GNU logs - #76835, boring messages

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Subject: [bug#76835] [PATCH python-team 00/15] Some further python fixes
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We might want to check out with Chris if nothing is broken with an
update of patchwork.

Nicolas Graves (12):
  gnu: gunicorn: Migrate 'check phase to pyproject-build-system.
  gnu: python-unyt: Avoid deprecation failure in tests.
  gnu: python-carbon: Update to 1.1.10.
  gnu: Add python-rrdtool.
  gnu: python-h2: Fix test-flags.
  gnu: graphite-web: Update to 1.1.10-2.49c28e2.
  gnu: python-nptyping: Ignore failing test.
  gnu: python-cfn-lint: Update to 1.28.0.
  gnu: patchwork: Update to 3.2.1.
  gnu: Remove python-django-3.2.
  gnu: python-uqbar: Update to 7.0.0.
  gnu: Remove python-sphinx-autodoc-typehints-5.

Nicolas Graves via Guix-patches via (3):
  gnu: python-sphinx-panels: Update input to python-sphinx-5.
  gnu: python-numpy-documentation: Update python-sphinx native-input.
  gnu: Remove python-sphinx-4.

 gnu/packages/django.scm         |  20 +----
 gnu/packages/graphviz.scm       |  11 +--
 gnu/packages/monitoring.scm     | 128 ++++++++++++++++++++++----------
 gnu/packages/patchutils.scm     |   6 +-
 gnu/packages/python-check.scm   |   2 +
 gnu/packages/python-science.scm |   3 +
 gnu/packages/python-web.scm     |  26 +++----
 gnu/packages/python-xyz.scm     |  14 +++-
 gnu/packages/sphinx.scm         |  36 +++------
 9 files changed, 132 insertions(+), 114 deletions(-)

-- 
2.48.1

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From: help-debbugs@HIDDEN (GNU bug Tracking System)
To: Nicolas Graves <ngraves@HIDDEN>
Subject: bug#76835: Acknowledgement ([PATCH python-team 00/15] Some
 further python fixes)
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Date: Fri, 07 Mar 2025 18:51:02 +0000

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76835: https://debbugs.gnu.org/cgi/bugreport.cgi?bug=3D76835
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Subject: [bug#76835] [PATCH 03/15] gnu: python-carbon: Update to 1.1.10.
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* gnu/packages/monitoring.scm (python-carbon): Update to 1.1.10.
---
 gnu/packages/monitoring.scm | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/gnu/packages/monitoring.scm b/gnu/packages/monitoring.scm
index 9813b5ca67..01b554d9aa 100644
--- a/gnu/packages/monitoring.scm
+++ b/gnu/packages/monitoring.scm
@@ -433,23 +433,24 @@ (define-public python-whisper
 (define-public python-carbon
   (package
     (name "python-carbon")
-    (version "1.1.8")
+    (version "1.1.10")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "carbon" version))
        (sha256
         (base32
-         "1wb91fipk1niciffq5xwqbh8g7rl7ghdam4m97cjbig12i5qr4cm"))))
-    (build-system python-build-system)
+         "0p6yjxif5ly5wkllnaw41w2zy9y0nffgfk91v861fn6c26lmnfy1"))))
+    (build-system pyproject-build-system)
     (arguments
      `(#:phases
        (modify-phases %standard-phases
          ;; Don't install to /opt
          (add-after 'unpack 'do-not-install-to-/opt
            (lambda _ (setenv "GRAPHITE_NO_PREFIX" "1") #t)))))
+    (native-inputs (list python-setuptools python-wheel))
     (propagated-inputs
-     (list python-cachetools python-txamqp python-urllib3 python-whisper))
+     (list python-cachetools python-twisted python-txamqp python-urllib3))
     (home-page "https://graphiteapp.org/")
     (synopsis "Backend data caching and persistence daemon for Graphite")
     (description "Carbon is a backend data caching and persistence daemon for
-- 
2.48.1

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Subject: [bug#76835] [PATCH 02/15] gnu: python-unyt: Avoid deprecation failure in tests.
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* gnu/packages/python-science.scm (python-unyt)[arguments]
{test-flags}: Ignore failing test.
---
 gnu/packages/python-science.scm | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm
index 2fa57f0ab5..ca259356cf 100644
--- a/gnu/packages/python-science.scm
+++ b/gnu/packages/python-science.scm
@@ -2526,6 +2526,9 @@ (define-public python-unyt
        (sha256
         (base32 "0jrq2vhan2h280h6cw1sm5hys2nzmf19w4py64k3nrkc320z9mni"))))
     (build-system pyproject-build-system)
+    (arguments
+     ;; This is a Numpy DeprecationWarning, remove it on next update.
+     (list #:test-flags ''("-k" "not test_h5_io")))
     ;; Pint is optional, but we do not propagate it due to its size.
     (native-inputs
      (list python-pint
-- 
2.48.1

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* gnu/packages/python-web.scm (gunicorn)[arguments]
{phases}: Remove 'check phase and migrate its flags to...
{test-flags}: ...here.
---
 gnu/packages/python-web.scm | 16 +++++-----------
 1 file changed, 5 insertions(+), 11 deletions(-)

diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm
index 7495616f2e..4765ab2358 100644
--- a/gnu/packages/python-web.scm
+++ b/gnu/packages/python-web.scm
@@ -7304,23 +7304,17 @@ (define-public gunicorn
     (outputs '("out" "doc"))
     (build-system pyproject-build-system)
     (arguments
-     `(#:phases
+     `(#:test-flags
+       ;; Disable the geventlet tests because eventlet uses dnspython, which
+       ;; does not work in the build container due to lack of /etc/resolv.conf
+       '("--ignore=tests/workers/test_geventlet.py")
+       #:phases
        (modify-phases %standard-phases
          (add-after 'build 'build-doc
            (lambda _
              (invoke "make" "-C" "docs" "PAPER=a4" "html" "info")
              (delete-file "docs/build/texinfo/Makefile")
              (delete-file "docs/build/texinfo/Gunicorn.texi")))
-         (replace 'check
-           (lambda* (#:key tests? #:allow-other-keys)
-             (if tests?
-                 (begin
-                   (invoke "pytest" "-vv"
-                           ;; Disable the geventlet tests because eventlet uses
-                           ;; dnspython, which does not work in the build
-                           ;; container due to lack of /etc/resolv.conf, etc.
-                           "--ignore=tests/workers/test_geventlet.py"))
-                 (format #t "test suite not run~%"))))
          (add-after 'install 'install-doc
            (lambda* (#:key outputs #:allow-other-keys)
              (let* ((doc (string-append (assoc-ref outputs "doc")
-- 
2.48.1

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* gnu/packages/monitoring.scm (python-rrdtool): New variable.
---
 gnu/packages/monitoring.scm | 20 ++++++++++++++++++++
 1 file changed, 20 insertions(+)

diff --git a/gnu/packages/monitoring.scm b/gnu/packages/monitoring.scm
index 01b554d9aa..b75500fc08 100644
--- a/gnu/packages/monitoring.scm
+++ b/gnu/packages/monitoring.scm
@@ -14,6 +14,7 @@
 ;;; Copyright © 2022 Hartmut Goebel <h.goebel@HIDDEN>
 ;;; Copyright © 2022 ( <paren@HIDDEN>
 ;;; Copyright © 2022 Mathieu Laparie <mlaparie@HIDDEN>
+;;; Copyright © 2025 Nicolas Graves <ngraves@HIDDEN>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -839,6 +840,25 @@ (define-public pw
 @end itemize")
     (license license:bsd-2)))
 
+(define-public python-rrdtool
+  (package
+    (name "python-rrdtool")
+    (version "0.1.16")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "rrdtool" version))
+       (sha256
+        (base32 "0l8lbarzfwbwnq9jm9gv4mmrxgjlb9hbz27sa8b703qa7s5zy2jz"))))
+    (build-system pyproject-build-system)
+    (arguments (list #:tests? #f)) ; No tests in pypi archive
+    (inputs (list rrdtool))
+    (native-inputs (list python-setuptools python-wheel))
+    (home-page "https://github.com/commx/python-rrdtool")
+    (synopsis "Python bindings for rrdtool")
+    (description "This package provides Python bindings for rrdtool.")
+    (license license:lgpl2.1)))
+
 (define-public python-statsd
   (package
     (name "python-statsd")
-- 
2.48.1

