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junifer/docs/whats_new.rst
Synchon Mandal b92c8197f3 docs: update docs and add deps
2026-03-31 11:37:03 +02:00

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.. include:: links.inc
.. include:: changes/contributors.inc
.. _whats_new:
What's new
==========
.. towncrier-draft-entries:: |release|
.. towncrier release notes start
Junifer 0.0.7 (2026-03-04)
--------------------------
Bugfixes
^^^^^^^^
- Allow ``timeseries_2d`` storage for :class:`.HDF5FeatureStorage` by `Fede
Raimondo`_ (:gh:`444`)
- Fix FSL presence checking status code by `Fede Raimondo`_ (:gh:`454`)
- Bypass warper check for callable masks on native data by `Synchon Mandal`_
(:gh:`481`)
- Fix mask specification check involving dicts in
:class:`junifer.data.MaskRegistry` when working in native space by `Synchon
Mandal`_ (:gh:`487`)
API Changes
^^^^^^^^^^^
- ``fname``, ``overwrite`` and ``output_format`` have been removed from
:func:`.configure_logging` by `Synchon Mandal`_ (:gh:`231`)
- ``ParcellationRegistry.get`` now returns labels as dictionary mapping from
values to labels instead of a list of labels by `Synchon Mandal`_ (:gh:`257`)
- :func:`.read_transform` has a new parameter ``nan_policy`` to handle NaN
values when transforming feature data by `Fede Raimondo`_ (:gh:`429`)
- :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`_ (:gh:`458`)
Improved Documentation
^^^^^^^^^^^^^^^^^^^^^^
- Add documentation on extending data registries by `Synchon Mandal`_
(:gh:`450`)
- Add documentation on adding data types by `Synchon Mandal`_ (:gh:`451`)
- Add documentation on :class:`.ConfigManager`, dumping data object and
extending data dump assets by `Synchon Mandal`_ (:gh:`452`)
Enhancements
^^^^^^^^^^^^
- Allow parcellation registration with non-continuous ranges as values by
`Synchon Mandal`_ (:gh:`257`)
- Add support for Chatterjee's xi correlation in
:class:`.JuniferConnectivityMeasure` by `Synchon Mandal`_ (:gh:`333`)
- Implement a NaN policy for :func:`.read_transform` by `Fede Raimondo`_
(:gh:`429`)
- Add FreeSurfer 7.4.1 aseg parcellation to :class:`.ParcellationRegistry` by
`Synchon Mandal`_ (:gh:`470`)
- Simplify ``Storage`` interface and implementations by `Synchon Mandal`_
(:gh:`472`)
- Simplify ``Preprocess`` interface and implementations by `Synchon Mandal`_
(:gh:`473`)
- Simplify :class:`.PipelineStepMixin` interface by `Synchon Mandal`_
(:gh:`476`)
- Improve ``Marker`` interface and implementations by `Synchon Mandal`_
(:gh:`477`)
- Add Glasser and Julich-Brain parcellations to :class:`.ParcellationRegistry`
by `Synchon Mandal`_ (:gh:`486`)
Features
^^^^^^^^
- Introduce :class:`.TemporalFilter` preprocessor for temporally filtering BOLD
data by `Fede Raimondo`_ (:gh:`432`)
- Introduce :class:`.TemporalSlicer` preprocessor for temporally slicing BOLD
data by `Synchon Mandal`_ (:gh:`443`)
- Enable data registries to be extended by exposing
:class:`.BasePipelineDataRegistry` and introducing
:func:`.register_data_registry` decorator by `Synchon Mandal`_ (:gh:`450`)
- Enable data types to be added by introducing :func:`.register_data_type` by
`Synchon Mandal`_ (:gh:`451`)
- 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`_ (:gh:`452`)
- Introduce :class:`.MapsRegistry` to centralise probabilistic atlas (maps)
data management by `Synchon Mandal`_ (:gh:`458`)
- Introduce :class:`.MapsAggregation`, :class:`.FunctionalConnectivityMaps`,
:class:`.EdgeCentricFCMaps`, :class:`.ReHoMaps`, :class:`.ALFFMaps` and
:class:`.TemporalSNRMaps` by `Synchon Mandal`_ (:gh:`460`)
- Enable :class:`.SpaceWarper` to warp data from native space to template
spaces via both FSL and ANTs by `Synchon Mandal`_ (:gh:`462`)
Miscellaneous
^^^^^^^^^^^^^
- Adopt ``structlog`` for logging infrastructure by `Synchon Mandal`_
(:gh:`231`)
- Regular repository maintenance by updating ``.pre-commit-config.yaml``,
replacing ``black`` with ``ruff-format`` and updating tool configs by
`Synchon Mandal`_ (:gh:`441`)
- Bump ``junifer-data`` to ``v3`` for Docker images by `Synchon Mandal`_
(:gh:`456`)
- Bump ``junifer-data`` to ``v3`` by `Synchon Mandal`_ (:gh:`457`)
- Constrain ``templateflow`` version to ``>=23.0.0,<25.0.0`` by `Synchon
Mandal`_ (:gh:`458`)
- Add a new GitHub Action to mark stale issues by `Synchon Mandal`_ (:gh:`464`)
- Bump ``junifer-data`` to ``v4`` for Docker images by `Synchon Mandal`_
(:gh:`465`)
- Bump ``junifer-data`` to ``v4`` by `Synchon Mandal`_ (:gh:`466`)
- Disable FSL installation for ``junifer-ci`` Docker image build with
``junifer-data`` v4 by `Synchon Mandal`_ (:gh:`467`)
- Pin ``junifer-ci`` Docker image to ``python:3.12-slim-bookworm`` and
re-enable FSL installation by `Synchon Mandal`_ (:gh:`468`)
- Bump ``junifer-data`` to ``v5`` by `Synchon Mandal`_ (:gh:`470`)
- Bump ``junifer-data`` to ``v6`` for Docker images by `Synchon Mandal`_
(:gh:`483`)
- Bump ``junifer-data`` to ``v7`` for Docker images by `Synchon Mandal`_
(:gh:`485`)
- Bump ``junifer-data`` to ``v7`` by `Synchon Mandal`_ (:gh:`486`)
- Add Dockerfile and a corresponding action for building and publishing the
image by `Fede Raimondo`_ and `Synchon Mandal`_ (:gh:`489`)
Junifer 0.0.6 (2025-03-24)
--------------------------
Bugfixes
^^^^^^^^
- Fix ``mri_binarize`` command preparation for structures with multiple indices
in :class:`.BrainPrint` by `Fede Raimondo`_ (:gh:`356`)
- Enable ``spike`` mapping from ``adhoc`` to ``fmriprep`` for
:class:`.fMRIPrepConfoundRemover` by `Leonard Sasse`_ and `Synchon Mandal`_
(:gh:`360`)
- Correct listing for :class:`.fMRIPrepConfoundRemover` in
``junifer.pipeline.registry`` by `Synchon Mandal`_ (:gh:`369`)
- Add ``'emomatching'`` task to :class:`.DataladAOMICPIOP2` by `Leonard Sasse`_
