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source bash configurations #36

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merged 4 commits into from
Jun 27, 2024
Merged

source bash configurations #36

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c0e8aaf
cherry pick and define EXPDIR
aerorahul Jun 26, 2024
bad1489
add EXPDIR in the validation dict
aerorahul Jun 26, 2024
bbe7ea8
define USER in the configuration test and watch it fail (maybe?)
aerorahul Jun 26, 2024
239773c
remove EXPDIR and USER from the config tests
aerorahul Jun 26, 2024
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4 changes: 3 additions & 1 deletion src/wxflow/configuration.py
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Original file line number Diff line number Diff line change
@@ -1,6 +1,7 @@
import glob
import os
import random
import shutil
import subprocess
from pathlib import Path
from pprint import pprint
Expand Down Expand Up @@ -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()
Expand Down
3 changes: 0 additions & 3 deletions tests/test_configuration.py
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Expand Up @@ -144,7 +144,6 @@ 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')]
Expand All @@ -157,14 +156,12 @@ 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'])
Expand Down