The installed test files contain the /gnu/store location, not the
+          ;; location of the discovered test files from the build directory.
+          ;; The test framework doesn't like this.  The easiest way around
+          ;; this mismatch is to jump to the output directory.
+          (add-before 'check 'check-chdir
+            (lambda _ (chdir #$output))))))
+    (propagated-inputs
+     (list python-click ;XXX required by python-dask
+           python-cloudpickle
+           python-dask
+           python-gatspy
+           python-joblib
+           python-numpy
+           python-pandas
+           python-scikit-learn
+           python-scipy
+           python-toolz))
+    (native-inputs (list python-cython python-pytest python-setuptools-scm
+                         python-setuptools python-wheel))
+    (home-page "https://pypi.org/project/cesium/")
+    (synopsis "Library for time-series feature extraction and processing")
+    (description
+     "Cesium is a library for time-series feature extraction and processing.")
+    (license license:bsd-3)))
+
 (define-public python-cmyt
   (package
     (name "python-cmyt")
@@ -3132,7 +3184,9 @@ zooming windows, star catalog access, cuts, star pick/FWHM, thumbnails, etc.")
               "--ignore=glue_astronomy/io/spectral_cube/tests/test_spectral_cube.py"
               "--ignore=glue_astronomy/io/spectral_cube/tests/test_spectral_cube.py"
               "--ignore=glue_astronomy/translators/tests/test_trace.py"
-              "--ignore=glue_astronomy/translators/tests/test_trace.py")))
+              "--ignore=glue_astronomy/translators/tests/test_trace.py"
+              ;; This is a Numpy DeprecationWarning, remove it on next update.
+              "-k" "not test_spectral_cube_io")))
     (propagated-inputs
      (list python-astropy
            python-glue-core

gnu/packages/audio.scm

@@ -647,17 +647,25 @@ Filter) modules follow the convention of 1V / Octave.")
                "1npks71ljc48w6858l9bq30kaf5nph8z0v61jkfb70xb9np850nl"))))
     (build-system waf-build-system)
     (arguments
-     `(#:tests? #f                      ; no check target
-       #:configure-flags
      (list
-        (string-append "LDFLAGS=-Wl,-rpath=" (assoc-ref %outputs "out") "/lib")
+      #:tests? #f                      ; no check target
+      #:configure-flags
+      #~(list
+         (string-append "LDFLAGS=-Wl,-rpath=" #$output "/lib")
          "--enable-fftw3f"
          "--enable-jack"
          "--enable-sndfile"
          "--enable-samplerate"
-        "--enable-avcodec")))
+         "--enable-avcodec")
+       #:phases
+       '(modify-phases %standard-phases
+          (add-after 'unpack 'python3.11-compatibility
+            (lambda _
+              (substitute* '("waflib/Context.py"
+                             "waflib/ConfigSet.py")
+                (("'rU'") "'r'")))))))
     (inputs
-     (list jack-1
+     (list jack-2
            libsndfile
            libsamplerate
            ffmpeg-4                     ;for libavcodec
@@ -2664,7 +2672,13 @@ partial release of the General MIDI sound set.")
            #:configure-flags
            #~(list
               ;; Add the output lib directory to the RUNPATH.
-              (string-append "--ldflags=-Wl,-rpath=" #$output "/lib"))))
+              (string-append "--ldflags=-Wl,-rpath=" #$output "/lib"))
+           #:phases
+           '(modify-phases %standard-phases
+              (add-after 'unpack 'python3.11-compatibility
+                (lambda _
+                  (substitute* "wscript"
+                    (("'rU'") "'r'")))))))
     (inputs
      (list libsndfile
            boost
@@ -2872,6 +2886,14 @@ synchronous execution of all clients, and low latency operation.")
        #: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

gnu/packages/backup.scm

@@ -1443,7 +1443,9 @@ borgmatic is powered by borg.")
            python-pytest-mock
            python-pytest-qt
            python-pytest-runner
-           python-setuptools-git))
+           python-setuptools
+           python-setuptools-git
+           python-wheel))
     (inputs
      (list borg
            python-appdirs

gnu/packages/benchmark.scm

@@ -402,7 +402,7 @@ setup against another one.")
 (define-public python-locust
   (package
     (name "python-locust")
-    (version "2.32.5")
+    (version "2.33.2")
     ;; The archive on Pypi has no tests.
     (source (origin
               (method git-fetch)
@@ -412,7 +412,7 @@ setup against another one.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "0nmhk2k0mbza9slqgms42s6hsfwwmyr275l90an02qaypx066l1n"))))
+                "055is6plxjajzp7v5q108n90j5mvdaylpna98kw9zsqn7mvfq7ms"))))
     (build-system pyproject-build-system)
     (arguments
      (list
@@ -484,10 +484,21 @@ setup against another one.")
                      "not test_ramp_up_from_0_to_100_000_users_with_50_user_classes_and_1000_workers_and_5000_spawn_rate"
                      ;; This test fails with "AssertionError:
                      ;; 'stopped' != 'stopping'".
-                     "not test_distributed_shape") " and "))
+                     "not test_distributed_shape"
+                     ;; This test fails with AssertionError:
+                     ;; "locust [...] != .locust-real"
+                     "not test_invalid_stop_timeout_string"
+                     ) " and "))
       #:phases
       #~(modify-phases %standard-phases
           ;; The build system attempts to detect the version by spawning git.
+          (add-after 'unpack 'pretend-version
+            (lambda _
+              (substitute* "pyproject.toml"
+                (("^dynamic = \\[\"version\"\\].*$")
+                 (format #f "version = ~s~%" #$version))
+                (("^source = \"vcs\".*$")
+                 "source = \"static\"\n"))))
           (add-after 'unpack 'fix-version
             (lambda _
               (let ((tuple (list
@@ -518,9 +529,15 @@ version_tuple = __version_tuple__
 
 ")))))
               (substitute* "pyproject.toml"
-                (("setuptools = \">=70.0.0\"") "setuptools = \">=67.0.0\"")
+                (("\"setuptools>=.*\",")
-                (("^version =.*") (string-append "version = \"" #$version "\"\n"))
+                 (string-append "\"setuptools>="
-                (("enable = true") "enable = false"))))
+                                #$(package-version
+                                   (this-package-input "python-setuptools"))
+                                "\","))
+                (("^version =.*")
+                 (string-append "version = \"" #$version "\"\n"))
+                (("enable = true")
+                 "enable = false"))))
           (add-before 'check 'increase-resource-limits
             (lambda _
               ;; XXX: Copied from ungoogled-chromium.
@@ -552,8 +569,8 @@ version_tuple = __version_tuple__
            python-werkzeug))
     (native-inputs
      (list nss-certs-for-test
-           python-poetry-core
+           python-hatchling
-           python-poetry-dynamic-versioning
+           python-hatch-vcs
            python-pyquery
            python-pytest
            python-retry))

gnu/packages/build-tools.scm

@@ -70,6 +70,7 @@
   #:use-module (gnu packages protobuf)
   #:use-module (gnu packages python)
   #:use-module (gnu packages python-build)
+  #:use-module (gnu packages python-check)
   #:use-module (gnu packages python-crypto)
   #:use-module (gnu packages python-web)
   #:use-module (gnu packages python-xyz)
@@ -79,6 +80,7 @@
   #:use-module (gnu packages tls)
   #:use-module (gnu packages unicode)
   #:use-module (gnu packages version-control)
+  #:use-module (gnu packages xml)
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system pyproject)
   #:use-module (guix build-system python))
@@ -436,7 +438,7 @@ other lower-level build files.")))
 (define-public scons
   (package
     (name "scons")
-    (version "4.4.0")
+    (version "4.5.0")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -446,7 +448,7 @@ other lower-level build files.")))
               (patches (search-patches "scons-test-environment.patch"))
               (sha256
                (base32
-                "1czswx1fj2j48rspkrvarkr43k0vii9rsmz054c9yby1dq362fgr"))))
+                "1skz1kzhwsp54i71jrsg46rkxwicfici7pq6qmfhlqd5zhrg21zb"))))
     (build-system python-build-system)
     (arguments
      (list
@@ -467,7 +469,9 @@ other lower-level build files.")))
           (replace 'check
             (lambda* (#:key tests? #:allow-other-keys)
               (when tests?
-                (invoke "python" "runtest.py" "--all" "--unit-only"))))
+                ;; remove these tests as they require a read/write filesystem
+                (delete-file "SCons/Variables/PathVariableTests.py")
+                (invoke "python" "runtest.py" "--all" "--unit-only" ))))
           (add-after 'install 'move-manuals
             (lambda _
               ;; XXX: For some reason manuals get installed to the top-level
@@ -483,7 +487,7 @@ other lower-level build files.")))
                             stray-manuals))))))))
     (native-inputs
      ;; TODO: Add 'fop' when available in Guix to generate manuals.
-     (list python-wheel
+     (list python-setuptools python-lxml python-wheel
            ;;For tests.
            python-psutil))
     (home-page "https://scons.org/")

gnu/packages/check.scm

@@ -1027,40 +1027,43 @@ definition language, a safe runtime engine for test suites and a powerful
 report generation engine.")
     (license license:bsd-3)))
 
-(define-public python-gixy
+(define-public python-gixy-ng
-  ;; The 0.1.20 release is missing some important fixes.
-  ;; XXX: Commit 'e9008dcbd11f43ccac109b0cf2bf98a94e76b449' breaks tests
-  ;; since it improperly removes an import.
-  (let ((commit "303eb6887ddecab18138b6e427b04ae77c41d2f1")
-        (revision "0")
-        (base-version "0.1.20"))
   (package
-      (name "python-gixy")
+    (name "python-gixy-ng")
-      (version (git-version base-version revision commit))
+    (version "0.2.7")
-      (source (origin
+    (source
+     (origin
        (method git-fetch)
        (uri (git-reference
-                      (url "https://github.com/yandex/gixy")
+             (url "https://github.com/dvershinin/gixy")
-                      (commit commit)))
+             (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-                 (base32
+        (base32 "0dipvy8y1nlhpka0cdk6hyv1j2388y7isbajpwskjrgqc5vayqx8"))))
-                  "0gymjcnvjx9snyrzdbmjnk93ibb161q72xam29vnl3yyac4r1330"))))
     (build-system pyproject-build-system)
-      (native-inputs (list python-nose python-setuptools python-wheel))
+    ;; This package currently doesn't test properly, but we can't add
-      (propagated-inputs
+    ;; pytest because it propagates another version of python-pyparsing
-       (list python-cached-property python-configargparse
+    ;; that takes precedence over the right one.
-             python-jinja2 python-six
+    (propagated-inputs (list python-configargparse
-             ;; XXX: gixy is incompatible with pyparsing >= 3.x.
+                             python-jinja2
-             ;; See <https://github.com/yandex/gixy/pull/132> and
+                             python-pyparsing-2.4.7
-             ;; <https://github.com/yandex/gixy/pull/122>.
+                             python-six))
-             python-pyparsing-2.4.7))
+    (native-inputs (list python-cached-property
-      (home-page "https://github.com/yandex/gixy")
+                         python-setuptools
+                         python-wheel))
+    (home-page "https://github.com/dvershinin/gixy")
     (synopsis "Static NGINX configuration analyzer")
     (description "Gixy is a static analyzer whose main goal is to help
 prevent common NGINX misconfigurations.  It provides the @command{gixy}
-command.")
+command.
-      (license license:mpl2.0))))
+
+Note: This is an actively maintained fork of the original @code{python-gixy}
+package.")
+    (license license:mpl2.0)))
+
+(define-deprecated/public python-gixy python-gixy-ng
+  (package/inherit python-gixy-ng
+    (name "python-gixy")))
 
 (define-public googletest
   (package
@@ -1413,34 +1416,6 @@ syntax validation, ...
 (define-public python-parameterized
   (package
     (name "python-parameterized")
-    (version "0.8.1")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (pypi-uri "parameterized" version))
-       (sha256
-        (base32 "0p1vhfw552rgd7gb2vy4l4l4k8mnbdz7f3chgzvk0r0qsqvzzfs1"))))
-    (build-system python-build-system)
-    (arguments
-     '(#:phases (modify-phases %standard-phases
-                  (replace 'check
-                    (lambda* (#:key tests? #:allow-other-keys)
-                      (if tests?
-                          (invoke "nosetests" "-v")
-                          (format #t "test suite not run~%"))
-                      #t)))))
-    (native-inputs
-     (list python-mock python-nose))
-    (home-page "https://github.com/wolever/parameterized")
-    (synopsis "Parameterized testing with any Python test framework")
-    (description
-     "Parameterized is a Python library that aims to fix parameterized testing
-for every Python test framework.  It supports nose, py.test, and unittest.")
-    (license license:bsd-2)))
-
-(define-public python-parameterized-next
-  (package
-    (inherit python-parameterized)
     (version "0.9.0")
     (source
      (origin
@@ -1450,18 +1425,29 @@ for every Python test framework.  It supports nose, py.test, and unittest.")
         (base32 "1c89vc40zj5aj2zvbvw875wqpyf0x6xrqhm3q5jg797g5hkhbjbz"))))
     (build-system pyproject-build-system)
     (arguments
-     '(#:phases
+     (list
-       (modify-phases %standard-phases
+      #:test-flags #~(list "parameterized/test.py")
-         (replace 'check
+      #:phases
-           (lambda* (#:key tests? #:allow-other-keys)
+      #~(modify-phases %standard-phases
-             (when tests?
+          (add-after 'unpack 'fix-tests
+            (lambda _
               (substitute* "parameterized/test.py"
-                 (("import mock") "from unittest import mock"))
+                ;; It's taken from NixOS package definition.
-               (invoke "python3" "-m" "unittest")))))))
+                ;; <https://github.com/wolever/parameterized/issues/167>,
+                ;; <https://github.com/wolever/parameterized/pull/162>.
+                (("assert_equal\\(missing, \\[\\])") "")
+                (("assertRaisesRegexp") "assertRaisesRegex")))))))
     (native-inputs
-     (list python-jinja2
+     (list python-pytest
+           python-mock
            python-setuptools
-           python-wheel))))
+           python-wheel))
+    (home-page "https://github.com/wolever/parameterized")
+    (synopsis "Parameterized testing with any Python test framework")
+    (description
+     "Parameterized is a Python library that aims to fix parameterized testing
+for every Python test framework.  It supports nose, py.test, and unittest.")
+    (license license:bsd-2)))
 
 (define-public python-minimock
   (package
@@ -2004,35 +1990,29 @@ Python's @code{random.seed}.")
 (define-public python-pytest-runner
   (package
     (name "python-pytest-runner")
-    (version "6.0.0")
+    (version "6.0.1")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "pytest-runner" version))
        (sha256
         (base32
-         "11dnhxnjmh4nf1j8rnvx944ha3wg8ggrgrwdcx4c7d19xmi57n5l"))))
+         "16zly218ij0n6fxzqsasia3vh9xkzl9w0cs9pwvqy057hnap7m3h"))))
     (build-system pyproject-build-system)
     (arguments
      (list
       ;; FIXME: The test suite requires 'python-pytest-virtualenv',
       ;; but that introduces a circular dependency.
-      #:tests? #f
+      #:tests? #f))
-      #:phases
-      #~(modify-phases %standard-phases
-          (replace 'build
-            (lambda _
-              (let ((circa-1980 (* 10 366 24 60 60)))
-                (setenv "SOURCE_DATE_EPOCH" (number->string circa-1980))
-                (invoke "python" "-m" "build" "--wheel" "--no-isolation" "."))))
-          (replace 'install
-            (lambda _
-              (let ((whl (car (find-files "dist" "\\.whl$"))))
-                (invoke "pip" "--no-cache-dir" "--no-input"
-                        "install" "--no-deps" "--prefix" #$output whl)))))))
     (native-inputs
-     (list python-pip python-pypa-build python-pytest
+     (list python-pytest
-           python-setuptools python-setuptools-scm python-wheel))
+           python-pytest-checkdocs
+           python-pytest-enabler
+           ;; python-pytest-virtualenv
+           python-setuptools
+           python-setuptools-scm
+           python-types-setuptools
+           python-wheel))
     (home-page "https://github.com/pytest-dev/pytest-runner")
     (synopsis "Invoke py.test as a distutils command")
     (description
@@ -2825,13 +2805,13 @@ instantly.")
 (define-public python-crosshair
   (package
     (name "python-crosshair")
-    (version "0.0.76")
+    (version "0.0.84")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "crosshair-tool" version))
        (sha256
-        (base32 "1yvbhzs7r85gn4d7drl7p7vi1f5cga1xyy3mzxy3fglyf8kxyakh"))))
+        (base32 "1j6icn5f206yld9871p7a3v45jg8d8v4bhxh09lq3kzi09gr7maz"))))
     (build-system pyproject-build-system)
     (arguments
      (list
@@ -2853,7 +2833,7 @@ instantly.")
                 (("typing-inspect>=0.7.1") "typing-inspect>=0.6.0")
                 ;; 'sanity-check fails for z3-solver, although it is
                 ;; included in 'propagated-inputs.
-                (("z3-solver==4.13.0.0") ""))))
+                (("z3-solver>=4.13.0.0") ""))))
           (add-before 'check 'set-test-env
             (lambda _
               (setenv "PYTHONHASHSEED" "0")))))) ;tests rely on this value
@@ -2863,10 +2843,16 @@ instantly.")
            python-mypy
            python-numpy
            python-pytest
-           python-pytest-xdist))
+           python-pytest-xdist
+           python-setuptools
+           python-wheel))
     (propagated-inputs
-     (list python-typeshed-client
+     (list python-importlib-metadata
+           python-packaging
+           ;; python-pygls
+           python-typeshed-client
            python-typing-inspect
+           python-typing-extensions
            z3))
     (home-page "https://crosshair.readthedocs.io")
     (synopsis "Analysis tool for Python using symbolic execution")
@@ -3132,39 +3118,6 @@ produces a given output.  As mypy can be told to display the type of an
 expression this allows you to check mypys type interference.")
     (license (list license:expat license:asl2.0))))
 
-(define-public python-pytest-pep8
-  (package
-    (name "python-pytest-pep8")
-    (version "1.0.6")
-    (source (origin
-              (method url-fetch)
-              (uri (pypi-uri "pytest-pep8" version))
-              (sha256
-               (base32
-                "06032agzhw1i9d9qlhfblnl3dw5hcyxhagn7b120zhrszbjzfbh3"))))
-    (build-system python-build-system)
-    (arguments
-     `(#:tests? #f ; Fails with recent pytest and pep8. See upstream issues #8 and #12.
-       #:phases
-       (modify-phases %standard-phases
-         (add-after 'unpack 'fix-dependencies
-           (lambda _
-             (substitute* "setup.py"
-               (("'pytest-cache', ") ""))))  ; Included in recent pytest
-         (replace 'check
-            (lambda* (#:key tests? inputs outputs #:allow-other-keys)
-              (when tests?
-                (add-installed-pythonpath inputs outputs)
-                (invoke "pytest" "-v")))))))
-    (native-inputs
-     (list python-pytest))
-    (propagated-inputs
-     (list python-pep8))
-    (home-page "https://bitbucket.org/pytest-dev/pytest-pep8")
-    (synopsis "Py.test plugin to check PEP8 requirements")
-    (description "Pytest plugin for checking PEP8 compliance.")
-    (license license:expat)))
-
 (define-public python-pytest-perf
   (package
     (name "python-pytest-perf")
@@ -3231,19 +3184,13 @@ each of the environments.")
               (sha256
                (base32
                 "0959qfxb4ayvfxvmpargvh4zfhwdq5l77gczhzv33bhmfblk8ccm"))))
-    (build-system python-build-system)
+    (build-system pyproject-build-system)
     (arguments
-     `(#:phases
+     (list
-       (modify-phases %standard-phases
+      #:test-flags
-         (delete 'check)
+      '(list "-k" "not test_syntax_error")))
-         (add-after 'install 'check
-           (lambda* (#:key outputs inputs #:allow-other-keys)
-             ;; It's easier to run tests after install.
-             ;; Make installed package available for running the tests
-             (add-installed-pythonpath inputs outputs)
-             (invoke "py.test" "-vv" "-k" "not test_syntax_error"))))))
     (native-inputs
-     (list python-coverage python-pytest python-pytest-pep8))
+     (list python-coverage python-pytest python-setuptools python-wheel))
     (propagated-inputs
      (list python-pyflakes))
     (home-page "https://github.com/fschulze/pytest-flakes")
@@ -3485,7 +3432,6 @@ backported from Python 2.7 for Python 2.4+.")
     (build-system pyproject-build-system)
     (native-inputs
      (list python-mock
-           python-nose
            python-assertpy
            python-pathpy
            python-pyhamcrest
@@ -3541,37 +3487,6 @@ tests written in a natural language style, backed up by Python code.")
 JSON APIs with Behave.")
     (license license:expat)))
 
-(define-public python-rednose
-  (package
-    (name "python-rednose")
-    (version "1.2.3")
-    (source
-      (origin
-        (method url-fetch)
-        (uri (pypi-uri "rednose" version))
-        (sha256
-          (base32
-            "11x5nx5b4wdq04s7vj1gcdl07jvvkfb37p0r5lg773gr5rr8mj6h"))))
-    (build-system python-build-system)
-    (arguments
-     `(#:phases (modify-phases %standard-phases
-                  (add-after 'unpack 'patch-setup.py
-                    (lambda _
-                      ;; Six is only required for tests and later versions
-                      ;; work fine.
-                      (substitute* "setup.py"
-                        (("six==1.10.0") "six"))
-                      #t)))))
-    (propagated-inputs
-     (list python-colorama python-termstyle))
-    (native-inputs
-     (list python-six python-nose))
-    (home-page "https://github.com/JBKahn/rednose")
-    (synopsis "Colored output for Python nosetests")
-    (description "This package provides colored output for the
-@command{nosetests} command of the Python Nose unit test framework.")
-    (license license:bsd-3)))
-
 (define-public python-nose-exclude
   (package
     (name "python-nose-exclude")
@@ -3632,30 +3547,6 @@ running your code against a large number of randomly generated input
 scenarios.")
     (license license:expat)))
 
-(define-public python-nose-randomly
-  (package
-    (name "python-nose-randomly")
-    (version "1.2.6")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (pypi-uri "nose-randomly" version))
-       (sha256
-        (base32 "0z662rqhfk4bjmg806mn4frb8nz4gbh7mrddsrhfffp1g4yklj3y"))))
-    (build-system python-build-system)
-    (native-inputs
-     (list python-nose python-numpy))
-    (home-page "https://github.com/adamchainz/nose-randomly")
-    (synopsis
-     "Nose plugin to randomly order tests and control random.seed")
-    (description
-     "This is a @code{Nose} plugin to randomly order tests which can be quite
-powerful in discovering hidden flaws in the tests themselves, while helping to
-reduce inter-test dependencies.  It also helps in controlling @code{random.seed},
-by resetting it to a repeatable number for each test, enabling the tests to
-create data based on random numbers and yet remain repeatable.")
-    (license license:bsd-3)))
-
 (define-public python-nose-timer
   (package
     (name "python-nose-timer")
@@ -4398,23 +4289,25 @@ directories and files.")
 (define-public python-pytest-regressions
   (package
     (name "python-pytest-regressions")
-    (version "2.5.0")
+    (version "2.7.0")
     (source
      (origin
        (method url-fetch)
-       (uri (pypi-uri "pytest-regressions" version))
+       (uri (pypi-uri "pytest_regressions" version))
        (sha256
-        (base32 "1nbg20m83jsj9p12fm4qn5b7hc3vqb5h5fzfi6zvmwygq627i341"))))
+        (base32 "0pph1935rq180ax0szwwf3c6zq2v40snypagr49914i31570cc2c"))))
     (build-system pyproject-build-system)
+    (arguments
+     (list
+      ;; Do not fail on warning.
+      ;; DeprecationWarning: module 'sre_constants' is deprecated
+      #:test-flags #~(list "-W" "ignore::DeprecationWarning")))
     (native-inputs
-     (list python-matplotlib
+     (list python-numpy
-           python-numpy
            python-pandas
-           python-pillow
+           python-pytest
-           python-restructuredtext-lint
            python-setuptools
-           python-setuptools-scm
+           python-setuptools-scm))
-           python-pytest))
     (propagated-inputs
      (list python-pytest-datadir
            python-pyyaml))

gnu/packages/cpp.scm

@@ -8,7 +8,7 @@
 ;;; Copyright © 2019 Jan Wielkiewicz <tona_kosmicznego_smiecia@interia.pl>
 ;;; Copyright © 2020, 2021 Nicolò Balzarotti <nicolo@nixo.xyz>
 ;;; Copyright © 2020 Roel Janssen <roel@gnu.org>
-;;; Copyright © 2020, 2021, 2023, 2024 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2020, 2021, 2023, 2024, 2025 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2020 Brice Waegeneire <brice@waegenei.re>
 ;;; Copyright © 2020, 2021, 2022, 2024 Vinicius Monego <monego@posteo.net>
 ;;; Copyright © 2020, 2022 Marius Bakke <marius@gnu.org>
@@ -45,6 +45,7 @@
 ;;; Copyright © 2025 Sharlatan Hellseher <sharlatanus@gmail.com>
 ;;; Copyright © 2025 Sergio Pastor Pérez <sergio.pastorperez@gmail.com>
 ;;; Copyright © 2025 Ashish SHUKLA <ashish.is@lostca.se>
+;;; Copyright © 2025 Nicolas Graves <ngraves@ngraves.fr>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -1549,7 +1550,7 @@ tools:
   ;; header
   (package
     (name "cpp-httplib")
-    (version "0.18.5")
+    (version "0.20.0")
     (source
      (origin
        (method git-fetch)
@@ -1557,7 +1558,7 @@ tools:
              (url "https://github.com/yhirose/cpp-httplib")
              (commit (string-append "v" version))))
        (sha256
-        (base32 "1jc31n4xdrknal4i1dvf8j6j9kafpczi0w5gbbi89xlir9dgm5kp"))
+        (base32 "0w5klyfsaws793xb0cbkjxg7lwrdm6f3m4z4v7pzkwl957f9q70m"))
        (file-name (git-file-name name version))))
     (build-system cmake-build-system)
     (arguments
@@ -1606,7 +1607,7 @@ library.")
 (define-public cpplint
   (package
     (name "cpplint")
-    (version "1.5.5")
+    (version "2.0.0")
     (source
      (origin
        (method git-fetch)
@@ -1616,7 +1617,7 @@ library.")
              (url "https://github.com/cpplint/cpplint")
              (commit version)))
        (sha256
-        (base32 "13l86aq0h1jga949k79k9x3hw2xqchjc162sclg2f99vz98zcz15"))
+        (base32 "06km4wh4944az1hk61g5w8pjhbvbccpgarz1dy7vhwkhfvmvggnk"))
        (file-name (git-file-name name version))))
     (build-system pyproject-build-system)
     (arguments
@@ -1625,6 +1626,11 @@ library.")
                        ,@%pyproject-build-system-modules)
            #:phases
            #~(modify-phases (@ (guix build pyproject-build-system) %standard-phases)
+               (add-after 'unpack 'patch-build-system
+                 (lambda _
+                   (substitute* "pyproject.toml"
+                     (("setuptools\\.build_meta:__legacy__")
+                      "setuptools.build_meta"))))
                (add-before 'wrap 'reduce-GUIX_PYTHONPATH
                  (lambda _
                    ;; Hide the transitive native inputs from GUIX_PYTHONPATH
@@ -1651,9 +1657,11 @@ library.")
                            (getenv "TMP_PYTHONPATH")))))))
     (native-inputs
      (list python-coverage
+           python-parameterized
            python-pytest
            python-pytest-cov
            python-pytest-runner
+           python-pytest-timeout
            python-setuptools
            python-testfixtures
            python-wheel))
@@ -2614,6 +2622,40 @@ union, difference & exclusive-or, and line & polygon offsetting.
 The library is based on Vatti's clipping algorithm.")
     (license license:boost1.0)))
 
+(define-public clipper2
+  (package
+    (inherit clipper)
+    (name "clipper2")
+    (version "1.5.2")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/AngusJohnson/Clipper2")
+             (commit (string-append "Clipper2_" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "1w8cmx712k45cb8gh9dakmbmybiwdx8c0b45mwpcldywx2lwxi2j"))
+       (modules '((guix build utils)))
+       (snippet #~(for-each
+                   delete-file-recursively
+                   '("CSharp" "DLL" "Delphi")))))
+    (build-system cmake-build-system)
+    (arguments
+     (list
+      #:configure-flags
+      #~(list "-DUSE_EXTERNAL_GTEST=ON"
+              "-DCLIPPER2_EXAMPLES=OFF")
+      #:phases #~(modify-phases %standard-phases
+                   (add-after 'unpack 'chdir
+                     (lambda _
+                       (chdir "CPP"))))))
+    (native-inputs (list googletest))
+    (home-page "https://github.com/AngusJohnson/Clipper2")
+    (description
+     (string-append (package-description clipper) "\
+Note: This package is a major update of the original clipper library."))))
+
 (define-public pcg-cpp
   (let ((commit "ffd522e7188bef30a00c74dc7eb9de5faff90092")
         (revision "2"))
@@ -3754,6 +3796,26 @@ file name and location, as well as filters with friendly names (such as
 \"source files\" or \"image files\") where supported.")
     (license license:zlib)))
 
+(define-public string-view-lite
+  (package
+    (name "string-view-lite")
+    (version "1.8.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/martinmoene/string-view-lite")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "1mfp3lmqx7ac0545akxd2v05rrapa3byz8q4gb9rqy94pcqbfyc5"))))
+    (build-system cmake-build-system)
+    (home-page "https://github.com/martinmoene/string-view-lite")
+    (synopsis "C++17 string-view for older C++")
+    (description "This package provides a compatibility header-only library
+for C++17 string-view.")
+    (license license:boost1.0)))
+
 (define-public tsl-hopscotch-map
   (package
     (name "tsl-hopscotch-map")

gnu/packages/crates-io.scm

@@ -47545,8 +47545,45 @@ without performing I/O.")
         ("rust-rustversion" ,rust-rustversion-1)
         ("rust-tempfile" ,rust-tempfile-3))))))
 
+(define-public rust-notify-7
+  (package
+    (name "rust-notify")
+    (version "7.0.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (crate-uri "notify" version))
+       (file-name (string-append name "-" version ".tar.gz"))
+       (sha256
+        (base32 "02a0a1n0raxqslwhfprwmz7w34v54r42006q0m8bmy89jz1v8cy5"))))
+    (build-system cargo-build-system)
+    (arguments
+     (list
+      #:cargo-inputs (list rust-bitflags-2
+                           rust-crossbeam-channel-0.5
+                           rust-filetime-0.2
+                           rust-fsevent-sys-4
+                           rust-inotify-0.10
+                           rust-kqueue-1
+                           rust-libc-0.2
+                           rust-log-0.4
+                           rust-mio-1
+                           rust-notify-types-1
+                           rust-walkdir-2
+                           rust-windows-sys-0.52)
+      #:cargo-development-inputs (list rust-insta-1
+                                       rust-nix-0.27
+                                       rust-serde-json-1
+                                       rust-tempfile-3)))
+    (home-page "https://github.com/notify-rs/notify")
+    (synopsis "Cross-platform filesystem notification library")
+    (description "This package contains a cross-platform filesystem
+notification library.")
+    (license license:cc0)))
+
 (define-public rust-notify-6
   (package
+    (inherit rust-notify-7)
     (name "rust-notify")
     (version "6.1.1")
     (source
@@ -47556,7 +47593,6 @@ without performing I/O.")
        (file-name (string-append name "-" version ".tar.gz"))
        (sha256
         (base32 "0bad98r0ilkhhq2jg3zs11zcqasgbvxia8224wpasm74n65vs1b2"))))
-    (build-system cargo-build-system)
     (arguments
      `(#:cargo-inputs (("rust-bitflags" ,rust-bitflags-2)
                        ("rust-crossbeam-channel" ,rust-crossbeam-channel-0.5)
@@ -47572,12 +47608,7 @@ without performing I/O.")
                        ("rust-windows-sys" ,rust-windows-sys-0.48))
        #:cargo-development-inputs (("rust-nix" ,rust-nix-0.23)
                                    ("rust-serde-json" ,rust-serde-json-1)
-                                   ("rust-tempfile" ,rust-tempfile-3))))
+                                   ("rust-tempfile" ,rust-tempfile-3))))))
-    (home-page "https://github.com/notify-rs/notify")
-    (synopsis "Cross-platform filesystem notification library")
-    (description "This package contains a cross-platform filesystem
-notification library.")
-    (license license:cc0)))
 
 (define-public rust-notify-5
   (package
@@ -47740,6 +47771,29 @@ client and server")
 Rust dbus client and server.")
     (license (list license:expat license:asl2.0))))
 
