GNU bug report logs - #76835
[PATCH python-team 00/15] Some further python fixes

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Message #5 received at submit <at> debbugs.gnu.org (full text, mbox):

From: Nicolas Graves <ngraves <at> ngraves.fr>
To: guix-patches <at> gnu.org
Cc: Nicolas Graves <ngraves <at> ngraves.fr>
Subject: [PATCH python-team 00/15] Some further python fixes
Date: Fri,  7 Mar 2025 19:48:39 +0100

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

Message #8 received at 76835 <at> debbugs.gnu.org (full text, mbox):

From: Nicolas Graves <ngraves <at> ngraves.fr>
To: 76835 <at> debbugs.gnu.org
Cc: Nicolas Graves <ngraves <at> ngraves.fr>
Subject: [PATCH 03/15] gnu: python-carbon: Update to 1.1.10.
Date: Fri,  7 Mar 2025 20:15:01 +0100

* 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

Message #11 received at 76835 <at> debbugs.gnu.org (full text, mbox):

From: Nicolas Graves <ngraves <at> ngraves.fr>
To: 76835 <at> debbugs.gnu.org
Cc: Nicolas Graves <ngraves <at> ngraves.fr>
Subject: [PATCH 02/15] gnu: python-unyt: Avoid deprecation failure in tests.
Date: Fri,  7 Mar 2025 20:15:00 +0100

* 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

Message #14 received at 76835 <at> debbugs.gnu.org (full text, mbox):

From: Nicolas Graves <ngraves <at> ngraves.fr>
To: 76835 <at> debbugs.gnu.org
Cc: Nicolas Graves <ngraves <at> ngraves.fr>
Subject: [PATCH 01/15] gnu: gunicorn: Migrate 'check phase to
 pyproject-build-system.
Date: Fri,  7 Mar 2025 20:14:59 +0100

* 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

Message #17 received at 76835 <at> debbugs.gnu.org (full text, mbox):

From: Nicolas Graves <ngraves <at> ngraves.fr>
To: 76835 <at> debbugs.gnu.org
Cc: Nicolas Graves <ngraves <at> ngraves.fr>
Subject: [PATCH 04/15] gnu: Add python-rrdtool.
Date: Fri,  7 Mar 2025 20:15:02 +0100

* 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 <at> crazy-compilers.com>
 ;;; Copyright © 2022 ( <paren <at> disroot.org>
 ;;; Copyright © 2022 Mathieu Laparie <mlaparie <at> disr.it>
+;;; Copyright © 2025 Nicolas Graves <ngraves <at> ngraves.fr>
 ;;;
 ;;; 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

Message #20 received at 76835 <at> debbugs.gnu.org (full text, mbox):

From: Nicolas Graves <ngraves <at> ngraves.fr>
To: 76835 <at> debbugs.gnu.org
Cc: Nicolas Graves <ngraves <at> ngraves.fr>
Subject: [PATCH 05/15] gnu: python-h2: Fix test-flags.
Date: Fri,  7 Mar 2025 20:15:03 +0100

* 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

Message #23 received at 76835 <at> debbugs.gnu.org (full text, mbox):

From: Nicolas Graves <ngraves <at> ngraves.fr>
To: 76835 <at> debbugs.gnu.org
Cc: Nicolas Graves <ngraves <at> ngraves.fr>
Subject: [PATCH 06/15] gnu: graphite-web: Update to 1.1.10-2.49c28e2.
Date: Fri,  7 Mar 2025 20:15:04 +0100

* 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

Message #26 received at 76835 <at> debbugs.gnu.org (full text, mbox):

From: Nicolas Graves <ngraves <at> ngraves.fr>
To: 76835 <at> debbugs.gnu.org
Cc: Nicolas Graves <ngraves <at> ngraves.fr>
Subject: [PATCH 08/15] gnu: python-cfn-lint: Update to 1.28.0.
Date: Fri,  7 Mar 2025 20:15:06 +0100

* 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

Message #29 received at 76835 <at> debbugs.gnu.org (full text, mbox):

From: Nicolas Graves <ngraves <at> ngraves.fr>
To: 76835 <at> debbugs.gnu.org
Cc: Nicolas Graves <ngraves <at> ngraves.fr>
Subject: [PATCH 07/15] gnu: python-nptyping: Ignore failing test.
Date: Fri,  7 Mar 2025 20:15:05 +0100

* 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

Message #32 received at 76835 <at> debbugs.gnu.org (full text, mbox):

From: Nicolas Graves <ngraves <at> ngraves.fr>
To: 76835 <at> debbugs.gnu.org
Cc: Nicolas Graves <ngraves <at> ngraves.fr>
Subject: [PATCH 09/15] gnu: patchwork: Update to 3.2.1.
Date: Fri,  7 Mar 2025 20:15:07 +0100

* 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

Message #35 received at 76835 <at> debbugs.gnu.org (full text, mbox):

From: Nicolas Graves <ngraves <at> ngraves.fr>
To: 76835 <at> debbugs.gnu.org
Cc: Nicolas Graves <ngraves <at> ngraves.fr>
Subject: [PATCH 10/15] gnu: Remove python-django-3.2.
Date: Fri,  7 Mar 2025 20:15:08 +0100

* 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

Message #38 received at 76835 <at> debbugs.gnu.org (full text, mbox):

From: Nicolas Graves <ngraves <at> ngraves.fr>
To: 76835 <at> debbugs.gnu.org
Cc: Nicolas Graves <ngraves <at> ngraves.fr>
Subject: [PATCH 11/15] gnu: python-uqbar: Update to 7.0.0.
Date: Fri,  7 Mar 2025 20:15:09 +0100

* 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

Message #41 received at 76835 <at> debbugs.gnu.org (full text, mbox):

From: Nicolas Graves <ngraves <at> ngraves.fr>
To: 76835 <at> debbugs.gnu.org
Cc: Nicolas Graves <ngraves <at> ngraves.fr>
Subject: [PATCH 12/15] gnu: Remove python-sphinx-autodoc-typehints-5.
Date: Fri,  7 Mar 2025 20:15:10 +0100

* 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

Message #44 received at 76835 <at> debbugs.gnu.org (full text, mbox):

From: Nicolas Graves <ngraves <at> ngraves.fr>
To: 76835 <at> debbugs.gnu.org
Cc: Nicolas Graves via Guix-patches via <guix-patches <at> gnu.org>
Subject: [PATCH 14/15] gnu: python-numpy-documentation: Update python-sphinx
 native-input.
Date: Fri,  7 Mar 2025 20:15:12 +0100

From: Nicolas Graves via Guix-patches via <guix-patches <at> gnu.org>

* 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

Message #47 received at 76835 <at> debbugs.gnu.org (full text, mbox):

From: Nicolas Graves <ngraves <at> ngraves.fr>
To: 76835 <at> debbugs.gnu.org
Cc: Nicolas Graves via Guix-patches via <guix-patches <at> gnu.org>
Subject: [PATCH 13/15] gnu: python-sphinx-panels: Update input to
 python-sphinx-5.
Date: Fri,  7 Mar 2025 20:15:11 +0100

From: Nicolas Graves via Guix-patches via <guix-patches <at> gnu.org>

* 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

Message #50 received at 76835 <at> debbugs.gnu.org (full text, mbox):

From: Nicolas Graves <ngraves <at> ngraves.fr>
To: 76835 <at> debbugs.gnu.org
Cc: Nicolas Graves via Guix-patches via <guix-patches <at> gnu.org>
Subject: [PATCH 15/15] gnu: Remove python-sphinx-4.
Date: Fri,  7 Mar 2025 20:15:13 +0100

From: Nicolas Graves via Guix-patches via <guix-patches <at> gnu.org>

* 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

Message #53 received at 76835 <at> debbugs.gnu.org (full text, mbox):

From: Nicolas Graves <ngraves <at> ngraves.fr>
To: 76835 <at> debbugs.gnu.org
Cc: Nicolas Graves <ngraves <at> ngraves.fr>
Subject: [PATCH v2 01/24] gnu: gunicorn: Migrate 'check phase to
 pyproject-build-system.
Date: Sun,  9 Mar 2025 23:11:09 +0100

* 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

Message #56 received at 76835 <at> debbugs.gnu.org (full text, mbox):

From: Nicolas Graves <ngraves <at> ngraves.fr>
To: 76835 <at> debbugs.gnu.org
Cc: Nicolas Graves <ngraves <at> ngraves.fr>
Subject: [PATCH v2 02/24] gnu: python-unyt: Avoid deprecation failure in tests.
Date: Sun,  9 Mar 2025 23:11:10 +0100

* 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

Message #59 received at 76835 <at> debbugs.gnu.org (full text, mbox):

From: Nicolas Graves <ngraves <at> ngraves.fr>
To: 76835 <at> debbugs.gnu.org
Cc: Nicolas Graves <ngraves <at> ngraves.fr>
Subject: [PATCH v2 03/24] gnu: python-carbon: Update to 1.1.10.
Date: Sun,  9 Mar 2025 23:11:11 +0100

* 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

Message #62 received at 76835 <at> debbugs.gnu.org (full text, mbox):

From: Nicolas Graves <ngraves <at> ngraves.fr>
To: 76835 <at> debbugs.gnu.org
Cc: Nicolas Graves <ngraves <at> ngraves.fr>
Subject: [PATCH v2 04/24] gnu: Add python-rrdtool.
Date: Sun,  9 Mar 2025 23:11:12 +0100

* 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 <at> crazy-compilers.com>
 ;;; Copyright © 2022 ( <paren <at> disroot.org>
 ;;; Copyright © 2022 Mathieu Laparie <mlaparie <at> disr.it>
+;;; Copyright © 2025 Nicolas Graves <ngraves <at> ngraves.fr>
 ;;;
 ;;; 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

Message #65 received at 76835 <at> debbugs.gnu.org (full text, mbox):

