Merge pull request #299223 from NixOS/python-updates

[python-updates] 2024-03-24 - selective updates

pkgs/applications/audio/miniplayer/default.nix

@@ -15,7 +15,11 @@ buildPythonApplication rec {
     hash = "sha256-iUUsVIDLQAiaMomfA2LvvJZ2ePhgADtC6GCwIpRC1MA=";
   };
 
-  propagatedBuildInputs = [
+  build-system = [
+    setuptools
+  ];
+
+  dependencies = [
     colorthief
     ffmpeg-python
     mpd2
@@ -25,6 +29,8 @@ buildPythonApplication rec {
     ueberzug
   ];
 
+  doCheck = false; # no tests
+
   # pythonImportsCheck is disabled because this package doesn't expose any modules.
 
   meta = with lib; {

pkgs/applications/misc/electron-cash/default.nix

@@ -12,6 +12,10 @@ python3Packages.buildPythonApplication rec {
     sha256 = "sha256-xOyj5XerOwgfvI0qj7+7oshDvd18h5IeZvcJTis8nWo=";
   };
 
+  build-system = with python3Packages; [
+    cython
+  ];
+
   propagatedBuildInputs = with python3Packages; [
     # requirements
     pyaes
@@ -36,7 +40,6 @@ python3Packages.buildPythonApplication rec {
     cryptography
 
     # requirements-hw
-    cython
     trezor
     keepkey
     btchip-python

pkgs/applications/science/biology/macs2/default.nix

@@ -21,7 +21,7 @@ python3.pkgs.buildPythonPackage rec {
   ];
 
   nativeBuildInputs = with python3.pkgs; [
-    cython
+    cython_0
     numpy
     setuptools
     wheel

pkgs/applications/science/math/sage/python-modules/sage-setup.nix

@@ -1,7 +1,7 @@
 { lib
 , buildPythonPackage
 , sage-src
-, cython_3
+, cython
 , jinja2
 , pkgconfig # the python module, not the pkg-config alias
 }:
@@ -11,7 +11,7 @@ buildPythonPackage rec {
   pname = "sage-setup";
   src = sage-src;
 
-  nativeBuildInputs = [ cython_3 ];
+  nativeBuildInputs = [ cython ];
   buildInputs = [ pkgconfig ];
   propagatedBuildInputs = [ jinja2 ];
 

pkgs/applications/science/math/sage/sagelib.nix

@@ -48,7 +48,7 @@
 , cvxopt
 , cypari2
 , cysignals
-, cython_3
+, cython
 , fpylll
 , gmpy2
 , importlib-metadata
@@ -153,7 +153,7 @@ buildPythonPackage rec {
     cvxopt
     cypari2
     cysignals
-    cython_3
+    cython
     fpylll
     gmpy2
     importlib-metadata

pkgs/applications/version-management/commitizen/default.nix

@@ -55,7 +55,7 @@ python3.pkgs.buildPythonApplication rec {
     pytest-freezer
     pytest-mock
     pytest-regressions
-    (pytestCheckHook.override { pytest = pytest_7; })
+    pytest7CheckHook
   ];
 
   doCheck = true;

pkgs/applications/version-management/git-up/default.nix

@@ -30,7 +30,7 @@ pythonPackages.buildPythonApplication rec {
 
   nativeCheckInputs = [
     git
-    pythonPackages.pytestCheckHook
+    pythonPackages.pytest7CheckHook
   ];
 
   # 1. git fails to run as it cannot detect the email address, so we set it

pkgs/applications/virtualization/virt-manager/default.nix

@@ -76,7 +76,7 @@ python3.pkgs.buildPythonApplication rec {
   '';
 
   nativeCheckInputs = with python3.pkgs; [
-    pytestCheckHook
+    pytest7CheckHook
     cpio
     cdrtools
     xorriso

pkgs/by-name/pr/pretalx/package.nix

@@ -86,6 +86,7 @@ python.pkgs.buildPythonApplication rec {
 
   pythonRelaxDeps = [
     "django-csp"
+    "django-filter"
     "python-dateutil"
   ];
 

pkgs/by-name/pr/pretix/package.nix

@@ -94,6 +94,7 @@ python.pkgs.buildPythonApplication rec {
       --replace-fail psycopg2-binary psycopg2 \
       --replace-fail vat_moss_forked==2020.3.20.0.11.0 vat-moss \
       --replace-fail "bleach==5.0.*" bleach \
+      --replace-fail "django-filter==23.5" django-filter \
       --replace-fail "dnspython==2.5.*" dnspython \
       --replace-fail "importlib_metadata==7.*" importlib_metadata \
       --replace-fail "protobuf==4.25.*" protobuf \
@@ -107,7 +108,6 @@ python.pkgs.buildPythonApplication rec {
   build-system = with python.pkgs; [
     gettext
     nodejs
-    pythonRelaxDepsHook
     setuptools
     tomli
   ];

pkgs/desktops/gnome/misc/gnome-extensions-cli/default.nix

@@ -33,6 +33,7 @@ buildPythonApplication rec {
 
   pythonRelaxDeps = [
     "more-itertools"
+    "packaging"
   ];
 
   propagatedBuildInputs = [

pkgs/development/compilers/vyper/default.nix

@@ -57,6 +57,7 @@ buildPythonPackage rec {
 
   pythonRelaxDeps = [
     "asttokens"
+    "packaging"
   ];
 
   propagatedBuildInputs = [

pkgs/development/python-modules/accelerate/default.nix

@@ -3,8 +3,7 @@
 , buildPythonPackage
 , fetchFromGitHub
 , pythonOlder
-, pytestCheckHook
+, pytest7CheckHook
-, pytest_7
 , setuptools
 , numpy
 , packaging
@@ -47,7 +46,7 @@ buildPythonPackage rec {
   nativeCheckInputs = [
     evaluate
     parameterized
-    (pytestCheckHook.override { pytest = pytest_7; })
+    pytest7CheckHook
     transformers
   ];
   preCheck = ''

pkgs/development/python-modules/aioesphomeapi/default.nix

@@ -4,7 +4,7 @@
 , pythonOlder
 
 # build-system
-, cython_3
+, cython
 , setuptools
 
 # dependencies
@@ -39,7 +39,7 @@ buildPythonPackage rec {
 
   build-system = [
     setuptools
-    cython_3
+    cython
   ];
 
   dependencies = [

pkgs/development/python-modules/aiohttp/default.nix

@@ -21,8 +21,7 @@
 , freezegun
 , gunicorn
 , pytest-mock
-, pytestCheckHook
+, pytest7CheckHook
-, pytest_7
 , python-on-whales
 , re-assert
 , trustme
@@ -83,7 +82,7 @@ buildPythonPackage rec {
     freezegun
     gunicorn
     pytest-mock
-    (pytestCheckHook.override { pytest = pytest_7; })
+    pytest7CheckHook
     python-on-whales
     re-assert
   ] ++ lib.optionals (!(stdenv.isDarwin && stdenv.isAarch64)) [

pkgs/development/python-modules/alembic/default.nix

@@ -14,7 +14,7 @@
 , typing-extensions
 
 # tests
-, pytestCheckHook
+, pytest7CheckHook
 , pytest-xdist
 , python-dateutil
 }:
@@ -49,7 +49,7 @@ buildPythonPackage rec {
   ];
 
   nativeCheckInputs = [
-    pytestCheckHook
+    pytest7CheckHook
     pytest-xdist
     python-dateutil
   ];

pkgs/development/python-modules/anytree/default.nix

@@ -4,7 +4,7 @@
 , fontconfig
 , graphviz
 , poetry-core
-, pytestCheckHook
+, pytest7CheckHook
 , pythonOlder
 , six
 , substituteAll
@@ -13,7 +13,7 @@
 
 buildPythonPackage rec {
   pname = "anytree";
-  version = "2.12.0";
+  version = "2.12.1";
   format = "pyproject";
 
   disabled = pythonOlder "3.7";
@@ -22,7 +22,7 @@ buildPythonPackage rec {
     owner = "c0fec0de";
     repo = "anytree";
     rev = "refs/tags/${version}";
-    hash = "sha256-8mV9Lf6NLPUDVurXCxG+tqe7+3TrIn2H+7tHa6BpTzk=";
+    hash = "sha256-5HU8kR3B2RHiGBraQ2FTgVtGHJi+Lha9U/7rpNsYCCI=";
   };
 
   patches = lib.optionals withGraphviz [
@@ -41,12 +41,7 @@ buildPythonPackage rec {
   ];
 
   nativeCheckInputs = [
-    pytestCheckHook
+    pytest7CheckHook
-  ];
-
-  pytestFlagsArray = [
-    # pytest.PytestRemovedIn8Warning: Support for nose tests is deprecated and will be removed in a future release.
-    "-W" "ignore::pytest.PytestRemovedIn8Warning"
   ];
 
