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Don't return the result dict from the CLI entry points #3

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Don't return the result dict from the CLI entry points #3

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Don't return the result dict from the CLI entry points 
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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@toresbe @claude
toresbe and claude committed Oct 8, 2026
commit b6132e7bf01fd97cf9d8a735f016e413b78db000
4 changes: 2 additions & 2 deletions copykat_py/cli.py
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Original file line number Diff line number Diff line change
Expand Up @@ -470,7 +470,7 @@ def main():
parser = _build_main_parser()
args = parser.parse_args()
rawmat = _load_matrix_input(args.input, args.genes, args.barcodes)
return _run_copykat_analysis(
_run_copykat_analysis(
args,
rawmat,
meta_csv=None,
Expand All @@ -485,7 +485,7 @@ def matrix_main():
parser = _build_matrix_parser()
args = parser.parse_args()
rawmat = _load_matrix_input(args.input, args.genes, args.barcodes)
return _run_copykat_analysis(
_run_copykat_analysis(
args,
rawmat,
meta_csv=args.meta,
Expand Down