[MAINT]: Release 0.0.7 #490
44 changed files with 119 additions and 43 deletions
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``fname``, ``overwrite`` and ``output_format`` have been removed from :func:`.configure_logging` by `Synchon Mandal`_
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Adopt ``structlog`` for logging infrastructure by `Synchon Mandal`_
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@ -1 +0,0 @@
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``ParcellationRegistry.get`` now returns labels as dictionary mapping from values to labels instead of a list of labels by `Synchon Mandal`_
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@ -1 +0,0 @@
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Allow parcellation registration with non-continuous ranges as values by `Synchon Mandal`_
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@ -1 +0,0 @@
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Add support for Chatterjee's xi correlation in :class:`.JuniferConnectivityMeasure` by `Synchon Mandal`_
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:func:`.read_transform` has a new parameter ``nan_policy`` to handle NaN values when transforming feature data by `Fede Raimondo`_
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@ -1 +0,0 @@
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Implement a NaN policy for :func:`.read_transform` by `Fede Raimondo`_
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@ -1 +0,0 @@
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Introduce :class:`.TemporalFilter` preprocessor for temporally filtering BOLD data by `Fede Raimondo`_
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Regular repository maintenance by updating ``.pre-commit-config.yaml``, replacing ``black`` with ``ruff-format`` and updating tool configs by `Synchon Mandal`_
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Introduce :class:`.TemporalSlicer` preprocessor for temporally slicing BOLD data by `Synchon Mandal`_
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@ -1 +0,0 @@
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Allow ``timeseries_2d`` storage for :class:`.HDF5FeatureStorage` by `Fede Raimondo`_
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@ -1 +0,0 @@
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Add documentation on extending data registries by `Synchon Mandal`_
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Enable data registries to be extended by exposing :class:`.BasePipelineDataRegistry` and introducing :func:`.register_data_registry` decorator by `Synchon Mandal`_
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@ -1 +0,0 @@
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Add documentation on adding data types by `Synchon Mandal`_
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Enable data types to be added by introducing :func:`.register_data_type` by `Synchon Mandal`_
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@ -1 +0,0 @@
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Add documentation on :class:`.ConfigManager`, dumping data object and extending data dump assets by `Synchon Mandal`_
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Allow pipeline data object to be dumped by introducing :class:`.DataObjectDumper` and available dumping / loading assets to be extended by introducing :func:`.register_data_dump_asset` decorator by `Synchon Mandal`_
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@ -1 +0,0 @@
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Fix FSL presence checking status code by `Fede Raimondo`_
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Bump ``junifer-data`` to ``v3`` for Docker images by `Synchon Mandal`_
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Bump ``junifer-data`` to ``v3`` by `Synchon Mandal`_
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:func:`.get_data`, :func:`.load_data`, :func:`.list_data`, :func:`.register_data` and :func:`.deregister_data` now support ``"maps"`` as a valid argument for ``kind`` by `Synchon Mandal`_
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Introduce :class:`.MapsRegistry` to centralise probabilistic atlas (maps) data management by `Synchon Mandal`_
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Constrain ``templateflow`` version to ``>=23.0.0,<25.0.0`` by `Synchon Mandal`_
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Introduce :class:`.MapsAggregation`, :class:`.FunctionalConnectivityMaps`, :class:`.EdgeCentricFCMaps`, :class:`.ReHoMaps`, :class:`.ALFFMaps` and :class:`.TemporalSNRMaps` by `Synchon Mandal`_
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Enable :class:`.SpaceWarper` to warp data from native space to template spaces via both FSL and ANTs by `Synchon Mandal`_
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@ -1 +0,0 @@
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Add a new GitHub Action to mark stale issues by `Synchon Mandal`_
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Bump ``junifer-data`` to ``v4`` for Docker images by `Synchon Mandal`_
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Bump ``junifer-data`` to ``v4`` by `Synchon Mandal`_
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Disable FSL installation for ``junifer-ci`` Docker image build with ``junifer-data`` v4 by `Synchon Mandal`_
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Pin ``junifer-ci`` Docker image to ``python:3.12-slim-bookworm`` and re-enable FSL installation by `Synchon Mandal`_
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Add FreeSurfer 7.4.1 aseg parcellation to :class:`.ParcellationRegistry` by `Synchon Mandal`_
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Bump ``junifer-data`` to ``v5`` by `Synchon Mandal`_
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Simplify ``Storage`` interface and implementations by `Synchon Mandal`_
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Simplify ``Preprocess`` interface and implementations by `Synchon Mandal`_
