gnu: python-mdx-gh-links: Update to 0.4.

* gnu/packages/python-xyz.scm (python-mdx-gh-links): Update to 0.4.
[build-system]: Switch to pyproject-build-system.
[native-inputs]: Add python-setuptools.

Change-Id: I98370aabb14c2465f0fed4399d57e87b3f7b0f69

gnu/local.mk

@@ -2037,6 +2037,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/python-clarabel-blas.patch		\
   %D%/packages/patches/python-docrepr-fix-tests.patch		\
   %D%/packages/patches/python-feedparser-missing-import.patch	\
+  %D%/packages/patches/python-hdmedians-replace-nose.patch	\
   %D%/packages/patches/python-louvain-fix-test.patch		\
   %D%/packages/patches/python-matplotlib-fix-legend-loc-best-test.patch	\
   %D%/packages/patches/python-mohawk-pytest.patch	\
@@ -2173,8 +2174,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/python-pytorch-system-libraries.patch	\
   %D%/packages/patches/python-pytorch-without-kineto.patch	\
   %D%/packages/patches/python-robotframework-sshlibrary-rf5-compat.patch \
-  %D%/packages/patches/python-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	\

gnu/packages/admin.scm

@@ -2874,7 +2874,7 @@ development, not the kernel implementation of ACPI.")
            python-setuptools
            python-wheel))
     (inputs
-     (list python-psutil-7
+     (list python-psutil
            python-urwid-3))
     (home-page "https://github.com/amanusk/s-tui")
     (synopsis "Interactive terminal stress test and monitoring tool")
@@ -5125,23 +5125,22 @@ cache of unix and unix-like systems.")
   (package
     (name "solaar")
     (version "1.1.14")
-    (source (origin
-              (method git-fetch)
-              (uri (git-reference
-                    (url "https://github.com/pwr-Solaar/Solaar")
-                    (commit version)))
-              (file-name (git-file-name name version))
-              (sha256
-               (base32
-                "000700waw4z6ab40naycapjgqz8yvz9ny1px94ni4pwf8f3kh0vh"))))
-    (build-system python-build-system)
-    (arguments
-     `(#:phases
-       (modify-phases %standard-phases
-         (add-before 'build 'setenv-PATH
-           (lambda _
-             (setenv "PYTHONPATH" "lib"))))))
-    (native-inputs (list python-pytest))
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/pwr-Solaar/Solaar")
+             (commit version)))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "000700waw4z6ab40naycapjgqz8yvz9ny1px94ni4pwf8f3kh0vh"))))
+    (build-system pyproject-build-system)
+    (native-inputs
+     (list python-pytest
+           python-pytest-mock
+           python-setuptools
+           python-typing-extensions
+           python-wheel))
     (propagated-inputs
      (list python-pygobject
            python-pyudev

gnu/packages/astronomy.scm

@@ -901,7 +901,7 @@ corrections.")
            python-pytest-doctestplus
            python-pytest-astropy
            python-pytest-astropy-header
-           python-setuptools-next))
+           python-setuptools))
     (inputs
      (list python-astropy
            python-numpy
@@ -1879,8 +1879,8 @@ model-fitting photometry or morphological analyses.")
            python-pytest-cov
            python-pytest-doctestplus
            python-pytest-xdist
-           python-setuptools-next
-           python-setuptools-scm-next))
+           python-setuptools
+           python-setuptools-scm))
     (propagated-inputs
      (list python-sunpy))
     (home-page "https://aia.lmsal.com/")
@@ -1976,8 +1976,8 @@ Main features:
            python-pytest-doctestplus
            python-pytest-remotedata
            python-pytest-xdist
-           python-setuptools-next
-           python-setuptools-scm-next
+           python-setuptools
+           python-setuptools-scm
            python-wheel))
     (propagated-inputs
      (list python-asdf-standard
@@ -2047,7 +2047,7 @@ implementation of the ASDF Standard.")
            python-pytest-astropy
            python-pytest-xdist
            python-scipy
-           python-setuptools-next
+           python-setuptools
            python-setuptools-scm
            python-wheel))
     (propagated-inputs
@@ -2073,7 +2073,7 @@ Astropy objects.")
             #:phases #~(modify-phases %standard-phases
                          (delete 'sanity-check))))
      (native-inputs
-      (list python-setuptools-next
+      (list python-setuptools
             python-wheel))
     (propagated-inputs
      (list python-importlib-metadata
@@ -2108,7 +2108,7 @@ Astropy objects.")
       (native-inputs
        (list python-numpy
              python-pytest
-             python-setuptools-next
+             python-setuptools
              python-setuptools-scm
              python-wheel))
       (propagated-inputs
@@ -2212,7 +2212,7 @@ up-front for extensibility.")
      (native-inputs
       (list python-asdf-bootstrap
             python-pytest
-            python-setuptools-next
+            python-setuptools
             python-setuptools-scm
             python-wheel))
      (propagated-inputs
@@ -2233,7 +2233,7 @@ implementation package such as asdf-astropy.")
             #:phases #~(modify-phases %standard-phases
                          (delete 'sanity-check))))
      (native-inputs
-      (list python-setuptools-next
+      (list python-setuptools
             python-wheel))
      (propagated-inputs '()))))
 
@@ -2256,7 +2256,7 @@ implementation package such as asdf-astropy.")
       (list python-asdf
             python-pytest
             python-pytest-openfiles
-            python-setuptools-next
+            python-setuptools
             python-setuptools-scm
             python-wheel))
      (propagated-inputs
@@ -2456,7 +2456,7 @@ astronomical images, especially when there is no WCS information available.")
            python-fsspec
            python-gwcs
            python-pillow
-           python-requests-next
+           python-requests
            python-roman-datamodels
            python-s3fs
            python-s3path
@@ -2685,8 +2685,12 @@ constraints (i.e., altitude, airmass, moon separation/illumination, etc.)
       #~(list "--pyargs" "astropy"
               ;; XXX: Tests are not thread save when they are more than 8.
               "--numprocesses" (number->string (min 8 (parallel-job-count)))
-              ;; Fails with  assert 13 == 1.
-              "-k" "not test_skip_meta")
+              "-k" (string-append
+                    ;; Fails with  assert 13 == 1.
+                    "not test_skip_meta"
+                    ;; Failed: DID NOT WARN. No warnings of type (<class
+                    ;; 'ResourceWarning'>,) were emitted.
+                    " and not test_ephemeris_local_file_not_ephemeris"))
       #:phases
       #~(modify-phases %standard-phases
           (add-after 'unpack 'preparations
@@ -2726,7 +2730,7 @@ constraints (i.e., altitude, airmass, moon separation/illumination, etc.)
            python-pytest-astropy-header
            python-pytest-doctestplus
            python-pytest-xdist
-           python-setuptools-scm-next
+           python-setuptools-scm
            python-sgp4
            python-skyfield
            python-threadpoolctl))
@@ -2795,7 +2799,10 @@ astronomy and astrophysics.")
            (with-directory-excursion "astropy/extern"
              (for-each delete-file-recursively '("ply" "configobj")))
            (with-directory-excursion "cextern"
-             (for-each delete-file-recursively '("expat" "wcslib")))))))))
+             (for-each delete-file-recursively '("expat" "wcslib")))))))
+    (propagated-inputs
+     (modify-inputs (package-propagated-inputs python-astropy)
+       (replace "python-jplephem" python-jplephem-2.22)))))
 
 (define-public python-astropy-healpix
   (package
@@ -2880,7 +2887,7 @@ celestial-to-terrestrial coordinate transformations.")
            pkg-config
            python-cython-3
            python-extension-helpers
-           python-setuptools-scm-next))
+           python-setuptools-scm))
     (propagated-inputs
      (list python-astropy-iers-data
            python-configobj      ;to replace custom module
@@ -3096,7 +3103,7 @@ Herschel.")
            python-pytest
            python-pytest-cov
            python-setuptools
-           python-setuptools-scm-next
+           python-setuptools-scm
            python-wheel))
     (propagated-inputs
      (list python-astropy
@@ -3134,7 +3141,7 @@ Origins Spectrograph}.")
     (native-inputs
      (list gfortran
            python-packaging
-           python-setuptools-next
+           python-setuptools
            python-wheel
            which)) ; for fortran/Makefile
     (propagated-inputs
@@ -3280,7 +3287,7 @@ bad pixel tracking throughout the reduction process.")
            python-pytest
            python-pytest-cov
            python-pytest-remotedata
-           python-setuptools-next
+           python-setuptools
            python-setuptools-scm
            python-xarray))
     (propagated-inputs
@@ -3366,8 +3373,8 @@ attempting to maintain ISTP compliance
     (native-inputs
      (list python-pytest-astropy-header
            python-pytest
-           python-setuptools-next
-           python-setuptools-scm-next
+           python-setuptools
+           python-setuptools-scm
            python-wheel))
     (propagated-inputs
      (list python-colorama
@@ -3674,7 +3681,7 @@ Spectrograph}.")
            python-pytest
            python-pytest-astropy
            python-pytest-doctestplus
-           python-setuptools-next
+           python-setuptools
            python-setuptools-scm
            python-stsynphot
            python-wheel))
@@ -3778,8 +3785,8 @@ Cesium.")
            python-pytest-mpl
            python-pytest-remotedata
            python-pytest-xdist
-           python-setuptools-next
-           python-setuptools-scm-next))
+           python-setuptools
+           python-setuptools-scm))
     (propagated-inputs
      (list python-aiohttp
            python-asdf
@@ -3836,8 +3843,9 @@ help you search, obtain and use DKIST data as part of your Python software.")
      (list python-astropy-minimal
            python-gwcs
            python-pytest
-           python-setuptools-next
-           python-setuptools-scm))
+           python-setuptools
+           python-setuptools-scm
+           python-wheel))
     (propagated-inputs
      (list python-numpy))
     (home-page "https://github.com/spacetelescope/drizzle")
@@ -3879,7 +3887,7 @@ code to be greatly simplified.")
            python-pytest
            python-pytest-remotedata
            python-setuptools
-           python-setuptools-scm-next
+           python-setuptools-scm
            python-wheel))
     (propagated-inputs
      (list python-astrocut
@@ -3895,7 +3903,7 @@ code to be greatly simplified.")
            python-photutils
            python-pypdf2
            python-regions
-           python-requests-next
+           python-requests
            python-scikit-image
            python-scikit-learn
            python-scipy
@@ -3933,7 +3941,7 @@ final image.")
      (list python-astropy-minimal
            python-pytest-astropy
            python-setuptools
-           python-setuptools-scm-next
+           python-setuptools-scm
            python-wheel))
     (propagated-inputs
      (list python-numpy
@@ -3962,7 +3970,7 @@ used with local NetDRMS sites.")
     (native-inputs
      (list python-pytest
            python-pytest-doctestplus
-           python-setuptools-next))
+           python-setuptools))
     (propagated-inputs
      (list python-astropy
            python-scipy))
@@ -3991,7 +3999,7 @@ implemented using the astropy.modeling framework.")
       #:tests? #f)) ;no tests in tarball
     (native-inputs
      (list python-pytest
-           python-setuptools-next))
+           python-setuptools))
     (propagated-inputs
      (list python-astropy
            python-fastapi
@@ -4027,10 +4035,23 @@ older EsoReflex environment.")
        (sha256
         (base32 "0rb0vc3kgmw5rzhfhxffg94bcwasm46sf814hv7l13ry8m7xckrw"))))
     (build-system pyproject-build-system)
+    (arguments
+     (list
+      #:test-flags
+      #~(list "--deselect=ephem/tests/test_jpl.py::JPLTest::runTest")
+      #:phases
+      #~(modify-phases %standard-phases
+          ;; XXX: See https://codeberg.org/guix/guix/issues/2108
+          (add-after 'install 'remove-installed-tests
+            (lambda* (#:key inputs outputs #:allow-other-keys)
+              (delete-file-recursively ".")
+              (mkdir-p "ephem")
+              (let* ((site (site-packages inputs outputs))
+                     (tests (string-append site "/ephem/tests")))
+                (copy-recursively tests "ephem/tests")
+                (delete-file-recursively tests)))))))
     (native-inputs
-     (list python-setuptools
-           python-wheel
-           tzdata))
+     (list python-pytest python-setuptools tzdata))
     (home-page "https://rhodesmill.org/pyephem/")
     (synopsis "Compute positions of the planets and stars")
     (description
@@ -4092,7 +4113,7 @@ tools for astronomers.")
     (native-inputs
      (list python-cython
            python-pytest
-           python-setuptools-next))
+           python-setuptools))
     (propagated-inputs
      (list python-numpy))
     (home-page "https://github.com/sncosmo/extinction")
@@ -4307,8 +4328,8 @@ astronomy-specific functionality")
     (native-inputs
      (list python-pytest
            python-pytest-mpl
-           python-setuptools-next
-           python-setuptools-scm-next))
+           python-setuptools
+           python-setuptools-scm))
     (propagated-inputs
      (list python-astrodendro
            python-astropy
@@ -4365,8 +4386,8 @@ across many files.")
     (native-inputs
      (list python-objgraph
            python-pytest
-           python-setuptools-next
-           python-setuptools-scm-next
+           python-setuptools
+           python-setuptools-scm
            xorg-server-for-tests))
     (propagated-inputs
      (list python-astropy
@@ -4490,8 +4511,10 @@ specifically pulsar timing array signals.")
     (native-inputs
      (list python-pytest
            python-pytest-astropy
-           python-setuptools-next
-           python-setuptools-scm-next))
+           python-pyyaml
+           python-setuptools
+           python-setuptools-scm
+           python-wheel))
     (propagated-inputs
      (list python-asdf
            python-asdf-astropy
@@ -4819,7 +4842,7 @@ observationally-derived galaxy merger catalogs.")
      (list ffmpeg
            python-pooch
            python-pytest-astropy
-           python-setuptools-next
+           python-setuptools
            python-setuptools-scm))
     (propagated-inputs
      (list python-dkist
@@ -4840,13 +4863,16 @@ satellite.")
 (define-public python-jplephem
   (package
     (name "python-jplephem")
-    (version "2.22")
+    (version "2.23")
     (source
      (origin
-       (method url-fetch)
-       (uri (pypi-uri "jplephem" version))
+       (method git-fetch)       ;no tests data in the PyPI tarball
+       (uri (git-reference
+              (url "https://github.com/brandon-rhodes/python-jplephem")
+              (commit version)))
+       (file-name (git-file-name name version))
        (sha256
-        (base32 "0b2rgb7pvwnl72pqjryf9c812mmdxr69fwiym7mnz05l2xrcr6hd"))))
+        (base32 "0mmd30cymb9f259c657d7jd65plirdsngnk14fbyjxd9vbryn2qa"))))
     (build-system pyproject-build-system)
     (arguments
      (list
@@ -4855,10 +4881,10 @@ satellite.")
           (replace 'check
             (lambda* (#:key tests? #:allow-other-keys)
               (when tests?
-                (invoke "python" "-m" "unittest" "discover" "-s" "test")))))))
+                (with-directory-excursion "ci"
+                  (invoke "python" "-m" "unittest" "test"))))))))
     (native-inputs
-     (list python-setuptools
-           python-wheel))
+     (list python-setuptools-next))
     (propagated-inputs
      (list python-numpy))
     (home-page "https://github.com/brandon-rhodes/python-jplephem")
@@ -4871,6 +4897,30 @@ Astronomical Almanac to within 0.0005 arcseconds (half a @emph{mas} or
 milliarcsecond).")
     (license license:expat)))
 
+;; The last compatible version for python-astropy-6.
+(define-public python-jplephem-2.22
+  (hidden-package
+   (package
+     (inherit python-jplephem)
+     (version "2.22")
+     (source
+      (origin
+        (method url-fetch)
+        (uri (pypi-uri "jplephem" version))
+        (sha256
+         (base32 "0b2rgb7pvwnl72pqjryf9c812mmdxr69fwiym7mnz05l2xrcr6hd"))))
+    (arguments
+     (list
+      #:phases
+      #~(modify-phases %standard-phases
+          (replace 'check
+            (lambda* (#:key tests? #:allow-other-keys)
+              (when tests?
+                (invoke "python" "-m" "unittest" "discover" "-s" "test")))))))
+    (native-inputs
+     (list python-setuptools
+           python-wheel)))))
+
 (define-public python-jwst
   (package
     (name "python-jwst")
@@ -4926,7 +4976,7 @@ milliarcsecond).")
            python-pytest-cov
            python-pytest-doctestplus
            python-requests-mock
-           python-setuptools-next
+           python-setuptools
            python-setuptools-scm
            python-wheel))
     (propagated-inputs
@@ -5452,7 +5502,7 @@ on:
            python-pytest-doctestplus
            python-pytest-mpl
            python-setuptools
-           python-setuptools-scm-next
+           python-setuptools-scm
            python-wheel))
     (propagated-inputs
      (list python-astropy
@@ -5550,7 +5600,7 @@ Carlo.")
            python-pytest-xdist
            python-scipy
            python-setuptools
-           python-setuptools-scm-next
+           python-setuptools-scm
            python-sunpy-minimal
            python-wheel))
     (propagated-inputs
@@ -6065,7 +6115,7 @@ position-frequency slice.")
            python-pandas
            python-pytest
            python-scipy
-           python-setuptools-next))
+           python-setuptools))
     (inputs
      (list cpl))
     (propagated-inputs
@@ -6144,7 +6194,7 @@ functions, so that they can be called with scalar or array inputs.")
     (build-system pyproject-build-system)
     (native-inputs
      (list python-pytest
-           python-setuptools-next))
+           python-setuptools))
     (propagated-inputs
      (list python-pycpl))
     (native-search-paths
@@ -6930,7 +6980,7 @@ PSF} describing how the optical system spreads light from sources.")
            python-pytest
            python-pytest-astropy
            python-pytest-xdist
-           python-setuptools-next
+           python-setuptools
            python-setuptools-scm
            python-stpreview))
     (propagated-inputs
@@ -7049,7 +7099,7 @@ well as ephemerides services
      (list python-cython
            python-pytest
            python-setuptools
-           python-setuptools-scm-next
+           python-setuptools-scm
            python-wheel))
     (propagated-inputs
      (list python-numpy))
@@ -7073,7 +7123,7 @@ well as ephemerides services
      (list python-cython
            python-pytest
            python-setuptools
-           python-setuptools-scm-next
+           python-setuptools-scm
            python-wheel))
     (propagated-inputs
      (list python-numpy
@@ -7471,7 +7521,7 @@ but has evolved to support other missions as well.")
               (setenv "NUMBA_CACHE_DIR" "/tmp"))))))
     (native-inputs
      (list ;; python-pytest
-           python-setuptools-next
+           python-setuptools
            python-wheel))
     (propagated-inputs
      (list python-astropy
@@ -7539,7 +7589,7 @@ Computing Cluster, HPCC}
     (native-inputs
      (list python-photutils
            python-pytest-astropy
-           python-setuptools-scm-next
+           python-setuptools-scm
            python-wheel))
     (propagated-inputs
      (list python-astropy
@@ -7756,7 +7806,7 @@ of axis order, spatial projections, and spectral units that exist in the wild.
     (native-inputs
      (list python-matplotlib
            python-pytest-astropy
-           python-setuptools-next
+           python-setuptools
            python-setuptools-scm
            python-spectral-cube))
     (propagated-inputs
@@ -7994,7 +8044,7 @@ and CAS statistics), as well as fitting 2D Sérsic profiles.")
            python-pytest
            python-pytest-xdist
            python-pytest-doctestplus
-           python-setuptools-next
+           python-setuptools
            python-setuptools-scm
            python-wheel))
     (propagated-inputs
@@ -8045,8 +8095,8 @@ and CAS statistics), as well as fitting 2D Sérsic profiles.")
            python-pytest-doctestplus
            python-pytest-xdist
            python-scipy
-           python-setuptools-next
-           python-setuptools-scm-next
+           python-setuptools
+           python-setuptools-scm
            python-wheel))
     (propagated-inputs
      (list python-asdf
@@ -8085,8 +8135,8 @@ implemented in the @acronym{JWST, James Webb Space Telescope} and
     (native-inputs
      (list python-pytest
            python-pytest-doctestplus
-           python-setuptools-next
-           python-setuptools-scm-next
+           python-setuptools
+           python-setuptools-scm
            python-wheel))
     (propagated-inputs
      (list python-asdf
@@ -8116,7 +8166,7 @@ implementing calibration pipeline software.")
     (native-inputs
      (list python-pytest
            python-roman-datamodels
-           python-setuptools-next
+           python-setuptools
            python-setuptools-scm
            python-wheel))
     (propagated-inputs
@@ -8153,7 +8203,7 @@ implementing calibration pipeline software.")
        ;; <https://github.com/spacetelescope/stpsf/issues/76>.
       #:tests? #f))
     (native-inputs
-     (list python-setuptools-next
+     (list python-setuptools
            python-setuptools-scm
            python-wheel))
     (propagated-inputs
@@ -8295,7 +8345,7 @@ spectra, and data.")
            python-pytest-doctestplus
            python-pytest-env
            python-pytest-xdist
-           python-setuptools-next
+           python-setuptools
            python-setuptools-scm
            python-wheel))
     (propagated-inputs
@@ -8342,8 +8392,8 @@ pipelines.")
               (invoke "python" "setup.py" "build_ext" "--inplace"))))))
     (native-inputs
      (list python-pytest
-           python-setuptools-next
-           python-setuptools-scm-next
+           python-setuptools
+           python-setuptools-scm
            python-wheel))
     (propagated-inputs
      (list python-numpy
@@ -8401,8 +8451,8 @@ task}.")
     (arguments
      (list #:tests? #f)) ; no tests in PyPI or git
     (native-inputs
-     (list python-setuptools-next
-           python-setuptools-scm-next))
+     (list python-setuptools
+           python-setuptools-scm))
     (propagated-inputs
      (list python-astropy
            python-numpy
@@ -8477,7 +8527,7 @@ processing functions: @code{xyxymatch}, @code{geomap}.")
            python-pytest-astropy-header
            python-pytest-doctestplus
            python-setuptools
-           python-setuptools-scm-next
+           python-setuptools-scm
            python-wheel))
     (propagated-inputs
      (list python-astropy
@@ -8585,7 +8635,7 @@ packages for HST.")
      (list nss-certs-for-test
            python-pytest
            python-setuptools
-           python-setuptools-scm-next
+           python-setuptools-scm
            python-wheel))
     (propagated-inputs
      (list python-astropy
@@ -8633,7 +8683,7 @@ Telescope, HST}).")
            python-pytest-mpl
            python-pytest-xdist
            python-setuptools
-           python-setuptools-scm-next
+           python-setuptools-scm
            python-wheel))
     (propagated-inputs
      (list python-astropy
@@ -8677,8 +8727,8 @@ Telescope, HST}).")
            python-pytest-doctestplus
            python-pytest-xdist
            python-reproject
-           python-setuptools-next
-           python-setuptools-scm-next
+           python-setuptools
+           python-setuptools-scm
            python-streamtracer
            python-sympy))
     (propagated-inputs
@@ -8734,7 +8784,7 @@ and @code{astropy}.")
           (delete 'sanity-check))))
     (native-inputs
      (list python-setuptools
-           python-setuptools-scm-next
+           python-setuptools-scm
            python-wheel))
     (propagated-inputs
      (list python-corner
@@ -8813,8 +8863,8 @@ SunPy.")
            python-pytest-mock
            python-pytest-mpl
            python-pytest-xdist
-           python-setuptools-next
-           python-setuptools-scm-next))
+           python-setuptools
+           python-setuptools-scm))
     (propagated-inputs
      (list python-asdf
            python-asdf-astropy
@@ -8836,7 +8886,7 @@ SunPy.")
            python-parfive
            python-pyerfa
            python-reproject
-           python-requests-next
+           python-requests
            python-scikit-image
            python-scipy
            ;; python-spiceypy ; Not packed yet in Guix, long journey.
@@ -8860,7 +8910,7 @@ to the SolarSoft data analysis environment.")
         ((#:tests? _ #t) #f)))
      (native-inputs
       (list python-setuptools
-            python-setuptools-scm-next
+            python-setuptools-scm
             python-wheel))
      (propagated-inputs
       (list python-astropy-minimal
@@ -8868,7 +8918,7 @@ to the SolarSoft data analysis environment.")
             python-mpl-animators
             python-parfive
             python-pyerfa
-            python-requests-next)))))
+            python-requests)))))
 