(:gh:`370`)
- Use correct return code for ANTs commands while checking presence of external
commands by `Synchon Mandal`_ (:gh:`385`)
- Use the :class:`junifer.pipeline.WorkDirManager` for temporary directories in
the :class:`.DataladDataGrabber` by `Fede Raimondo`_ (:gh:`386`)
- Fix coordinates space transformation using ANTs by `Synchon Mandal`_
(:gh:`388`)
- Fix metadata update for :class:`.MultipleDataGrabber` and adjust
:meth:`.PatternDataGrabber.get_elements` to check ``list``-like data type
values by `Fede Raimondo`_ and `Synchon Mandal`_ (:gh:`398`)
- Use correct file output suffices for AFNI-based markers by `Synchon Mandal`_
(:gh:`409`)
- Fix ``t_r`` tampering by :func:`nilearn.image.clean_img` in
:class:`.fMRIPrepConfoundRemover` by `Fede Raimondo`_ and `Synchon Mandal`_
(:gh:`420`)
- Fix coordinates fetching for Power and Dosenbach from ``junifer-data`` by
`Synchon Mandal`_ (:gh:`431`)
- Remove ``Power2013`` from :class:`.CoordinatesRegistry` by `Synchon Mandal`_
(:gh:`436`)
- Correct dispatch methods for ``*_data()`` functions by `Synchon Mandal`_
(:gh:`439`)
API Changes
^^^^^^^^^^^
- ``get_parcellation``, ``load_parcellation``, ``list_parcellation``,
``register_parcellation`` , ``get_coordinates``, ``load_coordinates``,
``list_coordinates``, ``register_coordinates``, ``get_mask``, ``load_mask``,
``list_mask``, ``register_mask`` have been removed in favour of
:func:`.get_data`, :func:`.load_data`, :func:`.list_data`,
:func:`.register_data` and :func:`.deregister_data` by `Synchon Mandal`_
(:gh:`387`)
- :class:`.SpaceWarper`'s ``using`` now supports ``"auto"`` allowing auto tool
selection based on DataGrabber specification by `Synchon Mandal`_ (:gh:`390`)
- Allow ``workdir`` to also be a mapping in YAML, with ``path`` and ``cleanup``
keys by `Synchon Mandal`_ (:gh:`402`)
- Add ``source`` parameter and resurrect ``extra_input`` parameter for
``compute_brain_mask`` by `Fede Raimondo`_ (:gh:`404`)
- ``native_t1w`` parameter has been replaced with ``space`` to allow
:class:`.DataladAOMICID1000`, :class:`.DataladAOMICPIOP1` and
:class:`.DataladAOMICPIOP2` to fetch data in all available spaces by `Fede
Raimondo`_ (:gh:`405`)
- :meth:`.ParcellationRegistry.load` now has a new parameter ``target_space``
to provide parcellation in highest possible resolution if it does not match
the space of the parcellation by `Fede Raimondo`_ and `Synchon Mandal`_
(:gh:`411`)
- Introduce new CLI parameter ``--verbose-datalad`` to control ``datalad``'s
logging handler by `Fede Raimondo`_ (:gh:`412`)
- ``target_data`` parameter of :func:`.get_template` has been replaced with
``target_img`` by `Fede Raimondo`_ (:gh:`413`)
- Add ``template_space`` parameter for ``compute_brain_mask`` and
``resolution`` parameter for :func:`.get_template` by `Fede Raimondo`_
(:gh:`415`)
- Add ``scrub``, ``fd_threshold`` and ``std_vars_threshold`` parameters to
:class:`.fMRIPrepConfoundRemover` and allow ``"scrubbing"`` key of type bool
for ``strategy`` by `Synchon Mandal`_ (:gh:`421`)
Improved Documentation
^^^^^^^^^^^^^^^^^^^^^^
- Improve Sphinx configuration and extensions by `Synchon Mandal`_ (:gh:`358`)
- Add documentation on analysing extracted features by `Synchon Mandal`_
(:gh:`359`)
- Add documentation on how to make a ``junifer`` plugin by `Synchon Mandal`_
(:gh:`366`)
Enhancements
^^^^^^^^^^^^
- Raise error when partial or complete element selectors are invalid when
running the pipeline by `Synchon Mandal`_ (:gh:`319`)
- Add support for Spearman's correlation in
:class:`.JuniferConnectivityMeasure` by `Leonard Sasse`_ (:gh:`335`)
- Set proper stdout encoding for :func:`.run_ext_cmd` to ease human readability
by `Fede Raimondo`_ (:gh:`357`)
- Adapt usage of ``junifer-data`` client API to fetch parcellations, masks,
coordinates and xfms by `Synchon Mandal`_ (:gh:`363`)
- Allow for external python files in the ``with`` section of the yaml to import
other files by `Fede Raimondo`_ (:gh:`367`)
- Use ``datalad``-enabled repository for template space transform files in
:func:`.get_xfm` by `Synchon Mandal`_ (:gh:`368`)
- Add a ``cleanup`` parameter to the :class:`junifer.pipeline.WorkDirManager`,
which allows to disable cleaning up temporary directories by `Fede Raimondo`_
(:gh:`389`)
- Update ``Warp`` data type to be a list of dictionaries and adapt to allow
multiple transforms to be specified by `Synchon Mandal`_ (:gh:`390`)
- Refactor the masking logic in the pipeline to account for and optimise space
transformations and merges by `Synchon Mandal`_ and `Fede Raimondo`_
(:gh:`395`)
- Allow ``workdir`` mapping form in YAML for easy debugging of single element
``run`` by disabling cleanup of :class:`junifer.pipeline.WorkDirManager` by
`Synchon Mandal`_ (:gh:`402`)
- Use :func:`junifer.utils.ConfigManager` to skip time-consuming dataset ID and
dirty checks for :class:`.DataladDataGrabber` by `Fede Raimondo`_ (:gh:`403`)
- Enable ``compute_brain_mask`` to use subject-specific probseg files by `Fede
Raimondo`_ (:gh:`404`)
- Update :class:`.DataladAOMICID1000`, :class:`.DataladAOMICPIOP1` and
:class:`.DataladAOMICPIOP2` to fetch data in all available spaces by `Fede
Raimondo`_ (:gh:`405`)
- Update Preprocessors to sync data their paths so that the results are
idempotent by `Synchon Mandal`_ (:gh:`408`)
- Ease asset storage for AFNI-based markers by `Synchon Mandal`_ (:gh:`409`)
- Refactor the parcellation logic in the pipeline to account for and optimise
space transformations and merges by `Synchon Mandal`_ and `Fede Raimondo`_
(:gh:`411`)
- Adapt mask warpers to use correct interpolation method based on the type of
data by `Synchon Mandal`_ and `Fede Raimondo`_ (:gh:`416`)
- Adapt usage of ``junifer-data`` DataLad dataset to fetch parcellations,
