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Recent Releases of nipoppy

nipoppy - 0.4.1

What's Changed

This release introduces some enhancements and minor bug fixes. Notable changes include: * A new --force flag to allow nipoppy init in a non-empty directory * A new nipoppy-gui command (need extra dependency, e.g. pip install nipoppy[gui]) for an in-Terminal "graphical" user interface * Usage of the "container-image" field in Boutiques descriptors (if specified) to launch containers. This means descriptors do not need to have Nipoppy-specific elements anymore (e.g. [[NIPOPPY_CONTAINER_COMMAND]] [[NIPOPPY_FPATH_CONTAINER]] in the "command-line" field). Usage of containers can be disabled by setting CONTAINER_CONFIG.COMMAND to null in the global config file. * This is a non-breaking change: existing descriptors do not have to be updated, but pipeline developers wishing to have descriptors usable outside of Nipoppy can make the following changes: * Remove [[NIPOPPY_CONTAINER_COMMAND]] [[NIPOPPY_FPATH_CONTAINER]] from the "command-line" field * Add executable name to the "command-line" field if not already present * Add "container-image" field * See here for an example

Features

  • [ENH]: allow forced dataset init on non-empty dirs by @asmacdo in https://github.com/nipoppy/nipoppy/pull/682
  • [ENH] Terminal user interface (GUI-ish) by @mathdugre in https://github.com/nipoppy/nipoppy/pull/651
  • [ENH] Let bosh handle container launching by @michellewang in https://github.com/nipoppy/nipoppy/pull/686
  • [ENH]: s/DATASETROOT/NIPOPPYPROJECT_ROOT by @asmacdo in https://github.com/nipoppy/nipoppy/pull/692
  • [ENH] Improve log error messages by @mathdugre in https://github.com/nipoppy/nipoppy/pull/630
  • [ENH] Expose more data in template HPC job script by @michellewang in https://github.com/nipoppy/nipoppy/pull/719 ### Bug Fixes
  • [BUG] Exit with non-zero code if no participants/sessions were found when running a pipeline by @michellewang in https://github.com/nipoppy/nipoppy/pull/690
  • [BUG] Fix Zenodo upload failure if user has no affiliation by @michellewang in https://github.com/nipoppy/nipoppy/pull/691
  • [BUG] Fix GitHub repo variable in test workflow by @michellewang in https://github.com/nipoppy/nipoppy/pull/702
  • [FIX] Update Nipoppy layout figure by @michellewang in https://github.com/nipoppy/nipoppy/pull/703
  • [BUG] Fix race condition in Zenodo API test by @michellewang in https://github.com/nipoppy/nipoppy/pull/705
  • [BUG] Fix incompatibility with pysqa 0.3.0 by @michellewang in https://github.com/nipoppy/nipoppy/pull/718
  • [BUG] Fix logfile being created even if layout validation fails by @michellewang in https://github.com/nipoppy/nipoppy/pull/724
  • [BUG] HPC command generation: run --> process by @jacobsanz97 in https://github.com/nipoppy/nipoppy/pull/725 ### Documentation
  • [DOC] Add "how-to" guide for creating a manifest file by @michellewang in https://github.com/nipoppy/nipoppy/pull/528
  • [DOC] Add tutorial: Nipoppy + MRIQC from BIDS dataset by @michellewang in https://github.com/nipoppy/nipoppy/pull/652
  • [DOC] added minimal guidelines to organize tabular data by @nikhil153 in https://github.com/nipoppy/nipoppy/pull/696
  • [DOC] Add DataLad + Nipoppy tutorial by @asmacdo in https://github.com/nipoppy/nipoppy/pull/685
  • [DOC] Add how-to guides for local/HPC parallelization by @michellewang in https://github.com/nipoppy/nipoppy/pull/713 ### Maintenance
  • [MAINT] Update version in CITATION.cff file by @nipoppy-bot[bot] in https://github.com/nipoppy/nipoppy/pull/655
  • [MAINT] Bump sigstore/gh-action-sigstore-python from 3.0.0 to 3.0.1 by @dependabot[bot] in https://github.com/nipoppy/nipoppy/pull/671
  • [MAINT] Bump fjogeleit/yaml-update-action from 0.16.0 to 0.16.1 by @dependabot[bot] in https://github.com/nipoppy/nipoppy/pull/660
  • [MAINT] Fix various small issues by @mathdugre in https://github.com/nipoppy/nipoppy/pull/695
  • [MAINT] Refactor Zenodo API tests and increase coverage by @michellewang in https://github.com/nipoppy/nipoppy/pull/697
  • [MAINT] restructure the test in folders. by @mathdugre in https://github.com/nipoppy/nipoppy/pull/698
  • [MAINT] Refactor cli structure and tests by @mathdugre in https://github.com/nipoppy/nipoppy/pull/699
  • [MAINT] Enable colors in GH actions. by @mathdugre in https://github.com/nipoppy/nipoppy/pull/730 ### Misc
  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci[bot] in https://github.com/nipoppy/nipoppy/pull/668
  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci[bot] in https://github.com/nipoppy/nipoppy/pull/721
  • Make copyright year dynamic by @mathdugre in https://github.com/nipoppy/nipoppy/pull/726

