ci: use uv in commit-triggered jobs

.github/workflows/ci.yml

@@ -22,24 +22,27 @@ 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 +52,27 @@ 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 +132,20 @@ 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 +157,23 @@ 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
 
       - 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 +184,7 @@ 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/"