 (define-public python-sunpy-soar
   (package
@@ -8924,7 +8974,7 @@ to the SolarSoft data analysis environment.")
            python-pytest-doctestplus
            python-responses
            python-setuptools
-           python-setuptools-scm-next
+           python-setuptools-scm
            python-wheel))
     (propagated-inputs
      (list python-astropy
@@ -8968,8 +9018,8 @@ to the SolarSoft data analysis environment.")
            python-pytest-astropy
            python-pytest-doctestplus
            python-pytest-xdist
-           python-setuptools-next
-           python-setuptools-scm-next
+           python-setuptools
+           python-setuptools-scm
            python-sunpy-minimal))
     (propagated-inputs
      (list python-astropy
@@ -9075,8 +9125,8 @@ of the old packages.")
     (native-inputs
      (list python-pytest
            python-scipy
-           python-setuptools-next
-           python-setuptools-scm-next
+           python-setuptools
+           python-setuptools-scm
            python-wheel))
     (propagated-inputs
      (list python-astropy

gnu/packages/audio.scm

@@ -3616,8 +3616,25 @@ included are the command line utilities @code{send_osc} and @code{dump_osc}.")
               (base32
                "1rr2m8jxa5yxyb3pw6h93kvdxg7x0m6sxxxvgn34vq8k8mg1kz21"))))
     (build-system pyproject-build-system)
-    (native-inputs (list python-cython python-setuptools python-wheel))
-    (inputs (list liblo))
+    (arguments
+     (list
+      #:test-backend #~'custom
+      #:test-flags #~(list "test/unit.py")
+      #:phases
+      #~(modify-phases %standard-phases
+          ;; long is not available and replaced by int, proposed in
+          ;; <https://github.com/gesellkammer/pyliblo3/pull/15>.
+          (add-after 'unpack 'fix-compilation
+            (lambda _
+              (substitute* "pyliblo3/_liblo.pyx"
+                (("long\\(") "int(")
+                ((", long") "")))))))
+    (native-inputs
+     (list python-cython
+           python-setuptools
+           python-wheel))
+    (inputs
+     (list liblo))
     (home-page "https://github.com/gesellkammer/pyliblo3")
     (synopsis "Python bindings for liblo")
     (description
@@ -3760,7 +3777,7 @@ files.")
     (native-inputs
      (list python-pytest
            python-pytest-cov
-           python-setuptools-next))
+           python-setuptools))
     (inputs
      (list libsndfile
            portaudio))
@@ -5715,6 +5732,8 @@ loudness of audio and video files to the same level.")
     (license license:gpl2+)))
 
 (define-public r128gain
+  ;; XXX: Upstream notice: This project was archived by the owner on Aug 17,
+  ;; 2023. It is now read-only.
   (package
     (name "r128gain")
     (version "1.0.7")
@@ -5730,6 +5749,7 @@ loudness of audio and video files to the same level.")
     (build-system pyproject-build-system)
     (arguments
        (list
+        #:tests? #f ;require a complex set up, see <.github/workflows/ci.yml>.
         #:phases
         #~(modify-phases %standard-phases
             (add-after 'unpack 'hardcode-ffmpeg
@@ -5743,8 +5763,7 @@ loudness of audio and video files to the same level.")
                   python-tqdm ffmpeg))
     (native-inputs (list python-future
                          python-requests
-                         python-setuptools
-                         python-wheel))
+                         python-setuptools))
     (home-page "https://github.com/desbma/r128gain")
     (synopsis "Fast audio loudness scanner & tagger")
     (description

gnu/packages/bioinformatics.scm

@@ -4742,35 +4742,30 @@ high-throughput sequencing of B cell and T cell repertoires.")
   (package
     (name "python-changeo")
     (version "1.3.4")
-    (home-page "https://github.com/immcantation/changeo")
     (source
      (origin
-       (method git-fetch)
-       (uri (git-reference
-              (url home-page)
-              (commit version)))
-       (file-name (git-file-name name version))
+       (method url-fetch)
+       (uri (pypi-uri "changeo" version))
        (sha256
-        (base32
-         "1230bb7672n6nqkrw2fvrprknchhlvvxb76l1r4g6ybrq0g7l0rb"))))
+        (base32 "0jm4chddpl929a8daicp9mv14nwzf2hajpjfhzckg6x8cpgc1087"))))
     (build-system pyproject-build-system)
+    (arguments
+     (list
+      #:build-backend "setuptools.build_meta"))
+    (native-inputs
+     (list python-pytest
+           python-setuptools))
     (propagated-inputs
      (list python-airr
            python-biopython
-           python-importlib-resources-6
+           python-importlib-resources
            python-numpy
            python-packaging
            python-pandas
            python-presto
            python-pyyaml
            python-scipy))
-    (native-inputs
-     (list python-airr
-           python-setuptools
-           python-wheel))
-    (arguments
-     (list
-      #:build-backend "setuptools.build_meta"))
+    (home-page "http://changeo.readthedocs.io")
     (synopsis "Repertoire clonal assignment toolkit")
     (description "Change-O is a collection of tools for processing the output
 of V(D)J alignment tools, assigning clonal clusters to immunoglobulin (Ig)
@@ -25694,7 +25689,7 @@ exclude =
     (inputs
      (cons python-wrapper (cargo-inputs 'python-gseapy)))
     (native-inputs
-     (list python-pytest python-wheel))
+     (list python-pytest python-setuptools))
     (propagated-inputs
      (list python-numpy
            python-scipy

gnu/packages/calendar.scm

@@ -248,8 +248,8 @@ data units.")
            python-importlib-metadata
            python-packaging
            python-pytest
-           python-setuptools-next
-           python-setuptools-scm-next
+           python-setuptools
+           python-setuptools-scm
            python-sphinx
            python-sphinxcontrib-newsfeed
            python-wheel))

gnu/packages/check.scm

@@ -777,7 +777,6 @@ pattern.")
 a multi-paradigm automated test framework for C++ and Objective-C.")
     (license license:boost1.0)))
 
-
 (define-public catch2-3
   (package
     (inherit catch2-3.8)
@@ -793,35 +792,6 @@ a multi-paradigm automated test framework for C++ and Objective-C.")
                (base32
                 "11yla93vm2896fzhm3fz8lk3y3iz5iy7vd6wa7wnwvhsfd2dbfq3"))))))
 
-(define-public cmdtest
-  (package
-    (name "cmdtest")
-    ;; Use the latest commit (from 2019) in order to get Python 3 support.
-    (version "0.32-14-gcdfe14e")
-    (source (origin
-              (method git-fetch)
-              (uri (git-reference
-                    (url "git://git.liw.fi/cmdtest/")
-                    (commit version)))
-              (file-name (git-file-name name version))
-              (sha256
-               (base32
-                "1yhcwsqcpckkq5kw3h07k0xg6infyiyzq9ni3nqphrzxis7hxjf1"))))
-    (build-system python-build-system)
-    (arguments `(#:tests? #f))          ;requires Python 2!
-    (native-inputs
-     (list python-coverage-test-runner python))
-    (inputs
-     (list python-cliapp python-markdown python-ttystatus))
-    (home-page "https://liw.fi/cmdtest/")
-    (synopsis "Black box Unix program tester")
-    (description
-     "@code{cmdtest} black box tests Unix command line tools.  Roughly, it is
-given a command line and input files, and the expected output, and it verifies
-that the command line produces the expected output.  If not, it reports a
-problem, and shows the differences.")
-    (license license:gpl3+)))
-
 (define-public cmocka
   (package
     (name "cmocka")
@@ -1089,44 +1059,6 @@ definition language, a safe runtime engine for test suites and a powerful
 report generation engine.")
     (license license:bsd-3)))
 
-(define-public python-gixy-ng
-  (package
-    (name "python-gixy-ng")
-    (version "0.2.7")
-    (source
-     (origin
-       (method git-fetch)
-       (uri (git-reference
-             (url "https://github.com/dvershinin/gixy")
-             (commit (string-append "v" version))))
-       (file-name (git-file-name name version))
-       (sha256
-        (base32 "0dipvy8y1nlhpka0cdk6hyv1j2388y7isbajpwskjrgqc5vayqx8"))))
-    (build-system pyproject-build-system)
-    ;; This package currently doesn't test properly, but we can't add
-    ;; pytest because it propagates another version of python-pyparsing
-    ;; that takes precedence over the right one.
-    (propagated-inputs (list python-configargparse
-                             python-jinja2
-                             python-pyparsing-2.4.7
-                             python-six))
-    (native-inputs (list python-cached-property
-                         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.
-
-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
     (name "googletest")
@@ -1625,36 +1557,6 @@ better plugin api, being easier for users to configure, and simplifying internal
 interfaces and processes.")
     (license license:bsd-2)))
 
-(define-public python-unittest2
-  (package
-    (name "python-unittest2")
-    (version "1.1.0")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (pypi-uri "unittest2" version))
-       (patches
-        (search-patches "python-unittest2-python3-compat.patch"
-                        "python-unittest2-remove-argparse.patch"))
-       (sha256
-        (base32
-         "0y855kmx7a8rnf81d3lh5lyxai1908xjp0laf4glwa4c8472m212"))))
-    (build-system python-build-system)
-    (arguments
-     '(#:phases
-       (modify-phases %standard-phases
-         (replace 'check
-           (lambda _
-             (zero? (system* "python" "-m" "unittest2" "discover" "--verbose")))))))
-    (propagated-inputs
-     (list python-six python-traceback2))
-    (home-page "https://pypi.org/project/unittest2/")
-    (synopsis "Python unit testing library")
-    (description
-     "Unittest2 is a replacement for the unittest module in the Python
-standard library.")
-    (license license:psfl)))
-
 (define-public python-pytest
   (package
     (name "python-pytest")
@@ -2206,6 +2108,7 @@ timeout has been exceeded.")
      ;; to fail (see: https://github.com/pytest-dev/pytest-forked/issues/54).
      (list python-pytest-bootstrap python-setuptools
            python-setuptools-scm python-wheel))
+    (propagated-inputs (list python-py))
     (home-page "https://github.com/pytest-dev/pytest-forked")
     (synopsis "Pytest plugin to run tests in isolated forked subprocesses")
     (description "This package provides a Pytest plugin which enables running
@@ -2237,268 +2140,241 @@ command-line applications.  With it you can run a script in a subprocess and
 see the output as well as any file modifications.")
     (license license:expat)))
 
-(define-public python-testtools-bootstrap
+(define-public python-testtools
   (package
-    (name "python-testtools-bootstrap")
+    (name "python-testtools")
     (version "2.7.2")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "testtools" version))
        (sha256
-        (base32
-         "18vy77n4ab2dvgx5ni6gfp2d0haxhh3yrkm6mih8n3zsy30vprav"))))
+        (base32 "18vy77n4ab2dvgx5ni6gfp2d0haxhh3yrkm6mih8n3zsy30vprav"))))
     (build-system pyproject-build-system)
-    (arguments (list #:tests? #f))
-    (propagated-inputs
-     (list python-fixtures-bootstrap python-pbr-minimal))
-    (native-inputs
-     (list python-hatchling python-hatch-vcs
-           python-setuptools)) ;due to python-pbr-minimal
-    (home-page "https://github.com/testing-cabal/testtools")
-    (synopsis
-     "Extensions to the Python standard library unit testing framework")
-    (description
-     "This package is only for bootstrapping.  Do not use this.")
-    (license license:psfl)))
-
-(define-public python-testtools
-  (package
-    (inherit python-testtools-bootstrap)
-    (name "python-testtools")
     (arguments
      (list
+      #:test-backend #~'custom
+      #:test-flags #~(list "-m" "testtools.run" "testtools.tests.test_suite")
       #:phases
-      '(modify-phases %standard-phases
-         (replace 'check
-           (lambda* (#:key tests? #:allow-other-keys)
-             (when tests?
-               ;; There are six failing tests:
-               ;; "test_fast_keyboard_interrupt_stops_test_run"
-               ;; "test_keyboard_interrupt_stops_test_run"
-               ;; "test_fast_sigint_raises_no_result_error"
-               ;; "test_fast_sigint_raises_no_result_error_second_time"
-               ;; "test_sigint_raises_no_result_error"
-               ;; "test_sigint_raises_no_result_error_second_time"
-               (substitute* "testtools/tests/twistedsupport/__init__.py"
-                 (("test_spinner,") "")
-                 (("test_runtest,") ""))
-               (invoke "python" "-m" "testtools.run"
-                       "testtools.tests.test_suite")))))))
-    (propagated-inputs
-     (list python-fixtures python-pbr))
+      #~(modify-phases %standard-phases
+          (add-before 'check 'pre-check
+            (lambda _
+              ;; There are six failing tests:
+              ;; "test_fast_keyboard_interrupt_stops_test_run"
+              ;; "test_keyboard_interrupt_stops_test_run"
+              ;; "test_fast_sigint_raises_no_result_error"
+              ;; "test_fast_sigint_raises_no_result_error_second_time"
+              ;; "test_sigint_raises_no_result_error"
+              ;; "test_sigint_raises_no_result_error_second_time"
+              (substitute* "testtools/tests/twistedsupport/__init__.py"
+                (("test_spinner,") "")
+                (("test_runtest,") "")))))))
     (native-inputs
-     (list python-hatchling python-hatch-vcs
-           python-testscenarios-bootstrap
+     (list python-hatch-vcs
+           python-hatchling
            python-twisted
-           python-setuptools)) ;due to python-pbr
+           python-testscenarios-bootstrap))
+    (propagated-inputs
+     (list python-fixtures))
+    (home-page "https://github.com/testing-cabal/testtools")
+    (synopsis "Extensions to the Python standard library unit testing framework")
     (description
      "Testtools extends the Python standard library unit testing framework to
 provide matchers, more debugging information, and cross-Python
-compatibility.")))
+compatibility.")
+    (license license:expat)))
 
-(define-public python-testscenarios-bootstrap
+(define-public python-testtools-bootstrap
+  (hidden-package
+   (package/inherit python-testtools
+     (arguments
+      ;; To break cycle with python-fixtures.
+      (list #:tests? #f))
+     (propagated-inputs '()))))
+
+;; XXX: The project is not maintained since 2015, consider to remove when
+;; nothing depends on it.
+(define-public python-testscenarios
   (package
-    (name "python-testscenarios-bootstrap")
+    (name "python-testscenarios")
     (version "0.5.0")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "testscenarios" version))
        (sha256
-        (base32
-         "1dm2aydqpv76vnsk1pw7k8n42hq58cfi4n1ixy7nyzpaj1mwnmy2"))))
-    (build-system python-build-system)
+        (base32 "1dm2aydqpv76vnsk1pw7k8n42hq58cfi4n1ixy7nyzpaj1mwnmy2"))))
+    (build-system pyproject-build-system)
     (arguments
-     `(#:phases (modify-phases %standard-phases
-                  (replace 'check
-                    (lambda _
-                      (invoke "python" "-m" "testtools.run"
-                              "testscenarios.test_suite"))))))
+     (list
+      #:test-backend #~'custom
+      #:test-flags #~(list "-m" "testtools.run" "testscenarios.test_suite")))
+    (native-inputs
+     (list python-setuptools))
     (propagated-inputs
-     `(("python-pbr" ,python-pbr-minimal)
-       ("python-testtools" ,python-testtools-bootstrap)))
+     (list python-pbr
+           python-testtools))
     (home-page "https://launchpad.net/testscenarios")
     (synopsis "Pyunit extension for dependency injection")
-    (description
-     "This package is only for bootstrapping.  Don't use this.")
-    (license (list license:bsd-3 license:asl2.0)))) ; at the user's option
-
-(define-public python-testscenarios
-  (package
-    (inherit python-testscenarios-bootstrap)
-    (name "python-testscenarios")
-    (propagated-inputs
-     (list python-pbr python-testtools))
     (description
      "Testscenarios provides clean dependency injection for Python unittest
-style tests.")))
-
-;; Testresources requires python-pbr at runtime, but pbr needs it for its
-;; own tests.  Hence this bootstrap variant.
-(define-public python-testresources-bootstrap
-  (package
-    (name "python-testresources-bootstrap")
-    (version "2.0.1")
-    (source (origin
-              (method url-fetch)
-              (uri (pypi-uri "testresources" version))
-              (sha256
-               (base32
-                "05s4dsli9g17m1r3b1gvwicbbgq011hnpb2b9qnj27ja2n11k7gf"))))
-    (build-system python-build-system)
-    (arguments '(#:tests? #f))
-    (propagated-inputs
-     `(("python-pbr" ,python-pbr-minimal)))
-    (home-page "https://launchpad.net/testresources")
-    (synopsis
-     "Pyunit extension for managing test resources")
-    (description
-     "This package is only here for bootstrapping purposes.  Use the regular
-testresources package instead.")
+style tests.")
     (license (list license:bsd-3 license:asl2.0)))) ; at the user's option
 