   # Tests print “Fontconfig error: Cannot load default config file”

pkgs/development/python-modules/apsw/default.nix

@@ -1,6 +1,7 @@
 { lib
 , buildPythonPackage
 , fetchFromGitHub
+, setuptools
 , sqlite
 , isPyPy
 , python
@@ -8,8 +9,8 @@
 
 buildPythonPackage rec {
   pname = "apsw";
-  version = "3.45.1.0";
+  version = "3.45.2.0";
-  format = "setuptools";
+  pyproject = true;
 
   disabled = isPyPy;
 
@@ -17,9 +18,13 @@ buildPythonPackage rec {
     owner = "rogerbinns";
     repo = "apsw";
     rev = "refs/tags/${version}";
-    hash = "sha256-NkpkciLR2TgfK/7UQHEzvQu8qRj4UJyOlGQbiV23qrc=";
+    hash = "sha256-tTi3/10W4OoGH6PQVhvPWc5o09on5BZrWoAvrfh4C/E=";
   };
 
+  build-system = [
+    setuptools
+  ];
+
   buildInputs = [
     sqlite
   ];
@@ -36,6 +41,7 @@ buildPythonPackage rec {
   ];
 
   meta = with lib; {
+    changelog = "https://github.com/rogerbinns/apsw/blob/${src.rev}/doc/changes.rst";
     description = "A Python wrapper for the SQLite embedded relational database engine";
     homepage = "https://github.com/rogerbinns/apsw";
     license = licenses.zlib;

pkgs/development/python-modules/astropy/default.nix

@@ -5,7 +5,7 @@
 
 # build time
 , astropy-extension-helpers
-, cython_3
+, cython
 , jinja2
 , oldest-supported-numpy
 , setuptools-scm
@@ -37,7 +37,7 @@ buildPythonPackage rec {
 
   nativeBuildInputs = [
     astropy-extension-helpers
-    cython_3
+    cython
     jinja2
     oldest-supported-numpy
     setuptools-scm

pkgs/development/python-modules/aws-encryption-sdk/default.nix

@@ -41,16 +41,17 @@ buildPythonPackage rec {
     pytestCheckHook
   ];
 
-  pytestFlagsArray = [
-    "-W" "ignore::pytest.PytestRemovedIn8Warning"
-  ];
-
   disabledTestPaths = [
     # Tests require networking
     "examples"
     "test/integration"
   ];
 
+  disabledTests = [
+    # pytest 8 compat issue
+    "test_happy_version"
+  ];
+
   pythonImportsCheck = [
     "aws_encryption_sdk"
   ];

pkgs/development/python-modules/awswrangler/default.nix

@@ -19,6 +19,7 @@
 , pyparsing
 , pytestCheckHook
 , pythonOlder
+, pythonRelaxDepsHook
 , redshift-connector
 , requests-aws4auth
 }:
@@ -39,6 +40,11 @@ buildPythonPackage rec {
 
   nativeBuildInputs = [
     poetry-core
+    pythonRelaxDepsHook
+  ];
+
+  pythonRelaxDeps = [
+    "packaging"
   ];
 
   propagatedBuildInputs = [

pkgs/development/python-modules/barectf/default.nix

@@ -2,7 +2,7 @@
 , buildPythonPackage
 , fetchFromGitHub
 , poetry-core
-, pytestCheckHook
+, pytest7CheckHook
 , pythonRelaxDepsHook
 , setuptools
 , jsonschema
@@ -47,11 +47,7 @@ buildPythonPackage rec {
   ];
 
   nativeCheckInputs = [
-    pytestCheckHook
+    pytest7CheckHook
-  ];
-
-  pytestFlagsArray = [
-    "-W" "ignore::pytest.PytestRemovedIn8Warning"
   ];
 
   meta = with lib; {

pkgs/development/python-modules/betterproto/default.nix

@@ -10,7 +10,7 @@
 , isort
 , python
 , pydantic
-, pytestCheckHook
+, pytest7CheckHook
 , pytest-asyncio
 , pytest-mock
 , typing-extensions
@@ -53,7 +53,7 @@ buildPythonPackage rec {
     pydantic
     pytest-asyncio
     pytest-mock
-    pytestCheckHook
+    pytest7CheckHook
     tomlkit
   ] ++ lib.flatten (builtins.attrValues passthru.optional-dependencies);
 

pkgs/development/python-modules/blis/default.nix

@@ -2,7 +2,7 @@
 , buildPythonPackage
 , fetchFromGitHub
 , setuptools
-, cython
+, cython_0
 , hypothesis
 , numpy
 , pytestCheckHook
@@ -38,7 +38,7 @@ buildPythonPackage rec {
 
   nativeBuildInputs = [
     setuptools
-    cython
+    cython_0
   ];
 
   propagatedBuildInputs = [

pkgs/development/python-modules/blosc2/default.nix

@@ -4,7 +4,7 @@
 
 # build-system
 , cmake
-, cython_3
+, cython
 , ninja
 , oldest-supported-numpy
 , pkg-config
@@ -47,7 +47,7 @@ buildPythonPackage rec {
 
   nativeBuildInputs = [
     cmake
-    cython_3
+    cython
     ninja
     oldest-supported-numpy
     pkg-config

pkgs/development/python-modules/bluetooth-data-tools/default.nix

@@ -2,7 +2,7 @@
 , buildPythonPackage
 , fetchFromGitHub
 , cryptography
-, cython_3
+, cython
 , poetry-core
 , pytestCheckHook
 , pythonOlder
@@ -28,7 +28,7 @@ buildPythonPackage rec {
   env.REQUIRE_CYTHON = 1;
 
   nativeBuildInputs = [
-    cython_3
+    cython
     poetry-core
     setuptools
   ];

pkgs/development/python-modules/cached-ipaddress/default.nix

@@ -1,6 +1,6 @@
 { lib
 , buildPythonPackage
-, cython_3
+, cython
 , fetchFromGitHub
 , poetry-core
 , pytestCheckHook
@@ -30,7 +30,7 @@ buildPythonPackage rec {
   '';
 
   nativeBuildInputs = [
-    cython_3
+    cython
     poetry-core
     setuptools
     wheel

pkgs/development/python-modules/cassandra-driver/default.nix

@@ -2,7 +2,7 @@
 , stdenv
 , buildPythonPackage
 , cryptography
-, cython
+, cython_0
 , eventlet
 , fetchFromGitHub
 , geomet
@@ -43,7 +43,7 @@ buildPythonPackage rec {
   '';
 
   nativeBuildInputs = [
-    cython
+    cython_0
   ];
 
   buildInputs = [

pkgs/development/python-modules/certifi/default.nix

@@ -9,7 +9,7 @@
 
 buildPythonPackage rec {
   pname = "certifi";
-  version = "2023.11.17";
+  version = "2024.02.02";
   pyproject = true;
 
   disabled = pythonOlder "3.6";
@@ -18,7 +18,7 @@ buildPythonPackage rec {
     owner = pname;
     repo = "python-certifi";
     rev = version;
-    hash = "sha256-H3zsFJjWt2+tT7yqQOOZZwSL5y0AtfDz6Fqxwpm4Wl8=";
+    hash = "sha256-gnWJjZy5E/0lvAeLftXNtcHH6RHL/dUomXOBgumiWX8=";
   };
 
   patches = [

pkgs/development/python-modules/certifi/env.patch

@@ -1,13 +1,17 @@
 diff --git a/certifi/core.py b/certifi/core.py
-index de02898..c033d20 100644
+index 91f538b..1110ce0 100644
 --- a/certifi/core.py
 +++ b/certifi/core.py
-@@ -4,15 +4,25 @@ certifi.py
+@@ -4,6 +4,7 @@ certifi.py
  
  This module returns the installation location of cacert.pem or its contents.
  """
 +import os
  import sys
+ import atexit
+ 
+@@ -11,12 +12,21 @@ def exit_cacert_ctx() -> None:
+     _CACERT_CTX.__exit__(None, None, None)  # type: ignore[union-attr]
  
  
 +def get_cacert_path_from_environ():
@@ -29,17 +33,16 @@ index de02898..c033d20 100644
  
      def where() -> str:
          # This is slightly terrible, but we want to delay extracting the file
-@@ -39,14 +49,16 @@ if sys.version_info >= (3, 11):
+@@ -44,6 +54,8 @@ if sys.version_info >= (3, 11):
          return _CACERT_PATH
  
      def contents() -> str:
--        return files("certifi").joinpath("cacert.pem").read_text(encoding="ascii")
 +        if _CACERT_PATH is not None:
 +            return open(_CACERT_PATH, encoding="utf-8").read()
-+        return files("certifi").joinpath("cacert.pem").read_text(encoding="utf-8")
+         return files("certifi").joinpath("cacert.pem").read_text(encoding="ascii")
  
  elif sys.version_info >= (3, 7):
- 
+@@ -51,7 +63,7 @@ elif sys.version_info >= (3, 7):
      from importlib.resources import path as get_path, read_text
  
