Release 2.5.7 — use the committed mmseqs indexes + version bump - #79
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Bug fix bundled with the release bump: the precompiled mmseqs DBs shipped in `database/vdj/*/mmseqs/` were never used. Their version marker was compared with an exact `==`, but `mmseqs version` prints the same release+commit with different punctuation across builds (static binary `18-8cc5c`, bioconda `18.8cc5c`), so the markers -- written under conda's mmseqs -- stopped matching once the toolchain moved to the static binary. Every run silently rebuilt a private cache instead. `mmseqs.version_key` normalizes the separator (`[\s._-]+` -> `-`, lowercased) so the comparison bridges the cosmetic difference while still rejecting a genuinely different version. Used in `_committed_index` and `build_index`. Also bumps the version to 2.5.7 across the eight places it lives (pyproject, `src/arda/__init__.py`, docs conf/pipeline, and the Nextflow module's main.nf / environment.yml / Dockerfile / README) and adds the 2.5.7 CHANGELOG entry, which also covers the already-merged stale-cache fix (#77) and uv toolchain switch (#78). Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
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Cuts 2.5.7. Headline fix + the version bump; the reference is unchanged.
Fix — the committed precompiled indexes were never used
The precompiled mmseqs DBs shipped in
database/vdj/*/mmseqs/are gated on a version marker compared with an exact==. Butmmseqs versionprints the same release+commit with different punctuation across builds — the official static binary says18-8cc5c, the bioconda build18.8cc5c. When arda's toolchain moved from conda's mmseqs to the static binary (#78), every committed marker (written under conda's mmseqs) stopped matching, so the shipped indexes were silently ignored and every run rebuilt a privatedata/mmseqs_dbcache._committed_indexandbuild_indexnow compare viammseqs.version_key— folds[\s._-]+→-and lowercases — bridging the cosmetic difference while still rejecting a genuinely different version (17-b804f≠18-8cc5c). Verified: the committed nt/aa indexes for every org are now selected, and the full unit + synthetic + realworld suite is green using them (303 passed).Version bump 2.5.6 → 2.5.7
All eight places:
pyproject.toml,src/arda/__init__.py,docs/conf.py,docs/pipeline_integration.rst, and the Nextflow module'smain.nf/environment.yml/Dockerfile/README.md. Thepypipublish job validates pyproject == tag.CHANGELOG
## 2.5.7covers this fix plus the two already-merged into master since 2.5.6: the stale-cache rebuild (#77) and the conda→uv toolchain switch (#78).Release checklist
scripts/pack_reference.shpre-flighted locally (2.8M, 53 members, verified — thereference-assetjob will attacharda-reference-vdj.tar.gz)v2.5.7→publish.ymlbuilds wheels/sdist and pauses at thepypienvironment gate for approval🤖 Generated with Claude Code