python3Packages.ruffus: drop (#501909)

{

  gevent,

  buildPythonPackage,

  fetchFromGitHub,

  hostname,

  pytest,

  pythonAtLeast,

  lib,

  stdenv,

}:

buildPythonPackage rec {

  pname = "ruffus";

  version = "2.8.4";

  format = "setuptools";

  src = fetchFromGitHub {

    owner = "cgat-developers";

    repo = "ruffus";

    rev = "v${version}";

    sha256 = "0fnzpchwwqsy5h18fs0n90s51w25n0dx0l74j0ka6lvhjl5sxn4c";

  };

  propagatedBuildInputs = [ gevent ];

  nativeCheckInputs = [

    hostname

    pytest

  ];

  # tests very flaky & hang often on darwin

  doCheck = !stdenv.hostPlatform.isDarwin;

  checkPhase =

    # https://docs.python.org/3/whatsnew/3.13.html#re

    lib.optionalString (pythonAtLeast "3.13") ''

      substituteInPlace ruffus/test/test_ruffus_utility.py \

        --replace-fail re.error re.PatternError

    ''

    # test files do indeed need to be executed separately

    + ''

      pushd ruffus/test

      rm test_with_logger.py  # spawns 500 processes

      for f in test_*.py ; do

        HOME=$TMPDIR pytest -v --disable-warnings $f

      done

      popd

    '';

  pythonImportsCheck = [ "ruffus" ];

  meta = {

    description = "Light-weight Python Computational Pipeline Management";

    homepage = "http://www.ruffus.org.uk";

    license = lib.licenses.mit;

    maintainers = [ ];

  };

}

  ruamel_base = throw "'ruamel_base' has been renamed to/replaced by 'ruamel-base'"; # Converted to throw 2025-10-29

  ruamel_yaml = throw "'ruamel_yaml' has been renamed to/replaced by 'ruamel-yaml'"; # Converted to throw 2025-10-29

  ruamel_yaml_clib = throw "'ruamel_yaml_clib' has been renamed to/replaced by 'ruamel-yaml-clib'"; # Converted to throw 2025-10-29

  ruffus = throw "'ruffus' has been removed as it was unmaintained and abandoned upstream"; # Added 2026-03-21

  sapi-python-client = throw "'sapi-python-client' has been renamed to/replaced by 'kbcstorage'"; # Converted to throw 2025-10-29

  schemainspect = throw "schemainspect has been removed because it has transitively been marked broken since May 2024, and is unmaintained upstream."; # Added 2025-10-11

  scikitimage = throw "'scikitimage' has been renamed to/replaced by 'scikit-image'"; # Converted to throw 2025-10-29

  ruff-api = callPackage ../development/python-modules/ruff-api { };

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

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

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