Reduce DeprecationWarnings in Testing

[cyschneck]

Describe the feature you'd like added to this project
Existing tests have a number of warnings being thrown due to DeprecationWarning and UserWarnings and some clean up for reducing redirects and refreshing docs

Describe the solution you'd like
Updated scripts to account for deprecation warnings for using setup.py as well as warnings associated with redirecting links in the docs
Test scripts will continue to throw warnings associated with dask data.chunks, heat_index, and interpolation out of bounds, since these will be handled in upcoming issues (#593 and #596)

[cyschneck]

Revisit DeprecationWarnings after #483 completed

[cyschneck]

test_climatologies.py (87 passed, 2 warnings in 33.44s)

• namespace packages (Packaging updates needed for namespace packages #547)

Outside packages:

python3.11/site-packages/xskillscore/__init__.py:2: 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

Internal Packages:

python3.11/site-packages/pkg_resources/__init__.py:2868: DeprecationWarning: Deprecated call to `pkg_resources.declare_namespace('geocat')`.
  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)

[cyschneck]

test_interpolation.py (25 passed, 19 warnings in 13.97s)

• interpolation.py DeprecationWarning for dimension-order tuples
• interpolation.py UserWarning interpolation out of data bounds

External Packages:

dataarray.py:6156: DeprecationWarning: Behaviour of argmin/argmax with neither dim nor axis argument will change to return a dict of indices of each dimension. To get a single, flat index, please use np.argmin(da.data) or np.argmax(da.data) instead of da.argmin() or da.argmax().
    result = self.variable.argmax(dim, axis, keep_attrs, skipna)

Internal Packages:

interpolation.py:470: DeprecationWarning: Supplying chunks as dimension-order tuples is deprecated. It will raise an error in the future. Instead use a dict with dimension names as keys.
    pressure = pressure.chunk(data.chunks)

interpolation.py:133: UserWarning: Interpolation point out of data bounds encountered
    return func_interpolate(new_levels, xcoords, data, axis=interp_axis)

[cyschneck]

test_meteorology.py (78 passed, 3 warnings in 10.94s)

• meteorology.py RunTime invalid sqrt

External Packages:

python3.11/site-packages/xarray/core/computation.py:822: RuntimeWarning: invalid value encountered in sqrt
    result_data = func(*input_data)

site-packages/dask/core.py:127: RuntimeWarning: invalid value encountered in sqrt
    return func(*(_execute_task(a, cache) for a in args))

Internal Packages:

meteorology.py:125: RuntimeWarning: invalid value encountered in sqrt
    heatindex - ((13 - relative_humidity) / 4) * np.sqrt(

[cyschneck]

test_gradient.py (7 passed, 3 warnings in 10.89s)

• test_gradient_xr RuntimeWarning

Internal Packages:

test/test_gradient.py::Test_Gradient::test_gradient_xr
  <frozen importlib._bootstrap>:241: RuntimeWarning: numpy.ndarray size changed, may indicate binary incompatibility. Expected 16 from C header, got 96 from PyObject

[cyschneck]

test_stats.py (24 passed, 21 warnings in 7.83s)

• eofunc will be deprecated
• test_01 RuntimeWarning numpy array size changed
• eofunc_ts will be deprecated soon (replace with eofunc_pcs)

Internal Packages:

stats.py:401: PendingDeprecationWarning: eofunc will be deprecated soon in a future version and may not currently generate proper results for some of its arguments including `pcrit`, `jopt=correlation`, and 'missing_value' other than np.nan. The output  and its attributes may thus not be as expected, too. Use `eofunc_eofs` instead.
    warnings.warn(

t_stats.py::Test_eof_ts::test_01
  <frozen importlib._bootstrap>:241: RuntimeWarning: numpy.ndarray size changed, may indicate binary incompatibility. Expected 16 from C header, got 96 from PyObject

stats.py:419: PendingDeprecationWarning: eofunc_ts will be deprecated soon in a future version and may not currently generate proper results for some of its arguments including `evec`, `jopt=correlation`, and 'missing_value' other than np.nan. The output  and its attributes may thus not be as expected, too. Use `eofunc_pcs` instead.
    warnings.warn(

External Packages:

python3.11/site-packages/eofs/xarray.py:130: DeprecationWarning: `product` is deprecated as of NumPy 1.25.0, and will be removed in NumPy 2.0. Please use `prod` instead.
    self._solver = standard.Eof(array.data,

python3.11/site-packages/eofs/xarray.py:130: DeprecationWarning: `product` is deprecated as of NumPy 1.25.0, and will be removed in NumPy 2.0. Please use `prod` instead.
    self._solver = standard.Eof(array.data,

[cyschneck]

CI.yml link checker

  contrib: line   51) broken    https://stackoverflow.com/help/minimal-reproducible-example - 403 Client Error: Forbidden for url: https://stackoverflow.com/help/minimal-reproducible-example

2024-02-16T00:06:50.6539501Z looking for now-outdated files... /home/runner/work/geocat-comp/geocat-comp/docs/release-notes.rst:23: WARNING: Title underline too short.

2024-02-16T00:06:50.6543193Z /home/runner/work/geocat-comp/geocat-comp/docs/release-notes.rst:23: WARNING: Title underline too short.

