CI update - Githubissues

omnideconv / SimBu

Simulate pseudo-bulk RNAseq samples from scRNAseq expression data

http://omnideconv.org/SimBu/

GNU General Public License v3.0

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CI update #31

Closed grst closed 2 years ago

grst commented 2 years ago

Copy files from immunedeconv
Reformat

TODO

[x] api key for coverage
[x] api key for netlify
[x] update badges

grst commented 2 years ago

@alex-d13, please look it through and LMK if anything is unclear.

pkgdown currently fails with an out-of-memory issue in the sfaira vignette. Maybe there's some low-hanging fruit for reducing memory consumption? Like setting a variable to NULL in R or a del of an unused object in Python?
The Check on windows fails also when rendering the sfaira vignette, but the error message is less clear to me. Maybe it also gets solved by reducing memory usage.

alex-d13 commented 2 years ago

Hi,

Thanks a lot for the help, everything seems to be clear to me.

Yeah the vignettes with sfaira are an issue on itself..i usually tried to pre-compile them locally, then push the compiled pkgdown vignette to its branch manually. Thats a really annoying workflow since I have to it before every push to main, but I dont really know how to solve it differently. The vignette first has to build a conda environment using basilisk and then downloads one example dataset from sfaira. I guess thats where pkgdown has its memory issue. Another reason for this pre-calculation is the time limit in Bioconductor. They give me timeout warnings if I build the vignette on their system. This is the blogpost I am using to precompile the vignettes: https://ropensci.org/blog/2019/12/08/precompute-vignettes/

grst commented 2 years ago

I see! We can of course somehow exclude the vignette from the CI. The memory limit on GH actions is 7GB, which is not too little.

Maybe a little downsampling or choosing a different example dataset will suffice?

alex-d13 commented 2 years ago

I could try that, let me see if I can find a smaller dataset.

But I don't think I can decrease the runtime, installing the python packages just takes some time. So maybe I can find a solution where pkgdown builds the vignettes and deploys them on one branch (main_deploy) and another branch to push to bioconductor (has to be the main branch i think). But i don't know if thats good 'git' solution :D

grst commented 2 years ago

If the vignette build runs on github, you could set it up to auto-commt the pre-compiled vignette, then bioconductor woudn't need to build it.

grst commented 2 years ago

You can take inspiration from the document action for that

github-actions[bot] commented 2 years ago

🚀 Deployed on https://632d79519b5e1b6cedc6f23c--simbu-pkgdown-pr-build.netlify.app