GNU bug report logs - #77575
[PATCH python-team 00/21] More patches

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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 00/21] More patches
Date: Sun,  6 Apr 2025 14:31:07 +0200

Please only select the ones you care about, some there can be skipped.
Big news :
wxpython fixed, pomegranate tests disabled, python-lap fixed.

Nicolas Graves (21):
  gnu: python-sanic: Update to 25.3.0.
  gnu: python-stem: Update to 1.8.2.
  gnu: python-lazr-delegates: Update to 2.1.1.
  gnu: python-lazr-config: Update to 3.1.
  gnu: python-lap: Update to 0.5.12.
  gnu: Remove python-pydiff.
  gnu: pomegranate: Disable tests.
  gnu: python-pymodbus: Update to 3.8.6.
  gnu: python-flufl-lock: Update to 8.1.0.
  gnu: python-flufl-i18n: Update to 5.1.0.
  gnu: cnvkit: Update to 0.9.12.
  gnu: python-authheaders: Update to 0.16.3.
  gnu: mailman: Update to 3.3.10.
  gnu: python-mailman-hyperkitty: Update to 1.2.1.
  gnu: python-ledgerblue: Fix version detection.
  gnu: ledger-agent: Switch to pyproject-build-system.
  gnu: python-gixy: Rename package to python-gixy-ng.
  gnu: python-ujson: Update to 5.10.0.
  gnu: bpytop: Switch to pyproject-build-system.
  gnu: python-redis: Ignore i686 failing test.
  gnu: python-wxpython: Update to 4.2.2.

 gnu/local.mk                                  |   1 -
 gnu/packages/admin.scm                        |  38 +--
 gnu/packages/bioinformatics.scm               |   6 +-
 gnu/packages/check.scm                        |  69 ++---
 gnu/packages/databases.scm                    |  37 +--
 gnu/packages/finance.scm                      |  13 +-
 gnu/packages/machine-learning.scm             |  39 ++-
 gnu/packages/mail.scm                         |  27 +-
 .../python-wxwidgets-type-errors.patch        |  42 ---
 gnu/packages/python-web.scm                   |  20 +-
 gnu/packages/python-xyz.scm                   | 264 ++++++++++--------
 gnu/packages/wxwidgets.scm                    |  51 +++-
 12 files changed, 329 insertions(+), 278 deletions(-)
 delete mode 100644 gnu/packages/patches/python-wxwidgets-type-errors.patch

-- 
2.49.0

Message #8 received at 77575 <at> debbugs.gnu.org (full text, mbox):

From: Nicolas Graves <ngraves <at> ngraves.fr>
To: 77575 <at> debbugs.gnu.org
Cc: Nicolas Graves <ngraves <at> ngraves.fr>
Subject: [PATCH 01/21] gnu: python-sanic: Update to 25.3.0.
Date: Sun,  6 Apr 2025 14:37:03 +0200

* gnu/packages/python-web.scm (python-sanic): Update to 25.3.0.
[source]: Add a snippet to loosen setuptools requirement.
[native-inputs]: Add python-chardet, python-cryptography,
python-docutils, python-mypy, python-pygments,
python-pytest-benchmark, python-pytest-sanic, python-slotscheck,
python-towncrier, python-types-ujson.
---
 gnu/packages/python-web.scm | 20 +++++++++++++++++---
 1 file changed, 17 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm
index bc35bc1c83..2fda55760f 100644
--- a/gnu/packages/python-web.scm
+++ b/gnu/packages/python-web.scm
@@ -9021,14 +9021,18 @@ (define-public python-sanic-testing
 (define-public python-sanic
   (package
     (name "python-sanic")
-    (version "23.12.1")
+    (version "25.3.0")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "sanic" version))
        (sha256
-        (base32
-         "115vnir4qijv89139g5h0i4l0n4w3bgh1ickgnk8xidxsa0wla15"))))
+        (base32 "1fv9wgsj54scbr7qhmwdgc4zqnqpwacpakcfxhsg10gc04h54pbp"))
+       ;; Loosen requirements for both python-sanic and python-sanic-bootstrap.
+       (modules '((guix build utils)))
+       (snippet #~(substitute* "setup.py"
+                    (("setuptools>=[0-9.]*")
+                     "setuptools")))))
     (build-system pyproject-build-system)
     (arguments
      (list
@@ -9081,10 +9085,20 @@ (define-public python-sanic
            python-websockets))
     (native-inputs
      (list python-beautifulsoup4
+           python-chardet
+           python-cryptography
+           python-docutils
+           python-mypy
+           python-pygments
            python-pytest
            python-pytest-asyncio
+           python-pytest-benchmark
+           python-pytest-sanic
            python-sanic-testing
            python-setuptools
+           python-slotscheck
+           python-towncrier
+           python-types-ujson
            python-uvicorn
            python-wheel))
     (home-page "https://github.com/sanic-org/sanic/")
-- 
2.49.0

Message #11 received at 77575 <at> debbugs.gnu.org (full text, mbox):

From: Nicolas Graves <ngraves <at> ngraves.fr>
To: 77575 <at> debbugs.gnu.org
Cc: Nicolas Graves <ngraves <at> ngraves.fr>
Subject: [PATCH 03/21] gnu: python-lazr-delegates: Update to 2.1.1.
Date: Sun,  6 Apr 2025 14:37:05 +0200

* gnu/packages/python-xyz.scm (python-lazr-delegates): Update to 2.1.1.
[build-system]: Switch to pyproject.
[arguments]{test-flags}: Run tests in output.
{phases}: Add a 'check-cleanup phase to remove tests from output.
[native-inputs]: Remove python-nose.  Add python-pytest,
python-setuptools, python-wheel.
---
 gnu/packages/python-xyz.scm | 30 +++++++++++++++++++-----------
 1 file changed, 19 insertions(+), 11 deletions(-)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 08d0eb6194..0cc189ce15 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -34617,23 +34617,31 @@ (define-public python-readme-renderer
 (define-public python-lazr-delegates
   (package
     (name "python-lazr-delegates")
-    (version "2.0.4")
+    (version "2.1.1")
     (source
       (origin
         (method url-fetch)
-        (uri (pypi-uri "lazr.delegates" version))
+        (uri (pypi-uri "lazr_delegates" version))
         (sha256
-         (base32
-          "1rdnl85j9ayp8n85l0ciip621j9dcziz5qnmv2m7krgwgcn31vfx"))))
-    (build-system python-build-system)
+         (base32 "1p02diwzn58jhpvf9m8bhb5p0xkx5gnc84mzgwr3zdsidrhv5kmf"))))
+    (build-system pyproject-build-system)
     (arguments
-     '(#:phases
-       (modify-phases %standard-phases
-         (replace 'check
-           (lambda* (#:key tests? #:allow-other-keys)
-             (when tests? (invoke "nosetests")))))))
+     (list
+      #:test-flags #~(list "-v" #$output)
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-after 'check 'check-cleanup
+            (lambda* (#:key tests? #:allow-other-keys)
+              (when tests?
+                (for-each
+                 delete-file-recursively
+                 (find-files #$output
+                             (lambda (file stat)
+                               (or (member (basename file)
+                                           '("tests" ".pytest_cache"))))
+                             #:directories? #t))))))))
     (native-inputs
-     (list python-nose))
+     (list python-pytest python-setuptools python-wheel))
     (propagated-inputs
      (list python-zope-interface))
     (home-page "https://launchpad.net/lazr.delegates")
-- 
2.49.0

Message #14 received at 77575 <at> debbugs.gnu.org (full text, mbox):

From: Nicolas Graves <ngraves <at> ngraves.fr>
To: 77575 <at> debbugs.gnu.org
Cc: Nicolas Graves <ngraves <at> ngraves.fr>
Subject: [PATCH 02/21] gnu: python-stem: Update to 1.8.2.
Date: Sun,  6 Apr 2025 14:37:04 +0200

