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monarch-initiative / monarchr

R package for easy access, manipulation, and analysis of Monarch KG data
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Add code coverage badges #4

Open oneilsh opened 1 year ago

bschilder commented 5 months ago

Since you're already using rworkflows, you could also use rworkflows::use_badges in your README, which collects and render all the badges for you.

I'll make a PR for this

bschilder commented 5 months ago

added here: #15

oneilsh commented 2 months ago

Thanks Brian - just making a note for this one that I have yet to link them to codecov.io

oneilsh commented 1 month ago

Hmm, so I could use some help getting the rworkflows checks and badges running properly. @bschilder, would you mind taking a look? I had previously removed Windows and OSX builds in rworkflows.yml as they were breaking (but not sure why), and I turned off run_rcmdcheck but I think it's ready to go now. I should be able to setup the link to codecov.io, but I don't remember how to trigger the codecov.yaml generation. And, I'm not sure if README.md is being properly built from README.Rmd.

Basically, I broke a lot of the rworkflows stuff to get the GH pages site to properly publish...

bschilder commented 1 month ago

The codecov.yaml should't be necessary anymore. Once rworkflows passes all the previous steps the codecov report should automatically be uploaded to Codecov and the badge will be updated.

That said, this only happens automatically when Codecov isn't having problems. We just added a new feature to rworkflows that allows you to supply the CODECOV token (which can be stored in the monarchr repo as a GitHub secret), just in case we need it.

https://github.com/neurogenomics/rworkflows/pull/132

bschilder commented 1 month ago

The reason the Codecov badge isn't updating here could be due to a permissions issue with the monarchr repo, or the monarch-initiative org in general (I see none of the repos have been activated for codecov). https://app.codecov.io/gh/monarch-initiative

Someone with admin permissions might need to follow some of these steps to let Codecov do its thing: https://docs.codecov.com/docs/quick-start