skb-arrow

A process host that exposes scikit-bio to non-Python callers. A caller runs skb-arrow, speaks JSON lines on its stdin and stdout, and exchanges tables as Arrow IPC in memory-mapped files. Each capability is one curated, typed, versioned scikit-bio operation: ancombc and mantel so far.

Platforms

• Linux x86_64, glibc 2.28 or later
• macOS 12 or later, on Apple silicon

Python 3.14 only. Every dependency installs from a wheel, and each is pinned exactly, so an answer is reproducible per skb-arrow version.

Install

Install uv 0.6.8 or later, then:

uv tool install --managed-python --python 3.14 skb-arrow
uv tool update-shell   # if uv says its tool directory isn't on PATH; then open a new shell
skb-arrow --doctor

• --python 3.14: uv 0.10 and later skip a default Python older than 3.14, but not a newer one: uv ignores the upper bound of the versions skb-arrow supports.
• --managed-python: uv's own CPython, not whichever 3.14 the machine has.

skb-arrow --doctor reports the interpreter, the platform, the pinned dependencies, numpy's BLAS, the thread settings, and where segments go, then a problem: line per fault. It exits 1 if there is one.

Use

A caller runs skb-arrow --segment-dir DIR. skb-arrow --version prints the version, the protocol version, and each capability with its schema version.

• Protocol: the control channel, the handshake, and versioning.
• Transport: segments, and where DIR goes.
• Capabilities: each capability's inputs, params, and output.
• Errors: error kinds and warnings.

These follow main. A release's own are under its tag: https://github.com/the-miint/skb-arrow/tree/v<version>/docs.

Threads

Each is read from the environment, and --doctor shows it:

• NUMBA_NUM_THREADS: numba's kernels (mantel); every core by default. Answers don't depend on it.
• OPENBLAS_NUM_THREADS for OpenBLAS (Linux, and macOS 12 and 13), VECLIB_MAXIMUM_THREADS for Accelerate (macOS 14 and later): numpy's and scipy's BLAS, which --doctor names. Answers are bit for bit on one machine at one count; across them, to floating-point tolerance.
• OMP_NUM_THREADS: OpenMP's.

Containers

On Linux, DIR lives in /dev/shm. Docker's default 64 MiB /dev/shm holds less than one default 256 MiB segment, and a call's inputs and outputs share DIR: run the container with a larger --shm-size, or on Kubernetes mount an emptyDir with medium: Memory at /dev/shm.

License

BSD-3-Clause.