masks, coordinates and xfms by `Synchon Mandal`_ (:gh:`418`)
- Add scrubbing support to :class:`.fMRIPrepConfoundRemover` by `Synchon
Mandal`_ (:gh:`421`)
- Add commit SHA check for ``junifer_data`` to simplify data fetching by `Fede
Raimondo`_ (:gh:`434`)
Features
^^^^^^^^
- Introduce :func:`.normalize` and :func:`.reweight` functions for downstream
BrainPrint analysis in :mod:`.onthefly._brainprint` by `Synchon Mandal`_
(:gh:`354`)
- Introduce :class:`junifer.pipeline.PipelineComponentRegistry` to centralise
pipeline component management by `Synchon Mandal`_ (:gh:`362`)
- Add support for plugins by `Synchon Mandal`_ (:gh:`366`)
- Introduce :class:`junifer.data.CoordinatesRegistry`,
:class:`junifer.data.ParcellationRegistry` and
:class:`junifer.data.MaskRegistry` to centralise data management by `Synchon
Mandal`_ (:gh:`387`)
- Introduce ``junifer.typing`` sub-module to organise internal and external
type hints by `Synchon Mandal`_ (:gh:`392`)
- Introduce :class:`junifer.utils.ConfigManager` singleton class to manage
global configuration by `Fede Raimondo`_ (:gh:`401`)
- Introduce ``BOLD.reference`` nested type and adapt :class:`.SpaceWarper` and
necessary data components by `Fede Raimondo`_ (:gh:`407`)
- Allow masks to be warped, if found, in :class:`.SpaceWarper` by `Synchon
Mandal`_ (:gh:`408`)
- Add support for coloured :class:`logging.Formatter` to use with ``junifer``'s
:class:`logging.StreamHandler` based on environment by `Fede Raimondo`_
(:gh:`412`)
- Allow storage of 2D timeseries, currently only supported by
HDF5FeatureStorage by `Fede Raimondo`_ (:gh:`422`)
Miscellaneous
^^^^^^^^^^^^^
- Adopt lazy-import mechanism for the package by `Synchon Mandal`_ (:gh:`355`)
- Refactor ``api`` sub-package and introduce new ``cli`` sub-package by
`Synchon Mandal`_ (:gh:`361`)
- Add ``junifer-data`` as a dependency by `Synchon Mandal`_ (:gh:`363`)
- Drop support for Python 3.8, add support for Python 3.13 and make Python 3.12
the base for code coverage by `Synchon Mandal`_ (:gh:`372`)
- Add Dockerfile for docs CI and a corresponding action for building and
publishing the image by `Synchon Mandal`_ (:gh:`373`)
- Adopt usage of custom docs CI image for building and previewing docs actions
by `Synchon Mandal`_ (:gh:`374`)
- Update Dependabot GitHub Action to support groups by `Synchon Mandal`_
(:gh:`380`)
- Add Dockerfile for CI and a corresponding action for building and publishing
the image by `Synchon Mandal`_ (:gh:`382`)
- Adopt usage of custom CI image for testing junifer action by `Synchon
Mandal`_ (:gh:`383`)
- Improve docs publishing action and add a manual trigger for it by `Synchon
Mandal`_ (:gh:`384`)
- Refactor ``Singleton`` class to use a metaclass instead of a class decorator
by `Fede Raimondo`_ (:gh:`391`)
- Update type hints across codebase to be Python>=3.9 compatible by `Synchon
Mandal`_ (:gh:`393`)
- Update Docker image recipes and GitHub Actions workflows by `Synchon Mandal`_
(:gh:`396`)
- Simplify logic for parcellation and mask space warping by `Synchon Mandal`_
(:gh:`414`)
- Remove ``httpx`` as a dependency by `Synchon Mandal`_ (:gh:`418`)
- Fix coverage in CI by `Fede Raimondo`_ (:gh:`424`)
- Use ``junifer-data`` in CI images by `Synchon Mandal`_ (:gh:`427`)
- Improve GitHub Actions workflows by `Synchon Mandal`_ (:gh:`428`)
- Bump ``junifer-data`` to ``v2`` for CI workflows, remove ``Power`` and add
``Seitzman2018`` to :class:`.CoordinatesRegistry` by `Synchon Mandal`_
(:gh:`437`)
- Bump ``junifer-data`` to ``v2`` for Docker images by `Synchon Mandal`_
(:gh:`438`)
Junifer 0.0.5 (2024-07-22)
--------------------------
Bugfixes
^^^^^^^^
- Remove extra dimension from parcellations warped via ANTs to other template
spaces by `Synchon Mandal`_ (:gh:`324`)
- Remove extra dimension from parcellations warped via ANTs when merging
parcellations by `Synchon Mandal`_ (:gh:`331`)
- Fix ``junifer reset`` to properly delete storage directory and handle
``junifer_jobs`` deletion if not empty by `Synchon Mandal`_ (:gh:`332`)
- Fix validation failure of multiple Preprocessors with different input data
types requirement by `Synchon Mandal`_ (:gh:`339`)
- Remove extra dimension from masks warped via ANTs by `Synchon Mandal`_
(:gh:`340`)
API Changes
^^^^^^^^^^^
- For :class:`.CrossParcellationFC`, ``aggregation_method`` and
``correlation_method`` have been renamed to ``agg_method`` and
``corr_method`` respectively and ``agg_method_params`` has been added; for
``FunctionalConnectivityBase``, :class:`.FunctionalConnectivityParcels`,
:class:`.FunctionalConnectivitySpheres`, :class:`.EdgeCentricFCParcels` and
:class:`.EdgeCentricFCSpheres`, ``cor_method`` and ``cor_method_params`` have
been renamed to ``conn_method`` and ``conn_method_params`` by `Synchon
Mandal`_ (:gh:`348`)
- ``fractional`` parameter for ``ALFFBase``, :class:`.ALFFParcels` and
:class:`.ALFFSpheres` have been removed in favour of returning both ALFF and
fALFF by `Synchon Mandal`_ (:gh:`349`)
- Add ``partial_pattern_ok`` argument to :class:`.PatternDataGrabber` to not
raise error on missing mandatory key checks for data types by `Synchon
Mandal`_ (:gh:`351`)
Improved Documentation
^^^^^^^^^^^^^^^^^^^^^^
- Improve sub-package level docstrings to better reflect their purposes by
`Synchon Mandal`_ (:gh:`115`)
- Update "Queueing Jobs (HPC, HTC)" section by `Synchon Mandal`_ (:gh:`327`)
- Add missing DataGrabber ``types`` options in respective docstrings of
:class:`.DataladAOMICID1000`, :class:`.DataladAOMICPIOP1`,
:class:`.DataladAOMICPIOP2` and :class:`.DMCC13Benchmark` by `Synchon
Mandal`_ (:gh:`330`)
Enhancements
^^^^^^^^^^^^
- Add test to be sure that :class:`.JuniferNiftiSpheresMasker` with mean
aggregation function behaves exactly as
