GNU bug report logs - #76571
[PATCH python-team 00/15] Some 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
Subject: [PATCH python-team 00/15] Some fixes 
Date: Tue, 25 Feb 2025 23:48:03 +0100

These patches were developped locally on 70858, but they should be
rather independent, and fix quite some things in the python-team branch.

There are still quite some failing packages scientific (bioinformatics
and astro packages), but those seem related to numpy deprecations and
updates.

Nicolas Graves (15):
  gnu: python-pillow-heif: Update test-flags.
  gnu: python-beartype: Update to 0.19.0.
  gnu: python-cftime: Update to 1.6.4.
  gnu: python-multiprocessing-on-dill: Use pyproject-build-system.
  gnu: python-pykdtree: Update to 1.3.9.
  gnu: python-peachpy: Update to 0.2.0-3.349e8f8.
  gnu: sdkmanager: Update python-urllib3.
  gnu: python-pytest-runner: Update to 6.0.1.
  gnu: Remove python-rednose.
  gnu: python-vcrpy: Update to 7.0.0.
  gnu: python-pyparsing: Update to 3.2.1.
  gnu: behave: Remove python-nose native-input.
  gnu: Remove python-dictpath.
  gnu: python-ipympl: Update to 0.9.2.
  gnu: python-anndata: Ignore failing test.

 gnu/packages/android.scm      |   5 +-
 gnu/packages/check.scm        |  60 ++++---------------
 gnu/packages/jupyter.scm      |   6 +-
 gnu/packages/python-build.scm |  10 ++--
 gnu/packages/python-check.scm |  37 +++++-------
 gnu/packages/python-web.scm   |   1 -
 gnu/packages/python-xyz.scm   | 109 ++++++++++++++--------------------
 gnu/packages/web.scm          |   7 ++-
 8 files changed, 91 insertions(+), 144 deletions(-)

-- 
2.48.1



-- 
Best regards,
Nicolas Graves

Message #8 received at 76571 <at> debbugs.gnu.org (full text, mbox):

From: Nicolas Graves <ngraves <at> ngraves.fr>
To: 76571 <at> debbugs.gnu.org
Subject: [PATCH 01/15] gnu: python-pillow-heif: Update test-flags.
Date: Thu, 20 Feb 2025 16:47:26 +0100

* gnu/packages/python-xyz.scm (python-pillow-heif)[arguments]{test-flags}:
Update them.
[native-inputs]: Remove uneeded python-pylint.
---
 gnu/packages/python-xyz.scm | 14 +++-----------
 1 file changed, 3 insertions(+), 11 deletions(-)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 9ba8220357..7d21beb4ce 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -11424,17 +11424,10 @@ (define-public python-pillow-heif
     (arguments
      (list
       #:test-flags
-      #~(list "-k"                      ; XXX: 10/12 bit tests fail
+      #~(list "-k"
               (string-append
-               "not test_save_bgr_16bit_to_10_12_bit"
-               " and not test_save_bgra_16bit_to_10_12_bit"
-               " and not test_open_heif_compare_non_standard_modes_data"
-               " and not test_open_save_disable_16bit"
-               " and not test_heif_read_images[image_path16]"
-               " and not test_heif_read_images[image_path43]"
-               " and not test_premultiplied_alpha"
-               " and not test_hdr_save"
-               " and not test_I_color_modes_to_10_12_bit"))))
+               "not test_heif_read_images[image_path25]"
+               " and not test_heif_read_images[image_path49]"))))
     (inputs (list libheif))
     (propagated-inputs (list python-pillow))
     (native-inputs (list opencv         ; for opencv-python
@@ -11443,7 +11436,6 @@ (define-public python-pillow-heif
                          python-numpy
                          python-packaging
                          python-pre-commit
-                         python-pylint
                          python-pympler
                          python-setuptools
                          python-pytest
-- 
2.48.1



-- 
Best regards,
Nicolas Graves

Message #11 received at 76571 <at> debbugs.gnu.org (full text, mbox):

From: Nicolas Graves <ngraves <at> ngraves.fr>
To: 76571 <at> debbugs.gnu.org
Subject: [PATCH 02/15] gnu: python-beartype: Update to 0.19.0.
Date: Thu, 20 Feb 2025 16:49:47 +0100

