Update copyrights

CMakeLists.txt

@@ -1,3 +1,35 @@
+# Copyright (c) 2005-2019, University of Oxford.
+# All rights reserved.
+# 
+# University of Oxford means the Chancellor, Masters and Scholars of the
+# University of Oxford, having an administrative office at Wellington
+# Square, Oxford OX1 2JD, UK.
+# 
+# This file is part of Chaste.
+# 
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted provided that the following conditions are met:
+#  * Redistributions of source code must retain the above copyright notice,
+#    this list of conditions and the following disclaimer.
+#  * Redistributions in binary form must reproduce the above copyright notice,
+#    this list of conditions and the following disclaimer in the documentation
+#    and/or other materials provided with the distribution.
+#  * Neither the name of the University of Oxford nor the names of its
+#    contributors may be used to endorse or promote products derived from this
+#    software without specific prior written permission.
+# 
+# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+# ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE
+# LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+# CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE
+# GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
+# HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+# LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+# OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+
 # Example CMake build configuration file for a Chaste user project.
 # See also https://chaste.cs.ox.ac.uk/trac/wiki/ChasteGuides/CmakeBuildGuide for full documentation.
 

SConscript

@@ -1,4 +1,4 @@
-"""Copyright (c) 2005-2018, University of Oxford.
+"""Copyright (c) 2005-2019, University of Oxford.
 All rights reserved.
 
 University of Oxford means the Chancellor, Masters and Scholars of the

apps/CMakeLists.txt

@@ -1,3 +1,35 @@
+# Copyright (c) 2005-2019, University of Oxford.
+# All rights reserved.
+# 
+# University of Oxford means the Chancellor, Masters and Scholars of the
+# University of Oxford, having an administrative office at Wellington
+# Square, Oxford OX1 2JD, UK.
+# 
+# This file is part of Chaste.
+# 
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted provided that the following conditions are met:
+#  * Redistributions of source code must retain the above copyright notice,
+#    this list of conditions and the following disclaimer.
+#  * Redistributions in binary form must reproduce the above copyright notice,
+#    this list of conditions and the following disclaimer in the documentation
+#    and/or other materials provided with the distribution.
+#  * Neither the name of the University of Oxford nor the names of its
+#    contributors may be used to endorse or promote products derived from this
+#    software without specific prior written permission.
+# 
+# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+# ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE
+# LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+# CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE
+# GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
+# HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+# LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
+# OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+
 # Example CMake build configuration file for a Chaste user project.
 # See also https://chaste.cs.ox.ac.uk/trac/wiki/ChasteGuides/CmakeBuildGuide for full documentation.
 

apps/src/ApPredict.cpp

@@ -1,6 +1,6 @@
 /*
 
-Copyright (c) 2005-2018, University of Oxford.
+Copyright (c) 2005-2019, University of Oxford.
 All rights reserved.
 
 University of Oxford means the Chancellor, Masters and Scholars of the

apps/src/DoseResponseFitter.cpp

@@ -1,6 +1,6 @@
 /*
 
-Copyright (c) 2005-2018, University of Oxford.
+Copyright (c) 2005-2019, University of Oxford.
 All rights reserved.
 
 University of Oxford means the Chancellor, Masters and Scholars of the

apps/src/TorsadePredict.cpp

@@ -1,6 +1,6 @@
 /*
 
-Copyright (c) 2005-2018, University of Oxford.
+Copyright (c) 2005-2019, University of Oxford.
 All rights reserved.
 
 University of Oxford means the Chancellor, Masters and Scholars of the

src/data_reading/AbstractDataStructure.cpp

@@ -1,6 +1,6 @@
 /*
 
-Copyright (c) 2005-2018, University of Oxford.
+Copyright (c) 2005-2019, University of Oxford.
 All rights reserved.
 
