refactor: 0-based indexing in Model::z2event_

models/model_calvetti_py/Jy.cpp

@@ -1,10 +1,7 @@
 #include "amici/symbolic_functions.h"
 #include "amici/defines.h"
-#include "sundials/sundials_types.h"
 
-#include <gsl/gsl-lite.hpp>
 #include <algorithm>
-
 #include "k.h"
 #include "y.h"
 #include "sigmay.h"

models/model_calvetti_py/create_splines.cpp

@@ -1,10 +1,7 @@
 #include "amici/symbolic_functions.h"
 #include "amici/defines.h"
-#include "sundials/sundials_types.h"
 
-#include <gsl/gsl-lite.hpp>
 #include <algorithm>
-
 #include "amici/splinefunctions.h"
 #include <vector>
 #include "k.h"

models/model_calvetti_py/dJydsigma.cpp

@@ -1,10 +1,7 @@
 #include "amici/symbolic_functions.h"
 #include "amici/defines.h"
-#include "sundials/sundials_types.h"
 
-#include <gsl/gsl-lite.hpp>
 #include <algorithm>
-
 #include "k.h"
 #include "y.h"
 #include "sigmay.h"

models/model_calvetti_py/dJydy.cpp

@@ -51,11 +51,10 @@ void dJydy_rowvals_model_calvetti_py(SUNMatrixWrapper &dJydy, int index){
 
 #include "amici/symbolic_functions.h"
 #include "amici/defines.h"
-#include "sundials/sundials_types.h"
 
-#include <gsl/gsl-lite.hpp>
 #include <algorithm>
-
+#include <sundials/sundials_types.h>
+#include <gsl/gsl-lite.hpp>
 #include "k.h"
 #include "y.h"
 #include "sigmay.h"

models/model_calvetti_py/dwdw.cpp

@@ -41,11 +41,10 @@ void dwdw_rowvals_model_calvetti_py(SUNMatrixWrapper &dwdw){
 
 #include "amici/symbolic_functions.h"
 #include "amici/defines.h"
-#include "sundials/sundials_types.h"
 
-#include <gsl/gsl-lite.hpp>
 #include <algorithm>
-
+#include <sundials/sundials_types.h>
+#include <gsl/gsl-lite.hpp>
 #include "x.h"
 #include "k.h"
 #include "h.h"

models/model_calvetti_py/dwdx.cpp

@@ -41,11 +41,10 @@ void dwdx_rowvals_model_calvetti_py(SUNMatrixWrapper &dwdx){
 
 #include "amici/symbolic_functions.h"
 #include "amici/defines.h"
-#include "sundials/sundials_types.h"
 
-#include <gsl/gsl-lite.hpp>
 #include <algorithm>
-
+#include <sundials/sundials_types.h>
+#include <gsl/gsl-lite.hpp>
 #include "x.h"
 #include "k.h"
 #include "h.h"

models/model_calvetti_py/dxdotdw.cpp

@@ -41,11 +41,10 @@ void dxdotdw_rowvals_model_calvetti_py(SUNMatrixWrapper &dxdotdw){
 
 #include "amici/symbolic_functions.h"
 #include "amici/defines.h"
-#include "sundials/sundials_types.h"
 
-#include <gsl/gsl-lite.hpp>
 #include <algorithm>
-
+#include <sundials/sundials_types.h>
+#include <gsl/gsl-lite.hpp>
 #include "x.h"
 #include "k.h"
 #include "h.h"

models/model_calvetti_py/dxdotdx_explicit.cpp

@@ -41,11 +41,10 @@ void dxdotdx_explicit_rowvals_model_calvetti_py(SUNMatrixWrapper &dxdotdx_explic
 
 #include "amici/symbolic_functions.h"
 #include "amici/defines.h"
-#include "sundials/sundials_types.h"
 
-#include <gsl/gsl-lite.hpp>
 #include <algorithm>
-
+#include <sundials/sundials_types.h>
+#include <gsl/gsl-lite.hpp>
 #include "x.h"
 #include "k.h"
 #include "h.h"

models/model_calvetti_py/dydx.cpp

@@ -1,10 +1,7 @@
 #include "amici/symbolic_functions.h"
 #include "amici/defines.h"
-#include "sundials/sundials_types.h"
 
-#include <gsl/gsl-lite.hpp>
 #include <algorithm>
-
 #include "x.h"
 #include "k.h"
 #include "h.h"

models/model_calvetti_py/explicit_roots.cpp

@@ -1,10 +1,7 @@
 #include "amici/symbolic_functions.h"
 #include "amici/defines.h"
-#include "sundials/sundials_types.h"
 