* gnu/packages/python-check.scm (python-beartype): Update to 0.19.0.
[arguments]: Remove former test-flags.
[native-inputs]: Remove python-setuptools, python-wheel. Add
python-hatchling, python-numpy and python-pygments.
---
 gnu/packages/python-check.scm | 16 ++++------------
 1 file changed, 4 insertions(+), 12 deletions(-)

diff --git a/gnu/packages/python-check.scm b/gnu/packages/python-check.scm
index 582f16ec1d..34125475ad 100644
--- a/gnu/packages/python-check.scm
+++ b/gnu/packages/python-check.scm
@@ -341,24 +341,16 @@ (define-public python-pytest-freezer
 (define-public python-beartype
   (package
     (name "python-beartype")
-    (version "0.10.4")
+    (version "0.19.0")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "beartype" version))
        (sha256
-        (base32 "0amzckgw9c93bl4jf0q6322j9wyyf3i8vl03yixfkrpllzv6kv14"))))
+        (base32 "0wv598iv9c2s6ivfiara9pnkdlnas8xjw063wvyi0dswpb0xyhny"))))
     (build-system pyproject-build-system)
-    (arguments
-     (list
-      #:test-flags
-      #~(list
-         "beartype_test"
-         ;; These tests rely on git through the "get_main_readme_file" helper.
-         "-k" (string-append "not test_doc_readme "
-                             "and not test_sphinx "
-                             "and not test_pep561_mypy"))))
-    (native-inputs (list python-pytest python-setuptools python-wheel))
+    (native-inputs
+     (list python-hatchling python-numpy python-pygments python-pytest))
     (home-page "https://github.com/beartype/beartype")
     (synopsis "Fast runtime type checking for Python")
     (description "Beartype aims to be a very fast runtime type checking tool
-- 
2.48.1



-- 
Best regards,
Nicolas Graves

Message #14 received at 76571 <at> debbugs.gnu.org (full text, mbox):

From: Nicolas Graves <ngraves <at> ngraves.fr>
To: 76571 <at> debbugs.gnu.org
Subject: [PATCH 03/15] gnu: python-cftime: Update to 1.6.4.
Date: Mon, 24 Feb 2025 07:54:50 +0100

* gnu/packages/python-xyz.scm (python-cftime): Update to 1.6.4.
[arguments]{phases}: Add phase 'remove-unwanted-dev-dependencies.
[native-inputs]: Remove python-check-manifest, python-pytest-cov. Add
python-setuptools.
---
 gnu/packages/python-xyz.scm | 20 +++++++++++++-------
 1 file changed, 13 insertions(+), 7 deletions(-)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 7d21beb4ce..6cf0862eed 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -3719,22 +3719,28 @@ (define-public python-sh
 (define-public python-cftime
   (package
     (name "python-cftime")
-    (version "1.6.2")
+    (version "1.6.4")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "cftime" version))
        (sha256
-        (base32 "1lp6jrjjgl18csn4bcnphn0l16ag4aynvn7x0kins155p07w0546"))))
+        (base32 "1p5fw25hjqpzwxw3662f72ga30kpf8pbbph8fgb7x2kmjdhl09g3"))))
     (build-system pyproject-build-system)
+    (arguments
+     (list #:phases
+           #~(modify-phases %standard-phases
+               (add-after 'unpack 'remove-unwanted-dev-dependencies
+                 (lambda _
+                   (substitute* "requirements-dev.txt"
+                     (("(check-manifest|coverage|coveralls|pytest-cov|twine)")
+                      "")))))))
     (propagated-inputs
      (list python-numpy))
     (native-inputs
-     (list python-check-manifest
-           python-coverage
-           python-coveralls
-           python-cython
-           python-pytest-cov
+     (list python-cython
+           python-pytest
+           python-setuptools
            python-sphinx
            python-twine
            python-wheel))
-- 
2.48.1



-- 
Best regards,
Nicolas Graves

Message #17 received at 76571 <at> debbugs.gnu.org (full text, mbox):

From: Nicolas Graves <ngraves <at> ngraves.fr>
To: 76571 <at> debbugs.gnu.org
Subject: [PATCH 04/15] gnu: python-multiprocessing-on-dill: Use
 pyproject-build-system.
Date: Mon, 24 Feb 2025 08:00:16 +0100

