Merge pull request #55 from zwicker-group/py3.12

Enable python 3.12 for package

.github/workflows/build.yml

@@ -9,20 +9,27 @@ jobs:
     strategy:
       matrix:
         os: [macos-latest, ubuntu-latest, windows-latest]
-        python-version: ['3.8', '3.11']
+        python-version: ['3.8', '3.12']
 
     steps:
     - uses: actions/checkout@v3
+
     - name: Set up Python ${{ matrix.python-version }}
       uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-version }}
+
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
         pip install -r requirements.txt
         pip install -r tests/requirements.txt
 
+    - name: Install optional dependencies
+      continue-on-error: true
+      run: |
+        pip install py-pde
+
     - name: Test with pytest
       env:
         NUMBA_WARNINGS: 1

docs/source/installation.rst

@@ -26,7 +26,7 @@ You can thus install it using
 
     conda install -c conda-forge py-modelrunner
 
-This installation includes all required dependencies to have all features of `py-pde`.
+This installation includes all required dependencies to have all features of `py-modelrunner`.
 
 
 Installing from source

modelrunner/py.typed

@@ -1 +1 @@
-# This file indicates that the py-pde package supports typing compliant with PEP 561 
+# This file indicates that the package supports typing compliant with PEP 561 

pyproject.toml

@@ -6,7 +6,7 @@ authors = [
 ]
 license = {text = "MIT"}
 readme = "README.md"
-requires-python = ">=3.8,<3.12"
+requires-python = ">=3.8,<3.13"
 dynamic = ["version"]
 
 classifiers = [
@@ -21,6 +21,7 @@ classifiers = [
     "Programming Language :: Python :: 3.9",
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
 ]
 
 # Requirements for setuptools

tests/helpers/storage.py

@@ -5,10 +5,9 @@
 """
 
 import importlib
-from typing import Any, Callable, List, Optional, Sequence, TypeVar, Union
+from typing import Any, Callable, List, Optional, TypeVar
 
 import numpy as np
-import pytest
 
 TFunc = TypeVar("TFunc", bound=Callable[..., Any])
 
@@ -31,33 +30,6 @@ def module_available(module_name: str) -> bool:
         return True
 
 
-def skipUnlessModule(
-    module_names: Union[Sequence[str], str]
-) -> Callable[[TFunc], TFunc]:
-    """decorator that skips a test when a module is not available
-
-    Args:
-        module_names (str):
-            The name of the required module(s)
-
-    Returns:
-        A function, so this can be used as a decorator
-    """
-    if isinstance(module_names, str):
-        module_names = [module_names]
-
-    for module_name in module_names:
-        if not module_available(module_name):
-            # return decorator skipping test
-            return pytest.skip(f"requires {module_name}")
-
-    # return no-op decorator if all modules are available
-    def wrapper(f: TFunc) -> TFunc:
-        return f
-
-    return wrapper
-
-
 def storage_extensions(
     incl_folder: bool = True, dot: bool = False, *, exclude: Optional[List] = None
 ):

tests/requirements.txt

@@ -4,5 +4,4 @@ isort>=5.1
 pytest>=5.4
 pytest-cov>=2.8
 pytest-xdist>=1.30
-py-pde>=0.33
 mypy>=0.770

tests/storage/test_storage_special.py

@@ -6,9 +6,8 @@
 
 import numpy as np
 import pytest
-from pde.tools.misc import skipUnlessModule
 
-from helpers import STORAGE_OBJECTS, assert_data_equals
+from helpers import STORAGE_OBJECTS, assert_data_equals, module_available
 from modelrunner.storage import MemoryStorage, open_storage
 
 
@@ -24,7 +23,7 @@ def test_memory_storage(obj):
         np.testing.assert_array_equal(storage.read_array("dyn", index=0), np.ones(2))
 
 
-@skipUnlessModule("h5py")
+@pytest.mark.skipif(not module_available("h5py"), reason="requires `h5py` module")
 def test_hdf_storage(tmp_path):
     """test HDFStorage"""
     import h5py
@@ -40,7 +39,7 @@ def test_hdf_storage(tmp_path):
         assert root.attrs["test"] == 5
 
 
-@skipUnlessModule("zarr")
+@pytest.mark.skipif(not module_available("zarr"), reason="requires `zarr` module")
 def test_zarr_storage(tmp_path):
     """test ZarrStorage"""
     import zarr
@@ -66,7 +65,7 @@ def test_json_storage(tmp_path):
         assert json.load(fp) == json.loads(json_txt)
 
 
-@skipUnlessModule("yaml")
+@pytest.mark.skipif(not module_available("yaml"), reason="requires `yaml` module")
 def test_yaml_storage(tmp_path):
     """test YAMLStorage"""
     import yaml

tests/test_results.py

@@ -5,7 +5,7 @@
 import numpy as np
 import pytest
 
-from helpers import assert_data_equals, skipUnlessModule, storage_extensions
+from helpers import assert_data_equals, module_available, storage_extensions
 from modelrunner.results import Result, ResultCollection
 
 STORAGE_EXT = storage_extensions(incl_folder=True, dot=True)
@@ -34,7 +34,7 @@ def test_result_serialization(ext, tmp_path):
     np.testing.assert_equal(read.data, result.data)
 
 
-@skipUnlessModule("pde")
+@pytest.mark.skipif(not module_available("pde"), reason="requires `pde` module")
 @pytest.mark.parametrize("ext", STORAGE_EXT)
 def test_pde_field_storage(ext, tmp_path):
     """test writing pde fields"""
@@ -59,7 +59,7 @@ def test_pde_field_storage(ext, tmp_path):
     np.testing.assert_equal(read.data, result.data)
 
 
-@skipUnlessModule("pde")
+@pytest.mark.skipif(not module_available("pde"), reason="requires `pde` module")
 @pytest.mark.parametrize("ext", STORAGE_EXT)
 def test_pde_trajectory_storage(ext, tmp_path):
     """test writing pde trajectories"""