Unverified Commit 51dd6b00 authored by Aleksana's avatar Aleksana Committed by GitHub
Browse files

pymol: fix build (#429447)

parents 42cf70e8 b46ff3e4

pkgs/by-name/py/pymol/package.nix

+31 −6
Original line number Diff line number Diff line
@@ -2,6 +2,7 @@ 
  stdenv,

  lib,

  fetchFromGitHub,

  fetchpatch,

  makeDesktopItem,

  cmake,

  python3Packages,
@@ -57,11 +58,31 @@ python3Packages.buildPythonApplication rec { 


  # A script is already created by the `[project.scripts]` directive

  # in `pyproject.toml`.

  patches = [ ./script-already-exists.patch ];

  patches = [

    ./script-already-exists.patch



    # Fix python3.13 and numpy 2 compatibility

    (fetchpatch {

      url = "https://github.com/schrodinger/pymol-open-source/commit/fef4a026425d195185e84d46ab88b2bbd6d96cf8.patch";

      hash = "sha256-F/5UcYwgHgcMQ+zeigedc1rr3WkN9rhxAxH+gQfWKIY=";

    })

    (fetchpatch {

      url = "https://github.com/schrodinger/pymol-open-source/commit/97cc1797695ee0850621762491e93dc611b04165.patch";

      hash = "sha256-H2PsRFn7brYTtLff/iMvJbZ+RZr7GYElMSINa4RDYdA=";

    })

    # Fixes failing test testLoadPWG

    (fetchpatch {

      url = "https://github.com/schrodinger/pymol-open-source/commit/17c6cbd96d52e9692fd298daec6c9bda273a8aad.patch";

      hash = "sha256-dcYRzUhiaGlR3CjQ0BktA5L+8lFyVdw0+hIz3Li7gDQ=";

    })

  ];



  postPatch = ''

    substituteInPlace setup.py \

      --replace-fail "self.install_libbase" '"${placeholder "out"}/${python3Packages.python.sitePackages}"'



    substituteInPlace pyproject.toml \

      --replace-fail '"cmake>=3.13.3",' ""

  '';



  env.PREFIX_PATH = lib.optionalString (!stdenv.hostPlatform.isDarwin) "${msgpack}";
@@ -74,8 +95,6 @@ python3Packages.buildPythonApplication rec { 
  ];



  buildInputs = [

    python3Packages.numpy_1

    python3Packages.pyqt5

    qt5.qtbase

    glew

    glm
@@ -89,6 +108,11 @@ python3Packages.buildPythonApplication rec { 
    msgpack

  ];



  dependencies = with python3Packages; [

    numpy

    pyqt5

  ];



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



  postInstall =
@@ -115,6 +139,7 @@ python3Packages.buildPythonApplication rec { 
    python3Packages.msgpack

    pillow

    pytestCheckHook

    requests

  ];



  # some tests hang for some reason
@@ -151,12 +176,12 @@ python3Packages.buildPythonApplication rec { 
    wrapQtApp "$out/bin/pymol"

  '';



  meta = with lib; {

  meta = {

    inherit description;

    mainProgram = "pymol";

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

    license = licenses.mit;

    maintainers = with maintainers; [

    license = lib.licenses.mit;

    maintainers = with lib.maintainers; [

      natsukium

      samlich

    ];