Set up skeleton API package

[pratikunterwegs]

This PR sets up {daedalus.api} with some skeleton API code taken from {odin.api}:

1. Updates the .lintr file to conform to modern {lintr} and tweak exclusions for;
2. Updates the GHA workflows;
3. Updates tests - removed {odin}-specific tests leaving only basic API tests;
4. Updates the Dockerfile and Rprofile.site to be use P3M.

Some outstanding points/issues:

1. I'm not having much luck updating to rocker/r-ver:4.4.1 as {R6} and {jsonlite} aren't installing which blocks {porcelain};
2. There's little to no Roxygen function documentation - is this something that needs to be added?
3. The Dockerfile still takes mrc-ide/drat as a repo, I can change this once we set up an R-universe;
4. The R CMD check GH workflow allows NOTEs to pass - this because {daedalus} is imported but not used (this will likely change?)

[richfitz]

tiny things, then let's get this merged

[richfitz]

if you set up .gitattributes with

R/porcelain.R linguist-generated=true

then this will not render in the diff view by default

[pratikunterwegs]

Added in 792b3e7

[richfitz]

This and prepare_code can be dropped I think?

[pratikunterwegs]

Removed in 9e12b17 - wasn't sure whether these would be needed later so kept them initially

[richfitz]

These were for uglifying js code returned from odin, but we removed the implementation in the end as it was hard to get it working as expected so I think I left it in as an empty skeleton and then forgot about it...

[richfitz]

Your queries:

I'm not having much luck updating to rocker/r-ver:4.4.1 as {R6} and {jsonlite} aren't installing which blocks {porcelain};

this is now fixed 🎉

There's little to no Roxygen function documentation - is this something that needs to be added?

that's fine, roxygen is just a tool for us to generate the interface for now

The Dockerfile still takes mrc-ide/drat as a repo, I can change this once we set up an R-universe;

this can be changed now, and you can also set up a jameel-institute one to pull daedalus itself in (now or later as you prefer)

The R CMD check GH workflow allows NOTEs to pass - this because {daedalus} is imported but not used (this will likely change?)

I never block on notes, because of notes like the "more than 5mb of compiled C++" one that blocks just about everything using Rcpp/cpp11

[pratikunterwegs]

this can be changed now, and you can also set up a jameel-institute one to pull daedalus itself in (now or later as you prefer)

I guess this can be left for now as {daedalus} is pulled direct from GH anyway as the remote is listed.

I think the more recent commits fix the other issues.

[richfitz]

I guess this can be left for now as {daedalus} is pulled direct from GH anyway as the remote is listed.

this is fine until we hit rate limits, as we can't get the token safely into the builder. if/once we hit that the fix is easy and by then we'll probably have the universe set up

[richfitz]

fabulous, thanks

[pratikunterwegs]

this is fine until we hit rate limits, as we can't get the token safely into the builder. if/once we hit that the fix is easy and by then we'll probably have the universe set up

I set it up yesterday/the day before - works alright. I can add the R-universe to the Dockerfile.