-#include <gsl/gsl-lite.hpp>
 #include <algorithm>
-
 #include <vector>
 #include "k.h"
 

models/model_calvetti_py/model_calvetti_py.h

@@ -557,7 +557,7 @@ class Model_model_calvetti_py : public amici::Model_DAE {
      * @return AMICI git commit hash
      */
     std::string getAmiciCommit() const override {
-        return "570c71d2a041ed15d548e826df3d97e05d124309";
+        return "d5492c37f7dbc5faa374128e3559b96518e9a937";
     }
 
     bool hasQuadraticLLH() const override {

models/model_calvetti_py/root.cpp

@@ -1,10 +1,7 @@
 #include "amici/symbolic_functions.h"
 #include "amici/defines.h"
-#include "sundials/sundials_types.h"
 
-#include <gsl/gsl-lite.hpp>
 #include <algorithm>
-
 #include "x.h"
 #include "k.h"
 #include "h.h"

models/model_calvetti_py/sigmay.cpp

@@ -1,10 +1,7 @@
 #include "amici/symbolic_functions.h"
 #include "amici/defines.h"
-#include "sundials/sundials_types.h"
 
-#include <gsl/gsl-lite.hpp>
 #include <algorithm>
-
 #include "k.h"
 #include "y.h"
 #include "sigmay.h"

models/model_calvetti_py/w.cpp

@@ -1,10 +1,7 @@
 #include "amici/symbolic_functions.h"
 #include "amici/defines.h"
-#include "sundials/sundials_types.h"
 
-#include <gsl/gsl-lite.hpp>
 #include <algorithm>
-
 #include "x.h"
 #include "k.h"
 #include "h.h"

models/model_calvetti_py/x0.cpp

@@ -1,10 +1,7 @@
 #include "amici/symbolic_functions.h"
 #include "amici/defines.h"
-#include "sundials/sundials_types.h"
 
-#include <gsl/gsl-lite.hpp>
 #include <algorithm>
-
 #include "k.h"
 
 namespace amici {

models/model_calvetti_py/x0_fixedParameters.cpp

@@ -1,10 +1,8 @@
 #include "amici/symbolic_functions.h"
 #include "amici/defines.h"
-#include "sundials/sundials_types.h"
 
-#include <gsl/gsl-lite.hpp>
 #include <algorithm>
-
+#include <gsl/gsl-lite.hpp>
 #include "k.h"
 
 namespace amici {

models/model_calvetti_py/x_rdata.cpp

@@ -1,10 +1,7 @@
 #include "amici/symbolic_functions.h"
 #include "amici/defines.h"
-#include "sundials/sundials_types.h"
 
-#include <gsl/gsl-lite.hpp>
 #include <algorithm>
-
 #include "x.h"
 #include "k.h"
 

models/model_calvetti_py/x_solver.cpp

@@ -1,10 +1,7 @@
 #include "amici/symbolic_functions.h"
 #include "amici/defines.h"
-#include "sundials/sundials_types.h"
 
-#include <gsl/gsl-lite.hpp>
 #include <algorithm>
-
 #include "x_rdata.h"
 
 namespace amici {

models/model_calvetti_py/xdot.cpp

@@ -1,10 +1,7 @@
 #include "amici/symbolic_functions.h"
 #include "amici/defines.h"
-#include "sundials/sundials_types.h"
 
-#include <gsl/gsl-lite.hpp>
 #include <algorithm>
-
 #include "x.h"
 #include "k.h"
 #include "h.h"

models/model_calvetti_py/y.cpp

@@ -1,10 +1,7 @@
 #include "amici/symbolic_functions.h"
 #include "amici/defines.h"
-#include "sundials/sundials_types.h"
 
-#include <gsl/gsl-lite.hpp>
 #include <algorithm>
-
 #include "x.h"
 #include "k.h"
 #include "h.h"

models/model_dirac_py/Jy.cpp

@@ -1,10 +1,7 @@
 #include "amici/symbolic_functions.h"
 #include "amici/defines.h"
-#include "sundials/sundials_types.h"
 
-#include <gsl/gsl-lite.hpp>
 #include <algorithm>
-
 #include "p.h"
 #include "y.h"
 #include "sigmay.h"

models/model_dirac_py/create_splines.cpp

@@ -1,10 +1,7 @@
 #include "amici/symbolic_functions.h"
 #include "amici/defines.h"
-#include "sundials/sundials_types.h"
 
-#include <gsl/gsl-lite.hpp>
 #include <algorithm>
-
 #include "amici/splinefunctions.h"
 #include <vector>
 #include "p.h"

models/model_dirac_py/dJydsigma.cpp

@@ -1,10 +1,7 @@
 #include "amici/symbolic_functions.h"
 #include "amici/defines.h"
-#include "sundials/sundials_types.h"
 
