add Ocean Gliders format output option to seaxexplorer processing

[callumrollo]

This PR is under development and is waiting on several currently active proposed edits to the Ocean Gliders format before it can be finalised

This will resolve #21

[codecov]

Codecov Report

Attention: Patch coverage is 13.20755% with 46 lines in your changes missing coverage. Please review.

Project coverage is 53.77%. Comparing base (7ec1b8e) to head (778a6b9).
Report is 7 commits behind head on main.

Files with missing lines	Patch %	Lines
pyglider/utils.py	4.87%	39 Missing ⚠️
pyglider/seaexplorer.py	41.66%	7 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #212      +/-   ##
==========================================
- Coverage   55.11%   53.77%   -1.35%     
==========================================
  Files           9        9              
  Lines        1700     1750      +50     
==========================================
+ Hits          937      941       +4     
- Misses        763      809      +46     

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[jklymak]

A quick skim - I'm not clear that a lot of this cannot be handled via the yaml.

For the rest, it would be nice to keep new variables like platform id in the yaml as well. I've not looked but perhaps that requires a new variable type that just accepts a constant value.

Maybe we should have a quick call, but I would rather see a general approach rather than special "og" carve outs

[jklymak]

For example, 'time'/'TIME' could be replaced by a time-encoder yaml entry. eg calls to ds.time could be replaced by ds[time_var_name] or similar?

Not sure about 'latitude' etc, but why do they need to be translated back and forth? For distance over ground? Maybe just use inside that function?

[callumrollo]

I can localise lon/lat to just change within those functions, I'll make a new PR with ds[time_var_name] and see what it looks like

[jklymak]

The yamls have a "conversion" field for each variable that tries to fine the method in utils.py. So this could look like

netcdf_variables:
    DEPLOYMENT_TIME:
         "long_name": "date of deployment"
         ...
         "conversion": "nanmin_time"

with the accompanying change in utils.py. We may want to think of a way to make that more general (np.nan_min, "DEPLOYMENT_TIME) if yaml accepts tuples.

[VeckoTheGecko]

6651931 (via #210) introduced a bunch of formatting changes that will likely cause merge conflicts. Here are merge and rebase workflows to avoid these conflicts (it depends on having pre-commit installed - see the contributing docs).

I recommend first creating a temp branch off of your branch of interest to test these workflows and make sure the output is as expected. I have tested these and they seem to work well.

# merge all the way up to the commit that introduced the formatting changes
git merge 66519318^1

# merge the commit that introduced the formatting changes, prioritising the working branch during conflicts
git merge -s ours 66519318 --no-commit 
pre-commit run --all-files
git commit --no-edit

# merge the rest of the way
git merge main

or by doing a rebase (if you want a clean history)

# Rebase up to the commit introducing formatting changes
git rebase 66519318^1

# Rebase onto the commit introducing formatting changes.
# Accept working branch changes (i.e., "theirs" during rebase
# - different to merge. See git rebase docs) during conflicts.
# During the rebase we will run the formatter after applying
# changes from commits, before committing so that everything is compliant.
git rebase -X theirs -i 66519318
# Replace all "pick" with "edit" or "e". Start the rebase...

# Repeatedly run
git add -u && pre-commit run --all-files && git rebase --continue
# to run pre-commit tooling, stage modified files, and continue
# until rebase is complete. Sometimes pre-commit can't autofix
# issues, then you need to fix them manually.
# If you make a mistake you can always do `git rebase --abort`

# Finally, rebase onto main
git rebase main

[callumrollo]

I'll try a different approach following Jody's suggestion of a new yaml entry that makes empty variables/variables with one value