fix(python) Fix python model compilation, add to ci, improve hdf5 sea…

…rch, python ci in venv (#337)

* fix(python) Rename dsigmaydp -> dsigma_ydp also in extern declaration

* ci(python) Include python-sbml import and simulation in CI (Closes #338)

* fix(*) Replace sigma_* by sigma* in all C++ code to have more uniform naming in python- and matlab-generated code

* Add missing newly created model files

* Fix typo

* ci(python) Set exit status according to test outcome (Fixes #339)

* ci(python) Disable building python package with cmake-generated libraries until they are repaired to work with current setup.py. Use plain setuptools package.

* ci(python) Don't run tests/testSBML.py twice. Is already run as part of scripts/run-codecov.sh -> tests/testCoverage.py

* debug(python) Print info if hdf5 was found

* feature(python) Check for HDF5 in standard location if pkgconfig is unsuccesful

* Fix variable name

* added standard osx include and library dir hints

* Fix hdf5 library path

* Adapt hdf5 library path, be verbose

* ci(): List hdf5 files

* ci() Maybe we can find the static hdf5 library

* ci() List brew hdf5 files

* Adapt hdf5 library path

* c() Add travis macOS hdf5 directories, remove debug output

* fix(cmake) Don't use PYTHON_INCLUDE_PATH which was already deprecated in cmake 3.0.2 or earlier

* cmake() VERSION_GREATER_EQUAL only introduced in cmake 3.7, making this check mostly useless

* cmake() VERSION_GREATER_EQUAL only introduced in cmake 3.7, making this check mostly useless

* Recreate example model code

* Revert mingw ::hypot hypot _hypot fix, since ncluding STL headers before Python.h is discouraged

This is an open python issue and should be fixed there (python/cpython#880). Windows workarounds exist.

* ci(python) Install amici package to virtual environment and run tests there (Closes #342)

* cmake() Add target for python source distribution

* ci() install h5py

* Revert "ci() install h5py"

This reverts commit ea79054.

* Install h5py in venv

* Squashed commit of the following:

commit 985646a
Author: Daniel Weindl <[email protected]>
Date:   Tue Jul 3 13:52:18 2018 +0200

    ci(python) no --user in venv; install wheel

commit f991ce6
Author: Daniel Weindl <[email protected]>
Date:   Tue Jul 3 13:51:35 2018 +0200

    ci(python) no --user in venv; install wheel

commit 62f828b
Author: Daniel Weindl <[email protected]>
Date:   Tue Jul 3 13:30:57 2018 +0200

    ci(python) install pkgconfig

commit b3d37c9
Author: Daniel Weindl <[email protected]>
Date:   Tue Jul 3 13:21:41 2018 +0200

    ci (python) correct package name

commit 039ebb0
Author: Daniel Weindl <[email protected]>
Date:   Tue Jul 3 13:11:55 2018 +0200

    ci (python) venv activate

commit 49d5412
Author: Daniel Weindl <[email protected]>
Date:   Tue Jul 3 13:05:03 2018 +0200

    ci (python) venv activate

commit d1f5824
Author: Daniel Weindl <[email protected]>
Date:   Tue Jul 3 12:57:45 2018 +0200

    ci (python) venv activate

commit 1446015
Author: Daniel Weindl <[email protected]>
Date:   Tue Jul 3 12:49:14 2018 +0200

    ci (python) h5py

commit b88701d
Author: Daniel Weindl <[email protected]>
Date:   Tue Jul 3 12:42:56 2018 +0200

    ci(python) install sdist

commit 220323b
Author: Daniel Weindl <[email protected]>
Date:   Tue Jul 3 12:15:40 2018 +0200

    ci(python) install --user

commit 190a270
Merge: 7adcc83 2e2e445
Author: Fabian Fröhlich <[email protected]>
Date:   Tue Jul 3 10:02:21 2018 +0200

    Merge branch 'master' into feature_venv

* ci(python) python 3.6 venv to find proper symengine wheel on osx?

