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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@@ -18,7 +18,7 @@ void print_usage(Logger &logger) {
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logger.Info("Options:");
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logger.Info(" -i<num> Number of images");
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logger.Info(" -N<num> Number of image processing threads (default: 8)");
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logger.Info(" -F{<txt>} Write file, optional parameter is name (default: lyso_lite_perf_test)");
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logger.Info(" -F{<txt>} Write file, optional parameter is name (default: lite_perf_test)");
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logger.Info(" -X<txt> Indexing (none|fft|fftw|ffbidx), ffbidx is default");
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logger.Info(" -t<num> Indexing thread pool size (default: 4)");
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logger.Info(" -f<num> FFT indexing search vectors");
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@@ -82,7 +82,7 @@ int main(int argc, char **argv) {
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if (optarg)
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filename = std::string(optarg);
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else
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filename = "lyso_lite_perf_test";
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filename = "lite_perf_test";
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break;
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case 'Q':
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quick_integrate = true;
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