Create NMFS completion certificates & use quarto for certificates

[ateucher]

This updates create_certificate() and create_batch_certificates() to create a certificate for the NMFS Openscapes champions using a nmfs-specific template, using Quarto with typst pdf output. It also switches the original certificate creation to use Quarto + typst instead of Rmarkdown + LaTeX.

The template (NMFS or standard Openscapes) is chosen via the new parameter cohort_type ("standard", the default, or "nmfs").

Because Quarto doesn't support writing to a different directory, I added code to match existing behaviour to move the file to a specified directory once it's created.

I also added some robustness to create_batch_certificates() with a tryCatch() inside the loop, and some more basic type checking and handling of dates.

Still TODO: Move pathways template here as well (#99) (NOTE: Will do in a separate PR after this is merged)

Closes #144

[stefaniebutland]

Dec 20

Thanks @ateucher for the screenshare to resolve this. I updated Quarto & RStudio & create_batch_certificates worked.

create_certificate gave error Error: argument "cohort_type" is missing, with no default

Out of date:

Error in my setup preventing me from testing.

create_certificate gives Error running quarto cli. I've got a newer version of Quarto installed but RStudio still using 1.4.4 (i.e. without typst?). Likely the source of error. I'll get Andy's help to clean up my setup

Session info

────────────────────────────────────────────────────────
 setting  value
 version  R version 4.4.1 (2024-06-14)
 os       macOS Ventura 13.7.1
 system   aarch64, darwin20
 ui       RStudio
 language (EN)
 collate  en_US.UTF-8
 ctype    en_US.UTF-8
 tz       America/Vancouver
 date     2024-12-16
 rstudio  2024.09.0+375 Cranberry Hibiscus (desktop)
 pandoc   3.2 @ /Applications/RStudio.app/Contents/Resources/app/quarto/bin/tools/aarch64/ (via rmarkdown)

