Further increase test coverage

6 files changed, 118 insertions, 5 deletions

diff --git a/tests/testthat/SFO_SFO_printed.txt b/tests/testthat/SFO_SFO_printed.txt
new file mode 100644
index 00000000..8a188152
--- /dev/null
+++ b/tests/testthat/SFO_SFO_printed.txt
@@ -0,0 +1,12 @@
+<mkinmod> model generated with
+Use of formation fractions $use_of_ff: min 
+Specification $spec:
+$parent
+$type: SFO; $to: m1; $sink: TRUE
+$m1
+$type: SFO; $sink: TRUE
+Coefficient matrix $coefmat available
+Compiled model $cf available
+Differential equations:
+d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent
+d_m1/dt = + k_parent_m1 * parent - k_m1_sink * m1
diff --git a/tests/testthat/test_from_max_mean.R b/tests/testthat/test_from_max_mean.R
index 8e5953b9..7529c5f2 100644
--- a/tests/testthat/test_from_max_mean.R
+++ b/tests/testthat/test_from_max_mean.R
@@ -1,3 +1,21 @@
+# Copyright (C) 2018 Johannes Ranke
+# Contact: jranke@uni-bremen.de
+
+# This file is part of the R package mkin
+
+# mkin is free software: you can redistribute it and/or modify it under the
+# terms of the GNU General Public License as published by the Free Software
+# Foundation, either version 3 of the License, or (at your option) any later
+# version.
+
+# This program is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+# FOR A PARTICULAR PURPOSE.  See the GNU General Public License for more
+# details.
+
+# You should have received a copy of the GNU General Public License along with
+# this program. If not, see <http://www.gnu.org/licenses/>
+
 context("Test fitting the decline of metabolites from their maximum")
 
 test_that("Fitting from maximum mean value works", {
diff --git a/tests/testthat/test_mkinds.R b/tests/testthat/test_mkinds.R
index e017301c..1046449b 100644
--- a/tests/testthat/test_mkinds.R
+++ b/tests/testthat/test_mkinds.R
@@ -1,3 +1,21 @@
+# Copyright (C) 2019 Johannes Ranke
+# Contact: jranke@uni-bremen.de
+
+# This file is part of the R package mkin
+
+# mkin is free software: you can redistribute it and/or modify it under the
+# terms of the GNU General Public License as published by the Free Software
+# Foundation, either version 3 of the License, or (at your option) any later
+# version.
+
+# This program is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+# FOR A PARTICULAR PURPOSE.  See the GNU General Public License for more
+# details.
+
+# You should have received a copy of the GNU General Public License along with
+# this program. If not, see <http://www.gnu.org/licenses/>
+
 context("Test dataset class mkinds used in gmkin")
 
 test_that("An mkinds object can be created and printed", {
diff --git a/tests/testthat/test_mkinfit_errors.R b/tests/testthat/test_mkinfit_errors.R
index 50032628..50d528e0 100644
--- a/tests/testthat/test_mkinfit_errors.R
+++ b/tests/testthat/test_mkinfit_errors.R
@@ -1,5 +1,20 @@
-library(mkin)
-library(testthat)
+# Copyright (C) 2019 Johannes Ranke
+# Contact: jranke@uni-bremen.de
+
+# This file is part of the R package mkin
+
+# mkin is free software: you can redistribute it and/or modify it under the
+# terms of the GNU General Public License as published by the Free Software
+# Foundation, either version 3 of the License, or (at your option) any later
+# version.
+
+# This program is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+# FOR A PARTICULAR PURPOSE.  See the GNU General Public License for more
+# details.
+
+# You should have received a copy of the GNU General Public License along with
+# this program. If not, see <http://www.gnu.org/licenses/>
 
 context("Special cases of mkinfit calls")
 
diff --git a/tests/testthat/test_mkinmod.R b/tests/testthat/test_mkinmod.R
new file mode 100644
index 00000000..430fad61
--- /dev/null
+++ b/tests/testthat/test_mkinmod.R
@@ -0,0 +1,52 @@
+# Copyright (C) 2019 Johannes Ranke
+# Contact: jranke@uni-bremen.de
+
+# This file is part of the R package mkin
+
+# mkin is free software: you can redistribute it and/or modify it under the
+# terms of the GNU General Public License as published by the Free Software
+# Foundation, either version 3 of the License, or (at your option) any later
+# version.
+
+# This program is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+# FOR A PARTICULAR PURPOSE.  See the GNU General Public License for more
+# details.
+
+# You should have received a copy of the GNU General Public License along with
+# this program. If not, see <http://www.gnu.org/licenses/>
+
+context("mkinmod model generation and printing")
+
+test_that("mkinmod stops to prevent and/or explain user errors", {
+  expect_error(mkinmod(compound_x = mkinsub("SFO", to = "compound_x_y"),
+                       compound_x_y = mkinsub("SFO")), 
+               "variable names can not contain each other")
+  expect_error(mkinmod(compound_to_x = mkinsub("SFO")),
+               "can not contain _to_")
+  expect_error(mkinmod(sink = mkinsub("SFO")),
+               "Naming")
+
+  expect_error(mkinmod(parent = mkinsub("SFO"), use_of_ff = "foo"))
+
+  expect_error(mkinmod(parent = mkinsub("foo")))
+
+  expect_error(mkinmod(parent = mkinsub("SFO", "m1"),
+                       m1 = mkinsub("FOMC")),
+               "only implemented for the first compartment")
+
+  expect_error(mkinmod(parent = mkinsub("IORE", "m1"),
+                       m1 = mkinsub("SFO"), use_of_ff = "min"),
+               "only supported with formation fractions")
+
+  expect_error(mkinmod(parent = mkinsub("SFORB", "m1"),
+                       m1 = mkinsub("SFO"), use_of_ff = "max"),
+               "not supported")
+})
+
+test_that("Printing mkinmod models is reproducible", {
+  expect_known_output(print(mkinmod(parent = mkinsub("SFO", "m1"), 
+                                    m1 = mkinsub("SFO"),
+                                    quiet = TRUE)),
+                      file = "SFO_SFO_printed.txt")
+})
diff --git a/tests/testthat/test_schaefer07_complex_case.R b/tests/testthat/test_schaefer07_complex_case.R
index 80306bbe..844dd88f 100644
--- a/tests/testthat/test_schaefer07_complex_case.R
+++ b/tests/testthat/test_schaefer07_complex_case.R
@@ -1,4 +1,4 @@
-# Copyright (C) 2014-2015,2018 Johannes Ranke

+# Copyright (C) 2014-2015,2018,2019 Johannes Ranke

 # Contact: jranke@uni-bremen.de

 

 # This file is part of the R package mkin

@@ -16,8 +16,6 @@
 # You should have received a copy of the GNU General Public License along with

 # this program. If not, see <http://www.gnu.org/licenses/>

 

-# This test was migrated from a RUnit test inst/unitTests/runit.mkinfit.R

-

 context("Complex test case from Schaefer et al. (2007) Piacenza paper")

 

 test_that("Complex test case from Schaefer (2007) can be reproduced (10% tolerance)", {