ci: use uv in commit-triggered jobs (#171)

Use UV in the CI test workflow. Also add a concurrency group constraint to the CI test workflow. Add dependency groups to `pyproject.toml` matching the extras groups. UV already supports dep groups. Eventually it seems like pip will too so at that point we can remove the extras.

Didn't use uv in the release workflow yet, will do that at next release time.

.github/workflows/ci.yml

@@ -13,6 +13,9 @@ on:
       - '**.md'
       - '.github/workflows/release.yml'
       - '.gitignore'
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
 jobs:
   lint:
     name: Lint
@@ -22,24 +25,27 @@ jobs:
       - name: Checkout repo
         uses: actions/checkout@v4
 
+      - name: Setup uv
+        uses: astral-sh/setup-uv@v5
+        with:
+          version: "0.5.18"
+
       - name: Setup Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
-          python-version: 3.x
-          cache: 'pip'
-          cache-dependency-path: pyproject.toml
+          python-version-file: pyproject.toml
 
-      - name: Install Python packages
-        run: pip install ".[lint]"
+      - name: Install project
+        run: uv sync --group lint
 
       - name: Run ruff check
-        run: ruff check
+        run: uv run ruff check
 
       - name: Run ruff format
-        run: ruff format --check
+        run: uv run ruff format --check
 
       - name: Check spelling
-        run: codespell
+        run: uv run codespell
 
   build:
     name: Build
@@ -49,24 +55,27 @@ jobs:
       - name: Checkout repo
         uses: actions/checkout@v3
 
+      - name: Setup uv
+        uses: astral-sh/setup-uv@v5
+        with:
+          version: "0.5.18"
+
       - name: Setup Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
-          python-version: 3.x
+          python-version-file: pyproject.toml
 
-      - name: Install Python packages
-        run: |
-          pip install --upgrade pip
-          pip install ".[build]"
+      - name: Install project
+        run: uv sync --group build
 
       - name: Print package version
-        run: python -c "import modflow_devtools; print(modflow_devtools.__version__)"
+        run: uv run python -c "import modflow_devtools; print(modflow_devtools.__version__)"
 
       - name: Build package
-        run: python -m build
+        run: uv run python -m build
 
       - name: Check distribution
-        run: twine check --strict dist/*
+        run: uv run twine check --strict dist/*
 
   test:
     name: Test
@@ -126,14 +135,20 @@ jobs:
           compiler: gcc
           version: ${{ env.GCC_V }}
 
-      - name: Setup Python
-        uses: actions/setup-python@v4
+      - name: Setup uv
+        uses: astral-sh/setup-uv@v5
         with:
+          version: "0.5.18"
           python-version: ${{ matrix.python }}
 
-      - name: Install Python packages
+      - name: Setup Python
+        uses: actions/setup-python@v5
+        with:
+          python-version-file: modflow-devtools/pyproject.toml
+
+      - name: Install project
         working-directory: modflow-devtools
-        run: pip install ".[dev]"
+        run: uv sync --all-extras
 
       - name: Cache modflow6 examples
         id: cache-examples
@@ -145,23 +160,23 @@ jobs:
       - name: Install extra Python packages
         working-directory: modflow6-examples/etc
         run: |
-          pip install -r requirements.pip.txt
-          pip install -r requirements.usgs.txt
+          uv pip install -r requirements.pip.txt
+          uv pip install -r requirements.usgs.txt
 
       - name: Update FloPy packages
-        run: python -m flopy.mf6.utils.generate_classes --ref develop --no-backup
+        run: uv run python -m flopy.mf6.utils.generate_classes --ref develop --no-backup
 
       - name: Build modflow6 example models
         if: steps.cache-examples.outputs.cache-hit != 'true'
         working-directory: modflow6-examples/autotest
-        run: pytest -v -n auto test_scripts.py --init
+        run: uv run pytest -v -n auto test_scripts.py --init
 
       - name: Run local tests
         working-directory: modflow-devtools/autotest
         env:
           REPOS_PATH: ${{ github.workspace }}
         # use --dist loadfile to so tests requiring pytest-virtualenv run on the same worker
-        run: pytest -v -n auto --dist loadfile --durations 0 --ignore test_download.py
+        run: uv run pytest -v -n auto --dist loadfile --durations 0 --ignore test_download.py
 
       - name: Run network-dependent tests
         # only invoke the GH API on one OS and Python version
@@ -172,7 +187,7 @@ jobs:
         env:
           REPOS_PATH: ${{ github.workspace }}
           GITHUB_TOKEN: ${{ github.token }}
-        run: pytest -v -n auto --durations 0 test_download.py
+        run: uv run pytest -v -n auto --durations 0 test_download.py
 
   rtd:
     name: Docs

modflow_devtools/fixtures.py

@@ -44,9 +44,9 @@ def function_tmpdir(tmpdir_factory, request) -> Generator[Path, None, None]:
 
 @pytest.fixture(scope="class")
 def class_tmpdir(tmpdir_factory, request) -> Generator[Path, None, None]:
-    assert (
-        request.cls is not None
-    ), "Class-scoped temp dir fixture must be used on class"
+    assert request.cls is not None, (
+        "Class-scoped temp dir fixture must be used on class"
+    )
     temp = Path(tmpdir_factory.mktemp(request.cls.__name__))
     yield temp
 

pyproject.toml

@@ -43,7 +43,6 @@ requires-python = ">=3.9"
 dynamic = ["version"]
 
 [project.optional-dependencies]
-dev=["modflow-devtools[lint,test,docs,dfn]"]
 build = [
     "build",
     "twine"
@@ -77,6 +76,49 @@ dfn = [
     "boltons",
     "tomlkit"
 ]
+dev = ["modflow-devtools[lint,test,docs,dfn]"]
+
+[dependency-groups]
+build = [
+    "build",
+    "twine"
+]
+lint = [
+    "codespell[toml]",
+    "ruff"
+]
+test = [
+    "modflow-devtools[lint]",
+    "coverage",
+    "flaky",
+    "filelock",
+    "meson!=0.63.0",
+    "ninja",
+    "numpy",
+    "pandas",
+    "pytest!=8.1.0",
+    "pytest-cov",
+    "pytest-dotenv",
+    "pytest-xdist",
+    "PyYaml",
+    "syrupy"
+]
+docs = [
+    "sphinx",
+    "sphinx-rtd-theme",
+    "myst-parser"
+]
+dfn = [
+    "boltons",
+    "tomlkit"
+]
+dev = [
+    {include-group = "build"},
+    {include-group = "lint"},
+    {include-group = "test"},
+    {include-group = "docs"},
+    {include-group = "dfn"}
+]
 
 [project.urls]
 "Documentation" = "https://modflow-devtools.readthedocs.io/en/latest/"