14. What’s new

14.1. Junifer 0.0.7.dev401 (2025-11-18)

14.1.1. Bugfixes

• Allow timeseries_2d storage for HDF5FeatureStorage by Fede Raimondo (#444)

• Fix FSL presence checking status code by Fede Raimondo (#454)

14.1.2. API Changes

• fname, overwrite and output_format have been removed from configure_logging() by Synchon Mandal (#231)

• ParcellationRegistry.get now returns labels as dictionary mapping from values to labels instead of a list of labels by Synchon Mandal (#257)

• read_transform() has a new parameter nan_policy to handle NaN values when transforming feature data by Fede Raimondo (#429)

• get_data(), load_data(), list_data(), register_data() and deregister_data() now support "maps" as a valid argument for kind by Synchon Mandal (#458)

14.1.3. Improved Documentation

• Add documentation on extending data registries by Synchon Mandal (#450)

• Add documentation on adding data types by Synchon Mandal (#451)

• Add documentation on ConfigManager, dumping data object and extending data dump assets by Synchon Mandal (#452)

14.1.4. Enhancements

• Allow parcellation registration with non-continuous ranges as values by Synchon Mandal (#257)

• Add support for Chatterjee’s xi correlation in JuniferConnectivityMeasure by Synchon Mandal (#333)

• Adopt Pydantic for user-facing core objects to perform automatic validation using typing annotations by Synchon Mandal (#364)

• Implement a NaN policy for read_transform() by Fede Raimondo (#429)

• Add FreeSurfer 7.4.1 aseg parcellation to ParcellationRegistry by Synchon Mandal (#470)

• Simplify Storage interface and implementations by Synchon Mandal (#472)

• Simplify Preprocess interface and implementations by Synchon Mandal (#473)

• Simplify PipelineStepMixin interface by Synchon Mandal (#476)

• Improve Marker interface and implementations by Synchon Mandal (#477)

14.1.5. Features

• Introduce TemporalFilter preprocessor for temporally filtering BOLD data by Fede Raimondo (#432)

• Introduce TemporalSlicer preprocessor for temporally slicing BOLD data by Synchon Mandal (#443)

• Enable data registries to be extended by exposing BasePipelineDataRegistry and introducing register_data_registry() decorator by Synchon Mandal (#450)

• Enable data types to be added by introducing register_data_type() by Synchon Mandal (#451)

• Allow pipeline data object to be dumped by introducing DataObjectDumper and available dumping / loading assets to be extended by introducing register_data_dump_asset() decorator by Synchon Mandal (#452)

• Introduce MapsRegistry to centralise probabilistic atlas (maps) data management by Synchon Mandal (#458)

• Introduce MapsAggregation, FunctionalConnectivityMaps, EdgeCentricFCMaps, ReHoMaps, ALFFMaps and TemporalSNRMaps by Synchon Mandal (#460)

• Enable SpaceWarper to warp data from native space to template spaces via both FSL and ANTs by Synchon Mandal (#462)

14.1.6. Miscellaneous

• Adopt structlog for logging infrastructure by Synchon Mandal (#231)

• Regular repository maintenance by updating .pre-commit-config.yaml, replacing black with ruff-format and updating tool configs by Synchon Mandal (#441)

• Bump junifer-data to v3 for Docker images by Synchon Mandal (#456)

• Bump junifer-data to v3 by Synchon Mandal (#457)

• Constrain templateflow version to >=23.0.0,<25.0.0 by Synchon Mandal (#458)

• Add a new GitHub Action to mark stale issues by Synchon Mandal (#464)

• Bump junifer-data to v4 for Docker images by Synchon Mandal (#465)

• Bump junifer-data to v4 by Synchon Mandal (#466)

• Disable FSL installation for junifer-ci Docker image build with junifer-data v4 by Synchon Mandal (#467)

• Pin junifer-ci Docker image to python:3.12-slim-bookworm and re-enable FSL installation by Synchon Mandal (#468)

• Bump junifer-data to v5 by Synchon Mandal (#470)

14.2. Junifer 0.0.6 (2025-03-24)

14.2.1. Bugfixes

• Fix mri_binarize command preparation for structures with multiple indices in BrainPrint by Fede Raimondo (#356)

• Enable spike mapping from adhoc to fmriprep for fMRIPrepConfoundRemover by Leonard Sasse and Synchon Mandal (#360)

• Correct listing for fMRIPrepConfoundRemover in junifer.pipeline.registry by Synchon Mandal (#369)

• Add 'emomatching' task to DataladAOMICPIOP2 by Leonard Sasse (#370)

