31.4 Settings

• A generic settings can be found in the PEcAn.all package

settings.xml <- system.file("pecan.biocro.xml", package = "PEcAn.BIOCRO")
settings <- read.settings(settings.xml)

• database settings can be specified, and tests run only if a connection is available

We currently use the following database to run tests against; tests that require access to a database should check db.exists() and be skipped if it returns FALSE to avoid failed tests on systems that do not have the database installed.

settings$database <- list(userid = "bety", 
                          passwd = "bety", 
                          name = "bety",     # database name 
                          host = "localhost" # server name)
test_that(..., {
  skip_if_not(db.exists(settings$database))
  ## write tests here
})

• instructions for installing this are available on the VM creation wiki

• examples can be found in the PEcAn.DB package (base/db/tests/testthat/).

• Model specific settings can go in the model-specific module, for example:

settings.xml <- system.file("extdata/pecan.biocro.xml", package = "PEcAn.BIOCRO")
settings <- read.settings(settings.xml)

• test-specific settings:

  • settings text can be specified inline:

    settings.text <- "
      <pecan>
        <nocheck>nope</nocheck> ## allows bypass of checks in the read.settings functions
        <pfts>
          <pft>
            <name>ebifarm.pavi</name>
            <outdir>test/</outdir>
          </pft>
        </pfts>
        <outdir>test/</outdir>
        <database>
          <userid>bety</userid>
          <passwd>bety</passwd>
          <location>localhost</location>
          <name>bety</name>
        </database>
      </pecan>"
    settings <- read.settings(settings.text)

  • values in settings can be updated:

    settings <- read.settings(settings.text)
    settings$outdir <- "/tmp" ## or any other settings