increment version 3.1.0 #84
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Pull Request Overview
This PR increments the package version to 3.1.0 and includes enhancements to the boxplot functionality along with some test configuration changes.
- Version bump from 3.0.2 to 3.1.0 in package metadata
- Enhanced boxplot function with alpha transparency parameter and improved point coloring
- Updated documentation to reflect new alpha parameter
Reviewed Changes
Copilot reviewed 5 out of 5 changed files in this pull request and generated 1 comment.
Show a summary per file
| File | Description |
|---|---|
| DESCRIPTION | Updates package version from 3.0.2 to 3.1.0 |
| NEWS.md | Adds version 3.1.0 section header |
| R/plot-pgs.R | Adds alpha parameter for point transparency and fixes point coloring logic |
| man/create.pgs.boxplot.Rd | Documents new alpha parameter |
| tests/testthat/test-plotting.R | Enables plotting tests by setting flags to FALSE |
Comments suppressed due to low confidence (1)
tests/testthat/test-plotting.R:2
- [nitpick] Enabling plotting tests in the test suite may significantly increase test execution time. Consider whether this should be enabled by default or only in specific CI environments.
SKIP.PLOTS <- FALSE;
| yaxis.lab = group.yaxis.formatting$axis.lab, | ||
| col = boxplot.colors | ||
| points.col = boxplot.colors[pgs.data[ , phenotype]] # color points by phenotype | ||
| #col = boxplot.colors |
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Remove commented-out code. Dead code should be deleted rather than commented out to maintain code cleanliness.
Suggested change
| #col = boxplot.colors |
rhughwhite
approved these changes
Jul 22, 2025
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In this PR:
a couple of small bug fixes
incrementing package version to 3.1.0 for various feature additions
I have read the code review guidelines and the code review best practice on GitHub check-list.
The name of the branch is meaningful and well formatted following the standards, using [AD_username (or 5 letters of AD if AD is too long)-[brief_description_of_branch].
I have set up or verified the branch protection rule following the github standards before opening this pull request.
I have added the changes included in this pull request to
NEWSunder the next release version or unreleased, and updated the date.I have updated the version number in
metadata.yamlandDESCRIPTION.Both
R CMD buildandR CMD checkrun successfully.Testing Results
Unit tests PASS and local R CMD Check passes.