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* gnu/packages/python-web.scm (python-h2)[arguments]{test-flags}:
Fix quoting.
---
 gnu/packages/python-web.scm | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm
index 4765ab2358..2438fba134 100644
--- a/gnu/packages/python-web.scm
+++ b/gnu/packages/python-web.scm
@@ -2483,9 +2483,9 @@ (define-public python-h2
               (string-join
                (list "not test_remotesettingschanged_repr"
                      ;; This test exceededs the Hypothesis deadline.
-                     ,@(if (target-riscv64?)
-                           `("test_changing_max_frame_size")
-                           '())
+                     #$@(if (target-riscv64?)
+                            #~("test_changing_max_frame_size")
+                            #~())
                      "test_streamreset_repr"
                      "test_settingsacknowledged_repr"
                      "test_connectionterminated_repr[None-None]"
-- 
2.48.1

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* gnu/packages/monitoring.scm (graphite-web): Update to 1.1.10-2.49c28e2.
---
 gnu/packages/monitoring.scm | 99 +++++++++++++++++++++++--------------
 1 file changed, 62 insertions(+), 37 deletions(-)

diff --git a/gnu/packages/monitoring.scm b/gnu/packages/monitoring.scm
index b75500fc08..1009c32783 100644
--- a/gnu/packages/monitoring.scm
+++ b/gnu/packages/monitoring.scm
@@ -69,6 +69,7 @@ (define-module (gnu packages monitoring)
   #:use-module (gnu packages prometheus)
   #:use-module (gnu packages python)
   #:use-module (gnu packages python-build)
+  #:use-module (gnu packages python-science)
   #:use-module (gnu packages python-web)
   #:use-module (gnu packages python-xyz)
   #:use-module (gnu packages rrdtool)
@@ -461,45 +462,69 @@ (define-public python-carbon
     (license license:asl2.0)))
 
 (define-public graphite-web
-  (package
-    (name "graphite-web")
-    (version "1.1.10")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (pypi-uri "graphite-web" version))
-       (sha256
-        (base32
-         "0nnk3kwn0b6bq9xnmv9bac6hpcbdgpgwf283c1ck5nm80panh61z"))))
-    (build-system python-build-system)
-    (arguments
-     `(#:tests? #f               ;XXX: not in PyPI release & requires database
-       #:phases
-       (modify-phases %standard-phases
-         (add-after 'unpack 'relax-requirements
-           (lambda _
-             (substitute* "setup.py"
-               ;; Allow newer versions of django-tagging.
-               (("django-tagging==") "django-tagging>=")
-               ;; And Django.
-               (("Django>=1\\.8,<3\\.1") "Django>=1.8,<4"))))
-         ;; Don't install to /opt
-         (add-after 'unpack 'do-not-install-to-/opt
-           (lambda _ (setenv "GRAPHITE_NO_PREFIX" "1") #t)))))
-    (propagated-inputs
-     (list python-cairocffi
-           python-django-3.2
-           python-django-tagging
-           python-pyparsing
-           python-pytz
-           python-six
-           python-urllib3))
-    (home-page "https://graphiteapp.org/")
-    (synopsis "Scalable realtime graphing system")
-    (description "Graphite is a scalable real-time graphing system that does
+  (let ((commit "49c28e2015d605ad9ec93524f7076dd924a4731a")
+        (revision "2"))
+    (package
+      (name "graphite-web")
+      (version (git-version "1.1.10" revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/graphite-project/graphite-web")
+               (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32 "0bcc6jh7gyp8f54dzy4zza1z46gk3530r952pi86irf834z106sg"))))
+      (build-system pyproject-build-system)
+      (arguments
+       `(#:tests? #f               ;XXX: Requires database, unable to run now
+         #:phases
+         (modify-phases %standard-phases
+           (add-after 'unpack 'relax-requirements
+             (lambda _
+               (substitute* "setup.py"
+                 ;; Allow newer versions of django-tagging.
+                 (("django-tagging==") "django-tagging>=")
+                 ;; And Django.
+                 (("Django>=3\\.2,<4") "Django>=4,<5"))))
+           ;; Don't install to /opt
+           (add-after 'unpack 'do-not-install-to-/opt
+             (lambda _ (setenv "GRAPHITE_NO_PREFIX" "1")))
+           (replace 'check
+             (lambda* (#:key tests? #:allow-other-keys)
+               (when tests?
+                 (mkdir-p "storage/log/webapp")
+                 (with-directory-excursion "webapp"
+                   (invoke "./manage.py" "test" "--pythonpath=." "tests"
+                           "-k" (string-join
+                                 (list
+                                  "not test_dashboard_save_temporary_xss_key"
+                                  "test_dashboard_save_temporary_xss_name")
+                                 " and not ")))))))))
+      (native-inputs
+       (list python-carbon
+             python-mock
+             python-pytest
+             python-rrdtool
+             python-setuptools
+             python-tzdata
+             python-wheel
+             python-whisper))
+      (propagated-inputs
+       (list python-cairocffi
+             python-django-4.2
+             python-django-tagging
+             python-pyparsing
+             python-pytz
+             python-six
+             python-urllib3))
+      (home-page "https://graphiteapp.org/")
+      (synopsis "Scalable realtime graphing system")
+      (description "Graphite is a scalable real-time graphing system that does
 two things: store numeric time-series data, and render graphs of this data on
 demand.")
-    (license license:asl2.0)))
+      (license license:asl2.0))))
 
 (define-public python-prometheus-client
   (package
-- 
2.48.1

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* gnu/packages/python-web.scm (python-cfn-lint): Update to 1.28.0.
---
 gnu/packages/python-web.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm
index 2438fba134..77a4e5c8f1 100644
--- a/gnu/packages/python-web.scm
+++ b/gnu/packages/python-web.scm
@@ -1659,7 +1659,7 @@ (define-public python-cbor2
 (define-public python-cfn-lint
   (package
     (name "python-cfn-lint")
-    (version "1.22.1")
+    (version "1.28.0")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -1668,7 +1668,7 @@ (define-public python-cfn-lint
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "1zz121r9yv1irwdbk07s7958fh43h3r3q39qcj0gv4kpgb0vdf32"))))
+                "0n1v05516s0zy64v1a7f7pj5h9lscvbkkwnlgmys7g8lydlgf0v4"))))
     (build-system pyproject-build-system)
     (arguments
      (list
-- 
2.48.1

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* gnu/packages/python-check.scm (python-nptyping)[arguments]
{test-flags}: Ignore failing test.
---
 gnu/packages/python-check.scm | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/gnu/packages/python-check.scm b/gnu/packages/python-check.scm
index c969499521..1138e287f1 100644
--- a/gnu/packages/python-check.scm
+++ b/gnu/packages/python-check.scm
@@ -2601,6 +2601,8 @@ (define-public python-nptyping
      (list
       #:test-flags
       #~(list
+         ;; This one started failing with the last update of Numpy.
+         "--ignore=tests/test_beartype.py"
          ;; Multiple failures due to undefined names (typing package must be
          ;; too outdated, or perhaps they use a newer pandas).
          "--ignore=tests/test_mypy.py"
-- 
2.48.1

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* gnu/packages/patchutils.scm (patchwork): Update to 3.2.1.
---
 gnu/packages/patchutils.scm | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/patchutils.scm b/gnu/packages/patchutils.scm
index 3cd3507b07..b2b84046b4 100644
--- a/gnu/packages/patchutils.scm
+++ b/gnu/packages/patchutils.scm
@@ -370,7 +370,7 @@ (define-public meld
 (define-public patchwork
   (package
     (name "patchwork")
-    (version "3.1.1")
+    (version "3.2.1")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -379,7 +379,7 @@ (define-public patchwork
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "0is9d4gf93jcbyshyj2k3kjyrjnvimrm6bai6dbcx630md222j5w"))))
+                "04ikawdyhjwspxvhazbp5f5vym672y0jcw8rd2m75h9ipcpnyxim"))))
     (build-system python-build-system)
     (arguments
      `(;; TODO: Tests require a running database
@@ -503,7 +503,7 @@ (define pythonpath
     (inputs
      (list python-wrapper))
     (propagated-inputs
-     (list python-django-3.2
+     (list python-django
            ;; TODO: Make this configurable
            python-psycopg2
            python-mysqlclient
-- 
2.48.1

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* gnu/packages/django.scm (python-django-3.2): Delete variable.
---
 gnu/packages/django.scm | 20 ++------------------
 1 file changed, 2 insertions(+), 18 deletions(-)

diff --git a/gnu/packages/django.scm b/gnu/packages/django.scm
index cb9df0d2df..20522231ac 100644
--- a/gnu/packages/django.scm
+++ b/gnu/packages/django.scm
@@ -148,26 +148,10 @@ (define-public python-django-4.2
                   ;; This CVE seems fixed since 4.2.1.
                   (lint-hidden-cve . ("CVE-2023-31047"))))))
 