+(define-public rust-notify-types-1
+  (package
+    (name "rust-notify-types")
+    (version "1.0.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (crate-uri "notify-types" version))
+       (file-name (string-append name "-" version ".tar.gz"))
+       (sha256
+        (base32 "0x5idrpxzf70ng88rz28dqmgx1jyddf0vxx1x3csw09fw6skqpaq"))))
+    (build-system cargo-build-system)
+    (arguments
+     `(#:cargo-inputs (("rust-instant" ,rust-instant-0.1)
+                       ("rust-serde" ,rust-serde-1))
+       #:cargo-development-inputs (("rust-insta" ,rust-insta-1)
+                                   ("rust-rstest" ,rust-rstest-0.21)
+                                   ("rust-serde-json" ,rust-serde-json-1))))
+    (home-page "https://github.com/notify-rs/notify")
+    (synopsis "Types used by the notify crate")
+    (description "This package provides rust types used by the notify crate.")
+    (license (list license:expat license:asl2.0))))
+
 (define-public rust-notmuch-0.8
   (package
     (name "rust-notmuch")

gnu/packages/cybersecurity.scm

@@ -3,6 +3,7 @@
 ;;; Copyright © 2020, 2021 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2021 c4droid <c4droid@foxmail.com>
 ;;; Copyright © 2021 Raghav Gururajan <rg@raghavgururajan.name>
+;;; Copyright © 2025 Nicolas Graves <ngraves@ngraves.fr>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -30,9 +31,11 @@
   #:use-module (gnu packages engineering)
   #:use-module (gnu packages pkg-config)
   #:use-module (gnu packages python)
-  #:use-module (gnu packages python-xyz)
+  #:use-module (gnu packages python-build)
+  #:use-module (gnu packages python-compression)
   #:use-module (gnu packages python-crypto)
   #:use-module (gnu packages python-web)
+  #:use-module (gnu packages python-xyz)
   #:use-module (gnu packages time)
   #:use-module (gnu packages bioinformatics)      ;python-intervaltree
   #:use-module (gnu packages emulators))
@@ -123,24 +126,26 @@ chains of gadgets to execute system calls.")
 (define-public pwntools
   (package
     (name "pwntools")
-    (version "4.4.0")
+    (version "4.15.0b1")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "pwntools" version))
        (sha256
         (base32
-         "1qw7j0wwm1878aia08gyw5xljjr26qsbp45w65n4qff672sha5n5"))))
+         "091fsk9rvbjkcsp8mmww0ka26dvznmj4pbqwaiygcw90g3v94zgd"))))
     (build-system python-build-system)
     (arguments
      '(#:tests? #f))                 ;XXX: needs a specific version of unicorn
     (propagated-inputs
      (list capstone
+           python-colored-traceback
            python-dateutil
            python-intervaltree
            python-mako
            python-packaging
            python-paramiko
+           python-pathlib2
            python-psutil
            python-pyelftools
            python-pygments
@@ -148,9 +153,14 @@ chains of gadgets to execute system calls.")
            python-pysocks
            python-requests
            ropgadget
+           python-rpyc
            python-six
            python-sortedcontainers
+           python-unix-ar
+           python-zstandard
            unicorn))
+    (native-inputs
+     (list python-setuptools python-toml python-wheel))
     (home-page "https://github.com/Gallopsled/pwntools")
     (synopsis
      "Capture-the-flag (CTF) framework and exploit development library")

gnu/packages/databases.scm

@@ -3371,20 +3371,24 @@ coroutine-specific markup.")
 (define-public python-asyncpg
   (package
     (name "python-asyncpg")
-    (version "0.25.0")
+    (version "0.30.0")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "asyncpg" version))
        (sha256
-        (base32 "0h1573lp4607nppflnnjrhn7yrfy6i54cm98gi4qbcikjykfdy33"))))
+        (base32 "0lf8xbrsb2ycpqx1vzlb05p48g5sh9zq24a8yh17cw5nia9fjlf5"))))
-    (build-system python-build-system)
+    (build-system pyproject-build-system)
-    (propagated-inputs (list python-typing-extensions))
     (native-inputs
      (list postgresql
            python-cython
            python-pytest
-           python-uvloop))
+           python-uvloop
+           python-distro
+           python-setuptools
+           python-wheel))
+    (propagated-inputs
+     (list python-async-timeout))
     (home-page "https://github.com/MagicStack/asyncpg")
     (synopsis "Fast PostgreSQL database client library for Python")
     (description "@code{asyncpg} is a database interface library designed
@@ -4574,7 +4578,11 @@ reasonable substitute.")
                      "test_tfunction_load_delete"
                      "test_tfunction_list"
                      ;; AssertionError: assert 3 == 2
-                     "test_acl_list")
+                     "test_acl_list"
+                     ;; XXX: This test occasionally fails on i686-linux
+                     #$@(if (target-x86-32?)
+                            '("test_geopos")
+                            '()))
                     " and not "))
       #:phases
       #~(modify-phases %standard-phases
@@ -4608,7 +4616,7 @@ reasonable substitute.")
 (define-public python-rq
   (package
     (name "python-rq")
-    (version "1.11.1")
+    (version "2.3.1")
     (source
      (origin
        (method git-fetch)
@@ -4617,24 +4625,20 @@ reasonable substitute.")
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "0dnjm2s036l4j4ypq0h903vh132dp2wiwjrn8jicz1nw829dqpzf"))))
+        (base32 "1w9aqvbvh1mfpgng0mdcskxl5y3ybcqqai5dnwgvg18am0xxhya6"))))
-    (build-system python-build-system)
+    (build-system pyproject-build-system)
     (arguments
-     '(#:phases (modify-phases %standard-phases
+     (list
+      #:phases #~(modify-phases %standard-phases
                    (add-before 'check 'start-redis
                      (lambda _
-                      (invoke "redis-server" "--daemonize" "yes")))
+                       (invoke "redis-server" "--daemonize" "yes"))))))
-                  (replace 'check
-                    (lambda* (#:key outputs #:allow-other-keys)
-                      (let ((out (assoc-ref outputs "out")))
-                        ;; Drop test that needs the SDK for Sentry.io.
-                        (delete-file "tests/test_sentry.py")
-                        ;; Ensure 'rq' and 'rqworker' ends up on PATH.
-                        (setenv "PATH" (string-append out "/bin:"
-                                                      (getenv "PATH")))
-                        (invoke "pytest" "-vv")))))))
     (native-inputs
-     (list python-mock python-psutil python-pytest redis))
+     (list python-hatchling
+           python-mock
+           python-psutil
+           python-pytest
+           redis))
     (propagated-inputs
      (list python-click python-redis))
     (home-page "https://python-rq.org/")
@@ -4648,7 +4652,7 @@ is designed to have a low barrier to entry.")
 (define-public python-rq-scheduler
   (package
     (name "python-rq-scheduler")
-    (version "0.10.0")
+    (version "0.14")
     (home-page "https://github.com/rq/rq-scheduler")
     (source (origin
               (method git-fetch)
@@ -4658,21 +4662,30 @@ is designed to have a low barrier to entry.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "0xg6yazqs5kbr2ayvhvljs1h5vgx5k5dds613fmhswln7gglf9hk"))))
+                "09fh9m2vcl1jndq35xp1x0j8ih009r71qmhn2pkl93fykrqfavyn"))))
-    (build-system python-build-system)
+    (build-system pyproject-build-system)
     (arguments
-     '(#:phases (modify-phases %standard-phases
+     (list
+      #:test-flags
+      #~(list "-k" (string-append "not test_cron"
+                                  " and not test_job_creation_with"
+                                  " and not test_job_with_crontab"))
+      #:phases #~(modify-phases %standard-phases
                    (add-before 'check 'start-redis
                      (lambda _
                        (invoke "redis-server" "--daemonize" "yes")))
-                  (replace 'check
+                   (add-after 'unpack 'loosen-requirements
                      (lambda _
-                      (substitute* "run_tests.py"
+                       (substitute* "setup.py"
-                        (("/usr/bin/env")
+                         (("crontab>=[0-9.]*")
-                         (which "env")))
+                          "python-crontab")))))))
-                      (invoke "./run_tests.py"))))))
     (native-inputs
-     (list redis which))
+     (list python-crontab
+           python-freezegun
+           python-pytest
+           python-setuptools
+           python-wheel
+           redis))
     (propagated-inputs
      (list python-croniter python-rq))
     (synopsis "Job scheduling capabilities for RQ (Redis Queue)")
@@ -4724,14 +4737,15 @@ provides support for parsing, splitting and formatting SQL statements.")
 (define-public python-sql
   (package
     (name "python-sql")
-    (version "1.3.0")
+    (version "1.5.2")
     (source
      (origin
        (method url-fetch)
-       (uri (pypi-uri "python-sql" version))
+       (uri (pypi-uri "python_sql" version))
        (sha256
-        (base32 "0xnimfzlxj1ddrb5xj3s4gaii278a0gpxrvwmdmrdxgjfdi3lq4x"))))
+        (base32 "0dnd0vai9z1fjkppv2xv2f4vlwwz0dqa137f39mrbjw744vm4pvk"))))
-    (build-system python-build-system)
+    (build-system pyproject-build-system)
+    (native-inputs (list python-setuptools python-wheel))
     (home-page "https://python-sql.tryton.org/")
     (synopsis "Library to write SQL queries in a pythonic way")
     (description "@code{python-sql} is a library to write SQL queries, that
@@ -5359,7 +5373,7 @@ other traditional Python scientific computing packages.")
 (define-public python-fastparquet
   (package
     (name "python-fastparquet")
-    (version "2024.2.0")
+    (version "2024.11.0")
     (source
      (origin
        ;; Fastparquet uses setuptools-scm to find the current version. This
@@ -5372,7 +5386,7 @@ other traditional Python scientific computing packages.")
              (commit version)))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "0f32dj1xvd11l0siznqd33dpjlhg9siylcjcfkcdlqfcy45jfj3v"))))
+        (base32 "0dhmyag06d073g1q58npbcikr9hjd6jgf05721gkl6m1gsprv7hq"))))
     (build-system pyproject-build-system)
     (arguments
      (list
@@ -5398,6 +5412,13 @@ other traditional Python scientific computing packages.")
             ;; Cython extensions need to be built for the check phase.
             (lambda _
               (invoke "python" "setup.py" "build_ext" "--inplace"))))))
+    (native-inputs
+     (list python-cython
+           python-pytest
+           python-pytest-xdist
+           python-setuptools
+           python-setuptools-scm
+           python-wheel))
     (propagated-inputs
      (list python-cramjam
            python-fsspec
@@ -5405,11 +5426,6 @@ other traditional Python scientific computing packages.")
            python-numpy
            python-packaging
            python-pandas))
-    (native-inputs
-     (list python-cython
-           python-pytest-runner
-           python-pytest-xdist
-           python-setuptools-scm))
     (home-page "https://github.com/dask/fastparquet")
     (synopsis "Python implementation of the Parquet file format")
     (description

gnu/packages/django.scm

@@ -148,26 +148,10 @@ to the @dfn{don't repeat yourself} (DRY) principle.")
                   ;; This CVE seems fixed since 4.2.1.
                   (lint-hidden-cve . ("CVE-2023-31047"))))))
 
-(define-public python-django-3.2
-  (package
-    (inherit python-django-4.2)
-    (version "3.2.21")
-    (source (origin
-              (method url-fetch)
-              (uri (pypi-uri "Django" version))
-              (sha256
-               (base32
-                "0g3zm2glh76g31q06g6fwkwvkrphjj3mnap5sgk1hx3v9r44rpm5"))))
-    (native-search-paths '())           ;no need for TZDIR
-    (propagated-inputs
-     (modify-inputs (package-propagated-inputs python-django-4.2)
-       ;; Django 4.0 deprecated pytz in favor of Pythons built-in zoneinfo.
-       (append python-pytz)))))
-
 ;; archivebox requires django>=3.1.3,<3.2
 (define-public python-django-3.1.14
   (package
-    (inherit python-django-3.2)
+    (inherit python-django-4.2)
     (version "3.1.14")
     (source (origin
               (method url-fetch)
@@ -176,7 +160,7 @@ to the @dfn{don't repeat yourself} (DRY) principle.")
                (base32
                 "0ix3v2wlnplv78zxjrlw8z3hiap2d5mxvk0ny2fc65526shsb93j"))))
     (propagated-inputs
-     (modify-inputs (package-propagated-inputs python-django-3.2)
+     (modify-inputs (package-propagated-inputs python-django-4.2)
        ;; Django 4.0 deprecated pytz in favor of Pythons built-in zoneinfo.
        (append python-pytz)))))
 
@@ -1055,35 +1039,37 @@ support, and optional data-URI image and font embedding.")
 (define-public python-django-rq
   (package
     (name "python-django-rq")
-    (version "2.7.0")
+    (version "3.0.0")
     (source (origin
               (method url-fetch)
               (uri (pypi-uri "django-rq" version))
               (sha256
                (base32
-                "0aw0fi0lg80qgdp9fhjbnlhvfh2p09rgy1nj6hxpyhi37kihni2h"))))
+                "1b371w4cdjlz83i2sg4gpx0z3svl3bfrn6zfy661374hv62xpnkv"))))
     (build-system pyproject-build-system)
     (arguments
      (list
+      #:test-flags
+      #~(list "-k" "not test_scheduled_jobs and not test_started_jobs")
       #:phases
-      '(modify-phases %standard-phases
+      #~(modify-phases %standard-phases
-         (replace 'check
+          (add-before 'check 'pre-check
             (lambda* (#:key tests? #:allow-other-keys)
               (when tests?
                 (invoke "redis-server" "--daemonize" "yes")
-               (invoke "django-admin" "test" "django_rq"
+                (setenv "DJANGO_SETTINGS_MODULE" "django_rq.tests.settings")
-                       "--settings=django_rq.tests.settings"
+                (setenv "PYTHONPATH" (getcwd))))))))
-                       "--pythonpath=.")))))))
     (native-inputs
      (list python-django-redis
-           python-mock
+           python-pytest
+           python-pytest-django
            python-rq-scheduler
            python-setuptools
            python-wheel
            redis
            tzdata-for-tests))
     (propagated-inputs
-     (list python-django python-rq))
+     (list python-django python-redis python-rq python-pyaml))
     (home-page "https://github.com/ui/django-rq")
     (synopsis "Django integration with RQ")
     (description

gnu/packages/documentation.scm

@@ -41,6 +41,7 @@
   #: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)
   #:use-module (guix utils)
@@ -51,6 +52,7 @@
   #:use-module (gnu packages bash)
   #:use-module (gnu packages check)
   #:use-module (gnu packages python)
+  #:use-module (gnu packages python-build)
   #:use-module (gnu packages python-xyz)
   #:use-module (gnu packages bison)
   #:use-module (gnu packages kde-frameworks)
@@ -315,6 +317,8 @@ format, and supports the file types JPG, GIF, TIFF, PNG, and PNM for embedded
 objects.")
     (license license:artistic2.0)))
 
+;; XXX: This project looks not maintained, and some tests fail to pass, see
+;; <https://github.com/spyder-ide/docrepr/issues/49>.
 (define-public python-docrepr
   (package
     (name "python-docrepr")
@@ -329,9 +333,10 @@ objects.")
                (base32
                 "1ma5gwy93m1djd3zdlnqfrwhgr8ic1qbsz5kkrb9f987ax40lfkd"))
               (patches (search-patches "python-docrepr-fix-tests.patch"))))
-    (build-system python-build-system)
+    (build-system pyproject-build-system)
     (arguments
      (list
+      #:tests? #f ; all tests fail
       #:phases
       #~(modify-phases %standard-phases
           (add-after 'unpack 'patch-sources
@@ -344,17 +349,13 @@ objects.")
               ;; https://github.com/spyder-ide/docrepr/issues/54).
               (substitute* "docrepr/utils.py"
                 (("except TypeError")
-                 "except (TypeError, shutil.Error)"))))
+                 "except (TypeError, shutil.Error)")))))))
-          (replace 'check
-            (lambda* (#:key tests? #:allow-other-keys)
-              (when tests?
-                (invoke "pytest" "-p" "no:warnings" "-vv")))))))
     (native-inputs
      (list python-ipython
            python-matplotlib
            python-numpy
-           python-pytest
+           python-setuptools
-           python-pytest-asyncio))
+           python-wheel))
     (propagated-inputs
      (list python-docutils
            python-jinja2

gnu/packages/ebook.scm

@@ -249,7 +249,7 @@ tags = [\"WS_X11\"]")
                  (string-append "[tool.sip.project]
 sip-include-dirs = [\""
                    #$(this-package-input "python-pyqt")
-                   "/lib/python3.10/site-packages/PyQt5/bindings\"]")))
+                   "/lib/python3.11/site-packages/PyQt5/bindings\"]")))
               (substitute* "src/calibre/ebooks/pdf/pdftohtml.py"
                 (("PDFTOHTML = 'pdftohtml'")
                  (string-append "PDFTOHTML = \""

gnu/packages/engineering.scm

@@ -3138,7 +3138,9 @@ Microwave engineering.")
                              python-scipy
                              python-sympy
                              python-wheel))
-    (native-inputs (list python-pytest))
+    (native-inputs (list python-pytest
+                         python-setuptools
+                         python-wheel))
     (home-page "https://github.com/mph-/lcapy")
     (synopsis "Symbolic linear circuit analysis")
     (description "Lcapy is a Python package for linear circuit analysis.  It
@@ -5188,22 +5190,23 @@ more.")
   (package
     (name "python-asyncua")
     (version "1.1.5")
-    (source (origin
+    (source
+     (origin
        (method git-fetch)
        (uri (git-reference
              (url "https://github.com/FreeOpcUa/opcua-asyncio.git")
              (commit (string-append "v" version))
+             ;; XXX: It clones <https://github.com/OPCFoundation/UA-Nodeset>
+             ;; submodule, check if it may be unbundled.
              (recursive? #t)))
        (file-name (git-file-name name version))
        (sha256
-               (base32
+        (base32 "0aisj8cpfhq50h4pv2p0c9iw5cqy3hxhn5adp8wd01c46dhg6y2x"))))
-                "0aisj8cpfhq50h4pv2p0c9iw5cqy3hxhn5adp8wd01c46dhg6y2x"))))
     (build-system pyproject-build-system)
     (native-inputs
-     (list python-asynctest
+     (list python-pytest
            python-pytest-asyncio-0.21
            python-pytest-mock
-           python-pytest-runner
            python-setuptools
            python-wheel))
     (propagated-inputs
@@ -5342,7 +5345,7 @@ and mogan.")
                (("'\" [+] python_path [+]")
                 (string-append "'\" + std::string(\""
                                (assoc-ref outputs "out")
-                               "/lib/python3.10/site-packages"
+                               "/lib/python3.11/site-packages"
                                "\") +")))))
           (add-before 'check 'prepare-checks
             (lambda _

gnu/packages/file-systems.scm

@@ -2035,33 +2035,6 @@ compatible directories.")
       (home-page "https://github.com/trapexit/mergerfs-tools")
       (license license:isc))))
 
-(define-public python-dropbox
-  (package
-    (name "python-dropbox")
-    (version "12.0.2")
-    (source
-      (origin
-        (method url-fetch)
-        (uri (pypi-uri "dropbox" version))
-        (sha256
-         (base32 "0qlrc2ykl7zmv808apqv5ycfzrwnm13ngz1daizh9kszmpapy1ah"))
-        (snippet
-         '(begin
-            (use-modules (guix build utils))
-            (substitute* "setup.py"
-              (("pytest-runner==5\\.2\\.0") "pytest-runner"))))))
-    (build-system python-build-system)
-    (arguments '(#:tests? #f))  ; Tests not included in the release tarball.
-    (native-inputs
-     (list python-pytest python-pytest-runner))
-    (propagated-inputs
-     (list python-requests python-six python-stone))
-    (home-page "https://www.dropbox.com/developers")
-    (synopsis "Official Dropbox API Client")
-    (description "This package provides a Python SDK for integrating with the
-Dropbox API v2.")
-    (license license:expat)))
-
 (define-public dbxfs
   (package
     (name "dbxfs")

gnu/packages/finance.scm

@@ -1039,15 +1039,23 @@ of Bitcoin BIP-0039.")
   (package
     (name "python-u2flib-host")
     (version "3.0.3")
-    (source (origin
+    (source
+     (origin
        (method url-fetch)
        (uri (pypi-uri "python-u2flib-host" version))
        (sha256
-               (base32
+        (base32 "02pwafd5kyjpc310ys0pgnd0adff1laz18naxxwsfrllqafqnrxb"))))
-                "02pwafd5kyjpc310ys0pgnd0adff1laz18naxxwsfrllqafqnrxb"))))
+    (build-system pyproject-build-system)
-    (build-system python-build-system)
+    (arguments
+     (list
+      #:test-flags
+        #~(list
+          "--deselect=test/test_soft.py::TestSoftU2FDevice::test_registeration"
+          "--deselect=test/test_reg_auth.py::TestRegister::test_register" "-k"
+          "not test_forget")))
     (propagated-inputs (list python-hidapi python-requests))
-    (native-inputs (list python-cryptography))
+    (native-inputs (list python-cryptography python-pytest python-setuptools
+                         python-wheel))
     (home-page "https://github.com/Yubico/python-u2flib-host")
     (synopsis "Python based U2F host library")
     (description
@@ -1063,15 +1071,19 @@ of Bitcoin BIP-0039.")
        (method url-fetch)
        (uri (pypi-uri "ledgerblue" version))
        (sha256
-          (base32
+        (base32 "0ghpvxgih1zarp788qi1xh5xmprv6yhaxglfbix4974i7r4pszqy"))))
-            "0ghpvxgih1zarp788qi1xh5xmprv6yhaxglfbix4974i7r4pszqy"))))
     (build-system pyproject-build-system)
     (arguments
-     `(#:tests? #f)) ; no tests
+     (list
-    (native-inputs
+      #:tests? #f
-     (list python-setuptools python-wheel))
+      #:phases
-    (propagated-inputs
+      #~(modify-phases %standard-phases
-     (list python-bleak
+          (add-before 'build 'pretend-version
+            (lambda _
+              (setenv "SETUPTOOLS_SCM_PRETEND_VERSION"
+                      #$version))))))
+    (native-inputs (list python-setuptools python-setuptools-scm python-wheel))
+    (propagated-inputs (list python-bleak
                              python-pyelftools
                              python-pycryptodome
                              python-ecpy
@@ -1216,9 +1228,11 @@ the KeepKey Hardware Wallet.")
        (sha256
         (base32
          "03zj602m2rln9yvr08dswy56vzkbldp8b074ixwzz525dafblr92"))))
-    (build-system python-build-system)
+    (build-system pyproject-build-system)
     (inputs
      (list python-ledgerblue python-trezor-agent))
+    (native-inputs
+     (list python-setuptools python-wheel))
     (home-page "https://github.com/romanz/trezor-agent")
     (synopsis "Ledger as hardware SSH/GPG agent")
     (description "This package allows using Ledger as hardware SSH/GPG agent.")
@@ -1414,42 +1428,22 @@ Luhn and family of ISO/IEC 7064 check digit algorithms.")
 (define-public python-duniterpy
   (package
     (name "python-duniterpy")
-    (version "1.1.1")
+    (version "1.2.1")
     (source
      (origin
-       (method url-fetch)
+       (method git-fetch)
-       (uri (pypi-uri "duniterpy" version))
+       (uri (git-reference
+             (url "https://git.duniter.org/clients/python/duniterpy")
+             (commit version)))
+       (file-name (git-file-name name version))
        (sha256
-        (base32 "0h0fsawsrjd50lb1bkysb21ph39qlhmiymd3r5vs695qxvbwaqaa"))))
+        (base32 "1ysh9b5lzg053hv4iw3zbn7hid05qssiwmrl8sir8qlk958r8x60"))))
     (build-system pyproject-build-system)
-    (arguments
-     ;; FIXME: Tests fail with: "TypeError: block_uid() missing 1 required
-     ;; positional argument: 'value'".
-     `(#:tests? #f
-       #:phases (modify-phases %standard-phases
-                  (add-after 'unpack 'loosen-requirements
-                    (lambda _
-                      (substitute* "pyproject.toml"
-                        (("mnemonic = \"\\^0\\.19")
-                         "mnemonic = \">=0.19")
-                        (("jsonschema = \"\\^3\\.2")
-                         "jsonschema = \">=3.2"))))
-                  (add-after 'unpack 'adjust-for-new-libnacl
-                    (lambda _
-                      ;; Mimic upstream commit ad8f6a26e9e7067; remove
-                      ;; for newer versions of duniterpy.
-                      (substitute* "pyproject.toml"
-                        (("libnacl = \"1\\.8")
-                         "libnacl = \">=1.9"))
-                      (substitute* "duniterpy/key/ascii_armor.py"
-                        (("from libnacl\\.version import version as libnacl_version")
-                         "import importlib.metadata
-libnacl_version = importlib.metadata.version('libnacl')")))))))
     (native-inputs
-     (list python-poetry-core))
+     (list python-poetry-core-next
+           python-pytest))
     (propagated-inputs
-     (list python-attrs
+     (list python-base58
-           python-base58
            python-graphql-core
            python-jsonschema
            python-libnacl

gnu/packages/fontutils.scm

@@ -505,14 +505,19 @@ subroutinizer for fontTools.")
        (uri (pypi-uri "cu2qu" version ".zip"))
        (sha256
         (base32 "1x762r7bf39g6aivfvrmq00h6f07abvs9x1xm0fz8l81vq8jz64c"))))
-    (build-system python-build-system)
+    (build-system pyproject-build-system)
+    (arguments
+     ;; XXX: Try to remove it when updating python-fonttools.
+     (list #:test-flags #~(list "-k" "not test_ignore_single_points")))
     (propagated-inputs (list python-fonttools))
     (native-inputs
      (list python-cython
            python-defcon
            python-pytest
            python-pytest-runner
+           python-setuptools
            python-setuptools-scm
+           python-wheel
            unzip))
     (home-page "https://github.com/googlefonts/cu2qu")
     (synopsis "Cubic-to-quadratic bezier curve conversion")

gnu/packages/freedesktop.scm

@@ -68,6 +68,7 @@
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system meson)
   #:use-module (guix build-system perl)
+  #:use-module (guix build-system pyproject)
   #:use-module (guix build-system python)
   #:use-module (guix build-system glib-or-gtk)
   #:use-module (guix build-system qt)
@@ -128,6 +129,7 @@
   #:use-module (gnu packages pkg-config)
   #:use-module (gnu packages polkit)
   #:use-module (gnu packages python)
+  #:use-module (gnu packages python-build)
   #:use-module (gnu packages python-crypto)
   #:use-module (gnu packages python-xyz)
   #:use-module (gnu packages qt)
@@ -789,7 +791,7 @@ other applications that need to directly deal with input devices.")
 (define-public libei
   (package
     (name "libei")
-    (version "1.3.0")
+    (version "1.4.0")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -797,7 +799,7 @@ other applications that need to directly deal with input devices.")
                     (commit version)))
               (sha256
                (base32
-                "0idbl20ax060s7m435rszfv7c0bvpinjvq45qbqwvcvp0hg8r9y8"))
+                "04ll43616pyfm7c835azdggx9x3vfykpcg3pzmsfz4f2vl5whalm"))
               (snippet
                #~(begin
                    (use-modules (guix build utils))
@@ -819,17 +821,18 @@ other applications that need to directly deal with input devices.")
      ;; liboeffis-1.0.pc requires.private libelogind
      (list elogind))
     (native-inputs
-     (list doxygen
+     (list dbus
+           doxygen
            libxml2
            munit
            pkg-config
            python
            python-attrs
-           python-black
            python-dbusmock
            python-jinja2
            python-pytest
            python-structlog
+           python-pyaml
            valgrind/interactive))
     (home-page "https://libinput.pages.freedesktop.org/libei/")
     (synopsis "Emulated Input protocol implementation")
@@ -2872,17 +2875,19 @@ encoding names are iconv-compatible.")
 (define-public python-cchardet
   (package
   (name "python-cchardet")
-  (version "2.1.7")
+  (version "2.2.0a2")
   (source
     (origin
       (method url-fetch)
       (uri (pypi-uri "cchardet" version))
       (sha256
         (base32
-          "1bqfz85cd51sw0bvhvdq9ikccxi2ld7g5jpni4jkq1a5clrvca64"))))
+          "08wq5yfaafbjipabfc6kpyvivkk2394w7isv0mwx5agcf8cbnwnx"))))
-  (build-system python-build-system)
+  (build-system pyproject-build-system)
   (inputs
    (list uchardet))
+  (native-inputs
+   (list python-setuptools python-wheel))
   (home-page "https://github.com/PyYoshi/cChardet")
   (synopsis "High-performance character encoding detection for Python")
   (description "cChardet is a character encoding detector, written in

gnu/packages/gnome-xyz.scm

@@ -67,10 +67,10 @@
   #:use-module (gnu packages ibus)
   #:use-module (gnu packages inkscape)
   #:use-module (gnu packages image)
+  #:use-module (gnu packages maths)
   #:use-module (gnu packages pcre)
   #:use-module (gnu packages pkg-config)
   #:use-module (gnu packages python)
-  #:use-module (gnu packages python-science)
   #:use-module (gnu packages python-xyz)
   #:use-module (gnu packages ssh)
   #:use-module (gnu packages tls)

gnu/packages/gnome.scm

@@ -7479,60 +7479,6 @@ almost all of them.")
 principles are simplicity and standards compliance.")
     (license license:gpl2+)))
 
-(define-public d-feet
-  (package
-    (name "d-feet")
-    (version "0.3.16")
-    (source (origin
-              (method url-fetch)
-              (uri (string-append "mirror://gnome/sources/" name "/"
-                                  (version-major+minor version) "/"
-                                  name "-" version ".tar.xz"))
-              (sha256
-               (base32
-                "1jqw5ndpgyb0zxh0g21ai1911lfrm56vz18xbccfqm4sk95wwcw7"))
-              (patches
-               (search-patches "d-feet-drop-unused-meson-argument.patch"))))
-    (build-system meson-build-system)
-    (arguments
-     (list
-      #:glib-or-gtk? #t
-      #:phases
-      #~(modify-phases %standard-phases
-          (add-before 'check 'pre-check
-            (lambda _
-              ;; The test suite requires a running X server.
-              (system "Xvfb :1 &")
-              (setenv "DISPLAY" ":1")))
-          (add-before 'install 'disable-gtk-update-icon-cache
-            (lambda _
-              (setenv "DESTDIR" "/")))
-          (add-after 'install 'wrap-program
-            (lambda* (#:key outputs #:allow-other-keys)
-              (wrap-program (search-input-file outputs "bin/d-feet")
-                `("GUIX_PYTHONPATH" = (,(getenv "GUIX_PYTHONPATH")))
-                `("GI_TYPELIB_PATH" = (,(getenv "GI_TYPELIB_PATH")))))))))
-    (native-inputs
-     (list `(,glib "bin")
-           intltool
-           itstool
-           libxml2
-           pkg-config
-           python-pep8
-           xorg-server-for-tests))
-    (inputs
-     (list bash-minimal
-           gobject-introspection
-           gtk+
-           python-wrapper
-           python-pygobject))
-    (home-page "https://wiki.gnome.org/Apps/DFeet")
-    (synopsis "D-Bus debugger")
-    (description
-     "D-Feet is a D-Bus debugger, which can be used to inspect D-Bus interfaces
-of running programs and invoke methods on those interfaces.")
-    (license license:gpl2+)))
-
 (define-public d-spy
   (package
     (name "d-spy")
@@ -7574,6 +7520,9 @@ programs via D-Bus.  It also ships a library for integration into development
 environments.")
     (license license:gpl2+)))
 
+(define-public d-feet
+  (deprecated-package "d-feet" d-spy))
+
 (define-public yelp-xsl
   (package
     (name "yelp-xsl")

gnu/packages/gnupg.scm

@@ -5,7 +5,7 @@
 ;;; Copyright © 2014, 2015, 2016, 2020 Mark H Weaver <mhw@netris.org>
 ;;; Copyright © 2015 Paul van der Walt <paul@denknerd.org>
 ;;; Copyright © 2015-2021, 2024 Efraim Flashner <efraim@flashner.co.il>
-;;; Copyright © 2015, 2016, 2017, 2019 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2015, 2016, 2017, 2019, 2025 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2016 Christine Lemmer-Webber <cwebber@dustycloud.org>
 ;;; Copyright © 2016, 2017 Nikita <nikita@n0.is>
 ;;; Copyright © 2016 Christopher Baines <mail@cbaines.net>
@@ -585,10 +585,17 @@ interface (FFI) of Guile.")
                 "1ji3ynhp36m1ccx7bmaq75dhij9frpn19v9mpi4aajn8csl194il"))))
     (build-system python-build-system)
     (arguments
-     '(#:phases
+     `(#:phases
        (modify-phases %standard-phases
          (add-before 'build 'set-environment
            (lambda _
+             ;; GPGME is built with large file support, so we need to set
+             ;; _FILE_OFFSET_BITS to 64 in all users of the GPGME library.
+             ,@(if (or (target-x86-32?) (target-arm32?))
+                   `((substitute* "setup.py"
+                       (("extra_macros = dict\\(\\)")
+                        "extra_macros = { \"_FILE_OFFSET_BITS\": 64 }")))
+                   '())
              (substitute* "setup.py"
                (("cc") (which "gcc")))
              #t)))

gnu/packages/gnuzilla.scm

@@ -8,7 +8,7 @@
 ;;; Copyright © 2017, 2023 Clément Lassieur <clement@lassieur.org>
 ;;; Copyright © 2017, 2018 Nikita <nikita@n0.is>
 ;;; Copyright © 2017, 2018, 2020 Tobias Geerinckx-Rice <me@tobias.gr>
-;;; Copyright © 2018, 2020 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2018, 2020, 2025 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2019 Ivan Petkov <ivanppetkov@gmail.com>
 ;;; Copyright © 2020, 2024 Oleg Pykhalov <go.wigust@gmail.com>
 ;;; Copyright © 2020 Jakub Kądziołka <kuba@kadziolka.net>
@@ -142,6 +142,14 @@
          "--with-intl-api")
       #:phases
       #~(modify-phases %standard-phases
+          (add-after 'unpack 'python-3.11-compatibility
+            (lambda _
+              (substitute* '("python/mozbuild/mozpack/files.py"
+                             "python/mozbuild/mozbuild/util.py"
+                             "python/mozbuild/mozbuild/action/process_define_files.py"
+                             "python/mozbuild/mozbuild/backend/base.py"
+                             "python/mozbuild/mozbuild/preprocessor.py")
+                (("\"rU\"") "\"r\""))))
           (add-after 'patch-source-shebangs 'patch-cargo-checksums
             (lambda _
               (let ((null-hash
@@ -278,6 +286,15 @@ in C/C++.")
      (substitute-keyword-arguments (package-arguments mozjs)
        ((#:phases phases)
         #~(modify-phases #$phases
+            (add-after 'unpack 'python-3.11-compatibility
+              (lambda _
+                (substitute* '("python/mozbuild/mozpack/files.py"
+                               "python/mozbuild/mozbuild/util.py"
+                               "python/mozbuild/mozbuild/action/process_define_files.py"
+                               "python/mozbuild/mozbuild/backend/base.py"
+                               "python/mozbuild/mozbuild/preprocessor.py"
+                               "python/mozbuild/mozbuild/virtualenv.py")
+                  (("'rU'") "'r'"))))
             (add-after 'unpack 'patch-for-python-3.10
               (lambda _
                 ;; Some classes were moved from collections to collections.abc
@@ -1650,7 +1667,7 @@ their corresponding VERSION, SOURCE and LOCALES variables."
                 (setenv "MACH_BUILD_PYTHON_NATIVE_PACKAGE_SOURCE" "system")
                 (setenv "GUIX_PYTHONPATH"
                         (string-append (getcwd)
-                                       "/obj/_virtualenvs/build/lib/python3.10/site-packages"))
+                                       "/obj/_virtualenvs/build/lib/python3.11/site-packages"))
                 (setenv "BUILD_BACKENDS" "FasterMake,RecursiveMake")))
             (replace 'build             ;build and install data files
               (lambda* (#:key outputs #:allow-other-keys)

gnu/packages/graph.scm

@@ -389,9 +389,9 @@ subplots, multiple-axes, polar charts, and bubble charts.")
        (patches (search-patches "python-louvain-fix-test.patch"))
        (sha256
         (base32 "0sx53l555rwq0z7if8agirjgw4ddp8r9b949wwz8vlig03sjvfmp"))))
-    (build-system python-build-system)
+    (build-system pyproject-build-system)
     (native-inputs
-     (list python-setuptools-57))       ;for use_2to3 support
+     (list python-setuptools python-wheel))
     (propagated-inputs
      (list python-networkx python-numpy))
     (home-page "https://github.com/taynaud/python-louvain")

gnu/packages/graphviz.scm

@@ -209,7 +209,7 @@ structure and layout algorithms.")
 (define-public python-uqbar
   (package
     (name "python-uqbar")
-    (version "0.6.9")
+    (version "0.7.2")
     (source
      (origin
        (method git-fetch)
@@ -218,27 +218,23 @@ structure and layout algorithms.")
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "037qj3rymm6xzdpklddfhmfp2p1bq9fi3jrvxj6gmharphd5z869"))))
+        (base32 "1limp2m2smg0l3v6vn2fwhjcw1d8gakw5v0q7krb03q539qiql87"))))
     (build-system pyproject-build-system)
-    (arguments  ; XXX: Disable failing tests.
+    (arguments
-     (list #:test-flags '(list "tests" "-k" "not test_find_executable \
+     (list
-and not test_sphinx_book_text_broken_strict")))
+      #:test-flags #~(list "--pyargs" "uqbar")))
     (native-inputs
      (list graphviz
-           python-flake8
+           python-defusedxml
-           python-isort
-           python-mypy
            python-pytest
            python-pytest-cov
            python-setuptools
+           python-typing-extensions
            python-wheel))
     (propagated-inputs
-     (list python-black python-sphinx-5 python-unidecode
+     (list python-black
-           (package/inherit python-sphinx-rtd-theme
+           python-sphinx
-             (propagated-inputs
+           python-unidecode))
-              (modify-inputs
-                  (package-propagated-inputs python-sphinx-rtd-theme)
-                (replace "python-sphinx" python-sphinx-5))))))
     (home-page "https://github.com/josiah-wolf-oberholtzer/uqbar")
     (synopsis "Tools for building documentation with Sphinx, Graphviz and LaTeX")
     (description

gnu/packages/image-processing.scm

@@ -1812,63 +1812,55 @@ processing pipelines.")
 (define-public labelme
   (package
     (name "labelme")
-    (version "4.5.13")
+    ;; It's the latest available version which does not require not packaged
+    ;; <https://github.com/wkentaro/osam>.
+    (version "5.2.1")
     (source
      (origin
        ;; PyPi tarball lacks tests.
        (method git-fetch)
        (uri (git-reference
-             (url "https://github.com/wkentaro/labelme.git")
+             (url "https://github.com/wkentaro/labelme")
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "0cmi2xb4dgh7738l259rgwhn9l134f0vnaaqc2gflc5yr3lqhrv2"))))
+        (base32 "1xpyad6rlkxyx51jaai4xhdy15k1gvm62xnkjn152hc1vj1c77sr"))))
-    (build-system python-build-system)
+    (build-system pyproject-build-system)
     (arguments
-     `(#:phases
+     (list
-       (modify-phases %standard-phases
+      #:test-flags
-         (add-after 'unpack 'loosen-requirements
+      #~(list "-m" "not gpu"
-           (lambda _
+              ;; Fails when invoking help2man for unknown reason.
-             ;; Don't require an outdated version of matplotlib.
+              "--ignore=tests/docs_tests/man_tests/test_labelme_1.py")
-             (substitute* "setup.py"
+      #:phases
-               (("matplotlib<3\\.3")
+      #~(modify-phases %standard-phases
-                "matplotlib"))))
           (add-before 'check 'start-xserver
             (lambda* (#:key inputs #:allow-other-keys)
-             (let ((xorg-server (assoc-ref inputs "xorg-server")))
+              (let ((xorg-server #$(this-package-native-input "xorg-server")))
                 ;; Options taken from CI workflow.
                 (system (string-append xorg-server "/bin/Xvfb :99 -screen 0 "
                                        "1920x1200x24 -ac +extension GLX +render "
                                        "-noreset &"))
-               (setenv "DISPLAY" ":99.0"))))
+                (setenv "DISPLAY" ":99.0")))))))
-         (replace 'check
+    (native-inputs
-           (lambda* (#:key inputs outputs tests? #:allow-other-keys)
+     (list python-pytest
-             (when tests?
+           python-pytest-qt
-               (add-installed-pythonpath inputs outputs)
+           xorg-server-for-tests
-               ;; Fails when invoking help2man for unknown reason.
+           python-wheel))
-               (delete-file "tests/docs_tests/man_tests/test_labelme_1.py")
-               ;; One test hangs.
-               (delete-file "tests/labelme_tests/widgets_tests/test_label_dialog.py")
-               ;; Calls incompatible function signatures.
-               (delete-file "tests/labelme_tests/widgets_tests/test_label_list_widget.py")
-               (setenv "MPLBACKEND" "agg")
-               (invoke "pytest" "-v" "tests" "-m" "not gpu")))))))
     (propagated-inputs
      (list python-imgviz
            python-matplotlib
+           python-natsort
            python-numpy
            python-pillow
            python-pyyaml
            python-qtpy
            python-termcolor))
-    (native-inputs
-      (list python-pytest python-pytest-qt xorg-server-for-tests))
     (home-page "https://github.com/wkentaro/labelme")
-    (synopsis
+    (synopsis "Image Polygonal Annotation")
-      "Image Polygonal Annotation")
     (description
-      "Image and video labeling tool supporting different shapes like
+     "Image and video labeling tool supporting different shapes like polygons,
-polygons, rectangles, circles, lines, points and VOC/COCO export.")
+rectangles, circles, lines, points and VOC/COCO export.")
     (license license:gpl3+)))
 
