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Use gtfparse 3 with explicit pandas 3 coverage - #485
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This was referenced Oct 6, 2026
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coverage: 93.289%. remained the same — deps/gtfparse3-pandas3 into master |
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Require gtfparse 3.0.2+ and PyEnsembl 2.24.1+ so Topiary can share the current annotation stack with Varcode. Both public GTF expression readers explicitly request pandas output, and their conformance test checks the same independently recorded StringTie transcript IDs and FPKM values.
Support pandas 2.2.2+ and 3.x. CI explicitly tests pandas 2 on Python 3.10/3.11 and pandas 3 on Python 3.11/3.12; coverage artifacts distinguish the two Python 3.11 jobs. Existing downstream Vaxrank and optional Isovar/PirlyGenes integration gates remain in place. Bumps Topiary to 5.94.2. Closes #484.
Validation:
./lint.sh, both paired GTF tests andpip checkpass../test.shin the documented release environment passed all 5,472 tests (no skips, 94% coverage), including installed Isovar 1.45.2 and PirlyGenes 6.0.8 with pandas 3.0.6, gtfparse 3.0.2 and PyEnsembl 2.24.1. Green GitHub CI also verifies the pandas matrix, packaging, released Vaxrank consumer and optional Isovar/PirlyGenes integrations.Coordinated Varcode hard-requirement PR: openvax/varcode#579. Publish Topiary first so joint installations can upgrade normally.