Commit 865bfd27 authored by Andreas Tille's avatar Andreas Tille
Browse files

New upstream version 1.5.4

parent 83347c0a

.travis.yml

+6 −4
Original line number Diff line number Diff line
@@ -28,10 +28,12 @@ before_install: 
  # install roadrunner dependencies via apt:

  - mkdir ~/debs

  - cd ~/debs

  - wget http://cdn.rawgit.com/sys-bio/roadrunner-debs/b8288d2f3e9623ad0f13ff8a1aa97fabf481413a/libroadrunner-deps_1.5_amd64.deb

  - sudo dpkg -i libroadrunner-deps_1.5_amd64.deb

  - sudo cp /usr/local/include/rr-libstruct/* /usr/local/include

  - sudo cp /usr/local/include/clapack/* /usr/local/include

  - wget http://cdn.rawgit.com/sys-bio/roadrunner-debs/db909c2b49a4897fbc95c6294be4d2550ec787ec/libroadrunner-deps_2.0.8_amd64.deb

  - sudo dpkg -i libroadrunner-deps_2.0.8_amd64.deb

  - wget http://cdn.rawgit.com/sys-bio/roadrunner-debs/db909c2b49a4897fbc95c6294be4d2550ec787ec/libroadrunner-deps-dev_2.0.8_amd64.deb

  - sudo dpkg -i libroadrunner-deps-dev_2.0.8_amd64.deb

  #- sudo cp /usr/local/include/rr-libstruct/* /usr/local/include

  #- sudo cp /usr/local/include/clapack/* /usr/local/include



  - mkdir ~/install

CMakeLists.txt

+1 −1
Original line number Diff line number Diff line
@@ -6,7 +6,7 @@ project(rr) 


set(ROADRUNNER_VERSION_MAJOR 1)

set(ROADRUNNER_VERSION_MINOR 5)

set(ROADRUNNER_VERSION_PATCH 1)

set(ROADRUNNER_VERSION_PATCH 4)



set(ROADRUNNER_VERSION "${ROADRUNNER_VERSION_MAJOR}.${ROADRUNNER_VERSION_MINOR}.${ROADRUNNER_VERSION_PATCH}")

apps/rr-sbml-benchmark/CMakeLists.txt

+2 −1
Original line number Diff line number Diff line
@@ -21,7 +21,8 @@ set_property(TARGET ${target} 
    STATIC_LIBSTRUCT

    STATIC_PUGI

    STATIC_RR

    STATIC_NLEQ

    STATIC_NLEQ1

    STATIC_NLEQ2

    )



link_directories(

apps/rr-sbml-benchmark/main.cpp

+64 −44
Original line number Diff line number Diff line
@@ -12,6 +12,7 @@ 


#include "rrRoadRunner.h"

#include "rrRoadRunnerOptions.h"

#include "wrappers/C/rrc_api.h"



#include <iostream>

#include <fstream>
@@ -111,8 +112,10 @@ int main(int argc, char** argv) 




    std::cout << "loading file: " << sbmlFile << std::endl;

    roadRunner.load(sbmlFile, &opt);



    try

    {

        roadRunner.load(sbmlFile, &opt);

	    SimulateOptions settings;

	    settings.loadSBMLSettings(settingsFile);
@@ -133,11 +136,7 @@ int main(int argc, char** argv) 
            }

        }



    for (int i = 0; i < argc; ++i) {

        if (string(argv[i]).find("stiff") != string::npos) {

			roadRunner.getIntegrator()->setValue("stiff", true);

        }

    }

	    roadRunner.getIntegrator()->setValue("stiff", false);



        std::cout << "running for " << settings.steps << ", duration " << settings.duration << std::endl;
@@ -158,11 +157,26 @@ int main(int argc, char** argv) 
            int rows = result.numRows();

            int cols = result.numCols();



        for (int i = 0; i < rows; ++i)

            for (int i = 0; i <= rows; ++i)

            {

                for (int j = 0; j < cols; ++j)

                {

                output << result(i, j);

                    if (i == 0)

                    {

                        output << result.getColNames()[j];



                        if (j + 1 < cols)

                        {

                            output << ", ";

                        }

                        else

                        {

                            output << "\n";

                        }

                    }

                    else

                    {

                        output << result(i-1, j);



                        if (j + 1 < cols)

                        {
@@ -175,6 +189,12 @@ int main(int argc, char** argv) 
                    }

                }

            }

        }

    }

    catch (std::exception& ex)

    {

        return false;

    }



    return 0;

}

apps/rr/CMakeLists.txt

+4 −2
Original line number Diff line number Diff line
@@ -13,7 +13,8 @@ add_definitions( 
#-DSTATIC_RR

-DSTATIC_LIBSTRUCT

-DLIBLAX_STATIC  

-DSTATIC_NLEQ

-DSTATIC_NLEQ1

-DSTATIC_NLEQ2

)



if(WIN32)
@@ -31,7 +32,8 @@ endif() 
if(UNIX)

target_link_libraries (${target} 

roadrunner-static

nleq-static.a

nleq1-static.a

nleq2-static.a

rr-libstruct-static

lapack

blas