Add --force-superseded collator option (issue #87) - #88
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Force all otherwise-unchanged crystals to 'superseded' status so they are re-processed and included in the next upload. This is needed when something that matters (e.g. assemblies.yaml) has changed but the PDB files have not. The flag is honoured both when determining status (_get_xtal_status) and when copying crystallographic files (_copy_files) so that the forced entries have their files re-copied into the current version dir and their metadata paths updated, rather than continuing to reference the previous upload. Includes unit tests for status determination and an integration test that excludes a dataset from upload_1, re-introduces it in upload_2 with --force-superseded, and checks the resulting status values, metadata file paths and copied files. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
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Closes #87.
What
Adds a per-run
--force-supersededflag to the collator that forces every crystal which would otherwise beunchangedtosupersededstatus, so it is re-processed and included in the next upload.This is needed when something that matters has changed but the PDB files have not — for example an edit to
assemblies.yaml. Normally such crystals are markedunchanged(based on a PDB SHA256 comparison), left out of the upload, and skipped by the aligner.How
The flag is honoured in two places:
_get_xtal_status— an otherwise-unchangedcrystal is promoted tosuperseded.newcrystals staynew; rejected crystals staydeprecated._copy_files— the PDB/MTZ/CIF/event-map copy decisions (previously driven solely by per-file SHA256 comparison, independent of status) also honour the flag, so the forced entries have their files re-copied into the current version dir and their metadata paths updated. Without this, the status flipped tosupersededbut the files stayed in the previous upload and the metadata kept pointing there.Tests
tests/test_collator_status.py— unit tests for_get_xtal_status(unchanged / superseded / force-promoted / rejected-stays-deprecated).tests/test_force_superseded.py— integration test: excludes a dataset from upload_1, re-introduces it in upload_2 withforce_superseded=True, and asserts the resulting status values, metadata file paths (upload_2/...) and that the files were actually copied.Full suite: 70 passed.
Docs
docs/source/USER-GUIDE.mdgains a "Forcing structures into an upload" subsection documenting the flag.🤖 Generated with Claude Code