Package dependency pins & test

.github/workflows/python-tilledbsoma-ml-compat.yml

@@ -0,0 +1,46 @@
+name: python-tiledbsoma-ml past tiledbsoma compat # Latest tiledbsoma version covered by another workflow
+
+on:
+ pull_request:
+ branches: ["*"]
+ paths-ignore:
+ - "scripts/**"
+ - "notebooks/**"
+ push:
+ branches: [main]
+ paths-ignore:
+ - "scripts/**"
+ - "notebooks/**"
+
+jobs:
+ unit_tests:
+ strategy:
+ fail-fast: false
+ matrix:
+ os: ["ubuntu-latest"] # could add 'macos-latest', but the matrix is already huge...
+ python-version: ["3.9", "3.10", "3.11"] # TODO: add 3.12 when tiledbsoma releases wheels for it.
+ pkg-version:
+ - "tiledbsoma~=1.9.0 'numpy<2.0.0'"
+ - "tiledbsoma~=1.10.0 'numpy<2.0.0'"
+ - "tiledbsoma~=1.11.0"
+ - "tiledbsoma~=1.12.0"
+ - "tiledbsoma~=1.13.0"
+ - "tiledbsoma~=1.14.0"
+
+ runs-on: ${{ matrix.os }}
+
+ steps:
+ - uses: actions/checkout@v4
+
+ - uses: actions/setup-python@v5
+ with:
+ python-version: ${{ matrix.python-version }}
+ cache: pip
+
+ - name: Install prereqs
+ run: |
+ pip install --upgrade pip pytest setuptools
+ pip install ${{ matrix.pkg-version }} .
+
+ - name: Run tests
+ run: pytest -v tests

CHANGELOG.md

@@ -8,12 +8,16 @@ and this project adheres to [Semantic Versioning](http://semver.org/).
 
 ## [Unreleased] - yyyy-mm-dd
 
-Porting and enhancing initial code contribution from the Chan Zuckerberg Initiative Foundation 
+Port and enhance contribution from the Chan Zuckerberg Initiative Foundation
 [CELLxGENE](https://cellxgene.cziscience.com/) project.
 
+This is not a one-for-one migration of the contributed code. Substantial changes have
+been made to the package utility (e.g., multi-GPU support), improve API usability, etc.
+
 ### Added
 
-- Initial commits via PR [#2823](https://github.com/single-cell-data/TileDB-SOMA/pull/2823)
+- Initial commits via [PR #1](https://github.com/single-cell-data/TileDB-SOMA-ML/pull/1)
+- Refine package dependency pins and compatibility tests via [PR #2](https://github.com/single-cell-data/TileDB-SOMA-ML/pull/2)
 
 ### Changed
 

pyproject.toml

@@ -6,9 +6,9 @@ build-backend = "setuptools.build_meta"
 name = "tiledbsoma-ml"
 dynamic = ["version"]
 dependencies = [
- "attrs",
- "tiledbsoma",
- "torch",
+ "attrs>=22.2",
+ "tiledbsoma>=1.9.0",
+ "torch>=2.0",
  "torchdata<=0.9",
  "numpy",
  "numba",