v0.3.3

🚀 Enhancements

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

Authors: 1

• Alyssa Dai (@alyssadai)

v0.3.2

🚀 Enhancements

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

Authors: 1

• Alyssa Dai (@alyssadai)

v0.3.1

🚀 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)

v0.3.0

💥 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)

v0.2.2

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)

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)

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

• @dependabot[bot]
• @pre-commit-ci[bot]
• @sam-gregz
• Alyssa Dai (@alyssadai)
• Sebastian Urchs (@surchs)

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)

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 #185
• [ENH] Provide overwritable output file path instead of directory path arg by @alyssadai in #216
• [REF] Refactor phenotypic/BIDS subjects check and add more intermediate stdout for bagel bids by @alyssadai in #227

Changes to the data model for inputs/outputs ⚙️

• [MNT] Capitalized age heuristics by @rmanaem in #219

Documentation updates 📜

• [DOC] Update example docker run commands + add submodule installation in README by @alyssadai in #186
• [DOC] Removed example expected CLI outputs table and synthetic TSV and JSON entries by @rmanaem in #204
• [MNT] Update help text and fix formatting issues in user messages by @alyssadai in #217

Bug fixes 🛠️

• [FIX] Add NCIT namespace by @alyssadai in #210
• [FIX] Gracefully handle user providing phenotypic file as .csv by @surchs in #212

Other changes 🧹

• [CI] Updated test workflow by @rmanaem in #194
• [MNT] Added neurobagel/neurobagel_examples as submodule by @rmanaem in #195

New Contributors

• @rmanaem made their first contribution in #194

Full Changelog: v0.1.0...v0.1.1

v0.1.0

First release 🎉

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 #10
• @alyssadai made their first contribution in #54
• @yarikoptic made their first contribution in #123
• @Remi-Gau made their first contribution in #130
• @dependabot made their first contribution in #133

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