Automatically sync the Rocrate and README content during pipelines lint #3688
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| # Ensure the fix rocrate_readme_sync is in the fix list | ||
| if "rocrate_readme_sync" not in self.fix: | ||
| self.fix += ("rocrate_readme_sync",) |
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if we are not using the --fix flag this can be removed, also the if at line 61
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Hi! I think this fix flag is not necessary anymore if we automate the update process. I.e. all the changes would be synchronized anyway during linting (according to my understanding, sorry if I'm wrong about it).
And in this case --fix is still available but always set to true, just in case we want to disable it again someday.
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I would remove it completely then, it makes the code more confusing to follow, at least for me 😄
| # Compare the two strings and add a linting error if they don't match | ||
| if readme_content != rc_description_graph: | ||
| # If the --fix flag is set, you could overwrite the RO-Crate description with the README content: | ||
| if "rocrate_readme_sync" in self.fix: |
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we don't need this check anymore
| assert len(results.get("failed", [])) == 0 | ||
| assert len(results.get("passed", [])) > 0 | ||
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| def test_rocrate_readme_sync_fail(self): |
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this test is still valid, no?
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I removed it because there won't be any "failed" cases anymore👀 shall I always keep the tests for all cases?
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We still have the error (at rocrate_readme_sync.py line 66), so I would keep the test.
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There won't be failed cases if I remove all the checks such as if "rocrate_readme_sync" in self.fix: ..., so I guess this test would anyway be not necessary anymore?
| fixed.append("Mismatch fixed: RO-Crate description updated from `README.md`.") | ||
| else: | ||
| failed.append( | ||
| "The RO-Crate descriptions do not match the README.md content. Use `nf-core pipelines lint --fix rocrate_readme_sync` to update." |
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update the error to remove mention to --fix flag
Sync the content automatically when there's any changes in the README file, as mentioned here. The flag
--fixis not available for this case anymore.PR checklist
CHANGELOG.mdis updateddocsis updated