+(define-public python-testscenarios-bootstrap
+  (hidden-package
+   (package/inherit python-testscenarios
+     (arguments
+      ;; To break cycle with python-testtols and python-subunit.
+      (list #:tests? #f
+            #:phases
+            #~(modify-phases %standard-phases
+                (delete 'sanity-check))))
+     (propagated-inputs
+      (list python-pbr)))))
+
 (define-public python-testresources
   (package
-    (inherit python-testresources-bootstrap)
     (name "python-testresources")
+    (version "2.0.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "testresources" version))
+       (sha256
+        (base32 "1v7a3mzi461v4cw4qil094j39wzn8hk10jkm9gi9ybmb01z3vgrc"))))
+    (build-system pyproject-build-system)
+    (arguments
+     (list
+      #:test-backend #~'custom
+      #:test-flags #~(list "-m" "testtools.run" "discover")))
+    (native-inputs
+     (list python-fixtures
+           python-setuptools
+           python-testtools))
     (propagated-inputs
      (list python-pbr))
-    (arguments '())
-    (native-inputs
-     (list python-fixtures python-testtools))
+    (home-page "https://github.com/testing-cabal/testresources")
+    (synopsis "Pyunit extension for managing test resources")
     (description
      "Testresources is an extension to Python's unittest to allow declarative
-use of resources by test cases.")))
+use of resources by test cases.")
+    (license (list license:bsd-3 license:asl2.0)))) ; at the user's option
 
-(define-public python-subunit-bootstrap
+(define-public python-subunit
   (package
-    (name "python-subunit-bootstrap")
-    (version "1.4.0")
+    (name "python-subunit")
+    (version "1.4.4")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "python-subunit" version))
        (sha256
-        (base32
-         "0j0ymmnc5nfxi1qzvy59j27viqca7l7xd0y9x29g7yr0h693j804"))))
-    (build-system python-build-system)
-    (propagated-inputs
-     (list python-extras python-testtools-bootstrap))
+        (base32 "0d7arni5h98x7mpgpv90bzipf6p6q9djcdwj4m2ky7da64qkcy8h"))))
+    (build-system pyproject-build-system)
+    (arguments
+     (list
+      #:test-backend #~'custom
+      #:test-flags #~(list "-m" "testtools.run" "subunit.test_suite")
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-after 'unpack 'disable-failing-tests
+            (lambda _
+              ;; There are two failing tests:
+              ;; subunit.tests.test_test_protocol.TestExecTestCase.test_args
+              ;; AssertionError: 1 != 0
+              ;;
+              ;; subunit.tests.test_test_protocol.TestExecTestCase.test_run
+              ;; AssertionError: Lists differ: [('startTest',
+              ;; <subunit.RemotedTestCase de[666 chars]r'>)] != []
+              (substitute* "python/subunit/tests/test_test_protocol.py"
+                (("test_args") "_off_test_args")
+                (("test_run") "_off_test_run"))))
+          (add-after 'disable-failing-tests 'disable-failing-console-scripts
+            (lambda _
+              (substitute* "setup.py"
+                ;; Requries not maintained python-junitxml.
+                (("'subunit2junitxml=.*subunit2junitxml:main',") "")
+                ;; To avoid Gtk in inputs.
+                (("'subunit-notify=.*subunit_notify:main',") "")
+                (("'subunit2gtk=.*subunit2gtk:main',") "")))))))
     (native-inputs
-     (list python-fixtures-bootstrap python-hypothesis
-           python-testscenarios-bootstrap))
-    (home-page "https://launchpad.net/subunit")
+     (list python-fixtures
+           python-setuptools
+           python-testscenarios))
+    (propagated-inputs
+     (list python-iso8601
+           python-pygobject
+           python-testtools))
+    (home-page "https://github.com/testing-cabal/subunit")
     (synopsis "Python implementation of the subunit protocol")
-    (description
-     "This package is here for bootstrapping purposes only.  Use the regular
-python-subunit package instead.")
-    (license (list license:bsd-3 license:asl2.0)))) ; at the user's option
-
-(define-public python-subunit
-  (package
-    (inherit python-subunit-bootstrap)
-    (name "python-subunit")
-    (propagated-inputs
-     (list python-extras python-testtools))
-    (native-inputs
-     (list python-fixtures python-hypothesis python-testscenarios))
     (description
      "Python-subunit is a Python implementation of the subunit test streaming
-protocol.")))
-
-;; Fixtures requires python-pbr at runtime, but pbr uses fixtures for its
-;; own tests.  Hence this bootstrap variant.
-(define-public python-fixtures-bootstrap
-  (package
-    (name "python-fixtures-bootstrap")
-    (version "3.0.0")
-    (source
-      (origin
-        (method url-fetch)
-        (uri (pypi-uri "fixtures" version))
-        (sha256
-         (base32
-          "1vxj29bzz3rd4pcy51d05wng9q9dh4jq6wx92yklsm7i6h1ddw7w"))
-        (patches (search-patches "python-fixtures-remove-monkeypatch-test.patch"))))
-    (build-system python-build-system)
-    (arguments
-      `(#:tests? #f
-        #:phases
-         (modify-phases %standard-phases
-           ;; Package is not loadable on its own at this stage.
-           (delete 'sanity-check))))
-    (propagated-inputs
-     (list python-pbr-minimal python-six python-extras))
-    (home-page "https://launchpad.net/python-fixtures")
-    (synopsis "Python test fixture library")
-    (description
-     "This package is only used for bootstrapping.  Use the regular
-python-fixtures package instead.")
-    (license (list license:bsd-3 license:asl2.0)))) ; at user's option
+protocol.")
+    (license (list license:bsd-3 license:asl2.0)))) ; at the user's option
 
 (define-public python-fixtures
   (package
-    (inherit python-fixtures-bootstrap)
     (name "python-fixtures")
-    (arguments
-     '(#:phases
-       (modify-phases %standard-phases
-         (replace 'check
-           (lambda* (#:key tests? #:allow-other-keys)
-             (when tests?
-               (invoke "python" "-m" "testtools.run"
-                       "fixtures.test_suite")))))))
-    (propagated-inputs
-     ;; Fixtures uses pbr at runtime to check versions, etc.
-     (list python-pbr python-six python-extras))
+    (version "4.2.6")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "fixtures" version))
+       (sha256
+        (base32 "02y92rnl2vyjcbc31mcpxkxjky6g9hjb2cxy5xkkl1j5n4ajniwm"))))
+    (build-system pyproject-build-system)
     (native-inputs
-     `(("python-mock" ,python-mock)
-       ("python-testtools" ,python-testtools-bootstrap)))
+     (list python-hatch-vcs
+           python-hatchling
+           python-testtools-bootstrap))
+    (home-page "https://github.com/testing-cabal/fixtures")
+    (synopsis "Python test fixture library")
     (description
      "Fixtures provides a way to create reusable state, useful when writing
-Python tests.")))
+Python tests.")
+    (license (list license:bsd-3 license:asl2.0)))) ; at user's option
 
-(define-public python-testrepository-bootstrap
+(define-public python-testrepository
   (package
-    (name "python-testrepository-bootstrap")
-     (version "0.0.20")
+    (name "python-testrepository")
+    (version "0.0.21")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "testrepository" version))
        (sha256
-        (base32
-         "1ssqb07c277010i6gzzkbdd46gd9mrj0bi0i8vn560n2k2y4j93m"))))
-    (build-system python-build-system)
-    (arguments '(#:tests? #f))
-    (propagated-inputs
-     `(("python-fixtures" ,python-fixtures-bootstrap)
-       ("python-subunit" ,python-subunit-bootstrap)
-       ("python-testtools" ,python-testtools-bootstrap)))
+        (base32 "1nd36zf1gz7rp5qqqvw15d8lwcdwcigs4m6ppn4cdcwhw3vzr2in"))))
+    (build-system pyproject-build-system)
+    (arguments
+     (list
+      #:phases
+      #~(modify-phases %standard-phases
+          (replace 'check
+            (lambda* (#:key tests? #:allow-other-keys)
+              (when tests?
+                (setenv "HOME" "/tmp")
+                (invoke "./testr" "init")
+                (invoke "./testr" "run")))))))
     (native-inputs
-     (list python-mimeparse))
-    (home-page "https://launchpad.net/testrepository")
+     (list python-hatch-vcs
+           python-hatchling
+           python-pytz
+           python-setuptools
+           python-testresources
+           python-testscenarios))
+    (propagated-inputs
+     (list python-fixtures
+           python-iso8601
+           python-subunit))
+    (home-page "https://github.com/testing-cabal/testrepository")
     (synopsis "Database for Python test results")
     (description
-     "Bootstrap package for python-testrepository.  Don't use this.")
+     "Testrepository provides a database of test results which can be used as
+part of a developer's workflow to check things such as what tests have failed
+since the last commit or what tests are currently failing.")
     (license (list license:bsd-3 license:asl2.0)))) ; at user's option
 
-(define-public python-testrepository
-  (package
-    (inherit python-testrepository-bootstrap)
-    (name "python-testrepository")
-    (arguments
-     ;; FIXME: Many tests are failing.
-     '(#:tests? #f))
-    (propagated-inputs
-     (list python-fixtures python-subunit python-testtools))
-    (native-inputs
-     (list python-mimeparse))
-    (description "Testrepository provides a database of test results which can
-be used as part of a developer's workflow to check things such as what tests
-have failed since the last commit or what tests are currently failing.")))
-
 (define-public python-coverage
   (package
     (name "python-coverage")
@@ -2705,26 +2581,6 @@ and commands.  It contains functions to check things on the file system, and
 tools for mocking system commands and recording calls to those.")
     (license license:expat)))
 
-;;; The software provided by this package was integrated into pytest 2.8.
-(define-public python-pytest-cache
-  (package
-    (name "python-pytest-cache")
-    (version "1.0")
-    (source (origin
-             (method url-fetch)
-             (uri (pypi-uri "pytest-cache" version))
-             (sha256
-              (base32
-               "1a873fihw4rhshc722j4h6j7g3nj7xpgsna9hhg3zn6ksknnhx5y"))))
-    (build-system python-build-system)
-    (propagated-inputs
-     (list python-apipkg python-execnet python-py python-pytest))
-    (synopsis "Py.test plugin with mechanisms for caching across test runs")
-    (description "The pytest-cache plugin provides tools to rerun failures from
-the last py.test invocation.")
-    (home-page "https://bitbucket.org/hpk42/pytest-cache/")
-    (license license:expat)))
-
 (define-public python-pytest-localserver
   (package
     (name "python-pytest-localserver")
@@ -2836,24 +2692,9 @@ instantly.")
 much larger range of examples than you would ever want to write by hand.  It’s
 based on the Haskell library, Quickcheck, and is designed to integrate
 seamlessly into your existing Python unit testing work flow.")
-    (home-page "https://hypothesis.works/")
     (license license:mpl2.0)))
 
-(define-public python-hypothesis-next
-  (package
-    (inherit python-hypothesis)
-    (name "python-hypothesis")
-    (version "6.131.8")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (pypi-uri "hypothesis" version))
-       (sha256
-        (base32 "1wx4ii5dxfp9gajfb5bqd3a2d1a38rbmvb620kj0cvlyvxkv5nk8"))))
-    (build-system pyproject-build-system)
-    (native-inputs
-     (list python-setuptools-next
-           python-wheel))))
+(define-public python-hypothesis-next python-hypothesis)
 
 ;; WARNING: This package is a dependency of mesa.
 (define-public python-lit
@@ -3210,29 +3051,6 @@ pragmas to control it from within your code.  Additionally, it is
 possible to write plugins to add your own checks.")
     (license license:gpl2+)))
 
-(define-public python-nosexcover
-  (package
-    (name "python-nosexcover")
-    (version "1.0.11")
-    (source (origin
-              (method url-fetch)
-              (uri (pypi-uri "nosexcover" version))
-              (sha256
-               (base32
-                "10xqr12qv62k2flxwqhh8cr00cjhn7sfjrm6p35gd1x5bmjkr319"))))
-    (build-system python-build-system)
-    (propagated-inputs
-     (list python-coverage python-nose))
-    (home-page "https://github.com/cmheisel/nose-xcover")
-    (synopsis "Extends nose.plugins.cover to add Cobertura-style XML reports")
-    (description "Nose-xcover is a companion to the built-in
-@code{nose.plugins.cover}.  This plugin will write out an XML coverage report
-to a file named coverage.xml.
-
-It will honor all the options you pass to the Nose coverage plugin,
-especially -cover-package.")
-    (license license:expat)))
-
 (define-public python-discover
   (package
     (name "python-discover")
@@ -3326,40 +3144,6 @@ tests written in a natural language style, backed up by Python code.")
 JSON APIs with Behave.")
     (license license:expat)))
 
-(define-public python-nose-exclude
-  (package
-    (name "python-nose-exclude")
-    (version "0.5.0")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (pypi-uri "nose-exclude" version))
-       (sha256
-        (base32 "0123x1lyv5b2p9civcfg8vilj2ga3q7p2ks1hq25z0gb3ssai3zp"))))
-    (build-system pyproject-build-system)
-    (arguments
-     (list
-      #:phases
-      #~(modify-phases %standard-phases
-          (add-before 'check 'disable-test
-            (lambda _
-              ;; Disable failing test: AssertionError.
-              (substitute* '("test_dirs/build/test.py"
-                            "test_dirs/test_not_me/test.py")
-                (("def test_i_should_never_run")
-                 "def off_i_should_never_run")))))))
-    (native-inputs
-     (list python-setuptools
-           python-wheel))
-    (propagated-inputs
-     (list python-nose))
-    (home-page "https://github.com/kgrandis/nose-exclude")
-    (synopsis "Exclude specific directories from nosetests runs")
-    (description
-     "@code{nose-exclude} is a Nose plugin that allows you to easily specify
-directories to be excluded from testing.")
-    (license license:lgpl2.1+)))
-
 (define-public python-nose-timer
   (package
     (name "python-nose-timer")

gnu/packages/code.scm

@@ -1118,7 +1118,7 @@ expressions, and its ability to generate emacs-style TAGS files.")
     ;; network access.
     (arguments (list #:tests? #f))
     (native-inputs
-     (list python-setuptools-next))
+     (list python-setuptools))
     (inputs
      (list python-pyyaml
            python-radon

gnu/packages/digest.scm

@@ -106,20 +106,24 @@ platforms (both big and little endian).")
 (define-public python-xxhash
   (package
     (name "python-xxhash")
-    (version "3.1.0")
+    (version "3.5.0")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "xxhash" version))
        (sha256
-        (base32
-         "1hdxcscry59gh0znlm71ya23mm9rfmvz8lvvlplzxzf63pib28dc"))))
+        (base32 "0pxlc37x0rrw3vl8yhf638wqcpfg9jfsh8ifvkwcpjaiz7fwmwl4"))))
     (build-system pyproject-build-system)
-    ;; Needed to embed the correct version string
+    (arguments
+     (list
+      #:test-backend #~'unittest
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-before 'check 'build-extensions
+            (lambda _
+              (invoke "python" "setup.py" "build_ext" "--inplace"))))))
     (native-inputs
-     (list python-setuptools-scm
-           python-setuptools
-           python-wheel))
+     (list python-setuptools))
     (home-page "https://github.com/ifduyue/python-xxhash")
     (synopsis "Python binding for xxHash")
     (description "This package provides Python bindings for the xxHash hash

gnu/packages/disk.scm

@@ -1698,41 +1698,6 @@ and a partitioning of the heap between kinds of memory (for NUMA).")
 inspecting MMC storage devices from userspace.")
       (license license:gpl2))))
 
-(define-public bmaptools
-  (package
-    (name "bmaptools")
-    (version "3.6")
-    (source (origin
-              (method git-fetch)
-              (uri (git-reference
-                    (url "https://github.com/intel/bmap-tools")
-                    (commit (string-append "v" version))))
-              (file-name (git-file-name name version))
-              (sha256
-               (base32
-                "01xzrv5nvd2nvj91lz4x9s91y9825j9pj96z0ap6yvy3w2dgvkkl"))))
-    (build-system python-build-system)
-    (arguments
-     '(#:phases
-       (modify-phases %standard-phases
-         (replace 'check
-           (lambda _
-             ;; XXX: Remove failing test.
-             (invoke "nosetests" "-v"
-                     "--exclude" "test_bmap_helpers"))))))
-    (native-inputs
-     (list python-mock python-nose))
-    (propagated-inputs
-     (list python-six))
-    (home-page "https://github.com/intel/bmap-tools")
-    (synopsis "Create block map for a file or copy a file using block map")
-    (description "Bmaptool is a tool for creating the block map (bmap) for a
-file and copying files using the block map.  The idea is that large files,
-like raw system image files, can be copied or flashed a lot faster and more
-reliably with @code{bmaptool} than with traditional tools, like @code{dd} or
-@code{cp}.")
-    (license license:gpl2)))
-
 (define-public duc
   (package
     (name "duc")

gnu/packages/django.scm

@@ -327,7 +327,7 @@ and adapters that are useful for non-trivial configuration scenarios.")
            python-pytest
            python-pytest-cov ; runs by default
            python-pytest-django
-           python-setuptools-next
+           python-setuptools
            python-shortuuid
            python-wheel))
     (home-page "https://github.com/django-extensions/django-extensions")
@@ -1026,7 +1026,7 @@ to asyncio and Pydantic.")
                 (invoke "django-admin" "test" "tests"
                         "--pythonpath=.")))))))
     (propagated-inputs (list python-asgiref python-django))
-    (native-inputs (list python-pytest python-setuptools-next python-wheel))
+    (native-inputs (list python-pytest python-setuptools python-wheel))
     (home-page "https://django-htmx.readthedocs.io/en/latest/")
     (synopsis "Extensions for using Django with htmx")
     (description "This package provides a Django extension to work with

gnu/packages/electronics.scm

@@ -1241,7 +1241,7 @@ verification.")
      (list iverilog
            nvc
            python-pytest
-           python-setuptools-next))
+           python-setuptools))
     (propagated-inputs
      (list python-find-libpython))
     (home-page "https://github.com/cocotb/cocotb")
@@ -1285,7 +1285,7 @@ and Verilog RTL using Python.")
        (list iverilog
              nvc
              python-pytest
-             python-setuptools-next))
+             python-setuptools))
       (propagated-inputs
        (list python-cocotb
              python-packaging
@@ -1323,7 +1323,7 @@ and reusable bus interfaces to be used with @code{cocotb}.")
                           "test_xcelium")
                     " and not "))))
     (native-inputs
-     (list python-pytest python-setuptools-next))
+     (list python-pytest python-setuptools))
     (propagated-inputs
      (list python-jinja2))
     (home-page "https://github.com/olofk/edalize/")
@@ -1359,7 +1359,7 @@ some tool-specific options are set.")
                                       (lambda _
                                         (chdir "testsuite"))))
                        #:test-flags #~(list "test_all.py")))
-      (native-inputs (list python-pytest python-setuptools-next))
+      (native-inputs (list python-pytest python-setuptools))
       (propagated-inputs (list python-networkx python-six))
       (home-page "https://ohwr.gitlab.io/project/hdl-make/")
       (synopsis "Generate multi-purpose makefiles for HDL projects")
@@ -1391,7 +1391,7 @@ and simulation Makefiles.")
       (build-system pyproject-build-system)
       (native-inputs
        (list python-pytest
-             python-setuptools-next))
+             python-setuptools))
       (propagated-inputs
        (list python-colorama))
       (home-page "https://m-labs.hk/gateware/migen/")
@@ -1430,7 +1430,7 @@ Python program.")
                   (invoke "make" "iverilog" "core")))))))
       (build-system pyproject-build-system)
       (native-inputs
-       (list iverilog python-setuptools-next python-pytest))
+       (list iverilog python-setuptools python-pytest))
       (home-page "http://www.myhdl.org/")
       (synopsis "Python as a Hardware Description Language")
       (description "This package provides a library to turn Python into
@@ -1534,7 +1534,7 @@ design.")
      (list python-pytest-cov
            python-pytest-html
            python-pytest-xdist
-           python-setuptools-next))
+           python-setuptools))
     (propagated-inputs
      (list python-pyyaml))
     (home-page "https://github.com/jeremiah-c-leary/vhdl-style-guide/")

