chore: drop py3.9, add py3.13, fix conftest.py, use uv in ci

Drop python 3.9 and add python 3.13. Fix the apparatus to download example models in conftest.py (hopefully soon to be replaced by devtools models API). Use uv in ci.

Author: wpbonelli

.github/workflows/ci.yml

@@ -26,22 +26,13 @@ jobs:
     - name: Checkout repo
       uses: actions/checkout@v3
 
-    - name: Setup Python
-      uses: actions/setup-python@v4
+    - name: Setup uv
+      uses: astral-sh/setup-uv@v5
       with:
-        python-version: 3.x
-
-    - name: Upgrade pip
-      run: |
-        python -m pip install --upgrade pip
-
-    - name: Base installation
-      run: |
-        pip install -e .
+        cache-dependency-glob: "**/pyproject.toml"
 
     - name: Print version
-      run: |
-        python -c "import modflowapi; print(modflowapi.__version__)"
+      run: uv run python -c "import modflowapi; print(modflowapi.__version__)"
 
   lint:
     name: lint
@@ -54,33 +45,21 @@ jobs:
         shell: bash
     steps:
     - name: Checkout repo
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
 
-    # Standard python fails on Windows without GDAL installation. Using
-    # standard python here since only linting on linux.
-    # Use standard bash shell with standard python
-    - name: Setup Python
-      uses: actions/setup-python@v4
+    - name: Setup uv
+      uses: astral-sh/setup-uv@v5
       with:
-        python-version: 3.x
-
-    - name: Print python version
-      run: |
-        python --version
-
-    - name: Install Python packages
-      run: |
-        python -m pip install --upgrade pip
-        pip install -e .[lint]
+        enable-cache: false
 
     - name: Lint
-      run: ruff check .
+      run: uvx ruff check .
 
-    - name: Check format
-      run: ruff format . --check
+    - name: Format
+      run: uvx ruff format . --check
 
-    - name: Check spelling
-      run: codespell
+    - name: Spelling
+      run: uvx codespell
 
   autotest_extensions:
     name: modflowapi extensions autotests
@@ -90,27 +69,27 @@ jobs:
       fail-fast: false
       matrix:
         os: [ ubuntu-latest, macos-latest, windows-latest ]
-        python-version: [ 3.9, "3.10", "3.11", "3.12" ]
+        python-version: [ "3.10", "3.11", "3.12", "3.13" ]
     defaults:
       run:
         shell: bash
     steps:
       - name: Checkout repo
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
-      - name: Setup Python
-        uses: actions/setup-python@v4
+      - name: Setup uv
+        uses: astral-sh/setup-uv@v5
         with:
+          cache-dependency-glob: "**/pyproject.toml"
           python-version: ${{ matrix.python-version }}
-          cache: 'pip'
-          cache-dependency-path: pyproject.toml
+
+      - name: Install
+        run: uv sync --all-extras
 
       - name: Install Python dependencies
         run: |
-          python -m pip install --upgrade pip
-          pip install git+https://[email protected]/Deltares/xmipy@develop
-          pip install git+https://[email protected]/MODFLOW-ORG/modflow-devtools@develop
-          pip install .[test]
+          uv pip install git+https://[email protected]/Deltares/xmipy@develop
+          uv pip install git+https://[email protected]/MODFLOW-ORG/modflow-devtools@develop
 
       - name: Install modflow executables
         uses: modflowpy/install-modflow-action@v1
@@ -121,7 +100,7 @@ jobs:
       - name: Run autotests
         working-directory: ./autotest
         shell: bash -l {0}
-        run: pytest -v -n auto -m "not mf6"
+        run: uv run pytest -v -n auto -m "not mf6"
 
   autotest_preidm_extensions:
     name: modflowapi pre-idm extensions autotests
@@ -131,27 +110,27 @@ jobs:
       fail-fast: false
       matrix:
         os: [ ubuntu-latest, macos-13, windows-latest ]
-        python-version: [ 3.9, "3.10", "3.11", "3.12" ]
+        python-version: [ "3.10", "3.11", "3.12", "3.13" ]
     defaults:
       run:
         shell: bash
     steps:
       - name: Checkout repo
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
-      - name: Setup Python
-        uses: actions/setup-python@v4
+      - name: Setup uv
+        uses: astral-sh/setup-uv@v5
         with:
+          cache-dependency-glob: "**/pyproject.toml"
           python-version: ${{ matrix.python-version }}
-          cache: 'pip'
-          cache-dependency-path: pyproject.toml
+
+      - name: Install
+        run: uv sync --all-extras
 
       - name: Install Python dependencies
         run: |
-          python -m pip install --upgrade pip
-          pip install git+https://[email protected]/Deltares/xmipy@develop
-          pip install git+https://[email protected]/MODFLOW-ORG/modflow-devtools@develop
-          pip install .[test]
+          uv pip install git+https://[email protected]/Deltares/xmipy@develop
+          uv pip install git+https://[email protected]/MODFLOW-ORG/modflow-devtools@develop
 
