Update strobealign index to format version 5 for strobealign 0.17.0#296
Update strobealign index to format version 5 for strobealign 0.17.0#296wwood wants to merge 2 commits into
Conversation
Regenerated tests/data/7seqs.fna.r100.sti using strobealign 0.17.0, which writes index format version 5. The old index was version 3, incompatible with strobealign >=0.17.0, causing test_strobealign_pregenerated_index to fail. Also bumped the minimum strobealign version in pixi.toml to >=0.17.0 to match the index format. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01BUkWFEp9YRYAVwvVDFudGU
![chatgpt-codex-connector[bot]](https://avatars.githubusercontent.com/in/1144995?s=60&v=4){kind=small}
There was a problem hiding this comment.
💡 Codex Review
Here are some automated review suggestions for this pull request.
Reviewed commit: 5da16a4d5f
ℹ️ About Codex in GitHub
Your team has set up Codex to review pull requests in this repo. Reviews are triggered when you
- Open a pull request for review
- Mark a draft as ready
- Comment "@codex review".
If Codex has suggestions, it will comment; otherwise it will react with 👍.
Codex can also answer questions or update the PR. Try commenting "@codex address that feedback".
| bwa-mem2 = "*" | ||
| dashing = ">=0.4.0,<1.0" # dashing 1.0 build gives illegal instruction errors | ||
| strobealign = ">=0.14.0" # tests use a pregenerated v3 database | ||
| strobealign = ">=0.17.0" # tests use a pregenerated v5 database |
There was a problem hiding this comment.
This constraint doesn't affect the locked Linux CI path because .github/workflows/test-coverm.yml:28 runs pixi run --frozen cargo test, and Pixi documents --frozen as installing from the lockfile without updating it. Since this commit leaves pixi.lock pinning bioconda/linux-64/strobealign-0.14.0 at pixi.lock:62, the frozen job will still install 0.14 and the new v5 pregenerated index remains unreadable; please regenerate and commit pixi.lock together with this manifest change.
Useful? React with 👍 / 👎.
Instead of storing a version-specific strobealign index in git (which breaks whenever strobealign is upgraded to a format that's incompatible with the stored file), generate the index at runtime before the test runs. This way the index always matches the currently-installed strobealign version. Also reverts the strobealign version constraint in pixi.toml back to >=0.14.0 (the >=0.17.0 bump caused a dependency conflict with dashing 0.4.0 over zlib version requirements). Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01BUkWFEp9YRYAVwvVDFudGU
2 participants
Regenerated tests/data/7seqs.fna.r100.sti using strobealign 0.17.0, which
writes index format version 5. The old index was version 3, incompatible
with strobealign >=0.17.0, causing test_strobealign_pregenerated_index to fail.
Also bumped the minimum strobealign version in pixi.toml to >=0.17.0 to
match the index format.
Co-Authored-By: Claude Sonnet 4.6 noreply@anthropic.com
Claude-Session: https://claude.ai/code/session_01BUkWFEp9YRYAVwvVDFudGU