v0.0.6

What's Changed

• [FIX]: Correct command for mri_binarize in BrainPrint by @synchon in #356
• [ENH]: Set proper stdout encoding for run_ext_cmd by @synchon in #357
• [ENH]: Add brainprint onthefly functions by @synchon in #354
• [ENH]: In-built support for spearman correlation for FunctionalConnectivity markers by @synchon in #335
• [DOC]: Add doc for analysing storage-like objects by @synchon in #359
• [FIX]: Enable spike for fMRIPrepConfoundRemover by @synchon in #360
• [DOC]: Improve Sphinx configuration and extensions by @synchon in #358
• [ENH]: Introduce new cli sub-package by @synchon in #361
• [ENH]: Allow for external modules to import other files by @fraimondo in #367
• [ENH]: Adapt junifer to have lazy imports by @synchon in #355
• [BUG]: Typo for fMRIPrepConfoundRemover pipeline registration by @synchon in #369
• Add emomatching task to AOMIC PIOP2 datagrabber by @LeSasse in #371
• [MAINT]: Drop Python 3.8 and support Python 3.13 by @synchon in #372
• [CI]: Add Dockerfile for building docs by @synchon in #373
• [ENH]: Use datalad human-template-xfms dataset for junifer.data.get_xfm() by @synchon in #368
• [CI]: Adopt custom CI image for junifer docs by @synchon in #374
• [CI]: Update dependabot.yml to support groups by @synchon in #380
• [CI]: Add Dockerfile for CI by @synchon in #382
• [MAINT]: Improve docs publishing by @synchon in #384
• [ENH]: Introduce PipelineComponentRegistry by @synchon in #362
• [ENH]: Introduce data registries by @synchon in #387
• [CI]: Adopt custom CI image for junifer test by @synchon in #383
• [BUG]: DataladDataGrabber is not using the WorkDirManager by @fraimondo in #386
• [ENH]: Refactor Singleton as a metaclass by @fraimondo in #391
• Bypass cleanup of temporary dirs if needed by @fraimondo in #389
• [ENH]: Introduce junfer.typing module by @synchon in #392
• [ENH]: Update Warp datatype schema and logic by @synchon in #390
• [MAINT]: Update type hints to be Python>=3.9 compatible by @synchon in #393
• [BUG]: Coordinates transforms to native space using ANTs are off by @synchon in #388
• [BUG]: Fix metadata update for MultipleDataGrabber by @synchon in #398
• [ENH]: Introduce ConfigManager by @fraimondo in #401
• [ENH]: Use junifer.utils.config to skip dataset id and dirty checks (time consuming) by @fraimondo in #403
• [ENH]: Allow workdir to forward parameters from YAML by @synchon in #402
• [ENH]: Introduce BOLD.reference nested data type by @synchon in #407
• Provide data in all spaces for AOMIC datasets by @fraimondo in #405
• [BUG]: External dependencies not found despite being there by @synchon in #385
• [ENH]: Refactor Preprocessors to sync data and their paths by @synchon in #408
• [BUG]: Correct file reading for AFNI outputs by @synchon in #409
• [ENH]: Logging with a color formatter by @fraimondo in #412
• [ENH]: Update get_template interface by @synchon in #413
• [ENH]: Rework masking logic by @synchon in #395
• [ENH]: Enable compute_brain_mask to use subject-specific probseg files by @fraimondo in #404
• [ENH]: Rework parcellation logic by @synchon in #411
• [ENH]: Simplify space warping for parcellations and masks by @synchon in #414
• [ENH]: Allow template space request for compute_brain_mask by @synchon in #415
• [ENH]: Add helper function for getting correct interpolator for masks by @synchon in #416
• [ENH]: Raise/warn if element is not ran by @synchon in #319
• [BUG]: fMRIPrepConfoundRemover sets incorrect t_r due to nilearn.image.clean_img by @synchon in #420
• [CI]: Upgrade Docker images and workflows by @synchon in #396
• chore(deps): bump the actions group across 1 directory with 6 updates by @dependabot in #419
• Allow to store 2d timeseries by @fraimondo in #422
• FIx CI coverage by @fraimondo in #424
• [ENH]: Use junifer-data datalad dataset for fetching data by @synchon in #418
• [ENH]: Move data downloading/handling to junifer-data package. by @synchon in #363
• [ENH]: Add scrubbing support in fMRIPrepConfoundRemover by @synchon in #421
• [CI]: Adapt usage of junifer-data for Docker images by @synchon in #427
• [CI]: Update CI workflows by @synchon in #428
• [BUG]: Cannot fetch Power2011 coordinates by @synchon in #431
• Use hexsha to verify junifer-data integrity by @fraimondo in #434
• chore(deps): bump the actions group across 1 directory with 4 updates by @dependabot in #433
• Power2011 and Power2013 files contain the same coordinates with mismatched ROI numbering by @synchon in #436
• [CI]: Bump junifer-data to v2 for building Docker images by @synchon in #438
• [MAINT]: Bump junifer-data version to v2 by @synchon in #437
• [BUG]: Correct methods for *_data() functions by @synchon in #439
• [ENH]: Prepare Junifer for extension support by @synchon in #366
• [MAINT]: Release 0.0.6 by @synchon in #442