gnu/packages/engineering.scm

@@ -2081,7 +2081,9 @@ bindings for Python, Java, OCaml and more.")
                              python-croniter
                              python-docutils
                              python-flask
-                             python-marshmallow
+                             ;; v4 is supported in upcomming release, see
+                             ;; <https://git.platypush.tech/platypush/platypush/issues/445>.
+                             python-marshmallow-3
                              python-pillow
                              python-pygments
                              python-pyotp
@@ -2112,7 +2114,7 @@ multiple services and devices with hundreds of supported integrations.")
 (define-public python-esptool
   (package
     (name "python-esptool")
-    (version "5.0.1")
+    (version "5.0.2")
     (source
      (origin
        (method git-fetch)
@@ -2121,7 +2123,7 @@ multiple services and devices with hundreds of supported integrations.")
               (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "04asqw6g4lhkz6fqn22wwk2wjq5q8c00m2k8wylksrc0v2f582i9"))))
+        (base32 "1wl75j6ncm5lahy9pzc38qivhaf9p42a2bijishdkwkw388fs6x1"))))
     (build-system pyproject-build-system)
     (arguments
      (list
@@ -2143,11 +2145,10 @@ multiple services and devices with hundreds of supported integrations.")
            python-pyserial
            python-pyyaml
            python-reedsolo
-           python-rich-click-next))
+           python-rich-click))
     (native-inputs (list python-pyelftools
                          python-pytest
-                         python-setuptools
-                         python-wheel))
+                         python-setuptools))
     (home-page "https://github.com/espressif/esptool")
     (synopsis "Bootloader utility for Espressif ESP8266 & ESP32 chips")
     (description

gnu/packages/fontutils.scm

@@ -14,6 +14,7 @@
 ;;; Copyright © 2020, 2021, 2024 Nicolas Goaziou <mail@nicolasgoaziou.fr>
 ;;; Copyright © 2021-2024 Maxim Cournoyer <maxim@guixotic.coop>
 ;;; Copyright © 2021 Sarah Morgensen <iskarian@mgsn.dev>
+;;; Copyright © 2022 Eric Bavier <bavier@posteo.net>
 ;;; Copyright © 2022 Felipe Balbi <balbi@kernel.org>
 ;;; Copyright © 2023 gemmaro <gemmaro.dev@gmail.com>
 ;;; Copyright © 2023 John Kehayias <john.kehayias@protonmail.com>
@@ -692,6 +693,47 @@ process.  FontParts is the successor of RoboFab.")
      (alist-delete 'hidden?
                    (package-properties python-fontparts-bootstrap)))))
 
+(define-public python-freetype-py
+  (package
+    (name "python-freetype-py")
+    (version "2.5.1")
+    (source
+     (origin
+       (method git-fetch)       ;no tests in PyPI archive
+       (uri (git-reference
+              (url "https://github.com/rougier/freetype-py")
+              (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "0cls0469zfqzwpq6k4pxa9vrczsqabqk4qh7444xybcyq9qgs1lp"))))
+    (build-system pyproject-build-system)
+    (arguments
+     (list
+      #:test-flags #~(list "tests")
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-after 'unpack 'patch-lib-paths
+            (lambda _
+              (substitute* "freetype/raw.py"
+                (("ctypes.util.find_library\\('freetype'\\)")
+                 (format #f "'~a/~a'" #$(this-package-input "freetype")
+                         "lib/libfreetype.so")))))
+          (add-before 'build 'set-version
+            (lambda _
+              (setenv "SETUPTOOLS_SCM_PRETEND_VERSION" #$version))))))
+    (native-inputs
+     (list python-pytest
+           python-setuptools
+           python-setuptools-scm))
+    (inputs
+     (list freetype))
+    (home-page "https://github.com/rougier/freetype-py")
+    (synopsis "Freetype python bindings")
+    (description
+     "Freetype Python provides bindings for the FreeType library.  Only the
+high-level API is bound.")
+    (license license:bsd-3)))
+
 (define-public python-glyphslib
   (package
     (name "python-glyphslib")

gnu/packages/game-development.scm

@@ -1565,7 +1565,7 @@ and multimedia programs in the Python language.")
               (setenv "HOME" "/tmp"))))))
     (native-inputs
      (list python-pytest
-           python-setuptools-next))
+           python-setuptools))
     (propagated-inputs
      (list python-pygame
            python-pyperclip

gnu/packages/gnome-xyz.scm

@@ -64,6 +64,7 @@
   #:use-module (gnu packages bash)
   #:use-module (gnu packages build-tools)
   #:use-module (gnu packages check)
+  #:use-module (gnu packages fontutils)
   #:use-module (gnu packages freedesktop)
   #:use-module (gnu packages gettext)
   #:use-module (gnu packages gl)

gnu/packages/jupyter.scm

@@ -1,16 +1,17 @@
 ;;; GNU Guix --- Functional package management for GNU
 ;;; Copyright © 2014 Danny Milosavljevic <dannym@friendly-machines.com>
+;;; Copyright © 2015 Federico Beffa <beffa@fbengineering.ch>
 ;;; Copyright © 2016, 2019 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2016, 2019, 2021-2025 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2016, 2021 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2018 Pierre-Antoine Rouby <pierre-antoine.rouby@inria.fr>
 ;;; Copyright © 2019, 2021-2023 Ludovic Courtès <ludo@gnu.org>
 ;;; Copyright © 2019, 2022 Andreas Enge <andreas@enge.fr>
-;;; Copyright © 2021 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2021 Hugo Lecomte <hugo.lecomte@inria.fr>
 ;;; Copyright © 2021 Lars-Dominik Braun <lars@6xq.net>
 ;;; Copyright © 2021 Nicolas Goaziou <mail@nicolasgoaziou.fr>
-;;; Copyright © 2022 Marius Bakke <marius@gnu.org>
-;;; Copyright © 2022 Maxim Cournoyer <maxim@guixotic.coop>
+;;; Copyright © 2021, 2022 Marius Bakke <marius@gnu.org>
+;;; Copyright © 2022 Maxim Cournoyer <maxim.cournoyer@gmail.com>
 ;;; Copyright © 2024 Nicolas Graves <ngraves@ngraves.fr>
 ;;; Copyright © 2024-2025 Sharlatan Hellseher <sharlatanus@gmail.com>
 ;;;
@@ -500,6 +501,34 @@ Messaging Protocol}.")
 extensions.")
     (license license:bsd-4)))
 
+(define-public python-terminado
+  (package
+    (name "python-terminado")
+    (version "0.18.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "terminado" version))
+       (sha256
+        (base32
+         "0bpxag3n0148vsgmi6wh3ynmprykazzqys0lfxgpdr2xp32g42fy"))))
+    (build-system pyproject-build-system)
+    (arguments
+     (list
+      #:test-flags #~(list "-W" "default")))    ;taken from pyproject.toml
+    (native-inputs
+     (list python-hatchling
+           python-pytest
+           python-pytest-timeout))
+    (propagated-inputs
+     (list python-ptyprocess
+           python-tornado-6))
+    (home-page "https://github.com/jupyter/terminado")
+    (synopsis "Terminals served to term.js using Tornado websockets")
+    (description "This package provides a Tornado websocket backend for the
+term.js Javascript terminal emulator library.")
+    (license license:bsd-2)))
+
 (define-public xeus
   (package
     (name "xeus")
@@ -835,15 +864,17 @@ endpoints—to Jupyter web applications.")
 (define-public python-jupyterlab-widgets
   (package
     (name "python-jupyterlab-widgets")
-    (version "3.0.10")
+    ;; XXX: Newer version requires python-jupyterlab, see guix/guix#2073.
+    (version "3.0.11")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "jupyterlab_widgets" version))
        (sha256
-        (base32
-         "1h04kln8hp56svdjjk2hbsb0z1mby71cv4gss3wy89v7jw2arwh4"))))
+        (base32 "09zfvqsw0svm6r3i2lhklnx44s7j4i60bvcvkkr9m5iwb5wwcnnx"))))
     (build-system pyproject-build-system)
+    (arguments
+     (list #:tests? #f)) ;no tests in PyPI
     (native-inputs
      (list python-jupyter-packaging))
     (home-page "https://github.com/jupyter-widgets/ipywidgets")
@@ -1073,7 +1104,7 @@ version to the original file.")
 (define-public repo2docker
   (package
     (name "repo2docker")
-    (version "2024.03.0")
+    (version "2024.07.0")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -1082,7 +1113,7 @@ version to the original file.")
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "1bcnl91j6p3315lk2mmn02jq6mjsn68m9rcw5rkln4c9fx1160rx"))))
+                "1fg71bldvfiln8h91sca4bjhwk7vdh80rhf0514qk6vqpikpx4cb"))))
     (outputs '("out" "doc"))
     (build-system pyproject-build-system)
     (arguments

gnu/packages/linux.scm

@@ -9717,7 +9717,7 @@ Text-based output formats: CSV, XML, Netfilter's LOG, Netfilter's conntrack
                          coreutils
                          pkg-config
                          ;; For rst2man, used to generate the manual page.
-                         python-docutils))
+                         python-docutils-0.19))
     (inputs (list libarchive talloc))
     (home-page "https://github.com/proot-me/PRoot")
     (synopsis "Unprivileged chroot, bind mount, and binfmt_misc")

gnu/packages/machine-learning.scm

@@ -243,7 +243,7 @@ family of functions.")
                              python-tqdm))
     (native-inputs (list python-numpy
                          python-pytest
-                         python-setuptools-next))
+                         python-setuptools))
     (home-page "https://github.com/SYSTRAN/faster-whisper")
     (synopsis "Whisper transcription reimplementation")
     (description
@@ -291,7 +291,7 @@ CTranslate2, which is a inference engine for transformer models.")
                          python-pytest
                          python-requests
                          python-scipy
-                         python-setuptools-next
+                         python-setuptools
                          python-torchvision))
     (home-page "https://github.com/pyro-ppl/funsor")
     (synopsis "Tensor-like library for functions and distributions")
@@ -1095,7 +1095,7 @@ cardinality matching from a bipartite graph.")
         (base32 "03d4kgakpgj54c3pl9dkqrkbmj6w13gmczkds5jagf3n85c1hgg1"))))
     (build-system pyproject-build-system)
     (native-inputs
-     (list python-pytest python-setuptools-next))
+     (list python-pytest python-setuptools))
     (propagated-inputs
      (list python-deprecated
            python-hopcroftkarp
@@ -1360,7 +1360,7 @@ storing tensors safely.")
             (lambda _
               (chdir "python"))))))
     (native-inputs
-     (list pkg-config protobuf python-pytest python-setuptools-next))
+     (list pkg-config protobuf python-pytest python-setuptools))
     (propagated-inputs (list sentencepiece))
     (synopsis "SentencePiece python wrapper")
     (description "This package provides a Python wrapper for the SentencePiece
@@ -1677,7 +1677,7 @@ operators and standard data types.")
      (append
       (list cmake-minimal
             python-pytest
-            python-setuptools-next)
+            python-setuptools)
       (filter
        (lambda (pkg)
          (member (or (%current-target-system)
@@ -1815,7 +1815,7 @@ with a single function call.")
            python-pytest
            python-pytorch
            python-sentencepiece
-           python-setuptools-next))
+           python-setuptools))
     (propagated-inputs
      (list python-coloredlogs
            python-flatbuffers
@@ -2323,7 +2323,7 @@ visualizing high-dimensional data sets.")
     ;; python-scikit-learn
     (arguments '(#:tests? #f))
     (native-inputs
-     (list python-setuptools-next))
+     (list python-setuptools))
     (propagated-inputs
      (list python-numpy python-scipy python-scikit-learn python-joblib))
     (home-page "https://epistasislab.github.io/scikit-rebate/")
@@ -2436,7 +2436,7 @@ data by providing clean labels during training.")
                           (lambda* (#:key tests? #:allow-other-keys)
                             (when tests?
                               (invoke "python" "-m" "cma.test")))))))
-    (native-inputs (list python-pytest python-setuptools-next))
+    (native-inputs (list python-pytest python-setuptools))
     (propagated-inputs (list python-numpy))
     (home-page "https://github.com/CMA-ES/pycma")
     (synopsis "Python implementation of CMA-ES")
@@ -3461,7 +3461,7 @@ in a fast and accurate way.")
     (propagated-inputs
      (list python-ipython python-numpy python-pandas python-scipy))
     (native-inputs
-     (list python-nose python-setuptools-next))
+     (list python-nose python-setuptools))
     (home-page "https://github.com/interpretable-ml/iml")
     (synopsis "Interpretable Machine Learning (iML) package")
     (description "Interpretable ML (iML) is a set of data type objects,
@@ -4954,7 +4954,7 @@ as torchvision, torchtext, and others.")
     (native-inputs
      (list python-pytest
            python-pytest-cov
-           python-setuptools-next))
+           python-setuptools))
     (home-page "https://github.com/magmax/python-readchar")
     (synopsis "Library to easily read single chars and key strokes")
     (description "This package provides a Python library to easily read single
@@ -5075,7 +5075,7 @@ feedback.")
              python-psutil
              python-requests-mock
              python-scikit-learn
-             python-setuptools-next))
+             python-setuptools))
       (home-page "https://lightning.ai/")
       (synopsis "Deep learning framework to train, deploy, and ship AI products")
       (description
@@ -5223,7 +5223,7 @@ and common image transformations for computer vision.")
                 (when tests?
                   (invoke "python3" "tests.py")))))))
       (propagated-inputs
-       (list python-numpy python-setuptools-next))
+       (list python-numpy python-setuptools))
       (home-page "https://github.com/bshillingford/python-torchfile")
       (synopsis "Torch7 binary serialized file parser")
       (description "This package enables you to deserialize Lua
@@ -5635,7 +5635,7 @@ algorithm for dense (LAPJV) or sparse (LAPMOD) matrices.")
     (build-system pyproject-build-system)
     (arguments (list #:tests? #f))      ;tests require launching the server
     (native-inputs
-     (list python-setuptools-next))
+     (list python-setuptools))
     (propagated-inputs
      (list python-jsonpatch
            python-networkx

gnu/packages/messaging.scm

@@ -3251,7 +3251,7 @@ designed for experienced users.")
     (native-inputs
      (list python-matrix-nio
            python-pytest
-           python-setuptools-next))
+           python-setuptools))
     (propagated-inputs
      (list python-click
            python-distro
@@ -3308,7 +3308,7 @@ designed for experienced users.")
      (list python-pytest
            python-pytest-cov
            python-pytest-mock
-           python-setuptools-next))
+           python-setuptools))
     (home-page "https://github.com/zulip/zulip-terminal")
     (synopsis "Zulip's official terminal client")
     (description "This package contains Zulip's official terminal client.")

gnu/packages/networking.scm

@@ -100,6 +100,7 @@
   #:use-module (guix build-system perl)
   #:use-module (guix build-system pyproject)
   #:use-module (guix build-system python)
+  #:use-module (guix build-system pyproject)
   #:use-module (guix build-system qt)
   #:use-module (guix build-system trivial)
   #:use-module (guix utils)
@@ -2021,9 +2022,9 @@ replies, fping will send out a ping packet and move on to the next target in a
 round-robin fashion.")
     (license license:expat)))
 
-(define-public gandi.cli
+(define-public gandi-cli
   (package
-    (name "gandi.cli")
+    (name "gandi-cli")
     (version "1.6")
     (source
      (origin
@@ -2031,34 +2032,41 @@ round-robin fashion.")
        (uri (pypi-uri name version))
        (sha256
         (base32 "1h36jahbp7273wn3yd747kbiwjc0bm3sja67bcxdsd54ln0vyndg"))))
-    (build-system python-build-system)
+    (build-system pyproject-build-system)
     (arguments
-     `(#:phases
-       (modify-phases %standard-phases
-         (add-after 'unpack 'embed-store-file-names
-           (lambda _
-             (substitute* (list "gandi/cli/modules/cert.py"
-                                "gandi/cli/tests/commands/test_certificate.py")
-               (("openssl") (which "openssl")))
-             #t))
-         (add-after 'install 'install-documentation
-           ;; The included man page may be outdated but we install it anyway,
-           ;; since it's mentioned in 'gandi --help' and better than nothing.
-           (lambda* (#:key outputs #:allow-other-keys)
-             (let* ((out  (assoc-ref outputs "out"))
-                    (man1 (string-append out "/share/man/man1")))
-               (mkdir-p man1)
-               (with-output-to-file (string-append man1 "/gandi.1")
-                 (lambda _
-                   (invoke "rst2man.py" "gandicli.man.rst")))
-               #t))))))
+     (list
+      #:test-flags
+      #~(list "--pyargs" "gandi.cli")
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-after 'unpack 'embed-store-file-names
+            (lambda _
+              (substitute* (list "gandi/cli/modules/cert.py"
+                                 "gandi/cli/tests/commands/test_certificate.py")
+                (("openssl") (which "openssl")))))
+          (add-after 'install 'install-documentation
+            ;; The included man page may be outdated but we install it anyway,
+            ;; since it's mentioned in 'gandi --help' and better than nothing.
+            (lambda _
+              (let* ((man1 (string-append #$output "/share/man/man1")))
+                (mkdir-p man1)
+                (with-output-to-file (string-append man1 "/gandi.1")
+                  (lambda _
+                    (invoke "rst2man.py" "gandicli.man.rst")))))))))
     (native-inputs
-     (list python-docutils ; for rst2man.py
-           python-pytest python-pytest-cov python-tox))
-    (propagated-inputs
-     (list openssh))           ; used by gandi/cli/modules/iass.py
+     (list python-docutils-0.19
+           python-pytest
+           python-pytest-cov
+           python-setuptools
+           python-wheel))
     (inputs
-     (list openssl python-click-7 python-ipy python-pyyaml python-requests))
+     (list openssl
+           python-click-7
+           python-ipy
+           python-pyyaml
+           python-requests))
+    (propagated-inputs
+     (list openssh))
     (home-page "https://cli.gandi.net")
     (synopsis "Command-line interface to the Gandi.net Web API")
     (description
@@ -2067,6 +2075,9 @@ manage, and delete Internet resources from Gandi.net such as domain names,
 virtual machines, and certificates.")
     (license license:gpl3+)))
 
+(define-public gandi.cli
+  (deprecated-package "gandi.cli" gandi-cli))
+
 (define-public go-sctp
   ;; docker-libnetwork-cmd-proxy requires this exact commit.
   ;; This commit is mentioned in docker-libnetwork-cmd-proxy's vendor.conf.

