Treat warnings as errors in tests (pyvista#7009)

edabor · tkoyama010 · pre-commit-ci[bot] · web-flow · commit e5eb840b4597 · 2025-01-18T07:46:58.000Z
* Remove depreciation warning ignore and make filter warnings as errors * Fix core tests * Fix camera tests * Fix some plotting tests * Add return_scalar to array_wrap for lut * Remove kwargs Path * Fix typing * Ignore pytest config warning for doc images tests * Fix warnings filter * Fix title offset deprecation * Add ignore warning for plotting tests * Ignore trame warning * Closing gif files * Fix typing * Fix cube axes actor test * Ignore matplotlib legend warning * Add conditional filter warnings for vtk 9.1 and numpy bool deprecation * Fix ignore regex * Fix vtk deprecation * Always print warnings for image regression * Fix last tests * Fix tests * Move warning ignore to configure since emitted during collection * Fix warning syntax * Ignore upstream matplotlib warning * Ignore already catched warning * Change warning type * Enlarge warning * Ignore warning from matplotlib * Change warning filter location for plotting * Add special ignore for 9.1 * Fix segfault for vtk < 9.1 * Change warning location * Fix warning in the docs * Fix docstring * Move image regression filter to pyproject * Add flaky test filter to always * Fix warning filter regex * Update pyvista/plotting/plotter.py Co-authored-by: Tetsuo Koyama <tkoyama010@gmail.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Apply suggestion from code review Co-authored-by: user27182 <89109579+user27182@users.noreply.github.com> * Apply suggestion from code review --------- Co-authored-by: Tetsuo Koyama <tkoyama010@gmail.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: user27182 <89109579+user27182@users.noreply.github.com>
diff --git a/pyproject.toml b/pyproject.toml
@@ -84,6 +84,7 @@ test = [
   'pytest-pyvista==0.1.8',
   'pytest-xdist<3.7.0',
   'pytest<8.4.0',
+  'pytest_cases<3.8.6',
   'pytest_mock<3.15.0',
   'pyvista[pinned]',
   'scipy<1.14.2',
@@ -198,15 +199,19 @@ omit = [
 
 [tool.pytest.ini_options]
 doctest_optionflags = 'NUMBER ELLIPSIS'
+
+# Keep spaces between filter warnings since order matters (see https://docs.pytest.org/en/stable/how-to/capture-warnings.html#controlling-warnings)
 filterwarnings = [
-  'error::pyvista.PyVistaDeprecationWarning',
-  'ignore:.*Given trait value dtype "float64":UserWarning', # bogus numpy ABI warning (see numpy/#432)
-  'ignore:.*The NumPy module was reloaded*:UserWarning',    # bogus numpy ABI warning (see numpy/#432)
-  'ignore:.*numpy.dtype size changed.*:RuntimeWarning',     # bogus numpy ABI warning (see numpy/#432)
-  'ignore:.*numpy.ufunc size changed.*:RuntimeWarning',     # bogus numpy ABI warning (see numpy/#432)
-  'ignore::DeprecationWarning',
-  'ignore::FutureWarning',
-  'ignore::PendingDeprecationWarning',
+  'error',
+
+  'ignore:.*Given trait value dtype "float64":UserWarning',                                   # bogus numpy ABI warning (see numpy/#432)
+  'ignore:.*The NumPy module was reloaded*:UserWarning',                                      # bogus numpy ABI warning (see numpy/#432)
+  'ignore:.*numpy.dtype size changed.*:RuntimeWarning',                                       # bogus numpy ABI warning (see numpy/#432)
+  'ignore:.*numpy.ufunc size changed.*:RuntimeWarning',                                       # bogus numpy ABI warning (see numpy/#432)
+  'ignore:Passing .{1}N.{1} to ListedColormap is deprecated since:DeprecationWarning',        # https://github.com/matplotlib/cmocean/pull/114
+  'ignore:pyvista test generated image dir.* does not yet exist.  Creating dir.:UserWarning',
+
+  'always:.*Exceeded image regression warning of .* with an image error of .*:UserWarning',
 ]
 image_cache_dir = 'tests/plotting/image_cache'
 junit_family = 'legacy'
diff --git a/pyvista/core/_validation/validate.py b/pyvista/core/_validation/validate.py
@@ -1231,7 +1231,7 @@ def validate_dimensionality(
         dimensionality_as_array = np.char.replace(dimensionality_as_array, 'D', '')
 
     try:
-        dimensionality_as_array = dimensionality_as_array.astype(np.integer)
+        dimensionality_as_array = dimensionality_as_array.astype(np.int64)
     except ValueError:
         raise ValueError(
             f'`{dimensionality}` is not a valid dimensionality.'
diff --git a/pyvista/core/filters/image_data.py b/pyvista/core/filters/image_data.py
@@ -2632,7 +2632,7 @@ def label_connectivity(
 
