Merge pull request #1120 from ICB-DCM/release_0.11.1

# Release 0.11.1

## Python
* Upgrade to sympy 1.6.0, which is now required minimum version  (#1098, #1103)
* Speed up model import 
  * Speed-up computation of sx0, reduce file size (#1109)
  * Replace terribly slow sympy.MutableDenseMatrix.is_zero_matrix by custom implementation (#1104)
* speedup dataframe creation in `get*AsDataFrame` (#1088)
* Allow caching edatas for simulate_petab (#1106)
* Fix wrong deprecation warning (Fixes #1093)
* Fix segmentation faults in NewtonSolver under certain conditions (#1089, #1090, #1097)
* fix wrong power function call in `unscale_parameter` (#1094)
* Fix MathML conversion (#1086)
* Fix deepcopy of SymPy objects (#1091)

## Matlab
* handle empty rdata->{pre|post}eq_numlinsteps (Closes #1113), which previously made the matlab interface unusable
* Fix generation of compileMexFile.m for matlab compilation of python code (#1115)

## C++
* Reduce memory requirements and speedup compilation of large models (#1105)
* Place generated code into own namespace (#937) (#1112)
* Fix several msvc compiler warnings (#1116) (Note that MSVC support is still experimental) **breaking change for users of C++ interface**
* Fix swig warning: ensure base class ContextManager is known before use (Fixes #1092) (#1101)

## CI
* Don't install/run valgrind on travis CI (done with github actions… (#1111)

Author: dweindl

.github/workflows/test-large-model.yml

@@ -4,6 +4,7 @@ on:
     branches:
       - develop
       - master
+      - fix_sx0_zeros
 
   pull_request:
     branches:

.travis.yml

@@ -32,8 +32,6 @@ matrix:
         - CI_PYTHON=TRUE
         - CI_ARCHIVE=TRUE
         - CI_NOTEBOOK=TRUE
-      before_install:
-        - ./scripts/buildValgrind.sh
       after_script:
         # cpputest coverage cpp
         - lcov --compat-libtool --no-external --directory ${BASE_DIR}/build/CMakeFiles/amici.dir/src --base-directory ${BASE_DIR} --capture --output-file coverage_cpp.info
@@ -182,8 +180,7 @@ script:
     - if [[ "$CI_PYTHON" == "TRUE" ]] && [[ "$ENABLE_GCOV_COVERAGE" == "TRUE" ]]; then $FOLD codecov ./scripts/run-codecov.sh; fi
     - if [[ "$CI_PYTHON" == "TRUE" ]] && [[ "$ENABLE_GCOV_COVERAGE" != "TRUE" ]]; then $FOLD python-tests ./scripts/run-python-tests.sh; fi
     # needs to be run after python tests
-    - if [[ "$CI_CPPUTEST" == "TRUE" ]] && [[ "$TRAVIS_OS_NAME" == "linux" ]]; then $FOLD valgrind ./scripts/run-valgrind.sh; fi
-    - if [[ "$CI_CPPUTEST" == "TRUE" ]] && [[ "$TRAVIS_OS_NAME" != "linux" ]]; then $FOLD cpputest ./scripts/run-cpputest.sh; fi
+    - if [[ "$CI_CPPUTEST" == "TRUE" ]]; then $FOLD cpputest ./scripts/run-cpputest.sh; fi
     - if [[ "$CI_DOC" == "TRUE" ]]; then $FOLD doxygen ./scripts/run-doxygen.sh; fi
     - if [[ "$CI_PYTHON" == "TRUE" ]]; then $FOLD sphinx ./scripts/run-sphinx.sh; fi
 

CMakeLists.txt

@@ -170,7 +170,10 @@ target_link_libraries(${PROJECT_NAME}
 
 # For matlab interface
 add_custom_target(matlabInterface
-    SOURCES src/interface_matlab.cpp src/returndata_matlab.cpp)
+    SOURCES
+    src/interface_matlab.cpp
+    src/returndata_matlab.cpp
+    include/amici/interface_matlab.h)
 set_target_properties(matlabInterface
     PROPERTIES INCLUDE_DIRECTORIES "${CMAKE_SOURCE_DIR}/include/")
 find_package(Matlab)
@@ -189,6 +192,7 @@ add_custom_target(
     src/CMakeLists.template.cmake
     src/main.template.cpp
     src/model_header.ODE_template.h
+    src/model.ODE_template.cpp
     src/wrapfunctions.ODE_template.h
     src/wrapfunctions.template.cpp
     swig/CMakeLists_model.cmake

