Remove Warnings

[j-c-c]

This PR resolves warning messages emitted during unit testing.

Python 3.8:

• tests/test_sinogram.py: 12 warnings
  /scratch/jc5485/miniconda3/envs/warnings_3.8/lib/python3.8/site-packages/skimage/transform/radon_transform.py:75: UserWarning: Radon transform: image must be zero outside the reconstruction circle
  warn('Radon transform: image must be zero outside the '

• tests/test_covar2d_denoiser.py: 15 warnings
  /scratch/jc5485/Work/ASPIRE-python.warnings_3.8/src/aspire/basis/steerable.py:524: UserWarning: BlkDiagMatrix.from_dense truncating values exceeding 0.001
  filt = BlkDiagMatrix.from_dense(

Python 3.9:

• tests/test_FFBbasis2D.py: 52 warnings

• tests/test_FBbasis2D.py: 70 warnings

• tests/test_FFBbasis3D.py: 4 warnings

• tests/test_FLEbasis2D.py: 18 warnings

• tests/test_FBbasis3D.py: 4 warnings

• tests/test_covar2d_denoiser.py: 664 warnings

• tests/test_mean_estimator.py: 24 warnings

• tests/test_mean_estimator_boosting.py: 11 warnings

• tests/test_steerable_bases_2d.py: 10 warnings

• tests/test_FPSWFbasis2D.py: 1 warning

• tests/test_PSWFbasis2D.py: 1 warning

• tests/test_weighted_mean_estimator.py: 24 warnings

• tests/test_array_image_source.py: 2 warnings
  /scratch/jc5485/Work/ASPIRE-python.warnings_3.9/src/aspire/numeric/scipy.py:17: DeprecationWarning: 'scipy.sparse.linalg.cg' keyword argument tol is deprecated in favor of rtol and will be removed in SciPy v1.14.0. Until then, if set, it will override rtol.
  return scipy.sparse.linalg.cg(*args, **kwargs)

• tests/test_fourier_correlation.py: 32 warnings

• tests/test_image.py: 1 warning

• tests/test_micrograph_source.py: 8 warnings

• tests/test_simulation.py: 3 warnings
  /scratch/jc5485/Work/ASPIRE-python.warnings_3.9/tests/test_utils.py:403: MatplotlibDeprecationWarning: Auto-close()ing of figures upon backend switching is deprecated since 3.8 and will be removed in 3.10. To suppress this warning, explicitly call plt.close('all') first.
  matplotlib.use(backend)

• tests/test_fourier_correlation.py::test_frc_img_plot[img_size=64-dtype=<class 'numpy.float64'>]

• tests/test_fourier_correlation.py::test_frc_img_plot[img_size=64-dtype=<class 'numpy.float32'>]

• tests/test_fourier_correlation.py::test_frc_img_plot[img_size=65-dtype=<class 'numpy.float64'>]

• tests/test_fourier_correlation.py::test_fsc_vol_plot[img_size=64-dtype=<class 'numpy.float64'>]

• tests/test_fourier_correlation.py::test_fsc_vol_plot[img_size=64-dtype=<class 'numpy.float32'>]

• tests/test_fourier_correlation.py::test_frc_img_plot[img_size=65-dtype=<class 'numpy.float32'>]

• tests/test_fourier_correlation.py::test_fsc_vol_plot[img_size=65-dtype=<class 'numpy.float64'>]

• tests/test_fourier_correlation.py::test_fsc_vol_plot[img_size=65-dtype=<class 'numpy.float32'>]
  /scratch/jc5485/Work/ASPIRE-python.warnings_3.9/src/aspire/utils/resolution_estimation.py:380: UserWarning: No artists with labels found to put in legend. Note that artists whose label start with an underscore are ignored when legend() is called with no argumen
  t.
  plt.legend(title=f"Method: {self.method}")

• tests/test_micrograph_source.py::test_rectangular_micrograph_source_files
  /scratch/jc5485/miniconda3/envs/warnings_3.9/lib/python3.9/site-packages/mrcfile/mrcobject.py:626: RuntimeWarning: Data array contains NaN values
  warnings.warn("Data array contains NaN values", RuntimeWarning)

