support om2 forcing file

[minghangli-uni]

closes #19

• Add a parser to parse json-format file,
• Add an updater for the om2 forcing configuration,
• Add more logic to _extract_run_specific_params in src/experiment_generator/om2_forcing_updater.py
• unittest

[codecov]

Codecov Report

❌ Patch coverage is 89.53488% with 9 lines in your changes missing coverage. Please review.
✅ Project coverage is 91.51%. Comparing base (21aef2e) to head (8e79c99).
⚠️ Report is 1 commits behind head on main.

Files with missing lines	Patch %	Lines
src/experiment_generator/tmp_parser/json_parser.py	36.36%	7 Missing ⚠️
src/experiment_generator/om2_forcing_updater.py	98.43%	0 Missing and 1 partial ⚠️
...rc/experiment_generator/perturbation_experiment.py	88.88%	0 Missing and 1 partial ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main      #20      +/-   ##
==========================================
- Coverage   91.78%   91.51%   -0.28%     
==========================================
  Files          15       18       +3     
  Lines         475      554      +79     
  Branches       96      112      +16     
==========================================
+ Hits          436      507      +71     
- Misses         18       25       +7     
- Partials       21       22       +1     

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[minghangli-uni]

Hi @aekiss can you review this PR related to the om2 forcing perturbation?

[aekiss]

Thanks @minghangli-uni - apart from the required temporal, spatial order for separable I didn't spot any other problems. I'm not a good person to review python code though, and only scanned over it.

[minghangli-uni]

Thanks @aekiss for your review. They look great! I've addressed your comments and suggestions. Could you have another look?

[aekiss]

LGTM, thanks @minghangli-uni

[aekiss]

not sure why you've got test fails though...

[minghangli-uni]

The coverage dropped because I added another json parser to the tmp_parser. That’s expected and it’s fine for now since all the parsers will eventually be replaced.

[dougiesquire]

The best way to resolve this is to add tests for the added code. If there's a reason not to do this, you could either skip this file from the codecov, or just merge with the reduced coverage

[minghangli-uni]

skip this file from the codecov

How can I skip this file?

[minghangli-uni]

I've added a codecov.yml file. The files in tmp_parser are still not being ignored, and I’m not sure if it will start working once this is merged into the main branch. I'll bypass rules and merge this to see if works.

 ignore:
   # https://docs.codecov.com/docs/ignoring-paths
   - "src/experiment_generator/tmp_parser/**/*"