New Contributors

  • @nipoppy-bot[bot] made their first contribution in https://github.com/nipoppy/nipoppy/pull/655
  • @asmacdo made their first contribution in https://github.com/nipoppy/nipoppy/pull/682

Full Changelog: https://github.com/nipoppy/nipoppy/compare/0.4.0...0.4.1

- Python
Published by nipoppy-bot[bot] 6 months ago

nipoppy - 0.4.0

What's Changed

🔴 BREAKING CHANGES 🔴

  • The doughnut.tsv file has been renamed to curation_status.tsv, and the bagel.tsv file has been renamed to processing_status.tsv
  • The global_config.json file schema and the internal organization of the <DATASET_ROOT>/pipelines directory has been changed
    • These changes were necessary for the move to the Zenodo catalog
    • The main change is that the pipeline configuration is no longer in the global_config.json file but rather in <DATASET_ROOT>/pipelines/<PIPELINE_NAME>-<PIPELINE_VERSION>/config.json
    • We provide a script to help migrate from 0.3.X to 0.4.0. Issues with the script can be reported on GitHub or Discord

Major new features

This release introduces two major new features: - nipoppy pipeline subcommands, which allow for installing/uploading pipeline configuration directories from a "pipeline catalog" on Zenodo - Related: nipoppy init will no longer include any default pipeline configurations in the new Nipoppy dataset - Support for launching jobs on high-performance computing systems using Slurm or SGE, using the --hpc option in nipoppy bidsify, nipoppy process, and nipoppy extract

Deprecation notices

Some of the existing subcommands have been renamed: - nipoppy doughnut --> nipoppy track-curation - nipoppy run --> nipoppy process - nipoppy track --> nipoppy track-processing The old command names still work for now (with a warning) but will cause an error in a future version.

Changelog

Features

  • Implement RABIES by @david-roper in https://github.com/nipoppy/nipoppy/pull/264
  • [ENH] Implement pipeline catalog by @mathdugre in https://github.com/nipoppy/nipoppy/pull/611
  • [ENH] Remove default pipeline configs by @michellewang in https://github.com/nipoppy/nipoppy/pull/604
  • [ENH] Add HPC integration by @michellewang in https://github.com/nipoppy/nipoppy/pull/587
  • [ENH] Automatically download container when running nipoppy pipeline install by @michellewang in https://github.com/nipoppy/nipoppy/pull/634
  • [ENH] Add indenting to rich Console printing by @michellewang in https://github.com/nipoppy/nipoppy/pull/638
  • [DOC] Update Quickstart and add file schemas by @michellewang in https://github.com/nipoppy/nipoppy/pull/649
  • [ENH] Implement pipeline create subcommand by @mathdugre in https://github.com/nipoppy/nipoppy/pull/636 #### Bug Fixes
  • [FIX] Restore substitutions behaviour for backward-compatibility by @michellewang in https://github.com/nipoppy/nipoppy/pull/605
  • [FIX] Make runners always bind dataset root directory in containers by @michellewang in https://github.com/nipoppy/nipoppy/pull/582
  • [BUG] Read-only BIDS datasets fail to init w/ README creation by @bcmcpher in https://github.com/nipoppy/nipoppy/pull/613
  • [FIX] Do not apply substitutions immediately when loading invocations by @michellewang in https://github.com/nipoppy/nipoppy/pull/627
  • [FIX] Do not create directories when running nipoppy track by @michellewang in https://github.com/nipoppy/nipoppy/pull/624
  • [FIX] Do not attempt to update the curation status file if ANALYSIS_LEVEL is not participant_session by @michellewang in https://github.com/nipoppy/nipoppy/pull/618
  • [FIX] Fix Zenodo upload bug where metadata check fails by @michellewang in https://github.com/nipoppy/nipoppy/pull/640
  • [FIX] Make pipeline config validation stricter by @michellewang in https://github.com/nipoppy/nipoppy/pull/648 #### Documentation
  • [DOC] High level docs by @nikhil153 in https://github.com/nipoppy/nipoppy/pull/621
  • [DOC] Add "how-to" guides for installing and running pipelines by @michellewang in https://github.com/nipoppy/nipoppy/pull/631 #### Maintenance
  • [MAINT] Fix Pydantic model_fields deprecations by @michellewang in https://github.com/nipoppy/nipoppy/pull/576
  • [MAINT] Fix dependabot username in release.yml by @michellewang in https://github.com/nipoppy/nipoppy/pull/580
  • [MAINT] Rename doughnut and bagel files by @michellewang in https://github.com/nipoppy/nipoppy/pull/585
  • [MAINT] Update release workflow to use Nipoppy bot token instead of default token by @michellewang in https://github.com/nipoppy/nipoppy/pull/581
  • [MAINT] Rename run and track subcommands and add aliases by @michellewang in https://github.com/nipoppy/nipoppy/pull/628 #### Misc
  • Enhance security and safeguard for Zenodo uploads. by @mathdugre in https://github.com/nipoppy/nipoppy/pull/626
  • Safeguard to prevent upload error + Fix test for Zenodo upload by @mathdugre in https://github.com/nipoppy/nipoppy/pull/629
  • Allow nipoppy commands to run anywhere within a nipoppy project by @mathdugre in https://github.com/nipoppy/nipoppy/pull/617

New Contributors

  • @david-roper made their first contribution in https://github.com/nipoppy/nipoppy/pull/264

Full Changelog: https://github.com/nipoppy/nipoppy/compare/0.3.4...0.4.0

- Python
Published by nipoppy-bot[bot] 9 months ago

nipoppy - 0.3.4

What's Changed

This is release introduces some enhancements and minor bug fixes. CLI updates include removing the large log dump with the Boutiques invocation/descriptor file contents, which should make the logs easier to navigate. Pipeline config updates include fixes for dcm2bids and fs_stats.

The next release should be 0.4.0, which will introduce a restructuring of the global config file as well a decoupling of sample pipeline config files from the Nipoppy Python package code base. Sample pipeline config files will be stored on Zenodo and the Nipoppy CLI will be able to download/upload them.