-(define-public python-django-3.2
-  (package
-    (inherit python-django-4.2)
-    (version "3.2.21")
-    (source (origin
-              (method url-fetch)
-              (uri (pypi-uri "Django" version))
-              (sha256
-               (base32
-                "0g3zm2glh76g31q06g6fwkwvkrphjj3mnap5sgk1hx3v9r44rpm5"))))
-    (native-search-paths '())           ;no need for TZDIR
-    (propagated-inputs
-     (modify-inputs (package-propagated-inputs python-django-4.2)
-       ;; Django 4.0 deprecated pytz in favor of Pythons built-in zoneinfo.
-       (append python-pytz)))))
-
 ;; archivebox requires django>=3.1.3,<3.2
 (define-public python-django-3.1.14
   (package
-    (inherit python-django-3.2)
+    (inherit python-django-4.2)
     (version "3.1.14")
     (source (origin
               (method url-fetch)
@@ -176,7 +160,7 @@ (define-public python-django-3.1.14
                (base32
                 "0ix3v2wlnplv78zxjrlw8z3hiap2d5mxvk0ny2fc65526shsb93j"))))
     (propagated-inputs
-     (modify-inputs (package-propagated-inputs python-django-3.2)
+     (modify-inputs (package-propagated-inputs python-django-4.2)
        ;; Django 4.0 deprecated pytz in favor of Pythons built-in zoneinfo.
        (append python-pytz)))))
 
-- 
2.48.1

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* gnu/packages/graphviz.scm (python-uqbar): Update to 7.0.0.
[propagated-inputs]: Replace python-sphinx-5 by python-sphinx,
recursively.
---
 gnu/packages/graphviz.scm | 11 +++--------
 1 file changed, 3 insertions(+), 8 deletions(-)

diff --git a/gnu/packages/graphviz.scm b/gnu/packages/graphviz.scm
index defd53df73..c23369acc4 100644
--- a/gnu/packages/graphviz.scm
+++ b/gnu/packages/graphviz.scm
@@ -208,7 +208,7 @@ (define-public python-pygraphviz
 (define-public python-uqbar
   (package
     (name "python-uqbar")
-    (version "0.6.9")
+    (version "7.0.0")
     (source
      (origin
        (method git-fetch)
@@ -217,7 +217,7 @@ (define-public python-uqbar
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "037qj3rymm6xzdpklddfhmfp2p1bq9fi3jrvxj6gmharphd5z869"))))
+        (base32 "0qa32d2z7bg3h26r18dv55g9lghw59wln7rkcciavyyjh553q430"))))
     (build-system pyproject-build-system)
     (arguments  ; XXX: Disable failing tests.
      (list #:test-flags '(list "tests" "-k" "not test_find_executable \
@@ -232,12 +232,7 @@ (define-public python-uqbar
            python-setuptools
            python-wheel))
     (propagated-inputs
-     (list python-black python-sphinx-5 python-unidecode
-           (package/inherit python-sphinx-rtd-theme
-             (propagated-inputs
-              (modify-inputs
-                  (package-propagated-inputs python-sphinx-rtd-theme)
-                (replace "python-sphinx" python-sphinx-5))))))
+     (list python-black python-sphinx python-unidecode python-sphinx-rtd-theme))
     (home-page "https://github.com/josiah-wolf-oberholtzer/uqbar")
     (synopsis "Tools for building documentation with Sphinx, Graphviz and LaTeX")
     (description
-- 
2.48.1

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* gnu/packages/sphinx.scm (python-sphinx-autodoc-typehints-5): Delete variable.
---
 gnu/packages/sphinx.scm | 7 -------
 1 file changed, 7 deletions(-)

diff --git a/gnu/packages/sphinx.scm b/gnu/packages/sphinx.scm
index 6847592a99..5f06cb04f5 100644
--- a/gnu/packages/sphinx.scm
+++ b/gnu/packages/sphinx.scm
@@ -1234,13 +1234,6 @@ (define-public python-sphinx-autodoc-typehints
 documenting acceptable argument types and return value types of functions.")
     (license license:expat)))
 
-(define-public python-sphinx-autodoc-typehints-5
-  (package/inherit python-sphinx-autodoc-typehints
-    (propagated-inputs
-     (modify-inputs
-         (package-propagated-inputs python-sphinx-autodoc-typehints)
-       (replace "python-sphinx" python-sphinx-5)))))
-
 (define-public python-sphinx-pytest
   (package
     (name "python-sphinx-pytest")
-- 
2.48.1

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From: Nicolas Graves via Guix-patches via <guix-patches@HIDDEN>

* gnu/packages/python-xyz.scm (python-numpy-documentation):
[arguments]{phases}: Add phase 'avoid-external-deps. Adapt phase
'install by removing sphinx.ext.autodoc extension.
[native-inputs]: Replace python-sphinx-4 by python-sphinx. Add
python-sphinx-design.
---
 gnu/packages/python-xyz.scm | 14 +++++++++++++-
 1 file changed, 13 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index bacfac6c42..6054a88562 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -9684,6 +9684,16 @@ (define-public python-numpy-documentation
       #:tests? #f                     ;we're only generating the documentation
       #:phases
       #~(modify-phases %standard-phases
+          (add-after 'unpack 'avoid-external-deps
+            (lambda _
+              ;; XXX: Avoid theme-switcher to avoid sphinx error
+              ;; TemplateNotFound('theme-switcher.html')
+              ;; XXX: Avoid version-switcher because it depends on the value
+              ;; of external https://numpy.org/doc/_static/versions.json
+              (substitute* "doc/source/conf.py"
+                (("\
+\"navbar_end\": \\[\"theme-switcher\", \"version-switcher\", ")
+                 "\"navbar_end\": ["))))
           (add-before 'build 'add-gnu-freefont-to-texmf
             (lambda _
               ;; XXX: The Sphinx-generated tex output specifies the GNU
@@ -9729,6 +9739,7 @@ (define-public python-numpy-documentation
                     (("\"contents\"") "'index'")
                     ;; Disable Sphinx extensions that produce broken Texinfo.
                     ((".*'numpydoc'.*") "")
+                    ((".*'sphinx.ext.autodoc'.*") "")
                     ((".*'sphinx.ext.autosummary'.*") ""))
                   (invoke "make" "info" sphinxopts)
                   ;; Install the HTML documentation.
@@ -9752,7 +9763,8 @@ (define-public python-numpy-documentation
            python-pandas
            python-pydata-sphinx-theme
            python-scipy                 ;used by matplotlib
-           python-sphinx-4
+           python-sphinx
+           python-sphinx-design
            python-sphinx-panels
            texinfo
            (texlive-updmap.cfg
-- 
2.48.1

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From: Nicolas Graves via Guix-patches via <guix-patches@HIDDEN>

* gnu/packages/sphinx.scm (python-sphinx-panels):
[arguments]{phases}: Add 'loosen-requirements phase.
[propagated-inputs]: Replace python-sphinx-4 by python-sphinx-5.
---
 gnu/packages/sphinx.scm | 10 +++++++++-
 1 file changed, 9 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/sphinx.scm b/gnu/packages/sphinx.scm
index 5f06cb04f5..024bfe986a 100644
--- a/gnu/packages/sphinx.scm
+++ b/gnu/packages/sphinx.scm
@@ -608,7 +608,15 @@ (define-public python-sphinx-panels
         (sha256
          (base32 "1ivqz6yv96a2jp59kylg1gbkrmzq6zwilppz3ij0zrkjn25zb97k"))))
     (build-system pyproject-build-system)
-    (propagated-inputs (list python-docutils-0.15 python-sphinx-4))
+    (arguments
+     (list #:phases
+           #~(modify-phases %standard-phases
+               (add-after 'unpack 'loosen-requirements
+                 (lambda _
+                   (substitute* "setup.py"
+                     (("sphinx>=2,<5")
+                      "sphinx>=2,<6")))))))
+    (propagated-inputs (list python-docutils-0.15 python-sphinx-5))
     (native-inputs
      (list python-pytest
            python-pytest-regressions
-- 
2.48.1

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From: Nicolas Graves via Guix-patches via <guix-patches@HIDDEN>

* gnu/packages/sphinx.scm (python-sphinx-4): Delete variable.
---
 gnu/packages/sphinx.scm | 19 -------------------
 1 file changed, 19 deletions(-)

diff --git a/gnu/packages/sphinx.scm b/gnu/packages/sphinx.scm
index 024bfe986a..58952049a1 100644
--- a/gnu/packages/sphinx.scm
+++ b/gnu/packages/sphinx.scm
@@ -267,25 +267,6 @@ (define-public python-sphinx-5
            (texlive-updmap.cfg
             (list texlive-cm-super texlive-tex-gyre))))))
 