* gnu/packages/python-xyz.scm (python-multiprocessing-on-dill): Use pyproject-build-system.
[arguments]: Remove field.
[native-inputs]: Remove uneeded python-check-manifest. Add python-pytest.
---
 gnu/packages/python-xyz.scm | 12 ++----------
 1 file changed, 2 insertions(+), 10 deletions(-)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 6cf0862eed..a5eefb8be2 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -30207,17 +30207,9 @@ (define-public python-multiprocessing-on-dill
               (sha256
                (base32
                 "1rs5a3hx1fcpfsxxkl5kx6g06c82wqjqgdqyny5l1ggl1wq0rmfn"))))
-    (build-system python-build-system)
-    (arguments
-     (list
-      #:phases
-      #~(modify-phases %standard-phases
-          (replace 'check
-            (lambda* (#:key tests? #:allow-other-keys)
-              (when tests?
-                (invoke "pytest" "-vv")))))))
+    (build-system pyproject-build-system)
     (propagated-inputs (list python-dill))
-    (native-inputs (list python-check-manifest python-pytest python-wheel))
+    (native-inputs (list python-pytest python-setuptools python-wheel))
     (home-page "https://github.com/sixty-north/multiprocessing_on_dill")
     (synopsis "Multiprocessing using dill instead of pickle")
     (description
-- 
2.48.1



-- 
Best regards,
Nicolas Graves

Message #20 received at 76571 <at> debbugs.gnu.org (full text, mbox):

From: Nicolas Graves <ngraves <at> ngraves.fr>
To: 76571 <at> debbugs.gnu.org
Subject: [PATCH 08/15] gnu: python-pytest-runner: Update to 6.0.1.
Date: Tue, 25 Feb 2025 08:11:27 +0100

* gnu/packages/check.scm (python-pytest-runner): Update to 6.0.1.
[arguments]: Remove {phases}.
[native-inputs]: Remove python-pip, python-pypa-build. Add
python-pytest-checkdocs, python-pytest-enabler,
python-types-setuptools.
---
 gnu/packages/check.scm | 28 +++++++++++-----------------
 1 file changed, 11 insertions(+), 17 deletions(-)

diff --git a/gnu/packages/check.scm b/gnu/packages/check.scm
index 61cacb98be..5e3ad744cc 100644
--- a/gnu/packages/check.scm
+++ b/gnu/packages/check.scm
@@ -1984,35 +1984,29 @@ (define-public python-pytest-randomly
 (define-public python-pytest-runner
   (package
     (name "python-pytest-runner")
-    (version "6.0.0")
+    (version "6.0.1")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "pytest-runner" version))
        (sha256
         (base32
-         "11dnhxnjmh4nf1j8rnvx944ha3wg8ggrgrwdcx4c7d19xmi57n5l"))))
+         "16zly218ij0n6fxzqsasia3vh9xkzl9w0cs9pwvqy057hnap7m3h"))))
     (build-system pyproject-build-system)
     (arguments
      (list
       ;; FIXME: The test suite requires 'python-pytest-virtualenv',
       ;; but that introduces a circular dependency.
-      #:tests? #f
-      #:phases
-      #~(modify-phases %standard-phases
-          (replace 'build
-            (lambda _
-              (let ((circa-1980 (* 10 366 24 60 60)))
-                (setenv "SOURCE_DATE_EPOCH" (number->string circa-1980))
-                (invoke "python" "-m" "build" "--wheel" "--no-isolation" "."))))
-          (replace 'install
-            (lambda _
-              (let ((whl (car (find-files "dist" "\\.whl$"))))
-                (invoke "pip" "--no-cache-dir" "--no-input"
-                        "install" "--no-deps" "--prefix" #$output whl)))))))
+      #:tests? #f))
     (native-inputs
-     (list python-pip python-pypa-build python-pytest
-           python-setuptools python-setuptools-scm python-wheel))
+     (list python-pytest
+           python-pytest-checkdocs
+           python-pytest-enabler
+           ;; python-pytest-virtualenv
+           python-setuptools
+           python-setuptools-scm
+           python-types-setuptools
+           python-wheel))
     (home-page "https://github.com/pytest-dev/pytest-runner")
     (synopsis "Invoke py.test as a distutils command")
     (description
-- 
2.48.1



-- 
Best regards,
Nicolas Graves

Message #23 received at 76571 <at> debbugs.gnu.org (full text, mbox):

From: Nicolas Graves <ngraves <at> ngraves.fr>
To: 76571 <at> debbugs.gnu.org
Subject: [PATCH 09/15] gnu: Remove python-rednose.
Date: Tue, 25 Feb 2025 08:13:28 +0100

This package is broken with the latest python version, and is easy to
remove.

