Merge pull request #198709 from fabaff/mezzanine-fix

python310Packages.mezzanine: add missing extra dependency

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

@@ -11,7 +11,7 @@
 
 buildPythonPackage rec {
   pname = "aeppl";
-  version = "0.0.35";
+  version = "0.0.38";
   format = "setuptools";
 
   disabled = pythonOlder "3.7";
@@ -20,7 +20,7 @@ buildPythonPackage rec {
     owner = "aesara-devs";
     repo = pname;
     rev = "refs/tags/v${version}";
-    hash = "sha256-HUcLa/9fTUBJYszo1SiG08t7DQiNSd8EsINkJpAeLsY=";
+    hash = "sha256-B9ZZEzGW4i0RRUaTAYiQ7+7pe4ArpSGcp/x4B6G7EYo=";
   };
 
   propagatedBuildInputs = [

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

@@ -30,7 +30,7 @@ buildPythonPackage rec {
     owner = "aesara-devs";
     repo = "aesara";
     rev = "refs/tags/rel-${version}";
-    hash = "sha256-Mt1IweQkPqxv+ynezdFHTJXU/oTOwhPkY49GzFJpPaM=";
+    hash = "sha256-xtnz+qKW2l8ze0EXdL9mkx0MzfAnmauC9042W2cVc5o=";
   };
 
   nativeBuildInputs = [
@@ -74,14 +74,15 @@ buildPythonPackage rec {
     "tests/scan/"
     "tests/tensor/"
     "tests/sandbox/"
+    "tests/sparse/sandbox/"
   ];
 
   meta = with lib; {
-    broken = (stdenv.isLinux && stdenv.isAarch64);
     description = "Python library to define, optimize, and efficiently evaluate mathematical expressions involving multi-dimensional arrays";
     homepage = "https://github.com/aesara-devs/aesara";
     changelog = "https://github.com/aesara-devs/aesara/releases";
     license = licenses.bsd3;
     maintainers = with maintainers; [ Etjean ];
+    broken = (stdenv.isLinux && stdenv.isAarch64);
   };
 }

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

@@ -31,7 +31,7 @@
 
 buildPythonPackage rec {
   pname = "arviz";
-  version = "0.12.1";
+  version = "0.13.0";
   format = "setuptools";
 
   disabled = pythonOlder "3.7";
@@ -40,7 +40,7 @@ buildPythonPackage rec {
     owner = "arviz-devs";
     repo = pname;
     rev = "v${version}";
-    hash = "sha256-5P6EXXAAS1Q2eNQuj/5JrDg0lPHfA5K4WaYfKaaXm9s=";
+    hash = "sha256-DGTGUMnkEQcwGR44WhmBpTBMcRcAtVIpM4YVnnlakE8=";
   };
 
   propagatedBuildInputs = [
@@ -90,6 +90,10 @@ buildPythonPackage rec {
     "test_plot_separation"
     "test_plot_trace_legend"
     "test_cov"
+    # countourpy is not available at the moment
+    "test_plot_kde"
+    "test_plot_kde_2d"
+    "test_plot_pair"
   ];
 
   pythonImportsCheck = [

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

@@ -5,14 +5,16 @@
 , six
 , html5lib
 , setuptools
+, tinycss2
 , packaging
 , pythonOlder
+, webencodings
 }:
 
 buildPythonPackage rec {
   pname = "bleach";
   version = "5.0.1";
-  disabled = pythonOlder "3.6";
+  disabled = pythonOlder "3.7";
 
   src = fetchPypi {
     inherit pname version;
@@ -20,12 +22,19 @@ buildPythonPackage rec {
   };
 
   propagatedBuildInputs = [
-    packaging
-    six
     html5lib
+    packaging
     setuptools
+    six
+    webencodings
   ];
 
+  passthru.optional-dependencies = {
+    css = [
+      tinycss2
+    ];
+  };
+
   checkInputs = [
     pytestCheckHook
   ];
@@ -35,7 +44,9 @@ buildPythonPackage rec {
     "protocols"
   ];
 
-  pythonImportsCheck = [ "bleach" ];
+  pythonImportsCheck = [
+    "bleach"
+  ];
 
   meta = with lib; {
     description = "An easy, HTML5, whitelisting HTML sanitizer";

