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Configure the default module repository, branch, and path from environment variables. #3481

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Merged
edanielson-ginkgo merged 4 commits into from
Mar 6, 2025
Merged

Configure the default module repository, branch, and path from environment variables. #3481

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d8ab00a
Take default component repo, branch, and org from environment variables
edanielson-ginkgo Mar 5, 2025
109291e
Add test for using the environment variables
edanielson-ginkgo Mar 5, 2025
cf27f83
[automated] Update CHANGELOG.md
nf-core-bot Mar 5, 2025
b221780
Clean up comments
edanielson-ginkgo Mar 5, 2025
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Clean up comments
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@edanielson-ginkgo
edanielson-ginkgo committed Mar 5, 2025
commit b221780cac2968bdbbe355f8f7b6c116ab2d5b27
4 changes: 0 additions & 4 deletions tests/components/test_components_utils.py
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Original file line number Diff line number Diff line change
Expand Up @@ -62,24 +62,20 @@ def test_get_biotools_ch_info_warn(self):

def test_environment_variables_override(self):
"""Test environment variables override default values"""
# Define environment variables to mock
mock_env = {
"NF_CORE_MODULES_NAME": "custom-name",
"NF_CORE_MODULES_REMOTE": "https://custom-repo.git",
"NF_CORE_MODULES_DEFAULT_BRANCH": "custom-branch",
}

# Use mock as a context manager
try:
with mock.patch.dict(os.environ, mock_env):
importlib.reload(nf_core.components.components_utils)
# Check custom values are used
assert nf_core.components.components_utils.NF_CORE_MODULES_NAME == mock_env["NF_CORE_MODULES_NAME"]
assert nf_core.components.components_utils.NF_CORE_MODULES_REMOTE == mock_env["NF_CORE_MODULES_REMOTE"]
assert (
nf_core.components.components_utils.NF_CORE_MODULES_DEFAULT_BRANCH
== mock_env["NF_CORE_MODULES_DEFAULT_BRANCH"]
)
finally:
# Restore original values
importlib.reload(nf_core.components.components_utils)
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