* gnu/packages/python-xyz.scm (python-stem): Update to 1.8.2.
[build-system]: Switch to pyproject.
[arguments]{phases}: Remove phase 'fix-tests.
[native-inputs]: Remove python-mock, python-pycodestyle,
python-pyflakes.  Add python-setuptools, python-wheel.
---
 gnu/packages/python-xyz.scm | 25 +++++++++----------------
 1 file changed, 9 insertions(+), 16 deletions(-)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index ceebb018d9..08d0eb6194 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -24353,30 +24353,23 @@ (define-public python-pyvirtualdisplay
 (define-public python-stem
   (package
     (name "python-stem")
-    (version "1.8.0")
+    (version "1.8.2")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "stem" version))
        (sha256
         (base32
-         "1hk8alc0r4m669ggngdfvryndd0fbx0w62sclcmg55af4ak8xd50"))))
-    (build-system python-build-system)
+         "10mm9qw4xv7d18086ivy38iaz04z72018186q03j5y69skzikyw3"))))
+    (build-system pyproject-build-system)
     (arguments
-     `(#:phases
-       (modify-phases %standard-phases
-         (add-after 'unpack 'fix-tests
-           ;; See https://github.com/torproject/stem/issues/56
-           (lambda _
-             (substitute* "run_tests.py"
-               (("test\\.task\\.MOCK_VERSION,")
-                ""))))
-         (replace 'check
-           (lambda _
-             (invoke "./run_tests.py" "--unit")
-             #t)))))
+     (list
+      #:phases #~(modify-phases %standard-phases
+                   (replace 'check
+                     (lambda _
+                       (invoke "./run_tests.py" "--unit"))))))
     (native-inputs
-     (list python-mock python-pycodestyle python-pyflakes))
+     (list python-setuptools python-wheel))
     (home-page "https://stem.torproject.org/")
     (synopsis
      "Python controller library that allows applications to interact with Tor")
-- 
2.49.0

Message #17 received at 77575 <at> debbugs.gnu.org (full text, mbox):

From: Nicolas Graves <ngraves <at> ngraves.fr>
To: 77575 <at> debbugs.gnu.org
Cc: Nicolas Graves <ngraves <at> ngraves.fr>
Subject: [PATCH 04/21] gnu: python-lazr-config: Update to 3.1.
Date: Sun,  6 Apr 2025 14:37:06 +0200

* gnu/packages/python-xyz.scm (python-lazr-config): Update to 3.1.
[build-system]: Switch to pyproject.
[arguments]{test-flags}: Run tests in output.
{phases}: Add a 'check-cleanup phase to remove tests from output.
[native-inputs]: Remove python-nose.  Add python-pytest,
python-setuptools, python-wheel.
---
 gnu/packages/python-xyz.scm | 30 +++++++++++++++++++-----------
 1 file changed, 19 insertions(+), 11 deletions(-)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 0cc189ce15..168ee456f0 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -34656,23 +34656,31 @@ (define-public python-lazr-delegates
 (define-public python-lazr-config
   (package
     (name "python-lazr-config")
-    (version "2.2.3")
+    (version "3.1")
     (source
       (origin
         (method url-fetch)
-        (uri (pypi-uri "lazr.config" version))
+        (uri (pypi-uri "lazr_config" version))
         (sha256
-         (base32
-          "1qdbrzl61q7cjhbnxvw9y3frcr935y7diwy15xrwcv9ynvw76jmp"))))
-    (build-system python-build-system)
+         (base32 "02xb4fs9rm6bf3f00qkq8pihgqvrvn2wfnvydn2vg9p73ddhcmvw"))))
+    (build-system pyproject-build-system)
     (arguments
-     '(#:phases
-       (modify-phases %standard-phases
-         (replace 'check
-           (lambda _
-             (invoke "python" "-s" "-m" "nose" "-P" "lazr"))))))
+     (list
+      #:test-flags #~(list "-v" #$output)
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-after 'check 'check-cleanup
+            (lambda* (#:key tests? #:allow-other-keys)
+              (when tests?
+                (for-each
+                 delete-file-recursively
+                 (find-files #$output
+                             (lambda (file stat)
+                               (or (member (basename file)
+                                           '("tests" ".pytest_cache"))))
+                             #:directories? #t))))))))
     (native-inputs
-     (list python-nose))
+     (list python-pytest python-setuptools python-wheel))
     (propagated-inputs
      (list python-lazr-delegates python-zope-interface))
     (home-page "https://launchpad.net/lazr.config")
-- 
2.49.0

Message #20 received at 77575 <at> debbugs.gnu.org (full text, mbox):

From: Nicolas Graves <ngraves <at> ngraves.fr>
To: 77575 <at> debbugs.gnu.org
Cc: Nicolas Graves <ngraves <at> ngraves.fr>
Subject: [PATCH 05/21] gnu: python-lap: Update to 0.5.12.
Date: Sun,  6 Apr 2025 14:37:07 +0200

* gnu/packages/machine-learning.scm (python-lap): Update to 0.5.12.
[build-system]: Switch to pyproject.
[arguments]{test-flags}: Run tests in output.
{phases}: Add a 'check-cleanup phase to remove tests from output.
[propagated-inputs]: Remove python-scipy.
[native-inputs]: Add python-setuptools, python-wheel.
---
 gnu/packages/machine-learning.scm | 39 +++++++++++++++----------------
 1 file changed, 19 insertions(+), 20 deletions(-)

diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm
index e62535d890..304e3bf87e 100644
--- a/gnu/packages/machine-learning.scm
+++ b/gnu/packages/machine-learning.scm
@@ -5976,34 +5976,33 @@ (define-public liblantern
 (define-public python-lap
   (package
     (name "python-lap")
-    (version "0.4.0")
+    (version "0.5.12")
     (source (origin
               (method url-fetch)
               (uri (pypi-uri "lap" version))
               (sha256
                (base32
-                "0fqfxpq4jg9h4wxjw540gjmvfg1ccc1nssk7i9njg7qfdybxknn4"))))
-    (build-system python-build-system)
+                "1za4mf5nd7vzwd24sy2mfxrk8mnwq7d8rv6h96yh8v5flx7422sp"))))
+    (build-system pyproject-build-system)
     (arguments
-     `(#:phases
-       (modify-phases %standard-phases
-         (replace 'build
-           (lambda* (#:key inputs #:allow-other-keys)
-             (invoke "python" "setup.py" "build"
-                     "--cpu-baseline=sse2")))
-         (replace 'check
-           (lambda* (#:key tests? #:allow-other-keys)
-             (when tests?
-               ;; The tests must be run from elsewhere.
-               (mkdir-p "/tmp/test")
-               (copy-recursively "lap/tests" "/tmp/test")
-               (with-directory-excursion "/tmp/test"
-                 (invoke "pytest" "-vv"))))))))
+     (list
+      #:test-flags #~(list "-v" #$output)
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-after 'check 'check-cleanup
+            (lambda* (#:key tests? #:allow-other-keys)
+              (when tests?
+                (for-each
+                 delete-file-recursively
+                 (find-files #$output
+                             (lambda (file stat)
+                               (or (member (basename file)
+                                           '("tests" ".pytest_cache"))))
+                             #:directories? #t))))))))
     (propagated-inputs
-     (list python-numpy
-           python-scipy))
+     (list python-numpy))
     (native-inputs
-     (list python-cython python-pytest))
+     (list python-cython python-pytest python-setuptools python-wheel))
     (home-page "https://github.com/gatagat/lap")
     (synopsis "Linear Assignment Problem solver (LAPJV/LAPMOD)")
     (description "Lap is a linear assignment problem solver using Jonker-Volgenant
-- 
2.49.0

Message #23 received at 77575 <at> debbugs.gnu.org (full text, mbox):

From: Nicolas Graves <ngraves <at> ngraves.fr>
To: 77575 <at> debbugs.gnu.org
Cc: Nicolas Graves <ngraves <at> ngraves.fr>
Subject: [PATCH 06/21] gnu: Remove python-pydiff.
Date: Sun,  6 Apr 2025 14:37:08 +0200

This package is a leaf package, stale for 11 years and not compatible
with the latest python.

