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juaml / junifer Public

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[ENH]: Adopt Pydantic for schema validation#364

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synchon wants to merge 130 commits intomainjuaml/junifer:mainfrom

feat/pydantic-validationjuaml/junifer:feat/pydantic-validationCopy head branch name to clipboard

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[ENH]: Adopt Pydantic for schema validation#364
synchon wants to merge 130 commits intomainfrom
feat/pydantic-validation

Commits

Commits on Mar 12, 2026

update: add pydantic to deps
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update: introduce DataType enum
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update: introduce StorageType enum
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update: adapt DataType and StorageType for markers
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update: introduce ExtDep enum
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update: adapt ExtDep for preprocessors
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update: adapt ExtDep for markers
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update: improve typing annotation for MarkerInOutMappings
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update: adapt DataType and StorageType for remaining markers
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update: introduce ConfoundsFormat enum
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update: introduce MatrixKind enum
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update: adapt MatrixKind
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update: introduce Upsert enum
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update: adapt Upsert enum
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chore: reorder storage imports
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update: adapt necessary enums in storage
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refactor: make storage interface and impls pydantic models
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chore: improve docstrings in storage
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update: introduce Confounds and Strategy types
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update: introduce and adapt SmoothingImpl enum
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update: introduce and adapt SpaceWarpingImpl enum
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update: adapt necessary enums in preprocess
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refactor: make preprocess interface and impls pydantic models
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chore: improve docstring for BasePreprocessor
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chore: add package guard for fMRIPrepConfoundRemover
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update: introduce and adapt ReHoImpl
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update: introduce and adapt ALFFImpl
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update: adapt ExtDep for remaining markers
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update: adapt necessary enums in markers
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refactor: make marker interface and impls pydantic models
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refactor: make datareader pydantic model
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chore: improve types
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refactor: make pipeline.utils.check_ext_dependencies validate via pydantic
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update: improve conditional deps declaration for markers
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update: introduce AOMICSpace and AOMICTask
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update: introduce HCP1200Task and HCP1200PhaseEncoding
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update: introduce DMCCSession, DMCCTask, DMCCPhaseEncoding and DMCCRun
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refactor: make datagrabber interface and impls pydantic models
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refactor: rename PipelineStepMixin validate to validate_component to avoid pydantic conflict
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chore: remove BaseFeatureStorage.get_valid_inputs
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update: rename BaseFeatureStroage.validate to validate_input to make intent clear
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chore: improve docstrings
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update: reorder marker params validation in BaseMarker
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fix: make on param for *Aggregation markers None by default
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update: make onthefly lazy during import
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update: fix tests for preprocess
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update: fix tests for markers
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update: fix tests for onthefly
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update: fix tests for storage
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chore: update tests for PipelineStepMixin
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update: add aenum as dependency and use it for DataType
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update: improve type handling for BaseDataGrabber.get_types
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update: fix tests for datagrabber
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update: allow DataType enum to be extended
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chore: improve docstrings for PatternValidationMixin
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chore: fix test for TemporalSNRBase
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chore: reorder import for pipeline
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chore: lint
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update: adapt maps_datagrabber fixture
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update: remove redundant tests in PatternValidationMixin
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chore: improve tests for PatternValidationMixin
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update: improve data type registration test
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chore: improve type annotation and docstring for PatternValidationMixin and test
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chore: adapt juseless datagrabbers
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chore: adapt validate_input for BaseFeatureStorage test
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chore: adapt validate_component for DefaultDataReader test
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update: adapt testing datagrabbers
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chore: update tests for testing datagrabbers
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update: improve tests for SQLiteFeatureStorage
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update: move MatrixKind and fix tests for storage.utils
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chore: update types for juseless datagrabbers
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chore: update type for HDF5FeatureStorage.store_matrix
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update: use pydantic model dump for UpdateMetaMixin
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fix: remove datadir from datagrabber meta when hashing for storage
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update: add new enums for queue_context
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update: make GnuParallelLocalAdapter pydantic model
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update: make HTCondorAdapter pydantic model
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chore: update docstring for QueueContextAdapter
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chore: make configs import lazy
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chore: make external import lazy
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chore: add py.typed to typing
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chore: lean up tests in configs
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chore: fix method in DataDispatcher
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chore: improve docstrings
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update: add pydantic.validate_call to get_aggfunc_by_name
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docs: update docs and add deps
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chore: add missing imports
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chore: add typing_extensions to deps
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docs: update extending docs
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chore: fix tests for pipeline
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chore: fix tests and data for cli
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chore: fix tests for api
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update: improve constraints for QueueContextEnv
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update: add guard for env.name in context adapters
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docs: update examples
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docs: update extending and using docs
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chore: add changelog 364.enh
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fix: conditional import for Required in queue_context_adapter.py
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fix: conditional import for TypedDict
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chore: reorganize MatrixKind
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update: improve cleanup for WorkDirManager
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update: improve cleanup for AFNIALFF and AFNIReHo
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refactor: allow direct usage of MultipleDataGrabber from yaml
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chore: remove unnecessary comments
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chore: add missing decorator for DataladDataGrabber
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chore: improve docstring for BrainPrint
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chore: improve logging for DataladDataGrabber
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refactor: make parcellation accept str or list of str across codebase
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docs: clarify preprocessor extension parameters
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refactor: make datagrabber list params as item or list of them
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refactor: make markers accept `on` as DataType or list of DataType
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refactor: make preprocess accept `on` and `required_data_types` as DataType or list of DataType
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update: improve DataType conversion in BaseMarker
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update: improve DataType conversion in BasePreprocessor
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chore: remove redundant `on` declaration across markers
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fix: correct import for ALFFParcels
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docs: simplify preprocessor extension
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update: replace HttpUrl with AnyUrl across codebase
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docs: simplify datagrabber extension
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docs: simplify example
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update: make datalad tempdir creation less prone to user defined dir conflict
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refactor: make `masks` param accept item or list of item
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docs: update nitpick ignore in conf.py
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update: improve test params for test_masks.py
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chore: fix log message formatting in DataladDataGrabber
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fix: remove datadir from meta only for datalad-based datagrabbers
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chore: clarify datagrabber parameters
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chore: update docstring for DataladDataGrabber
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chore: update uv.lock
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chore: lint
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