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

@@ -3,17 +3,21 @@
 , fetchFromGitHub
 , numpy
 , python
+, pythonOlder
 }:
 
 buildPythonPackage rec {
   pname = "cma";
   version = "3.2.2";
+  format = "setuptools";
+
+  disabled = pythonOlder "3.7";
 
   src = fetchFromGitHub {
     owner = "CMA-ES";
     repo = "pycma";
     rev = "refs/tags/r${version}";
-    sha256 = "sha256-STF7jtLqI2KiWvvI9/reRjP1XyW8l4/qy9uAPpE9mTs=";
+    hash = "sha256-STF7jtLqI2KiWvvI9/reRjP1XyW8l4/qy9uAPpE9mTs=";
   };
 
   propagatedBuildInputs = [
@@ -21,13 +25,18 @@ buildPythonPackage rec {
   ];
 
   checkPhase = ''
-    ${python.executable} -m cma.test
+    # At least one doctest fails, thus only limited amount of files is tested
+    ${python.executable} -m cma.test interfaces.py purecma.py logger.py optimization_tools.py transformations.py
   '';
 
+  pythonImportsCheck = [
+    "cma"
+  ];
+
   meta = with lib; {
-    description = "CMA-ES, Covariance Matrix Adaptation Evolution Strategy for non-linear numerical optimization in Python";
+    description = "Library for Covariance Matrix Adaptation Evolution Strategy for non-linear numerical optimization";
     homepage = "https://github.com/CMA-ES/pycma";
     license = licenses.bsd3;
-    maintainers = [ maintainers.costrouc ];
+    maintainers = with maintainers; [ costrouc ];
   };
 }

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

@@ -24,7 +24,7 @@ buildPythonPackage rec {
   version = "6.0.0";
   format = "setuptools";
 
-  disabled = pythonOlder "3.6" || isPyPy;
+  disabled = pythonOlder "3.7" || isPyPy;
 
   src = fetchPypi {
     pname = "Mezzanine";
@@ -50,10 +50,11 @@ buildPythonPackage rec {
     requests
     requests-oauthlib
     tzlocal
-  ];
+  ] ++ bleach.optional-dependencies.css;
 
   # Tests Fail Due to Syntax Warning, Fixed for v3.1.11+
   doCheck = false;
+
   # sed calls will be unecessary in v3.1.11+
   preConfigure = ''
     sed -i 's/==/>=/' setup.py

pkgs/development/python-modules/pylsp-mypy/default.nix

@@ -1,39 +1,49 @@
 { lib
 , buildPythonPackage
 , fetchFromGitHub
-, mock
 , mypy
 , pytestCheckHook
 , python-lsp-server
 , pythonOlder
+, toml
 }:
 
 buildPythonPackage rec {
   pname = "pylsp-mypy";
   version = "0.6.3";
-  disabled = pythonOlder "3.6";
+  format = "setuptools";
+
+  disabled = pythonOlder "3.7";
 
   src = fetchFromGitHub {
     owner = "Richardk2n";
     repo = "pylsp-mypy";
     rev = "refs/tags/${version}";
-    sha256 = "sha256-fZ2bPPjBK/H2jMI4S3EhvWJaNl4tK7HstxcHSAkoFW4=";
+    hash = "sha256-fZ2bPPjBK/H2jMI4S3EhvWJaNl4tK7HstxcHSAkoFW4=";
   };
 
+  propagatedBuildInputs = [
+    mypy
+    python-lsp-server
+    toml
+  ];
+
+  checkInputs = [
+    pytestCheckHook
+  ];
+
+  pythonImportsCheck = [
+    "pylsp_mypy"
+  ];
+
   disabledTests = [
-    "test_multiple_workspaces"
+    # Tests wants to call dmypy
     "test_option_overrides_dmypy"
   ];
 
-  checkInputs = [ pytestCheckHook mock ];
-
-  propagatedBuildInputs = [ mypy python-lsp-server ];
-
-  pythonImportsCheck = [ "pylsp_mypy" ];
-
   meta = with lib; {
-    homepage = "https://github.com/Richardk2n/pylsp-mypy";
     description = "Mypy plugin for the Python LSP Server";
+    homepage = "https://github.com/Richardk2n/pylsp-mypy";
     license = licenses.mit;
     maintainers = with maintainers; [ cpcloud ];
   };

