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test: implement testing and benchmarking #12
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-Moved drug application test examples -Supressed Expected Warning in process_gene() test-dgidb.R: -Now Uses testthat package for R unit testing -Supports three unique tests -get_interactions(search='genes') -get_interactions(search='drugs') -get_drug_applications() -Currently the tests only expect that no error occurs during the test -Moved to seperate test folder -Now Uses microbenchmark package for R benchmarking -A benchmark is run on the each test function following the inital test -Currently the benchmark samples 10 runs of the function and reports the average,min,max,etc execution time
Performed lintr styling to test.dgidb.R
Fixed testthat file structure using usethis::use_testthat()
Used usethis::create_package() to setup barebone structure of an R package
in testthat.R: library(rdgidb) does not function, as rdgidb needs to be installed locally as a package to be loaded. Now: the devtools package is used to load the local instance of rdgidb and use it for testing without need for installing the package.
One important thing with this PR is that the parent directory/repo name 'r-dgidb' should, at least for now, be renamed to 'rdgidb', as 'r-dgidb' is considered to be an invalid package name. |
Added project dependencies in DESCRIPTION. Additionally, the sub package of tidyverse, tidyr, was specified as a dependency, as opposed to all of tidyverse.
Added data.table and httr to imports in DESCRIPTION
@jsstevenson any clues on why the lint.yaml github action is failing? We tried doing some googling and dependency resolution but it still is failing. Not sure would love some help on this. |
update: @rbasu101 found the fix (comma placement error) but now the test seems to be installing every R package under the sun while testing the lock file? These are not all dependencies for this package. Is it somehow grabbing these from his environment or something |
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