* ci(python) install python3.6

* ci(python) install python3.6

.travis.yml

@@ -38,7 +38,7 @@ matrix:
         - brew update # without this homebrew can stumble over wrong ruby version
         - travis_wait brew install gcc || brew link --overwrite gcc # fix linker warning regarding /usr/local/include/c++
         - brew install hdf5 cppcheck swig doxygen ragel graphviz homebrew/cask/mactex
-        - brew upgrade python
+        - brew install zoidbergwill/python/python36
       after_success: 
         - cd $BASE_DIR # cd to base dir for correct relative pah in deploy
       deploy:
@@ -65,9 +65,9 @@ install:
     - ./scripts/buildAmici.sh
 
 script:  
-    - cd $BASE_DIR/python/sdist
-    - python3 setup.py sdist --dist-dir=$BASE_DIR/build/python/
-    - python3 -m pip install $BASE_DIR/build/python/amici-*.tar.gz --verbose
+#    - cd $BASE_DIR/python/sdist
+#    - python3 setup.py sdist --dist-dir=$BASE_DIR/build/python/
+#    - python3 -m pip install $BASE_DIR/build/python/amici-*.tar.gz --verbose
     - cd $BASE_DIR
     - ./scripts/run-cpputest.sh
     - ./scripts/run-cppcheck.sh

include/amici/model.h

@@ -229,14 +229,14 @@ namespace amici {
         void fdeltaqB(const int ie, const realtype t, const AmiVector *x, const AmiVector *xB,
                               const AmiVector *xdot, const AmiVector *xdot_old);
 
-        void fsigma_y(const int it, const ExpData *edata, ReturnData *rdata);
+        void fsigmay(const int it, const ExpData *edata, ReturnData *rdata);
 
-        void fdsigma_ydp(const int it, ReturnData *rdata, const ExpData *edata);
+        void fdsigmaydp(const int it, ReturnData *rdata, const ExpData *edata);
 
-        void fsigma_z(const realtype t, const int ie, const int *nroots,
+        void fsigmaz(const realtype t, const int ie, const int *nroots,
                       const ExpData *edata, ReturnData *rdata);
 
-        void fdsigma_zdp(const realtype t);
+        void fdsigmazdp(const realtype t);
 
         void fJy(const int it, ReturnData *rdata, const ExpData *edata);
 
@@ -836,7 +836,7 @@ namespace amici {
          * @param p parameter vector
          * @param k constant vector
          **/
-        virtual void fsigma_y(realtype *sigmay, const realtype t, const realtype *p, const realtype *k) {
+        virtual void fsigmay(realtype *sigmay, const realtype t, const realtype *p, const realtype *k) {
             throw AmiException("Requested functionality is not supported as (%s) is not implemented for this model!",__func__);
         }
 
@@ -847,7 +847,7 @@ namespace amici {
          * @param k constant vector
          * @param ip sensitivity index
          **/
-        virtual void fdsigma_ydp(realtype *dsigmaydp, const realtype t, const realtype *p, const realtype *k, const int ip) {
+        virtual void fdsigmaydp(realtype *dsigmaydp, const realtype t, const realtype *p, const realtype *k, const int ip) {
             throw AmiException("Requested functionality is not supported as (%s) is not implemented for this model!",__func__);
         }
 
@@ -857,7 +857,7 @@ namespace amici {
          * @param p parameter vector
          * @param k constant vector
          **/
-        virtual void fsigma_z(realtype *sigmaz, const realtype t, const realtype *p, const realtype *k) {
+        virtual void fsigmaz(realtype *sigmaz, const realtype t, const realtype *p, const realtype *k) {
             throw AmiException("Requested functionality is not supported as (%s) is not implemented for this model!",__func__);
         }
 
