Add rworkflows

[bschilder]

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Hi there!

Thanks so much for making signac, it's been a huge help in our lab's sc epigenomic work!

I wanted to offer using rworkflows for your CI workflow. It's a centrally maintained GItHub Action for R package development that can:

• Run Bioc and/or CRAN checks
• Run unit tests
• Build/push your docs site.
• Build/push a docker container.

Each step is optional and easily configurable with flags: https://github.com/bschilder/signac/blob/31a3a344300d7de6d2214e697fd05c796c0764f1/.github/workflows/rworkflows.yml#L42

Let me know if you have any questions or feature requests!

All the best, and thanks again, Brian

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[bschilder]

Hey @timoast I noticed you're experiencing the same errors as I am regarding actions/checkout:

https://github.com/stuart-lab/signac/actions/runs/6070764287

Download action repository 'actions/checkout@v3' (SHA:f43a0e5ff2bd294095638e18286ca9a3d1956744)
Error: '/Users/runner/work/_actions/_temp_95e52419-9535-4675-a265-8b319d07b381/13f2683d-2fff-41db-aa3f-7566fd58b426.tar.gz' contains '0' directories

I've just pushed a fix to the rworkflows action by switching to the actions/checkout@v4, which works well. All changes should automatically be propagated to you the next time you run rworkflows.

[bschilder]

Btw, I was just having a look at the signac vignette that seems to be producing an error, and I think it's happening bc it can't find the right file path: https://github.com/stuart-lab/signac/blob/2ad6c3c9c0c8dd31f7e1433b2efd5050d8606f27/vignettes/cicero.Rmd#L59

# load the object created in the Monocle 3 vignette
bone <- readRDS("../vignette_data/cd34.rds")

I think here would help in this case, because it can more easily find your base directory across a variety of scenarios:

# load the object created in the Monocle 3 vignette
bone <- readRDS(here::here("vignette_data","cd34.rds"))

Though this doesn't necessarily guarantee that the vignettes will be run in the necessary order such that the object is created before it's referenced.

I suppose another option would be to add the data as a built-in dataset to Signac, or store it in the "inst/extdata" subfolder (assuming the file is small enough).

[bschilder]

@timoast any thoughts on this?