Features

  • [ENH] Add dcm2bids 3.2.0 by @michellewang in https://github.com/nipoppy/nipoppy/pull/436
  • [ENH] Add bids-validator 2.0.3 by @michellewang in https://github.com/nipoppy/nipoppy/pull/534
  • [ENH] group options in cli help. by @mathdugre in https://github.com/nipoppy/nipoppy/pull/491
  • [ENH] Remove Boutiques descriptor/invocation file content dumps by @michellewang in https://github.com/nipoppy/nipoppy/pull/542
  • [ENH] Print container-pulling command and change global config container substitution by @michellewang in https://github.com/nipoppy/nipoppy/pull/540
  • [ENH] Improve fs_stats extractor pipeline by @michellewang in https://github.com/nipoppy/nipoppy/pull/550 ### Bug Fixes
  • [BUG] Update Sigstore action version by @michellewang in https://github.com/nipoppy/nipoppy/pull/479
  • [BUG] Ensure that --verbose option is a flag in the CLI by @michellewang in https://github.com/nipoppy/nipoppy/pull/481
  • [BUG] Fix paths in fs_stats extractor default invocation by @michellewang in https://github.com/nipoppy/nipoppy/pull/485
  • [BUG] Status command session indexing fix by @nikhil153 in https://github.com/nipoppy/nipoppy/pull/492
  • [BUG] Fix nipoppy init in existing dirs. by @mathdugre in https://github.com/nipoppy/nipoppy/pull/490
  • [BUG] Fix bug in invocation file for dcm2bids's prepare step by @michellewang in https://github.com/nipoppy/nipoppy/pull/495
  • [BUG] Add validation for non-alphanumeric characters in participant_id and session_id in manifest by @michellewang in https://github.com/nipoppy/nipoppy/pull/546 ### Documentation
  • [DOC] Use SVG path for logo text by @michellewang in https://github.com/nipoppy/nipoppy/pull/499
  • [DOC] Add "how-to" guide for dataset initialization by @michellewang in https://github.com/nipoppy/nipoppy/pull/489
  • [DOC] Add a CLI reference page for nipoppy status by @michellewang in https://github.com/nipoppy/nipoppy/pull/529
  • [DOC] Add tooltips for glossary terms by @michellewang in https://github.com/nipoppy/nipoppy/pull/526
  • [DOC] Do not include extractor scripts in autodocs by @michellewang in https://github.com/nipoppy/nipoppy/pull/525
  • [DOC] Add external link checking for docs build + fix broken links by @michellewang in https://github.com/nipoppy/nipoppy/pull/524 ### Maintenance
  • [MAINT] Add dependabot for GitHub actions by @michellewang in https://github.com/nipoppy/nipoppy/pull/511
  • [MAINT] Fix/update issue labeller by @michellewang in https://github.com/nipoppy/nipoppy/pull/509
  • [MAINT] Use Nipoppy bot instead of PAT for projects automation workflow by @michellewang in https://github.com/nipoppy/nipoppy/pull/508
  • [MAINT] Add GitHub Actions workflow to automatically update CITATION.cff version after release by @michellewang in https://github.com/nipoppy/nipoppy/pull/512
  • Bump actions/stale from 9.0.0 to 9.1.0 by @dependabot in https://github.com/nipoppy/nipoppy/pull/515
  • Bump actions/checkout from 3 to 4 by @dependabot in https://github.com/nipoppy/nipoppy/pull/514
  • Bump actions/setup-python from 4 to 5 by @dependabot in https://github.com/nipoppy/nipoppy/pull/516
  • Bump codecov/codecov-action from 4 to 5 by @dependabot in https://github.com/nipoppy/nipoppy/pull/513
  • [MAINT] Clean up .gitignore by @michellewang in https://github.com/nipoppy/nipoppy/pull/521
  • [MAINT] Add CI workflow for Read the docs preview link by @michellewang in https://github.com/nipoppy/nipoppy/pull/536

New Contributors

  • @dependabot made their first contribution in https://github.com/nipoppy/nipoppy/pull/515

Full Changelog: https://github.com/nipoppy/nipoppy/compare/0.3.3...0.3.4

- Python
Published by github-actions[bot] 11 months ago

nipoppy - 0.3.3

What's Changed

This release includes a refactor of the CLI to use click instead of argparse, which changes the look of the CLI.