 (define-public charls

gnu/packages/image.scm

@@ -2761,6 +2761,10 @@ GIF, TIFF, WEBP, BMP, PNG, XPM formats.")
                   (guix build utils))
        #:phases
        (modify-phases %standard-phases
+         (add-after 'unpack 'python3.11-compatibility
+           (lambda _
+             (substitute* "setup.py"
+               (("\"rU\"") "\"r\""))))
          (add-after 'install 'glib-or-gtk-wrap
            (assoc-ref glib-or-gtk:%standard-phases 'glib-or-gtk-wrap))
          (add-after 'install 'wrap-program

gnu/packages/irc.scm

@@ -919,7 +919,7 @@ parsers")
           ;; unmaintained clone of <https://github.com/ircdocs/parser-tests>
           ;; which is packed in Guix as python-irc-parser-tests.  Tests data
           ;; (YAML files) are distributed as Python package and located in
-          ;; <lib/python3.10/site-packages/parser_tests/data/>.
+          ;; <lib/python3.11/site-packages/parser_tests/data/>.
           (add-before 'check 'install-testcases-data
             (lambda* (#:key import-path #:allow-other-keys)
               (with-directory-excursion (string-append "src/" import-path)

gnu/packages/iso-codes.scm

@@ -122,7 +122,8 @@ information.")
     (build-system pyproject-build-system)
     (native-inputs
      (list python-pytest
-           python-setuptools))
+           python-setuptools
+           python-wheel))
     (propagated-inputs
      (list python-pandas))
     (home-page "https://github.com/IndEcol/country_converter")

gnu/packages/jupyter.scm

@@ -64,13 +64,6 @@
        (sha256
         (base32 "1qrhzazq10dz64y9mawr3ns595fsdhrj1wvbb42xhmcl66r1xq8a"))))
     (build-system pyproject-build-system)
-    (arguments
-     (list
-      #:phases
-      ;; Because python-jsonschema has an old python-webcolor.  Remove this
-      ;; when python-team branch is merged.
-      '(modify-phases %standard-phases
-         (delete 'sanity-check))))
     (propagated-inputs (list python-argon2-cffi
                              python-ipykernel
                              python-ipython-genutils
@@ -96,7 +89,7 @@
                          python-pytest-jupyter
                          python-pytest-tornasync
                          python-requests
-                         python-requests-unixsocket
+                         python-requests-unixsocket2
                          python-testpath))
     (home-page "https://github.com/jupyter/nbclassic")
     (synopsis "Jupyter Notebook as a Jupyter Server extension")
@@ -601,7 +594,7 @@ JavaScript build steps.")
               (setenv "PATH"
                       (string-append #$output "/bin:" (getenv "PATH"))))))))
     (propagated-inputs
-     (list python-anyio/without-dataclasses
+     (list python-anyio
            python-argon2-cffi
            python-jinja2
            python-jupyter-client
@@ -1062,13 +1055,13 @@ a notebook.")
 (define-public python-ipympl
   (package
     (name "python-ipympl")
-    (version "0.9.1")
+    (version "0.9.2")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "ipympl" version))
        (sha256
-        (base32 "11rppjdqzgs4pfiq8gww5xkpbk21fp86vvv839v56b9rqq06j2b4"))))
+        (base32 "12qgiy08klqb5gipm23yzh09p5g2k8ihcq2bprprdya84acw2rf8"))))
     (build-system python-build-system)
     (propagated-inputs
      (list python-ipython
@@ -1079,7 +1072,7 @@ a notebook.")
            python-pillow
            python-traitlets))
     (native-inputs
-     (list python-jupyter-packaging))
+     (list python-hatchling python-jupyter-packaging))
     (home-page "https://matplotlib.org/ipympl/")
     (synopsis "Matplotlib Jupyter Extension")
     (description "Leveraging the Jupyter interactive widgets framework, ipympl

gnu/packages/llvm.scm

@@ -663,7 +663,7 @@ output), and Binutils.")
                   (rename-file (string-append #$output "/share/opt-viewer")
                                opt-viewer-share))))
             ;; The build daemon goes OOM on i686-linux on this phase.
-            #$@(if (and (version>=? version "16.0")
+            #$@(if (and (version>=? version "15.0")
                         (target-x86-32?))
                    #~((delete 'make-dynamic-linker-cache))
                    #~()))))

gnu/packages/machine-learning.scm

@@ -234,8 +234,16 @@ family of functions.")
        (sha256
         (base32 "0cgysij0dix0fikyz2x4f8jvaskm5s5a04s07chzaz2dw1fpxdq8"))))
     (build-system pyproject-build-system)
-    (arguments  ; disable flaky test
+    (arguments
-     (list #:test-flags '(list "-k" "not test_integrate_variable[x23-i]")))
+     (list
+      #:test-flags
+      '(list "-k"
+             (string-append
+              ;; Disable flaky test
+              "not test_integrate_variable[x23-i]"
+              ;; XXX This test fails because the length of arguments
+              ;; is longer than the length of inputs.
+              " and not test_function_of_numeric_array"))))
     (propagated-inputs (list python-makefun python-multipledispatch
                              python-numpy python-opt-einsum
                              python-typing-extensions))
@@ -423,33 +431,25 @@ machine learning algorithms based on GPs.")
 (define-public python-ml-collections
   (package
     (name "python-ml-collections")
-    (version "0.1.1")
+    (version "1.0.0")
     (source
      (origin
-       (method url-fetch)
+       (method git-fetch)
-       (uri (pypi-uri "ml_collections" version))
+       (uri (git-reference
+             (url "https://github.com/google/ml_collections")
+             (commit (string-append "v" version))))
        (sha256
-        (base32 "1k38psfzqsqnl99fl578bd07zdmvfkja61r3sgjs2fj3xircrvrz"))))
+        (base32 "1f3rwbgnnvgh2jgnkwxfjdw18yly41hlx9fy56h0x36zyy8p0j21"))))
     (build-system pyproject-build-system)
     (arguments
      (list
-      #:phases
+      #:test-flags '(list "--pyargs" "ml_collections/config_dict/tests")))
-      #~(modify-phases %standard-phases
-          (replace 'check
-            (lambda* (#:key tests? #:allow-other-keys)
-              (when tests?
-                ;; TODO: we can't seem to run the config_flags tests, because
-                ;; the installed Python files conflict with those from the
-                ;; source directory, resulting in constants to be defined more
-                ;; than once.
-                (invoke "pytest" "ml_collections/config_dict/tests"
-                        ;; This one fails because we're testing the __main__
-                        ;; class, not config_dict_test.
-                        "-k" "not testJSONConversionBestEffort")))))))
     (propagated-inputs
-     (list python-absl-py python-contextlib2 python-pyyaml python-six))
+     (list python-absl-py python-pyyaml))
-    (native-inputs (list python-mock python-pytest python-setuptools
+    (native-inputs (list python-pylint
-                         python-wheel))
+                         python-pytest
+                         python-pytest-xdist
+                         python-flit-core))
     (home-page "https://github.com/google/ml_collections")
     (synopsis "Python collections designed for Machine Learning usecases")
     (description
@@ -1843,7 +1843,7 @@ in terms of new algorithms.")
             pybind11
             python-coverage
             python-fb-re2
-            python-parameterized-next
+            python-parameterized
             python-pytest
             python-pytest-runner
             python-setuptools
@@ -2553,7 +2553,7 @@ standard feature selection algorithms.")
 (define-public python-cleanlab
   (package
     (name "python-cleanlab")
-    (version "2.7.0")
+    (version "2.7.1")
     ;; The version on pypi does not come with tests.
     (source (origin
               (method git-fetch)
@@ -2563,7 +2563,7 @@ standard feature selection algorithms.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "0f8v5246nzy22r7zswv9vbpxc7wxaqjwry9iq0fqjp2ffch88h6j"))))
+                "073w45azq496x4bhrh8mdywcrg3gk33n13w1pqh1kiykw826ld9b"))))
     (build-system pyproject-build-system)
     (arguments
      (list
@@ -2681,37 +2681,37 @@ Covariance Matrix Adaptation Evolution Strategy (CMA-ES) for Python.")
     (license license:expat)))
 
 (define-public python-autograd
-  (let* ((commit "c6d81ce7eede6db801d4e9a92b27ec5d409d0eab")
-         (revision "0")
-         (version (git-version "1.5" revision commit)))
   (package
     (name "python-autograd")
-      (home-page "https://github.com/HIPS/autograd")
+    (version "1.7.0")
-      (source (origin
+    (source
+     (origin
        (method git-fetch)
        (uri (git-reference
-                      (url home-page)
+             (url "https://github.com/HIPS/autograd")
-                      (commit commit)))
+             (commit (string-append "v" version))))
        (sha256
-                 (base32
+        (base32 "1fpnmm3mzw355iq7w751j4mjfcr0yh324cxidba1l22652gg8r8m"))
-                  "04kljgydng42xlg044h6nbzxpban1ivd6jzb8ydkngfq88ppipfk"))
        (file-name (git-file-name name version))))
-      (version version)
     (build-system pyproject-build-system)
     (native-inputs
-       (list python-nose python-pytest python-setuptools python-wheel))
+     (list python-hatchling
+           python-pytest))
     (propagated-inputs
-       (list python-future python-numpy))
+     (list python-future
+           python-numpy))
+    (home-page "https://github.com/HIPS/autograd")
     (synopsis "Efficiently computes derivatives of NumPy code")
-      (description "Autograd can automatically differentiate native Python and
+    (description
-NumPy code.  It can handle a large subset of Python's features, including loops,
+     "Autograd can automatically differentiate native Python and NumPy code.
-ifs, recursion and closures, and it can even take derivatives of derivatives
+It can handle a large subset of Python's features, including loops, ifs,
-of derivatives.  It supports reverse-mode differentiation
+recursion and closures, and it can even take derivatives of derivatives of
+derivatives.  It supports reverse-mode differentiation
 (a.k.a. backpropagation), which means it can efficiently take gradients of
 scalar-valued functions with respect to array-valued arguments, as well as
 forward-mode differentiation, and the two can be composed arbitrarily.  The
 main intended application of Autograd is gradient-based optimization.")
-      (license license:expat))))
+    (license license:expat)))
 
 (define-public lightgbm
   (package
@@ -3370,8 +3370,14 @@ Python.")
            ;; SOURCE_DATE_EPOCH is respected, which we set to some time in
            ;; 1980.
            (lambda _ (setenv "SOURCE_DATE_EPOCH" "315532800")))
-         (add-after 'unpack 'python3.10-compatibility
+         (add-after 'unpack 'python3.11-compatibility
            (lambda _
+             ;; Py_TYPE was changed to an inline static function in Python
+             ;; 3.11, so it cannot be used on the left-hand side.
+             (substitute* "tensorflow/python/lib/core/bfloat16.cc"
+               (("Py_TYPE\\(&NPyBfloat16_Descr\\) = &PyArrayDescr_Type;")
+                "Py_SET_TYPE(&NPyBfloat16_Descr, &PyArrayDescr_Type);"))
+
              ;; See https://github.com/tensorflow/tensorflow/issues/20517#issuecomment-406373913
              (substitute* '("tensorflow/python/eager/pywrap_tfe_src.cc"
                             "tensorflow/python/lib/core/ndarray_tensor.cc"
@@ -3421,6 +3427,16 @@ Python.")
                 (string-append m
                                " and not isinstance(existing, type(object.__or__))")))
 
+             ;; ArgSpec has been replaced with FullArgSpec.
+             (substitute* "tensorflow/python/util/tf_inspect.py"
+               (("ArgSpec = _inspect.ArgSpec") "\
+ArgSpec = namedtuple('ArgSpec', [ 'args', 'varargs', 'keywords', 'defaults' ])
+def makeargspec(s):
+  return ArgSpec(args=s.args, varargs=s.varargs, keywords=s.varkw, defaults=s.defaults)
+")
+               (("_inspect.getargspec\\((.*)\\)" m target)
+                (string-append "makeargspec(_inspect.getfullargspec(" target "))")))
+
              ;; Fix the build with numpy >= 1.19.
              ;; Suggested in https://github.com/tensorflow/tensorflow/issues/41086#issuecomment-656833081
              (substitute* "tensorflow/python/lib/core/bfloat16.cc"
@@ -3441,7 +3457,22 @@ Python.")
              (substitute* '("tensorflow/python/framework/fast_tensor_util.pyx"
                             "tensorflow/python/estimator/canned/linear_testing_utils.py")
                (("np.asscalar") "np.ndarray.item"))))
-         (add-after 'python3.10-compatibility 'chdir
+         (add-after 'python3.11-compatibility 'numpy-compatibility
+           (lambda _
+             (substitute* (cons* "tensorflow/compiler/xla/python/xla_client.py"
+                                 "tensorflow/contrib/layers/python/ops/sparse_ops_test.py"
+                                 (find-files "tensorflow/python/" "\\.py$"))
+               (("np.object") "object"))
+             (substitute* (append
+                           '("tensorflow/compiler/tests/unary_ops_test.py"
+                             "tensorflow/compiler/xla/python/xla_client.py"
+                             "tensorflow/compiler/xla/python/xla_client_test.py")
+                           (find-files "tensorflow/python/" "\\.py$")
+                           (find-files "tensorflow/contrib/" "\\.py$"))
+               (("np.bool,") "bool,")
+               (("np.bool\\)") "bool)")
+               (("np.bool:") "bool:"))))
+         (add-after 'numpy-compatibility 'chdir
            (lambda _ (chdir "tensorflow/contrib/cmake")))
          (add-after 'chdir 'disable-downloads
            (lambda* (#:key inputs #:allow-other-keys)
@@ -4169,7 +4200,7 @@ project, and it will potentially also do the same for the Lime project.")
     (propagated-inputs
      (list python-h5py python-numpy))
     (native-inputs
-     (list python-pytest python-pytest-cov python-pytest-pep8
+     (list python-pytest python-pytest-cov
            python-pytest-xdist))
     (home-page "https://github.com/keras-team/keras-applications")
     (synopsis "Reference implementations of popular deep learning models")
@@ -4339,7 +4370,6 @@ with image data, text data, and sequence data.")
            python-pandas
            python-pytest
            python-pytest-cov
-           python-pytest-pep8
            python-pytest-timeout
            python-pytest-xdist
            python-pyux
@@ -5558,7 +5588,10 @@ Note: currently this package does not provide GPU support.")
                    ;; These refuse to be run on CPU and really want a GPU
                    " and not test_add_random_walk_pe"
                    " and not test_asap"
-                   " and not test_two_hop"))
+                   " and not test_two_hop"
+                   ;; Failed when switched to python@3.11
+                   ;; typing module internals
+                   " and not test_type_repr"))
       #:phases
       '(modify-phases %standard-phases
          (add-after 'unpack 'delete-top-level-directories
@@ -6315,7 +6348,7 @@ tokenizers, @code{rust-tokenizers}.")
            python-tokenizers
            python-tqdm))
     (native-inputs
-     (list python-parameterized-next
+     (list python-parameterized
            python-pytest python-setuptools python-wheel))
     (home-page "https://github.com/huggingface/transformers")
     (synopsis "Machine Learning for PyTorch and TensorFlow")
@@ -6459,34 +6492,33 @@ of Hidden Markov Models.")
 (define-public python-lap
   (package
     (name "python-lap")
-    (version "0.4.0")
+    (version "0.5.12")
     (source (origin
               (method url-fetch)
               (uri (pypi-uri "lap" version))
               (sha256
                (base32
-                "0fqfxpq4jg9h4wxjw540gjmvfg1ccc1nssk7i9njg7qfdybxknn4"))))
+                "1za4mf5nd7vzwd24sy2mfxrk8mnwq7d8rv6h96yh8v5flx7422sp"))))
-    (build-system python-build-system)
+    (build-system pyproject-build-system)
     (arguments
-     `(#:phases
+     (list
-       (modify-phases %standard-phases
+      #:test-flags #~(list "-v" #$output)
-         (replace 'build
+      #:phases
-           (lambda* (#:key inputs #:allow-other-keys)
+      #~(modify-phases %standard-phases
-             (invoke "python" "setup.py" "build"
+          (add-after 'check 'check-cleanup
-                     "--cpu-baseline=sse2")))
-         (replace 'check
             (lambda* (#:key tests? #:allow-other-keys)
               (when tests?
-               ;; The tests must be run from elsewhere.
+                (for-each
-               (mkdir-p "/tmp/test")
+                 delete-file-recursively
-               (copy-recursively "lap/tests" "/tmp/test")
+                 (find-files #$output
-               (with-directory-excursion "/tmp/test"
+                             (lambda (file stat)
-                 (invoke "pytest" "-vv"))))))))
+                               (or (member (basename file)
+                                           '("tests" ".pytest_cache"))))
+                             #:directories? #t))))))))
     (propagated-inputs
-     (list python-numpy
+     (list python-numpy))
-           python-scipy))
     (native-inputs
-     (list python-cython python-pytest))
+     (list python-cython python-pytest python-setuptools python-wheel))
     (home-page "https://github.com/gatagat/lap")
     (synopsis "Linear Assignment Problem solver (LAPJV/LAPMOD)")
     (description "Lap is a linear assignment problem solver using Jonker-Volgenant
@@ -6581,24 +6613,23 @@ inference.")
 (define-public python-linear-operator
   (package
     (name "python-linear-operator")
-    (version "0.5.2")
+    (version "0.6")
     (source (origin
               (method url-fetch)
               (uri (pypi-uri "linear_operator" version))
               (sha256
                (base32
-                "03drb4hn9nn8jrqd9vbalihhahgpdm956hbs05bix7svradhknaw"))))
+                "0m56f3zrm8xh1bpwh4g7jfc79rf4j94g6zmz663b58pig4w6dqm9"))))
     (build-system pyproject-build-system)
     (propagated-inputs (list python-jaxtyping
+                             python-mpmath
                              python-pytorch
-                             python-scipy
+                             python-scipy))
-                             python-typeguard))
+    (native-inputs (list python-pytest
-    (native-inputs (list python-flake8
-                         python-flake8-print
-                         python-pytest
                          python-setuptools
                          python-setuptools-scm
-                         python-twine))
+                         python-typeguard
+                         python-wheel))
     (home-page "https://github.com/cornellius-gp/linear_operator/")
     (synopsis "Linear operator implementation")
     (description "LinearOperator is a PyTorch package for abstracting away the
@@ -6608,29 +6639,34 @@ linear algebra routines needed for structured matrices (or operators).")
 (define-public python-gpytorch
   (package
     (name "python-gpytorch")
-    (version "1.12")
+    (version "1.14")
     (source (origin
               (method url-fetch)
               (uri (pypi-uri "gpytorch" version))
               (sha256
                (base32
-                "1pwsccll1hrgkifdmlxzcn6cvnwvyq2cimqzbfgihr13yw51cb6w"))))
+                "13cs6dx8qa5j4ygji9w5xbmaqc68ihqyzz33fyyf9qa6d8gc2b03"))))
     (build-system pyproject-build-system)
     (arguments
      (list #:test-flags
+           #~(list "-k" (string-append
                          ;; test_deprecated_methods fails with an AssertionError.
-           #~(list "-k" (string-append "not test_deprecated_methods"))))
+                         "not test_deprecated_methods"
-    (propagated-inputs (list python-linear-operator
+                         ;; This test is flaky: Expects gradients of 0 exactly,
+                         ;; can get negligible ones (e-10 to e-16).
+                         " and not test_optimization_optimal_error")
+                   ;; Ignore lenghty tests of little relevance.
+                   "--ignore=test/examples/")))
+    (propagated-inputs (list python-jaxtyping
+                             python-linear-operator
                              python-mpmath
                              python-scikit-learn
                              python-scipy))
-    (native-inputs (list python-coverage
+    (native-inputs (list python-nbval
-                         python-flake8
-                         python-flake8-print
-                         python-nbval
                          python-pytest
                          python-setuptools
-                         python-twine))
+                         python-setuptools-scm
+                         python-wheel))
     (home-page "https://gpytorch.ai")
     (synopsis "Implementation of Gaussian Processes in PyTorch")
     (description
@@ -6640,7 +6676,7 @@ linear algebra routines needed for structured matrices (or operators).")
 (define-public python-botorch
   (package
     (name "python-botorch")
-    (version "0.11.3")
+    (version "0.13.0")
     (source (origin
               (method git-fetch) ;no tests in PyPI
               (uri (git-reference
@@ -6649,7 +6685,7 @@ linear algebra routines needed for structured matrices (or operators).")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "0nf9zrg1khvckb8kdpffqc3bnlhc0x03jd1560qmjamwl3j59m02"))))
+                "1sxgxdq892vg5xj30kb86003b9rwsipc95c7p1zdv865y4f38a8y"))))
     (build-system pyproject-build-system)
     (arguments
      (list #:test-flags #~(list "-k" "not test_all_cases_covered")
@@ -6668,9 +6704,12 @@ linear algebra routines needed for structured matrices (or operators).")
                              python-pyro-ppl
                              python-pytorch
                              python-scipy))
-    (native-inputs (list python-pytest
+    (native-inputs (list python-pyre-extensions
+                         python-pytest
                          python-pytest-cov
-                         python-setuptools-scm))
+                         python-setuptools
+                         python-setuptools-scm
+                         python-wheel))
     (home-page "https://botorch.org")
     (synopsis "Bayesian Optimization in PyTorch")
     (description
@@ -6779,7 +6818,7 @@ simple speech recognition.")
                   "library_dirs=["
                   "'" #$vosk-api "/lib'"
                   "],\n\t"
-                  "libraries=['vosk', 'python3.10'],\n\t"
+                  "libraries=['vosk', 'python3.11'],\n\t"
                   "include_dirs=["
                   "'" #$vosk-api "/src'" "])")))
               (substitute* "vosk/__init__.py"

gnu/packages/mail.scm

@@ -3588,14 +3588,17 @@ an SMTP transaction before a message is committed to queue.")
 (define-public mailman
   (package
     (name "mailman")
-    (version "3.3.2")
+    (version "3.3.10")
     (source
       (origin
         (method url-fetch)
         (uri (pypi-uri "mailman" version))
         (sha256
-         (base32 "0a5ckbf8hc3y28b7p5psp0d4bxk601jlr5pd3hhh545xd8d9f0dg"))))
+         (base32 "0cjn8karkgrapgiv3ra6ddcngkf5c5779hrq369mvwi6ygy7ir0d"))))
-    (build-system python-build-system)
+    (build-system pyproject-build-system)
+    (arguments
+     ;; XXX: Too much failing tests to try and isolate them.
+     (list #:tests? #f))
     (propagated-inputs
      (list gunicorn
            python-aiosmtpd
@@ -3620,7 +3623,7 @@ an SMTP transaction before a message is committed to queue.")
            python-zope-event
            python-zope-interface))
     (native-inputs
-     (list python-nose))
+     (list python-pytest python-pdm-backend))
     (home-page "https://www.list.org")
     (synopsis "Mailing list manager")
     (description
@@ -3755,21 +3758,17 @@ interfaces interacting with Mailman.")
 (define-public python-mailman-hyperkitty
   (package
     (name "python-mailman-hyperkitty")
-    (version "1.2.0")
+    (version "1.2.1")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "mailman-hyperkitty" version))
        (sha256
-         (base32
+        (base32 "0f6c1fs28w3r9k9mbg7gsv6pa45aayaadaa0dn4q5dfcqvxrvmpq"))))
-          "1ni6vf1yi14c0l895fk278x4na7ymhpkl1q0vnpzbkzplpa7200i"))))
+    (build-system pyproject-build-system)
-    (build-system python-build-system)
+    (propagated-inputs (list python-requests python-zope-interface))
-    (propagated-inputs
+    (inputs (list mailman))
-     (list python-requests python-zope-interface))
+    (native-inputs (list python-nose2 python-setuptools python-wheel))
-    (inputs
-     (list mailman))
-    (native-inputs
-     (list python-mock python-nose python-nose2))
     (home-page "https://gitlab.com/mailman/mailman-hyperkitty/")
     (synopsis "Mailman archiver plugin for HyperKitty")
     (description
@@ -4681,18 +4680,20 @@ the RFC 8617 Authenticated Received Chain (ARC) protocol.")
 (define-public python-authheaders
   (package
     (name "python-authheaders")
-    (version "0.13.0")
+    (version "0.16.3")
     (source
       (origin
         (method url-fetch)
         (uri (pypi-uri "authheaders" version))
         (sha256
          (base32
-          "14k6i72k5f8dyvps8vc0aq0cczc8lvqpgjfjzsy6qqychjvjcmwk"))))
+          "12hl93336w64iyqalpv4rma2ijigav68qy1xmgziibdi7inxr3hi"))))
-    (build-system python-build-system)
+    (build-system pyproject-build-system)
     (propagated-inputs
      (list python-authres python-dkimpy python-dnspython
            python-publicsuffix2))
+    (native-inputs
+     (list python-setuptools python-wheel))
     (home-page "https://github.com/ValiMail/authentication-headers")
     (synopsis "Library wrapping email authentication header verification and generation")
     (description
@@ -4707,30 +4708,27 @@ DKIM and ARC sign messages and output the corresponding signature headers.")
 (define-public python-aiosmtpd
   (package
     (name "python-aiosmtpd")
-    (version "1.2.2")
+    (version "1.4.6")
     (source
      (origin
        (method git-fetch)
        (uri (git-reference
              (url "https://github.com/aio-libs/aiosmtpd")
-             (commit version)))
+             (commit (string-append "v" version))))
        (sha256
-        (base32 "0083d6nf75xv8nq1il6jabz36v6c452svy4p402csxwwih5pw6sk"))
+        (base32 "0b5y94zc8pq75sjwsifblzgjnliyclkwypi68b2zffrxcdnz27r2"))
        (file-name (git-file-name name version))))
-    (build-system python-build-system)
+    (build-system pyproject-build-system)
     (arguments
-     '(#:phases
+     ;; This QA test requires git.
-       (modify-phases %standard-phases
+     (list #:test-flags ''("-k" "not test_ge_master")))
-         (add-after 'unpack 'delete-failing-tests
-           (lambda _
-             ;; This test uses an expired certificate.
-             (delete-file "aiosmtpd/tests/test_smtps.py")
-             #t))
-         (replace 'check
-           (lambda _
-             (invoke "python" "-m" "nose2" "-v"))))))
     (native-inputs
-     (list python-flufl-testing python-nose2))
+     (list python-pytest
+           python-pytest-asyncio
+           python-pytest-cov
+           python-pytest-mock
+           python-setuptools
+           python-wheel))
     (propagated-inputs
      (list python-atpublic))
     (home-page "https://aiosmtpd.readthedocs.io/")

gnu/packages/maths.scm

@@ -108,6 +108,7 @@
   #:use-module (guix build-system python)
   #:use-module (guix build-system ruby)
   #:use-module (gnu packages algebra)
+  #:use-module (gnu packages astronomy)
   #:use-module (gnu packages audio)
   #:use-module (gnu packages autotools)
   #:use-module (gnu packages backup)
@@ -3551,46 +3552,51 @@ ASCII text files using Gmsh's own scripting language.")
 (define-public veusz
   (package
     (name "veusz")
-    (version "3.3.1")
+    (version "3.6.2")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "veusz" version))
        (sha256
-        (base32 "1q7hi1qwwg4pgiz62isvv1pia85m13bspdpp1q3mrnwl11in0ag0"))))
+        (base32 "1lcmcfr0dcam8g1fp5qip8jnxglxx7i62ln3ix6l4c2bbv21l5y2"))))
-    (build-system python-build-system)
+    (build-system pyproject-build-system)
     (arguments
-     `(;; Tests will fail because they depend on optional packages like
+     (list
-       ;; python-astropy, which is not packaged.
+      ;; Tests currently fail with exception TypeError:
+      ;; calling <function version ...> returned 3.6.2, not a test
       #:tests? #f
       #:phases
-       (modify-phases %standard-phases
+      #~(modify-phases %standard-phases
-         ;; Veusz will append 'PyQt5' to sip_dir by default. That is not how
+          ;; Veusz uses python's site-packages to look for pyqt5_include_dir.
-         ;; the path is defined in Guix, therefore we have to change it.
+          (add-after 'unpack 'fix-pyqt5-include-dir
-         (add-after 'unpack 'fix-sip-dir
             (lambda _
-             (substitute* "pyqtdistutils.py"
+              (substitute* "pyqt_setuptools.py"
-               (("os.path.join\\(sip_dir, 'PyQt5'\\)") "sip_dir"))))
+                (("get_path\\('platlib'\\)")
-         ;; Now we have to pass the correct sip_dir to setup.py.
+                 (format #f "~s"
-         (replace 'build
+                         (string-append
-           (lambda* (#:key inputs #:allow-other-keys)
+                          #$(this-package-input "python-pyqt")
-             ;; We need to tell setup.py where to locate QtCoremod.sip
+                          "/lib/python"
-             ((@@ (guix build python-build-system) call-setuppy)
+                          #$(version-major+minor
-              "build_ext"
+                             (package-version python-wrapper))
-              (list (string-append "--sip-dir="
+                          "/site-packages"))))))
-                                   (search-input-directory inputs "share/sip"))))))
           ;; Ensure that icons are found at runtime.
-         (add-after 'install 'wrap-executable
+          (add-after 'wrap 'wrap-executable
-           (lambda* (#:key inputs outputs #:allow-other-keys)
+            (lambda* (#:key inputs #:allow-other-keys)
-             (let ((out (assoc-ref outputs "out")))
+              (wrap-program (string-append #$output "/bin/veusz")
-               (wrap-program (string-append out "/bin/veusz")
                 `("QT_PLUGIN_PATH" prefix
-                   ,(list (string-append (assoc-ref inputs "qtsvg")
+                  ,(list (string-append
-                                         "/lib/qt5/plugins/"))))))))))
+                          (string-join
+                           (list #$(this-package-input "qtbase")
+                                 #$(this-package-input "qtsvg")
+                                 #$(this-package-input "qtwayland"))
+                           "/lib/qt5/plugins:")
+                          "/lib/qt5/plugins")))))))))
     (native-inputs
      (list pkg-config
-           ;;("python-astropy" ,python-astropy) ;; FIXME: Package this.
+           python-astropy
-           qttools-5 python-sip-4))
+           python-setuptools
+           python-wheel
+           qttools-5))
     (inputs
      (list bash-minimal
            ghostscript ;optional, for EPS/PS output
@@ -3598,7 +3604,8 @@ ASCII text files using Gmsh's own scripting language.")
            python-h5py ;optional, for HDF5 data
            python-pyqt
            qtbase-5
-           qtsvg-5))
+           qtsvg-5
+           qtwayland-5))
     (propagated-inputs
      (list python-numpy))
     (home-page "https://veusz.github.io/")
@@ -4346,7 +4353,15 @@ recurrence relations.")
       ;; These tests fails with unexpected keyword arguments
       ;; in calls to cplot.
       #~(list "--deselect" "tests/test_u3.py::test_write_single"
-              "--deselect" "tests/test_u3.py::test_write_tree")))
+              "--deselect" "tests/test_u3.py::test_write_tree"
+              "-k" (string-join
+                    ;; Tests fail in arrays comprising.
+                    (list "not test_chebyshev1_p11[2-y2]"
+                          "test_chebyshev1_p11[4-y4]"
+                          "test_eval[1-ref1]"
+                          "test_eval[t2-ref2]"
+                          "test_eval[t3-ref3]")
+                    " and not "))))
     (native-inputs
      (list python-matplotx
            python-meshio
@@ -4437,6 +4452,35 @@ bindings to almost all functions of PETSc.")
     ;; <https://github.com/dimpase/primecountpy/issues/16>.
     (license license:gpl2+)))
 
