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Project improvements and VERTEX code migration#2

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sr-murthy merged 1 commit into
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project-improvements
Apr 10, 2026
Merged

Project improvements and VERTEX code migration#2
sr-murthy merged 1 commit into
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project-improvements

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@sr-murthy sr-murthy commented Apr 7, 2026

  • Update and clean up project TOML, inlcluding adding a pylock TOML - ✅
  • Update and clean up CI wofkflows - ✅
  • Set up Sphinx docs - ✅
  • Copy VERTEX logging (vertex.logging) REDCap data retrievel (vertex.getREDCapData.py), analytics (vertex.IsaricAnalytics.py) and visualisation (vertex.IsaricDraw.py) libraries into the repo - ✅
  • Remove unused or placeholder libraries (including tests), folders and assets from the repo; some of these may be added back later following a code review - ✅

@sr-murthy sr-murthy self-assigned this Apr 7, 2026
@sr-murthy sr-murthy added the enhancement New feature or request label Apr 7, 2026
@sr-murthy sr-murthy force-pushed the project-improvements branch 2 times, most recently from 0db6e16 to e110dff Compare April 7, 2026 14:51
Comment thread .github/workflows/test-python-versions-coverage.yml Fixed
@sr-murthy sr-murthy force-pushed the project-improvements branch 2 times, most recently from e618c05 to e8331cd Compare April 7, 2026 14:58
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codecov Bot commented Apr 7, 2026

Welcome to Codecov 🎉

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@sr-murthy sr-murthy force-pushed the project-improvements branch from e8331cd to 6619703 Compare April 7, 2026 15:01
@sr-murthy sr-murthy changed the title VERTEX analytics code migration Project improvements Apr 7, 2026
@sr-murthy sr-murthy force-pushed the project-improvements branch 11 times, most recently from e101159 to 2faf023 Compare April 8, 2026 09:47
@sr-murthy sr-murthy marked this pull request as draft April 8, 2026 09:50
@sr-murthy sr-murthy changed the title Project improvements DRAFT: Project improvements Apr 8, 2026
Comment thread docs/conf.py Dismissed
@sr-murthy sr-murthy force-pushed the project-improvements branch from a8aceb5 to 8659f5f Compare April 8, 2026 10:19
Comment thread isaricanalytics/IsaricDraw.py Fixed
Comment thread isaricanalytics/IsaricDraw.py Fixed
Comment thread isaricanalytics/IsaricDraw.py Fixed
Comment thread isaricanalytics/IsaricDraw.py Fixed
Comment thread isaricanalytics/IsaricAnalytics.py Fixed
Comment thread isaricanalytics/IsaricDraw.py Fixed
Comment thread isaricanalytics/IsaricAnalytics.py Fixed
Comment thread isaricanalytics/IsaricAnalytics.py Fixed
@sr-murthy sr-murthy force-pushed the project-improvements branch from 8659f5f to a8f57a4 Compare April 8, 2026 10:38
Comment thread isaricanalytics/IsaricDraw.py Fixed
Comment thread isaricanalytics/IsaricDraw.py Dismissed
@sr-murthy sr-murthy marked this pull request as ready for review April 8, 2026 12:23
@sr-murthy sr-murthy changed the title DRAFT: Project improvements Project improvements Apr 8, 2026
@sr-murthy sr-murthy changed the title Project improvements Project improvements and code migration Apr 8, 2026
@sr-murthy sr-murthy requested review from EstebanGarciaG, ISARICData and alasdairwilson and removed request for ISARICData April 8, 2026 12:25
@sr-murthy sr-murthy force-pushed the project-improvements branch 2 times, most recently from f3e0e96 to eec3e98 Compare April 8, 2026 13:44
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@alasdairwilson alasdairwilson left a comment

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I think we should keep the structure::

If i was the one that was trying to redistribute the functions from the veretx IA/ID files then I would rather have categories to insert into, this means you can do it in a much more iterative way without reverting early changes. rather than have to try and group the functions together adhoc as you go, having to rework early categorisations as you make later iterative changes. To me, useful work was done and it is just gonna need done again.

I am not really invested either way though, so you can keep the change if you want.

Comment thread isaricanalytics/IsaricAnalytics.py
@sr-murthy sr-murthy force-pushed the project-improvements branch 2 times, most recently from 9dc6141 to bae65f0 Compare April 10, 2026 07:25
Comment thread isaricanalytics/getREDCapData.py Fixed
Comment thread isaricanalytics/getREDCapData.py Fixed
Comment thread isaricanalytics/getREDCapData.py Fixed
Comment thread isaricanalytics/getREDCapData.py Fixed
Comment thread isaricanalytics/getREDCapData.py Fixed
@sr-murthy sr-murthy force-pushed the project-improvements branch 2 times, most recently from 9cb3dc8 to 3e0eb5a Compare April 10, 2026 07:42
Comment thread isaricanalytics/getREDCapData.py Dismissed
Comment thread isaricanalytics/getREDCapData.py Dismissed
chore: update README with status badges

test: add Codecov YML

chore: clean up deps in project TOML

docs: Set up Sphinx docs

style: lint

docs: clean up conf

ci: clean up tests step in test workflow to use PDM + remove the install package step

chore: add security policy

chore: add keywords to project TOML

refactor: copy analytics and visualisation libraries (and the tests) from VERTEX + update project TOML with Plotly dep

chore: remove commented out code from analytics and draw

chore: delete all unusued libraries (including tests) and assets from the repo

chore(deps): add pylock TOML

Various project improvements

chore: add missing `getREDCapData` lib. + `logging` subpackage from VERTEX

VERTEX code migration for REDCap data retrieval, analytics and visualisation libraries

chore(deps): add `requests` to deps

Project improvements and VERTEX code migration

chore: remove commented out code in `getREDCapData`

Project improvements and VERTEX code migration

chore: add license badge to README

Project improvements and VERTEX code migration
@sr-murthy sr-murthy force-pushed the project-improvements branch from 3e0eb5a to 5be28a1 Compare April 10, 2026 07:49
@sr-murthy sr-murthy changed the title Project improvements and code migration Project improvements and VERTEX code migration Apr 10, 2026
@sr-murthy sr-murthy merged commit f62c5ca into main Apr 10, 2026
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@sr-murthy sr-murthy deleted the project-improvements branch April 10, 2026 08:15
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4 participants