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0.8/pydantic2 (Sourcery refactored)#1369

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Commits

Commits on Oct 14, 2023

• Implement model.item with pydantic.

  

  joernweissenborn

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  jsnel

  committed
  bc97571

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

  Show description for 7b794f8
  

  pre-commit-ci[bot]

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  jsnel

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  7b794f8

• Create model.library

  

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  645975d

• Redesign megacomplex and dataset model.

  

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  a8ab614

• Implemented experiment model.

  

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  bc1d869

• Create library from megacomplex.

  

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  d0ea1ed

• Library create datamodels for megacomplex.

  

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  ec28457

• Add DataModel.from_dict.

  

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  c71721d

• Add ExperimentModel.from_dict

  

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  7899171

• Adapted experiment items to new item types.

  

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  e735ada

• Add validation logic for items.

  

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  7e9c868

• Remove old model and items.

  

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  7e77d9e

• Move dataset scale to ExperimentModel

  

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  5c2e09e

• Move weight to data_model.

  

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  d464a2f

• Resolve parameters.

  

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  c2028c9

• Remove link_clp.

  

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  93e3df3

• Rewrite optimization test models.

  

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  a73b568

• Adapt data provider.

  

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  8115364

• Also resolve resolved items.

  

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  ac5e915

• Created OptimizationData.

  

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  f5a4fbe

• Created OptimizationMatrix

  

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  72be264

• Added OptimizationEstimation

  

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  930af5b

• Refactored tests.

  

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  41363ee

• Added penalty

  

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  02684d3

• Create OptimizationObjective.

  

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  eec2250

• Created Optimization

  

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  f325fc7

• Subtract number of clp from dgrees of freedom.

  

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  187f5e7

• Make parameter type optional float for handy constant.

  

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  a958cb0

• Finetuning.

  

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  1eb6eeb

• Added test for OptimizationObjective

  

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  382a20d

• Remove weights from linked data.

  

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  44bca3c

• Refactored simulation.

  

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  a2cfb94

• Added first test for optimization.

  

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  efdf6f6

• Added OptimnizationMatrix.from_global_data.

  

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  a368460

• Add global path to Objective.

  

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  a569360

• Added test for penalties.

  

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  315d3a6

• Added optimization test for global model.

  

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  5186489

• Added test for multiple experiments.

  

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  b61b5ec

• Cleanup.

  

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  59efdea

• Added model issue guard to optimization

  

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  4bbe690

• Added Optimization.dry_run

  

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  f4b1ffb

• Renamed clp_labels to clp_axis.

  

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  a0948a4

• Tempery deactivated mypy and darglint precommit checks.

  

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  f94c6c0

• Added test for megacomplex result.

  

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  7b48327

• Added Parameters.close_or_equal

  

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  4798ca0

• Fixed resolving of none library items.

  

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  6e9a244

• Fixed result resolving of clp.

  

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  c38cdc3

• Fixed datamodel model dimension for None case.

  

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  f215a78

• Support item iteration over Annoted types.

  

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  e4fa9e3

• Make OptimizationResult pydantic model

  

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  b14778b

• Created Activation item

  

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  14edfed

• Add item Kinetic.

  

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  53e7877

• Add KineticMegacomplex

  

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  dc6bcf1

• Refactored if parameter calculation.

  

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  ea20504

• Refactored kinetic megacomplex calculation.

  

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  1d3dc7a

• Ported tests from k matrix to kinetic item.

  

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  7dad053

• Added tests for gaussian action.

  

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  d4bdeda

• Added test for kinetic megacomplex

  

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  d7d0f41

• Adapted baseline megacomplex

  

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  b76d581

• Adapted clp guide megacomplex

  

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  28dae9a

• Adapted coherent artifact.

  

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  6e947e6

• Adapdet damped oscillation megacomplex

  

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  8c94431

• Adapted spectral megacomplex.

  

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  7f2f45b

• Add resultdata for kinetic megacomplex.

  

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  3963a72

• Removed decay megacomplex

  

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  a2359f3

• Added register_as to megacomplexes

  

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  0f9df73

• Created basic new scheme.

  

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  ac512c5

• Add new result class.

  

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  20772e5

• Changend name of experiment.validate to avoid pydantiv conflict

  

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  10a7463

• Added basic test for scheme.

  

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  2b0fe3a

• Remove old scheme and result.

  

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  682369d

• Removed model related things from plugin and io.

  

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  564e5c8

• Remove folder plugin.

  

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  6f83257

• Cleanded Model from YML io.

  

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  7703c33

• Reimplemented load_scheme.

  

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  b02c28f

• Fix activation.

