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
+4 -4
View File
@@ -25,7 +25,7 @@ namespace {
public:
using Catch::EventListenerBase::EventListenerBase;
void testRunStarting(Catch::TestRunInfo const &) override {
const bool rot = jfjoch_test::LargeDataFile("lyso_rotation_master.h5").has_value();
const bool rot = jfjoch_test::LargeDataFile("rotation_master.h5").has_value();
std::cout << "[jfjoch_test] large dataset in " << jfjoch_test::LargeDataDir()
<< ": rotation=" << (rot ? "yes" : "no")
<< " ([large] tests skip when absent)" << std::endl;
@@ -40,10 +40,10 @@ namespace {
CATCH_REGISTER_LISTENER(LargeDataListener)
TEST_CASE("Rugnux_LysoRotation", "[large]") {
const auto master = jfjoch_test::LargeDataFile("lyso_rotation_master.h5");
TEST_CASE("Rugnux_Rotation", "[large]") {
const auto master = jfjoch_test::LargeDataFile("rotation_master.h5");
if (!master)
SKIP("lyso_rotation_master.h5 not available (git-lfs data not pulled)");
SKIP("rotation_master.h5 not available (git-lfs data not pulled)");
RegisterHDF5Filter();
JFJochHDF5Reader reader;