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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@@ -38,7 +38,7 @@ const gemmi::Mtz::Column* SelectDefaultColumn(const gemmi::Mtz& mtz, bool& squar
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}
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// Fall back to a plain structure-factor amplitude (type F): a deposited/observed FP or FOBS, or a
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// lone FC, squared to an intensity like F-model. Lets a reference MTZ that carries only amplitudes
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// (no F-model or IMEAN/I - e.g. the KR2 8cl8 deposition, which has only FP) still seed CCref
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// (no F-model or IMEAN/I - e.g. a deposition that has only FP) still seed CCref
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// without an explicit --reference-column.
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for (const char* label : {"FP", "FOBS", "F", "FC", "Fobs", "F-obs"}) {
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if (const auto* col = mtz.column_with_label(label, nullptr, 'F')) {
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