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
@@ -366,7 +366,7 @@ TEST_CASE("ZstdHuff_MaskLike", "[ZSTD]") {
RequireHuffRoundTrip(image);
}
TEST_CASE("ZstdHuff_LysoImage", "[ZSTD]") {
TEST_CASE("ZstdHuff_BenchmarkImage", "[ZSTD]") {
RegisterHDF5Filter(); // bitshuffle filter, needed to read the compressed benchmark dataset
HDF5ReadOnlyFile data("../../tests/test_data/compression_benchmark.h5");
HDF5DataSet dataset(data, "/entry/data/data");