Fix warnings

[shntnu]

Fix these these warnings that pop up upon testing

pytest
======================================================================== test session starts ========================================================================
platform darwin -- Python 3.9.6, pytest-7.1.1, pluggy-1.0.0
rootdir: /Users/shsingh/work/repos/software/cytominer/cytomining/pycytominer
collected 129 items                                                                                                                                                 

pycytominer/tests/test_aggregate.py .........                                                                                                                 [  6%]
pycytominer/tests/test_annotate.py ...                                                                                                                        [  9%]
pycytominer/tests/test_consensus.py ..                                                                                                                        [ 10%]
pycytominer/tests/test_feature_select.py .........                                                                                                            [ 17%]
pycytominer/tests/test_normalize.py ...........                                                                                                               [ 26%]
pycytominer/tests/test_cyto_utils/test_DeepProfiler_processing.py .....                                                                                       [ 30%]
pycytominer/tests/test_cyto_utils/test_annotate_custom.py ......                                                                                              [ 34%]
pycytominer/tests/test_cyto_utils/test_cells.py .................                                                                                             [ 48%]
pycytominer/tests/test_cyto_utils/test_cp_image_features.py ..                                                                                                [ 49%]
pycytominer/tests/test_cyto_utils/test_feature_blocklist.py ..                                                                                                [ 51%]
pycytominer/tests/test_cyto_utils/test_feature_drop_outlier.py ....                                                                                           [ 54%]
pycytominer/tests/test_cyto_utils/test_feature_infer.py .....                                                                                                 [ 58%]
pycytominer/tests/test_cyto_utils/test_features_count_na.py .                                                                                                 [ 58%]
pycytominer/tests/test_cyto_utils/test_features_util.py .                                                                                                     [ 59%]
pycytominer/tests/test_cyto_utils/test_load.py ....                                                                                                           [ 62%]
pycytominer/tests/test_cyto_utils/test_modz.py .......                                                                                                        [ 68%]
pycytominer/tests/test_cyto_utils/test_output.py ......                                                                                                       [ 72%]
pycytominer/tests/test_cyto_utils/test_single_cell_ingest_utils.py ...                                                                                        [ 75%]
pycytominer/tests/test_cyto_utils/test_util.py ............                                                                                                   [ 84%]
pycytominer/tests/test_cyto_utils/test_write_gct.py ....                                                                                                      [ 87%]
pycytominer/tests/test_operations/test_correlation_threshold.py ....                                                                                          [ 90%]
pycytominer/tests/test_operations/test_get_na_columns.py ...                                                                                                  [ 93%]
pycytominer/tests/test_operations/test_sparse_random_projection.py ..                                                                                         [ 94%]
pycytominer/tests/test_operations/test_transform.py ....                                                                                                      [ 97%]
pycytominer/tests/test_operations/test_variance_threshold.py ...                                                                                              [100%]

========================================================================= warnings summary ==========================================================================
pycytominer/cyto_utils/util.py:61
  /Users/shsingh/work/repos/software/cytominer/cytomining/pycytominer/pycytominer/cyto_utils/util.py:61: UserWarning: Non-canonical compartment detected: new
    warnings.warn(warn_str)

pycytominer/tests/test_consensus.py: 6 warnings
pycytominer/tests/test_feature_select.py: 5 warnings
pycytominer/tests/test_cyto_utils/test_modz.py: 20 warnings
pycytominer/tests/test_cyto_utils/test_util.py: 1 warning
pycytominer/tests/test_operations/test_correlation_threshold.py: 5 warnings
  /Users/shsingh/work/repos/software/cytominer/cytomining/pycytominer/pycytominer/cyto_utils/util.py:338: DeprecationWarning: `np.bool` is a deprecated alias for the builtin `bool`. To silence this warning, use `bool` by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use `np.bool_` here.
  Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
    np.tril(np.ones(data_cor_natri_df.shape), k=-1).astype(np.bool)

pycytominer/tests/test_feature_select.py::test_feature_select_noise_removal
pycytominer/tests/test_feature_select.py::test_feature_select_noise_removal
pycytominer/tests/test_feature_select.py::test_feature_select_noise_removal
pycytominer/tests/test_feature_select.py::test_feature_select_noise_removal
pycytominer/tests/test_feature_select.py::test_feature_select_noise_removal
pycytominer/tests/test_feature_select.py::test_feature_select_noise_removal
pycytominer/tests/test_feature_select.py::test_feature_select_noise_removal
  /usr/local/lib/python3.9/site-packages/numpy/core/fromnumeric.py:3613: FutureWarning: Dropping of nuisance columns in DataFrame reductions (with 'numeric_only=None') is deprecated; in a future version this will raise TypeError.  Select only valid columns before calling the reduction.
    return std(axis=axis, dtype=dtype, out=out, ddof=ddof, **kwargs)

pycytominer/tests/test_normalize.py::test_normalize_robustize_mad_allsamples
pycytominer/tests/test_normalize.py::test_normalize_robustize_mad_allsamples_novar
pycytominer/tests/test_operations/test_transform.py::test_robust_mad
  /Users/shsingh/work/repos/software/cytominer/cytomining/pycytominer/pycytominer/operations/transform.py:131: DeprecationWarning: `median_absolute_deviation` is deprecated, use `median_abs_deviation` instead!
  
