Unverified Commit a9ba7631 authored by Tom Hunze's avatar Tom Hunze
Browse files

python3Packages.ruffus: drop

ruffus has been abandoned upstream since July 2021 [1], is broken with
Python 3.14 [2], and is unmaintained in nixpkgs.

[1] https://github.com/cgat-developers/ruffus
[2] https://hydra.nixos.org/build/323541184/nixlog/1
parent 09061f74
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+0 −56
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{
  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 = [ ];
  };
}
+1 −0
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@@ -497,6 +497,7 @@ mapAliases {
  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
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@@ -17089,8 +17089,6 @@ self: super: with self; {
  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 { };