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NIEHS / chopin

Scalable GIS methods for environmental and climate data analysis
https://niehs.github.io/chopin/
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0.0.2 rev and workflow integration #15

Closed sigmafelix closed 9 months ago

sigmafelix commented 9 months ago

Still figuring out YAML file settings for running the test.

kyle-messier commented 9 months ago

@sigmafelix I don't think we need the codecov.yaml - the test-coverage calls covr and should apply the codecov.io test coverage report.

sigmafelix commented 9 months ago

R CMD check keeps failing. I will revisit the error codes and try to run R CMD check locally before push any changes.

kyle-messier commented 9 months ago

@sigmafelix The R CMD Check has 5 warnings which causes it to fail. It has lots of suggestions, but it is not always straight forward to debug. One thing that may alleviate a lot of this is proper folder naming. R CMD check will expect all of the R scipts to be in R with no other subfolders. As it is in scromps/R/ that be a source of many issues. One drastic option is to start from scratch with R package building (e.g. use_this) and let it build things as it expects from the ground up.

kyle-messier commented 9 months ago

@sigmafelix I see what you mean now. You have scomps set up as an R package within our repo name. Should I rename the repo to scomps and then you can make the necessary folder changes to move scomps to be the package and repo root?

codecov[bot] commented 9 months ago

The author of this PR, sigmafelix, is not an activated member of this organization on Codecov. Please activate this user on Codecov to display this PR comment. Coverage data is still being uploaded to Codecov.io for purposes of overall coverage calculations. Please don't hesitate to email us at support@codecov.io with any questions.

sigmafelix commented 9 months ago

@Spatiotemporal-Exposures-and-Toxicology I think the repo name was properly reflected in *.yaml files for GitHub Actions. The push just I made returned no warnings when R CMD check was done in my local system. Let's see how it turns out. For naming the package, [s]calable [comp]utation for geo[s]patial health studies was my initial thought, but I will be happy to discuss a proper name.

sigmafelix commented 9 months ago

@Spatiotemporal-Exposures-and-Toxicology Finally the recent push passed the test. I will keep the directory layout of this repo as-is for the time being. I think I will do R CMD check locally to make the pull request process efficient from now on.

kyle-messier commented 9 months ago

@sigmafelix codecov.io is working, but I think the nested package is causing an issue with giving line-by-line coverage. Let me know if you can see the line coverage at codecov.io. See similar issue here: https://community.codecov.com/t/codecov-website-can-not-show-line-by-line-coverage/3809/3

sigmafelix commented 9 months ago

@Spatiotemporal-Exposures-and-Toxicology I think that is because I disabled covr::codecov run in the yaml file. I will close this one and reopen a PR with the full yaml file.