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juaml / junifer Public

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[ENH]: Consistency of logging#239

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synchon wants to merge 111 commits intomainjuaml/junifer:mainfrom

update/logging-consistencyjuaml/junifer:update/logging-consistencyCopy head branch name to clipboard

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[ENH]: Consistency of logging#239
synchon wants to merge 111 commits intomainfrom
update/logging-consistency

Commits

Commits on Nov 17, 2025

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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Commits on Nov 18, 2025

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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Commits on Nov 21, 2025

update: improve logging for datagrabber params
synchon
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update: improve logging for datareader params
synchon
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update: improve logging for marker params
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update: improve logging for preprocess params
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update: improve logging for storage params
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update: improve logging for stats
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update: improve logging for api
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update: improve logging for cli
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update: improve logging for data
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update: improve logging for pipeline
synchon
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update: improve logging for onthefly
synchon
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update: improve logging for utils
synchon
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