.travis.yml

@@ -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

@@ -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

@@ -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

@@ -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

@@ -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

debian/changelog

-libroadrunner (1.5.1-1) UNRELEASED; urgency=medium
+libroadrunner (1.5.4-1) unstable; urgency=medium
 
   * Initial release (Closes: #<bug>)
 
- -- Andreas Tille <tille@debian.org>  Mon, 29 Oct 2018 08:45:58 +0100
+ -- Andreas Tille <tille@debian.org>  Wed, 04 Sep 2019 11:46:58 +0200

debian/compat

-11

debian/control

@@ -4,21 +4,21 @@ Uploaders: Andreas Tille <tille@debian.org>
 Section: science
 Testsuite: autopkgtest-pkg-python
 Priority: optional
-Build-Depends: debhelper (>= 11~),
+Build-Depends: debhelper-compat (= 12),
                llvm-dev,
                cmake,
                libncurses5-dev,
                zlib1g-dev,
                libbz2-dev,
-               python-dev,
-               python-llvmlite,
-               python-numpy,
+               python3-dev,
+               python3-llvmlite,
+               python3-numpy,
                swig,
                libsbml5-dev,
                libxml2-dev,
                libsundials-dev,
                libpoco-dev
-Standards-Version: 4.2.1
+Standards-Version: 4.4.0
 Vcs-Browser: https://salsa.debian.org/med-team/libroadrunner
 Vcs-Git: https://salsa.debian.org/med-team/libroadrunner.git
 Homepage: http://libroadrunner.org/
@@ -41,7 +41,6 @@ Description: simulation engine for systems and synthetic biology
 Package: libroadrunner-dev
 Architecture: any
 Section: libdevel
-Testsuite: autopkgtest-pkg-python
 Depends: libroadrunner (= ${binary:Version})
 Description: simulation engine for systems and synthetic biology (development)
  LibRoadRunner is a high performance and portable simulation engine for
@@ -56,13 +55,12 @@ Description: simulation engine for systems and synthetic biology (development)
  .
  This package contains the header files for libroadrunner.
 
-Package: python-roadrunner
+Package: python3-roadrunner
 Architecture: any
 Section: python
-Testsuite: autopkgtest-pkg-python
 Depends: libroadrunner (= ${binary:Version}),
-         python-numpy
-Description: Python bindings for libroadrunner
+         python3-numpy
+Description: Python 3 bindings for libroadrunner
  LibRoadRunner is a high performance and portable simulation engine for
  systems and synthetic biology. I can run on many platforms including
  Windows, Mac OS, and Linux. libRoadRunner is major rewrite of the
@@ -73,4 +71,4 @@ Description: Python bindings for libroadrunner
  end design, better event handling, new C++ API and stochastic
  simulation support.
  .
- This package contains the Python bindings for libroadrunner.
+ This package contains the Python 3 bindings for libroadrunner.

examples/load_model_dll/CMakeLists.txt

@@ -12,7 +12,8 @@ add_definitions(
 -DSTATIC_RR
 -DSTATIC_LIBSTRUCT
 -DLIBLAX_STATIC  
--DSTATIC_NLEQ
+-DSTATIC_NLEQ1
+-DSTATIC_NLEQ2
 )
 
 if(WIN32)
@@ -29,7 +30,8 @@ endif()
 if(UNIX)
 target_link_libraries (${target} 
 roadrunner-static
-nleq-static.a
+nleq1-static.a
+nleq2-static.a
 rr-libstruct-static
 lapack
 blas

examples/one_rr/CMakeLists.txt

@@ -12,7 +12,8 @@ add_definitions(
 -DSTATIC_RR
 -DSTATIC_LIBSTRUCT
 -DLIBLAX_STATIC  
--DSTATIC_NLEQ
+-DSTATIC_NLEQ1
+-DSTATIC_NLEQ2
 )
 
 if(WIN32)
@@ -29,7 +30,8 @@ endif()
 if(UNIX)
 target_link_libraries (${target} 
 roadrunner-static
-nleq-static.a
+nleq1-static.a
+nleq2-static.a
 rr-libstruct-static
 lapack
 blas