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
@@ -18,7 +18,7 @@ void print_usage(Logger &logger) {
logger.Info("Options:");
logger.Info(" -i<num> Number of images");
logger.Info(" -N<num> Number of image processing threads (default: 8)");
logger.Info(" -F{<txt>} Write file, optional parameter is name (default: lyso_lite_perf_test)");
logger.Info(" -F{<txt>} Write file, optional parameter is name (default: lite_perf_test)");
logger.Info(" -X<txt> Indexing (none|fft|fftw|ffbidx), ffbidx is default");
logger.Info(" -t<num> Indexing thread pool size (default: 4)");
logger.Info(" -f<num> FFT indexing search vectors");
@@ -82,7 +82,7 @@ int main(int argc, char **argv) {
if (optarg)
filename = std::string(optarg);
else
filename = "lyso_lite_perf_test";
filename = "lite_perf_test";
break;
case 'Q':
quick_integrate = true;