no dep groups (too soon), pin vtk and use prerelease for now, update …

…ci, add lockfile

.github/workflows/commit.yml

@@ -32,11 +32,11 @@ jobs:
 
       - name: Install Python dependencies
         run: |
-          uv sync --group build
+          uv sync --extra build
           uv run python -c "import flopy; print(f'{flopy.__version__}')"
 
       - name: Build package
-        run: uv run python -m build
+        run: uv build
 
       - name: Check package
         run: uv run twine check --strict dist/*
@@ -64,7 +64,7 @@ jobs:
           python-version-file: pyproject.toml
 
       - name: Install Python dependencies
-        run: uv sync --group lint
+        run: uv sync --extra lint
 
       - name: Lint
         run: uv run ruff check .
@@ -106,7 +106,8 @@ jobs:
           python-version-file: pyproject.toml
 
       - name: Install Python dependencies
-        run: uv sync --group test --group optional
+        # temp. allow prereleases for vtk on aarch64
+        run: uv sync --all-extras --prerelease=allow
 
       - name: Install Modflow executables
         uses: modflowpy/install-modflow-action@v1

pyproject.toml

@@ -35,69 +35,6 @@ dependencies = [
 ]
 dynamic = ["version", "readme"]
 
-[dependency-groups]
-build = ["build", "twine"]
-lint = ["cffconvert", "codespell[toml] >=2.2.2", "ruff"]
-test = [
-    "flopy[lint]",
-    "coverage !=7.6.5",
-    "flaky",
-    "filelock",
-    "jupyter",
-    "jupyter_client >=8.4.0", # avoid datetime.utcnow() deprecation warning
-    "jupytext",
-    "modflow-devtools",
-    "pytest !=8.1.0",
-    "pytest-benchmark",
-    "pytest-cov",
-    "pytest-dotenv",
-    "pytest-xdist",
-    "pyzmq >=25.1.2",
-    "syrupy",
-    "virtualenv"
-]
-optional = [
-    "affine",
-    "descartes",
-    "fiona",
-    "geojson",
-    "geopandas",
-    "GitPython",
-    "imageio",
-    "netcdf4",
-    "pooch",
-    "pymetis ; platform_system != 'Windows'",
-    "pyproj",
-    "pyshp",
-    "pyvista",
-    "rasterio",
-    "rasterstats",
-    "scipy",
-    "shapely >=2.0",
-    "vtk",
-    "xmipy",
-]
-doc = [
-    "flopy[optional]",
-    "ipython[kernel]",
-    "jupytext",
-    "myst-parser",
-    "nbconvert <7.14.0",
-    "nbsphinx",
-    "PyYAML",
-    "rtds-action",
-    "sphinx ==7.1.2",
-    "sphinx-rtd-theme >=1",
-]
-dev = [
-    {include-group = "build"},
-    {include-group = "lint"},
-    {include-group = "test"},
-    {include-group = "optional"},
-    {include-group = "doc"},
-    "tach"
-]
-
 [project.optional-dependencies]
 dev = ["flopy[build,lint,test,optional,doc]", "tach"]
 build = ["build", "twine"]
@@ -138,7 +75,7 @@ optional = [
     "rasterstats",
     "scipy",
     "shapely >=2.0",
-    "vtk",
+    "vtk >=9.4.0",
     "xmipy",
 ]
 doc = [