What’s new

0.3.2

Released on 2024-12-12 - GitHub - PyPI

What's Changed

This release introduces two new commands:

• nipoppy status: get summary information about the dataset, including how many participants/sessions are in the manifest, have been BIDSified, or have been processed
• nipoppy extract: run extraction pipelines that depend on certain processing pipelines (configured in the global config file)

Features

• [ENH] Add status command to display high-level participant counts by @nikhil153 in #419
• [ENH] add nipoppy extract command by @michellewang in #399
• [ENH] Add FreeSurfer aparc/aseg stats extractor by @michellewang in #342

Documentation

• [DOC] Add icon/link to GitHub repo in docs footer by @michellewang in #434

Maintenance

• [MAINT] Exclude PyBIDS version 0.18.0 from dependencies by @michellewang in #449

Full Changelog: 0.3.1...0.3.2

0.3.1

Released on 2024-11-12 - GitHub - PyPI

What's Changed

Features

• [ENH] Allow BIDS datasets without session level by @mtorabi59 in #420
• [ENH] Add fMRIPrep 24.1.1 by @michellewang in #426

Maintenance

• [MAINT] refactor pipeline steps. by @mathdugre in #418

Full Changelog: 0.3.0...0.3.1

0.3.0

Released on 2024-10-31 - GitHub - PyPI

What's Changed

Breaking changes

• [ENH] Add _id suffix to bids_participant and bids_session by @michellewang in #382
• [ENH] Make TRACKER_CONFIG_FILE part of pipeline step config instead of pipeline config by @michellewang in #352
• [API] make --dataset-root and positional arg. by @mathdugre in #390
• [ENH] Update pipeline config layout by @michellewang in #383
• [ENH] Use TSV instead of CSV for tabular files by @michellewang in #381
• [ENH] Update layout by @michellewang in #379
• [ENH] Rename doughnut columns by @michellewang in #404
• [ENH] Update bagel columns by @michellewang in #354

Documentation

• [DOC] Update dataset layout figure by @michellewang in #412
• [DOC] Update file trees in user guide page for DICOM reorg by @michellewang in #408

Misc

• [REL] Fix merge conflict for REL 0.3.0 by @mathdugre in #417
• [REL] Release 0.3.0 by @mathdugre in #416

Full Changelog: 0.2.3...0.3.0

0.2.3

Released on 2024-10-10 - GitHub - PyPI

What's Changed

Features

• [ENH] make fmriprep --fs-no-reconall value-key and id more intuitive. by @mathdugre in #406

Bug Fixes

• [BUG] keep working directory on failed run / flag to keep pipeline working directory on success by @bcmcpher in #345
• [BUG] Do not pool BIDS and PROC pipelines together when searching pipeline configs by @michellewang in #391
• [FIX] Do not enable markup language processing when logging messages related to subprocesses by @michellewang in #410

Maintenance

• [MAINT] Only move PRs to pending review. by @mathdugre in #389

Full Changelog: 0.2.2...0.2.3

0.2.2

Released on 2024-09-27 - GitHub - PyPI

What's Changed

Features

• [ENH] Init a Nipoppy dataset with a BIDS dataset by @Remi-Gau in #358

Bug Fixes

• [BUG] Fix logging issues by @michellewang in #356
• [FIX] Support latest version of doc dependencies by @michellewang in #365
• [BUG] Fix logo path by @mathdugre in #376
• [BUG] Fix logo again... by @mathdugre in #377

Documentation

• [DOC] Add auto-generated changelog page to docs by @michellewang in #361
• [DOC] Update contribution guide by @michellewang in #375
• [DOC] Add logo by @michellewang in #347

Maintenance

• [MAINT] Refactor pipeline step config in workflow classes by @michellewang in #362
• [MAINT] test with python 3.13 by @Remi-Gau in #359

Misc

• [ENH] Pybids database creation toggle (fixed) for issue #253 by @jacobsanz97 in #371

New Contributors

• @jacobsanz97 made their first contribution in #371

Full Changelog: 0.2.1...0.2.2

0.2.1

Released on 2024-09-12 - GitHub - PyPI

What's Changed

Breaking Changes

• [MAINT] Clean up legacy files by @michellewang in #339

Features

• [ENH] add automatic release notes for GitHub. by @mathdugre in #322
• [ENH] Add "ANALYSIS_LEVEL" field to pipeline step config to allow group-level processing by @michellewang in #341

Bug Fixes

• [FIX] Improve pipeline config substitutions by @michellewang in #300
• [FIX] Fix various bugs in sample JSON config files by @michellewang in #299
• [BUG] Fix error when using invalid verbosity level by @michellewang in #330
• [BUG] Heudiconv invocation fix by @nikhil153 in #314
• [BUG] Fix label_new_issue.yml failing by @michellewang in #344

