more updates to tests PecanProject#158

all/tests/run.all.R → all/tests/testthat.R

@@ -7,7 +7,7 @@
 # http://opensource.ncsa.illinois.edu/license.html
 #-------------------------------------------------------------------------------
 library(testthat)
-library(PEcAn.all)
+library(PEcAn.utils)
 
 logger.setQuitOnSevere(FALSE)
-test_package("PEcAn.all")
+test_check("PEcAn.all")

models/biocro/tests/testthat.R

@@ -0,0 +1,13 @@
+#-------------------------------------------------------------------------------
+# Copyright (c) 2012 University of Illinois, NCSA.
+# All rights reserved. This program and the accompanying materials
+# are made available under the terms of the 
+# University of Illinois/NCSA Open Source License
+# which accompanies this distribution, and is available at
+# http://opensource.ncsa.illinois.edu/license.html
+#-------------------------------------------------------------------------------
+library(testthat)
+library(PEcAn.utils)
+
+logger.setQuitOnSevere(FALSE)
+# test_check("PEcAn.BIOCRO")

models/biocro/inst/extdata/pecan.biocro.xml → models/biocro/tests/testthat/data/pecan.biocro.xml

@@ -12,7 +12,7 @@
       <password>bety</password>
       <dbname>bety</dbname>
       <host>localhost</host>
-      <dbfiles>$HOME/.pecan/dbfiles</dbfiles>
+      <dbfiles>/tmp/dbfiles</dbfiles>
     </bety>
   </database>
   <meta.analysis>
@@ -33,7 +33,7 @@
       <name>Sapelo Island</name>
       <lat>31.40</lat>
       <lon>-81.28</lon>
-      <met>$HOME/.pecan/dbfiles/met/31.397Nx81.28W/weather.csv</met>
+      <met>data/weather.csv</met>
     </site>
     <start.date>2004-01-01 06:00:00</start.date>
     <end.date>2005-12-31 05:59:00</end.date>

models/biocro/inst/tests/test.model2netcdf.BIOCRO.R → models/biocro/tests/testthat/test.model2netcdf.BIOCRO.R

@@ -3,12 +3,9 @@ context("check output from model2netcdf.BIOCRO")
 outdir <- file.path(tempdir(), "biocro")
 dir.create(outdir, showWarnings = FALSE, recursive = TRUE)
 
-settings.file <- system.file("extdata/pecan.biocro.xml", package = "PEcAn.BIOCRO")
-settings <- read.settings(settings.file)
+file.copy(from = "data/result.RData", to = outdir)
 
-result.file <- system.file("data/result.RData", package = "PEcAn.BIOCRO")
-
-file.copy(from = result.file, to = outdir)
+settings <- read.settings("data/pecan.biocro.xml")
 
 start_date <- settings$run$start.date
 model2netcdf.BIOCRO(outdir = outdir, sitelat=1, sitelon=2, 

models/biocro/inst/tests/test.write.configs.BIOCRO.R → models/biocro/tests/testthat/test.write.configs.BIOCRO.R

@@ -1,8 +1,6 @@
 
-extdir <-  system.file("extdata", package = "PEcAn.BIOCRO")
-settings.xml <- file.path(extdir, "pecan.biocro.xml")
-settings <- read.settings(settings.xml)
-settings$site$met <- file.path(extdir, "weather.csv")
+settings.xml <- file.path(data, )
+settings <- read.settings("data/pecan.biocro.xml")
 
 samples <- list(
   biocro.saof = (data.frame(

modules/data.hydrology/tests/run.all.R → models/ed/tests/testthat.R

@@ -7,7 +7,7 @@
 # http://opensource.ncsa.illinois.edu/license.html
 #-------------------------------------------------------------------------------
 library(testthat)
-library(PEcAn.DB)
+library(PEcAn.utils)
 
 logger.setQuitOnSevere(FALSE)
-#test_package("foo")
+test_check("PEcAn.ED2")

models/ed/inst/tests/test.model2netcdf.ED2.R → models/ed/tests/testthat/test.model2netcdf.ED2.R

@@ -1,10 +1,8 @@
-context("check output from model2netcdf.BIOCRO")
+context("check output from model2netcdf.ED2")
 
