Repository navigation
Require gtfparse 3 with coordinated Topiary support - #579
Merged
Merged
Conversation
This was referenced Oct 6, 2026
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
1 participant
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Make gtfparse 3.0.2+ mandatory alongside PyEnsembl 2.24.1+, including every pandas 2/3 CI configuration. Remove the temporary gtfparse 2.9.1 fallback and document Topiary 5.94.2 as the compatible downstream floor. Bumps Varcode to 10.11.9.
Coordinated with openvax/topiary#484 and Topiary's gtfparse 3 migration. Publish Topiary first so joint installations can upgrade normally.
Validation:
./lint.shandgit diff --checkpass. This final branch's./test.shpassed all 3,240 tests (92% coverage) with pandas 3.0.6, gtfparse 3.0.2 and PyEnsembl 2.24.1. The full CI matrix includes pandas 2/3 and the pandas 3 cross-annotator parity gate. Topiary migration PR: openvax/topiary#485.