From 11ccea1fdd7fbdf34f51edb132e58957538a68f1 Mon Sep 17 00:00:00 2001 From: Gary Mirams Date: Wed, 2 Jan 2019 15:11:25 +0000 Subject: [PATCH] Update copyrights --- CMakeLists.txt | 32 +++++++++++++++++++ SConscript | 2 +- apps/CMakeLists.txt | 32 +++++++++++++++++++ apps/src/ApPredict.cpp | 2 +- apps/src/DoseResponseFitter.cpp | 2 +- apps/src/TorsadePredict.cpp | 2 +- src/data_reading/AbstractDataStructure.cpp | 2 +- src/data_reading/AbstractDataStructure.hpp | 2 +- .../AbstractDrugDataStructure.cpp | 2 +- .../AbstractDrugDataStructure.hpp | 2 +- .../CardiovascRes2011DataStructure.hpp | 2 +- src/data_reading/DaviesDogDataStructure.cpp | 2 +- src/data_reading/DaviesDogDataStructure.hpp | 2 +- src/data_reading/PkpdDataStructure.hpp | 2 +- src/dose_response_fitter/HillFunction.cpp | 2 +- src/dose_response_fitter/HillFunction.hpp | 2 +- .../NelderMeadMinimizer.cpp | 2 +- .../NelderMeadMinimizer.hpp | 2 +- .../RunHillFunctionMinimization.cpp | 2 +- .../RunHillFunctionMinimization.hpp | 2 +- src/fortests/ActionPotentialDownsampler.cpp | 2 +- src/fortests/ActionPotentialDownsampler.hpp | 2 +- src/fortests/DoseCalculator.cpp | 2 +- src/fortests/DoseCalculator.hpp | 2 +- src/fortests/SetupModel.cpp | 2 +- src/fortests/SetupModel.hpp | 2 +- ...bstractUntemplatedLookupTableGenerator.hpp | 2 +- src/lookup/LookupTableGenerator.cpp | 2 +- src/lookup/LookupTableGenerator.hpp | 2 +- src/lookup/LookupTableLoader.cpp | 2 +- src/lookup/LookupTableLoader.hpp | 2 +- src/lookup/ParameterBox.cpp | 2 +- src/lookup/ParameterBox.hpp | 2 +- src/lookup/ParameterPointData.hpp | 2 +- src/lookup/QuantityOfInterest.hpp | 2 +- .../AbstractActionPotentialMethod.cpp | 10 +++--- .../AbstractActionPotentialMethod.hpp | 2 +- src/single_cell/ApPredictMethods.cpp | 2 +- src/single_cell/ApPredictMethods.hpp | 2 +- src/single_cell/CipaQNetCalculator.cpp | 2 +- src/single_cell/CipaQNetCalculator.hpp | 2 +- .../SingleActionPotentialPrediction.hpp | 2 +- src/single_cell/TorsadePredictMethods.cpp | 2 +- src/single_cell/TorsadePredictMethods.hpp | 2 +- src/stats/AbstractDistribution.hpp | 2 +- src/stats/BayesianInferer.cpp | 2 +- src/stats/BayesianInferer.hpp | 2 +- src/stats/DoseResponseParameterTypes.hpp | 2 +- src/stats/LinearDiscriminantAnalysis.cpp | 2 +- src/stats/LinearDiscriminantAnalysis.hpp | 2 +- src/stats/LogLogisticDistribution.hpp | 2 +- src/stats/LogisticDistribution.hpp | 2 +- test/CMakeLists.txt | 32 +++++++++++++++++++ test/TestActionPotentialDownsampler.hpp | 2 +- test/TestApPredict.hpp | 2 +- test/TestApPredictLong.hpp | 2 +- test/TestBayesianInferer.hpp | 2 +- test/TestCipaQNetCalculator.hpp | 2 +- .../TestConvertLookupTableArchiveToBinary.hpp | 2 +- test/TestDataReaders.hpp | 2 +- test/TestDavies2012Paper.hpp | 2 +- test/TestDoseCalculator.hpp | 2 +- test/TestDoseResponseFitting.hpp | 2 +- test/TestLinearDiscriminantAnalysis.hpp | 2 +- test/TestLogisticDistribution.hpp | 2 +- test/TestLookupTableGenerator.hpp | 2 +- test/TestMakeALookupTable.hpp | 2 +- test/TestMetadataCellmlModels.hpp | 2 +- test/TestParameterBox.hpp | 2 +- test/TestPkpdInterpolations.hpp | 2 +- test/TestPkpdReader.hpp | 2 +- test/TestTorsadePredict.hpp | 2 +- test/TestTorsadePredictLong.hpp | 2 +- test/TestTroublesomeApEvaluations.hpp | 2 +- 74 files changed, 171 insertions(+), 75 deletions(-) diff --git a/CMakeLists.txt b/CMakeLists.txt index b745e04..6d74cee 100644 --- a/CMakeLists.txt +++ b/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. diff --git a/SConscript b/SConscript index f51e504..e3028d3 100644 --- a/SConscript +++ b/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 diff --git a/apps/CMakeLists.txt b/apps/CMakeLists.txt index 5959930..f894d23 100644 --- a/apps/CMakeLists.txt +++ b/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. diff --git a/apps/src/ApPredict.cpp b/apps/src/ApPredict.cpp index f35a39a..a30b2c0 100644 --- a/apps/src/ApPredict.cpp +++ b/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 diff --git a/apps/src/DoseResponseFitter.cpp b/apps/src/DoseResponseFitter.cpp index eb70f13..fe522d7 100644 --- a/apps/src/DoseResponseFitter.cpp +++ b/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 diff --git a/apps/src/TorsadePredict.cpp b/apps/src/TorsadePredict.cpp index 20b096f..5bbf693 100644 --- a/apps/src/TorsadePredict.cpp +++ b/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 diff --git a/src/data_reading/AbstractDataStructure.cpp b/src/data_reading/AbstractDataStructure.cpp index 1766500..d443266 100644 --- a/src/data_reading/AbstractDataStructure.cpp +++ b/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 diff --git a/src/data_reading/AbstractDataStructure.hpp b/src/data_reading/AbstractDataStructure.hpp index daf212e..c90d5a4 100644 --- a/src/data_reading/AbstractDataStructure.hpp +++ b/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 diff --git a/src/data_reading/AbstractDrugDataStructure.cpp b/src/data_reading/AbstractDrugDataStructure.cpp index 3838124..00ed63e 100644 --- a/src/data_reading/AbstractDrugDataStructure.cpp +++ b/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 diff --git a/src/data_reading/AbstractDrugDataStructure.hpp b/src/data_reading/AbstractDrugDataStructure.hpp index 46402da..1c27ca5 100644 --- a/src/data_reading/AbstractDrugDataStructure.hpp +++ b/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 diff --git a/src/data_reading/CardiovascRes2011DataStructure.hpp b/src/data_reading/CardiovascRes2011DataStructure.hpp index 7a2d4f1..5a93361 100644 --- a/src/data_reading/CardiovascRes2011DataStructure.hpp +++ b/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 diff --git a/src/data_reading/DaviesDogDataStructure.cpp b/src/data_reading/DaviesDogDataStructure.cpp index 3ac9aec..c8470c2 100644 --- a/src/data_reading/DaviesDogDataStructure.cpp +++ b/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 diff --git a/src/data_reading/DaviesDogDataStructure.hpp b/src/data_reading/DaviesDogDataStructure.hpp index ae48ea6..8d7bf7b 100644 --- a/src/data_reading/DaviesDogDataStructure.hpp +++ b/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 diff --git a/src/data_reading/PkpdDataStructure.hpp b/src/data_reading/PkpdDataStructure.hpp index 35b5877..303d0d9 100644 --- a/src/data_reading/PkpdDataStructure.hpp +++ b/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 diff --git a/src/dose_response_fitter/HillFunction.cpp b/src/dose_response_fitter/HillFunction.cpp index eb6e38f..c613902 100644 --- a/src/dose_response_fitter/HillFunction.cpp +++ b/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 diff --git a/src/dose_response_fitter/HillFunction.hpp b/src/dose_response_fitter/HillFunction.hpp index 4595f70..66f0661 100644 --- a/src/dose_response_fitter/HillFunction.hpp +++ b/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 diff --git a/src/dose_response_fitter/NelderMeadMinimizer.cpp b/src/dose_response_fitter/NelderMeadMinimizer.cpp index be83a72..756034f 100644 --- a/src/dose_response_fitter/NelderMeadMinimizer.cpp +++ b/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 diff --git a/src/dose_response_fitter/NelderMeadMinimizer.hpp b/src/dose_response_fitter/NelderMeadMinimizer.hpp index 4b56af8..b760916 100644 --- a/src/dose_response_fitter/NelderMeadMinimizer.hpp +++ b/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 diff --git a/src/dose_response_fitter/RunHillFunctionMinimization.cpp b/src/dose_response_fitter/RunHillFunctionMinimization.cpp index 9eb2a56..57eeba8 100644 --- a/src/dose_response_fitter/RunHillFunctionMinimization.cpp +++ b/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 diff --git a/src/dose_response_fitter/RunHillFunctionMinimization.hpp b/src/dose_response_fitter/RunHillFunctionMinimization.hpp index 36561cc..aa13e7d 100644 --- a/src/dose_response_fitter/RunHillFunctionMinimization.hpp +++ b/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 diff --git a/src/fortests/ActionPotentialDownsampler.cpp b/src/fortests/ActionPotentialDownsampler.cpp index 56d7586..bc40a03 100644 --- a/src/fortests/ActionPotentialDownsampler.cpp +++ b/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 diff --git a/src/fortests/ActionPotentialDownsampler.hpp b/src/fortests/ActionPotentialDownsampler.hpp