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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 #4301

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1779554
fix: use repo-root-relative path in git restore call in container_con…
Copilot May 26, 2026
388429e
Merge remote-tracking branch 'origin/dev' into copilot/fix-container-…
Copilot May 26, 2026
4c9af23
fix: replace git-diff detection with content comparison in container_…
Copilot May 26, 2026
7f82f8b
fix: correct type annotation for snapshot dict (str, not str | None)
Copilot May 26, 2026
e11140f
test: add relative wf-path test for container_configs lint
Copilot May 26, 2026
cfae19d
test: properly test relative wf_path in container_configs
Copilot May 26, 2026
2eebf84
fix: use Path.cwd() instead of os.getcwd() for lint compliance
Copilot May 26, 2026
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3 changes: 2 additions & 1 deletion nf_core/pipelines/lint/container_configs.py
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Original file line number Diff line number Diff line change
Expand Up @@ -78,8 +78,9 @@ def container_configs(self):
if not fixing:
# Restore working tree: reset modified tracked files and delete new untracked ones
log.debug(f"Restoring working tree: resetting {len(modified)} modified, removing {len(new)} new file(s)")
repo_root = Path(repo.working_tree_dir).resolve()
for name in modified:
repo.git.restore(str(conf_dir / name))
repo.git.restore(str((conf_dir / name).resolve().relative_to(repo_root)))
for name in new:
(conf_dir / name).unlink(missing_ok=True)

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