Update workflows to use uv (missing updates to tests) (#334)

* feat(workflow docs): use uv to build env & call mkdocs build

* feat(build): use uv for build workflow and add pytest dependencies to pyproject.toml

Author: ssenan

.github/workflows/build.yml

@@ -1,39 +1,33 @@
+---
 name: Build
-
 on:
   workflow_dispatch:
   push:
-    branches:
-      - main
+  branches: [main]
   pull_request:
-
 jobs:
-  test:
-
+  build:
     runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        python_version: ['3.10']
-
-    steps:
+  steps:
     - uses: actions/checkout@v4
-    - name: Set up Python
-      uses: actions/setup-python@v4
+    - name: Install uv
+      uses: astral-sh/setup-uv@v6
       with:
-        python-version: ${{ matrix.python_version }}
-    - name: Install dependencies
+        enable-cache: true
+        cache-dependency-glob: uv.lock
+    - name: Setup python
+      uses: uv python install
+    - name: Install the project
+      run: uv sync --locked --all-extras --dev
+    - name: Lint check
       run: |
-        python -m pip install --upgrade pip
-        pip install hatch
-        hatch env create
-    - name: Lint and typecheck
-      run: |
-        hatch run lint-check
+        uv run ruff format --check .
+        uv run ruff  .
     - name: Test
       run: |
-        hatch run test-cov-xml
-    - uses: codecov/codecov-action@v4
-      with:
+        uv run pytest -rA --cov-report=xml
+    - uses: codecov/codecov-action@v5
+        with:
         token: ${{ secrets.CODECOV_TOKEN }}
         fail_ci_if_error: true
         verbose: true

.github/workflows/documentation.yml

@@ -1,57 +1,38 @@
-name: Build documentation
-
+---
+name: Build and deploy docs
 on:
   workflow_dispatch:
   push:
-    branches:
-      - main
-
-# Sets permissions of the GITHUB_TOKEN to allow deployment to GitHub Pages
+    branches: [main]
 permissions:
   contents: read
   pages: write
   id-token: write
-
-# Allow one concurrent deployment
 concurrency:
-  group: "pages"
+  group: pages
   cancel-in-progress: true
-
-# Default to bash
 defaults:
   run:
     shell: bash
-
 jobs:
   build:
-
     runs-on: ubuntu-latest
-
-    steps:
-    - uses: actions/checkout@v4
-    - name: Set up Python
-      uses: actions/setup-python@v4
-      with:
-        python-version: '3.10'
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        pip install hatch
-        hatch env create
-    - name: Build
-      run: hatch run docs-build
-    - name: Upload artifact
-      uses: actions/upload-pages-artifact@v2
-      with:
-        path: ./site
-
-  deploy:
-    environment:
-      name: github-pages
-      url: ${{ steps.deployment.outputs.page_url }}
-    runs-on: ubuntu-latest
-    needs: build
     steps:
+      - uses: actions/checkout@v4
+      - name: Set up uv
+        uses: astral-sh/setup-uv@v6
+        with:
+          enable-cache: true
+          cache-dependency-glob: uv.lock
+      - name: Set up Python
+        run: uv python install
+      - name: Install project + dev deps
+        run: uv sync --locked --all-extras --dev
+      - name: Build documentation
+        run: uv run mkdocs build
+      - name: Upload Pages artifact
+        uses: actions/upload-pages-artifact@v3
+        with:
+          path: site
       - name: Deploy to GitHub Pages
-        id: deployment
-        uses: actions/deploy-pages@v2
+        uses: actions/deploy-pages@v4

pyproject.toml

@@ -35,20 +35,20 @@ Source = "https://github.com/pinellolab/DNA-Diffusion"
 target-version = "py312"
 line-length = 120
 extend-include = ["*.ipynb"]
-select = ["E", "F", "I"]
-ignore = ["E721", "E731", "E741", "E742", "E743"]
+lint.select = ["E", "F", "I"]
+lint.ignore = ["E721", "E731", "E741", "E742", "E743"]
 exclude = ["src/refactor"]
 
-[tool.ruff.isort]
+[tool.ruff.lint.isort]
 known-first-party = ["dnadiffusion"]
 
 [tool.ruff.format]
 quote-style = "double"
 
-[tool.ruff.flake8-tidy-imports]
+[tool.ruff.lint.flake8-tidy-imports]
 ban-relative-imports = "all"
 
-[tool.ruff.per-file-ignores]
+[tool.ruff.lint.per-file-ignores]
 # Tests can use magic values, assertions, and relative imports
 "tests/**/*" = ["PLR2004", "S101", "TID252"]
 
@@ -87,4 +87,7 @@ dev = [
     "pytest-cov>=6.1.1",
     "pytest>=8.3.5",
     "ruff>=0.11.5",
+    "mkdocs-material>=9.6.12",
+    "mkdocstrings>=0.29.1",
+    "pytest-asyncio>=0.26.0",
 ]