         Label only the regions that include seed points, by seed order.
 
-        >>> points = [(2, 1, 0), (0, 0, 1)]
+        >>> points = [(2.0, 1.0, 0.0), (0.0, 0.0, 1.0)]
         >>> connected, labels, sizes = segmented_grid.label_connectivity(
         ...     scalar_range='foreground',
         ...     extraction_mode='seeded',
diff --git a/pyvista/core/pointset.py b/pyvista/core/pointset.py
@@ -2488,7 +2488,9 @@ def dimensions(self):  # numpydoc ignore=RT01
         (20, 10, 4)
 
         """
-        return tuple(self.GetDimensions())
+        dims = [0, 0, 0]
+        self.GetDimensions(dims)
+        return tuple(dims)
 
     @dimensions.setter
     def dimensions(self, dims) -> None:
diff --git a/pyvista/core/utilities/fileio.py b/pyvista/core/utilities/fileio.py
@@ -1241,7 +1241,7 @@ def _try_imageio_imread(filename: str | Path) -> imageio.core.util.Array:
 
     """
     try:
-        from imageio import imread
+        from imageio.v2 import imread
     except ModuleNotFoundError:  # pragma: no cover
         raise ModuleNotFoundError(
             'Problem reading the image with VTK. Install imageio to try to read the '
diff --git a/pyvista/core/utilities/reader.py b/pyvista/core/utilities/reader.py
@@ -2622,6 +2622,8 @@ def Update(self) -> None:
         if 'frame0' in self._data_object.point_data:
             self._data_object.point_data.active_scalars_name = 'frame0'
 
+        img.close()
+
 
 class GIFReader(BaseReader):
     """GIFReader for .gif files.
diff --git a/pyvista/core/utilities/transform.py b/pyvista/core/utilities/transform.py
@@ -1562,7 +1562,7 @@ def apply(
 
         Apply a transformation to a points array.
 
-        >>> points = np.array([[1, 2, 3], [4, 5, 6]])
+        >>> points = np.array([[1.0, 2.0, 3.0], [4.0, 5.0, 6.0]])
         >>> transformed_points = transform.apply(points)
         >>> transformed_points
         array([[ 2.,  4.,  6.],
@@ -1574,14 +1574,14 @@ def apply(
         >>> transformed_dataset = transform.apply(dataset)
         >>> transformed_dataset.points
         pyvista_ndarray([[ 2.,  4.,  6.],
-                         [ 8., 10., 12.]], dtype=float32)
+                         [ 8., 10., 12.]])
 
         Apply the inverse.
 
         >>> inverted_dataset = transform.apply(dataset, inverse=True)
         >>> inverted_dataset.points
         pyvista_ndarray([[0.5, 1. , 1.5],
-                         [2. , 2.5, 3. ]], dtype=float32)
+                         [2. , 2.5, 3. ]])
 
         """
         inplace = not copy
diff --git a/pyvista/examples/downloads.py b/pyvista/examples/downloads.py
@@ -93,7 +93,7 @@
     # provide helpful message if pooch path is inaccessible
     if not Path(USER_DATA_PATH).is_dir():  # pragma: no cover
         try:
-            Path(USER_DATA_PATH, exist_ok=True).mkdir()
+            Path(USER_DATA_PATH).mkdir(exist_ok=True)
             if not os.access(USER_DATA_PATH, os.W_OK):
                 raise OSError
         except (PermissionError, OSError):
diff --git a/pyvista/plotting/axes_assembly.py b/pyvista/plotting/axes_assembly.py
@@ -1961,7 +1961,8 @@ def __init__(self):
         self.SetUseBounds(False)
 