      _CACERT_CTX = None
@@ -48,7 +51,7 @@ index de02898..c033d20 100644
  
      def where() -> str:
          # This is slightly terrible, but we want to delay extracting the
-@@ -74,7 +86,9 @@ elif sys.version_info >= (3, 7):
+@@ -80,7 +92,9 @@ elif sys.version_info >= (3, 7):
          return _CACERT_PATH
  
      def contents() -> str:
@@ -59,7 +62,7 @@ index de02898..c033d20 100644
  
  else:
      import os
-@@ -84,6 +98,8 @@ else:
+@@ -90,6 +104,8 @@ else:
      Package = Union[types.ModuleType, str]
      Resource = Union[str, "os.PathLike"]
  
@@ -68,7 +71,7 @@ index de02898..c033d20 100644
      # This fallback will work for Python versions prior to 3.7 that lack the
      # importlib.resources module but relies on the existing `where` function
      # so won't address issues with environments like PyOxidizer that don't set
-@@ -102,7 +118,14 @@ else:
+@@ -108,7 +124,13 @@ else:
      def where() -> str:
          f = os.path.dirname(__file__)
  
@@ -78,9 +81,7 @@ index de02898..c033d20 100644
          return os.path.join(f, "cacert.pem")
  
      def contents() -> str:
--        return read_text("certifi", "cacert.pem", encoding="ascii")
 +        if _CACERT_PATH is not None:
 +            with open(_CACERT_PATH, encoding="utf-8") as data:
 +                return data.read()
-+
+         return read_text("certifi", "cacert.pem", encoding="ascii")
-+        return read_text("certifi", "cacert.pem", encoding="utf-8")

pkgs/development/python-modules/chacha20poly1305-reuseable/default.nix

@@ -4,7 +4,7 @@
 , pythonOlder
 
 # build-system
-, cython_3
+, cython
 , poetry-core
 , setuptools
 
@@ -34,7 +34,7 @@ buildPythonPackage {
   };
 
   nativeBuildInputs = [
-    cython_3
+    cython
     poetry-core
     setuptools
   ];

pkgs/development/python-modules/chalice/default.nix

@@ -10,7 +10,7 @@
 , mock
 , mypy-extensions
 , pip
-, pytestCheckHook
+, pytest7CheckHook
 , pythonOlder
 , pyyaml
 , requests
@@ -61,15 +61,11 @@ buildPythonPackage rec {
   nativeCheckInputs = [
     hypothesis
     mock
-    pytestCheckHook
+    pytest7CheckHook
     requests
     websocket-client
   ];
 
-  pytestFlagsArray = [
-    "-W" "ignore::pytest.PytestRemovedIn8Warning"
-  ];
-
   disabledTestPaths = [
     # Don't check the templates and the sample app
     "chalice/templates"

pkgs/development/python-modules/chart-studio/default.nix

@@ -21,7 +21,7 @@ buildPythonPackage rec {
     owner = "plotly";
     repo = "plotly.py";
     rev = "refs/tags/v${version}";
-    hash = "sha256-LSZGaefxQC6h9VAJ2wgZyaQPR6vs0wrp2oxd51I3pL8=";
+    hash = "sha256-i//LKTNmoIrusBnpfSGc9cDijPxg/dY/7fumV3kfTAY=";
   };
 
   sourceRoot = "${src.name}/packages/python/chart-studio";

pkgs/development/python-modules/chex/default.nix

@@ -2,6 +2,7 @@
 , buildPythonPackage
 , pythonOlder
 , fetchFromGitHub
+, setuptools
 , absl-py
 , cloudpickle
 , dm-tree
@@ -15,8 +16,8 @@
 
 buildPythonPackage rec {
   pname = "chex";
-  version = "0.1.85";
+  version = "0.1.86";
-  format = "setuptools";
+  pyproject = true;
 
   disabled = pythonOlder "3.9";
 
@@ -24,10 +25,14 @@ buildPythonPackage rec {
     owner = "deepmind";
     repo = "chex";
     rev = "refs/tags/v${version}";
-    hash = "sha256-7k/+2dNNbPBXtbabuOEVpAI7T1SuM4JDf074dmTg/vs=";
+    hash = "sha256-Z5Ns4fG5pC99I4xdGjDMKX6YZpTtd1y0TWcIOtr7dug=";
   };
 
-  propagatedBuildInputs = [
+  build-system = [
+    setuptools
+  ];
+
+  dependencies = [
     absl-py
     jaxlib
     jax

pkgs/development/python-modules/clickhouse-cityhash/default.nix

@@ -1,6 +1,6 @@
 { lib
 , buildPythonPackage
-, cython_3
+, cython
 , fetchPypi
 , pythonOlder
 , setuptools
@@ -19,7 +19,7 @@ buildPythonPackage rec {
   };
 
   nativeBuildInputs = [
-    cython_3
+    cython
     setuptools
   ];
 

pkgs/development/python-modules/clickhouse-connect/default.nix

@@ -4,7 +4,7 @@
 , pythonOlder
 , pytestCheckHook
   # build_requires
-, cython_3
+, cython
   # install_requires
 , certifi
 , importlib-metadata
@@ -36,7 +36,7 @@ buildPythonPackage rec {
     hash = "sha256-YEtcM9+GO8mYv2pyaBYmXdmWLXVuteKtQIJR4H+Xsd4=";
   };
 
-  nativeBuildInputs = [ cython_3 ];
+  nativeBuildInputs = [ cython ];
   setupPyBuildFlags = [ "--inplace" ];
   enableParallelBuilding = true;
 

pkgs/development/python-modules/clickhouse-driver/default.nix

@@ -1,7 +1,7 @@
 { lib
 , buildPythonPackage
 , clickhouse-cityhash
-, cython_3
+, cython
 , fetchFromGitHub
 , freezegun
 , lz4
@@ -29,7 +29,7 @@ buildPythonPackage rec {
   };
 
   nativeBuildInputs = [
-    cython_3
+    cython
     setuptools
   ];
 

pkgs/development/python-modules/cloudpathlib/default.nix

@@ -11,8 +11,7 @@
 , boto3
 , psutil
 , pydantic
-, pytestCheckHook
+, pytest7CheckHook
-, pytest_7
 , pytest-cases
 , pytest-cov
 , pytest-xdist
@@ -66,7 +65,7 @@ buildPythonPackage rec {
     google-cloud-storage
     psutil
     pydantic
-    (pytestCheckHook.override { pytest = pytest_7; })
+    pytest7CheckHook
     pytest-cases
     pytest-cov
     pytest-xdist

pkgs/development/python-modules/colorcet/default.nix

@@ -1,6 +1,8 @@
 { lib
 , buildPythonPackage
 , fetchPypi
+, setuptools
+, setuptools-scm
 , param
 , pyct
 , pytest-mpl
@@ -10,14 +12,19 @@
 buildPythonPackage rec {
   pname = "colorcet";
   version = "3.1.0";
-  format = "setuptools";
+  pyproject = true;
 
   src = fetchPypi {
     inherit pname version;
     hash = "sha256-KSGzzYGiKIqvLWPbwM48JtzYgujDicxQXWiGv3qppOs=";
   };
 
-  propagatedBuildInputs = [
+  build-system = [
+    setuptools
+    setuptools-scm
+  ];
+
+  dependencies = [
     param
     pyct
   ];

pkgs/development/python-modules/cpyparsing/default.nix

@@ -1,7 +1,7 @@
 { lib
 , buildPythonPackage
 , fetchFromGitHub
-, cython_3
+, cython
 , pexpect
 , python
 , pythonOlder
@@ -23,7 +23,7 @@ buildPythonPackage rec {
   };
 
   nativeBuildInputs = [
-    cython_3
+    cython
     setuptools
   ];
 

pkgs/development/python-modules/cssutils/default.nix

@@ -1,8 +1,6 @@
 { lib
 , buildPythonPackage
-, pythonAtLeast
 , pythonOlder
-, fetchpatch
 , fetchPypi
 , setuptools
 , setuptools-scm
@@ -10,7 +8,7 @@
 , jaraco-test
 , lxml
 , mock
-, pytestCheckHook
+, pytest7CheckHook
 , importlib-resources
 }:
 
@@ -37,16 +35,11 @@ buildPythonPackage rec {
     jaraco-test
     lxml
     mock
-    pytestCheckHook
+    pytest7CheckHook
   ] ++ lib.optionals (pythonOlder "3.9") [
     importlib-resources
   ];
 
-  pytestFlagsArray = [
-    # pytest.PytestRemovedIn8Warning: Support for nose tests is deprecated and will be removed in a future release.
-    "-W" "ignore::pytest.PytestRemovedIn8Warning"
-  ];
-
   disabledTests = [
     # access network
     "test_parseUrl"

pkgs/development/python-modules/cypari2/default.nix

@@ -5,7 +5,7 @@
 , fetchPypi
 , pari
 , gmp
-, cython_3
+, cython
 , cysignals
 }:
 
