Releases | Open Source Science

🚀 Enhancements

[ENH] Warn when only ID columns are annotated, simplify log messages #514 (@alyssadai)

🐛 Bug Fixes

[FIX] Remove custom entrypoint that checks for within-container BIDS path #515 (@alyssadai)

Authors: 1

Alyssa Dai (@alyssadai)

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

💥 Breaking Changes

[ENH] Add bids2tsv command to convert a BIDS dir into a minimal TSV, and update bids command to read from TSV #481 (@alyssadai)

🚀 Enhancements

[ENH] Support custom vocabs for pheno via --config option & defer errors from resource fetching #498 (@alyssadai)
[MODEL] Add a pandera schema for the BIDS metadata table #503 (@alyssadai)
[ENH] More user-friendly error messages for pheno command input validation #508 (@alyssadai)

Authors: 1

Alyssa Dai (@alyssadai)

- Python
Published by neurobagel-bot[bot] 7 months ago

🚀 Enhancements

[MNT] Set up bagel CLI for publishing on PyPI #460 (@alyssadai)

🏠 Internal

[CI] Release the CLI #465 (@alyssadai)

Authors: 1

Alyssa Dai (@alyssadai)

- Python
Published by neurobagel-bot[bot] 8 months ago

🚀 Enhancements

[ENH] Rename "Transformation" to "Format" in data dictionary model #459 (@alyssadai)
[ENH] Split --bids-dir into input and host path options #449 (@alyssadai @rmanaem)

Authors: 2

Alyssa Dai (@alyssadai)
Arman Jahanpour (@rmanaem)

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

🚀 Enhancements

[REF] Switch to logging for errors and add --verbosity option for log level #446 (@alyssadai)
[REF] Switch to logging for warnings and info messages #444 (@alyssadai)

Authors: 1

Alyssa Dai (@alyssadai)

- Python
Published by neurobagel-bot[bot] 11 months ago

🚀 Enhancements

[ENH] Support ranged ages with nb:FromRange #437 (@alyssadai)

Authors: 1

Alyssa Dai (@alyssadai)

- Python
Published by neurobagel-bot[bot] 12 months ago

🏠 Internal

[ENH] Add docker image build for arm64 architecture #429 (@rmanaem @surchs)

Authors: 2

Arman Jahanpour (@rmanaem)
Sebastian Urchs (@surchs)

- Python
Published by neurobagel-bot[bot] about 1 year ago

🐛 Bug Fixes

[FIX] Disallow empty string/whitespace-only pheno --name values #426 (@alyssadai)

🏠 Internal

[MNT] Configure mypy in pre-commit for type checking #423 (@alyssadai)

Authors: 1

Alyssa Dai (@alyssadai)

- Python
Published by neurobagel-bot[bot] about 1 year ago

💥 Breaking Changes

[MNT] Deprecate Cognitive Atlas vocab namespace & add check for unsupported namespaces #410 (@alyssadai)

Authors: 1

Alyssa Dai (@alyssadai)

- Python
Published by neurobagel-bot[bot] about 1 year ago

🚀 Enhancements

[ENH] Allow unrecognized pipeline names and versions in processing status file #401 (@alyssadai)
[MNT] Remind about missing value annotation in age parsing error #402 (@alyssadai)

Authors: 1

Alyssa Dai (@alyssadai)

- Python
Published by neurobagel-bot[bot] about 1 year ago

🚀 Enhancements

[ENH] Load pipeline catalog dynamically and error out when it is empty/not found #391 (@surchs @alyssadai)

🏠 Internal

[REF] Refactor utilities #385 (@alyssadai)

🔩 Dependency Updates

[REF] Upgrade codebase to Pydantic>2 #389 (@alyssadai)

Authors: 2

Alyssa Dai (@alyssadai)
Sebastian Urchs (@surchs)

- Python
Published by neurobagel-bot[bot] over 1 year ago

🚀 Enhancements

[FIX] Package pipeline-catalog as data files in CLI installation #379 (@alyssadai)

Authors: 1

Alyssa Dai (@alyssadai)

- Python
Published by neurobagel-bot[bot] over 1 year ago

🚀 Enhancements

[FIX] Make pipeline-catalog submodule available to built Docker image #373 (@alyssadai)

Authors: 1

Alyssa Dai (@alyssadai)

- Python
Published by neurobagel-bot[bot] over 1 year ago

🚀 Enhancements

[FIX] Add missing _id suffix to processing status file column mappings #370 (@alyssadai)

📝 Documentation

[DOC] Move pre-commit setup to README.md #368 (@alyssadai)

Authors: 1

Alyssa Dai (@alyssadai)

- Python
Published by neurobagel-bot[bot] over 1 year ago

💥 Breaking Changes

[MODEL] Model basic pipeline availability info in imaging session #347 (@alyssadai)

🚀 Enhancements

[ENH] Add derivatives command and pipeline-catalog submodule #349 (@alyssadai)
[REF] Rename Neurobagel-created session to ses-unnamed #358 (@alyssadai)
[ENH] More user-friendly handling of input decoding/reading errors #337 (@alyssadai)

🏠 Internal

[INF] Add script to generate nb_vocab.ttl #360 (@alyssadai)
[MNT] Removed build docker nightly workflow file #348 (@rmanaem)

📝 Documentation

[DOC] Remove usage instructions & update development environment section in README #365 (@alyssadai)

Authors: 2

Alyssa Dai (@alyssadai)
Arman Jahanpour (@rmanaem)

- Python
Published by neurobagel-bot[bot] over 1 year ago

Release Notes

[CI] Release the CLI (#330)

This release introduces short option names for CLI commands and fixes a bug that prevented hyphens in column names from being parsed.