gnu/packages/openstack.scm

@@ -911,15 +911,24 @@ documentation from the OpenStack project.")
        (sha256
         (base32 "1vp85v81p2vx66j973hc7fa65shp0ilhaypyyny01jwcip94152s"))))
     (build-system pyproject-build-system)
-    (propagated-inputs
-     (list python-fixtures python-subunit python-testtools))
+    (arguments
+     (list
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-after 'unpack 'remove-sub-package
+            ;; error: Multiple top-level packages discovered in a flat-layout:
+            ;; ['oslotest', 'releasenotes'].
+            (lambda _
+              (delete-file-recursively "releasenotes"))))))
     (native-inputs
-     (list python-coverage
-           python-debtcollector
+     (list python-debtcollector
            python-oslo-config
            python-stestr
-           python-setuptools
-           python-wheel))
+           python-setuptools))
+    (propagated-inputs
+     (list python-fixtures
+           python-subunit
+           python-testtools))
     (home-page "https://launchpad.net/oslo")
     (synopsis "Oslo test framework")
     (description "The Oslo Test framework provides common fixtures, support

gnu/packages/parallel.scm

@@ -425,7 +425,7 @@ cluster/resource management systems.")
               (when tests?
                 (invoke "python" "./pathos/tests/__main__.py")))))))
     (native-inputs
-     (list python-setuptools-next))
+     (list python-setuptools))
     (propagated-inputs
      (list python-dill
            python-multiprocess
@@ -464,7 +464,7 @@ execution environment.")
               (when tests?
                 (invoke "python" "./ppft/tests/__main__.py")))))))
     (native-inputs
-     (list python-setuptools-next))
+     (list python-setuptools))
     (home-page "https://pypi.org/project/ppft/")
     (synopsis "Fork of Parallel Python")
     (description

gnu/packages/patches/python-hdmedians-replace-nose.patch

@@ -0,0 +1,95 @@
+This patch is from the upstream pull request.
+https://github.com/daleroberts/hdmedians/pull/10.
+It adds compatibility with Pytest and drops Nose.
+
+diff --git a/hdmedians/tests/test_geomedian.py b/hdmedians/tests/test_geomedian.py
+index 0bc37e9..ff5f938 100644
+--- a/hdmedians/tests/test_geomedian.py
++++ b/hdmedians/tests/test_geomedian.py
+@@ -4,9 +4,9 @@ Tests.
+ 
+ import numpy as np
+ import hdmedians as hd
++import pytest
+ 
+ from numpy.testing import assert_equal, assert_array_almost_equal
+-from nose.tools import assert_true, assert_raises
+ 
+ # shape (6, 25)
+ DATA1 = np.array([[693, 990, 1281, 2101, 3524, 2577],
+@@ -124,10 +124,12 @@ def test_nangeomedian_axis_one_two_good():
+ def test_nangeomedian_axis_bad():
+     data = np.array([[1.0, np.nan, 1.0],
+                      [2.0, 1.0, 1.0]])
+-    assert_raises(IndexError, hd.nangeomedian, data, axis=2)
++    with pytest.raises(IndexError):
++        hd.nangeomedian(data, axis=2)
+ 
+ 
+ def test_nangeomedian_all_nan():
+     data = np.array([[np.nan, np.nan, np.nan],
+                      [np.nan, np.nan, np.nan]])
+-    assert_raises(ValueError, hd.nangeomedian, data)
++    with pytest.raises(ValueError):
++        hd.nangeomedian(data)
+diff --git a/hdmedians/tests/test_medoid.py b/hdmedians/tests/test_medoid.py
+index c5e0a7f..4fbdf80 100644
+--- a/hdmedians/tests/test_medoid.py
++++ b/hdmedians/tests/test_medoid.py
+@@ -4,9 +4,9 @@ Tests.
+ 
+ import numpy as np
+ import hdmedians as hd
++import pytest
+ 
+ from numpy.testing import assert_equal, assert_array_almost_equal
+-from nose.tools import assert_true, assert_raises
+ 
+ # shape (6, 25)
+ DATA1 = np.array([[693, 990, 1281, 2101, 3524, 2577],
+@@ -59,7 +59,7 @@ def test_medoid_in_set_random():
+     s = [list(x) for x in a.T]
+     m = hd.medoid(a)
+     idx = s.index(list(m))
+-    assert_true(idx > -1)
++    assert(idx > -1)
+ 
+ 
+ def test_medoid_noaxis():
+@@ -85,7 +85,8 @@ def test_medoid_axis_one():
+ 
+ 
+ def test_medoid_axis_bad():
+-    assert_raises(IndexError, hd.medoid, DATA1, axis=2)
++    with pytest.raises(IndexError):
++        hd.medoid(DATA1, axis=2)
+ 
+ 
+ def test_medoid_noaxis_indexonly():
+@@ -136,7 +137,8 @@ def test_nanmedoid_two_obs():
+ def test_nanmedoid_all_nan():
+     data = np.array([[np.nan, np.nan, np.nan],
+                      [np.nan, np.nan, np.nan]])
+-    assert_raises(ValueError, hd.nanmedoid, data)
++    with pytest.raises(ValueError):
++        hd.nanmedoid(data)
+ 
+ 
+ def test_nanmedoid_axis_zero():
+@@ -170,7 +172,8 @@ def test_nanmedoid_axis_one_indexonly():
+ 
+ 
+ def test_nanmedoid_axis_bad():
+-    assert_raises(IndexError, hd.nanmedoid, DATA1, axis=2)
++    with pytest.raises(IndexError):
++        hd.nanmedoid(DATA1, axis=2)
+ 
+ 
+ def test_nanmedoid_two_obs():
+@@ -184,4 +187,5 @@ def test_nanmedoid_two_obs():
+ def test_nanmedoid_all_nan():
+     data = np.array([[np.nan, np.nan, np.nan],
+                      [np.nan, np.nan, np.nan]])
+-    assert_raises(ValueError, hd.nanmedoid, data)
++    with pytest.raises(ValueError):
++        hd.nanmedoid(data)

gnu/packages/patches/python-unittest2-python3-compat.patch

@@ -1,46 +0,0 @@
-Skip tests that fail with newer versions of Python.
-
-Patch copied from Gentoo:
-
-https://gitweb.gentoo.org/repo/gentoo.git/tree/dev-python/unittest2/files/unittest2-1.1.0-python3.5-test.patch
-
-diff --git a/unittest2/test/test_loader.py b/unittest2/test/test_loader.py
-index 683f662..347eea5 100644
---- a/unittest2/test/test_loader.py
-+++ b/unittest2/test/test_loader.py
-@@ -509,6 +509,7 @@ class Test_TestLoader(unittest2.TestCase):
-     #
-     # What happens when an impossible name is given, relative to the provided
-     # `module`?
-+    @unittest.skipIf(sys.version_info[:2] >= (3, 5), "python 3.5 has problems here")
-     def test_loadTestsFromName__relative_malformed_name(self):
-         loader = unittest.TestLoader()
- 
-@@ -811,6 +812,7 @@ class Test_TestLoader(unittest2.TestCase):
-     # TestCase or TestSuite instance."
-     #
-     # What happens when presented with an impossible module name?
-+    @unittest.skipIf(sys.version_info[:2] >= (3, 5), "python 3.5 has problems here")
-     def test_loadTestsFromNames__malformed_name(self):
-         loader = unittest2.TestLoader()
- 
-@@ -918,6 +920,7 @@ class Test_TestLoader(unittest2.TestCase):
-     # "The method optionally resolves name relative to the given module"
-     #
-     # What happens when presented with an impossible attribute name?
-+    @unittest.skipIf(sys.version_info[:2] >= (3, 5), "python 3.5 has problems here")
-     def test_loadTestsFromNames__relative_malformed_name(self):
-         loader = unittest.TestLoader()
- 
-diff --git a/unittest2/compatibility.py b/unittest2/compatibility.py
-index 9e5f1a5..2d20c19 100644
---- a/unittest2/compatibility.py
-+++ b/unittest2/compatibility.py
-@@ -140,6 +140,6 @@ except ImportError:
- ###  ChainMap (helper for configparser and string.Template)
- ########################################################################
- 
--class ChainMap(collections.MutableMapping):
-+class ChainMap(collections.abc.MutableMapping):
-     ''' A ChainMap groups multiple dicts (or other mappings) together
-     to create a single, updateable view.

gnu/packages/patches/python-unittest2-remove-argparse.patch

@@ -1,11 +0,0 @@
---- a/setup.py	2017-09-12 01:22:06.273997788 +0200
-+++ b/setup.py	2017-09-12 01:22:14.297918757 +0200
-@@ -57,7 +57,7 @@
- # Both install and setup requires - because we read VERSION from within the
- # package, and the package also exports all the APIs.
- # six for compat helpers
--REQUIRES = ['argparse', 'six>=1.4', 'traceback2'],
-+REQUIRES = ['six>=1.4', 'traceback2'],
- 
- params = dict(
-     name=NAME,

gnu/packages/python-build.scm

@@ -237,19 +237,7 @@ Included are implementations of:
 @end enumerate\n")
     (license license:psfl)))
 
-(define-public python-typing-extensions-next
-  (package
-    (inherit python-typing-extensions)
-    (version "4.15.0")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (pypi-uri "typing_extensions" version))
-       (sha256
-        (base32 "0rhlhs28jndgp9fghdhidn6g7xiwx8vvihxbxhlgl4ncfg8lishc"))))
-    (native-inputs
-     (modify-inputs (package-native-inputs python-typing-extensions)
-       (replace "python-flit-core" python-flit-core-next)))))
+(define-public python-typing-extensions-next python-typing-extensions)
 
 
 ;;;
@@ -361,23 +349,7 @@ facilitate packaging Python projects, where packaging includes:
     (native-inputs
      (list python-wheel-0.40))))
 
-(define-public python-setuptools-next
-  (package
-    (inherit python-setuptools)
-    (name "python-setuptools")
-    (version "79.0.1")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (pypi-uri "setuptools" version))
-       (sha256
-        (base32 "127svm8cdpvmq37gcrbvdr9fhrhs0nscnzh63gypjc1wyfwfg30j"))
-       (modules '((guix build utils)))
-       (snippet
-        #~(begin
-            (for-each delete-file
-                      (find-files "setuptools" "^(cli|gui).*\\.exe$"))))))
-    (build-system pyproject-build-system)))
+(define-public python-setuptools-next python-setuptools)
 
 (define-public python-wheel
   (package
@@ -488,19 +460,6 @@ of regular expressions.  The pyparsing module provides a library of classes
 that client code uses to construct the grammar directly in Python code.")
     (license license:expat)))
 
-;;; This is the last release compatible with Python 2.
-(define-public python-pyparsing-2.4.7
-  (package
-    (inherit python-pyparsing)
-    (version "2.4.7")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (pypi-uri "pyparsing" version))
-       (sha256
-        (base32 "1hgc8qrbq1ymxbwfbjghv01fm3fbpjwpjwi0bcailxxzhf3yq0y2"))))
-    (native-inputs (list python-setuptools python-wheel))))
-
 (define-public python-packaging-bootstrap
   (package
     (name "python-packaging-bootstrap")
@@ -601,15 +560,7 @@ 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"))))))
+(define-public python-poetry-core-next python-poetry-core)
 
 ;;; This package exists to bootstrap python-tomli.
 (define-public python-flit-core-bootstrap
@@ -663,16 +614,7 @@ specified by PEP 517, @code{flit_core.buildapi}.")
        (delete "python-toml")
        (prepend python-tomli)))))
 
-(define-public python-flit-core-next
-  (package/inherit python-flit-core
-    (name "python-flit-core")
-    (version "3.12.0")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (pypi-uri "flit" version))
-       (sha256
-        (base32 "0h1pxi2hgr95321bgl45l86693zl14l3shj0idsyg4k9v56z700w"))))))
+(define-public python-flit-core-next python-flit-core)
 
 (define-public python-flit-scm
   (package
@@ -740,36 +682,7 @@ system, then @code{flit_core} to build the package.")
 them as the version argument or in a SCM managed file.")
     (license license:expat)))
 
-(define-public python-setuptools-scm-next
-  (package
-    (inherit python-setuptools-scm)
-    (name "python-setuptools-scm")
-    (version "8.1.0")
-    (source (origin
-              (method url-fetch)
-              (uri (pypi-uri "setuptools_scm" version))
-              (sha256
-               (base32 "19y84rzqwb2rd88bjrlafrhfail2bnk6apaig8xskjviayva3pj2"))))
-    (build-system pyproject-build-system)
-    (arguments (list
-                ;; pyproject-build-system will error handle forms such as
-                ;; "module:object", so we set it.
-                #:build-backend "setuptools.build_meta"
-                #:phases
-                #~(modify-phases %standard-phases
-                    (add-before 'build 'setenv
-                      (lambda _
-                        ;; pyproject-build-system ignore backend-path,
-                        ;; and __import__ ignore GUIX_PYTHONPATH, so set
-                        ;; PYTHONPATH.
-                        (setenv "PYTHONPATH"
-                                (string-append
-                                 (getcwd)
-                                 ":"
-                                 (getcwd) "/src:"
-                                 (getenv "GUIX_PYTHONPATH"))))))
-                #:tests? #f))    ;avoid extra dependencies such as pytest
-    (native-inputs (list python-setuptools python-wheel))))
+(define-public python-setuptools-scm-next python-setuptools-scm)
 
 (define-public python-editables
   (package

gnu/packages/python-check.scm

@@ -303,33 +303,21 @@ Avocado machine readable outputs this one is streamlined (per test results).
 (define-public python-bandit
   (package
     (name "python-bandit")
-    (version "1.8.3")
+    (version "1.8.6")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "bandit" version))
        (sha256
-        (base32 "0fhr0rsvh44ix31dwxjw8aj0wklj95368djwk0i98c2dcpmpp17m"))))
+        (base32 "0sz5lkg9anqz6ir157xr8ng9ymgj37ymbplkhl3w4qb9zhjrrznv"))))
     (build-system pyproject-build-system)
     (arguments
-     (list
-      #:test-flags
-      ;; XXX: Two tests fail.
-      #~(list "--exclude-regex" "test_no_arguments|test_help_arg")))
+     (list #:tests? #f))         ;tests require complex setup and networking
     (native-inputs
-     (list python-beautifulsoup4
-           python-fixtures
-           python-setuptools
-           python-stestr
-           python-testscenarios
-           python-testtools
-           python-wheel))
+     (list python-setuptools))
     (propagated-inputs
-     (list python-gitpython
-           python-jschema-to-python
-           python-pyyaml
+     (list python-pyyaml
            python-rich
-           python-sarif-om
            python-stevedore))
     (home-page "https://github.com/PyCQA/bandit")
     (synopsis "Security oriented static analyser for python code")
@@ -343,16 +331,16 @@ all the files it generates a report.")
 (define-public python-beartype
   (package
     (name "python-beartype")
-    (version "0.19.0")
+    (version "0.21.0")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "beartype" version))
        (sha256
-        (base32 "0wv598iv9c2s6ivfiara9pnkdlnas8xjw063wvyi0dswpb0xyhny"))))
+        (base32 "0i1j1mkcw0fgms9qg7j30nlgcr0b0ndx2l98sb162wp8bj7hg9gr"))))
     (build-system pyproject-build-system)
     (native-inputs
-     (list python-hatchling python-numpy python-pygments python-pytest))
+     (list python-hatchling python-pytest))
     (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
@@ -1582,19 +1570,21 @@ flake8 to check PEP-8 naming conventions.")
     (version "1.2.0")
     (source
      (origin
-       (method url-fetch)
-       (uri (pypi-uri "pyannotate" version))
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/dropbox/pyannotate")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
        (sha256
-        (base32 "16bm0mf7wxvy0lgmcs1p8n1ji8pnvj1jvj8zk3am70dkp825iv84"))))
+        (base32 "0gmhl4ldan0p774dhrs9a7bmjjphlsy3hhfqq84gak15rdjs59ga"))))
     (build-system pyproject-build-system)
-    (native-inputs
-     (list python-setuptools python-wheel))
-    (propagated-inputs
-     (list python-mypy-extensions python-six))
+    (arguments (list #:test-backend #~'unittest))
+    (native-inputs (list python-setuptools))
+    (propagated-inputs (list python-mypy-extensions python-six))
     (home-page "https://github.com/dropbox/pyannotate")
     (synopsis "Auto-generate PEP-484 annotations")
-    (description "This package, PyAnnotate, is used to auto-generate PEP-484
-annotations.")
+    (description
+     "This package, PyAnnotate, is used to auto-generate PEP-484 annotations.")
     (license license:asl2.0)))
 
 (define-public python-pycotap
@@ -2935,17 +2925,6 @@ times.")
 eliminate flaky failures.")
     (license license:mpl2.0)))
 
-(define-public python-pytest-rerunfailures-13
-  (package
-    (inherit python-pytest-rerunfailures)
-    (version "13.0")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (pypi-uri "pytest-rerunfailures" version))
-       (sha256
-        (base32 "16cin0chv59w4rvnd6r0fisp0s8avmp07rwn9da6yixw43jdncp1"))))))
-
 ;; This is only used by python-sanic
 (define-public python-pytest-sanic
   (package

gnu/packages/python-compression.scm

@@ -118,17 +118,16 @@ This Python package wraps the Blosc library.")
        (uri (pypi-uri "blosc2" version))
        (sha256
         (base32 "1s4gpdf1hfbw5w3hpx0g8bfwjrws1b8wgmh7snafh5ivai0lvnrl"))))
-    (build-system python-build-system)
+    (build-system pyproject-build-system)
     (arguments
-     (list #:phases #~(modify-phases %standard-phases
-                        (replace 'build
-                          (lambda* (#:key inputs #:allow-other-keys)
-                            (invoke "python" "setup.py" "build"
-                                    "-DUSE_SYSTEM_BLOSC2=ON")))
-                        (replace 'check
-                          (lambda* (#:key tests? #:allow-other-keys)
-                            (when tests?
-                              (invoke "python" "-m" "pytest" "-vv")))))))
+     (list
+      #:test-flags
+      #~(list "--pyargs" "blosc2")
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-before 'build 'configure
+            (lambda _
+              (setenv "USE_SYSTEM_BLOSC2" "ON"))))))
     (inputs (list c-blosc2))
     (propagated-inputs
      (list python-msgpack
@@ -141,7 +140,8 @@ This Python package wraps the Blosc library.")
            pkg-config
            python-cython-3
            python-pytest
-           python-scikit-build))
+           python-scikit-build
+           python-setuptools))
     (home-page "https://github.com/blosc/python-blosc2")
     (synopsis "Python wrapper for the Blosc2 data compressor library")
     (description
@@ -467,13 +467,16 @@ compression algorithm.")
        ;; Remove bundled isa-l source code
        (modules '((guix build utils)))
        (snippet
-        '(delete-file-recursively "src/isal/isa-l"))))
+        #~(delete-file-recursively "src/isal/isa-l"))))
     (build-system pyproject-build-system)
     (arguments
-     `(#:phases
-       (modify-phases %standard-phases
-         (add-after 'unpack 'use-dynamic-linking
-           (lambda _ (setenv "PYTHON_ISAL_LINK_DYNAMIC" "1"))))))
+     (list
+      #:test-backend #~'unittest
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-after 'unpack 'use-dynamic-linking
+            (lambda _
+              (setenv "PYTHON_ISAL_LINK_DYNAMIC" "1"))))))
     (inputs (list isa-l))
     (native-inputs (list python-cython python-setuptools python-wheel))
     (home-page "https://github.com/pycompression/python-isal")
@@ -827,7 +830,7 @@ install: libbitshuffle.so
     (arguments
      (list #:tests? #f)) ;no tests
     (native-inputs
-     (list python-setuptools-next))
+     (list python-setuptools))
     (home-page "https://github.com/kYwzor/uncompresspy")
     (synopsis "Uncompressing LZW files in Python")
     (description

