Merge pull request OSOceanAcoustics#398 from OSOceanAcoustics/release…

…/v0.5.2

Adding commits for release/v0.5.2

docs/source/contributing.rst

@@ -43,7 +43,7 @@ Create a `conda <https://docs.conda.io>`_ environment for echopype development
 
 .. code-block:: bash
 
-    conda install -c conda-forge -n echopype --yes python=3.8 --file requirements.txt --file requirements-dev.txt
+    conda create -c conda-forge -n echopype --yes python=3.8 --file requirements.txt --file requirements-dev.txt
     conda activate echopype
     # ipykernel is recommended, in order to use with JupyterLab and IPython
     # to aid with development. We recommend you install JupyterLab separately

docs/source/whats-new.rst

@@ -4,20 +4,43 @@ What's new
 See `GitHub releases page <https://github.com/OSOceanAcoustics/echopype/releases>`_ for the complete history.
 
 
+v0.5.2 (2021 Jul 18)
+--------------------
+
+Overview
+~~~~~~~~
+
+This is a minor release that addresses issues related to time encoding for data variables related to platform locations and data conversion/encoding for AD2CP data files.
+
+Bug fixes and improvements
+~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+- Fixed the ``location_time`` encoding in the ``Platform`` group for latitude and longitude data variables (#393)
+- Fixed the ``location_time`` encoding in the ``Platform/NMEA`` group (#395)
+- Updated ``EchoData`` repr to show ``Platform/NMEA`` (#395, #396)
+- Improved AD2CP data parsing and conversion (#388)
+
+   - Cleaned up organization of data from different sampling modes and their corresponding time coordinates
+   - Fixed parsing issues that generated spikes in parsed echosounder mode amplitude data
+   - Removed the ``Beam_complex`` group and put raw IQ samples in the ``Vendor`` group per convention requirements
+   - Populated the ``Sonar`` group with AD2CP information
+
+
+
 v0.5.1 (2021 Jun 16)
 --------------------
 
 Overview
 ~~~~~~~~
 
-This is a minor release that addresses a couple of issues from the last major version (0.5.0) 
+This is a minor release that addresses a couple of issues from the last major version (0.5.0)
 and improves code maintenance and testing procedures.
 
 
 New features
 ~~~~~~~~~~~~
 
-- Added experimental functions to detect and correct ``ping_time`` reversals. 
+- Added experimental functions to detect and correct ``ping_time`` reversals.
   See `qc` subpackage (#297)
 
 
@@ -160,16 +183,23 @@ New features
 ~~~~~~~~~~~~
 
 - Add EK80 support:
+
   - File conversion from EK80 `.raw` files to netCDF and zarr formats
   - "Simple" calibration to frequency-average Sv based on pulse compression output is implemented but needs to be thoroughly tested.
+
 - Rename subpackage `echopype.model` to `echopype.process`
+
   - The new name better describes the subpackage's function to process data for further analysis
   - Also rename class `EchoData` to `Process` to mirror the structure in `Convert` better.
   - Importing using the old names will be deprecated in the next release.
+
 - Overhaul converting multiple files with `combine_opt=True`
+
   - If target format is netCDF, temporary files will be created and finally combined to a single netCDF. This is due to current restriction that xarray does not allow simply appending new data to an existing file.
   - If target format is zarr, data in each file are unpacked and appended to the same output file.
+
 - Allow reading Zarr into `Process` in addition to netCDF: thanks @lsetiawan!
+
 - Add a logo!
 
 Bug fixes

echopype/convert/api.py

@@ -279,17 +279,6 @@ def _save_groups_to_file(echodata, output_path, engine, compress=True):
             compression_settings=COMPRESSION_SETTINGS[engine] if compress else None,
         )
 
-    # Beam Complex Group: only AD2CP has Beam Complex
-    if hasattr(echodata, "beam_complex") and echodata.beam_complex is not None:
-        io.save_file(
-            echodata.beam_complex,
-            path=output_path,
-            mode="a",
-            engine=engine,
-            group="Beam_complex",
-            compression_settings=COMPRESSION_SETTINGS[engine] if compress else None,
-        )
-
     # Platform group
     io.save_file(
         echodata.platform,  # TODO: chunking necessary? location_time and mru_time (EK80) only
@@ -301,7 +290,7 @@ def _save_groups_to_file(echodata, output_path, engine, compress=True):
     )
 
     # Platform/NMEA group: some sonar model does not produce NMEA data
-    if hasattr(echodata, "nmea"):
+    if echodata.nmea is not None:
         io.save_file(
             echodata.nmea,  # TODO: chunking necessary?
             path=output_path,
@@ -547,8 +536,6 @@ def open_raw(
         echodata.beam, echodata.beam_power = setgrouper.set_beam()
     else:
         echodata.beam = setgrouper.set_beam()
-    if sonar_model == "AD2CP":
-        echodata.beam_complex = setgrouper.set_beam_complex()
     echodata.vendor = setgrouper.set_vendor()
 
     return echodata