@@ -868,7 +868,7 @@ namespace amici {
          * @param k constant vector
          * @param ip sensitivity index
          **/
-        virtual void fdsigma_zdp(realtype *dsigmazdp, const realtype t, const realtype *p, const realtype *k, const int ip) {
+        virtual void fdsigmazdp(realtype *dsigmazdp, const realtype t, const realtype *p, const realtype *k, const int ip) {
             throw AmiException("Requested functionality is not supported as (%s) is not implemented for this model!",__func__);
         }
 

matlab/@amimodel/compileAndLinkModel.m

@@ -70,7 +70,7 @@ function compileAndLinkModel(modelname, modelSourceFolder, coptim, debug, funs,
 
     %% Model-specific files
     for j=1:length(funs)
-        baseFileName = [modelname '_' funs{j}];
+        baseFileName = [modelname '_' strrep(funs{j}, 'sigma_', 'sigma')];
         cfun(1).(funs{j}) = sourceNeedsRecompilation(modelSourceFolder, modelObjectFolder, baseFileName, objectFileSuffix);
     end
 
@@ -114,6 +114,7 @@ function compileAndLinkModel(modelname, modelSourceFolder, coptim, debug, funs,
             end
         end
         funsForRecompile = funs(structfun(@(x) logical(x), cfun(1)));
+        funsForRecompile = cellfun(@(x) strrep(x, 'sigma_', 'sigma'), funsForRecompile, 'UniformOutput', false);
     end
 
     if(numel(funsForRecompile))
@@ -131,15 +132,15 @@ function compileAndLinkModel(modelname, modelSourceFolder, coptim, debug, funs,
 
     % append model object files
     for j=1:length(funs)
-        filename = fullfile(modelObjectFolder, [modelname '_' funs{j} objectFileSuffix]);
+        filename = fullfile(modelObjectFolder, [modelname '_' strrep(funs{j}, 'sigma_', 'sigma') objectFileSuffix]);
         if(exist(filename,'file'))
             objectsstr = strcat(objectsstr,...
                 ' "',filename,'"');
         end
     end    
 
     % compile the wrapfunctions object
-    fprintf('wrapfunctions | '); 
+    fprintf('wrapfunctions | ');
     eval(['mex ' DEBUG COPT ...
         ' -c -outdir ' modelObjectFolder ' ' ...
         fullfile(modelSourceFolder,'wrapfunctions.cpp') ' ' ...

matlab/@amimodel/generateC.m

@@ -17,6 +17,7 @@ function generateC(this)
 % write fun ccode
 
 for ifun = this.funs
+    cppFunctionName = strrep(ifun{1}, 'sigma_', 'sigma');
     if(isfield(this.fun,ifun{1}))
         bodyNotEmpty = any(this.fun.(ifun{1}).sym(:)~=0);
         if(strcmp(ifun{1},'JSparse'))
@@ -28,7 +29,7 @@ function generateC(this)
 
         if(bodyNotEmpty)
             fprintf([ifun{1} ' | ']);
-            fid = fopen(fullfile(this.wrap_path,'models',this.modelname,[this.modelname '_' ifun{1} '.cpp']),'w');
+            fid = fopen(fullfile(this.wrap_path,'models',this.modelname,[this.modelname '_' cppFunctionName '.cpp']),'w');
             fprintf(fid,'\n');
             fprintf(fid,'#include "amici/symbolic_functions.h"\n');
             fprintf(fid,'#include "amici/defines.h" //realtype definition\n');
@@ -44,7 +45,7 @@ function generateC(this)
             fprintf(fid,'\n');
 
             % function definition
-            fprintf(fid,['void ' ifun{1} '_' this.modelname '' this.fun.(ifun{1}).argstr ' {\n']);
+            fprintf(fid,['void ' cppFunctionName '_' this.modelname '' this.fun.(ifun{1}).argstr ' {\n']);
             if(strcmp(ifun{1},'JSparse'))
                 for i = 1:length(this.rowvals)
                     fprintf(fid,['  JSparse->indexvals[' num2str(i-1) '] = ' num2str(this.rowvals(i)) ';\n']);
@@ -132,7 +133,8 @@ function generateC(this)
         % access argstr
     end
     if(checkIfFunctionBodyIsNonEmpty(this,ifun{1}))
-        fprintf(fid,['extern void ' ifun{1} '_' this.modelname this.fun.(ifun{1}).argstr ';\n']);
+        cppFunctionName = strrep(ifun{1}, 'sigma_', 'sigma');
+        fprintf(fid,['extern void ' cppFunctionName '_' this.modelname this.fun.(ifun{1}).argstr ';\n']);
     end
 end
 