Full Changelog: v0.0.5...v0.0.6

v0.0.5

What's Changed

• [ENH]: Specify which shell to use when using junifer queue by @synchon in #273
• [ENH]: Smoothing images as a preprocessing step by @synchon in #161
• [BUG]: Extra dimension added to parcellation after warping to another template space via ANTs by @synchon in #324
• [ENH]: Add junifer list-elements for listing out elements of an YAML's DataGrabber by @synchon in #323
• [DOC]: Change __init__.py docstrings to reflect sub-packages by @synchon in #115
• [DOC]: Add missing types in DataGrabber types docstrings by @synchon in #330
• [BUG]: junifer reset fails as it tries to delete junifer_jobs directory by @synchon in #332
• [MAINT]: Remove deprecations from 0.0.3 and 0.0.4 by @synchon in #336
• [BUG]: Merge parcellations fail with extra dimensions by @synchon in #331
• [BUG]: Extra dimension added to mask after warping via ANTs by @synchon in #340
• chore(deps): bump peaceiris/actions-gh-pages from 3 to 4 by @dependabot in #329
• [BUG]: Validation failure of multiple pre-processing steps with different input data types requirement by @synchon in #339
• [ENH]: Add support for FreeSurfer via Docker by @synchon in #342
• [ENH]: Refactor DataGrabber patterns by @synchon in #341
• [ENH]: Add scalar table storage support for HDF5FeatureStorage by @synchon in #343
• [ENH]: Unix path expansion directives support for PatternDataGrabber by @synchon in #345
• [ENH]: Add support for FreeSurfer data type by @synchon in #346
• [ENH]: Add support for BrainPrint by @synchon in #344
• [MAINT]: Regular repository maintenance by @synchon in #337
• [MAINT]: Update dependencies by @synchon in #347
• [ENH]: Add test for JuniferNiftiSpheresMasker against nilearn's version by @synchon in #136
• [DOC]: venv example by @synchon in #327
• [CI]: Improve CI by @synchon in #318
• [ENH]: Add UKB_15K_GM mask by @synchon in #350
• [ENH]: Enable Markers to extract multiple features by @synchon in #349
• [CI]: Fix examples by @fraimondo in #352
• [ENH]: Introduce JuniferConnectivityMeasure by @synchon in #348
• [ENH]: Adapt MultipleDataGrabber to patterns with nested data types by @synchon in #351
• [MAINT]: Release 0.0.5 by @synchon in #353

