✨ Complete internal rewrite - new result API by jsnel · Pull Request #1562 · glotaran/pyglotaran

Commits on Oct 14, 2023

Implement model.item with pydantic.

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

pre-commit-ci[bot]
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Create model.library

joernweissenborn
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Redesign megacomplex and dataset model.

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Implemented experiment model.

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Create library from megacomplex.

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Library create datamodels for megacomplex.

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Add DataModel.from_dict.

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Add ExperimentModel.from_dict

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Adapted experiment items to new item types.

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Add validation logic for items.

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Remove old model and items.

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Move dataset scale to ExperimentModel

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Move weight to data_model.

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Resolve parameters.

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Remove link_clp.

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Rewrite optimization test models.

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Adapt data provider.

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Also resolve resolved items.

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Created OptimizationData.

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Created OptimizationMatrix

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Added OptimizationEstimation

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Refactored tests.

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Added penalty

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Create OptimizationObjective.

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Created Optimization

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Subtract number of clp from dgrees of freedom.

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Make parameter type optional float for handy constant.

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Finetuning.

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Added test for OptimizationObjective

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Remove weights from linked data.

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Refactored simulation.

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Added first test for optimization.

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Added OptimnizationMatrix.from_global_data.

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Add global path to Objective.

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Added test for penalties.

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Added optimization test for global model.

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Added test for multiple experiments.

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Cleanup.

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Added model issue guard to optimization

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Added Optimization.dry_run

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Renamed clp_labels to clp_axis.

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Tempery deactivated mypy and darglint precommit checks.

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Added test for megacomplex result.

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Added Parameters.close_or_equal

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Fixed resolving of none library items.

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Fixed result resolving of clp.

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Fixed datamodel model dimension for None case.

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Support item iteration over Annoted types.

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Make OptimizationResult pydantic model

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Created Activation item

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Add item Kinetic.

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Add KineticMegacomplex

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Refactored if parameter calculation.

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Refactored kinetic megacomplex calculation.

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Ported tests from k matrix to kinetic item.

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Added tests for gaussian action.

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Added test for kinetic megacomplex

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Adapted baseline megacomplex

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Adapted clp guide megacomplex

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Adapted coherent artifact.

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Adapdet damped oscillation megacomplex

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Adapted spectral megacomplex.

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Add resultdata for kinetic megacomplex.

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Removed decay megacomplex

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Added register_as to megacomplexes

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Created basic new scheme.

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Add new result class.

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Changend name of experiment.validate to avoid pydantiv conflict

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Added basic test for scheme.

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Remove old scheme and result.

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Removed model related things from plugin and io.

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Remove folder plugin.

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Cleanded Model from YML io.

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Reimplemented load_scheme.

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Fix activation.

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Fix baseline register

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Fix kinetic megacomplex

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Fix OptimizationMatrix

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Fix scheme

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Merge Kinetic part with megacomplex.

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Remove library.

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Remove OptimizationGroup

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Renamed megacomplex to model.

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Adapted optimization to latest changes.

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Rename megacomplex plugins to models.

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Adapted scheme test.

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Removed obsolete yml tests.

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Make scheme library use get_annotated_type

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Enable per activation coherent_artifact

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Rename model to element.

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Made scheme experiments dict.

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Create Result.save

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Updated nix flake.

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Added ExtendableElement.

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Cleanup.

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Made kinetic element extendable

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Remove generators,

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Remove dataclass helpers.

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Remove project.

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Remove benchmark.

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Remove cli.

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Fixed flake init.

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Adapted test for full model.

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Adapt simulated data.

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Cleanup.

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More cleanup.

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Add test for Result.save

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Fix simulation test.

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Update flake.

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Fix typing of ArrayLike.

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Change element scale to dict.

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Add parameters from expressions tp initial parameters.

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Add fitted data to result.

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Fixed mypy override issues.

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Fix pydantic-field mypy errors.

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Fixed damped oscillation issues.

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Fix datamodel creation.

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Fix get parameter dependencies.

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Fix mypy errors in coherent-artifact.

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Add scale to result data.

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Fixed mypy issues in kinetic element.

joernweissenborn
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Fixed mypy errors in activation.

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Fixed mypy issues in spectral.

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Small fixes.

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Cleanup yml io.

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Fix project mypy issues.

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Fix mypy errors in optimization.

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Fix mypy issues for model.

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Final mypy fixes.
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Precommit fixes.

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Add allow_overwrite to Result.save.

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Commits on Oct 15, 2023

Fix bug with nested extensions.

joernweissenborn
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Commits on Oct 17, 2023

Commits on Oct 20, 2023

Add call to calculate_parameter_errors before returning Result (glotaran#1373 )
jsnel
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Commits on Oct 21, 2023

Commits on Oct 22, 2023

Commits on Jan 27, 2024

Commits on Feb 3, 2024

🧹 Use element plugin registry to define LibraryType (glotaran#1427 )
s-weigand
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Commits on Mar 17, 2024

⬆️🧰 Autoupdate pre-commit config staging (glotaran#1438 )
s-weigand
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Commits on Jun 1, 2024

Staging fix relations (glotaran#1455 )

joernweissenborn
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s-weigand
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Commits on Jun 2, 2024

🚇 Use pyglotaran-examples@staging_rewrite for CI integration tests (glotaran#1462 )
s-weigand
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Commits on Jun 8, 2024

Commits on Jun 15, 2024

Commits on Jun 22, 2024

🩹 Fix scaling for linked dataset case (glotaran#1461 )

jsnel
and
s-weigand
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Commits on Jul 6, 2024

Commits on Jul 7, 2024

Add additional penalty to result.
joernweissenborn
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Commits on Jul 13, 2024

Commits on Jul 14, 2024

🩹Fix order of parameters involved in parameters expresssion (glotaran#1500 )
jsnel
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