:class:`nilearn.maskers.NiftiSpheresMasker` by `Synchon Mandal`_ (:gh:`136`)
- Refactor DataGrabber ``patterns`` to make helper types like ``*_mask`` as
"nested types" of the actual data type by `Synchon Mandal`_ (:gh:`341`)
- Adapt :class:`.DataladAOMICID1000`, :class:`.DataladAOMICPIOP1` and
:class:`.DataladAOMICPIOP2` to support ``FreeSurfer`` data type by `Synchon
Mandal`_ (:gh:`346`)
- ``FunctionalConnectivity``-family Markers now use
:class:`sklearn.covariance.EmpiricalCovariance` as the default covariance
estimator and ``correlation`` as the default connecivity matrix kind by
`Synchon Mandal`_ (:gh:`348`)
- Enable Markers to output multiple features by `Synchon Mandal`_ (:gh:`349`)
- Add support for ``UKB_15K_GM`` mask by `Synchon Mandal`_ (:gh:`350`)
- Adapt :class:`.MultipleDataGrabber` to handle "nested types" introduced in
:gh:`341` by `Synchon Mandal`_ (:gh:`351`)
Features
^^^^^^^^
- Introduce :class:`.Smoothing` for smoothing / blurring images as a
preprocessing step by `Synchon Mandal`_ (:gh:`161`)
- Add support for choosing between ``bash`` and ``zsh`` shells when queueing by
`Synchon Mandal`_ (:gh:`273`)
- Add ``junifer list-elements`` to list out available elements for a
DataGrabber based on filtering via ``--element`` by `Synchon Mandal`_
(:gh:`323`)
- Introduce new storage type ``scalar_table`` and adapt
:class:`.HDF5FeatureStorage` to support it by `Synchon Mandal`_ (:gh:`343`)
- Add support for `BrainPrint
<https://github.com/Deep-MI/BrainPrint?tab=readme-ov-file>`_ marker by
`Synchon Mandal`_ (:gh:`344`)
- Allow Unix path expansion directives to be used in
:class:`.PatternDataGrabber` ``patterns`` by `Synchon Mandal`_ (:gh:`345`)
- Add support for ``FreeSurfer`` data type for :class:`.PatternDataGrabber` by
`Synchon Mandal`_ (:gh:`346`)
- Introduce :class:`.JuniferConnectivityMeasure` for customising functional
connectivity matrix kinds and measurements by `Synchon Mandal`_ (:gh:`348`)
- Introduce :class:`.PatternValidationMixin` to simplify validation for
pattern-based DataGrabbers and :func:`.deep_update` for updating dictionary
with varying width and depth by `Synchon Mandal`_ (:gh:`351`)
Miscellaneous
^^^^^^^^^^^^^
- Improve CI to allow external tool installation to fail gracefully and update
necessary dependency version and conditional checks by `Synchon Mandal`_
(:gh:`318`)
- Update ``pre-commit`` dependency versions, add ``blacken-docs`` to
``pre-commit``, add ``__all__`` for modules, sub-packages and package, update
``ruff`` and ``pytest`` configs in ``pyproject.toml`` by `Synchon Mandal`_
(:gh:`337`)
- Add support for accessing FreeSurfer via Docker wrapper along with
``mri_binarize``, ``mri_pretess``, ``mri_mc`` and ``mris_convert`` by
`Synchon Mandal`_ (:gh:`342`)
- Update core and docs dependencies by `Synchon Mandal`_ (:gh:`347`)
- Integrate ``warnings`` with ``logging`` respecting filters by `Fede
Raimondo`_ (:gh:`351`)
Deprecations and Removals
^^^^^^^^^^^^^^^^^^^^^^^^^
- Remove ``Power`` coordinates, ``fetch_icbm152_brain_gm_mask`` mask,
``BOLDWarper`` Preprocessor by `Synchon Mandal`_ (:gh:`336`)
Junifer 0.0.4 (2024-04-05)
--------------------------
Bugfixes
^^^^^^^^
- Make copying of assets in ``with`` block of YAML, relative to YAML and not to
current working directory by `Fede Raimondo`_ and `Synchon Mandal`_
(:gh:`224`)
- Adapt ``junifer queue`` to properly use HTCondor >=10.4.0
``condor_submit_dag`` by `Fede Raimondo`_ and `Synchon Mandal`_ (:gh:`233`)
- Use 1 instead of 0 for successful FSL commands in ``_check_fsl()`` by
`Synchon Mandal`_ (:gh:`272`)
- Store native warped parcellations, coordinates and masks in element-scoped
tempdirs for the pipeline to work by `Synchon Mandal`_ (:gh:`274`)
- Change interpolation scheme for parcel and mask native space transformation
to nearest neighbour by `Synchon Mandal`_ (:gh:`276`)
- Bypass FSL ``std2imgcoord`` stdin bug and use recommended piped input for
coordinates transformation by `Synchon Mandal`_ (:gh:`278`)
- Add ``-std`` to FSL ``std2imgcoord`` for coordinates transformation by
`Synchon Mandal`_ (:gh:`280`)
- Replace FSL ``std2imgcoord`` with ``img2imgcoord`` as the former is incorrect
for coordinates transformation to other template spaces. (:gh:`281`)
- Propagate ReHo and fALFF maps, for aggregation to convert to other template
spaces when required by `Synchon Mandal`_ (:gh:`282`)
- Allow :class:`junifer.pipeline.WorkDirManager` to accept str via the
``workdir`` parameter by `Synchon Mandal`_ (:gh:`283`)
- Avoid warping mask preprocessed with :class:`.fMRIPrepConfoundRemover` and
used by markers with ``mask="inherit"`` in subject-native template space by
`Fede Raimondo`_ and `Synchon Mandal`_ (:gh:`284`)
- Pass down input path if input space is "native" for ``ReHoEstimator`` and
``ALFFEstimator``, else use respective compute maps by `Fede Raimondo`_ and
`Synchon Mandal`_ (:gh:`286`)
- Fix :class:`.HTCondorAdapter`'s script generation to use double quotes
instead of single quotes for HTCondor's ``VARS`` by `Synchon Mandal`_
(:gh:`312`)
- Fix element access for :class:`.DMCC13Benchmark` DataGrabber by `Synchon
Mandal`_ (:gh:`314`)
- Add a validation step on the :func:`.run` function to validate the marker
collection by `Fede Raimondo`_ (:gh:`320`)
- Add the executable flag to the ants docker scripts, fsl docker scripts and
other running scripts by `Fede Raimondo`_ (:gh:`321`)
- Force ``str`` dtype when parsing elements from file by `Synchon Mandal`_
(:gh:`322`)
API Changes
^^^^^^^^^^^
- Rename ``Power`` coordinates to ``Power2011`` by `Synchon Mandal`_
(:gh:`245`)
- Add ``feature_md5`` argument to :func:`.read_transform()` by `Synchon
Mandal`_ (:gh:`248`)
- Add ``native_t1w`` parameter to :class:`.DataladAOMICID1000`,