• Use correct return code for ANTs commands while checking presence of external commands by Synchon Mandal (#385)

• Use the junifer.pipeline.WorkDirManager for temporary directories in the DataladDataGrabber by Fede Raimondo (#386)

• Fix coordinates space transformation using ANTs by Synchon Mandal (#388)

• Fix metadata update for MultipleDataGrabber and adjust PatternDataGrabber.get_elements() to check list-like data type values by Fede Raimondo and Synchon Mandal (#398)

• Use correct file output suffices for AFNI-based markers by Synchon Mandal (#409)

• Fix t_r tampering by nilearn.image.clean_img() in fMRIPrepConfoundRemover by Fede Raimondo and Synchon Mandal (#420)

• Fix coordinates fetching for Power and Dosenbach from junifer-data by Synchon Mandal (#431)

• Remove Power2013 from CoordinatesRegistry by Synchon Mandal (#436)

• Correct dispatch methods for *_data() functions by Synchon Mandal (#439)

14.2.2. 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 get_data(), load_data(), list_data(), register_data() and deregister_data() by Synchon Mandal (#387)

• SpaceWarper’s using now supports "auto" allowing auto tool selection based on DataGrabber specification by Synchon Mandal (#390)

• Allow workdir to also be a mapping in YAML, with path and cleanup keys by Synchon Mandal (#402)

• Add source parameter and resurrect extra_input parameter for compute_brain_mask by Fede Raimondo (#404)

• native_t1w parameter has been replaced with space to allow DataladAOMICID1000, DataladAOMICPIOP1 and DataladAOMICPIOP2 to fetch data in all available spaces by Fede Raimondo (#405)

• 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 (#411)

• Introduce new CLI parameter --verbose-datalad to control datalad’s logging handler by Fede Raimondo (#412)

• target_data parameter of get_template() has been replaced with target_img by Fede Raimondo (#413)

• Add template_space parameter for compute_brain_mask and resolution parameter for get_template() by Fede Raimondo (#415)

• Add scrub, fd_threshold and std_vars_threshold parameters to fMRIPrepConfoundRemover and allow "scrubbing" key of type bool for strategy by Synchon Mandal (#421)

14.2.3. Improved Documentation

• Improve Sphinx configuration and extensions by Synchon Mandal (#358)

• Add documentation on analysing extracted features by Synchon Mandal (#359)

• Add documentation on how to make a junifer plugin by Synchon Mandal (#366)

14.2.4. Enhancements

• Raise error when partial or complete element selectors are invalid when running the pipeline by Synchon Mandal (#319)

• Add support for Spearman’s correlation in JuniferConnectivityMeasure by Leonard Sasse (#335)

• Set proper stdout encoding for run_ext_cmd() to ease human readability by Fede Raimondo (#357)

• Adapt usage of junifer-data client API to fetch parcellations, masks, coordinates and xfms by Synchon Mandal (#363)

• Allow for external python files in the with section of the yaml to import other files by Fede Raimondo (#367)

• Use datalad-enabled repository for template space transform files in get_xfm() by Synchon Mandal (#368)

• Add a cleanup parameter to the junifer.pipeline.WorkDirManager, which allows to disable cleaning up temporary directories by Fede Raimondo (#389)

• Update Warp data type to be a list of dictionaries and adapt to allow multiple transforms to be specified by Synchon Mandal (#390)

• Refactor the masking logic in the pipeline to account for and optimise space transformations and merges by Synchon Mandal and Fede Raimondo (#395)

• Allow workdir mapping form in YAML for easy debugging of single element run by disabling cleanup of junifer.pipeline.WorkDirManager by Synchon Mandal (#402)

• Use junifer.utils.ConfigManager() to skip time-consuming dataset ID and dirty checks for DataladDataGrabber by Fede Raimondo (#403)

• Enable compute_brain_mask to use subject-specific probseg files by Fede Raimondo (#404)

• Update DataladAOMICID1000, DataladAOMICPIOP1 and DataladAOMICPIOP2 to fetch data in all available spaces by Fede Raimondo (#405)

• Update Preprocessors to sync data their paths so that the results are idempotent by Synchon Mandal (#408)

• Ease asset storage for AFNI-based markers by Synchon Mandal (#409)

• Refactor the parcellation logic in the pipeline to account for and optimise space transformations and merges by Synchon Mandal and Fede Raimondo (#411)

• Adapt mask warpers to use correct interpolation method based on the type of data by Synchon Mandal and Fede Raimondo (#416)

