build: release 2026.6.9 (+ fix CITATION pre-commit hook portability)#74
Merged
Conversation
added 2 commits
June 9, 2026 17:26
The pre-commit hook auto-updates CITATION.cff whenever pyproject.toml
changes, but two bugs caused it to silently corrupt the file on
macOS/BSD:
1. The version-extraction regex used \s (GNU-only) in grep -E / sed -E.
On BSD this matches a literal 's', so the capture fails and VERSION
falls back to the entire matched line ('version = "X.Y.Z"').
2. The CITATION.cff substitution `s/version: .*/.../` was unanchored,
so it also rewrote the `cff-version:` line.
Together these turned `cff-version: 1.2.0` and `version: X.Y.Z` into
`cff-version: version = "X.Y.Z"` and `version: version = "X.Y.Z"`,
which is invalid CFF (this is what PR #73 had to repair).
Fix both by using POSIX [[:space:]] and anchoring the substitutions
with ^.
Release cut after #73. Switches to CalVer (YYYY.M.D) matching the prior v2025.11.1 tag rather than the intermediate YY.M.DD form used in 26.5.22. - pyproject.toml: 26.5.22 -> 2026.6.9 - CITATION.cff: version + date-released for today's tag
nextgenusfs
pushed a commit
that referenced
this pull request
Jun 10, 2026
Mis-typed the version in #74 as 2026.6.9 (full-year CalVer) instead of 26.6.9 (YY.M.D), which is the form actually used by this project (prior on-PyPI release was 26.5.22). The wrong tag v2026.6.9 is being removed; replacing it with v26.6.9. TestPyPI already received funannotate2-2026.6.9 from the bad tag; that artifact is left in place on TestPyPI (irreversible there) and will simply be ignored. PyPI was not affected (production release is workflow_dispatch only).
nextgenusfs
pushed a commit
that referenced
this pull request
Jun 10, 2026
The version bump in #74 missed updating pixi.lock, which kept funannotate2 pinned at 26.5.22. That broke `pixi install --locked` in the Docker build (docker.yml is the only workflow that consumes the lockfile). Regenerated with `pixi install` (default env). Only the funannotate2 package version line changed; transitive deps are untouched. The v26.6.9 tag is being force-moved to this commit so the Docker push-on-tag trigger picks up the fixed lockfile.
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.
Summary
Release cut for
2026.6.9(today). Two commits:fix(hooks): make pre-commit CITATION sync portable— The.githooks/pre-commithook auto-updatesCITATION.cffwheneverpyproject.tomlchanges, but two bugs caused it to silently corruptthe file on macOS/BSD:
\s(GNU-only) ingrep -E/sed -E. On BSD this matches a literals, so the capture failsand
VERSIONfalls back to the entire matched line(
version = "X.Y.Z").s/version: .*/.../was unanchored,so it also rewrote the
cff-version:line.Together these produced the malformed CFF that fix: repair CITATION.cff and clarify BAM contig-map comment #73 had to repair.
Fix is
[[:space:]]instead of\sand^-anchored substitutions.build: bump version to 2026.6.9—pyproject.tomlandCITATION.cffbumped from26.5.22to2026.6.9, matching theCalVer (
YYYY.M.D) form of the priorv2025.11.1tag.Test plan
cffconvert --validate -i CITATION.cff→ valid against schema 1.2.0.pyproject.toml; itextracted
2026.6.9correctly and updated only theversion:anddate-released:lines (cff-version line untouched).Follow-up
Once merged, I'll tag
v2026.6.9onmainto triggerproduction-release.ymlanddocker.yml.