[pyOpenSci] Tests

[nicoguaro]

When I run the tests in my computer with a newly installed Felupe, I get the following

tests/test_constitution.py::test_optimize
  C:\Users\nguarinz\Workspace\felupe\.tox\py3\Lib\site-packages\tensortrax\math\_math_tensor.py:228: RuntimeWarning: invalid value encountered in log
    x = np.log(f(A))

tests/test_constitution.py::test_plot_negative_stretches
  C:\Users\nguarinz\Workspace\felupe\.tox\py3\Lib\site-packages\felupe\constitution\_view.py:77: RuntimeWarning: More than 20 figures have been opened. Figures created through the pyplot interface (`matplotlib.pyplot.figure`) are retained until explicitly closed and may consume too much memory. (To control this warning, see the rcParam `figure.max_open_warning`). Consider using `matplotlib.pyplot.close()`.
    fig, ax = plt.subplots()

tests/test_job.py::test_job_xdmf
  C:\Users\nguarinz\Workspace\felupe\tests\test_job.py:20: DeprecationWarning: felupe.SolidBodyGravity is deprecated, use felupe.SolidBodyForce instead.
    gravity = SolidBodyForce(field, [0, 0, 0], 0)

tests/test_job.py: 11 warnings
  C:\Users\nguarinz\Workspace\felupe\.tox\py3\Lib\site-packages\felupe\mechanics\_solidbody_gravity.py:98: DeprecationWarning: felupe.SolidBodyGravity is deprecated, use felupe.SolidBodyForce instead.
    self.__init__(self.field, gravity, self.results.density)

tests/test_region.py::test_region
  C:\Users\nguarinz\Workspace\felupe\.tox\py3\Lib\site-packages\felupe\math\_tensor.py:417: RuntimeWarning: divide by zero encountered in divide
    return np.divide(detAinvA, detA, out=detAinvA)

tests/test_region.py::test_region
  C:\Users\nguarinz\Workspace\felupe\.tox\py3\Lib\site-packages\felupe\math\_tensor.py:417: RuntimeWarning: invalid value encountered in divide
    return np.divide(detAinvA, detA, out=detAinvA)

tests/test_region.py::test_region
  C:\Users\nguarinz\Workspace\felupe\.tox\py3\Lib\site-packages\felupe\region\_region.py:381: UserWarning: Negative volumes for cells
   [0]
  Try ``mesh.flip(np.any(region.dV < 0, axis=0))`` and re-create the region.
    warnings.warn(message_negative_volumes)

-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
====================================================================================== 155 passed, 17 warnings in 51.14s =======================================================================================
  core: OK (95.30=setup[82.97]+cmd[12.33] seconds)
  py3: OK (120.30=setup[67.59]+cmd[52.70] seconds)
  congratulations :) (215.72 seconds)

There are some warnings regarding deprecation and negative jacobians, is this because of some updates in the test suite?

[adtzlr]

Hi @nicoguaro!

• SolidBodyGravity: I keep the deprecated SolidBodyGravity in the tests, just to be sure it's tested until it is removed. The deprecation warning is okay. The warning is now captured in the tests as part of Fix RegionQuadraticQuadBoundary #933.
• The negative volumes for cells (Jacobians) and divide-by-zero warnings are part of the test suite - but actually this was a bug in the gradient-evaluation of a boundary-region for quadratic-quad elements. Resolved in Fix RegionQuadraticQuadBoundary #933.
• All figures are now closed in the constitution-tests. Resolved in Fix RegionQuadraticQuadBoundary #933 and Don't create a figure if error in umat.plot() #934.

Thanks!

P.S.: The invalid value (log) is due to a not well-defined (but original!) hyperelastic model using automatic differentiation. The warning is captured in #933.

[adtzlr]

@nicoguaro, how would you like to handle the pyOpenSci-related Issues? Should I keep them open? Should I close them when I think they are finished? Would you like to close them once the fixes / enhancements are okay for you?

[nicoguaro]

I think that you should handle them and let me know.

[adtzlr]

Okay, @nicoguaro, then let's close this issue, all warnings are captured in in the tests now. One bug in the boundary-region for quadratic quads was detected in the warnings and is fixed now.