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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@@ -1473,7 +1473,7 @@ TEST_CASE("JFJochReader_InstrumentMetadata_Sample_RingCurrent", "[HDF5][Full]")
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InstrumentMetadata metadata;
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metadata.InstrumentName("PXI").SourceName("SLS");
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x.ImportInstrumentMetadata(metadata).SampleName("Lysozyme").RingCurrent_mA(399.5); // 0.3995 A
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x.ImportInstrumentMetadata(metadata).SampleName("test_sample").RingCurrent_mA(399.5); // 0.3995 A
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x.TotalFlux(1e7).AttenuatorTransmission(0.56);
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x.DetectIceRings(false);
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@@ -1511,7 +1511,7 @@ TEST_CASE("JFJochReader_InstrumentMetadata_Sample_RingCurrent", "[HDF5][Full]")
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CHECK(dataset->experiment.GetTotalFlux() == Catch::Approx(1e7));
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// Sample name
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CHECK(dataset->experiment.GetSampleName() == "Lysozyme");
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CHECK(dataset->experiment.GetSampleName() == "test_sample");
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// Ring current read back in mA; allow small fp tolerance
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CHECK(dataset->experiment.GetRingCurrent_mA().has_value());
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