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

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 168ee456f0..ebcb30a611 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -27913,25 +27913,6 @@ (define-public python-pysocks
 version of @code{SocksiPy} with bug fixes and extra features.")
     (license license:bsd-3)))
 
-(define-public python-pydiff
-  (package
-    (name "python-pydiff")
-    (version "0.2")
-    (source
-      (origin
-        (method url-fetch)
-        (uri (pypi-uri "pydiff" version))
-        (sha256
-          (base32
-            "1als83h9w0gab24ipyna6khm390qmpnpkc5jksmdbs2xc8hp2z44"))))
-    (build-system python-build-system)
-    (home-page "https://github.com/myint/pydiff")
-    (synopsis "Library to diff two Python files at the bytecode level")
-    (description
-      "@code{pydiff} makes it easy to look for actual code changes while
-ignoring formatting changes.")
-    (license license:expat)))
-
 (define-public python-pydub
   (package
     (name "python-pydub")
-- 
2.49.0

Message #26 received at 77575 <at> debbugs.gnu.org (full text, mbox):

From: Nicolas Graves <ngraves <at> ngraves.fr>
To: 77575 <at> debbugs.gnu.org
Cc: Nicolas Graves <ngraves <at> ngraves.fr>
Subject: [PATCH 07/21] gnu: pomegranate: Disable tests.
Date: Sun,  6 Apr 2025 14:37:09 +0200

* gnu/packages/python-xyz.scm (pomegranate): Disable tests.
[build-system]: Switch to pyproject.
[arguments]{tests?}: Disable them.
{phases}: Remove 'check phase replacement.
[native-inputs]: Add python-setuptools, python-wheel.  Remove python-nose.
---
 gnu/packages/python-xyz.scm | 16 +++++++---------
 1 file changed, 7 insertions(+), 9 deletions(-)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index ebcb30a611..d457d89de7 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -5925,15 +5925,12 @@ (define-public python-pomegranate
               ;; Delete generated Cython C files.
               (snippet
                '(for-each delete-file (find-files "." "\\.c$")))))
-    (build-system python-build-system)
+    (build-system pyproject-build-system)
     (arguments
      (list
-      #:phases
-      '(modify-phases %standard-phases
-         (replace 'check
-           (lambda* (#:key tests? #:allow-other-keys)
-             (when tests?
-               (invoke "python" "setup.py" "test")))))))
+      ;; XXX: Update to python <at> 3.11 broke some python-nose functionality.
+      ;; Tests are broken but the package itself is most likely fine.
+      #:tests? #f))
     (propagated-inputs
      (list python-joblib
            python-networkx
@@ -5942,8 +5939,9 @@ (define-public python-pomegranate
            python-scipy))
     (native-inputs
      (list python-cython
-           python-nose
-           python-pandas))
+           python-pandas
+           python-setuptools
+           python-wheel))
     (home-page "https://pypi.python.org/pypi/pomegranate/")
     (synopsis "Graphical models library for Python")
     (description
-- 
2.49.0

Message #29 received at 77575 <at> debbugs.gnu.org (full text, mbox):

From: Nicolas Graves <ngraves <at> ngraves.fr>
To: 77575 <at> debbugs.gnu.org
Cc: Nicolas Graves <ngraves <at> ngraves.fr>
Subject: [PATCH 08/21] gnu: python-pymodbus: Update to 3.8.6.
Date: Sun,  6 Apr 2025 14:37:10 +0200

* gnu/packages/python-xyz.scm (python-pymodbus): Update to 3.8.6.
[build-system]: Swith to pyproject.
[arguments]{test-flags}: Ignore failing tests.
{phases}: Remove field, use test-flags instead.
[native-inputs]: Add python-pytest-asyncio, python-pytest-cov,
python-pytest-xdist, python-setuptools, python-wheel.
---
 gnu/packages/python-xyz.scm | 37 +++++++++++++++----------------------
 1 file changed, 15 insertions(+), 22 deletions(-)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index d457d89de7..efdf82e58c 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -24448,7 +24448,7 @@ (define-public python-pymemcache
 (define-public python-pymodbus
   (package
     (name "python-pymodbus")
-    (version "2.5.3")
+    (version "3.8.6")
     (source
      (origin
        (method git-fetch)
@@ -24457,34 +24457,27 @@ (define-public python-pymodbus
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32
-         "0kjjrx7xrlx0pf3y67hhr4xvqrly3xzmvf6ic5as61m6z19m7zd5"))))
-    (build-system python-build-system)
+        (base32 "1sncllh01c6vqq4fh9k3yg9fchmmw661rcp0066l7fis6sp4yw82"))))
+    (build-system pyproject-build-system)
     (arguments
-     `(#:phases (modify-phases %standard-phases
-                  (add-after 'unpack 'disable-problematic-tests
-                    (lambda _
-                      ;; The following test modules rely on Python's own
-                      ;; 'test' module, which is not distributed in the Python
-                      ;; package of Guix.
-                      (delete-file "test/test_client_async_asyncio.py")
-                      (delete-file "test/test_client_sync_diag.py")
-                      ;; The following test module requires the asynctest
-                      ;; library, abandoned without support for Python 3.9+
-                      ;; (see:
-                      ;; https://github.com/riptideio/pymodbus/issues/681).
-                      (delete-file "test/test_server_asyncio.py")))
-                  (replace 'check
-                    (lambda* (#:key tests? #:allow-other-keys)
-                      (when tests?
-                        (invoke "python" "-m" "pytest")))))))
+     (list
+      #:test-flags
+      #~(list "--ignore" "test/server/test_simulator_api.py"
+              ;; These tests require the presence of a certificate.
+              "--ignore-glob" "test/examples/*"
+              "--ignore" "test/client/test_client.py")))
     (native-inputs
      (list python-mock
            python-pytest
+           python-pytest-asyncio
+           python-pytest-cov
+           python-pytest-xdist
            python-redis
+           python-setuptools
            python-sqlalchemy
            python-tornado
-           python-twisted))
+           python-twisted
+           python-wheel))
     (propagated-inputs
      (list python-pyserial
            python-six
-- 
2.49.0

Message #32 received at 77575 <at> debbugs.gnu.org (full text, mbox):

From: Nicolas Graves <ngraves <at> ngraves.fr>
To: 77575 <at> debbugs.gnu.org
Cc: Nicolas Graves <ngraves <at> ngraves.fr>
Subject: [PATCH 09/21] gnu: python-flufl-lock: Update to 8.1.0.
Date: Sun,  6 Apr 2025 14:37:11 +0200

* gnu/packages/python-xyz.scm (python-flufl-lock): Update to 8.1.0.
[build-system]: Switch to pyproject.
[arguments]{test-flags}: Ignore docs and coverage tests.
{phases}: Add phase 'add-custom-dist-info.
[native-inputs]: Add python-hatchling, python-pytest,
python-pytest-cov, python-sybil.
---
 gnu/packages/python-xyz.scm | 31 +++++++++++++++++++++++++++----
 1 file changed, 27 insertions(+), 4 deletions(-)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index efdf82e58c..f779acd4df 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -34729,15 +34729,38 @@ (define-public python-flufl-i18n
 (define-public python-flufl-lock
   (package
     (name "python-flufl-lock")
-    (version "4.0")
+    (version "8.1.0")
     (source
       (origin
         (method url-fetch)
         (uri (pypi-uri "flufl.lock" version))
         (sha256
-         (base32
-          "055941zyma3wfx25jhm8wcsghpv3jc3iwi1gdrdjhzcnfhn62lxq"))))
-    (build-system python-build-system)
+         (base32 "1jz7vipjga4x803gfsb9mvnfb6q8my7ib000nsc3v9ljaq0050yq"))))
+    (build-system pyproject-build-system)
+    (arguments
+     (list #:test-flags
+           #~(list "--no-cov" "--ignore-glob=docs/*")
+           #:phases
+           #~(modify-phases %standard-phases
+               ;; This phase add a symlink of dist-info dir for packages
+               ;; expecting flufl.lock rather than flufl_lock (mailman).
+               (add-after 'install 'add-custom-dist-info
+                 (lambda _
+                   (for-each
+                    (lambda (dir)
+                      (with-directory-excursion (dirname dir)
+                        (let ((base (basename dir)))
+                          (symlink base
+                                   (string-join (string-split base #\_) ".")))))
+                    (find-files #$output
+                                (lambda (file stat)
+                                  (string-suffix? ".dist-info" file))
+                                #:directories? #t)))))))
+    (native-inputs
+     (list python-hatchling
+           python-pytest
+           python-pytest-cov
+           python-sybil))
     (propagated-inputs
      (list python-atpublic python-psutil))
     (home-page "https://flufllock.readthedocs.io")
-- 
2.49.0

