calc_* and process_hms functions; .gitignore

[mitchellmanware]

I was unable to resolve errors in previous pull requests, so with new branch (v2) I will commit small changes to evaluate how they do/do not pass pull request tests.

[mitchellmanware]

@Spatiotemporal-Exposures-and-Toxicology

All checks are failing due to:

 Error: 
  ! error in pak subprocess
  Caused by error in `verify_extracted_package(filename, pkg_cache)`:
  ! 
  '/tmp/RtmpyxpY6v/file13cf7aaebd0c/src/contrib/x86_64-pc-linux-gnu-ubuntu-22.04/4.3/withr_3.0.0.tar.gz'
  is not a valid binary, it is missing withr/Meta/package.rds.
  ---
  Backtrace:
  1. pak::lockfile_install(".github/pkg.lock")
  2. pak:::remote(function(...) { …
  3. err$throw(res$error)

Unclear why this is occurring, and seems weird that 4 R files (which pass local lints and are not subject to testing) and edits to the .gitignore cause these issues. Do you have any idea why this is happening?

[kyle-messier]

@mitchellmanware Not sure why. Did you need to add all of those sub-paths to the .gitignore?

[mitchellmanware]

@Spatiotemporal-Exposures-and-Toxicology
Those are the folders with raw covariate data, but I guess those can be put into one single raw_data/ folder and have just that on the .gitignore.

[mitchellmanware]

Seems to be an issue with the new version of the withr package published yesterday. GitHub dialogue has opened for fixes- I will keep updating.

Package- https://cran.r-project.org/web/packages/withr/index.html
Discussion- r-lib/withr#253

@Spatiotemporal-Exposures-and-Toxicology @sigmafelix @eva0marques @dzilber @MAKassien @dawranadeep @Sanisha003

[codecov]

Codecov Report

Attention: 37 lines in your changes are missing coverage. Please review.

Comparison is base (b1273f3) 91.06% compared to head (5c6233c) 91.78%.

Files	Patch %	Lines
R/download.R	91.72%	37 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #264      +/-   ##
==========================================
+ Coverage   91.06%   91.78%   +0.72%     
==========================================
  Files          14       14              
  Lines        1735     1839     +104     
==========================================
+ Hits         1580     1688     +108     
+ Misses        155      151       -4     

☔ View full report in Codecov by Sentry.
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[mitchellmanware]

• R-CMD-check build finally passes due to updates to withr package.
• URL checks within download functions are not covered by unit tests
• pkgdown fail- may be due to .qmd file in vignettes
  • Note: pkgdown does not like Quarto documents for vignettes

[mitchellmanware]

URLs generated by download_sedac* always return HTTP status 200 because the httr::GET() returns the NASA EarthData login page. Removed for now but will continue to work on these within function URL checks.