Investigate and fix warnings that are thrown during testing

[davidrudlstorfer]

During testing a few warnings are thrown which

1. do come from 3rd party packages
2. could be deactivated because we purposefully get them during testing

Therefore, the warnings should be checked and "removed"

During our regular test suite the following warnings are there:

=============================== warnings summary ===============================
<frozen importlib._bootstrap>:241
  <frozen importlib._bootstrap>:241: DeprecationWarning: builtin type SwigPyPacked has no __module__ attribute

<frozen importlib._bootstrap>:241
  <frozen importlib._bootstrap>:241: DeprecationWarning: builtin type SwigPyObject has no __module__ attribute

<frozen importlib._bootstrap>:241
  <frozen importlib._bootstrap>:241: DeprecationWarning: builtin type swigvarlink has no __module__ attribute

tests/integration/test_integration_core_mesh.py::test_integration_core_mesh_transformations_with_solid[True-0.2-False-context2]
  /home/runner/work/beamme/beamme/src/beamme/core/mesh.py:538: UserWarning: There are elements which are not parallel to the y-z or x-y plane. This will lead to distorted elements!
    _warnings.warn(

-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html

On windows also this warning is thrown:

[7](https://github.com/beamme-py/beamme/actions/runs/21199690791/job/60982692361#step:5:99)
tests/other/test_other_examples.py::test_other_examples_notebooks[examples/example_1_finite_rotations.ipynb]
  C:\hostedtoolcache\windows\Python\3.13.11\x64\Lib\site-packages\zmq\_future.py:718: RuntimeWarning: Proactor event loop does not implement add_reader family of methods required for zmq. Registering an additional selector thread for add_reader support via tornado. Use `asyncio.set_event_loop_policy(WindowsSelectorEventLoopPolicy())` to avoid this warning.
    self._get_loop()

During our full test suite (with cubit) we get this additional warning:

tests/other/test_other_logo.py::test_other_logo
  /__w/beamme/beamme/src/beamme/mesh_creation_functions/beam_parametric_curve.py:156: IntegrationWarning: The maximum number of subdivisions (50) has been achieved.
    If increasing the limit yields no improvement it is advised to analyze 
    the integrand in order to determine the difficulties.  If the position of a 
    local difficulty can be determined (singularity, discontinuity) one will 
    probably gain from splitting up the interval and calling the integrator 
    on the subranges.  Perhaps a special-purpose integrator should be used.
    return _integrate.quad(ds, st, t)[0] + sS

And during our performance tests we get these warnings at runtime

WARNING: >>>>Poor Quality Shape Face Generated!<<<< on Surface 3
    (For example, the Shape metric for Face 10856 is 0.19802 .)
    The threshold for a Face is 0.2

WARNING: >>>>Poor Quality Shape Face Generated!<<<< on Surface 5
    (For example, the Shape metric for Face 12356 is 0.19802 .)
    The threshold for a Face is 0.2

and these additional warnings:

[4](https://github.com/beamme-py/beamme/actions/runs/21199478783/job/60982445846#step:7:56)
tests/performance/test_performance_beamme.py::test_performance_beamme_mespy_wrap_around_cylinder
  /github/home/miniconda3/envs/beamme/lib/python3.13/site-packages/beamme/core/mesh.py:538: UserWarning: There are elements which are not parallel to the y-z or x-y plane. This will lead to distorted elements!
    _warnings.warn(

tests/performance/test_performance_beamme.py::test_performance_beamme_wrap_around_cylinder_without_check
  /github/home/miniconda3/envs/beamme/lib/python3.13/site-packages/beamme/core/mesh.py:544: UserWarning: The nodes are not on the same y-z plane. This may lead to distorted elements!
    _warnings.warn(

[davidrudlstorfer]

@isteinbrecher are the warnings you experienced on macOS with numpy still there with an updated env and current install of beamme?