Message #35 received at 77575 <at> debbugs.gnu.org (full text, mbox):

From: Nicolas Graves <ngraves <at> ngraves.fr>
To: 77575 <at> debbugs.gnu.org
Cc: Nicolas Graves <ngraves <at> ngraves.fr>
Subject: [PATCH 10/21] gnu: python-flufl-i18n: Update to 5.1.0.
Date: Sun,  6 Apr 2025 14:37:12 +0200

* gnu/packages/python-xyz.scm (python-flufl-i18n): Update to 5.1.0.
[build-system]: Switch to pyproject.
[arguments]{test-flags}: Ignore docs and coverage tests.
{phases}: Add phase 'add-custom-dist-info.
[native-inputs]: Add python-hatchling, python-pytest,
python-pytest-cov, python-sybil.
---
 gnu/packages/python-xyz.scm | 32 ++++++++++++++++++++++++++++----
 1 file changed, 28 insertions(+), 4 deletions(-)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index f779acd4df..374d10a8d8 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -34703,17 +34703,41 @@ (define-public python-flufl-bounce
 (define-public python-flufl-i18n
   (package
     (name "python-flufl-i18n")
-    (version "3.0")
+    (version "5.1.0")
     (source
       (origin
         (method url-fetch)
-        (uri (pypi-uri "flufl.i18n" version))
+        (uri (pypi-uri "flufl_i18n" version))
         (sha256
          (base32
-          "1flwpn1xhgc957zj3zxw92dhdjh0lsy0hdvzq32dzqpsajfsvq1r"))))
-    (build-system python-build-system)
+          "0bm4kmi04gm164y5nmadmrg79y1l1cs9iwxcv9y7gq0dgyr20xms"))))
+    (build-system pyproject-build-system)
+    (arguments
+     (list #:test-flags
+           #~(list "--no-cov" "--ignore-glob=docs/*")
+           #:phases
+           #~(modify-phases %standard-phases
+               ;; This phase add a symlink of dist-info dir for packages
+               ;; expecting flufl.i18n rather than flufl_i18n (mailman).
+               (add-after 'install 'add-custom-dist-info
+                 (lambda _
+                   (for-each
+                    (lambda (dir)
+                      (with-directory-excursion (dirname dir)
+                        (let ((base (basename dir)))
+                          (symlink base
+                                   (string-join (string-split base #\_) ".")))))
+                    (find-files #$output
+                                (lambda (file stat)
+                                  (string-suffix? ".dist-info" file))
+                                #:directories? #t)))))))
     (propagated-inputs
      (list python-atpublic))
+    (native-inputs
+     (list python-hatchling
+           python-pytest
+           python-pytest-cov
+           python-sybil))
     (home-page "https://flufli18n.readthedocs.io")
     (synopsis "API for Python internationalization")
     (description
-- 
2.49.0

Message #38 received at 77575 <at> debbugs.gnu.org (full text, mbox):

From: Nicolas Graves <ngraves <at> ngraves.fr>
To: 77575 <at> debbugs.gnu.org
Cc: Nicolas Graves <ngraves <at> ngraves.fr>
Subject: [PATCH 11/21] gnu: cnvkit: Update to 0.9.12.
Date: Sun,  6 Apr 2025 14:37:13 +0200

* gnu/packages/bioinformatics.scm (cnvkit): Update to 0.9.12.
[build-system]: Switch to pyproject.
[native-inputs]: Add python-setuptools, python-wheel.
---
 gnu/packages/bioinformatics.scm | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 5c5106b21a..cbb7aa1b11 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -21156,7 +21156,7 @@ (define-public nanopolish
 (define-public cnvkit
   (package
     (name "cnvkit")
-    (version "0.9.10")
+    (version "0.9.12")
     (source
      (origin
        (method git-fetch)
@@ -21165,7 +21165,7 @@ (define-public cnvkit
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "0r303pqjg70zpxa564bavbfj99c6di0dafgqqwx2vh4vfsiif94q"))))
+        (base32 "090yh17symcahddx399kcx0mcw4gdrcc2jil3p8lb92r8c8kglb5"))))
     (build-system pyproject-build-system)
     (propagated-inputs
      (list python-biopython
@@ -21182,7 +21182,7 @@ (define-public cnvkit
            ;; R packages
            r-dnacopy))
     (inputs (list r-minimal)) ;for tests
-    (native-inputs (list python-setuptools python-wheel))
+    (native-inputs (list python-pytest python-setuptools python-wheel))
     (home-page "https://cnvkit.readthedocs.org/")
     (synopsis "Copy number variant detection from targeted DNA sequencing")
     (description
-- 
2.49.0

Message #41 received at 77575 <at> debbugs.gnu.org (full text, mbox):

From: Nicolas Graves <ngraves <at> ngraves.fr>
To: 77575 <at> debbugs.gnu.org
Cc: Nicolas Graves <ngraves <at> ngraves.fr>
Subject: [PATCH 12/21] gnu: python-authheaders: Update to 0.16.3.
Date: Sun,  6 Apr 2025 14:37:14 +0200

* gnu/packages/mail.scm (python-authheaders): Update to 0.16.3.
[build-system]: Switch to pyproject.
[native-inputs]: Add python-setuptools, python-wheel.
---
 gnu/packages/mail.scm | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/mail.scm b/gnu/packages/mail.scm
index c031548216..217ffa8d01 100644
--- a/gnu/packages/mail.scm
+++ b/gnu/packages/mail.scm
@@ -4680,18 +4680,20 @@ (define-public python-dkimpy
 (define-public python-authheaders
   (package
     (name "python-authheaders")
-    (version "0.13.0")
+    (version "0.16.3")
     (source
       (origin
         (method url-fetch)
         (uri (pypi-uri "authheaders" version))
         (sha256
          (base32
-          "14k6i72k5f8dyvps8vc0aq0cczc8lvqpgjfjzsy6qqychjvjcmwk"))))
-    (build-system python-build-system)
+          "12hl93336w64iyqalpv4rma2ijigav68qy1xmgziibdi7inxr3hi"))))
+    (build-system pyproject-build-system)
     (propagated-inputs
      (list python-authres python-dkimpy python-dnspython
            python-publicsuffix2))
+    (native-inputs
+     (list python-setuptools python-wheel))
     (home-page "https://github.com/ValiMail/authentication-headers")
     (synopsis "Library wrapping email authentication header verification and generation")
     (description
-- 
2.49.0

Message #44 received at 77575 <at> debbugs.gnu.org (full text, mbox):

From: Nicolas Graves <ngraves <at> ngraves.fr>
To: 77575 <at> debbugs.gnu.org
Cc: Nicolas Graves <ngraves <at> ngraves.fr>
Subject: [PATCH 13/21] gnu: mailman: Update to 3.3.10.
Date: Sun,  6 Apr 2025 14:37:15 +0200

* gnu/packages/mail.scm (mailman): Update to 3.3.10.
[build-system]: Switch to pyproject.
[arguments]{tests?}: Disable tests?
[native-inputs]: Remove python-nose.  Add python-pytest,
python-pdm-backend.
---
 gnu/packages/mail.scm | 11 +++++++----
 1 file changed, 7 insertions(+), 4 deletions(-)

diff --git a/gnu/packages/mail.scm b/gnu/packages/mail.scm
index 217ffa8d01..e4b874078b 100644
--- a/gnu/packages/mail.scm
+++ b/gnu/packages/mail.scm
@@ -3587,14 +3587,17 @@ (define-public opensmtpd-filter-rspamd
 (define-public mailman
   (package
     (name "mailman")
-    (version "3.3.2")
+    (version "3.3.10")
     (source
       (origin
         (method url-fetch)
         (uri (pypi-uri "mailman" version))
         (sha256
-         (base32 "0a5ckbf8hc3y28b7p5psp0d4bxk601jlr5pd3hhh545xd8d9f0dg"))))
-    (build-system python-build-system)
+         (base32 "0cjn8karkgrapgiv3ra6ddcngkf5c5779hrq369mvwi6ygy7ir0d"))))
+    (build-system pyproject-build-system)
+    (arguments
+     ;; XXX: Too much failing tests to try and isolate them.
+     (list #:tests? #f))
     (propagated-inputs
      (list gunicorn
            python-aiosmtpd
@@ -3619,7 +3622,7 @@ (define-public mailman
            python-zope-event
            python-zope-interface))
     (native-inputs
-     (list python-nose))
+     (list python-pytest python-pdm-backend))
     (home-page "https://www.list.org")
     (synopsis "Mailing list manager")
     (description
-- 
2.49.0

