Address warnings

[tsalo]

Summary

There are a number of warnings that are raised when running ASLPrep. In many cases, these warnings may come from dependencies, but it would be nice to fix the ones we can.

WARNING  py.warnings:_warnings.py:37 WARNING: The behavior of affine_transform with a 1-D array supplied for the matrix parameter has changed in SciPy 0.18.0.

WARNING  py.warnings:_warnings.py:37 WARNING: `np.bool8` is a deprecated alias for `np.bool_`.  (Deprecated NumPy 1.24)

WARNING  nipype.interface:bids.py:714 Changing /usr/local/miniconda/lib/python3.9/site-packages/aslprep/aslprep/tests/pytests/out/test_001/aslprep/sub-01/perf/sub-01_space-T1w_desc-brain_mask.nii.gz dtype from float64 to uint8

WARNING  py.warnings:_warnings.py:37 WARNING: Starting in version 0.12, 3D images will be transformed to 1D arrays. Until then, 3D images will be coerced to 2D arrays, with a singleton first dimension representing time.

WARNING  py.warnings:_warnings.py:37 WARNING: Degrees of freedom <= 0 for slice

WARNING  py.warnings:_warnings.py:37 WARNING: invalid value encountered in divide

WARNING  py.warnings:_warnings.py:37 WARNING: invalid value encountered in scalar divide

WARNING  py.warnings:_warnings.py:37 WARNING: `rcond` parameter will change to the default of machine precision times ``max(M, N)`` where M and N are the input matrix dimensions.
To use the future default and silence this warning we advise to pass `rcond=None`, to keep using the old, explicitly pass `rcond=-1`.

WARNING  py.warnings:_warnings.py:37 WARNING: Applying "mask_img" before signal extraction may result in empty region signals in the output. These are currently kept. Starting from version 0.13, the default behavior will be changed to remove them by setting "keep_masked_labels=False". "keep_masked_labels" parameter will be removed in version 0.15.

WARNING  py.warnings:_warnings.py:37 WARNING: Data array used to create a new image contains 64-bit ints. This is likely due to creating the array with numpy and passing `int` as the `dtype`. Many tools such as FSL and SPM cannot deal with int64 in Nifti images, so for compatibility the data has been converted to int32.

WARNING  py.warnings:_warnings.py:37 WARNING: Passing `palette` without assigning `hue` is deprecated and will be removed in v0.14.0. Assign the `x` variable to `hue` and set `legend=False` for the same effect.

WARNING  py.warnings:_warnings.py:37 WARNING: Attempting to set identical low and high ylims makes transformation singular; automatically expanding.

WARNING  py.warnings:_warnings.py:37 WARNING: The get_cmap function was deprecated in Matplotlib 3.7 and will be removed two minor releases later. Use ``matplotlib.colormaps[name]`` or ``matplotlib.colormaps.get_cmap(obj)`` instead.

[tsalo]

Some more:

aslprep/tests/test_cli.py:7
  /src/aslprep/aslprep/tests/test_cli.py:7: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html
    from pkg_resources import resource_filename as pkgrf

../../usr/local/miniconda/lib/python3.10/site-packages/niworkflows/viz/__init__.py:12
  /usr/local/miniconda/lib/python3.10/site-packages/niworkflows/viz/__init__.py:12: PendingDeprecationWarning: Niworkflows will be deprecating visualizations in favor of a standalone library "nireports".
    warnings.warn(msg, PendingDeprecationWarning)

WARNING: Reference space not set

aslprep/tests/test_interfaces_cbf.py::test_computecbf_casl
  /src/aslprep/aslprep/utils/cbf.py:752: RuntimeWarning: divide by zero encountered in divide
    cbf_by_pld[:, i_pld] = pld_num_factor / pld_denom_factor