-#include <gsl/gsl-lite.hpp>
 #include <algorithm>
-
 #include "p.h"
 #include "y.h"
 #include "sigmay.h"

models/model_dirac_py/dJydy.cpp

@@ -41,11 +41,10 @@ void dJydy_rowvals_model_dirac_py(SUNMatrixWrapper &dJydy, int index){
 
 #include "amici/symbolic_functions.h"
 #include "amici/defines.h"
-#include "sundials/sundials_types.h"
 
-#include <gsl/gsl-lite.hpp>
 #include <algorithm>
-
+#include <sundials/sundials_types.h>
+#include <gsl/gsl-lite.hpp>
 #include "p.h"
 #include "y.h"
 #include "sigmay.h"

models/model_dirac_py/deltaqB.cpp

@@ -1,10 +1,7 @@
 #include "amici/symbolic_functions.h"
 #include "amici/defines.h"
-#include "sundials/sundials_types.h"
 
-#include <gsl/gsl-lite.hpp>
 #include <algorithm>
-
 #include "x.h"
 #include "p.h"
 #include "h.h"

models/model_dirac_py/deltasx.cpp

@@ -1,10 +1,7 @@
 #include "amici/symbolic_functions.h"
 #include "amici/defines.h"
-#include "sundials/sundials_types.h"
 
-#include <gsl/gsl-lite.hpp>
 #include <algorithm>
-
 #include "x.h"
 #include "p.h"
 #include "h.h"

models/model_dirac_py/deltax.cpp

@@ -1,10 +1,7 @@
 #include "amici/symbolic_functions.h"
 #include "amici/defines.h"
-#include "sundials/sundials_types.h"
 
-#include <gsl/gsl-lite.hpp>
 #include <algorithm>
-
 #include "x.h"
 #include "p.h"
 #include "h.h"

models/model_dirac_py/dxdotdp_explicit.cpp

@@ -41,11 +41,10 @@ void dxdotdp_explicit_rowvals_model_dirac_py(SUNMatrixWrapper &dxdotdp_explicit)
 
 #include "amici/symbolic_functions.h"
 #include "amici/defines.h"
-#include "sundials/sundials_types.h"
 
-#include <gsl/gsl-lite.hpp>
 #include <algorithm>
-
+#include <sundials/sundials_types.h>
+#include <gsl/gsl-lite.hpp>
 #include "x.h"
 #include "p.h"
 #include "h.h"

models/model_dirac_py/dxdotdx_explicit.cpp

@@ -41,11 +41,10 @@ void dxdotdx_explicit_rowvals_model_dirac_py(SUNMatrixWrapper &dxdotdx_explicit)
 
 #include "amici/symbolic_functions.h"
 #include "amici/defines.h"
-#include "sundials/sundials_types.h"
 
-#include <gsl/gsl-lite.hpp>
 #include <algorithm>
-
+#include <sundials/sundials_types.h>
+#include <gsl/gsl-lite.hpp>
 #include "x.h"
 #include "p.h"
 #include "h.h"

models/model_dirac_py/dydx.cpp

@@ -1,10 +1,7 @@
 #include "amici/symbolic_functions.h"
 #include "amici/defines.h"
-#include "sundials/sundials_types.h"
 
-#include <gsl/gsl-lite.hpp>
 #include <algorithm>
-
 #include "x.h"
 #include "p.h"
 #include "h.h"

models/model_dirac_py/explicit_roots.cpp

@@ -1,10 +1,7 @@
 #include "amici/symbolic_functions.h"
 #include "amici/defines.h"
-#include "sundials/sundials_types.h"
 
-#include <gsl/gsl-lite.hpp>
 #include <algorithm>
-
 #include <vector>
 #include "p.h"
 

models/model_dirac_py/model_dirac_py.h

@@ -544,7 +544,7 @@ class Model_model_dirac_py : public amici::Model_ODE {
      * @return AMICI git commit hash
      */
     std::string getAmiciCommit() const override {
-        return "570c71d2a041ed15d548e826df3d97e05d124309";
+        return "d5492c37f7dbc5faa374128e3559b96518e9a937";
     }
 
     bool hasQuadraticLLH() const override {

models/model_dirac_py/root.cpp

@@ -1,10 +1,7 @@
 #include "amici/symbolic_functions.h"
 #include "amici/defines.h"
-#include "sundials/sundials_types.h"
 
-#include <gsl/gsl-lite.hpp>
 #include <algorithm>
-
 #include "x.h"
 #include "p.h"
 #include "h.h"

models/model_dirac_py/sigmay.cpp

@@ -1,10 +1,7 @@
 #include "amici/symbolic_functions.h"
 #include "amici/defines.h"
-#include "sundials/sundials_types.h"
 
-#include <gsl/gsl-lite.hpp>
 #include <algorithm>
-
 #include "p.h"
 #include "y.h"
 #include "sigmay.h"