setup.md

In iDigBio/idb-us-collections: Interface to the iDigBio Collections API

Setup for installing and then running tests (WIP)

Note for commands below:

• $ denotes bash prompt
• r> is the r prompt

Install r packages

You'll need some r packages installed. Below is a partial list. Some of these need to be compiled but the system will do it automatically.

install.packages("testthat", "progress", "jsonlite", "devtools")

Temporary workaround for paths

update the cwd line in ./tests/testthat/test_json.R to your system's cwd. (todo: improve this)

build, check, and test

Build the package used for testing:

$ R CMD build .
* checking for file ‘./DESCRIPTION’ ... OK
* preparing ‘idbCollections’:
* checking DESCRIPTION meta-information ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* creating default NAMESPACE file
* building ‘idbCollections_0.0.1.tar.gz’

run a check. Technically, the command can be done through R CMD but it's better to run it through devtools because it does some extra cleanup:

devtools::check()

Now run tests. If you're familiar with testthat, don't try to run test_dir() or test_file(), it won't find the package.

r> devtools::test()

ideally, you'll see something similar to the following, where n = our number of collections, including the one just added:

Loading idbCollections
Testing idbCollections
✔ |  OK F W S | Context
✔ |  n        | test attributes [27.0 s]

══ Results ═════════════════════
Duration: 27.0 s

OK:       n
Failed:   0
Warnings: 0
Skipped:  0

Note that update-json-index.sh cannot yet be run locally, so this is the end of the local process for now.

iDigBio/idb-us-collections documentation built on June 6, 2020, 11:03 a.m.