skb-arrow 0.1.0__tar.gz

skb_arrow-0.1.0/.gitignore

@@ -0,0 +1,7 @@
+__pycache__/
+.venv/
+dist/
+.pytest_cache/
+.ruff_cache/
+.mypy_cache/
+.DS_Store

skb_arrow-0.1.0/LICENSE

@@ -0,0 +1,32 @@
+=================================
+ The skb-arrow licensing terms
+=================================
+
+The skb-arrow project is licensed under the terms of the Modified BSD License
+(also known as New or Revised BSD), as follows:
+
+Copyright (c) 2026-, The skb-arrow Development Team <damcdonald@ucsd.edu>
+
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+    * Redistributions of source code must retain the above copyright
+      notice, this list of conditions and the following disclaimer.
+    * Redistributions in binary form must reproduce the above copyright
+      notice, this list of conditions and the following disclaimer in the
+      documentation and/or other materials provided with the distribution.
+    * Neither the name of the skb-arrow development team nor the names of its
+      contributors may be used to endorse or promote products derived from this
+      software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
+ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE SKB-ARROW DEVELOPMENT TEAM BE LIABLE FOR
+ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

skb_arrow-0.1.0/PKG-INFO

@@ -0,0 +1,109 @@
+Metadata-Version: 2.5
+Name: skb-arrow
+Version: 0.1.0
+Summary: Process host exposing scikit-bio to non-Python callers over Arrow
+Project-URL: Repository, https://github.com/the-miint/skb-arrow
+Project-URL: Documentation, https://github.com/the-miint/skb-arrow/tree/main/docs
+Project-URL: Issues, https://github.com/the-miint/skb-arrow/issues
+Author-email: Daniel McDonald <damcdonald@ucsd.edu>
+License-Expression: BSD-3-Clause
+License-File: LICENSE
+Keywords: apache-arrow,bioinformatics,microbiome,scikit-bio
+Classifier: Development Status :: 3 - Alpha
+Classifier: Operating System :: MacOS
+Classifier: Operating System :: POSIX :: Linux
+Classifier: Programming Language :: Python :: 3.14
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Requires-Python: ==3.14.*
+Requires-Dist: array-api-compat==1.15.0
+Requires-Dist: biom-format==2.1.18
+Requires-Dist: certifi==2026.7.22
+Requires-Dist: charset-normalizer==3.5.2
+Requires-Dist: click==8.5.0
+Requires-Dist: decorator==5.3.1
+Requires-Dist: formulaic==1.2.2
+Requires-Dist: h5py==3.16.0
+Requires-Dist: idna==3.20
+Requires-Dist: interface-meta==2.0.1
+Requires-Dist: llvmlite==0.50.0
+Requires-Dist: narwhals==2.26.0
+Requires-Dist: numba==0.68.0
+Requires-Dist: numpy==2.5.3
+Requires-Dist: packaging==26.3
+Requires-Dist: pandas==3.0.6
+Requires-Dist: patsy==1.0.3
+Requires-Dist: pyarrow==25.0.1
+Requires-Dist: python-dateutil==2.9.0.post0
+Requires-Dist: requests==2.34.2
+Requires-Dist: scikit-bio==0.7.4
+Requires-Dist: scipy==1.18.1
+Requires-Dist: six==1.17.0
+Requires-Dist: statsmodels==0.15.0
+Requires-Dist: typing-extensions==4.16.0
+Requires-Dist: urllib3==2.8.0
+Requires-Dist: wrapt==2.5.0
+Description-Content-Type: text/markdown
+
+# skb-arrow
+
+A process host that exposes [scikit-bio](https://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](https://docs.astral.sh/uv/getting-started/installation/) 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](https://github.com/the-miint/skb-arrow/blob/main/docs/protocol.md): the control
+  channel, the handshake, and versioning.
+- [Transport](https://github.com/the-miint/skb-arrow/blob/main/docs/transport.md): segments,
+  and where DIR goes.
+- [Capabilities](https://github.com/the-miint/skb-arrow/blob/main/docs/capabilities.md): each
+  capability's inputs, params, and output.
+- [Errors](https://github.com/the-miint/skb-arrow/blob/main/docs/errors.md): 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.

skb_arrow-0.1.0/README.md

@@ -0,0 +1,63 @@
+# skb-arrow
+
+A process host that exposes [scikit-bio](https://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](https://docs.astral.sh/uv/getting-started/installation/) 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](https://github.com/the-miint/skb-arrow/blob/main/docs/protocol.md): the control
+  channel, the handshake, and versioning.
+- [Transport](https://github.com/the-miint/skb-arrow/blob/main/docs/transport.md): segments,
+  and where DIR goes.
+- [Capabilities](https://github.com/the-miint/skb-arrow/blob/main/docs/capabilities.md): each
+  capability's inputs, params, and output.
+- [Errors](https://github.com/the-miint/skb-arrow/blob/main/docs/errors.md): 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.