:class:`.DataladAOMICPIOP1`, :class:`.DataladAOMICPIOP2`, enabling fetching
of T1w data in subject-native space by `Synchon Mandal`_ (:gh:`252`)
- Modify ``preprocessor`` to ``preprocessors`` in :func:`.run` and
``preprocessing`` to ``preprocessors`` in :class:`.MarkerCollection` to
accept multiple preprocessors by `Synchon Mandal`_ (:gh:`263`)
- Add ``space`` parameter to ``register_coordinates``,
``register_parcellation`` and ``register_mask`` and return space
from ``load_coordinates``, ``load_parcellation`` and
``load_mask`` by `Synchon Mandal`_ and `Fede Raimondo`_ (:gh:`268`)
- Add ``template_type`` parameter to :func:`.get_template` by `Synchon Mandal`_
(:gh:`299`)
- Change :meth:`.BasePreprocessor.preprocess` return values to preprocessed
target data and "helper" data types as a dictionary by `Synchon Mandal`_
(:gh:`310`)
- Add a positional argument ``using`` for Markers and Preprocessors having
implementation-based variations, in particular :class:`.ReHoParcels`,
:class:`.ReHoSpheres`, :class:`.ALFFParcels`, :class:`.ALFFSpheres` and
``BOLDWarper`` by `Synchon Mandal`_ (:gh:`311`)
- Change all ``probseg_`` types to ``VBM_`` types by `Fede Raimondo`_
(:gh:`320`)
- Change the subject and session patterns for :class:`.DataladAOMICID1000`,
:class:`.DataladAOMICPIOP1`, :class:`.DataladAOMICPIOP2` and
:class:`.DMCC13Benchmark` so that they are consistent with their own
``"participants.tsv"`` file by `Fede Raimondo`_ (:gh:`325`)
Improved Documentation
^^^^^^^^^^^^^^^^^^^^^^
- Add Zenodo badge in ``README`` and improve general documentation by `Synchon
Mandal`_ (:gh:`247`)
- Rename ``extMDN`` to ``extDMN`` (extended default mode network) and fix
listing for ``eMDN`` (extended multiple-demand network) by `Synchon Mandal`_
(:gh:`251`)
- Fixed typo in code example for adding masks from "register_custom_mask" to
"register_mask" by `Tobias Muganga`_ (:gh:`291`)
- Rename ``Misc`` section to ``Miscellaneous`` in ``docs/whats_new.rst`` by
`Synchon Mandal`_ (:gh:`300`)
- Improve documentation by adding information about space transformation and
writing custom Preprocessors by `Synchon Mandal`_ (:gh:`317`)
Enhancements
^^^^^^^^^^^^
- Support element(s) to be specified via text file for ``--element`` option of
``junifer run`` by `Synchon Mandal`_ (:gh:`182`)
- Support element-scoped directory and temporary directories for
:class:`junifer.pipeline.WorkDirManager` by `Synchon Mandal`_ (:gh:`258`)
- Improve element directory cleanup via
``junifer.pipeline.WorkDirManager.cleanup_elementdir`` method by `Synchon
Mandal`_ (:gh:`259`)
- Improve :class:`.BasePreprocessor` for easy subclassing and adapt
:class:`.fMRIPrepConfoundRemover` to it by `Synchon Mandal`_ (:gh:`260`)
- Add ``space`` information to existing datagrabbers, masks, parcellations and
coordinates by `Synchon Mandal`_ and `Fede Raimondo`_ (:gh:`268`)
- Add ``mode`` as an aggregation function option in
:func:`.get_aggfunc_by_name` by `Synchon Mandal`_ (:gh:`287`)
- Adapt ``BOLDWarper`` to use FSL or ANTs depending on warp file
extension by `Synchon Mandal`_ (:gh:`293`)
- Rewrite ``compute_brain_mask`` to allow variable template fetching via
templateflow, according to target data by `Synchon Mandal`_ (:gh:`299`)
- Replace ``requests`` with ``httpx`` for fetching parcellations by `Synchon
Mandal`_ (:gh:`300`)
- Allow ``BOLDWarper`` to warp BOLD data to other MNI spaces by `Synchon
Mandal`_ (:gh:`302`)
- Add support for local ``junifer queue`` via GNU Parallel by `Synchon Mandal`_
(:gh:`306`)
- Improve :class:`.PatternDataGrabber` and
:class:`.PatternDataladDataGrabber`'s ``patterns`` to enable ``space``,
``format``, ``mask_item`` and other metadata description handling via YAML by
`Synchon Mandal`_ (:gh:`308`)
- Improve :class:`.BasePreprocessor` by revamping
:meth:`.BasePreprocessor.preprocess` and ``BasePreprocessor._fit_transform``
to handle "helper" data types better and make the pipeline explicit where
data is being altered by `Synchon Mandal`_ (:gh:`310`)
- Improve external dependency handling for :class:`.PipelineStepMixin`-derived
objects having implementation-based variations by `Synchon Mandal`_
(:gh:`311`)
Features
^^^^^^^^
- Introduce complexity markers: :class:`.HurstExponent`,
:class:`.MultiscaleEntropyAUC`, :class:`.PermEntropy`,
:class:`.RangeEntropy`, :class:`.RangeEntropyAUC` and :class:`.SampleEntropy`
by `Amir Omidvarnia`_ (:gh:`145`)
- Add ``junifer reset`` to reset storage and jobs directory by `Synchon
Mandal`_ (:gh:`240`)
- Add support for ``Power2013`` coordinates by `Synchon Mandal`_ (:gh:`245`)
- Support ``venv`` as environment kind for queueing jobs by `Synchon Mandal`_
(:gh:`249`)
- Add support for ``AutobiographicalMemory`` coordinates by `Synchon Mandal`_
(:gh:`250`)
- Add support for subject-native space by `Synchon Mandal`_ and `Fede
Raimondo`_ (:gh:`252`)
- Introduce :class:`junifer.pipeline.WorkDirManager` singleton class to manage
working and temporary directories across pipeline by `Synchon Mandal`_
(:gh:`254`)
- Introduce ``get_parcellation`` to fetch parcellation tailored for the
data by `Synchon Mandal`_ (:gh:`264`)
- Introduce ``get_coordinates`` to fetch coordinates tailored for the data
by `Synchon Mandal`_ (:gh:`265`)
- Introduce ``junifer.preprocess.fsl.apply_warper._ApplyWarper`` to wrap FSL's
``applywarp`` by `Synchon Mandal`_ (:gh:`266`)
- Introduce ``BOLDWarper`` for warping BOLD data via FSL's ``applywarp``
by `Synchon Mandal`_ (:gh:`267`)
- Introduce :class:`.DMCC13Benchmark` to access `DMCC13benchmark dataset
<https://openneuro.org/datasets/ds003452/versions/1.0.1>`_ by `Synchon
Mandal`_ (:gh:`271`)
- Add ``Brainnetome 246`` parcellation to ``junifer.data`` by `Synchon Mandal`_
(:gh:`275`)
- Introduce
