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
@@ -40,8 +40,8 @@ TEST_CASE("CBORSerialize_Start", "[CBOR]") {
.storage_cell_delay_ns = 15345,
.pixel_mask_enabled = true,
.arm_date = "abc",
.sample_name = "lyso",
.file_prefix = "lyso1/dir/file",
.sample_name = "test_sample",
.file_prefix = "test_sample/dir/file",
.images_per_file = 12345,
.channels = {"default", "sc2"},
.detector_description = "EIGER 16M",