AZFP ULS6 beta version, ULS5 fixes

[dash-uvic]

ULS5 Bug fixes:

• fixed recursive bug for corrupted files
• fixed RepeatedField not applying correctly
  ULS6 updates:
• Added AZFP Nano (single channel) compatibility
• Added compatibility for beta version of ULS6 standard
• Refractored code to inherit ULS5 as a base class
• Added additional tests for ULS6 to include Paros sensors

[leewujung]

I haven't gotten around to upload the test data to GitHub release assets just yet. Traveling tomorrow, so will try Wednesday...

[leewujung]

Hey @dash-uvic : I got the test data you sent me as a staged asset in #1582. It’s merged so if you pull from main now you should have all the right files.

[codecov-commenter]

Codecov Report

❌ Patch coverage is 94.03748% with 35 lines in your changes missing coverage. Please review.
✅ Project coverage is 85.27%. Comparing base (d371686) to head (e1ab28e).
⚠️ Report is 24 commits behind head on main.

Files with missing lines	Patch %	Lines
echopype/convert/parse_uls6.py	89.43%	26 Missing ⚠️
echopype/convert/parse_azfp.py	92.06%	5 Missing ⚠️
echopype/convert/parse_uls5.py	97.22%	4 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #1581      +/-   ##
==========================================
+ Coverage   84.95%   85.27%   +0.32%     
==========================================
  Files          79       80       +1     
  Lines        6998     7042      +44     
==========================================
+ Hits         5945     6005      +60     
+ Misses       1053     1037      -16     

Flag	Coverage Δ
unittests	85.27% <94.03%> (+0.32%)	⬆️

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[leewujung]

@dash-uvic: I pulled the update assets in and the current tests all passed. Are there additional tests or code you want to add?

[leewujung]

@dash-uvic : Thanks for the PR! I went through the changes quickly, and have one more substantial suggestion and a couple small ones below.

I think it'd be better from the maintenance point of view to have a parent class parse_AZFP and have 2 child classes, one parse_ULS5 and the other parse_ULS6. What you have under the current parse_AZFP (largely from existing code) can largely stay in this parent class, with both child classes being pretty slim with only the differences on the header and XLM handling.

Small comments:

• I don't see this constant used in the ULS6 code: FILENAME_DATETIME_AZFP = "\\w+_\\w+.[azfp|aps6]". Could you confirm? This is linked to the parent class suggestion above. It'll be cleaner to have all shared constants in the parent class and only the differences showing up in the child class. We did the same thing for the EK classes.
• There are these couple lines in multiple functions that I think are redundant, since the parse object is called from convert/api.py and will ALWAYS execute parse.parse_raw() for all sonar models.

  if not self.unpacked_data:
    self.parse_raw()

  As you make changes re the parent/child classes, could you also remove these?

[dash-uvic]

@leewujung I've done the suggested changes and included comments from [1505] and moved the Sv_offset to calibration. Just need to write a test for the new Sv interpolation and I'll push.

[leewujung]

@dash-uvic : Awesome. Looking forward to it!

[LOCEANlloydizard]

Hi @dash-uvic, the error currently raised in the tests is fixed in #1591, so fetching the latest from upstream should resolve it!
Cheers!

[leewujung]

@dash-uvic: I pulled in the upstream and everything runs through fine, so you should be good to go on adding additional tests for Sv offset.

[dash-uvic]

Sorry just got back from vacation. I just did a pull and ran the tests and everything looks good (Sv offset tests were in the last push). I did a minor code cleanup push just now to remove a few commented out asserts.