Replaced decorator skipUnlessModule (#510)

* Replaced decorator `skipUnlessModule`

pde/tools/__init__.py

@@ -19,6 +19,6 @@
    plotting
    spectral
    typing
-   
+
 .. codeauthor:: David Zwicker <[email protected]> 
 """

pde/tools/config.py

@@ -10,7 +10,7 @@
    check_package_version
    packages_from_requirements
    environment
-   
+
 .. codeauthor:: David Zwicker <[email protected]>
 """
 

pde/tools/misc.py

@@ -8,7 +8,6 @@
    ensure_directory_exists
    preserve_scalars
    decorator_arguments
-   skipUnlessModule
    import_class
    classproperty
    hybridmethod
@@ -29,6 +28,7 @@
 import json
 import os
 import unittest
+import warnings
 from pathlib import Path
 from typing import Any, Callable, Dict, Optional, Sequence, TypeVar
 
@@ -135,6 +135,13 @@ def skipUnlessModule(module_names: str | Sequence[str]) -> Callable[[TFunc], TFu
     Returns:
         A function, so this can be used as a decorator
     """
+    # deprecated since 2024-01-03
+    warnings.warn(
+        "`skipUnlessModule` is deprecated. Use "
+        '`@pytest.mark.skipif(not module_available("module"))` instead.',
+        DeprecationWarning,
+    )
+
     if isinstance(module_names, str):
         module_names = [module_names]
 

tests/fields/test_field_collections.py

@@ -8,7 +8,7 @@
 from fixtures.fields import iter_grids
 from pde import FieldCollection, ScalarField, Tensor2Field, UnitGrid, VectorField
 from pde.fields.base import FieldBase
-from pde.tools.misc import skipUnlessModule
+from pde.tools.misc import module_available
 
 
 @pytest.mark.parametrize("grid", iter_grids())
@@ -224,7 +224,7 @@ def test_from_scalar_expressions():
     np.testing.assert_allclose(fc[1].data, 1)
 
 
-@skipUnlessModule("napari")
+@pytest.mark.skipif(not module_available("napari"), reason="requires `napari` module")
 @pytest.mark.interactive
 def test_interactive_collection_plotting(rng):
     """test the interactive plotting"""

tests/fields/test_generic_fields.py

@@ -17,7 +17,7 @@
     SphericalSymGrid,
     UnitGrid,
 )
-from pde.tools.misc import skipUnlessModule
+from pde.tools.misc import module_available
 
 
 @pytest.mark.parametrize("field_class", [ScalarField, VectorField, Tensor2Field])
@@ -214,7 +214,7 @@ def test_complex_fields(field_class, rng):
     assert field_copy.dtype == np.dtype("complex")
 
 
-@skipUnlessModule("h5py")
+@pytest.mark.skipif(not module_available("h5py"), reason="requires `h5py` module")
 def test_hdf_input_output(tmp_path, rng):
     """test writing and reading files"""
     grid = UnitGrid([4, 4])

tests/fields/test_scalar_fields.py

@@ -13,7 +13,7 @@
 from pde.grids import CartesianGrid, PolarSymGrid, UnitGrid, boundaries
 from pde.grids._mesh import GridMesh
 from pde.tools import mpi
-from pde.tools.misc import module_available, skipUnlessModule
+from pde.tools.misc import module_available
 
 
 def test_interpolation_singular():
@@ -240,7 +240,6 @@ def f(x, y):
     np.testing.assert_allclose(sf.data, [[0.25, 0.75]])
 
 
-@skipUnlessModule("matplotlib")
 def test_from_image(tmp_path, rng):
     from matplotlib.pyplot import imsave
 
@@ -410,7 +409,7 @@ def test_plotting_2d(rng):
     field._update_plot(ref)
 
 
-@skipUnlessModule("napari")
+@pytest.mark.skipif(not module_available("napari"), reason="requires `napari` module")
 @pytest.mark.interactive
 def test_interactive_plotting(rng):
     """test the interactive plotting"""

tests/fields/test_vectorial_fields.py

@@ -7,7 +7,7 @@
 
 from pde import CartesianGrid, ScalarField, Tensor2Field, UnitGrid, VectorField
 from pde.fields.base import FieldBase
-from pde.tools.misc import module_available, skipUnlessModule
+from pde.tools.misc import module_available
 
 
 def test_vectors_basic():
@@ -238,7 +238,7 @@ def test_vector_plotting_2d(transpose, rng):
     field.get_vector_data(transpose=transpose, max_points=7)
 