@@ -45,7 +45,7 @@ buildPythonPackage rec {
 
   propagatedBuildInputs = [
     cysignals
-    cython_3
+    cython
   ];
 
   checkPhase = ''

pkgs/development/python-modules/cysignals/default.nix

@@ -2,7 +2,7 @@
 , autoreconfHook
 , fetchPypi
 , buildPythonPackage
-, cython_3
+, cython
 , pariSupport ? true, pari # for interfacing with the PARI/GP signal handler
 }:
 
@@ -34,7 +34,7 @@ buildPythonPackage rec {
   '';
 
   propagatedBuildInputs = [
-    cython_3
+    cython
   ] ++ lib.optionals pariSupport [
     # When cysignals is built with pari, including cysignals into the
     # buildInputs of another python package will cause cython to link against

pkgs/development/python-modules/cython/0.nix

@@ -0,0 +1,91 @@
+{ lib
+, stdenv
+, buildPythonPackage
+, fetchPypi
+, fetchpatch
+, setuptools
+, python
+, pkg-config
+, gdb
+, numpy
+, ncurses
+}:
+
+let
+  excludedTests = [ "reimport_from_subinterpreter" ]
+    # cython's testsuite is not working very well with libc++
+    # We are however optimistic about things outside of testsuite still working
+    ++ lib.optionals (stdenv.cc.isClang or false) [ "cpdef_extern_func" "libcpp_algo" ]
+    # Some tests in the test suite isn't working on aarch64. Disable them for
+    # now until upstream finds a workaround.
+    # Upstream issue here: https://github.com/cython/cython/issues/2308
+    ++ lib.optionals stdenv.isAarch64 [ "numpy_memoryview" ]
+    ++ lib.optionals stdenv.isi686 [ "future_division" "overflow_check_longlong" ]
+  ;
+
+in buildPythonPackage rec {
+  pname = "cython";
+  version = "0.29.36";
+  pyproject = true;
+
+  src = fetchPypi {
+    pname = "Cython";
+    inherit version;
+    hash = "sha256-QcDP0tdU44PJ7rle/8mqSrhH0Ml0cHfd18Dctow7wB8=";
+  };
+
+  nativeBuildInputs = [
+    pkg-config
+    setuptools
+  ];
+
+  nativeCheckInputs = [
+    gdb numpy ncurses
+  ];
+
+  LC_ALL = "en_US.UTF-8";
+
+  patches = [
+    # backport Cython 3.0 trashcan support (https://github.com/cython/cython/pull/2842) to 0.X series.
+    # it does not affect Python code unless the code explicitly uses the feature.
+    # trashcan support is needed to avoid stack overflows during object deallocation in sage (https://trac.sagemath.org/ticket/27267)
+    ./trashcan.patch
+    # The above commit introduces custom trashcan macros, as well as
+    # compiler changes to use them in Cython-emitted code. The latter
+    # change is still useful, but the former has been upstreamed as of
+    # Python 3.8, and the patch below makes Cython use the upstream
+    # trashcan macros whenever available. This is needed for Python
+    # 3.11 support, because the API used in Cython's implementation
+    # changed: https://github.com/cython/cython/pull/4475
+    (fetchpatch {
+      name = "disable-trashcan.patch";
+      url = "https://github.com/cython/cython/commit/e337825cdcf5e94d38ba06a0cb0188e99ce0cc92.patch";
+      hash = "sha256-q0f63eetKrDpmP5Z4v8EuGxg26heSyp/62OYqhRoSso=";
+    })
+  ];
+
+  checkPhase = ''
+    export HOME="$NIX_BUILD_TOP"
+    ${python.interpreter} runtests.py -j$NIX_BUILD_CORES \
+      --no-code-style \
+      ${lib.optionalString (builtins.length excludedTests != 0)
+        ''--exclude="(${builtins.concatStringsSep "|" excludedTests})"''}
+  '';
+
+  # https://github.com/cython/cython/issues/2785
+  # Temporary solution
+  doCheck = false;
+  # doCheck = !stdenv.isDarwin;
+
+  # force regeneration of generated code in source distributions
+  # https://github.com/cython/cython/issues/5089
+  setupHook = ./setup-hook.sh;
+
+  meta = {
+    changelog = "https://github.com/cython/cython/blob/${version}/CHANGES.rst";
+    description = "An optimising static compiler for both the Python programming language and the extended Cython programming language";
+    homepage = "https://cython.org";
+    license = lib.licenses.asl20;
+    maintainers = with lib.maintainers; [ fridh ];
+  };
+}

pkgs/development/python-modules/cython/default.nix

@@ -2,7 +2,6 @@
 , stdenv
 , buildPythonPackage
 , fetchPypi
-, fetchpatch
 , setuptools
 , python
 , pkg-config
@@ -25,16 +24,16 @@ let
 
 in buildPythonPackage rec {
   pname = "cython";
-  version = "0.29.36";
+  version = "3.0.9";
   pyproject = true;
 
   src = fetchPypi {
     pname = "Cython";
     inherit version;
-    hash = "sha256-QcDP0tdU44PJ7rle/8mqSrhH0Ml0cHfd18Dctow7wB8=";
+    hash = "sha256-otNU8FnR8FXTTPqmLFtovHisLOq2QHFI1H+1CM87pPM=";
   };
 
-  nativeBuildInputs = [
+  build-system = [
     pkg-config
     setuptools
   ];
@@ -43,26 +42,7 @@ in buildPythonPackage rec {
     gdb numpy ncurses
   ];
 
-  LC_ALL = "en_US.UTF-8";
+  env.LC_ALL = "en_US.UTF-8";
-
-  patches = [
-    # backport Cython 3.0 trashcan support (https://github.com/cython/cython/pull/2842) to 0.X series.
-    # it does not affect Python code unless the code explicitly uses the feature.
-    # trashcan support is needed to avoid stack overflows during object deallocation in sage (https://trac.sagemath.org/ticket/27267)
-    ./trashcan.patch
-    # The above commit introduces custom trashcan macros, as well as
-    # compiler changes to use them in Cython-emitted code. The latter
-    # change is still useful, but the former has been upstreamed as of
-    # Python 3.8, and the patch below makes Cython use the upstream
-    # trashcan macros whenever available. This is needed for Python
-    # 3.11 support, because the API used in Cython's implementation
-    # changed: https://github.com/cython/cython/pull/4475
-    (fetchpatch {
-      name = "disable-trashcan.patch";
-      url = "https://github.com/cython/cython/commit/e337825cdcf5e94d38ba06a0cb0188e99ce0cc92.patch";
-      hash = "sha256-q0f63eetKrDpmP5Z4v8EuGxg26heSyp/62OYqhRoSso=";
-    })
-  ];
 
   checkPhase = ''
     export HOME="$NIX_BUILD_TOP"

pkgs/development/python-modules/daqp/default.nix

@@ -1,9 +1,8 @@
 { lib
-, stdenv
 , fetchFromGitHub
 , buildPythonPackage
 , unittestCheckHook
-, cython
+, cython_0
 , setuptools
 , wheel
 , numpy
@@ -32,7 +31,7 @@ buildPythonPackage rec {
   unittestFlagsArray = [ "-s" "test" "-p" "'*.py'" "-v" ];
 
   nativeBuildInputs = [
-    cython
+    cython_0
     setuptools
     wheel
   ];

pkgs/development/python-modules/dask/default.nix

@@ -38,7 +38,7 @@
 
 buildPythonPackage rec {
   pname = "dask";
-  version = "2024.1.1";
+  version = "2024.2.1";
   pyproject = true;
 
   disabled = pythonOlder "3.9";
@@ -47,7 +47,7 @@ buildPythonPackage rec {
     owner = "dask";
     repo = "dask";
     rev = "refs/tags/${version}";
-    hash = "sha256-L8bRh2bx36CYrAFXYJF67rCeCRfm5ufhTkMFRJo0yYo=";
+    hash = "sha256-8VFtKPaF0PqCjqFB+plFe1GjUno5j7j86+wxKhzByyw=";
   };
 
   nativeBuildInputs = [
@@ -127,8 +127,6 @@ buildPythonPackage rec {
     "--reruns 3"
     # Don't run tests that require network access
     "-m 'not network'"
-    # pytest.PytestRemovedIn8Warning: Passing None has been deprecated.
-    "-W" "ignore::pytest.PytestRemovedIn8Warning"
   ];
 
   disabledTests = lib.optionals stdenv.isDarwin [

pkgs/development/python-modules/dbt-core/default.nix

@@ -58,6 +58,7 @@ buildPythonPackage rec {
     "mashumaro"
     "networkx"
     "logbook"
+    "pathspec"
     "urllib3"
   ];
 

pkgs/development/python-modules/dbus-fast/default.nix

@@ -1,7 +1,7 @@
 { lib
 , async-timeout
 , buildPythonPackage
-, cython_3
+, cython
 , fetchFromGitHub
 , poetry-core
 , pytest-asyncio
@@ -30,7 +30,7 @@ buildPythonPackage rec {
   env.REQUIRE_CYTHON = 1;
 
   nativeBuildInputs = [
-    cython_3
+    cython
     poetry-core
     setuptools
     wheel

pkgs/development/python-modules/deal/default.nix

@@ -19,7 +19,7 @@
 
 buildPythonPackage rec {
   pname = "deal";
-  version = "4.24.3";
+  version = "4.24.4";
   format = "pyproject";
   disabled = pythonOlder "3.7";
 