• tests/test_sinogram.py: 60 warnings
  /scratch/jc5485/Work/ASPIRE-python.warnings_3.9/src/aspire/image/image.py:243: DeprecationWarning: product is deprecated as of NumPy 1.25.0, and will be removed in NumPy 2.0. Please use prod instead.
  return aspire.sinogram.Sinogram(xp.asnumpy(image_rt))

• tests/test_sinogram.py: 20 warnings
  /scratch/jc5485/Work/ASPIRE-python.warnings_3.9/src/aspire/sinogram/sinogram.py:62: DeprecationWarning: product is deprecated as of NumPy 1.25.0, and will be removed in NumPy 2.0. Please use prod instead.
  return self.class(self._data[key])

• tests/test_sinogram.py: 22 warnings
  /scratch/jc5485/Work/ASPIRE-python.warnings_3.9/src/aspire/sinogram/sinogram.py:90: DeprecationWarning: product is deprecated as of NumPy 1.25.0, and will be removed in NumPy 2.0. Please use prod instead.
  return self.class(self._data.reshape(*shape, *self._data.shape[-2:]))

• tests/test_sinogram.py: 12 warnings
  /scratch/jc5485/miniconda3/envs/warnings_3.9/lib/python3.9/site-packages/skimage/transform/radon_transform.py:74: UserWarning: Radon transform: image must be zero outside the reconstruction circle
  warn(

• tests/test_covar2d_denoiser.py: 15 warnings
  /scratch/jc5485/Work/ASPIRE-python.warnings_3.9/src/aspire/basis/steerable.py:524: UserWarning: BlkDiagMatrix.from_dense truncatin
  g values exceeding 0.001
  filt = BlkDiagMatrix.from_dense(

• tests/test_orient_symmetric.py: 2970 warnings
  /scratch/jc5485/Work/ASPIRE-python.warnings_3.9/tests/test_orient_symmetric.py:641: DeprecationWarning: Conversion of an array wit
  h ndim > 0 to a scalar is deprecated, and will error in future. Ensure you extract a single element from your array before performin
  g this operation. (Deprecated NumPy 1.25.)
  clmatrix_gt[idx, i, j] = CLSymmetryC3C4.cl_angles_to_ind(

• tests/test_orient_symmetric.py: 2970 warnings
  /scratch/jc5485/Work/ASPIRE-python.warnings_3.9/tests/test_orient_symmetric.py:644: DeprecationWarning: Conversion of an array wit
  h ndim > 0 to a scalar is deprecated, and will error in future. Ensure you extract a single element from your array before performin
  g this operation. (Deprecated NumPy 1.25.)
  clmatrix_gt[idx, j, i] = CLSymmetryC3C4.cl_angles_to_ind(

• tests/test_orient_symmetric.py: 1932 warnings
  /scratch/jc5485/Work/ASPIRE-python.warnings_3.9/tests/test_orient_symmetric.py:158: DeprecationWarning: Conversion of an array wit
  h ndim > 0 to a scalar is deprecated, and will error in future. Ensure you extract a single element from your array before performin
  g this operation. (Deprecated NumPy 1.25.)
  dist[s] = np.minimum(

• tests/test_orient_symmetric.py: 192 warnings
  /scratch/jc5485/Work/ASPIRE-python.warnings_3.9/tests/test_orient_symmetric.py:195: DeprecationWarning: Conversion of an array wit
  h ndim > 0 to a scalar is deprecated, and will error in future. Ensure you extract a single element from your array before performin
  g this operation. (Deprecated NumPy 1.25.)
  dist[i] = Rotation.angle_dist(estimate, Rii_gt)

Python 3.10:

• tests/test_fourier_correlation.py: 32 warnings

• tests/test_image.py: 1 warning

• tests/test_micrograph_source.py: 8 warnings

• tests/test_simulation.py: 3 warnings
  /scratch/jc5485/Work/ASPIRE-python.warnings_3.10/tests/test_utils.py:403: MatplotlibDeprecationWarning: Auto-close()ing of figures
  upon backend switching is deprecated since 3.8 and will be removed in 3.10. To suppress this warning, explicitly call plt.close('a
  ll') first.
  matplotlib.use(backend)

• tests/test_fourier_correlation.py::test_frc_img_plot[img_size=64-dtype=<class 'numpy.float64'>]

• tests/test_fourier_correlation.py::test_frc_img_plot[img_size=64-dtype=<class 'numpy.float32'>]

• tests/test_fourier_correlation.py::test_frc_img_plot[img_size=65-dtype=<class 'numpy.float64'>]

• tests/test_fourier_correlation.py::test_frc_img_plot[img_size=65-dtype=<class 'numpy.float32'>]

• tests/test_fourier_correlation.py::test_fsc_vol_plot[img_size=64-dtype=<class 'numpy.float64'>]

• tests/test_fourier_correlation.py::test_fsc_vol_plot[img_size=64-dtype=<class 'numpy.float32'>]

• tests/test_fourier_correlation.py::test_fsc_vol_plot[img_size=65-dtype=<class 'numpy.float64'>]

• tests/test_fourier_correlation.py::test_fsc_vol_plot[img_size=65-dtype=<class 'numpy.float32'>]
  /scratch/jc5485/Work/ASPIRE-python.warnings_3.10/src/aspire/utils/resolution_estimation.py:380: UserWarning: No artists with label
  s found to put in legend. Note that artists whose label start with an underscore are ignored when legend() is called with no argume
  nt.
  plt.legend(title=f"Method: {self.method}")

• tests/test_sinogram.py: 60 warnings
  /scratch/jc5485/Work/ASPIRE-python.warnings_3.10/src/aspire/image/image.py:243: DeprecationWarning: product is deprecated as of
  NumPy 1.25.0, and will be removed in NumPy 2.0. Please use prod instead.
  return aspire.sinogram.Sinogram(xp.asnumpy(image_rt))

• tests/test_sinogram.py: 20 warnings
  /scratch/jc5485/Work/ASPIRE-python.warnings_3.10/src/aspire/sinogram/sinogram.py:62: DeprecationWarning: product is deprecated a
  s of NumPy 1.25.0, and will be removed in NumPy 2.0. Please use prod instead.
  return self.class(self._data[key])

• tests/test_sinogram.py: 22 warnings
  /scratch/jc5485/Work/ASPIRE-python.warnings_3.10/src/aspire/sinogram/sinogram.py:90: DeprecationWarning: product is deprecated a
  s of NumPy 1.25.0, and will be removed in NumPy 2.0. Please use prod instead.
  return self.class(self._data.reshape(*shape, *self._data.shape[-2:]))

• tests/test_sinogram.py: 12 warnings
  /scratch/jc5485/miniconda3/envs/warnings_3.10/lib/python3.10/site-packages/skimage/transform/radon_transform.py:74: UserWarning: R
  adon transform: image must be zero outside the reconstruction circle
  warn(

• tests/test_covar2d_denoiser.py: 15 warnings
  /scratch/jc5485/Work/ASPIRE-python.warnings_3.10/src/aspire/basis/steerable.py:524: UserWarning: BlkDiagMatrix.from_dense truncati
  ng values exceeding 0.001
  filt = BlkDiagMatrix.from_dense(

• tests/test_orient_symmetric.py: 1932 warnings
  /scratch/jc5485/Work/ASPIRE-python.warnings_3.10/tests/test_orient_symmetric.py:158: DeprecationWarning: Conversion of an array wi
  th ndim > 0 to a scalar is deprecated, and will error in future. Ensure you extract a single element from your array before performi
  ng this operation. (Deprecated NumPy 1.25.)
  dist[s] = np.minimum(