Message #47 received at 77575 <at> debbugs.gnu.org (full text, mbox):

From: Nicolas Graves <ngraves <at> ngraves.fr>
To: 77575 <at> debbugs.gnu.org
Cc: Nicolas Graves <ngraves <at> ngraves.fr>
Subject: [PATCH 14/21] gnu: python-mailman-hyperkitty: Update to 1.2.1.
Date: Sun,  6 Apr 2025 14:37:16 +0200

* gnu/packages/mail.scm (python-mailman-hyperkitty): Update to 1.2.1.
[build-system] :Swtich to pyproject.
[native-inputs]: Remove python-mock, python-nose.  Add
python-setuptools, python-wheel.
---
 gnu/packages/mail.scm | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/gnu/packages/mail.scm b/gnu/packages/mail.scm
index e4b874078b..3d2085b59e 100644
--- a/gnu/packages/mail.scm
+++ b/gnu/packages/mail.scm
@@ -3757,21 +3757,21 @@ (define-public python-django-mailman3
 (define-public python-mailman-hyperkitty
   (package
     (name "python-mailman-hyperkitty")
-    (version "1.2.0")
+    (version "1.2.1")
     (source
       (origin
         (method url-fetch)
         (uri (pypi-uri "mailman-hyperkitty" version))
         (sha256
          (base32
-          "1ni6vf1yi14c0l895fk278x4na7ymhpkl1q0vnpzbkzplpa7200i"))))
-    (build-system python-build-system)
+          "0f6c1fs28w3r9k9mbg7gsv6pa45aayaadaa0dn4q5dfcqvxrvmpq"))))
+    (build-system pyproject-build-system)
     (propagated-inputs
      (list python-requests python-zope-interface))
     (inputs
      (list mailman))
     (native-inputs
-     (list python-mock python-nose python-nose2))
+     (list python-nose2 python-setuptools python-wheel))
     (home-page "https://gitlab.com/mailman/mailman-hyperkitty/")
     (synopsis "Mailman archiver plugin for HyperKitty")
     (description
-- 
2.49.0

Message #50 received at 77575 <at> debbugs.gnu.org (full text, mbox):

From: Nicolas Graves <ngraves <at> ngraves.fr>
To: 77575 <at> debbugs.gnu.org
Cc: Nicolas Graves <ngraves <at> ngraves.fr>
Subject: [PATCH 15/21] gnu: python-ledgerblue: Fix version detection.
Date: Sun,  6 Apr 2025 14:37:17 +0200

* gnu/packages/finance.scm (python-ledgerblue): Fix version detection.
[arguments]{phases}: Add 'pretend-version phase.
[native-inputs]: Add python-setuptools-scm.
---
 gnu/packages/finance.scm | 9 +++++++--
 1 file changed, 7 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/finance.scm b/gnu/packages/finance.scm
index 680ebe467c..f7e7ca1fff 100644
--- a/gnu/packages/finance.scm
+++ b/gnu/packages/finance.scm
@@ -1065,9 +1065,14 @@ (define-public python-ledgerblue
             "0ghpvxgih1zarp788qi1xh5xmprv6yhaxglfbix4974i7r4pszqy"))))
     (build-system pyproject-build-system)
     (arguments
-     `(#:tests? #f)) ; no tests
+     (list #:tests? #f
+           #:phases
+           #~(modify-phases %standard-phases
+               (add-before 'build 'pretend-version
+                 (lambda _
+                   (setenv "SETUPTOOLS_SCM_PRETEND_VERSION" #$version))))))
     (native-inputs
-     (list python-setuptools python-wheel))
+     (list python-setuptools python-setuptools-scm python-wheel))
     (propagated-inputs
      (list python-bleak
            python-pyelftools
-- 
2.49.0

Message #53 received at 77575 <at> debbugs.gnu.org (full text, mbox):

From: Nicolas Graves <ngraves <at> ngraves.fr>
To: 77575 <at> debbugs.gnu.org
Cc: Nicolas Graves <ngraves <at> ngraves.fr>
Subject: [PATCH 16/21] gnu: ledger-agent: Switch to pyproject-build-system.
Date: Sun,  6 Apr 2025 14:37:18 +0200

* gnu/packages/finance.scm (ledger-agent)[build-system]: Switch to
pyproject.
[native-inputs]: Add python-setuptools, python-wheel.
---
 gnu/packages/finance.scm | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/finance.scm b/gnu/packages/finance.scm
index f7e7ca1fff..f0536d3f3d 100644
--- a/gnu/packages/finance.scm
+++ b/gnu/packages/finance.scm
@@ -1219,9 +1219,11 @@ (define-public ledger-agent
        (sha256
         (base32
          "03zj602m2rln9yvr08dswy56vzkbldp8b074ixwzz525dafblr92"))))
-    (build-system python-build-system)
+    (build-system pyproject-build-system)
     (inputs
      (list python-ledgerblue python-trezor-agent))
+    (native-inputs
+     (list python-setuptools python-wheel))
     (home-page "https://github.com/romanz/trezor-agent")
     (synopsis "Ledger as hardware SSH/GPG agent")
     (description "This package allows using Ledger as hardware SSH/GPG agent.")
-- 
2.49.0

Message #56 received at 77575 <at> debbugs.gnu.org (full text, mbox):

From: Nicolas Graves <ngraves <at> ngraves.fr>
To: 77575 <at> debbugs.gnu.org
Cc: Nicolas Graves <ngraves <at> ngraves.fr>
Subject: [PATCH 17/21] gnu: python-gixy: Rename package to python-gixy-ng.
Date: Sun,  6 Apr 2025 14:37:19 +0200

* gnu/packages/check.scm (python-gixy): Deprecate package, defaults to
python-gixy-ng.
(python-gixy-ng): New variable.
---
 gnu/packages/check.scm | 69 ++++++++++++++++++++++--------------------
 1 file changed, 36 insertions(+), 33 deletions(-)

diff --git a/gnu/packages/check.scm b/gnu/packages/check.scm
index c9b96c14bd..ef5a23de86 100644
--- a/gnu/packages/check.scm
+++ b/gnu/packages/check.scm
@@ -1027,40 +1027,43 @@ (define-public kyua
 report generation engine.")
     (license license:bsd-3)))
 
-(define-public python-gixy
-  ;; The 0.1.20 release is missing some important fixes.
-  ;; XXX: Commit 'e9008dcbd11f43ccac109b0cf2bf98a94e76b449' breaks tests
-  ;; since it improperly removes an import.
-  (let ((commit "303eb6887ddecab18138b6e427b04ae77c41d2f1")
-        (revision "0")
-        (base-version "0.1.20"))
-    (package
-      (name "python-gixy")
-      (version (git-version base-version revision commit))
-      (source (origin
-                (method git-fetch)
-                (uri (git-reference
-                      (url "https://github.com/yandex/gixy")
-                      (commit commit)))
-                (file-name (git-file-name name version))
-                (sha256
-                 (base32
-                  "0gymjcnvjx9snyrzdbmjnk93ibb161q72xam29vnl3yyac4r1330"))))
-      (build-system pyproject-build-system)
-      (native-inputs (list python-nose python-setuptools python-wheel))
-      (propagated-inputs
-       (list python-cached-property python-configargparse
-             python-jinja2 python-six
-             ;; XXX: gixy is incompatible with pyparsing >= 3.x.
-             ;; See <https://github.com/yandex/gixy/pull/132> and
-             ;; <https://github.com/yandex/gixy/pull/122>.
-             python-pyparsing-2.4.7))
-      (home-page "https://github.com/yandex/gixy")
-      (synopsis "Static NGINX configuration analyzer")
-      (description "Gixy is a static analyzer whose main goal is to help
+(define-public python-gixy-ng
+  (package
+    (name "python-gixy-ng")
+    (version "0.2.7")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/dvershinin/gixy")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "0dipvy8y1nlhpka0cdk6hyv1j2388y7isbajpwskjrgqc5vayqx8"))))
+    (build-system pyproject-build-system)
+    ;; This package currently doesn't test properly, but we can't add
+    ;; pytest because it propagates another version of python-pyparsing
+    ;; that takes precedence over the right one.
+    (propagated-inputs (list python-configargparse
+                             python-jinja2
+                             python-pyparsing-2.4.7
+                             python-six))
+    (native-inputs (list python-cached-property
+                         python-setuptools
+                         python-wheel))
+    (home-page "https://github.com/dvershinin/gixy")
+    (synopsis "Static NGINX configuration analyzer")
+    (description "Gixy is a static analyzer whose main goal is to help
 prevent common NGINX misconfigurations.  It provides the @command{gixy}
-command.")
-      (license license:mpl2.0))))
+command.
+
+Note: This is an actively maintained fork of the original @code{python-gixy}
+package.")
+    (license license:mpl2.0)))
+
+(define-deprecated/public python-gixy python-gixy-ng
+  (package/inherit python-gixy-ng
+    (name "python-gixy")))
 