@@ -27,7 +27,7 @@ buildPythonPackage rec {
     owner = "life4";
     repo = pname;
     rev = "refs/tags/${version}";
-    hash = "sha256-QlM3d/jmg6v3L3D45+cgcCej71U1dl4uZ6sAYGGm3tU=";
+    hash = "sha256-4orpoYfPGSvquhg9w63uUe8QbBa2RUpxaEJ9uy28+fU=";
   };
 
   postPatch = ''
@@ -62,10 +62,6 @@ buildPythonPackage rec {
     flake8
   ];
 
-  pytestFlagsArray = [
-    "-W" "ignore::pytest.PytestRemovedIn8Warning"
-  ];
-
   disabledTests = [
     # needs internet access
     "test_smoke_has"

pkgs/development/python-modules/demes/default.nix

@@ -5,7 +5,7 @@
 , ruamel-yaml
 , attrs
 , pythonOlder
-, pytestCheckHook
+, pytest7CheckHook
 , pytest-xdist
 , numpy
 }:
@@ -36,16 +36,11 @@ buildPythonPackage rec {
   '';
 
   nativeCheckInputs = [
-    pytestCheckHook
+    pytest7CheckHook
     pytest-xdist
     numpy
   ];
 
-  pytestFlagsArray = [
-    # pytest.PytestRemovedIn8Warning: Passing None has been deprecated.
-    "-W" "ignore::pytest.PytestRemovedIn8Warning"
-  ];
-
   disabledTestPaths = [
     "tests/test_spec.py"
   ];

pkgs/development/python-modules/detect-secrets/default.nix

@@ -5,7 +5,7 @@
 , mock
 , pkgs
 , pyahocorasick
-, pytestCheckHook
+, pytest7CheckHook
 , pythonOlder
 , pyyaml
 , requests
@@ -37,17 +37,12 @@ buildPythonPackage rec {
 
   nativeCheckInputs = [
     mock
-    pytestCheckHook
+    pytest7CheckHook
     responses
     unidiff
     pkgs.gitMinimal
   ];
 
-  pytestFlagsArray = [
-    # Pytest.PytestRemovedIn8Warning: Support for nose tests is deprecated and will be removed in a future release.
-    "-W" "ignore::pytest.PytestRemovedIn8Warning"
-  ];
-
   preCheck = ''
     export HOME=$(mktemp -d);
   '';

pkgs/development/python-modules/devtools/default.nix

@@ -39,11 +39,6 @@ buildPythonPackage rec {
     pytest-mock
   ];
 
-  pytestFlagsArray = [
-    # pytest.PytestRemovedIn8Warning: Passing None has been deprecated.
-    "-W ignore::pytest.PytestRemovedIn8Warning"
-  ];
-
   disabledTests = [
     # Test for Windows32
     "test_print_subprocess"

pkgs/development/python-modules/diffsync/default.nix

@@ -27,6 +27,11 @@ buildPythonPackage rec {
     pythonRelaxDepsHook
   ];
 
+  pythonRelaxDeps = [
+    "packaging"
+    "structlog"
+  ];
+
   propagatedBuildInputs = [
     colorama
     packaging
@@ -35,10 +40,6 @@ buildPythonPackage rec {
     structlog
   ];
 
-  pythonRelaxDeps = [
-    "structlog"
-  ];
-
   pythonImportsCheck = [
     "diffsync"
   ];

pkgs/development/python-modules/django-filter/default.nix

@@ -6,22 +6,22 @@
 , djangorestframework
 , pytestCheckHook
 , pytest-django
-, python
+, pytz
 }:
 
 buildPythonPackage rec {
   pname = "django-filter";
-  version = "23.5";
+  version = "24.1";
-  format = "pyproject";
+  pyproject = true;
 
   src = fetchPypi {
     inherit pname version;
-    hash = "sha256-Z1g6pDuR/oxJ90qDLZX02EQr5ij9TG1l6fgR9RU6Tlw=";
+    hash = "sha256-ZctDzicgd+Wsaq4QVNdsEhzWtVLilqgqE5Iek3G6+ME=";
   };
 
-  nativeBuildInputs = [ flit-core ];
+  build-system = [ flit-core ];
 
-  propagatedBuildInputs = [ django ];
+  dependencies = [ django ];
 
   pythonImportsCheck = [
     "django_filters"
@@ -31,6 +31,7 @@ buildPythonPackage rec {
     djangorestframework
     pytestCheckHook
     pytest-django
+    pytz
   ];
 
   env.DJANGO_SETTINGS_MODULE = "tests.settings";

pkgs/development/python-modules/djangorestframework/default.nix

@@ -6,7 +6,7 @@
 , django-guardian
 , pythonOlder
 , pytest-django
-, pytestCheckHook
+, pytest7CheckHook
 , pytz
 , pyyaml
 , uritemplate
@@ -32,7 +32,7 @@ buildPythonPackage rec {
 
   nativeCheckInputs = [
     pytest-django
-    pytestCheckHook
+    pytest7CheckHook
 
     # optional tests
     coreapi
@@ -41,11 +41,6 @@ buildPythonPackage rec {
     uritemplate
   ];
 
-  pytestFlagsArray = [
-    # ytest.PytestRemovedIn8Warning: Support for nose tests is deprecated and will be removed in a future release.
-    "-W" "ignore::pytest.PytestRemovedIn8Warning"
-  ];
-
   pythonImportsCheck = [ "rest_framework" ];
 
   meta = with lib; {

pkgs/development/python-modules/dtlssocket/default.nix

@@ -2,7 +2,7 @@
 , buildPythonPackage
 , fetchPypi
 , autoconf
-, cython
+, cython_0
 , setuptools
 }:
 
@@ -20,7 +20,7 @@ buildPythonPackage rec {
 
   nativeBuildInputs = [
     autoconf
-    cython
+    cython_0
     setuptools
   ];
 

pkgs/development/python-modules/ed25519/default.nix

@@ -1,10 +1,13 @@
-{ lib, fetchPypi, buildPythonPackage }:
+{ lib, fetchPypi, buildPythonPackage, pythonAtLeast }:
 
 buildPythonPackage rec {
   pname = "ed25519";
   version = "1.5";
   format = "setuptools";
 
+  # last commit in 2019, various compat issues with 3.12
+  disabled = pythonAtLeast "3.12";
+
   src = fetchPypi {
     inherit pname version;
     sha256 = "0n1k83ww0pr4q6z0h7p8hvy21hcgb96jvgllfbwhvvyf37h3w182";

pkgs/development/python-modules/editdistance/default.nix

@@ -2,7 +2,7 @@
 , buildPythonPackage
 , fetchFromGitHub
 , pytestCheckHook
-, cython_3
+, cython
 , pdm-backend
 , setuptools
 , pythonOlder
@@ -23,7 +23,7 @@ buildPythonPackage rec {
   };
 
   nativeBuildInputs = [
-    cython_3
+    cython
     pdm-backend
     setuptools
   ];

pkgs/development/python-modules/editdistpy/default.nix

@@ -7,7 +7,7 @@
 , pythonOlder
 
 , setuptools
-, cython_3
+, cython
 
 , symspellpy
 , numpy
@@ -30,7 +30,7 @@ buildPythonPackage rec {
 
   build-system = [
     setuptools
-    cython_3
+    cython
   ];
 
   # error: infinite recursion encountered

pkgs/development/python-modules/falcon/default.nix

@@ -6,7 +6,7 @@
 , fetchFromGitHub
 
 # build
-, cython_3
+, cython
 , setuptools
 
 # tests
@@ -17,8 +17,7 @@
 , mujson
 , orjson
 , pytest-asyncio
-, pytestCheckHook
+, pytest7CheckHook
-, pytest_7
 , pyyaml
 , rapidjson
 , requests
@@ -44,7 +43,7 @@ buildPythonPackage rec {
   nativeBuildInputs = [
     setuptools
   ] ++ lib.optionals (!isPyPy) [
-    cython_3
+    cython
   ];
 
   __darwinAllowLocalNetworking = true;
@@ -61,7 +60,7 @@ buildPythonPackage rec {
 
   nativeCheckInputs = [
     # https://github.com/falconry/falcon/blob/master/requirements/tests
-    (pytestCheckHook.override { pytest = pytest_7; })
+    pytest7CheckHook
     pyyaml
     requests
     rapidjson

pkgs/development/python-modules/fastjsonschema/default.nix

@@ -2,13 +2,14 @@
 , stdenv
 , buildPythonPackage
 , fetchFromGitHub
+, fetchpatch2
 , pytestCheckHook
 , pythonOlder
 }:
 
 buildPythonPackage rec {
   pname = "fastjsonschema";
-  version = "2.18.1";
+  version = "2.19.1";
   format = "setuptools";
 
   disabled = pythonOlder "3.7";
@@ -18,17 +19,21 @@ buildPythonPackage rec {
     repo = "python-fastjsonschema";
     rev = "v${version}";
     fetchSubmodules = true;
-    hash = "sha256-t6JnqQgsWAL8oL8+LO0xrXMYsZOlTF3DlXkRiqUzYtU=";
+    hash = "sha256-UxcxVB4ldnGAYJKWEccivon1CwZD588mNiVJOJPNeN8=";
   };
 