From: Nicolas Graves <ngraves <at> ngraves.fr>
To: 76835 <at> debbugs.gnu.org
Cc: Nicolas Graves <ngraves <at> ngraves.fr>
Subject: [PATCH v2 05/24] gnu: python-h2: Fix test-flags.
Date: Sun,  9 Mar 2025 23:11:13 +0100

* 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

Message #68 received at 76835 <at> debbugs.gnu.org (full text, mbox):

From: Nicolas Graves <ngraves <at> ngraves.fr>
To: 76835 <at> debbugs.gnu.org
Cc: Nicolas Graves <ngraves <at> ngraves.fr>
Subject: [PATCH v2 06/24] gnu: graphite-web: Update to 1.1.10-2.49c28e2.
Date: Sun,  9 Mar 2025 23:11:14 +0100

* 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

Message #71 received at 76835 <at> debbugs.gnu.org (full text, mbox):

From: Nicolas Graves <ngraves <at> ngraves.fr>
To: 76835 <at> debbugs.gnu.org
Cc: Nicolas Graves <ngraves <at> ngraves.fr>
Subject: [PATCH v2 08/24] gnu: python-cfn-lint: Update to 1.28.0.
Date: Sun,  9 Mar 2025 23:11:16 +0100

* 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

Message #74 received at 76835 <at> debbugs.gnu.org (full text, mbox):

From: Nicolas Graves <ngraves <at> ngraves.fr>
To: 76835 <at> debbugs.gnu.org
Cc: Nicolas Graves <ngraves <at> ngraves.fr>
Subject: [PATCH v2 09/24] gnu: patchwork: Update to 3.2.1.
Date: Sun,  9 Mar 2025 23:11:17 +0100

* 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

Message #77 received at 76835 <at> debbugs.gnu.org (full text, mbox):

From: Nicolas Graves <ngraves <at> ngraves.fr>
To: 76835 <at> debbugs.gnu.org
Cc: Nicolas Graves <ngraves <at> ngraves.fr>
Subject: [PATCH v2 10/24] gnu: Remove python-django-3.2.
Date: Sun,  9 Mar 2025 23:11:18 +0100

* 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

Message #80 received at 76835 <at> debbugs.gnu.org (full text, mbox):

From: Nicolas Graves <ngraves <at> ngraves.fr>
To: 76835 <at> debbugs.gnu.org
Cc: Nicolas Graves <ngraves <at> ngraves.fr>
Subject: [PATCH v2 07/24] gnu: python-nptyping: Ignore failing test.
Date: Sun,  9 Mar 2025 23:11:15 +0100

* 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

Message #83 received at 76835 <at> debbugs.gnu.org (full text, mbox):

From: Nicolas Graves <ngraves <at> ngraves.fr>
To: 76835 <at> debbugs.gnu.org
Cc: Nicolas Graves <ngraves <at> ngraves.fr>
Subject: [PATCH v2 11/24] gnu: python-uqbar: Update to 7.0.0.
Date: Sun,  9 Mar 2025 23:11:19 +0100

* 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

Message #86 received at 76835 <at> debbugs.gnu.org (full text, mbox):

From: Nicolas Graves <ngraves <at> ngraves.fr>
To: 76835 <at> debbugs.gnu.org
Cc: Nicolas Graves <ngraves <at> ngraves.fr>
Subject: [PATCH v2 12/24] gnu: Remove python-sphinx-autodoc-typehints-5.
Date: Sun,  9 Mar 2025 23:11:20 +0100

* 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

Message #89 received at 76835 <at> debbugs.gnu.org (full text, mbox):

From: Nicolas Graves <ngraves <at> ngraves.fr>
To: 76835 <at> debbugs.gnu.org
Cc: Nicolas Graves <ngraves <at> ngraves.fr>
Subject: [PATCH v2 13/24] gnu: python-sphinx-panels: Update input to
 python-sphinx-5.
Date: Sun,  9 Mar 2025 23:11:21 +0100

* 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

Message #92 received at 76835 <at> debbugs.gnu.org (full text, mbox):

From: Nicolas Graves <ngraves <at> ngraves.fr>
To: 76835 <at> debbugs.gnu.org
Cc: Nicolas Graves <ngraves <at> ngraves.fr>
Subject: [PATCH v2 14/24] gnu: python-numpy-documentation: Update
 python-sphinx native-input.
Date: Sun,  9 Mar 2025 23:11:22 +0100

* 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

Message #95 received at 76835 <at> debbugs.gnu.org (full text, mbox):

From: Nicolas Graves <ngraves <at> ngraves.fr>
To: 76835 <at> debbugs.gnu.org
Cc: Nicolas Graves <ngraves <at> ngraves.fr>
Subject: [PATCH v2 15/24] gnu: Remove python-sphinx-4.
Date: Sun,  9 Mar 2025 23:11:23 +0100

* 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

Message #98 received at 76835 <at> debbugs.gnu.org (full text, mbox):

From: Nicolas Graves <ngraves <at> ngraves.fr>
To: 76835 <at> debbugs.gnu.org
Cc: Nicolas Graves <ngraves <at> ngraves.fr>
Subject: [PATCH v2 16/24] gnu: Remove python-anyjson.
Date: Sun,  9 Mar 2025 23:11:24 +0100

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

Message #101 received at 76835 <at> debbugs.gnu.org (full text, mbox):

From: Nicolas Graves <ngraves <at> ngraves.fr>
To: 76835 <at> debbugs.gnu.org
Cc: Nicolas Graves <ngraves <at> ngraves.fr>
Subject: [PATCH v2 17/24] gnu: Remove python-parameterizedtestcase.
Date: Sun,  9 Mar 2025 23:11:25 +0100

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

Message #104 received at 76835 <at> debbugs.gnu.org (full text, mbox):

From: Nicolas Graves <ngraves <at> ngraves.fr>
To: 76835 <at> debbugs.gnu.org
Cc: Nicolas Graves <ngraves <at> ngraves.fr>
Subject: [PATCH v2 18/24] gnu: python-pyvcf: Rename package to python-pyvcf3.
Date: Sun,  9 Mar 2025 23:11:26 +0100

* 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

Message #107 received at 76835 <at> debbugs.gnu.org (full text, mbox):

From: Nicolas Graves <ngraves <at> ngraves.fr>
To: 76835 <at> debbugs.gnu.org
Cc: Nicolas Graves <ngraves <at> ngraves.fr>
Subject: [PATCH v2 19/24] gnu: gdal: Update to 3.10.2.
Date: Sun,  9 Mar 2025 23:11:27 +0100

* 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

Message #110 received at 76835 <at> debbugs.gnu.org (full text, mbox):

From: Nicolas Graves <ngraves <at> ngraves.fr>
To: 76835 <at> debbugs.gnu.org
Cc: Nicolas Graves <ngraves <at> ngraves.fr>
Subject: [PATCH v2 21/24] gnu: sphinx-5: Ignore failing test.
Date: Sun,  9 Mar 2025 23:11:29 +0100

* gnu/packages/sphinx.scm (sphinx-5)[arguments]{test-flags}: Ignore
test test_autodoc_default_options (also ignored in sphinx <at> 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 <at> 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

Message #113 received at 76835 <at> debbugs.gnu.org (full text, mbox):

From: Nicolas Graves <ngraves <at> ngraves.fr>
To: 76835 <at> debbugs.gnu.org
Cc: Nicolas Graves <ngraves <at> ngraves.fr>
Subject: [PATCH v2 20/24] gnu: python-docutils-0.15: Update to 0.16.
Date: Sun,  9 Mar 2025 23:11:28 +0100

* 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

Message #116 received at 76835 <at> debbugs.gnu.org (full text, mbox):

From: Nicolas Graves <ngraves <at> ngraves.fr>
To: 76835 <at> debbugs.gnu.org
Cc: Nicolas Graves <ngraves <at> ngraves.fr>
Subject: [PATCH v2 22/24] gnu: python-importlib-resources: Update
 python-setuptools input.
Date: Sun,  9 Mar 2025 23:11:30 +0100

* 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

Message #119 received at 76835 <at> debbugs.gnu.org (full text, mbox):

From: Nicolas Graves <ngraves <at> ngraves.fr>
To: 76835 <at> debbugs.gnu.org
Cc: Nicolas Graves <ngraves <at> ngraves.fr>
Subject: [PATCH v2 23/24] gnu: python-louvain: Use pyproject-build-system.
Date: Sun,  9 Mar 2025 23:11:31 +0100

* 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

Message #122 received at 76835 <at> debbugs.gnu.org (full text, mbox):

From: Nicolas Graves <ngraves <at> ngraves.fr>
To: 76835 <at> debbugs.gnu.org
Cc: Nicolas Graves <ngraves <at> ngraves.fr>
Subject: [PATCH v2 24/24] gnu: Remove python-setuptools-57.
Date: Sun,  9 Mar 2025 23:11:32 +0100

* 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

Message #125 received at 76835 <at> debbugs.gnu.org (full text, mbox):

From: Nicolas Graves <ngraves <at> ngraves.fr>
To: 76835 <at> debbugs.gnu.org
Cc: Nicolas Graves <ngraves <at> ngraves.fr>
Subject: [PATCH v3 01/40] gnu: gunicorn: Migrate 'check phase to
 pyproject-build-system.
Date: Mon, 10 Mar 2025 03:16:06 +0100

* 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

Message #128 received at 76835 <at> debbugs.gnu.org (full text, mbox):

From: Nicolas Graves <ngraves <at> ngraves.fr>
To: 76835 <at> debbugs.gnu.org
Cc: Nicolas Graves <ngraves <at> ngraves.fr>
Subject: [PATCH v3 03/40] gnu: python-carbon: Update to 1.1.10.
Date: Mon, 10 Mar 2025 03:16:08 +0100

* 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

Message #131 received at 76835 <at> debbugs.gnu.org (full text, mbox):

