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v2.0.0#46

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jmtang2018 merged 31 commits intomainfrom
develop
Apr 17, 2025
Merged

v2.0.0#46
jmtang2018 merged 31 commits intomainfrom
develop

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@alexsigaras alexsigaras commented Apr 17, 2025

This pull request includes updates to metadata, documentation, and project structure for the Bridge2AI Voice Project. Key changes include updates to author affiliations, versioning updates, and the removal of legacy files related to phenotype data and dataset descriptions.

Metadata Updates:

  • Updated author affiliations in the CITATION.cff file to remove abbreviations from institutional names and added a new author, Jamie Toghranegar, with their details. [1] [2] [3]

Documentation Updates:

  • Updated the project version badge in README.md to reflect the new version 2.0.0.
  • Updated the SECURITY.md file to indicate that version v2.0.0 is now supported with security updates, while earlier versions are no longer supported.

Removal of Legacy Files:

  • Removed the README.md file from src/b2ai-data-bids-like-template that described the project directory structure.
  • Deleted the dataset_description.json file, which included metadata about the dataset.
  • Removed phenotype-related JSON and TSV files (adhd.json, adhd.tsv, airwaystenosis.json, airwaystenosis.tsv, als.json) from the src/b2ai-data-bids-like-template/phenotype directory. These files contained metadata and structure for phenotype data that is no longer needed. [1] [2] [3] [4] [5]

dependabot Bot and others added 29 commits April 4, 2025 14:58
@dependabot
Bump jinja2 from 3.1.4 to 3.1.5 in the pip group across 1 directory
39eaf94 
Bumps the pip group with 1 update in the / directory: [jinja2](https://github.com/pallets/jinja).


Updates `jinja2` from 3.1.4 to 3.1.5
- [Release notes](https://github.com/pallets/jinja/releases)
- [Changelog](https://github.com/pallets/jinja/blob/main/CHANGES.rst)
- [Commits](pallets/jinja@3.1.4...3.1.5)

---
updated-dependencies:
- dependency-name: jinja2
  dependency-type: direct:production
  dependency-group: pip
...

Signed-off-by: dependabot[bot] <support@github.com>
@alexsigaras
Merge pull request #32 from eipm/dependabot/pip/pip-e49d2f513e
d73d465 
Bump jinja2 from 3.1.4 to 3.1.6 in the pip group across 1 directory
@alexsigaras
version bump
8027360
@alexsigaras
fix grammar errors
71a48b9
@satra
Update data_pre_processing.py
29816b5
@satra
Delete src/b2ai-data-bids-like-template directory
16d675e
@satra
Update overview.py
c13272f
@alexsigaras
bumped to version v2.0.0
efb8935
@alexsigaras
Merge branch 'develop' into patch-4
73449d4
@alexsigaras
Update src/tabs/overview.py
3ebff29 
Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
@alexsigaras
Update src/tabs/overview.py
280fe77 
Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
@alexsigaras
Update src/tabs/data_pre_processing.py
1d468c9 
Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
@alexsigaras
Updated CITATION.cff
337bdb7
@jmtang2018
Merge pull request #44 from eipm/v2.0.0-rc
0ce2d2c 
V2.0.0 rc
@satra
adjust description of removed elements
fd3993a
@satra
Merge branch 'develop' into patch-2
18dde97
@alexsigaras
Merge pull request #41 from satra/patch-3
907cc43 
Delete src/b2ai-data-bids-like-template directory
@alexsigaras
Merge pull request #40 from satra/patch-2
a7b6464 
Update data_pre_processing tab
@JamieToghranegar @alistairewj
Add test heading
58f5ece
@JamieToghranegar @alistairewj
Update study_metadata.py
35c3df2 
Change text from v1 to v2
@JamieToghranegar @alistairewj
Update data_governance.py
0d379ac 
updated options for two data access options for v2 dataset, need to add links however to DARF and DUA
@alexsigaras @alistairewj
Update src/tabs/overview.py
353ddad
@JamieToghranegar @alistairewj
Update data_governance.py
006b4b2 
Update text
@alistairewj
update content for v2 release
9d869ac
@alexsigaras
Update src/dashboard.py
330a4e8
@alexsigaras
Merge branch 'develop' into alistair/update_docs_v2
8ca7064
@alexsigaras
Merge pull request #45 from alistairewj/alistair/update_docs_v2
3c5c65f 
Update docs for v2
@alexsigaras
Updated logo
4de4144
@alexsigaras
Added buttons in overview
364e34c
@alexsigaras alexsigaras added the enhancement New feature or request label Apr 17, 2025
@alexsigaras alexsigaras requested a review from Copilot April 17, 2025 14:59
Copilot AI reviewed Apr 17, 2025
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Copilot reviewed 86 out of 98 changed files in this pull request and generated no comments.

