Add GitHub actions for checks, pkgdown & codecov

[jemus42]

In theory, this PR supersedes existing Travis CI and Appveyor setup.

It adds 3 GitHub Actions workflows (see .github/workflows), which

• Run R CMD check on windows/macOS/Ubuntu on R release and devel (R-CMD-check.yaml)
• Run covr::codecov (with the same args as previous .travis.yaml) (test-coverage.yaml)
• Build the pkgdown site and deploy to GH pages (For a preview, see my fork's deployment) (pkgdown.yaml)

All workflows are based on (or unmodified copies of) the example actions available at r-lib/actions/examples

Notably, this PR also adds various packages required for the vignettes to the Suggests: field in DESCRIPTION, which seems to helps with dependency discovery in the workflows.

The recurrent-events vignette was added to the article index in _pkgdown.yml to avoid pkgdown warnings. This may be undesirable, depending on the vignette's status.
In addition, the following pkgdown notes were not adressed:

Topics missing from index: 
* add_tdc
* as.data.frame.crps
* daily
* extub_event
* geom_hazard
* geom_stepribbon
* get_intervals
* get_plotinfo
* get_terms
* pammtools
* patient
* predictSurvProb.pamm
* simdf_elra
* staph 

[adibender]

Thx, looks good 👍🏻 Is the modification of the Suggests: necessary? Currently I omit the vignettes from the official package on purpose (i.e. it's in .buildignore), because it would make package checks etc. on CRAN more tedious and increases the amount of dependencies. Is it possible to keep it that way?

[fabian-s]

Thx, looks good 👍🏻 Is the modification of the Suggests: necessary? Currently I omit the vignettes from the official package on purpose (i.e. it's in .buildignore), because it would make package checks etc. on CRAN more tedious and increases the amount of dependencies. Is it possible to keep it that way?

could pre-compute the vignettes: https://ropensci.org/blog/2019/12/08/precompute-vignettes/ and add GH action for recompiling them, e.g by running something like this: https://github.com/ropensci/eia/blob/master/vignettes/precompile.R

[jemus42]

I added the packages to Suggests: on a hunch because manual dependency installation in the pkgdown workflow might have been related to an Rmd issue I couldn't quite reproduce locally, I can try without the changes to Suggests: again to see if I can make it work.

I'll take a look at precompilation, that might be the least intrusive option.

[jemus42]

Welp, looks like it works just as well without the changes to Suggests: with the vignette dependencies installed ad-hoc in the pkgdown workflow.

Future vignette dependencies will need to be added to .github/workflows/pkgdown.yaml.

[adibender]

Welp, looks like it works just as well without the changes to Suggests: with the vignette dependencies installed ad-hoc in the pkgdown workflow.

This is good, isn't it?

[jemus42]

This is good, isn't it?

I guess so? It means no DESCRIPTION changes, no extra CRAN-dependencies for the vignettes, and the .Rbuildignore'd vignettes remain .Rbuildignore'd while still being rendered/deployed via GH Actions.

Unless I missed something, this should achieve the goal of "replace travis & appveyor at no extra cost" 🤔

[adibender]

perfect, thx!