gnu/packages/python-crypto.scm

@@ -340,59 +340,21 @@ production use.  Include this module and use its backends at your own risk.")
     (arguments
      (list
       #:install-source? #f
+      #:imported-modules `(,@%pyproject-build-system-modules
+                           ,@%cargo-build-system-modules)
+      #:modules `((guix build cargo-build-system)
+                  ((guix build pyproject-build-system) #:prefix py:)
+                  (guix build utils))
       #:phases
       #~(modify-phases %standard-phases
-          (add-after 'install 'build-python-module
-            (lambda _
-              ;; We don't use maturin.
-              (delete-file "pyproject.toml")
-              (call-with-output-file "pyproject.toml"
-                (lambda (port)
-                  (format port "\
-[build-system]
-build-backend = 'setuptools.build_meta'
-requires = ['setuptools']
-")))
-              (call-with-output-file "setup.cfg"
-                (lambda (port)
-                  (format port "\
-
-[metadata]
-name = blake3
-version = ~a
-
-[options]
-packages = find:
-
-[options.packages.find]
-exclude =
-  src*
-  c_impl*
-  tests*
-  Cargo.toml
-" #$version)))
-              ;; ZIP does not support timestamps before 1980.
-              (setenv "SOURCE_DATE_EPOCH" "315532800")
-              (invoke "python" "-m" "build" "--wheel" "--no-isolation" ".")))
+          (add-after 'build 'build-python-module
+            (assoc-ref py:%standard-phases 'build))
           (add-after 'build-python-module 'install-python-module
-            (lambda* (#:key outputs #:allow-other-keys)
-              (let ((whl (car (find-files "dist" "\\.whl$"))))
-                (invoke "pip" "--no-cache-dir" "--no-input"
-                        "install" "--no-deps" "--prefix" #$output whl))))
-          (add-after 'install-python-module 'install-python-library
-            (lambda _
-              (let ((site (string-append #$output "/lib/python"
-                                         #$(version-major+minor
-                                            (package-version python))
-                                         "/site-packages")))
-                (mkdir-p site)
-                (copy-file "target/release/libblake3.so"
-                           (string-append site "/blake3.so"))))))))
-    (inputs (cargo-inputs 'python-blake3))
+            (assoc-ref py:%standard-phases 'install)))))
     (native-inputs
      (list python-wrapper
-           python-pypa-build
-           python-wheel))
+           maturin))
+    (inputs (cargo-inputs 'python-blake3))
     (home-page "https://github.com/oconnor663/blake3-py")
     (synopsis "Python bindings for the Rust blake3 crate")
     (description "This package provides Python bindings for the Rust crate of

gnu/packages/python-science.scm

@@ -904,21 +904,15 @@ optimization and generally improved organization.")
                  (string-append "version = \"" #$version "\""))))))))
     (propagated-inputs (list python-dask
                              python-numpy
-                             python-pandas-2
+                             python-pandas
                              python-pims
                              python-scipy
                              python-tifffile))
     (native-inputs
-     (list python-coverage
-           python-flake8
-           python-pytest
-           python-pytest-cov
-           python-pytest-flake8
+     (list python-pytest
            python-pytest-timeout
            python-setuptools
-           python-setuptools-scm
-           python-twine
-           python-wheel))
+           python-setuptools-scm))
     (home-page "https://github.com/dask/dask-image")
     (synopsis "Distributed image processing")
     (description "This is a package for image processing with Dask arrays.
@@ -2954,7 +2948,7 @@ swarm algorithm.")
     (native-inputs
      (list python-pytest
            python-pytest-xdist
-           python-setuptools-next))
+           python-setuptools))
     (propagated-inputs
      (list python-joblib
            python-matplotlib
@@ -3377,7 +3371,7 @@ Snakemake and its storage plugins.")
            python-pytest
            python-pytest-cov
            python-setuptools
-           python-setuptools-scm-next
+           python-setuptools-scm
            python-wheel))
     (home-page "https://github.com/pydata/sparse/")
     (synopsis "Library for multi-dimensional sparse arrays")
@@ -3588,108 +3582,6 @@ library.")
 tissue-specificity metrics for gene expression.")
     (license license:gpl3+)))
 
-(define-public python-pandas-1
-  (package
-    (name "python-pandas")
-    (version "1.5.3")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (pypi-uri "pandas" version))
-       (sha256
-        (base32 "1cdhngylzh352wx5s3sjyznn7a6kmjqcfg97hgqm5h3yb9zgv8vl"))))
-    (build-system pyproject-build-system)
-    (arguments
-     (list
-      #:test-flags
-      '(list "--pyargs" "pandas"
-             "-n" (number->string (parallel-job-count))
-             "-m" "not slow and not network and not db"
-             "-k"
-             (string-append
-              ;; TODO: Missing input
-              "not TestS3"
-              " and not s3"
-              ;; No module named 'pandas.io.sas._sas'
-              " and not test_read_expands_user_home_dir"
-              " and not test_read_non_existent"
-              ;; Unknown failures
-              " and not test_switch_options"
-              ;; These fail with: td64 doesn't return NotImplemented, see numpy#17017
-              " and not test_nat_comparisons"
-              ;; Crashes
-              " and not test_bytes_exceed_2gb"
-              ;; get_subplotspec() returns None; possibly related to
-              ;; https://github.com/pandas-dev/pandas/issues/54577
-              " and not test_plain_axes"
-              ;; This test fails when run with pytest-xdist
-              ;; (see https://github.com/pandas-dev/pandas/issues/39096).
-              " and not test_memory_usage"))
-      #:phases
-       #~(modify-phases %standard-phases
-           (add-after 'unpack 'patch-build-system
-             (lambda _
-               (substitute* "pyproject.toml"
-                 ;; Not all data files are distributed with the tarball.
-                 (("--strict-data-files ") "")
-                 ;; Unknown property "asyncio_mode"
-                 (("asyncio_mode = \"strict\"") ""))))
-           (add-after 'unpack 'patch-which
-             (lambda* (#:key inputs #:allow-other-keys)
-               (substitute* "pandas/io/clipboard/__init__.py"
-                 (("^WHICH_CMD = .*")
-                  (string-append "WHICH_CMD = \""
-                                 (search-input-file inputs "/bin/which")
-                                 "\"\n")))))
-           (add-before 'check 'prepare-x
-             (lambda _
-               (system "Xvfb &")
-               (setenv "DISPLAY" ":0")
-               ;; xsel needs to write a log file.
-               (setenv "HOME" "/tmp")))
-           ;; The compiled libraries are only in the output at this point,
-           ;; but they are needed to run tests.
-           ;; FIXME: This should be handled by the pyargs pytest argument,
-           ;; but is not for some reason.
-           (add-before 'check 'pre-check
-             (lambda* (#:key inputs outputs #:allow-other-keys)
-               (copy-recursively
-                (string-append (site-packages inputs outputs)
-                               "/pandas/_libs")
-                "pandas/_libs"))))))
-    (propagated-inputs
-     (list python-jinja2
-           python-matplotlib
-           python-numpy
-           python-openpyxl
-           python-pytz
-           python-dateutil
-           python-xlrd
-           python-xlsxwriter))
-    (inputs
-     (list which xclip xsel))
-    (native-inputs
-     (list python-cython-0.29.35
-           python-beautifulsoup4
-           python-lxml
-           python-html5lib
-           python-pytest
-           python-pytest-mock
-           python-pytest-xdist
-           python-setuptools
-           python-wheel
-           ;; Needed to test clipboard support.
-           xorg-server-for-tests))
-    (home-page "https://pandas.pydata.org")
-    (synopsis "Data structures for data analysis, time series, and statistics")
-    (description
-     "Pandas is a Python package providing fast, flexible, and expressive data
-structures designed to make working with structured (tabular,
-multidimensional, potentially heterogeneous) and time series data both easy
-and intuitive.  It aims to be the fundamental high-level building block for
-doing practical, real world data analysis in Python.")
-    (license license:bsd-3)))
-
 (define-public python-pandas-2
   (package
     (name "python-pandas")

gnu/packages/python-web.scm

@@ -1689,18 +1689,6 @@ The package includes a module with full coverage of JSON RPC versions 1.0 and
 comes with a SOCKS proxy client.")
     (license (list license:expat license:bsd-2))))
 
-(define-public python-aiorpcx-0.18
-  (package
-    (inherit python-aiorpcx)
-    (version "0.18.7")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (pypi-uri "aiorpcX" version))
-       (sha256
-        (base32
-         "1rswrspv27x33xa5bnhrkjqzhv0sknv5kd7pl1vidw9d2z4rx2l0"))))))
-
 (define-public python-aiostream
   (package
     (name "python-aiostream")
@@ -2060,9 +2048,8 @@ emit information from within their applications to the AWS X-Ray service.")
        (sha256
         (base32 "0llam7g7sv08lcfgy18iph8br8ldjmy2qbjaykc9pd3z4iisb0yd"))))
     (build-system pyproject-build-system)
-    (native-inputs
-     (list python-setuptools
-           python-wheel))
+    (arguments (list #:test-backend #~'unittest))
+    (native-inputs (list python-setuptools))
     (home-page "https://github.com/ko-zu/psl")
     (synopsis "Public suffix list for Python")
     (description
@@ -2207,7 +2194,9 @@ decode and default on encode.
                     (list "not test_build_graph"
                           "test_good_template"
                           "test_success_run"
-                          "test_update_docs")
+                          "test_update_docs"
+                          ;; ImportError: Missing optional dependencies sarif
+                          "test_sarif_formatter")
                     " and not "))
       #:phases
       #~(modify-phases %standard-phases
@@ -2230,9 +2219,7 @@ decode and default on encode.
            python-sympy
            python-typing-extensions
            ;; [optional]
-           python-jschema-to-python
-           python-junit-xml
-           python-sarif-om))
+           python-junit-xml))
     (home-page "https://github.com/aws-cloudformation/cfn-lint")
     (synopsis "Validate CloudFormation templates")
     (description
@@ -2241,25 +2228,6 @@ the CloudFormation spec and additional checks.  Includes checking valid values
 for resource properties and best practices.")
     (license license:expat)))
 
-(define-public python-jschema-to-python
-  (package
-    (name "python-jschema-to-python")
-    (version "1.2.3")
-    (source (origin
-              (method url-fetch)
-              (uri (pypi-uri "jschema_to_python" version))
-              (sha256
-               (base32
-                "14cvaiwm56g0v6p7zviikaa5i9ln3yqy910jmp60hirhbpz19zvn"))))
-    (build-system python-build-system)
-    (propagated-inputs (list python-attrs python-jsonpickle python-pbr))
-    (native-inputs (list python-pytest))
-    (home-page "https://github.com/microsoft/jschema-to-python")
-    (synopsis "Generate Python classes from a JSON schema")
-    (description "This package generates source code for Python classes from a
-@url{http://jschema.org,JSchema} JSON schema.")
-    (license license:expat)))
-
 (define-public python-requests-cache
   (package
     (name "python-requests-cache")
@@ -2323,6 +2291,33 @@ responses as planin JSON/YAML file or save responses as plain JSON/YAML
 files.")
     (license license:bsd-2)))
 
+(define-public python-requests-futures
+  (package
+    (name "python-requests-futures")
+    (version "1.0.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "requests_futures" version))
+       (sha256
+        (base32 "1njqfjmd72l5f32jvcppg2afrvb0cd8angdwmq7q0vik81wvazkb"))))
+    (build-system pyproject-build-system)
+    (native-inputs
+     (list python-greenlet
+           python-pytest
+           python-pytest-httpbin
+           python-readme-renderer
+           python-setuptools
+           python-twine
+           python-werkzeug))
+    (propagated-inputs (list python-requests))
+    (home-page "https://github.com/ross/requests-futures")
+    (synopsis "Asynchronous Python HTTP for Humans")
+    (description
+     "This package provides and add-on the Python Requests HTTP library to run
+code asynchronously.")
+    (license license:asl2.0)))
+
 (define-public python-s3path
   (package
     (name "python-s3path")
@@ -2351,26 +2346,6 @@ files.")
 AWS S3 Service using boto3 S3 resource as a driver.")
     (license license:asl2.0)))
 
-(define-public python-sarif-om
-  (package
-    (name "python-sarif-om")
-    (version "1.0.4")
-    (source (origin
-              (method url-fetch)
-              (uri (pypi-uri "sarif_om" version))
-              (sha256
-               (base32
-                "167gb8xjm0310km3w1s12bqldbv7zyklkr4j5900vq4361ml2pyd"))))
-    (build-system python-build-system)
-    (propagated-inputs (list python-attrs))
-    (native-inputs (list python-pbr))
-    (home-page "https://github.com/microsoft/sarif-python-om")
-    (synopsis "Python implementation of the SARIF 2.1.0 object model")
-    (description "This module contains classes for the object model defined
-by the @url{https://sarifweb.azurewebsites.net,Static Analysis Results
-Interchange Format (SARIF)} file format.")
-    (license license:expat)))
-
 (define-public python-falcon
   (package
     (name "python-falcon")
@@ -2675,7 +2650,7 @@ HTTP servers, RESTful APIs, and web services.")
            python-pytest-localserver
            python-pytest-socket
            python-setuptools
-           python-setuptools-scm-next
+           python-setuptools-scm
            python-wheel))
     (propagated-inputs
      (list python-aiofiles
@@ -3397,7 +3372,7 @@ be written directly in Python without templates.")
       #:test-flags
       ;; XXX: requires network access.
       #~(list "--ignore=tests/unit/credentials_test.py")))
-    (native-inputs (list python-pytest python-setuptools-next))
+    (native-inputs (list python-pytest python-setuptools))
     (propagated-inputs
      (list python-certifi python-dateutil python-pytz python-urllib3))
     (home-page "https://github.com/minio/minio-py")
@@ -3477,32 +3452,27 @@ high-speed transfers via libcurl and frequently outperforms alternatives.")
 (define-public python-url-normalize
   (package
     (name "python-url-normalize")
-    (version "1.4.3")
+    (version "2.2.1")
     (source
      (origin
        (method git-fetch)               ; no tests in PyPI release
        (uri (git-reference
-             (url "https://github.com/niksite/url-normalize")
-             (commit version)))
+              (url "https://github.com/niksite/url-normalize")
+              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "09nac5nh94x0n4bfazjfxk96b20mfsx6r1fnvqv85gkzs0rwqkaq"))))
+        (base32 "1yhsf4sk6l6nznpnqigisbfz690a4g342dsk2n6dggh7q4l3amk4"))))
     (build-system pyproject-build-system)
     (arguments
      (list
-      #:phases
-      #~(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")))))))
+      #:test-flags #~(list "--ignore=tests/test_cli.py")))
     (native-inputs
-     (list python-poetry-core
-           python-pytest
-           python-pytest-flakes
+     (list python-pytest
            python-pytest-cov
-           python-pytest-socket))
+           python-pytest-socket
+           python-setuptools))
+    (propagated-inputs
+     (list python-idna))
     (home-page "https://github.com/niksite/url-normalize")
     (synopsis "URL normalization for Python")
     (description
@@ -4287,34 +4257,6 @@ connection to each user.")
 web framework, either via the basic or digest authentication schemes.")
     (license license:asl2.0)))
 
-(define-public python-terminado
-  (package
-    (name "python-terminado")
-    (version "0.18.1")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (pypi-uri "terminado" version))
-       (sha256
-        (base32
-         "0bpxag3n0148vsgmi6wh3ynmprykazzqys0lfxgpdr2xp32g42fy"))))
-    (build-system pyproject-build-system)
-    (arguments
-     (list
-      #:test-flags #~(list "-W" "default")))    ;taken from pyproject.toml
-    (native-inputs
-     (list python-hatchling
-           python-pytest
-           python-pytest-timeout))
-    (propagated-inputs
-     (list python-ptyprocess
-           python-tornado-6))
-    (home-page "https://github.com/jupyter/terminado")
-    (synopsis "Terminals served to term.js using Tornado websockets")
-    (description "This package provides a Tornado websocket backend for the
-term.js Javascript terminal emulator library.")
-    (license license:bsd-2)))
-
 (define-public python-wsgi-intercept
   (package
     (name "python-wsgi-intercept")
@@ -5128,7 +5070,7 @@ sanitizer Rust crate.")
        (sha256
         (base32 "0sqgg8jmg2j14f4h96h0rs42kr460v65lhanps6lhdvj5zp81cbh"))))
     (build-system pyproject-build-system)
-    (native-inputs (list python-psutil python-pytest python-setuptools-next))
+    (native-inputs (list python-psutil python-pytest python-setuptools))
     (home-page "https://github.com/daanzu/py-webrtcvad-wheels")
     (synopsis "Python interface to the WebRTC Voice Activity Detector (VAD)")
     (description
@@ -5239,7 +5181,7 @@ APIs.")
     (arguments
      ;; The test tries to open a connection to a remote server.
      `(#:tests? #f))
-    (native-inputs (list python-setuptools-next))
+    (native-inputs (list python-setuptools))
     (propagated-inputs (list python-apiron))
     (home-page "https://github.com/teffalump/beren")
     (synopsis "REST client for Orthanc DICOM servers")
@@ -5283,20 +5225,7 @@ APIs.")
 than Python’s urllib2 library.")
     (license license:asl2.0)))
 
-(define-public python-requests-next
-  (package
-    (inherit python-requests)
-    (name "python-requests")
-    (version "2.32.3")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (pypi-uri "requests" version))
-       (sha256
-        (base32 "0q5742pnibwy74169kacin3dmqg9jzmzk7qab5aq5caffcbm8djm"))))
-     (native-inputs
-      (modify-inputs (package-native-inputs python-requests)
-        (prepend nss-certs-for-test)))))
+(define-public python-requests-next python-requests)
 
 (define-public python-requests-kerberos
   (package
@@ -5343,8 +5272,8 @@ python-requests.")
            python-pytest
            python-waitress))
     (propagated-inputs
-     (list python-requests-next
-           python-urllib3-next))
+     (list python-requests
+           python-urllib3))
     (home-page "https://gitlab.com/thelabnyc/requests-unixsocket2")
     (synopsis "Talk HTTP via a UNIX domain socket")
     (description
@@ -5380,27 +5309,23 @@ library.")
 (define-public python-requests-mock
   (package
     (name "python-requests-mock")
-    (version "1.8.0")
+    (version "1.12.1")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "requests-mock" version))
        (sha256
-        (base32
-         "09nj8fmyj7xz2mgwyvbw0fl9zybmx2d3qd2hf529vvjc9s24d3z6"))))
-    (build-system python-build-system)
-    (propagated-inputs
-     (list python-requests python-six))
+        (base32 "008l6xysgs6ax56lairg1li5i4bb04i2z19w5bl5claj7crjxqg9"))))
+    (build-system pyproject-build-system)
     (native-inputs
-     (list python-pbr
-           python-discover
-           python-docutils
-           python-fixtures
-           python-mock
-           python-purl
+     (list python-purl
            python-pytest
-           python-sphinx
-           python-testrepository))
+           python-requests-futures
+           python-setuptools
+           python-setuptools-scm
+           python-testtools))
+    (propagated-inputs
+     (list python-requests))
     (home-page "https://requests-mock.readthedocs.org/")
     (synopsis "Mock out responses from the requests package")
     (description
@@ -5523,7 +5448,7 @@ protocol, both client and server for Python asyncio module.
       (build-system pyproject-build-system)
       (arguments
        (list #:test-flags #~(list "mohawk/tests.py")))
-      (native-inputs (list python-pytest python-setuptools-next))
+      (native-inputs (list python-pytest python-setuptools))
       (home-page "https://github.com/kumar303/mohawk")
       (synopsis "Library for Hawk HTTP authorization")
       (description
@@ -5721,21 +5646,7 @@ can reuse the same socket connection for multiple requests, it can POST files,
 supports url redirection and retries, and also gzip and deflate decoding.")
     (license license:expat)))
 
-(define-public python-urllib3-next
-  (package
-    (inherit python-urllib3)
-    (version "2.5.0")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (pypi-uri "urllib3" version))
-       (sha256
-        (base32
-         "0q17z6zlpyjv9ax5c3d30qwp9fwhz2sc4gbb7yyd86g4qwrpgi1z"))))
-    (native-inputs
-     (list python-hatch-vcs
-           python-hatchling
-           python-setuptools-scm))))
+(define-public python-urllib3-next python-urllib3)
 
 (define-public python-urllib3-1.25
   (package
@@ -6480,20 +6391,6 @@ provide an easy-to-use Python interface for building OAuth1 and OAuth2 clients."
 @code{httplib2} for use with @code{requests} session objects.")
     (license license:asl2.0)))
 
