Fix 'Division by Zero' error when converting EK80 files without Sound Velocity Profile Depth value(s)

[ctuguinay]

When trying to save an Echodata object to Zarr that was missing the Sound Velocity Profile Depth coordinate in the Environment group, I got the following error:

{
	"name": "ZeroDivisionError",
	"message": "division by zero",
	"stack": "---------------------------------------------------------------------------
ZeroDivisionError                         Traceback (most recent call last)
Cell In[6], line 1
----> 1 ed.to_zarr(\"test.zarr\")

File ~/echopype/echopype/echodata/echodata.py:602, in EchoData.to_zarr(self, save_path, compress, overwrite, parallel, output_storage_options, consolidated, **kwargs)
    577 \"\"\"Save content of EchoData to zarr.
    578 
    579 Parameters
   (...)
    598     xarray's documentation for a list of all possible arguments.
    599 \"\"\"
    600 from ..convert.api import to_file
--> 602 return to_file(
    603     echodata=self,
    604     engine=\"zarr\",
    605     save_path=save_path,
    606     compress=compress,
    607     overwrite=overwrite,
    608     parallel=parallel,
    609     output_storage_options=output_storage_options,
    610     consolidated=consolidated,
    611     **kwargs,
    612 )

File ~/echopype/echopype/convert/api.py:88, in to_file(echodata, engine, save_path, compress, overwrite, parallel, output_storage_options, **kwargs)
     86     else:
     87         logger.info(f\"saving {output_file}\")
---> 88     _save_groups_to_file(
     89         echodata,
     90         output_path=io.sanitize_file_path(
     91             file_path=output_file, storage_options=output_storage_options
     92         ),
     93         engine=engine,
     94         compress=compress,
     95         **kwargs,
     96     )
     98 # Link path to saved file with attribute as if from open_converted
     99 echodata.converted_raw_path = output_file

File ~/echopype/echopype/convert/api.py:118, in _save_groups_to_file(echodata, output_path, engine, compress, **kwargs)
    108 io.save_file(
    109     echodata[\"Top-level\"],
    110     path=output_path,
   (...)
    114     **kwargs,
    115 )
    117 # Environment group
--> 118 io.save_file(
    119     echodata[\"Environment\"],  # TODO: chunking necessary?
    120     path=output_path,
    121     mode=\"a\",
    122     engine=engine,
    123     group=\"Environment\",
    124     compression_settings=COMPRESSION_SETTINGS[engine] if compress else None,
    125     **kwargs,
    126 )
    128 # Platform group
    129 io.save_file(
    130     echodata[\"Platform\"],  # TODO: chunking necessary? time1 and time2 (EK80) only
    131     path=output_path,
   (...)
    136     **kwargs,
    137 )

File ~/echopype/echopype/utils/io.py:78, in save_file(ds, path, mode, engine, group, compression_settings, **kwargs)
     76         if isinstance(ds[var].data, DaskArray):
     77             ds[var] = ds[var].chunk(enc.get(\"chunks\", {}))
---> 78     ds.to_zarr(store=path, mode=mode, group=group, encoding=encoding, **kwargs)
     79 else:
     80     raise ValueError(f\"{engine} is not a supported save format\")

File ~/miniforge3/envs/echopype/lib/python3.9/site-packages/xarray/core/dataset.py:2549, in Dataset.to_zarr(self, store, chunk_store, mode, synchronizer, group, encoding, compute, consolidated, append_dim, region, safe_chunks, storage_options, zarr_version, write_empty_chunks, chunkmanager_store_kwargs)
   2404 \"\"\"Write dataset contents to a zarr group.
   2405 
   2406 Zarr chunks are determined in the following way:
   (...)
   2545     The I/O user guide, with more details and examples.
   2546 \"\"\"
   2547 from xarray.backends.api import to_zarr
-> 2549 return to_zarr(  # type: ignore[call-overload,misc]
   2550     self,
   2551     store=store,
   2552     chunk_store=chunk_store,
   2553     storage_options=storage_options,
   2554     mode=mode,
   2555     synchronizer=synchronizer,
   2556     group=group,
   2557     encoding=encoding,
   2558     compute=compute,
   2559     consolidated=consolidated,
   2560     append_dim=append_dim,
   2561     region=region,
   2562     safe_chunks=safe_chunks,
   2563     zarr_version=zarr_version,
   2564     write_empty_chunks=write_empty_chunks,
   2565     chunkmanager_store_kwargs=chunkmanager_store_kwargs,
   2566 )

...

File ~/miniforge3/envs/echopype/lib/python3.9/site-packages/zarr/indexing.py:181, in SliceDimIndexer.__init__(self, dim_sel, dim_len, dim_chunk_len)
    179 self.dim_chunk_len = dim_chunk_len
    180 self.nitems = max(0, ceildiv((self.stop - self.start), self.step))
--> 181 self.nchunks = ceildiv(self.dim_len, self.dim_chunk_len)

File ~/miniforge3/envs/echopype/lib/python3.9/site-packages/zarr/indexing.py:167, in ceildiv(a, b)
    166 def ceildiv(a, b):
--> 167     return math.ceil(a / b)

ZeroDivisionError: division by zero"
}

Zarr doesn't seem to like it when a coordinate has no associated value(s):

So instead of setting sound_velocity_profile_depth to [] in set groups when the parser contains no associated values, I set it to [np.nan].

[codecov-commenter]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 80.22%. Comparing base (9f56124) to head (c916fe9).
Report is 141 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #1381      +/-   ##
==========================================
- Coverage   83.52%   80.22%   -3.31%     
==========================================
  Files          64       18      -46     
  Lines        5686     3089    -2597     
==========================================
- Hits         4749     2478    -2271     
+ Misses        937      611     -326     

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[ctuguinay]

@leewujung This should be ready for review

[leewujung]

@ctuguinay : This looks good. I agree [np.nan] is better than []. There may be something else we need to change further on this due to the newly discovered Environment datagram variability (only the first one in a .raw file contain the full set of data and the later ones containing only a subset).

The only comment I have is whether we need 3 test files. If these are identical in what the content is like, let's just keep one.

[ctuguinay]

@leewujung Thanks for the review! Just made the change to use just one test (since the content was identical).

[leewujung]

Great, thanks @ctuguinay! I resolved one merge conflict and this should be ready to go!