[isteinbrecher]

From the warnings that you posted I have some more information:

tests/integration/test_integration_core_mesh.py::test_integration_core_mesh_transformations_with_solid[True-0.2-False-context2]
  /home/runner/work/beamme/beamme/src/beamme/core/mesh.py:538: UserWarning: There are elements which are not parallel to the y-z or x-y plane. This will lead to distorted elements!
    _warnings.warn(

[4](https://github.com/beamme-py/beamme/actions/runs/21199478783/job/60982445846#step:7:56)
tests/performance/test_performance_beamme.py::test_performance_beamme_mespy_wrap_around_cylinder
  /github/home/miniconda3/envs/beamme/lib/python3.13/site-packages/beamme/core/mesh.py:538: UserWarning: There are elements which are not parallel to the y-z or x-y plane. This will lead to distorted elements!
    _warnings.warn(

tests/performance/test_performance_beamme.py::test_performance_beamme_wrap_around_cylinder_without_check
  /github/home/miniconda3/envs/beamme/lib/python3.13/site-packages/beamme/core/mesh.py:544: UserWarning: The nodes are not on the same y-z plane. This may lead to distorted elements!
    _warnings.warn(

these are warnings from within BeamMe, they come from the wrap_around_cylinder function. We currently don't have a way to suppress this warning, but it should be relatively easy.

These warnings are from Cubit itself, I am not sure if there

WARNING: >>>>Poor Quality Shape Face Generated!<<<< on Surface 3
    (For example, the Shape metric for Face 10856 is 0.19802 .)
    The threshold for a Face is 0.2

WARNING: >>>>Poor Quality Shape Face Generated!<<<< on Surface 5
    (For example, the Shape metric for Face 12356 is 0.19802 .)
    The threshold for a Face is 0.2

I am not sure about the others.

[isteinbrecher]

I just released a new Cubit version today, so we will likely also soon get this warning:

tests/performance/test_performance_beamme.py: 1 warning
  /Users/ivosteinbrecher/miniforge3/envs/tmp/lib/python3.13/site-packages/cubitpy/conf.py:171: DeprecationWarning: CubitPy configuration file not found.Using default config: local
    warnings.warn(

[isteinbrecher]

I just installed the current main (v0.1.4) and ran the tests with pytest --performance-tests --CubitPy. I get same warnings as you report, the other ones with numpy are gone.

[isteinbrecher]

And one last comment, when I build the Python code with python setup.py build_ext --inplace I get the following warning (I have never seen that one before):

!!

        ********************************************************************************
        Please use a simple string containing a SPDX expression for `project.license`. You can also use `project.license-files`. (Both options available on setuptools>=77.0.0).

        By 2026-Feb-18, you need to update your project and remove deprecated calls
        or your builds will no longer be supported.

        See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.
        ********************************************************************************

!!

And the ArborX build also gives a lot of warnings - but they are mostly related to the c++ side of how we use ArborX and how we set the build options in our CMake.

[davidrudlstorfer]

And one last comment, when I build the Python code with python setup.py build_ext --inplace I get the following warning (I have never seen that one before):

I also already saw that one in the pipeline 😅

[davidrudlstorfer]

I tried to tackle down the swig warnings but I am not able to find which package or import is the culprit...

[davidrudlstorfer]

This comments collects an overview of all warnings and associated pull request

• license warning => fixed in fix: update to new license format in pyproject.toml #582

!!

        ********************************************************************************
        Please use a simple string containing a SPDX expression for `project.license`. You can also use `project.license-files`. (Both options available on setuptools>=77.0.0).

        By 2026-Feb-18, you need to update your project and remove deprecated calls
        or your builds will no longer be supported.

        See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.
        ********************************************************************************

!!

• pytest double import warning => fixed in fix: remove pytest warning for double import #583

../../../github/home/miniconda3/envs/beamme/lib/python3.13/site-packages/_pytest/config/__init__.py:852
  /github/home/miniconda3/envs/beamme/lib/python3.13/site-packages/_pytest/config/__init__.py:852: PytestAssertRewriteWarning: Module already imported so cannot be rewritten; tests.conftest_performance_tests
    self.import_plugin(import_spec)

• integration warning => fixed in Refactor parametric curve generation #576

tests/other/test_other_logo.py::test_other_logo
  /__w/beamme/beamme/src/beamme/mesh_creation_functions/beam_parametric_curve.py:156: IntegrationWarning: The maximum number of subdivisions (50) has been achieved.
    If increasing the limit yields no improvement it is advised to analyze 
    the integrand in order to determine the difficulties.  If the position of a 
    local difficulty can be determined (singularity, discontinuity) one will 
    probably gain from splitting up the interval and calling the integrator 
    on the subranges.  Perhaps a special-purpose integrator should be used.
    return _integrate.quad(ds, st, t)[0] + sS

• swig warning

<frozen importlib._bootstrap>:241
  <frozen importlib._bootstrap>:241: DeprecationWarning: builtin type SwigPyPacked has no __module__ attribute