@@ -180,9 +182,10 @@ function generateC(this)
 fprintf(fid,['    const  char* getAmiciVersion() const { return "' getCommitHash(fileparts(fileparts(mfilename('fullpath')))) '"; };\n\n']);
 
 for ifun = this.funs
-    fprintf(fid,['    virtual void f' ifun{1} this.fun.(ifun{1}).argstr ' override {\n']);
+    cppFunctionName = strrep(ifun{1}, 'sigma_', 'sigma');
+    fprintf(fid,['    virtual void f' cppFunctionName this.fun.(ifun{1}).argstr ' override {\n']);
     if(checkIfFunctionBodyIsNonEmpty(this,ifun{1}))
-        fprintf(fid,['        ' ifun{1} '_' this.modelname '' removeTypes(this.fun.(ifun{1}).argstr) ';\n']);
+        fprintf(fid,['        ' cppFunctionName '_' this.modelname '' removeTypes(this.fun.(ifun{1}).argstr) ';\n']);
     end
     fprintf(fid,'    }\n\n');
 end
@@ -241,7 +244,8 @@ function generateCMakeFile(this)
     for j=1:length(this.funs)
         funcName = this.funs{j};
         if(checkIfFunctionBodyIsNonEmpty(this,funcName))
-            sourceStr = [ sourceStr, sprintf('${MODEL_DIR}/%s_%s.cpp\n', this.modelname, funcName) ];
+            cppFunctionName = strrep(funcName, 'sigma_', 'sigma');
+            sourceStr = [ sourceStr, sprintf('${MODEL_DIR}/%s_%s.cpp\n', this.modelname, cppFunctionName) ];
         end
     end
 
@@ -287,5 +291,6 @@ function generateMainC(this)
 function nonempty = checkIfFunctionBodyIsNonEmpty(this,ifun)
     % if we don't have symbolic variables, it might have been generated before and symbolic expressions were simply not
     % regenerated. any() for empty (no generated) variables is always false.
-    nonempty = or(exist(fullfile(this.wrap_path,'models',this.modelname,[this.modelname '_' ifun '.cpp']),'file'),any(this.fun.(ifun).sym(:)~=0));
+    cppFunctionName = strrep(ifun, 'sigma_', 'sigma');
+    nonempty = or(exist(fullfile(this.wrap_path,'models',this.modelname,[this.modelname '_' cppFunctionName '.cpp']),'file'),any(this.fun.(ifun).sym(:)~=0));
 end

models/model_dirac/CMakeLists.txt

@@ -37,7 +37,7 @@ ${MODEL_DIR}/model_dirac_dxdotdp.cpp
 ${MODEL_DIR}/model_dirac_dydx.cpp
 ${MODEL_DIR}/model_dirac_qBdot.cpp
 ${MODEL_DIR}/model_dirac_root.cpp
-${MODEL_DIR}/model_dirac_sigma_y.cpp
+${MODEL_DIR}/model_dirac_sigmay.cpp
 ${MODEL_DIR}/model_dirac_stau.cpp
 ${MODEL_DIR}/model_dirac_sxdot.cpp
 ${MODEL_DIR}/model_dirac_xBdot.cpp
@@ -69,7 +69,7 @@ endif()
 ## SWIG
 option(ENABLE_SWIG "Build swig/python library?" ON)
 if(ENABLE_SWIG)
-    if(${CMAKE_VERSION} VERSION_GREATER_EQUAL 3.8)
+    if(NOT(${CMAKE_VERSION} VERSION_LESS 3.8))
         add_subdirectory(swig)
     else()
         message(WARNING "Unable to build SWIG interface, upgrade CMake to >=3.8.")