 University of Oxford means the Chancellor, Masters and Scholars of the

src/data_reading/AbstractDataStructure.hpp

@@ -1,6 +1,6 @@
 /*
 
-Copyright (c) 2005-2018, University of Oxford.
+Copyright (c) 2005-2019, University of Oxford.
 All rights reserved.
 
 University of Oxford means the Chancellor, Masters and Scholars of the

src/data_reading/AbstractDrugDataStructure.cpp

@@ -1,6 +1,6 @@
 /*
 
-Copyright (c) 2005-2018, University of Oxford.
+Copyright (c) 2005-2019, University of Oxford.
 All rights reserved.
 
 University of Oxford means the Chancellor, Masters and Scholars of the

src/data_reading/AbstractDrugDataStructure.hpp

@@ -1,6 +1,6 @@
 /*
 
-Copyright (c) 2005-2018, University of Oxford.
+Copyright (c) 2005-2019, University of Oxford.
 All rights reserved.
 
 University of Oxford means the Chancellor, Masters and Scholars of the

src/data_reading/CardiovascRes2011DataStructure.hpp

@@ -1,6 +1,6 @@
 /*
 
-Copyright (c) 2005-2018, University of Oxford.
+Copyright (c) 2005-2019, University of Oxford.
 All rights reserved.
 
 University of Oxford means the Chancellor, Masters and Scholars of the

src/data_reading/DaviesDogDataStructure.cpp

@@ -1,6 +1,6 @@
 /*
 
-Copyright (c) 2005-2018, University of Oxford.
+Copyright (c) 2005-2019, University of Oxford.
 All rights reserved.
 
 University of Oxford means the Chancellor, Masters and Scholars of the

src/data_reading/DaviesDogDataStructure.hpp

@@ -1,6 +1,6 @@
 /*
 
-Copyright (c) 2005-2018, University of Oxford.
+Copyright (c) 2005-2019, University of Oxford.
 All rights reserved.
 
 University of Oxford means the Chancellor, Masters and Scholars of the

src/data_reading/PkpdDataStructure.hpp

@@ -1,6 +1,6 @@
 /*
 
-Copyright (c) 2005-2018, University of Oxford.
+Copyright (c) 2005-2019, University of Oxford.
 All rights reserved.
 
 University of Oxford means the Chancellor, Masters and Scholars of the

src/dose_response_fitter/HillFunction.cpp

@@ -1,6 +1,6 @@
 /*
 
-Copyright (c) 2005-2018, University of Oxford.
+Copyright (c) 2005-2019, University of Oxford.
 All rights reserved.
 
 University of Oxford means the Chancellor, Masters and Scholars of the

src/dose_response_fitter/HillFunction.hpp

@@ -1,6 +1,6 @@
 /*
 
-Copyright (c) 2005-2018, University of Oxford.
+Copyright (c) 2005-2019, University of Oxford.
 All rights reserved.
 
 University of Oxford means the Chancellor, Masters and Scholars of the

src/dose_response_fitter/NelderMeadMinimizer.cpp

@@ -1,6 +1,6 @@
 /*
 
-Copyright (c) 2005-2018, University of Oxford.
+Copyright (c) 2005-2019, University of Oxford.
 All rights reserved.
 
 University of Oxford means the Chancellor, Masters and Scholars of the

src/dose_response_fitter/NelderMeadMinimizer.hpp

@@ -1,6 +1,6 @@
 /*
 
-Copyright (c) 2005-2018, University of Oxford.
+Copyright (c) 2005-2019, University of Oxford.
 All rights reserved.
 
 University of Oxford means the Chancellor, Masters and Scholars of the

src/dose_response_fitter/RunHillFunctionMinimization.cpp

@@ -1,6 +1,6 @@
 /*
 
-Copyright (c) 2005-2018, University of Oxford.
+Copyright (c) 2005-2019, University of Oxford.
 All rights reserved.
 