         # Format title positioning
-        self.SetTitleOffset(0)
+        offset = (0,) if pv.vtk_version_info < (9, 3) else (0, 0)
+        self.SetTitleOffset(*offset)
         self.SetLabelOffset(0)
 
         # For 2D mode only
diff --git a/pyvista/plotting/cube_axes_actor.py b/pyvista/plotting/cube_axes_actor.py
@@ -2,8 +2,10 @@
 
 from __future__ import annotations
 
+from collections.abc import MutableSequence
 from typing import TYPE_CHECKING
 from typing import cast
+import warnings
 
 import numpy as np
 
@@ -289,12 +291,34 @@ def label_offset(self, offset: float):
         self.SetLabelOffset(offset)
 
     @property
-    def title_offset(self) -> float:  # numpydoc ignore=RT01
+    def title_offset(self) -> float | tuple[float, float]:  # numpydoc ignore=RT01
         """Return or set the distance between title and labels."""
+        if pyvista.vtk_version_info >= (9, 3):
+            offx, offy = (_vtk.reference(0.0), _vtk.reference(0.0))
+            self.GetTitleOffset(offx, offy)  # type: ignore[call-overload]
+            return offx, offy  # type: ignore[return-value]
+
         return self.GetTitleOffset()
 
     @title_offset.setter
-    def title_offset(self, offset: float):
+    def title_offset(self, offset: float | MutableSequence[float]):
+        vtk_geq_9_3 = pyvista.vtk_version_info >= (9, 3)
+
+        if vtk_geq_9_3:
+            if isinstance(offset, float):
+                msg = f'Setting title_offset with a float is deprecated from vtk >= 9.3. Accepts now a sequence of (x,y) offsets. Setting the x offset to {(x:=0.0)}'
+                warnings.warn(msg, UserWarning)
+                self.SetTitleOffset([x, offset])
+            else:
+                self.SetTitleOffset(offset)
+            return
+
+        if isinstance(offset, MutableSequence):
+            msg = f'Setting title_offset with a sequence is only supported from vtk >= 9.3. Considering only the second value (ie. y-offset) of {(y:=offset[1])}'
+            warnings.warn(msg, UserWarning)
+            self.SetTitleOffset(y)
+            return
+
         self.SetTitleOffset(offset)
 
     @property
diff --git a/pyvista/plotting/lookup_table.py b/pyvista/plotting/lookup_table.py
@@ -76,14 +76,14 @@ def __setitem__(self, key, value):
             # internal VTK array
             self.table.Get().values = self
 
-    def __array_wrap__(self, out_arr, context=None):  # type: ignore[override]
+    def __array_wrap__(self, out_arr, context=None, return_scalar: bool = False):
         """Return a numpy scalar if array is 0d.
 
         See https://github.com/numpy/numpy/issues/5819
 
         """
         if out_arr.ndim:
-            return np.ndarray.__array_wrap__(self, out_arr, context)
+            return np.ndarray.__array_wrap__(self, out_arr, context, return_scalar)
 
         # Match numpy's behavior and return a numpy dtype scalar
         return out_arr[()]
diff --git a/pyvista/plotting/plotter.py b/pyvista/plotting/plotter.py
@@ -2206,12 +2206,18 @@ def key_press_event(self, *args, **kwargs) -> None:  # numpydoc ignore=PR01,RT01
 
     def left_button_down(self, *args):
         """Register the event for a left button down click."""
+        attr = (
+            'GetOffScreenFramebuffer'
+            if pyvista.vtk_version_info < (9, 1)
+            else 'GetRenderFramebuffer'
+        )
         if (
-            hasattr(self.render_window, 'GetOffScreenFramebuffer')
-            and not self.render_window.GetOffScreenFramebuffer().GetFBOIndex()  # type: ignore[union-attr]
+            hasattr(renwin := self.render_window, attr)
+            and not getattr(renwin, attr)().GetFBOIndex()
         ):
             # must raise a runtime error as this causes a segfault on VTK9
             raise ValueError('Invoking helper with no framebuffer')
+
         # Get 2D click location on window
         click_pos = self.iren.get_event_position()  # type: ignore[has-type]
 
diff --git a/tests/conftest.py b/tests/conftest.py
@@ -2,6 +2,7 @@
 
 import functools
 from importlib import metadata
+from pathlib import Path
 import re
 
 import numpy as np
@@ -260,18 +261,33 @@ def pytest_addoption(parser):
     parser.addoption('--test_downloads', action='store_true', default=False)
 
