feat: sync MA python with Rust#118
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The core rewrite in #107 changed the API out from under the pyo3 wrapper. Qualities are a SmallVec now and names an Arc<str>, from_tags/to_tags lost the old AL slot, and add_annotations takes an Encoding (always Ma from python). Also give the crate its own empty [workspace] table so maturin stops walking up to the root Cargo.toml when it builds.
The MM/ML parse/emit code was stuck behind the htslib feature because it read straight off a bam::Record. Move the actual algorithm behind a new mmml feature that works on plain slices (the MM string, ML bytes, and forward sequence); from_record just grabs those off the record now and hands them over. pyMA turns on mmml and exposes parse_mm_ml/to_mm_ml, and pysam_utils.from_record reads the tags and reverse-complements the sequence for reverse reads. The algorithm didn't change, so the existing htslib tests still pass; new ones cover the record-free path, reverse strand, and a byte-identical round trip.
Reads fibertools-rs all.bam through pysam and from_record and checks the known nuc/msp/m6a/5mC counts on the first read, that base mods land in range with reference coords, and that writing back out round-trips the MA tag while leaving MM/ML untouched. Also covers adding an annotation to a parsed record and writing it. Skips when the bam isn't there (outside the repo).
Builds the molecular-annotation Python wheels + sdist with maturin and publishes to PyPI via OIDC trusted publishing (no API token) on molecular-annotation-py-v* tags.
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Jul 21, 2026
## 🤖 New release * `molecular-annotation`: 0.0.1 -> 0.0.2 (✓ API compatible changes) * `fibertools-rs`: 0.11.0 -> 0.12.0 (✓ API compatible changes) <details><summary><i><b>Changelog</b></i></summary><p> ## `molecular-annotation` <blockquote> ## [0.0.2](molecular-annotation-v0.0.1...molecular-annotation-v0.0.2) - 2026-07-21 ### Added - sync MA python with Rust ([#118](#118)) </blockquote> ## `fibertools-rs` <blockquote> ## [0.12.0](v0.11.0...v0.12.0) - 2026-07-21 ### Added - sync MA python with Rust ([#118](#118)) </blockquote> </p></details> --- This PR was generated with [release-plz](https://github.com/release-plz/release-plz/). Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
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This PR gets the Python MA library up to date with the Rust crate.