Update jmodel: model cards, invalid value masking

[iulusoy]

This closes #32
This addresses #22 #20

• update pre-commit hooks to use ruff
• apply zero value to masked values for J-model
  • here we need two different masks: one for nan -> should result in empty values
  • one mask for negative temperatures: should result in zero values
• do not use random values in array for testing run_model for J-model
• test that masked values get set to the correct values for R0
• add model cards and model readme

Also: fix some Jmodel tests, plus we need to see if we do need the geometry cropping (see discussion on file).

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 94.89%. Comparing base (11bf4c8) to head (475fe60).
⚠️ Report is 1 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main      #48      +/-   ##
==========================================
+ Coverage   94.46%   94.89%   +0.42%     
==========================================
  Files          10       10              
  Lines         705      686      -19     
  Branches       78       73       -5     
==========================================
- Hits          666      651      -15     
+ Misses         24       22       -2     
+ Partials       15       13       -2     

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[Copilot]

Pull request overview

This pull request updates the J-model implementation to improve handling of invalid temperature values and adds comprehensive model card documentation for the HeiPlanet modeling suite. The PR also modernizes the pre-commit hooks to use ruff instead of black and flake8.

Changes:

• Implemented distinct masking for NaN (water areas) vs. out-of-range temperatures in J-model R0 calculation
• Updated pre-commit hooks from black/flake8 to ruff for linting and formatting
• Added model cards (YAML and Markdown) for WNV-R0 and Aedes albopictus population models

Reviewed changes

Copilot reviewed 14 out of 15 changed files in this pull request and generated 9 comments.

Show a summary per file

File	Description
.pre-commit-config.yaml	Replaced black and flake8 with ruff for linting and formatting
src/heiplanet_models/Jmodel.py	Modified _interpolate_r0 to handle NaN and out-of-range temperatures differently; commented out geometry clipping
src/heiplanet_models/utils.py	Reformatted lambda function parameters across multiple lines
test/test_JModel.py	Updated tests to verify masking behavior and corrected coordinate assertions
test/test_utils.py	Reformatted lambda function parameters across multiple lines
test/conftest.py	Changed test data from random to deterministic with deliberate NaN insertion
test/Pmodel/test_Pmodel_initial.py	Added noqa comments to lambda functions
docs/sources/model_jmodel_python.ipynb	Minor formatting changes and kernel version update
model_cards/WNV-R0_model_card.yaml	New comprehensive model card for WNV-R0 model
model_cards/WNV-R0_model_card.md	New markdown version of WNV-R0 model card
model_cards/Aedes_albopictus_population_model_card.md	New model card for Aedes albopictus population model
model_cards/README.md	New overview README for the model card suite
model_cards/HeiPlanet_model_comparison.yaml	New file comparing the two models
model_cards/HeiPlanet_harmonized_model_cards.yaml	New harmonized model card schema

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[iulusoy]

@MaHaWo please review and make changes as you seem fit, I can also do the refactor of the geometry issues if needed.

[MaHaWo]

looks good, thank you! the only comment I have is about the -10/ 0.0 values for the masking, which is an implemenation detail though and no game breaker. I can implement the changes mentioned, but pls add your comments to existing discussions first as you see fit.

[iulusoy]

looks good, thank you! the only comment I have is about the -10/ 0.0 values for the masking, which is an implemenation detail though and no game breaker. I can implement the changes mentioned, but pls add your comments to existing discussions first as you see fit.

So, there are two more changes for this PR:

• change the -10 to NaN, and the tests accordingly
• remove the geometry checks and NUTS region functionality

I've added the comments above. Also Copilot was highlighting some more issues, which I did not check in detail.

[MaHaWo]

• implemented changes mentioned
  • changed missing values indicator
  • adjusted tests
  • additional refactoring done for issues I noticed during this pass: correct some things with read_data, add explicit error handling
  • added explicit tests for failure modes
• copilot comments where not particularly useful. all closed.

do you want to have another look @iulusoy ?

[iulusoy]

do you want to have another look @iulusoy ?

Thank you @MaHaWo , I will look at this later!

[sonarqubecloud]

Quality Gate passed

Issues
2 New issues
0 Accepted issues

Measures
0 Security Hotspots
0.0% Coverage on New Code
0.0% Duplication on New Code

See analysis details on SonarQube Cloud