 University of Oxford means the Chancellor, Masters and Scholars of the

src/dose_response_fitter/RunHillFunctionMinimization.hpp

@@ -1,6 +1,6 @@
 /*
 
-Copyright (c) 2005-2018, University of Oxford.
+Copyright (c) 2005-2019, University of Oxford.
 All rights reserved.
 
 University of Oxford means the Chancellor, Masters and Scholars of the

src/fortests/ActionPotentialDownsampler.cpp

@@ -1,6 +1,6 @@
 /*
 
-Copyright (c) 2005-2018, University of Oxford.
+Copyright (c) 2005-2019, University of Oxford.
 All rights reserved.
 
 University of Oxford means the Chancellor, Masters and Scholars of the

src/fortests/ActionPotentialDownsampler.hpp

@@ -1,6 +1,6 @@
 /*
 
-Copyright (c) 2005-2018, University of Oxford.
+Copyright (c) 2005-2019, University of Oxford.
 All rights reserved.
 
 University of Oxford means the Chancellor, Masters and Scholars of the

src/fortests/DoseCalculator.cpp

@@ -1,6 +1,6 @@
 /*
 
-Copyright (c) 2005-2018, University of Oxford.
+Copyright (c) 2005-2019, University of Oxford.
 All rights reserved.
 
 University of Oxford means the Chancellor, Masters and Scholars of the

src/fortests/DoseCalculator.hpp

@@ -1,6 +1,6 @@
 /*
 
-Copyright (c) 2005-2018, University of Oxford.
+Copyright (c) 2005-2019, University of Oxford.
 All rights reserved.
 
 University of Oxford means the Chancellor, Masters and Scholars of the

src/fortests/SetupModel.cpp

@@ -1,6 +1,6 @@
 /*
 
-Copyright (c) 2005-2018, University of Oxford.
+Copyright (c) 2005-2019, University of Oxford.
 All rights reserved.
 
 University of Oxford means the Chancellor, Masters and Scholars of the

src/fortests/SetupModel.hpp

@@ -1,6 +1,6 @@
 /*
 
-Copyright (c) 2005-2018, University of Oxford.
+Copyright (c) 2005-2019, University of Oxford.
 All rights reserved.
 
 University of Oxford means the Chancellor, Masters and Scholars of the

src/lookup/AbstractUntemplatedLookupTableGenerator.hpp

@@ -1,6 +1,6 @@
 /*
 
-Copyright (c) 2005-2018, University of Oxford.
+Copyright (c) 2005-2019, University of Oxford.
 All rights reserved.
 
 University of Oxford means the Chancellor, Masters and Scholars of the

src/lookup/LookupTableGenerator.cpp

@@ -1,6 +1,6 @@
 /*
 
-Copyright (c) 2005-2018, University of Oxford.
+Copyright (c) 2005-2019, University of Oxford.
 All rights reserved.
 
 University of Oxford means the Chancellor, Masters and Scholars of the

src/lookup/LookupTableGenerator.hpp

@@ -1,6 +1,6 @@
 /*
 
-Copyright (c) 2005-2018, University of Oxford.
+Copyright (c) 2005-2019, University of Oxford.
 All rights reserved.
 
 University of Oxford means the Chancellor, Masters and Scholars of the

src/lookup/LookupTableLoader.cpp

@@ -1,6 +1,6 @@
 /*
 
-Copyright (c) 2005-2018, University of Oxford.
+Copyright (c) 2005-2019, University of Oxford.
 All rights reserved.
 
 University of Oxford means the Chancellor, Masters and Scholars of the

src/lookup/LookupTableLoader.hpp

@@ -1,6 +1,6 @@
 /*
 
-Copyright (c) 2005-2018, University of Oxford.
+Copyright (c) 2005-2019, University of Oxford.
 All rights reserved.
 
 University of Oxford means the Chancellor, Masters and Scholars of the

src/lookup/ParameterBox.cpp

@@ -1,6 +1,6 @@
 /*
 
-Copyright (c) 2005-2018, University of Oxford.
+Copyright (c) 2005-2019, University of Oxford.
 All rights reserved.
 
