Convert FIMS to a pkgdown site

[Andrea-Havron-NOAA]

The https://noaa-fims.github.io/ site is not built using pkgdown. Using pkgdown is preferred for the following reasons:

• pkgdown is the recommended method for publishing R vignettes online
• NOAA NMFS has a pkgdown template. Using this template would allow the FIMS website to match NOAA branding

[timjmiller]

Started to work on this but there are issues with the vignettes. I think a good approach would be to have the vignettes not do any heavy computation so that the build runs faster. In wham we have example scripts that mirror the Rmds and the example scripts are where users can run the commands. So the vignettes would be a lot of r chunks with eval=F and then stored objects with necessary results are loaded as needed (in r chunks with include = FALSE).

[Bai-Li-NOAA]

Great! I will continue working on the issue by adding a GHA workflow to automatically update pkgdown website. I agree that we should convert some r chunks with eval = F if it takes long time to run the vignette.

[Bai-Li-NOAA]

I updated the pkgdown site through commits 1e5ab91 and 098a2b5:

• added .github/workflows/call-update-pkgdown.yml to automatically update the pkgdown site when there is a change in main branch. We need help from @ChristineStawitz-NOAA to update GitHub settings and publish the website after merging those changes to main.
• added home, reference, articles, and news sections in pkgdown/_pkgdown.yml following examples from tidyverse packages (e.g., ggplot2 and dplyr)
  • home section includes links to C++ doxygen documentation page and collaborative workflow book
  • reference section includes built-in dataset and functions for package development
  • articles section includes articles that describe FIMS design and demos for developers
  • new section includes information of releases

I am able to run pkgdown::build_site() locally to build the site in 28.32 secs.
@timjmiller, please feel free to update the website. I wonder if we should create a new issue to let the implementation team go over the R functions and update the names of some functions for topic matching. We can use starts_with("prefix") to select all functions with common prefix when creating a pkgdown website. Or we can add @keywords in roxygen documentation and then use has_keyword("x") in _pkgdown.yml file to select all topics with keyword "x" (see FIMS examples here and here).