Reivew and Reorganize internals

[karissawhiting]

What changes are proposed in this pull request?

Here is a run down of the updates:

• More explicit separation between which are exported vs internal-only functions.

  • All internal functions start with a period (eg. .check_required_cols()) and are removed from NAMESPACE export list. If these are internal helpers for create_gene_binary(), they are in utils-gene-binary.R. Otherwise, they are in utils.R.
  • Other user-facing and exported helpers/utilities are in utils-exported-helpers.R.

• I’ve removed the sanitize_mutations(), sanitize_cna(), sanitize_fusions() functions and instead replaced them with smaller, more modular and explicit functions that do all the same tasks. This helps test, debug and troubleshoot some of the more complicated processing pipelines and now we have nice explicit pipes like this:

If there is an GitHub issue associated with this pull request, please provide link.
#328

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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

[michaelcurry1123]

I took a look and it looks great I will do the checklist in a bit but will approve today

[michaelcurry1123]

@karissawhiting the checks aren't passing can you try to run them to see if it is an issue with my access?