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
+1 -1
View File
@@ -221,7 +221,7 @@ ModelValidationResult ValidateAgainstModel(const std::vector<MergedReflection> &
// intensities (at the merge stage for rotation data, per image in stills scaling), and that
// choice is authoritative - we keep it. Only with a model and NO reference do we resolve the
// ambiguity here, as a fallback, by fitting each candidate reindexing and keeping the lowest
// R-free. A no-op either way for a holohedral crystal (no twin laws), e.g. lysozyme. The
// R-free. A no-op either way for a holohedral crystal (no twin laws). The
// enantiomorph/screw ambiguity is never probed by R-free: |Fcalc| is the same for both hands, so
// it cannot distinguish them - that is taken from the model hand above.
Fit best = fit_model(obs);