• Adapt usage of junifer-data DataLad dataset to fetch parcellations, masks, coordinates and xfms by Synchon Mandal (#418)

• Add scrubbing support to fMRIPrepConfoundRemover by Synchon Mandal (#421)

• Add commit SHA check for junifer_data to simplify data fetching by Fede Raimondo (#434)

14.2.5. Features

• Introduce normalize() and reweight() functions for downstream BrainPrint analysis in onthefly._brainprint by Synchon Mandal (#354)

• Introduce junifer.pipeline.PipelineComponentRegistry to centralise pipeline component management by Synchon Mandal (#362)

• Add support for plugins by Synchon Mandal (#366)

• Introduce junifer.data.CoordinatesRegistry, junifer.data.ParcellationRegistry and junifer.data.MaskRegistry to centralise data management by Synchon Mandal (#387)

• Introduce junifer.typing sub-module to organise internal and external type hints by Synchon Mandal (#392)

• Introduce junifer.utils.ConfigManager singleton class to manage global configuration by Fede Raimondo (#401)

• Introduce BOLD.reference nested type and adapt SpaceWarper and necessary data components by Fede Raimondo (#407)

• Allow masks to be warped, if found, in SpaceWarper by Synchon Mandal (#408)

• Add support for coloured logging.Formatter to use with junifer’s logging.StreamHandler based on environment by Fede Raimondo (#412)

• Allow storage of 2D timeseries, currently only supported by HDF5FeatureStorage by Fede Raimondo (#422)

14.2.6. Miscellaneous

• Adopt lazy-import mechanism for the package by Synchon Mandal (#355)

• Refactor api sub-package and introduce new cli sub-package by Synchon Mandal (#361)

• Add junifer-data as a dependency by Synchon Mandal (#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 (#372)

• Add Dockerfile for docs CI and a corresponding action for building and publishing the image by Synchon Mandal (#373)

• Adopt usage of custom docs CI image for building and previewing docs actions by Synchon Mandal (#374)

• Update Dependabot GitHub Action to support groups by Synchon Mandal (#380)

• Add Dockerfile for CI and a corresponding action for building and publishing the image by Synchon Mandal (#382)

• Adopt usage of custom CI image for testing junifer action by Synchon Mandal (#383)

• Improve docs publishing action and add a manual trigger for it by Synchon Mandal (#384)

• Refactor Singleton class to use a metaclass instead of a class decorator by Fede Raimondo (#391)

• Update type hints across codebase to be Python>=3.9 compatible by Synchon Mandal (#393)

• Update Docker image recipes and GitHub Actions workflows by Synchon Mandal (#396)

• Simplify logic for parcellation and mask space warping by Synchon Mandal (#414)

• Remove httpx as a dependency by Synchon Mandal (#418)

• Fix coverage in CI by Fede Raimondo (#424)

• Use junifer-data in CI images by Synchon Mandal (#427)

• Improve GitHub Actions workflows by Synchon Mandal (#428)

• Bump junifer-data to v2 for CI workflows, remove Power and add Seitzman2018 to CoordinatesRegistry by Synchon Mandal (#437)

• Bump junifer-data to v2 for Docker images by Synchon Mandal (#438)

14.3. Junifer 0.0.5 (2024-07-22)

14.3.1. Bugfixes

• Remove extra dimension from parcellations warped via ANTs to other template spaces by Synchon Mandal (#324)

• Remove extra dimension from parcellations warped via ANTs when merging parcellations by Synchon Mandal (#331)

• Fix junifer reset to properly delete storage directory and handle junifer_jobs deletion if not empty by Synchon Mandal (#332)

• Fix validation failure of multiple Preprocessors with different input data types requirement by Synchon Mandal (#339)

• Remove extra dimension from masks warped via ANTs by Synchon Mandal (#340)

14.3.2. API Changes

• For 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, FunctionalConnectivityParcels, FunctionalConnectivitySpheres, EdgeCentricFCParcels and EdgeCentricFCSpheres, cor_method and cor_method_params have been renamed to conn_method and conn_method_params by Synchon Mandal (#348)

• fractional parameter for ALFFBase, ALFFParcels and ALFFSpheres have been removed in favour of returning both ALFF and fALFF by Synchon Mandal (#349)

• Add partial_pattern_ok argument to PatternDataGrabber to not raise error on missing mandatory key checks for data types by Synchon Mandal (#351)

14.3.3. Improved Documentation

• Improve sub-package level docstrings to better reflect their purposes by Synchon Mandal (#115)

• Update “Queueing Jobs (HPC, HTC)” section by Synchon Mandal (#327)

