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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@@ -151,7 +151,7 @@ TEST_CASE("RugnuxCommandLine_Full", "[process]") {
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config.rotation_indexing_image_count = 30;
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config.spot_finding = DiffractionExperiment::DefaultDataProcessingSettings();
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const std::string cmd = RugnuxCommandLine(config, x, "/data/lyso_master.h5");
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const std::string cmd = RugnuxCommandLine(config, x, "/data/test_master.h5");
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CHECK(cmd.rfind("rugnux", 0) == 0);
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CHECK(cmd.find("-N 8") != std::string::npos);
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CHECK(cmd.find("-e 500") != std::string::npos);
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@@ -162,7 +162,7 @@ TEST_CASE("RugnuxCommandLine_Full", "[process]") {
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// would not re-parse (getopt would leave 30 as a positional and drop the count).
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CHECK(cmd.find("-R30") != std::string::npos);
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CHECK(cmd.find("-R 30") == std::string::npos);
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CHECK(cmd.find("/data/lyso_master.h5") != std::string::npos);
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CHECK(cmd.find("/data/test_master.h5") != std::string::npos);
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}
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TEST_CASE("RugnuxCommandLine_AzInt", "[process]") {
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