include/amici/defines.h

@@ -29,6 +29,7 @@ constexpr int AMICI_ERR_FAILURE=              -3;
 constexpr int AMICI_CONV_FAILURE=             -4;
 constexpr int AMICI_ILL_INPUT=               -22;
 constexpr int AMICI_ERROR=                   -99;
+constexpr int AMICI_SINGULAR_JACOBIAN=      -807;
 constexpr int AMICI_NOT_IMPLEMENTED=        -999;
 constexpr int AMICI_SUCCESS=                   0;
 constexpr int AMICI_DATA_RETURN=               1;

include/amici/forwardproblem.h

@@ -213,23 +213,23 @@ class ForwardProblem {
      * @return index
      */
     int getTimepointCounter() const {
-        return timepoint_states.size() - 1;
+        return static_cast<int>(timepoint_states.size() - 1);
     }
 
     /**
      * @brief Returns maximal event index for which simulations are available
      * @return index
      */
     int getEventCounter() const {
-        return event_states.size() - 1;
+        return static_cast<int>(event_states.size() - 1);
     }
 
     /**
      * @brief Returns maximal event index for which the timepoint is available
      * @return index
      */
     int getRootCounter() const {
-        return discs.size() - 1;
+        return static_cast<int>(discs.size() - 1);
     }
 
     /**

include/amici/interface_matlab.h

@@ -6,11 +6,14 @@
 #include <mex.h>
 #include <memory>
 
-class Model;
-extern std::unique_ptr<amici::Model> getModel();
 
-namespace amici {    
+namespace amici {
+
+namespace generic_model {
+extern std::unique_ptr<amici::Model> getModel();
+} // namespace generic_model
 
+class Model;
 class ReturnDataMatlab;
 
 
@@ -39,7 +42,7 @@ void setSolverOptions(const mxArray *prhs[], int nrhs, Solver& solver);
  */
 ReturnDataMatlab *setupReturnData(mxArray *plhs[], int nlhs);
 
-    
+
 /*!
  * @brief expDataFromMatlabCall parses the experimental data from the matlab
  * call and writes it to an ExpData class object

include/amici/misc.h

@@ -61,7 +61,8 @@ const gsl::span<const T> slice(const std::vector<T> &data,
  * @param expected_size expected size of the buffer
  */
 template <class T>
-void checkBufferSize(gsl::span<T> buffer, unsigned expected_size) {
+void checkBufferSize(gsl::span<T> buffer,
+                     typename gsl::span<T>::index_type expected_size) {
     if (buffer.size() != expected_size)
         throw AmiException("Incorrect buffer size! Was %u, expected %u.",
                            buffer.size(), expected_size);

include/amici/steadystateproblem.h

@@ -211,6 +211,9 @@ class SteadystateProblem {
     /** state differential sensitivities */
     AmiVectorArray sdx;
 
+    /** maximum number of steps for Newton solver for allocating numlinsteps */
+    int maxSteps = 0;
+
     /** weighted root-mean-square error */
     realtype wrms = NAN;
 

matlab/@amimodel/compileAndLinkModel.m

@@ -143,13 +143,24 @@ function compileAndLinkModel(modelname, modelSourceFolder, coptim, debug, funs,
         end
     end
 
+    % in case we compile python-generated code, there is a modelname.cpp
+    model_cpp = fullfile(modelSourceFolder, [modelname '.cpp']);
+    if(exist(model_cpp, 'file'))
+        model_cpp = ['"' model_cpp '" '];
+        model_cpp_obj = [' "' fullfile(modelObjectFolder,[modelname objectFileSuffix]) '" '];
+    else
+        model_cpp = '';
+        model_cpp_obj = '';
+    end
+
+
     % compile the wrapfunctions object
     fprintf('wrapfunctions | ');
     eval(['mex ' DEBUG COPT ...
         ' -c -outdir "' modelObjectFolder '" "' ...
-        fullfile(modelSourceFolder,'wrapfunctions.cpp') '" ' ...
+        fullfile(modelSourceFolder,'wrapfunctions.cpp') '" ' model_cpp ...
         includesstr]);
-    objectsstr = [objectsstr, ' "' fullfile(modelObjectFolder,['wrapfunctions' objectFileSuffix]) '"'];
+    objectsstr = [objectsstr, ' "' fullfile(modelObjectFolder,['wrapfunctions' objectFileSuffix]) '" ' model_cpp_obj];
 