Full Changelog: v0.0.4...v0.0.5

v0.0.4

What's Changed

• [DOC]: Add Zenodo shield and improve documentation by @synchon in #247
• [BUG]: Jobs fail with new condor_submit_dag changes by @synchon in #233
• [ENH]: Add feature_md5 argument to read_transform() by @synchon in #248
• [ENH]: Bump dependencies by @fraimondo in #253
• [ENH]: Support for Power 2013 coordinates by @synchon in #245
• [BUG]: extMDN coordinates are falsely registered as extDMN coordinates in junifer by @synchon in #251
• [ENH]: Add support for subject(s) file for junifer run by @synchon in #182
• [ENH]: Introduce WorkDirManager by @synchon in #254
• [ENH]: Add element-scoped directories for WorkDirManager by @synchon in #258
• [ENH]: Improve element-specific directory cleanup for WorkDirManager by @synchon in #259
• [MAINT]: Pin ruff and update housekeeping configs by @synchon in #261
• [ENH]: Improve BasePreprocessor and fMRIPrepConfoundRemover by @synchon in #260
• [ENH]: Add support for FSL via Docker by @synchon in #262
• [ENH]: Introduce junifer.data.get_parcellation() by @synchon in #264
• [ENH]: Introduce junifer.data.get_coordinates() by @synchon in #265
• [ENH]: Add support for multiple preprocessors in the pipeline by @synchon in #263
• [ENH]: Introduce _ApplyWarper by @synchon in #266
• [ENH]: Introduce BOLDWarper by @synchon in #267
• [ENH]: Add space awareness to existing components by @synchon in #268
• [ENH]: Add support for native space by @synchon in #252
• [MAINT]: Improve docs, packaging and code style by @synchon in #269
• [ENH]: Add DMCC13Benchmark DataGrabber by @synchon in #271
• [FIX]: Fix _check_fsl() by @synchon in #272
• [FIX]: Make native warped components persist by @synchon in #274
• [ENH]: Complexity features by @omidvarnia in #145
• [BUG]: relative path in with block in YAML is interpreted relative from YAML, but copy operation to junifer jobs directory interprets relative to working directory. by @synchon in #224
• [BUG]: Fix interpolation scheme for native parcellation and mask by @synchon in #276
• [ENH]: Add support for ANTs via Docker by @synchon in #277
• [BUG]: Fix FSL std2imgcoord I/O by @synchon in #278
• [ENH]: Use stderr for external tool wrappers' output by @synchon in #279
• [BUG]: Fix FSL std2imgcoord source image by @synchon in #280
• [BUG]: Replace FSL std2imgcoord with img2imgcoord by @synchon in #281
• [BUG]: Propagate ReHo and fALFF maps' file paths by @synchon in #282
• [BUG]: WorkDirManager does not accept string as workdir by @synchon in #283
• update: correct register_mask import in code example by @tomug in #291
• [MAINT]: Make BOLDWarper tool-agnostic by @synchon in #288
• [BUG]: Correct path propagation logic for ReHoEstimator and ALFFEstimator by @synchon in #286
• [MAINT]: Update README and pyproject.toml by @synchon in #294
• [ENH]: Add mode as an aggregation function for get_aggfunc_by_name by @synchon in #287
• [BUG]: Mask "inherit" will be warped twice if working in native space. by @synchon in #284
• [ENH]: Introduce _AntsApplyTransformsWarper by @synchon in #293
• [ENH]: Introduce run_ext_cmd for running external commands by @synchon in #295
• [ENH]: Introduce get_xfm for fetching transformation files by @synchon in #297
• [MAINT]: Improve repository by @synchon in #300
• chore(deps): bump actions/setup-python from 4 to 5 by @dependabot in #303
• chore(deps): bump actions/checkout from 3 to 4 by @dependabot in #304
• chore(deps): bump codecov/codecov-action from 3 to 4 by @dependabot in #305
• [ENH]: Introduce get_template for getting templates by @synchon in #298
• [ENH]: Allow BOLDWarper to warp between MNI spaces by @synchon in #302
• [ENH]: Allow for using venv in queue kind by @synchon in #249
• [ENH]: Coordinates - Autobiographical Memory by @synchon in #250
• [ENH]: Support Brainnetome 246 parcellation by @synchon in #275
• [ENH]: Implement junifer reset to delete job/results file. by @synchon in #240
• [ENH]: Introduce QueueContextAdapter and HTCondorAdapter by @synchon in #309
• [ENH]: Improve BasePreprocessor by @synchon in #310
• Improve external dependency handling of PipelineStepMixin by @synchon in #311
• [MAINT]: Add support for Python 3.12 by @synchon in #270
• [FIX]: Element parsing for HTCondor via VARS by @synchon in #312
• [ENH]: Preprocessing step to warp any image to any standard space by @synchon in #301
• [FIX]: Element access for DMCC13Benchmark by @synchon in #314
• [ENH]: Allow for local queue using GNU parallel by @synchon in #306
• [DOC]: Improve documentation by @synchon in #317
• [ENH]: Add support for on-the-fly template space transformation by @synchon in #299
• [ENH]: Improving DataGrabber patterns by @synchon in #308
• [FIX] change files to executables. by @fraimondo in #321
• [FIX]: Change all probseg_ appearances with VBM_ for consistency by @fraimondo in #320
• [BUG]: subject ID truncated incorrectly in condor submit dag file by @synchon in #322
• Follow the datasets BIDS convention for participants/sessions by @fraimondo in #325
• [MAINT]: Release 0.0.4 by @synchon in #328

