[wwood]

Summary

Addresses #303: makes it clear that the bioconda package installs only the default mappers, so the others must be installed separately. Also fixes a strobealign 0.18 test failure in the unlocked CI job.

Key Changes

• README.md:
  • The bioconda section now lists what the package includes: strobealign, minimap2, bwa, samtools, skani and FastANI. It explains how to install the optional mappers (bwa-mem2, minibwa, rammap) separately.
  • The dependencies list marks strobealign as the default mapper and adds bwa and minibwa. A note says which mappers bioconda installs.
• src/cli.rs: a shared bioconda_mappers_note() is added to the -p/--mapper help of genome, contig, make and makedb. The HTML in docs/ will pick it up at the next release.
• tests/test_cmdline.rs: test_sharded_contig_input_reads_strobealign now accepts either the pre-0.18 or the strobealign 0.18.0 output. 0.18.0 gives slightly different mean coverages, which failed the test_dependencies_optimistic job.

Bioconda recipe check

The current recipe (0.8.0) already includes the default mappers: strobealign (default for genome/contig), minimap2 (default for makedb) and bwa. It also has skani, the default dereplication precluster method. No change is needed.

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[wwood]

Pixi test_dependencies_optimistic (3.11, ubuntu-latest) is failing for a reason that isn't this PR's.

That job deletes pixi.lock before installing, so it picked up strobealign 0.18.0; the lockfile pins 0.17.0. tests::test_sharded_contig_input_reads_strobealign then gets slightly different mean coverages, e.g. genome3~random_sequence_length_11001 0.11057869 → 0.110588886. This PR only changes help text and the README. The locked jobs pass, and so does pixi run cargo test locally. main would fail this job the same way now.

No fix exists yet. Two options for a separate PR:

1. Update the expected values in tests/test_cmdline.rs (test_sharded_contig_input_reads_strobealign) to the 0.18.0 output and bump strobealign in pixi.lock; or
2. Cap strobealign = ">=0.14.0,<0.18" in pixi.toml until the test is updated.

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