+  patches = [
+    (fetchpatch2 {
+      name = "fastjsonschema-pytest8-compat.patch";
+      url = "https://github.com/horejsek/python-fastjsonschema/commit/efc04daf4124a598182dfcfd497615cd1e633d18.patch";
+      hash = "sha256-G1/PIpdN+KFfRP9pUFf/ANXLq3mzrocEHyBNWQMVOZM=";
+    })
+  ];
+
   nativeCheckInputs = [
     pytestCheckHook
   ];
 
-  pytestFlagsArray = [
-    "-W" "ignore::pytest.PytestRemovedIn8Warning"
-  ];
-
   dontUseSetuptoolsCheck = true;
 
   disabledTests = [

pkgs/development/python-modules/favicon/default.nix

@@ -2,7 +2,7 @@
 , beautifulsoup4
 , buildPythonPackage
 , fetchPypi
-, pytestCheckHook
+, pytest7CheckHook
 , pythonOlder
 , requests
 , requests-mock
@@ -30,14 +30,10 @@ buildPythonPackage rec {
   ];
 
   nativeCheckInputs = [
-    pytestCheckHook
+    pytest7CheckHook
     requests-mock
   ];
 
-  pytestFlagsArray = [
-    "-W" "ignore::pytest.PytestRemovedIn8Warning"
-  ];
-
   pythonImportsCheck = [
     "favicon"
   ];

pkgs/development/python-modules/fiona/default.nix

@@ -2,7 +2,7 @@
 , buildPythonPackage
 , pythonOlder
 , fetchFromGitHub
-, cython_3
+, cython
 , gdal
 , oldest-supported-numpy
 , setuptools
@@ -34,7 +34,7 @@ buildPythonPackage rec {
   };
 
   nativeBuildInputs = [
-    cython_3
+    cython
     gdal # for gdal-config
     oldest-supported-numpy
     setuptools

pkgs/development/python-modules/flaky/default.nix

@@ -1,20 +1,25 @@
 { lib
 , buildPythonPackage
 , fetchPypi
+, setuptools
 , mock
 , pytest
 }:
 
 buildPythonPackage rec {
   pname = "flaky";
-  version = "3.7.0";
+  version = "3.8.1";
-  format = "setuptools";
+  pyproject = true;
 
   src = fetchPypi {
     inherit pname version;
-    hash = "sha256-OtEAeAchoZEfV6FlgJt+omWnhjMFrLZnCCIIIMr4qg0=";
+    hash = "sha256-RyBKgeyQXz1az71h2uq8raj51AMWFtm8sGGEYXKWmfU=";
   };
 
+  build-system = [
+    setuptools
+  ];
+
   nativeCheckInputs = [
     mock
     pytest
@@ -29,6 +34,7 @@ buildPythonPackage rec {
   '';
 
   meta = with lib; {
+    changelog = "https://github.com/box/flaky/blob/v${version}/HISTORY.rst";
     homepage = "https://github.com/box/flaky";
     description = "Plugin for nose or py.test that automatically reruns flaky tests";
     license = licenses.asl20;

pkgs/development/python-modules/flet/default.nix

@@ -36,9 +36,10 @@ buildPythonPackage rec {
   ];
 
   pythonRelaxDeps = [
-    "websockets"
     "cookiecutter"
+    "packaging"
     "watchdog"
+    "websockets"
   ];
 
   propagatedBuildInputs = [

pkgs/development/python-modules/flexmock/default.nix

@@ -3,32 +3,33 @@
 , fetchPypi
 , pytestCheckHook
 , pythonOlder
+, poetry-core
 , teamcity-messages
 , testtools
 }:
 
 buildPythonPackage rec {
   pname = "flexmock";
-  version = "0.11.3";
+  version = "0.12.0";
-  format = "setuptools";
+  pyproject = true;
 
   disabled = pythonOlder "3.6";
 
   src = fetchPypi {
     inherit pname version;
-    hash = "sha256-sf419qXzJUe1zTGhXAYNmrhj3Aiv8BjNc9x40bZR7dQ=";
+    hash = "sha256-YdBvPRRCuBW3qoWh9HvoONBW9fXRTO/teuv7A0c9FKs=";
   };
 
+  build-system = [
+    poetry-core
+  ];
+
   nativeCheckInputs = [
     pytestCheckHook
     teamcity-messages
     testtools
   ];
 
-  disabledTests = [
-    "test_failed_test_case"
-  ];
-
   pythonImportsCheck = [
     "flexmock"
   ];

pkgs/development/python-modules/flow-record/default.nix

@@ -5,8 +5,7 @@
 , fetchFromGitHub
 , lz4
 , msgpack
-, pytestCheckHook
+, pytest7CheckHook
-, pytest_7
 , pythonOlder
 , setuptools
 , setuptools-scm
@@ -52,7 +51,7 @@ buildPythonPackage rec {
   };
 
   nativeCheckInputs = [
-    (pytestCheckHook.override { pytest = pytest_7; })
+    pytest7CheckHook
   ] ++ lib.flatten (builtins.attrValues passthru.optional-dependencies);
 
   pythonImportsCheck = [

pkgs/development/python-modules/fonttools/default.nix

@@ -21,8 +21,7 @@
 , xattr
 , skia-pathops
 , uharfbuzz
-, pytestCheckHook
+, pytest7CheckHook
-, pytest_7
 }:
 
 buildPythonPackage rec {
@@ -65,7 +64,7 @@ buildPythonPackage rec {
   nativeCheckInputs = [
     # test suite fails with pytest>=8.0.1
     # https://github.com/fonttools/fonttools/issues/3458
-    (pytestCheckHook.override { pytest = pytest_7; })
+    pytest7CheckHook
   ] ++ lib.concatLists (lib.attrVals ([
     "woff"
     # "interpolatable" is not included because it only contains 2 tests at the time of writing but adds 270 extra dependencies

pkgs/development/python-modules/fpylll/default.nix

@@ -5,7 +5,7 @@
 
 # build-system
 , cysignals
-, cython_3
+, cython
 , pkgconfig
 , setuptools
 
@@ -43,7 +43,7 @@ buildPythonPackage rec {
   ];
 
   nativeBuildInputs = [
-    cython_3
+    cython
     cysignals
     pkgconfig
     setuptools

pkgs/development/python-modules/frozenlist/default.nix

@@ -1,6 +1,6 @@
 { lib
 , buildPythonPackage
-, cython_3
+, cython
 , expandvars
 , fetchFromGitHub
 , pep517
@@ -30,7 +30,7 @@ buildPythonPackage rec {
 
   nativeBuildInputs = [
     expandvars
-    cython_3
+    cython
     pep517
     setuptools
     wheel

pkgs/development/python-modules/fugashi/default.nix

@@ -3,7 +3,7 @@
 , pythonOlder
 , pytestCheckHook
 , buildPythonPackage
-, cython
+, cython_0
 , mecab
 , setuptools-scm
 , ipadic
@@ -24,7 +24,7 @@ buildPythonPackage rec {
     hash = "sha256-4i7Q+TtXTQNSJ1EIcS8KHrVPdCJAgZh86Y6lB8772XU=";
   };
 
-  nativeBuildInputs = [ cython mecab setuptools-scm ];
+  nativeBuildInputs = [ cython_0 mecab setuptools-scm ];
 
   nativeCheckInputs = [ ipadic pytestCheckHook ]
     ++ passthru.optional-dependencies.unidic-lite;

pkgs/development/python-modules/gbinder-python/default.nix

@@ -1,7 +1,7 @@
 { lib
 , fetchFromGitHub
 , buildPythonPackage
-, cython
+, cython_0
 , pkg-config
 , libgbinder
 }:
@@ -23,7 +23,7 @@ buildPythonPackage rec {
   ];
 
   nativeBuildInputs = [
-    cython
+    cython_0
     pkg-config
   ];
 

pkgs/development/python-modules/gevent/default.nix

@@ -5,7 +5,7 @@
 , python
 , libev
 , cffi
-, cython_3
+, cython
 , greenlet
 , importlib-metadata
 , setuptools
@@ -34,7 +34,7 @@ buildPythonPackage rec {
   };
 
   nativeBuildInputs = [
-    cython_3
+    cython
     setuptools
     wheel
   ] ++ lib.optionals (!isPyPy) [

pkgs/development/python-modules/graphene-django/default.nix

@@ -1,7 +1,6 @@
 { stdenv
 , lib
 , buildPythonPackage
-, pythonAtLeast
 , pythonOlder
 , fetchFromGitHub
 