 (define-public googletest
   (package
-- 
2.49.0

Message #59 received at 77575 <at> debbugs.gnu.org (full text, mbox):

From: Nicolas Graves <ngraves <at> ngraves.fr>
To: 77575 <at> debbugs.gnu.org
Cc: Nicolas Graves <ngraves <at> ngraves.fr>
Subject: [PATCH 18/21] gnu: python-ujson: Update to 5.10.0.
Date: Sun,  6 Apr 2025 14:37:20 +0200

* gnu/packages/python-xyz.scm (python-ujson): Update to 5.10.0.
[build-system]: Switch to pyproject.
[native-inputs]: Add python-pytest, python-setuptools, python-wheel.
---
 gnu/packages/python-xyz.scm | 44 ++++++++++++++++++-------------------
 1 file changed, 22 insertions(+), 22 deletions(-)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 374d10a8d8..5508ab1511 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -32429,38 +32429,38 @@ (define-public python-jsonplus
 (define-public python-ujson
   (package
     (name "python-ujson")
-    (version "5.7.0")
+    (version "5.10.0")
     (source
       (origin
         (method url-fetch)
         (uri (pypi-uri "ujson" version))
         (sha256
          (base32
-          "08vvyfyg4qvjy2vxrvc0qix5zmd0j6wd0icvmhc633xfvkayb277"))
+          "1habmn3bmmv2ym4ldiijcavdkdzp8h28h60hgwjkhxwcbly8zkdk"))
         (modules '((guix build utils)))
         (snippet
-         '(begin (delete-file-recursively "deps") #t))))
-    (build-system python-build-system)
+         #~(begin (delete-file-recursively "deps")))))
+    (build-system pyproject-build-system)
     (arguments
-     `(#:phases
-       (modify-phases %standard-phases
-         (add-after 'unpack 'link-to-system-double-conversion
-           (lambda* (#:key inputs #:allow-other-keys)
-             (let ((d-c (assoc-ref inputs "double-conversion")))
-               (substitute* "setup.py"
-                 (("./deps/double-conversion/double-conversion\"")
-                  (string-append d-c "/include/double-conversion\""))
-                 (("-lstdc++" stdc)
-                  (string-append "-L" d-c "/lib\","
-                                 " \"-ldouble-conversion\","
-                                 " \"" stdc)))
-               #t)))
-         (replace 'check
-           (lambda* (#:key inputs outputs #:allow-other-keys)
-             (add-installed-pythonpath inputs outputs)
-             (invoke "pytest"))))))
+     (list
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-after 'unpack 'link-to-system-double-conversion
+            (lambda* (#:key inputs #:allow-other-keys)
+              (let ((d-c (assoc-ref inputs "double-conversion")))
+                (substitute* "setup.py"
+                  (("./deps/double-conversion/double-conversion\"")
+                   (string-append d-c "/include/double-conversion\""))
+                  (("-lstdc++" stdc)
+                   (string-append "-L" d-c "/lib\","
+                                  " \"-ldouble-conversion\","
+                                  " \"" stdc)))))))))
     (native-inputs
-     (list double-conversion python-setuptools-scm python-pytest))
+     (list double-conversion
+           python-pytest
+           python-setuptools
+           python-setuptools-scm
+           python-wheel))
     (home-page "https://github.com/ultrajson/ultrajson")
     (synopsis "Ultra fast JSON encoder and decoder for Python")
     (description
-- 
2.49.0

Message #62 received at 77575 <at> debbugs.gnu.org (full text, mbox):

From: Nicolas Graves <ngraves <at> ngraves.fr>
To: 77575 <at> debbugs.gnu.org
Cc: Nicolas Graves <ngraves <at> ngraves.fr>
Subject: [PATCH 19/21] gnu: bpytop: Switch to pyproject-build-system.
Date: Sun,  6 Apr 2025 14:37:21 +0200

* gnu/packages/admin.scm (bpytop)
[build-system]: Swith to pyproject.
[arguments]{tests?}: Disable tests.
{phases}: Add phase 'use-poetry-core. Improve phase 'install-theme.
[native-inputs]: Add python-poetry-core.
---
 gnu/packages/admin.scm | 38 +++++++++++++++++++++-----------------
 1 file changed, 21 insertions(+), 17 deletions(-)

diff --git a/gnu/packages/admin.scm b/gnu/packages/admin.scm
index 9aa71f8cf9..ce34477749 100644
--- a/gnu/packages/admin.scm
+++ b/gnu/packages/admin.scm
@@ -1065,25 +1065,29 @@ (define-public bpytop
        (uri (pypi-uri "bpytop" version))
        (sha256
         (base32 "1clvajbv7pzlya9s1xs6dvjic8rv3kx7aqiwnjxapiypx246gdjk"))))
-    (build-system python-build-system)
+    (build-system pyproject-build-system)
+    (arguments
+     (list
+      #:tests? #f ; No tests in Pypi archive.
+      #:phases
+      #~(modify-phases %standard-phases
+          (add-after 'unpack 'use-poetry-core
+            (lambda _
+              ;; Patch to use the core poetry API.
+              (substitute* "pyproject.toml"
+                (("poetry.masonry.api")
+                 "poetry.core.masonry.api"))))
+          (add-after 'install 'install-themes
+            (lambda* (#:key inputs outputs #:allow-other-keys)
+              (let ((themes (string-append (site-packages inputs outputs)
+                                           "/bpytop-themes")))
+                (mkdir-p themes)
+                (copy-recursively "themes" themes)))))))
     (inputs
      (list python-psutil))
-    (arguments
-     `(#:phases
-       (modify-phases %standard-phases
-         ;; sanity-check phase fail, but the application seems to be working
-         (delete 'sanity-check)
-         (add-after 'install 'install-themes
-           (lambda* (#:key outputs #:allow-other-keys)
-             (let ((themes (string-append (assoc-ref outputs "out")
-                                          "/lib/python"
-                                          ,(version-major+minor
-                                            (package-version python))
-                                          "/site-packages/bpytop-themes")))
-               (mkdir-p themes)
-               (copy-recursively "themes" themes)))))))
-    (home-page
-     "https://github.com/aristocratos/bpytop")
+    (native-inputs
+     (list python-poetry-core))
+    (home-page "https://github.com/aristocratos/bpytop")
     (synopsis "Resource monitor")
     (description "Resource monitor that shows usage and stats for processor,
 memory, disks, network and processes.  It's a Python port and continuation of
-- 
2.49.0

Message #65 received at 77575 <at> debbugs.gnu.org (full text, mbox):

From: Nicolas Graves <ngraves <at> ngraves.fr>
To: 77575 <at> debbugs.gnu.org
Cc: Nicolas Graves <ngraves <at> ngraves.fr>
Subject: [PATCH 20/21] gnu: python-redis: Ignore i686 failing test.
Date: Sun,  6 Apr 2025 14:37:22 +0200