-
-extdata.dir <- system.file("extdata", package = "PEcAn.ED2")
 outdir <- file.path(tempdir(), "ed")
 dir.create(outdir, showWarnings = FALSE, recursive = TRUE) 
-file.copy(dir(extdata.dir, pattern = "*.h5$", full.names = TRUE), outdir)
+file.copy(dir("data", pattern = "*.h5$", full.names = TRUE), outdir)
 
 model2netcdf.ED2(outdir, 40, -88.5, "2010-01-01", "2010-12-31")
 

models/sipnet/tests/testthat.R

@@ -0,0 +1,13 @@
+#-------------------------------------------------------------------------------
+# Copyright (c) 2012 University of Illinois, NCSA.
+# All rights reserved. This program and the accompanying materials
+# are made available under the terms of the 
+# University of Illinois/NCSA Open Source License
+# which accompanies this distribution, and is available at
+# http://opensource.ncsa.illinois.edu/license.html
+#-------------------------------------------------------------------------------
+library(testthat)
+library(PEcAn.utils)
+
+logger.setQuitOnSevere(FALSE)
+test_check("PEcAn.SIPNET")

models/template/tests/testthat.R

@@ -0,0 +1,13 @@
+#-------------------------------------------------------------------------------
+# Copyright (c) 2012 University of Illinois, NCSA.
+# All rights reserved. This program and the accompanying materials
+# are made available under the terms of the 
+# University of Illinois/NCSA Open Source License
+# which accompanies this distribution, and is available at
+# http://opensource.ncsa.illinois.edu/license.html
+#-------------------------------------------------------------------------------
+library(testthat)
+library(PEcAn.utils)
+
+logger.setQuitOnSevere(FALSE)
+test_check("PEcAn.SIPNET")

models/template/tests/testthat/README.txt

@@ -0,0 +1,3 @@
+Place your tests here. They will be executed in this folder, so you
+can place any data you need in this folder as well (or in a subfolder
+called data).

modules/allometry/tests/testthat.R

@@ -0,0 +1,13 @@
+#-------------------------------------------------------------------------------
+# Copyright (c) 2012 University of Illinois, NCSA.
+# All rights reserved. This program and the accompanying materials
+# are made available under the terms of the 
+# University of Illinois/NCSA Open Source License
+# which accompanies this distribution, and is available at
+# http://opensource.ncsa.illinois.edu/license.html
+#-------------------------------------------------------------------------------
+library(testthat)
+library(PEcAn.utils)
+
+logger.setQuitOnSevere(FALSE)
+test_check("PEcAn.allometry")

modules/benchmark/tests/testthat.R

@@ -0,0 +1,13 @@
+#-------------------------------------------------------------------------------
+# Copyright (c) 2012 University of Illinois, NCSA.
+# All rights reserved. This program and the accompanying materials
+# are made available under the terms of the 
+# University of Illinois/NCSA Open Source License
+# which accompanies this distribution, and is available at
+# http://opensource.ncsa.illinois.edu/license.html
+#-------------------------------------------------------------------------------
+library(testthat)
+library(PEcAn.utils)
+
+logger.setQuitOnSevere(FALSE)
+test_check("PEcAn.benchmark")

modules/data.atmosphere/tests/testthat.R

@@ -0,0 +1,13 @@
+#-------------------------------------------------------------------------------
+# Copyright (c) 2012 University of Illinois, NCSA.
+# All rights reserved. This program and the accompanying materials
+# are made available under the terms of the 
+# University of Illinois/NCSA Open Source License
+# which accompanies this distribution, and is available at
+# http://opensource.ncsa.illinois.edu/license.html
+#-------------------------------------------------------------------------------
+library(testthat)
+library(PEcAn.utils)
+
+logger.setQuitOnSevere(FALSE)
+test_check("PEcAn.data.atmosphere")

modules/data.hydrology/DESCRIPTION

@@ -1,4 +1,4 @@
-Package: PEcAn.DB
+Package: PEcAn.data.hydrology
 Type: Package
 Title: PEcAn functions used for ecological forecasts and reanalysis
 Version: 1.3.3

modules/data.hydrology/tests/testthat.R

@@ -0,0 +1,13 @@
+#-------------------------------------------------------------------------------
+# Copyright (c) 2012 University of Illinois, NCSA.
+# All rights reserved. This program and the accompanying materials
+# are made available under the terms of the 
+# University of Illinois/NCSA Open Source License
+# which accompanies this distribution, and is available at
+# http://opensource.ncsa.illinois.edu/license.html
+#-------------------------------------------------------------------------------
+library(testthat)
+library(PEcAn.utils)
+
+logger.setQuitOnSevere(FALSE)
+test_check("PEcAn.data.hydrology")

