Unverified Commit 4e37a233 authored by Mario Rodas's avatar Mario Rodas Committed by GitHub
Browse files

Merge pull request #283019 from bcdarwin/update-mne 

python311Packages.mne-python: 1.6.0 -> 1.6.1; unbreak
parents 78ca9473 9f56eed7

pkgs/development/python-modules/h5io/default.nix

0 → 100644
+52 −0
Original line number Diff line number Diff line 
{ lib

, buildPythonPackage

, fetchFromGitHub

, pythonOlder

, setuptools

, numpy

, h5py

, pytestCheckHook

}:



buildPythonPackage rec {

  pname = "h5io";

  version = "0.2.1";

  pyproject = true;



  disabled = pythonOlder "3.7";



  src = fetchFromGitHub {

    owner = "h5io";

    repo = "h5io";

    rev = "refs/tags/h5io-${version}";

    hash = "sha256-3mrHIkfaXq06mMzUwudRO81DWTk0TO/e15IQA5fxxNc=";

  };



  postPatch = ''

    substituteInPlace pyproject.toml  \

      --replace "--cov-report=" ""  \

      --replace "--cov-branch" ""  \

      --replace "--cov=h5io" ""

  '';



  nativeBuildInputs = [ setuptools ];



  propagatedBuildInputs = [

    numpy

    h5py

  ];



  nativeCheckInputs = [

    pytestCheckHook

  ];



  pythonImportsCheck = [ "h5io" ];



  meta = with lib; {

    description = "Read and write simple Python objects using HDF5";

    homepage = "https://github.com/h5io/h5io";

    changelog = "https://github.com/h5io/h5io/releases/tag/${src.rev}";

    license = licenses.bsd3;

    maintainers = with maintainers; [ mbalatsko ];

  };

}

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

+44 −25
Original line number Diff line number Diff line 
{ lib

, buildPythonPackage

, fetchFromGitHub

, setuptools

, setuptools-scm

, numpy

, scipy

, pytestCheckHook

, pytest-timeout

, h5py

, pytest-harvest

, matplotlib

, nibabel

, pandas

, scikit-learn

, decorator

, jinja2

, pooch

, tqdm

, setuptools

, packaging

, importlib-resources

, lazy-loader

, h5io

, pymatreader

, pythonOlder

}:



buildPythonPackage rec {

  pname = "mne-python";

  version = "1.6.0";

  format = "setuptools";

  version = "1.6.1";

  pyproject = true;



  disabled = pythonOlder "3.7";

  disabled = pythonOlder "3.8";



  src = fetchFromGitHub {

    owner = "mne-tools";

    repo = pname;

    repo = "mne-python";

    rev = "refs/tags/v${version}";

    hash = "sha256-OoaXNHGL2svOpNL5GHcVRfQc9GxIRpZRhpZ5Hi1JTzM=";

    hash = "sha256-U1aMqcUZ3BcwqwOYh/qfG5PhacwBVioAgNc52uaoJL0";

  };



  postPatch = ''

    substituteInPlace pyproject.toml  \

      --replace "--cov-report=" ""  \

      --replace "--cov-branch" ""

  '';



  nativeBuildInputs = [

    setuptools

    setuptools-scm

  ];



  propagatedBuildInputs = [

    decorator

    jinja2

    matplotlib

    numpy

    pooch

    scipy

    setuptools

    matplotlib

    tqdm

    pooch

    decorator

    packaging

    jinja2

    lazy-loader

  ] ++ lib.optionals (pythonOlder "3.9") [

    importlib-resources

  ];



  passthru.optional-dependencies = {

    hdf5 = [

      h5io

      pymatreader

    ];

  };



  nativeCheckInputs = [

    h5py

    nibabel

    pandas

    pytestCheckHook

    scikit-learn

    pytest-timeout

  ];

    pytest-harvest

  ] ++ lib.flatten (builtins.attrValues passthru.optional-dependencies);



  preCheck = ''

    export HOME=$TMP

    export HOME=$(mktemp -d)

    export MNE_SKIP_TESTING_DATASET_TESTS=true

    export MNE_SKIP_NETWORK_TESTS=1

  '';



  # All tests pass, but Pytest hangs afterwards - probably some thread hasn't terminated

  doCheck = false;



  pythonImportsCheck = [

    "mne"

  ];
@@ -68,7 +86,8 @@ buildPythonPackage rec { 
  meta = with lib; {

    description = "Magnetoencephelography and electroencephalography in Python";

    homepage = "https://mne.tools";

    changelog = "https://mne.tools/stable/changes/v${version}.html";

    license = licenses.bsd3;

    maintainers = with maintainers; [ bcdarwin ];

    maintainers = with maintainers; [ bcdarwin mbalatsko ];