Documentation

• [DOC] Update installation instructions by @mathdugre in #326

Maintenance

• [MAINT] automatically label issue and PRs based on prefixes by @mathdugre in #338

Misc

• [ENH] Add GitHub Project automation by @michellewang in #333
• [FIX] Add changes erased by force-push by @michellewang in #336

Full Changelog: 0.2.0...0.2.1

0.2.0

Released on 2024-08-15 - GitHub - PyPI

What's Changed

• codespell: config, workflow and typos fixed by @yarikoptic in #104
• renamed fmriprep hpc run scripts by @nikhil153 in #96
• Add nimhans_serb repo to update_dataset_repos.yml by @michellewang in #108
• Make small changes to check_dicom_status.py by @michellewang in #98
• Move README.md to docs by @michellewang in #110
• [DOC] add zenodo DOI badge to README.md by @Remi-Gau in #106
• Merge TractoFlow Workflow by @bcmcpher in #112
• TractoFlow Adjustments by @bcmcpher in #113
• Fix dicom_org issues and update bids_conv by @michellewang in #111
• add nipoppy_nimhans to update_dataset_repos.yml by @michellewang in #114
• Added MAGeT Brain scripts by @nikhil153 in #123
• Update repo names in GitHub actions for updating dataset forks by @michellewang in #125
• Renamed mr_proc mentions by @nikhil153 in #127
• Fix small issues with DICOM-to-BIDS conversion by @michellewang in #128
• added requests module and fixed import path in check_dicom_status.py by @nikhil153 in #130
• [MAINT] add test to run in ci for fmriprep workflow by @Remi-Gau in #132
• Attempt to fix merge conflicts after #132 by @michellewang in #136
• moving sample_global_configs.json and tree.json to the nipoppy subdir by @nikhil153 in #137
• fixed import paths after refactor by @nikhil153 in #139
• Use bids_id in doughnut file only instead of manifest and doughnut by @michellewang in #133
• Minor fixes to files and check_dicom_status.py by @michellewang in #140
• Do not run Codespell on *.ipynb files by @michellewang in #142
• refactored and cleaned up mriqc run script by @nikhil153 in #143
• Add GitHub Actions workflow to prevent downstream forks changing files tracked in main repo by @michellewang in #146
• Fix bug where doughnut.csv loses rows after BIDS conversion by @michellewang in #145
• Do not check changed files when syncing with downstream forks by @michellewang in #154
• Make Codespell ignore HTML files and PPMI-specific file by @michellewang in #153
• Update trackers following changes in dashboard schema (+ other improvements) by @michellewang in #95
• Started tracker refactoring to use doughnut by @nikhil153 in #148
• Do not trigger Codespell on push events by @michellewang in #161
• Assume dicom_dir is participant_id if custom function is not provided by @michellewang in #157
• add session_id to participant_id_to_dicom_dir() by @michellewang in #165
• update to tractoflow run for bval parsing by @bcmcpher in #166
• Make backups of bagel.csv and check it when tracking pipelines (+ refactor status -> doughnut) by @michellewang in #162
• Updates to trackers and global variable handling by @nikhil153 in #163
• Issue 172 by @bcmcpher in #173
• fixed errors from previous merge conflict resolution by @nikhil153 in #170
• Make parent directory of output file in make_squash.sh by @michellewang in #158
• Minor fixes to trackers by @nikhil153 in #177
• Quick fix for tractoflow data parsing missing valid T1s by @bcmcpher in #179
• Update trackers to use manifest and handle tar archives by @michellewang in #181
• use doughnut file to get BIDS ID in run_tracker.py (create if needed) by @michellewang in #185
• FC run_script by @mtorabi59 in #183
• removed version (i.e. v) prefix from run scripts to match trackers and refactored FS extractor by @nikhil153 in #188
• add "ses-" prefix to sample_global_configs.json by @michellewang in #195
• Fix Tractoflow runscript bugs by @michellewang in #198
• Fix MRIQC (and fMRIPrep) runscript bugs by @michellewang in #194
• Remove symlinks from tractoflow output by @bcmcpher in #200
• Fix TractoFlow symlink bugs by @michellewang in #202
• Add dcm2bids conversion by @danyluik in #189
• [MAINT] Expand testing and add coverage by @Remi-Gau in #144
• add checks for dir exist by @mtorabi59 in #207
• Refactor into a CLI by @michellewang in #205
• Add docs built with Sphinx by @michellewang in #209
• [DOC] make install command more robust by @Remi-Gau in #215
• [DOC] fix edit button and unpin doc dependencies by @Remi-Gau in #216
• [DOC] build schema before doc and ignore autodoc related warnings by @Remi-Gau in #218
• fixed bugs related to maget-brain data prep and tracking options by @nikhil153 in #196
• [MAINT] use official fids by @Remi-Gau in #220
• [FIX] Make sure Python >=3.9 is supported by @michellewang in #237
• [ENH] Add DICOM header checking and DicomDirMap to DicomReorgWorkflow by @michellewang in #229
• [ENH] Update global config specification by @michellewang in #238
• [ENH] Make sure workflows do not run again for participant/sessions that already have expected output by @michellewang in #259
• [ENH] Rename tabular file columns to visit_id and session_id by @michellewang in #263
• [FIX] Write updated doughnut file to disk at the end of DicomReorgWorkflow and BidsConversionWorkflow by @michellewang in #260
• [ENH] Add default tracker config files for fMRIPrep and FreeSurfer, and update default invocation files by @michellewang in #265
• [FIX] Fix doughnut path and other bugs by @michellewang in #274
• [ENH] Add descriptors and sample invocations for BIDScoin by @michellewang in #267
• [FIX] Fix command-line for fMRIPrep, MRIQC and HeuDiConv descriptors by @michellewang in #275
• [FIX] Fix nipoppy run creating empty PyBIDS database on second (and later) loop iteration by @michellewang in #283
• [FIX] Add pipeline_starttime to bagel file by @michellewang in #286
• [FIX] Remove working directory in PipelineRunner instead of BasePipelineWorkflow by @michellewang in #288
• [ENH] [REFACTOR] imports to improve performance of the cli. by @mathdugre in #281
• [MAINT] Stop syncing with dataset fork repositories by @michellewang in #303
• [DOC] Add user guide by @michellewang in #243
• [MAINT] change linting config and apply pre-commit by @Remi-Gau in #311
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #313
• [ENH] Add workflow for releases by @michellewang in #308
• [ENH] Add success/summary message at the end of each workflow by @michellewang in #261
• [ENH] add version to cli by @Remi-Gau in #319
• [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in #320
• [MAINT] Fix (?) release workflow by @michellewang in #317

