Merge pull request #305464 from natsukium/pymol/update

in

python3Packages.buildPythonApplication rec {

  inherit pname;

  version = "2.5.0";

  version = "3.0.0";

  pyproject = true;

  src = fetchFromGitHub {

    owner = "schrodinger";

    repo = "pymol-open-source";

    rev = "v${version}";

    sha256 = "sha256-JdsgcVF1w1xFPZxVcyS+GcWg4a1Bd4SvxFOuSdlz9SM=";

    hash = "sha256-GhTHxacjGN7XklZ6gileBMRZAGq4Pp4JknNL+qGqrVE=";

  };

  postPatch = ''

    substituteInPlace setup.py \

      --replace-fail "self.install_libbase" '"${placeholder "out"}/${python3.sitePackages}"'

  '';

  build-system = [

    python3Packages.setuptools

  ];

  nativeBuildInputs = [ qt5.wrapQtAppsHook ];

  buildInputs = [ python3Packages.numpy python3Packages.pyqt5 glew glm libpng libxml2 freetype msgpack netcdf ];

  env.NIX_CFLAGS_COMPILE = "-I ${libxml2.dev}/include/libxml2";

  hardeningDisable = [ "format" ];

  installPhase = ''

    python setup.py install --home="$out"

    runHook postInstall

  '';

  postInstall = with python3Packages; ''

    wrapProgram $out/bin/pymol \

      --prefix PYTHONPATH : ${lib.makeSearchPathOutput "lib" python3.sitePackages [ pyqt5 pyqt5.pyqt5-sip ]}

    mkdir -p "$out/share/icons/"

    ln -s ../../lib/python/pymol/pymol_path/data/pymol/icons/icon2.svg "$out/share/icons/pymol.svg"

    ln -s $out/${python3.sitePackages}/pymol/pymol_path/data/pymol/icons/icon2.svg "$out/share/icons/pymol.svg"

  '' + lib.optionalString stdenv.hostPlatform.isLinux ''

    cp -r "${desktopItem}/share/applications/" "$out/share/"

  '';

  pythonImportsCheck = [

    "pymol"

  ];

  nativeCheckInputs = with python3Packages; [

    python3Packages.msgpack

    pillow

    pytestCheckHook

  ];

  # some tests hang for some reason

  doCheck = !(stdenv.hostPlatform.isLinux && stdenv.hostPlatform.isAarch64);

  disabledTestPaths = [

    # require biopython which is broken as of 2024-04-20

    "tests/api/seqalign.py"

  ];

  disabledTests = [

    # the output image does not exactly match

    "test_commands"

    # touch the network

    "testFetch"

    # requires collada2gltf which is not included in nixpkgs

    "testglTF"

    # require mmtf-cpp which does not support darwin

    "testMMTF"

    "testSave_symmetry__mmtf"

  ];

  preCheck = ''

    cd testing

  '';

  __darwinAllowLocalNetworking = true;

  preFixup = ''

    wrapQtApp "$out/bin/pymol"

  '';

    mainProgram = "pymol";

    homepage = "https://www.pymol.org/";

    license = licenses.mit;

    maintainers = with maintainers; [ samlich ];

    maintainers = with maintainers; [ natsukium samlich ];

  };

}