-;; Some packages do not support Sphinx 5 yet.  Remove when unused.
-(define-public python-sphinx-4
-  (package
-    (inherit python-sphinx-5)
-    (version "4.5.0")
-    (source (origin
-              (method url-fetch)
-              (uri (pypi-uri "Sphinx" version))
-              (sha256
-               (base32
-                "1rp28jryxwy24y8vpacclqihbizyi6b1s6id86pibvm46ybcmy3v"))))
-    (propagated-inputs
-     (modify-inputs (package-propagated-inputs python-sphinx)
-       (replace "python-docutils" python-docutils-0.15)))
-    (native-inputs
-     (modify-inputs (package-native-inputs python-sphinx)
-       (delete python-flit-core)
-       (append python-setuptools python-wheel)))))
-
 (define-public python-sphinxcontrib-apidoc
   (package
     (name "python-sphinxcontrib-apidoc")
-- 
2.48.1

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* gnu/packages/python-web.scm (gunicorn)[arguments]
{phases}: Remove 'check phase and migrate its flags to...
{test-flags}: ...here.
---
 gnu/packages/python-web.scm | 16 +++++-----------
 1 file changed, 5 insertions(+), 11 deletions(-)

diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm
index 7495616f2e..4765ab2358 100644
--- a/gnu/packages/python-web.scm
+++ b/gnu/packages/python-web.scm
@@ -7304,23 +7304,17 @@ (define-public gunicorn
     (outputs '("out" "doc"))
     (build-system pyproject-build-system)
     (arguments
-     `(#:phases
+     `(#:test-flags
+       ;; Disable the geventlet tests because eventlet uses dnspython, which
+       ;; does not work in the build container due to lack of /etc/resolv.conf
+       '("--ignore=tests/workers/test_geventlet.py")
+       #:phases
        (modify-phases %standard-phases
          (add-after 'build 'build-doc
            (lambda _
              (invoke "make" "-C" "docs" "PAPER=a4" "html" "info")
              (delete-file "docs/build/texinfo/Makefile")
              (delete-file "docs/build/texinfo/Gunicorn.texi")))
-         (replace 'check
-           (lambda* (#:key tests? #:allow-other-keys)
-             (if tests?
-                 (begin
-                   (invoke "pytest" "-vv"
-                           ;; Disable the geventlet tests because eventlet uses
-                           ;; dnspython, which does not work in the build
-                           ;; container due to lack of /etc/resolv.conf, etc.
-                           "--ignore=tests/workers/test_geventlet.py"))
-                 (format #t "test suite not run~%"))))
          (add-after 'install 'install-doc
            (lambda* (#:key outputs #:allow-other-keys)
              (let* ((doc (string-append (assoc-ref outputs "doc")
-- 
2.48.1

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* gnu/packages/python-science.scm (python-unyt)[arguments]
{test-flags}: Ignore failing test.
---
 gnu/packages/python-science.scm | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm
index 2fa57f0ab5..ca259356cf 100644
--- a/gnu/packages/python-science.scm
+++ b/gnu/packages/python-science.scm
@@ -2526,6 +2526,9 @@ (define-public python-unyt
        (sha256
         (base32 "0jrq2vhan2h280h6cw1sm5hys2nzmf19w4py64k3nrkc320z9mni"))))
     (build-system pyproject-build-system)
+    (arguments
+     ;; This is a Numpy DeprecationWarning, remove it on next update.
+     (list #:test-flags ''("-k" "not test_h5_io")))
     ;; Pint is optional, but we do not propagate it due to its size.
     (native-inputs
      (list python-pint
-- 
2.48.1

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* gnu/packages/monitoring.scm (python-carbon): Update to 1.1.10.
---
 gnu/packages/monitoring.scm | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/gnu/packages/monitoring.scm b/gnu/packages/monitoring.scm
index 9813b5ca67..01b554d9aa 100644
--- a/gnu/packages/monitoring.scm
+++ b/gnu/packages/monitoring.scm
@@ -433,23 +433,24 @@ (define-public python-whisper
 (define-public python-carbon
   (package
     (name "python-carbon")
-    (version "1.1.8")
+    (version "1.1.10")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "carbon" version))
        (sha256
         (base32
-         "1wb91fipk1niciffq5xwqbh8g7rl7ghdam4m97cjbig12i5qr4cm"))))
-    (build-system python-build-system)
+         "0p6yjxif5ly5wkllnaw41w2zy9y0nffgfk91v861fn6c26lmnfy1"))))
+    (build-system pyproject-build-system)
     (arguments
      `(#:phases
        (modify-phases %standard-phases
          ;; Don't install to /opt
          (add-after 'unpack 'do-not-install-to-/opt
            (lambda _ (setenv "GRAPHITE_NO_PREFIX" "1") #t)))))
+    (native-inputs (list python-setuptools python-wheel))
     (propagated-inputs
-     (list python-cachetools python-txamqp python-urllib3 python-whisper))
+     (list python-cachetools python-twisted python-txamqp python-urllib3))
     (home-page "https://graphiteapp.org/")
     (synopsis "Backend data caching and persistence daemon for Graphite")
     (description "Carbon is a backend data caching and persistence daemon for
-- 
2.48.1

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* gnu/packages/monitoring.scm (python-rrdtool): New variable.
---
 gnu/packages/monitoring.scm | 20 ++++++++++++++++++++
 1 file changed, 20 insertions(+)

diff --git a/gnu/packages/monitoring.scm b/gnu/packages/monitoring.scm
index 01b554d9aa..b75500fc08 100644
--- a/gnu/packages/monitoring.scm
+++ b/gnu/packages/monitoring.scm
@@ -14,6 +14,7 @@
 ;;; Copyright © 2022 Hartmut Goebel <h.goebel@HIDDEN>
 ;;; Copyright © 2022 ( <paren@HIDDEN>
 ;;; Copyright © 2022 Mathieu Laparie <mlaparie@HIDDEN>
+;;; Copyright © 2025 Nicolas Graves <ngraves@HIDDEN>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -839,6 +840,25 @@ (define-public pw
 @end itemize")
     (license license:bsd-2)))
 
+(define-public python-rrdtool
+  (package
+    (name "python-rrdtool")
+    (version "0.1.16")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "rrdtool" version))
+       (sha256
+        (base32 "0l8lbarzfwbwnq9jm9gv4mmrxgjlb9hbz27sa8b703qa7s5zy2jz"))))
+    (build-system pyproject-build-system)
+    (arguments (list #:tests? #f)) ; No tests in pypi archive
+    (inputs (list rrdtool))
+    (native-inputs (list python-setuptools python-wheel))
+    (home-page "https://github.com/commx/python-rrdtool")
+    (synopsis "Python bindings for rrdtool")
+    (description "This package provides Python bindings for rrdtool.")
+    (license license:lgpl2.1)))
+
 (define-public python-statsd
   (package
     (name "python-statsd")
-- 
2.48.1

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* gnu/packages/python-web.scm (python-h2)[arguments]{test-flags}:
Fix quoting.
---
 gnu/packages/python-web.scm | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm
index 4765ab2358..2438fba134 100644
--- a/gnu/packages/python-web.scm
+++ b/gnu/packages/python-web.scm
@@ -2483,9 +2483,9 @@ (define-public python-h2
               (string-join
                (list "not test_remotesettingschanged_repr"
                      ;; This test exceededs the Hypothesis deadline.
-                     ,@(if (target-riscv64?)
-                           `("test_changing_max_frame_size")
-                           '())
+                     #$@(if (target-riscv64?)
+                            #~("test_changing_max_frame_size")
+                            #~())
                      "test_streamreset_repr"
                      "test_settingsacknowledged_repr"
                      "test_connectionterminated_repr[None-None]"
-- 
2.48.1

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* gnu/packages/monitoring.scm (graphite-web): Update to 1.1.10-2.49c28e2.
---
 gnu/packages/monitoring.scm | 99 +++++++++++++++++++++++--------------
 1 file changed, 62 insertions(+), 37 deletions(-)

diff --git a/gnu/packages/monitoring.scm b/gnu/packages/monitoring.scm
index b75500fc08..1009c32783 100644
--- a/gnu/packages/monitoring.scm
+++ b/gnu/packages/monitoring.scm
@@ -69,6 +69,7 @@ (define-module (gnu packages monitoring)
   #:use-module (gnu packages prometheus)
   #:use-module (gnu packages python)
   #:use-module (gnu packages python-build)
+  #:use-module (gnu packages python-science)
   #:use-module (gnu packages python-web)
   #:use-module (gnu packages python-xyz)
   #:use-module (gnu packages rrdtool)
@@ -461,45 +462,69 @@ (define-public python-carbon
     (license license:asl2.0)))
 