The nipoppy run command also has a new --tar argument which enables tarring of a participant-session directory upon successful completion of a processing pipeline (path configured in tracker config files). Tracking will take into account the tarball contents too.

We have also added a --write-list flag to nipoppy bidsify, nipoppy run, and nipoppy extract, which will write to a CSV file the list of participant and session IDs to run (may be helpful for parallel processing and HPC job submission).

Features

  • [ENH] Rename some input IDs in MRIQC descriptor by @michellewang in https://github.com/nipoppy/nipoppy/pull/428
  • [ENH] Add --tar option to nipoppy run by @michellewang in https://github.com/nipoppy/nipoppy/pull/430
  • [ENH] add QSIPrep by @michellewang in https://github.com/nipoppy/nipoppy/pull/266
  • [ENH] Make trackers handle tarball in pipeline output by @michellewang in https://github.com/nipoppy/nipoppy/pull/466
  • [ENH] Improve DicomReorgWorkflow customization flexibility and logging by @michellewang in https://github.com/nipoppy/nipoppy/pull/467
  • [ENH] Update Freesurfer stats/QC extractor by @michellewang in https://github.com/nipoppy/nipoppy/pull/464
  • [ENH] Add flag for writing HPC participant-session list by @michellewang in https://github.com/nipoppy/nipoppy/pull/462
  • [ENH] Add static FC extractor by @mtorabi59 in https://github.com/nipoppy/nipoppy/pull/413
  • [ENH] Add "symlink" option to init by @bcmcpher in https://github.com/nipoppy/nipoppy/pull/478 ### Bug Fixes
  • [BUG] Make PARTICIPANT_SESSION_DIR field relative to pipeline output directory by @michellewang in https://github.com/nipoppy/nipoppy/pull/461
  • [BUG] Make PipelineRunner exit/throw exception if container is specified but not found by @michellewang in https://github.com/nipoppy/nipoppy/pull/443
  • [BUG] Fix wrong container config being used in runners by @michellewang in https://github.com/nipoppy/nipoppy/pull/442
  • [BUG] Update Heudiconv descriptor and invocation files by @michellewang in https://github.com/nipoppy/nipoppy/pull/471 ### Documentation
  • [DOC] Add Plausible analytics by @michellewang in https://github.com/nipoppy/nipoppy/pull/459 ### Maintenance
  • [MAINT] Fix PerformanceWarning in BaseTabular class by @michellewang in https://github.com/nipoppy/nipoppy/pull/425
  • [MAINT] Refactor CLI to use Click by @mathdugre in https://github.com/nipoppy/nipoppy/pull/444 ### Misc
  • [ENH] Add --mode=move option to nipoppy init with --bids-source by @mtorabi59 in https://github.com/nipoppy/nipoppy/pull/475

Full Changelog: https://github.com/nipoppy/nipoppy/compare/0.3.2...0.3.3

- Python
Published by michellewang about 1 year ago

nipoppy - 0.3.2

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 https://github.com/nipoppy/nipoppy/pull/419
  • [ENH] add nipoppy extract command by @michellewang in https://github.com/nipoppy/nipoppy/pull/399
  • [ENH] Add FreeSurfer aparc/aseg stats extractor by @michellewang in https://github.com/nipoppy/nipoppy/pull/342 ### Documentation
  • [DOC] Add icon/link to GitHub repo in docs footer by @michellewang in https://github.com/nipoppy/nipoppy/pull/434 ### Maintenance
  • [MAINT] Exclude PyBIDS version 0.18.0 from dependencies by @michellewang in https://github.com/nipoppy/nipoppy/pull/449