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Simplify :class:`.PipelineStepMixin` interface by `Synchon Mandal`_
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@ -1 +0,0 @@
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Improve ``Marker`` interface and implementations by `Synchon Mandal`_
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Bypass warper check for callable masks on native data by `Synchon Mandal`_
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Bump ``junifer-data`` to ``v6`` for Docker images by `Synchon Mandal`_
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Bump ``junifer-data`` to ``v7`` for Docker images by `Synchon Mandal`_
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@ -1 +0,0 @@
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Add Glasser and Julich-Brain parcellations to :class:`.ParcellationRegistry` by `Synchon Mandal`_
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@ -1 +0,0 @@
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Bump ``junifer-data`` to ``v7`` by `Synchon Mandal`_
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@ -1 +0,0 @@
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Fix mask specification check involving dicts in `:class:`junifer.data.MaskRegistry` when working in native space by `Synchon Mandal`_
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Add Dockerfile and a corresponding action for building and publishing the image by `Fede Raimondo`_ and `Synchon Mandal`_
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@ -10,6 +10,125 @@ What's new
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.. towncrier release notes start
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Junifer 0.0.7 (2026-03-04)
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--------------------------
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Bugfixes
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^^^^^^^^
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- Allow ``timeseries_2d`` storage for :class:`.HDF5FeatureStorage` by `Fede
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Raimondo`_ (:gh:`444`)
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- Fix FSL presence checking status code by `Fede Raimondo`_ (:gh:`454`)
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- Bypass warper check for callable masks on native data by `Synchon Mandal`_
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(:gh:`481`)
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- Fix mask specification check involving dicts in
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:class:`junifer.data.MaskRegistry` when working in native space by `Synchon
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Mandal`_ (:gh:`487`)
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API Changes
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^^^^^^^^^^^
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- ``fname``, ``overwrite`` and ``output_format`` have been removed from
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:func:`.configure_logging` by `Synchon Mandal`_ (:gh:`231`)
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- ``ParcellationRegistry.get`` now returns labels as dictionary mapping from
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values to labels instead of a list of labels by `Synchon Mandal`_ (:gh:`257`)
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- :func:`.read_transform` has a new parameter ``nan_policy`` to handle NaN
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values when transforming feature data by `Fede Raimondo`_ (:gh:`429`)
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- :func:`.get_data`, :func:`.load_data`, :func:`.list_data`,
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:func:`.register_data` and :func:`.deregister_data` now support ``"maps"`` as
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a valid argument for ``kind`` by `Synchon Mandal`_ (:gh:`458`)
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Improved Documentation
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^^^^^^^^^^^^^^^^^^^^^^
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- Add documentation on extending data registries by `Synchon Mandal`_
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(:gh:`450`)
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- Add documentation on adding data types by `Synchon Mandal`_ (:gh:`451`)
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- Add documentation on :class:`.ConfigManager`, dumping data object and
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extending data dump assets by `Synchon Mandal`_ (:gh:`452`)
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Enhancements
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^^^^^^^^^^^^
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- Allow parcellation registration with non-continuous ranges as values by
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`Synchon Mandal`_ (:gh:`257`)
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- Add support for Chatterjee's xi correlation in
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:class:`.JuniferConnectivityMeasure` by `Synchon Mandal`_ (:gh:`333`)
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- Implement a NaN policy for :func:`.read_transform` by `Fede Raimondo`_
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(:gh:`429`)
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- Add FreeSurfer 7.4.1 aseg parcellation to :class:`.ParcellationRegistry` by
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`Synchon Mandal`_ (:gh:`470`)
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- Simplify ``Storage`` interface and implementations by `Synchon Mandal`_
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(:gh:`472`)
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- Simplify ``Preprocess`` interface and implementations by `Synchon Mandal`_
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(:gh:`473`)
