osx_arm updates

[garrettwrong]

Now that I have removed PyFFTW, pyshtools, and updated to FINUFFT 2.3.0 I think ASPIRE should be good to run native M1 out of the box. This PR patches the CI and removes the mention of the x86_64 conda install/workarounds.

I'll confirm with my own M1 machine a little later this morning before sending this for review.

[garrettwrong]

Had to patch a few more tests than I hoped, but overall I don't think we did too bad for a totally different architecture 😎 .

We may find a few more as it begins to run regularly, but they should mainly just be adding an appropriate tolerance (1e-6 seems to be working well for stuff; mainly seeing small diffs in singles).

Here is the run from my M1 mini:

(test_osx) ➜  ASPIRE-Python git:(osx_arm_update) ✗ git log | head
commit 8ae41ed233d371dd40a0c7796b24577f3c48d77a
Author: Garrett Wright <garrettwrong@gmail.com>
Date:   Fri Sep 13 08:33:59 2024 -0400

    Another test file tweak for arm64

commit 967f79cb44d87a5caf9afa5e9c152d45d3c4bf50
Author: Garrett Wright <garrettwrong@gmail.com>
Date:   Fri Sep 13 08:30:15 2024 -0400

(test_osx) ➜  ASPIRE-Python git:(osx_arm_update) ✗ time pytest -n10
====================================================================== test session starts ======================================================================
platform darwin -- Python 3.11.10, pytest-8.3.3, pluggy-1.5.0
Test order randomisation NOT enabled. Enable with --random-order or --random-order-bucket=<bucket_type>
rootdir: /Users/garrett/work/ASPIRE-Python
configfile: tox.ini
testpaths: tests
plugins: cov-5.0.0, random-order-1.1.1, anyio-4.4.0, xdist-3.6.1
10 workers [5664 items] kipped                                                                                                                                  
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======================================================================= warnings summary ========================================================================
tests/test_image.py: 1 warning
tests/test_micrograph_source.py: 8 warnings
tests/test_simulation.py: 3 warnings
  /Users/garrett/work/ASPIRE-Python/src/aspire/image/image.py:691: UserWarning: FigureCanvasAgg is non-interactive, and thus cannot be shown
    plt.show()

tests/test_image.py: 1 warning
tests/test_fourier_correlation.py: 32 warnings
tests/test_micrograph_source.py: 8 warnings
tests/test_simulation.py: 3 warnings
  /Users/garrett/work/ASPIRE-Python/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: 32 warnings
  /Users/garrett/work/ASPIRE-Python/src/aspire/utils/resolution_estimation.py:386: UserWarning: FigureCanvasAgg is non-interactive, and thus cannot be shown
    plt.show()

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'>]
  /Users/garrett/work/ASPIRE-Python/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 argument.
    plt.legend(title=f"Method: {self.method}")

tests/test_micrograph_source.py::test_rectangular_micrograph_source_files
  /Users/garrett/miniconda3/envs/test_osx/lib/python3.11/site-packages/mrcfile/mrcobject.py:626: RuntimeWarning: Data array contains NaN values
    warnings.warn("Data array contains NaN values", RuntimeWarning)

tests/test_covar2d_denoiser.py: 15 warnings
  /Users/garrett/work/ASPIRE-Python/src/aspire/basis/steerable.py:524: UserWarning: BlkDiagMatrix.from_dense truncating values exceeding 0.001
    filt = BlkDiagMatrix.from_dense(

tests/test_sinogram.py: 60 warnings
  /Users/garrett/work/ASPIRE-Python/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
  /Users/garrett/work/ASPIRE-Python/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
  /Users/garrett/work/ASPIRE-Python/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
  /Users/garrett/miniconda3/envs/test_osx/lib/python3.11/site-packages/skimage/transform/radon_transform.py:74: UserWarning: Radon transform: image must be zero outside the reconstruction circle
    warn(

tests/test_commonline_sync3n.py::test_estimate_rotations[resolution=40-offsets=0-dtype=<class 'numpy.float32'>]
  /Users/garrett/work/ASPIRE-Python/src/aspire/abinitio/commonline_sync3n.py:730: RuntimeWarning: overflow encountered in exp
    Pij = 1 / (1 + (1 - P) / P * np.exp(ln_f_arb - ln_f_ind))

tests/test_orient_symmetric.py: 1932 warnings
  /Users/garrett/work/ASPIRE-Python/tests/test_orient_symmetric.py:158: DeprecationWarning: Conversion of an array with ndim > 0 to a scalar is deprecated, and will error in future. Ensure you extract a single element from your array before performing this operation. (Deprecated NumPy 1.25.)
    dist[s] = np.minimum(

tests/test_orient_symmetric.py: 192 warnings
  /Users/garrett/work/ASPIRE-Python/tests/test_orient_symmetric.py:195: DeprecationWarning: Conversion of an array with ndim > 0 to a scalar is deprecated, and will error in future. Ensure you extract a single element from your array before performing this operation. (Deprecated NumPy 1.25.)
    dist[i] = Rotation.angle_dist(estimate, Rii_gt)

tests/test_orient_symmetric.py: 2970 warnings
  /Users/garrett/work/ASPIRE-Python/tests/test_orient_symmetric.py:641: DeprecationWarning: Conversion of an array with ndim > 0 to a scalar is deprecated, and will error in future. Ensure you extract a single element from your array before performing this operation. (Deprecated NumPy 1.25.)
    clmatrix_gt[idx, i, j] = CLSymmetryC3C4.cl_angles_to_ind(

tests/test_orient_symmetric.py: 2970 warnings
  /Users/garrett/work/ASPIRE-Python/tests/test_orient_symmetric.py:644: DeprecationWarning: Conversion of an array with ndim > 0 to a scalar is deprecated, and will error in future. Ensure you extract a single element from your array before performing this operation. (Deprecated NumPy 1.25.)
    clmatrix_gt[idx, j, i] = CLSymmetryC3C4.cl_angles_to_ind(

-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
====================================== 5551 passed, 32 skipped, 82 xfailed, 1 xpassed, 8291 warnings in 185.03s (0:03:05) =======================================
pytest -n10  936.99s user 137.56s system 579% cpu 3:05.40 total

[j-c-c]

Looks good! Just one comment.

[j-c-c]

Looks good!

[garrettwrong]

No functional changes, just the CI and some testing tolerances. Merging.