• Add missing DataGrabber types options in respective docstrings of DataladAOMICID1000, DataladAOMICPIOP1, DataladAOMICPIOP2 and DMCC13Benchmark by Synchon Mandal (#330)

14.3.4. Enhancements

• Add test to be sure that JuniferNiftiSpheresMasker with mean aggregation function behaves exactly as nilearn.maskers.NiftiSpheresMasker by Synchon Mandal (#136)

• Refactor DataGrabber patterns to make helper types like *_mask as “nested types” of the actual data type by Synchon Mandal (#341)

• Adapt DataladAOMICID1000, DataladAOMICPIOP1 and DataladAOMICPIOP2 to support FreeSurfer data type by Synchon Mandal (#346)

• FunctionalConnectivity-family Markers now use sklearn.covariance.EmpiricalCovariance as the default covariance estimator and correlation as the default connecivity matrix kind by Synchon Mandal (#348)

• Enable Markers to output multiple features by Synchon Mandal (#349)

• Add support for UKB_15K_GM mask by Synchon Mandal (#350)

• Adapt MultipleDataGrabber to handle “nested types” introduced in #341 by Synchon Mandal (#351)

14.3.5. Features

• Introduce Smoothing for smoothing / blurring images as a preprocessing step by Synchon Mandal (#161)

• Add support for choosing between bash and zsh shells when queueing by Synchon Mandal (#273)

• Add junifer list-elements to list out available elements for a DataGrabber based on filtering via --element by Synchon Mandal (#323)

• Introduce new storage type scalar_table and adapt HDF5FeatureStorage to support it by Synchon Mandal (#343)

• Add support for BrainPrint marker by Synchon Mandal (#344)

• Allow Unix path expansion directives to be used in PatternDataGrabber patterns by Synchon Mandal (#345)

• Add support for FreeSurfer data type for PatternDataGrabber by Synchon Mandal (#346)

• Introduce JuniferConnectivityMeasure for customising functional connectivity matrix kinds and measurements by Synchon Mandal (#348)

• Introduce PatternValidationMixin to simplify validation for pattern-based DataGrabbers and deep_update() for updating dictionary with varying width and depth by Synchon Mandal (#351)

14.3.6. Miscellaneous

• Improve CI to allow external tool installation to fail gracefully and update necessary dependency version and conditional checks by Synchon Mandal (#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 (#337)

• Add support for accessing FreeSurfer via Docker wrapper along with mri_binarize, mri_pretess, mri_mc and mris_convert by Synchon Mandal (#342)

• Update core and docs dependencies by Synchon Mandal (#347)

• Integrate warnings with logging respecting filters by Fede Raimondo (#351)

14.3.7. Deprecations and Removals

• Remove Power coordinates, fetch_icbm152_brain_gm_mask mask, BOLDWarper Preprocessor by Synchon Mandal (#336)

14.4. Junifer 0.0.4 (2024-04-05)

14.4.1. 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 (#224)

• Adapt junifer queue to properly use HTCondor >=10.4.0 condor_submit_dag by Fede Raimondo and Synchon Mandal (#233)

• Use 1 instead of 0 for successful FSL commands in _check_fsl() by Synchon Mandal (#272)

• Store native warped parcellations, coordinates and masks in element-scoped tempdirs for the pipeline to work by Synchon Mandal (#274)

• Change interpolation scheme for parcel and mask native space transformation to nearest neighbour by Synchon Mandal (#276)

• Bypass FSL std2imgcoord stdin bug and use recommended piped input for coordinates transformation by Synchon Mandal (#278)

• Add -std to FSL std2imgcoord for coordinates transformation by Synchon Mandal (#280)

• Replace FSL std2imgcoord with img2imgcoord as the former is incorrect for coordinates transformation to other template spaces. (#281)

• Propagate ReHo and fALFF maps, for aggregation to convert to other template spaces when required by Synchon Mandal (#282)

• Allow junifer.pipeline.WorkDirManager to accept str via the workdir parameter by Synchon Mandal (#283)

• Avoid warping mask preprocessed with fMRIPrepConfoundRemover and used by markers with mask="inherit" in subject-native template space by Fede Raimondo and Synchon Mandal (#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 (#286)

• Fix HTCondorAdapter’s script generation to use double quotes instead of single quotes for HTCondor’s VARS by Synchon Mandal (#312)

• Fix element access for DMCC13Benchmark DataGrabber by Synchon Mandal (#314)

• Add a validation step on the run() function to validate the marker collection by Fede Raimondo (#320)