* gnu/packages/check.scm (python-rednose): Delete variable.
* gnu/packages/python-xyz.scm (python-sure) and
* gnu/packages/web.scm (python-httpretty):
[arguments]: Add 'remove-rednose-dependency in {phases}.
[native-inputs]: Remove python-rednose.
---
 gnu/packages/check.scm      | 31 -------------------------------
 gnu/packages/python-xyz.scm | 12 +++++++++++-
 gnu/packages/web.scm        |  7 ++++++-
 3 files changed, 17 insertions(+), 33 deletions(-)

diff --git a/gnu/packages/check.scm b/gnu/packages/check.scm
index 5e3ad744cc..eb1923e8ad 100644
--- a/gnu/packages/check.scm
+++ b/gnu/packages/check.scm
@@ -3496,37 +3496,6 @@ (define-public python-behave-web-api
 JSON APIs with Behave.")
     (license license:expat)))
 
-(define-public python-rednose
-  (package
-    (name "python-rednose")
-    (version "1.2.3")
-    (source
-      (origin
-        (method url-fetch)
-        (uri (pypi-uri "rednose" version))
-        (sha256
-          (base32
-            "11x5nx5b4wdq04s7vj1gcdl07jvvkfb37p0r5lg773gr5rr8mj6h"))))
-    (build-system python-build-system)
-    (arguments
-     `(#:phases (modify-phases %standard-phases
-                  (add-after 'unpack 'patch-setup.py
-                    (lambda _
-                      ;; Six is only required for tests and later versions
-                      ;; work fine.
-                      (substitute* "setup.py"
-                        (("six==1.10.0") "six"))
-                      #t)))))
-    (propagated-inputs
-     (list python-colorama python-termstyle))
-    (native-inputs
-     (list python-six python-nose))
-    (home-page "https://github.com/JBKahn/rednose")
-    (synopsis "Colored output for Python nosetests")
-    (description "This package provides colored output for the
-@command{nosetests} command of the Python Nose unit test framework.")
-    (license license:bsd-3)))
-
 (define-public python-nose-exclude
   (package
     (name "python-nose-exclude")
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 271e52df34..0aa5b23278 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -26659,10 +26659,20 @@ (define-public python-sure
         (base32
          "1jmrskj399idw1czx6dvy2zfaijnwi02b55vx979ixp7q2mnzz68"))))
     (build-system python-build-system)
+    (arguments
+     (list
+      #:phases
+      '(modify-phases %standard-phases
+         (add-after 'unpack 'remove-rednose-dependency
+           (lambda _
+             (substitute* "setup.py"
+               (("'rednose'") ""))
+             (substitute* '("requirements.txt" "setup.cfg")
+               (("rednose.*") "")))))))
     (propagated-inputs
      (list python-mock python-six))
     (native-inputs
-     (list python-nose python-rednose))
+     (list python-nose))
     (home-page "https://github.com/gabrielfalcao/sure")
     (synopsis "Automated testing library in python for python")
     (description
diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm
index 0030e152b4..fdb7753ba6 100644
--- a/gnu/packages/web.scm
+++ b/gnu/packages/web.scm
@@ -7159,6 +7159,12 @@ (define-public python-httpretty
      (list
       #:phases
       '(modify-phases %standard-phases
+         (add-after 'unpack 'remove-rednose-dependency
+           (lambda _
+             (substitute* "setup.py"
+               (("'rednose'") ""))
+             (substitute* '("requirements.txt" "setup.cfg")
+               (("rednose.*") ""))))
          (replace 'check
            (lambda* (#:key tests? #:allow-other-keys)
              (when tests?
@@ -7172,7 +7178,6 @@ (define-public python-httpretty
            python-httplib2
            python-nose
            python-pyparsing
-           python-rednose
            python-requests
            python-sure
            python-tornado))
-- 
2.48.1



-- 
Best regards,
Nicolas Graves

Message #26 received at 76571 <at> debbugs.gnu.org (full text, mbox):