From: Nicolas Graves <ngraves <at> ngraves.fr>
To: 76835 <at> debbugs.gnu.org
Cc: Nicolas Graves <ngraves <at> ngraves.fr>
Subject: [PATCH v3 05/40] gnu: python-h2: Fix test-flags.
Date: Mon, 10 Mar 2025 03:16:10 +0100

* 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

Message #134 received at 76835 <at> debbugs.gnu.org (full text, mbox):

From: Nicolas Graves <ngraves <at> ngraves.fr>
To: 76835 <at> debbugs.gnu.org
Cc: Nicolas Graves <ngraves <at> ngraves.fr>
Subject: [PATCH v3 02/40] gnu: python-unyt: Avoid deprecation failure in tests.
Date: Mon, 10 Mar 2025 03:16:07 +0100

* 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

Message #137 received at 76835 <at> debbugs.gnu.org (full text, mbox):

From: Nicolas Graves <ngraves <at> ngraves.fr>
To: 76835 <at> debbugs.gnu.org
Cc: Nicolas Graves <ngraves <at> ngraves.fr>
Subject: [PATCH v3 04/40] gnu: Add python-rrdtool.
Date: Mon, 10 Mar 2025 03:16:09 +0100

* 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 <at> crazy-compilers.com>
 ;;; Copyright © 2022 ( <paren <at> disroot.org>
 ;;; Copyright © 2022 Mathieu Laparie <mlaparie <at> disr.it>
+;;; Copyright © 2025 Nicolas Graves <ngraves <at> ngraves.fr>
 ;;;
 ;;; 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

Message #140 received at 76835 <at> debbugs.gnu.org (full text, mbox):

From: Nicolas Graves <ngraves <at> ngraves.fr>
To: 76835 <at> debbugs.gnu.org
Cc: Nicolas Graves <ngraves <at> ngraves.fr>
Subject: [PATCH v3 06/40] gnu: graphite-web: Update to 1.1.10-2.49c28e2.
Date: Mon, 10 Mar 2025 03:16:11 +0100

* 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

Message #143 received at 76835 <at> debbugs.gnu.org (full text, mbox):

From: Nicolas Graves <ngraves <at> ngraves.fr>
To: 76835 <at> debbugs.gnu.org
Cc: Nicolas Graves <ngraves <at> ngraves.fr>
Subject: [PATCH v3 08/40] gnu: python-cfn-lint: Update to 1.28.0.
Date: Mon, 10 Mar 2025 03:16:13 +0100

* 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

Message #146 received at 76835 <at> debbugs.gnu.org (full text, mbox):

From: Nicolas Graves <ngraves <at> ngraves.fr>
To: 76835 <at> debbugs.gnu.org
Cc: Nicolas Graves <ngraves <at> ngraves.fr>
Subject: [PATCH v3 07/40] gnu: python-nptyping: Ignore failing test.
Date: Mon, 10 Mar 2025 03:16:12 +0100

* 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

Message #149 received at 76835 <at> debbugs.gnu.org (full text, mbox):

From: Nicolas Graves <ngraves <at> ngraves.fr>
To: 76835 <at> debbugs.gnu.org
Cc: Nicolas Graves <ngraves <at> ngraves.fr>
Subject: [PATCH v3 09/40] gnu: patchwork: Update to 3.2.1.
Date: Mon, 10 Mar 2025 03:16:14 +0100

* 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

Message #152 received at 76835 <at> debbugs.gnu.org (full text, mbox):

From: Nicolas Graves <ngraves <at> ngraves.fr>
To: 76835 <at> debbugs.gnu.org
Cc: Nicolas Graves <ngraves <at> ngraves.fr>
Subject: [PATCH v3 10/40] gnu: Remove python-django-3.2.
Date: Mon, 10 Mar 2025 03:16:15 +0100

* 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

Message #155 received at 76835 <at> debbugs.gnu.org (full text, mbox):

From: Nicolas Graves <ngraves <at> ngraves.fr>
To: 76835 <at> debbugs.gnu.org
Cc: Nicolas Graves <ngraves <at> ngraves.fr>
Subject: [PATCH v3 11/40] gnu: python-uqbar: Update to 7.0.0.
Date: Mon, 10 Mar 2025 03:16:16 +0100

* 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

Message #158 received at 76835 <at> debbugs.gnu.org (full text, mbox):

From: Nicolas Graves <ngraves <at> ngraves.fr>
To: 76835 <at> debbugs.gnu.org
Cc: Nicolas Graves <ngraves <at> ngraves.fr>
Subject: [PATCH v3 12/40] gnu: Remove python-sphinx-autodoc-typehints-5.
Date: Mon, 10 Mar 2025 03:16:17 +0100

* 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

Message #161 received at 76835 <at> debbugs.gnu.org (full text, mbox):

From: Nicolas Graves <ngraves <at> ngraves.fr>
To: 76835 <at> debbugs.gnu.org
Cc: Nicolas Graves <ngraves <at> ngraves.fr>
Subject: [PATCH v3 13/40] gnu: python-sphinx-panels: Update input to
 python-sphinx-5.
Date: Mon, 10 Mar 2025 03:16:18 +0100

* 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

Message #164 received at 76835 <at> debbugs.gnu.org (full text, mbox):

From: Nicolas Graves <ngraves <at> ngraves.fr>
To: 76835 <at> debbugs.gnu.org
Cc: Nicolas Graves <ngraves <at> ngraves.fr>
Subject: [PATCH v3 14/40] gnu: python-numpy-documentation: Update
 python-sphinx native-input.
Date: Mon, 10 Mar 2025 03:16:19 +0100

* 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

Message #167 received at 76835 <at> debbugs.gnu.org (full text, mbox):

From: Nicolas Graves <ngraves <at> ngraves.fr>
To: 76835 <at> debbugs.gnu.org
Cc: Nicolas Graves <ngraves <at> ngraves.fr>
Subject: [PATCH v3 15/40] gnu: Remove python-sphinx-4.
Date: Mon, 10 Mar 2025 03:16:20 +0100

* 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

Message #170 received at 76835 <at> debbugs.gnu.org (full text, mbox):

From: Nicolas Graves <ngraves <at> ngraves.fr>
To: 76835 <at> debbugs.gnu.org
Cc: Nicolas Graves <ngraves <at> ngraves.fr>
Subject: [PATCH v3 16/40] gnu: Remove python-anyjson.
Date: Mon, 10 Mar 2025 03:16:21 +0100

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

Message #173 received at 76835 <at> debbugs.gnu.org (full text, mbox):

From: Nicolas Graves <ngraves <at> ngraves.fr>
To: 76835 <at> debbugs.gnu.org
Cc: Nicolas Graves <ngraves <at> ngraves.fr>
Subject: [PATCH v3 17/40] gnu: Remove python-parameterizedtestcase.
Date: Mon, 10 Mar 2025 03:16:22 +0100

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

Message #176 received at 76835 <at> debbugs.gnu.org (full text, mbox):

From: Nicolas Graves <ngraves <at> ngraves.fr>
To: 76835 <at> debbugs.gnu.org
Cc: Nicolas Graves <ngraves <at> ngraves.fr>
Subject: [PATCH v3 18/40] gnu: python-pyvcf: Rename package to python-pyvcf3.
Date: Mon, 10 Mar 2025 03:16:23 +0100

* 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

Message #179 received at 76835 <at> debbugs.gnu.org (full text, mbox):

From: Nicolas Graves <ngraves <at> ngraves.fr>
To: 76835 <at> debbugs.gnu.org
Cc: Nicolas Graves <ngraves <at> ngraves.fr>
Subject: [PATCH v3 19/40] gnu: gdal: Update to 3.10.2.
Date: Mon, 10 Mar 2025 03:16:24 +0100

* 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

Message #182 received at 76835 <at> debbugs.gnu.org (full text, mbox):

From: Nicolas Graves <ngraves <at> ngraves.fr>
To: 76835 <at> debbugs.gnu.org
Cc: Nicolas Graves <ngraves <at> ngraves.fr>
Subject: [PATCH v3 21/40] gnu: sphinx-5: Ignore failing test.
Date: Mon, 10 Mar 2025 03:16:26 +0100

* gnu/packages/sphinx.scm (sphinx-5)[arguments]{test-flags}: Ignore
test test_autodoc_default_options (also ignored in sphinx <at> 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 <at> 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

Message #185 received at 76835 <at> debbugs.gnu.org (full text, mbox):

From: Nicolas Graves <ngraves <at> ngraves.fr>
To: 76835 <at> debbugs.gnu.org
Cc: Nicolas Graves <ngraves <at> ngraves.fr>
Subject: [PATCH v3 20/40] gnu: python-docutils-0.15: Update to 0.16.
Date: Mon, 10 Mar 2025 03:16:25 +0100

* 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

Message #188 received at 76835 <at> debbugs.gnu.org (full text, mbox):

From: Nicolas Graves <ngraves <at> ngraves.fr>
To: 76835 <at> debbugs.gnu.org
Cc: Nicolas Graves <ngraves <at> ngraves.fr>
Subject: [PATCH v3 22/40] gnu: python-importlib-resources: Update
 python-setuptools input.
Date: Mon, 10 Mar 2025 03:16:27 +0100

* 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

Message #191 received at 76835 <at> debbugs.gnu.org (full text, mbox):

From: Nicolas Graves <ngraves <at> ngraves.fr>
To: 76835 <at> debbugs.gnu.org
Cc: Nicolas Graves <ngraves <at> ngraves.fr>
Subject: [PATCH v3 23/40] gnu: python-louvain: Use pyproject-build-system.
Date: Mon, 10 Mar 2025 03:16:28 +0100

* 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

Message #194 received at 76835 <at> debbugs.gnu.org (full text, mbox):

From: Nicolas Graves <ngraves <at> ngraves.fr>
To: 76835 <at> debbugs.gnu.org
Cc: Nicolas Graves <ngraves <at> ngraves.fr>
Subject: [PATCH v3 24/40] gnu: Remove python-setuptools-57.
Date: Mon, 10 Mar 2025 03:16:29 +0100