 (define-public graphite-web
-  (package
-    (name "graphite-web")
-    (version "1.1.10")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (pypi-uri "graphite-web" version))
-       (sha256
-        (base32
-         "0nnk3kwn0b6bq9xnmv9bac6hpcbdgpgwf283c1ck5nm80panh61z"))))
-    (build-system python-build-system)
-    (arguments
-     `(#:tests? #f               ;XXX: not in PyPI release & requires database
-       #:phases
-       (modify-phases %standard-phases
-         (add-after 'unpack 'relax-requirements
-           (lambda _
-             (substitute* "setup.py"
-               ;; Allow newer versions of django-tagging.
-               (("django-tagging==") "django-tagging>=")
-               ;; And Django.
-               (("Django>=1\\.8,<3\\.1") "Django>=1.8,<4"))))
-         ;; Don't install to /opt
-         (add-after 'unpack 'do-not-install-to-/opt
-           (lambda _ (setenv "GRAPHITE_NO_PREFIX" "1") #t)))))
-    (propagated-inputs
-     (list python-cairocffi
-           python-django-3.2
-           python-django-tagging
-           python-pyparsing
-           python-pytz
-           python-six
-           python-urllib3))
-    (home-page "https://graphiteapp.org/")
-    (synopsis "Scalable realtime graphing system")
-    (description "Graphite is a scalable real-time graphing system that does
+  (let ((commit "49c28e2015d605ad9ec93524f7076dd924a4731a")
+        (revision "2"))
+    (package
+      (name "graphite-web")
+      (version (git-version "1.1.10" revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/graphite-project/graphite-web")
+               (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32 "0bcc6jh7gyp8f54dzy4zza1z46gk3530r952pi86irf834z106sg"))))
+      (build-system pyproject-build-system)
+      (arguments
+       `(#:tests? #f               ;XXX: Requires database, unable to run now
+         #:phases
+         (modify-phases %standard-phases
+           (add-after 'unpack 'relax-requirements
+             (lambda _
+               (substitute* "setup.py"
+                 ;; Allow newer versions of django-tagging.
+                 (("django-tagging==") "django-tagging>=")
+                 ;; And Django.
+                 (("Django>=3\\.2,<4") "Django>=4,<5"))))
+           ;; Don't install to /opt
+           (add-after 'unpack 'do-not-install-to-/opt
+             (lambda _ (setenv "GRAPHITE_NO_PREFIX" "1")))
+           (replace 'check
+             (lambda* (#:key tests? #:allow-other-keys)
+               (when tests?
+                 (mkdir-p "storage/log/webapp")
+                 (with-directory-excursion "webapp"
+                   (invoke "./manage.py" "test" "--pythonpath=." "tests"
+                           "-k" (string-join
+                                 (list
+                                  "not test_dashboard_save_temporary_xss_key"
+                                  "test_dashboard_save_temporary_xss_name")
+                                 " and not ")))))))))
+      (native-inputs
+       (list python-carbon
+             python-mock
+             python-pytest
+             python-rrdtool
+             python-setuptools
+             python-tzdata
+             python-wheel
+             python-whisper))
+      (propagated-inputs
+       (list python-cairocffi
+             python-django-4.2
+             python-django-tagging
+             python-pyparsing
+             python-pytz
+             python-six
+             python-urllib3))
+      (home-page "https://graphiteapp.org/")
+      (synopsis "Scalable realtime graphing system")
+      (description "Graphite is a scalable real-time graphing system that does
 two things: store numeric time-series data, and render graphs of this data on
 demand.")
-    (license license:asl2.0)))
+      (license license:asl2.0))))
 
 (define-public python-prometheus-client
   (package
-- 
2.48.1

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* gnu/packages/python-web.scm (python-cfn-lint): Update to 1.28.0.
---
 gnu/packages/python-web.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm
index 2438fba134..77a4e5c8f1 100644
--- a/gnu/packages/python-web.scm
+++ b/gnu/packages/python-web.scm
@@ -1659,7 +1659,7 @@ (define-public python-cbor2
 (define-public python-cfn-lint
   (package
     (name "python-cfn-lint")
-    (version "1.22.1")
+    (version "1.28.0")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -1668,7 +1668,7 @@ (define-public python-cfn-lint
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "1zz121r9yv1irwdbk07s7958fh43h3r3q39qcj0gv4kpgb0vdf32"))))
+                "0n1v05516s0zy64v1a7f7pj5h9lscvbkkwnlgmys7g8lydlgf0v4"))))
     (build-system pyproject-build-system)
     (arguments
      (list
-- 
2.48.1

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* gnu/packages/patchutils.scm (patchwork): Update to 3.2.1.
---
 gnu/packages/patchutils.scm | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/patchutils.scm b/gnu/packages/patchutils.scm
index 3cd3507b07..b2b84046b4 100644
--- a/gnu/packages/patchutils.scm
+++ b/gnu/packages/patchutils.scm
@@ -370,7 +370,7 @@ (define-public meld
 (define-public patchwork
   (package
     (name "patchwork")
-    (version "3.1.1")
+    (version "3.2.1")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -379,7 +379,7 @@ (define-public patchwork
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "0is9d4gf93jcbyshyj2k3kjyrjnvimrm6bai6dbcx630md222j5w"))))
+                "04ikawdyhjwspxvhazbp5f5vym672y0jcw8rd2m75h9ipcpnyxim"))))
     (build-system python-build-system)
     (arguments
      `(;; TODO: Tests require a running database
@@ -503,7 +503,7 @@ (define pythonpath
     (inputs
      (list python-wrapper))
     (propagated-inputs
-     (list python-django-3.2
+     (list python-django
            ;; TODO: Make this configurable
            python-psycopg2
            python-mysqlclient
-- 
2.48.1

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* gnu/packages/django.scm (python-django-3.2): Delete variable.
---
 gnu/packages/django.scm | 20 ++------------------
 1 file changed, 2 insertions(+), 18 deletions(-)

diff --git a/gnu/packages/django.scm b/gnu/packages/django.scm
index cb9df0d2df..20522231ac 100644
--- a/gnu/packages/django.scm
+++ b/gnu/packages/django.scm
@@ -148,26 +148,10 @@ (define-public python-django-4.2
                   ;; This CVE seems fixed since 4.2.1.
                   (lint-hidden-cve . ("CVE-2023-31047"))))))
 
-(define-public python-django-3.2
-  (package
-    (inherit python-django-4.2)
-    (version "3.2.21")
-    (source (origin
-              (method url-fetch)
-              (uri (pypi-uri "Django" version))
-              (sha256
-               (base32
-                "0g3zm2glh76g31q06g6fwkwvkrphjj3mnap5sgk1hx3v9r44rpm5"))))
-    (native-search-paths '())           ;no need for TZDIR
-    (propagated-inputs
-     (modify-inputs (package-propagated-inputs python-django-4.2)
-       ;; Django 4.0 deprecated pytz in favor of Pythons built-in zoneinfo.
-       (append python-pytz)))))
-
 ;; archivebox requires django>=3.1.3,<3.2
 (define-public python-django-3.1.14
   (package
-    (inherit python-django-3.2)
+    (inherit python-django-4.2)
     (version "3.1.14")
     (source (origin
               (method url-fetch)
@@ -176,7 +160,7 @@ (define-public python-django-3.1.14
                (base32
                 "0ix3v2wlnplv78zxjrlw8z3hiap2d5mxvk0ny2fc65526shsb93j"))))
     (propagated-inputs
-     (modify-inputs (package-propagated-inputs python-django-3.2)
+     (modify-inputs (package-propagated-inputs python-django-4.2)
        ;; Django 4.0 deprecated pytz in favor of Pythons built-in zoneinfo.
        (append python-pytz)))))
 
-- 
2.48.1

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* gnu/packages/python-check.scm (python-nptyping)[arguments]
{test-flags}: Ignore failing test.
---
 gnu/packages/python-check.scm | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/gnu/packages/python-check.scm b/gnu/packages/python-check.scm
index c969499521..1138e287f1 100644
--- a/gnu/packages/python-check.scm
+++ b/gnu/packages/python-check.scm
@@ -2601,6 +2601,8 @@ (define-public python-nptyping
      (list
       #:test-flags
       #~(list
+         ;; This one started failing with the last update of Numpy.
+         "--ignore=tests/test_beartype.py"
          ;; Multiple failures due to undefined names (typing package must be
          ;; too outdated, or perhaps they use a newer pandas).
          "--ignore=tests/test_mypy.py"
-- 
2.48.1

