fix(lint): use repo-root-relative path in git restore call in container_configs#4301
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fix(lint): use repo-root-relative path in git restore call in container_configs#4301Copilot wants to merge 7 commits into
git restore call in container_configs#4301Copilot wants to merge 7 commits into
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…figs.py Agent-Logs-Url: https://github.com/nf-core/tools/sessions/1d9f4c7e-f5d1-42ae-9baa-8e581e139ebb Co-authored-by: jpfeuffer <8102638+jpfeuffer@users.noreply.github.com>
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@copilot resolve the merge conflicts in this pull request |
…configs-bug # Conflicts: # nf_core/pipelines/lint/container_configs.py Co-authored-by: jpfeuffer <8102638+jpfeuffer@users.noreply.github.com>
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please add a test to tests/pipelines/lint/test_container_configs.py to test this scenario.
…configs lint The old approach used repo.index.diff(None) to detect stale configs, which compared the working tree against HEAD. This caused false 'out of date' failures when configs were already regenerated (e.g. by modules update) but not yet committed. The new approach: 1. Snapshots file content on disk before generation 2. Generates new configs 3. Compares new content to the snapshot 4. If unchanged → pass; if different → fail This makes the lint correct regardless of the git commit state. The restore logic now simply writes back the saved content instead of using git restore, which also fixes the original repo-root-relative path bug. Also adds two new tests: - test_container_configs_uncommitted_but_correct_passes: verifies that uncommitted but correct configs don't produce false failures - test_container_configs_working_tree_restored_after_lint: verifies the working tree is properly restored after lint Agent-Logs-Url: https://github.com/nf-core/tools/sessions/e3bf8950-f65b-4a3d-9b94-e3a275b359eb Co-authored-by: jpfeuffer <8102638+jpfeuffer@users.noreply.github.com>
Agent-Logs-Url: https://github.com/nf-core/tools/sessions/e3bf8950-f65b-4a3d-9b94-e3a275b359eb Co-authored-by: jpfeuffer <8102638+jpfeuffer@users.noreply.github.com>
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Agent-Logs-Url: https://github.com/nf-core/tools/sessions/f898f098-3f2a-4e3f-8bbd-2fe45e5fed00 Co-authored-by: jpfeuffer <8102638+jpfeuffer@users.noreply.github.com>
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Agent-Logs-Url: https://github.com/nf-core/tools/sessions/0c47257c-1ebc-4639-95c8-377dc2159244 Co-authored-by: jpfeuffer <8102638+jpfeuffer@users.noreply.github.com>
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Completed Fixes for container_configs lint
Fixes Implemented
I think this is the right thing to do, even if you do not need testing of older releases. It just did not come up because your container configs were always update during checkout already and modules update did not change anything.
git restorewith relative pathsTests Added
test_container_configs_uncommitted_but_correct_passes: Key scenario where modules update regenerated configs without committingtest_container_configs_working_tree_restored_after_lint: Verifies working tree restorationtest_container_configs_restore_with_relative_wf_path: Verifies relative path handlingPR Status
copilot/fix-container-configs-buggit restorecall incontainer_configs#4301