* gnu/packages/databases.scm (python-redis)
[arguments]{test-flags}: Ignore i686 failing test.
---
 gnu/packages/databases.scm | 37 +++++++++++++++++++++----------------
 1 file changed, 21 insertions(+), 16 deletions(-)

diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm
index 1aebf982ae..a7c83e5ea3 100644
--- a/gnu/packages/databases.scm
+++ b/gnu/packages/databases.scm
@@ -4562,22 +4562,27 @@ (define-public python-redis
                              "and not ssl "
                              "and not graph")
               "-k" (string-join
-                    (list
-                     ;; The autoclaim test fails with "AssertionError: assert
-                     ;; [b'0-0', [], []] == [b'0-0', []]".
-                     "not test_xautoclaim "
-                     ;; These tests cause the following error: "Error 111
-                     ;; connecting to localhost:6380. Connection refused."
-                     ;; (see: https://github.com/redis/redis-py/issues/2109).
-                     "test_sync"
-                     "test_psync"
-                     ;; Same with: "Error 111 connecting to
-                     ;; localhost:6479. Connection refused."
-                     "test_tfcall"
-                     "test_tfunction_load_delete"
-                     "test_tfunction_list"
-                     ;; AssertionError: assert 3 == 2
-                     "test_acl_list")
+                    (append
+                     (list
+                      ;; The autoclaim test fails with "AssertionError: assert
+                      ;; [b'0-0', [], []] == [b'0-0', []]".
+                      "not test_xautoclaim "
+                      ;; These tests cause the following error: "Error 111
+                      ;; connecting to localhost:6380. Connection refused."
+                      ;; (see: https://github.com/redis/redis-py/issues/2109).
+                      "test_sync"
+                      "test_psync"
+                      ;; Same with: "Error 111 connecting to
+                      ;; localhost:6479. Connection refused."
+                      "test_tfcall"
+                      "test_tfunction_load_delete"
+                      "test_tfunction_list"
+                      ;; AssertionError: assert 3 == 2
+                      "test_acl_list")
+                     ;; XXX: This test occasionally fails on i686-linux
+                     (if (string-prefix? "i686" (%current-system))
+                         '("test_geopos")
+                         '()))
                     " and not "))
       #:phases
       #~(modify-phases %standard-phases
-- 
2.49.0

Message #68 received at 77575 <at> debbugs.gnu.org (full text, mbox):

From: Nicolas Graves <ngraves <at> ngraves.fr>
To: 77575 <at> debbugs.gnu.org
Cc: Nicolas Graves <ngraves <at> ngraves.fr>
Subject: [PATCH 21/21] gnu: python-wxpython: Update to 4.2.2.
Date: Sun,  6 Apr 2025 14:37:23 +0200

* gnu/packages/wxwidgets.scm (python-wxpython): Update to 4.2.2.
[source]: Remove uneeded patch.
[arguments]{phases}: Add phase 'patch-avoid-circular-import. Add phase
'add-missing.so.
{modules}: Add necessary modules for new phases.
[native-inputs]: Add python-setuptools, python-wheel.
* gnu/packages/patches/python-wxwidgets-type-errors.patch: Remove
patch.
* gnu/local.mk: Unregister patch.
---
 gnu/local.mk                                  |  1 -
 .../python-wxwidgets-type-errors.patch        | 42 ---------------
 gnu/packages/wxwidgets.scm                    | 51 +++++++++++++++----
 3 files changed, 40 insertions(+), 54 deletions(-)
 delete mode 100644 gnu/packages/patches/python-wxwidgets-type-errors.patch

diff --git a/gnu/local.mk b/gnu/local.mk
index 6c2466114d..01dd31c328 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -2023,7 +2023,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/python-sgmllib3k-assertions.patch	\
   %D%/packages/patches/python-sphobjinv-defer-ssl-import.patch	\
   %D%/packages/patches/python-sphinx-prompt-docutils-0.19.patch	\
-  %D%/packages/patches/python-wxwidgets-type-errors.patch	\
   %D%/packages/patches/qcodeeditor-qt6.patch			\
   %D%/packages/patches/qtdeclarative-5-disable-qmlcache.patch	\
   %D%/packages/patches/qtdeclarative-disable-qmlcache.patch	\
diff --git a/gnu/packages/patches/python-wxwidgets-type-errors.patch b/gnu/packages/patches/python-wxwidgets-type-errors.patch
deleted file mode 100644
index 53e48c0886..0000000000
--- a/gnu/packages/patches/python-wxwidgets-type-errors.patch
+++ /dev/null
@@ -1,42 +0,0 @@
-Merged upstream but not yet released (see:
-https://github.com/wxWidgets/Phoenix/pull/2387/commits/5d9f7aa185cd18da3e93ae1d0033fb9172d7a714).
-
-From 5d9f7aa185cd18da3e93ae1d0033fb9172d7a714 Mon Sep 17 00:00:00 2001
-From: Maxim Cournoyer <maxim.cournoyer <at> gmail.com>
-Date: Mon, 1 May 2023 13:53:55 -0400
-Subject: [PATCH] agw: Fix TypeError caused by floats with Python 3.10
- extensions.
-
-This fixes the following error:
-
-   File "/lib/python3.10/site-packages/wx/lib/agw/pygauge.py", line 380, in OnPaint
-       dc.DrawText(drawString, textXPos, textYPos)
-   TypeError: DC.DrawText(): arguments did not match any overloaded call:
-     overload 1: argument 2 has unexpected type 'float'
-     overload 2: argument 2 has unexpected type 'float'
-   TimeLeft: 3.0
-
-Visible when using Python 3.10 or newer.
----
- wx/lib/agw/pygauge.py | 4 ++--
- 1 file changed, 2 insertions(+), 2 deletions(-)
-
-diff --git a/wx/lib/agw/pygauge.py b/wx/lib/agw/pygauge.py
-index b8654436a..da42e6f61 100644
---- a/wx/lib/agw/pygauge.py
-+++ b/wx/lib/agw/pygauge.py
-@@ -367,12 +367,12 @@ def OnPaint(self, event):
-             drawString = self._drawIndicatorText_formatString.format(drawValue)
-             rect = self.GetClientRect()
-             (textWidth, textHeight, descent, extraLeading) = dc.GetFullTextExtent(drawString)
--            textYPos = (rect.height-textHeight)/2
-+            textYPos = (rect.height-textHeight)//2
- 
-             if textHeight > rect.height:
-                 textYPos = 0-descent+extraLeading
- 
--            textXPos = (rect.width-textWidth)/2
-+            textXPos = (rect.width-textWidth)//2
- 
-             if textWidth>rect.width:
-                 textXPos = 0
diff --git a/gnu/packages/wxwidgets.scm b/gnu/packages/wxwidgets.scm
index 7bbdafeb89..2f806482f9 100644
--- a/gnu/packages/wxwidgets.scm
+++ b/gnu/packages/wxwidgets.scm
@@ -13,6 +13,7 @@
 ;;; Copyright © 2023 Malte Frank Gerdes <malte.f.gerdes <at> gmail.com>
 ;;; Copyright © 2023 Maxim Cournoyer <maxim.cournoyer <at> gmail.com>
 ;;; Copyright © 2025 Ekaitz Zarraga <ekaitz <at> elenq.tech>
+;;; Copyright © 2025 Nicolas Graves <ngraves <at> ngraves.fr>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -37,6 +38,7 @@ (define-module (gnu packages wxwidgets)
   #:use-module ((guix licenses) #:prefix l:)
   #:use-module (guix build-system glib-or-gtk)
   #:use-module (guix build-system perl)
+  #:use-module (guix build-system pyproject)
   #:use-module (guix build-system python)
   #:use-module (guix utils)
   #:use-module (gnu packages)
@@ -57,7 +59,9 @@ (define-module (gnu packages wxwidgets)
   #:use-module (gnu packages photo)
   #:use-module (gnu packages pkg-config)
   #:use-module (gnu packages python)
+  #:use-module (gnu packages python-build)
   #:use-module (gnu packages python-xyz)
+  #:use-module (gnu packages qt)
   #:use-module (gnu packages sdl)
   #:use-module (gnu packages video)
   #:use-module (gnu packages web)
@@ -318,26 +322,38 @@ (define-public prusa-wxwidgets
 (define-public python-wxpython
   (package
     (name "python-wxpython")
-    (version "4.2.0")
+    (version "4.2.2")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "wxPython" version))
        (sha256
-        (base32
-         "1iw6xp76b3fmdqwbqmsx9i1razzpfki5z1hq6l8mszlxa32fng36"))
+        (base32 "1fp2717a96hd5pdai6hlzc4pngdazxas55apjv2w5zb71xjv1g2x"))
        (modules '((guix build utils)))
-       (snippet
-        '(begin
-           ;; Remove bundled wxwidgets
-           (delete-file-recursively "ext/wxWidgets")))
-       (patches (search-patches "python-wxwidgets-type-errors.patch"))))
-    (build-system python-build-system)
+       (snippet #~(begin
+                    ;; Remove bundled wxWidgets
+                    (delete-file-recursively "ext/wxWidgets")))))
+    (build-system pyproject-build-system)
     (outputs '("out" "debug"))
     (arguments
      (list
+      #:modules '((guix build pyproject-build-system)
+                  (guix build utils)
+                  (ice-9 ftw)
+                  (ice-9 match)
+                  (srfi srfi-26))
       #:phases
       #~(modify-phases %standard-phases
+          (add-after 'unpack 'patch-avoid-circular-import
+            (lambda _
+              (substitute* "wx/__init__.py"
+                (("^import wx\\.__version__.*$") "\
+try:
+    import wx.__version__
+except ImportError:
+    pass\n")
+                (("^__version__ = .*")
+                 (format #f "__version__ = ~s~%" #$version)))))
           (add-before 'build 'configure
             (lambda* (#:key inputs #:allow-other-keys)
               ;; Configure the build options provided to the 'build.py' build
@@ -357,11 +373,24 @@ (define-public python-wxpython
                  (string-append "#" all)))
               ;; The build script tries to write to demo/version.py. So, we set
               ;; correct write permissions.
-              (chmod "demo/version.py" #o644))))))
+              (chmod "demo/version.py" #o644)))
+          (add-before 'check 'add-missing-.so
+            (lambda* (#:key inputs outputs #:allow-other-keys)
+              (let ((site (site-packages inputs outputs)))
+                (with-directory-excursion (string-append site "/wx")
+                  (for-each
+                   (match-lambda
+                     ("siplib"
+                      (rename-file "siplib" "siplib.so"))
+                     ((? (cut string-prefix? "_" <>) file)
+                      (unless (string-prefix? "__" file)
+                        (rename-file file (string-append file ".so"))))
+                     (_ #t))
+                   (scandir ".")))))))))
     (inputs
      (list gtk+ wxwidgets))
     (native-inputs
-     (list pkg-config python-waf))
+     (list pkg-config python-setuptools python-waf python-wheel))
     (propagated-inputs
      (list python-attrdict3 python-numpy python-pillow python-six))
     (home-page "https://wxpython.org/")
-- 
2.49.0

