- [MNT] Deprecate Cognitive Atlas vocab namespace & add check for unsupported namespaces #410 (@alyssadai)
- Alyssa Dai (@alyssadai)
- [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)
- Alyssa Dai (@alyssadai)
- [ENH] Load pipeline catalog dynamically and error out when it is empty/not found #391 (@surchs @alyssadai)
- [REF] Refactor utilities #385 (@alyssadai)
- [REF] Upgrade codebase to Pydantic>2 #389 (@alyssadai)
- Alyssa Dai (@alyssadai)
- Sebastian Urchs (@surchs)
- [FIX] Package
pipeline-catalogas data files in CLI installation #379 (@alyssadai)
- Alyssa Dai (@alyssadai)
- [FIX] Make
pipeline-catalogsubmodule available to built Docker image #373 (@alyssadai)
- Alyssa Dai (@alyssadai)
- [FIX] Add missing
_idsuffix to processing status file column mappings #370 (@alyssadai)
- [DOC] Move pre-commit setup to README.md #368 (@alyssadai)
- Alyssa Dai (@alyssadai)
- [MODEL] Model basic pipeline availability info in imaging session #347 (@alyssadai)
- [ENH] Add derivatives command and
pipeline-catalogsubmodule #349 (@alyssadai) - [REF] Rename Neurobagel-created session to
ses-unnamed#358 (@alyssadai) - [ENH] More user-friendly handling of input decoding/reading errors #337 (@alyssadai)
- [INF] Add script to generate
nb_vocab.ttl#360 (@alyssadai) - [MNT] Removed build docker nightly workflow file #348 (@rmanaem)
- [DOC] Remove usage instructions & update development environment section in README #365 (@alyssadai)
- Alyssa Dai (@alyssadai)
- Arman Jahanpour (@rmanaem)
[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.
- [CI] Release the CLI #330 (@alyssadai)
- [ENH] Update help text and add short CLI options #316 (@alyssadai)
- [FIX] Handle dashes (/any chars that are not python variable valid) in column names #313 (@alyssadai)
- [DOC] Note case sensitivity of subject IDs in
bidsIDs check error #317 (@alyssadai)
- Alyssa Dai (@alyssadai)
[MNT] Release the CLI (#291)
We have updated the Neurobagel data model to allow users to specify phenotypic information at the session level (neurobagel/planning#83). This release updates the CLI so you can create .jsonld files according to the new data model.
- [ENH] Update help text and add short CLI options #316 (@alyssadai)
- [MNT] Release the CLI #291 (@alyssadai @surchs)
- [FIX] Handle dashes (/any chars that are not python variable valid) in column names #313 (@alyssadai)
- [DOC] Note case sensitivity of subject IDs in
bidsIDs check error #317 (@alyssadai)
- Alyssa Dai (@alyssadai)
- Sebastian Urchs (@surchs)
[MNT] Release the CLI (#291)
We have updated the Neurobagel data model to allow users to specify phenotypic information at the session level (neurobagel/planning#83). This release updates the CLI so you can create .jsonld files according to the new data model.
- [MNT] Release the CLI #291 (@alyssadai @surchs)
- Alyssa Dai (@alyssadai)
- Sebastian Urchs (@surchs)
- [FIX] Use different reviewer token in release.yaml #268 (@alyssadai)
- [ENH] Handle multi-column attribute annotations #264 (@alyssadai)
- Bump bids-examples from
1a000d6toeff47f1#265 (@dependabot[bot]) - [CI] Allow auto to push on protected branch #261 (@alyssadai)
- Bump bids-examples from
b6e5234to1a000d6#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)
- @dependabot[bot]
- Alyssa Dai (@alyssadai)
- Sebastian Urchs (@surchs)
- [MODEL] Update data model to include longitudinal pheno data when sessions exist in TSV #250 (@alyssadai @surchs @pre-commit-ci[bot])
- [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
f1b00e5to94282f1#249 (@dependabot[bot]) - [MNT] Update the neurobagel examples #247 (@surchs)
- Delete .github/workflows/add_pr2project.yml #244 (@surchs)
- @dependabot[bot]
- @pre-commit-ci[bot]
- @sam-gregz
- Alyssa Dai (@alyssadai)
- Sebastian Urchs (@surchs)
- Bump actions/stale from 8 to 9 #245 (@dependabot[bot])
- Bump neurobagel_examples from
f1b00e5to94282f1#249 (@dependabot[bot]) - [MNT] Update the neurobagel examples #247 (@surchs)
- Delete .github/workflows/add_pr2project.yml #244 (@surchs)
- @dependabot[bot]
- Sebastian Urchs (@surchs)
- Bump neurobagel_examples from
f1b00e5to94282f1#249 (@dependabot[bot])
- [MNT] Update the neurobagel examples #247 (@surchs)
- Delete .github/workflows/add_pr2project.yml #244 (@surchs)
- Sebastian Urchs (@surchs)
- Sebastian Urchs (@surchs)
- [CI] Added
releaseworkflow #243 (@rmanaem) - [DOC] Added link to official docs #237 (@surchs)
- Bump bids-examples from
e073115tob6e5234#232 (@dependabot[bot]) - [ENH] Change assessment tool availability heuristic to
any()#234 (@alyssadai)
- [CI] Update image tag for default build + add wf to build on release #242 (@alyssadai)
- @dependabot[bot]
- Alyssa Dai (@alyssadai)
- Arman Jahanpour (@rmanaem)
- Sebastian Urchs (@surchs)