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

pkgs/development/python-modules/ruffus/default.nix

deleted100644 → 0
+0 −56
Original line number Diff line number Diff line 
{

  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 = [ ];

  };

}

pkgs/top-level/python-aliases.nix

+1 −0
Original line number Diff line number Diff line
@@ -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

pkgs/top-level/python-packages.nix

+0 −2
Original line number Diff line number Diff line
@@ -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 { };