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NIEHS / beethoven

BEETHOVEN is: Building an Extensible, rEproducible, Test-driven, Harmonized, Open-source, Versioned, ENsemble model for air quality
https://niehs.github.io/beethoven/
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Standardize relative/absolute path reference with a script? #214

Closed sigmafelix closed 7 months ago

sigmafelix commented 8 months ago

@Spatiotemporal-Exposures-and-Toxicology

I have been writing path reference in covariate calculation functions with the assumption of the working directory being the root directory of the project. Considering that this project will be packaged and the large datasets will be stored in ddn at the moment, I think it would be helpful for all to have a configuration script that assigns the data directories (./input) with one or two user inputs (e.g., user names for ddn reference). This issue can also be related to writing a pipeline with targets.

kyle-messier commented 8 months ago

@sigmafelix sounds like a good idea. I'd like to learn more about this technique.

sigmafelix commented 7 months ago

We could control reused elements in _targets.R file for targets pipeline. For tests, using testthat::test_path() will be helpful to run tests locally and in GitHub CI Action without manually changing path strings. I will close this issue.