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Develop#75

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jreps merged 42 commits into
mainfrom
develop
Sep 9, 2025
Merged

Develop#75
jreps merged 42 commits into
mainfrom
develop

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@jreps
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@jreps jreps commented May 8, 2025

Before you do a pull request, you should always file an issue and make sure the package maintainer agrees that it’s a problem, and is happy with your basic proposal for fixing it. We don’t want you to spend a bunch of time on something that we don’t think is a good idea.

Additional requirements for pull requests:

  • Adhere to the Developer Guidelines as well as the OHDSI Code Style.

  • If possible, add unit tests for new functionality you add.

  • Restrict your pull request to solving the issue at hand. Do not try to 'improve' parts of the code that are not related to the issue. If you feel other parts of the code need better organization, create a separate issue for that.

  • Make sure you pass R check without errors and warnings before submitting.

  • Always target the develop branch, and make sure you are up-to-date with the develop branch.

msuchard and others added 18 commits November 5, 2024 12:01
Cast datediff as bigint to prevent arithmetic overflow
turning off progress bar
trying to fix github actions
updating vignettes to try and pass actions
adding ubuntu latest as 20.04 depreciated
preparing for 2.1.4 release
putting examples in own directories
fixing example doc
using the new FE that fixes the Andromeda issue
adding failed case series csv test
changing version ready for release
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codecov Bot commented May 8, 2025

Codecov Report

❌ Patch coverage is 84.26396% with 62 lines in your changes missing coverage. Please review.
✅ Project coverage is 91.29%. Comparing base (213d736) to head (f9e5c41).
⚠️ Report is 82 commits behind head on main.

Files with missing lines Patch % Lines
R/CustomCovariates.R 50.00% 22 Missing ⚠️
R/ViewShiny.R 76.47% 16 Missing ⚠️
R/Database.R 57.89% 8 Missing ⚠️
R/SaveLoad.R 76.47% 8 Missing ⚠️
R/AggregateCovariates.R 96.15% 3 Missing ⚠️
R/DechallengeRechallenge.R 83.33% 2 Missing ⚠️
R/RunCharacterization.R 97.77% 2 Missing ⚠️
R/TimeToEvent.R 85.71% 1 Missing ⚠️
Additional details and impacted files
@@            Coverage Diff             @@
##             main      #75      +/-   ##
==========================================
+ Coverage   86.99%   91.29%   +4.30%     
==========================================
  Files           8       10       +2     
  Lines        1384     2688    +1304     
==========================================
+ Hits         1204     2454    +1250     
- Misses        180      234      +54     

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jreps and others added 11 commits June 26, 2025 15:58
-  changing aggregate csv to be done in batches
- adding example results into testdata for testing the aggregate csv function
- changing append logic to only append if it is not the first time writing to the file or not the first chunk
- adding more tests to the csv aggregation
Fix inconsistent PK designation in RDMS
- fixing progressBar to default to interactive() when possible or turned off when not possible to specify as an input.
- added code to ensure all the result csv files are created
updating GHA with curl fix part 1 (thanks Anthony Sena!)
@jreps jreps merged commit a59629e into main Sep 9, 2025
10 of 11 checks passed
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4 participants