* 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

Message #197 received at 76835 <at> debbugs.gnu.org (full text, mbox):

From: Nicolas Graves <ngraves <at> ngraves.fr>
To: 76835 <at> debbugs.gnu.org
Cc: Nicolas Graves <ngraves <at> ngraves.fr>
Subject: [PATCH v3 25/40] gnu: python-dpath: Update to 2.2.0.
Date: Mon, 10 Mar 2025 03:16:30 +0100

* gnu/packages/python-xyz.scm (python-dpath): Update to 2.2.0.
[source]: Switch to git-fetch.
[build-system]: Switch from python-build-system to
pyproject-build-system.
[native-inputs]: Remove python-mock. Replace python-nose by
python-nose2. Add python-setuptools and python-wheel.
---
 gnu/packages/python-xyz.scm | 27 ++++++++++++---------------
 1 file changed, 12 insertions(+), 15 deletions(-)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index ace13dd419..58b2436f7a 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -34488,25 +34488,22 @@ (define-public python-dparse
 (define-public python-dpath
   (package
     (name "python-dpath")
-    (version "2.0.1")
+    (version "2.2.0")
     (source
      (origin
-       (method url-fetch)
-       (uri (pypi-uri "dpath" version))
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/akesterson/dpath-python")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
        (sha256
-        (base32
-         "1ymi9ssk7i0mx3mviplf4csfvzibdd6wyj4qzj6s487n9xgnp85y"))))
-    (build-system python-build-system)
+        (base32 "1rxgkn2dzakwdw5idkx0092yrmf46zcqx3xp87xksvxpzbsvz4nf"))))
+    (build-system pyproject-build-system)
     (native-inputs
-     (list python-hypothesis python-mock python-nose))
-    (arguments
-     '(#:phases
-       (modify-phases %standard-phases
-         (replace 'check
-           (lambda* (#:key inputs outputs #:allow-other-keys)
-             (add-installed-pythonpath inputs outputs)
-             ;; This invocation is taken from tox.ini.
-             (invoke "nosetests" "-d" "-v" "tests/"))))))
+     (list python-hypothesis
+           python-nose2
+           python-setuptools
+           python-wheel))
     (home-page "https://github.com/akesterson/dpath-python")
     (synopsis "File-system-like pathing and searching for dictionaries")
     (description
-- 
2.48.1

Message #200 received at 76835 <at> debbugs.gnu.org (full text, mbox):

From: Nicolas Graves <ngraves <at> ngraves.fr>
To: 76835 <at> debbugs.gnu.org
Cc: Nicolas Graves <ngraves <at> ngraves.fr>
Subject: [PATCH v3 26/40] gnu: python-yte: Update to 1.7.0.
Date: Mon, 10 Mar 2025 03:16:31 +0100

* gnu/packages/python-xyz.scm (python-yte): Update to 1.7.0.
---
 gnu/packages/python-xyz.scm | 26 ++++++++++++++++----------
 1 file changed, 16 insertions(+), 10 deletions(-)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 58b2436f7a..347dee36bc 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -15319,20 +15319,26 @@ (define-public python-plac
 (define-public python-yte
   (package
     (name "python-yte")
-    (version "1.2.0")
+    (version "1.7.0")
     (source
      (origin
-       (method url-fetch)
-       (uri (pypi-uri "yte" version))
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/koesterlab/yte")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
        (sha256
-        (base32 "07hm1warpqi4ifqgkaz5sg887x4a44yhxafmpf835ywnpchg4s03"))))
-    (build-system python-build-system)
+        (base32 "01hxl47bfb0jp2rh6qb6wrm6m8p5rfk21gksqb8qxxv9a037dnsv"))))
+    (build-system pyproject-build-system)
     (arguments
-     '(#:phases
-       (modify-phases %standard-phases
-         (add-after 'unpack 'set-HOME
-           (lambda _ (setenv "HOME" "/tmp"))))))
-    (propagated-inputs (list python-plac python-pyyaml))
+     (list #:phases
+           #~(modify-phases %standard-phases
+               (replace 'check
+                 (lambda* (#:key tests? #:allow-other-keys)
+                   (when tests?
+                     (invoke "python" "tests.py")))))))
+    (native-inputs (list python-numpy python-poetry-core python-pytest))
+    (propagated-inputs (list python-dpath python-plac python-pyyaml))
     (home-page "https://github.com/koesterlab/yte")
     (synopsis "YAML template engine with Python expressions")
     (description
-- 
2.48.1

Message #203 received at 76835 <at> debbugs.gnu.org (full text, mbox):

From: Nicolas Graves <ngraves <at> ngraves.fr>
To: 76835 <at> debbugs.gnu.org
Cc: Nicolas Graves <ngraves <at> ngraves.fr>
Subject: [PATCH v3 27/40] gnu: Add python-argparse-dataclass.
Date: Mon, 10 Mar 2025 03:16:32 +0100

* gnu/packages/python-xyz.scm (python-argparse-dataclass): New variable.
---
 gnu/packages/python-xyz.scm | 18 ++++++++++++++++++
 1 file changed, 18 insertions(+)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 347dee36bc..c6d90fe1ac 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -19682,6 +19682,24 @@ (define-public python-connection-pool
 connection pool.")
     (license license:expat)))
 
+(define-public python-argparse-dataclass
+  (package
+    (name "python-argparse-dataclass")
+    (version "2.0.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "argparse_dataclass" version))
+       (sha256
+        (base32 "0zr9r4n00x2wi5kyzw3bxvrdp5k113jw7f9p4f414bsaj4f69aq9"))))
+    (build-system pyproject-build-system)
+    (native-inputs (list python-setuptools python-wheel))
+    (home-page "https://github.com/mivade/argparse_dataclass")
+    (synopsis "Declarative CLIs with argparse and dataclasses")
+    (description
+     "This package provides declarative CLIs with argparse and dataclasses.")
+    (license license:expat)))
+
 (define-public python-argparse-manpage
   (package
     (name "python-argparse-manpage")
-- 
2.48.1

Message #206 received at 76835 <at> debbugs.gnu.org (full text, mbox):

From: Nicolas Graves <ngraves <at> ngraves.fr>
To: 76835 <at> debbugs.gnu.org
Cc: Nicolas Graves <ngraves <at> ngraves.fr>
Subject: [PATCH v3 28/40] gnu: Add python-snakemake-interface-common.
Date: Mon, 10 Mar 2025 03:16:33 +0100

* gnu/packages/python-science.scm (python-snakemake-interface-common):
New variable.
---
 gnu/packages/python-science.scm | 29 +++++++++++++++++++++++++++++
 1 file changed, 29 insertions(+)

diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm
index ca259356cf..d0a354a8c6 100644
--- a/gnu/packages/python-science.scm
+++ b/gnu/packages/python-science.scm
@@ -933,6 +933,35 @@ (define-public python-scikit-survival
 cross-validation.")
       (license license:gpl3+))))
 
+(define-public python-snakemake-interface-common
+  (package
+    (name "python-snakemake-interface-common")
+    (version "1.17.4")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/snakemake/snakemake-interface-common")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "19fyqs048zdvrmq5sdayzch850kwsyv2x6xn57cjjzcm4zpjrh9w"))))
+    (build-system pyproject-build-system)
+    (arguments
+     (list #:phases
+           #~(modify-phases %standard-phases
+               (replace 'check
+                 (lambda* (#:key tests? #:allow-other-keys)
+                   (when tests?
+                     (invoke "python3" "tests/tests.py")))))))
+    (native-inputs (list python-poetry-core python-pytest))
+    (propagated-inputs (list python-argparse-dataclass python-configargparse))
+    (home-page "https://github.com/snakemake/snakemake-interface-common")
+    (synopsis "Common functions and classes for Snakemake and its plugins")
+    (description "This package provides common functions and classes
+for Snakemake and its plugins.")
+    (license license:expat)))
+
 (define-public python-tdda
   (package
     (name "python-tdda")
-- 
2.48.1

Message #209 received at 76835 <at> debbugs.gnu.org (full text, mbox):

From: Nicolas Graves <ngraves <at> ngraves.fr>
To: 76835 <at> debbugs.gnu.org
Cc: Nicolas Graves <ngraves <at> ngraves.fr>
Subject: [PATCH v3 29/40] gnu: Add python-snakemake-interface-executor-plugins.
Date: Mon, 10 Mar 2025 03:16:34 +0100

* gnu/packages/python-science.scm
(python-snakemake-interface-executor-plugins): New variable.
---
 gnu/packages/python-science.scm | 34 +++++++++++++++++++++++++++++++++
 1 file changed, 34 insertions(+)

diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm
index d0a354a8c6..54b04abf71 100644
--- a/gnu/packages/python-science.scm
+++ b/gnu/packages/python-science.scm
@@ -962,6 +962,40 @@ (define-public python-snakemake-interface-common
 for Snakemake and its plugins.")
     (license license:expat)))
 
+(define-public python-snakemake-interface-executor-plugins
+  (package
+    (name "python-snakemake-interface-executor-plugins")
+    (version "9.3.3")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "\
+https://github.com/snakemake/snakemake-interface-executor-plugins")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "1kjjcgkk1rbavb687x5ayw35ayhsnhpg9262k317x911wqpsj2fm"))))
+    (build-system pyproject-build-system)
+    (arguments
+     (list #:phases
+           #~(modify-phases %standard-phases
+               (replace 'check
+                 (lambda* (#:key tests? #:allow-other-keys)
+                   (when tests?
+                     (invoke "python3" "tests/tests.py")))))))
+    (propagated-inputs (list python-argparse-dataclass
+                             python-snakemake-interface-common
+                             python-throttler))
+    (native-inputs (list python-poetry-core python-pytest))
+    (home-page "\
+https://github.com/snakemake/python-snakemake-interface-executor-plugins")
+    (synopsis "Interface for Snakemake executor plugins")
+    (description
+     "This package provides a stable interface for interactions between Snakemake and
+its executor plugins.")
+    (license license:expat)))
+
 (define-public python-tdda
   (package
     (name "python-tdda")
-- 
2.48.1