🚀 Enhancements

[ENH] Update help text and add short CLI options #316 (@alyssadai)

🐛 Bug Fixes

[FIX] Handle dashes (/any chars that are not python variable valid) in column names #313 (@alyssadai)

📝 Documentation

[DOC] Note case sensitivity of subject IDs in bids IDs check error #317 (@alyssadai)

Authors: 1

Alyssa Dai (@alyssadai)

- Python
Published by neurobagel-chef-bot[bot] over 1 year ago

Release Notes

[MNT] Release the CLI (#291)

We have updated the Neurobagel data model to allow users to specify phenotypic information at the session level (https://github.com/neurobagel/planning/issues/83). This release updates the CLI so you can create .jsonld files according to the new data model.

🚀 Enhancements

[MNT] Release the CLI #291 (@alyssadai @surchs)

Authors: 2

Alyssa Dai (@alyssadai)
Sebastian Urchs (@surchs)

- Python
Published by surchs almost 2 years ago

bagel-cli - v0.2.1

🐛 Bug Fix

[FIX] Use different reviewer token in release.yaml #268 (@alyssadai)
[ENH] Handle multi-column attribute annotations #264 (@alyssadai)
Bump bids-examples from 1a000d6 to eff47f1 #265 (@dependabot[bot])
[CI] Allow auto to push on protected branch #261 (@alyssadai)
Bump bids-examples from b6e5234 to 1a000d6 #256 (@dependabot[bot])
[CI] Switch to parallel build config for coveralls #263 (@alyssadai)
[MODEL] Handle phenotypic inputs with no session column in the TSV #260 (@alyssadai)
[MNT] Stop pre-commit from pushing to PR branches #253 (@surchs)

Authors: 3

@dependabot[bot]
Alyssa Dai (@alyssadai)
Sebastian Urchs (@surchs)

- Python
Published by surchs about 2 years ago

bagel-cli - v0.2.0

🚀 Enhancement

[MODEL] Update data model to include longitudinal pheno data when sessions exist in TSV #250 (@alyssadai @surchs @pre-commit-ci[bot])

🐛 Bug Fix

[CI] give auto-release permissions to launch build #255 (@surchs)
[CI] Add Codecov to test workflow #254 (@alyssadai)
[TST] Added a test to ensure correct labelling of phenotypic sessions #251 (@sam-gregz)
Bump actions/setup-python from 4 to 5 #246 (@dependabot[bot])
[CI] Update .autorc to release with release label #248 (@alyssadai @surchs @pre-commit-ci[bot])
Bump actions/stale from 8 to 9 #245 (@dependabot[bot])
Bump neurobagel_examples from f1b00e5 to 94282f1 #249 (@dependabot[bot])
[MNT] Update the neurobagel examples #247 (@surchs)
Delete .github/workflows/add_pr2project.yml #244 (@surchs)

Authors: 5

- Python
Published by surchs about 2 years ago

bagel-cli - v0.1.3

🐛 Bug Fix

Delete .github/workflows/add_pr2project.yml #244 (@surchs)

Authors: 1

Sebastian Urchs (@surchs)

- Python
Published by github-actions[bot] about 2 years ago

bagel-cli - v0.1.2

🐛 Bug Fix

[CI] Added release workflow #243 (@rmanaem)
[DOC] Added link to official docs #237 (@surchs)
Bump bids-examples from e073115 to b6e5234 #232 (@dependabot[bot])
[ENH] Change assessment tool availability heuristic to any() #234 (@alyssadai)

🏠 Internal

[CI] Update image tag for default build + add wf to build on release #242 (@alyssadai)

Authors: 4

@dependabot[bot]
Alyssa Dai (@alyssadai)
Arman Jahanpour (@rmanaem)
Sebastian Urchs (@surchs)

- Python
Published by github-actions[bot] about 2 years ago

bagel-cli - v0.1.1

Summary

This release introduces user-configurable output filenames and the option to overwrite an existing output file. Also introduced are clearer and more detailed help text and more efficient validation of input data.

This release includes a breaking change to the expected names of age transformations in data dictionaries.