index f39ca99..573e195 100644 --- a/src/fortests/ActionPotentialDownsampler.hpp +++ b/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 diff --git a/src/fortests/DoseCalculator.cpp b/src/fortests/DoseCalculator.cpp index 1294eb4..022ad62 100644 --- a/src/fortests/DoseCalculator.cpp +++ b/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 diff --git a/src/fortests/DoseCalculator.hpp b/src/fortests/DoseCalculator.hpp index 04d0675..6928bf3 100644 --- a/src/fortests/DoseCalculator.hpp +++ b/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 diff --git a/src/fortests/SetupModel.cpp b/src/fortests/SetupModel.cpp index 72dd05c..9cec1d3 100644 --- a/src/fortests/SetupModel.cpp +++ b/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 diff --git a/src/fortests/SetupModel.hpp b/src/fortests/SetupModel.hpp index 8dcbe34..ff1ac16 100644 --- a/src/fortests/SetupModel.hpp +++ b/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 diff --git a/src/lookup/AbstractUntemplatedLookupTableGenerator.hpp b/src/lookup/AbstractUntemplatedLookupTableGenerator.hpp index 6f149fd..da96e08 100644 --- a/src/lookup/AbstractUntemplatedLookupTableGenerator.hpp +++ b/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 diff --git a/src/lookup/LookupTableGenerator.cpp b/src/lookup/LookupTableGenerator.cpp index 51fd9e6..6d3ece2 100644 --- a/src/lookup/LookupTableGenerator.cpp +++ b/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 diff --git a/src/lookup/LookupTableGenerator.hpp b/src/lookup/LookupTableGenerator.hpp index 7ebfd18..13e9820 100644 --- a/src/lookup/LookupTableGenerator.hpp +++ b/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 diff --git a/src/lookup/LookupTableLoader.cpp b/src/lookup/LookupTableLoader.cpp index c49998f..5a7e8df 100644 --- a/src/lookup/LookupTableLoader.cpp +++ b/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 diff --git a/src/lookup/LookupTableLoader.hpp b/src/lookup/LookupTableLoader.hpp index 0293d7c..828ae44 100644 --- a/src/lookup/LookupTableLoader.hpp +++ b/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 diff --git a/src/lookup/ParameterBox.cpp b/src/lookup/ParameterBox.cpp index e2798aa..d71e4a4 100644 --- a/src/lookup/ParameterBox.cpp +++ b/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 diff --git a/src/lookup/ParameterBox.hpp b/src/lookup/ParameterBox.hpp index 540c1af..28b833a 100644 --- a/src/lookup/ParameterBox.hpp +++ b/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 diff --git a/src/lookup/ParameterPointData.hpp b/src/lookup/ParameterPointData.hpp index ca39384..bed52ef 100644 --- a/src/lookup/ParameterPointData.hpp +++ b/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 diff --git a/src/lookup/QuantityOfInterest.hpp b/src/lookup/QuantityOfInterest.hpp index 425bccd..522cefb 100644 --- a/src/lookup/QuantityOfInterest.hpp +++ b/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 diff --git a/src/single_cell/AbstractActionPotentialMethod.cpp b/src/single_cell/AbstractActionPotentialMethod.cpp index 0ae6d0d..919224e 100644 --- a/src/single_cell/AbstractActionPotentialMethod.cpp +++ b/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; } diff --git a/src/single_cell/AbstractActionPotentialMethod.hpp b/src/single_cell/AbstractActionPotentialMethod.hpp index 2da72f7..9b3829a 100644 --- a/src/single_cell/AbstractActionPotentialMethod.hpp +++ b/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 diff --git a/src/single_cell/ApPredictMethods.cpp b/src/single_cell/ApPredictMethods.cpp index 9eba92e..0b3f872 100644 --- a/src/single_cell/ApPredictMethods.cpp +++ b/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 diff --git a/src/single_cell/ApPredictMethods.hpp b/src/single_cell/ApPredictMethods.hpp index 60bfedb..5fc366f 100644 --- a/src/single_cell/ApPredictMethods.hpp +++ b/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 diff --git a/src/single_cell/CipaQNetCalculator.cpp b/src/single_cell/CipaQNetCalculator.cpp index 969cfb9..75f80e3 100644 --- a/src/single_cell/CipaQNetCalculator.cpp +++ b/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 diff --git a/src/single_cell/CipaQNetCalculator.hpp b/src/single_cell/CipaQNetCalculator.hpp index 565d68e..4ae42fb 100644 --- a/src/single_cell/CipaQNetCalculator.hpp +++ b/src/single_cell/CipaQNetCalculator.