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>
This commit is contained in:
2026-07-15 17:19:43 +02:00
co-authored by Claude Opus 4.8
parent 0f3ccda779
commit abbee2d4dc
27 changed files with 159 additions and 4079 deletions
+2 -2
View File
@@ -1473,7 +1473,7 @@ TEST_CASE("JFJochReader_InstrumentMetadata_Sample_RingCurrent", "[HDF5][Full]")
InstrumentMetadata metadata;
metadata.InstrumentName("PXI").SourceName("SLS");
x.ImportInstrumentMetadata(metadata).SampleName("Lysozyme").RingCurrent_mA(399.5); // 0.3995 A
x.ImportInstrumentMetadata(metadata).SampleName("test_sample").RingCurrent_mA(399.5); // 0.3995 A
x.TotalFlux(1e7).AttenuatorTransmission(0.56);
x.DetectIceRings(false);
@@ -1511,7 +1511,7 @@ TEST_CASE("JFJochReader_InstrumentMetadata_Sample_RingCurrent", "[HDF5][Full]")
CHECK(dataset->experiment.GetTotalFlux() == Catch::Approx(1e7));
// Sample name
CHECK(dataset->experiment.GetSampleName() == "Lysozyme");
CHECK(dataset->experiment.GetSampleName() == "test_sample");
// Ring current read back in mA; allow small fp tolerance
CHECK(dataset->experiment.GetRingCurrent_mA().has_value());