From: Nicolas Graves <ngraves <at> ngraves.fr>
To: 76571 <at> debbugs.gnu.org
Subject: [PATCH 10/15] gnu: python-vcrpy: Update to 7.0.0.
Date: Tue, 25 Feb 2025 10:58:01 +0100

* gnu/packages/python-check.scm (python-vcrpy): Update to 7.0.0.
[native-inputs]: Remove python-flask, python-ipaddress, python-mock.
Add python-aiohttp, python-boto3, python-httpx, python-pytest-aiohttp,
python-pytest-asyncio, python-requests, python-tornado,
python-werkzeug.
[propagated-inputs]: Remove python-six.
---
 gnu/packages/python-check.scm | 21 +++++++++++----------
 1 file changed, 11 insertions(+), 10 deletions(-)

diff --git a/gnu/packages/python-check.scm b/gnu/packages/python-check.scm
index 34125475ad..d0319fcbc0 100644
--- a/gnu/packages/python-check.scm
+++ b/gnu/packages/python-check.scm
@@ -3244,13 +3244,13 @@ (define-public python-pycotap
 (define-public python-vcrpy
   (package
     (name "python-vcrpy")
-    (version "6.0.2")
+    (version "7.0.0")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "vcrpy" version))
        (sha256
-        (base32 "02fwmmc33qqybzbj1lvdz458g1fffm5cgnqihj4larw4268kvqc8"))))
+        (base32 "0l1sdfc51024jclqv9104nagpirxx8w0gcn5h0bdxv950jnr2qqp"))))
     (build-system pyproject-build-system)
     (arguments
      (list
@@ -3263,22 +3263,23 @@ (define-public python-vcrpy
                           "test_testcase_playback")
                     " and not "))))
     (native-inputs
-     (list nss-certs-for-test
-           python-flask
+     (list python-aiohttp
+           python-boto3
            python-httplib2
-           python-ipaddress
-           python-mock
+           python-httpx
            python-pytest
            python-pytest-cov
+           python-pytest-aiohttp
+           python-pytest-asyncio
            python-pytest-httpbin
+           python-requests
            python-setuptools
+           python-tornado
            python-urllib3
+           python-werkzeug
            python-wheel))
     (propagated-inputs
-     (list python-pyyaml
-           python-six
-           python-wrapt
-           python-yarl))
+     (list python-pyyaml python-wrapt python-yarl))
     (home-page "https://github.com/kevin1024/vcrpy")
     (synopsis "Automatically mock your HTTP interactions")
     (description
-- 
2.48.1



-- 
Best regards,
Nicolas Graves

Message #29 received at 76571 <at> debbugs.gnu.org (full text, mbox):

From: Nicolas Graves <ngraves <at> ngraves.fr>
To: 76571 <at> debbugs.gnu.org
Subject: [PATCH 12/15] gnu: behave: Remove python-nose native-input.
Date: Tue, 25 Feb 2025 11:14:55 +0100

* gnu/packages/check.scm (behave)[native-inputs]: Remove python-nose.
---
 gnu/packages/check.scm | 1 -
 1 file changed, 1 deletion(-)

diff --git a/gnu/packages/check.scm b/gnu/packages/check.scm
index eb1923e8ad..98f950142d 100644
--- a/gnu/packages/check.scm
+++ b/gnu/packages/check.scm
@@ -3440,7 +3440,6 @@ (define-public behave
     (build-system pyproject-build-system)
     (native-inputs
      (list python-mock
-           python-nose
            python-assertpy
            python-pathpy
            python-pyhamcrest
-- 
2.48.1



-- 
Best regards,
Nicolas Graves

Message #32 received at 76571 <at> debbugs.gnu.org (full text, mbox):

From: Nicolas Graves <ngraves <at> ngraves.fr>
To: 76571 <at> debbugs.gnu.org
Subject: [PATCH 11/15] gnu: python-pyparsing: Update to 3.2.1.
Date: Tue, 25 Feb 2025 11:11:07 +0100