 University of Oxford means the Chancellor, Masters and Scholars of the

src/lookup/ParameterBox.hpp

@@ -1,6 +1,6 @@
 /*
 
-Copyright (c) 2005-2018, University of Oxford.
+Copyright (c) 2005-2019, University of Oxford.
 All rights reserved.
 
 University of Oxford means the Chancellor, Masters and Scholars of the

src/lookup/ParameterPointData.hpp

@@ -1,6 +1,6 @@
 /*
 
-Copyright (c) 2005-2018, University of Oxford.
+Copyright (c) 2005-2019, University of Oxford.
 All rights reserved.
 
 University of Oxford means the Chancellor, Masters and Scholars of the

src/lookup/QuantityOfInterest.hpp

@@ -1,6 +1,6 @@
 /*
 
-Copyright (c) 2005-2018, University of Oxford.
+Copyright (c) 2005-2019, University of Oxford.
 All rights reserved.
 
 University of Oxford means the Chancellor, Masters and Scholars of the

src/single_cell/AbstractActionPotentialMethod.cpp

@@ -1,6 +1,6 @@
 /*
 
-Copyright (c) 2005-2018, University of Oxford.
+Copyright (c) 2005-2019, University of Oxford.
 All rights reserved.
 
 University of Oxford means the Chancellor, Masters and Scholars of the
@@ -298,8 +298,7 @@ OdeSolution AbstractActionPotentialMethod::SteadyStatePacingExperiment(
 
     if (mRepeat)
     {
-        // std::cout << "Repeating simulation to order alternans APs
-        // consistently...\n";
+        // std::cout << "Repeating simulation to order alternans APs consistently...\n";
         // If we might benefit from pushing forward one period and re-analysing...
         PushModelForwardOneS1Interval(pModel, s1_period, maximum_time_step);
 
@@ -412,8 +411,9 @@ OdeSolution AbstractActionPotentialMethod::PerformAnalysisOfTwoPaces(
         // We didn't get back any action potentials,
         // which should be because of one of the following errors (if not throw the
         // exception).
-        if (e.GetShortMessage() != "AP did not occur, never exceeded threshold voltage." && e.GetShortMessage() != "No full action potential was recorded" && e.GetShortMessage() != "No MaxUpstrokeVelocity matching a full action potential was "
-                                                                                                                                                                                     "recorded.")
+        if (e.GetShortMessage() != "AP did not occur, never exceeded threshold voltage."
+            && e.GetShortMessage() != "No full action potential was recorded"
+            && e.GetShortMessage() != "No MaxUpstrokeVelocity matching a full action potential was recorded.")
         {
             throw e;
         }

src/single_cell/AbstractActionPotentialMethod.hpp

@@ -1,6 +1,6 @@
 /*
 
-Copyright (c) 2005-2018, University of Oxford.
+Copyright (c) 2005-2019, University of Oxford.
 All rights reserved.
 
 University of Oxford means the Chancellor, Masters and Scholars of the

src/single_cell/ApPredictMethods.cpp

@@ -1,6 +1,6 @@
 /*
 
-Copyright (c) 2005-2018, University of Oxford.
+Copyright (c) 2005-2019, University of Oxford.
 All rights reserved.
 
 University of Oxford means the Chancellor, Masters and Scholars of the

src/single_cell/ApPredictMethods.hpp

@@ -1,6 +1,6 @@
 /*
 
-Copyright (c) 2005-2018, University of Oxford.
+Copyright (c) 2005-2019, University of Oxford.
 All rights reserved.
 
 University of Oxford means the Chancellor, Masters and Scholars of the

src/single_cell/CipaQNetCalculator.cpp

@@ -1,6 +1,6 @@
 /*
 
-Copyright (c) 2005-2018, University of Oxford.
+Copyright (c) 2005-2019, University of Oxford.
 All rights reserved.
 
 University of Oxford means the Chancellor, Masters and Scholars of the