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* gnu/packages/graphviz.scm (python-uqbar): Update to 7.0.0.
[propagated-inputs]: Replace python-sphinx-5 by python-sphinx,
recursively.
---
 gnu/packages/graphviz.scm | 11 +++--------
 1 file changed, 3 insertions(+), 8 deletions(-)

diff --git a/gnu/packages/graphviz.scm b/gnu/packages/graphviz.scm
index defd53df73..c23369acc4 100644
--- a/gnu/packages/graphviz.scm
+++ b/gnu/packages/graphviz.scm
@@ -208,7 +208,7 @@ (define-public python-pygraphviz
 (define-public python-uqbar
   (package
     (name "python-uqbar")
-    (version "0.6.9")
+    (version "7.0.0")
     (source
      (origin
        (method git-fetch)
@@ -217,7 +217,7 @@ (define-public python-uqbar
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "037qj3rymm6xzdpklddfhmfp2p1bq9fi3jrvxj6gmharphd5z869"))))
+        (base32 "0qa32d2z7bg3h26r18dv55g9lghw59wln7rkcciavyyjh553q430"))))
     (build-system pyproject-build-system)
     (arguments  ; XXX: Disable failing tests.
      (list #:test-flags '(list "tests" "-k" "not test_find_executable \
@@ -232,12 +232,7 @@ (define-public python-uqbar
            python-setuptools
            python-wheel))
     (propagated-inputs
-     (list python-black python-sphinx-5 python-unidecode
-           (package/inherit python-sphinx-rtd-theme
-             (propagated-inputs
-              (modify-inputs
-                  (package-propagated-inputs python-sphinx-rtd-theme)
-                (replace "python-sphinx" python-sphinx-5))))))
+     (list python-black python-sphinx python-unidecode python-sphinx-rtd-theme))
     (home-page "https://github.com/josiah-wolf-oberholtzer/uqbar")
     (synopsis "Tools for building documentation with Sphinx, Graphviz and LaTeX")
     (description
-- 
2.48.1

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* gnu/packages/sphinx.scm (python-sphinx-autodoc-typehints-5): Delete variable.
---
 gnu/packages/sphinx.scm | 7 -------
 1 file changed, 7 deletions(-)

diff --git a/gnu/packages/sphinx.scm b/gnu/packages/sphinx.scm
index 6847592a99..5f06cb04f5 100644
--- a/gnu/packages/sphinx.scm
+++ b/gnu/packages/sphinx.scm
@@ -1234,13 +1234,6 @@ (define-public python-sphinx-autodoc-typehints
 documenting acceptable argument types and return value types of functions.")
     (license license:expat)))
 
-(define-public python-sphinx-autodoc-typehints-5
-  (package/inherit python-sphinx-autodoc-typehints
-    (propagated-inputs
-     (modify-inputs
-         (package-propagated-inputs python-sphinx-autodoc-typehints)
-       (replace "python-sphinx" python-sphinx-5)))))
-
 (define-public python-sphinx-pytest
   (package
     (name "python-sphinx-pytest")
-- 
2.48.1

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* gnu/packages/sphinx.scm (python-sphinx-panels):
[arguments]{phases}: Add 'loosen-requirements phase.
[propagated-inputs]: Replace python-sphinx-4 by python-sphinx-5.
---
 gnu/packages/sphinx.scm | 10 +++++++++-
 1 file changed, 9 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/sphinx.scm b/gnu/packages/sphinx.scm
index 5f06cb04f5..024bfe986a 100644
--- a/gnu/packages/sphinx.scm
+++ b/gnu/packages/sphinx.scm
@@ -608,7 +608,15 @@ (define-public python-sphinx-panels
         (sha256
          (base32 "1ivqz6yv96a2jp59kylg1gbkrmzq6zwilppz3ij0zrkjn25zb97k"))))
     (build-system pyproject-build-system)
-    (propagated-inputs (list python-docutils-0.15 python-sphinx-4))
+    (arguments
+     (list #:phases
+           #~(modify-phases %standard-phases
+               (add-after 'unpack 'loosen-requirements
+                 (lambda _
+                   (substitute* "setup.py"
+                     (("sphinx>=2,<5")
+                      "sphinx>=2,<6")))))))
+    (propagated-inputs (list python-docutils-0.15 python-sphinx-5))
     (native-inputs
      (list python-pytest
            python-pytest-regressions
-- 
2.48.1

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* gnu/packages/python-xyz.scm (python-numpy-documentation):
[arguments]{phases}: Add phase 'avoid-external-deps. Adapt phase
'install by removing sphinx.ext.autodoc extension.
[native-inputs]: Replace python-sphinx-4 by python-sphinx. Add
python-sphinx-design.
---
 gnu/packages/python-xyz.scm | 14 +++++++++++++-
 1 file changed, 13 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index bacfac6c42..6054a88562 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -9684,6 +9684,16 @@ (define-public python-numpy-documentation
       #:tests? #f                     ;we're only generating the documentation
       #:phases
       #~(modify-phases %standard-phases
+          (add-after 'unpack 'avoid-external-deps
+            (lambda _
+              ;; XXX: Avoid theme-switcher to avoid sphinx error
+              ;; TemplateNotFound('theme-switcher.html')
+              ;; XXX: Avoid version-switcher because it depends on the value
+              ;; of external https://numpy.org/doc/_static/versions.json
+              (substitute* "doc/source/conf.py"
+                (("\
+\"navbar_end\": \\[\"theme-switcher\", \"version-switcher\", ")
+                 "\"navbar_end\": ["))))
           (add-before 'build 'add-gnu-freefont-to-texmf
             (lambda _
               ;; XXX: The Sphinx-generated tex output specifies the GNU
@@ -9729,6 +9739,7 @@ (define-public python-numpy-documentation
                     (("\"contents\"") "'index'")
                     ;; Disable Sphinx extensions that produce broken Texinfo.
                     ((".*'numpydoc'.*") "")
+                    ((".*'sphinx.ext.autodoc'.*") "")
                     ((".*'sphinx.ext.autosummary'.*") ""))
                   (invoke "make" "info" sphinxopts)
                   ;; Install the HTML documentation.
@@ -9752,7 +9763,8 @@ (define-public python-numpy-documentation
            python-pandas
            python-pydata-sphinx-theme
            python-scipy                 ;used by matplotlib
-           python-sphinx-4
+           python-sphinx
+           python-sphinx-design
            python-sphinx-panels
            texinfo
            (texlive-updmap.cfg
-- 
2.48.1

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* gnu/packages/sphinx.scm (python-sphinx-4): Delete variable.
---
 gnu/packages/sphinx.scm | 19 -------------------
 1 file changed, 19 deletions(-)

diff --git a/gnu/packages/sphinx.scm b/gnu/packages/sphinx.scm
index 024bfe986a..58952049a1 100644
--- a/gnu/packages/sphinx.scm
+++ b/gnu/packages/sphinx.scm
@@ -267,25 +267,6 @@ (define-public python-sphinx-5
            (texlive-updmap.cfg
             (list texlive-cm-super texlive-tex-gyre))))))
 
-;; Some packages do not support Sphinx 5 yet.  Remove when unused.
-(define-public python-sphinx-4
-  (package
-    (inherit python-sphinx-5)
-    (version "4.5.0")
-    (source (origin
-              (method url-fetch)
-              (uri (pypi-uri "Sphinx" version))
-              (sha256
-               (base32
-                "1rp28jryxwy24y8vpacclqihbizyi6b1s6id86pibvm46ybcmy3v"))))
-    (propagated-inputs
-     (modify-inputs (package-propagated-inputs python-sphinx)
-       (replace "python-docutils" python-docutils-0.15)))
-    (native-inputs
-     (modify-inputs (package-native-inputs python-sphinx)
-       (delete python-flit-core)
-       (append python-setuptools python-wheel)))))
-
 (define-public python-sphinxcontrib-apidoc
   (package
     (name "python-sphinxcontrib-apidoc")
-- 
2.48.1

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This package is a leaf package in Guix, is stale for 13 years, and its
upstream repository is not even up anymore.