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

@@ -16,7 +16,7 @@
 
 buildPythonPackage rec {
   pname = "pymc";
-  version = "4.1.3";
+  version = "4.3.0";
   format = "setuptools";
 
   disabled = pythonOlder "3.7";
@@ -25,7 +25,7 @@ buildPythonPackage rec {
     owner = "pymc-devs";
     repo = "pymc";
     rev = "refs/tags/v${version}";
-    hash = "sha256-fqhtfMGopzVgonF5+qyFhm72KV0hX8QE95slI/HBZYU=";
+    hash = "sha256-pkeAcsdVBDc7eKC03+FDJCYT48PaVcXT8K8U8T4gGKo=";
   };
 
   nativeBuildInputs = [

pkgs/development/python-modules/python-lsp-server/default.nix

@@ -1,4 +1,5 @@
 { lib
+, stdenv
 , autopep8
 , buildPythonPackage
 , fetchFromGitHub
@@ -21,19 +22,10 @@
 , rope
 , setuptools
 , setuptools-scm
-, stdenv
 , ujson
+, websockets
 , whatthepatch
 , yapf
-, withAutopep8 ? true
-, withFlake8 ? true
-, withMccabe ? true
-, withPycodestyle ? true
-, withPydocstyle ? true
-, withPyflakes ? true
-, withPylint ? true
-, withRope ? true
-, withYapf ? true
 }:
 
 buildPythonPackage rec {
@@ -54,7 +46,11 @@ buildPythonPackage rec {
     substituteInPlace pyproject.toml \
       --replace "--cov-report html --cov-report term --junitxml=pytest.xml" "" \
       --replace "--cov pylsp --cov test" "" \
-      --replace "mccabe>=0.6.0,<0.7.0" "mccabe"
+      --replace "autopep8>=1.6.0,<1.7.0" "autopep8" \
+      --replace "flake8>=4.0.0,<4.1.0" "flake8" \
+      --replace "mccabe>=0.6.0,<0.7.0" "mccabe" \
+      --replace "pycodestyle>=2.8.0,<2.9.0" "pycodestyle" \
+      --replace "pyflakes>=2.4.0,<2.5.0" "pyflakes"
   '';
 
   preBuild = ''
@@ -68,15 +64,53 @@ buildPythonPackage rec {
     setuptools
     setuptools-scm
     ujson
-  ] ++ lib.optional withAutopep8 autopep8
-  ++ lib.optional withFlake8 flake8
-  ++ lib.optional withMccabe mccabe
-  ++ lib.optional withPycodestyle pycodestyle
-  ++ lib.optional withPydocstyle pydocstyle
-  ++ lib.optional withPyflakes pyflakes
-  ++ lib.optional withPylint pylint
-  ++ lib.optional withRope rope
-  ++ lib.optionals withYapf [ whatthepatch yapf ];
+  ];
+
+  passthru.optional-dependencies = {
+    all = [
+      autopep8
+      flake8
+      mccabe
+      pycodestyle
+      pydocstyle
+      pyflakes
+      pylint
+      rope
+      whatthepatch
+      yapf
+    ];
+    autopep8 = [
+      autopep8
+    ];
+    flake8 = [
+      flake8
+    ];
+    mccabe = [
+      mccabe
+    ];
+    pycodestyle = [
+      pycodestyle
+    ];
+    pydocstyle = [
+      pydocstyle
+    ];
+    pyflakes = [
+      pyflakes
+    ];
+    pylint = [
+      pylint
+    ];
+    rope = [
+      rope
+    ];
+    yapf = [
+      whatthepatch
+      yapf
+    ];
+    websockets = [
+      websockets
+    ];
+  };
 
   checkInputs = [
     flaky
@@ -84,26 +118,20 @@ buildPythonPackage rec {
     numpy
     pandas
     pytestCheckHook
-  ]
+  ] ++ passthru.optional-dependencies.all
   # pyqt5 is broken on aarch64-darwin
-  ++ lib.optionals (!stdenv.isDarwin || !stdenv.isAarch64) [ pyqt5 ];
+  ++ lib.optionals (!stdenv.isDarwin || !stdenv.isAarch64) [
+    pyqt5
+  ];
 