+(define-public python-pyglm
+  (package
+    (name "python-pyglm")
+    (version "2.8.1")
+    (source
+     (origin
+       ;; Test files are not included in the archive in pypi.
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/Zuzu-Typ/PyGLM")
+             (commit version)
+             ;; XXX: Attempt to use Guix's glm@1.0.1 failed, try to figure out
+             ;; how to fix it.
+             (recursive? #t)))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32
+         "1ra54m0pb5aca7q6ymappjsyxdzdy17yz8rrhlql04k0p9lnf1v8"))))
+    (build-system pyproject-build-system)
+    (native-inputs
+     (list python-pytest
+           python-setuptools
+           python-wheel))
+    (home-page "https://github.com/Zuzu-Typ/PyGLM")
+    (synopsis "OpenGL Mathematics library for Python")
+    (description "PyGLM is a Python extension library which brings the OpenGL
+Mathematics (GLM) library to Python.")
+    (license license:zlib)))
+
 (define-public python-quadpy
   (package
     (name "python-quadpy")
@@ -4454,6 +4498,12 @@ bindings to almost all functions of PETSc.")
           (base32
             "1f989dipv7lqxvalfrvvlmhlxyl67a87lavyyqrr1mh88glhl592"))))
     (build-system pyproject-build-system)
+    (arguments
+     (list
+      #:test-flags
+      ;; AssertionError: Lebedev(047) -- observed: 41, expected: 47 (max err:
+      ;; 4.910e-15).
+      #~(list "--deselect=tests/test_u3.py::test_scheme_spherical[lebedev_047]")))
     (native-inputs
      (list python-accupy
            python-pytest
@@ -7171,39 +7221,29 @@ with C89.")
 (define-public glm
   (package
     (name "glm")
-    (version "0.9.9.8")
+    (version "1.0.1")
     (source
      (origin
-       (method url-fetch)
+       (method git-fetch)
-       (uri (string-append "https://github.com/g-truc/glm/releases/download/"
+       (uri (git-reference
-                           version  "/glm-" version ".zip"))
+             (url "https://github.com/g-truc/glm")
+             (commit version)))
+       (file-name (git-file-name name version))
        (sha256
-        (base32 "0k6yk9v46h690rshdx49x98y5qspkzibld1wb51jwcm35vba7qip"))))
+        (base32 "0890rvv3czi3nqj11dc2m3wcdfv0dm0nr63wfcpfikk9sk6b4w8s"))))
     (build-system cmake-build-system)
     (arguments
-     `(#:phases (modify-phases %standard-phases
+     (list
-                  (add-before 'configure 'set-environment
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-after 'install 'post-install
             (lambda _
-                      ;; Pass "-fno-ipa-modref" flag to the compiler to work
+              (let* ((doc (string-append #$output "/share/doc/glm"))
-                      ;; around a test failure with GCC 11.  This is a
+                     (pkgconfig (string-append #$output "/lib/pkgconfig")))
-                      ;; header-only library so these flags only affect tests.
+                (mkdir-p doc)
-                      ;; See <https://github.com/g-truc/glm/pull/1087>.
-                      (setenv "CXXFLAGS" "-O2 -g -fno-ipa-modref")))
-                  (replace 'install
-                    (lambda* (#:key outputs #:allow-other-keys)
-                      ;; Since version 0.9.9.6, 'make install' is not supported
-                      ;; and we have to do it "manually".  Upstream discussion:
-                      ;; <https://github.com/g-truc/glm/pull/968>.
-                      (let* ((source (string-append "../glm"))
-                             (out (assoc-ref outputs "out"))
-                             (inc (string-append out "/include"))
-                             (lib (string-append out "/lib"))
-                             (pkgconfig (string-append lib "/pkgconfig")))
-                        (with-directory-excursion source
-                          (mkdir-p inc)
                 (mkdir-p pkgconfig)
-                          (copy-recursively "glm" (string-append inc "/glm"))
+                (copy-recursively "../source/doc/api" (string-append doc "/html"))
-                          (copy-recursively "cmake" (string-append lib "/cmake"))
+                (install-file "../source/doc/manual.pdf" doc)
                 (call-with-output-file (string-append pkgconfig "/glm.pc")
                   (lambda (port)
                     (format port
@@ -7213,8 +7253,7 @@ includedir=${prefix}/include
 Name: GLM
 Description: OpenGL Mathematics
 Version: ~a
-Cflags: -I${includedir}~%" out ,(version-prefix version 3)))))
+Cflags: -I${includedir}~%" #$output #$version)))))))))
-                        #t))))))
     (native-inputs
      (list unzip))
     (home-page "https://glm.g-truc.net/")
@@ -11079,7 +11118,7 @@ Mathics3.")
     (propagated-inputs (list python-django-4.2
                              python-mathics-scanner
                              python-mathics-core
-                             python-networkx-next
+                             python-networkx
                              python-pygments
                              python-requests))
     (native-inputs (list python-pytest python-setuptools python-wheel))

gnu/packages/medical.scm

@@ -19,6 +19,7 @@
 ;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
 
 (define-module (gnu packages medical)
+  #:use-module (guix build-system pyproject)
   #:use-module (guix build-system python)
   #:use-module (guix build-system qt)
   #:use-module (guix download)
@@ -29,6 +30,7 @@
   #:use-module (gnu packages databases)
   #:use-module (gnu packages kde-frameworks) ; kirigami
   #:use-module (gnu packages python)
+  #:use-module (gnu packages python-build)
   #:use-module (gnu packages python-crypto)
   #:use-module (gnu packages python-web)
   #:use-module (gnu packages python-xyz)
@@ -93,18 +95,26 @@ Health Federation.")
              ".tar.gz"))
        (sha256
         (base32 "09vrfqn511vswnj2q9m7srlwdgz066qvqpmja6sg1yl1ibh3cbpr"))))
-    (build-system python-build-system)
+    (build-system pyproject-build-system)
     (arguments
-     `(#:use-setuptools? #f
+     (list
-       #:phases (modify-phases %standard-phases
+      #:phases
+      #~(modify-phases %standard-phases
           (add-after 'unpack 'patch-/usr
             (lambda* (#:key outputs #:allow-other-keys)
               (substitute* '("setup.py"
                              "src/openmolar/settings/localsettings.py")
-                        (("/usr")
+                (("/usr") #$output))))
-                         (assoc-ref outputs "out"))) #t)))))
+          (add-after 'unpack 'set-acceptable-version
-    (inputs (list python-pyqtwebengine python-pyqt+qscintilla
+            (lambda _
-                  python-mysqlclient qscintilla))
+              (substitute* "src/openmolar/settings/version.py"
+                ((#$version) "1.1.6")))))))
+    (native-inputs
+     (list python-setuptools python-wheel))
+    (inputs (list python-pyqtwebengine
+                  python-pyqt+qscintilla
+                  python-mysqlclient
+                  qscintilla))
     (propagated-inputs (list qtwebengine-5))
     (home-page "https://openmolar.com/om1")
     (synopsis "Dental practice management software")

gnu/packages/monitoring.scm

@@ -14,6 +14,7 @@
 ;;; Copyright © 2022 Hartmut Goebel <h.goebel@crazy-compilers.com>
 ;;; Copyright © 2022 ( <paren@disroot.org>
 ;;; Copyright © 2022 Mathieu Laparie <mlaparie@disr.it>
+;;; Copyright © 2025 Nicolas Graves <ngraves@ngraves.fr>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -68,6 +69,7 @@
   #:use-module (gnu packages prometheus)
   #:use-module (gnu packages python)
   #:use-module (gnu packages python-build)
+  #:use-module (gnu packages python-science)
   #:use-module (gnu packages python-web)
   #:use-module (gnu packages python-xyz)
   #:use-module (gnu packages rrdtool)
@@ -433,23 +435,24 @@ historical data.")
 (define-public python-carbon
   (package
     (name "python-carbon")
-    (version "1.1.8")
+    (version "1.1.10")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "carbon" version))
        (sha256
         (base32
-         "1wb91fipk1niciffq5xwqbh8g7rl7ghdam4m97cjbig12i5qr4cm"))))
+         "0p6yjxif5ly5wkllnaw41w2zy9y0nffgfk91v861fn6c26lmnfy1"))))
-    (build-system python-build-system)
+    (build-system pyproject-build-system)
     (arguments
      `(#:phases
        (modify-phases %standard-phases
          ;; Don't install to /opt
          (add-after 'unpack 'do-not-install-to-/opt
            (lambda _ (setenv "GRAPHITE_NO_PREFIX" "1") #t)))))
+    (native-inputs (list python-setuptools python-wheel))
     (propagated-inputs
-     (list python-cachetools python-txamqp python-urllib3 python-whisper))
+     (list python-cachetools python-twisted python-txamqp python-urllib3))
     (home-page "https://graphiteapp.org/")
     (synopsis "Backend data caching and persistence daemon for Graphite")
     (description "Carbon is a backend data caching and persistence daemon for
@@ -459,19 +462,23 @@ and persisting them to disk using the Whisper time-series library.")
     (license license:asl2.0)))
 
 (define-public graphite-web
+  (let ((commit "49c28e2015d605ad9ec93524f7076dd924a4731a")
+        (revision "2"))
     (package
       (name "graphite-web")
-    (version "1.1.10")
+      (version (git-version "1.1.10" revision commit))
       (source
        (origin
-       (method url-fetch)
+         (method git-fetch)
-       (uri (pypi-uri "graphite-web" version))
+         (uri (git-reference
+               (url "https://github.com/graphite-project/graphite-web")
+               (commit commit)))
+         (file-name (git-file-name name version))
          (sha256
-        (base32
+          (base32 "0bcc6jh7gyp8f54dzy4zza1z46gk3530r952pi86irf834z106sg"))))
-         "0nnk3kwn0b6bq9xnmv9bac6hpcbdgpgwf283c1ck5nm80panh61z"))))
+      (build-system pyproject-build-system)
-    (build-system python-build-system)
       (arguments
-     `(#:tests? #f               ;XXX: not in PyPI release & requires database
+       `(#:tests? #f               ;XXX: Requires database, unable to run now
          #:phases
          (modify-phases %standard-phases
            (add-after 'unpack 'relax-requirements
@@ -480,13 +487,33 @@ and persisting them to disk using the Whisper time-series library.")
                  ;; Allow newer versions of django-tagging.
                  (("django-tagging==") "django-tagging>=")
                  ;; And Django.
-               (("Django>=1\\.8,<3\\.1") "Django>=1.8,<4"))))
+                 (("Django>=3\\.2,<4") "Django>=4,<5"))))
            ;; Don't install to /opt
            (add-after 'unpack 'do-not-install-to-/opt
-           (lambda _ (setenv "GRAPHITE_NO_PREFIX" "1") #t)))))
+             (lambda _ (setenv "GRAPHITE_NO_PREFIX" "1")))
+           (replace 'check
+             (lambda* (#:key tests? #:allow-other-keys)
+               (when tests?
+                 (mkdir-p "storage/log/webapp")
+                 (with-directory-excursion "webapp"
+                   (invoke "./manage.py" "test" "--pythonpath=." "tests"
+                           "-k" (string-join
+                                 (list
+                                  "not test_dashboard_save_temporary_xss_key"
+                                  "test_dashboard_save_temporary_xss_name")
+                                 " and not ")))))))))
+      (native-inputs
+       (list python-carbon
+             python-mock
+             python-pytest
+             python-rrdtool
+             python-setuptools
+             python-tzdata
+             python-wheel
+             python-whisper))
       (propagated-inputs
        (list python-cairocffi
-           python-django-3.2
+             python-django-4.2
              python-django-tagging
              python-pyparsing
              python-pytz
@@ -497,7 +524,7 @@ and persisting them to disk using the Whisper time-series library.")
       (description "Graphite is a scalable real-time graphing system that does
 two things: store numeric time-series data, and render graphs of this data on
 demand.")
-    (license license:asl2.0)))
+      (license license:asl2.0))))
 
 (define-public python-prometheus-client
   (package
@@ -838,6 +865,25 @@ display resumes.
 @end itemize")
     (license license:bsd-2)))
 
+(define-public python-rrdtool
+  (package
+    (name "python-rrdtool")
+    (version "0.1.16")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "rrdtool" version))
+       (sha256
+        (base32 "0l8lbarzfwbwnq9jm9gv4mmrxgjlb9hbz27sa8b703qa7s5zy2jz"))))
+    (build-system pyproject-build-system)
+    (arguments (list #:tests? #f)) ; No tests in pypi archive
+    (inputs (list rrdtool))
+    (native-inputs (list python-setuptools python-wheel))
+    (home-page "https://github.com/commx/python-rrdtool")
+    (synopsis "Python bindings for rrdtool")
+    (description "This package provides Python bindings for rrdtool.")
+    (license license:lgpl2.1)))
+
 (define-public python-statsd
   (package
     (name "python-statsd")

gnu/packages/music.scm

@@ -1858,7 +1858,11 @@ typographic detail of symbols on the page.")
         (base32 "1y8s55b4mlsigm0xkk6qjpp08c75rv0swvjp0lj3cs6lgqdjxdjl"))))
     (build-system pyproject-build-system)
     (native-inputs
-     (list lilypond python-pytest python-setuptools python-wheel))
+     (list lilypond
+           python-pytest
+           python-pytest-cov
+           python-setuptools
+           python-wheel))
     (propagated-inputs
      (list abjad))
     (home-page "https://abjad.github.io")
@@ -3809,8 +3813,14 @@ follows a traditional multi-track tape recorder control paradigm.")
         (base32 "1lz2mvk4gqsyf92yxd3aaldx0d0qi28h4rnnvsaz4ls0ccqm80nk"))))
     (build-system waf-build-system)
     (arguments
-     `(#:phases
+     (list
-       (modify-phases %standard-phases
+      #:phases
+      '(modify-phases %standard-phases
+         (add-after 'unpack 'python3.11-compatibility
+           (lambda _
+             (substitute* '("waflib/Context.py"
+                            "waflib/ConfigSet.py")
+               (("'rU'") "'r'"))))
          (add-after 'unpack 'remove-sse-flags
            (lambda* (#:key system #:allow-other-keys)
              (unless (or (string-prefix? "x86_64" system)
@@ -4617,8 +4627,8 @@ standard MIDI file with the csvmidi program.")
     (license license:public-domain)))
 
 (define-public mididings
-  (let ((commit "d98265be8afe7da20a5c7cfd0515f0d5fae5c53a")
+  (let ((commit "bc71ea9c86bdc0b02364b11ab7331e8b3a86bb4f")
-        (revision "1"))
+        (revision "2"))
     (package
       (name "mididings")
       (version (git-version "0" revision commit))
@@ -4630,8 +4640,8 @@ standard MIDI file with the csvmidi program.")
                 (file-name (git-file-name name version))
                 (sha256
                  (base32
-                  "1a8i4yac5jjkq0vh73nwkv0j7vnvfwbzzagam4xdl1gpnc26n5xi"))))
+                  "1f0f8bpqbc1av0ggv6wjicymc2klliwdl1m5blmjcvy39q3cwd59"))))
-      (build-system pyproject-build-system)
+      (build-system meson-build-system)
       (arguments
        (list
         #:phases
@@ -4647,6 +4657,7 @@ standard MIDI file with the csvmidi program.")
        (list alsa-lib
              boost
              jack-2
+             python
              `(,python "tk")
              python-dbus
              python-decorator

gnu/packages/networking.scm

@@ -1,6 +1,6 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2014, 2017, 2018, 2021 Ludovic Courtès <ludo@gnu.org>
-;;; Copyright © 2015, 2016, 2017, 2018, 2020, 2024 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2015, 2016, 2017, 2018, 2020, 2024, 2025 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2015 Mark H Weaver <mhw@netris.org>
 ;;; Copyright © 2015, 2016, 2017, 2021 Stefan Reichör <stefan@xsteve.at>
 ;;; Copyright © 2016 Raimon Grau <raimonster@gmail.com>
@@ -911,21 +911,22 @@ systems with no further dependencies.")
 (define-public blueman
   (package
     (name "blueman")
-    (version "2.3.4")
+    (version "2.4.4")
     (source
      (origin
        (method url-fetch)
        (uri (string-append "https://github.com/blueman-project/blueman/releases"
                            "/download/" version "/blueman-" version ".tar.xz"))
        (sha256
-        (base32 "0lh1aqpdq6vi4agrgmm7fifjbxz2s5qcs3hr7nfjrwrp2j1361n2"))))
+        (base32 "1w45dr2cmy32cvxwqaybf5m2ziraj929f4lxcwapv266r1a92kyk"))))
     (build-system glib-or-gtk-build-system)
     (arguments
-     `(#:configure-flags (list "--enable-polkit"
+     (list
+      #:configure-flags '(list "--enable-polkit"
                                "--without-systemdsystemunitdir" ; Not required
                                "--without-systemduserunitdir")  ; Not required
       #:phases
-       (modify-phases %standard-phases
+      #~(modify-phases %standard-phases
           ;; Python references are not being patched in patch-phase of build,
           ;; despite using python-wrapper as input. So we patch them manually.
           (add-after 'unpack 'patch-python-references
@@ -939,8 +940,8 @@ systems with no further dependencies.")
                    (search-input-file inputs
                                       (string-append
                                        "/bin/python"
-                                      ,(version-major+minor
+                                       #$(version-major+minor
-                                        (package-version python)))))))))
+                                          (package-version (this-package-input "python-wrapper"))))))))))
           ;; Fix loading of external programs.
           (add-after 'unpack 'patch-external-programs
             (lambda* (#:key inputs #:allow-other-keys)
@@ -956,7 +957,7 @@ systems with no further dependencies.")
           ;; Fix loading of pulseaudio libraries.
           (add-after 'unpack 'patch-pulseaudio-libraries
             (lambda* (#:key inputs #:allow-other-keys)
-             (let* ((pulseaudio (assoc-ref inputs "pulseaudio"))
+              (let* ((pulseaudio #$(this-package-input "pulseaudio"))
                      (pulse (string-append pulseaudio "/lib/libpulse.so.0"))
                      (pulse-glib (string-append pulseaudio
                                                 "/lib/libpulse-mainloop-glib.so.0")))
@@ -967,12 +968,11 @@ systems with no further dependencies.")
           ;; Fix running of blueman programs.
           (add-after 'glib-or-gtk-wrap 'wrap-blueman-progs
             (lambda* (#:key outputs #:allow-other-keys)
-             (let* ((out (assoc-ref outputs "out"))
+              (let* ((bin (string-append #$output "/bin/blueman-"))
-                    (bin (string-append out "/bin/blueman-"))
+                     (libexec (string-append #$output "/libexec/blueman-"))
-                    (libexec (string-append out "/libexec/blueman-"))
+                     (lib (string-append #$output "/lib/python"
-                    (lib (string-append out "/lib/python"
+                                         #$(version-major+minor
-                                        ,(version-major+minor
+                                            (package-version (this-package-input "python-wrapper")))
-                                          (package-version python))
                                          "/site-packages")))
                 (for-each
                  (lambda (program)

gnu/packages/openstack.scm

@@ -115,20 +115,30 @@ formatters, and other extensions.")
 (define-public python-debtcollector
   (package
     (name "python-debtcollector")
-    (version "1.19.0")
+    (version "3.0.0")
     (source
       (origin
         (method url-fetch)
         (uri (pypi-uri "debtcollector" version))
         (sha256
-          (base32
+         (base32 "0vzarkvjclci98d8lvkix6qj59f7rxp1qg2x6q6is7qfbg91g29a"))
-           "06c7vyn184y9f0lsrwaz13aq63hdz5fjrd191b8nifx6acsni42f"))))
+        (modules '((guix build utils)))
-    (build-system python-build-system)
+        (snippet #~(begin
+                     (substitute* "test-requirements.txt"
+                       (("^(coverage|hacking|pre-commit).*")
+                        ""))))))
+    (build-system pyproject-build-system)
     (propagated-inputs
-     (list python-pbr python-six python-wrapt))
+     (list python-pbr python-wrapt))
     (native-inputs
-     (list ;; Tests.
+     (list python-doc8
-           python-subunit python-testrepository python-testtools))
+           python-fixtures
+           python-openstackdocstheme
+           python-reno
+           python-setuptools
+           python-stestr
+           python-testtools
+           python-wheel))
     (home-page "https://www.openstack.org/")
     (synopsis
      "Find deprecated patterns and strategies in Python code")
@@ -386,11 +396,11 @@ extensions.")
                              python-fixtures
                              python-jsonschema
                              python-netaddr
-                             python-oslo.concurrency
+                             python-oslo-concurrency
-                             python-oslo.config
+                             python-oslo-config
-                             python-oslo.log
+                             python-oslo-log
-                             python-oslo.serialization
+                             python-oslo-serialization
-                             python-oslo.utils
+                             python-oslo-utils
                              python-paramiko
                              python-prettytable
                              python-pyyaml
@@ -437,7 +447,7 @@ OpenStack deployment.")
             python-httplib2
             python-iso8601
             python-jsonschema
-            python-oslo.log
+            python-oslo-log
             python-paramiko
             python-six))
     (native-inputs
@@ -455,9 +465,9 @@ common features used in Tempest.")
 ;;; Packages from the Oslo library
 ;;;
 
-(define-public python-oslo.concurrency
+(define-public python-oslo-concurrency
   (package
-    (name "python-oslo.concurrency")
+    (name "python-oslo-concurrency")
     (version "5.0.0")
     (source (origin
               (method url-fetch)
@@ -490,8 +500,8 @@ common features used in Tempest.")
                          python-fixtures
                          python-stestr
                          python-eventlet))
-    (propagated-inputs (list python-fasteners python-oslo.config
+    (propagated-inputs (list python-fasteners python-oslo-config
-                             python-oslo.i18n python-oslo.utils))
+                             python-oslo-i18n python-oslo-utils))
     (home-page "https://docs.openstack.org/oslo.concurrency/latest/")
     (synopsis "Oslo Concurrency library")
     (description "The Oslo Concurrency Library provides utilities for safely
@@ -499,9 +509,9 @@ running multi-thread, multi-process applications using locking mechanisms and
 for running external processes.")
     (license asl2.0)))
 
-(define-public python-oslo.config
+(define-public python-oslo-config
   (package
-    (name "python-oslo.config")
+    (name "python-oslo-config")
     (version "8.7.1")
     (source
      (origin
@@ -515,7 +525,7 @@ for running external processes.")
     (propagated-inputs
      (list python-debtcollector
            python-netaddr
-           python-oslo.i18n
+           python-oslo-i18n
            python-rfc3986
            python-requests
            python-stevedore
@@ -527,9 +537,9 @@ for running external processes.")
 .ini style configuration files.")
     (license asl2.0)))
 
-(define-public python-oslo.context
+(define-public python-oslo-context
   (package
-    (name "python-oslo.context")
+    (name "python-oslo-context")
     (version "5.0.0")
     (source
      (origin
@@ -566,9 +576,9 @@ about a request context.  The request context is usually populated in the WSGI
 pipeline and used by various modules such as logging.")
     (license asl2.0)))
 
-(define-public python-oslo.i18n
+(define-public python-oslo-i18n
   (package
-    (name "python-oslo.i18n")
+    (name "python-oslo-i18n")
     (version "3.20.0")
     (source
      (origin
@@ -592,9 +602,9 @@ internationalization (i18n) features, especially translation for text strings
 in an application or library.")
     (license asl2.0)))
 
-(define-public python-oslo.log
+(define-public python-oslo-log
   (package
-  (name "python-oslo.log")
+  (name "python-oslo-log")
   (version "5.0.0")
   (source
     (origin
@@ -612,11 +622,11 @@ in an application or library.")
   (propagated-inputs
    (list python-dateutil
          python-debtcollector
-         python-oslo.config
+         python-oslo-config
-         python-oslo.context
+         python-oslo-context
-         python-oslo.i18n
+         python-oslo-i18n
-         python-oslo.utils
+         python-oslo-utils
-         python-oslo.serialization
+         python-oslo-serialization
          python-pyinotify))
   (native-inputs
    (list python-fixtures python-oslotest python-stestr python-testtools
@@ -629,9 +639,9 @@ configuration for all OpenStack projects.  It also provides custom formatters,
 handlers and support for context specific logging (like resource id’s etc).")
   (license asl2.0)))
 
-(define-public python-oslo.serialization
+(define-public python-oslo-serialization
   (package
-    (name "python-oslo.serialization")
+    (name "python-oslo-serialization")
     (version "4.2.0")
     (source
      (origin
@@ -647,10 +657,10 @@ handlers and support for context specific logging (like resource id’s etc).")
                     (lambda* (#:key tests? #:allow-other-keys)
                       (when tests? (invoke "stestr" "run")))))))
     (propagated-inputs
-      (list python-msgpack python-oslo.utils python-pbr python-pytz))
+      (list python-msgpack python-oslo-utils python-pbr python-pytz))
     (native-inputs
      ;; For tests.
-      (list python-netaddr python-oslo.i18n python-oslotest python-stestr))
+      (list python-netaddr python-oslo-i18n python-oslotest python-stestr))
     (home-page "https://launchpad.net/oslo")
     (synopsis "Oslo serialization library")
     (description
@@ -757,9 +767,9 @@ documentation from the OpenStack project.")
 for debugging, and better support for mocking results.")
     (license asl2.0)))
 
-(define-public python-oslo.utils
+(define-public python-oslo-utils
   (package
-    (name "python-oslo.utils")
+    (name "python-oslo-utils")
     (version "4.12.0")
     (source
       (origin
@@ -776,7 +786,7 @@ for debugging, and better support for mocking results.")
                       (when tests? (invoke "stestr" "run")))))))
     (propagated-inputs
       (list python-debtcollector
-            python-oslo.i18n
+            python-oslo-i18n
             python-iso8601
             python-netaddr
             python-netifaces
@@ -843,8 +853,8 @@ handling.")
                          python-hacking
                          python-lxml
                          python-oauthlib
-                         python-oslo.config
+                         python-oslo-config
-                         python-oslo.utils
+                         python-oslo-utils
                          python-oslotest
                          python-pbr
                          python-pyyaml
@@ -907,10 +917,10 @@ process of writing new clients.")
            python-iso8601
            python-keystoneauth1
            python-netaddr
-           python-oslo.config
+           python-oslo-config
-           python-oslo.i18n
+           python-oslo-i18n
-           python-oslo.serialization
+           python-oslo-serialization
-           python-oslo.utils
+           python-oslo-utils
            python-prettytable
            python-requests
            python-six
@@ -1071,7 +1081,7 @@ regardless of whether they are bundled or not.")
                          python-statsd
                          python-stestr
                          python-testscenarios
-                         python-oslo.config
+                         python-oslo-config
                          python-oslotest))
     (propagated-inputs (list python-appdirs
                              python-cryptography

gnu/packages/orange.scm

@@ -31,6 +31,7 @@
   #:use-module (gnu packages graph)
   #:use-module (gnu packages machine-learning)
   #:use-module (gnu packages python-build)
+  #:use-module (gnu packages python-check)
   #:use-module (gnu packages python-crypto)
   #:use-module (gnu packages python-science)
   #:use-module (gnu packages python-web)
@@ -59,7 +60,19 @@
                      "test_copy_cut_paste"
                      ;; AttributeError: 'NoneType' object has no attribute
                      ;; 'isEnabled'
-                     "test_item_context_menu")
+                     "test_item_context_menu"
+                     ;; Tests fail with error: Failed: CALL ERROR: Exceptions
+                     ;; caught in Qt event loop.
+                     "test_create_new_window"
+                     "test_new_window"
+                     "test_dont_load_swp_on_new_window"
+                     "test_toolbox"
+                     "test_widgettoolgrid"
+                     "test_editlinksnode"
+                     "test_links_edit"
+                     "test_links_edit_widget"
+                     "test_flattened"
+                     "test_tooltree_registry")
                     " and not "))
       #:phases
       #~(modify-phases %standard-phases
@@ -71,12 +84,18 @@
           (add-before 'check 'pre-check
             (lambda _
               (setenv "HOME" "/tmp")
+              (setenv "QT_PLUGIN_PATH"
+                      (string-append #$(this-package-input "qtbase") "/lib/qt6/plugins:"
+                                     (getenv "QT_PLUGIN_PATH")))
               (setenv "QT_QPA_PLATFORM" "offscreen"))))))
     (native-inputs
      (list python-pytest
+           python-pytest-qt
            python-setuptools
            python-trubar
            python-wheel))
+    (inputs
+     (list qtbase))
     (propagated-inputs
      (list python-anyqt
            python-cachecontrol

gnu/packages/package-management.scm

@@ -1123,6 +1123,34 @@ Anaconda Cloud.  Anaconda Cloud is useful for sharing packages, notebooks and
 environments.")
     (license license:bsd-3)))
 
+(define-public python-conda-inject
+  (package
+    (name "python-conda-inject")
+    (version "1.3.2")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/koesterlab/conda-inject")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "1aig9l676wc2sjb20y7rdqf0hfcfjhh92yfiy82mf7kfnv7rp3rk"))))
+    (build-system pyproject-build-system)
+    (arguments
+     (list #:tests? #f)) ; tests require setting up Conda
+    (native-inputs
+     (list python-poetry-core))
+    (propagated-inputs
+     (list python-pyyaml))
+    (home-page "https://github.com/koesterlab/conda-inject")
+    (synopsis "Inject a conda environment into the current python environment")
+    (description
+     "This package provides helper functions for injecting a conda
+environment into the current python environment (by modifying @code{sys.path},
+without actually changing the current python environment).")
+    (license license:expat)))
+
 (define-public python-conda-package-handling
   (package
     (name "python-conda-package-handling")
@@ -1315,7 +1343,7 @@ written entirely in Python.")
 (define-public conan
   (package
     (name "conan")
-    (version "2.0.9")
+    (version "2.7.1")
     (source
      (origin
        (method git-fetch)               ; no tests in PyPI archive
@@ -1324,13 +1352,74 @@ written entirely in Python.")
              (commit version)))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "1ykfj7c3i0b57s7ql3p2lawxdzd2cn36f3k8p64lyzla8rwv4xdx"))))
+        (base32 "00mrx1ighvf6r6fy2iqxr286w3jfd0gwlzcqsw15cm9axblx5av9"))))
-    (build-system python-build-system)
+    (build-system pyproject-build-system)
     (arguments
      (list
-      #:modules '((guix build python-build-system)
+      #:modules '((guix build pyproject-build-system)
                   (guix build utils)
                   (ice-9 format))
+      #:test-flags
+      (let ((system (or (%current-target-system)
+                        (%current-system))))
+        #~(list "-n" (number->string (parallel-job-count))
+                "-m" "not slow"
+                "--ignore=test/performance/"
+                ;; E   ModuleNotFoundError: No module named 'docker'
+                "--ignore=test/functional/command/runner_test.py"
+                ;; Disable problematic tests.
+                "-k"
+                (string-append
+                 ;; These tests rely on networking.
+                 "not download_retries_errors "
+                 "and not ftp "
+                 ;; These tests are for old versions of cmake.
+                 "and not test_custom_cmake_3_16 "
+                 "and not test_custom_cmake_3_17 "
+                 "and not test_custom_cmake_3_19 "
+                 ;; Guix sets PKG_CONFIG_PATH itself, which is not
+                 ;; expected by the following test.
+                 "and not pkg_config_path "
+                 "and not compare " ;caused by newer node-semver?
+                 ;; This test hard-codes a compiler version.
+                 "and not test_toolchain "
+                 ;; The 'test_list' tests may fail
+                 ;; non-deterministically (see:
+                 ;; https://github.com/conan-io/conan/issues/13583).
+                 "and not test_list "
+                 ;; These tests fail when Autoconf attempt to load a
+                 ;; shared library in the same directory (see:
+                 ;; https://github.com/conan-io/conan/issues/13577).
+                 "and not test_other_client_can_link_autotools "
+                 "and not test_autotools_lib_template "
+                 ;; Sometimes fail: https://github.com/conan-io/conan/issues/15936
+                 "and not test_basic_parallel_install "
+                 ;; These tests require additional build tools
+                 "and not test_premake "
+                 "and not test_sconsdeps "
+                 ;; Unclear why libc is not found properly
+                 "and not test_profile_detect_libc "
+                 #$(if (not (string-prefix? "x86_64" system))
+                       ;; These tests either assume the machine is
+                       ;; x86_64, or require a cross-compiler to target
+                       ;; it.
+                       (string-append
+                        "and not cpp_package "
+                        "and not exclude_code_analysis "
+                        "and not cmakedeps_multi "
+                        "and not locally_build_linux "
+                        "and not custom_configuration "
+                        "and not package_from_system "
+                        "and not cross_build_command "
+                        "and not test_package "
+                        "and not test_same ")
+                       "")
+                 #$(if (not (or (string-prefix? "x86_64" system)
+                                (string-prefix? "i686" system)))
+                       ;; This test only works with default arch "x86",
+                       ;; "x86_64", "sparc" or "sparcv9".
+                       "and not settings_as_a_dict_conanfile "
+                       ""))))
       #:phases
       #~(modify-phases %standard-phases
           (add-after 'unpack 'patch-paths
@@ -1345,21 +1434,22 @@ written entirely in Python.")
               ;; The test suite expects GCC 9 to be used (see:
               ;; https://github.com/conan-io/conan/issues/13575).  Render the
               ;; check version agnostic.
-              (substitute* "conans/test/functional/toolchains/meson/_base.py"
+              (substitute* "test/functional/toolchains/meson/_base.py"
                 (("__GNUC__9")
                  "__GNUC__"))))
           (add-after 'unpack 'use-current-cmake-for-tests
             (lambda _
-              (substitute* (find-files "conans/test" "\\.py$")
+              (substitute* (find-files "test" "\\.py$")
-                (("@pytest.mark.tool\\(\"cmake\", \"3.23\")")
+                (("@pytest.mark.tool\\(\"cmake\", \".*\")")
                  "@pytest.mark.tool(\"cmake\")"))))
           (add-before 'check 'configure-tests
             (lambda _
               (let* ((cmake-version #$(version-major+minor
-                                       (package-version cmake)))
+                                       (package-version
+                                        (this-package-native-input "cmake"))))
                      (pkg-config-version #$(version-major+minor
                                             (package-version pkg-config))))
-                (call-with-output-file "conans/test/conftest_user.py"
+                (call-with-output-file "test/conftest_user.py"
                   (lambda (port)
                     (format port "\
 tools_locations = {
@@ -1378,61 +1468,12 @@ tools_locations = {
           (add-before 'check 'set-home
             (lambda _
               (setenv "HOME" "/tmp")))
-          (replace 'check
+          (add-before 'check 'configure-tests
-            (lambda* (#:key tests? outputs #:allow-other-keys)
+            (lambda* (#:key tests? #:allow-other-keys)
-              (define system #$(or (%current-target-system)
-                                   (%current-system)))
               (when tests?
                 (setenv "CONFIG_SHELL" (which "sh"))
                 (setenv "PATH" (string-append (getenv "PATH") ":"
-                                              #$output "/bin"))
+                                              #$output "/bin"))))))))
-                (invoke "python" "-m" "pytest" "-vv"
-                        "-n" (number->string (parallel-job-count))
-                        "-m" "not slow"
-                        ;; Disable problematic tests.
-                        "-k"
-                        (string-append
-                         ;; These tests rely on networking.
-                         "not download_retries_errors "
-                         "and not ftp "
-                         ;; Guix sets PKG_CONFIG_PATH itself, which is not
-                         ;; expected by the following test.
-                         "and not pkg_config_path "
-                         "and not compare " ;caused by newer node-semver?
-                         ;; This test hard-codes a compiler version.
-                         "and not test_toolchain "
-                         ;; The 'test_list' tests may fail
-                         ;; non-deterministically (see:
-                         ;; https://github.com/conan-io/conan/issues/13583).
-                         "and not test_list "
-                         ;; These tests fail when Autoconf attempt to load a
-                         ;; shared library in the same directory (see:
-                         ;; https://github.com/conan-io/conan/issues/13577).
-                         "and not test_other_client_can_link_autotools "
-                         "and not test_autotools_lib_template "
-                         ;; Sometimes fail: https://github.com/conan-io/conan/issues/15936
-                         "and not test_basic_parallel_install "
-                         (if (not (string-prefix? "x86_64" system))
-                             ;; These tests either assume the machine is
-                             ;; x86_64, or require a cross-compiler to target
-                             ;; it.
-                             (string-append
-                              "and not cpp_package "
-                              "and not exclude_code_analysis "
-                              "and not cmakedeps_multi "
-                              "and not locally_build_linux "
-                              "and not custom_configuration "
-                              "and not package_from_system "
-                              "and not cross_build_command "
-                              "and not test_package "
-                              "and not test_same ")
-                             "")
-                         (if (not (or (string-prefix? "x86_64" system)
-                                      (string-prefix? "i686" system)))
-                             ;; This test only works with default arch "x86",
-                             ;; "x86_64", "sparc" or "sparcv9".
-                             "and not settings_as_a_dict_conanfile "
-                             "")))))))))
     (propagated-inputs
      (list python-bottle
            python-colorama
@@ -1450,7 +1491,7 @@ tools_locations = {
            python-requests
            python-six
            python-tqdm
-           python-urllib3))
+           python-urllib3-1.26))
     (inputs
      (list coreutils))                  ;for printenv
     (native-inputs
@@ -1467,7 +1508,9 @@ tools_locations = {
            python-parameterized
            python-pytest
            python-pytest-xdist
+           python-setuptools
            python-webtest
+           python-wheel
            which))
     (home-page "https://conan.io")
     (synopsis "Decentralized C/C++ package manager")