* gnu/packages/python-xyz.scm (python-anyjson): Delete variable.
---
 gnu/packages/python-xyz.scm | 28 ----------------------------
 1 file changed, 28 deletions(-)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 6054a88562..558131fee6 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -21048,34 +21048,6 @@ (define-public python-pyquery
 fast xml and html manipulation.")
     (license license:bsd-3)))
 
-(define-public python-anyjson
-  (package
-    (name "python-anyjson")
-    (version "0.3.3")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (pypi-uri "anyjson" version))
-       (sha256
-        (base32
-         "1fjph4alvcscsl5d4b6qpv1yh31jy05jxi1l0xff7lws7j32v09p"))))
-    (build-system python-build-system)
-    (arguments
-     `(;; We could possibly get tests working, but on Python 3 it's not so easy.
-       ;; Very strangely, 2to3 is run *during setup.py install* (or bdist, or
-       ;; whatever) so this transformation needs to be done before the tests
-       ;; can be run.  Maybe we could add a build step to transform beforehand
-       ;; but it could be annoying/difficult.
-       #:tests? #f))
-    (native-inputs (list python-setuptools-57)) ;for use_2to3 support
-    (home-page "https://bitbucket.org/runeh/anyjson/")
-    (synopsis
-     "Wraps best available JSON implementation in a common interface")
-    (description
-     "Anyjson loads whichever is the fastest JSON module installed
-and provides a uniform API regardless of which JSON implementation is used.")
-    (license license:bsd-3)))
-
 (define-public python-amqp
   (package
     (name "python-amqp")
-- 
2.48.1

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This package is a leaf package in Guix, has been abandonned for 11
years (aside from a License change).

* gnu/packages/python-check.scm (python-parameterizedtestcase): Delete variable.
---
 gnu/packages/python-check.scm | 19 -------------------
 1 file changed, 19 deletions(-)

diff --git a/gnu/packages/python-check.scm b/gnu/packages/python-check.scm
index 1138e287f1..d8fa37b9f6 100644
--- a/gnu/packages/python-check.scm
+++ b/gnu/packages/python-check.scm
@@ -2925,25 +2925,6 @@ (define-public python-pandas-vet
 in an opinionated way.")
     (license license:expat)))
 
-(define-public python-parameterizedtestcase
-  (package
-    (name "python-parameterizedtestcase")
-    (version "0.1.0")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (pypi-uri "parameterizedtestcase" version))
-       (sha256
-        (base32 "0zhjmsd16xacg4vd7zb75kw8q9khn52wvad634v1bvz7swaivk2c"))))
-    (build-system python-build-system)
-    (native-inputs (list python-setuptools-57)) ;for use_2to3
-    (home-page
-     "https://github.com/msabramo/python_unittest_parameterized_test_case")
-    (synopsis "Parameterized tests for Python's unittest module")
-    (description "This package provides parameterized tests for Python's
-@code{unittest} module taking inspiration from pytest.")
-    (license license:expat)))
-
 (define-public python-pytest-rerunfailures
   (package
     (name "python-pytest-rerunfailures")
-- 
2.48.1

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* gnu/packages/bioinformatics.scm (python-pyvcf): Define in terms of
'deprecated-package'.
(python-pyvcf3): New variable, formerly known as "python-pyvcf".
---
 gnu/packages/bioinformatics.scm | 65 +++++++++++----------------------
 1 file changed, 21 insertions(+), 44 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 6f4c5053b6..c593c37d35 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -23715,50 +23715,27 @@ (define-public tombo
     ;; Some parts may be BSD-3-licensed.
     (license license:mpl2.0)))
 
-(define-public python-pyvcf
-  (let ((commit "476169cd457ba0caa6b998b301a4d91e975251d9")
-        (revision "0"))
-    (package
-      (name "python-pyvcf")
-      (version (git-version "0.6.8" revision commit))
-      ;; Use git, because the PyPI tarballs lack test data.
-      (source
-       (origin
-         (method git-fetch)
-         (uri (git-reference
-               (url "https://github.com/jamescasbon/PyVCF.git")
-               ;; Latest release is not tagged.
-               (commit commit)))
-         (file-name (git-file-name name version))
-         (sha256
-          (base32
-           "0qf9lwj7r2hjjp4bd4vc7nayrhblfm4qcqs4dbd43a6p4bj2jv5p"))))
-      (build-system python-build-system)
-      (arguments
-       `(#:phases
-         (modify-phases %standard-phases
-           (add-after 'unpack 'patch-sample-script
-             (lambda _
-               ;; Add Python 3 compatibility to this sample script.
-               (substitute* "scripts/vcf_sample_filter.py"
-                 (("print (.*)\n" _ arg)
-                  (string-append "print(" arg ")\n")))))
-           (add-after 'install 'remove-installed-tests
-             ;; Do not install test files.
-             (lambda* (#:key inputs outputs #:allow-other-keys)
-               (delete-file-recursively (string-append
-                                         (site-packages inputs outputs)
-                                         "/vcf/test")))))))
-      (native-inputs
-       ;; Older setuptools is needed for use_2to3.
-       (list python-cython python-setuptools-57))
-      (propagated-inputs
-       (list python-pysam python-rpy2))
-      (home-page "https://github.com/jamescasbon/PyVCF")
-      (synopsis "Variant Call Format parser for Python")
-      (description "This package provides a @acronym{VCF,Variant Call Format}
+;; This is a fork of the original unmaintained python-pyvcf.
+(define-public python-pyvcf3
+  (package
+    (name "python-pyvcf3")
+    (version "1.0.3")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "PyVCF3" version))
+       (sha256
+        (base32 "0783pb2p5qx3vgwksc9b9vxbpdq7ax6znff9wa3h80cpicfdf5jb"))))
+    (build-system pyproject-build-system)
+    (propagated-inputs (list python-setuptools))
+    (native-inputs (list python-setuptools python-wheel))
+    (home-page "https://github.com/dridk/PyVCF3")
+    (synopsis "Variant Call Format parser for Python")
+    (description "This package provides a @acronym{VCF,Variant Call Format}
 parser for Python.")
-      (license license:expat))))
+    (license license:expat)))
+
+(define-deprecated/public-alias python-pyvcf python-pyvcf3)
 
 (define-public nanosv
   (package
@@ -23772,7 +23749,7 @@ (define-public nanosv
               "1wl2daj0bwrl8fx5xi8j8hfs3mp3vg3qycy66538n032v1qkc6xg"))))
    (build-system python-build-system)
    (inputs
-    (list python-configparser python-pysam python-pyvcf))
+    (list python-configparser python-pysam python-pyvcf3))
    (home-page "https://github.com/mroosmalen/nanosv")
    (synopsis "Structural variation detection tool for Oxford Nanopore data")
    (description "NanoSV is a software package that can be used to identify
-- 
2.48.1

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* gnu/packages/geo.scm (gdal): Update to 3.10.2.
[source]: Bundle zlib back, as it's now using a custom fork.
[arguments]: Add 'patch-runpath phase and {modules} in order to patch
the runpaths of the swig generated python bindings. Improve style.
[inputs]: Add gcc:lib, hdf5, librasterlite2, libspatialite.
[native-inputs]: Add bison.
---
 gnu/packages/geo.scm | 66 ++++++++++++++++++++++++++++++--------------
 1 file changed, 45 insertions(+), 21 deletions(-)