Message #212 received at 76835 <at> debbugs.gnu.org (full text, mbox):

From: Nicolas Graves <ngraves <at> ngraves.fr>
To: 76835 <at> debbugs.gnu.org
Cc: Nicolas Graves <ngraves <at> ngraves.fr>
Subject: [PATCH v3 30/40] gnu: Add python-snakemake-interface-report-plugins.
Date: Mon, 10 Mar 2025 03:16:35 +0100

* gnu/packages/python-science.scm
(python-snakemake-interface-report-plugins): New variable.
---
 gnu/packages/python-science.scm | 32 ++++++++++++++++++++++++++++++++
 1 file changed, 32 insertions(+)

diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm
index 54b04abf71..41ce2a3689 100644
--- a/gnu/packages/python-science.scm
+++ b/gnu/packages/python-science.scm
@@ -996,6 +996,38 @@ (define-public python-snakemake-interface-executor-plugins
 its executor plugins.")
     (license license:expat)))
 
+(define-public python-snakemake-interface-report-plugins
+  (package
+    (name "python-snakemake-interface-report-plugins")
+    (version "1.1.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "\
+https://github.com/snakemake/snakemake-interface-report-plugins")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "0i6z9vk6nv2m3jsym0glrb7h9isdlfza2yq14vbqcslybdi9ykfa"))))
+    (build-system pyproject-build-system)
+    (arguments
+     (list #:tests? #f  ;XXX: Circular dependency on snakemake
+           #:phases
+           #~(modify-phases %standard-phases
+               (replace 'check
+                 (lambda* (#:key tests? #:allow-other-keys)
+                   (when tests?
+                     (invoke "python3" "tests/tests.py")))))))
+    (propagated-inputs (list python-snakemake-interface-common python-pytest))
+    (native-inputs (list python-poetry-core))
+    (home-page "\
+https://github.com/snakemake/python-snakemake-interface-report-plugins")
+    (synopsis "Interface for Snakemake report plugins")
+    (description "This package provides a stable interface for interactions
+between Snakemake and its report plugins.")
+    (license license:expat)))
+
 (define-public python-tdda
   (package
     (name "python-tdda")
-- 
2.48.1

Message #215 received at 76835 <at> debbugs.gnu.org (full text, mbox):

From: Nicolas Graves <ngraves <at> ngraves.fr>
To: 76835 <at> debbugs.gnu.org
Cc: Nicolas Graves <ngraves <at> ngraves.fr>
Subject: [PATCH v3 32/40] gnu: Add python-snakemake-interface-storage-plugins.
Date: Mon, 10 Mar 2025 03:16:37 +0100

* gnu/packages/python-science.scm
(python-snakemake-interface-storage-plugins): New variable.
---
 gnu/packages/python-science.scm | 34 +++++++++++++++++++++++++++++++++
 1 file changed, 34 insertions(+)

diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm
index 3ac753f55e..ac16401254 100644
--- a/gnu/packages/python-science.scm
+++ b/gnu/packages/python-science.scm
@@ -1060,6 +1060,40 @@ (define-public python-snakemake-interface-software-deployment-plugins
 its software deployment plugins.")
     (license license:expat)))
 
+(define-public python-snakemake-interface-storage-plugins
+  (package
+    (name "python-snakemake-interface-storage-plugins")
+    (version "3.3.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "\
+https://github.com/snakemake/snakemake-interface-storage-plugins")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "05n5xgwagb01nyzi8xfvp0nvdfl24lxidgksm7k86p68n1rijd5a"))))
+    (build-system pyproject-build-system)
+    (arguments
+     (list #:tests? #f  ;XXX: Circular dependency on snakemake
+           #:phases
+           #~(modify-phases %standard-phases
+               (replace 'check
+                 (lambda* (#:key tests? #:allow-other-keys)
+                   (when tests?
+                     (invoke "python3" "tests/tests.py")))))))
+    (propagated-inputs (list python-reretry python-snakemake-interface-common
+                             python-throttler python-wrapt))
+    (native-inputs (list python-poetry-core python-pytest))
+    (home-page
+     "https://github.com/snakemake/snakemake-interface-storage-plugins")
+    (synopsis "Interface for Snakemake storage plugins")
+    (description
+     "This package provides a stable interface for interactions between
+Snakemake and its storage plugins.")
+    (license license:expat)))
+
 (define-public python-tdda
   (package
     (name "python-tdda")
-- 
2.48.1

Message #218 received at 76835 <at> debbugs.gnu.org (full text, mbox):

From: Nicolas Graves <ngraves <at> ngraves.fr>
To: 76835 <at> debbugs.gnu.org
Cc: Nicolas Graves <ngraves <at> ngraves.fr>
Subject: [PATCH v3 31/40] gnu: Add
 python-snakemake-interface-software-deployment-plugins.
Date: Mon, 10 Mar 2025 03:16:36 +0100

* gnu/packages/python-science.scm
(python-snakemake-interface-software-deployment-plugins): New variable.
---
 gnu/packages/python-science.scm | 32 ++++++++++++++++++++++++++++++++
 1 file changed, 32 insertions(+)

diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm
index 41ce2a3689..3ac753f55e 100644
--- a/gnu/packages/python-science.scm
+++ b/gnu/packages/python-science.scm
@@ -1028,6 +1028,38 @@ (define-public python-snakemake-interface-report-plugins
 between Snakemake and its report plugins.")
     (license license:expat)))
 
+(define-public python-snakemake-interface-software-deployment-plugins
+  (package
+    (name "python-snakemake-interface-software-deployment-plugins")
+    (version "0.6.1")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/snakemake/snakemake-interface-software-deployment-plugins")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "0b4kkznfyfck9f92pkimhyl13ljisfn67rsilm1a5inq2ywpmxba"))))
+    (build-system pyproject-build-system)
+    (arguments
+     (list #:phases
+           #~(modify-phases %standard-phases
+               (replace 'check
+                 (lambda* (#:key tests? #:allow-other-keys)
+                   (when tests?
+                     (invoke "python3" "tests/tests.py")))))))
+    (propagated-inputs (list python-argparse-dataclass
+                             python-snakemake-interface-common))
+    (native-inputs (list python-poetry-core))
+    (home-page "\
+https://github.com/snakemake/snakemake-interface-software-deployment-plugins")
+    (synopsis "Interface for Snakemake software deployment plugins")
+    (description
+     "This package provides a stable interface for interactions between Snakemake and
+its software deployment plugins.")
+    (license license:expat)))
+
 (define-public python-tdda
   (package
     (name "python-tdda")
-- 
2.48.1

Message #221 received at 76835 <at> debbugs.gnu.org (full text, mbox):

From: Nicolas Graves <ngraves <at> ngraves.fr>
To: 76835 <at> debbugs.gnu.org
Cc: Nicolas Graves <ngraves <at> ngraves.fr>
Subject: [PATCH v3 33/40] gnu: Add python-throttler.
Date: Mon, 10 Mar 2025 03:16:38 +0100

* gnu/packages/python-xyz.scm (python-throttler): New variable.
---
 gnu/packages/python-xyz.scm | 27 +++++++++++++++++++++++++++
 1 file changed, 27 insertions(+)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index c6d90fe1ac..540ea1b379 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -14869,6 +14869,33 @@ (define-public python-three-merge
 approach.")
     (license license:expat)))
 
+(define-public python-throttler
+  (package
+    (name "python-throttler")
+    (version "1.2.2")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/uburuntu/throttler")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "1gn21x0zkm7rr7qijlz7nvw7z0mm1j2r0r2lslg7wln1z36gjkbw"))))
+    (build-system pyproject-build-system)
+    (native-inputs (list python-aiohttp
+                         python-pytest
+                         python-pytest-asyncio
+                         python-pytest-cov
+                         python-setuptools
+                         python-wheel))
+    (home-page "https://github.com/uburuntu/throttler")
+    (synopsis "Throttling with asyncio support in Python")
+    (description
+     "This package provides a zero-dependency Python package for easy
+throttling with asyncio support.")
+    (license license:expat)))
+
 (define-public snakemake
   (package
     (name "snakemake")
-- 
2.48.1

Message #224 received at 76835 <at> debbugs.gnu.org (full text, mbox):

From: Nicolas Graves <ngraves <at> ngraves.fr>
To: 76835 <at> debbugs.gnu.org
Cc: Nicolas Graves <ngraves <at> ngraves.fr>
Subject: [PATCH v3 34/40] gnu: Add python-reretry.
Date: Mon, 10 Mar 2025 03:16:39 +0100

* gnu/packages/python-xyz.scm (python-reretry): New variable.
---
 gnu/packages/python-xyz.scm | 19 +++++++++++++++++++
 1 file changed, 19 insertions(+)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 540ea1b379..a12edc7ab0 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -7895,6 +7895,25 @@ (define-public python-repoze-lru
      "This package provides a tiny LRU cache implementation and decorator.")
     (license license:bsd-4)))
 
+(define-public python-reretry
+  (package
+    (name "python-reretry")
+    (version "0.11.8")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "reretry" version))
+       (sha256
+        (base32 "1qrjsjzah8gw1bciqn8bhrj80fjjg13qg8jks7qs4bjipv71yygj"))))
+    (build-system pyproject-build-system)
+    (native-inputs (list python-setuptools python-wheel))
+    (home-page "https://github.com/leshchenko1979/reretry")
+    (synopsis "Python decorator for retrying on exceptions")
+    (description
+     "This provides an easy to use, but functional decorator for retrying on
+exceptions.")
+    (license license:asl2.0)))
+
 (define-public python-restructuredtext-lint
   (package
     (name "python-restructuredtext-lint")
-- 
2.48.1