gnu/packages/patches/onionshare-cli-async-mode.patch

@@ -1,25 +0,0 @@
-Specifying the `async_mode` parameter seems to have been a workaround for
-packaging on Windows and macOS.  If not given, flask_socketio.SocketIO will
-probe for an available asynchronous model, e.g. `eventlet`, and otherwise gets
-stuck if `gevent-socketio` is not available.
-
-c.f. https://github.com/onionshare/onionshare/commit/ec7fa4ef16c9e1ba6028ee927c23f76c399a17a6
-and  https://github.com/onionshare/onionshare/issues/1510
-
-diff --git a/cli/onionshare_cli/web/web.py b/cli/onionshare_cli/web/web.py
-index 64844b5..7e1b095 100644
---- a/cli/onionshare_cli/web/web.py
-+++ b/cli/onionshare_cli/web/web.py
-@@ -164,10 +164,10 @@ class Web:
-         elif self.mode == "chat":
-             if self.common.verbose:
-                 self.socketio = SocketIO(
--                    async_mode="gevent", logger=True, engineio_logger=True
-+                    logger=True, engineio_logger=True
-                 )
-             else:
--                self.socketio = SocketIO(async_mode="gevent")
-+                self.socketio = SocketIO()
-             self.socketio.init_app(self.app)
-             self.chat_mode = ChatModeWeb(self.common, self)
- 

gnu/packages/patches/python-3.11-fix-tests.patch

@@ -0,0 +1,430 @@
+From f0698133e7d6c353a3e6ae0fc62e57ba558a9bc0 Mon Sep 17 00:00:00 2001
+From: Maxim Cournoyer <maxim.cournoyer@gmail.com>
+Date: Wed, 28 Oct 2020 22:55:05 -0400
+Subject: [PATCH] Skip problematic Python 3 tests in Guix.
+
+A subset of the hunks in this patch is tracked upstream at
+https://bugs.python.org/issue38845, which was contributed by Tanguy Le
+Carrour <tanguy@bioneland.org>.
+---
+ Lib/ctypes/test/test_callbacks.py         | 3 +++
+ Lib/ctypes/test/test_find.py              | 1 +
+ Lib/ctypes/test/test_libc.py              | 3 +++
+ Lib/distutils/tests/test_archive_util.py  | 2 ++
+ Lib/distutils/tests/test_sdist.py         | 1 +
+ Lib/test/_test_multiprocessing.py         | 2 ++
+ Lib/test/test_asyncio/test_base_events.py | 2 ++
+ Lib/test/test_generators.py               | 1 +
+ Lib/test/test_pathlib.py                  | 3 +--
+ Lib/test/test_pdb.py                      | 4 ++--
+ Lib/test/test_regrtest.py                 | 2 ++
+ Lib/test/test_resource.py                 | 1 +
+ Lib/test/test_shutil.py                   | 2 ++
+ Lib/test/test_signal.py                   | 4 ++++
+ Lib/test/test_socket.py                   | 8 ++++++++
+ Lib/test/test_spwd.py                     | 6 ++----
+ Lib/test/test_tarfile.py                  | 9 ++++++---
+ Lib/test/test_threading.py                | 3 +++
+ Lib/test/test_unicodedata.py              | 1 +
+ Tools/scripts/run_tests.py                | 2 +-
+ 20 files changed, 48 insertions(+), 12 deletions(-)
+
+diff --git a/Lib/ctypes/test/test_callbacks.py b/Lib/ctypes/test/test_callbacks.py
+index d8e9c5a760..94fc5929c9 100644
+--- a/Lib/ctypes/test/test_callbacks.py
++++ b/Lib/ctypes/test/test_callbacks.py
+@@ -5,6 +5,7 @@ from test import support
+ from ctypes import *
+ from ctypes.test import need_symbol
+ import _ctypes_test
++import platform
+ 
+ class Callbacks(unittest.TestCase):
+     functype = CFUNCTYPE
+@@ -178,6 +179,8 @@ class SampleCallbacksTestCase(unittest.TestCase):
+ 
+         self.assertLess(diff, 0.01, "%s not less than 0.01" % diff)
+ 
++    @unittest.skipIf(platform.machine() in ['mips64'],
++                     "This test fails on this platform")
+     def test_issue_8959_a(self):
+         from ctypes.util import find_library
+         libc_path = find_library("c")
+diff --git a/Lib/ctypes/test/test_find.py b/Lib/ctypes/test/test_find.py
+index 92ac1840ad..c8eb75dedd 100644
+--- a/Lib/ctypes/test/test_find.py
++++ b/Lib/ctypes/test/test_find.py
+@@ -116,6 +116,7 @@ class FindLibraryLinux(unittest.TestCase):
+         with unittest.mock.patch("ctypes.util._findSoname_ldconfig", lambda *args: None):
+             self.assertNotEqual(find_library('c'), None)
+ 
++    @unittest.skipIf(True, "ldconfig is not used on Guix")
+     def test_find_library_with_ld(self):
+         with unittest.mock.patch("ctypes.util._findSoname_ldconfig", lambda *args: None), \
+              unittest.mock.patch("ctypes.util._findLib_gcc", lambda *args: None):
+diff --git a/Lib/ctypes/test/test_libc.py b/Lib/ctypes/test/test_libc.py
+index 56285b5ff8..c088ab3db8 100644
+--- a/Lib/ctypes/test/test_libc.py
++++ b/Lib/ctypes/test/test_libc.py
+@@ -2,6 +2,7 @@ import unittest
+ 
+ from ctypes import *
+ import _ctypes_test
++import platform
+ 
+ lib = CDLL(_ctypes_test.__file__)
+ 
+@@ -17,6 +18,8 @@ class LibTest(unittest.TestCase):
+         import math
+         self.assertEqual(lib.my_sqrt(2.0), math.sqrt(2.0))
+ 
++    @unittest.skipIf(platform.machine() in ['mips64'],
++                     "This test fails on this platform")
+     def test_qsort(self):
+         comparefunc = CFUNCTYPE(c_int, POINTER(c_char), POINTER(c_char))
+         lib.my_qsort.argtypes = c_void_p, c_size_t, c_size_t, comparefunc
+diff --git a/Lib/distutils/tests/test_archive_util.py b/Lib/distutils/tests/test_archive_util.py
+index e9aad0e40f..8bbaa51ee5 100644
+--- a/Lib/distutils/tests/test_archive_util.py
++++ b/Lib/distutils/tests/test_archive_util.py
+@@ -333,6 +333,7 @@ class ArchiveUtilTestCase(support.TempdirManager,
+         self.assertEqual(os.path.basename(res), 'archive.tar.xz')
+         self.assertEqual(self._tarinfo(res), self._created_files)
+ 
++    @unittest.skipIf(True, "getgrgid(0)[0] raises a KeyError on Guix")
+     def test_make_archive_owner_group(self):
+         # testing make_archive with owner and group, with various combinations
+         # this works even if there's not gid/uid support
+@@ -362,6 +363,7 @@ class ArchiveUtilTestCase(support.TempdirManager,
+ 
+     @unittest.skipUnless(ZLIB_SUPPORT, "Requires zlib")
+     @unittest.skipUnless(UID_GID_SUPPORT, "Requires grp and pwd support")
++    @unittest.skipIf(True, "getgrgid(0)[0] raises a KeyError on Guix")
+     def test_tarfile_root_owner(self):
+         tmpdir =  self._create_files()
+         base_name = os.path.join(self.mkdtemp(), 'archive')
+diff --git a/Lib/distutils/tests/test_sdist.py b/Lib/distutils/tests/test_sdist.py
+index 23db126959..6e2329df7d 100644
+--- a/Lib/distutils/tests/test_sdist.py
++++ b/Lib/distutils/tests/test_sdist.py
+@@ -443,6 +443,7 @@ class SDistTestCase(BasePyPIRCCommandTestCase):
+                      "The tar command is not found")
+     @unittest.skipIf(find_executable('gzip') is None,
+                      "The gzip command is not found")
++    @unittest.skipIf(True, "getgrgid(0)[0] raises a KeyError on Guix")
+     def test_make_distribution_owner_group(self):
+         # now building a sdist
+         dist, cmd = self.get_cmd()
+diff --git a/Lib/test/_test_multiprocessing.py b/Lib/test/_test_multiprocessing.py
+index e47905c863..31a5a9c308 100644
+--- a/Lib/test/_test_multiprocessing.py
++++ b/Lib/test/_test_multiprocessing.py
+@@ -1577,6 +1577,7 @@ class _TestCondition(BaseTestCase):
+         if pid is not None:
+             os.kill(pid, signal.SIGINT)
+ 
++    @unittest.skipIf(True, "This fails for unknown reasons on Guix")
+     def test_wait_result(self):
+         if isinstance(self, ProcessesMixin) and sys.platform != 'win32':
+             pid = os.getpid()
+@@ -3905,6 +3906,7 @@ class _TestSharedMemory(BaseTestCase):
+         sms.close()
+ 
+     @unittest.skipIf(os.name != "posix", "not feasible in non-posix platforms")
++    @unittest.skipUnless(sys.stdin.isatty(), "KeyboardInterrupts require a TTY device")
+     def test_shared_memory_SharedMemoryServer_ignores_sigint(self):
+         # bpo-36368: protect SharedMemoryManager server process from
+         # KeyboardInterrupt signals.
+diff --git a/Lib/test/test_asyncio/test_base_events.py b/Lib/test/test_asyncio/test_base_events.py
+index 533d5cc7f5..c4f860cc3b 100644
+--- a/Lib/test/test_asyncio/test_base_events.py
++++ b/Lib/test/test_asyncio/test_base_events.py
+@@ -1341,6 +1341,8 @@ class BaseEventLoopWithSelectorTests(test_utils.TestCase):
+         self._test_create_connection_ip_addr(m_socket, False)
+ 
+     @patch_socket
++    @unittest.skipUnless(support.is_resource_enabled('network'),
++                         'network is not enabled')
+     def test_create_connection_service_name(self, m_socket):
+         m_socket.getaddrinfo = socket.getaddrinfo
+         sock = m_socket.socket.return_value
+diff --git a/Lib/test/test_generators.py b/Lib/test/test_generators.py
+index 3bf1522808..04bac8a7db 100644
+--- a/Lib/test/test_generators.py
++++ b/Lib/test/test_generators.py
+@@ -33,6 +33,7 @@ class SignalAndYieldFromTest(unittest.TestCase):
+         else:
+             return "FAILED"
+ 
++    @unittest.skipIf(True, 'Keyboard interrupts do not work in the Guix build environment')
+     def test_raise_and_yield_from(self):
+         gen = self.generator1()
+         gen.send(None)
+diff --git a/Lib/test/test_pathlib.py b/Lib/test/test_pathlib.py
+index 3da35710b9..5404f9193d 100644
+--- a/Lib/test/test_pathlib.py
++++ b/Lib/test/test_pathlib.py
+@@ -2408,10 +2408,7 @@ class PosixPathTest(_BasePathTest, unittest.TestCase):
+         self.assertEqual(given, expect)
+         self.assertEqual(set(p.rglob("FILEd*")), set())
+ 
+-    @unittest.skipUnless(hasattr(pwd, 'getpwall'),
+-                         'pwd module does not expose getpwall()')
+-    @unittest.skipIf(sys.platform == "vxworks",
+-                     "no home directory on VxWorks")
++    @unittest.skipIf(True, "Guix builder home is '/' which causes trouble for these tests")
+     def test_expanduser(self):
+         P = self.cls
+         support.import_module('pwd')
+diff --git a/Lib/test/test_pdb.py b/Lib/test/test_pdb.py
+index 8016f81e5a..10190486b4 100644
+--- a/Lib/test/test_pdb.py
++++ b/Lib/test/test_pdb.py
+@@ -1219,11 +1219,11 @@ def test_pdb_issue_20766():
+     > <doctest test.test_pdb.test_pdb_issue_20766[0]>(6)test_function()
+     -> print('pdb %d: %s' % (i, sess._previous_sigint_handler))
+     (Pdb) continue
+-    pdb 1: <built-in function default_int_handler>
++    pdb 1: 1
+     > <doctest test.test_pdb.test_pdb_issue_20766[0]>(6)test_function()
+     -> print('pdb %d: %s' % (i, sess._previous_sigint_handler))
+     (Pdb) continue
+-    pdb 2: <built-in function default_int_handler>
++    pdb 2: 1
+     """
+ 
+ 
+diff --git a/Lib/test/test_regrtest.py b/Lib/test/test_regrtest.py
+index a77638b10a..2069b349a8 100644
+--- a/Lib/test/test_regrtest.py
++++ b/Lib/test/test_regrtest.py
+@@ -811,6 +811,7 @@ class ArgsTestCase(BaseTestCase):
+         output = self.run_tests('--fromfile', filename)
+         self.check_executed_tests(output, tests)
+ 
++    @unittest.skipIf(True, 'Keyboard interrupts do not work in the Guix build environment.')
+     def test_interrupted(self):
+         code = TEST_INTERRUPTED
+         test = self.create_test('sigint', code=code)
+@@ -828,6 +829,7 @@ class ArgsTestCase(BaseTestCase):
+                  % (self.TESTNAME_REGEX, len(tests)))
+         self.check_line(output, regex)
+ 
++    @unittest.skipIf(True, 'Keyboard interrupts do not work in the Guix build environment.')
+     def test_slowest_interrupted(self):
+         # Issue #25373: test --slowest with an interrupted test
+         code = TEST_INTERRUPTED
+diff --git a/Lib/test/test_resource.py b/Lib/test/test_resource.py
+index e5ece5284c..5299e54507 100644
+--- a/Lib/test/test_resource.py
++++ b/Lib/test/test_resource.py
+@@ -148,6 +148,7 @@ class ResourceTest(unittest.TestCase):
+ 
+     @unittest.skipUnless(hasattr(resource, 'prlimit'), 'no prlimit')
+     @support.requires_linux_version(2, 6, 36)
++    @unittest.skipIf(True, "Bug: the PermissionError is not raised")
+     def test_prlimit(self):
+         self.assertRaises(TypeError, resource.prlimit)
+         self.assertRaises(ProcessLookupError, resource.prlimit,
+diff --git a/Lib/test/test_shutil.py b/Lib/test/test_shutil.py
+index e19af64be0..1b893df6fa 100644
+--- a/Lib/test/test_shutil.py
++++ b/Lib/test/test_shutil.py
+@@ -1427,6 +1427,7 @@ class TestArchives(BaseTest, unittest.TestCase):
+         base_name = os.path.join(tmpdir, 'archive')
+         self.assertRaises(ValueError, make_archive, base_name, 'xxx')
+ 
++    @unittest.skipIf(True, "The Guix build container has no root user")
+     @support.requires_zlib()
+     def test_make_archive_owner_group(self):
+         # testing make_archive with owner and group, with various combinations
+@@ -1455,6 +1456,7 @@ class TestArchives(BaseTest, unittest.TestCase):
+         self.assertTrue(os.path.isfile(res))
+ 
+ 
++    @unittest.skipIf(True, "The Guix build container has no root user")
+     @support.requires_zlib()
+     @unittest.skipUnless(UID_GID_SUPPORT, "Requires grp and pwd support")
+     def test_tarfile_root_owner(self):
+diff --git a/Lib/test/test_signal.py b/Lib/test/test_signal.py
+index 45553a6a42..55623f01a3 100644
+--- a/Lib/test/test_signal.py
++++ b/Lib/test/test_signal.py
+@@ -78,7 +78,8 @@ class PosixTests(unittest.TestCase):
+         self.assertLess(len(s), signal.NSIG)
+ 
+     @unittest.skipUnless(sys.executable, "sys.executable required.")
+     @support.requires_subprocess()
++    @unittest.skipUnless(sys.stdin.isatty(), "KeyboardInterrupts require a TTY device")
+     def test_keyboard_interrupt_exit_code(self):
+         """KeyboardInterrupt triggers exit via SIGINT."""
+         process = subprocess.run(
+@@ -128,7 +129,8 @@ class WindowsSignalTests(unittest.TestCase):
+             signal.signal(7, handler)
+ 
+     @unittest.skipUnless(sys.executable, "sys.executable required.")
+     @support.requires_subprocess()
++    @unittest.skipUnless(sys.stdin.isatty(), "KeyboardInterrupts require a TTY device")
+     def test_keyboard_interrupt_exit_code(self):
+         """KeyboardInterrupt triggers an exit using STATUS_CONTROL_C_EXIT."""
+         # We don't test via os.kill(os.getpid(), signal.CTRL_C_EVENT) here
+@@ -1245,6 +1247,7 @@ class StressTest(unittest.TestCase):
+ 
+ class RaiseSignalTest(unittest.TestCase):
+ 
++    @unittest.skipUnless(sys.stdin.isatty(), "KeyboardInterrupts require a TTY device")
+     def test_sigint(self):
+         with self.assertRaises(KeyboardInterrupt):
+             signal.raise_signal(signal.SIGINT)
+@@ -1275,6 +1278,7 @@ class RaiseSignalTest(unittest.TestCase):
+ 
+ class PidfdSignalTest(unittest.TestCase):
+ 
++    @unittest.skipUnless(sys.stdin.isatty(), "KeyboardInterrupts require a TTY device")
+     @unittest.skipUnless(
+         hasattr(signal, "pidfd_send_signal"),
+         "pidfd support not built in",
+diff --git a/Lib/test/test_socket.py b/Lib/test/test_socket.py
+index aefba4f397..6c89f558d5 100755
+--- a/Lib/test/test_socket.py
++++ b/Lib/test/test_socket.py
+@@ -1009,6 +1009,8 @@ class GeneralModuleTests(unittest.TestCase):
+         if not fqhn in all_host_names:
+             self.fail("Error testing host resolution mechanisms. (fqdn: %s, all: %s)" % (fqhn, repr(all_host_names)))
+ 
++    @unittest.skipUnless(support.is_resource_enabled('network'),
++                         'network is not enabled')
+     def test_host_resolution(self):
+         for addr in [socket_helper.HOSTv4, '10.0.0.1', '255.255.255.255']:
+             self.assertEqual(socket.gethostbyname(addr), addr)
+@@ -1140,6 +1142,8 @@ class GeneralModuleTests(unittest.TestCase):
+             self.assertWarns(DeprecationWarning, socket.ntohs, k)
+             self.assertWarns(DeprecationWarning, socket.htons, k)
+ 
++    @unittest.skipUnless(os.path.exists("/etc/services"),
++                         "getservbyname uses /etc/services, which is not in the chroot")
+     def testGetServBy(self):
+         eq = self.assertEqual
+         # Find one service that exists, then check all the related interfaces.
+@@ -1489,6 +1493,8 @@ class GeneralModuleTests(unittest.TestCase):
+             raise
+         self.assertRaises(TypeError, s.ioctl, socket.SIO_LOOPBACK_FAST_PATH, None)
+ 
++    @unittest.skipUnless(os.path.exists("/etc/gai.conf"),
++                         "getaddrinfo() will fail")
+     def testGetaddrinfo(self):
+         try:
+             socket.getaddrinfo('localhost', 80)
+@@ -1571,6 +1577,8 @@ class GeneralModuleTests(unittest.TestCase):
+         # only IP addresses are allowed
+         self.assertRaises(OSError, socket.getnameinfo, ('mail.python.org',0), 0)
+ 
++    @unittest.skipUnless(os.path.exists("/etc/gai.conf"),
++                         "getaddrinfo() will fail")
+     @unittest.skipUnless(support.is_resource_enabled('network'),
+                          'network is not enabled')
+     def test_idna(self):
+diff --git a/Lib/test/test_spwd.py b/Lib/test/test_spwd.py
+index 07793c84c8..fec672bcbe 100644
+--- a/Lib/test/test_spwd.py
++++ b/Lib/test/test_spwd.py
+@@ -5,8 +5,7 @@ from test import support
+ spwd = support.import_module('spwd')
+ 
+ 
+-@unittest.skipUnless(hasattr(os, 'geteuid') and os.geteuid() == 0,
+-                     'root privileges required')
++@unittest.skipUnless(os.path.exists("/etc/shadow"), 'spwd tests require /etc/shadow')
+ class TestSpwdRoot(unittest.TestCase):
+ 
+     def test_getspall(self):
+@@ -56,8 +55,7 @@ class TestSpwdRoot(unittest.TestCase):
+             self.assertRaises(TypeError, spwd.getspnam, bytes_name)
+ 
+ 
+-@unittest.skipUnless(hasattr(os, 'geteuid') and os.geteuid() != 0,
+-                     'non-root user required')
++@unittest.skipUnless(os.path.exists("/etc/shadow"), 'spwd tests require /etc/shadow')
+ class TestSpwdNonRoot(unittest.TestCase):
+ 
+     def test_getspnam_exception(self):
+diff --git a/Lib/test/test_tarfile.py b/Lib/test/test_tarfile.py
+index 29cde91bf7..8d0f20e8bf 100644
+--- a/Lib/test/test_tarfile.py
++++ b/Lib/test/test_tarfile.py
+@@ -2607,9 +2607,12 @@ def root_is_uid_gid_0():
+         import pwd, grp
+     except ImportError:
+         return False
+-    if pwd.getpwuid(0)[0] != 'root':
+-        return False
+-    if grp.getgrgid(0)[0] != 'root':
++    try:
++        if pwd.getpwuid(0)[0] != 'root':
++            return False
++        if grp.getgrgid(0)[0] != 'root':
++            return False
++    except KeyError:
+         return False
+     return True
+ 
+diff --git a/Lib/test/test_tools/test_freeze.py b/Lib/test/test_tools/test_freeze.py
+index 0e7ed67de7..6539a2983b 100644
+--- a/Lib/test/test_tools/test_freeze.py
++++ b/Lib/test/test_tools/test_freeze.py
+@@ -23,6 +23,7 @@
+                  'test is too slow with PGO')
+ class TestFreeze(unittest.TestCase):
+
++    @unittest.skipIf(True, 'Fails on Guix.')
+     @support.requires_resource('cpu') # Building Python is slow
+     def test_freeze_simple_script(self):
+         script = textwrap.dedent("""
+diff --git a/Lib/test/test_threading.py b/Lib/test/test_threading.py
+index c21cdf8eb7..6c9d575032 100644
+--- a/Lib/test/test_threading.py
++++ b/Lib/test/test_threading.py
+@@ -1398,5 +1398,6 @@ class MiscTestCase(unittest.TestCase):
+             signal.signal(signum, handler) 
+ 
++    @unittest.skipIf(True, 'Keyboard interrupts do not work in the Guix build container.')
+     def test_interrupt_main_subthread(self):
+         # Calling start_new_thread with a function that executes interrupt_main
+         # should raise KeyboardInterrupt upon completion.
+@@ -1409,6 +1410,8 @@ class InterruptMainTests(unittest.TestCase):
+             t.join()
+         t.join()
+ 
++
++    @unittest.skipIf(True, 'Keyboard interrupts do not work in the Guix build container.')
+     def test_interrupt_main_mainthread(self):
+         # Make sure that if interrupt_main is called in main thread that
+         # KeyboardInterrupt is raised instantly.
+diff --git a/Lib/test/test_unicodedata.py b/Lib/test/test_unicodedata.py
+index b552d2bd17..28b1144e15 100644
+--- a/Lib/test/test_unicodedata.py
++++ b/Lib/test/test_unicodedata.py
+@@ -309,6 +309,7 @@ class UnicodeMiscTest(UnicodeDatabaseTest):
+                 self.assertEqual(len(lines), 1,
+                                  r"\u%.4x should not be a linebreak" % i)
+ 
++@requires_resource('network')
+ class NormalizationTest(unittest.TestCase):
+     @staticmethod
+     def check_version(testfile):
+diff --git a/Tools/scripts/run_tests.py b/Tools/scripts/run_tests.py
+index bcfa5e943b..1f2484971b 100644
+--- a/Tools/scripts/run_tests.py
++++ b/Tools/scripts/run_tests.py
+@@ -41,7 +41,7 @@ def main(regrtest_args):
+         else:
+             args.extend(['-j', '0'])  # Use all CPU cores
+     if not any(is_resource_use_flag(arg) for arg in regrtest_args):
+-        args.extend(['-u', 'all,-largefile,-audio,-gui'])
++        args.extend(['-u', 'all,-largefile,-audio,-gui,-network'])
+
+     if cross_compile and hostrunner:
+         # If HOSTRUNNER is set and -p/--python option is not given, then
+-- 
+2.29.2
+

gnu/packages/patches/python-bed-reader-use-store-samples.patch

@@ -0,0 +1,147 @@
+From 7e6bcdfeed54500ca533d2f0eb12078248c43c77 Mon Sep 17 00:00:00 2001
+Message-ID: <7e6bcdfeed54500ca533d2f0eb12078248c43c77.1743682382.git.ngraves@ngraves.fr>
+From: Nicolas Graves <ngraves@ngraves.fr>
+Date: Thu, 3 Apr 2025 11:33:58 +0200
+Subject: [PATCH] samples: Use deterministic samples in Guix.
+
+---
+ bed_reader/_sample_data.py | 86 +++++++++-----------------------------
+ 1 file changed, 19 insertions(+), 67 deletions(-)
+
+diff --git a/bed_reader/_sample_data.py b/bed_reader/_sample_data.py
+index 6ca4cc0..6a1146e 100644
+--- a/bed_reader/_sample_data.py
++++ b/bed_reader/_sample_data.py
+@@ -1,33 +1,8 @@
++import os
+ import tempfile
+ from pathlib import Path, PurePath
+ from typing import Union
+ 
+-try:
+-    import pooch
+-
+-    """
+-    Load sample data.
+-    """
+-
+-    POOCH = pooch.create(
+-        # Use the default cache folder for the OS
+-        path=pooch.os_cache("bed_reader"),
+-        # The remote data is on Github
+-        base_url="https://raw.githubusercontent.com/"
+-        + "fastlmm/bed-sample-files/main/",
+-        # If this is a development version, get the data from the master branch
+-        version_dev="main",
+-        # The registry specifies the files that can be fetched
+-        env="BED_READER_DATA_DIR",
+-    )
+-
+-    # Get registry file from package_data
+-    registry_file = Path(__file__).parent / "tests/registry.txt"
+-    # Load this registry file
+-    POOCH.load_registry(registry_file)
+-except ImportError:
+-    pooch = None
+-
+ 
+ def sample_file(filepath: Union[str, Path]) -> str:
+     """Retrieve a sample .bed file. (Also retrieves associated .fam and .bim files).
+@@ -40,50 +15,41 @@ def sample_file(filepath: Union[str, Path]) -> str:
+     Returns
+     -------
+     str
+-        Local name of sample .bed file.
+-
+-
+-    .. note::
+-        This function requires the :mod:`pooch` package. Install `pooch` with:
+-
+-        .. code-block:: bash
+-
+-            pip install --upgrade bed-reader[samples]
+-
+-
+-    By default this function puts files under the user's cache directory.
+-    Override this by setting
+-    the `BED_READER_DATA_DIR` environment variable.
++        Local path of sample .bed file.
+ 
+     Example
+     --------
+ 
+     .. doctest::
+ 
+-        >>> # pip install bed-reader[samples]  # if needed
+         >>> from bed_reader import sample_file
+         >>>
+         >>> file_name = sample_file("small.bed")
+         >>> print(f"The local file name is '{file_name}'")
+         The local file name is '...small.bed'
+-
+     """
+-    if pooch is None:
+-        raise ImportError(
+-            "The function sample_file() requires pooch. "
+-            + "Install it with 'pip install --upgrade bed-reader[samples]'.",
++    filepath = Path(filepath)
++    sample_dir = os.environ.get("BED_READER_DATA_DIR")
++    if sample_dir is None:
++        raise EnvironmentError(
++            "BED_READER_DATA_DIR environment variable is not set. "
++            "This should point to the directory containing the sample files."
+         )
+ 
+-    filepath = Path(filepath)
+-    file_string = str(filepath)
+-    if file_string.lower().endswith(".bed"):
+-        POOCH.fetch(file_string[:-4] + ".fam")
+-        POOCH.fetch(file_string[:-4] + ".bim")
+-    return POOCH.fetch(file_string)
++    file_path = Path(sample_dir) / filepath
++
++    # Check if file exists
++    if not file_path.exists():
++        raise FileNotFoundError(
++            f"Sample file '{filepath}' not found in {sample_dir}. "
++            f"Make sure you're using the latest samples in BED_READER_DATA_DIR."
++        )
++
++    return str(file_path)
+ 
+ 
+ def sample_url(filepath: Union[str, Path]) -> str:
+-    """Retrieve a URL to a sample .bed file. (Also makes ready associated .fam and .bim files).
++    """Retrieve a URL to a sample .bed file.
+ 
+     Parameters
+     ----------
+@@ -95,25 +61,11 @@ def sample_url(filepath: Union[str, Path]) -> str:
+     str
+         URL to sample .bed file.
+ 
+-
+-    .. note::
+-        This function requires the :mod:`pooch` package. Install `pooch` with:
+-
+-        .. code-block:: bash
+-
+-            pip install --upgrade bed-reader[samples]
+-
+-
+-    By default this function puts files under the user's cache directory.
+-    Override this by setting
+-    the `BED_READER_DATA_DIR` environment variable.
+-
+     Example
+     --------
+ 
+     .. doctest::
+ 
+-        >>> # pip install bed-reader[samples]  # if needed
+         >>> from bed_reader import sample_url
+         >>>
+         >>> url = sample_url("small.bed")
+-- 
+2.49.0
+

gnu/packages/patches/python-property-cached-asyncio-3_11.patch

@@ -0,0 +1,201 @@
+From d89186b47dc25c5ef5907c146edf3f792d50774b Mon Sep 17 00:00:00 2001
+Message-ID: <d89186b47dc25c5ef5907c146edf3f792d50774b.1743608515.git.ngraves@ngraves.fr>
+From: Nicolas Graves <ngraves@ngraves.fr>
+Date: Wed, 2 Apr 2025 17:29:45 +0200
+Subject: [PATCH] Update to python 3.11
+
+---
+ property_cached/__init__.py             | 21 +++-------
+ tests/test_async_cached_property.py     |  3 +-
+ tests/test_coroutine_cached_property.py | 51 ++++++++++---------------
+ 3 files changed, 27 insertions(+), 48 deletions(-)
+
+diff --git a/property_cached/__init__.py b/property_cached/__init__.py
+index 3353048..c033542 100644
+--- a/property_cached/__init__.py
++++ b/property_cached/__init__.py
+@@ -3,6 +3,7 @@ import functools
+ import pkg_resources
+ import threading
+ import weakref
++from inspect import iscoroutinefunction
+ from time import time
+ 
+ 
+@@ -31,12 +32,12 @@ class cached_property(property):
+         if obj is None:
+             return self
+ 
+-        if asyncio and asyncio.iscoroutinefunction(self.func):
+-            return self._wrap_in_coroutine(obj)
+-
+         value = self.cache.get(obj, self._sentinel)
+         if value is self._sentinel:
+-            value = self.cache[obj] = self.func(obj)
++            if iscoroutinefunction(self.func):
++                self.cache[obj] = value = asyncio.ensure_future(self.func(obj))
++            else:
++                self.cache[obj] = value = self.func(obj)
+ 
+         return value
+ 
+@@ -49,18 +50,6 @@ class cached_property(property):
+     def __delete__(self, obj):
+         del self.cache[obj]
+ 
+-    def _wrap_in_coroutine(self, obj):
+-
+-        @functools.wraps(obj)
+-        @asyncio.coroutine
+-        def wrapper():
+-            value = self.cache.get(obj, self._sentinel)
+-            if value is self._sentinel:
+-                self.cache[obj] = value = asyncio.ensure_future(self.func(obj))
+-            return value
+-
+-        return wrapper()
+-
+ 
+ class threaded_cached_property(cached_property):
+     """
+diff --git a/tests/test_async_cached_property.py b/tests/test_async_cached_property.py
+index 1af139d..32b3410 100644
+--- a/tests/test_async_cached_property.py
++++ b/tests/test_async_cached_property.py
+@@ -9,8 +9,7 @@ import property_cached as cached_property
+ 
+ def unittest_run_loop(f):
+     def wrapper(*args, **kwargs):
+-        coro = asyncio.coroutine(f)
+-        future = coro(*args, **kwargs)
++        future = f(*args, **kwargs)
+         loop = asyncio.get_event_loop()
+         loop.run_until_complete(future)
+ 
+diff --git a/tests/test_coroutine_cached_property.py b/tests/test_coroutine_cached_property.py
+index 40e443b..5864301 100644
+--- a/tests/test_coroutine_cached_property.py
++++ b/tests/test_coroutine_cached_property.py
+@@ -14,8 +14,7 @@ import property_cached as cached_property
+ 
+ def unittest_run_loop(f):
+     def wrapper(*args, **kwargs):
+-        coro = asyncio.coroutine(f)
+-        future = coro(*args, **kwargs)
++        future = f(*args, **kwargs)
+         loop = asyncio.get_event_loop()
+         loop.run_until_complete(future)
+ 
+@@ -33,14 +32,12 @@ def CheckFactory(cached_property_decorator):
+             self.control_total = 0
+             self.cached_total = 0
+ 
+-        @asyncio.coroutine
+-        def add_control(self):
++        async def add_control(self):
+             self.control_total += 1
+             return self.control_total
+ 
+         @cached_property_decorator
+-        @asyncio.coroutine
+-        def add_cached(self):
++        async def add_cached(self):
+             self.cached_total += 1
+             return self.cached_total
+ 
+@@ -52,74 +49,68 @@ class TestCachedProperty(unittest.TestCase):
+ 
+     cached_property_factory = cached_property.cached_property
+ 
+-    @asyncio.coroutine
+-    def assert_control(self, check, expected):
++    async def assert_control(self, check, expected):
+         """
+         Assert that both `add_control` and 'control_total` equal `expected`
+         """
+-        value = yield from check.add_control()
++        value = await check.add_control()
+         self.assertEqual(value, expected)
+         self.assertEqual(check.control_total, expected)
+ 
+-    @asyncio.coroutine
+-    def assert_cached(self, check, expected):
++    async def assert_cached(self, check, expected):
+         """
+         Assert that both `add_cached` and 'cached_total` equal `expected`
+         """
+         print("assert_cached", check.add_cached)
+-        value = yield from check.add_cached
++        value = await check.add_cached
+         self.assertEqual(value, expected)
+         self.assertEqual(check.cached_total, expected)
+ 
+     @unittest_run_loop
+-    @asyncio.coroutine
+-    def test_cached_property(self):
++    async def test_cached_property(self):
+         Check = CheckFactory(self.cached_property_factory)
+         check = Check()
+ 
+         # The control shows that we can continue to add 1
+-        yield from self.assert_control(check, 1)
+-        yield from self.assert_control(check, 2)
++        await self.assert_control(check, 1)
++        await self.assert_control(check, 2)
+ 
+         # The cached version demonstrates how nothing is added after the first
+-        yield from self.assert_cached(check, 1)
+-        yield from self.assert_cached(check, 1)
++        await self.assert_cached(check, 1)
++        await self.assert_cached(check, 1)
+ 
+         # The cache does not expire
+         with freeze_time("9999-01-01"):
+-            yield from self.assert_cached(check, 1)
++            await self.assert_cached(check, 1)
+ 
+         # Typically descriptors return themselves if accessed though the class
+         # rather than through an instance.
+         self.assertTrue(isinstance(Check.add_cached, self.cached_property_factory))
+ 
+     @unittest_run_loop
+-    @asyncio.coroutine
+-    def test_reset_cached_property(self):
++    async def test_reset_cached_property(self):
+         Check = CheckFactory(self.cached_property_factory)
+         check = Check()
+ 
+         # Run standard cache assertion
+-        yield from self.assert_cached(check, 1)
+-        yield from self.assert_cached(check, 1)
++        await self.assert_cached(check, 1)
++        await self.assert_cached(check, 1)
+ 
+         # Clear the cache
+         del check.add_cached
+ 
+         # Value is cached again after the next access
+-        yield from self.assert_cached(check, 2)
+-        yield from self.assert_cached(check, 2)
++        await self.assert_cached(check, 2)
++        await self.assert_cached(check, 2)
+ 
+     @unittest_run_loop
+-    @asyncio.coroutine
+-    def test_none_cached_property(self):
++    async def test_none_cached_property(self):
+         class Check(object):
+             def __init__(self):
+                 self.cached_total = None
+ 
+             @self.cached_property_factory
+-            @asyncio.coroutine
+-            def add_cached(self):
++            async def add_cached(self):
+                 return self.cached_total
+ 
+-        yield from self.assert_cached(Check(), None)
++        await self.assert_cached(Check(), None)
+-- 
+2.49.0
+

gnu/packages/patches/python-sip-include-dirs.patch

@@ -5,16 +5,15 @@ It seems that we cannot easily change the destination folder of these
 files though, so this variable must be set on a per-package basis (and
 non through search-path).
 
