increment version 3.1.0 - #84
Merged
Merged
Conversation
There was a problem hiding this comment.
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 |
There was a problem hiding this comment.
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
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
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.