Refactor Element Result Saving

joernweissenborn commented 1 week ago

This PR refactors the way element results are stored. Now every element stores it's own items. They return

@dataclass
class ElementResult:
    amplitudes: dict[str, xr.DataArray]
    concentrations: dict[str, xr.DataArray]
    extra: dict[str, xr.DataArray] = field(default_factory=dict)

The Kinetic element eg, stores amplitudes and contractions each with key "species" and "decay". This means in the final result this will be stored as eg species_associated_amplitude_ELEMENTNAME. K matrices etc are part of extra and only get the element name suffixed.

IMPORTANT To avoid collisions, all coords which are not the model or the global dim also get suffixed with the name, species coord will be renamend to species_ELEMENTNAME.

Checklist

[ ] ✔️ Passing the tests (mandatory for all PR's)
[ ] 🚧 Added changes to changelog (mandatory for all PR's)
[ ] 👌 Closes issue (mandatory for ✨ feature and 🩹 bug fix PR's)
[ ] 🧪 Adds new tests for the feature (mandatory for ✨ feature and 🩹 bug fix PR's)
[ ] 📚 Adds documentation of the feature

Closes issues

closes #1498

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github-actions[bot] commented 1 week ago

:point_left: Launch a binder notebook on branch _joernweissenborn/pyglotaran/staging1474

joernweissenborn commented 1 week ago

I have checked the sonar cloud issues, this will be fixed in the cleanup when I add doc etc.

codecov[bot] commented 4 days ago

Codecov Report

Attention: Patch coverage is 94.51477% with 13 lines in your changes missing coverage. Please review.

Project coverage is 85.3%. Comparing base (06d4c98) to head (f41fd12).

Files with missing lines	Patch %	Lines
glotaran/builtin/items/activation/data_model.py	88.5%	2 Missing and 2 partials :warning:
...aran/builtin/elements/coherent_artifact/element.py	86.3%	1 Missing and 2 partials :warning:
glotaran/optimization/data.py	77.7%	1 Missing and 1 partial :warning:
glotaran/optimization/objective.py	98.1%	1 Missing and 1 partial :warning:
glotaran/builtin/elements/baseline/element.py	66.6%	1 Missing :warning:
glotaran/optimization/optimization.py	50.0%	1 Missing :warning:

Additional details and impacted files

```diff @@ Coverage Diff @@ ## staging #1534 +/- ## ========================================= - Coverage 85.3% 85.3% -0.1% ========================================= Files 91 91 Lines 3752 3746 -6 Branches 734 719 -15 ========================================= - Hits 3203 3197 -6 - Misses 438 445 +7 + Partials 111 104 -7 ```

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