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
Loading
Loading
Loading
Loading
+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 ];
  };
}
+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 ];
  };
}
+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 ];
  };
}
+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 ];
  };
}
+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 { };