@@ -17,7 +16,7 @@
 , py
 , pytest-django
 , pytest-random-order
-, pytestCheckHook
+, pytest7CheckHook
 }:
 
 buildPythonPackage rec {
@@ -58,20 +57,15 @@ buildPythonPackage rec {
     py
     pytest-django
     pytest-random-order
-    pytestCheckHook
+    pytest7CheckHook
   ];
 
-  pytestFlagsArray = [
+  disabledTests = [
-    # pytest.PytestRemovedIn8Warning: Passing None has been deprecated.
+    # https://github.com/graphql-python/graphene-django/issues/1510
-    "-W" "ignore::pytest.PytestRemovedIn8Warning"
+    "test_should_filepath_convert_string"
-  ];
+    "test_should_choice_convert_enum"
-
+    "test_should_multiplechoicefield_convert_to_list_of_enum"
-  disabledTests = lib.optionals (pythonAtLeast "3.11") [
+    "test_perform_mutate_success_with_enum_choice_field"
-    # Python 3.11 support, https://github.com/graphql-python/graphene-django/pull/1365
-    "test_django_objecttype_convert_choices_enum_naming_collisions"
-    "test_django_objecttype_choices_custom_enum_name"
-    "test_django_objecttype_convert_choices_enum_list"
-    "test_schema_representation"
   ] ++ lib.optionals stdenv.isDarwin [
     # this test touches files in the "/" directory and fails in darwin sandbox
     "test_should_filepath_convert_string"

pkgs/development/python-modules/graphene/default.nix

@@ -8,7 +8,7 @@
 , pytest-asyncio
 , pytest-benchmark
 , pytest-mock
-, pytestCheckHook
+, pytest7CheckHook
 , pythonOlder
 , pytz
 , snapshottest
@@ -39,7 +39,7 @@ buildPythonPackage rec {
   ];
 
   nativeCheckInputs = [
-    pytestCheckHook
+    pytest7CheckHook
     pytest-asyncio
     pytest-benchmark
     pytest-mock
@@ -49,7 +49,6 @@ buildPythonPackage rec {
 
   pytestFlagsArray = [
     "--benchmark-disable"
-    "-W ignore::pytest.PytestRemovedIn8Warning"
   ];
 
   pythonImportsCheck = [

pkgs/development/python-modules/h5py/default.nix

@@ -7,7 +7,7 @@
 , wheel
 , numpy
 , hdf5
-, cython
+, cython_0
 , pkgconfig
 , mpi4py ? null
 , openssh
@@ -50,7 +50,7 @@ in buildPythonPackage rec {
   preBuild = lib.optionalString mpiSupport "export CC=${lib.getDev mpi}/bin/mpicc";
 
   nativeBuildInputs = [
-    cython
+    cython_0
     oldest-supported-numpy
     pkgconfig
     setuptools

pkgs/development/python-modules/hatchling/default.nix

@@ -20,13 +20,13 @@
 
 buildPythonPackage rec {
   pname = "hatchling";
-  version = "1.21.1";
+  version = "1.22.4";
   format = "pyproject";
   disabled = pythonOlder "3.8";
 
   src = fetchPypi {
     inherit pname version;
-    hash = "sha256-u6RARToiTn1EeEV/oujYw2M3Zbr6Apdaa1O5v5F5gLw=";
+    hash = "sha256-ii3OyW1/uEg4LvWEjlrEP9rmQfNaCKP6tRFr1JXzQW4=";
   };
 
   # listed in backend/pyproject.toml

pkgs/development/python-modules/hid-parser/default.nix

@@ -2,7 +2,7 @@
 , buildPythonPackage
 , fetchPypi
 , setuptools
-, pytestCheckHook
+, pytest7CheckHook
 , hypothesis
 }:
 
@@ -21,14 +21,10 @@ buildPythonPackage rec {
   ];
 
   nativeCheckInputs = [
-    pytestCheckHook
+    pytest7CheckHook
     hypothesis
   ];
 
-  pytestFlagsArray = [
-    "-W" "ignore::pytest.PytestRemovedIn8Warning"
-  ];
-
   pythonImportsCheck = [ "hid_parser" ];
 
   meta = with lib; {

pkgs/development/python-modules/hidapi/default.nix

@@ -3,7 +3,7 @@
 , buildPythonPackage
 , fetchPypi
 , xcbuild
-, cython
+, cython_0
 , libusb1
 , udev
 , darwin
@@ -19,10 +19,10 @@ buildPythonPackage rec {
     sha256 = "a7cb029286ced5426a381286526d9501846409701a29c2538615c3d1a612b8be";
   };
 
-  nativeBuildInputs = lib.optionals stdenv.isDarwin [ xcbuild ];
+  nativeBuildInputs = [ cython_0 ]
+    ++ lib.optionals stdenv.isDarwin [ xcbuild ];
 
-  propagatedBuildInputs = [ cython ]
+  propagatedBuildInputs = lib.optionals stdenv.isLinux [ libusb1 udev ]
-    ++ lib.optionals stdenv.isLinux [ libusb1 udev ]
     ++ lib.optionals stdenv.isDarwin (with darwin.apple_sdk.frameworks; [ AppKit CoreFoundation IOKit ]);
 
   # Fix the USB backend library lookup

pkgs/development/python-modules/homematicip/default.nix

@@ -5,8 +5,7 @@
 , async-timeout
 , buildPythonPackage
 , fetchFromGitHub
-, pytestCheckHook
+, pytest7CheckHook
-, pytest_7
 , pythonAtLeast
 , pythonOlder
 , pytest-aiohttp
@@ -50,7 +49,7 @@ buildPythonPackage rec {
     aiohttp-wsgi
     pytest-aiohttp
     pytest-asyncio
-    (pytestCheckHook.override { pytest = pytest_7; })
+    pytest7CheckHook
   ];
 
   pytestFlagsArray = [

pkgs/development/python-modules/hypothesis/default.nix

@@ -22,7 +22,7 @@
 
 buildPythonPackage rec {
   pname = "hypothesis";
-  version = "6.98.17";
+  version = "6.99.12";
   pyproject = true;
 
   disabled = pythonOlder "3.7";
@@ -31,7 +31,7 @@ buildPythonPackage rec {
     owner = "HypothesisWorks";
     repo = "hypothesis";
     rev = "hypothesis-python-${version}";
-    hash = "sha256-2knFmaa334vFo8bbLCmrWAXRDXFcC+GPRqj7RG3FqEQ=";
+    hash = "sha256-0nzjRDv4L3bxxnC0lBY5S7FP9CFhyzHzNchWXoX91Zg=";
   };
 
   # I tried to package sphinx-selective-exclude, but it throws

pkgs/development/python-modules/in-n-out/default.nix

@@ -1,6 +1,6 @@
 { lib
 , buildPythonPackage
-, cython_3
+, cython
 , fetchPypi
 , future
 , pytestCheckHook
@@ -25,7 +25,7 @@ buildPythonPackage rec {
   };
 
   nativeBuildInputs = [
-    cython_3
+    cython
     hatchling
     hatch-vcs
   ];

pkgs/development/python-modules/ipython/default.nix

@@ -22,8 +22,7 @@
 # Test dependencies
 , pickleshare
 , pytest-asyncio
-, pytestCheckHook
+, pytest7CheckHook
-, pytest_7
 , testpath
 }:
 
@@ -72,7 +71,7 @@ buildPythonPackage rec {
   nativeCheckInputs = [
     pickleshare
     pytest-asyncio
-    (pytestCheckHook.override { pytest = pytest_7; })
+    pytest7CheckHook
     testpath
   ];
 

pkgs/development/python-modules/ipywidgets/default.nix

@@ -8,7 +8,7 @@
 , jsonschema
 , jupyterlab-widgets
 , lib
-, pytestCheckHook
+, pytest7CheckHook
 , pytz
 , traitlets
 , widgetsnbextension
@@ -40,15 +40,10 @@ buildPythonPackage rec {
   nativeCheckInputs = [
     ipykernel
     jsonschema
-    pytestCheckHook
+    pytest7CheckHook
     pytz
   ];
 