Message #227 received at 76835 <at> debbugs.gnu.org (full text, mbox):

From: Nicolas Graves <ngraves <at> ngraves.fr>
To: 76835 <at> debbugs.gnu.org
Cc: Nicolas Graves <ngraves <at> ngraves.fr>
Subject: [PATCH v3 35/40] gnu: Add python-conda-inject.
Date: Mon, 10 Mar 2025 03:16:40 +0100

* gnu/packages/package-management.scm (python-conda-inject): New variable.
---
 gnu/packages/package-management.scm | 32 +++++++++++++++++++++++++++++
 1 file changed, 32 insertions(+)

diff --git a/gnu/packages/package-management.scm b/gnu/packages/package-management.scm
index da50de8788..13cc7aa073 100644
--- a/gnu/packages/package-management.scm
+++ b/gnu/packages/package-management.scm
@@ -1123,6 +1123,38 @@ (define-public python-anaconda-client
 environments.")
     (license license:bsd-3)))
 
+(define-public python-conda-inject
+  (package
+    (name "python-conda-inject")
+    (version "1.3.2")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/koesterlab/conda-inject")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "1aig9l676wc2sjb20y7rdqf0hfcfjhh92yfiy82mf7kfnv7rp3rk"))))
+    (build-system pyproject-build-system)
+    (arguments
+     (list #:phases
+           #~(modify-phases %standard-phases
+               (replace 'check
+                 (lambda* (#:key tests? #:allow-other-keys)
+                   (when tests?
+                     (invoke "python3" "tests/tests.py")))))))
+    (propagated-inputs (list python-pyyaml))
+    (native-inputs (list python-poetry-core python-pytest))
+    (home-page "https://github.com/koesterlab/conda-inject")
+    (synopsis
+     "Inject a conda environment into the current python environment")
+    (description
+     "This package provides helper functions for injecting a conda
+environment into the current python environment (by modifying @code{sys.path},
+without actually changing the current python environment).")
+    (license license:expat)))
+
 (define-public python-conda-package-handling
   (package
     (name "python-conda-package-handling")
-- 
2.48.1

Message #230 received at 76835 <at> debbugs.gnu.org (full text, mbox):

From: Nicolas Graves <ngraves <at> ngraves.fr>
To: 76835 <at> debbugs.gnu.org
Cc: Nicolas Graves <ngraves <at> ngraves.fr>
Subject: [PATCH v3 36/40] gnu: Add snakemake.
Date: Mon, 10 Mar 2025 03:16:41 +0100

* gnu/packages/python-science.scm (snakemake): New variable.
---
 gnu/packages/python-science.scm | 122 ++++++++++++++++++++++++++++++++
 1 file changed, 122 insertions(+)

diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm
index ac16401254..7ccd991478 100644
--- a/gnu/packages/python-science.scm
+++ b/gnu/packages/python-science.scm
@@ -27,6 +27,7 @@
 ;;; Copyright © 2024 Marco Baggio <marco.baggio <at> mdc-berlin.de>
 ;;; Copyright © 2024 Nicolas Graves <ngraves <at> ngraves.fr>
 ;;; Copyright © 2024 Rick Huijzer <ikbenrickhuyzer <at> gmail.com>
+;;; Copyright © 2025 Nicolas Graves <ngraves <at> ngraves.fr>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -67,6 +68,7 @@ (define-module (gnu packages python-science)
   #:use-module (gnu packages maths)
   #:use-module (gnu packages mpi)
   #:use-module (gnu packages pcre)
+  #:use-module (gnu packages package-management)
   #:use-module (gnu packages perl)
   #:use-module (gnu packages pkg-config)
   #:use-module (gnu packages python)
@@ -82,6 +84,7 @@ (define-module (gnu packages python-science)
   #:use-module (gnu packages ssh)
   #:use-module (gnu packages statistics)
   #:use-module (gnu packages time)
+  #:use-module (gnu packages version-control)
   #:use-module (gnu packages xdisorg)
   #:use-module (gnu packages xml)
   #:use-module (gnu packages xorg)
@@ -4410,6 +4413,125 @@ (define-public python-libneuroml
 neuronal models")
     (license license:bsd-3)))
 
+(define-public snakemake
+  (package
+    (name "snakemake")
+    (version "8.29.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "snakemake" version))
+       (sha256
+        (base32 "1ilpmrjmnc529p4gw2x23ik1d8b5pm6k1dhq08dknvfjsf3vgyjr"))))
+    (build-system pyproject-build-system)
+    (arguments
+     (list
+      #:test-flags
+      #~(list
+         ;; XXX: Unclear why these tests fail.
+         "--ignore=tests/test_report_href/test_script.py"
+         "--ignore=tests/test_script_py/scripts/test_explicit_import.py"
+         "--ignore=tests/test_output_index.py"
+         ;; We don't care about testing old python <at> 3.7 on Guix.
+         "--ignore=tests/test_conda_python_3_7_script/test_script.py"
+         ;; Those require additional snakemake plugins.
+         "--ignore=tests/test_api.py"
+         "--ignore=tests/test_executor_test_suite.py"
+         ;; We don't care about lints.
+         "--ignore=tests/test_linting.py"
+         ;; These tests attempt to change S3 buckets on AWS and fail
+         ;; because there are no AWS credentials.
+         "--ignore=tests/test_tibanna"
+         ;; It's a similar story with this test, which requires access
+         ;; to the Google Storage service.
+         "--ignore=tests/test_google_lifesciences")
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-after 'unpack 'avoid-assets-download
+            (lambda _
+              (substitute* "setup.py"
+                (("^from assets import Assets") "")
+                (("^Assets\\.deploy\\(\\)") ""))))
+          ;; For cluster execution Snakemake will call Python.  Since there is
+          ;; no suitable GUIX_PYTHONPATH set, cluster execution will fail.  We
+          ;; fix this by calling the snakemake wrapper instead.
+          (add-after 'unpack 'call-wrapper-not-wrapped-snakemake
+            (lambda _
+              (substitute* "snakemake/executors/__init__.py"
+                (("self\\.get_python_executable\\(\\),")
+                 "")
+                (("\"-m snakemake\"")
+                 (string-append "\"" #$output
+                                "/bin/snakemake" "\""))
+                ;; The snakemake command produced by format_job_exec contains
+                ;; references to /gnu/store.  Prior to patching above that's
+                ;; just a reference to Python; after patching it's a reference
+                ;; to the snakemake executable.
+                ;;
+                ;; In Tibanna execution mode Snakemake arranges for a certain
+                ;; Docker image to be deployed to AWS.  It then passes its own
+                ;; command line to Tibanna.  This is misguided because it only
+                ;; ever works if the local Snakemake command was run inside
+                ;; the same Docker image.  In the case of using Guix this is
+                ;; never correct, so we need to replace the store reference.
+                (("tibanna_args.command = command")
+                 (string-append
+                  "tibanna_args.command = command.replace('"
+                  #$output "/bin/snakemake', 'python3 -m snakemake')")))))
+          (add-after 'unpack 'patch-version
+            (lambda _
+              (substitute* "setup.py"
+                (("version=versioneer.get_version\\(\\)")
+                 (format #f "version=~s" #$version)))
+              (substitute* '("snakemake/_version.py"
+                             "versioneer.py")
+                (("0\\+unknown") #$version))))
+          (add-before 'check 'pre-check
+            (lambda* (#:key tests?  #:allow-other-keys)
+              (when tests?
+                (setenv "HOME" "/tmp")))))))
+    (inputs
+     (list python-appdirs
+           python-conda-inject
+           python-configargparse
+           python-connection-pool
+           python-docutils
+           python-dpath
+           python-gitpython
+           python-humanfriendly
+           python-immutables
+           python-jinja2
+           python-jsonschema
+           python-nbformat
+           python-packaging
+           python-psutil
+           python-pulp
+           python-pyyaml
+           python-requests
+           python-reretry
+           python-smart-open
+           python-snakemake-interface-common
+           python-snakemake-interface-executor-plugins
+           python-snakemake-interface-report-plugins
+           python-snakemake-interface-storage-plugins
+           python-tabulate
+           python-throttler
+           python-wrapt
+           python-yte))
+    (native-inputs
+     (list python-numpy
+           python-pandas
+           python-setuptools
+           python-tomli
+           python-wheel))
+    (home-page "https://snakemake.readthedocs.io")
+    (synopsis "Python-based execution environment for make-like workflows")
+    (description
+     "Snakemake aims to reduce the complexity of creating workflows by
+providing a clean and modern domain specific specification language (DSL) in
+Python style, together with a fast and comfortable execution environment.")
+    (license license:expat)))
+
 ;;;
 ;;; Avoid adding new packages to the end of this file. To reduce the chances
 ;;; of a merge conflict, place them above by existing packages with similar
-- 
2.48.1

Message #233 received at 76835 <at> debbugs.gnu.org (full text, mbox):

From: Nicolas Graves <ngraves <at> ngraves.fr>
To: 76835 <at> debbugs.gnu.org
Cc: Nicolas Graves <ngraves <at> ngraves.fr>
Subject: [PATCH v3 37/40] gnu: python-ratelimiter: Update to 1.2.0-0.da78a45.
Date: Mon, 10 Mar 2025 03:16:42 +0100

* gnu/packages/python-xyz.scm (python-ratelimiter): Update to 1.2.0-0.da78a45.
[native-inputs]: Add python-pytest, python-pytest-asyncio,
python-setuptools, python-wheel.
[arguments]{phases}: Add 'patch phase.
---
 gnu/packages/python-xyz.scm | 62 ++++++++++++++++++++++++++-----------
 1 file changed, 44 insertions(+), 18 deletions(-)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index a12edc7ab0..81b8386049 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -27885,25 +27885,51 @@ (define-public python-tracerite
     (license license:unlicense)))
 
