Commit cea6a8bf authored by dflores1's avatar dflores1
Browse files

multiqc: 1.29 -> 1.30

parent 3bb3bf51

pkgs/by-name/mu/multiqc/package.nix

+43 −28
Original line number Diff line number Diff line
@@ -8,27 +8,28 @@ 
  addBinToPathHook,

}:



let

  test-data = fetchFromGitHub {

    name = "test-data";

    owner = "MultiQC";

    repo = "test-data";

    rev = "d775b73c106d48726653f2fd02e473b7acbd93d8";

    hash = "sha256-uxBpMx22gWJmnbF9tVuVIdYdiqUh7n51swzu5hnfZQ0=";

  };

in

python3Packages.buildPythonApplication rec {

  pname = "multiqc";

  version = "1.29";

  version = "1.30";

  pyproject = true;



  src = fetchFromGitHub {

  # Two data sources. One for the code, another for the test data

  srcs = [

    (fetchFromGitHub {

      name = "multiqc";

      owner = "MultiQC";

      repo = "MultiQC";

      tag = "v${version}";

    hash = "sha256-KKLdDNf889lEbCyNpJFZoE8rNO50CRzNP4hKpKHRAcE=";

  };

      hash = "sha256-TR5YFoWj97gpsykIzc1lqtYVePsVLRIT0HXw+VPJ7o4=";

    })

    (fetchFromGitHub {

      owner = "MultiQC";

      repo = "test-data";

      rev = "cc9f853e7892eb537e91505e0e847ff63669138d";

      hash = "sha256-/MiNnPayG6wpF2S09ENYTlEBF7Km4aH1RjdGOfMgZcA=";

      name = "test-data";

    })

  ];



  # Multiqc cannot remove temporary directories in some case.

  # Default is 10 retries, lower it to 2
@@ -37,9 +38,16 @@ python3Packages.buildPythonApplication rec { 
      --replace-fail \

        "max_retries: int = 10," \

        "max_retries: int = 2,"

    substituteInPlace pyproject.toml \

      --replace 'polars-lts-cpu' 'polars'

  '';



  build-system = with python3Packages; [ setuptools ];

  sourceRoot = "multiqc";



  nativeBuildInputs = with python3Packages; [

    setuptools

    wheel

  ];



  dependencies = with python3Packages; [

    boto3
@@ -49,25 +57,25 @@ python3Packages.buildPythonApplication rec { 
    jinja2

    kaleido

    markdown

    natsort

    numpy

    packaging

    requests

    polars

    pillow

    plotly

    pyarrow

    pyyaml

    rich

    rich-click

    coloredlogs

    spectra

    pydantic

    tiktoken

    typeguard

    tqdm

    python-dotenv

    natsort

    tiktoken

    jsonschema

    polars

    pyarrow

  ];



  optional-dependencies = {
@@ -89,19 +97,26 @@ python3Packages.buildPythonApplication rec { 
    ];

  };



  # Some tests run subprocess.run() with "multiqc"

  preCheck = ''

    ln -s ${test-data} ./test-data

    chmod -R u+w ../test-data

    ln -s ../test-data .

  '';



  # Some tests run subprocess.run() with "ps"

  nativeCheckInputs =

    (with python3Packages; [

    with python3Packages;

    [

      pytest-cov-stub

      pytest-xdist

      pytestCheckHook

    ])

    ++ [

      addBinToPathHook # Some tests run subprocess.run() with "multiqc"

      procps # Some tests run subprocess.run() with "ps"

      syrupy

      pygithub

      versionCheckHook

    ]

    ++ [

      procps

      addBinToPathHook

    ];



  versionCheckProgramArg = "--version";