 
-def marker_names(item):
+def pytest_configure(config: pytest.Config):
+    """Add filterwarnings for vtk < 9.1 and numpy bool deprecation"""
+    warnings = config.getini('filterwarnings')
+
+    if pyvista.vtk_version_info < (9, 1):
+        warnings.append(
+            r'ignore:.*np\.bool.{1} is a deprecated alias for the builtin .{1}bool.*:DeprecationWarning'
+        )
+    if any(Path(a).stem == 'tst_doc_images' for a in config.args):
+        # Warning is emitted because `pytest-pyvista` is not installed (and is not required for this test)
+        warnings.append(
+            'ignore:Unknown config option.*image_cache_dir.*:pytest.PytestConfigWarning'
+        )
+
+
+def marker_names(item: pytest.Item):
     return [marker.name for marker in item.iter_markers()]
 
 
-def pytest_collection_modifyitems(config, items):
+def pytest_collection_modifyitems(config: pytest.Config, items: list[pytest.Item]):
     test_downloads = config.getoption('--test_downloads')
 
-    # skip all tests that need downloads
-    if not test_downloads:
-        skip_downloads = pytest.mark.skip('Downloads not enabled with --test_downloads')
-        for item in items:
+    for item in items:
+        # skip all tests that need downloads
+        if not test_downloads:
             if 'needs_download' in marker_names(item):
+                skip_downloads = pytest.mark.skip('Downloads not enabled with --test_downloads')
                 item.add_marker(skip_downloads)
 
 
diff --git a/tests/core/test_dataset_filters.py b/tests/core/test_dataset_filters.py
@@ -4570,6 +4570,7 @@ def test_align_xyz_three_axis_directions(planar_mesh):
         )
 
 
+@pytest.mark.filterwarnings('ignore:Points is not a float type.*:UserWarning')
 def test_align_xyz_swap_axes():
     # create planar data with equal variance in x and z
     points = np.array([[1, 0, 0], [-1, 0, 0], [0, 0, 1], [0, 0, -1]])
diff --git a/tests/core/test_utilities.py b/tests/core/test_utilities.py
@@ -14,6 +14,8 @@
 
 import numpy as np
 import pytest
+from pytest_cases import parametrize
+from pytest_cases import parametrize_with_cases
 import vtk
 
 import pyvista as pv
@@ -1058,6 +1060,8 @@ def test_principal_axes_return_std():
     assert np.allclose(ratios_in, ratios_out, atol=0.02)
 
 
+@pytest.mark.filterwarnings('ignore:Mean of empty slice:RuntimeWarning')
+@pytest.mark.filterwarnings('ignore:invalid value encountered in divide:RuntimeWarning')
 def test_principal_axes_empty():
     axes = principal_axes(np.empty((0, 3)))
     assert np.allclose(axes, DEFAULT_PRINCIPAL_AXES)
@@ -1370,38 +1374,48 @@ def test_transform_invert(transform):
     assert transform.is_inverted is False
 
