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epiverse-trace / episoap

[Not published - under active development] A Store of Outbreak Analytics Pipelines Provided as Rmarkdown Report Templates
https://epiverse-trace.github.io/episoap/
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`git-lfs` dependency not documented #121

Open chartgerink opened 5 months ago

chartgerink commented 5 months ago

To clone the repository, one needs to have git-lfs installed. This was a surprise to me, as the documentation does not mention this at all.

Might it be worth mentioning this dependency? I am honestly also a bit surprised to learn afterwards that all the files are <5MB, which would mean it does not necessarily require git-lfs - but I might be missing some historical context surrounding https://github.com/epiverse-trace/episoap/pull/87 and before.

Bisaloo commented 5 months ago

Thanks for the report! Ideally, the dependency on git-lfs should be removed but here is some history behind its presence:

git-lfs is used to store the png images in the vignettes/ folder. While the image size is not absolutely unmanageable, there is a risk they end up increasing the total git repo size a lot since images don't diff well.

Ideally though, we wouldn't store these images at all. The whole idea is to show two reports with different parameters side by side in the intro vignette. Creating screenshots on the fly via webshot doesn't work well due to an annoying interaction on file paths with pkgdown & GHA containers.

We could think about alternatives though. E.g., create the reports and include them in an iframe, or something similar. It's quite likely to bump into the same path issues though :thinking: