PecanProject
Fix remaining check warnings from PEcAn.photosynthesis (fixes #2819)
this pull request is directed towards getting the photosynthesis package ready to be released to CRAN! I will be constantly updating this pull request as we move forward until the task is finished!
Currently failing build because the vignette is too large. This will need to be fixed before it can go to CRAN, but we may want to consider merging this and tackling that separately.
Per @mdietze in Slack discussion about reducing vignette size:
"I think you could safely drop the gelman.plots from the vignette. If that's not enough then I'd comment out the plot(fit$params) in the second and third examples, and the plot_photo in the third, with a note encouraging folks to run those if they're doing the vignette interactively. But the reality is that once you see mcmc output in the first you don't need to see it in the 2nd and 3rd and the fits to the A-Ci curves in the 3rd look pretty identical to the 2nd"
You can also pre-compile vignettes so CRAN doesn't have to: https://ropensci.org/blog/2019/12/08/precompute-vignettes/
@Aariq At the moment compilation time is a secondary problem and the main issue, which precompilation won't fix, is that the finished vignette PDF is by itself larger than CRAN's 5 MB limit for a whole package! To resolve this we need to do some combination of (a) reducing the number of images and/or (b) making each image use fewer bytes.
Are we sure this is the images and not this: https://github.com/PecanProject/pecan/pull/2836#issuecomment-1182523692 ?
Looks like the branch this PR was coming from doesn't exist anymore. Should this PR be closed?
This PR has a lot of good changes in it, so I'd like to keep it open until someone (me) has time to push a replacement and work out the minimal changes needed to merge.
That sounds good. I was just trying to take a look at it and couldn't figure out how to with my usual avoid-commandline-git workflow which said the branch didn't exist anymore.
Please accept my apologies here! I don't know what I was thinking when I deleted my pecan fork 😞. @infotroph please let me know how I can recover the work done in this branch.
I've opened #3015 to be the mergeable continuation of this work and am closing this PR, but please refer back to the discussion here when planning any further work in #3015.