* gnu/packages/python-build.scm (python-pyparsing): Update to 3.2.1.
[build-system]: Switch to pyproject-build-system.
[native-inputs]: Add python-flit-core.
(python-pyparsing-2.4.7)[native-inputs]: Add python-setuptools,
python-wheel.
---
 gnu/packages/python-build.scm | 10 ++++++----
 1 file changed, 6 insertions(+), 4 deletions(-)

diff --git a/gnu/packages/python-build.scm b/gnu/packages/python-build.scm
index 375896a76a..6bea44fee6 100644
--- a/gnu/packages/python-build.scm
+++ b/gnu/packages/python-build.scm
@@ -412,14 +412,14 @@ (define-public python-pep517-bootstrap
 (define-public python-pyparsing
   (package
     (name "python-pyparsing")
-    (version "3.0.6")
+    (version "3.2.1")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "pyparsing" version))
        (sha256
-        (base32 "109b9r802wb472hgmxclljprh5cid0w3p6mk9alba7pg2c0frgfr"))))
-    (build-system python-build-system)
+        (base32 "02jz5rv3vx46xvjszda467l269jz9narlrwd0a83mpk6zma0i631"))))
+    (build-system pyproject-build-system)
     (outputs '("out" "doc"))
     (arguments
      `(#:tests? #f                      ;no test target
@@ -440,6 +440,7 @@ (define-public python-pyparsing
                        (find-files dir ".*")))
                 (list "docs" "htmldoc" "examples")
                 (list doc html-doc examples))))))))
+    (native-inputs (list python-flit-core))
     (home-page "https://github.com/pyparsing/pyparsing")
     (synopsis "Python parsing class library")
     (description
@@ -459,7 +460,8 @@ (define-public python-pyparsing-2.4.7
        (method url-fetch)
        (uri (pypi-uri "pyparsing" version))
        (sha256
-        (base32 "1hgc8qrbq1ymxbwfbjghv01fm3fbpjwpjwi0bcailxxzhf3yq0y2"))))))
+        (base32 "1hgc8qrbq1ymxbwfbjghv01fm3fbpjwpjwi0bcailxxzhf3yq0y2"))))
+    (native-inputs (list python-setuptools python-wheel))))
 
 (define-public python-packaging-bootstrap
   (package
-- 
2.48.1



-- 
Best regards,
Nicolas Graves

Message #35 received at 76571 <at> debbugs.gnu.org (full text, mbox):

From: Nicolas Graves <ngraves <at> ngraves.fr>
To: 76571 <at> debbugs.gnu.org
Subject: [PATCH 13/15] gnu: Remove python-dictpath.
Date: Tue, 25 Feb 2025 17:42:53 +0100

* gnu/packages/python-xyz.scm (python-dictpath): Remove variable.
* gnu/packages/python-web.scm (python-openapi-core)[propagated-inputs]:
Remove unecessary python-dictpath.
---
 gnu/packages/python-web.scm |  1 -
 gnu/packages/python-xyz.scm | 19 -------------------
 2 files changed, 20 deletions(-)

diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm
index 9db9f46638..e6918a530e 100644
--- a/gnu/packages/python-web.scm
+++ b/gnu/packages/python-web.scm
@@ -3160,7 +3160,6 @@ (define-public python-openapi-core
     (propagated-inputs
      (list python-attrs
            python-aiohttp
-           python-dictpath
            python-isodate
            python-jsonschema
            python-lazy-object-proxy
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 0aa5b23278..28e0545f26 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -33748,25 +33748,6 @@ (define-public python-dictdiffer
 dictionaries.")
     (license license:expat)))
 
-(define-public python-dictpath
-  (package
-    (name "python-dictpath")
-    (version "0.1.3")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (pypi-uri "dictpath" version))
-       (sha256
-        (base32 "1n4hq4wbgaw59bbb16nhkgg5wk8sl4iw940vjrgx4xmifqxxw73m"))))
-    (build-system python-build-system)
-    (native-inputs (list python-pytest python-pytest-cov python-pytest-flake8))
-    (home-page "https://github.com/p1c2u/pathable")
-    (synopsis "Object-oriented path library for Python")
-    (description "This object-oriented dictionary path Python library enables
-traversing resources like paths or accessing resources on demand with separate
-accessor layer.")
-    (license license:asl2.0)))
-
 (define-public pyzo
   (package
     (name "pyzo")
-- 
2.48.1



-- 
Best regards,
Nicolas Graves

Message #38 received at 76571 <at> debbugs.gnu.org (full text, mbox):

From: Nicolas Graves <ngraves <at> ngraves.fr>
To: 76571 <at> debbugs.gnu.org
Subject: [PATCH 14/15] gnu: python-ipympl: Update to 0.9.2.
Date: Tue, 25 Feb 2025 18:04:42 +0100