``junifer.preprocess.ants.ants_apply_transforms_warper._AntsApplyTransformsWarper``
to wrap ANTs' ``antsApplyTransforms`` by `Synchon Mandal`_ (:gh:`293`)
- Introduce :func:`.run_ext_cmd` to take care of the boilerplate code for
running external commands from FSL, ANTs and others by `Synchon Mandal`_
(:gh:`295`)
- Introduce :func:`.get_xfm` to fetch transformation files for moving between
template spaces by `Synchon Mandal`_ (:gh:`297`)
- Introduce :func:`.get_template` to fetch template space image tailored to a
target data by `Synchon Mandal`_ (:gh:`298`)
- Add support for on-the-fly template space transformation in
``get_parcellation`` and ``get_mask`` to allow parcellation and
mask in different template spaces to work with a ``DataGrabber``'s data in a
specified template space. (:gh:`299`)
- Introduce :class:`.SpaceWarper` for warping ``T1w``, ``BOLD``, ``VBM_GM``,
``VBM_WM``, ``fALFF``, ``GCOR`` and ``LCOR`` data to other spaces by `Synchon
Mandal`_ (:gh:`301`)
- Introduce :class:`.QueueContextAdapter` as an abstract base class for job
queueing and :class:`.HTCondorAdapter` as its implementation for HTCondor by
`Synchon Mandal`_ (:gh:`309`)
Miscellaneous
^^^^^^^^^^^^^
- Update dependencies requirements by `Fede Raimondo`_ (:gh:`253`)
- Pin ``ruff`` to ``0.1.0`` as the lowest version and update ``pre-commit``
config by `Synchon Mandal`_ (:gh:`261`)
- Add support for accessing FSL via Docker wrapper along with ``flirt``,
``applywarp`` and ``std2imgcoord`` commands by `Synchon Mandal`_ (:gh:`262`)
- Improve documentation, packaging and code style by `Synchon Mandal`_
(:gh:`269`)
- Add support for Python 3.12 and make Python 3.11 the base for code coverage
and CI checks by `Synchon Mandal`_ (:gh:`270`)
- Add support for accessing ANTs via Docker wrapper along with
``antsApplyTransforms`` and ``antsApplyTransformsToPoints`` by `Synchon
Mandal`_ (:gh:`277`)
- Make the external tool wrappers output to stderr instead of stdout by
`Synchon Mandal`_ (:gh:`279`)
- Add support for accessing FSL ``img2imgcoord`` via Docker wrapper command by
`Synchon Mandal`_ (:gh:`281`)
- Make ``BOLDWarper`` tool-agnostic by moving it from
``junifer.preprocess.fsl`` to :mod:`junifer.preprocess` by `Synchon Mandal`_
(:gh:`288`)
- Add support for accessing ANTs' ``ResampleImage`` via Docker wrapper by
`Synchon Mandal`_ (:gh:`293`)
- Update ``pyproject.toml`` and add FAIR shield in ``README.md`` by `Synchon
Mandal`_ (:gh:`294`)
- Update dependency listing in ``pyproject.toml``, add
``.github/dependabot.yml`` to auto-update GitHub Actions, add ``ANTs`` and
``FSL`` installation in CI and improve general code style by `Synchon
Mandal`_ (:gh:`300`)
Deprecations and Removals
^^^^^^^^^^^^^^^^^^^^^^^^^
- Deprecate ``BOLDWarper`` and mark for removal in v0.0.4 by `Synchon
Mandal`_ (:gh:`301`)
Junifer 0.0.3 (2023-07-21)
--------------------------
Bugfixes
^^^^^^^^
- Enable YAML 1.2 support and allow multiline strings in YAML which would not
work earlier by `Synchon Mandal`_ (:gh:`223`)
- Handle ``datalad.IncompleteResultsError`` exception for partial clone in
:class:`.DataladDataGrabber` by `Synchon Mandal`_ (:gh:`235`)
API Changes
^^^^^^^^^^^
- Expose ``types`` parameter for :class:`.DataladAOMICID1000`,
:class:`.DataladAOMICPIOP1`, :class:`.DataladAOMICPIOP2` and
:class:`.JuselessUCLA` by `Synchon Mandal`_ (:gh:`132`)
- Rename ``junifer.testing.datagrabbers.SPMAuditoryTestingDatagrabber`` to
:class:`.SPMAuditoryTestingDataGrabber` and
``junifer.testing.datagrabbers.OasisVBMTestingDatagrabber`` to
:class:`.OasisVBMTestingDataGrabber` by `Synchon Mandal`_ (:gh:`222`)
- Add :meth:`.BaseFeatureStorage.read` method for storage-like objects by
`Synchon Mandal`_ (:gh:`236`)
Improved Documentation
^^^^^^^^^^^^^^^^^^^^^^
- Improve general prose, formatting and code blocks in docs and set line length
for ``.rst`` files to 80 by `Synchon Mandal`_ (:gh:`220`)
- Update ``julearn`` example under ``examples`` by `Synchon Mandal`_
(:gh:`242`)
Enhancements
^^^^^^^^^^^^
- Change validation of ``types`` against ``patterns`` to allow a subset of
``patterns``'s types to be used for ``DataGrabber`` data fetch by `Synchon
Mandal`_ (:gh:`132`)
- Rename instances of "Datagrabber" to "DataGrabber" especially in
``junifer.testing`` to be consistent by `Synchon Mandal`_ (:gh:`222`)
- Use ``ruamel.yaml`` instead of ``pyyaml`` as YAML I/O library by `Synchon
Mandal`_ (:gh:`223`)
- Adopt ``DataGrabber`` consistently throughout codebase to match with the
documentation by `Synchon Mandal`_ (:gh:`226`)
- Adopt ``DataReader`` consistently throughout codebase to match with the
documentation by `Synchon Mandal`_ (:gh:`227`)
- Enable ``stdout`` and ``stderr`` capture for AFNI commands by `Synchon
Mandal`_ (:gh:`234`)
- Adapt :meth:`.HDF5FeatureStorage.read_df` due to addition of
:meth:`.HDF5FeatureStorage.read` by `Synchon Mandal`_ (:gh:`236`)
Features
^^^^^^^^
- Add ``AICHA v1`` and ``AICHA v2`` parcellations to ``junifer.data`` by
`Synchon Mandal`_ (:gh:`173`)
- Add ``Shen 2013``, ``Shen 2015`` and ``Shen 2019`` parcellations to
``junifer.data`` by `Synchon Mandal`_ (:gh:`184`)
- Add ``Yan 2023`` parcellation to ``junifer.data`` by `Synchon Mandal`_
(:gh:`225`)
- Introduce :mod:`.onthefly` sub-module and :func:`.read_transform` for quick
transform operations on stored data by `Synchon Mandal`_ (:gh:`237`)
Miscellaneous
^^^^^^^^^^^^^
- Consistent docstrings for pytest fixtures used in the test suite by `Synchon
Mandal`_ (:gh:`228`)
- Adopt ``ruff`` as the only linter for the codebase by `Synchon Mandal`_
(:gh:`229`)
- Improve ``codespell`` support by fixing typos in documentation by `Synchon
Mandal`_ (:gh:`230`)
- Adopt ``pre-commit`` for adding and managing git pre-commit hooks by
`Synchon Mandal`_ (:gh:`232`)
