pod5 conda package incompatible with pyarrow >=23

[jayhesselberth]

Problem

The pod5 conda package (bioconda) bundles lib_pod5 compiled against libarrow.so.2000 (pyarrow ~20.x). When installed alongside pyarrow >=23.0.0, importing pod5 fails:

ImportError: libarrow.so.2000: cannot open shared object file: No such file or directory

The environment has libarrow.so.2300 (from pyarrow 23.x) but pod5 expects the older ABI.

Context

This was hit when adding pod5 as a dependency to the outer pixi.toml in 2026-aars-in-vitro, which already pins pyarrow = ">=23.0.0,<24". The pipeline submodule's own pixi environment has a compatible pyarrow/pod5 combination and works fine.

Impact

Scripts that need both pod5 and the outer environment's packages (e.g., scripts/calc_signal_per_nt.py) must either:

• Run from the submodule env (cd aa-tRNA-seq-pipeline && pixi run ...) for POD5 access
• Run from the outer env with --n_verify 0 to skip POD5 verification

Possible fixes

• Pin pyarrow to a version compatible with the latest pod5 conda build
• Use pod5 from PyPI instead of conda (may have its own bundled arrow)
• Wait for an updated pod5 conda package built against arrow 23.x