---- sip/sipbuild/builder.py	2023-03-22 09:06:37.588792878 +0100
+--- sip/sipbuild/builder.py
-+++ sip/sipbuild/builder.py	2023-03-22 09:10:35.830181134 +0100
++++ sip/sipbuild/builder.py
-@@ -254,6 +254,10 @@
+@@ -227,5 +227,9 @@
                      os.path.join(project.target_dir,
                              project.get_bindings_dir()))
  
-+            # Add extra bindings from environment for GNU Guix.
++        # Add extra bindings from environment for GNU Guix
 +        if 'SIP_INCLUDE_DIRS' in os.environ:
 +            sip_include_dirs.extend(os.environ['SIP_INCLUDE_DIRS'].split(os.pathsep))
 +
-             # Generate the sip.h file for the shared sip module.
+         # Generate the code for each set of bindings.
-             copy_sip_h(abi_major_version, project.build_dir,
+         api_files = []
-                     project.sip_module, version_info=project.version_info)

gnu/packages/patches/python-vaex-core-fix-tsl-use.patch

@@ -0,0 +1,67 @@
+From 8cb8808b3ceccf4ab3ac542739ef490abe7e76b3 Mon Sep 17 00:00:00 2001
+Message-ID: <8cb8808b3ceccf4ab3ac542739ef490abe7e76b3.1743597010.git.ngraves@ngraves.fr>
+From: Nicolas Graves <ngraves@ngraves.fr>
+Date: Wed, 2 Apr 2025 14:29:40 +0200
+Subject: [PATCH] Fix tsl map use
+
+---
+ packages/vaex-core/src/hash_string.hpp | 25 ++++++++++++++++---------
+ 1 file changed, 16 insertions(+), 9 deletions(-)
+
+diff --git a/packages/vaex-core/src/hash_string.hpp b/packages/vaex-core/src/hash_string.hpp
+index d3b60199..0ed69d1c 100644
+--- a/packages/vaex-core/src/hash_string.hpp
++++ b/packages/vaex-core/src/hash_string.hpp
+@@ -39,13 +39,15 @@ class hash_base : public hash_common<Derived, T, hashmap<T, int64_t>> {
+         for (int i = 0; i < nmaps; i++) {
+             string_arrays.emplace_back(std::make_shared<StringList64>());
+             StringList64 *strings = string_arrays[i].get();
+-            // equal_to<string_ref>& eq = this->maps[i].key_eq();
+-            this->maps[i].m_ht.strings_equals = strings;
+-            this->maps[i].m_ht.strings_hash = strings;
++            equal_to<key_type> eq;
++            eq.strings_equals = strings;
++            hash<key_type> h;
++            h.strings_hash = strings;
++            this->maps[i] = hashmap_type(8, h, eq);
+         }
+     };
+ 
+-    virtual std::string _get(hashmap_type &map, typename hashmap_type::key_type key) override { return map.m_ht.strings_equals->get(key.index); };
++    virtual std::string _get(hashmap_type &map, typename hashmap_type::key_type key) override { return string_arrays[0]->get(key.index); };
+ 
+     size_t bytes_used() const {
+         int64_t buffer_size = 0; // collect buffer size
+@@ -391,9 +393,12 @@ class ordered_set : public hash_base<ordered_set<T>, T, T, V> {
+     template <class SL>
+     static ordered_set *create(std::shared_ptr<SL> keys, int64_t null_value, int64_t nan_count, int64_t null_count, std::string *fingerprint) {
+         ordered_set *set = new ordered_set(1);
+-        set->maps[0].m_ht.strings_equals = keys.get();
+-        set->maps[0].m_ht.strings_hash = keys.get();
+         set->string_arrays[0] = keys;
++        equal_to<key_type> eq;
++        eq.strings_equals = keys.get();
++        hash<key_type> h;
++        h.strings_hash = keys.get();
++        set->maps[0] = hashmap_type(keys->length, h, eq);
+         {
+             size_t size = keys->length;
+             set->maps[0].reserve(size);
+@@ -701,9 +706,11 @@ class index_hash : public hash_base<index_hash<T>, T, T, V> {
+             // string_arrays_overflow.emplace_back(std::make_shared<StringList64>());
+             // for each key in overflow, it should be present in the main string array
+             StringList64 *strings = this->string_arrays[i].get();
+-            // equal_to<string_ref>& eq = this->maps[i].key_eq();
+-            overflows[i].m_ht.strings_equals = strings;
+-            overflows[i].m_ht.strings_hash = strings;
++            equal_to<key_type> eq;
++            eq.strings_equals = strings;
++            hash<key_type> h;
++            h.strings_hash = strings;
++            overflows[i] = overflow_type(8, h, eq);
+         }
+     }
+ 
+-- 
+2.49.0
+

gnu/packages/patches/python-wxwidgets-type-errors.patch

@@ -1,42 +0,0 @@
-Merged upstream but not yet released (see:
-https://github.com/wxWidgets/Phoenix/pull/2387/commits/5d9f7aa185cd18da3e93ae1d0033fb9172d7a714).
-
-From 5d9f7aa185cd18da3e93ae1d0033fb9172d7a714 Mon Sep 17 00:00:00 2001
-From: Maxim Cournoyer <maxim.cournoyer@gmail.com>
-Date: Mon, 1 May 2023 13:53:55 -0400
-Subject: [PATCH] agw: Fix TypeError caused by floats with Python 3.10
- extensions.
-
-This fixes the following error:
-
-   File "/lib/python3.10/site-packages/wx/lib/agw/pygauge.py", line 380, in OnPaint
-       dc.DrawText(drawString, textXPos, textYPos)
-   TypeError: DC.DrawText(): arguments did not match any overloaded call:
-     overload 1: argument 2 has unexpected type 'float'
-     overload 2: argument 2 has unexpected type 'float'
-   TimeLeft: 3.0
-
-Visible when using Python 3.10 or newer.
----
- wx/lib/agw/pygauge.py | 4 ++--
- 1 file changed, 2 insertions(+), 2 deletions(-)
-
-diff --git a/wx/lib/agw/pygauge.py b/wx/lib/agw/pygauge.py
-index b8654436a..da42e6f61 100644
---- a/wx/lib/agw/pygauge.py
-+++ b/wx/lib/agw/pygauge.py
-@@ -367,12 +367,12 @@ def OnPaint(self, event):
-             drawString = self._drawIndicatorText_formatString.format(drawValue)
-             rect = self.GetClientRect()
-             (textWidth, textHeight, descent, extraLeading) = dc.GetFullTextExtent(drawString)
--            textYPos = (rect.height-textHeight)/2
-+            textYPos = (rect.height-textHeight)//2
- 
-             if textHeight > rect.height:
-                 textYPos = 0-descent+extraLeading
- 
--            textXPos = (rect.width-textWidth)/2
-+            textXPos = (rect.width-textWidth)//2
- 
-             if textWidth>rect.width:
-                 textXPos = 0

gnu/packages/patches/trytond-add-egg-modules-to-path.patch

@@ -1,22 +0,0 @@
-Work around trytond.module not being a real namespace module.
-
-Solution is to add all trytond module's locations to
-trytond.modules._path__. This will make trytond.module behave much
-like a namespace module.
-Adding to __path__ is done in update_egg_modules() to ensure __path__
-is updated whenever the list of egg modules is updated.
-
-*** a/trytond/modules/__init__.py	1970-01-01 01:00:01.000000000 +0100
---- b/trytond/modules/__init__.py	2021-12-02 18:12:15.385101986 +0100
-***************
-*** 38,43 ****
---- 38,46 ----
-          import pkg_resources
-          for ep in pkg_resources.iter_entry_points('trytond.modules'):
-              EGG_MODULES[ep.name] = ep
-+             path = os.path.join(ep.dist.location, 'trytond', 'modules')
-+             if not path in __path__ and os.path.isdir(path):
-+                 __path__.append(path)
-      except ImportError:
-          pass
-  

gnu/packages/patchutils.scm

@@ -366,7 +366,7 @@ you to figure out what is going on in that merge you keep avoiding.")
 (define-public patchwork
   (package
     (name "patchwork")
-    (version "3.1.1")
+    (version "3.2.1")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -375,7 +375,7 @@ you to figure out what is going on in that merge you keep avoiding.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "0is9d4gf93jcbyshyj2k3kjyrjnvimrm6bai6dbcx630md222j5w"))))
+                "04ikawdyhjwspxvhazbp5f5vym672y0jcw8rd2m75h9ipcpnyxim"))))
     (build-system python-build-system)
     (arguments
      `(;; TODO: Tests require a running database
@@ -499,7 +499,7 @@ if __name__ == \"__main__\":
     (inputs
      (list python-wrapper))
     (propagated-inputs
-     (list python-django-3.2
+     (list python-django
            ;; TODO: Make this configurable
            python-psycopg2
            python-mysqlclient

gnu/packages/protobuf.scm

@@ -2,7 +2,7 @@
 ;;; Copyright © 2014, 2022 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2016 Daniel Pimentel <d4n1@d4n1.org>
 ;;; Copyright © 2016 Leo Famulari <leo@famulari.name>
-;;; Copyright © 2017, 2018, 2019, 2022, 2023 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2017-2019, 2022-2025 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2017, 2018, 2019, 2020 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2020, 2021, 2022, 2023 Maxim Cournoyer <maxim.cournoyer@gmail.com>
 ;;; Copyright © 2020 Vinicius Monego <monego@posteo.net>
@@ -175,7 +175,7 @@ internal RPC protocols and file formats.")
   (package
     (inherit protobuf)
     (name "protobuf")
-    (version "3.20.2")
+    (version "3.20.3")
     (source (origin
               (method url-fetch)
               (uri (string-append
@@ -186,7 +186,7 @@ internal RPC protocols and file formats.")
               (snippet '(delete-file-recursively "third_party"))
               (sha256
                (base32
-                "1hsscx9jm8qv3afgwc764rx9sx1ylkrr54xw1wc0mfjbl8mpw5m0"))))
+                "0ggyfrfal7wms4n8pba224jwpjxn19rigd5y90m3x2bg97ych775"))))
     (build-system gnu-build-system)
     (arguments (substitute-keyword-arguments (package-arguments protobuf)
                  ;; XXX: insists on using bundled googletest
@@ -467,21 +467,18 @@ mechanism for serializing structured data.")
 (define-public python-protobuf
   (package
     (name "python-protobuf")
-    (version "3.20.2")
+    (version "3.20.3")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "protobuf" version))
        (sha256
         (base32
-         "0l0p2lczs5iahgkhzm3298pjl49bk9iiwngkglg7ll7fkqqwlbbi"))))
+         "1wh5f4rnzbv46xy1rx62cprhg5hqf2py06s9b7rfpzwwki12fd1f"))))
     (build-system python-build-system)
-    (inputs (list protobuf))
+    ;; The C++ implementation is not compatible with Python 3.11, so we cannot
-    (arguments
+    ;; pass --cpp_implementation any more.
-     `(;; Favor C++ implementation from protobuf over the native Python
+    (inputs (list protobuf-3.20))
-       ;; implementation. The additional dependency yields significant
-       ;; performance improvements for some workloads.
-       #:configure-flags '("--cpp_implementation")))
     (home-page "https://github.com/google/protobuf")
     (synopsis "Protocol buffers is a data interchange format")
     (description

gnu/packages/python-build.scm

@@ -344,18 +344,6 @@ facilitate packaging Python projects, where packaging includes:
                    license:asl2.0       ;packaging is dual ASL2/BSD-2
                    license:bsd-2))))
 
-;; This is the last version with use_2to3 support.
-(define-public python-setuptools-57
-  (package
-    (inherit python-setuptools)
-    (version "57.5.0")
-    (source (origin
-              (inherit (package-source python-setuptools))
-              (uri (pypi-uri "setuptools" version))
-              (sha256
-               (base32
-                "091sp8lrin7qllrhhx7y0iiv5gdb1d3l8a1ip5knk77ma1njdlyr"))))))
-
 (define-public python-wheel
   (package
     (name "python-wheel")
@@ -412,14 +400,14 @@ installed with a newer @code{pip} or with wheel's own command line utility.")
 (define-public python-pyparsing
   (package
     (name "python-pyparsing")
-    (version "3.0.6")
+    (version "3.2.1")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "pyparsing" version))
        (sha256
-        (base32 "109b9r802wb472hgmxclljprh5cid0w3p6mk9alba7pg2c0frgfr"))))
+        (base32 "02jz5rv3vx46xvjszda467l269jz9narlrwd0a83mpk6zma0i631"))))
-    (build-system python-build-system)
+    (build-system pyproject-build-system)
     (outputs '("out" "doc"))
     (arguments
      `(#:tests? #f                      ;no test target
@@ -440,6 +428,7 @@ installed with a newer @code{pip} or with wheel's own command line utility.")
                        (find-files dir ".*")))
                 (list "docs" "htmldoc" "examples")
                 (list doc html-doc examples))))))))
+    (native-inputs (list python-flit-core))
     (home-page "https://github.com/pyparsing/pyparsing")
     (synopsis "Python parsing class library")
     (description
@@ -459,7 +448,8 @@ that client code uses to construct the grammar directly in Python code.")
        (method url-fetch)
        (uri (pypi-uri "pyparsing" version))
        (sha256
-        (base32 "1hgc8qrbq1ymxbwfbjghv01fm3fbpjwpjwi0bcailxxzhf3yq0y2"))))))
+        (base32 "1hgc8qrbq1ymxbwfbjghv01fm3fbpjwpjwi0bcailxxzhf3yq0y2"))))
+    (native-inputs (list python-setuptools python-wheel))))
 
 (define-public python-packaging-bootstrap
   (package
@@ -569,6 +559,16 @@ a light weight, fully compliant, self-contained package allowing PEP 517
 compatible build front-ends to build Poetry managed projects.")
     (license license:expat)))
 
+(define-public python-poetry-core-next
+  (package/inherit python-poetry-core
+    (version "2.1.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "poetry_core" version))
+       (sha256
+        (base32 "015a0802radb2x5wsbywm4fggv4s1srh8zyml5v58xgrxg8bpnzr"))))))
+
 ;;; This package exists to bootstrap python-tomli.
 (define-public python-flit-core-bootstrap
   (package

gnu/packages/python-check.scm

@@ -288,27 +288,70 @@ Avocado machine readable outputs this one is streamlined (per test results).
 @end table")
     (license license:gpl2)))            ;some files are under GPLv2 only
 
+(define-public python-pytest-black
+  (package
+    (name "python-pytest-black")
+    (version "0.6.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "pytest_black" version))
+       (sha256
+        (base32
+         "04dmhv8dzh356qdxz6hrwfz3nk3mlc9shicgpns5r03rydap9dzc"))))
+    (build-system pyproject-build-system)
+    (native-inputs
+     (list python-setuptools
+           python-wheel))
+    (propagated-inputs
+     (list python-black
+           python-pytest
+           python-toml))
+    ;; Project maintenance has been changed, see
+    ;; <https://github.com/shopkeep/pytest-black/issues/70>.
+    (home-page "https://github.com/coherent-oss/pytest-black")
+    (synopsis "Pytest plugin to enable format checking with black")
+    (description
+     "This package provides a pytest plugin to enable format checking with the
+Python code formatter \"black\".")
+    (license license:expat)))
+
+(define-public python-pytest-freezer
+  (package
+    (name "python-pytest-freezer")
+    (version "0.4.9")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "pytest_freezer" version))
+       (sha256
+        (base32 "0an8y6ri3bhij4137gphdw2yg6rq7if4nb1qjj7zjsy4kjy1dgr1"))))
+    (build-system pyproject-build-system)
+    (native-inputs
+     (list python-flit-core))
+    (propagated-inputs
+     (list python-freezegun
+           python-pytest))
+    (home-page "https://github.com/pytest-dev/pytest-freezer/")
+    (synopsis "Pytest plugin providing a fixture interface for spulec/freezegun")
+    (description
+     "Pytest plugin providing a fixture interface for
+@url{https://github.com/spulec/freezegun, freezegun}.")
+    (license license:expat)))
+
 (define-public python-beartype
   (package
     (name "python-beartype")
-    (version "0.10.4")
+    (version "0.19.0")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "beartype" version))
        (sha256
-        (base32 "0amzckgw9c93bl4jf0q6322j9wyyf3i8vl03yixfkrpllzv6kv14"))))
+        (base32 "0wv598iv9c2s6ivfiara9pnkdlnas8xjw063wvyi0dswpb0xyhny"))))
     (build-system pyproject-build-system)
-    (arguments
+    (native-inputs
-     (list
+     (list python-hatchling python-numpy python-pygments python-pytest))
-      #:test-flags
-      #~(list
-         "beartype_test"
-         ;; These tests rely on git through the "get_main_readme_file" helper.
-         "-k" (string-append "not test_doc_readme "
-                             "and not test_sphinx "
-                             "and not test_pep561_mypy"))))
-    (native-inputs (list python-pytest python-setuptools python-wheel))
     (home-page "https://github.com/beartype/beartype")
     (synopsis "Fast runtime type checking for Python")
     (description "Beartype aims to be a very fast runtime type checking tool
@@ -2628,6 +2671,8 @@ them using any Python VM with basically no runtime overhead.")
      (list
       #:test-flags
       #~(list
+         ;; This one started failing with the last update of Numpy.
+         "--ignore=tests/test_beartype.py"
          ;; Multiple failures due to undefined names (typing package must be
          ;; too outdated, or perhaps they use a newer pandas).
          "--ignore=tests/test_mypy.py"
@@ -2846,7 +2891,7 @@ help in debugging failures and optimizing the scheduler to improve speed.")
 (define-public python-pytest-subprocess
   (package
     (name "python-pytest-subprocess")
-    (version "1.5.2")
+    (version "1.5.3")
     (source
      (origin
        (method git-fetch)               ;no tests in PyPI archive
@@ -2856,16 +2901,16 @@ help in debugging failures and optimizing the scheduler to improve speed.")
        (file-name (git-file-name name version))
        (sha256
         (base32
-         "1mncfyn0vkbf7d03zc8wmv7nl354ck5i9gfblp9220ihc52whhy0"))))
+         "1yb5y6dqzf6k5a07yzdpw8w50bm7zbsdvv06ii7c7vyg9wx5iw6y"))))
     (build-system pyproject-build-system)
-    (native-inputs (list python-anyio
+    (native-inputs
-                         python-coverage
+     (list python-anyio
            python-docutils
-                         python-nox
            python-pygments
            python-pytest
            python-pytest-asyncio
            python-pytest-rerunfailures
+           python-setuptools
            python-wheel))
     (home-page "https://github.com/aklajnert/pytest-subprocess")
     (synopsis "Fake subprocess for Pytest")
@@ -2950,25 +2995,6 @@ __version_tuple__ = version_tuple = (~a)~%" version version-tuple)))))))))
 in an opinionated way.")
     (license license:expat)))
 
-(define-public python-parameterizedtestcase
-  (package
-    (name "python-parameterizedtestcase")
-    (version "0.1.0")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (pypi-uri "parameterizedtestcase" version))
-       (sha256
-        (base32 "0zhjmsd16xacg4vd7zb75kw8q9khn52wvad634v1bvz7swaivk2c"))))
-    (build-system python-build-system)
-    (native-inputs (list python-setuptools-57)) ;for use_2to3
-    (home-page
-     "https://github.com/msabramo/python_unittest_parameterized_test_case")
-    (synopsis "Parameterized tests for Python's unittest module")
-    (description "This package provides parameterized tests for Python's
-@code{unittest} module taking inspiration from pytest.")
-    (license license:expat)))
-
 (define-public python-pytest-rerunfailures
   (package
     (name "python-pytest-rerunfailures")
@@ -3271,13 +3297,13 @@ attachments).
 (define-public python-vcrpy
   (package
     (name "python-vcrpy")
-    (version "6.0.2")
+    (version "7.0.0")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "vcrpy" version))
        (sha256
-        (base32 "02fwmmc33qqybzbj1lvdz458g1fffm5cgnqihj4larw4268kvqc8"))))
+        (base32 "0l1sdfc51024jclqv9104nagpirxx8w0gcn5h0bdxv950jnr2qqp"))))
     (build-system pyproject-build-system)
     (arguments
      (list
@@ -3290,22 +3316,23 @@ attachments).
                           "test_testcase_playback")
                     " and not "))))
     (native-inputs
-     (list nss-certs-for-test
+     (list python-aiohttp
-           python-flask
+           python-boto3
            python-httplib2
-           python-ipaddress
+           python-httpx
-           python-mock
            python-pytest
            python-pytest-cov
+           python-pytest-aiohttp
+           python-pytest-asyncio
            python-pytest-httpbin
+           python-requests
            python-setuptools
+           python-tornado
            python-urllib3
+           python-werkzeug
            python-wheel))
     (propagated-inputs
-     (list python-pyyaml
+     (list python-pyyaml python-wrapt python-yarl))
-           python-six
-           python-wrapt
-           python-yarl))
     (home-page "https://github.com/kevin1024/vcrpy")
     (synopsis "Automatically mock your HTTP interactions")
     (description

gnu/packages/python-compression.scm

@@ -11,6 +11,7 @@
 ;;; Copyright © 2024 TakeV <takev@disroot.org>
 ;;; Copyright © 2023 Ivan Vilata i Balaguer <ivan@selidor.net>
 ;;; Copyright © 2024 Maxim Cournoyer <maxim.cournoyer@gmail.com>
+;;; Copyright © 2025 Nicolas Graves <ngraves@ngraves.fr>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -764,6 +765,33 @@ install: libbitshuffle.so
     (inputs '())
     (native-inputs '())))
 
+(define-public python-unix-ar
+  (package
+    (name "python-unix-ar")
+    (version "0.2.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "unix_ar" version))
+       (sha256
+        (base32 "0kicwxsh28x8r34a7cgzv2i65gsd4qjw2vf29pwq4fpsf3n2i4xz"))))
+    (build-system pyproject-build-system)
+    (arguments
+     ;; These tests have timestamp-related issues.
+     (list #:test-flags
+           #~(list "-m" "unittest" "-k" "not test_add and not test_addfile")
+           #:phases
+           #~(modify-phases %standard-phases
+               (replace 'check
+                 (lambda* (#:key tests? test-flags #:allow-other-keys)
+                   (apply invoke "python" test-flags))))))
+    (native-inputs (list python-pytest python-setuptools python-wheel))
+    (home-page "https://github.com/getninjas/unix_ar")
+    (synopsis "AR file handling in Python")
+    (description "This package provides utilities to handle AR files in
+Python.")
+    (license license:bsd-3)))
+
 (define-public python-zipp
   (package
     (name "python-zipp")

gnu/packages/python-crypto.scm

@@ -11,7 +11,7 @@
 ;;; Copyright © 2016, 2017, 2018, 2019, 2020 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2016, 2017 Nikita <nikita@n0.is>
 ;;; Copyright © 2014, 2015 Mark H Weaver <mhw@netris.org>
-;;; Copyright © 2015, 2016, 2017, 2019, 2022, 2024 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2015, 2016, 2017, 2019, 2022, 2024, 2025 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2016 Danny Milosavljevic <dannym+a@scratchpost.org>
 ;;; Copyright © 2016, 2017, 2020 Arun Isaac <arunisaac@systemreboot.net>
 ;;; Copyright © 2017 Carlo Zancanaro <carlo@zancanaro.id.au>
@@ -57,6 +57,7 @@
   #:use-module (guix build-system python)
   #:use-module (guix utils)
   #:use-module (gnu packages)
+  #:use-module (gnu packages certs)
   #:use-module (gnu packages check)
   #:use-module (gnu packages crates-io)
   #:use-module (gnu packages crates-tls)
@@ -141,17 +142,19 @@ Password Scheme\"} by Niels Provos and David Mazieres.")
        (uri (pypi-uri "passlib" version))
        (sha256
         (base32 "015y5qaw9qnxr29lg60dml1g5rbqd4586wy5n8m41ib55gvm1zfy"))))
-    (build-system python-build-system)
+    (build-system pyproject-build-system)
-    (native-inputs
-     (list python-nose))
-    (propagated-inputs
-     (list python-bcrypt))
     (arguments
-     `(#:phases
+     (list
-       (modify-phases %standard-phases
+      #:phases
+      #~(modify-phases %standard-phases
           (add-before 'check 'set-PYTHON_EGG_CACHE
             ;; Some tests require access to "$HOME/.cython".
-           (lambda _ (setenv "PYTHON_EGG_CACHE" "/tmp"))))))
+            (lambda _
+              (setenv "PYTHON_EGG_CACHE" "/tmp"))))))
+    (native-inputs
+     (list python-nose python-setuptools python-wheel))
+    (propagated-inputs
+     (list python-argon2-cffi python-bcrypt python-cryptography))
     (home-page "https://bitbucket.org/ecollins/passlib")
     (synopsis "Comprehensive password hashing framework")
     (description
@@ -162,32 +165,6 @@ useful for a wide range of tasks, from verifying a hash found in /etc/shadow,
 to providing full-strength password hashing for multi-user application.")
     (license license:bsd-3)))
 
-(define-public python-pyblake2
-  (package
-    (name "python-pyblake2")
-    (version "1.1.2")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (pypi-uri "pyblake2" version))
-       (sha256
-        (base32
-         "0gz9hgznv5zw4qjq43xa56y0yikimx30gffvibxzm0nv5sq7xk2w"))))
-    (build-system python-build-system)
-    (home-page "https://github.com/dchest/pyblake2")
-    (synopsis "BLAKE2 hash function for Python")
-    (description "BLAKE2 is a cryptographic hash function, which offers
-stronger security while being as fast as MD5 or SHA-1, and comes in two
-flavors: @code{BLAKE2b}, optimized for 64-bit platforms and produces digests
-of any size between 1 and 64 bytes, and @code{BLAKE2s}, optimized for 8- to
-32-bit platforms and produces digests of any size between 1 and 32 bytes.
-
-This package provides a Python interface for BLAKE2.")
-    ;; The COPYING file declares it as public domain, with the option to
-    ;; alternatively use and redistribute it under a variety of permissive
-    ;; licenses. cc0 is explicitly mentioned in setup.py and pyblake2module.c.
-    (license (list license:public-domain license:cc0))))
-
 (define-public python-paramiko
   (package
     (name "python-paramiko")
@@ -455,13 +432,7 @@ blake3, a cryptographic hash function.")
                      ;; Those tests uses PKCS12, which has been removed in
                      ;; pyopenssl 23.3.0:
                      "not test_custom_not_before_not_after"
-                     "test_ca_cert_in_mem"
+                     "test_ca_cert_in_mem")
-                     ;; Those tests try to download certificates:
-                     "test_file_wildcard"
-                     "test_file_wildcard_subdomains"
-                     "test_in_mem_parent_wildcard_cert"
-                     "test_in_mem_parent_wildcard_cert_at_tld"
-                     "test_in_mem_parent_wildcard_cert_2")
                     " and not "))
       #:phases
       #~(modify-phases %standard-phases
@@ -474,7 +445,7 @@ blake3, a cryptographic hash function.")
     (propagated-inputs
      (list python-pyopenssl python-tldextract))
     (native-inputs
-     (list python-pytest-cov python-setuptools python-wheel))
+     (list nss-certs-for-test python-pytest-cov python-setuptools python-wheel))
     (home-page "https://github.com/ikreymer/certauth")
     (synopsis "Certificate authority creation tool")
     (description "This package provides a small library, built on top of
@@ -658,7 +629,13 @@ ciphers, message digests and key derivation functions.")
                 ;; PyOpenSSL runs tests against a certificate with a fixed
                 ;; expiry time.  To ensure successful builds in the future,
                 ;; set the time to roughly the release date.
-                (invoke "faketime" "2024-07-20" "pytest" "-vv" "-k"
+                (invoke "faketime" "2024-07-20" "pytest" "-vv"
+                        "--deselect"
+                        ;; This test seems to fail when using faketime, at
+                        ;; least on aarch64-linux with OSError: [Errno 22]
+                        ;; Invalid argument
+                        "tests/test_ssl.py::TestDTLS::test_timeout"
+                        "-k"
                         ;; This test tries to look up certificates from
                         ;; the compiled-in default path in OpenSSL, which
                         ;; does not exist in the build environment.
@@ -1657,17 +1634,14 @@ signatures.")
         (uri (pypi-uri "PGPy" version))
         (sha256
          (base32 "10w3h934fi1ijx72ppn67a50yhkf8n1db6xx02gk2fjc7wsjx717"))))
-    (build-system python-build-system)
+    (build-system pyproject-build-system)
     (arguments
-     `(#:phases
+     (list #:test-flags
-       (modify-phases %standard-phases
+           ;; All broken tests are in this file.
-         (replace 'check
+           ;; They fail with ValueError: key_size must be at least 1024-bits.
-           (lambda* (#:key tests? #:allow-other-keys)
+           #~(list "--ignore" "tests/test_10_exceptions.py")))
-             (when tests?
-               (invoke "pytest")))))))
     (native-inputs
-     (list python-pytest
+     (list python-pytest python-setuptools python-wheel))
-           python-wheel))
     (propagated-inputs (list python-cryptography python-pyasn1))
     (home-page "https://github.com/SecurityInnovation/PGPy")
     (synopsis "Python implementation of OpenPGP")

gnu/packages/python-science.scm

@@ -27,6 +27,7 @@
 ;;; Copyright © 2024 Marco Baggio <marco.baggio@mdc-berlin.de>
 ;;; Copyright © 2024 Nicolas Graves <ngraves@ngraves.fr>
 ;;; Copyright © 2024 Rick Huijzer <ikbenrickhuyzer@gmail.com>
+;;; Copyright © 2025 Nicolas Graves <ngraves@ngraves.fr>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -67,6 +68,7 @@
   #:use-module (gnu packages maths)
   #:use-module (gnu packages mpi)
   #:use-module (gnu packages pcre)
+  #:use-module (gnu packages package-management)
   #:use-module (gnu packages perl)
   #:use-module (gnu packages pkg-config)
   #:use-module (gnu packages python)
@@ -82,6 +84,7 @@
   #:use-module (gnu packages ssh)
   #:use-module (gnu packages statistics)
   #:use-module (gnu packages time)
+  #:use-module (gnu packages version-control)
   #:use-module (gnu packages xdisorg)
   #:use-module (gnu packages xml)
   #:use-module (gnu packages xorg)
@@ -372,7 +375,21 @@ Features:
     (build-system pyproject-build-system)
     (arguments
      (list
-      #:test-flags #~(list "--pyargs" "numdifftools")
+      #:test-flags
+      #~(list "--pyargs" "numdifftools"
+              "-k" (string-join
+                    ;; Tests failing with error: TypeError: a must be an array
+                    ;; of real numbers, see
+                    ;; <https://github.com/pbrod/numdifftools/issues/72>.
+                    (list "not test_high_order_derivative"
+                          "test_low_order_derivative_on_example_functions"
+                          "test_sinx_div_x"
+                          "test_complex_hessian_issue_35"
+
+                          "numdifftools.fornberg.Taylor"
+                          "numdifftools.fornberg.derivative"
+                          "numdifftools.fornberg.taylor")
+                    " and not "))
       #:phases
       #~(modify-phases %standard-phases
           (add-after 'unpack 'relax-requirements
@@ -1052,6 +1069,172 @@ utilizing the power of scikit-learn, e.g., for pre-processing or doing
 cross-validation.")
       (license license:gpl3+))))
 
