Merge pull request #10 from tomwhite/ci

Basic CI for tests

Author: jeromekelleher

.github/workflows/ci.yml

@@ -0,0 +1,64 @@
+name: CI
+
+on:
+  pull_request:
+  push:
+    branches:
+      - main
+
+jobs:
+  test:
+    name: Test
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        # Use macos-13 because pip binary packages for ARM aren't
+        # available for many dependencies
+        os: [macos-13, macos-14, ubuntu-latest]
+        python-version: ["3.9", "3.10", "3.11"]
+        exclude:
+          # Just run macos tests on one Python version
+          - os: macos-13
+            python-version: "3.10"
+          - os: macos-13
+            python-version: "3.11"
+          - os: macos-14
+            python-version: "3.9"
+          - os: macos-14
+            python-version: "3.10"
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install '.[dev]'
+      - name: Run tests
+        run: |
+          pytest
+
+  packaging:
+    name: Packaging
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: '3.11'
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install build twine validate-pyproject[all]
+      - name: Check and install package
+        run: |
+          validate-pyproject pyproject.toml
+          python -m build
+          python -m twine check --strict dist/*
+          python -m pip install dist/*.whl
+      - name: Check vcztools CLI
+        run: |
+          vcztools --help
+          python -m vcztools --help

pyproject.toml

@@ -6,12 +6,22 @@ build-backend = "setuptools.build_meta"
 name = "vcztools"
 version = "0.0.1"
 dependencies = [
-    "numpy>=1.23.5",
+  "numpy>=1.23.5,<2",
+  "numba",
+  "zarr>=2.17,<3",
+  "click",
 ]
 requires-python = ">=3.9"
 
 [project.scripts]
-vcztools = "vcztools.__main__:main"
+vcztools = "vcztools.cli:vcztools_main"
+
+[project.optional-dependencies]
+dev = [
+  "bio2zarr @ git+https://github.com/sgkit-dev/bio2zarr.git",
+  "pytest",
+  "pytest-datadir",
+]
 
 [tool.setuptools]
 packages = ["vcztools"]