modules/data.land/tests/testthat.R

@@ -0,0 +1,13 @@
+#-------------------------------------------------------------------------------
+# Copyright (c) 2012 University of Illinois, NCSA.
+# All rights reserved. This program and the accompanying materials
+# are made available under the terms of the 
+# University of Illinois/NCSA Open Source License
+# which accompanies this distribution, and is available at
+# http://opensource.ncsa.illinois.edu/license.html
+#-------------------------------------------------------------------------------
+library(testthat)
+library(PEcAn.utils)
+
+logger.setQuitOnSevere(FALSE)
+test_check("PEcAn.data.land")

modules/data.mining/tests/testthat.R

@@ -0,0 +1,13 @@
+#-------------------------------------------------------------------------------
+# Copyright (c) 2012 University of Illinois, NCSA.
+# All rights reserved. This program and the accompanying materials
+# are made available under the terms of the 
+# University of Illinois/NCSA Open Source License
+# which accompanies this distribution, and is available at
+# http://opensource.ncsa.illinois.edu/license.html
+#-------------------------------------------------------------------------------
+library(testthat)
+library(PEcAn.utils)
+
+logger.setQuitOnSevere(FALSE)
+test_check("PEcAn.data.mining")

modules/meta.analysis/tests/run.all.R → modules/meta.analysis/tests/testthat.R

@@ -7,7 +7,7 @@
 # http://opensource.ncsa.illinois.edu/license.html
 #-------------------------------------------------------------------------------
 library(testthat)
-library(PEcAn.MA)
+library(PEcAn.utils)
 
 logger.setQuitOnSevere(FALSE)
-test_package("PEcAn.MA")
+test_check("PEcAn.MA")

modules/priors/tests/testthat.R

@@ -0,0 +1,13 @@
+#-------------------------------------------------------------------------------
+# Copyright (c) 2012 University of Illinois, NCSA.
+# All rights reserved. This program and the accompanying materials
+# are made available under the terms of the 
+# University of Illinois/NCSA Open Source License
+# which accompanies this distribution, and is available at
+# http://opensource.ncsa.illinois.edu/license.html
+#-------------------------------------------------------------------------------
+library(testthat)
+library(PEcAn.utils)
+
+logger.setQuitOnSevere(FALSE)
+test_check("PEcAn.priors")

models/ed/tests/run.all.R → modules/rtm/tests/testthat.R

@@ -7,7 +7,7 @@
 # http://opensource.ncsa.illinois.edu/license.html
 #-------------------------------------------------------------------------------
 library(testthat)
-library(PEcAn.ED2)
+library(PEcAn.utils)
 
 logger.setQuitOnSevere(FALSE)
-test_package("PEcAn.ED2")
+test_check("PEcAn.rtm")

modules/uncertainty/tests/testthat.R

@@ -0,0 +1,13 @@
+#-------------------------------------------------------------------------------
+# Copyright (c) 2012 University of Illinois, NCSA.
+# All rights reserved. This program and the accompanying materials
+# are made available under the terms of the 
+# University of Illinois/NCSA Open Source License
+# which accompanies this distribution, and is available at
+# http://opensource.ncsa.illinois.edu/license.html
+#-------------------------------------------------------------------------------
+library(testthat)
+library(PEcAn.utils)
+
+logger.setQuitOnSevere(FALSE)
+test_check("PEcAn.uncertainty")

qaqc/tests/testthat.R

@@ -0,0 +1,13 @@
+#-------------------------------------------------------------------------------
+# Copyright (c) 2012 University of Illinois, NCSA.
+# All rights reserved. This program and the accompanying materials
+# are made available under the terms of the 
+# University of Illinois/NCSA Open Source License
+# which accompanies this distribution, and is available at
+# http://opensource.ncsa.illinois.edu/license.html
+#-------------------------------------------------------------------------------
+library(testthat)
+library(PEcAn.utils)
+
+logger.setQuitOnSevere(FALSE)
+#test_check("PEcAn.qaqc")

settings/tests/testthat.R

@@ -6,7 +6,8 @@
 # which accompanies this distribution, and is available at
 # http://opensource.ncsa.illinois.edu/license.html
 #-------------------------------------------------------------------------------
-
 library(testthat)
+library(PEcAn.utils)
 
+logger.setQuitOnSevere(FALSE)
 test_check("PEcAn.settings")