     % now we have compiled everything model-specific, so we can replace hashes.mat to prevent recompilation
     try

matlab/@amimodel/generateC.m

@@ -43,6 +43,8 @@ function generateC(this)
             fprintf(fid,'\n');
             fprintf(fid,'using namespace amici;\n');
             fprintf(fid,'\n');
+            fprintf(fid,'namespace amici {\n\n');
+            fprintf(fid,['namespace model_' this.modelname '{\n\n']);
 
             % function definition
             fprintf(fid,['void ' cppFunctionName '_' this.modelname '' this.fun.(ifun{1}).argstr ' {\n']);
@@ -82,19 +84,28 @@ function generateC(this)
             end
             fprintf(fid,'}\n');
             fprintf(fid,'\n');
+            fprintf(fid,['} // namespace model_' this.modelname '\n\n']);
+            fprintf(fid,'} // namespace amici\n\n');
+
             fclose(fid);
         end
     end
 end
 
+% wrapfunctions.h
+
 fid = fopen(fullfile(this.wrap_path,'models',this.modelname,'wrapfunctions.h'),'w');
 fprintf(fid,'#ifndef _amici_wrapfunctions_h\n');
 fprintf(fid,'#define _amici_wrapfunctions_h\n');
 fprintf(fid,'\n');
 fprintf(fid,['#include "' this.modelname '.h"\n']);
 fprintf(fid,'\n');
+fprintf(fid,'namespace amici {\n\n');
+fprintf(fid,'namespace generic_model {\n\n');
 fprintf(fid,'std::unique_ptr<amici::Model> getModel();\n');
 fprintf(fid,'\n');
+fprintf(fid,'} // namespace generic_model\n\n');
+fprintf(fid,'} // namespace amici \n\n');
 fprintf(fid,'#endif /* _amici_wrapfunctions_h */\n');
 fclose(fid);
 
@@ -121,9 +132,9 @@ function generateC(this)
     fprintf(fid,'#include "amici/model_dae.h"\n');
 end
 fprintf(fid,'\n');
-fprintf(fid,'namespace amici {\nclass Solver;\n}\n');
-fprintf(fid,'\n');
-fprintf(fid,'\n');
+fprintf(fid,'namespace amici {\n\n');
+fprintf(fid,'class Solver;\n\n');
+fprintf(fid,['namespace model_' this.modelname '{\n\n']);
 
 for ifun = this.funs
     if(~isfield(this.fun,ifun{1}))
@@ -194,17 +205,23 @@ function generateC(this)
     fprintf(fid,'    }\n\n');
 end
 fprintf(fid,'};\n\n');
-
+fprintf(fid,['} // namespace model_' this.modelname '\n\n']);
+fprintf(fid,'} // namespace amici \n\n');
 fprintf(fid,['#endif /* _amici_' this.modelname '_h */\n']);
 fclose(fid);
 
-
+% wrapfunctions.cpp
 fid = fopen(fullfile(this.wrap_path,'models',this.modelname,'wrapfunctions.cpp'),'w');
 fprintf(fid,'#include "amici/model.h"\n');
 fprintf(fid,'#include "wrapfunctions.h"\n\n');
+fprintf(fid,'namespace amici {\n\n');
+fprintf(fid,'namespace generic_model {\n\n');
 fprintf(fid,'std::unique_ptr<amici::Model> getModel() {\n');
-fprintf(fid, ['    return std::unique_ptr<amici::Model>(new Model_' this.modelname '());\n']);
+fprintf(fid,'    return std::unique_ptr<amici::Model>(\n');
+fprintf(fid,['        new amici::model_' this.modelname '::Model_' this.modelname '());\n']);
 fprintf(fid,'}\n\n');
+fprintf(fid,'} // namespace generic_model\n\n');
+fprintf(fid,'} // namespace amici \n\n');
 fclose(fid);
 
 fprintf('CMakeLists | ');