R-local-dev

Container for local development of all things R in MicrobiomeDB.

Quick start - work on one MicrobiomeDB R Package

Let's say we wanted to work on the plot.data package.

1. Run make build to build the docker image that contains all packages necessary for development.
2. Run make start-shell to start an interactive R session within the development container. R should start automatically and the output should end with something like the following

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

>

3. Now we're ready to load and/or install MicrobiomeDB packages. If we want to work on the main package, MicrobiomeDB, for example run load_all([path-to-MicrobiomeDB]). You may first need to load any dependencies you haven't chosen to install in the Dockerfile.
4. Make changes to the package, reload changes with load_all('MicrobiomeDB') (or other package nameor location).
5. Once you're happy with the changes, run all the testthat changes using devtools::test('MicrobiomeDB'). Alternatively, run all the tests in one file using test_file.
6. All done? Quit using quit().

NOTE: Keep in mind that you still need to make a PR against the package you're developing and once GitHub Actions are passing ask for a review.