Files not reviewed (12)
  • src/b2ai-data-bids-like-template/dataset_description.json: Language not supported
  • src/b2ai-data-bids-like-template/phenotype/adhd.json: Language not supported
  • src/b2ai-data-bids-like-template/phenotype/adhd.tsv: Language not supported
  • src/b2ai-data-bids-like-template/phenotype/airwaystenosis.json: Language not supported
  • src/b2ai-data-bids-like-template/phenotype/airwaystenosis.tsv: Language not supported
  • src/b2ai-data-bids-like-template/phenotype/als.json: Language not supported
  • src/b2ai-data-bids-like-template/phenotype/als.tsv: Language not supported
  • src/b2ai-data-bids-like-template/phenotype/alzheimers.json: Language not supported
  • src/b2ai-data-bids-like-template/phenotype/alzheimers.tsv: Language not supported
  • src/b2ai-data-bids-like-template/phenotype/benignLesion.json: Language not supported
  • src/b2ai-data-bids-like-template/phenotype/benignLesion.tsv: Language not supported
  • src/b2ai-data-bids-like-template/phenotype/bipolar.json: Language not supported
Comments suppressed due to low confidence (1)

README.md:5

  • [nitpick] Consider updating the badge text to use 'GitHub' instead of 'Github' for consistent branding across the project.
[![Github](https://img.shields.io/badge/github-2.0.0-green?style=flat&logo=github)](https://github.com/eipm/bridge2ai-docs)

@alexsigaras alexsigaras requested a review from jmtang2018 April 17, 2025 15:03
@alexsigaras alexsigaras requested a review from Copilot April 17, 2025 15:03
Copilot AI reviewed Apr 17, 2025
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Copilot reviewed 86 out of 98 changed files in this pull request and generated 1 comment.

Files not reviewed (12)
  • src/b2ai-data-bids-like-template/dataset_description.json: Language not supported
  • src/b2ai-data-bids-like-template/phenotype/adhd.json: Language not supported
  • src/b2ai-data-bids-like-template/phenotype/adhd.tsv: Language not supported
  • src/b2ai-data-bids-like-template/phenotype/airwaystenosis.json: Language not supported
  • src/b2ai-data-bids-like-template/phenotype/airwaystenosis.tsv: Language not supported
  • src/b2ai-data-bids-like-template/phenotype/als.json: Language not supported
  • src/b2ai-data-bids-like-template/phenotype/als.tsv: Language not supported
  • src/b2ai-data-bids-like-template/phenotype/alzheimers.json: Language not supported
  • src/b2ai-data-bids-like-template/phenotype/alzheimers.tsv: Language not supported
  • src/b2ai-data-bids-like-template/phenotype/benignLesion.json: Language not supported
  • src/b2ai-data-bids-like-template/phenotype/benignLesion.tsv: Language not supported
  • src/b2ai-data-bids-like-template/phenotype/bipolar.json: Language not supported

Comment thread README.md Outdated
@alexsigaras alexsigaras requested a review from Copilot April 17, 2025 15:08
Copilot AI reviewed Apr 17, 2025
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Copilot reviewed 86 out of 98 changed files in this pull request and generated no comments.

Files not reviewed (12)
  • src/b2ai-data-bids-like-template/dataset_description.json: Language not supported
  • src/b2ai-data-bids-like-template/phenotype/adhd.json: Language not supported
  • src/b2ai-data-bids-like-template/phenotype/adhd.tsv: Language not supported
  • src/b2ai-data-bids-like-template/phenotype/airwaystenosis.json: Language not supported
  • src/b2ai-data-bids-like-template/phenotype/airwaystenosis.tsv: Language not supported
  • src/b2ai-data-bids-like-template/phenotype/als.json: Language not supported
  • src/b2ai-data-bids-like-template/phenotype/als.tsv: Language not supported
  • src/b2ai-data-bids-like-template/phenotype/alzheimers.json: Language not supported
  • src/b2ai-data-bids-like-template/phenotype/alzheimers.tsv: Language not supported
  • src/b2ai-data-bids-like-template/phenotype/benignLesion.json: Language not supported
  • src/b2ai-data-bids-like-template/phenotype/benignLesion.tsv: Language not supported
  • src/b2ai-data-bids-like-template/phenotype/bipolar.json: Language not supported
Comments suppressed due to low confidence (1)

src/b2ai-data-bids-like-template/README.md:1

  • Verify that any documentation references to this legacy README file are updated or removed to avoid broken links.
Deleted legacy README file

@jmtang2018 jmtang2018 merged commit f283fc5 into main Apr 17, 2025
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@alexsigaras @jmtang2018 @satra @JamieToghranegar @alistairewj