Update maximal Python version to 3.13 in workflows and configuration files (#653)

* Update maximal Python version to 3.13 in workflows and configuration files
* Update py-modelrunner version to 0.19 in requirements files
* Rename build job to serial_tests and update dependency installation process in tests_all.yml
* Improve dependency installation process in Github actions to handle installation failures gracefully

Author: david-zwicker

.github/workflows/coverage_report.yml

@@ -19,9 +19,14 @@ jobs:
       uses: AnimMouse/setup-ffmpeg@v1
 
     - name: Install dependencies
+      # install all requirements. Note that the full requirements are installed separately
+      # so the job does not fail if one of the packages cannot be installed. This allows
+      # testing the package for newer python version even when some of the optional
+      # packages are not yet available.
       run: |
         python -m pip install --upgrade pip
-        pip install -r tests/requirements_full.txt
+        pip install -r requirements.txt
+        cat tests/requirements_full.txt | sed -e '/^\s*#.*$/d' -e '/^\s*$/d' | xargs -n 1 -I % sh -c "pip install % || true"
         pip install -r tests/requirements.txt
 
     - name: Generate serial coverage report

.github/workflows/tests_all.yml

@@ -29,7 +29,7 @@ jobs:
       run: |
         python -m pip install --upgrade pip
         pip install -r requirements.txt
-        cat tests/requirements_full.txt | sed -e '/^\s*#.*$/d' -e '/^\s*$/d' | xargs -n 1 pip install
+        cat tests/requirements_full.txt | sed -e '/^\s*#.*$/d' -e '/^\s*$/d' | xargs -n 1 -I % sh -c "pip install % || true"
         pip install -r tests/requirements.txt
 
     - name: Run serial tests with pytest

.github/workflows/tests_mpi.yml

@@ -22,7 +22,7 @@ jobs:
     - name: Set up Python
       uses: actions/setup-python@v5
       with:
-        python-version: '3.12'
+        python-version: '3.13'
 
     - name: Setup MPI]
       uses: mpi4py/setup-mpi@v1

.github/workflows/tests_types.yml

@@ -7,7 +7,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        pyversion: ['3.9', '3.12']
+        pyversion: ['3.9', '3.13']
     timeout-minutes: 30
 
     steps:
@@ -19,11 +19,15 @@ jobs:
         python-version: ${{ matrix.pyversion }}
 
     - name: Install dependencies
-      # install all requirements
+      # install all requirements. Note that the full requirements are installed separately
+      # so the job does not fail if one of the packages cannot be installed. This allows
+      # testing the package for newer python version even when some of the optional
+      # packages are not yet available.
       run: |
         python -m pip install --upgrade pip
+        pip install -r requirements.txt
+        cat tests/requirements_full.txt | sed -e '/^\s*#.*$/d' -e '/^\s*$/d' | xargs -n 1 -I % sh -c "pip install % || true"
         pip install -r tests/requirements.txt
-        pip install -r tests/requirements_full.txt
         pip install types-PyYAML
 
     - name: Test types with mypy

docs/requirements.txt

@@ -3,7 +3,7 @@ ffmpeg-python>=0.2
 h5py>=2.10
 pandas>=2
 Pillow>=7.0
-py-modelrunner>=0.18.3
+py-modelrunner>=0.19
 Sphinx>=4
 sphinx-autodoc-annotation>=1.0
 sphinx-gallery>=0.6

docs/source/_static/requirements_optional.csv

@@ -6,6 +6,6 @@ mpi4py,3,Parallel processing using MPI
 napari,0.4.8,Displaying images interactively
 numba-mpi,0.22,Parallel processing using MPI+numba
 pandas,2,Handling tabular data
-py-modelrunner,0.18.3,Running simulations and handling I/O
+py-modelrunner,0.19,Running simulations and handling I/O
 pyfftw,0.12,Faster Fourier transforms
 rocket-fft,0.2.4,Numba-compiled fast Fourier transforms

pde/tools/resources/requirements_full.txt

@@ -6,7 +6,7 @@ matplotlib>=3.1
 numba>=0.59
 numpy>=1.22
 pandas>=2
-py-modelrunner>=0.18.3
+py-modelrunner>=0.19
 rocket-fft>=0.2.4
 scipy>=1.10
 sympy>=1.9

pyproject.toml

@@ -9,7 +9,7 @@ authors = [
 ]
 license = {text = "MIT"}
 readme = "README.md"
-requires-python = ">=3.9,<3.13"
+requires-python = ">=3.9,<3.14"
 dynamic = ["version"]
 
 keywords = ["pdes", "partial-differential-equations", "dynamical-systems"]
@@ -24,6 +24,7 @@ classifiers = [
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
     "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
 ]
 
 # Requirements for setuptools
@@ -84,7 +85,7 @@ select = [
     "SIM", # flake8-simplify
     "PTH", # flake8-use-pathlib
 ]
-ignore = ["A005", "B007", "B027", "B028", "SIM108", "ISC001", "PT006", "PT011", "RET504", "RET505", "RET506"]
+ignore = ["B007", "B027", "B028", "SIM108", "ISC001", "PT006", "PT011", "RET504", "RET505", "RET506"]
 
 [tool.ruff.lint.isort]
 section-order = ["future", "standard-library", "third-party", "first-party", "self", "local-folder"]

scripts/_templates/_pyproject.toml

@@ -21,6 +21,7 @@ classifiers = [
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
     "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
 ]
 
 # Requirements for setuptools

scripts/create_requirements.py

@@ -11,7 +11,7 @@
 
 PACKAGE_PATH = Path(__file__).resolve().parents[1]
 MIN_PYTHON_VERSION = "3.9"
-MAX_PYTHON_VERSION = "3.12"
+MAX_PYTHON_VERSION = "3.13"
 
 
 @dataclass
@@ -107,7 +107,7 @@ def line(self, relation: str = ">=") -> str:
     ),
     Requirement(
         name="py-modelrunner",
-        version_min="0.18.3",
+        version_min="0.19",
         usage="Running simulations and handling I/O",
         collections={"full", "docs"},
     ),