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