depot/third_party/nixpkgs/pkgs/development/python-modules/meeko/default.nix

{
  lib,
  buildPythonPackage,
  fetchFromGitHub,
  fetchpatch,
  numpy,
  pytestCheckHook,
  pythonOlder,
  rdkit,
  scipy,
}:

buildPythonPackage rec {
  pname = "meeko";
  version = "0.5.1";
  format = "setuptools";

  disabled = pythonOlder "3.5";

  src = fetchFromGitHub {
    owner = "forlilab";
    repo = "Meeko";
    rev = "refs/tags/v${version}";
    hash = "sha256-I/kAO0a6DbDqmzjS36ETuoH/Z1gR2eNpyE3herHDKMs=";
  };

  patches = [
    # https://github.com/forlilab/Meeko/issues/60
    (fetchpatch {
      name = "fix-unknown-sidechains.patch";
      url = "https://github.com/forlilab/Meeko/commit/28c9fbfe3b778aa1bd5e8d7e4f3e6edf44633a0c.patch";
      hash = "sha256-EJbLnbKTTOsTxKtLiU7Af07yjfY63ungGUHbGvrm0AU=";
    })
    (fetchpatch {
      name = "add-test-data.patch";
      url = "https://github.com/forlilab/Meeko/commit/57b52e3afffb82685cdd1ef1bf6820d55924b97a.patch";
      hash = "sha256-nLnyIjT68iaY3lAEbH9EJ5jZflhxABBwDqw8kaRKf3k=";
    })
  ];

  propagatedBuildInputs = [
    # setup.py only requires numpy but others are needed at runtime
    numpy
    rdkit
    scipy
  ];

  nativeCheckInputs = [ pytestCheckHook ];

  pythonImportsCheck = [ "meeko" ];

  meta = {
    description = "Python package for preparing small molecule for docking";
    homepage = "https://github.com/forlilab/Meeko";
    changelog = "https://github.com/forlilab/Meeko/releases/tag/${lib.removePrefix "refs/tags/" src.rev}";
    license = lib.licenses.lgpl21Only;
    maintainers = with lib.maintainers; [ natsukium ];
  };
}