  To preserve the existing default behavior, use
  `scipy.stats.median_abs_deviation(..., scale=1/1.4826)`.
  The value 1.4826 is not numerically precise for scaling
  with a normal distribution. For a numerically precise value, use
  `scipy.stats.median_abs_deviation(..., scale='normal')`.
  
    median_absolute_deviation(X, nan_policy="omit"), index=self.median.index

pycytominer/tests/test_cyto_utils/test_cells.py::test_merge_single_cells
pycytominer/tests/test_cyto_utils/test_cells.py::test_merge_single_cells
pycytominer/tests/test_cyto_utils/test_cells.py::test_merge_single_cells
pycytominer/tests/test_cyto_utils/test_cells.py::test_merge_single_cells
  /Users/shsingh/work/repos/software/cytominer/cytomining/pycytominer/pycytominer/cyto_utils/cells.py:693: FutureWarning: Passing 'suffixes' which cause duplicate columns {'ObjectNumber_cytoplasm'} in the result is deprecated and will raise a MergeError in a future version.
    sc_df = sc_df.merge(

pycytominer/tests/test_cyto_utils/test_modz.py::test_modz_base
  /Users/shsingh/work/repos/software/cytominer/cytomining/pycytominer/pycytominer/tests/test_cyto_utils/test_modz.py:48: FutureWarning: The 'check_less_precise' keyword in testing.assert_*_equal is deprecated and will be removed in a future version. You can stop passing 'check_less_precise' to silence this warning.
    pd.testing.assert_series_equal(

pycytominer/tests/test_cyto_utils/test_modz.py::test_modz
  /Users/shsingh/work/repos/software/cytominer/cytomining/pycytominer/pycytominer/tests/test_cyto_utils/test_modz.py:71: FutureWarning: The 'check_less_precise' keyword in testing.assert_*_equal is deprecated and will be removed in a future version. You can stop passing 'check_less_precise' to silence this warning.
    pd.testing.assert_frame_equal(

pycytominer/tests/test_cyto_utils/test_modz.py::test_modz_multiple_columns
  /Users/shsingh/work/repos/software/cytominer/cytomining/pycytominer/pycytominer/tests/test_cyto_utils/test_modz.py:118: FutureWarning: The 'check_less_precise' keyword in testing.assert_*_equal is deprecated and will be removed in a future version. You can stop passing 'check_less_precise' to silence this warning.
    pd.testing.assert_frame_equal(

pycytominer/tests/test_cyto_utils/test_modz.py::test_modz_multiple_columns_one_metadata_column
  /Users/shsingh/work/repos/software/cytominer/cytomining/pycytominer/pycytominer/tests/test_cyto_utils/test_modz.py:148: FutureWarning: The 'check_less_precise' keyword in testing.assert_*_equal is deprecated and will be removed in a future version. You can stop passing 'check_less_precise' to silence this warning.
    pd.testing.assert_frame_equal(

pycytominer/tests/test_cyto_utils/test_output.py::test_compress
  /Users/shsingh/work/repos/software/cytominer/cytomining/pycytominer/pycytominer/tests/test_cyto_utils/test_output.py:57: FutureWarning: The 'check_less_precise' keyword in testing.assert_*_equal is deprecated and will be removed in a future version. You can stop passing 'check_less_precise' to silence this warning.
    pd.testing.assert_frame_equal(

pycytominer/tests/test_cyto_utils/test_output.py::test_compress_tsv
  /Users/shsingh/work/repos/software/cytominer/cytomining/pycytominer/pycytominer/tests/test_cyto_utils/test_output.py:74: FutureWarning: The 'check_less_precise' keyword in testing.assert_*_equal is deprecated and will be removed in a future version. You can stop passing 'check_less_precise' to silence this warning.
    pd.testing.assert_frame_equal(

pycytominer/tests/test_cyto_utils/test_output.py::test_output_none
  /Users/shsingh/work/repos/software/cytominer/cytomining/pycytominer/pycytominer/tests/test_cyto_utils/test_output.py:90: FutureWarning: The 'check_less_precise' keyword in testing.assert_*_equal is deprecated and will be removed in a future version. You can stop passing 'check_less_precise' to silence this warning.
    pd.testing.assert_frame_equal(

pycytominer/tests/test_operations/test_transform.py::test_low_variance_spherize
  /usr/local/lib/python3.9/site-packages/numpy/lib/function_base.py:2829: RuntimeWarning: invalid value encountered in true_divide
    c /= stddev[:, None]

pycytominer/tests/test_operations/test_transform.py::test_low_variance_spherize
  /usr/local/lib/python3.9/site-packages/numpy/lib/function_base.py:2830: RuntimeWarning: invalid value encountered in true_divide
    c /= stddev[None, :]

pycytominer/tests/test_operations/test_transform.py::test_robust_mad
  /Users/shsingh/work/repos/software/cytominer/cytomining/pycytominer/pycytominer/tests/test_operations/test_transform.py:86: DeprecationWarning: `median_absolute_deviation` is deprecated, use `median_abs_deviation` instead!
  
  To preserve the existing default behavior, use
  `scipy.stats.median_abs_deviation(..., scale=1/1.4826)`.
  The value 1.4826 is not numerically precise for scaling
  with a normal distribution. For a numerically precise value, use
  `scipy.stats.median_abs_deviation(..., scale='normal')`.
  
    result = median_absolute_deviation(transform_df).sum()

-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
============================================================ 129 passed, 62 warnings in 63.04s (0:01:03) ============================================================
(pycytominer) pycytominer$