-  pytestFlagsArray = [
-    # pytest.PytestRemovedIn8Warning: Support for nose tests is deprecated and will be removed in a future release.
-    "-W" "ignore::pytest.PytestRemovedIn8Warning"
-  ];
-
   meta = {
     description = "IPython HTML widgets for Jupyter";
     homepage = "https://github.com/jupyter-widgets/ipywidgets";

pkgs/development/python-modules/isort/default.nix

@@ -52,8 +52,6 @@ buildPythonPackage rec {
     "--ignore=tests/benchmark/" # requires pytest-benchmark
     "--ignore=tests/integration/" # pulls in 10 other packages
     "--ignore=tests/unit/profiles/test_black.py" # causes infinite recursion to include black
-    # pytest.PytestRemovedIn8Warning: Passing None has been deprecated.
-    "-W" "ignore::pytest.PytestRemovedIn8Warning"
   ];
 
   disabledTests = [
@@ -74,6 +72,8 @@ buildPythonPackage rec {
     "test_value_assignment_list"
     # profiles not available
     "test_isort_supports_shared_profiles_issue_970"
+    # https://github.com/PyCQA/isort/issues/2234
+    "test_isort_should_warn_on_empty_custom_config_issue_1433"
   ];
 
   meta = with lib; {

pkgs/development/python-modules/json-tricks/default.nix

@@ -2,7 +2,7 @@
 , fetchFromGitHub
 , buildPythonPackage
 , pythonOlder
-, pytestCheckHook
+, pytest7CheckHook
 , numpy
 , pandas
 , pytz
@@ -26,11 +26,7 @@ buildPythonPackage rec {
     numpy
     pandas
     pytz
-    pytestCheckHook
+    pytest7CheckHook
-  ];
-
-  pytestFlagsArray = [
-    "-W" "ignore::pytest.PytestRemovedIn8Warning"
   ];
 
   pythonImportsCheck = [

pkgs/development/python-modules/kivy/default.nix

@@ -1,6 +1,6 @@
 { lib, stdenv
 , buildPythonPackage, fetchFromGitHub, fetchpatch
-, pkg-config, cython, docutils
+, pkg-config, cython_0, docutils
 , kivy-garden
 , mesa, mtdev, SDL2, SDL2_image, SDL2_ttf, SDL2_mixer
 , Accelerate, ApplicationServices, AVFoundation, libcxx
@@ -31,7 +31,7 @@ buildPythonPackage rec {
 
   nativeBuildInputs = [
     pkg-config
-    cython
+    cython_0
     docutils
   ];
 

pkgs/development/python-modules/kombu/default.nix

@@ -15,7 +15,7 @@
 , pycurl
 , pymongo
   #, pyro4
-, pytestCheckHook
+, pytest7CheckHook
 , pythonOlder
 , pyyaml
 , redis
@@ -89,14 +89,9 @@ buildPythonPackage rec {
   nativeCheckInputs = [
     case
     hypothesis
-    pytestCheckHook
+    pytest7CheckHook
   ] ++ lib.flatten (builtins.attrValues passthru.optional-dependencies);
 
-  pytestFlagsArray = [
-    # pytest.PytestRemovedIn8Warning: Support for nose tests is deprecated and will be removed in a future release.
-    "-W" "ignore::pytest.PytestRemovedIn8Warning"
-  ];
-
   pythonImportsCheck = [
     "kombu"
   ];

pkgs/development/python-modules/kubernetes/default.nix

@@ -36,6 +36,11 @@ buildPythonPackage rec {
     hash = "sha256-NKrxv5a5gkgpNG7yViTKYBYnU249taWl6fkPJa7/Rzo=";
   };
 
+  postPatch = ''
+    substituteInPlace ./kubernetes/base/config/kube_config_test.py \
+      --replace-fail assertEquals assertEqual
+  '';
+
   propagatedBuildInputs = [
     adal
     certifi

pkgs/development/python-modules/langchain-core/default.nix

@@ -16,7 +16,7 @@
 
 buildPythonPackage rec {
   pname = "langchain-core";
-  version = "0.1.32";
+  version = "0.1.33";
   pyproject = true;
 
   disabled = pythonOlder "3.8";
@@ -24,11 +24,12 @@ buildPythonPackage rec {
   src = fetchPypi {
     pname = "langchain_core";
     inherit version;
-    hash = "sha256-1iaDvsvyD1HxKHV5GgQjIPReqgyHomfTC8A7waB/XsI=";
+    hash = "sha256-VF7/Peg8xYIxvSsMbWcjI/wgd7lNMmuhoyGRGK8dGmY=";
   };
 
   pythonRelaxDeps = [
     "langsmith"
+    "packaging"
   ];
 
   nativeBuildInputs = [

pkgs/development/python-modules/levenshtein/default.nix

@@ -2,7 +2,7 @@
 , stdenv
 , buildPythonPackage
 , cmake
-, cython_3
+, cython
 , fetchFromGitHub
 , pytestCheckHook
 , pythonOlder
@@ -28,7 +28,7 @@ buildPythonPackage rec {
 
   nativeBuildInputs = [
     cmake
-    cython_3
+    cython
     scikit-build
   ];
 

pkgs/development/python-modules/libgpuarray/default.nix

@@ -4,7 +4,7 @@
 , buildPythonPackage
 , fetchFromGitHub
 , cmake
-, cython
+, cython_0
 , numpy
 , six
 , nose
@@ -67,13 +67,13 @@ buildPythonPackage rec {
 
   nativeBuildInputs = [
     cmake
+    cython_0
   ] ++ lib.optionals cudaSupport [
     addOpenGLRunpath
   ];
 
 
   buildInputs = [
-    cython
     nose
   ];
 

pkgs/development/python-modules/librouteros/default.nix

@@ -2,7 +2,7 @@
 , buildPythonPackage
 , fetchFromGitHub
 , pytest-xdist
-, pytestCheckHook
+, pytest7CheckHook
 , pythonOlder
 , setuptools
 }:
@@ -27,12 +27,7 @@ buildPythonPackage rec {
 
   nativeCheckInputs = [
     pytest-xdist
-    pytestCheckHook
+    pytest7CheckHook
-  ];
-
-  pytestFlagsArray = [
-    # pytest.PytestRemovedIn8Warning: Support for nose tests is deprecated and will be removed in a future release.
-    "-W" "ignore::pytest.PytestRemovedIn8Warning"
   ];
 
   disabledTests = [

pkgs/development/python-modules/lightning-utilities/default.nix

@@ -11,8 +11,7 @@
 
 # tests
 , pytest-timeout
-, pytestCheckHook
+, pytest7CheckHook
-, pytest_7
 }:
 
 buildPythonPackage rec {
@@ -42,7 +41,7 @@ buildPythonPackage rec {
 
   nativeCheckInputs = [
     pytest-timeout
-    (pytestCheckHook.override { pytest = pytest_7; })
+    pytest7CheckHook
   ];
 
   disabledTests = [

pkgs/development/python-modules/limits/default.nix

@@ -22,7 +22,7 @@
 
 buildPythonPackage rec {
   pname = "limits";
-  version = "3.9.0";
+  version = "3.10.1";
   pyproject = true;
 
   disabled = pythonOlder "3.7";
@@ -37,7 +37,7 @@ buildPythonPackage rec {
     postFetch = ''
       rm "$out/limits/_version.py"
     '';
-    hash = "sha256-X4nf9ifhJjTNKnQuAxRNK9j/MzfAC58kv+19zMWtKg8=";
+    hash = "sha256-Ax0P9rYTPOrhtOw7FLElSNTGQ3WWCboM3FodTOGZWu8=";
   };
 
   postPatch = ''

pkgs/development/python-modules/line-profiler/default.nix

@@ -1,7 +1,7 @@
 { lib
 , buildPythonPackage
 , fetchPypi
-, cython_3
+, cython
 , isPyPy
 , ipython
 , scikit-build
@@ -25,7 +25,7 @@ buildPythonPackage rec {
   };
 
   nativeBuildInputs = [
-    cython_3
+    cython
     cmake
     scikit-build
   ];

pkgs/development/python-modules/llfuse/default.nix

@@ -3,7 +3,7 @@
 , buildPythonPackage
 , pythonOlder
 , fetchFromGitHub
-, cython_3
+, cython
 , fuse
 , pkg-config
 , pytestCheckHook
@@ -27,7 +27,7 @@ buildPythonPackage rec {
     hash = "sha256-6/iW5eHmX6ODVPLFkOo3bN9yW8ixqy2MHwQ2r9FA0iI=";
   };
 
-  nativeBuildInputs = [ cython_3 pkg-config setuptools ];
+  nativeBuildInputs = [ cython pkg-config setuptools ];
 
   buildInputs = [ fuse ];
 

pkgs/development/python-modules/logical-unification/default.nix

@@ -1,6 +1,7 @@
 { lib
 , buildPythonPackage
 , fetchFromGitHub
+, pythonAtLeast
 , toolz
 , multipledispatch
 , py
@@ -33,6 +34,11 @@ buildPythonPackage rec {
     pytest-benchmark  # Needed for the `--benchmark-skip` flag
   ];
 
+  disabledTests = lib.optionals (pythonAtLeast "3.12") [
+    # Failed: DID NOT RAISE <class 'RecursionError'>
+    "test_reify_recursion_limit"
+  ];
+
   pytestFlagsArray = [
     "--benchmark-skip"
     "--html=testing-report.html"

pkgs/development/python-modules/lupa/default.nix

@@ -1,6 +1,6 @@
 { lib
 , buildPythonPackage
-, cython_3
+, cython
 , fetchPypi
 , pythonOlder
 , setuptools
@@ -19,7 +19,7 @@ buildPythonPackage rec {
   };
 
   build-system = [
-    cython_3
+    cython
     setuptools
   ];