Ensure env_params intake for calibration

[leewujung]

Overview

This PR fixes a regression bug in v0.6.4 and ensures env_params are taken up correctly for EK60 echosounder.

It turned out that the bug was not an omission, but that the env_params used for EK60 cal in v0.6.4 was not passed in from the correctly sanitized ones from the parent class method. This is now in a PR with minimal scope #987.

Therefore, I am putting in work in this PR to address #965 more comprehensively.

Details

• Overhaul functions in env_params.py to address the core of Improve env_params intake and add test #965
• Remove redundancy in passing in extra ed_beam_group in _cal_power_samples and _cal_complex_samples
• Create integration tests for the get_env_params_* functions in env_params_integration.py
  • These verify that user-provided params are taken in to the calibration objects and stored in the final Sv output correctly
• Create unit tests for the get_env_params_* functions in env_params.py

[codecov-commenter]

Codecov Report

Merging #985 (ad0551c) into dev (8aca475) will increase coverage by 6.17%.
The diff coverage is 90.47%.

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@@            Coverage Diff             @@
##              dev     #985      +/-   ##
==========================================
+ Coverage   79.64%   85.82%   +6.17%     
==========================================
  Files          62       19      -43     
  Lines        5680     1199    -4481     
==========================================
- Hits         4524     1029    -3495     
+ Misses       1156      170     -986     

Flag	Coverage Δ
unittests	85.82% <90.47%> (+6.17%)	⬆️

Flags with carried forward coverage won't be shown. Click here to find out more.

Impacted Files	Coverage Δ
echopype/calibrate/cal_params.py	92.30% <ø> (ø)
echopype/calibrate/env_params.py	89.10% <87.17%> (+0.58%)	⬆️
echopype/calibrate/calibrate_azfp.py	97.29% <100.00%> (ø)
echopype/calibrate/calibrate_ek.py	98.68% <100.00%> (+<0.01%)	⬆️
echopype/calibrate/range.py	86.15% <100.00%> (ø)
echopype/consolidate/api.py	72.60% <100.00%> (-19.18%)	⬇️

... and 50 files with indirect coverage changes

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[leewujung]

@emiliom : I think this is ready for a review when you are available. I will add that one integration test tomorrow morning.

[leewujung]

@emiliom : This one is ready for a thorough review.

[emiliom]

I wasn't thorough, but I think it looks good. I made a bunch of comments, most of them stylistic.

There's just one where I think you're missing something important, an inistance(). Take a look.

[leewujung]

@emiliom : Thanks for reviewing this! I've made the following changes:

• made all but one of the suggested changes (that one was incorrect even though the pattern looks similar, so I reverted)
• added missed test cases for test_sanitize_user_env_dict
• remove redundancy in passing in ed_beam_group in _cal_power_samples and _cal_complex_samples

I had questions about two of your comments so left them open.