       - name: Install modflow executables
         uses: modflowpy/install-modflow-action@v1
@@ -173,7 +152,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [ ubuntu-latest, macos-latest, windows-latest ]
-        python-version: [ 3.9, "3.10", "3.11", "3.12" ]
+        python-version: [ "3.10", "3.11", "3.12", "3.13" ]
     defaults:
       run:
         shell: bash
@@ -187,23 +166,23 @@ jobs:
           repository: MODFLOW-ORG/modflow6-examples
           path: modflow6-examples
 
-      - name: Setup Python
-        uses: actions/setup-python@v5
+      - name: Setup uv
+        uses: astral-sh/setup-uv@v5
         with:
+          cache-dependency-glob: "**/pyproject.toml"
           python-version: ${{ matrix.python-version }}
-          cache: 'pip'
-          cache-dependency-path: pyproject.toml
+
+      - name: Install
+        run: uv sync --all-extras
 
       - name: Install Python dependencies
         run: |
-          python -m pip install --upgrade pip
-          pip install git+https://[email protected]/Deltares/xmipy@develop
-          pip install git+https://[email protected]/MODFLOW-ORG/modflow-devtools@develop
-          pip install git+https://[email protected]/modflowpy/flopy@develop
-          pip install .[test]
+          uv pip install git+https://[email protected]/Deltares/xmipy@develop
+          uv pip install git+https://[email protected]/MODFLOW-ORG/modflow-devtools@develop
+          uv pip install git+https://[email protected]/modflowpy/flopy@develop
 
       - name: update flopy for mf6-examples
-        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: Install modflow6 for modflow6-examples
         uses: modflowpy/install-modflow-action@v1
@@ -213,7 +192,7 @@ jobs:
       - name: Build mf6-examples
         working-directory: modflow6-examples/autotest
         run: |
-          pytest -v -n=auto --init test_scripts.py -k "not synthetic-valley"
+          uv run pytest -v -n=auto --init test_scripts.py -k "not synthetic-valley"
 
       - name: Install modflow6 nightly build
         uses: modflowpy/install-modflow-action@v1
@@ -224,4 +203,4 @@ jobs:
       - name: Run autotests
         working-directory: ./autotest
         shell: bash -l {0}
-        run: pytest -v -n=auto test_mf6_examples.py --mf6-examples-path=../modflow6-examples/examples
+        run: uv run pytest -v -n=auto test_mf6_examples.py --mf6-examples-path=../modflow6-examples/examples

.github/workflows/release.yml

@@ -28,7 +28,7 @@ jobs:
       - name: Setup Python
         uses: actions/setup-python@v4
         with:
-          python-version: 3.9
+          python-version: '3.10'
           cache: 'pip'
           cache-dependency-path: pyproject.toml
 
@@ -138,7 +138,7 @@ jobs:
       - name: Setup Python
         uses: actions/setup-python@v4
         with:
-          python-version: 3.9
+          python-version: '3.10'
 
       - name: Install Python dependencies
         run: |
@@ -186,7 +186,7 @@ jobs:
       - name: Setup Python
         uses: actions/setup-python@v4
         with:
-          python-version: 3.9
+          python-version: '3.10'
 
       - name: Install Python dependencies
         run: |

README.md

@@ -33,7 +33,7 @@ and additional functionality specific to the MODFLOW API. Currently it is a join
 
 ## Installation
 
-`modflowapi` requires Python 3.9+, with:
+`modflowapi` requires Python 3.10+, with:
 
 ```shell
 numpy

autotest/conftest.py

@@ -24,7 +24,7 @@ def get_mf6_examples_path() -> Path:
         if not __mf6_examples_path.is_dir():
             __mf6_examples_path.mkdir(exist_ok=True)
             download_and_unzip(
-                url="https://github.com/MODFLOW-ORG/modflow6-examples/releases/download/current/modflow6-examples.zip",
+                url="https://github.com/MODFLOW-ORG/modflow6-examples/releases/download/current/mf6examples.zip",
                 path=__mf6_examples_path,
                 verbose=True,
             )

pyproject.toml

@@ -25,13 +25,13 @@ classifiers = [
     "License :: CC0 1.0 Universal (CC0 1.0) Public Domain Dedication",
     "Programming Language :: Python :: 3",
     "Programming Language :: Python :: 3 :: Only",
-    "Programming Language :: Python :: 3.9",
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
     "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
     "Topic :: Scientific/Engineering :: Hydrology",
 ]
-requires-python = ">=3.9"
+requires-python = ">=3.10"
 dependencies = [
     "numpy",
     "pandas",
@@ -42,7 +42,7 @@ dependencies = [
 dev = ["modflowapi[test,lint]"]
 test = [
     "filelock",
-    "modflow-devtools",
+    "modflow-devtools[dfn] @ git+https://github.com/MODFLOW-ORG/modflow-devtools.git",
     "pytest!=8.1.0",
     "pytest-order",
     "pytest-xdist",
@@ -72,6 +72,10 @@ packages = ["modflowapi"]
 [tool.hatch.version]
 path = "modflowapi/version.py"
 
+[tool.hatch.metadata]
+# temporary, until new devtools release
+allow-direct-references = true
+
 [tool.ruff]
 line-length = 88