Rename tpm to cpm throughout the API (breaking) (2.1.0) - #45
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Everywhere "tpm" appeared, the formula was count / total_reads * 1e6 -- CPM, with no transcript-length normalization. Only the name was wrong; for full-length long reads this is the right metric already, since read count is already a direct proxy for molecule count. Also updated tutorial notebooks referencing the old tpm= API, since there's no deprecated alias. Bumps to 2.1.0 (minor, since this breaks existing code).
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Summary
Everywhere "tpm" appeared in the API, the formula was
count / total_reads_in_sample * 1e6-- CPM, with no transcript-length normalization. Renamed throughout to match:transcript_table(cpm=..., cpm_pseudocount=...),_cpm/_sum_cpmcolumns,Gene.cpm(),estimate_cpm_threshold(was in__init__.py's__all__), therun_isotoolsCLI, and all docstrings/plot labels.Clean break, no deprecated alias --
tpm=now raisesTypeError. The computation itself is unchanged (still CPM), so this is a rename, not a math change.Also updated the 6 tutorial notebooks referencing the old
tpm=API/wording, so the published tutorials don't show broken code.Bumps to 2.1.0 (minor, not patch, since this breaks existing user code).
Test plan
pytestsuite passes (20 passed), including a new regression test verifying the CPM formula andGene.cpm()tpm=now raisesTypeErrorflake8/blackcleanpython -m build+twine check dist/*pass at 2.1.0