Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Internal colname messages #324

Merged
merged 12 commits into from
Oct 9, 2023
Merged

Internal colname messages #324

merged 12 commits into from
Oct 9, 2023

Conversation

karissawhiting
Copy link
Collaborator

@karissawhiting karissawhiting commented Sep 18, 2023

What changes are proposed in this pull request?

Update internal processing of input data set names. Currently any passed genomic data is resolved to a set of internal data field names for all functions. This makes it confusing when warnings are thrown using internal assigned names, not original data set names.

If there is an GitHub issue associated with this pull request, please provide link.

#302


Reviewer Checklist (if item does not apply, mark is as complete)

  • PR branch has pulled the most recent updates from main branch. Ensure the pull request branch and your local version match and both have the latest updates from the main branch.
  • If a new function was added, function included in _pkgdown.yml
  • If a bug was fixed, a unit test was added for the bug check
  • Run pkgdown::build_site(). Check the R console for errors, and review the rendered website.
  • Code coverage is suitable for any new functions/features. Review coverage with withr::with_envvar(new = c("NOT_CRAN" = "true"), covr::report()). Begin in a fresh R session without any packages loaded.
  • R CMD Check runs without errors, warnings, and notes
  • usethis::use_spell_check() runs with no spelling errors in documentation

When the branch is ready to be merged into master:

  • Update NEWS.md with the changes from this pull request under the heading "# cbioportalR (development version)". If there is an issue associated with the pull request, reference it in parentheses at the end update (see NEWS.md for examples).
  • Run codemetar::write_codemeta()
  • Run usethis::use_spell_check() again
  • Approve Pull Request
  • Merge the PR

@hfuchs5 hfuchs5 self-assigned this Sep 21, 2023
@karissawhiting
Copy link
Collaborator Author

@hfuchs5 - Could you double check there aren't any spots where I missed this column name replacement? I updated it in sanitize data functions and also create_gene_binary()

Also if you could stress test it a little more that would be great as I did end up changing quite a few internals. Thank you!!!!

@hfuchs5 hfuchs5 merged commit 2408e08 into main Oct 9, 2023
6 checks passed
@hfuchs5 hfuchs5 deleted the internal-colname-messages branch October 9, 2023 19:50
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

Successfully merging this pull request may close these issues.

2 participants