Move preprocess functions and tests new clean and commongrid subpackages

[emiliom]

Moved noise functions (public API: estimate_noise and remove_noise) from preprocess to filter. Split off noise tests in preprocess/test_preprocess.py to filter/test_noise.py

Fully addresses #889, moving functions from preprocess to filter or commongrid. We agreed to call the new subpackage commongrid rather than unify (I'll make a note of it in #889). Updated all tests.

See #817 (comment), but note that I did not carry out the filter.noise hierarchy proposed there. Looking through all subpackages, there are only a couple of cases of another subpackage (folder) under a subpackage, and those are not publicly exposed.

NOTE: We'll likely need to revisit the subpackage name filter, because filter is a Python reserved word!

Partly addresses #889. This PR could be treated as stand-alone, with a follow up PR to address the rest of #889. Or we could add those other changes on top of this PR, when ready.

[codecov-commenter]

Codecov Report

Merging #993 (295111b) into dev (edc1d15) will decrease coverage by 55.71%.
The diff coverage is 82.92%.

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@@             Coverage Diff             @@
##              dev     #993       +/-   ##
===========================================
- Coverage   79.72%   24.01%   -55.71%     
===========================================
  Files          62       66        +4     
  Lines        5721     5738       +17     
===========================================
- Hits         4561     1378     -3183     
- Misses       1160     4360     +3200     

Flag	Coverage Δ
unittests	24.01% <82.92%> (-55.71%)	⬇️

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

Impacted Files	Coverage Δ
echopype/clean/noise_est.py	94.73% <ø> (ø)
echopype/commongrid/mvbs.py	84.37% <ø> (ø)
echopype/preprocess/api.py	47.05% <47.05%> (-44.17%)	⬇️
echopype/clean/api.py	78.57% <78.57%> (ø)
echopype/commongrid/api.py	95.45% <95.45%> (ø)
echopype/__init__.py	100.00% <100.00%> (ø)
echopype/clean/__init__.py	100.00% <100.00%> (ø)
echopype/commongrid/__init__.py	100.00% <100.00%> (ø)
echopype/consolidate/api.py	91.78% <100.00%> (ø)
echopype/preprocess/__init__.py	100.00% <100.00%> (ø)

... and 43 files with indirect coverage changes

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[leewujung]

Partly addresses #889. This PR could be treated as stand-alone, with a follow up PR to address the rest of #889. Or we could add those other changes on top of this PR, when ready.

Hey @emiliom : thanks for submitting this! I think we could keep this PR open so that you could add the rest of #889 on top of this? I can review this PR again at that time. I did look through the changes in this one quickly and your proposed changes to where estimate_noise sits is fine by me.

[emiliom]

Alright, it took me much more work than I anticipated to complete the rest of this PR, but here it is.

• All preprocess functions have now been distributed to either filter or commongrid
• All tests were updated and renamed as needed
• .ci_helpers/run-test.py is updated
• Added stub, pass-through functions to preprocess with a deprecation warning saying that they'll be removed in 0.7.1. I didn't add tests for these stub functions, since they seem unnecessary. I did test them locally, manually.
• Updated the provenance attribute statements to replace "preprocess" with "filter" or "commongrid". Note that I didn't make other changes to that code, since we're having a parallel conversation about the future of those attributes.

All tests ran locally.

[emiliom]

New commit to change filter subpackage to clean. See #889 (comment)

[leewujung]

@emiliom : Thanks for this PR! I think this is ready to be merged once you address the estimate_noise docstring change (which I know didn't come from you...). My other comments were just questions which may or may not lead to further changes.

[emiliom]

I think the only open issue is whether to reorder the __all__ strings in echopype/__init__.py. Any preference?

[leewujung]

whether to reorder the __all__ strings in echopype/__init__.py. Any preference?

I think it will be good to reorder that as well! :)

[emiliom]

whether to reorder the all strings in echopype/init.py. Any preference?

I think it will be good to reorder that as well! :)

Done. Everything else is also taken care of. I'll merge the PR once the tests are completed. Thanks!!