 
-@skipUnlessModule("napari")
+@pytest.mark.skipif(not module_available("napari"), reason="requires `napari` module")
 @pytest.mark.interactive
 def test_interactive_vector_plotting(rng):
     """test the interactive plotting"""

tests/grids/operators/test_cartesian_operators.py

@@ -18,7 +18,7 @@
 )
 from pde.grids.operators import cartesian as ops
 from pde.grids.operators.common import make_laplace_from_matrix
-from pde.tools.misc import skipUnlessModule
+from pde.tools.misc import module_available
 
 π = np.pi
 
@@ -85,7 +85,7 @@ def test_laplace_1d(periodic, rng):
     np.testing.assert_allclose(l1.data, l2.data)
 
 
-@skipUnlessModule("rocket_fft")
+@pytest.mark.skipif(not module_available("rocket_fft"), reason="requires `rocket_fft`")
 @pytest.mark.parametrize("ndim", [1, 2])
 @pytest.mark.parametrize("dtype", [float, complex])
 def test_laplace_spectral(ndim, dtype, rng):

tests/grids/test_generic_grids.py

@@ -15,7 +15,6 @@
     discretize_interval,
     registered_operators,
 )
-from pde.tools.misc import skipUnlessModule
 
 
 def iter_grids():
@@ -118,7 +117,6 @@ def test_integration_serial(grid, rng):
         assert res == pytest.approx(grid.integrate(arr, axes=range(grid.num_axes)))
 
 
-@skipUnlessModule("matplotlib")
 def test_grid_plotting():
     """test plotting of grids"""
     grids.UnitGrid([4]).plot()

tests/storage/test_file_storages.py

@@ -7,10 +7,10 @@
 
 import pde
 from pde import DiffusionPDE, FileStorage, ScalarField, UnitGrid
-from pde.tools.misc import skipUnlessModule
+from pde.tools.misc import module_available
 
 
-@skipUnlessModule("h5py")
+@pytest.mark.skipif(not module_available("napari"), reason="requires `napari` module")
 @pytest.mark.parametrize("collection", [True, False])
 def test_storage_persistence(collection, tmp_path):
     """test writing to persistent trackers"""
@@ -76,7 +76,7 @@ def assert_storage_content(storage, expect):
                 assert info.items() <= reader.info.items()
 
 
-@skipUnlessModule("h5py")
+@pytest.mark.skipif(not module_available("napari"), reason="requires `napari` module")
 @pytest.mark.parametrize("compression", [True, False])
 def test_simulation_persistence(compression, tmp_path, rng):
     """test whether a tracker can accurately store information about simulation"""
@@ -101,7 +101,7 @@ def test_simulation_persistence(compression, tmp_path, rng):
     assert grid == grid_res
 
 
-@skipUnlessModule("h5py")
+@pytest.mark.skipif(not module_available("napari"), reason="requires `napari` module")
 @pytest.mark.parametrize("compression", [True, False])
 def test_storage_fixed_size(compression, tmp_path):
     """test setting fixed size of FileStorage objects"""
@@ -130,7 +130,7 @@ def test_storage_fixed_size(compression, tmp_path):
             np.testing.assert_allclose(storage.times, [0, 1])
 
 
-@skipUnlessModule("h5py")
+@pytest.mark.skipif(not module_available("napari"), reason="requires `napari` module")
 def test_appending(tmp_path):
     """test the appending data"""
     path = tmp_path / "test_appending.hdf5"
@@ -152,7 +152,7 @@ def test_appending(tmp_path):
     assert len(storage2) == 2
 
 
-@skipUnlessModule("h5py")
+@pytest.mark.skipif(not module_available("napari"), reason="requires `napari` module")
 def test_keep_opened(tmp_path):
     """test the keep opened option"""
     path = tmp_path / "test_keep_opened.hdf5"
@@ -180,7 +180,7 @@ def test_keep_opened(tmp_path):
     np.testing.assert_allclose(storage2.times, np.arange(3))
 
