cherry pick and define EXPDIR

src/wxflow/configuration.py

@@ -1,6 +1,7 @@
 import glob
 import os
 import random
+import shutil
 import subprocess
 from pathlib import Path
 from pprint import pprint
@@ -107,8 +108,9 @@ def _get_shell_env(scripts: List) -> Dict[str, Any]:
         runme = ''.join([f'source {s} ; ' for s in scripts])
         magic = f'--- ENVIRONMENT BEGIN {random.randint(0,64**5)} ---'
         runme += f'/bin/echo -n "{magic}" ; /usr/bin/env -0'
+        bash_path = shutil.which('bash')
         with open('/dev/null', 'w') as null:
-            env = subprocess.Popen(runme, shell=True, stdin=null.fileno(),
+            env = subprocess.Popen(runme, shell=True, executable=bash_path, stdin=null.fileno(),
                                    stdout=subprocess.PIPE)
             (out, err) = env.communicate()
         out = out.decode()

tests/test_configuration.py

@@ -27,6 +27,7 @@
 export SOME_BOOL4=NO
 export SOME_BOOL5=.false.
 export SOME_BOOL6=.F.
+export EXPDIR="SOME_VALUE_FOR_EXPDIR"
 """
 
 file1 = """#!/bin/bash
@@ -144,7 +145,6 @@ def test_configuration_config_dir(tmp_path, create_configs):
     assert cfg.config_dir == tmp_path
 
 
-@pytest.mark.skip(reason="fails in GH runner, passes on localhost")
 def test_configuration_config_files(tmp_path, create_configs):
     cfg = Configuration(tmp_path)
     config_files = [str(tmp_path / 'config.file0'), str(tmp_path / 'config.file1')]
@@ -157,14 +157,12 @@ def test_find_config(tmp_path, create_configs):
     assert str(tmp_path / 'config.file0') == file0
 
 
-@pytest.mark.skip(reason="fails in GH runner, passes on localhost")
 def test_parse_config1(tmp_path, create_configs):
     cfg = Configuration(tmp_path)
     f0 = cfg.parse_config('config.file0')
     assert file0_dict == f0
 
 
-@pytest.mark.skip(reason="fails in GH runner, passes on localhost")
 def test_parse_config2(tmp_path, create_configs):
     cfg = Configuration(tmp_path)
     ff = cfg.parse_config(['config.file0', 'config.file1'])