Djm/summer cleaning

[dajmcdon]

Checklist

Please:

• Make sure this PR is against "dev", not "main".
• Request a review from one of the current epipredict main reviewers:
  dajmcdon.
• Make sure to bump the version number in DESCRIPTION and NEWS.md.
  Always increment the patch version number (the third number), unless you are
  making a release PR from dev to main, in which case increment the minor
  version number (the second number).
• Describe changes made in NEWS.md, making sure breaking changes
  (backwards-incompatible changes to the documented interface) are noted.
  Collect the changes under the next release number (e.g. if you are on
  0.7.2, then write your changes under the 0.8 heading).
• Consider pinning the epiprocess version in the DESCRIPTION file if
  • You anticipate breaking changes in epiprocess soon
  • You want to co-develop features in epipredict and epiprocess

[dajmcdon]

@JavierMtzRdz Most of the changes are coming from the Air R formatter. The actual changes are (I think):

1. checkout action in the github actions;
2. Some changes to autoplot() that got out of sync with epiprocess.
3. Some changes to broken URLs in documentation.
4. Some changes to the README to avoid pulling from the API, and make autoplot() work on the forecasts.

[JavierMtzRdz]

/preview-docs

[github-actions]

🚀 Deployed on https://6a467ac7e81902b110d77428--epipredict.netlify.app

[JavierMtzRdz]

The GitHub Actions seem to render the documentation correctly, all updated links work for me on the rendered page, and the style changes look good to me.

RE .max_keys, it is still active in epiprocess, as shown here. I believe the error was caused by using an outdated version of epiprocess, which was the only way to reproduce the issue on the dev branch, as shown below.

> pak::pkg_install("cmu-delphi/epiprocess@main")

#> → Will update 1 package.
#> → The package (0 B) is cached.
#> + epiprocess 0.12.0.9999 → 0.12.0 👷🏼‍♀️🔧 (GitHub: adaa348)
#> 
#> ! epiprocess is loaded in the current R session, you probably need to
#> restart R after the installation.
#> 
#> ? Do you want to continue (Y/n) 
#> y
#> ℹ No downloads are needed, 1 pkg is cached
#> ✔ Installed epiprocess 0.12.0 (github::cmu-delphi/epiprocess@adaa348) (82ms)
#> ✔ 1 pkg + 42 deps: kept 41, upd 1 [5.1s]                               
#> R 4.5.1 exited (preparing for restart)
#> R 4.5.1 restarted.
> rmarkdown::render("README.Rmd")


#> processing file: README.Rmd
#> 1/30                       
#> 2/30 [unnamed-chunk-1]     
#> 3/30 [pkgs]                
#> 4/30                       
#> 5/30 [coloration]          
#> 6/30                       
#> 7/30 [install]             
#> 8/30                       
#> 9/30 [subset_geos]         
#> 10/30                       
#> 11/30 [fc_date]             
#> 12/30                       
#> 13/30 [case_death]          
#> 14/30                       
#> 15/30 [date]                
#> 16/30                       
#> 17/30 [outlier]             
#> 18/30                       
#> 19/30 [plot_locs]           
#> 20/30                       
#> 21/30 [show-processed-data] 
#> 22/30                       
#> 23/30 [make-forecasts]      
#> Registered S3 methods overwritten by 'epipredict':
#>   method                          from   
#> print.step_naomit               recipes
#> vec_arith.quantile_pred         hardhat
#> vec_arith.numeric.quantile_pred hardhat
#> vec_math.quantile_pred          hardhat
#> 24/30                       
#> 25/30 [plotting_forecast]   
#> Warning messages:
#>   1: package 'parsnip' was built under R version 4.5.2 
#> 2: package 'data.table' was built under R version 4.5.2 
#> 3: package 'dplyr' was built under R version 4.5.2 
#> 4: package 'tidyr' was built under R version 4.5.2 
#> 5: package 'ggplot2' was built under R version 4.5.2 
#> 6: package 'magrittr' was built under R version 4.5.2 
#> 7: package 'purrr' was built under R version 4.5.2 
#> 8: package 'tibble' was built under R version 4.5.2 
#> 9: package 'readr' was built under R version 4.5.2 
#> 10: package 'lubridate' was built under R version 4.5.2 
#> 
#> Quitting from README.Rmd:305-322 [plotting_forecast]
#> Error in `autoplot_check_viable_response_vars()`:
#>   ! Can't select columns with `Inf`.
#> ✖ Can't convert from `Inf` <double> to <integer> due to loss of precision.
#> 
#> Show Traceback
> pak::pkg_install("cmu-delphi/epiprocess@dev")
#> ✔ Loading metadata database ... done                                  
#> 
#> → Will update 1 package.
#> → The package (0 B) is cached.
#> + epiprocess 0.12.0 → 0.12.0.9999 👷🏾🔧 (GitHub: 364e390)
#> 
#> ! epiprocess is loaded in the current R session, you probably need to
#> restart R after the installation.
#> 
#> ? Do you want to continue (Y/n) 
#> y
#> ℹ No downloads are needed, 1 pkg is cached
#> ✔ Installed epiprocess 0.12.0.9999 (github::cmu-delphi/epiprocess@364e390) (37ms)
#> ✔ 1 pkg + 75 deps: kept 72, upd 1 [9.2s]                               
#> R 4.5.1 exited (preparing for restart)
#> R 4.5.1 restarted.
> rmarkdown::render("README.Rmd")