─ Packages ────────────────────────────────────────────────────────────
 ! package       * version  date (UTC) lib source
   askpass         1.2.1    2024-10-04 [1] CRAN (R 4.4.1)
   brio            1.1.5    2024-04-24 [1] CRAN (R 4.4.0)
   cachem          1.1.0    2024-05-16 [1] CRAN (R 4.4.0)
   cellranger      1.1.0    2016-07-27 [1] CRAN (R 4.4.0)
   cli             3.6.3    2024-06-21 [1] CRAN (R 4.4.0)
   credentials     2.0.2    2024-10-04 [1] CRAN (R 4.4.1)
   curl            6.0.1    2024-11-14 [1] CRAN (R 4.4.1)
   desc            1.4.3    2023-12-10 [1] CRAN (R 4.4.0)
   devtools      * 2.4.5    2022-10-11 [1] CRAN (R 4.4.0)
   digest          0.6.37   2024-08-19 [1] CRAN (R 4.4.1)
   dplyr         * 1.1.4    2023-11-17 [1] CRAN (R 4.4.0)
   ellipsis        0.3.2    2021-04-29 [1] CRAN (R 4.4.0)
   evaluate        1.0.1    2024-10-10 [1] CRAN (R 4.4.1)
   fansi           1.0.6    2023-12-08 [1] CRAN (R 4.4.0)
   fastmap         1.2.0    2024-05-15 [1] CRAN (R 4.4.0)
   fs              1.6.5    2024-10-30 [1] CRAN (R 4.4.1)
   gargle          1.5.2    2023-07-20 [1] CRAN (R 4.4.0)
   generics        0.1.3    2022-07-05 [1] CRAN (R 4.4.0)
   gert            2.1.4    2024-10-14 [1] CRAN (R 4.4.1)
   gh              1.4.1    2024-03-28 [1] CRAN (R 4.4.0)
   gitcreds        0.1.2    2022-09-08 [1] CRAN (R 4.4.0)
   glue            1.8.0    2024-09-30 [1] CRAN (R 4.4.1)
   googledrive     2.1.1    2023-06-11 [1] CRAN (R 4.4.0)
   googlesheets4 * 1.1.1    2023-06-11 [1] CRAN (R 4.4.0)
   htmltools       0.5.8.1  2024-04-04 [1] CRAN (R 4.4.0)
   htmlwidgets     1.6.4    2023-12-06 [1] CRAN (R 4.4.0)
   httpuv          1.6.15   2024-03-26 [1] CRAN (R 4.4.0)
   httr            1.4.7    2023-08-15 [1] CRAN (R 4.4.0)
   jsonlite        1.8.9    2024-09-20 [1] CRAN (R 4.4.1)
   knitr           1.49     2024-11-08 [1] CRAN (R 4.4.1)
 P kyber         * 0.1.0    2024-12-09 [?] Github (openscapes/kyber@ee5f27d)
   later           1.4.1    2024-11-27 [1] CRAN (R 4.4.1)
   lifecycle       1.0.4    2023-11-07 [1] CRAN (R 4.4.0)
   lubridate       1.9.4    2024-12-08 [1] CRAN (R 4.4.1)
   magrittr        2.0.3    2022-03-30 [1] CRAN (R 4.4.0)
   memoise         2.0.1    2021-11-26 [1] CRAN (R 4.4.0)
   mime            0.12     2021-09-28 [1] CRAN (R 4.4.0)
   miniUI          0.1.1.1  2018-05-18 [1] CRAN (R 4.4.0)
   openssl         2.2.2    2024-09-20 [1] CRAN (R 4.4.1)
   parsermd        0.1.3    2024-01-16 [1] CRAN (R 4.4.0)
   pillar          1.9.0    2023-03-22 [1] CRAN (R 4.4.0)
   pkgbuild        1.4.5    2024-10-28 [1] CRAN (R 4.4.1)
   pkgconfig       2.0.3    2019-09-22 [1] CRAN (R 4.4.0)
   pkgload         1.4.0    2024-06-28 [1] CRAN (R 4.4.0)
   processx        3.8.4    2024-03-16 [1] CRAN (R 4.4.0)
   profvis         0.4.0    2024-09-20 [1] CRAN (R 4.4.1)
   promises        1.3.2    2024-11-28 [1] CRAN (R 4.4.1)
   ps              1.8.1    2024-10-28 [1] CRAN (R 4.4.1)
   purrr           1.0.2    2023-08-10 [1] CRAN (R 4.4.0)
   quarto        * 1.4.4    2024-07-20 [1] CRAN (R 4.4.0)
   R6              2.5.1    2021-08-19 [1] CRAN (R 4.4.0)
   rappdirs        0.3.3    2021-01-31 [1] CRAN (R 4.4.0)
   Rcpp            1.0.13-1 2024-11-02 [1] CRAN (R 4.4.1)
   remotes         2.5.0    2024-03-17 [1] CRAN (R 4.4.0)
   rlang           1.1.4    2024-06-04 [1] CRAN (R 4.4.0)
   rmarkdown       2.29     2024-11-04 [1] CRAN (R 4.4.1)
   rprojroot       2.0.4    2023-11-05 [1] CRAN (R 4.4.0)
   rstudioapi      0.17.1   2024-10-22 [1] CRAN (R 4.4.1)
   sessioninfo     1.2.2    2021-12-06 [1] CRAN (R 4.4.0)
   shiny           1.9.1    2024-08-01 [1] CRAN (R 4.4.0)
   stringi         1.8.4    2024-05-06 [1] CRAN (R 4.4.0)
   stringr         1.5.1    2023-11-14 [1] CRAN (R 4.4.0)
   sys             3.4.3    2024-10-04 [1] CRAN (R 4.4.1)
   testthat      * 3.2.1.1  2024-04-14 [1] CRAN (R 4.4.0)
   tibble          3.2.1    2023-03-20 [1] CRAN (R 4.4.0)
   tidyselect      1.2.1    2024-03-11 [1] CRAN (R 4.4.0)
   timechange      0.3.0    2024-01-18 [1] CRAN (R 4.4.0)
   urlchecker      1.0.1    2021-11-30 [1] CRAN (R 4.4.0)
   usethis       * 3.1.0    2024-11-26 [1] CRAN (R 4.4.1)
   utf8            1.2.4    2023-10-22 [1] CRAN (R 4.4.0)
   vctrs           0.6.5    2023-12-01 [1] CRAN (R 4.4.0)
   withr           3.0.2    2024-10-28 [1] CRAN (R 4.4.1)
   xfun            0.49     2024-10-31 [1] CRAN (R 4.4.1)
   xtable          1.8-4    2019-04-21 [1] CRAN (R 4.4.0)
   yaml            2.3.10   2024-07-26 [1] CRAN (R 4.4.0)

 [1] /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library

[stefaniebutland]

UPDATE: copied from comment above

create_certificate gave error Error: argument "cohort_type" is missing, with no default

Worked well for me in our late-Dec screenshare. Thank you @ateucher !