Remove deprecated preprocess subpackage [all tests ci] (OSOceanAcoustics#1082)

* Remove deprecated preprocess subpackage

* docs: replace references to preprocess with clean and commongrid

* docs: add attention box about removal of preprocess subpackage

Author: emiliom

docs/source/api.rst

@@ -58,10 +58,17 @@ calibrate
    :no-inheritance-diagram:
    :no-heading:
 
-preprocess
+clean
+^^^^^
+
+.. automodapi:: echopype.clean
+   :no-inheritance-diagram:
+   :no-heading:
+
+commongrid
 ^^^^^^^^^^
 
-.. automodapi:: echopype.preprocess
+.. automodapi:: echopype.commongrid
    :no-inheritance-diagram:
    :no-heading:
 

docs/source/process.rst

@@ -54,14 +54,14 @@ The steps for performing these analyses are summarized below:
    .. code-block:: python
 
       # Reduce data based on physical units
-      ds_MVBS = ep.preprocess.compute_MVBS(
+      ds_MVBS = ep.commongrid.compute_MVBS(
            ds_Sv,               # calibrated Sv dataset
            range_meter_bin=20,  # bin size to average along echo_range in meters
            ping_time_bin='20S'  # bin size to average along ping_time in seconds
        )
 
       # Reduce data based on sample number
-      ds_MVBS = ep.preprocess.compute_MVBS_index_binning(
+      ds_MVBS = ep.commongrid.compute_MVBS_index_binning(
            ds_Sv,             # calibrated Sv dataset
            range_sample_num=30,  # number of sample bins to average along the range_sample dimensionm
            ping_num=5         # number of pings to average
@@ -72,21 +72,27 @@ The steps for performing these analyses are summarized below:
    .. code-block:: python
 
       # Remove noise
-      ds_Sv_clean = ep.preprocess.remove_noise(    # obtain a denoised Sv dataset
+      ds_Sv_clean = ep.clean.remove_noise(    # obtain a denoised Sv dataset
          ds_Sv,             # calibrated Sv dataset
          range_sample_num=30,  # number of samples along the range_sample dimension for estimating noise
          ping_num=5,        # number of pings for estimating noise
       )
 
+.. attention::
+
+   The ``clean`` and ``commongrid`` subpackages were introduced in version 0.7.0.
+   They contain functions previously found in the deprecated ``preprocess`` subpackage;
+   ``preprocess`` was removed in version 0.8.0.
+
 The functions in the ``calibrate`` subpackage take in an ``EchoData`` object,
 which is essentially a container for multiple xarray ``Dataset`` instances,
 and return a single xarray ``Dataset`` containing the calibrated backscatter
 quantities and the samples' corresponding range in meters.
-The input and output of all functions in the ``preprocess``
-subpackage are xarray ``Dataset`` instances, with the input being a ``Dataset``
+The input and output of all functions in the ``clean`` and ``commongrid``
+subpackages are xarray ``Dataset`` instances, with the input being a ``Dataset``
 containing ``Sv`` and ``echo_range`` generated from calibration.
 
-The ``calibrate`` and ``preprocess`` functions do not save the calculation results to disk,
+The ``calibrate``, ``clean`` and ``commongrid`` functions do not save the calculation results to disk,
 but the returned xarray ``Dataset`` can be saved using native xarray methods
 such as ``to_netcdf`` and ``to_zarr``.
 
@@ -98,7 +104,9 @@ For example, to save the Sv and MVBS results to disk:
    ds_MVBS.to_netcdf('file_MVBS.nc')
 
 
-.. note:: Echopype's data processing functionality is being developed actively.
+.. note::
+
+   Echopype's data processing functionality is being developed actively.
    Be sure to check back here often!
 
 

echopype/__init__.py

@@ -2,7 +2,7 @@
 
 from _echopype_version import version as __version__  # noqa
 
-from . import calibrate, clean, commongrid, consolidate, mask, preprocess, utils
+from . import calibrate, clean, commongrid, consolidate, mask, utils
 from .convert.api import open_raw
 from .echodata.api import open_converted
 from .echodata.combine import combine_echodata
@@ -23,7 +23,6 @@
     "mask",
     "open_converted",
     "open_raw",
-    "preprocess",
     "utils",
     "verbose",
 ]