pliers
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a single test failing with permission denied when running in docker as a "pliers" user
on top of #347 decided to add running tests while building docker image from within WORKDIR... the only one failing is
=================================== FAILURES ===================================
________________________ test_load_from_standard_paths _________________________
def test_load_from_standard_paths():
# Verify defaults
reset_options(update_from_file=False)
assert pliers.config._settings == pliers.config._default_settings
# Verify that PLIERS_CONFIG and local dir take precedence
env_config = {"n_jobs": 200, "log_transformations": False}
cwd_config = {"log_transformations": True, "parallelize": True}
handle, f = tempfile.mkstemp(suffix='.json')
json.dump(env_config, open(f, 'w'))
os.environ['PLIERS_CONFIG'] = f
target = 'pliers_config.json'
if os.path.exists(target):
pytest.skip("Cannot test pliers config because the default config file"
" (pliers_config.json) already exists in the current "
"working directory. Skipping test to avoid overwriting.")
> json.dump(cwd_config, open(target, 'w'))
E PermissionError: [Errno 13] Permission denied: 'pliers_config.json'
/opt/pliers/pliers/tests/test_config.py:28: PermissionError
=============================== warnings summary ===============================
shouldn't it just skip the test then?
or ideally never write in the current directory. also it would fail now if config exists but a broken symlink (annexed file) -- use lexists
not just exists
for that