models/model_dirac/model_dirac.h

@@ -1,6 +1,6 @@
 #ifndef _amici_model_dirac_h
 #define _amici_model_dirac_h
-/* Generated by amiwrap (R2017b) 32ff5874402bf4335dcd258191c251105e377de4 */
+/* Generated by amiwrap (R2017b) 413f6c54d956e878a95406f02808fafd1272c1cd */
 #include <cmath>
 #include <memory>
 #include "amici/defines.h"
@@ -29,7 +29,7 @@ extern void dxdotdp_model_dirac(realtype *dxdotdp, const realtype t, const realt
 extern void dydx_model_dirac(double *dydx, const realtype t, const realtype *x, const realtype *p, const realtype *k, const realtype *h);
 extern void qBdot_model_dirac(realtype *qBdot, const int ip, const realtype t, const realtype *x, const realtype *p, const realtype *k, const realtype *h, const realtype *xB, const realtype *w, const realtype *dwdp);
 extern void root_model_dirac(realtype *root, const realtype t, const realtype *x, const realtype *p, const realtype *k, const realtype *h);
-extern void sigma_y_model_dirac(double *sigmay, const realtype t, const realtype *p, const realtype *k);
+extern void sigmay_model_dirac(double *sigmay, const realtype t, const realtype *p, const realtype *k);
 extern void stau_model_dirac(double *stau, const realtype t, const realtype *x, const realtype *p, const realtype *k, const realtype *h, const realtype *sx, const int ip, const int ie);
 extern void sxdot_model_dirac(realtype *sxdot, const realtype t, const realtype *x, const realtype *p, const realtype *k, const realtype *h, const int ip, const realtype *sx, const realtype *w, const realtype *dwdx, const realtype *J, const realtype *dxdotdp);
 extern void xBdot_model_dirac(realtype *xBdot, const realtype t, const realtype *x, const realtype *p, const realtype *k, const realtype *h, const realtype *xB, const realtype *w, const realtype *dwdx);
@@ -62,7 +62,7 @@ class Model_model_dirac : public amici::Model_ODE {
 
     virtual amici::Model* clone() const override { return new Model_model_dirac(*this); };
 
-    const  char* getAmiciVersion() const { return "32ff5874402bf4335dcd258191c251105e377de4"; };
+    const  char* getAmiciVersion() const { return "413f6c54d956e878a95406f02808fafd1272c1cd"; };
 
     virtual void fJ(realtype *J, const realtype t, const realtype *x, const double *p, const double *k, const realtype *h, const realtype *w, const realtype *dwdx) override {
         J_model_dirac(J, t, x, p, k, h, w, dwdx);
@@ -142,10 +142,10 @@ class Model_model_dirac : public amici::Model_ODE {
     virtual void fdrzdx(double *drzdx, const int ie, const realtype t, const realtype *x, const realtype *p, const realtype *k, const realtype *h) override {
     }
 
-    virtual void fdsigma_ydp(double *dsigmaydp, const realtype t, const realtype *p, const realtype *k, const int ip) override {
+    virtual void fdsigmaydp(double *dsigmaydp, const realtype t, const realtype *p, const realtype *k, const int ip) override {
     }
 
-    virtual void fdsigma_zdp(double *dsigmazdp, const realtype t, const realtype *p, const realtype *k, const int ip) override {
+    virtual void fdsigmazdp(double *dsigmazdp, const realtype t, const realtype *p, const realtype *k, const int ip) override {
     }
 
     virtual void fdwdp(realtype *dwdp, const realtype t, const realtype *x, const realtype *p, const realtype *k, const realtype *h, const realtype *w) override {
@@ -182,11 +182,11 @@ class Model_model_dirac : public amici::Model_ODE {
     virtual void frz(double *rz, const int ie, const realtype t, const realtype *x, const realtype *p, const realtype *k, const realtype *h) override {
     }
 
-    virtual void fsigma_y(double *sigmay, const realtype t, const realtype *p, const realtype *k) override {
-        sigma_y_model_dirac(sigmay, t, p, k);
+    virtual void fsigmay(double *sigmay, const realtype t, const realtype *p, const realtype *k) override {
+        sigmay_model_dirac(sigmay, t, p, k);
     }
 