- Improve docstrings and code style and parametrize remaining tests for
``junifer.data.parcellations`` by `Synchon Mandal`_ (:gh:`238`)
- Bump ``numpy`` version constraint to ``>=1.24,<1.26`` by `Synchon Mandal`_
(:gh:`241`)
Junifer 0.0.2 (2023-03-31)
--------------------------
Bugfixes
^^^^^^^^
- Fix a bug in which relative storage URIs will be computed relative to the CWD
and not to the location of the YAML file by `Fede Raimondo`_. (:gh:`127`)
- Fix ``junifer run`` to respect preprocess step specified in the pipeline by
`Synchon Mandal`_ (:gh:`159`)
- Fix a bug in which only ``REST1`` and ``REST2`` tasks could be accessed in
:class:`.DataladHCP1200` and :class:`.HCP1200` datagrabbers by `Fede
Raimondo`_ (:gh:`183`)
- Fix a bug in which fitting a marker (e.g. ``SphereAggregation``) on a
specific type (e.g.: ``BOLD``) will fail if another non-supported type (e.g.:
``BOLD_confounds``) is present in the data object by `Fede Raimondo`_
(:gh:`185`)
- Fix :class:`.ALFFParcels`, :class:`.ALFFSpheres`, :class:`.ReHoSpheres` and
:class:`.ReHoParcels` pass the ``extra_input`` parameter by `Fede Raimondo`_
(:gh:`187`)
- Fix several markers that did not properly handle the ``extra_input``
parameter by `Fede Raimondo`_ (:gh:`189`)
- Fix a bug in which relative paths in the YAML ``with`` directive would be
computed relative to the current working directory of the process instead of
the location of the YAML file by `Fede Raimondo`_. (:gh:`191`)
- Fix an issue with datalad cache and locks in which the user-specific
configuration might create a conflict in high throughput systems by `Fede
Raimondo`_ (:gh:`192`)
- Fix a bug in which :class:`.ParcelAggregation` could yield duplicated column
names if two or more parcels were used and label names were not unique by
`Fede Raimondo`_ (:gh:`194`)
- Fix a bug in which :func:`.count` will not be correctly applied across an
axis by `Fede Raimondo`_ (:gh:`195`)
- Fix an issue with datalad cache and locks in which the overridden settings in
Junifer were not propagated to subprocesses, resulting in using the default
settings by `Fede Raimondo`_ (:gh:`199`)
- Fix a bug in which ``get_mask`` fails for ``FunctionalConnectivityBase``
class, because of missing extra_input parameter by `Leonard Sasse`_
(:gh:`200`)
- Fix the output of :class:`.RSSETSMarker` to be 2D by `Synchon Mandal`_
(:gh:`215`)
API Changes
^^^^^^^^^^^
- Add ``confounds_format`` parameter to :class:`.PatternDataGrabber`
constructor for improved handling of confounds specified via
``BOLD_confounds`` data type by `Synchon Mandal`_ (:gh:`158`)
- Rename ``store_table()`` to ``store_vector()`` for storage-like objects and
adapt marker-like objects to use ``"vector"`` in place of ``"table"`` for
storage. Also, improve the logic of storing vectors by `Synchon Mandal`_
(:gh:`181`)
- Add ``ica_fix`` parameter to :class:`.DataladHCP1200` and :class:`.HCP1200`
datagrabbers to allow for selecting data processed with ICA+FIX. Default
value is ``False`` which changes behaviour since 0.0.1 release. By `Fede
Raimondo`_ (:gh:`183`)
- Add ``pre_run`` parameter to ``_queue_condor`` by `Fede Raimondo`_
(:gh:`188`)
- Expose ``allow_overlap`` parameter in :class:`.SphereAggregation` and
related markers by `Fede Raimondo`_ (:gh:`190`)
- Rename ``AmplitudeLowFrequencyFluctuationParcels`` and
``AmplitudeLowFrequencyFluctuationSpheres`` to :class:`.ALFFParcels` and
:class:`.ALFFSpheres` by `Synchon Mandal`_ (:gh:`216`)
Improved Documentation
^^^^^^^^^^^^^^^^^^^^^^
- Add more documentation on registering parcellations, coordinates, and masks
by `Leonard Sasse`_ (:gh:`166`)
- Migrate and document changelog creation and maintenance via ``towncrier`` by
`Synchon Mandal`_ (:gh:`203`)
- Add copy button to documentation code blocks by `Synchon Mandal`_ (:gh:`205`)
- Add sections *starting* and *help* in the documentation by `Fede Raimondo`_
(:gh:`210`)
- Shorten Sphinx references across code and docs, and add ``black`` shield in
README by `Synchon Mandal`_ (:gh:`218`)
Enhancements
^^^^^^^^^^^^
- Organize functional connectivity markers in
``junifer.markers.functional_connectivity`` by `Synchon Mandal`_ (:gh:`107`)
- Change HCP datagrabber tests to decrease CI running time by `Fede Raimondo`_
(:gh:`155`)
- Allow :class:`.PartlyCloudyTestingDataGrabber` to be accessible via ``import
junifer.testing.registry`` by `Synchon Mandal`_ (:gh:`160`)
- Update docstrings and fix typo in log message by `Synchon Mandal`_
(:gh:`165`)
- Add fMRIPrep brain masks to the datagrabber patterns for all datagrabbers in
the aomic sub-package by `Leonard Sasse`_ (:gh:`177`)
- Improved logging output for preprocessing, collecting and pipeline building
from YAML by `Fede Raimondo`_ (:gh:`185`)
- Allow for empty spheres in :class:`.JuniferNiftiSpheresMasker`, that will
result in NaNs. Also, modify the behaviour of the ``collect`` parameter in
HTCondor ``queue`` function to run a collect job even if some of the previous
jobs fail. This is useful to collect the results of a pipeline even if some
of the jobs fail by `Fede Raimondo`_ (:gh:`190`)
- Allow for empty parcels in :class:`.ParcelAggregation`, that will result in
NaNs by `Fede Raimondo`_ (:gh:`194`)
- Improve metadata and data I/O for :class:`.HDF5FeatureStorage` by `Synchon
Mandal`_ (:gh:`196`)
- Force datalad to be non-interactive on *queued* jobs by `Fede Raimondo`_
(:gh:`201`)
- Add missing ``abstractmethod`` decorators for ``get_valid_inputs`` methods of
:class:`.BaseMarker` and :class:`.BasePreprocessor` by `Synchon Mandal`_
(:gh:`214`)
Features
^^^^^^^^
- Add :class:`.EdgeCentricFCParcels` and :class:`.EdgeCentricFCSpheres` by
`Leonard Sasse`_ (:gh:`64`)
- Expose a ``merge_parcellations`` function to merge a list of