* gnu/packages/jupyter.scm (python-ipympl): Update to 0.9.2.
[native-inputs]: Add python-hatchling.
---
 gnu/packages/jupyter.scm | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/jupyter.scm b/gnu/packages/jupyter.scm
index d5c298056c..6c2f549583 100644
--- a/gnu/packages/jupyter.scm
+++ b/gnu/packages/jupyter.scm
@@ -1055,13 +1055,13 @@ (define-public python-sparqlkernel
 (define-public python-ipympl
   (package
     (name "python-ipympl")
-    (version "0.9.1")
+    (version "0.9.2")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "ipympl" version))
        (sha256
-        (base32 "11rppjdqzgs4pfiq8gww5xkpbk21fp86vvv839v56b9rqq06j2b4"))))
+        (base32 "12qgiy08klqb5gipm23yzh09p5g2k8ihcq2bprprdya84acw2rf8"))))
     (build-system python-build-system)
     (propagated-inputs
      (list python-ipython
@@ -1072,7 +1072,7 @@ (define-public python-ipympl
            python-pillow
            python-traitlets))
     (native-inputs
-     (list python-jupyter-packaging))
+     (list python-hatchling python-jupyter-packaging))
     (home-page "https://matplotlib.org/ipympl/")
     (synopsis "Matplotlib Jupyter Extension")
     (description "Leveraging the Jupyter interactive widgets framework, ipympl
-- 
2.48.1



-- 
Best regards,
Nicolas Graves

Message #41 received at 76571 <at> debbugs.gnu.org (full text, mbox):

From: Nicolas Graves <ngraves <at> ngraves.fr>
To: 76571 <at> debbugs.gnu.org
Subject: [PATCH 15/15] gnu: python-anndata: Ignore failing test.
Date: Tue, 25 Feb 2025 22:45:27 +0100

* gnu/packages/python-xyz.scm (python-anndata)[arguments]{test-flags}:
Ignore test_read_write_X test.
---
 gnu/packages/python-xyz.scm | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 28e0545f26..2063dceeea 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -30064,8 +30064,12 @@ (define-public python-anndata
     (arguments
      (list
       #:test-flags
-      ;; This one test seemingly freezes
-      '(list "-k" "not test_read_lazy_h5_cluster")
+      #~(list "-k" #$(string-append
+                      ;; This one test seemingly freezes
+                      "not test_read_lazy_h5_cluster"
+                      ;; Fails with a numpy deprecation warning
+                      ;; but not an actual failure
+                      " and not test_read_write_X"))
       #:phases
       #~(modify-phases %standard-phases
           ;; Doctests require scanpy from (gnu packages bioinformatics)
-- 
2.48.1



-- 
Best regards,
Nicolas Graves

Message #44 received at 76571 <at> debbugs.gnu.org (full text, mbox):

From: Nicolas Graves <ngraves <at> ngraves.fr>
To: 76571 <at> debbugs.gnu.org
Subject: [PATCH 05/15] gnu: python-pykdtree: Update to 1.3.9.
Date: Tue, 25 Feb 2025 00:20:32 +0100

* gnu/packages/python-xyz.scm (python-pykdtree): Update to 1.3.9.
[native-inputs]: Remove python-nose. Add python-cython, python-pytest,
python-setuptools, python-wheel.
---
 gnu/packages/python-xyz.scm | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index a5eefb8be2..f57a7c6bd6 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -10783,16 +10783,16 @@ (define-public python-perfplot
 (define-public python-pykdtree
   (package
     (name "python-pykdtree")
-    (version "1.3.4")
+    (version "1.3.9")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "pykdtree" version))
        (sha256
-        (base32 "0p8n2ljdacfixkiw092974dmhy4s1c0h032ii1z9kwi9h5h5rgmy"))))
+        (base32 "0q4zrqdn8ad6f710yggkhvx4avf2h1hsbg9qa7ghly54v4vhpgd7"))))
     (build-system python-build-system)
     (native-inputs
-     (list python-nose))
+     (list python-cython python-pytest python-setuptools python-wheel))
     (propagated-inputs
      (list python-numpy))
     (home-page "https://github.com/storpipfugl/pykdtree")
-- 
2.48.1



-- 
Best regards,
Nicolas Graves

Message #47 received at 76571 <at> debbugs.gnu.org (full text, mbox):

