Resolve deprecation warnings re: datatree, xr.drop_var, numpy.array_equal

[leewujung]

There are multiple deprecation warnings that we should address in the next release.

One of the warning is related to the use of pkg_resources in datatree, but our datatree version is pinned to a pretty old version. This one may take some more time.

../../miniconda3/envs/echopype_20240415/lib/python3.9/site-packages/datatree/__init__.py:4
  /Users/wujung/miniconda3/envs/echopype_20240415/lib/python3.9/site-packages/datatree/__init__.py:4: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html
    from pkg_resources import DistributionNotFound, get_distribution

../../miniconda3/envs/echopype_20240415/lib/python3.9/site-packages/pkg_resources/__init__.py:2832
../../miniconda3/envs/echopype_20240415/lib/python3.9/site-packages/pkg_resources/__init__.py:2832
../../miniconda3/envs/echopype_20240415/lib/python3.9/site-packages/pkg_resources/__init__.py:2832
../../miniconda3/envs/echopype_20240415/lib/python3.9/site-packages/pkg_resources/__init__.py:2832
../../miniconda3/envs/echopype_20240415/lib/python3.9/site-packages/pkg_resources/__init__.py:2832
../../miniconda3/envs/echopype_20240415/lib/python3.9/site-packages/pkg_resources/__init__.py:2832
  /Users/wujung/miniconda3/envs/echopype_20240415/lib/python3.9/site-packages/pkg_resources/__init__.py:2832: DeprecationWarning: Deprecated call to `pkg_resources.declare_namespace('sphinxcontrib')`.
  Implementing implicit namespace packages (as specified in PEP 420) is preferred to `pkg_resources.declare_namespace`. See https://setuptools.pypa.io/en/latest/references/keywords.html#keyword-namespace-packages
    declare_namespace(pkg)

echopype/tests/calibrate/test_calibrate_ek80.py::test_ek80_BB_complex_multiplex_NaNs_and_non_NaNs[NYOS2105-D20210525-T213648.raw-target_channel_ping_pattern0]
echopype/tests/calibrate/test_calibrate_ek80.py::test_ek80_BB_complex_multiplex_NaNs_and_non_NaNs[NYOS2105-D20210525-T213648.raw-target_channel_ping_pattern0]
  /Users/wujung/code_git/echopype/echopype/calibrate/cal_params.py:318: DeprecationWarning: dropping variables using `drop` is deprecated; use drop_vars.
    da_param = da_param.drop(plb_var)

echopype/tests/calibrate/test_calibrate_ek80.py::test_ek80_BB_complex_multiplex_NaNs_and_non_NaNs[NYOS2105-D20210525-T213648.raw-target_channel_ping_pattern0]
  /Users/wujung/code_git/echopype/echopype/calibrate/range.py:187: DeprecationWarning: dropping variables using `drop` is deprecated; use drop_vars.
    valid_idx = ~beam["backscatter_r"].isel(beam=0).drop("beam").isnull()

echopype/tests/calibrate/test_calibrate_ek80.py::test_ek80_BB_complex_multiplex_NaNs_and_non_NaNs[NYOS2105-D20210525-T213648.raw-target_channel_ping_pattern0]
  /Users/wujung/miniconda3/envs/echopype_20240415/lib/python3.9/site-packages/dask/array/core.py:1712: FutureWarning: The `numpy.array_equal` function is not implemented by Dask array. You may want to use the da.map_blocks function or something similar to silence this warning. Your code may stop working in a future release.
    warnings.warn(

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

[ctuguinay]

The test echopype/tests/calibrate/test_calibrate_ek80.py::test_ek80_BB_complex_multiplex_NaNs_and_non_NaNs also produces:

/home/exouser/echopype/echopype/calibrate/ek80_complex.py:34: 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.)
    L = int(np.round(tau * fs * slope * 2.0))  # Length of hanning window

[ctuguinay]

Also I'm unable to recreate the following warnings:

echopype/tests/calibrate/test_calibrate_ek80.py::test_ek80_BB_complex_multiplex_NaNs_and_non_NaNs[NYOS2105-D20210525-T213648.raw-target_channel_ping_pattern0]
  /Users/wujung/miniconda3/envs/echopype_20240415/lib/python3.9/site-packages/dask/array/core.py:1712: FutureWarning: The `numpy.array_equal` function is not implemented by Dask array. You may want to use the da.map_blocks function or something similar to silence this warning. Your code may stop working in a future release.
    warnings.warn(

Looking at this test, it doesn't seem to use np.array_equal with any Dask Arrays. I printed out the types of the arrays passed into the np.array_equal lines and they were all numpy arrays.

[ctuguinay]

Also, I'll give the datatree unpinning a try tomorrow. We can just put it in 0.9.1 if it's too much to fix.

[leewujung]

What do you think we push the datatree component to later, maybe not even v0.9.1? Since xarray-datatree is official now, we should probably do a more thorough investigation before diving in to changes.

[ctuguinay]

Oh yeah, you're right, let's do that