• Add the executable flag to the ants docker scripts, fsl docker scripts and other running scripts by Fede Raimondo (#321)

• Force str dtype when parsing elements from file by Synchon Mandal (#322)

14.4.2. API Changes

• Rename Power coordinates to Power2011 by Synchon Mandal (#245)

• Add feature_md5 argument to read_transform() by Synchon Mandal (#248)

• Add native_t1w parameter to DataladAOMICID1000, DataladAOMICPIOP1, DataladAOMICPIOP2, enabling fetching of T1w data in subject-native space by Synchon Mandal (#252)

• Modify preprocessor to preprocessors in run() and preprocessing to preprocessors in MarkerCollection to accept multiple preprocessors by Synchon Mandal (#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 (#268)

• Add template_type parameter to get_template() by Synchon Mandal (#299)

• Change BasePreprocessor.preprocess() return values to preprocessed target data and “helper” data types as a dictionary by Synchon Mandal (#310)

• Add a positional argument using for Markers and Preprocessors having implementation-based variations, in particular ReHoParcels, ReHoSpheres, ALFFParcels, ALFFSpheres and BOLDWarper by Synchon Mandal (#311)

• Change all probseg_ types to VBM_ types by Fede Raimondo (#320)

• Change the subject and session patterns for DataladAOMICID1000, DataladAOMICPIOP1, DataladAOMICPIOP2 and DMCC13Benchmark so that they are consistent with their own "participants.tsv" file by Fede Raimondo (#325)

14.4.3. Improved Documentation

• Add Zenodo badge in README and improve general documentation by Synchon Mandal (#247)

• Rename extMDN to extDMN (extended default mode network) and fix listing for eMDN (extended multiple-demand network) by Synchon Mandal (#251)

• Fixed typo in code example for adding masks from “register_custom_mask” to “register_mask” by Tobias Muganga (#291)

• Rename Misc section to Miscellaneous in docs/whats_new.rst by Synchon Mandal (#300)

• Improve documentation by adding information about space transformation and writing custom Preprocessors by Synchon Mandal (#317)

14.4.4. Enhancements

• Support element(s) to be specified via text file for --element option of junifer run by Synchon Mandal (#182)

• Support element-scoped directory and temporary directories for junifer.pipeline.WorkDirManager by Synchon Mandal (#258)

• Improve element directory cleanup via junifer.pipeline.WorkDirManager.cleanup_elementdir method by Synchon Mandal (#259)

• Improve BasePreprocessor for easy subclassing and adapt fMRIPrepConfoundRemover to it by Synchon Mandal (#260)

• Add space information to existing datagrabbers, masks, parcellations and coordinates by Synchon Mandal and Fede Raimondo (#268)

• Add mode as an aggregation function option in get_aggfunc_by_name() by Synchon Mandal (#287)

• Adapt BOLDWarper to use FSL or ANTs depending on warp file extension by Synchon Mandal (#293)

• Rewrite compute_brain_mask to allow variable template fetching via templateflow, according to target data by Synchon Mandal (#299)

• Replace requests with httpx for fetching parcellations by Synchon Mandal (#300)

• Allow BOLDWarper to warp BOLD data to other MNI spaces by Synchon Mandal (#302)

• Add support for local junifer queue via GNU Parallel by Synchon Mandal (#306)

• Improve PatternDataGrabber and PatternDataladDataGrabber’s patterns to enable space, format, mask_item and other metadata description handling via YAML by Synchon Mandal (#308)

• Improve BasePreprocessor by revamping 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 (#310)

• Improve external dependency handling for PipelineStepMixin-derived objects having implementation-based variations by Synchon Mandal (#311)

14.4.5. Features

• Introduce complexity markers: HurstExponent, MultiscaleEntropyAUC, PermEntropy, RangeEntropy, RangeEntropyAUC and SampleEntropy by Amir Omidvarnia (#145)

• Add junifer reset to reset storage and jobs directory by Synchon Mandal (#240)

• Add support for Power2013 coordinates by Synchon Mandal (#245)

• Support venv as environment kind for queueing jobs by Synchon Mandal (#249)

• Add support for AutobiographicalMemory coordinates by Synchon Mandal (#250)

• Add support for subject-native space by Synchon Mandal and Fede Raimondo (#252)

• Introduce junifer.pipeline.WorkDirManager singleton class to manage working and temporary directories across pipeline by Synchon Mandal (#254)

• Introduce get_parcellation to fetch parcellation tailored for the data by Synchon Mandal (#264)

