Remove sample identities from the repository; document the rule
Datasets may be confidential; sample names and measured unit cells committed to the repo can leak outside the group working on them. Scrub existing occurrences and add a "No sample identities in the repository" section to CLAUDE.md (forbidden: sample/dataset names, internal codes, measured cells tied to a sample; fine: space group / lattice / twinning descriptors). - Comments: replace internal dataset codes and protein names with the crystallographic situation they illustrate (centred vs pseudo-symmetric, holohedral, cubic, F-cubic/hexagonal, ...). - Docs: same, in the analysis/writer/stream references and example configs. - Tests: rename sample-named identifiers, TEST_CASE names, file prefixes and asserted labels to neutral crystallographic names (e.g. tetragonal_uc); behaviour unchanged. Reduce the CrystFEL reference PDB to a bare CRYST1 cell file (cell.pdb) and rename the reference data file. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
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@@ -221,7 +221,7 @@ ModelValidationResult ValidateAgainstModel(const std::vector<MergedReflection> &
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// intensities (at the merge stage for rotation data, per image in stills scaling), and that
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// choice is authoritative - we keep it. Only with a model and NO reference do we resolve the
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// ambiguity here, as a fallback, by fitting each candidate reindexing and keeping the lowest
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// R-free. A no-op either way for a holohedral crystal (no twin laws), e.g. lysozyme. The
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// R-free. A no-op either way for a holohedral crystal (no twin laws). The
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// enantiomorph/screw ambiguity is never probed by R-free: |Fcalc| is the same for both hands, so
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// it cannot distinguish them - that is taken from the model hand above.
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Fit best = fit_model(obs);
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