   disabledTests = [
-    "test_numpy_completions" # https://github.com/python-lsp/python-lsp-server/issues/243
-  ] ++ lib.optional (!withPycodestyle) "test_workspace_loads_pycodestyle_config"
-  # pyqt5 is broken on aarch64-darwin
-  ++ lib.optional (stdenv.isDarwin && stdenv.isAarch64) "test_pyqt_completion";
-
-  disabledTestPaths = lib.optional (!withAutopep8) "test/plugins/test_autopep8_format.py"
-    ++ lib.optional (!withRope) "test/plugins/test_completion.py"
-    ++ lib.optional (!withFlake8) "test/plugins/test_flake8_lint.py"
-    ++ lib.optional (!withMccabe) "test/plugins/test_mccabe_lint.py"
-    ++ lib.optional (!withPycodestyle) "test/plugins/test_pycodestyle_lint.py"
-    ++ lib.optional (!withPydocstyle) "test/plugins/test_pydocstyle_lint.py"
-    ++ lib.optional (!withPyflakes) "test/plugins/test_pyflakes_lint.py"
-    ++ lib.optional (!withPylint) "test/plugins/test_pylint_lint.py"
-    ++ lib.optional (!withRope) "test/plugins/test_rope_rename.py"
-    ++ lib.optional (!withYapf) "test/plugins/test_yapf_format.py";
+    # https://github.com/python-lsp/python-lsp-server/issues/243
+    "test_numpy_completions"
+    "test_workspace_loads_pycodestyle_config"
+  ] ++ lib.optional (stdenv.isDarwin && stdenv.isAarch64) [
+    # pyqt5 is broken on aarch64-darwin
+    "test_pyqt_completion"
+  ];
 
   preCheck = ''
     export HOME=$(mktemp -d);

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

@@ -41,21 +41,23 @@
 , textdistance
 , three-merge
 , watchdog
-, pytestCheckHook
 }:
 
 buildPythonPackage rec {
   pname = "spyder";
   version = "5.3.3";
+  format = "setuptools";
 
   disabled = pythonOlder "3.7";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "sha256-vWhwn07zgHX7/7uAz0ekNwnAiKLECCBzBq47TtTaHfE=";
+    hash = "sha256-vWhwn07zgHX7/7uAz0ekNwnAiKLECCBzBq47TtTaHfE=";
   };
 
-  nativeBuildInputs = [ pyqtwebengine.wrapQtAppsHook ];
+  nativeBuildInputs = [
+    pyqtwebengine.wrapQtAppsHook
+  ];
 
   propagatedBuildInputs = [
     atomicwrites
@@ -63,19 +65,16 @@ buildPythonPackage rec {
     cloudpickle
     cookiecutter
     diff-match-patch
-    flake8
     intervaltree
     jedi
     jellyfish
     keyring
     matplotlib
-    mccabe
     nbconvert
     numpy
     numpydoc
     psutil
     pygments
-    pylint
     pyls-spyder
     pyopengl
     pyqtwebengine
@@ -83,7 +82,6 @@ buildPythonPackage rec {
     python-lsp-server
     pyxdg
     pyzmq
-    pycodestyle
     qdarkstyle
     qstylizer
     qtawesome
@@ -96,7 +94,7 @@ buildPythonPackage rec {
     textdistance
     three-merge
     watchdog
-  ];
+  ] ++ python-lsp-server.optional-dependencies.all;
 
   # There is no test for spyder
   doCheck = false;
@@ -112,15 +110,16 @@ buildPythonPackage rec {
   };
 
   postPatch = ''
-    # remove dependency on pyqtwebengine
-    # this is still part of the pyqt 5.11 version we have in nixpkgs
+    # Remove dependency on pyqtwebengine
+    # This is still part of the pyqt 5.11 version we have in nixpkgs
     sed -i /pyqtwebengine/d setup.py
     substituteInPlace setup.py \
+      --replace "qdarkstyle>=3.0.2,<3.1.0" "qdarkstyle" \
       --replace "ipython>=7.31.1,<8.0.0" "ipython"
   '';
 
   postInstall = ''
-    # add Python libs to env so Spyder subprocesses
+    # Add Python libs to env so Spyder subprocesses
     # created to run compute kernels don't fail with ImportErrors
     wrapProgram $out/bin/spyder --prefix PYTHONPATH : "$PYTHONPATH"
 
@@ -147,7 +146,7 @@ buildPythonPackage rec {
     downloadPage = "https://github.com/spyder-ide/spyder/releases";
     changelog = "https://github.com/spyder-ide/spyder/blob/master/CHANGELOG.md";
     license = licenses.mit;
-    platforms = platforms.linux;
     maintainers = with maintainers; [ gebner ];
+    platforms = platforms.linux;
   };
 }