  

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  789d51b

• Fix baseline register

  

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  bf2619c

• Fix kinetic megacomplex

  

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  2b9bd27

• Fix OptimizationMatrix

  

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  d70e8ca

• Fix scheme

  

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  3f4da66

• Merge Kinetic part with megacomplex.

  

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  1523450

• Remove library.

  

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  ea593b4

• Remove OptimizationGroup

  

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  44970c0

• Renamed megacomplex to model.

  

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  815134d

• Adapted optimization to latest changes.

  

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  968a42b

• Rename megacomplex plugins to models.

  

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  290d42f

• Adapted scheme test.

  

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  7182330

• Removed obsolete yml tests.

  

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  8e00bc2

• Make scheme library use get_annotated_type

  

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  93b0d1c

• Enable per activation coherent_artifact

  

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  b0e002f

• Rename model to element.

  

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  d9d67e5

• Made scheme experiments dict.

  

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  a41ae90

• Create Result.save

  

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  bcb9a9f

• Updated nix flake.

  

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  561b512

• Added ExtendableElement.

  

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  5de6cdc

• Cleanup.

  

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  a7eb023

• Made kinetic element extendable

  

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  75f2d08

• Remove generators,

  

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  be7a8d4

• Remove dataclass helpers.

  

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  4659901

• Remove project.

  

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  a2b41e8

• Remove benchmark.

  

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  1fadbab

• Remove cli.

  

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  deb8243

• Fixed flake init.

  

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  04b2fca

• Adapted test for full model.

  

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  4b62a7a

• Adapt simulated data.

  

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  ccd95c1

• Cleanup.

  

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  1c4e05a

• More cleanup.

  

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  c930100

• Add test for Result.save

  

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  f9bb72e

• Fix simulation test.

  

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  72a0ab5

• Update flake.

  

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  b2e2df4

• Fix typing of ArrayLike.

  

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  92bfb7e

• Change element scale to dict.

  

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  8c9e83f

• Add parameters from expressions tp initial parameters.

  

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  9de1f78

• Add fitted data to result.

  

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  62fae03

• Fixed mypy override issues.

  

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  0e74f1e

• Fix pydantic-field mypy errors.

  

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  0480f2d

• Fixed damped oscillation issues.

  

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  31d24f7

• Fix datamodel creation.

  

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  b2cb780

• Fix get parameter dependencies.

  

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  3e73ce5

• Fix mypy errors in coherent-artifact.

  

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  2f96fb8

• Add scale to result data.

  

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  ad3bfc6

• Fixed mypy issues in kinetic element.

  

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  54c0519

• Fixed mypy errors in activation.

  

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  7eebb3f

• Fixed mypy issues in spectral.

  

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  0b42fb3

• Small fixes.

  

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  cd5d83b

• Cleanup yml io.

  

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  18f5930

• Fix project mypy issues.

  

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  6b560ee

• Fix mypy errors in optimization.

  

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  b2881fd

• Fix mypy issues for model.

  

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  c648185

• Final mypy fixes.

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  cf66ce6

• Precommit fixes.

  

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  c58222d

• Add allow_overwrite to Result.save.

  

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  6b1b751

Commits on Oct 15, 2023

• Fix bug with nested extensions.

  

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  1aa3d6a

Commits on Oct 17, 2023

• Fix clp constraints (#1366)

  Show description for a2211d6
  

  jsnel

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  a2211d6

• Autoconvert to pydantic 2.

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  9f62fbe

• Replace missing clasing with any.

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  142c23b

• Adapted typing for pydantic 2.

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  211988d

• Check if Factory is needed

  Show description for d671497
  jsnel

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  d671497

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

  Show description for 1d86119
  pre-commit-ci[bot]

  committed
  1d86119

Commits on Oct 20, 2023

• 🩹 Fix assignment of literal type to type attribute

  s-weigand

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  cf167a7

• 🩹 Use RootModel instead of BaseModel and __root__

  Show description for 99e74be
  s-weigand

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  99e74be

• 🩹 Replace deprecated parse_obj with model_validate

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  4cf056d

• 🩹 Fix accessing of element data_model_type

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  5b52160

• 🩹 Undefined -> PydanticUndefined

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  c2465ca

• 🩹 Adjust to removal of ModelField

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  143a9bf

• 🧪🩹 Adapt to schema changes

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  2d96f5d

• 🧪🩹 Fix pydantic validation error in test

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  53220c0

• 🧪🩹 Fix definition MockElementWithDataModel.data_model_type

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  be3f0c3

• 🧹 Replace .dict with .model_dump

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• 🧹 Replace .copy with .model_copy

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  ac85e89

• 'Refactored by Sourcery'

  

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