pythonPackages.rds2py: init at 0.7.3 (#442058)

{

  lib,

  buildPythonPackage,

  stdenv,

  fetchFromGitHub,

  cmake,

  zlib,

  pybind11,

  pytestCheckHook,

  pytest-cov-stub,

  pkg-config,

  setuptools,

  setuptools-scm,

  biocutils,

  biocframe,

  pandas,

  scipy,

}:

buildPythonPackage rec {

  pname = "rds2py";

  version = "0.7.3";

  pyproject = true;

  src = fetchFromGitHub {

    owner = "BiocPy";

    repo = "rds2py";

    tag = version;

    hash = "sha256-GbRpkt+K2HXuAT7KtI4h1SnZ4RtSo5hrea2L92VZj/o=";

  };

  rds2cpp-src = fetchFromGitHub {

    owner = "LTLA";

    repo = "rds2cpp";

    rev = "v1.1.0";

    hash = "sha256-q7C/oORmhgXlqnZnslhyrxBc3RRF2gdgGuQU4TimxtI=";

  };

  byteme-src = fetchFromGitHub {

    owner = "LTLA";

    repo = "byteme";

    rev = "v1.2.2";

    hash = "sha256-rM/pSMGlaMWE69lYORaa8SQYGQyzhdyQnXImmAesxFA=";

  };

  # Upstream uses CMake's FetchContent to download rds2cpp and byteme into

  # build/_deps at configure time. We pre-fetch both repos and copy them

  # into build/_deps manually. This way the build tree matches what upstream expects.

  prePatch = ''

    mkdir -p build/_deps

    cp -r ${rds2cpp-src} build/_deps/rds2cpp-src

    cp -r ${byteme-src} build/_deps/byteme-src

    chmod -R u+w build/_deps

  '';

  # Patch upstream CMakeLists.txt files to use our vendored sources instead of

  # calling FetchContent. We point add_subdirectory() to the copies staged in

  # build/_deps above. We also patch rds2cpp's own extern/CMakeLists.txt to

  # disable its nested FetchContent call for byteme, since we already provide it.

  postPatch = ''

    substituteInPlace lib/CMakeLists.txt \

      --replace-fail \

        "FetchContent_MakeAvailable(byteme)" \

        "add_subdirectory(\''${CMAKE_BINARY_DIR}/../_deps/byteme-src \''${CMAKE_CURRENT_BINARY_DIR}/byteme)" \

      --replace-fail \

        "FetchContent_MakeAvailable(rds2cpp)" \

        "add_subdirectory(\''${CMAKE_BINARY_DIR}/../_deps/rds2cpp-src \''${CMAKE_CURRENT_BINARY_DIR}/rds2cpp)"

    substituteInPlace build/_deps/rds2cpp-src/extern/CMakeLists.txt \

      --replace-fail "FetchContent_MakeAvailable(byteme)" "# FetchContent_MakeAvailable(byteme) -- Patched by Nix"

  '';

  # We use the MORE_CMAKE_OPTIONS environment variable, which is a hook provided

  # by the upstream setup.py, to pass our zlib flags to the CMake configure step.

  preConfigure = ''

    export MORE_CMAKE_OPTIONS="-DZLIB_INCLUDE_DIR=${lib.getDev zlib}/include -DZLIB_LIBRARY=${lib.getLib zlib}/lib/libz.so"

  '';

  nativeBuildInputs = [

    cmake

    pkg-config

    pybind11

    zlib

  ];

  build-system = [

    setuptools

    setuptools-scm

  ];

  dependencies = [

    biocutils

  ];

  nativeCheckInputs = [

    pytest-cov-stub

    pytestCheckHook

    biocframe

    pandas

    scipy

  ];

  disabledTestPaths = [

    # Requires packages not in Nixpkgs

    "tests/test_delayedmatrices.py"

    "tests/test_granges.py"

    "tests/test_mae.py"

    "tests/test_sce.py"

    "tests/test_se.py"

  ];

  # setuptools drives the build, so disable cmake configure hook

  dontUseCmakeConfigure = true;

  pythonImportsCheck = [ "rds2py" ];

  meta = {

    description = "Read RDS files, in Python";

    homepage = "https://github.com/BiocPy/rds2py";

    license = lib.licenses.mit;

    maintainers = with lib.maintainers; [ b-rodrigues ];

  };

}

    };

  };

  rds2py = callPackage ../development/python-modules/rds2py { };

  re-assert = callPackage ../development/python-modules/re-assert { };

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