From 85e6474eeec3d510aac82c15b55d249731a22b7b Mon Sep 17 00:00:00 2001
From: Robert Scott <code@humanleg.org.uk>
Date: Fri, 25 Sep 2020 23:37:08 +0100
Subject: [PATCH] pythonPackages.ruffus: 2.8.1 -> 2.8.4, fix build

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.
---
 .../python-modules/ruffus/default.nix         | 29 ++++++++-----------
 1 file changed, 12 insertions(+), 17 deletions(-)

diff --git a/pkgs/development/python-modules/ruffus/default.nix b/pkgs/development/python-modules/ruffus/default.nix
index b3f09ee88ff..da905f7ab47 100644
--- a/pkgs/development/python-modules/ruffus/default.nix
+++ b/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";