Full Changelog: https://github.com/nipoppy/nipoppy/compare/0.3.1...0.3.2

- Python
Published by github-actions[bot] about 1 year ago

nipoppy - 0.3.1

What's Changed

Features

  • [ENH] Allow BIDS datasets without session level by @mtorabi59 in https://github.com/nipoppy/nipoppy/pull/420
  • [ENH] Add fMRIPrep 24.1.1 by @michellewang in https://github.com/nipoppy/nipoppy/pull/426 ### Maintenance
  • [MAINT] refactor pipeline steps. by @mathdugre in https://github.com/nipoppy/nipoppy/pull/418

Full Changelog: https://github.com/nipoppy/nipoppy/compare/0.3.0...0.3.1

- Python
Published by github-actions[bot] over 1 year ago

nipoppy - 0.3.0

What's Changed

Breaking changes

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

Documentation

  • [DOC] Update dataset layout figure by @michellewang in https://github.com/nipoppy/nipoppy/pull/412
  • [DOC] Update file trees in user guide page for DICOM reorg by @michellewang in https://github.com/nipoppy/nipoppy/pull/408

Misc

  • [REL] Fix merge conflict for REL 0.3.0 by @mathdugre in https://github.com/nipoppy/nipoppy/pull/417
  • [REL] Release 0.3.0 by @mathdugre in https://github.com/nipoppy/nipoppy/pull/416

Full Changelog: https://github.com/nipoppy/nipoppy/compare/0.2.3...0.3.0

- Python
Published by github-actions[bot] over 1 year ago

nipoppy - 0.2.3

What's Changed

Features

  • [ENH] make fmriprep --fs-no-reconall value-key and id more intuitive. by @mathdugre in https://github.com/nipoppy/nipoppy/pull/406 ### Bug Fixes
  • [BUG] keep working directory on failed run / flag to keep pipeline working directory on success by @bcmcpher in https://github.com/nipoppy/nipoppy/pull/345
  • [BUG] Do not pool BIDS and PROC pipelines together when searching pipeline configs by @michellewang in https://github.com/nipoppy/nipoppy/pull/391
  • [FIX] Do not enable markup language processing when logging messages related to subprocesses by @michellewang in https://github.com/nipoppy/nipoppy/pull/410 ### Maintenance
  • [MAINT] Only move PRs to pending review. by @mathdugre in https://github.com/nipoppy/nipoppy/pull/389

Full Changelog: https://github.com/nipoppy/nipoppy/compare/0.2.2...0.2.3

What's Changed

Features

  • [ENH] make fmriprep --fs-no-reconall value-key and id more intuitive. by @mathdugre in https://github.com/nipoppy/nipoppy/pull/406 ### Bug Fixes
  • [BUG] keep working directory on failed run / flag to keep pipeline working directory on success by @bcmcpher in https://github.com/nipoppy/nipoppy/pull/345
  • [BUG] Do not pool BIDS and PROC pipelines together when searching pipeline configs by @michellewang in https://github.com/nipoppy/nipoppy/pull/391
  • [FIX] Do not enable markup language processing when logging messages related to subprocesses by @michellewang in https://github.com/nipoppy/nipoppy/pull/410 ### Maintenance
  • [MAINT] Only move PRs to pending review. by @mathdugre in https://github.com/nipoppy/nipoppy/pull/389