Message #71 received at 77575-submitter <at> debbugs.gnu.org (full text, mbox):

From: Steve George <steve <at> futurile.net>
To: 77575-submitter <at> debbugs.gnu.org
Subject: RE: python-team build patches
Date: Tue, 8 Apr 2025 18:07:36 +0100

Hi Nicolas,

They all built correctly, and their dependents built as well. Except for the python-redis patch, where I get:

  223:20  1 (proc #<directory (guile-user) 7ffff7850c80>)
  In unknown file:
             0 (%resolve-variable (7 . %current-system) #<directory (g?>)

             ERROR: In procedure %resolve-variable:
             Unbound variable: %current-system

Can you check it please?

Thanks,

Steve / Futurile

Message #74 received at 77575 <at> debbugs.gnu.org (full text, mbox):

From: Steve George <steve <at> futurile.net>
To: 77575 <at> debbugs.gnu.org, 77575-submitter <at> debbugs.gnu.org
Cc: Nicolas Graves <ngraves <at> ngraves.fr>
Subject: Re: [bug#77575] [PATCH python-team 00/21] More patches
Date: Tue, 8 Apr 2025 20:20:47 +0100

Hi,

Everything applied except for the python-redis patch as mentioned earlier.

Commits are:

[01/21] gnu: python-sanic: Update to 25.3.0.
        commit: 4836b39947381853feac58d97688425d2f4ad1ce
[02/21] gnu: python-stem: Update to 1.8.2.
        commit: ffcfb322690598f8f2d2884941e374189ee9ecb4
[03/21] gnu: python-lazr-delegates: Update to 2.1.1.
        commit: 997b90ed7ed50f015da2802e778dda3224e3f3d3
[04/21] gnu: python-lazr-config: Update to 3.1.
        commit: 32a060479b62b4599995962d22bc53f930d912fd
[05/21] gnu: python-lap: Update to 0.5.12.
        commit: df985f3107b3cc8e6eb81d9a3aaa334c7998f9c0
[06/21] gnu: Remove python-pydiff.
        commit: 04cbdbc3faf70cd8f35168e8bbc0c89bc49d581c
[07/21] gnu: pomegranate: Disable tests.
        commit: a872c47eae0b036577d5a21455b6ae02d74d7135
[08/21] gnu: python-pymodbus: Update to 3.8.6.
        commit: f1012d6451c0fe42ca81b777b1ed3309c48aa71e
[09/21] gnu: python-flufl-lock: Update to 8.1.0.
        commit: 59f4ab7911b06d314ce1ccb498568f1dc1f38760
[10/21] gnu: python-flufl-i18n: Update to 5.1.0.
        commit: 8d06615eb62ce02a13c20f2eefc57c158698cfb4
[11/21] gnu: cnvkit: Update to 0.9.12.
        commit: b4a2507e1611b51589a295e194acf8868aeefdea
[12/21] gnu: python-authheaders: Update to 0.16.3.
        commit: 622aa0aed15df87bf31a1158ce11705776ba987d
[13/21] gnu: mailman: Update to 3.3.10.
        commit: 008173787113e6ca7aa7492efa888af7cf8cf86a
[14/21] gnu: python-mailman-hyperkitty: Update to 1.2.1.
        commit: 87549b8453b0c871665465051ff5c8885e9cdf40
[15/21] gnu: python-ledgerblue: Fix version detection.
        commit: 95d1600ecc9971ea3de62e505f7bee94a2e4e06f
[16/21] gnu: ledger-agent: Switch to pyproject-build-system.
        commit: 9b21d0dd7ca8c5c5c47860ab946be73346b57b28
[17/21] gnu: python-gixy: Rename package to python-gixy-ng.
        commit: 226c9d7f256fd4d5d1a18468bf969c6ab281af7a
[18/21] gnu: python-ujson: Update to 5.10.0.
        commit: bb5907ffc8144bd7c2e2b541aa1f6f7d53b6e346
[19/21] gnu: bpytop: Switch to pyproject-build-system.
        commit: 9c392708edb92cc5c0c8f98a5af9fbc5aa20e81b
[20/21] gnu: python-redis: Ignore i686 failing test.
        (no commit info)
[21/21] gnu: python-wxpython: Update to 4.2.2.
        commit: d382c62902bbb97e9cdb11ba710e311157eb2f3b

Best regards,
-- 
Steve George <steve <at> futurile.net>

Message #82 received at 77575-done <at> debbugs.gnu.org (full text, mbox):

From: Andreas Enge <andreas <at> enge.fr>
To: Steve George <steve <at> futurile.net>
Cc: 77575-done <at> debbugs.gnu.org, Nicolas Graves <ngraves <at> ngraves.fr>,
 77575-submitter <at> debbugs.gnu.org
Subject: Re: [bug#77575] [PATCH python-team 00/21] More patches
Date: Wed, 9 Apr 2025 10:37:23 +0200

Hello,

Am Tue, Apr 08, 2025 at 08:20:47PM +0100 schrieb Steve George:
> Everything applied except for the python-redis patch as mentioned earlier.

as far as I can see, this has been handled by a modified patch in commit
576c81eaa49f97a1b53c72fd946768dce79d0d46 on the python-team branch.

Closing this issue; thanks to Nicolas and Steve for your heroic efforts!

Andreas

Message #88 received at 77575-done <at> debbugs.gnu.org (full text, mbox):

From: Steve George <steve <at> futurile.net>
To: 77575-done <at> debbugs.gnu.org
Subject: Closing
Date: Thu, 10 Apr 2025 22:21:53 +0100

Hi,

Looks like Sharlatan applied the last patch, so we're all done on this. Thanks for sending them!

Steve / Futurile

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