✨ Complete internal rewrite - new result API #1562

jsnel · 2024-12-10T20:43:23Z

TODO: summarize the close to 200 commits.

Joined effort from maintainers:

Change summary

TODO1 - WIP
TODO1 - WIP

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 #XXXX

for more information, see https://pre-commit.ci

to be more consistent with model/scheme definition

Make calculate_parameter_errors a seperate function

On the basis of user feedback

- removes extras - add activations - unpack (what was in) data to top level including: -- input_data -- residual(s) - make fitted_data a property (computed on the fly) - make keyword arguments only

and fix some formatting

DatasetResult -> OptimizationResult (possible because of precious optimization_info refactor) Give DOAS and kinetic test more meaningful names

Reduced of 3 fails in total unit tests

Co-authored-by: s-weigand <s.weigand.phy@gmail.com>

Maybe rename it at some point ^^

🧰✨ Add toml formatter and linter hook

sonarqubecloud · 2024-12-10T20:44:06Z

Quality Gate failed

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E Reliability Rating on New Code (required ≥ A)

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joernweissenborn and others added 30 commits October 14, 2023 11:17

Implement model.item with pydantic.

bc97571

[pre-commit.ci] auto fixes from pre-commit.com hooks

7b794f8

for more information, see https://pre-commit.ci

Create model.library

645975d

Redesign megacomplex and dataset model.

a8ab614

Implemented experiment model.

bc1d869

Create library from megacomplex.

d0ea1ed

Library create datamodels for megacomplex.

ec28457

Add DataModel.from_dict.

c71721d

Add ExperimentModel.from_dict

7899171

Adapted experiment items to new item types.

e735ada

Add validation logic for items.

7e9c868

Remove old model and items.

7e77d9e

Move dataset scale to ExperimentModel

5c2e09e

Move weight to data_model.

d464a2f

Resolve parameters.

c2028c9

Remove link_clp.

93e3df3

Rewrite optimization test models.

a73b568

Adapt data provider.

8115364

Also resolve resolved items.

ac5e915

Created OptimizationData.

f5a4fbe

Created OptimizationMatrix

72be264

Added OptimizationEstimation

930af5b

Refactored tests.

41363ee

Added penalty

02684d3

Create OptimizationObjective.

eec2250

Created Optimization

f325fc7

Subtract number of clp from dgrees of freedom.

187f5e7

Make parameter type optional float for handy constant.

a958cb0

Finetuning.

1eb6eeb

Added test for OptimizationObjective

382a20d

joernweissenborn and others added 28 commits September 29, 2024 12:51

fix

e1aeb6a

[pre-commit.ci] auto fixes from pre-commit.com hooks

f58bb9a

for more information, see https://pre-commit.ci

WIP: Unflatten result.

c47ec65

Fix result data type

1c39372

Rename result.data to result.datasets

c839a34

to be more consistent with model/scheme definition

Rename OptimizationResult to OptimizationInfo

f3e51c9

Make calculate_parameter_errors a seperate function

Rename parameters in Results back to what it was

809189f

On the basis of user feedback

Refactor DatasetResults

ec35a58

- removes extras - add activations - unpack (what was in) data to top level including: -- input_data -- residual(s) - make fitted_data a property (computed on the fly) - make keyword arguments only

Change DatasetResult type to pydantic BaseModels instead of dataclass

85ee779

and fix some formatting

Removed ElementResults in favor of xr.Dataset

4d274dc

Rename residual to residuals

fabd900

♻️ Refactor for more meaning function/class/method names

4042737

DatasetResult -> OptimizationResult (possible because of precious optimization_info refactor) Give DOAS and kinetic test more meaningful names

Start refactor coordinate species to compartment

99c7b21

Rename optimization_result to optimization_results in objective

1a975c8

Fix kinetic element unit tests

4598f79

Reduced of 3 fails in total unit tests

WIP ♻️ Rename activation to activations and use dict instead of a list

a02b1e5

Co-authored-by: s-weigand <s.weigand.phy@gmail.com>

Adapt to changed to dict like ActiviationDataModel

3138c49

Finish refactoring of activations

5da2676

Fix coherent_artifact unit tests

265f63d

Fix typo

6cdb9d9

Refactor coherent-artifact element compartment and coord labeling

d71f3ee

Fixed unit test for damped-oscillation element

66e9deb

Fix unit test for spectral element

9482cc5

Fix most remaining unit tests

f12a1be

Disable test_result with warning that it needs to be fixed

f5af4df

Maybe rename it at some point ^^

🧰⬆️ Update pre-commit config

4925c74

🧰✨ Add toml formatter and linter hook

🧹 Fix typo

8c52c70

🧹 Fix pre-commit issues outside of result saving

fdec279

jsnel mentioned this pull request Dec 10, 2024

[WIP] Staging new result api [DRAFT] joernweissenborn/pyglotaran#7

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✨ Complete internal rewrite - new result API #1562

✨ Complete internal rewrite - new result API #1562

jsnel commented Dec 10, 2024

sonarqubecloud bot commented Dec 10, 2024

✨ Complete internal rewrite - new result API #1562

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✨ Complete internal rewrite - new result API #1562

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jsnel commented Dec 10, 2024

Change summary

Checklist

Closes issues

sonarqubecloud bot commented Dec 10, 2024

Quality Gate failed