-    virtual void fsigma_z(double *sigmaz, const realtype t, const realtype *p, const realtype *k) override {
+    virtual void fsigmaz(double *sigmaz, const realtype t, const realtype *p, const realtype *k) override {
     }
 
     virtual void fsrz(double *srz, const int ie, const realtype t, const realtype *x, const realtype *p, const realtype *k, const realtype *h, const realtype *sx, const int ip) override {

models/model_events/model_events_sigma_y.cpp → models/model_dirac/model_dirac_sigmay.cpp

@@ -6,7 +6,7 @@ typedef amici::realtype realtype;
 
 using namespace amici;
 
-void sigma_y_model_events(double *sigmay, const realtype t, const realtype *p, const realtype *k) {
+void sigmay_model_dirac(double *sigmay, const realtype t, const realtype *p, const realtype *k) {
   sigmay[0] = 1.0;
 }
 

models/model_dirac/swig/CMakeLists.txt

@@ -4,7 +4,7 @@ find_package(SWIG REQUIRED)
 include(${SWIG_USE_FILE})
 
 FIND_PACKAGE(PythonLibs REQUIRED)
-INCLUDE_DIRECTORIES(${PYTHON_INCLUDE_PATH})
+include_directories(${PYTHON_INCLUDE_DIRS})
 
 SET(CMAKE_SWIG_FLAGS "")
 SET_SOURCE_FILES_PROPERTIES(${PROJECT_NAME}.i PROPERTIES CPLUSPLUS ON)

models/model_events/CMakeLists.txt

@@ -46,8 +46,8 @@ ${MODEL_DIR}/model_events_dzdx.cpp
 ${MODEL_DIR}/model_events_qBdot.cpp
 ${MODEL_DIR}/model_events_root.cpp
 ${MODEL_DIR}/model_events_rz.cpp
-${MODEL_DIR}/model_events_sigma_y.cpp
-${MODEL_DIR}/model_events_sigma_z.cpp
+${MODEL_DIR}/model_events_sigmay.cpp
+${MODEL_DIR}/model_events_sigmaz.cpp
 ${MODEL_DIR}/model_events_srz.cpp
 ${MODEL_DIR}/model_events_stau.cpp
 ${MODEL_DIR}/model_events_sxdot.cpp
@@ -83,7 +83,7 @@ endif()
 ## SWIG
 option(ENABLE_SWIG "Build swig/python library?" ON)
 if(ENABLE_SWIG)
-    if(${CMAKE_VERSION} VERSION_GREATER_EQUAL 3.8)
+    if(NOT(${CMAKE_VERSION} VERSION_LESS 3.8))
         add_subdirectory(swig)
     else()
         message(WARNING "Unable to build SWIG interface, upgrade CMake to >=3.8.")

models/model_events/model_events.h

@@ -1,6 +1,6 @@
 #ifndef _amici_model_events_h
 #define _amici_model_events_h
-/* Generated by amiwrap (R2017b) 32ff5874402bf4335dcd258191c251105e377de4 */
+/* Generated by amiwrap (R2017b) 413f6c54d956e878a95406f02808fafd1272c1cd */
 #include <cmath>
 #include <memory>
 #include "amici/defines.h"
@@ -38,8 +38,8 @@ extern void dzdx_model_events(double *dzdx, const int ie, const realtype t, cons
 extern void qBdot_model_events(realtype *qBdot, const int ip, const realtype t, const realtype *x, const realtype *p, const realtype *k, const realtype *h, const realtype *xB, const realtype *w, const realtype *dwdp);
 extern void root_model_events(realtype *root, const realtype t, const realtype *x, const realtype *p, const realtype *k, const realtype *h);
 extern void rz_model_events(double *rz, const int ie, const realtype t, const realtype *x, const realtype *p, const realtype *k, const realtype *h);
-extern void sigma_y_model_events(double *sigmay, const realtype t, const realtype *p, const realtype *k);
-extern void sigma_z_model_events(double *sigmaz, const realtype t, const realtype *p, const realtype *k);
+extern void sigmay_model_events(double *sigmay, const realtype t, const realtype *p, const realtype *k);
+extern void sigmaz_model_events(double *sigmaz, const realtype t, const realtype *p, const realtype *k);
 extern void srz_model_events(double *srz, const int ie, const realtype t, const realtype *x, const realtype *p, const realtype *k, const realtype *h, const realtype *sx, const int ip);
 extern void stau_model_events(double *stau, const realtype t, const realtype *x, const realtype *p, const realtype *k, const realtype *h, const realtype *sx, const int ip, const int ie);
 extern void sxdot_model_events(realtype *sxdot, const realtype t, const realtype *x, const realtype *p, const realtype *k, const realtype *h, const int ip, const realtype *sx, const realtype *w, const realtype *dwdx, const realtype *J, const realtype *dxdotdp);
@@ -76,7 +76,7 @@ class Model_model_events : public amici::Model_ODE {
 