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 diff --git a/src/single_cell/SingleActionPotentialPrediction.hpp b/src/single_cell/SingleActionPotentialPrediction.hpp index 5021066..2844560 100644 --- a/src/single_cell/SingleActionPotentialPrediction.hpp +++ b/src/single_cell/SingleActionPotentialPrediction.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 diff --git a/src/single_cell/TorsadePredictMethods.cpp b/src/single_cell/TorsadePredictMethods.cpp index b5f68c4..f645a69 100644 --- a/src/single_cell/TorsadePredictMethods.cpp +++ b/src/single_cell/TorsadePredictMethods.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 diff --git a/src/single_cell/TorsadePredictMethods.hpp b/src/single_cell/TorsadePredictMethods.hpp index 1d3e80f..35ed412 100644 --- a/src/single_cell/TorsadePredictMethods.hpp +++ b/src/single_cell/TorsadePredictMethods.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 diff --git a/src/stats/AbstractDistribution.hpp b/src/stats/AbstractDistribution.hpp index a55e20b..20f5da3 100644 --- a/src/stats/AbstractDistribution.hpp +++ b/src/stats/AbstractDistribution.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 diff --git a/src/stats/BayesianInferer.cpp b/src/stats/BayesianInferer.cpp index 02dc7ed..6236e63 100644 --- a/src/stats/BayesianInferer.cpp +++ b/src/stats/BayesianInferer.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 diff --git a/src/stats/BayesianInferer.hpp b/src/stats/BayesianInferer.hpp index 6701c91..660e4e5 100644 --- a/src/stats/BayesianInferer.hpp +++ b/src/stats/BayesianInferer.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 diff --git a/src/stats/DoseResponseParameterTypes.hpp b/src/stats/DoseResponseParameterTypes.hpp index 2472011..7b446b5 100644 --- a/src/stats/DoseResponseParameterTypes.hpp +++ b/src/stats/DoseResponseParameterTypes.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 diff --git a/src/stats/LinearDiscriminantAnalysis.cpp b/src/stats/LinearDiscriminantAnalysis.cpp index 03e1b52..6c34f93 100644 --- a/src/stats/LinearDiscriminantAnalysis.cpp +++ b/src/stats/LinearDiscriminantAnalysis.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 diff --git a/src/stats/LinearDiscriminantAnalysis.hpp b/src/stats/LinearDiscriminantAnalysis.hpp index 38eaca7..d413ec3 100644 --- a/src/stats/LinearDiscriminantAnalysis.hpp +++ b/src/stats/LinearDiscriminantAnalysis.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 diff --git a/src/stats/LogLogisticDistribution.hpp b/src/stats/LogLogisticDistribution.hpp index a919ae3..55e3e8d 100644 --- a/src/stats/LogLogisticDistribution.hpp +++ b/src/stats/LogLogisticDistribution.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 diff --git a/src/stats/LogisticDistribution.hpp b/src/stats/LogisticDistribution.hpp index 37f05e2..4549005 100644 --- a/src/stats/LogisticDistribution.hpp +++ b/src/stats/LogisticDistribution.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 diff --git a/test/CMakeLists.txt b/test/CMakeLists.txt index a226236..7c9cc29 100644 --- a/test/CMakeLists.txt +++ b/test/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. diff --git a/test/TestActionPotentialDownsampler.hpp b/test/TestActionPotentialDownsampler.hpp index 6187c0a..3a95e2d 100644 --- a/test/TestActionPotentialDownsampler.hpp +++ b/test/TestActionPotentialDownsampler.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 diff --git a/test/TestApPredict.hpp b/test/TestApPredict.hpp index 16eac0c..15877f2 100644 --- a/test/TestApPredict.hpp +++ b/test/TestApPredict.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 diff --git a/test/TestApPredictLong.hpp b/test/TestApPredictLong.hpp index fb6f913..aee9152 100644 --- a/test/TestApPredictLong.hpp +++ b/test/TestApPredictLong.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 diff --git a/test/TestBayesianInferer.hpp b/test/TestBayesianInferer.hpp index a359012..b31e9fd 100644 --- a/test/TestBayesianInferer.hpp +++ b/test/TestBayesianInferer.