Code

Migrate models to pydantic 2#17262

Code

Merged

mvdbeek merged 182 commits intogalaxyproject:devgalaxyproject/galaxy:devfrom mvdbeek:pydantic_v2_2024mvdbeek/galaxy:pydantic_v2_2024Copy head branch name to clipboardJan 11, 2024

+4,854-5,471

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Commits on Jan 8, 2024

• Temp

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  aae0376

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• Port OffsetNaiveDatetime to pydantic2

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  5673cbc

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• Fix up remaining pydantic issues

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  181c5e1

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• Remove DecodedDatabaseIdField instance check

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• Replace DecodedDatabaseIdField.encode with Security.security.encode_id

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• Fix example -> examples

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  0fc981c

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• Fix valid_id validator

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• Fix validation error transform

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• Drop explicit json encoder

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• Fix ValidationError import

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  0c3c760

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• Adapt as_form decorator

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• Drop more Required

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• Fix one more ValidationError import

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  87a7b77

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• Also override validation schema

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• Revert me: drop custom schema generation

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• Use model_construct and model_dump

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• Field fixes

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• Validation error fix

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  7f38e1c

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• Fix use of HistoryIDPathParam

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• Re-use more path params

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• Update user api path param

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• Fix double encoding of user ids

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• Rename id to workflow_id parameter

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• Fix one more case of __root__ in pydantic RootModel

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• Optional attributes are still required

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  3fcc810

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• Don't double-encode user id

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• Fix collection type optionality in collection payload

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• Create new type from annotated types

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• Use model_rebuild instead of update_forward_refs

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  970bbf4

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• Fix fetch_data schema unit tests

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  ed1c30a

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• Drop custom required handling

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• TEMP: schema dumpt fix

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  23ff26b

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• Remove more __root__ and construct calls

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  8a3d805

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• Make more fields optional and not required

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• Add (fallback?) serializer for DecodedDatabaseIdField

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• More root and model fixes

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• Fix DataResult optionality

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• Fix DatasetStorageDetails construction

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• Regenerate DRS schema

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• Drop library folder id encoding

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• Fix share with status responses for history sharing

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• Fix folder id encoding and decoding

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• Make sure ValidationErrors are serialized cleanly

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  b80fbbd

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• Fix id encoding via type

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• Drop more deprecated .dict() and .construct() calls

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  79f1c29

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• Fix WithJsonSchema import

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  87a1d5f

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• Fix library permission model

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• Fix LibraryFolderMetadata model

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• Fix PageSummary model

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• .dict() -> .model_dump()

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• Improve validation error

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• Really test missing name in role payload test

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• Fix page response models

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• Fix tour models

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• Fix refactoring models

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• Allow passing non-string value as paste_content and element name

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• Use alias instead of getter_dict

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• .from_orm() -> .model_validate()

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• Fix wrong model_dump_json argument

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  a2e3c6b

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• Fix invocation export response models

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  04bce0a

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• Update fastapi and pydantic dependencies

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  e63c3ba

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• Fix id field unit tests

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• Fix ToolDataEntryList

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• Make OptionalExclusionList not required

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  f8d4dc3

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• Fix LibraryPermissionsPayload parsing

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• Bump pydantic typecheck dependency

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• Use upstream openapi for now

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• Update fastapi-utils requirement to use git

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  7ff74bf

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• Fix refactoring action models

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  cc8ea86

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• Fix double id encoding in quota endpoints

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• Temp fix for notifications

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  a13ef3e

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• Fix double encoding of repository ids

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  0fb6851

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• Fix JobIdResponse model construction

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• Make username and email optional in LimitedUserModel

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• Fix ValidationError exception casting

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  c1a44c7

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• WIP: examples

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  31a6529

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• Fix pydantic v1 usage remote_files.py

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• Remove Required added in new code

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• Undo dependency changes

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• More RootModel refactoring

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• Drop NotificationGetter

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• CBV fix for pydantic 2

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• Drop TypeAliasType

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• Drop deprecated const keyword

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• Use concrete IDs instead of EntityIdField where it makes sense

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• Use UserIdPathParam

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• Use model_dump

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• Fix import

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  c46293a

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• Fix UserID usage

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  1b2b9dd

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• Use EncodedDatabaseId for responses, don't by pass validation

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• More type fixes

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  ee3c349

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• Fix parent_id decoding

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• More type fixes

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• example -> examples

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• Fix group id encoding

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• More example -> examples

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• Use Annotated

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• Fix encoding of copied_from_ldda_id

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• Fix group and role id handling

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• Fix library and folder id handling

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• Fix tag id handling

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• Fix workflow id handling

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  544e51a

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• Encode ids in models

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  7be79d0

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• Fix minor things

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  d1efd29

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• Various workflow fixes

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  b6fa550

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• Fix job index response

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• Fix VisualizationIdPathParam double validation

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• Fix remaining API tests

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• Undo dependency changes

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• Update dependencies

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• Drop gravity temporarily

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• Drop unused import

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• Fix security type

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• Drop unnecessary TypeAliasType

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• Fix JobSummary import

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• Fix root model iteration

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• More example->examples:

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• Fix strip tzinfo typing

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• Fix more types

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• Fix optionality

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• Use FastAPI ValidationException

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• Fix import

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• Fix share_with_status_cls type annotation

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• Delete openapi.utils copy

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• Fix _hack_fastapi_4428 type annotation

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• Revert "Use FastAPI ValidationException"

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• Fix optionality

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• Use validator to set default model_class

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• Fix removed deprecated Field argument

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• Fix model_class default

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• Drop ModelClassField from where it isn't needed

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• Fix encoded id unit test

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• Drop outdated todo

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• Use model_construct for MaterializeDatasetInstanceTaskRequest

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• Properly serialize workfow import response

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• Fix show_invocation_report_pdf arguments

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• Update pydantic package dependencies

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• Fix exception handler middleware

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• Use model_dump(mode="json") when values are going to be encoded

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• Fix validation exception types

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• Add pycryptodome dependency to galaxy-schema

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• Update dependencies

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• Update pydantic in type-check dependencies

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• Unhide force field

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• Fix Validation type catching

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• Use pydantic v1/v2 compat branch

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• Fix minimal history view

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• Drop more deprecated things

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• Eliminate namespace warning for model_class

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• example -> examples

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• Fix double id encoding in summarize_job_parameters

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• Use unambiguous workflow steps api route

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• Guarantee that JobsService.get_job returns job

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• Fix double decoding of repository id

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• Use ConfigDict

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• Use field_validator

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• Use released gravity dependency

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• Fix dataset hash construction

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• WIP improve schema generation

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• Encode TS repo user_id

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• Customize generics schema

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• Adjust client types for more precise schema

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• Fix test_install_info test

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• Customize generics schema

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• Rebuild schema

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• Fix dataset_id type

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Commits on Jan 9, 2024

• Update redocly ignore list

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• Fix model refs

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Commits on Jan 10, 2024

• Add explicit public keyword

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• Mark public methods that don't use trans as public in schema

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• Fix type hints for get_dbkeys

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• Don't expose unimplemented method

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• Require session or API key for forum searches

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• Update client schema

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• Update _shed_schema.yaml ignore list

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• Fix wether typo

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• Fix accidental pydot downgrade

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• Delete TRS openapi document that was included by mistake

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• Import IdEncodingHelper for type-checking only

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• Fix merge conflicts in packages/web_apps/setup.cfg

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• Drop unused code from dump_openapi_schema.py

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• Construct RepositoryMetadata inline

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