python312Packages.monty: cleanup & add missing test dependency (#382662)

  lib,

  buildPythonPackage,

  fetchFromGitHub,

  msgpack,

  numpy,

  pandas,

  pydantic,

  pymongo,

  pytestCheckHook,

  pythonOlder,

  ruamel-yaml,

  # build-system

  setuptools,

  setuptools-scm,

  # dependencies

  msgpack,

  ruamel-yaml,

  # optional-dependencies

  coverage,

  pymongo,

  pytest,

  pytest-cov,

  types-requests,

  sphinx,

  sphinx-rtd-theme,

  orjson,

  pandas,

  pydantic,

  pint,

  torch,

  tqdm,

  invoke,

  requests,

  # tests

  ipython,

  numpy,

  pytestCheckHook,

}:

buildPythonPackage rec {

  version = "2025.1.9";

  pyproject = true;

  disabled = pythonOlder "3.9";

  src = fetchFromGitHub {

    owner = "materialsvirtuallab";

    repo = "monty";

    hash = "sha256-+9nxuvrtl04Fb+GQJUn+fxg4sq1pXK59UkUTkKH16YQ=";

  };

  postPatch = ''

    substituteInPlace tests/test_os.py \

      --replace 'self.assertEqual("/usr/bin/find", which("/usr/bin/find"))' '#'

  '';

  nativeBuildInputs = [

  build-system = [

    setuptools

    setuptools-scm

  ];

  propagatedBuildInputs = [

  dependencies = [

    msgpack

    ruamel-yaml

    tqdm

  ];

  optional-dependencies = rec {

    ci = [

      coverage

      pymongo

      pytest

      pytest-cov

      types-requests

    ] ++ optional;

    dev = [ ipython ];

    docs = [

      sphinx

      sphinx-rtd-theme

    ];

    json =

      [

        orjson

        pandas

        pydantic

        pymongo

      ]

      ++ lib.optionals (pythonOlder "3.13") [

        pint

        torch

      ];

    multiprocessing = [ tqdm ];

    optional = dev ++ json ++ multiprocessing ++ serialization;

    serialization = [ msgpack ];

    task = [

      invoke

      requests

    ];

  };

  nativeCheckInputs = [

    ipython

    numpy

    pandas

    pydantic

    pymongo

    pytestCheckHook

    torch

    tqdm

  ];

  pythonImportsCheck = [ "monty" ];

  disabledTests = [

    # Test file was removed and re-added after 2022.9.9

    "test_reverse_readfile_gz"

    "test_Path_objects"

    "test_zopen"

    "test_zpath"

    # flaky, precision/rounding error

    "TestJson.test_datetime"

  ];

  meta = with lib; {

  meta = {

    description = "Serves as a complement to the Python standard library by providing a suite of tools to solve many common problems";

    longDescription = "

      Monty implements supplementary useful functions for Python that are not part of the

      patterns such as singleton and cached_class, and many more.

    ";

    homepage = "https://github.com/materialsvirtuallab/monty";

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

    license = licenses.mit;

    maintainers = with maintainers; [ psyanticy ];

    changelog = "https://github.com/materialsvirtuallab/monty/releases/tag/v${version}";

    license = lib.licenses.mit;

    maintainers = with lib.maintainers; [ psyanticy ];

  };

}

{

  lib,

  ase,

  stdenv,

  buildPythonPackage,

  cython,

  pythonAtLeast,

  fetchFromGitHub,

  # build-system

  setuptools,

  # nativeBuildInputs

  cython,

  glibcLocales,

  # dependencies

  joblib,

  matplotlib,

  monty,

  networkx,

  oldest-supported-numpy,

  numpy,

  palettable,

  pandas,

  plotly,

  pybtex,

  pydispatcher,

  pytest-xdist,

  pytestCheckHook,

  pythonOlder,

  requests,

  ruamel-yaml,

  scipy,

  seekpath,

  setuptools,

  spglib,

  sympy,

  tabulate,

  tqdm,

  uncertainties,

  # optional-dependencies

  netcdf4,

  ase,

  pytest,

  pytest-cov,

  invoke,

  sphinx,

  sphinx-rtd-theme,

  numba,

  vtk,

  # tests

  addBinToPathHook,

  pytest-xdist,

  pytestCheckHook,

}:

buildPythonPackage rec {

  pname = "pymatgen";

  version = "2025.1.9";

  version = "2025.1.24";

  pyproject = true;

  disabled = pythonOlder "3.8";

  disabled = pythonAtLeast "3.13";

  src = fetchFromGitHub {

    owner = "materialsproject";

    repo = "pymatgen";

    tag = "v${version}";

    hash = "sha256-mbXnuqgve8YjktJ2PSaMNk8ADioaGe+W12bYm/chpzE=";

    hash = "sha256-0P3/M6VI2RKPArMwXD95sjW7dYOTXxUeu4tOliN0IGk=";

  };

  build-system = [ setuptools ];

  ];

  dependencies = [

    joblib

    matplotlib

    monty

    networkx

    oldest-supported-numpy

    numpy

    palettable

    pandas

    plotly

    pybtex

    pydispatcher

    requests

    ruamel-yaml

    scipy

    spglib

    sympy

    tabulate

    tqdm

    uncertainties

  ];

  optional-dependencies = {

    abinit = [ netcdf4 ];

    ase = [ ase ];

    joblib = [ joblib ];

    seekpath = [ seekpath ];

    ci = [

      pytest

      pytest-cov

      # pytest-split

    ];

    docs = [

      invoke

      sphinx

      # sphinx_markdown_builder

      sphinx-rtd-theme

    ];

    electronic_structure = [

      # fdint

    ];

    mlp = [

      # chgnet

      # matgl

    ];

    numba = [ numba ];

    vis = [ vtk ];

  };

  pythonImportsCheck = [ "pymatgen" ];

  nativeCheckInputs = [

    addBinToPathHook

    pytestCheckHook

    pytest-xdist

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

  preCheck = ''

  preCheck =

    # ensure tests can find these

    ''

      export PMG_TEST_FILES_DIR="$(realpath ./tests/files)"

    # some tests cover the command-line scripts

    export PATH=$out/bin:$PATH

    '';

  pythonImportsCheck = [ "pymatgen" ];

  disabledTests =

    [

      # Flaky

      "test_numerical_eos_values"

      "test_pca"

      "test_static_si_no_kgrid"

      "test_thermal_conductivity"

    ]

    ++ lib.optionals (stdenv.hostPlatform.isLinux && stdenv.hostPlatform.isAarch64) [

      # AttributeError: 'NoneType' object has no attribute 'items'

      "test_mean_field"

    ]

    ++ lib.optionals stdenv.hostPlatform.isDarwin [

      # Fatal Python error: Aborted

      # matplotlib/backend_bases.py", line 2654 in create_with_canvas

      "test_angle"

      "test_as_dict_from_dict"

      "test_attributes"

      "test_basic"

      "test_core_state_eigen"

      "test_eos_func"

      "test_get_info_cohps_to_neighbors"

      "test_get_plot"

      "test_get_point_group_operations"

      "test_matplotlib_plots"

      "test_ph_plot_w_gruneisen"

      "test_plot"

      "test_proj_bandstructure_plot"

      "test_structure"

      "test_structure_environments"

    ];

  disabledTestPaths = lib.optionals stdenv.hostPlatform.isDarwin [

    # Crash when running the pmg command

    # Critical error: required built-in appearance SystemAppearance not found

    "tests/cli/test_pmg_plot.py"

  ];

  meta = with lib; {

  meta = {

    description = "Robust materials analysis code that defines core object representations for structures and molecules";

    homepage = "https://pymatgen.org/";

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

    license = licenses.mit;

    maintainers = with maintainers; [ psyanticy ];

    changelog = "https://github.com/materialsproject/pymatgen/releases/tag/v${version}";

    license = lib.licenses.mit;

    maintainers = with lib.maintainers; [ psyanticy ];

  };

}