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The copykat-py and copykat_matrix console scripts returned the result dict from main(), so the generated `sys.exit(main())` wrapper printed the whole dict to stderr and exited 1 on every successful run. They now return None. pyproject.toml declared GPL-2.0 while the shipped LICENSE file is MIT; the metadata now uses the SPDX expression "MIT" with license-files (the old license table is deprecated by setuptools). The version is read from copykat_py.__version__ so it lives in one place, and project URLs and classifiers are added. Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_015f962qieP31uEsiDVYuZ6L
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Before:
pip install .already produced a working wheel, with the genome annotations and example data bundled and all five console scripts installed. But every successful run ofcopykat-pyorcopykat_matrixexited with status 1 and printed the whole result dict to stderr, so the CLIs broke shell pipelines and job schedulers. The package metadata also said GPL-2.0 while the LICENSE file it ships is MIT, and setuptools warned that the license table form is deprecated.After: both CLIs exit 0 with an empty stderr. The wheel declares
License-Expression: MITand carries the LICENSE file, the version comes fromcopykat_py.__version__alone, and the metadata has project URLs and classifiers. The build runs without warnings.The console-script wrapper setuptools generates is
sys.exit(main()), andsys.exittreats any non-None, non-int value as an error message, somain()andmatrix_main()now return None. Nothing in the repo used their return value.How:
pyproject.tomlswitches to the SPDXlicense = "MIT"withlicense-files(which needs setuptools>=77, so the build requirement is raised and the unneededwheelrequirement is dropped), movesversionto[tool.setuptools.dynamic], and adds[project.urls]and classifiers..gitignorenow ignores*.egg-info/.Verified: I built the sdist and wheel with
python -m build, installed the wheel into a fresh Python 3.13 venv and importedcopykat_pythere. I rancopykat(load_example_data(), ...)end to end. I rancopykat-pyon the bundled example matrix: exit code 0 and an empty stderr, where the same command exited 1 before this change.ruffpasses on the touched file, themypyerror count is unchanged from main (147 errors, already there), andpytest testspasses (122 tests).Not changed here: the README install section belongs to the README work going on separately. Two notes for it: the README tells users to run
copykat_anndata --help, butcopykat_anndatais a Python function, not an installed command, and the README describes thegpuextra in terms of CuPy, while the extra installs torch and triton.🤖 Generated with Claude Code
https://claude.ai/code/session_015f962qieP31uEsiDVYuZ6L
Generated by Claude Code