Add test suite and CI#7
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Adds a pytest battery (32 tests) covering: - the per-segment metric helpers (identity, matched, query length, MD-tag detection) against hand-crafted segments with known values; - filterSAMbyIdentity / filterSAMbyPercentMatched retention at several cutoffs, on both SAM and BAM input, and that MD-less reads are dropped; - output-format selection (SAM stays text, BAM is binary, and the *output* extension wins over the input one) — guarding the single-process fixes; - default output-path naming for filenames containing 'sam'/'bam'; - filterSAM dispatch: invalid filter / out-of-range cutoff raising, and the single-vs-parallel routing, including that n_processes<=1 never invokes the splitting machinery (regression guard for #3), plus an end-to-end parallel run that matches the serial result. Adds a GitHub Actions workflow (conda + bioconda samtools/pysam, pip parallelbam) running pytest on push and PRs. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
The conda-based workflow failed to solve: with channel-priority strict and the action's implicit `defaults` channel, the solver pulled ancient `defaults` pysam builds (pysam 0.7.7 needs python <3.0) and hit a libdeflate conflict. Switch to actions/setup-python + apt samtools + pip (pysam, numpy, pytest, parallelbam all have wheels / are pure-python). Simpler, faster, and avoids the conda channel/ToS mess. Verified locally against the PyPI pysam 0.24.0 wheel: 32 passed. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
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Summary
Adds the pytest battery + CI that was written alongside #6 but didn't make it into
main(PR #6 merged at the-p 1fix commit only). This is a tests-only change — no production code is modified.What's covered (32 tests)
percent_identity,percent_matched,getQueryLength,getNumberOfMatches,sumMatchesAndMismatches,has_MD_tag) against hand-crafted segments with values verified via pysam.filterSAMbyIdentity/filterSAMbyPercentMatchedretention at several cutoffs, on both SAM and BAM input, and MD-less reads always dropped.sam/bam(guard for the suffix-based extension fix).filterSAMdispatch — invalid filter / out-of-range cutoff raising; single-vs-parallel routing, including thatn_processes <= 1never invokes the splitting machinery (regression guard for performance in multiprocessing mode much worse than single processor #3); and an end-to-end parallel run matching the serial result.CI
GitHub Actions workflow (
.github/workflows/tests.yml): conda + biocondasamtools/pysam, pipparallelbam, thenpyteston push tomainand on PRs. It will register and run once merged to the default branch.🤖 Generated with Claude Code