 
-@skipUnlessModule("h5py")
+@pytest.mark.skipif(not module_available("napari"), reason="requires `napari` module")
 @pytest.mark.parametrize("dtype", [bool, float, complex])
 def test_write_types(dtype, tmp_path, rng):
     """test whether complex data can be written"""

tests/test_examples.py

@@ -10,7 +10,7 @@
 
 import pytest
 
-from pde.tools.misc import module_available, skipUnlessModule
+from pde.tools.misc import module_available
 from pde.visualization.movies import Movie
 
 PACKAGE_PATH = Path(__file__).resolve().parents[1]
@@ -67,7 +67,10 @@ def test_example_scripts(path):
 
 @pytest.mark.slow
 @pytest.mark.no_cover
-@skipUnlessModule(["h5py", "jupyter", "notebook", "nbconvert"])
+@pytest.mark.skipif(not module_available("h5py"), reason="requires `h5py`")
+@pytest.mark.skipif(not module_available("jupyter"), reason="requires `jupyter`")
+@pytest.mark.skipif(not module_available("notebook"), reason="requires `notebook`")
+@pytest.mark.skipif(not module_available("nbconvert"), reason="requires `nbconvert`")
 @pytest.mark.parametrize("path", NOTEBOOKS)
 def test_jupyter_notebooks(path, tmp_path):
     """run the jupyter notebooks"""

tests/test_integration.py

@@ -11,7 +11,7 @@
 from pde.tools import misc, mpi, numba
 
 
-@misc.skipUnlessModule("h5py")
+@pytest.mark.skipif(not misc.module_available("h5py"), reason="requires `h5py` module")
 def test_writing_to_storage(tmp_path, rng):
     """test whether data is written to storage"""
     state = ScalarField.random_uniform(UnitGrid([3]), rng=rng)

tests/tools/test_misc.py

@@ -82,7 +82,7 @@ def value(cls):  # @NoSelf
     assert Test.value == 2
 
 
-@misc.skipUnlessModule("h5py")
+@pytest.mark.skipif(not misc.module_available("h5py"), reason="requires `h5py` module")
 def test_hdf_write_attributes(tmp_path):
     """test hdf_write_attributes function"""
     import h5py
@@ -110,3 +110,9 @@ def test_hdf_write_attributes(tmp_path):
             misc.hdf_write_attributes(
                 hdf_file, {"a": object()}, raise_serialization_error=True
             )
+
+
+@misc.skipUnlessModule("undefined_module_name")
+def test_skipUnlessModule():
+    """test skipUnlessModule decorator"""
+    raise RuntimeError  # test should never run

tests/visualization/test_plotting.py

@@ -7,11 +7,10 @@
 from pde.fields import FieldCollection, ScalarField
 from pde.grids import UnitGrid
 from pde.storage import get_memory_storage
-from pde.tools.misc import skipUnlessModule
+from pde.tools.misc import module_available
 from pde.visualization import plotting
 
 
-@skipUnlessModule("matplotlib")
 def test_scalar_field_plot(tmp_path, rng):
     """test ScalarFieldPlot class"""
     path = tmp_path / "test_scalar_field_plot.png"
@@ -28,7 +27,6 @@ def test_scalar_field_plot(tmp_path, rng):
     assert path.stat().st_size > 0
 
 
-@skipUnlessModule("matplotlib")
 def test_scalar_plot(tmp_path, rng):
     """test Simple simulation"""
     path = tmp_path / "test_scalar_plot.png"
@@ -48,7 +46,6 @@ def test_scalar_plot(tmp_path, rng):
     assert path.stat().st_size > 0
 
 
-@skipUnlessModule("matplotlib")
 def test_collection_plot(tmp_path):
     """test Simple simulation"""
     # create some data
@@ -107,7 +104,7 @@ def test_kymograph_collection(tmp_path):
     assert path.stat().st_size > 0
 
 
-@skipUnlessModule("napari")
+@pytest.mark.skipif(not module_available("napari"), reason="requires `napari` module")
 @pytest.mark.interactive
 def test_interactive_plotting(rng):
     """test plot_interactive"""