• Introduce get_coordinates to fetch coordinates tailored for the data by Synchon Mandal (#265)

• Introduce junifer.preprocess.fsl.apply_warper._ApplyWarper to wrap FSL’s applywarp by Synchon Mandal (#266)

• Introduce BOLDWarper for warping BOLD data via FSL’s applywarp by Synchon Mandal (#267)

• Introduce DMCC13Benchmark to access DMCC13benchmark dataset by Synchon Mandal (#271)

• Add Brainnetome 246 parcellation to junifer.data by Synchon Mandal (#275)

• Introduce junifer.preprocess.ants.ants_apply_transforms_warper._AntsApplyTransformsWarper to wrap ANTs’ antsApplyTransforms by Synchon Mandal (#293)

• Introduce run_ext_cmd() to take care of the boilerplate code for running external commands from FSL, ANTs and others by Synchon Mandal (#295)

• Introduce get_xfm() to fetch transformation files for moving between template spaces by Synchon Mandal (#297)

• Introduce get_template() to fetch template space image tailored to a target data by Synchon Mandal (#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. (#299)

• Introduce SpaceWarper for warping T1w, BOLD, VBM_GM, VBM_WM, fALFF, GCOR and LCOR data to other spaces by Synchon Mandal (#301)

• Introduce QueueContextAdapter as an abstract base class for job queueing and HTCondorAdapter as its implementation for HTCondor by Synchon Mandal (#309)

14.4.6. Miscellaneous

• Update dependencies requirements by Fede Raimondo (#253)

• Pin ruff to 0.1.0 as the lowest version and update pre-commit config by Synchon Mandal (#261)

• Add support for accessing FSL via Docker wrapper along with flirt, applywarp and std2imgcoord commands by Synchon Mandal (#262)

• Improve documentation, packaging and code style by Synchon Mandal (#269)

• Add support for Python 3.12 and make Python 3.11 the base for code coverage and CI checks by Synchon Mandal (#270)

• Add support for accessing ANTs via Docker wrapper along with antsApplyTransforms and antsApplyTransformsToPoints by Synchon Mandal (#277)

• Make the external tool wrappers output to stderr instead of stdout by Synchon Mandal (#279)

• Add support for accessing FSL img2imgcoord via Docker wrapper command by Synchon Mandal (#281)

• Make BOLDWarper tool-agnostic by moving it from junifer.preprocess.fsl to junifer.preprocess by Synchon Mandal (#288)

• Add support for accessing ANTs’ ResampleImage via Docker wrapper by Synchon Mandal (#293)

• Update pyproject.toml and add FAIR shield in README.md by Synchon Mandal (#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 (#300)

14.4.7. Deprecations and Removals

• Deprecate BOLDWarper and mark for removal in v0.0.4 by Synchon Mandal (#301)

14.5. Junifer 0.0.3 (2023-07-21)

14.5.1. Bugfixes

• Enable YAML 1.2 support and allow multiline strings in YAML which would not work earlier by Synchon Mandal (#223)

• Handle datalad.IncompleteResultsError exception for partial clone in DataladDataGrabber by Synchon Mandal (#235)

14.5.2. API Changes

• Expose types parameter for DataladAOMICID1000, DataladAOMICPIOP1, DataladAOMICPIOP2 and JuselessUCLA by Synchon Mandal (#132)

• Rename junifer.testing.datagrabbers.SPMAuditoryTestingDatagrabber to SPMAuditoryTestingDataGrabber and junifer.testing.datagrabbers.OasisVBMTestingDatagrabber to OasisVBMTestingDataGrabber by Synchon Mandal (#222)

• Add BaseFeatureStorage.read() method for storage-like objects by Synchon Mandal (#236)

14.5.3. Improved Documentation

• Improve general prose, formatting and code blocks in docs and set line length for .rst files to 80 by Synchon Mandal (#220)

• Update julearn example under examples by Synchon Mandal (#242)

14.5.4. 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 (#132)

• Rename instances of “Datagrabber” to “DataGrabber” especially in junifer.testing to be consistent by Synchon Mandal (#222)

• Use ruamel.yaml instead of pyyaml as YAML I/O library by Synchon Mandal (#223)

• Adopt DataGrabber consistently throughout codebase to match with the documentation by Synchon Mandal (#226)

• Adopt DataReader consistently throughout codebase to match with the documentation by Synchon Mandal (#227)

• Enable stdout and stderr capture for AFNI commands by Synchon Mandal (#234)

• Adapt HDF5FeatureStorage.read_df() due to addition of HDF5FeatureStorage.read() by Synchon Mandal (#236)