-(define-public python-cachecontrol-0.11
-  (package
-    (inherit python-cachecontrol)
-    (name "python-cachecontrol")
-    (version "0.11.7")
-    (source
-      (origin
-        (method url-fetch)
-        (uri (pypi-uri "CacheControl" version))
-        (sha256
-         (base32
-          "07jsfhlbcwgqg6ayz8nznzaqg5rmxqblbzxz1qvg5wc44pcjjy4g"))))
-    (native-inputs (list python-setuptools python-wheel))))
-
 (define-public python-betamax
   (package
     (name "python-betamax")
@@ -6582,26 +6479,23 @@ Betamax that may possibly end up in the main package.")
 (define-public python-s3fs
   (package
     (name "python-s3fs")
-    (version "2024.12.0")
+    (version "2025.7.0")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "s3fs" version))
        (sha256
-        (base32 "0mpxk4xvg0gwzapdh9r3fvnjhi8ymf96f7c756xabk26b67kl3qv"))))
+        (base32 "0b82wqf70q1srsjb7xbbjhlzm08lbghzm1pbwdam2x6prb09wzsy"))))
     (build-system pyproject-build-system)
-    ;; Many tests fail with "No such file or directory" raised by the HTTP
-    ;; client.
+    ;; TODO: Many tests fail with "No such file or directory" raised by the
+    ;; HTTP client.
     (arguments (list #:tests? #false))
-    (propagated-inputs (list python-aiobotocore python-aiohttp python-fsspec))
     (native-inputs
-     (list python-flask ;for moto
-           python-flask-cors
-           python-moto
-           python-pytest
-           python-pytest-asyncio
-           python-setuptools
-           python-wheel))
+     (list python-setuptools))
+    (propagated-inputs
+     (list python-aiobotocore
+           python-aiohttp
+           python-fsspec))
     (home-page "https://github.com/fsspec/s3fs/")
     (synopsis "Convenient filesystem interface over S3")
     (description "This package provides a convenient filesystem interface over
@@ -7554,7 +7448,7 @@ users, gradebooks, and more.")
         (base32 "1gncv3l11za0mpxvmpaf5n5j3jzp282rz62yml4ha4z55q930d8l"))))
     (build-system pyproject-build-system)
     (arguments (list #:tests? #f))      ;There are no tests.
-    (native-inputs (list python-setuptools-next))
+    (native-inputs (list python-setuptools))
     (propagated-inputs (list python-beautifulsoup4))
     (home-page "https://breakingcode.wordpress.com/")
     (synopsis "Python bindings to the Google search engine")
@@ -9180,40 +9074,47 @@ requests.")
     (name "python-flask-restx")
     (version "1.3.0")
     (source
-     ;; We fetch from the Git repo because there are no tests in the PyPI
-     ;; archive.
      (origin
-       (method git-fetch)
+       (method git-fetch)       ;no tests in PyPI archive
        (uri (git-reference
-             (url "https://github.com/python-restx/flask-restx")
-             (commit version)))
+              (url "https://github.com/python-restx/flask-restx")
+              (commit version)))
        (file-name (git-file-name name version))
        (sha256
         (base32 "1qmm3i1cdv0bvzsc1gn4ql2dsf1fbx85fk69vcmzpsdxzczmw508"))))
-    (build-system python-build-system)
-    (propagated-inputs
-     (list python-aniso8601 python-flask python-jsonschema python-pytz))
+    (build-system pyproject-build-system)
+    (arguments
+     (list
+      ;; 1214 passed, 6 skipped, 16 deselected, 3 warnings
+      #:test-flags
+      #~(list "--benchmark-skip"
+              ;; ValueError: http://www.google.com is not a valid URL. Domain
+              ;; does not exists.
+              "--deselect=tests/test_inputs.py::URLTest::test_check"
+              "-k" (string-join
+                    ;; See: <https://github.com/python-restx/flask-restx/issues/620>.
+                    (list "not test_rfc822_value"
+                          "test_iso8601_value"
+                          ;; assert 404 == 2000
+                          "test_specs_endpoint_host_and_subdomain"
+                          ;; ValueError: test@gmail.com is not a valid email
+                          "test_valid_value_check")
+                    " and not "))))
     (native-inputs
      (list python-blinker
            python-faker
            python-pytest
            python-pytest-benchmark
            python-pytest-flask
-           python-pytest-mock))
-    (arguments
-     `(#:phases
-       (modify-phases %standard-phases
-         (replace 'check
-           (lambda _
-             (invoke "pytest" "--benchmark-skip" "-k"
-                     ;; Those tests need internet access
-                     (string-join
-                      '("not test_check"
-                        "not test_valid_value_check"
-                        "not test_override_app_level"
-                        "not test_redirect"
-                        "not test_swagger")
-                      " and ")))))))
+           python-pytest-mock
+           python-setuptools))
+    (propagated-inputs
+     (list python-aniso8601
+           python-flask
+           python-importlib-resources
+           python-jsonschema
+           python-pytz
+           python-werkzeug))
     (home-page "https://github.com/python-restx/flask-restx")
     (synopsis
      "Framework for fast, easy and documented API development with Flask")
@@ -9724,7 +9625,7 @@ over IMAP:
        (sha256
         (base32 "1fdbxp176p17sn5xc1418mz2vk00hlcsd5qmi2fdcfphqal6raan"))))
     (build-system pyproject-build-system)
-    (native-inputs (list python-pytest python-setuptools-next))
+    (native-inputs (list python-pytest python-setuptools))
     (home-page "https://github.com/nephila/giturlparse")
     (synopsis "Git URL parsing module")
     (description
@@ -9747,7 +9648,7 @@ and rewriting of remote git URLs from various hosting providers.")
         (base32 "02mdzhgdz3sprgc26qb084zy639h2zw2yc8d2vm1r18ap9k51ayq"))))
     (build-system pyproject-build-system)
     (arguments (list #:tests? #f))      ; tests require external resources.
-    (native-inputs (list python-setuptools-next))
+    (native-inputs (list python-setuptools))
     (home-page "https://github.com/sethmlarson/hstspreload")
     (synopsis "Chromium HSTS Preload list as a Python package")
     (description
@@ -10112,7 +10013,7 @@ SOCKS5(h), HTTP tunnel).")
     (build-system pyproject-build-system)
     (arguments
      (list #:tests? #f))         ;no tests in PyPI archive
-    (native-inputs (list python-setuptools-next))
+    (native-inputs (list python-setuptools))
     (propagated-inputs (list python-azure-nspkg))
     (home-page "https://github.com/Azure/azure-storage-python")
     (synopsis "Microsoft Azure Storage Namespace package")
@@ -10662,7 +10563,7 @@ real-life projects with legacy data and diverse storage providers.")
        (sha256
         (base32 "083ir0nccm14431mmn243862gq731ww98fwpd95zm1yccvpzdy68"))))
     (build-system pyproject-build-system)
-    (native-inputs (list python-pytest python-setuptools-next))
+    (native-inputs (list python-pytest python-setuptools))
     (home-page "https://github.com/earwig/mwparserfromhell")
     (synopsis "Python parser for MediaWiki wikicode")
     (description
@@ -11318,7 +11219,7 @@ and FastAPI.")
         (base32 "0psrlvax8249ccs2rvgdygpckzz22vxjcyzr2pql06d48k61gk54"))))
     (build-system pyproject-build-system)
     (arguments (list #:tests? #false)) ; There are no tests.
-    (native-inputs (list python-setuptools-next))
+    (native-inputs (list python-setuptools))
     (home-page "https://pypi.org/project/whereismyip/")
     (synopsis "Queries multiple geolocation services until one succeeds")
     (description

gnu/packages/shells.scm

@@ -669,7 +669,7 @@ ksh, and tcsh.")
            python-pytest-subprocess
            python-pytest-timeout
            python-requests
-           python-setuptools-next))
+           python-setuptools))
     (inputs
      (list python-distro
            python-ply

gnu/packages/sphinx.scm

@@ -273,111 +273,6 @@ sources.")
            (texlive-local-tree
             (list texlive-anyfontsize texlive-cm-super texlive-tex-gyre))))))
 
-(define-public python-sphinx-5
-  (package
-    (inherit python-sphinx)
-    (version "5.3.0")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (pypi-uri "Sphinx" version))
-       (sha256
-        (base32
-         "1dclwwz5rsvlw5rzyad1ar7i0zh4csni6jfp0lyc37zzm7h6s0ji"))))
-    (arguments
-     (list
-      #:test-flags
-      ;; These require Internet access.
-      '(list "--ignore=tests/test_build_linkcheck.py"
-             "-k"
-             (string-append
-              "not test_latex_images"
-              ;; XXX: Not clear why this fails with a version comparison
-              ;; failure.
-              " and not test_needs_sphinx"
-              ;; This fails on some machines with the failed assertion
-              ;; '5:11:17\u202fAM' == '5:11:17 AM'.
-              " and not test_format_date"
-              ;; This is a harmless failure.  The expected output looks for a
-              ;; long string that happens to contain a literal space
-              ;; character, but in the actual output the space character is
-              ;; wrapped in <span class="w"> </span>.
-              " 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"
-              ;; 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
-           (lambda _
-             ;; for test_cython
-             (setenv "HOME" "/tmp"))))))
-    (propagated-inputs
-     (list python-babel
-           python-colorama
-           python-docutils
-           python-filelock
-           python-html5lib
-           python-imagesize
-           python-importlib-metadata
-           python-jinja2
-           python-packaging
-           python-pygments
-           python-requests
-           python-snowballstemmer
-           python-sphinx-alabaster-theme
-           python-sphinxcontrib-applehelp
-           python-sphinxcontrib-devhelp
-           python-sphinxcontrib-htmlhelp
-           python-sphinxcontrib-jsmath
-           python-sphinxcontrib-qthelp
-           python-sphinxcontrib-serializinghtml
-           python-sphinxcontrib-websupport
-           python-types-requests
-
-           ;; The Sphinx LaTeX library '\RequirePackage' or \\usepackage
-           ;; these:
-           texlive-scheme-basic         ;for a valid TeX Live tree
-           texlive-anyfontsize
-           texlive-capt-of
-           texlive-cm-super
-           texlive-cmap
-           texlive-etoolbox
-           texlive-fancyvrb
-           texlive-float
-           texlive-fncychap
-           texlive-fontspec
-           texlive-framed
-           texlive-luatex85
-           texlive-luatexbase
-           texlive-needspace
-           texlive-parskip
-           texlive-polyglossia
-           texlive-preview
-           texlive-tabulary
-           texlive-tex-gyre
-           texlive-titlesec
-           texlive-upquote
-           texlive-varwidth
-           texlive-wrapfig
-           texlive-xcolor))
-    (native-inputs
-     (list fontconfig
-           font-gnu-freefont
-           ;; imagemagick is added for "convert".  The store item does not
-           ;; retain a reference to imagemagick, so it should be safe to use
-           ;; 'imagemagick/stable' instead of 'imagemagick'.  This is enforced
-           ;; by the '#:disallowed-references' above.
-           imagemagick/stable
-           python-cython
-           python-flit-core
-           python-pytest
-           (texlive-local-tree
-            (list texlive-anyfontsize texlive-cm-super texlive-tex-gyre))))))
-
 (define-public python-sphinxcontrib-apidoc
   (package
     (name "python-sphinxcontrib-apidoc")
@@ -560,9 +455,14 @@ size responsive web components.")
        (sha256
         (base32
          "1x9af78vamjjcdrrhiah3wg613jv7gm8yh9vvqfrmf4vam6mimyg"))))
-    (build-system python-build-system)
+    (build-system pyproject-build-system)
+    (arguments
+     `(#:tests? #f))    ;no tests
+    (native-inputs
+     (list python-flit-core))
     (propagated-inputs
-     (list python-docutils python-sphinx))
+     (list python-docutils
+           python-sphinx))
     (home-page "https://github.com/jupyter/sphinxcontrib_github_alt")
     (synopsis "Link to GitHub pages from Sphinx docs")
     (description
@@ -744,43 +644,6 @@ user profiles.  Support for GitHub is built-in, but other services can also be
 supported with @code{sphinx-issues}.")
     (license license:expat)))
 
-(define-public python-sphinx-panels
-  (package
-    (name "python-sphinx-panels")
-    (version "0.6.0")
-    (source
-      (origin
-        ;; Tests not included in the pypi release.
-        (method git-fetch)
-        (uri (git-reference
-               (url "https://github.com/executablebooks/sphinx-panels")
-               (commit (string-append "v" version))))
-        (file-name (git-file-name name version))
-        (sha256
-         (base32 "1ivqz6yv96a2jp59kylg1gbkrmzq6zwilppz3ij0zrkjn25zb97k"))))
-    (build-system pyproject-build-system)
-    (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
-           python-setuptools
-           python-wheel))
-    (home-page "https://github.com/executablebooks/sphinx-panels")
-    (synopsis "Sphinx extension for creating panels in a grid layout")
-    (description
-     "This package provides a sphinx extension for creating panels in a
-grid layout.  It is no longer maintained and users are encouraged to use
-@code{sphinx-design} instead.")
-    (license license:expat)))
-
 (define-public python-sphinx-tabs
   (package
     (name "python-sphinx-tabs")

gnu/packages/statistics.scm

@@ -671,7 +671,7 @@ and a lot more.")
               "dcor/tests")))
     (native-inputs
      (list python-pytest
-           python-setuptools-next))
+           python-setuptools))
     (propagated-inputs
      (list python-joblib
            python-numba
@@ -1100,19 +1100,19 @@ correlated samples from Markov Chain Monte Carlo (MCMC).")
               (uri (pypi-uri "hdmedians" version))
               (sha256
                (base32
-                "1mn2k8srnmfy451l7zvb2l4hn9701bc5awjm6q3vmqbicyqyqyml"))))
+                "1mn2k8srnmfy451l7zvb2l4hn9701bc5awjm6q3vmqbicyqyqyml"))
+       (patches (search-patches "python-hdmedians-replace-nose.patch"))))
     (build-system pyproject-build-system)
     (arguments
      (list
-      #:phases
-      '(modify-phases %standard-phases
-         (add-before 'check 'build-extensions
-           (lambda _
-             ;; Cython extensions have to be built before running the tests.
-             (invoke "python" "setup.py" "build_ext" "--inplace"))))))
-    (propagated-inputs (list python-cython python-numpy python-setuptools
-                             python-wheel))
-    (native-inputs (list python-nose))
+      #:test-flags #~(list "--pyargs" "hdmedians")))
+    (native-inputs
+     (list python-pytest))
+    (propagated-inputs
+     (list python-cython
+           python-numpy
+           python-setuptools
+           python-wheel))
     (home-page "http://github.com/daleroberts/hdmedians")
     (synopsis "High-dimensional medians")
     (description "Various definitions for a high-dimensional median exist and
@@ -1349,7 +1349,7 @@ Meier, Nelson Aalen and regression.")
                (base32
                 "1bkikqjya6gkds3n4qj6svvyz6czkwrc5s66ffb62l6wi4v2f89a"))))
     (build-system pyproject-build-system)
-    (native-inputs (list python-pandas python-pytest python-setuptools-next
+    (native-inputs (list python-pandas python-pytest python-setuptools
                          python-wheel))
     (propagated-inputs (list python-numpy python-scikit-learn))
     (home-page "https://github.com/scikit-learn-contrib/MAPIE")
@@ -1404,7 +1404,7 @@ conformal prediction methods intervals.")
     (native-inputs
      (list python-cython-3
            python-matplotlib
-           python-setuptools-next
+           python-setuptools
            python-setuptools-scm))
     (home-page
      (string-append "https://www.statsmodels.org/v" version "/"))

gnu/packages/sugar.scm

@@ -443,7 +443,7 @@ the Sugar Toolkit.")
               (lambda _
                 (invoke "python" "setup.py" "install"
                         (string-append "--prefix=" #$output)))))))
-      (native-inputs (list python-setuptools-next))
+      (native-inputs (list python-setuptools))
       (propagated-inputs
        (list gtk+
              gstreamer
@@ -504,7 +504,7 @@ a Tetris-like game.")
            telepathy-glib
            webkitgtk-for-gtk3))
     (inputs (list (list glib "bin")))
-    (native-inputs (list gettext-minimal python-setuptools-next))
+    (native-inputs (list gettext-minimal python-setuptools))
     (home-page "https://help.sugarlabs.org/browse.html")
     (synopsis "Sugar activity to browse the internet")
     (description "Browse is a web browser activity for the Sugar desktop.")
@@ -563,7 +563,7 @@ import pygame
       ;; All these libraries are accessed via gobject introspection.
       (propagated-inputs (list gtk+ sugar-toolkit-gtk3))
       (inputs (list python-pygame))
-      (native-inputs (list gettext-minimal python-setuptools-next))
+      (native-inputs (list gettext-minimal python-setuptools))
       (home-page "https://github.com/sugarlabs/cellgame")
       (synopsis "Cell game for Sugar")
       (description "This game for the Sugar desktop is based on the mechanisms
@@ -616,7 +616,7 @@ present in gene regulatory networks.")
              python-pygobject
              sugar-toolkit-gtk3
              telepathy-glib))
-      (native-inputs (list gettext-minimal python-setuptools-next))
+      (native-inputs (list gettext-minimal python-setuptools))
       (home-page "https://help.sugarlabs.org/chat.html")
       (synopsis "Sugar activity to chat")
       (description "Chat is an activity used to exchange messages with friends
@@ -664,7 +664,7 @@ or classmates.")
              gtk+
              python-pygobject
              sugar-toolkit-gtk3))
-      (native-inputs (list gettext-minimal python-setuptools-next))
+      (native-inputs (list gettext-minimal python-setuptools))
       (home-page "https://github.com/sugarlabs/classify-cats")
       (synopsis "Classify cats based on various criteria")
       (description "This is a Sugar activity where players classify cats based
@@ -727,7 +727,7 @@ import logging
              python-pygobject
              sugar-toolkit-gtk3))
       (inputs (list python-pygame))
-      (native-inputs (list gettext-minimal python-setuptools-next))
+      (native-inputs (list gettext-minimal python-setuptools))
       (home-page "https://github.com/sugarlabs/sugar-commander")
       (synopsis "Manage your Sugar journal")
       (description
@@ -780,7 +780,7 @@ the Journal.")
                 (invoke "python" "setup.py" "install"
                         (string-append "--prefix=" #$output)))))))
       (native-inputs
-       (list sugar-toolkit-gtk3 python-sphinx python-setuptools-next))
+       (list sugar-toolkit-gtk3 python-sphinx python-setuptools))
       (propagated-inputs (list webkitgtk-for-gtk3))
       (home-page "https://github.com/sugarlabs/help-activity")
       (synopsis "Sugar activity for accessing documentation and manuals")
@@ -823,7 +823,7 @@ users with easy access to documentation and manuals.")
                 (setenv "HOME" "/tmp")
                 (invoke "python" "setup.py" "install"
                         (string-append "--prefix=" #$output)))))))
-      (native-inputs (list python-setuptools-next))
+      (native-inputs (list python-setuptools))
       ;; All these libraries are accessed via gobject introspection.
       (propagated-inputs
        (list gtk+
@@ -901,7 +901,7 @@ and @file{.pls}.")
       ;; All these libraries are accessed via gobject introspection.
       (propagated-inputs (list gtk+ sugar-toolkit-gtk3))
       (inputs (list coreutils net-tools procps))
-      (native-inputs (list gettext-minimal python-setuptools-next))
+      (native-inputs (list gettext-minimal python-setuptools))
       (home-page "https://help.sugarlabs.org/log.html")
       (synopsis "Log activity for the Sugar learning environment")
       (description
@@ -942,7 +942,7 @@ looking for why an activity or Sugar is not working properly.")
               (setenv "HOME" "/tmp")
               (invoke "python" "setup.py" "install"
                       (string-append "--prefix=" #$output)))))))
-    (native-inputs (list python-setuptools-next))
+    (native-inputs (list python-setuptools))
     ;; All these libraries are accessed via gobject introspection.
     (propagated-inputs (list gtk+ telepathy-glib))
     (inputs (list sugar-toolkit-gtk3 gettext-minimal))
@@ -999,7 +999,7 @@ for directory in \"" (getenv "GUIX_PYTHONPATH") "\".split(\":\"):
                 (setenv "HOME" "/tmp")
                 (invoke "python" "setup.py" "install"
                         (string-append "--prefix=" #$output)))))))
-      (native-inputs (list python-setuptools-next))
+      (native-inputs (list python-setuptools))
       ;; All these libraries are accessed via gobject introspection.
       (propagated-inputs (list gtk+ gdk-pixbuf))
       (inputs (list python-pybox2d python-pygame sugar-toolkit-gtk3
@@ -1047,7 +1047,7 @@ life with forces (think gravity, Newton!), friction (scrrrrape), and inertia
                 (setenv "HOME" "/tmp")
                 (invoke "python" "setup.py" "install"
                         (string-append "--prefix=" #$output)))))))
-      (native-inputs (list python-setuptools-next))
+      (native-inputs (list python-setuptools))
       ;; All these libraries are accessed via gobject introspection.
       (propagated-inputs
        (list cairo
@@ -1101,7 +1101,7 @@ Journal entries that have been ‘starred’.")
               (setenv "HOME" "/tmp")
               (invoke "python" "setup.py" "install"
                       (string-append "--prefix=" #$output)))))))
-    (native-inputs (list python-setuptools-next))
+    (native-inputs (list python-setuptools))
     ;; All these libraries are accessed via gobject introspection.
     (propagated-inputs
      (list evince
@@ -1166,7 +1166,7 @@ import pygame
                 (setenv "HOME" "/tmp")
                 (invoke "python" "setup.py" "install"
                         (string-append "--prefix=" #$output)))))))
-      (native-inputs (list python-setuptools-next))
+      (native-inputs (list python-setuptools))
       ;; These libraries are accessed via gobject introspection.
       (propagated-inputs (list gtk+))
       (inputs (list python-pygame sugar-toolkit-gtk3 gettext-minimal))
@@ -1214,7 +1214,7 @@ hesitate to feast on the goat.")
                 (setenv "HOME" "/tmp")
                 (invoke "python" "setup.py" "install"
                         (string-append "--prefix=" #$output)))))))
-      (native-inputs (list python-setuptools-next))
+      (native-inputs (list python-setuptools))
       ;; All these libraries are accessed via gobject introspection.
       (propagated-inputs (list gtk+ vte/gtk+-3 sugar-toolkit-gtk3))
       (inputs (list gettext-minimal))
@@ -1293,7 +1293,7 @@ a Command-Line Interface (CLI) to the system.")
                 (setenv "HOME" "/tmp")
                 (invoke "python" "setup.py" "install"
                         (string-append "--prefix=" #$output)))))))
-      (native-inputs (list python-setuptools-next))
+      (native-inputs (list python-setuptools))
       ;; All these libraries are accessed via gobject introspection.
       (propagated-inputs
        (list gstreamer
@@ -1375,7 +1375,7 @@ import logging
              gtk+
              python-pygobject
              sugar-toolkit-gtk3))
-      (native-inputs (list gettext-minimal python-setuptools-next))
+      (native-inputs (list gettext-minimal python-setuptools))
       (home-page "https://github.com/sugarlabs/turtlepond")
       (synopsis "Turtle-based strategy game")
       (description "Turtle in a Pond is a strategy game.  The goal is to
@@ -1420,7 +1420,7 @@ surround the turtle before it runs off the screen.")
               (invoke "python" "setup.py" "install"
                       (string-append "--prefix=" #$output)))))))
     (native-inputs
-     (list gettext-minimal sugar-toolkit-gtk3 python-setuptools-next))
+     (list gettext-minimal sugar-toolkit-gtk3 python-setuptools))
     (inputs (list setxkbmap))
     (home-page "https://help.sugarlabs.org/en/typing_turtle.html")
     (synopsis "Learn typing")
@@ -1465,7 +1465,7 @@ typist.")
                 (setenv "HOME" "/tmp")
                 (invoke "python" "setup.py" "install"
                         (string-append "--prefix=" #$output)))))))
-      (native-inputs (list python-setuptools-next))
+      (native-inputs (list python-setuptools))
       ;; All these libraries are accessed via gobject introspection.
       (propagated-inputs
        (list abiword

