Update CI and code QA

.github/workflows/pr.yml

@@ -0,0 +1,35 @@
+name: Lint and Test
+
+on: pull_request
+
+jobs:
+  lint:
+    name: Lint
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - uses: psf/black@stable
+        with:
+          src: "viscy"
+          options: "--check --verbose"
+      - uses: chartboost/ruff-action@v1
+        with:
+          src: "viscy"
+
+  test:
+    needs: [lint]
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.9", "3.10"]
+    steps:
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install ".[metrics,dev]"
+      - name: Test with pytest
+        run: pytest -v

CONTRIBUTING.md

@@ -0,0 +1,9 @@
+# Contributing to viscy
+
+## Testing
+
+Run tests with `pytest`:
+
+```sh
+pytest
+```

pyproject.toml

@@ -6,7 +6,8 @@ build-backend = "setuptools.build_meta"
 name = "viscy"
 description = "Learning vision for cells"
 readme = "README.md"
-requires-python = ">=3.9"
+# cannot build on 3.11 due to https://github.com/cheind/py-lapsolver/pull/18
+requires-python = ">=3.9,!=3.11"
 license = { file = "LICENSE" }
 authors = [{ name = "CZ Biohub SF", email = "compmicro@czbiohub.org" }]
 dependencies = [
@@ -29,7 +30,7 @@ metrics = [
     "scikit-learn>=1.1.3",
     "scipy>=1.8.0",
 ]
-dev = ["profilehooks", "onnxruntime"]
+dev = ["pytest", "hypothesis", "profilehooks", "onnxruntime"]
 
 [project.scripts]
 viscy = "viscy.cli.cli:main"
@@ -38,8 +39,12 @@ viscy = "viscy.cli.cli:main"
 write_to = "viscy/_version.py"
 
 [tool.black]
+src = ["viscy"]
 line-length = 88
 
-[tool.isort]
-profile = "black"
-line_length = 88
+[tool.ruff]
+src = ["viscy", "tests"]
+extend-select = ["I001"]
+
+[tool.ruff.isort]
+known-first-party = ["viscy"]

tests/__init__.py

@@ -1 +1 @@
-"""Tests for viscy"""
+"""Tests for viscy"""