 
-@pytest.mark.parametrize('copy', [True, False])
-@pytest.mark.parametrize(
-    ('obj', 'return_self', 'return_type', 'return_dtype'),
-    [
-        (list(VECTOR), False, np.ndarray, float),
-        (VECTOR, False, np.ndarray, float),
-        (np.array(VECTOR), False, np.ndarray, float),
-        (np.array([VECTOR]), False, np.ndarray, float),
-        (np.array(VECTOR, dtype=float), True, np.ndarray, float),
-        (np.array([VECTOR], dtype=float), True, np.ndarray, float),
-        (pv.PolyData(np.atleast_2d(VECTOR)), True, pv.PolyData, np.float32),
-        (pv.PolyData(np.atleast_2d(VECTOR).astype(int)), True, pv.PolyData, np.float32),
-        (pv.PolyData(np.atleast_2d(VECTOR).astype(float)), True, pv.PolyData, float),
-        (
+class CasesTransformApply:
+    def case_list_int(self):
+        return list(VECTOR), False, np.ndarray, float
+
+    def case_tuple_int(self):
+        return VECTOR, False, np.ndarray, float
+
+    def case_array1d_int(self):
+        return np.array(VECTOR), False, np.ndarray, float
+
+    def case_array2d_int(self):
+        return np.array([VECTOR]), False, np.ndarray, float
+
+    def case_array1d_float(self):
+        return np.array(VECTOR, dtype=float), True, np.ndarray, float
+
+    def case_array2d_float(self):
+        return np.array([VECTOR], dtype=float), True, np.ndarray, float
+
+    @pytest.mark.filterwarnings('ignore:Points is not a float type.*:UserWarning')
+    def case_polydata_float32(self):
+        return pv.PolyData(np.atleast_2d(VECTOR)), True, pv.PolyData, np.float32
+
+    @pytest.mark.filterwarnings('ignore:Points is not a float type.*:UserWarning')
+    def case_polydata_int(self):
+        return pv.PolyData(np.atleast_2d(VECTOR).astype(int)), True, pv.PolyData, np.float32
+
+    def case_polydata_float(self):
+        return pv.PolyData(np.atleast_2d(VECTOR).astype(float)), True, pv.PolyData, float
+
+    def case_multiblock_float(self):
+        return (
             pv.MultiBlock([pv.PolyData(np.atleast_2d(VECTOR).astype(float))]),
             True,
             pv.MultiBlock,
             float,
-        ),
-    ],
-    ids=[
-        'list-int',
-        'tuple-int',
-        'array1d-int',
-        'array2d-int',
-        'array1d-float',
-        'array2d-float',
-        'polydata-float32',
-        'polydata-int',
-        'polydata-float',
-        'multiblock-float',
-    ],
+        )
+
+
+@parametrize(copy=[True, False])
+@parametrize_with_cases(
+    ('obj', 'return_self', 'return_type', 'return_dtype'), cases=CasesTransformApply
 )
 def test_transform_apply(transform, obj, return_self, return_type, return_dtype, copy):
     def _get_points_from_object(obj_):
diff --git a/tests/core/test_validation.py b/tests/core/test_validation.py
@@ -124,6 +124,9 @@ def test_check_subdtype():
         check_subdtype(np.array([1 + 1j, 2, 3]), (np.integer, np.floating))
 
 
+@pytest.mark.filterwarnings(
+    'ignore:Converting `np.inexact` or `np.floating` to a dtype is deprecated. The current result is `float64` which is not strictly correct.:DeprecationWarning'
+)
 def test_check_subdtype_changes_type():
     # test coercing some types (e.g. np.number) can lead to unexpected
     # failed `np.issubtype` checks due to an implicit change of type
@@ -1017,6 +1020,7 @@ def test_cast_to_numpy(as_any, copy, dtype):
         assert array_out.dtype.type is np.dtype(dtype).type
 
 
+@pytest.mark.filterwarnings('ignore:Creating an ndarray from ragged nested sequences:UserWarning')
 def test_cast_to_numpy_raises():
     if NUMPY_VERSION_INFO < (1, 26) and sys.platform == 'linux':
         err = TypeError
diff --git a/tests/doc/tst_doc_images.py b/tests/doc/tst_doc_images.py
@@ -25,6 +25,8 @@
     path for path in os.listdir(FLAKY_IMAGE_DIR) if Path(FLAKY_IMAGE_DIR, path).is_dir()
 ]
 
+pytestmark = [pytest.mark.filterwarnings(r'always:.*\n.*THIS IS A FLAKY TEST.*:UserWarning')]
+
 
 class _TestCaseTuple(NamedTuple):
     test_name: str
diff --git a/tests/plotting/jupyter/test_trame.py b/tests/plotting/jupyter/test_trame.py
diff --git a/tests/plotting/test_camera.py b/tests/plotting/test_camera.py
diff --git a/tests/plotting/test_charts.py b/tests/plotting/test_charts.py
diff --git a/tests/plotting/test_cube_axes_actor.py b/tests/plotting/test_cube_axes_actor.py
diff --git a/tests/plotting/test_plotting.py b/tests/plotting/test_plotting.py
diff --git a/tests/plotting/test_plotting_utilities.py b/tests/plotting/test_plotting_utilities.py
diff --git a/tests/plotting/test_theme.py b/tests/plotting/test_theme.py