14.5.5. Features

• Add AICHA v1 and AICHA v2 parcellations to junifer.data by Synchon Mandal (#173)

• Add Shen 2013, Shen 2015 and Shen 2019 parcellations to junifer.data by Synchon Mandal (#184)

• Add Yan 2023 parcellation to junifer.data by Synchon Mandal (#225)

• Introduce onthefly sub-module and read_transform() for quick transform operations on stored data by Synchon Mandal (#237)

14.5.6. Miscellaneous

• Consistent docstrings for pytest fixtures used in the test suite by Synchon Mandal (#228)

• Adopt ruff as the only linter for the codebase by Synchon Mandal (#229)

• Improve codespell support by fixing typos in documentation by Synchon Mandal (#230)

• Adopt pre-commit for adding and managing git pre-commit hooks by Synchon Mandal (#232)

• Improve docstrings and code style and parametrize remaining tests for junifer.data.parcellations by Synchon Mandal (#238)

• Bump numpy version constraint to >=1.24,<1.26 by Synchon Mandal (#241)

14.6. Junifer 0.0.2 (2023-03-31)

14.6.1. 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. (#127)

• Fix junifer run to respect preprocess step specified in the pipeline by Synchon Mandal (#159)

• Fix a bug in which only REST1 and REST2 tasks could be accessed in DataladHCP1200 and HCP1200 datagrabbers by Fede Raimondo (#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 (#185)

• Fix ALFFParcels, ALFFSpheres, ReHoSpheres and ReHoParcels pass the extra_input parameter by Fede Raimondo (#187)

• Fix several markers that did not properly handle the extra_input parameter by Fede Raimondo (#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. (#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 (#192)

• Fix a bug in which ParcelAggregation could yield duplicated column names if two or more parcels were used and label names were not unique by Fede Raimondo (#194)

• Fix a bug in which count() will not be correctly applied across an axis by Fede Raimondo (#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 (#199)

• Fix a bug in which get_mask fails for FunctionalConnectivityBase class, because of missing extra_input parameter by Leonard Sasse (#200)

• Fix the output of RSSETSMarker to be 2D by Synchon Mandal (#215)

14.6.2. API Changes

• Add confounds_format parameter to PatternDataGrabber constructor for improved handling of confounds specified via BOLD_confounds data type by Synchon Mandal (#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 (#181)

• Add ica_fix parameter to DataladHCP1200 and 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 (#183)

• Add pre_run parameter to _queue_condor by Fede Raimondo (#188)

• Expose allow_overlap parameter in SphereAggregation and related markers by Fede Raimondo (#190)

• Rename AmplitudeLowFrequencyFluctuationParcels and AmplitudeLowFrequencyFluctuationSpheres to ALFFParcels and ALFFSpheres by Synchon Mandal (#216)

14.6.3. Improved Documentation

• Add more documentation on registering parcellations, coordinates, and masks by Leonard Sasse (#166)

• Migrate and document changelog creation and maintenance via towncrier by Synchon Mandal (#203)

• Add copy button to documentation code blocks by Synchon Mandal (#205)

• Add sections starting and help in the documentation by Fede Raimondo (#210)

• Shorten Sphinx references across code and docs, and add black shield in README by Synchon Mandal (#218)

14.6.4. Enhancements

• Organize functional connectivity markers in junifer.markers.functional_connectivity by Synchon Mandal (#107)

• Change HCP datagrabber tests to decrease CI running time by Fede Raimondo (#155)

• Allow PartlyCloudyTestingDataGrabber to be accessible via import junifer.testing.registry by Synchon Mandal (#160)

• Update docstrings and fix typo in log message by Synchon Mandal (#165)

• Add fMRIPrep brain masks to the datagrabber patterns for all datagrabbers in the aomic sub-package by Leonard Sasse (#177)

• Improved logging output for preprocessing, collecting and pipeline building from YAML by Fede Raimondo (#185)

• Allow for empty spheres in 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 (#190)

• Allow for empty parcels in ParcelAggregation, that will result in NaNs by Fede Raimondo (#194)

• Improve metadata and data I/O for HDF5FeatureStorage by Synchon Mandal (#196)

• Force datalad to be non-interactive on queued jobs by Fede Raimondo (#201)

• Add missing abstractmethod decorators for get_valid_inputs methods of BaseMarker and BasePreprocessor by Synchon Mandal (#214)

14.6.5. Features

• Add EdgeCentricFCParcels and EdgeCentricFCSpheres by Leonard Sasse (#64)