 (define-public python-ratelimiter
-  (package
-    (name "python-ratelimiter")
-    (version "1.2.0")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (pypi-uri "ratelimiter" version))
-       (sha256
-        (base32
-         "1dhz85mj5bqd2mij84ncs6pz32hgidr79hay4aqfmzaa4rbb497p"))))
-    (build-system python-build-system)
-    (arguments
-     '(#:tests? #f))          ; There are no tests in the pypi archive.
-    (home-page "https://github.com/RazerM/ratelimiter")
-    (synopsis "Simple rate limiting object")
-    (description
-     "The @code{ratelimiter} module ensures that an operation will not be
+  ;; Latest commit of the archived repository.
+  (let ((commit "da78a45867c3a204083c6ea8ee74f6b3e78ef524")
+        (revision "0"))
+    (package
+      (name "python-ratelimiter")
+      (version (git-version "1.2.0" revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/RazerM/ratelimiter")
+               (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32 "1dhfp170wzbn2pfgha5bacc8cmibs5vq4cdgpbibqbwpxm797xrb"))))
+      (build-system pyproject-build-system)
+      (arguments
+       (list #:phases
+             #~(modify-phases %standard-phases
+                 (add-after 'unpack 'patch
+                   (lambda _
+                     ;; Patch for pytest <at> 7 support
+                     ;; Taken from /pull/13
+                     (substitute* "tests/conftest.py"
+                       (("pytest\\.collect\\.File")
+                        "pytest.File"))
+                     ;; Patch for python <at> 3.8+ support
+                     ;; Taken from /pull/11
+                     (substitute* "ratelimiter/_async.py"
+                       (("with await self\\._alock:")
+                        "async with self._alock:")
+                       (("__aexit__ = asyncio\\.coroutine\\(.*\\)") "\
+async def __aexit__(self, exc_type, exc_value, traceback):
+         return super(AsyncRateLimiter, self).\
+__exit__(exc_type, exc_value, traceback)")))))))
+      (native-inputs (list python-pytest
+                           python-pytest-asyncio
+                           python-setuptools
+                           python-wheel))
+      (home-page "https://github.com/RazerM/ratelimiter")
+      (synopsis "Simple rate limiting object")
+      (description
+       "The @code{ratelimiter} module ensures that an operation will not be
 executed more than a given number of times during a given period.")
-    (license license:asl2.0)))
+      (license license:asl2.0))))
 
 (define-public python-jsonrpclib-pelix
   (package
-- 
2.48.1

Message #236 received at 76835 <at> debbugs.gnu.org (full text, mbox):

From: Nicolas Graves <ngraves <at> ngraves.fr>
To: 76835 <at> debbugs.gnu.org
Cc: Nicolas Graves <ngraves <at> ngraves.fr>
Subject: [PATCH v3 38/40] gnu: snakemake-7: Move to (gnu packages
 python-science).
Date: Mon, 10 Mar 2025 03:16:43 +0100

* gnu/packages/python-xyz.scm (snakemake-7): Move from here…
* gnu/packages/python-science.scm (snakemake-7): …to here.
Inherit from snakemake <at> 8.
---
 gnu/packages/python-science.scm |  70 +++++++++++++++++++++
 gnu/packages/python-xyz.scm     | 104 --------------------------------
 2 files changed, 70 insertions(+), 104 deletions(-)

diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm
index 7ccd991478..5acead6523 100644
--- a/gnu/packages/python-science.scm
+++ b/gnu/packages/python-science.scm
@@ -4532,6 +4532,76 @@ (define-public snakemake
 Python style, together with a fast and comfortable execution environment.")
     (license license:expat)))
 
+(define-public snakemake-7
+  (package
+    (inherit snakemake)
+    (name "snakemake")
+    (version "7.7.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/snakemake/snakemake")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "1qrqbmx4cbis0wxr6dl2rdjv9v627sbirsz6v5c31vlbqwkvs04q"))))
+    (build-system pyproject-build-system)
+    (arguments
+     (substitute-keyword-arguments (package-arguments snakemake)
+       ((#:test-flags test-flags)
+        #~(list
+           ;; We don't care about lints.
+           "--ignore=tests/test_linting.py"
+           ;; These tests attempt to change S3 buckets on AWS and fail
+           ;; because there are no AWS credentials.
+           "--ignore=tests/test_tibanna.py"
+           ;; It's a similar story with this test, which requires access
+           ;; to the Google Storage service.
+           "--ignore=tests/test_google_lifesciences.py"))
+       ((#:phases phases)
+        #~(modify-phases #$phases
+            (delete 'avoid-assets-download)
+            ;; No longer needed with 7.15.2+
+            (add-after 'unpack 'tabulate-compatibility
+              (lambda _
+                (substitute* "snakemake/dag.py"
+                  (("\"job\": rule,")
+                   "\"job\": rule.name,"))))))))
+    (propagated-inputs
+     (list python-appdirs
+           python-configargparse
+           python-connection-pool
+           python-datrie
+           python-docutils
+           python-filelock
+           python-gitpython
+           python-jinja2
+           python-jsonschema
+           python-nbformat
+           python-networkx
+           python-psutil
+           python-pulp
+           python-pyyaml
+           python-py-tes
+           python-ratelimiter
+           python-requests
+           python-retry
+           python-smart-open
+           python-stopit
+           python-tabulate
+           python-toposort
+           python-wrapt
+           python-yte))
+    (native-inputs
+     (list git-minimal
+           python-wrapper
+           python-pytest
+           python-pandas
+           python-requests-mock
+           python-setuptools
+           python-wheel))))
+
 ;;;
 ;;; Avoid adding new packages to the end of this file. To reduce the chances
 ;;; of a merge conflict, place them above by existing packages with similar
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 81b8386049..740e6cfd33 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -15082,110 +15082,6 @@ (define-public snakemake-6
            python-setuptools
            python-wheel))))
 
-(define-public snakemake-7
-  (package
-    (inherit snakemake-6)
-    (name "snakemake")
-    (version "7.7.0")
-    (source
-     (origin
-       (method git-fetch)
-       (uri (git-reference
-             (url "https://github.com/snakemake/snakemake")
-             (commit (string-append "v" version))))
-       (file-name (git-file-name name version))
-       (sha256
-        (base32 "1qrqbmx4cbis0wxr6dl2rdjv9v627sbirsz6v5c31vlbqwkvs04q"))))
-    (build-system pyproject-build-system)
-    (arguments
-     (list
-      #:phases
-      #~(modify-phases %standard-phases
-          ;; For cluster execution Snakemake will call Python.  Since there is
-          ;; no suitable GUIX_PYTHONPATH set, cluster execution will fail.  We
-          ;; fix this by calling the snakemake wrapper instead.
-          (add-after 'unpack 'call-wrapper-not-wrapped-snakemake
-            (lambda* (#:key outputs #:allow-other-keys)
-              (substitute* "snakemake/executors/__init__.py"
-                (("self\\.get_python_executable\\(\\),")
-                 "")
-                (("\"-m snakemake\"")
-                 (string-append "\"" #$output
-                                "/bin/snakemake" "\""))
-                ;; The snakemake command produced by format_job_exec contains
-                ;; references to /gnu/store.  Prior to patching above that's
-                ;; just a reference to Python; after patching it's a reference
-                ;; to the snakemake executable.
-                ;;
-                ;; In Tibanna execution mode Snakemake arranges for a certain
-                ;; Docker image to be deployed to AWS.  It then passes its own
-                ;; command line to Tibanna.  This is misguided because it only
-                ;; ever works if the local Snakemake command was run inside
-                ;; the same Docker image.  In the case of using Guix this is
-                ;; never correct, so we need to replace the store reference.
-                (("tibanna_args.command = command")
-                 (string-append
-                  "tibanna_args.command = command.replace('"
-                  #$output "/bin/snakemake', 'python3 -m snakemake')")))))
-          ;; No longer needed with 7.15.2+
-          (add-after 'unpack 'tabulate-compatibility
-            (lambda _
-              (substitute* "snakemake/dag.py"
-                (("\"job\": rule,")
-                 "\"job\": rule.name,"))))
-          (add-after 'unpack 'patch-version
-            (lambda _
-              (substitute* "setup.py"
-                (("version=versioneer.get_version\\(\\)")
-                 (format #f "version=~s" #$version)))
-              (substitute* '("snakemake/_version.py"
-                             "versioneer.py")
-                (("0\\+unknown") #$version))))
-          (replace 'check
-            (lambda* (#:key tests? #:allow-other-keys)
-              (when tests?
-                (setenv "HOME" "/tmp")
-                ;; This test attempts to change S3 buckets on AWS and fails
-                ;; because there are no AWS credentials.
-                (delete-file "tests/test_tibanna.py")
-                ;; It's a similar story with this test, which requires access
-                ;; to the Google Storage service.
-                (delete-file "tests/test_google_lifesciences.py")
-                (invoke "pytest")))))))
-    (propagated-inputs
-     (list python-appdirs
-           python-configargparse
-           python-connection-pool
-           python-datrie
-           python-docutils
-           python-filelock
-           python-gitpython
-           python-jinja2
-           python-jsonschema
-           python-nbformat
-           python-networkx
-           python-psutil
-           python-pulp
-           python-pyyaml
-           python-py-tes
-           python-ratelimiter
-           python-requests
-           python-retry
-           python-smart-open
-           python-stopit
-           python-tabulate
-           python-toposort
-           python-wrapt
-           python-yte))
-    (native-inputs
-     (list git-minimal
-           python-wrapper
-           python-pytest
-           python-pandas
-           python-requests-mock
-           python-setuptools
-           python-wheel))))
-
 (define-public python-pyqrcode
   (package
     (name "python-pyqrcode")
-- 
2.48.1

Message #239 received at 76835 <at> debbugs.gnu.org (full text, mbox):

From: Nicolas Graves <ngraves <at> ngraves.fr>
To: 76835 <at> debbugs.gnu.org
Cc: Nicolas Graves <ngraves <at> ngraves.fr>
Subject: [PATCH v3 39/40] gnu: snakemake-6: Move to (gnu packages
 python-science).
Date: Mon, 10 Mar 2025 03:16:44 +0100