<frozen importlib._bootstrap>:241
  <frozen importlib._bootstrap>:241: DeprecationWarning: builtin type SwigPyObject has no __module__ attribute

<frozen importlib._bootstrap>:241
  <frozen importlib._bootstrap>:241: DeprecationWarning: builtin type swigvarlink has no __module__ attribute

• unparallel elements warning

tests/integration/test_integration_core_mesh.py::test_integration_core_mesh_transformations_with_solid[True-0.2-False-context2]
  /home/runner/work/beamme/beamme/src/beamme/core/mesh.py:538: UserWarning: There are elements which are not parallel to the y-z or x-y plane. This will lead to distorted elements!
    _warnings.warn(

• windows warning

[7](https://github.com/beamme-py/beamme/actions/runs/21199690791/job/60982692361#step:5:99)
tests/other/test_other_examples.py::test_other_examples_notebooks[examples/example_1_finite_rotations.ipynb]
  C:\hostedtoolcache\windows\Python\3.13.11\x64\Lib\site-packages\zmq\_future.py:718: RuntimeWarning: Proactor event loop does not implement add_reader family of methods required for zmq. Registering an additional selector thread for add_reader support via tornado. Use `asyncio.set_event_loop_policy(WindowsSelectorEventLoopPolicy())` to avoid this warning.
    self._get_loop()

• cubit poor quality shape face generated

WARNING: >>>>Poor Quality Shape Face Generated!<<<< on Surface 3
    (For example, the Shape metric for Face 10856 is 0.19802 .)
    The threshold for a Face is 0.2

WARNING: >>>>Poor Quality Shape Face Generated!<<<< on Surface 5
    (For example, the Shape metric for Face 12356 is 0.19802 .)
    The threshold for a Face is 0.2

• nodes not on the same plane warning

tests/performance/test_performance_beamme.py::test_performance_beamme_wrap_around_cylinder_without_check
  /github/home/miniconda3/envs/beamme/lib/python3.13/site-packages/beamme/core/mesh.py:544: UserWarning: The nodes are not on the same y-z plane. This may lead to distorted elements!
    _warnings.warn(

• cubit warning

tests/performance/test_performance_beamme.py: 1 warning
  /Users/ivosteinbrecher/miniforge3/envs/tmp/lib/python3.13/site-packages/cubitpy/conf.py:171: DeprecationWarning: CubitPy configuration file not found.Using default config: local
    warnings.warn(

• pyvista warning

tests/integration/test_integration_core_mesh.py::test_integration_core_mesh_display_pyvista
tests/other/test_other_readme.py::test_other_readme_getting_started
  /__w/beamme/beamme/src/beamme/core/mesh.py:963: PyVistaFutureWarning: The default value of `algorithm` for the filter
  `UnstructuredGrid.extract_surface` will change in the future. It currently defaults to
  `'dataset_surface'`, but will change to `None`. Explicitly set the `algorithm` keyword to
  silence this warning.
    surface = beam_grid.extract_surface()

• vistools warning

  /github/home/miniconda3/envs/beamme/lib/python3.13/site-packages/vistools/vtk/compare_grids.py:131: DeprecationWarning: Call to deprecated method GetData. (Use ExportLegacyFormat, or GetOffsetsArray/GetConnectivityArray instead.) -- Deprecated since version 9.6.0.
    grid_1.GetCells().GetData(), grid_2.GetCells().GetData(), "cell_connectivity"

• ArborX compilation warnings (very low priority): There are a lot of ArborX compilation warnings.

@isteinbrecher I think these are all warnings, maybe you could take a brief look which warnings should be tackled in which manner

[davidrudlstorfer]

So the swig warning actually comes from the rapidyaml import via FourCIPP => biojppm/rapidyaml#570

[isteinbrecher]

unparallel elements warning
nodes not on the same plane warning

This is related to the warp around cylinder function and should be made optional - I can take care of that.

cubit poor quality shape face generated

These are coming directly from Cubit. I don't know if we can get rid of them easily. Is this actually a warning or is this "just" printed in the terminal output.

cubit warning

That is due to a change in CubitPy, I will also look at this.

Regarding the other warnings, I don't have an idea.

[davidrudlstorfer]

That sounds perfect ;)

I will take care of the remaining warnings :)

[isteinbrecher]

@davidrudlstorfer with #593 the warnings in the logo are removed. Unfortunately there are now some other additional warnings... I added them to the comment above.