• tests/test_orient_symmetric.py: 192 warnings
  /scratch/jc5485/Work/ASPIRE-python.warnings_3.10/tests/test_orient_symmetric.py:195: DeprecationWarning: Conversion of an array wi
  th ndim > 0 to a scalar is deprecated, and will error in future. Ensure you extract a single element from your array before performi
  ng this operation. (Deprecated NumPy 1.25.)
  dist[i] = Rotation.angle_dist(estimate, Rii_gt)

• tests/test_orient_symmetric.py: 2970 warnings
  /scratch/jc5485/Work/ASPIRE-python.warnings_3.10/tests/test_orient_symmetric.py:641: DeprecationWarning: Conversion of an array wi
  th ndim > 0 to a scalar is deprecated, and will error in future. Ensure you extract a single element from your array before performi
  ng this operation. (Deprecated NumPy 1.25.)
  clmatrix_gt[idx, i, j] = CLSymmetryC3C4.cl_angles_to_ind(

• tests/test_orient_symmetric.py: 2970 warnings
  /scratch/jc5485/Work/ASPIRE-python.warnings_3.10/tests/test_orient_symmetric.py:644: DeprecationWarning: Conversion of an array wi
  th ndim > 0 to a scalar is deprecated, and will error in future. Ensure you extract a single element from your array before performi
  ng this operation. (Deprecated NumPy 1.25.)
  clmatrix_gt[idx, j, i] = CLSymmetryC3C4.cl_angles_to_ind(

[j-c-c]

I've resolved all warnings for Python 3.8 - 3.11.

There are 2 remaining warnings on the ampere job. One is related to an external package not importing a pandas dependency and the other set of warnings are from cufinufft warning about copying arrays.

=============================== warnings summary ===============================
../../../../../u/gbwright/.local/lib/python3.9/site-packages/xarray/testing/assertions.py:8
  /u/gbwright/.local/lib/python3.9/site-packages/xarray/testing/assertions.py:8: DeprecationWarning: 
  Pyarrow will become a required dependency of pandas in the next major release of pandas (pandas 3.0),
  (to allow more performant data types, such as the Arrow string type, and better interoperability with other libraries)
  but was not found to be installed on your system.
  If this would cause problems for you,
  please provide us feedback at https://github.com/pandas-dev/pandas/issues/54466
          
    import pandas as pd

tests/test_FFBbasis2D.py: 6 warnings
tests/test_FLEbasis2D.py: 1 warning
tests/test_anisotropic_noise.py: 2 warnings
tests/test_bot_align.py: 2 warnings
tests/test_covar2d.py: 30 warnings
tests/test_covar3d.py: 3 warnings
tests/test_relion_interop.py: 4 warnings
tests/test_simulation.py: 7 warnings
tests/test_volume.py: 4 warnings
  /u/gbwright/.local/lib/python3.9/site-packages/cufinufft/_plan.py:336: UserWarning: Argument `data` does not satisfy the following requirement: C. Copying array (this may reduce performance)
    warnings.warn(f"Argument `{name}` does not satisfy the "

[garrettwrong]

Why not fix all the errors? We should be able to fix both the remaining ones you mentioned pretty easily to make this whole.

Also, we seem to be missing the part about putting new warnings under test so the CI indicates we have warnings to address.

[j-c-c]

Why not fix all the errors? We should be able to fix both the remaining ones you mentioned pretty easily to make this whole.

Good point. Fixed those remaining warnings.

Also, we seem to be missing the part about putting new warnings under test so the CI indicates we have warnings to address.
Ok, I adjusted the CI workflows to fail on new warnings. In most of the CI jobs this just meant adding a --strict-warnings flag to pytest. However, on the jobs where we use python to execute pytest this flag did not work so I ended up using the environment variable PYTHONWARNINGS=error.

[j-c-c]

@garrettwrong as discussed in meeting, I've changed this to fail on warnings for the ampere job only. This should be good to go now. Thanks.

[garrettwrong]

This looks good thanks! Just two questions and it can move on.

[garrettwrong]

Awesome, thanks!

[janden]

Looks great! Just one question, really.

[j-c-c]

Had to resolve a conflict related to purging pyshtools. Once CI passes I'll merge.