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 diff --git a/test/TestCipaQNetCalculator.hpp b/test/TestCipaQNetCalculator.hpp index f159581..e9b0564 100644 --- a/test/TestCipaQNetCalculator.hpp +++ b/test/TestCipaQNetCalculator.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 diff --git a/test/TestConvertLookupTableArchiveToBinary.hpp b/test/TestConvertLookupTableArchiveToBinary.hpp index 206d77e..c112b28 100644 --- a/test/TestConvertLookupTableArchiveToBinary.hpp +++ b/test/TestConvertLookupTableArchiveToBinary.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 diff --git a/test/TestDataReaders.hpp b/test/TestDataReaders.hpp index c3f9966..56d1574 100644 --- a/test/TestDataReaders.hpp +++ b/test/TestDataReaders.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 diff --git a/test/TestDavies2012Paper.hpp b/test/TestDavies2012Paper.hpp index d014bc3..5afca19 100644 --- a/test/TestDavies2012Paper.hpp +++ b/test/TestDavies2012Paper.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 diff --git a/test/TestDoseCalculator.hpp b/test/TestDoseCalculator.hpp index 50bbaa1..7f0b547 100644 --- a/test/TestDoseCalculator.hpp +++ b/test/TestDoseCalculator.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 diff --git a/test/TestDoseResponseFitting.hpp b/test/TestDoseResponseFitting.hpp index fc09bbe..b461d79 100644 --- a/test/TestDoseResponseFitting.hpp +++ b/test/TestDoseResponseFitting.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 diff --git a/test/TestLinearDiscriminantAnalysis.hpp b/test/TestLinearDiscriminantAnalysis.hpp index 7bd5f99..6551712 100644 --- a/test/TestLinearDiscriminantAnalysis.hpp +++ b/test/TestLinearDiscriminantAnalysis.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 diff --git a/test/TestLogisticDistribution.hpp b/test/TestLogisticDistribution.hpp index de267c3..e429014 100644 --- a/test/TestLogisticDistribution.hpp +++ b/test/TestLogisticDistribution.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 diff --git a/test/TestLookupTableGenerator.hpp b/test/TestLookupTableGenerator.hpp index ec65bd5..235c96e 100644 --- a/test/TestLookupTableGenerator.hpp +++ b/test/TestLookupTableGenerator.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 diff --git a/test/TestMakeALookupTable.hpp b/test/TestMakeALookupTable.hpp index 2ffe34b..02b566b 100644 --- a/test/TestMakeALookupTable.hpp +++ b/test/TestMakeALookupTable.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 diff --git a/test/TestMetadataCellmlModels.hpp b/test/TestMetadataCellmlModels.hpp index 18dc52e..c8c1e94 100644 --- a/test/TestMetadataCellmlModels.hpp +++ b/test/TestMetadataCellmlModels.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 diff --git a/test/TestParameterBox.hpp b/test/TestParameterBox.hpp index 5ed80d1..4c6ad09 100644 --- a/test/TestParameterBox.hpp +++ b/test/TestParameterBox.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 diff --git a/test/TestPkpdInterpolations.hpp b/test/TestPkpdInterpolations.hpp index 0ee3ede..0c35924 100644 --- a/test/TestPkpdInterpolations.hpp +++ b/test/TestPkpdInterpolations.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 diff --git a/test/TestPkpdReader.hpp b/test/TestPkpdReader.hpp index a0ce126..3a37910 100644 --- a/test/TestPkpdReader.hpp +++ b/test/TestPkpdReader.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 diff --git a/test/TestTorsadePredict.hpp b/test/TestTorsadePredict.hpp index 48319a3..bb93868 100644 --- a/test/TestTorsadePredict.hpp +++ b/test/TestTorsadePredict.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 diff --git a/test/TestTorsadePredictLong.hpp b/test/TestTorsadePredictLong.hpp index 5136726..f51fe17 100644 --- a/test/TestTorsadePredictLong.hpp +++ b/test/TestTorsadePredictLong.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 diff --git a/test/TestTroublesomeApEvaluations.hpp b/test/TestTroublesomeApEvaluations.hpp index 0ab803c..40c0293 100644 --- a/test/TestTroublesomeApEvaluations.hpp +++ b/test/TestTroublesomeApEvaluations.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