From: Nicolas Graves <ngraves <at> ngraves.fr>
To: 76571 <at> debbugs.gnu.org
Subject: [PATCH 07/15] gnu: sdkmanager: Update python-urllib3.
Date: Tue, 25 Feb 2025 08:05:54 +0100

* gnu/packages/android.scm (sdkmanager)[inputs]: Switch to
python-urllib3-next.
---
 gnu/packages/android.scm | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/android.scm b/gnu/packages/android.scm
index cb699b06dc..bafca18abe 100644
--- a/gnu/packages/android.scm
+++ b/gnu/packages/android.scm
@@ -738,7 +738,10 @@ (define-public sdkmanager
                (base32
                 "11as7n2mj3nbqsqb3ivyv9985n73i022s748qvjg36cs8ig50afx"))))
     (build-system pyproject-build-system)
-    (inputs (list python-requests python-argcomplete python-urllib3 gnupg))
+    (inputs (list python-requests
+                  python-argcomplete
+                  python-urllib3-next
+                  gnupg))
     (native-inputs (list python-setuptools python-wheel))
     (arguments
      (list #:phases #~(modify-phases %standard-phases
-- 
2.48.1



-- 
Best regards,
Nicolas Graves

Message #50 received at 76571 <at> debbugs.gnu.org (full text, mbox):

From: Nicolas Graves <ngraves <at> ngraves.fr>
To: 76571 <at> debbugs.gnu.org
Subject: [PATCH 06/15] gnu: python-peachpy: Update to 0.2.0-3.349e8f8.
Date: Tue, 25 Feb 2025 01:15:22 +0100

* gnu/packages/python-xyz.scm (python-peachpy): Update to
0.2.0-3.349e8f8.
[build-system]: Switch to pyproject-build-system.
[arguments]: Remove {phases}. Add {test-target} to ignore a failing
test.
[native-inputs]: Remove python-nose, python-rednose. Add
python-pytest, python-wheel.
---
 gnu/packages/python-xyz.scm | 18 ++++++++----------
 1 file changed, 8 insertions(+), 10 deletions(-)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index f57a7c6bd6..271e52df34 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -36569,9 +36569,9 @@ (define-public python-angr
 
 (define-public python-peachpy
   ;; There is no tag in this repo.
-  (let ((commit "913d74c35a6b1d330e90bfc055208ce5b06b35a0")
+  (let ((commit "349e8f836142b2ed0efeb6bb99b1b715d87202e9")
         (version "0.2.0")                         ;from 'peachpy/__init__.py'
-        (revision "2"))
+        (revision "3"))
     (package
       (name "python-peachpy")
       (version (git-version version revision commit))
@@ -36582,17 +36582,15 @@ (define-public python-peachpy
                 (file-name (git-file-name name version))
                 (sha256
                  (base32
-                  "1wnqxspxsacw4556q0b9fbw11nhrkgn6gs8g43jdnpa35f3z9kb6"))
+                  "16pnkghmqjc7pbws0yhyrwlz43d5pffb5c6v2bb4jk0j537gwzbi"))
                 (patches (search-patches "python-peachpy-determinism.patch"))))
-      (build-system python-build-system)
+      (build-system pyproject-build-system)
       (arguments
-       '(#:phases (modify-phases %standard-phases
-                    (replace 'check
-                      (lambda* (#:key tests? #:allow-other-keys)
-                        (when tests?
-                          (invoke "nosetests")))))))
+       ;; The issue is known and the test will probably never be fixed.
+       ;; https://github.com/Maratyszcza/PeachPy/issues/131
+       (list #:test-flags ''("--ignore=tests/arm/test_arm.py")))
       (native-inputs
-       (list python-nose python-rednose python-setuptools))
+       (list python-pytest python-setuptools python-wheel))
       (propagated-inputs
        (list python-six python-opcodes))
       (synopsis "Efficient assembly code generation in Python")
-- 
2.48.1



-- 
Best regards,
Nicolas Graves

Message #57 received at 76571-done <at> debbugs.gnu.org (full text, mbox):

From: Ricardo Wurmus <rekado <at> elephly.net>
To: 76571-done <at> debbugs.gnu.org
Subject: [PATCH python-team 00/15] Some fixes
Date: Wed, 26 Feb 2025 14:57:38 +0100

Applied to python-team branch, thank you!

-- 
Ricardo

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