+(define-public python-snakemake-interface-common
+  (package
+    (name "python-snakemake-interface-common")
+    (version "1.17.4")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/snakemake/snakemake-interface-common")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "19fyqs048zdvrmq5sdayzch850kwsyv2x6xn57cjjzcm4zpjrh9w"))))
+    (build-system pyproject-build-system)
+    (arguments
+     (list #:phases
+           #~(modify-phases %standard-phases
+               (replace 'check
+                 (lambda* (#:key tests? #:allow-other-keys)
+                   (when tests?
+                     (invoke "python3" "tests/tests.py")))))))
+    (native-inputs (list python-poetry-core python-pytest))
+    (propagated-inputs (list python-argparse-dataclass python-configargparse))
+    (home-page "https://github.com/snakemake/snakemake-interface-common")
+    (synopsis "Common functions and classes for Snakemake and its plugins")
+    (description "This package provides common functions and classes
+for Snakemake and its plugins.")
+    (license license:expat)))
+
+(define-public python-snakemake-interface-executor-plugins
+  (package
+    (name "python-snakemake-interface-executor-plugins")
+    (version "9.3.3")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url (string-append "https://github.com/snakemake/"
+                                 "snakemake-interface-executor-plugins"))
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "1kjjcgkk1rbavb687x5ayw35ayhsnhpg9262k317x911wqpsj2fm"))))
+    (build-system pyproject-build-system)
+    (arguments
+     (list
+      #:phases
+      #~(modify-phases %standard-phases
+          (replace 'check
+            (lambda* (#:key tests? #:allow-other-keys)
+              (when tests?
+                (invoke "python3" "tests/tests.py")))))))
+    (propagated-inputs (list python-argparse-dataclass
+                             python-snakemake-interface-common
+                             python-throttler))
+    (native-inputs (list python-poetry-core python-pytest))
+    (home-page (string-append "https://github.com/snakemake/"
+                              "python-snakemake-interface-executor-plugins"))
+    (synopsis "Interface for Snakemake executor plugins")
+    (description
+     "This package provides a stable interface for interactions between Snakemake and
+its executor plugins.")
+    (license license:expat)))
+
+(define-public python-snakemake-interface-report-plugins
+  (package
+    (name "python-snakemake-interface-report-plugins")
+    (version "1.1.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url (string-append "https://github.com/snakemake/"
+                                 "snakemake-interface-report-plugins"))
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "0i6z9vk6nv2m3jsym0glrb7h9isdlfza2yq14vbqcslybdi9ykfa"))))
+    (build-system pyproject-build-system)
+    (arguments
+     (list
+      #:tests? #f ;circular dependency on snakemake
+      #:phases
+      #~(modify-phases %standard-phases
+          (replace 'check
+            (lambda* (#:key tests? #:allow-other-keys)
+              (when tests?
+                (invoke "python3" "tests/tests.py")))))))
+    (propagated-inputs (list python-snakemake-interface-common python-pytest))
+    (native-inputs (list python-poetry-core))
+    (home-page (string-append "https://github.com/snakemake/"
+                              "python-snakemake-interface-report-plugins"))
+    (synopsis "Interface for Snakemake report plugins")
+    (description "This package provides a stable interface for interactions
+between Snakemake and its report plugins.")
+    (license license:expat)))
+
+(define-public python-snakemake-interface-software-deployment-plugins
+  (package
+    (name "python-snakemake-interface-software-deployment-plugins")
+    (version "0.6.1")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url (string-append "https://github.com/snakemake/"
+                   "snakemake-interface-software-deployment-plugins"))
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "0b4kkznfyfck9f92pkimhyl13ljisfn67rsilm1a5inq2ywpmxba"))))
+    (build-system pyproject-build-system)
+    (arguments
+     (list
+      #:phases
+      #~(modify-phases %standard-phases
+          (replace 'check
+            (lambda* (#:key tests? #:allow-other-keys)
+              (when tests?
+                (invoke "python3" "tests/tests.py")))))))
+    (propagated-inputs (list python-argparse-dataclass
+                             python-snakemake-interface-common))
+    (native-inputs (list python-poetry-core))
+    (home-page (string-append "https://github.com/snakemake/"
+                "snakemake-interface-software-deployment-plugins"))
+    (synopsis "Interface for Snakemake software deployment plugins")
+    (description
+     "This package provides a stable interface for interactions between Snakemake and
+its software deployment plugins.")
+    (license license:expat)))
+
+(define-public python-snakemake-interface-storage-plugins
+  (package
+    (name "python-snakemake-interface-storage-plugins")
+    (version "3.3.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url (string-append "https://github.com/snakemake/"
+                                 "snakemake-interface-storage-plugins"))
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "05n5xgwagb01nyzi8xfvp0nvdfl24lxidgksm7k86p68n1rijd5a"))))
+    (build-system pyproject-build-system)
+    (arguments
+     (list
+      #:tests? #f ;circular dependency on snakemake
+      #:phases
+      #~(modify-phases %standard-phases
+          (replace 'check
+            (lambda* (#:key tests? #:allow-other-keys)
+              (when tests?
+                (invoke "python3" "tests/tests.py")))))))
+    (propagated-inputs (list python-reretry python-snakemake-interface-common
+                             python-throttler python-wrapt))
+    (native-inputs (list python-poetry-core python-pytest))
+    (home-page (string-append "https://github.com/snakemake/"
+                              "snakemake-interface-storage-plugins"))
+    (synopsis "Interface for Snakemake storage plugins")
+    (description
+     "This package provides a stable interface for interactions between
+Snakemake and its storage plugins.")
+    (license license:expat)))
+
 (define-public python-tdda
   (package
     (name "python-tdda")
@@ -1643,7 +1826,7 @@ doing practical, real world data analysis in Python.")
             (lambda _
               (copy-recursively
                (string-append #$output
-                              "/lib/python3.10/site-packages/pandas/_libs")
+                              "/lib/python3.11/site-packages/pandas/_libs")
                "pandas/_libs"))))))
     (propagated-inputs
      (list python-dateutil
@@ -2465,7 +2648,7 @@ objects.")
 (define-public python-pytensor
   (package
     (name "python-pytensor")
-    (version "2.18.1")
+    (version "2.28.3") ; the minimal version supporting SciPy 1.12.0
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -2474,52 +2657,65 @@ objects.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "0qa0y13xfm6w7ry7gp0lv84c8blyg34a9ns7ynwqyhf9majq08s5"))))
+                "1yz1yslms6kdmy4sgnvbnghhclcpkc80z3vaw9c2y3b3j1fs9b4v"))))
     (build-system pyproject-build-system)
     (arguments
      (list
+      #:test-flags
+      ;; XXX: Full test suite takes about 20-30min to complete in single
+      ;; thread, attempt to run tests in parallel with pytest-xdist fails even
+      ;; so upstream provides a support for that, try to figure out how to
+      ;; improve it.
+      ;;
+      ;; Upstream implements a script, showing slow tests which may be used to
+      ;; exclude even more hanging/slow ones, see
+      ;; <scripts/slowest_tests/extract-slow-tests.py>.
+      ;;
+      ;; Skip computationally intensive tests.
+      #~(list "--ignore" "tests/scan/"
+              "--ignore" "tests/tensor/"
+              "--ignore" "tests/sandbox/"
+              "--ignore" "tests/sparse/sandbox/"
+              ;; Tests hang while running from these files.
+              "--ignore" "tests/compile/test_compilelock.py"
+              "--ignore" "tests/link/jax/test_tensor_basic.py"
+              ;; XXX: Tests finish with error in these files, check why.
+              "--ignore" "tests/compile/function/test_types.py"
+              "--ignore" "tests/link/numba/test_basic.py"
+              "--ignore" "tests/link/numba/test_blockwise.py"
+              "--ignore" "tests/link/numba/test_elemwise.py"
+              "-k" (string-join
+                    ;; Skip benchmark tests.
+                    (list "not test_elemwise_speed"
+                          "test_logsumexp_benchmark"
+                          "test_fused_elemwise_benchmark"
+                          "test_scan_multiple_output"
+                          "test_vector_taps_benchmark"
+                          "test_cython_performance"
+                          ;; Assertion fails in tests.
+                          "test_choose_signature"
+                          "test_fgraph_to_python_names")
+                    " and not ")
+              ;; Tests collection selects pytensor, which does not contain
+              ;; tests and fails to pass; manually provide a test directory
+              ;; instead.
+              "tests")
       #:phases
       #~(modify-phases %standard-phases
           ;; Replace version manually because pytensor uses
           ;; versioneer, which requires git metadata.
           (add-after 'unpack 'versioneer
             (lambda _
-              (with-output-to-file "setup.cfg"
-                (lambda ()
-                  (display "\
-[versioneer]
-VCS = git
-style = pep440
-versionfile_source = pytensor/_version.py
-versionfile_build = pytensor/_version.py
-tag_prefix =
-parentdir_prefix = pytensor-
-")))
               (invoke "versioneer" "install")
               (substitute* "setup.py"
-                (("versioneer.get_version\\(\\)")
+                (("version=versioneer.get_version\\(),")
-                 (string-append "\"" #$version "\"")))))
+                 (format #f "version=~s," #$version)))))
-          (replace 'check
+          (add-before 'check 'pre-check
-            (lambda* (#:key tests? #:allow-other-keys)
+            (lambda _
-              (when tests?
+              ;; It is required for most tests.
-                (setenv "HOME" "/tmp") ; required for most tests
+              (setenv "HOME" "/tmp")
-                ;; Test discovery fails, have to call pytest by hand.
+              ;; Cython extensions have to be built before running the tests.
-                ;; test_tensor_basic.py file requires JAX.
+              (invoke "python" "setup.py" "build_ext" "--inplace"))))))
-                (invoke "python" "-m" "pytest" "-vv"
-                        "--ignore" "tests/link/jax/test_tensor_basic.py"
-                        ;; Skip benchmark tests.
-                        "-k" (string-append
-                              "not test_elemwise_speed"
-                              " and not test_logsumexp_benchmark"
-                              " and not test_fused_elemwise_benchmark"
-                              " and not test_scan_multiple_output"
-                              " and not test_vector_taps_benchmark"
-                              " and not test_cython_performance")
-                        ;; Skip computationally intensive tests.
-                        "--ignore" "tests/scan/"
-                        "--ignore" "tests/tensor/"
-                        "--ignore" "tests/sandbox/"
-                        "--ignore" "tests/sparse/sandbox/")))))))
     (native-inputs (list python-cython
                          python-pytest
                          python-pytest-mock
@@ -2663,6 +2859,9 @@ annotations on an existing boxplots and barplots generated by seaborn.")
        (sha256
         (base32 "0jrq2vhan2h280h6cw1sm5hys2nzmf19w4py64k3nrkc320z9mni"))))
     (build-system pyproject-build-system)
+    (arguments
+     ;; This is a Numpy DeprecationWarning, remove it on next update.
+     (list #:test-flags ''("-k" "not test_h5_io")))
     ;; Pint is optional, but we do not propagate it due to its size.
     (native-inputs
      (list python-pint
@@ -2878,32 +3077,6 @@ and more
 @end itemize")
     (license license:gpl3)))
 
-(define-public python-pyglm
-  (package
-    (name "python-pyglm")
-    (version "2.5.7")
-    (source
-     (origin
-       ;; Test files are not included in the archive in pypi.
-       (method git-fetch)
-       (uri (git-reference
-             (url "https://github.com/Zuzu-Typ/PyGLM")
-             (commit version)
-             ;; Checkout the bundled `glm` submodule.  PyGLM uses the
-             ;; currently unreleased GLM_EXT_matrix_integer feature.  Can
-             ;; maybe unbundle once glm@0.9.9.9 is released.
-             (recursive? #t)))
-       (file-name (git-file-name name version))
-       (sha256
-        (base32
-         "08v0cgkwsf8rxscx5g9c5p1dy38rvak2fy3q6hg985if1nj6d9ks"))))
-    (build-system python-build-system)
-    (home-page "https://github.com/Zuzu-Typ/PyGLM")
-    (synopsis "OpenGL Mathematics library for Python")
-    (description "PyGLM is a Python extension library which brings the OpenGL
-Mathematics (GLM) library to Python.")
-    (license license:zlib)))
-
 (define-public python-dask-expr
   (package
     (name "python-dask-expr")
@@ -3794,18 +3967,37 @@ it can be used for displaying many qualitatively different samples.")
   (package
     (name "python-paramz")
     (version "0.9.6")
-    (source (origin
+    (source
+     (origin
        (method git-fetch)
        (uri (git-reference
              (url "https://github.com/sods/paramz")
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-               (base32
+        (base32 "1ywc2jzj40m6wmq227j3snxvp4434s0m1xk1abg6v6mr87pv2sa9"))))
-                "1ywc2jzj40m6wmq227j3snxvp4434s0m1xk1abg6v6mr87pv2sa9"))))
     (build-system pyproject-build-system)
+    (arguments
+     (list
+      #:test-flags
+      #~(list "-k"
+              ;; Two tests fail with error: TypeError: arrays to stack must be
+              ;; passed as a "sequence" type such as list or tuple.
+              (string-append "not test_raveled_index"
+                             " and not test_regular_expression_misc")
+              "paramz/tests/array_core_tests.py"
+              "paramz/tests/cacher_tests.py"
+              "paramz/tests/examples_tests.py"
+              "paramz/tests/index_operations_tests.py"
+              "paramz/tests/init_tests.py"
+              "paramz/tests/lists_and_dicts_tests.py"
+              "paramz/tests/model_tests.py"
+              "paramz/tests/observable_tests.py"
+              "paramz/tests/parameterized_tests.py"
+              "paramz/tests/pickle_tests.py"
+              "paramz/tests/verbose_optimize_tests.py")))
     (native-inputs
-     (list python-nose
+     (list python-pytest
            python-setuptools
            python-wheel))
     (propagated-inputs
@@ -4055,16 +4247,10 @@ numerical computation.")
               (sha256
                (base32
                 "0jb5lia0q742d1713jk33vlj41y61sf52j6pgk7pvhxvfxglgxjr"))))
-    (build-system python-build-system)
+    (build-system pyproject-build-system)
-    (arguments
-     '(#:phases
-       (modify-phases %standard-phases
-         (replace 'check
-           (lambda* (#:key tests? #:allow-other-keys)
-             (when tests?
-               (invoke "pytest" "-vv")))))))
     (propagated-inputs (list python-numpy))
-    (native-inputs (list python-pytest python-pytest-cov python-pytest-pep8))
+    (native-inputs
+     (list python-pytest python-pytest-cov python-setuptools python-wheel))
     (home-page "https://github.com/dgasmith/opt_einsum")
     (synopsis "Optimizing numpys einsum function")
     (description
@@ -4080,24 +4266,44 @@ documentation for more information.")
 (define-public python-vaex-core
   (package
     (name "python-vaex-core")
-    (version "4.17.1")
+    (version "4.18.1")
     (source
      (origin
-       (method url-fetch)
+       (method git-fetch)
-       (uri (pypi-uri "vaex-core" version))
+       (uri (git-reference
+             (url "https://www.github.com/maartenbreddels/vaex")
+             (commit (string-append "core-v" version))))
+       (file-name (git-file-name name version))
        (sha256
-        (base32 "1rzx5px3fwi5mh1z8y91brvffk7dkhj287lnmqp8zp6836kkqhya"))
+        (base32 "1sp096msbzgjlwi8c1ink2bp4pjff9pvikqz1y1li8d3in4gpgdr"))
-       (modules '((guix build utils)))
+       (patches
+        (search-patches "python-vaex-core-fix-tsl-use.patch"))
+       (modules '((guix build utils)
+                  (ice-9 ftw)))
        (snippet
-        ;; Remove bundled libraries
+        #~(begin
-        '(for-each delete-file-recursively
+            ;; Delete everything except for vaex-core itself:
-                   (list "vendor/boost"
+            (define (delete-except exception)
-                         "vendor/pcre"
+              (lambda (file)
-                         "vendor/pybind11")))))
+                (unless (member file `("." ".." ,exception))
+                  (delete-file-recursively file))))
+            (for-each (delete-except "packages") (scandir "."))
+            (with-directory-excursion "packages"
+              (for-each (delete-except "vaex-core") (scandir ".")))
+            (for-each (lambda (file)
+                        (unless (member file '("." ".."))
+                          (rename-file
+                           (string-append "packages/vaex-core/" file)
+                           file)))
+                      (scandir "packages/vaex-core"))
+            (delete-file-recursively "packages")
+            (delete-file-recursively "vendor")))))
     (build-system pyproject-build-system)
-    (arguments (list #:tests? #false)) ;require vaex.server and others, which require vaex-core.
+    (arguments
+     ;; require vaex.server and others, which require vaex-core.
+     (list #:tests? #false))
     (inputs
-     (list boost pcre pybind11-2.3))
+     (list boost pcre pybind11 string-view-lite tsl-hopscotch-map))
     (propagated-inputs
      (list python-aplus
            python-blake3
@@ -4321,6 +4527,125 @@ compagnies.")
 neuronal models")
     (license license:bsd-3)))
 
+(define-public snakemake
+  (package
+    (name "snakemake")
+    (version "8.29.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "snakemake" version))
+       (sha256
+        (base32 "1ilpmrjmnc529p4gw2x23ik1d8b5pm6k1dhq08dknvfjsf3vgyjr"))))
+    (build-system pyproject-build-system)
+    (arguments
+     (list
+      #:test-flags
+      #~(list
+         ;; XXX: Unclear why these tests fail.
+         "--ignore=tests/test_report_href/test_script.py"
+         "--ignore=tests/test_script_py/scripts/test_explicit_import.py"
+         "--ignore=tests/test_output_index.py"
+         ;; We don't care about testing old python@3.7 on Guix.
+         "--ignore=tests/test_conda_python_3_7_script/test_script.py"
+         ;; Those require additional snakemake plugins.
+         "--ignore=tests/test_api.py"
+         "--ignore=tests/test_executor_test_suite.py"
+         ;; We don't care about lints.
+         "--ignore=tests/test_linting.py"
+         ;; These tests attempt to change S3 buckets on AWS and fail
+         ;; because there are no AWS credentials.
+         "--ignore=tests/test_tibanna"
+         ;; It's a similar story with this test, which requires access
+         ;; to the Google Storage service.
+         "--ignore=tests/test_google_lifesciences")
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-after 'unpack 'avoid-assets-download
+            (lambda _
+              (substitute* "setup.py"
+                (("^from assets import Assets") "")
+                (("^Assets\\.deploy\\(\\)") ""))))
+          ;; For cluster execution Snakemake will call Python.  Since there is
+          ;; no suitable GUIX_PYTHONPATH set, cluster execution will fail.  We
+          ;; fix this by calling the snakemake wrapper instead.
+          (add-after 'unpack 'call-wrapper-not-wrapped-snakemake
+            (lambda _
+              (substitute* "snakemake/executors/__init__.py"
+                (("self\\.get_python_executable\\(\\),")
+                 "")
+                (("\"-m snakemake\"")
+                 (string-append "\"" #$output
+                                "/bin/snakemake" "\""))
+                ;; The snakemake command produced by format_job_exec contains
+                ;; references to /gnu/store.  Prior to patching above that's
+                ;; just a reference to Python; after patching it's a reference
+                ;; to the snakemake executable.
+                ;;
+                ;; In Tibanna execution mode Snakemake arranges for a certain
+                ;; Docker image to be deployed to AWS.  It then passes its own
+                ;; command line to Tibanna.  This is misguided because it only
+                ;; ever works if the local Snakemake command was run inside
+                ;; the same Docker image.  In the case of using Guix this is
+                ;; never correct, so we need to replace the store reference.
+                (("tibanna_args.command = command")
+                 (string-append
+                  "tibanna_args.command = command.replace('"
+                  #$output "/bin/snakemake', 'python3 -m snakemake')")))))
+          (add-after 'unpack 'patch-version
+            (lambda _
+              (substitute* "setup.py"
+                (("version=versioneer.get_version\\(\\)")
+                 (format #f "version=~s" #$version)))
+              (substitute* '("snakemake/_version.py"
+                             "versioneer.py")
+                (("0\\+unknown") #$version))))
+          (add-before 'check 'pre-check
+            (lambda* (#:key tests?  #:allow-other-keys)
+              (when tests?
+                (setenv "HOME" "/tmp")))))))
+    (propagated-inputs
+     (list python-appdirs
+           python-conda-inject
+           python-configargparse
+           python-connection-pool
+           python-dpath
+           python-gitpython
+           python-humanfriendly
+           python-immutables
+           python-jinja2
+           python-jsonschema
+           python-nbformat
+           python-packaging
+           python-psutil
+           python-pulp
+           python-pyyaml
+           python-requests
+           python-reretry
+           python-smart-open
+           python-snakemake-interface-common
+           python-snakemake-interface-executor-plugins
+           python-snakemake-interface-report-plugins
+           python-snakemake-interface-storage-plugins
+           python-tabulate
+           python-throttler
+           python-wrapt
+           python-yte))
+    (native-inputs
+     (list python-docutils
+           python-numpy
+           python-pandas
+           python-setuptools
+           python-tomli
+           python-wheel))
+    (home-page "https://snakemake.readthedocs.io")
+    (synopsis "Python-based execution environment for make-like workflows")
+    (description
+     "Snakemake aims to reduce the complexity of creating workflows by
+providing a clean and modern domain specific specification language (DSL) in
+Python style, together with a fast and comfortable execution environment.")
+    (license license:expat)))
+
 ;;;
 ;;; Avoid adding new packages to the end of this file. To reduce the chances
 ;;; of a merge conflict, place them above by existing packages with similar

gnu/packages/python.scm

@@ -660,6 +660,405 @@ def contents() -> str:
             (variable "PYTHONTZPATH")
             (files (list "share/zoneinfo")))))))
 
+(define-public python-3.11
+  (package
+    (inherit python-3.10)
+    (name "python")
+    (version "3.11.11")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append "https://www.python.org/ftp/python/"
+                                  version "/Python-" version ".tar.xz"))
+              (patches (search-patches
+                        "python-3-deterministic-build-info.patch"
+                        "python-3.11-fix-tests.patch"
+                        "python-3-hurd-configure.patch"
+                        "python-3-search-paths.patch"))
+              (sha256
+               (base32
+                "1qrvsxg5g0b0pgz2iigxic2j3g6b2c59iva46vins8ydl33j169a"))
+              (modules '((guix build utils)))
+              (snippet
+               '(begin
+                  ;; Delete the bundled copy of libexpat.
+                  (delete-file-recursively "Modules/expat")
+                  (substitute* "Modules/Setup"
+                    ;; Link Expat instead of embedding the bundled one.
+                    (("^#pyexpat.*") "pyexpat pyexpat.c -lexpat\n"))
+                  ;; Delete windows binaries
+                  (for-each delete-file
+                            (find-files "Lib/distutils/command" "\\.exe$"))))))
+    (arguments
+     (list
+      #:test-target "test"
+      #:configure-flags
+      #~(list "--enable-shared"          ;allow embedding
+              "--with-system-expat"      ;for XML support
+              "--with-system-ffi"        ;build ctypes
+              "--with-ensurepip=install" ;install pip and setuptools
+              "--with-computed-gotos"    ;main interpreter loop optimization
+              "--enable-unicode=ucs4"
+              "--without-static-libpython"
+              "--enable-loadable-sqlite-extensions"
+
+              ;; FIXME: These flags makes Python significantly faster,
+              ;; but leads to non-reproducible binaries.
+              ;; "--with-lto"   ;increase size by 20MB, but 15% speedup
+              ;; "--enable-optimizations"
+
+              ;; Prevent the installed _sysconfigdata.py from retaining
+              ;; a reference to coreutils.
+              "INSTALL=install -c"
+              "MKDIR_P=mkdir -p"
+
+              ;; Add a reference to libxcrypt in LIBS so that the
+              ;; sysconfigdata file records it and propagates it to programs
+              ;; linking against Python.
+              (let ((libxcrypt
+                     (false-if-exception
+                      (dirname
+                       (search-input-file %build-inputs
+                                          "lib/libcrypt.so.1")))))
+                (string-append
+                 "LIBS="
+                 (if libxcrypt
+                     (string-append "-L" libxcrypt)
+                     "")))
+
+              ;; Disable runtime check failing if cross-compiling, see:
+              ;; https://lists.yoctoproject.org/pipermail/poky/2013-June/008997.html
+              #$@(if (%current-target-system)
+                     '("ac_cv_buggy_getaddrinfo=no"
+                       "ac_cv_file__dev_ptmx=no"
+                       "ac_cv_file__dev_ptc=no")
+                     '())
+              ;; -fno-semantic-interposition reinstates some
+              ;; optimizations by gcc leading to around 15% speedup.
+              ;; This is the default starting from python 3.10.
+              "CFLAGS=-fno-semantic-interposition"
+              (string-append "LDFLAGS=-Wl,-rpath=" #$output "/lib"
+                             " -fno-semantic-interposition"))
+      ;; With no -j argument tests use all available cpus, so provide one.
+      #:make-flags
+      `(list (string-append (format #f "TESTOPTS=-j~d"
+                                    (parallel-job-count))
+                            ;; those tests fail on low-memory systems
+                            " --exclude"
+                            " test_mmap"
+                            " test_socket"
+                            " test_threading"
+                            " test_asyncio"
+                            " test_shutdown"
+                            ,@(if (system-hurd?)
+                                  '(" test_posix" ;multiple errors
+                                    " test_time"
+                                    " test_pty"
+                                    " test_shutil"
+                                    " test_tempfile" ;chflags: invalid argument:
+                                    ;; tbv14c9t/dir0/dir0/dir0/test0.txt
+                                    " test_os" ;stty: 'standard input':
+                                    ;; Inappropriate ioctl for device
+                                    " test_openpty" ;No such file or directory
+                                    " test_selectors" ;assertEqual(NUM_FDS // 2, len(fds))
+                                    ;; 32752 != 4
+                                    " test_compileall" ;multiple errors
+                                    " test_poll" ;list index out of range
+                                    " test_subprocess" ;runs over 10min
+                                    " test_asyncore"   ;multiple errors
+                                    " test_threadsignals"
+                                    " test_eintr" ;Process return code is -14
+                                    " test_io"    ;multiple errors
+                                    " test_logging"
+                                    " test_signal"
+                                    " test_flags" ;ERROR
+                                    " test_bidirectional_pty"
+                                    " test_create_unix_connection"
+                                    " test_unix_sock_client_ops"
+                                    " test_open_unix_connection"
+                                    " test_open_unix_connection_error"
+                                    " test_read_pty_output"
+                                    " test_write_pty"
+                                    " test_concurrent_futures" ;freeze
+                                    " test_venv"               ;freeze
+                                    " test_multiprocessing_forkserver" ;runs over 10min
+                                    " test_multiprocessing_spawn" ;runs over 10min
+                                    " test_builtin"
+                                    " test_capi"
+                                    " test_dbm_ndbm"
+                                    " test_exceptions"
+                                    " test_faulthandler"
+                                    " test_getopt"
+                                    " test_importlib"
+                                    " test_json"
+                                    " test_multiprocessing_fork"
+                                    " test_multiprocessing_main_handling"
+                                    " test_pdb "
+                                    " test_regrtest"
+                                    " test_sqlite")
+                                  '())))
+
+      #:modules
+      '((ice-9 ftw)
+        (ice-9 match)
+        (guix build utils)
+        (guix build gnu-build-system))
+
+      #:phases
+      #~(modify-phases %standard-phases
+          #$@(if (system-hurd?)
+                 `((add-after 'unpack
+                       'disable-multi-processing
+                     (lambda _
+                       (substitute* "Makefile.pre.in"
+                         (("-j0")
+                          "-j1")))))
+                 '())
+          (add-before 'configure 'patch-lib-shells
+            (lambda _
+              ;; This variable is used in setup.py to enable cross compilation
+              ;; specific switches. As it is not set properly by configure
+              ;; script, set it manually.
+              #$@(if (%current-target-system)
+                     '((setenv "_PYTHON_HOST_PLATFORM" ""))
+                     '())
+              ;; Filter for existing files, since some may not exist in all
+              ;; versions of python that are built with this recipe.
+              (substitute* (filter file-exists?
+                                   '("Lib/subprocess.py"
+                                     "Lib/popen2.py"
+                                     "Lib/distutils/tests/test_spawn.py"
+                                     "Lib/test/support/__init__.py"
+                                     "Lib/test/test_subprocess.py"))
+                (("/bin/sh")
+                 (which "sh")))))
+          (add-before 'configure 'do-not-record-configure-flags
+            (lambda* (#:key configure-flags #:allow-other-keys)
+              ;; Remove configure flags from the installed '_sysconfigdata.py'
+              ;; and 'Makefile' so we don't end up keeping references to the
+              ;; build tools.
+              ;;
+              ;; Preserve at least '--with-system-ffi' since otherwise the
+              ;; thing tries to build libffi, fails, and we end up with a
+              ;; Python that lacks ctypes.
+              (substitute* "configure"
+                (("^CONFIG_ARGS=.*$")
+                 (format #f "CONFIG_ARGS='~a'\n"
+                         (if (member "--with-system-ffi"
+                                     configure-flags)
+                             "--with-system-ffi" ""))))))
+          (add-before 'check 'pre-check
+            (lambda _
+              ;; 'Lib/test/test_site.py' needs a valid $HOME
+              (setenv "HOME"
+                      (getcwd))))
+          (add-after 'unpack 'set-source-file-times-to-1980
+            ;; XXX One of the tests uses a ZIP library to pack up some of the
+            ;; source tree, and fails with "ZIP does not support timestamps
+            ;; before 1980".  Work around this by setting the file times in the
+            ;; source tree to sometime in early 1980.
+            (lambda _
+              (let ((circa-1980 (* 10 366 24 60 60)))
+                (ftw "."
+                     (lambda (file stat flag)
+                       (utime file circa-1980 circa-1980) #t)))))
+          (add-after 'unpack 'remove-windows-binaries
+            (lambda _
+              ;; Delete .exe from embedded .whl (zip) files
+              (for-each (lambda (whl)
+                          (let ((dir "whl-content")
+                                (circa-1980 (* 10 366 24 60 60)))
+                            (mkdir-p dir)
+                            (with-directory-excursion dir
+                              (let ((whl (string-append "../" whl)))
+                                (invoke "unzip" whl)
+                                (for-each delete-file
+                                          (find-files "." "\\.exe$"))
+                                (delete-file whl)
+                                ;; Reset timestamps to prevent them from ending
+                                ;; up in the Zip archive.
+                                (ftw "."
+                                     (lambda (file stat flag)
+                                       (utime file circa-1980
+                                              circa-1980) #t))
+                                (apply invoke "zip" "-X" whl
+                                       (find-files "."
+                                                   #:directories? #t))))
+                            (delete-file-recursively dir)))
+                        (find-files "Lib/ensurepip" "\\.whl$"))))
+          (add-after 'install 'remove-tests
+            ;; Remove 25 MiB of unneeded unit tests.  Keep test_support.*
+            ;; because these files are used by some libraries out there.
+            (lambda* (#:key outputs #:allow-other-keys)
+              (let ((out (assoc-ref outputs "out")))
+                (match (scandir (string-append out "/lib")
+                                (lambda (name)
+                                  (string-prefix? "python" name)))
+                  ((pythonX.Y)
+                   (let ((testdir (string-append out "/lib/" pythonX.Y
+                                                 "/test")))
+                     (with-directory-excursion testdir
+                       (for-each delete-file-recursively
+                                 (scandir testdir
+                                          (match-lambda
+                                            ((or "." "..")
+                                             #f)
+                                            ("support" #f)
+                                            (file (not (string-prefix?
+                                                        "test_support."
+                                                        file))))))
+                       (call-with-output-file "__init__.py"
+                         (const #t))))
+                   (let ((libdir (string-append out "/lib/" pythonX.Y)))
+                     (for-each (lambda (directory)
+                                 (let ((dir (string-append libdir "/"
+                                                           directory)))
+                                   (when (file-exists? dir)
+                                     (delete-file-recursively dir))))
+                               '("email/test" "ctypes/test"
+                                 "unittest/test"
+                                 "tkinter/test"
+                                 "sqlite3/test"
+                                 "bsddb/test"
+                                 "lib-tk/test"
+                                 "json/tests"
+                                 "distutils/tests"))))))))
+          (add-after 'remove-tests 'move-tk-inter
+            (lambda* (#:key outputs inputs #:allow-other-keys)
+              ;; When Tkinter support is built move it to a separate output so
+              ;; that the main output doesn't contain a reference to Tcl/Tk.
+              (let ((out (assoc-ref outputs "out"))
+                    (tk (assoc-ref outputs "tk")))
+                (when tk
+                  (match (find-files out "tkinter.*\\.so")
+                    ((tkinter.so)
+                     ;; The .so is in OUT/lib/pythonX.Y/lib-dynload, but we
+                     ;; want it under TK/lib/pythonX.Y/site-packages.
+                     (let* ((len (string-length out))
+                            (target (string-append tk "/"
+                                                   (string-drop (dirname
+                                                                 (dirname
+                                                                  tkinter.so))
+                                                                len)
+                                                   "/site-packages")))
+                       (install-file tkinter.so target)
+                       (delete-file tkinter.so))))
+                  ;; Remove explicit store path references.
+                  (let ((tcl (assoc-ref inputs "tcl"))
+                        (tk (assoc-ref inputs "tk")))
+                    (substitute* (find-files (string-append out "/lib")
+                                             "^(_sysconfigdata_.*\\.py|Makefile)$")
+                      (((string-append "-L" tk "/lib"))
+                       "")
+                      (((string-append "-L" tcl "/lib"))
+                       "")))))))
+          (add-after 'move-tk-inter 'move-idle
+            (lambda* (#:key outputs #:allow-other-keys)
+              ;; when idle is built, move it to a separate output to save some
+              ;; space (5MB)
+              (let ((out (assoc-ref outputs "out"))
+                    (idle (assoc-ref outputs "idle")))
+                (when idle
+                  (for-each (lambda (file)
+                              (let ((target (string-append idle
+                                                           "/bin/"
+                                                           (basename
+                                                            file))))
+                                (install-file file
+                                              (dirname target))
+                                (delete-file file)))
+                            (find-files (string-append out "/bin")
+                                        "^idle"))
+                  (match (find-files out "^idlelib$"
+                                     #:directories? #t)
+                    ((idlelib)
+                     (let* ((len (string-length out))
+                            (target (string-append idle "/"
+                                                   (string-drop
+                                                    idlelib len)
+                                                   "/site-packages")))
+                       (mkdir-p (dirname target))
+                       (rename-file idlelib target))))))))
+          (add-after 'move-idle 'rebuild-bytecode
+            (lambda* (#:key outputs #:allow-other-keys)
+              ;; Disable hash randomization to ensure the generated .pycs
+              ;; are reproducible.
+              (setenv "PYTHONHASHSEED" "0")
+
+              (for-each (lambda (output)
+                          ;; XXX: Delete existing pycs generated by the build
+                          ;; system beforehand because the -f argument does
+                          ;; not necessarily overwrite all files, leading to
+                          ;; indeterministic results.
+                          (for-each (lambda (pyc)
+                                      (delete-file pyc))
+                                    (find-files output "\\.pyc$"))
+
+                          (apply invoke
+                                 #$(if (%current-target-system)
+                                       "python3"
+                                       #~(string-append #$output "/bin/python3"))
+                                 `("-m" "compileall"
+                                   "-o" "0"
+                                   "-o" "1"
+                                   "-o" "2"
+                                   "-f" ;force rebuild
+                                   "--invalidation-mode=unchecked-hash"
+                                   ;; Don't build lib2to3, because it's Python
+                                   ;; 2 code.
+                                   "-x" "lib2to3/.*"
+                                   ,output)))
+                        (map cdr outputs))))
+          (add-before 'check 'set-TZDIR
+            (lambda* (#:key inputs native-inputs #:allow-other-keys)
+              ;; test_email requires the Olson time zone database.
+              (setenv "TZDIR"
+                      (string-append (assoc-ref (or native-inputs
+                                                    inputs) "tzdata")
+                                     "/share/zoneinfo"))))
+          (add-after 'install 'add-libxcrypt-reference-pkgconfig
+            (lambda* (#:key inputs #:allow-other-keys)
+              (let ((libxcrypt
+                     (false-if-exception
+                      (dirname
+                       (search-input-file inputs "lib/libcrypt.so.1")))))
+                (when libxcrypt
+                  (substitute*
+                      (find-files (string-append #$output "/lib/pkgconfig")
+                                  ".*\\.pc")
+                    (("Libs:")
+                     (string-append "Libs: " "-L" libxcrypt " -lcrypt")))))))
+          (add-after 'install 'install-sitecustomize.py
+            #$(customize-site version)))))
+    (inputs (list bzip2
+                  expat
+                  gdbm
+                  libffi                ;for ctypes
+                  libxcrypt             ;crypto module slated for removal in 3.13
+                  sqlite                ;for sqlite extension
+                  openssl
+                  readline
+                  zlib
+                  tcl
+                  tk))                  ;for tkinter
+    (native-inputs `(("tzdata" ,tzdata-for-tests)
+                     ("unzip" ,unzip)
+                     ("zip" ,(@ (gnu packages compression) zip))
+                     ("pkg-config" ,pkg-config)
+                     ("sitecustomize.py" ,(local-file (search-auxiliary-file
+                                                       "python/sitecustomize.py")))
+                     ;; When cross-compiling, a native version of Python itself is needed.
+                     ,@(if (%current-target-system)
+                           `(("python" ,this-package)
+                             ("which" ,which))
+                           '())))
+    (native-search-paths
+     (list (guix-pythonpath-search-path version)
+           ;; Used to locate tzdata by the zoneinfo module introduced in
+           ;; Python 3.9.
+           (search-path-specification
+            (variable "PYTHONTZPATH")
+            (files (list "share/zoneinfo")))))))
+
 (define-public python-3.12
   (package
     (name "python-next")
@@ -1051,7 +1450,7 @@ data types.")
 (define-public python-next python-3.12)
 