  };

}

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

0 → 100644
+46 −0
Original line number Diff line number Diff line 
{ lib

, buildPythonPackage

, fetchFromGitLab

, setuptools

, h5py

, numpy

, scipy

, xmltodict

, pytestCheckHook

}:



buildPythonPackage rec {

  pname = "pymatreader";

  version = "0.0.31";

  pyproject = true;



  src = fetchFromGitLab {

    owner = "obob";

    repo = "pymatreader";

    rev = "refs/tags/v${version}";

    hash = "sha256-pYObmvqA49sHjpZcwXkN828R/N5CSpmr0OyyxzDiodQ=";

  };



  nativeBuildInputs = [ setuptools ];



  propagatedBuildInputs = [

    h5py

    numpy

    scipy

    xmltodict

  ];



  nativeCheckInputs = [

    pytestCheckHook

  ];



  pythonImportsCheck = [ "pymatreader" ];



  meta = with lib; {

    description = "A python package to read all kinds and all versions of Matlab mat files";

    homepage = "https://gitlab.com/obob/pymatreader/";

    changelog = "https://gitlab.com/obob/pymatreader/-/blob/${src.rev}/CHANGELOG.md";

    license = licenses.bsd2;

    maintainers = with maintainers; [ mbalatsko ];

  };

}

pkgs/development/python-modules/pytest-harvest/default.nix

0 → 100644
+68 −0
Original line number Diff line number Diff line 
{ lib

, buildPythonPackage

, fetchFromGitHub

, setuptools-scm

, pytest-runner

, pytest

, decopatch

, makefun

, six

, pytestCheckHook

, numpy

, pandas

, tabulate

, pytest-cases

, pythonOlder

}:



buildPythonPackage rec {

  pname = "pytest-harvest";

  version = "1.10.4";

  pyproject = true;



  disabled = pythonOlder "3.6";



  src = fetchFromGitHub {

    owner = "smarie";

    repo = "python-pytest-harvest";

    rev = "refs/tags/${version}";

    hash = "sha256-ebzE63d7zt9G9HgbLHaE/USZZpUd3y3vd0kNdT/wWw0=";

  };



  # create file, that is created by setuptools_scm

  # we disable this file creation as it touches internet

  postPatch = ''

    echo "version = '${version}'" > pytest_harvest/_version.py

  '';



  nativeBuildInputs = [

    setuptools-scm

    pytest-runner

  ];



  buildInputs = [ pytest ];



  propagatedBuildInputs = [

    decopatch

    makefun

    six

  ];



  nativeCheckInputs = [

    pytestCheckHook

    numpy

    pandas

    tabulate

    pytest-cases

  ];



  pythonImportsCheck = [ "pytest_harvest" ];



  meta = with lib; {

    description = "Store data created during your `pytest` tests execution, and retrieve it at the end of the session, e.g. for applicative benchmarking purposes";

    homepage = "https://github.com/smarie/python-pytest-harvest";

    changelog = "https://github.com/smarie/python-pytest-harvest/releases/tag/${src.rev}";

    license = licenses.bsd3;

    maintainers = with maintainers; [ mbalatsko ];

  };

}

pkgs/top-level/python-packages.nix

+6 −0
Original line number Diff line number Diff line
@@ -5055,6 +5055,8 @@ self: super: with self; { 
    inherit (pkgs) h3;

  };













  h5io = callPackage ../development/python-modules/h5io { };



























  h5netcdf = callPackage ../development/python-modules/h5netcdf { };





























  h5py = callPackage ../development/python-modules/h5py { };










@@ -10813,6 +10815,8 @@ self: super: with self; {



























  pymatgen = callPackage ../development/python-modules/pymatgen { };



























  pymatreader = callPackage ../development/python-modules/pymatreader { };



























  pymatting = callPackage ../development/python-modules/pymatting { };





























  pymaven-patch = callPackage ../development/python-modules/pymaven-patch { };










@@ -11585,6 +11589,8 @@ self: super: with self; {



























  pytest-grpc = callPackage ../development/python-modules/pytest-grpc { };



























  pytest-harvest = callPackage ../development/python-modules/pytest-harvest { };



























  pytest-helpers-namespace = callPackage ../development/python-modules/pytest-helpers-namespace { };





























  pytest-html = callPackage ../development/python-modules/pytest-html { };