• Expose a merge_parcellations function to merge a list of parcellations by Leonard Sasse (#146)

• Add support for HDF5 feature storage via HDF5FeatureStorage by Synchon Mandal (#147)

• Add TemporalSNRParcels and TemporalSNRSpheres by Leonard Sasse (#163)

• Add support for Power coordinates by Synchon Mandal (#167)

• Add support for Dosenbach coordinates by Synchon Mandal (#168)

• Add support for nilearn computed masks (compute_epi_mask, compute_brain_mask, compute_background_mask, fetch_icbm152_brain_gm_mask) by Fede Raimondo (#175)

• Add aggregation function 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 (#190)

14.7. Junifer 0.0.1 (2022-12-20)

14.7.1. Bugfixes

• Fix a bug in which a PatternDataGrabber would now work with relative datadir paths (reported by Leonard Sasse, fixed by Fede Raimondo) (#96, #98)

• Fix a bug in which DataladAOMICPIOP2 datagrabber did not use user input to constrain elements based on tasks by Leonard Sasse (#105)

• Fix a bug in which a datalad dataset could remove a user-cloned dataset by Fede Raimondo (#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 (#143)

14.7.2. API Changes

• Change the single_output default parameter in storage classes from False to True by Fede Raimondo (#134)

14.7.3. 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 (#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 (#114)

14.7.4. Enhancements

• Add comments to DataladDataGrabber datagrabber and change to use datalad-clone instead of datalad-install by Benjamin Poldrack (#55)

• Upgrade storage interface for storage-like objects by Synchon Mandal (#84)

• Add missing type annotations by Synchon Mandal (#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 DataladHCP1200 datagrabber by Synchon Mandal (#93)

• Refactor DataladAOMICID1000 slightly by Leonard Sasse (#94)

• Rename “atlas” to “parcellation” by Fede Raimondo (#116)

• Refactor the BaseDataGrabber class to allow for easier subclassing by Fede Raimondo (#123)

• Allow custom aggregation method for SphereAggregation by Synchon Mandal (#102)

• Add support for “masks” by Fede Raimondo (#79)

• Allow ParcelAggregation to apply multiple parcellations at once by Fede Raimondo (#131)

• Refactor PipelineStepMixin to improve its implementation and validation for pipeline steps by Synchon Mandal (#152)

14.7.5. Features

• Implement SPMAuditoryTestingDataGrabber datagrabber by Fede Raimondo (#52)

• Implement matrix storage in SQliteFeatureStorage by Fede Raimondo (#42)

• Implement FunctionalConnectivityParcels marker for functional connectivity using a parcellation by Amir Omidvarnia and Kaustubh R. Patil (#41)

• Implement register_coordinates, list_coordinates and load_coordinates by Fede Raimondo (#11)

• Add DataladAOMICID1000 datagrabber for AOMIC ID1000 dataset including tests and creation of mock dataset for testing by Vera Komeyer and Xuan Li (#60)

• Add support to access other input in the data object in the compute method by Fede Raimondo

• Implement RSSETSMarker marker by Leonard Sasse, Nicolas Nieto and Sami Hamdan (#51)

• Implement SphereAggregation marker by Fede Raimondo (#83)

• Implement DataladAOMICPIOP1 and DataladAOMICPIOP2 datagrabbers for AOMIC PIOP1 and PIOP2 datasets respectively by Leonard Sasse (#94)

• Implement JuselessDataladCamCANVBM datagrabber by Leonard Sasse (#99)

• Implement JuselessDataladIXIVBM CAT output datagrabber for juseless by Leonard Sasse (#48)

• Add junifer wtf to report environment details by Synchon Mandal (#33)

• Add junifer selftest to report environment details by Synchon Mandal (#9)

• Implement JuselessDataladAOMICID1000VBM datagrabber for accessing AOMIC ID1000 VBM from juseless by Felix Hoffstaedter and Synchon Mandal (#57)

• Add fMRIPrepConfoundRemover by Fede Raimondo and Leonard Sasse (#111)

• Implement CrossParcellationFC marker by Leonard Sasse and Kaustubh R. Patil (#85)

• Add JuselessUCLA datagrabber for the UCLA dataset available on juseless by Leonard Sasse (#118)

• Introduce a singleton decorator for marker computations by Synchon Mandal (#151)

• Implement ReHoParcels and ReHoSpheres markers by Synchon Mandal (#36)

• Implement ALFFParcels and ALFFSpheres markers by Fede Raimondo (#35)

14.7.6. Miscellaneous

• Create the repository based on the mockup by Fede Raimondo