Update pytest config (#5576)

Ignores some warnings outside Holoviews and moves the configuration to pyproject.

I added flaky to test examples because it sometimes gives this Runtime error `Kernel died before replying to kernel_info`. 

Also, ignoring some warnings emitted by the latest numpy release (1.24).

.github/workflows/test.yaml

@@ -82,7 +82,7 @@ jobs:
         if: matrix.python-version == '3.11'
         run: |
           conda activate test-environment
-          pytest -n auto --dist loadscope --nbval-lax examples/reference/elements
+          pytest -n auto --dist loadscope --nbval-lax examples/reference/elements --force-flaky
       - name: codecov
         run: |
           conda activate test-environment

holoviews/core/util.py

@@ -2010,7 +2010,7 @@ def bound_range(vals, density, time_unit='us'):
         invert = True
     if not density:
         with warnings.catch_warnings():
-            warnings.filterwarnings('ignore', r'invalid value encountered in double_scalars')
+            warnings.filterwarnings('ignore', r'invalid value encountered in (double_scalars|scalar divide)')
             full_precision_density = compute_density(low, high, len(vals)-1)
             with np.errstate(over='ignore'):
                 density = round(full_precision_density, sys.float_info.dig)

pyproject.toml

@@ -4,3 +4,22 @@ requires = [
     "pyct >=0.4.4",
     "setuptools >=30.3.0",
 ]
+
+[tool.pytest.ini_options]
+addopts = "-p no:dash"
+filterwarnings = [
+    # Numpy warning triggered in Bokeh, when timedelta or datetime numpy scalar are compared to a numerical scalar
+    "ignore:elementwise comparison failed:DeprecationWarning:bokeh.core.property.bases",
+    "ignore:dropping variables using `drop` will be deprecated; using drop_vars is encouraged:PendingDeprecationWarning:xarray.core.dataarray",
+    # 2022-12-27: Plotly don't use packagings version yet
+    "ignore:distutils Version classes are deprecated:DeprecationWarning:plotly.graph_objs",
+    # 2022-12-27: A weird warning which could be related to Datashader
+    "ignore:Please use `append` from the:DeprecationWarning:pickle",
+    # 2022-12-27: Warnings which should be fixed in Panel
+    "ignore:make_current is deprecated; start the event loop first:DeprecationWarning:panel.io.server",
+    # 2023-01-02: Numpy 1.24 warnings
+    "ignore:`.+?` is a deprecated alias for `.+?`.:DeprecationWarning:bokeh",  # https://github.com/bokeh/bokeh/pull/12690
+    "ignore:`.+?` is a deprecated alias for `.+?`.:DeprecationWarning:cupy",  # https://github.com/cupy/cupy/issues/7211
+    "ignore:`.+?` is a deprecated alias for `.+?`.:DeprecationWarning:plotly.express.imshow_utils",  # https://github.com/plotly/plotly.py/pull/3997
+    "ignore:`.+?` is a deprecated alias for `.+?`.:DeprecationWarning:skimage.util.dtype",  # https://github.com/scikit-image/scikit-image/pull/6637
+]

setup.py

@@ -32,6 +32,7 @@
     'pytest',
     'pytest-cov',
     'pytest-xdist',
+    'flaky',
     'matplotlib >=3',
     'nbconvert',
     'bokeh',

tox.ini

@@ -28,10 +28,11 @@ commands = pytest holoviews --cov=./holoviews -vv
 [_examples]
 description = Test that default examples run
 deps = .[examples_tests]
-commands = pytest -n auto --dist loadscope --nbval-lax examples -k "not Plotting_with_Bokeh and not 17-Dashboards and not Plots_and_Renderers"
+commands = pytest -n auto --dist loadscope --nbval-lax examples -k "not Plotting_with_Bokeh and not 17-Dashboards and not Plots_and_Renderers" --force-flaky
 # 'Plotting_with_Bokeh' needs selenium, phantomjs, firefox and geckodriver to save a png picture.
 # '17-Dashboards' can give a timeout error.
 # 'Plots_and_Renderers' can give file not found here.
+# --force-flaky is because of "RuntimeError: Kernel died before replying to kernel_info"
 
 [_all_recommended]
 description = Run all recommended tests