New Contributors

• @omidvarnia made their first contribution in #145
• @tomug made their first contribution in #291
• @dependabot made their first contribution in #303

Full Changelog: v0.0.3...v0.0.4

v0.0.3

What's Changed

• [DOC]: Improve documentation by @synchon in #220
• [ENH]: Consistent DataGrabber naming in testing by @synchon in #222
• [MAIN]: Add junifer to conda-forge by @synchon in #221
• [ENH]: Use ruamel.yaml in place of pyyaml by @synchon in #223
• [MAINT]: Improve codespell support by @synchon in #230
• [MAINT]: Consistent use of DataGrabber by @synchon in #226
• [MAINT]: Consistent use of DataReader by @synchon in #227
• [MAINT]: Consistent pytest fixture naming by @synchon in #228
• [ENH]: Add support for ruff linter by @synchon in #229
• [ENH]: Add support for pre-commit by @synchon in #232
• [ENH]: Enable stdout and stderr capturing for AFNI commands by @synchon in #234
• [BUG]: No error is logged if datalad fails to clone a repository by @synchon in #235
• [ENH]: Add read() method for storage-like objects by @synchon in #236
• [ENH]: Homotopic AICHA parcellation (version 2) by @synchon in #173
• [ENH]: 268 ROIs Shen Parcellation from Finn et al. (2015) by @synchon in #184
• [ENH]: Introduce new onthefly sub-module for quick transforms for analyses by @synchon in #237
• [ENH]: Homotopic Version of Schaefer Parcellation by @synchon in #225
• [MAINT]: junifer.data.parcellations cleanup by @synchon in #238
• [MAINT]: Bump numpy version by @synchon in #241
• [MAINT]: Bump and update julearn example by @synchon in #242
• [ENH]: Allow users to select types for datagrabbers in order to avoid downloading unnecesary data. by @synchon in #132
• [MAINT]: Release 0.0.3 by @synchon in #246

Full Changelog: v0.0.2...v0.0.3

v0.0.2

Full Changelog: v0.0.1...v0.0.2

v0.0.1

New Contributors

• @bpoldrack made their first contribution in #55
• @samihamdan made their first contribution in #72
• @kaurao made their first contribution in #62
• @verakye made their first contribution in #76
• @susanneweis made their first contribution in #70
• @FeHoff made their first contribution in #57

Full Changelog: https://github.com/juaml/junifer/commits/v0.0.1