     virtual amici::Model* clone() const override { return new Model_model_events(*this); };
 
-    const  char* getAmiciVersion() const { return "32ff5874402bf4335dcd258191c251105e377de4"; };
+    const  char* getAmiciVersion() const { return "413f6c54d956e878a95406f02808fafd1272c1cd"; };
 
     virtual void fJ(realtype *J, const realtype t, const realtype *x, const double *p, const double *k, const realtype *h, const realtype *w, const realtype *dwdx) override {
         J_model_events(J, t, x, p, k, h, w, dwdx);
@@ -162,10 +162,10 @@ class Model_model_events : public amici::Model_ODE {
         drzdx_model_events(drzdx, ie, t, x, p, k, h);
     }
 
-    virtual void fdsigma_ydp(double *dsigmaydp, const realtype t, const realtype *p, const realtype *k, const int ip) override {
+    virtual void fdsigmaydp(double *dsigmaydp, const realtype t, const realtype *p, const realtype *k, const int ip) override {
     }
 
-    virtual void fdsigma_zdp(double *dsigmazdp, const realtype t, const realtype *p, const realtype *k, const int ip) override {
+    virtual void fdsigmazdp(double *dsigmazdp, const realtype t, const realtype *p, const realtype *k, const int ip) override {
     }
 
     virtual void fdwdp(realtype *dwdp, const realtype t, const realtype *x, const realtype *p, const realtype *k, const realtype *h, const realtype *w) override {
@@ -205,12 +205,12 @@ class Model_model_events : public amici::Model_ODE {
         rz_model_events(rz, ie, t, x, p, k, h);
     }
 
-    virtual void fsigma_y(double *sigmay, const realtype t, const realtype *p, const realtype *k) override {
-        sigma_y_model_events(sigmay, t, p, k);
+    virtual void fsigmay(double *sigmay, const realtype t, const realtype *p, const realtype *k) override {
+        sigmay_model_events(sigmay, t, p, k);
     }
 
-    virtual void fsigma_z(double *sigmaz, const realtype t, const realtype *p, const realtype *k) override {
-        sigma_z_model_events(sigmaz, t, p, k);
+    virtual void fsigmaz(double *sigmaz, const realtype t, const realtype *p, const realtype *k) override {
+        sigmaz_model_events(sigmaz, t, p, k);
     }
 
     virtual void fsrz(double *srz, const int ie, const realtype t, const realtype *x, const realtype *p, const realtype *k, const realtype *h, const realtype *sx, const int ip) override {

models/model_dirac/model_dirac_sigma_y.cpp → models/model_events/model_events_sigmay.cpp

@@ -6,7 +6,7 @@ typedef amici::realtype realtype;
 
 using namespace amici;
 
-void sigma_y_model_dirac(double *sigmay, const realtype t, const realtype *p, const realtype *k) {
+void sigmay_model_events(double *sigmay, const realtype t, const realtype *p, const realtype *k) {
   sigmay[0] = 1.0;
 }