gnu/packages/terminals.scm

@@ -30,7 +30,6 @@
 ;;; Copyright © 2021 Brice Waegeneire <brice@waegenei.re>
 ;;; Copyright © 2021 Solene Rapenne <solene@perso.pw>
 ;;; Copyright © 2021 Petr Hodina <phodina@protonmail.com>
-;;; Copyright © 2021 Stefan Reichör <stefan@xsteve.at>
 ;;; Copyright © 2022 Felipe Balbi <balbi@kernel.org>
 ;;; Copyright © 2022 ( <paren@disroot.org>
 ;;; Copyright © 2022, 2023 jgart <jgart@dismail.de>
@@ -1064,161 +1063,6 @@ minimalistic.")
 usable with any list--including files, command history, processes and more.")
     (license license:expat)))
 
-(define-public python-pyte
-  (package
-    (name "python-pyte")
-    (version "0.8.2")
-    (source
-     (origin
-       (method git-fetch)
-       (uri (git-reference
-              (url "https://github.com/selectel/pyte")
-              (commit version)))
-       (file-name (git-file-name name version))
-       (sha256
-        (base32 "1cdhnl6rp4kcbs3s766519k80pf5ma18mgv6cyidf4nbgysjavmv"))))
-    (build-system pyproject-build-system)
-    (propagated-inputs (list python-wcwidth))
-    (native-inputs (list python-pytest python-setuptools python-wheel))
-    (home-page "https://pyte.readthedocs.io/")
-    (synopsis "Simple VTXXX-compatible terminal emulator")
-    (description "@code{pyte} is an in-memory VTxxx-compatible terminal
-emulator.  @var{VTxxx} stands for a series of video terminals, developed by
-DEC between 1970 and 1995.  The first and probably most famous one was the
-VT100 terminal, which is now a de-facto standard for all virtual terminal
-emulators.
-
-pyte is a fork of vt102, which was an incomplete pure Python implementation
-of VT100 terminal.")
-    (license license:lgpl3+)))
-
-(define-public python-blessings
-  (package
-    (name "python-blessings")
-    (version "1.7")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (pypi-uri "blessings" version))
-       (sha256
-        (base32
-         "0z8mgkbmisxs10rz88qg46l1c9a8n08k8cy2iassal2zh16qbrcq"))))
-    (build-system python-build-system)
-    (arguments
-     ;; FIXME: Test suite is unable to detect TTY conditions.
-     `(#:tests? #f))
-    (native-inputs
-     (list python-nose python-six))
-    (home-page "https://github.com/erikrose/blessings")
-    (synopsis "Python module to manage terminal color, styling, and
-positioning")
-    (description "Blessings is a pythonic API to manipulate terminal color,
-styling, and positioning.  It provides similar features to curses but avoids
-some of curses’s limitations: it does not require clearing the whole screen
-for little changes, provides a scroll-back buffer after the program exits, and
-avoids styling altogether when the output is redirected to something other
-than a terminal.")
-    (license license:expat)))
-
-(define-public python-curtsies
-  (package
-    (name "python-curtsies")
-    (version "0.4.3")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (pypi-uri "curtsies" version))
-       (sha256
-        (base32 "09c8c4vssm2zkq017xj99vhcrisfva4nkz92w8dly4jjz7xhyahh"))))
-    (build-system pyproject-build-system)
-    (native-inputs
-     (list python-pyte
-           python-pytest
-           python-setuptools
-           python-wheel))
-    (propagated-inputs
-     (list python-blessed
-           python-cwcwidth))
-    (home-page "https://github.com/bpython/curtsies")
-    (synopsis "Library for curses-like terminal interaction with colored strings")
-    (description
-     "Curtsies is a Python library for interacting with the terminal.  It
-features string-like objects which carry formatting information, per-line
-fullscreen terminal rendering, and keyboard input event reporting.")
-    (license license:expat)))
-
-(define-public python-halo
-  (package
-    (name "python-halo")
-    (version "0.0.31")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (pypi-uri "halo" version))
-       (sha256
-        (base32 "1mn97h370ggbc9vi6x8r6akd5q8i512y6kid2nvm67g93r9a6rvv"))))
-    (build-system pyproject-build-system)
-    (arguments
-     (list #:tests? #f))         ;no tests in PyPI archive, no tags in Git
-    (native-inputs
-     (list python-setuptools))
-    (propagated-inputs
-     (list python-colorama
-           python-log-symbols
-           python-six
-           python-spinners
-           python-termcolor))
-    (home-page "https://github.com/manrajgrover/halo")
-    (synopsis "Python library to display graphical spinners in the terminal")
-    (description "Halo is a Python library to display graphical spinners in
-the terminal.  It also supports IPython/Jupyter.")
-    (license license:expat)))
-
-(define-public python-log-symbols
-  (package
-    (name "python-log-symbols")
-    (version "0.0.14")
-    (source (origin
-              (method url-fetch)
-              (uri (pypi-uri "log_symbols" version))
-              (sha256
-               (base32
-                "0mh5d0igw33libfmbsr1ri1p1y644p36nwaa2w6kzrd8w5pvq2yg"))))
-    (build-system pyproject-build-system)
-    (arguments
-     (list #:tests? #f))         ;no tests in PyPI archive, tests depend on Nose
-    (native-inputs
-     (list python-setuptools))
-    (propagated-inputs
-     (list python-colorama))
-    (home-page "https://github.com/manrajgrover/py-log-symbols")
-    (synopsis "Python library with graphical symbols for logging on the terminal")
-    (description "This package provides a Python library with graphical symbols
-that can be displayed on the terminal, with color if possible, for logging
-purposes.")
-    (license license:expat)))
-
-(define-public python-spinners
-  (package
-    (name "python-spinners")
-    (version "0.0.24")
-    (source (origin
-              (method url-fetch)
-              (uri (pypi-uri "spinners" version))
-              (sha256
-               (base32
-                "0zz2z6dpdjdq5z8m8w8dfi8by0ih1zrdq0caxm1anwhxg2saxdhy"))))
-    (build-system pyproject-build-system)
-    (arguments
-     (list #:tests? #f))         ;no tests in PyPI archive, tests depend on Nose
-    (native-inputs
-     (list python-setuptools))
-    (home-page "https://github.com/manrajgrover/py-spinners")
-    (synopsis "Python library with graphical spinners for the terminal")
-    (description "Spinners is a Python library that contains graphical spinners
-that can be displayed terminal.")
-    (license license:expat)))
-
 (define-public tmate
   (package
     (name "tmate")

gnu/packages/textutils.scm

@@ -1058,43 +1058,6 @@ Eclipse and NetBeans.  Completion information is typically specified in an XML
 file, but can even be dynamic.")
     (license license:bsd-3)))
 
-;; We use the sources from git instead of the tarball from pypi, because the
-;; latter does not include the Cython source file from which bycython.cpp is
-;; generated.
-(define-public python-editdistance
-  (let ((commit "3ea84a7dd3258c76aa3be851ef3d50e59c886846")
-        (revision "1"))
-    (package
-      (name "python-editdistance")
-      (version (string-append "0.3.1-" revision "." (string-take commit 7)))
-      (source
-       (origin
-         (method git-fetch)
-         (uri (git-reference
-               (url "https://github.com/aflc/editdistance")
-               (commit commit)))
-         (file-name (git-file-name name version))
-         (sha256
-          (base32
-           "1l43svsv12crvzphrgi6x435z6xg8m086c64armp8wzb4l8ccm7g"))))
-      (build-system python-build-system)
-      (arguments
-       `(#:phases
-         (modify-phases %standard-phases
-           (add-after 'unpack 'build-cython-code
-             (lambda _
-               (with-directory-excursion "editdistance"
-                 (delete-file "bycython.cpp")
-                 (invoke "cython" "--cplus" "bycython.pyx")))))))
-      (native-inputs
-       (list python-cython))
-      (home-page "https://www.github.com/aflc/editdistance")
-      (synopsis "Fast implementation of the edit distance (Levenshtein distance)")
-      (description
-       "This library simply implements Levenshtein distance algorithm with C++
-and Cython.")
-      (license license:expat))))
-
 (define-public txt2tags
   (package
     (name "txt2tags")

gnu/packages/time.scm

@@ -387,6 +387,8 @@ datetime module, available in Python 2.3+.")
     (license (list bsd-3 asl2.0))))
 
 (define-public python-dateutils
+  ;; XXX: The last release was in 2021, no development on the master
+  ;; branch. consider to remove when nothing depends on it.
   (package
     (name "python-dateutils")
     (version "0.6.12")
@@ -397,8 +399,9 @@ datetime module, available in Python 2.3+.")
                (base32
                 "1wg3f3imjq3snvjccv64h5498pqv9xz664xhni7bsh8mnay91p83"))))
     (build-system pyproject-build-system)
+    (arguments (list #:tests? #f)) ;requires twine
     (propagated-inputs (list python-dateutil python-pytz))
-    (native-inputs (list python-setuptools python-wheel))
+    (native-inputs (list python-setuptools))
     (home-page "https://github.com/jmcantrell/python-dateutils")
     (synopsis "Various utilities for working with date and datetime objects")
     (description

gnu/packages/tor.scm

@@ -301,7 +301,7 @@ networks.")
            python-setuptools
            python-stem
            python-unidecode
-           python-urllib3-next
+           python-urllib3
            python-waitress
            python-werkzeug
            tor))

gnu/packages/version-control.scm

@@ -2833,7 +2833,7 @@ execution of any hook written in any language before every commit.")
     (native-inputs
      (list python-docutils
            ;; The following inputs are only needed to run the tests.
-           python-setuptools-next python-setuptools-scm-next python-wheel unzip which))
+           python-setuptools python-setuptools-scm python-wheel unzip which))
     (inputs
      (list python-wrapper))
     ;; Find third-party extensions.

gnu/packages/video.scm

@@ -3203,7 +3203,7 @@ video streaming services of the Finnish national broadcasting company Yle.")
                   python-certifi
                   python-mutagen
                   python-pycryptodomex
-                  python-requests-next ; TODO Remove this special package
+                  python-requests ; TODO Remove this special package
                   python-urllib3
                   python-websockets))
     (native-inputs
@@ -3373,7 +3373,7 @@ Both command-line and GTK2 interface are available.")
            python-wcwidth
            python-websockets
            python-urllib3
-           python-requests-next
+           python-requests
            python-pycryptodomex
            python-mutagen
            python-brotli
@@ -6592,7 +6592,7 @@ can also directly record to WebM or MP4 if you prefer.")
      (list python-dbus
            python-pygobject
            python-pytest
-           python-setuptools-next
+           python-setuptools
            python-wheel))
     (propagated-inputs
      (list python-pylast

gnu/packages/xdisorg.scm

@@ -2166,64 +2166,80 @@ connectivity of the X server running on a particular @code{DISPLAY}.")
     (license license:gpl3+)))
 
 (define-public ulauncher
-  (package
-    (name "ulauncher")
-    (version "6.0.0")
-    (source (origin
-              (method git-fetch)
-              (uri (git-reference
-                    (url "https://github.com/Ulauncher/Ulauncher")
-                    (commit "1e68d47473f8e77d375cb4eca644c3cda68ed7e9")))
-              (file-name (git-file-name name version))
-              (sha256
-               (base32
-                "1c2czlrsf5aq8c88qliqbnqvf04q9cnjc1j6hivqa0w260mzjll1"))))
-    (build-system python-build-system)
-    (arguments
-     (list #:phases #~(modify-phases %standard-phases
-                        (add-after 'unpack 'fix-libX11
-                          (lambda* (#:key inputs #:allow-other-keys)
-                            (substitute* "ulauncher/utils/xinit.py"
-                              (("libX11.so.6")
-                               (search-input-file inputs "/lib/libX11.so")))))
-                        (add-after 'unpack 'fix-usr
-                          (lambda _
-                            (substitute* "setup.py"
-                              (("\\{sys.prefix\\}")
-                               (string-append #$output)))))
-                        (add-after 'unpack 'fix-os-release
-                          (lambda _
-                            (define (touch file)
-                              (call-with-output-file file
-                                (const #t)))
-                            (let* ((hard-path "/etc/os-release")
-                                   (fixed-path (string-append #$output
-                                                              hard-path)))
-                              ;; Make it relative
-                              ;; Update hardcoded path to something
-                              ;; within the build enviroment.
-                              (substitute* "ulauncher/utils/environment.py"
-                                ((hard-path)
-                                 fixed-path))
-                              ;; Create directory for the dummy file.
-                              (mkdir-p (string-append #$output "/etc"))
-                              (touch fixed-path))))
-                        (add-before 'check 'env-setup
-                          ;; The test require access to home to put temporary files.
-                          (lambda _
-                            (setenv "HOME"
-                                    (getcwd)))))))
-    (native-inputs (list intltool python-distutils-extra python-mock))
-    (inputs (list libx11 python-levenshtein python-pycairo))
-    (propagated-inputs (list keybinder libwnck gsettings-desktop-schemas
-                             python-pygobject webkitgtk-with-libsoup2))
-    (home-page "https://ulauncher.io")
-    (synopsis "Application launcher for Linux")
-    (description
-     "Ulauncher is a fast application launcher for Linux.  It is written in
+  (let ((commit "901ce03beb157ff8fb354558594495eb74c6de7b")
+        (revision "18"))
+    (package
+      (name "ulauncher")
+      (version (git-version "6.0.0" revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/Ulauncher/Ulauncher")
+               (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32 "0qrqpbqrrklfgqr48zafzggrbzns2q6h27nh63skfd9w582nsajg"))))
+      (build-system pyproject-build-system)
+      (arguments
+       (list
+        #:test-flags
+        ;; XXX: Most likely require a running X server.
+        #~(list "--ignore=tests/ui/test_preferences_server.py"
+                "--ignore=tests/ui/test_result_widget.py")
+        #:phases
+        #~(modify-phases %standard-phases
+            (add-after 'unpack 'fix-libX11
+              (lambda* (#:key inputs #:allow-other-keys)
+                (substitute* "ulauncher/utils/xinit.py"
+                  (("libX11.so.6")
+                   (search-input-file inputs "/lib/libX11.so")))))
+            (add-after 'unpack 'fix-bash
+              (lambda* (#:key inputs #:allow-other-keys)
+                (substitute* "tests/modes/shortcuts/test_run_script.py"
+                  (("/bin/bash")
+                   (search-input-file inputs "bin/bash")))))
+            (add-after 'unpack 'fix-os-release
+              (lambda _
+                (define (touch file)
+                  (call-with-output-file file
+                    (const #t)))
+                (let* ((hard-path "/etc/os-release")
+                       (fixed-path (string-append #$output hard-path)))
+                  ;; Make it relative
+                  ;; Update hardcoded path to something
+                  ;; within the build enviroment.
+                  (substitute* "ulauncher/utils/environment.py"
+                    ((hard-path)
+                     fixed-path))
+                  ;; Create directory for the dummy file.
+                  (mkdir-p (string-append #$output "/etc"))
+                  (touch fixed-path))))
+            (add-before 'check 'env-setup
+              ;; The test require access to home to put temporary files.
+              (lambda _
+                (setenv "HOME"
+                        (getcwd)))))))
+      (native-inputs (list intltool
+                           python-mock
+                           python-pytest
+                           python-pytest-mock
+                           python-setuptools
+                           python-wheel))
+      (inputs (list libx11 python-levenshtein python-pycairo))
+      (propagated-inputs (list keybinder
+                               libwnck
+                               gsettings-desktop-schemas
+                               python-pygobject
+                               python-xlib
+                               webkitgtk-with-libsoup2))
+      (home-page "https://ulauncher.io")
+      (synopsis "Application launcher for Linux")
+      (description
+       "Ulauncher is a fast application launcher for Linux.  It is written in
 Python, using GTK+, and features: App Search (fuzzy matching), Calculator,
 Extensions, Shortcuts, File browser mode and Custom Color Themes.")
-    (license license:gpl3+)))
+      (license license:gpl3+))))
 
 (define-public rofi
   (package
@@ -2834,7 +2850,7 @@ both binary and text data.")
     (arguments
      '(#:tests? #f)) ; Not clear how to make tests pass.
     (native-inputs
-     (list python-setuptools-next))
+     (list python-setuptools))
     (inputs
      (list xclip xsel))
     (home-page "https://github.com/asweigart/pyperclip")

gnu/packages/xorg.scm

@@ -2109,7 +2109,7 @@ server.")
     (inputs
      (list libxmu libxext libxau libx11))
     (native-inputs
-     (list cmdtest pkg-config))
+     (list pkg-config))
     (home-page "https://www.x.org/wiki/")
     (synopsis "X authority file utility")
     (description