New Contributors

• @yarikoptic made their first contribution in #104
• @danyluik made their first contribution in #189
• @mathdugre made their first contribution in #281
• @pre-commit-ci made their first contribution in #313

Full Changelog: 0.1.0...0.2.0

0.1.0

Released on 2023-06-27 - GitHub - PyPI

What's Changed

• Add some notes and tab data folders. by @Vincent-wq in #1
• Upload of the original pipeline. by @Vincent-wq in #2
• updating heudiconv scripts for PPMI by @Vincent-wq in #3
• PPMI BIDS conversion complete. by @Vincent-wq in #4
• Adding sge support and updating heuristics with Nikhil. by @Vincent-wq in #5
• Create session reorganization before conversion. by @Vincent-wq in #6
• BIC server sge scripts finished with correct sessions. by @Vincent-wq in #7
• Ppmi preproc branch established by @Vincent-wq in #9
• Revert "Ppmi preproc branch established" by @Vincent-wq in #10
• Revert "Ppmi preproc branch established" by @Vincent-wq in #11
• Merge workflow template with amin branch by @nikhil153 in #13
• Nimhans added by @nikhil153 in #37
• mriqc run and evaluate scripts by @InesGP in #38
• Update function name by @InesGP in #40
• Adding nimhans changes to the main branch by @nikhil153 in #44
• Nimhans by @nikhil153 in #45
• converted SGE script to python script by @InesGP in #46
• updated mriqc scripts by @InesGP in #47
• mriqc tracker by @InesGP in #55
• Update .gitignore and remove dataset-specific files by @michellewang in #68
• Update README.md by @nikhil153 in #71
• GitHub Actions workflow to update downstream dataset repos by @michellewang in #70
• Fix GitHub Actions for updating dataset repos by @michellewang in #72
• added exploratory analysis of QPN visits by @nikhil153 in #74
• Revert "added exploratory analysis of QPN visits" by @nikhil153 in #76
• refactored run script of fmriprep to remove shell script dependency by @nikhil153 in #73
• Updated mr_proc_manifest path and column names in catalog, dicom_reorg, and bids_conv by @nikhil153 in #78
• Update README.md by @michellewang in #82
• added pybids as dependency by @bcmcpher in #84
• updated run_mriqc to use global config by @InesGP in #77
• refactored run scripts and added extractor module by @nikhil153 in #79
• Fix/update trackers by @michellewang in #81
• resolving harmonization issues with mriqc run script by @InesGP in #88
• Small leftover changes after refactoring of shell scripts into python run scripts and and trackers by @nikhil153 in #91
• Refactor DICOM-to-BIDS conversion to use doughnut.csv by @michellewang in #89
• Update sample global configs by @michellewang in #101
• [MAINT] add citation file and validation workflow by @Remi-Gau in #105

New Contributors

• @michellewang made their first contribution in #68
• @Remi-Gau made their first contribution in #105

Full Changelog: https://github.com/neurodatascience/mr_proc/commits/0.1.0