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- Simplify :class:`.PipelineStepMixin` interface by `Synchon Mandal`_
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(:gh:`476`)
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- Improve ``Marker`` interface and implementations by `Synchon Mandal`_
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(:gh:`477`)
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- Add Glasser and Julich-Brain parcellations to :class:`.ParcellationRegistry`
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by `Synchon Mandal`_ (:gh:`486`)
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Features
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^^^^^^^^
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- Introduce :class:`.TemporalFilter` preprocessor for temporally filtering BOLD
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data by `Fede Raimondo`_ (:gh:`432`)
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- Introduce :class:`.TemporalSlicer` preprocessor for temporally slicing BOLD
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data by `Synchon Mandal`_ (:gh:`443`)
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- Enable data registries to be extended by exposing
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:class:`.BasePipelineDataRegistry` and introducing
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:func:`.register_data_registry` decorator by `Synchon Mandal`_ (:gh:`450`)
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- Enable data types to be added by introducing :func:`.register_data_type` by
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`Synchon Mandal`_ (:gh:`451`)
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- Allow pipeline data object to be dumped by introducing
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:class:`.DataObjectDumper` and available dumping / loading assets to be
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extended by introducing :func:`.register_data_dump_asset` decorator by
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`Synchon Mandal`_ (:gh:`452`)
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- Introduce :class:`.MapsRegistry` to centralise probabilistic atlas (maps)
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data management by `Synchon Mandal`_ (:gh:`458`)
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- Introduce :class:`.MapsAggregation`, :class:`.FunctionalConnectivityMaps`,
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:class:`.EdgeCentricFCMaps`, :class:`.ReHoMaps`, :class:`.ALFFMaps` and
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:class:`.TemporalSNRMaps` by `Synchon Mandal`_ (:gh:`460`)
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- Enable :class:`.SpaceWarper` to warp data from native space to template
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spaces via both FSL and ANTs by `Synchon Mandal`_ (:gh:`462`)
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Miscellaneous
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^^^^^^^^^^^^^
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- Adopt ``structlog`` for logging infrastructure by `Synchon Mandal`_
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(:gh:`231`)
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- Regular repository maintenance by updating ``.pre-commit-config.yaml``,
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replacing ``black`` with ``ruff-format`` and updating tool configs by
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`Synchon Mandal`_ (:gh:`441`)
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- Bump ``junifer-data`` to ``v3`` for Docker images by `Synchon Mandal`_
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(:gh:`456`)
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- Bump ``junifer-data`` to ``v3`` by `Synchon Mandal`_ (:gh:`457`)
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- Constrain ``templateflow`` version to ``>=23.0.0,<25.0.0`` by `Synchon
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Mandal`_ (:gh:`458`)
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- Add a new GitHub Action to mark stale issues by `Synchon Mandal`_ (:gh:`464`)
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- Bump ``junifer-data`` to ``v4`` for Docker images by `Synchon Mandal`_
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(:gh:`465`)
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- Bump ``junifer-data`` to ``v4`` by `Synchon Mandal`_ (:gh:`466`)
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- Disable FSL installation for ``junifer-ci`` Docker image build with
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``junifer-data`` v4 by `Synchon Mandal`_ (:gh:`467`)
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- Pin ``junifer-ci`` Docker image to ``python:3.12-slim-bookworm`` and
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re-enable FSL installation by `Synchon Mandal`_ (:gh:`468`)
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- Bump ``junifer-data`` to ``v5`` by `Synchon Mandal`_ (:gh:`470`)
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- Bump ``junifer-data`` to ``v6`` for Docker images by `Synchon Mandal`_
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(:gh:`483`)
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- Bump ``junifer-data`` to ``v7`` for Docker images by `Synchon Mandal`_
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(:gh:`485`)
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- Bump ``junifer-data`` to ``v7`` by `Synchon Mandal`_ (:gh:`486`)
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- Add Dockerfile and a corresponding action for building and publishing the
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image by `Fede Raimondo`_ and `Synchon Mandal`_ (:gh:`489`)
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Junifer 0.0.6 (2025-03-24)
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--------------------------
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