b12f/nixpkgs
1
0
Fork 0
Code Issues Pull requests Packages Projects Releases Wiki Activity

pythonPackages.ruffus: 2.8.1 -> 2.8.4, fix build

Browse source 
simplify test execution by skipping their makefile entirely. disable tests
on darwin as they are very flaky & hang often. this is probably ok because
we're not hacking this package's source to get it installed, and the user
is probably getting something very similar as they would get using a
regular pip installation.
This commit is contained in:
Robert Scott 2020-09-25 23:37:08 +01:00 committed by Jon
parent 6efc71f17b
commit 85e6474eee
1 changed files with 12 additions and 17 deletions
Show stats Download patch file Download diff file Expand all files Collapse all files

29
pkgs/development/python-modules/ruffus/default.nix
View file

@ -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";