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main() and matrix_main() returned the result of _run_copykat_analysis(). The console scripts generated for [project.scripts] call sys.exit(main()), and sys.exit() given a non-integer prints it to stderr and exits with status 1, so every successful copykat-py / copykat_matrix run printed the whole result dict to stderr and reported failure. Python callers who want the results use copykat() or copykat_anndata(), which are unchanged. Fixes #2 Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
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Fixes #2.
main()andmatrix_main()returned the result dict from_run_copykat_analysis(). The console scripts generated for[project.scripts]callsys.exit(main()), andsys.exit()given a non-integer exits with status 1, so every successfulcopykat-py/copykat_matrixrun reported failure to the shell, workflow managers and schedulers.The two entry points now just run the analysis without returning its result.
copykat()andcopykat_anndata(), the Python APIs, still return the results as before.Checked, with the package installed normally (so the generated console scripts are used) and the 302-cell built-in example exported as
.mtx:maincopykat-pyexit statuscopykat_matrixexit statusprediction.txt,CNA_results.txtandCNA_raw_results_gene_by_cell.txtare byte-identical tomainfor both commands.🤖 Generated with Claude Code