diff options
Diffstat (limited to 'nixpkgs/pkgs/development/python-modules/ruffus/default.nix')
| -rw-r--r-- | nixpkgs/pkgs/development/python-modules/ruffus/default.nix | 29 |
1 files changed, 12 insertions, 17 deletions
diff --git a/nixpkgs/pkgs/development/python-modules/ruffus/default.nix b/nixpkgs/pkgs/development/python-modules/ruffus/default.nix index b3f09ee88ffa..da905f7ab477 100644 --- a/nixpkgs/pkgs/development/python-modules/ruffus/default.nix +++ b/nixpkgs/pkgs/development/python-modules/ruffus/default.nix @@ -9,39 +9,34 @@ buildPythonPackage rec { pname = "ruffus"; - version = "2.8.1"; + version = "2.8.4"; src = fetchFromGitHub { owner = "cgat-developers"; repo = pname; rev = "v${version}"; - sha256 = "1gyabqafq4s2sy0prh3k1m8859shzjmfxr7fimx10liflvki96a9"; + sha256 = "0fnzpchwwqsy5h18fs0n90s51w25n0dx0l74j0ka6lvhjl5sxn4c"; }; propagatedBuildInputs = [ gevent ]; - postPatch = '' - sed -i -e 's|/bin/bash|${stdenv.shell}|' ruffus/test/Makefile - sed -i -e 's|\tpytest|\t${pytest}/bin/pytest|' ruffus/test/Makefile - sed -i -e 's|\tpython|\t${python.interpreter}|' ruffus/test/Makefile - sed -i -e 's|/usr/bin/env bash|${stdenv.shell}|' ruffus/test/run_all_unit_tests.cmd - sed -i -e 's|python3|${python.interpreter}|' ruffus/test/run_all_unit_tests3.cmd - sed -i -e 's|python %s|${python.interpreter} %s|' ruffus/test/test_drmaa_wrapper_run_job_locally.py - ''; - - makefile = "ruffus/test/Makefile"; - checkInputs = [ - gevent hostname pytest ]; + # tests very flaky & hang often on darwin + doCheck = !stdenv.isDarwin; + # test files do indeed need to be executed separately checkPhase = '' - export HOME=$TMPDIR - cd ruffus/test - make all PYTEST_OPTIONS="-q --disable-warnings" + 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 = with stdenv.lib; { description = "Light-weight Python Computational Pipeline Management"; |