* gnu/packages/python-xyz.scm (snakemake-6): Move from here…
* gnu/packages/python-science.scm (snakemake-6): …to here.
Inherit from snakemake-7.
---
 gnu/packages/python-science.scm | 19 ++++++++
 gnu/packages/python-xyz.scm     | 83 ---------------------------------
 2 files changed, 19 insertions(+), 83 deletions(-)

diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm
index 5acead6523..509e77b765 100644
--- a/gnu/packages/python-science.scm
+++ b/gnu/packages/python-science.scm
@@ -4602,6 +4602,25 @@ (define-public snakemake-7
            python-setuptools
            python-wheel))))
 
+(define-public snakemake-6
+  (package
+    (inherit snakemake-7)
+    (name "snakemake")
+    (version "6.15.5")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/snakemake/snakemake")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "09yrpi9f86r9yvcm2dfjs5zy87c4j31bxama77kfd6y8yfrrjlai"))))
+    (build-system pyproject-build-system)
+    (propagated-inputs
+     (modify-inputs (package-propagated-inputs snakemake-7)
+       (delete "python-retry" "python-yte")))))
+
 ;;;
 ;;; Avoid adding new packages to the end of this file. To reduce the chances
 ;;; of a merge conflict, place them above by existing packages with similar
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 740e6cfd33..fa73a189ce 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -14999,89 +14999,6 @@ (define-public snakemake
 Python style, together with a fast and comfortable execution environment.")
     (license license:expat)))
 
-(define-public snakemake-6
-  (package
-    (inherit snakemake)
-    (name "snakemake")
-    (version "6.15.5")
-    (source
-     (origin
-       (method git-fetch)
-       (uri (git-reference
-             (url "https://github.com/snakemake/snakemake")
-             (commit (string-append "v" version))))
-       (file-name (git-file-name name version))
-       (sha256
-        (base32 "09yrpi9f86r9yvcm2dfjs5zy87c4j31bxama77kfd6y8yfrrjlai"))))
-    (build-system pyproject-build-system)
-    (arguments
-     (list
-      #:phases
-      #~(modify-phases %standard-phases
-          ;; For cluster execution Snakemake will call Python.  Since there is
-          ;; no suitable GUIX_PYTHONPATH set, cluster execution will fail.  We
-          ;; fix this by calling the snakemake wrapper instead.
-
-          ;; XXX: There is another instance of sys.executable on line 692, but
-          ;; it is not clear how to patch it.
-          (add-after 'unpack 'call-wrapper-not-wrapped-snakemake
-            (lambda* (#:key outputs #:allow-other-keys)
-              (substitute* "snakemake/executors/__init__.py"
-                (("\\{sys.executable\\} -m snakemake")
-                 (string-append #$output "/bin/snakemake")))))
-          (add-after 'unpack 'tabulate-compatibility
-            (lambda _
-              (substitute* "snakemake/dag.py"
-                (("\"job\": rule,")
-                 "\"job\": rule.name,"))))
-          (add-after 'unpack 'patch-version
-            (lambda _
-              (substitute* "setup.py"
-                (("version=versioneer.get_version\\(\\)")
-                 (format #f "version=~s" #$version)))
-              (substitute* '("snakemake/_version.py"
-                             "versioneer.py")
-                (("0\\+unknown") #$version))))
-          (replace 'check
-            (lambda* (#:key tests? #:allow-other-keys)
-              (when tests?
-                (setenv "HOME" "/tmp")
-                ;; This test attempts to change S3 buckets on AWS and fails
-                ;; because there are no AWS credentials.
-                (delete-file "tests/test_tibanna.py")
-                (invoke "pytest")))))))
-    (propagated-inputs
-     (list python-appdirs
-           python-configargparse
-           python-connection-pool
-           python-datrie
-           python-docutils
-           python-filelock
-           python-gitpython
-           python-jinja2
-           python-jsonschema
-           python-nbformat
-           python-networkx
-           python-psutil
-           python-pulp
-           python-pyyaml
-           python-py-tes
-           python-ratelimiter
-           python-requests
-           python-smart-open
-           python-stopit
-           python-tabulate
-           python-toposort
-           python-wrapt))
-    (native-inputs
-     (list git-minimal
-           python-wrapper
-           python-pytest
-           python-pandas
-           python-requests-mock
-           python-setuptools
-           python-wheel))))
-
 (define-public python-pyqrcode
   (package
     (name "python-pyqrcode")
-- 
2.48.1

Message #242 received at 76835 <at> debbugs.gnu.org (full text, mbox):

From: Nicolas Graves <ngraves <at> ngraves.fr>
To: 76835 <at> debbugs.gnu.org
Cc: Nicolas Graves <ngraves <at> ngraves.fr>
Subject: [PATCH v3 40/40] gnu: Remove snakemake.
Date: Mon, 10 Mar 2025 03:16:45 +0100

* gnu/packages/python-xyz.scm (snakemake): Delete variable.
---
 gnu/packages/python-xyz.scm | 84 -------------------------------------
 1 file changed, 84 deletions(-)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index fa73a189ce..91c662c35c 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -14915,90 +14915,6 @@ (define-public python-throttler
 throttling with asyncio support.")
     (license license:expat)))
 
-(define-public snakemake
-  (package
-    (name "snakemake")
-    (version "5.32.2")
-    (source
-     (origin
-       (method git-fetch)
-       (uri (git-reference
-             (url "https://github.com/snakemake/snakemake")
-             (commit (string-append "v" version))))
-       (file-name (git-file-name name version))
-       (sha256
-        (base32 "0nxp4z81vykv07kv2b6zrwk7ns8s10zqsb7vcignp8695yq3nlcm"))))
-    (build-system pyproject-build-system)
-    (arguments
-     (list
-      #:test-flags
-      '(list
-        ;; We have no TES support.
-        "--ignore=tests/test_tes.py"
-        ;; This test attempts to change S3 buckets on AWS and fails
-        ;; because there are no AWS credentials.
-        "--ignore=tests/test_tibanna.py"
-        ;; It's a similar story with this test, which requires access
-        ;; to the Google Storage service.
-        "--ignore=tests/test_google_lifesciences.py")
-      #:phases
-      #~(modify-phases %standard-phases
-          (add-after 'unpack 'tabulate-compatibility
-            (lambda _
-              (substitute* "snakemake/dag.py"
-                (("\"job\": rule,")
-                 "\"job\": rule.name,"))))
-          (add-after 'unpack 'patch-version
-            (lambda _
-              (substitute* "setup.py"
-                (("version=versioneer.get_version\\(\\)")
-                 (format #f "version=~s" #$version)))
-              (substitute* '("snakemake/_version.py"
-                             "versioneer.py")
-                (("0\\+unknown") #$version))))
-          ;; For cluster execution Snakemake will call Python.  Since there is
-          ;; no suitable PYTHONPATH set, cluster execution will fail.  We fix
-          ;; this by calling the snakemake wrapper instead.
-          (add-after 'unpack 'call-wrapper-not-wrapped-snakemake
-            (lambda _
-              (substitute* "snakemake/executors/__init__.py"
-                (("\\{sys.executable\\} -m snakemake")
-                 (string-append #$output "/bin/snakemake")))))
-          (add-before 'check 'pre-check
-            (lambda _ (setenv "HOME" "/tmp"))))))
-    (propagated-inputs
-     (list python-appdirs
-           python-configargparse
-           python-datrie
-           python-docutils
-           python-gitpython
-           python-jinja2
-           python-jsonschema
-           python-nbformat
-           python-networkx
-           python-psutil
-           python-pulp
-           python-pyyaml
-           python-ratelimiter
-           python-requests
-           python-toposort
-           python-wrapt))
-    (native-inputs
-     (list git-minimal
-           python-wrapper
-           python-pytest
-           python-pandas
-           python-requests-mock
-           python-setuptools
-           python-wheel))
-    (home-page "https://snakemake.readthedocs.io")
-    (synopsis "Python-based execution environment for make-like workflows")
-    (description
-      "Snakemake aims to reduce the complexity of creating workflows by
-providing a clean and modern domain specific specification language (DSL) in
-Python style, together with a fast and comfortable execution environment.")
-    (license license:expat)))
-
 (define-public python-pyqrcode
   (package
     (name "python-pyqrcode")
-- 
2.48.1

Message #245 received at 76835 <at> debbugs.gnu.org (full text, mbox):

From: Sharlatan Hellseher <sharlatanus <at> gmail.com>
To: 76835 <at> debbugs.gnu.org
Cc: Nicolas Graves <ngraves <at> ngraves.fr>
Subject: [PATCH python-team 00/15] Some further python fixes
Date: Wed, 12 Mar 2025 19:30:36 +0000

[Message part 1 (text/plain, inline)]

Hi

While nothing is working right now (mumi and patchwork) I'm about to
pull v3 patches like this:

--8<---------------cut here---------------start------------->8---
seq 1 79 | while read -r i; do curl https://issues.guix.gnu.org/issue/76835/raw/$i -o $i & done

grep -ow "PATCH.v3..." -r . | sed -e 's/PATCH//' -e 's/v3 /v3-0/' -e 's/: / /' | while read -r of nf; do cp $of $nf; done
--8<---------------cut here---------------end--------------->8---

--
Oleg

[signature.asc (application/pgp-signature, inline)]

Message #250 received at 76835-done <at> debbugs.gnu.org (full text, mbox):

From: Steve George <steve <at> futurile.net>
To: 76835-done <at> debbugs.gnu.org
Subject: RE: Some further python fixes
Date: Tue, 15 Apr 2025 00:43:01 +0100

Hi Nicolas,

Done in 985fe12efd4f60f006dfabd4f9314dc2f1cead38 

Lets see how the tree is with these added, hopefully we're moving in the right direction!

Thanks,

Futurile / Steve

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