parcellations by `Leonard Sasse`_ (:gh:`146`)
- Add support for HDF5 feature storage via :class:`.HDF5FeatureStorage` by
`Synchon Mandal`_ (:gh:`147`)
- Add :class:`.TemporalSNRParcels` and :class:`.TemporalSNRSpheres` by `Leonard
Sasse`_ (:gh:`163`)
- Add support for ``Power`` coordinates by `Synchon Mandal`_ (:gh:`167`)
- Add support for ``Dosenbach`` coordinates by `Synchon Mandal`_ (:gh:`168`)
- Add support for nilearn computed masks (``compute_epi_mask``,
``compute_brain_mask``, ``compute_background_mask``,
``fetch_icbm152_brain_gm_mask``) by `Fede Raimondo`_ (:gh:`175`)
- Add aggregation function :func:`.count` that returns the number of elements
in a given axis. This allows to count the number of voxels per sphere/parcel
when used as ``method`` in markers by `Fede Raimondo`_ (:gh:`190`)
Junifer 0.0.1 (2022-12-20)
--------------------------
Bugfixes
^^^^^^^^
- Fix a bug in which a :class:`.PatternDataGrabber` would now work with
relative ``datadir`` paths (reported by `Leonard Sasse`_, fixed by
`Fede Raimondo`_) (:gh:`96`, :gh:`98`)
- Fix a bug in which :class:`.DataladAOMICPIOP2` datagrabber did not use user
input to constrain elements based on tasks by `Leonard Sasse`_ (:gh:`105`)
- Fix a bug in which a datalad dataset could remove a user-cloned dataset by
`Fede Raimondo`_ (:gh:`53`)
- Fix a bug in which CLI command would not work using elements with more than
one field by `Fede Raimondo`_
- Fix a bug in which the generated DAG for HTCondor will not work by
`Fede Raimondo`_ (:gh:`143`)
API Changes
^^^^^^^^^^^
- Change the ``single_output`` default parameter in storage classes from
``False`` to ``True`` by `Fede Raimondo`_ (:gh:`134`)
Improved Documentation
^^^^^^^^^^^^^^^^^^^^^^
- Add an example how to use ``junifer`` and ``julearn`` in one pipeline to
extract features and do machine learning by `Leonard Sasse`_,
`Nicolas Nieto`_, and `Sami Hamdan`_ (:gh:`40`)
- Add documentation for the datagrabbers by `Leonard Sasse`_,
`Nicolas Nieto`_, and `Sami Hamdan`_
- Change documentation template to furo. Fix references and standardize
documentation by `Fede Raimondo`_ (:gh:`114`)
Enhancements
^^^^^^^^^^^^
- Add comments to :class:`.DataladDataGrabber` datagrabber and change to use
``datalad-clone`` instead of ``datalad-install`` by `Benjamin Poldrack`_
(:gh:`55`)
- Upgrade storage interface for storage-like objects by `Synchon Mandal`_
(:gh:`84`)
- Add missing type annotations by `Synchon Mandal`_ (:gh:`74`)
- Refactor markers ``on`` attribute and ``get_valid_inputs`` to verify that the
marker can be computed on the input data types by `Fede Raimondo`_
- Add test for :class:`.DataladHCP1200` datagrabber by `Synchon Mandal`_
(:gh:`93`)
- Refactor :class:`.DataladAOMICID1000` slightly by `Leonard Sasse`_ (:gh:`94`)
- Rename "atlas" to "parcellation" by `Fede Raimondo`_ (:gh:`116`)
- Refactor the :class:`.BaseDataGrabber` class to allow for easier subclassing
by `Fede Raimondo`_ (:gh:`123`)
- Allow custom aggregation method for :class:`.SphereAggregation` by
`Synchon Mandal`_ (:gh:`102`)
- Add support for "masks" by `Fede Raimondo`_ (:gh:`79`)
- Allow :class:`.ParcelAggregation` to apply multiple parcellations at once by
`Fede Raimondo`_ (:gh:`131`)
- Refactor :class:`.PipelineStepMixin` to improve its implementation and
validation for pipeline steps by `Synchon Mandal`_ (:gh:`152`)
Features
^^^^^^^^
- Implement :class:`.SPMAuditoryTestingDataGrabber` datagrabber by
`Fede Raimondo`_ (:gh:`52`)
- Implement matrix storage in SQliteFeatureStorage by `Fede Raimondo`_
(:gh:`42`)
- Implement :class:`.FunctionalConnectivityParcels` marker for functional
connectivity using a parcellation by `Amir Omidvarnia`_ and
`Kaustubh R. Patil`_ (:gh:`41`)
- Implement ``register_coordinates``, ``list_coordinates`` and
``load_coordinates`` by `Fede Raimondo`_ (:gh:`11`)
- Add :class:`.DataladAOMICID1000` datagrabber for AOMIC ID1000 dataset
including tests and creation of mock dataset for testing by
`Vera Komeyer`_ and `Xuan Li`_ (:gh:`60`)
- Add support to access other input in the data object in the ``compute`` method
by `Fede Raimondo`_
- Implement :class:`.RSSETSMarker` marker by `Leonard Sasse`_, `Nicolas Nieto`_
and `Sami Hamdan`_ (:gh:`51`)
- Implement :class:`.SphereAggregation` marker by `Fede Raimondo`_ (:gh:`83`)
- Implement :class:`.DataladAOMICPIOP1` and :class:`.DataladAOMICPIOP2`
datagrabbers for AOMIC PIOP1 and PIOP2 datasets respectively by
`Leonard Sasse`_ (:gh:`94`)
- Implement :class:`.JuselessDataladCamCANVBM` datagrabber by `Leonard Sasse`_
(:gh:`99`)
- Implement :class:`.JuselessDataladIXIVBM` CAT output datagrabber for juseless
by `Leonard Sasse`_ (:gh:`48`)
- Add ``junifer wtf`` to report environment details by `Synchon Mandal`_
(:gh:`33`)
- Add ``junifer selftest`` to report environment details by `Synchon Mandal`_
(:gh:`9`)
- Implement :class:`.JuselessDataladAOMICID1000VBM` datagrabber for accessing
AOMIC ID1000 VBM from juseless by `Felix Hoffstaedter`_ and `Synchon Mandal`_
(:gh:`57`)
- Add :class:`.fMRIPrepConfoundRemover` by `Fede Raimondo`_ and `Leonard Sasse`_
(:gh:`111`)
- Implement :class:`.CrossParcellationFC` marker by `Leonard Sasse`_ and
`Kaustubh R. Patil`_ (:gh:`85`)
- Add :class:`.JuselessUCLA` datagrabber for the UCLA dataset available on
juseless by `Leonard Sasse`_ (:gh:`118`)
- Introduce a singleton decorator for marker computations by `Synchon Mandal`_
(:gh:`151`)
- Implement :class:`.ReHoParcels` and :class:`.ReHoSpheres` markers by
`Synchon Mandal`_ (:gh:`36`)
- Implement :class:`.ALFFParcels` and :class:`.ALFFSpheres` markers by
`Fede Raimondo`_ (:gh:`35`)
Miscellaneous
^^^^^^^^^^^^^
- Create the repository based on the mockup by `Fede Raimondo`_
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