Full Changelog: https://github.com/nipoppy/nipoppy/compare/0.2.2...0.2.3

- Python
Published by michellewang over 1 year ago

nipoppy - 0.2.2

What's Changed

Features

  • [ENH] Init a Nipoppy dataset with a BIDS dataset by @Remi-Gau in https://github.com/nipoppy/nipoppy/pull/358 ### Bug Fixes
  • [BUG] Fix logging issues by @michellewang in https://github.com/nipoppy/nipoppy/pull/356
  • [FIX] Support latest version of doc dependencies by @michellewang in https://github.com/nipoppy/nipoppy/pull/365
  • [BUG] Fix logo path by @mathdugre in https://github.com/nipoppy/nipoppy/pull/376
  • [BUG] Fix logo again... by @mathdugre in https://github.com/nipoppy/nipoppy/pull/377 ### Documentation
  • [DOC] Add auto-generated changelog page to docs by @michellewang in https://github.com/nipoppy/nipoppy/pull/361
  • [DOC] Update contribution guide by @michellewang in https://github.com/nipoppy/nipoppy/pull/375
  • [DOC] Add logo by @michellewang in https://github.com/nipoppy/nipoppy/pull/347 ### Maintenance
  • [MAINT] Refactor pipeline step config in workflow classes by @michellewang in https://github.com/nipoppy/nipoppy/pull/362
  • [MAINT] test with python 3.13 by @Remi-Gau in https://github.com/nipoppy/nipoppy/pull/359 ### Misc
  • [ENH] Pybids database creation toggle (fixed) for issue #253 by @jacobsanz97 in https://github.com/nipoppy/nipoppy/pull/371

New Contributors

  • @jacobsanz97 made their first contribution in https://github.com/nipoppy/nipoppy/pull/371

Full Changelog: https://github.com/nipoppy/nipoppy/compare/0.2.1...0.2.2

- Python
Published by michellewang over 1 year ago

nipoppy - 0.2.1

What's Changed

Breaking Changes

  • [MAINT] Clean up legacy files by @michellewang in https://github.com/nipoppy/nipoppy/pull/339 ### Features
  • [ENH] add automatic release notes for GitHub. by @mathdugre in https://github.com/nipoppy/nipoppy/pull/322
  • [ENH] Add "ANALYSIS_LEVEL" field to pipeline step config to allow group-level processing by @michellewang in https://github.com/nipoppy/nipoppy/pull/341 ### Bug Fixes
  • [FIX] Improve pipeline config substitutions by @michellewang in https://github.com/nipoppy/nipoppy/pull/300
  • [FIX] Fix various bugs in sample JSON config files by @michellewang in https://github.com/nipoppy/nipoppy/pull/299
  • [BUG] Fix error when using invalid verbosity level by @michellewang in https://github.com/nipoppy/nipoppy/pull/330
  • [BUG] Heudiconv invocation fix by @nikhil153 in https://github.com/nipoppy/nipoppy/pull/314
  • [BUG] Fix label_new_issue.yml failing by @michellewang in https://github.com/nipoppy/nipoppy/pull/344 ### Documentation
  • [DOC] Update installation instructions by @mathdugre in https://github.com/nipoppy/nipoppy/pull/326 ### Maintenance
  • [MAINT] automatically label issue and PRs based on prefixes by @mathdugre in https://github.com/nipoppy/nipoppy/pull/338 ### Misc
  • [ENH] Add GitHub Project automation by @michellewang in https://github.com/nipoppy/nipoppy/pull/333
  • [FIX] Add changes erased by force-push by @michellewang in https://github.com/nipoppy/nipoppy/pull/336

Full Changelog: https://github.com/nipoppy/nipoppy/compare/0.2.0...0.2.1

- Python
Published by github-actions[bot] over 1 year ago

nipoppy - 0.2.0

What's Changed

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

New Contributors

  • @yarikoptic made their first contribution in https://github.com/nipoppy/nipoppy/pull/104
  • @danyluik made their first contribution in https://github.com/nipoppy/nipoppy/pull/189
  • @mathdugre made their first contribution in https://github.com/nipoppy/nipoppy/pull/281
  • @pre-commit-ci made their first contribution in https://github.com/nipoppy/nipoppy/pull/313

Full Changelog: https://github.com/nipoppy/nipoppy/compare/0.1.0...0.2.0

- Python
Published by github-actions[bot] over 1 year ago

nipoppy - 0.1.0

What's Changed

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

New Contributors

  • @michellewang made their first contribution in https://github.com/neurodatascience/mr_proc/pull/68
  • @Remi-Gau made their first contribution in https://github.com/neurodatascience/mr_proc/pull/105

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

- Python
Published by Remi-Gau over 2 years ago