What's Changed

New or improved features ✨

[ENH] Pinning dependencies for deterministic Docker builds by @surchs in https://github.com/neurobagel/bagel-cli/pull/185
[ENH] Provide overwritable output file path instead of directory path arg by @alyssadai in https://github.com/neurobagel/bagel-cli/pull/216
[REF] Refactor phenotypic/BIDS subjects check and add more intermediate stdout for bagel bids by @alyssadai in https://github.com/neurobagel/bagel-cli/pull/227

Changes to the data model for inputs/outputs :gear:

[MNT] Capitalized age heuristics by @rmanaem in https://github.com/neurobagel/bagel-cli/pull/219

Documentation updates 📜

[DOC] Update example docker run commands + add submodule installation in README by @alyssadai in https://github.com/neurobagel/bagel-cli/pull/186
[DOC] Removed example expected CLI outputs table and synthetic TSV and JSON entries by @rmanaem in https://github.com/neurobagel/bagel-cli/pull/204
[MNT] Update help text and fix formatting issues in user messages by @alyssadai in https://github.com/neurobagel/bagel-cli/pull/217

Bug fixes 🛠️

[FIX] Add NCIT namespace by @alyssadai in https://github.com/neurobagel/bagel-cli/pull/210
[FIX] Gracefully handle user providing phenotypic file as .csv by @surchs in https://github.com/neurobagel/bagel-cli/pull/212

Other changes 🧹

[CI] Updated test workflow by @rmanaem in https://github.com/neurobagel/bagel-cli/pull/194
[MNT] Added neurobagel/neurobagel_examples as submodule by @rmanaem in https://github.com/neurobagel/bagel-cli/pull/195

New Contributors

@rmanaem made their first contribution in https://github.com/neurobagel/bagel-cli/pull/194

Full Changelog: https://github.com/neurobagel/bagel-cli/compare/v0.1.0...v0.1.1

- Python
Published by alyssadai over 2 years ago

bagel-cli - v0.1.0

First release :tada:

This is the first release of the neurobagel CLI. In this release, we introduce the bagel command and two subcommands:

bagel pheno for reading and processing a BIDS compatible participants.tsv file and a Neurobagel augmented participants.json data dictionary. The pheno subcommand will create a Neurobagel graph instance in the form of a .jsonld file that describes the phenotypic information in a machine readable form
bagel bids for reading the .jsonld file created by bagel pheno and a BIDS dataset with imaging data. This subcommand adds the imaging metadata from the BIDS dataset to the existing phenotypic descriptions, and creates an augmented .jsonld graph file that can be uploaded to the Neurobagel graph.

New Contributors

@surchs made their first contribution in https://github.com/neurobagel/bagel-cli/pull/10
@alyssadai made their first contribution in https://github.com/neurobagel/bagel-cli/pull/54
@yarikoptic made their first contribution in https://github.com/neurobagel/bagel-cli/pull/123
@Remi-Gau made their first contribution in https://github.com/neurobagel/bagel-cli/pull/130
@dependabot made their first contribution in https://github.com/neurobagel/bagel-cli/pull/133

Full Changelog: https://github.com/neurobagel/bagel-cli/commits/v0.1.0

- Python
Published by surchs over 2 years ago

Recent Releases of bagel-cli

bagel-cli - v0.7.1

🚀 Enhancements

🐛 Bug Fixes

Authors: 1

bagel-cli - v0.7.0

💥 Breaking Changes

🚀 Enhancements

Authors: 1

bagel-cli - v0.6.0

🚀 Enhancements

🏠 Internal

Authors: 1

bagel-cli - v0.5.0

🚀 Enhancements

Authors: 2

bagel-cli - v0.4.4

🚀 Enhancements

Authors: 1

bagel-cli - v0.4.3

🚀 Enhancements

Authors: 1

bagel-cli - v0.4.2

🏠 Internal

Authors: 2

bagel-cli - v0.4.1

🐛 Bug Fixes

🏠 Internal

Authors: 1

bagel-cli - v0.4.0

💥 Breaking Changes

Authors: 1

bagel-cli - v0.3.5

🚀 Enhancements

Authors: 1

bagel-cli - v0.3.4

🚀 Enhancements

🏠 Internal

🔩 Dependency Updates

Authors: 2

bagel-cli - v0.3.3

🚀 Enhancements

Authors: 1

bagel-cli - v0.3.2

🚀 Enhancements

Authors: 1

bagel-cli - v0.3.1

🚀 Enhancements

📝 Documentation

Authors: 1

bagel-cli - v0.3.0

💥 Breaking Changes

🚀 Enhancements

🏠 Internal

📝 Documentation

Authors: 2

bagel-cli - v0.2.2

Release Notes

[CI] Release the CLI (#330)

🚀 Enhancements

🐛 Bug Fixes

📝 Documentation

Authors: 1

bagel-cli - v0.2.2

Release Notes

[MNT] Release the CLI (#291)

🚀 Enhancements

Authors: 2

bagel-cli - v0.2.1

🐛 Bug Fix

Authors: 3

bagel-cli - v0.2.0

🚀 Enhancement

🐛 Bug Fix

Authors: 5

bagel-cli - v0.1.3

🐛 Bug Fix

Authors: 1

bagel-cli - v0.1.2

🐛 Bug Fix