2024-02-16T00:07:49.5980038Z checking consistency... /home/runner/work/geocat-comp/geocat-comp/docs/_build/jupyter_execute/_build/jupyter_execute/examples/calendar_average.ipynb: WARNING: document isn't included in any toctree
2024-02-16T00:07:49.5984842Z /home/runner/work/geocat-comp/geocat-comp/docs/_build/jupyter_execute/_build/jupyter_execute/examples/climatology_average.ipynb: WARNING: document isn't included in any toctree
2024-02-16T00:07:49.5989272Z /home/runner/work/geocat-comp/geocat-comp/docs/_build/jupyter_execute/_build/jupyter_execute/examples/fourier_filter.ipynb: WARNING: document isn't included in any toctree
2024-02-16T00:07:49.5992249Z /home/runner/work/geocat-comp/geocat-comp/docs/_build/jupyter_execute/_build/jupyter_execute/examples/vimfc.ipynb: WARNING: document isn't included in any toctree
2024-02-16T00:07:49.5993788Z /home/runner/work/geocat-comp/geocat-comp/docs/_build/jupyter_execute/examples/calendar_average.ipynb: WARNING: document isn't included in any toctree
2024-02-16T00:07:49.5995278Z /home/runner/work/geocat-comp/geocat-comp/docs/_build/jupyter_execute/examples/climatology_average.ipynb: WARNING: document isn't included in any toctree
2024-02-16T00:07:49.5996774Z /home/runner/work/geocat-comp/geocat-comp/docs/_build/jupyter_execute/examples/fourier_filter.ipynb: WARNING: document isn't included in any toctree
2024-02-16T00:07:49.5998177Z /home/runner/work/geocat-comp/geocat-comp/docs/_build/jupyter_execute/examples/vimfc.ipynb: WARNING: document isn't included in any toctree

[cyschneck]

CI Upstream

test/test_stats.py::Test_pearson_r::test_keep_attrs PASSED               [100%]/home/runner/micromamba/envs/geocat_comp_build/lib/python3.11/site-packages/coverage/control.py:887: CoverageWarning: No data was collected. (no-data-collected)
2024-02-16T00:22:45.6079842Z   self._warn("No data was collected.", slug="no-data-collected")

/home/runner/micromamba/envs/geocat_comp_build/lib/python3.11/site-packages/geocat/comp/interpolation.py:470: DeprecationWarning: Supplying chunks as dimension-order tuples is deprecated. It will raise an error in the future. Instead use a dict with dimension names as keys. (pressure = pressure.chunk(data.chunks)

/home/runner/micromamba/envs/geocat_comp_build/lib/python3.11/site-packages/geocat/comp/interpolation.py:133: UserWarning: Interpolation point out of data bounds encountered
2024-02-16T00:22:45.6946236Z     return func_interpolate(new_levels, xcoords, data, axis=interp_axis)

/home/runner/micromamba/envs/geocat_comp_build/lib/python3.11/site-packages/xarray/core/dataarray.py:6149: DeprecationWarning: Behaviour of argmin/argmax with neither dim nor axis argument will change to return a dict of indices of each dimension. To get a single, flat index, please use np.argmin(da.data) or np.argmax(da.data) instead of da.argmin() or da.argmax().
2024-02-16T00:22:45.6957710Z     result = self.variable.argmax(dim, axis, keep_attrs, skipna)

/home/runner/micromamba/envs/geocat_comp_build/lib/python3.11/site-packages/geocat/comp/meteorology.py:125: RuntimeWarning: invalid value encountered in sqrt
2024-02-16T00:22:45.6965745Z     heatindex - ((13 - relative_humidity) / 4) * np.sqrt(

/home/runner/micromamba/envs/geocat_comp_build/lib/python3.11/site-packages/xarray/core/computation.py:825: RuntimeWarning: invalid value encountered in sqrt
2024-02-16T00:22:45.6970418Z     result_data = func(*input_data

/home/runner/micromamba/envs/geocat_comp_build/lib/python3.11/site-packages/eofs/xarray.py:130: DeprecationWarning: `product` is deprecated as of NumPy 1.25.0, and will be removed in NumPy 2.0. Please use `prod` instead.

test/test_stats.py::Test_eof::test_eof_deprecated
2024-02-16T00:22:45.6982489Z   /home/runner/micromamba/envs/geocat_comp_build/lib/python3.11/site-packages/geocat/comp/stats.py:401: PendingDeprecationWarning: eofunc will be deprecated soon in a future version and may not currently generate proper results for some of its arguments including `pcrit`, `jopt=correlation`, and 'missing_value' other than np.nan. The output  and its attributes may thus not be as expected, too. Use `eofunc_eofs` instead.

test/test_stats.py::Test_eof_ts::test_01_deprecated
2024-02-16T00:22:45.6990003Z   /home/runner/micromamba/envs/geocat_comp_build/lib/python3.11/site-packages/geocat/comp/stats.py:419: PendingDeprecationWarning: eofunc_ts will be deprecated soon in a future version and may not currently generate proper results for some of its arguments including `evec`, `jopt=correlation`, and 'missing_value' other than np.nan. The output  and its attributes may thus not be as expected, too. Use `eofunc_pcs` instead.

[cyschneck]

Upload geocat-comp to PyPi

Newline warning

2024-01-30T21:03:06.4652795Z /opt/hostedtoolcache/Python/3.10.13/x64/lib/python3.10/site-packages/setuptools/dist.py:160: UserWarning: newlines not allowed and will break in the future
2024-01-30T21:03:06.4654709Z   warnings.warn("newlines not allowed and will break in the future")
2024-01-30T21:03:06.4658101Z Writing geocat.comp-2024.1.0/setup.cfg

/opt/hostedtoolcache/Python/3.10.13/x64/lib/python3.10/site-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools.
2024-01-30T21:03:06.5753553Z   warnings.warn(