fix(lint): use repo-root-relative path in `git restore` call in `container_configs` by Copilot · Pull Request #4301 · nf-core/tools

Copilot · 2026-05-26T14:40:46Z

Completed Fixes for container_configs lint

Fixes Implemented

Primary fix: Replaced git-diff detection with content comparison
- Use-case: Enable testing of patches etc. to stable releases of nf-core/tools not just dev
- Snapshots file content before generation
- Compares new content to snapshot after generation
- Eliminates false "out of date" failures when configs are regenerated but not committed

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.

Secondary fix: Removed git restore dependency
- No longer uses git restore with relative paths
- Writes back snapshotted content directly
- Fixes relative wf_path bugs

Tests Added

test_container_configs_uncommitted_but_correct_passes: Key scenario where modules update regenerated configs without committing
test_container_configs_working_tree_restored_after_lint: Verifies working tree restoration
test_container_configs_restore_with_relative_wf_path: Verifies relative path handling

PR Status

Branch: copilot/fix-container-configs-bug
PR: fix(lint): use repo-root-relative path in git restore call in container_configs #4301
Ready for review and merge

jpfeuffer · 2026-05-26T14:42:44Z

@copilot resolve the merge conflicts in this pull request

Copilot · 2026-05-26T14:44:52Z

@copilot resolve the merge conflicts in this pull request

Merge conflicts resolved in 388429e. The only conflicting file was container_configs.py — the resolution keeps all log.debug calls from dev alongside the repo_root fix from this branch.

mashehu

please add a test to tests/pipelines/lint/test_container_configs.py to test this scenario.

codecov · 2026-05-26T15:21:13Z

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✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 70.68%. Comparing base (f2f69f4) to head (e11140f).

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codecov · 2026-05-26T15:44:41Z

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 78.39%. Comparing base (3f64b31) to head (f121a46).
⚠️ Report is 1 commits behind head on dev.

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mashehu · 2026-07-01T13:45:01Z

nice fix! I guess the PR title needs to be updated.

We actually have a similar logic already in files_unchanged.py, where we use filecmp.cmp().
Could you switch to that way of comparing files please?

github-actions · 2026-09-06T00:08:26Z

This PR has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment if it is still useful.

mashehu · 2026-10-13T09:44:09Z

went back to an in-memory only checking of differences. These files are not in the template, so it is different than what files_unchanged.py does. Sorry for the back and forth.

mashehu · 2026-10-13T10:25:38Z

@nf-core-bot changelog

…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> # Conflicts: # nf_core/pipelines/lint/container_configs.py

…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>

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>

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>

Agent-Logs-Url: https://github.com/nf-core/tools/sessions/660f217b-3360-4cc5-8f61-35616aadd65e Co-authored-by: jpfeuffer <8102638+jpfeuffer@users.noreply.github.com>

Sorry for the back and forth

Co-authored-by: JulianFlesch <julian.flesch@qbic.uni-tuebingen.de>

Copilot AI assigned Copilot and jpfeuffer May 26, 2026

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jpfeuffer changed the base branch from main to dev May 26, 2026 14:41

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mashehu force-pushed the copilot/fix-container-configs-bug branch from 3f59ea5 to 974a0fd Compare October 9, 2026 15:02

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Copilot AI and others added 9 commits October 13, 2026 12:28

fix: correct type annotation for snapshot dict (str, not str | None)

a671daa

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>

test: add relative wf-path test for container_configs lint

a3afd10

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>

test: properly test relative wf_path in container_configs

d9dd26a

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>

fix: use Path.cwd() instead of os.getcwd() for lint compliance

84ef74f

Agent-Logs-Url: https://github.com/nf-core/tools/sessions/660f217b-3360-4cc5-8f61-35616aadd65e Co-authored-by: jpfeuffer <8102638+jpfeuffer@users.noreply.github.com>

rewrite to use filecmp like we do in file_unchanged

c47f624

go back to in-memory handling of comparison checks

dc913df

Sorry for the back and forth

[automated] Update CHANGELOG.md [skip ci]

465ec20

mashehu force-pushed the copilot/fix-container-configs-bug branch from 923d492 to 465ec20 Compare October 13, 2026 10:28

[automated] Update Template snapshots

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mashehu and others added 2 commits October 13, 2026 14:20

Update nf_core/pipelines/lint/container_configs.py

8f863be

Co-authored-by: JulianFlesch <julian.flesch@qbic.uni-tuebingen.de>

update snapshots

f121a46

mashehu enabled auto-merge (squash) October 13, 2026 12:47

mashehu merged commit cfba18b into dev Oct 13, 2026
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codspeed Bot mentioned this pull request Oct 15, 2026

Resolve template merge conflicts in nf-core pipelines sync #4519

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fix(lint): use repo-root-relative path in `git restore` call in `container_configs` - #4301

fix(lint): use repo-root-relative path in `git restore` call in `container_configs`#4301
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Completed Fixes for container_configs lint

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