 ;; Current 3.x version.
-(define-public python-3 python-3.10)
+(define-public python-3 python-3.11)
 
 ;; Current major version.
 (define-public python python-3)
@@ -1088,10 +1487,10 @@ data types.")
     (build-system gnu-build-system)
     (arguments
      (substitute-keyword-arguments (package-arguments python)
-       ((#:configure-flags flags '())
+       ((#:configure-flags configure-flags)
-        `(cons "--with-pydebug" ,flags))))
+        #~(append #$configure-flags
-    (synopsis
+                  (list "--with-pydebug")))))
-     "Python with the debug hooks enabled")
+    (synopsis "Python with the debug hooks enabled")
     (description
      "This variant of Python provides an interpreter built with
 @code{--with-pydebug} to help develop and debug extensions.  See

gnu/packages/qt.scm

@@ -4033,7 +4033,7 @@ Python.")
 (define-public python-sip
   (package
     (name "python-sip")
-    (version "6.8.6")
+    (version "6.10.0")
     (source
      (origin
        (method url-fetch)
@@ -4043,18 +4043,20 @@ Python.")
                                  "/sip-" version ".tar.gz")))
        (sha256
         (base32
-         "0ykxq0607f2sdwbl5cxbp0y8pl14bsgzc9nhifpxbibfivj5kjbz"))
+         "176jylhzs2ci2r9f3l75k9dpwhp1dn0qv2cy9phdp62cgmlia1gs"))
+       (modules '((guix build utils)))
+       (snippet
+        ;; Relax setuptools dependency
+        #~(substitute* "pyproject.toml"
+            (("\"setuptools>=.*\",") "\"setuptools\",")))
        (patches (search-patches "python-sip-include-dirs.patch"))))
     (build-system pyproject-build-system)
     (arguments
      (list #:tests? #f))        ; No test system found.
     (native-inputs
-     (list python-wrapper python-setuptools python-setuptools-scm-next))
+     (list python-setuptools python-setuptools-scm-next python-wheel))
     (propagated-inputs
-     (list python-tomli
+     (list python-packaging python-setuptools))
-           python-packaging
-           python-setuptools
-           python-wheel))
     (home-page "https://www.riverbankcomputing.com/software/sip/intro")
     (synopsis "Python binding creator for C and C++ libraries")
     (description
@@ -5137,7 +5139,7 @@ color-related widgets.")
 (define-public python-shiboken-2
   (package
     (name "python-shiboken-2")
-    (version "5.15.10")
+    (version "5.15.16")
     (source (origin
               (method url-fetch)
               (uri (string-append "mirror://qt/QtForPython/pyside2/PySide2-"
@@ -5145,7 +5147,7 @@ color-related widgets.")
                                   version ".tar.xz"))
               (sha256
                (base32
-                "0fnkx8ax2lkin3bpqbz4zbdrdin2ixb4d6s3c0xghh9sc79r3xia"))))
+                "0q3ky0fai3wr8kr1q82vdg5byhbn5sfdymmb554afpi72zyxcgkd"))))
     (build-system cmake-build-system)
     (inputs
      (list clang-toolchain

gnu/packages/radio.scm

@@ -3272,7 +3272,6 @@ satellites.")
       (native-inputs
        (list python-mock
              python-mox3
-             python-pep8
              python-pytest
              python-pytest-mock
              python-pyyaml

gnu/packages/sphinx.scm

@@ -81,10 +81,15 @@
     (arguments
      (list
       #:test-flags
+      #~(list "-k" (string-join
+                    (list
                      ;; These require Internet access.
-      #~(list "-k" (string-append "not test_latex_images"
+                     "not test_latex_images"
-                                  " and not test_build_latex_doc[lualatex-manual]"
+                     "test_build_latex_doc[lualatex-manual]"
-                                  " and not est_build_latex_doc[lualatex-howto]"))
+                     "est_build_latex_doc[lualatex-howto]"
+                     ;; AssertionError: assert...list of weak references to the object...
+                     "test_autodoc_default_options")
+                    " and not "))
       #:phases
       #~(modify-phases %standard-phases
           (add-before 'check 'pre-check
@@ -192,7 +197,10 @@ sources.")
               " and not test_viewcode"
               ;; These fail with pygments 2.10+.  They are harmless.
               " and not test_additional_targets_should_not_be_translated"
-              " and not test_additional_targets_should_be_translated"))
+              " and not test_additional_targets_should_be_translated"
+              ;; As in Sphinx@6:
+              ;; AssertionError: assert...list of weak references to the object...
+              " and not test_autodoc_default_options"))
       #:phases
       '(modify-phases %standard-phases
          (add-before 'check 'pre-check
@@ -262,25 +270,6 @@ sources.")
            (texlive-updmap.cfg
             (list texlive-cm-super texlive-tex-gyre))))))
 
-;; Some packages do not support Sphinx 5 yet.  Remove when unused.
-(define-public python-sphinx-4
-  (package
-    (inherit python-sphinx-5)
-    (version "4.5.0")
-    (source (origin
-              (method url-fetch)
-              (uri (pypi-uri "Sphinx" version))
-              (sha256
-               (base32
-                "1rp28jryxwy24y8vpacclqihbizyi6b1s6id86pibvm46ybcmy3v"))))
-    (propagated-inputs
-     (modify-inputs (package-propagated-inputs python-sphinx)
-       (replace "python-docutils" python-docutils-0.15)))
-    (native-inputs
-     (modify-inputs (package-native-inputs python-sphinx)
-       (delete python-flit-core)
-       (append python-setuptools python-wheel)))))
-
 (define-public python-sphinxcontrib-apidoc
   (package
     (name "python-sphinxcontrib-apidoc")
@@ -603,7 +592,15 @@ supported with @code{sphinx-issues}.")
         (sha256
          (base32 "1ivqz6yv96a2jp59kylg1gbkrmzq6zwilppz3ij0zrkjn25zb97k"))))
     (build-system pyproject-build-system)
-    (propagated-inputs (list python-docutils-0.15 python-sphinx-4))
+    (arguments
+     (list #:phases
+           #~(modify-phases %standard-phases
+               (add-after 'unpack 'loosen-requirements
+                 (lambda _
+                   (substitute* "setup.py"
+                     (("sphinx>=2,<5")
+                      "sphinx>=2,<6")))))))
+    (propagated-inputs (list python-docutils-0.16 python-sphinx-5))
     (native-inputs
      (list python-pytest
            python-pytest-regressions
@@ -1229,13 +1226,6 @@ enabled web server.")
 documenting acceptable argument types and return value types of functions.")
     (license license:expat)))
 
-(define-public python-sphinx-autodoc-typehints-5
-  (package/inherit python-sphinx-autodoc-typehints
-    (propagated-inputs
-     (modify-inputs
-         (package-propagated-inputs python-sphinx-autodoc-typehints)
-       (replace "python-sphinx" python-sphinx-5)))))
-
 (define-public python-sphinx-pytest
   (package
     (name "python-sphinx-pytest")

gnu/packages/statistics.scm

@@ -916,7 +916,7 @@ comparison and diagnostics.")
 (define-public python-pymc
   (package
     (name "python-pymc")
-    (version "5.11.0")
+    (version "5.21.0")
     (source (origin
               (method git-fetch)        ; no tests in PyPI
               (uri (git-reference
@@ -925,28 +925,17 @@ comparison and diagnostics.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "0x94qzq3z02fxlliz1xfdpb2pbn7nhp4skzcxz6qdavbj9xqcxys"))))
+                "0azkbl0mpanza35ibdqdm21bf45n3xi26wy01lnxzxqblcjcny9l"))))
     (build-system pyproject-build-system)
     (arguments
      (list #:tests? #f ; tests are too computationally intensive
            #:phases #~(modify-phases %standard-phases
                         (add-after 'unpack 'versioneer
                           (lambda _
-                            (with-output-to-file "setup.cfg"
-                (lambda ()
-                  (display "\
-[versioneer]
-VCS = git
-style = pep440
-versionfile_source = pymc/_version.py
-versionfile_build = pymc/_version.py
-tag_prefix =
-parentdir_prefix = pymc-
-")))
                             (invoke "versioneer" "install")
                             (substitute* "setup.py"
-                (("versioneer.get_version\\(\\)")
+                              (("version=versioneer.get_version\\(),")
-                 (string-append "\"" #$version "\"")))))
+                               (format #f "version=~s," #$version)))))
                         ;; To create the compiledir for tests.
                         (add-before 'check 'write-permissions
                           (lambda* (#:key tests? #:allow-other-keys)
@@ -1009,24 +998,18 @@ and a lot more.")
 (define-public python-patsy
   (package
     (name "python-patsy")
-    (version "0.5.2")
+    (version "1.0.1")
     (source (origin
               (method url-fetch)
               (uri (pypi-uri "patsy" version))
               (sha256
                (base32
-                "17dn72519gvwifw3i8mzwlslxmxkl8ihzfrxg1iblsk70iwdwlsh"))))
+                "1i60b6s8zj0w2ks63ip4mr8z14p6pixp76rm9q2qr0gc3qwsk1p7"))))
-    (build-system python-build-system)
+    (build-system pyproject-build-system)
-    (arguments
-     `(#:phases
-       (modify-phases %standard-phases
-         (replace 'check
-           (lambda* (#:key tests? #:allow-other-keys)
-             (when tests? (invoke "pytest" "-vv")))))))
     (propagated-inputs
-     (list python-numpy python-scipy python-six))
+     (list python-numpy python-scipy))
     (native-inputs
-     (list python-pytest))
+     (list python-pytest python-pytest-cov python-setuptools python-wheel))
     (home-page "https://github.com/pydata/patsy")
     (synopsis "Describe statistical models and build design matrices")
     (description
@@ -3333,7 +3316,7 @@ statistical summary in arrays and enumerables.")
 (define-public python-pgmpy
   (package
     (name "python-pgmpy")
-    (version "0.1.24")
+    (version "1.0.0")
     (source
      (origin
        (method git-fetch)  ;pypi package does not include test data
@@ -3343,8 +3326,14 @@ statistical summary in arrays and enumerables.")
        (file-name (git-file-name name version))
        (sha256
         (base32
-         "0fvzh6v0yhgdryczamvzhfy2ymywkh0ssx4rl47xnfvi43hnij90"))))
+         "1hg6wrg3jcac71zn4gknni1wrn38wa86ka3sgp2bndz59mx6sr2s"))))
     (build-system pyproject-build-system)
+    (arguments
+     (list #:test-flags
+           #~(list "-k" (string-append
+                         "not test_pillai"
+                         " and not test_estimate_with_cache_no_llm_calls"
+                         " and not test_estimate_with_orientations"))))
     (propagated-inputs (list python-daft
                              python-joblib
                              python-networkx
@@ -3358,7 +3347,11 @@ statistical summary in arrays and enumerables.")
                              python-statsmodels
                              python-tqdm))
     (native-inputs (list python-mock
-                         python-pytest))
+                         python-pyro-ppl
+                         python-pytest
+                         python-setuptools
+                         python-wheel
+                         python-xgboost))
     (home-page "https://github.com/pgmpy/pgmpy")
     (synopsis "Probabilistic Graphical Models library")
     (description "This package provides a library for Probabilistic

gnu/packages/tor.scm

@@ -44,6 +44,7 @@
   #:use-module (gnu packages)
   #:use-module (gnu packages base)
   #:use-module (gnu packages libevent)
+  #:use-module (gnu packages libffi)
   #:use-module (gnu packages linux)
   #:use-module (gnu packages check)
   #:use-module (gnu packages compression)
@@ -261,7 +262,7 @@ networks.")
 (define-public onionshare-cli
   (package
     (name "onionshare-cli")
-    (version "2.6")
+    (version "2.6.3")
     (source
      (origin
        (method git-fetch)
@@ -270,32 +271,53 @@ networks.")
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "1bhrp019a0923h7dnfxhgvgvdp81blvnsbnvzy34hp827abxf3ic"))
+        (base32 "16yr25llnbgl2iwk458ca0rhrxsmpfx72q4gdg4a52i6g546p3hd"))))
-       (patches (search-patches "onionshare-cli-async-mode.patch"))))
+    (build-system pyproject-build-system)
-    (build-system python-build-system)
     (native-inputs
-     (list python-pytest))
+     (list python-cython-3
+           python-poetry-core
+           python-pytest
+           python-wheel))
     (inputs
-     ;; TODO: obfs4proxy
      (list python-click
+           python-cffi
            python-colorama
            python-eventlet
            python-flask
-           python-flask-httpauth
+           python-flask-compress
            python-flask-socketio
-           python-pynacl
+           python-gevent
+           python-gevent-websocket
+           python-packaging
            python-psutil
-           python-pycryptodome
+           python-pynacl
            python-pysocks
+           python-qrcode
            python-requests
+           python-setuptools
            python-stem
            python-unidecode
-           python-urllib3
+           python-urllib3-next
+           python-waitress
+           python-werkzeug
            tor))
     (arguments
      (list
       #:phases
       #~(modify-phases %standard-phases
+          (add-after 'unpack 'relax-requirements
+            (lambda _
+              ;; All tests passed, and the CLI is working in runtime, relax
+              ;; Poetry way too strict requirements.
+              (substitute* "cli/pyproject.toml"
+                (("2.3.2") "^3.0.0")     ; flask = "2.3.2"
+                (("5.3.4") "5.5.1")      ; flask-socketio = "5.3.4"
+                (("23.9.1") "24.11.1")   ; gevent = "^23.9.1"
+                (("7.4.2") "8.0.0")      ; qrcode = "^7.4.2"
+                (("70.0.0") "67.6.1")    ; setuptools = ">=70.0.0"
+                (("1.8.1") "^1.8.1")     ; stem = "1.8.1"
+                (("3.0.6") "^3.0.6")     ; werkzeug = "3.0.6"
+                (("0.41.2") "0.40.0")))) ; wheel = "^0.41.2"
           (add-after 'unpack 'bake-tor
             (lambda* (#:key inputs #:allow-other-keys)
               (substitute* (list "cli/onionshare_cli/common.py"
@@ -307,16 +329,15 @@ networks.")
                  (search-input-directory inputs "share/tor")))))
           (add-before 'build 'change-directory
             (lambda _ (chdir "cli")))
-          (replace 'check
+          (add-before 'check 'pre-check
             (lambda* (#:key tests? #:allow-other-keys)
               (when tests?
                 (setenv "HOME" "/tmp")
-                ;; Greendns is not needed for testing, and if eventlet tries to
+                ;; Greendns is not needed for testing, and if eventlet tries
-                ;; load it, an OSError is thrown when getprotobyname is called.
+                ;; to load it, an OSError is thrown when getprotobyname is
-                ;; Thankfully there is an environment variable to disable the
+                ;; called.  Thankfully there is an environment variable to
-                ;; greendns import, so use it:
+                ;; disable the greendns import, so use it:
-                (setenv "EVENTLET_NO_GREENDNS" "yes")
+                (setenv "EVENTLET_NO_GREENDNS" "yes")))))))
-                (invoke "pytest" "-v" "./tests")))))))
     (home-page "https://onionshare.org/")
     (synopsis "Securely and anonymously share files")
     (description "OnionShare lets you securely and anonymously share files,

gnu/packages/tryton.scm

@@ -4,6 +4,7 @@
 ;;; Copyright © 2021 Maxime Devos <maximedevos@telenet.be>
 ;;; Copyright © 2021 Hartmut Goebel <h.goebel@crazy-compilers.com>
 ;;; Copyright © 2021 Maxim Cournoyer <maxim.cournoyer@gmail.com>
+;;; Copyright © 2025 Ricardo Wurmus <rekado@elephly.net>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -23,24 +24,29 @@
 (define-module (gnu packages tryton)
   #:use-module ((guix licenses) #:prefix license:)
   #:use-module (gnu packages)
+  #:use-module (gnu packages base)
   #:use-module (gnu packages bash)
   #:use-module (gnu packages check)
   #:use-module (gnu packages databases)
   #:use-module (gnu packages finance)
   #:use-module (gnu packages glib)
   #:use-module (gnu packages gnome)
+  #:use-module (gnu packages graphviz)
   #:use-module (gnu packages gtk)
   #:use-module (gnu packages pdf)
   #:use-module (gnu packages python)
+  #:use-module (gnu packages python-build)
   #:use-module (gnu packages python-crypto)
   #:use-module (gnu packages python-web)
   #:use-module (gnu packages python-xyz)
   #:use-module (gnu packages time)
   #:use-module (gnu packages xml)
+  #:use-module (guix gexp)
   #:use-module (guix packages)
   #:use-module (guix download)
   #:use-module (guix utils)
-  #:use-module (guix build-system python))
+  #:use-module (guix build-system python)
+  #:use-module (guix build-system pyproject))
 
 (define (guix-trytonpath-search-path version)
   "Generate a GUIX_TRYTOND_MODULES_PATH search path specification, using
@@ -58,41 +64,49 @@ installed in the same environments.  Collecting only paths actually containing
 (define-public trytond
   (package
     (name "trytond")
-    (version "6.2.10")
+    (version "7.4.4")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "trytond" version))
        (sha256
-        (base32 "0s53ig8snbs9936h99pwa0lwhcrd3j3cbpwlmf90mf1chrif7zca"))
+        (base32 "1bwa631qz07k6s5fbki3ph6sx0ch9yss2q4sa1jb67z6angiwv5f"))
-       (patches (search-patches "trytond-add-egg-modules-to-path.patch"
+       (patches (search-patches "trytond-add-guix_trytond_path.patch"))))
-                                "trytond-add-guix_trytond_path.patch"))))
+    (build-system pyproject-build-system)
-    (build-system python-build-system)
+    (arguments
+     (list
+      #:test-flags
+      '(list "-k"
+             (string-append
+              ;; "modules" is [None], but should be a list of modules.
+              "not ModuleTestCase"
+                            ;; fixture 'self' not found
+                            " and not test_method"))
+      #:phases
+      '(modify-phases %standard-phases
+         (add-before 'check 'preparations
+           (lambda _
+             (setenv "DB_NAME" ":memory:")
+             (setenv "HOME" "/tmp"))))))
     (propagated-inputs
      (list python-dateutil
            python-defusedxml
            python-genshi
            python-lxml
-           python-magic
            python-passlib
            python-polib
-           python-psycopg2
            python-relatorio
            python-sql
-           python-werkzeug-1.0 ;setup.py requires werkzeug<2
+           python-werkzeug))
-           python-wrapt))
     (native-inputs
-     (list python-mock python-pillow))
+     (list python-pillow
+           python-pydot
+           python-pytest
+           python-setuptools
+           python-wheel
+           tzdata-for-tests))
     (native-search-paths
      (list (guix-trytonpath-search-path (package-version python))))
-    (arguments
-     `(#:phases
-       (modify-phases %standard-phases
-         (add-before 'check 'preparations
-           (lambda _
-             (setenv "DB_NAME" ":memory:")
-             (setenv "HOME" "/tmp")
-             #t)))))
     (home-page "https://www.tryton.org/")
     (synopsis "Tryton Server")
     (description "Tryton is a three-tier high-level general purpose
@@ -104,30 +118,33 @@ and security.")
 (define-public tryton
   (package
     (name "tryton")
-    (version "6.2.7")
+    (version "7.4.4")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "tryton" version))
        (sha256
-        (base32 "1bvwkrj2mmnddaif60g2np2jpx8lq5ka32xlhd4rlnshnbryrm5q"))))
+        (base32 "0q0qa4pjbpc0h8r9hlnm5dh315w5i7mzqpdrlw1c8qvigpl1rf7g"))))
-    (build-system python-build-system)
+    (build-system pyproject-build-system)
     (arguments
-     `(#:phases
+     (list
-       (modify-phases %standard-phases
+      #:phases
+      #~(modify-phases %standard-phases
           (add-before 'check 'change-home
             (lambda _
               ;; Change from /homeless-shelter to /tmp for write permission.
               (setenv "HOME" "/tmp")))
           (add-after 'install 'wrap-gi-python
-           (lambda* (#:key inputs outputs #:allow-other-keys)
+            (lambda _
-             (let ((out               (assoc-ref outputs "out"))
+              (let ((gi-typelib-path   (getenv "GI_TYPELIB_PATH")))
-                   (gi-typelib-path   (getenv "GI_TYPELIB_PATH")))
+                (wrap-program (string-append #$output "/bin/tryton")
-               (wrap-program (string-append out "/bin/tryton")
                   `("GI_TYPELIB_PATH" ":" prefix (,gi-typelib-path)))))))))
     (native-inputs
      (list `(,glib "bin")
-           gobject-introspection))
+           gobject-introspection
+           python-pytest
+           python-setuptools
+           python-wheel))
     (inputs (list bash-minimal))        ;for wrap-program
     (propagated-inputs
      (list (librsvg-for-system)
@@ -145,19 +162,20 @@ and security.")
 (define-public python-proteus
   (package
     (name "python-proteus")
-    (version "6.2.3")
+    (version "7.4.1")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "proteus" version))
        (sha256
-        (base32 "0xx8kqzgs66rgz6bk5favnjs0akz6znz81vmjwpwp2wpq7094fsr"))))
+        (base32 "1q3d0hkvmfsmxbx2qqp8zpslyy11mzwh0q2dkrh958yfyrzi1550"))))
-    (build-system python-build-system)
+    (build-system pyproject-build-system)
     ;; Tests require python-trytond-party which requires python-proteus.
     (arguments
      `(#:tests? #f))
     (propagated-inputs
      (list python-dateutil python-defusedxml))
+    (native-inputs (list python-setuptools python-wheel))
     (home-page "http://www.tryton.org/")
     (synopsis "Library to access a Tryton server as a client")
     (description

gnu/packages/version-control.scm

@@ -2702,7 +2702,7 @@ execution of any hook written in any language before every commit.")
     (native-search-paths
      (list (search-path-specification
             (variable "HGEXTENSIONPATH")
-            (files '("lib/python3.10/site-packages/hgext3rd")))))
+            (files '("lib/python3.11/site-packages/hgext3rd")))))
     (home-page "https://www.mercurial-scm.org/")
     (synopsis "Decentralized version control system")
     (description
@@ -4312,50 +4312,47 @@ defects faster.")
     (license license:expat)))
 
 (define-public gita
-  (let ((commit "e41b504dca90a25e9be27f296da7ce22e5782893")
-        (revision "1"))
   (package
     (name "gita")
-      (version (git-version "0.12.9" revision commit))
+    (version "0.16.7.2")
-      (source (origin
+    (source
+     (origin
        (method git-fetch)
        (uri (git-reference
              (url "https://github.com/nosarthur/gita")
-                      (commit commit)))
+             (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-                 (base32
+        (base32 "118dzmjgml0c32yllr2178ash2hvgn201i463bv4y0qbywajm9ax"))))
-                  "1k03zgcbhl91cgyh4k7ywyjp00y63q4bqbimncqh5b3lni8l8j5l"))))
+    (build-system pyproject-build-system)
-      (build-system python-build-system)
-      (native-inputs
-       (list git ;for tests
-             python-pytest))
-      (propagated-inputs
-       (list python-pyyaml))
     (arguments
-       `(#:phases
+     (list
-         (modify-phases %standard-phases
+      #:test-flags #~(list "--ignore" "tests/test_main.py")
-           (replace 'check
+      #:phases
-             (lambda* (#:key inputs outputs #:allow-other-keys)
+      #~(modify-phases %standard-phases
-               (substitute* "tests/test_main.py"
+          (add-before 'check 'pre-check
-                 (("'gita\\\\n'") "'source\\n'")
+            (lambda _
-                 (("'gita'") "'source'"))
+              (invoke (string-append
-               (invoke (search-input-file inputs "/bin/git")
+                       #$(this-package-native-input "git-minimal") "/bin/git")
-                       "init")
+                      "init")))
-               (add-installed-pythonpath inputs outputs)
-               (invoke (search-input-file inputs "/bin/pytest")
-                       "-vv" "tests")))
           (add-after 'install 'install-shell-completions
-             (lambda* (#:key outputs #:allow-other-keys)
+            (lambda _
-               (let* ((out (assoc-ref outputs "out"))
+              (let* ((out #$output)
                      (bash-completion (string-append out "/etc/bash_completion.d"))
                      (zsh-completion (string-append out "/etc/zsh/site-functions")))
                 (mkdir-p bash-completion)
-                 (copy-file ".gita-completion.bash"
+                (copy-file "auto-completion/bash/.gita-completion.bash"
                            (string-append bash-completion "/gita"))
                 (mkdir-p zsh-completion)
-                 (copy-file ".gita-completion.zsh"
+                (copy-file "auto-completion/zsh/.gita-completion.zsh"
                            (string-append zsh-completion "/_gita"))))))))
+    (native-inputs
+     (list git-minimal/pinned ;for tests
+           python-pytest
+           python-setuptools
+           python-wheel))
+    (propagated-inputs
+     (list python-argcomplete))
     (home-page "https://github.com/nosarthur/gita")
     (synopsis "Command-line tool to manage multiple Git repos")
     (description "This package provides a command-line tool to manage
@@ -4369,7 +4366,7 @@ commit message side by side
 @end itemize
 
 If several repos are related, it helps to see their status together.")
-      (license license:expat))))
+    (license license:expat)))
 
 (define-public ghq
   (package

gnu/packages/video.scm

@@ -3221,7 +3221,7 @@ YouTube.com and many more sites.")
                   python-mutagen
                   python-pycryptodomex
                   python-requests-next ; TODO Remove this special package
-                  python-urllib3-next  ; TODO Remove this one too
+                  python-urllib3-1.26  ; TODO Remove this one too
                   python-websockets))
     (native-inputs
      (append
@@ -3799,34 +3799,28 @@ and custom quantization matrices.")
 (define-public streamlink
   (package
     (name "streamlink")
-    (version "6.3.1")
+    (version "7.1.2")
     (source
       (origin
         (method url-fetch)
         (uri (pypi-uri "streamlink" version))
         (sha256
          (base32
-          "0i2qym2plm4gpcq50vl67j69m8a4zz9mb8gi2xryx28pbnpdzh4k"))
+          "1mvg8lw3rkng6ciryziqh9r4ffj0ls7k0sv3byk3439s5d2qxh31"))))
-        (snippet
+    (build-system pyproject-build-system)
-         #~(begin (use-modules (guix build utils))
-                  (substitute* "pyproject.toml"
-                    (("trio >=0\\.22") "trio >=0.21"))))))
-    (build-system python-build-system)
     (arguments
-     `(#:phases
+     (list
-       (modify-phases %standard-phases
+      #:test-flags #~(list "-k" "not test_no_cache")))
-         (replace 'check
-          (lambda* (#:key tests? #:allow-other-keys)
-              (when tests?
-                  (invoke "python" "-m" "pytest")))))))
     (native-inputs
      (list python-freezegun
-           python-requests-mock
            python-pytest
-           python-pytest-asyncio
+           python-pytest-trio
-           python-pytest-trio))
+           python-requests-mock
+           python-setuptools
+           python-wheel))
     (propagated-inputs
      (list python-certifi
+           python-exceptiongroup
            python-isodate
            python-lxml
            python-pycountry
@@ -3835,7 +3829,6 @@ and custom quantization matrices.")
            python-requests
            python-trio
            python-trio-websocket
-           python-typing-extensions
            python-urllib3
            python-websocket-client))
     (home-page "https://github.com/streamlink/streamlink")

gnu/packages/web.scm

@@ -7217,6 +7217,12 @@ efficient where possible.")
      (list
       #:phases
       '(modify-phases %standard-phases
+         (add-after 'unpack 'remove-rednose-dependency
+           (lambda _
+             (substitute* "setup.py"
+               (("'rednose'") ""))
+             (substitute* '("requirements.txt" "setup.cfg")
+               (("rednose.*") ""))))
          (replace 'check
            (lambda* (#:key tests? #:allow-other-keys)
              (when tests?
@@ -7230,7 +7236,6 @@ efficient where possible.")
            python-httplib2
            python-nose
            python-pyparsing
-           python-rednose
            python-requests
            python-sure
            python-tornado))

gnu/packages/wxwidgets.scm

@@ -13,6 +13,7 @@
 ;;; Copyright © 2023 Malte Frank Gerdes <malte.f.gerdes@gmail.com>
 ;;; Copyright © 2023 Maxim Cournoyer <maxim.cournoyer@gmail.com>
 ;;; Copyright © 2025 Ekaitz Zarraga <ekaitz@elenq.tech>
+;;; Copyright © 2025 Nicolas Graves <ngraves@ngraves.fr>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -37,6 +38,7 @@
   #:use-module ((guix licenses) #:prefix l:)
   #:use-module (guix build-system glib-or-gtk)
   #:use-module (guix build-system perl)
+  #:use-module (guix build-system pyproject)
   #:use-module (guix build-system python)
   #:use-module (guix utils)
   #:use-module (gnu packages)
@@ -57,7 +59,9 @@
   #:use-module (gnu packages photo)
   #:use-module (gnu packages pkg-config)
   #:use-module (gnu packages python)
+  #:use-module (gnu packages python-build)
   #:use-module (gnu packages python-xyz)
+  #:use-module (gnu packages qt)
   #:use-module (gnu packages sdl)
   #:use-module (gnu packages video)
   #:use-module (gnu packages web)
@@ -318,26 +322,38 @@ and many other languages.")
 (define-public python-wxpython
   (package
     (name "python-wxpython")
-    (version "4.2.0")
+    (version "4.2.2")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "wxPython" version))
        (sha256
-        (base32
+        (base32 "1fp2717a96hd5pdai6hlzc4pngdazxas55apjv2w5zb71xjv1g2x"))
-         "1iw6xp76b3fmdqwbqmsx9i1razzpfki5z1hq6l8mszlxa32fng36"))
        (modules '((guix build utils)))
-       (snippet
+       (snippet #~(begin
-        '(begin
+                    ;; Remove bundled wxWidgets
-           ;; Remove bundled wxwidgets
+                    (delete-file-recursively "ext/wxWidgets")))))
-           (delete-file-recursively "ext/wxWidgets")))
+    (build-system pyproject-build-system)
-       (patches (search-patches "python-wxwidgets-type-errors.patch"))))
-    (build-system python-build-system)
     (outputs '("out" "debug"))
     (arguments
      (list
+      #:modules '((guix build pyproject-build-system)
+                  (guix build utils)
+                  (ice-9 ftw)
+                  (ice-9 match)
+                  (srfi srfi-26))
       #:phases
       #~(modify-phases %standard-phases
+          (add-after 'unpack 'patch-avoid-circular-import
+            (lambda _
+              (substitute* "wx/__init__.py"
+                (("^import wx\\.__version__.*$") "\
+try:
+    import wx.__version__
+except ImportError:
+    pass\n")
+                (("^__version__ = .*")
+                 (format #f "__version__ = ~s~%" #$version)))))
           (add-before 'build 'configure
             (lambda* (#:key inputs #:allow-other-keys)
               ;; Configure the build options provided to the 'build.py' build
@@ -357,11 +373,24 @@ and many other languages.")
                  (string-append "#" all)))
               ;; The build script tries to write to demo/version.py. So, we set
               ;; correct write permissions.
-              (chmod "demo/version.py" #o644))))))
+              (chmod "demo/version.py" #o644)))
+          (add-before 'check 'add-missing-.so
+            (lambda* (#:key inputs outputs #:allow-other-keys)
+              (let ((site (site-packages inputs outputs)))
+                (with-directory-excursion (string-append site "/wx")
+                  (for-each
+                   (match-lambda
+                     ("siplib"
+                      (rename-file "siplib" "siplib.so"))
+                     ((? (cut string-prefix? "_" <>) file)
+                      (unless (string-prefix? "__" file)
+                        (rename-file file (string-append file ".so"))))
+                     (_ #t))
+                   (scandir ".")))))))))
     (inputs
      (list gtk+ wxwidgets))
     (native-inputs
-     (list pkg-config python-waf))
+     (list pkg-config python-setuptools python-waf python-wheel))
     (propagated-inputs
      (list python-attrdict3 python-numpy python-pillow python-six))
     (home-page "https://wxpython.org/")