diff --git a/gnu/packages/geo.scm b/gnu/packages/geo.scm
index 251ef5ced9..7e9b1da2e3 100644
--- a/gnu/packages/geo.scm
+++ b/gnu/packages/geo.scm
@@ -1408,46 +1408,69 @@ (define-public pdal
 (define-public gdal
   (package
     (name "gdal")
-    (version "3.6.1")
+    (version "3.10.2")
     (source (origin
               (method url-fetch)
               (uri (string-append
-                     "http://download.osgeo.org/gdal/" version "/gdal-"
-                     version ".tar.gz"))
+                    "http://download.osgeo.org/gdal/" version "/gdal-"
+                    version ".tar.gz"))
               (sha256
                (base32
-                "1qckwnygszxkkq40bf87s3m1sab6jj9jyakdvskh0qf7dq8zjarf"))
+                "1nmh92vbcrp9qnld98vkxsvaw0mrska06kxxbn7n6kgbh6mhlwfa"))
               (modules '((guix build utils)))
               (snippet
-                `(begin
-                   ;; TODO: frmts contains a lot more bundled code.
-                   (for-each delete-file-recursively
-                     ;; bundled code
-                     '("frmts/png/libpng"
-                       "frmts/gif/giflib"
-                       "frmts/jpeg/libjpeg"
-                       "frmts/jpeg/libjpeg12"
-                       "frmts/gtiff/libtiff"
-                       "frmts/gtiff/libgeotiff"
-                       "frmts/zlib"
-                       "ogr/ogrsf_frmts/geojson/libjson"))))))
+               `(begin
+                  ;; TODO: frmts contains a lot more bundled code.
+                  (for-each delete-file-recursively
+                            ;; bundled code
+                            '("frmts/png/libpng"
+                              "frmts/gif/giflib"
+                              "frmts/jpeg/libjpeg"
+                              "frmts/jpeg/libjpeg12"
+                              "frmts/gtiff/libtiff"
+                              "frmts/gtiff/libgeotiff"
+                              "ogr/ogrsf_frmts/geojson/libjson"))))))
     (build-system cmake-build-system)
     (arguments
-     `(#:tests? #f
-       #:configure-flags
-       (list "-DGDAL_USE_INTERNAL_LIBS=WHEN_NO_EXTERNAL"
-             "-DGDAL_USE_JPEG12_INTERNAL=OFF")))
+     (list
+      #:tests? #f
+      #:configure-flags '(list "-DGDAL_USE_INTERNAL_LIBS=WHEN_NO_EXTERNAL"
+                               "-DGDAL_USE_JPEG12_INTERNAL=OFF")
+      #:modules '((guix build cmake-build-system)
+                  (guix build gremlin)
+                  (guix build utils)
+                  (srfi srfi-26))
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-before 'strip 'patch-runpath
+            (lambda* (#:key inputs #:allow-other-keys)
+              (for-each
+               (cut set-file-runpath <>
+                    (list (string-append #$output "/lib")
+                          (dirname (search-input-file
+                                    inputs "/lib/libgcc_s.so"))
+                          (dirname (search-input-file
+                                    inputs "/lib/libc.so.6"))))
+               (find-files
+                #$output
+                (lambda (file stat)
+                  (and (string-suffix? ".so" file)
+                       (string-contains file "site-packages"))))))))))
     (inputs
      (list curl
            expat
            freexl
+           `(,gcc "lib")
            geos
            giflib
+           hdf5
            json-c
            libgeotiff
            libjpeg-turbo
            libjxl
            libpng
+           librasterlite2
+           libspatialite
            libtiff
            libwebp
            lz4
@@ -1463,7 +1486,8 @@ (define-public gdal
            zlib
            zstd))
     (native-inputs
-     (list pkg-config
+     (list bison
+           pkg-config
            python))
     (propagated-inputs
      (list python-numpy))
-- 
2.48.1

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* gnu/packages/sphinx.scm (sphinx-5)[arguments]{test-flags}: Ignore
test test_autodoc_default_options (also ignored in sphinx@6).
---
 gnu/packages/sphinx.scm | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/sphinx.scm b/gnu/packages/sphinx.scm
index 239a2cc780..4b3e598e38 100644
--- a/gnu/packages/sphinx.scm
+++ b/gnu/packages/sphinx.scm
@@ -197,7 +197,10 @@ (define-public python-sphinx-5
               " and not test_viewcode"
               ;; These fail with pygments 2.10+.  They are harmless.
               " and not test_additional_targets_should_not_be_translated"
-              " and not test_additional_targets_should_be_translated"))
+              " and not test_additional_targets_should_be_translated"
+              ;; As in Sphinx@6:
+              ;; AssertionError: assert...list of weak references to the object...
+              " and not test_autodoc_default_options"))
       #:phases
       '(modify-phases %standard-phases
          (add-before 'check 'pre-check
-- 
2.48.1

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* gnu/packages/python-xyz.scm (python-docutils-0.15): Update to 0.16.
[native-inputs]: Replace python-setuptools-57 by python-setuptools.
* gnu/packages/python-web.scm (awscli)[inputs]: Update accordingly.
* gnu/packages/sphinx.scm (python-sphinx-panels)[propagated-inputs]:
Update accordingly.
---
 gnu/packages/python-web.scm |  2 +-
 gnu/packages/python-xyz.scm | 10 +++++-----
 gnu/packages/sphinx.scm     |  2 +-
 3 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm
index 77a4e5c8f1..42f98df644 100644
--- a/gnu/packages/python-web.scm
+++ b/gnu/packages/python-web.scm
@@ -5165,7 +5165,7 @@ (define-public awscli
      (list groff-minimal
            python-botocore
            python-colorama
-           python-docutils-0.15
+           python-docutils-0.16
            python-pyyaml
            python-rsa
            python-s3transfer))
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 558131fee6..72906d7b37 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -7835,21 +7835,21 @@ (define-public python-docutils
     ;; licensed under the PFSL, BSD 2-clause, and GPLv3+ licenses.
     (license (list license:public-domain license:psfl license:bsd-2 license:gpl3+))))
 
-;; awscli refuses to be built with docutils < 0.16.
-(define-public python-docutils-0.15
+;; awscli refuses to be built with docutils < 0.17.
+(define-public python-docutils-0.16
   (package
     (inherit python-docutils)
-    (version "0.15")
+    (version "0.16")
     (source (origin
               (method url-fetch)
               (uri (pypi-uri "docutils" version))
               (sha256
                (base32
-                "0ja8q6mdj6xv62jjw3phv8j5nfqi5x8hnfy4pqfcjcgz4b34k8sl"))))
+                "1z3qliszqca9m719q3qhdkh0ghh90g500avzdgi7pl77x5h3mpn2"))))
     ;; tests contain Python 2 syntax.
     (arguments '(#:tests? #false))
     (native-inputs
-     (list python-setuptools-57))))
+     (list python-setuptools))))
 
 (define-public python-docx
   (package
diff --git a/gnu/packages/sphinx.scm b/gnu/packages/sphinx.scm
index 58952049a1..239a2cc780 100644
--- a/gnu/packages/sphinx.scm
+++ b/gnu/packages/sphinx.scm
@@ -597,7 +597,7 @@ (define-public python-sphinx-panels
                    (substitute* "setup.py"
                      (("sphinx>=2,<5")
                       "sphinx>=2,<6")))))))
-    (propagated-inputs (list python-docutils-0.15 python-sphinx-5))
+    (propagated-inputs (list python-docutils-0.16 python-sphinx-5))
     (native-inputs
      (list python-pytest
            python-pytest-regressions
-- 
2.48.1

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* gnu/packages/python-xyz.scm (python-importlib-resource)
[native-inputs]: Replace python-setuptools-57 by python-setuptools.
---
 gnu/packages/python-xyz.scm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 72906d7b37..ace13dd419 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -12913,7 +12913,7 @@ (define-public python-importlib-resources
            python-pytest-enabler
            python-pytest-flake8
            python-pytest-mypy
-           python-setuptools-57
+           python-setuptools
            python-setuptools-scm))
     (propagated-inputs
      (list python-zipp))
-- 
2.48.1

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* gnu/packages/graph.scm (python-louvain)
[build-system]: Switch from python-build-system to
pyproject-build-system.
[native-inputs]: Replace python-setuptools-57 by
python-setuptools. Add python-wheel.
---
 gnu/packages/graph.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/graph.scm b/gnu/packages/graph.scm
index f29a71c0d7..22fbf07229 100644
--- a/gnu/packages/graph.scm
+++ b/gnu/packages/graph.scm
@@ -388,9 +388,9 @@ (define-public python-louvain
        (patches (search-patches "python-louvain-fix-test.patch"))
        (sha256
         (base32 "0sx53l555rwq0z7if8agirjgw4ddp8r9b949wwz8vlig03sjvfmp"))))
-    (build-system python-build-system)
+    (build-system pyproject-build-system)
     (native-inputs
-     (list python-setuptools-57))       ;for use_2to3 support
+     (list python-setuptools python-wheel))
     (propagated-inputs
      (list python-networkx python-numpy))
     (home-page "https://github.com/taynaud/python-louvain")
-- 
2.48.1

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* gnu/packages/python-build.scm (python-setuptools-57): Delete variable.
---
 gnu/packages/python-build.scm | 12 ------------
 1 file changed, 12 deletions(-)

diff --git a/gnu/packages/python-build.scm b/gnu/packages/python-build.scm
index 6bea44fee6..85115afe25 100644
--- a/gnu/packages/python-build.scm
+++ b/gnu/packages/python-build.scm
@@ -344,18 +344,6 @@ (define-public python-setuptools
                    license:asl2.0       ;packaging is dual ASL2/BSD-2
                    license:bsd-2))))
 
-;; This is the last version with use_2to3 support.
-(define-public python-setuptools-57
-  (package
-    (inherit python-setuptools)
-    (version "57.5.0")
-    (source (origin
-              (inherit (package-source python-setuptools))
-              (uri (pypi-uri "setuptools" version))
-              (sha256
-               (base32
-                "091sp8lrin7qllrhhx7y0iiv5gdb1d3l8a1ip5knk77ma1njdlyr"))))))
-
 (define-public python-wheel
   (package
     (name "python-wheel")
-- 
2.48.1

Last modified: Sun, 9 Mar 2025 22:15:01 UTC

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Copyright (C) 1999 Darren O. Benham, 1997 nCipher Corporation Ltd, 1994-97 Ian Jackson.