#> processing file: README.Rmd
#> 1/30                       
#> 2/30 [unnamed-chunk-1]     
#> 3/30 [pkgs]                
#> 4/30                       
#> 5/30 [coloration]          
#> 6/30                       
#> 7/30 [install]             
#> 8/30                       
#> 9/30 [subset_geos]         
#> 10/30                       
#> 11/30 [fc_date]             
#> 12/30                       
#> 13/30 [case_death]          
#> 14/30                       
#> 15/30 [date]                
#> 16/30                       
#> 17/30 [outlier]             
#> 18/30                       
#> 19/30 [plot_locs]           
#> 20/30                       
#> 21/30 [show-processed-data] 
#> 22/30                       
#> 23/30 [make-forecasts]      
#> Registered S3 methods overwritten by 'epipredict':
#>   method                          from   
#> print.step_naomit               recipes
#> vec_arith.quantile_pred         hardhat
#> vec_arith.numeric.quantile_pred hardhat
#> vec_math.quantile_pred          hardhat
#> 24/30                       
#> 25/30 [plotting_forecast]   
#> 26/30                       
#> 27/30 [show-single-forecast]
#> 28/30                       
#> 29/30 [pivot_wider]         
#> 30/30                       
#> output file: README.knit.md
#> 
#> /Applications/Positron.app/Contents/Resources/app/quarto/bin/tools/aarch64/pandoc +RTS #> -K512m -RTS README.knit.md --to gfm-tex_math_gfm-yaml_metadata_block --from markdown#> +autolink_bare_uris+tex_math_single_backslash --output README.md --template /Library#> /Frameworks/R.framework/Versions/4.5-arm64/Resources/library/rmarkdown/rmarkdown#> /templates/github_document/resources/default.md 
#> /Applications/Positron.app/Contents/Resources/app/quarto/bin/tools/aarch64/pandoc +RTS #> -K512m -RTS README.md --to html4 --from gfm-tex_math_gfm --output README.html --embed#> -resources --standalone --syntax-highlighting pygments --template /Library/Frameworks/R#> .framework/Versions/4.5-arm64/Resources/library/rmarkdown/rmarkdown/templates#> /github_document/resources/preview.html --variable 'github-markdown-css:/Library#> /Frameworks/R.framework/Versions/4.5-arm64/Resources/library/rmarkdown/rmarkdown#> /templates/github_document/resources/github.css' --metadata pagetitle=PREVIEW --mathjax #> 
#> 
#> Preview created: README.html
#> 
#> Output created: README.md
#> Warning messages:
#>   1: package 'parsnip' was built under R version 4.5.2 
#> 2: package 'data.table' was built under R version 4.5.2 
#> 3: package 'dplyr' was built under R version 4.5.2 
#> 4: package 'tidyr' was built under R version 4.5.2 
#> 5: package 'ggplot2' was built under R version 4.5.2 
#> 6: package 'magrittr' was built under R version 4.5.2 
#> 7: package 'purrr' was built under R version 4.5.2 
#> 8: package 'tibble' was built under R version 4.5.2 
#> 9: package 'readr' was built under R version 4.5.2 
#> 10: package 'lubridate' was built under R version 4.5.2 

.max_keys subsamples the displayed location-key combinations to prevent autoplot.epi_df from getting stuck when plotting too many locations. However, because this feature is not integrated into autoplot.epi_workflow, it may return forecasts without the observed response data if we remove .max_keys = Inf. To address this, I submitted PR #483 that restores .max_keys = Inf and adds a test to verify that autoplot.epi_workflow is working. I avoided using expect_snapshot_file because it might trigger warnings if ggplot undergoes upstream changes.

If the reintegration of .max_keys = Inf looks good to you, we can proceed to merge.