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Remove auto-generated flux_r0 expression in models without reactions #3057

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Merged
dweindl merged 1 commit into from
Nov 24, 2025
Merged

Remove auto-generated flux_r0 expression in models without reactions #3057

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4 changes: 2 additions & 2 deletions models/model_calvetti_py/dwdw.cpp
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Expand Up @@ -7,8 +7,8 @@
namespace amici {
namespace model_model_calvetti_py {

static constexpr std::array<sunindextype, 18> dwdw_colptrs_model_calvetti_py_ = {
0, 1, 2, 3, 4, 5, 6, 6, 6, 7, 9, 12, 16, 16, 16, 16, 16, 16
static constexpr std::array<sunindextype, 17> dwdw_colptrs_model_calvetti_py_ = {
0, 1, 2, 3, 4, 5, 6, 6, 6, 7, 9, 12, 16, 16, 16, 16, 16
};

void dwdw_colptrs_model_calvetti_py(SUNMatrixWrapper &dwdw){
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4 changes: 2 additions & 2 deletions models/model_calvetti_py/dxdotdw.cpp
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Expand Up @@ -7,8 +7,8 @@
namespace amici {
namespace model_model_calvetti_py {

static constexpr std::array<sunindextype, 18> dxdotdw_colptrs_model_calvetti_py_ = {
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 3, 5, 7, 7
static constexpr std::array<sunindextype, 17> dxdotdw_colptrs_model_calvetti_py_ = {
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 3, 5, 7
};

void dxdotdw_colptrs_model_calvetti_py(SUNMatrixWrapper &dxdotdw){
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6 changes: 2 additions & 4 deletions models/model_calvetti_py/model_calvetti_py.cpp
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Expand Up @@ -45,7 +45,7 @@ ObservableScaling::lin, // y[4]
ObservableScaling::lin, // y[5]
};

std::array<const char*, 17> expression_names = {
std::array<const char*, 16> expression_names = {
"C1ss", // w[0]
"C2ss", // w[1]
"C3ss", // w[2]
Expand All @@ -62,7 +62,6 @@ std::array<const char*, 17> expression_names = {
"rate_of_V1", // w[13]
"rate_of_V2", // w[14]
"rate_of_V3", // w[15]
"flux_r0", // w[16]
};

std::array<const char*, 0> free_parameter_ids = {
Expand Down Expand Up @@ -96,7 +95,7 @@ std::array<const char*, 6> observable_ids = {
"obs_f2", // y[5]
};

std::array<const char*, 17> expression_ids = {
std::array<const char*, 16> expression_ids = {
"C1ss", // w[0]
"C2ss", // w[1]
"C3ss", // w[2]
Expand All @@ -113,7 +112,6 @@ std::array<const char*, 17> expression_ids = {
"rate_of_V1", // w[13]
"rate_of_V2", // w[14]
"rate_of_V3", // w[15]
"flux_r0", // w[16]
};

std::array<int, 6> state_idxs_solver = {
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8 changes: 4 additions & 4 deletions models/model_calvetti_py/model_calvetti_py.h
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Expand Up @@ -19,12 +19,12 @@ extern std::array<const char*, 6> fixed_parameter_names;
extern std::array<const char*, 6> state_names;
extern std::array<const char*, 6> observable_names;
extern std::array<const ObservableScaling, 6> observable_scalings;
extern std::array<const char*, 17> expression_names;
extern std::array<const char*, 16> expression_names;
extern std::array<const char*, 0> free_parameter_ids;
extern std::array<const char*, 6> fixed_parameter_ids;
extern std::array<const char*, 6> state_ids;
extern std::array<const char*, 6> observable_ids;
extern std::array<const char*, 17> expression_ids;
extern std::array<const char*, 16> expression_ids;
extern std::array<int, 6> state_idxs_solver;

extern void Jy_model_calvetti_py(realtype *Jy, const int iy, const realtype *p, const realtype *k, const realtype *y, const realtype *sigmay, const realtype *my);
Expand Down Expand Up @@ -125,7 +125,7 @@ class Model_model_calvetti_py : public amici::Model_DAE {
.ne = 4,
.ne_solver = 0,
.nspl = 0,
.nw = 17,
.nw = 16,
.ndwdx = 15,
.ndwdp = 0,
.ndwdw = 16,
Expand Down Expand Up @@ -557,7 +557,7 @@ class Model_model_calvetti_py : public amici::Model_DAE {
* @return AMICI git commit hash
*/
std::string get_amici_commit() const override {
return "63f2e78a186ee722a79b0da2797e0c116ec81065";
return "c4a395b6462dc1f26ad1472e6b2fa71fe0d54382";
}

bool has_quadratic_llh() const override {
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1 change: 0 additions & 1 deletion models/model_calvetti_py/w.h
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Expand Up @@ -14,4 +14,3 @@
#define rate_of_V1 w[13]
#define rate_of_V2 w[14]
#define rate_of_V3 w[15]
#define flux_r0 w[16]
1 change: 0 additions & 1 deletion models/model_dirac_py/CMakeLists.txt
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Expand Up @@ -88,7 +88,6 @@ sigmay.h
stau.cpp
stau.h
sx.h
w.h
wrapfunctions.cpp
wrapfunctions.h
x.h
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1 change: 0 additions & 1 deletion models/model_dirac_py/deltaqB.cpp
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Expand Up @@ -5,7 +5,6 @@
#include "x.h"
#include "p.h"
#include "h.h"
#include "w.h"
#include "xdot.h"
#include "xdot_old.h"
#include "x_old.h"
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1 change: 0 additions & 1 deletion models/model_dirac_py/dxdotdp_explicit.cpp
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Expand Up @@ -48,7 +48,6 @@ void dxdotdp_explicit_rowvals_model_dirac_py(SUNMatrixWrapper &dxdotdp_explicit)
#include "x.h"
#include "p.h"
#include "h.h"
#include "w.h"
#include "dxdotdp_explicit.h"

namespace amici {
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1 change: 0 additions & 1 deletion models/model_dirac_py/dxdotdx_explicit.cpp
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Expand Up @@ -48,7 +48,6 @@ void dxdotdx_explicit_rowvals_model_dirac_py(SUNMatrixWrapper &dxdotdx_explicit)
#include "x.h"
#include "p.h"
#include "h.h"
#include "w.h"
#include "dxdotdx_explicit.h"

namespace amici {
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8 changes: 4 additions & 4 deletions models/model_dirac_py/model_dirac_py.cpp
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Expand Up @@ -29,8 +29,8 @@ std::array<const ObservableScaling, 1> observable_scalings = {
ObservableScaling::lin, // y[0]
};

std::array<const char*, 1> expression_names = {
"flux_r0", // w[0]
std::array<const char*, 0> expression_names = {

};

std::array<const char*, 4> free_parameter_ids = {
Expand All @@ -53,8 +53,8 @@ std::array<const char*, 1> observable_ids = {
"obs_x2", // y[0]
};

std::array<const char*, 1> expression_ids = {
"flux_r0", // w[0]
std::array<const char*, 0> expression_ids = {

};

std::array<int, 2> state_idxs_solver = {
Expand Down
8 changes: 4 additions & 4 deletions models/model_dirac_py/model_dirac_py.h
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Expand Up @@ -19,12 +19,12 @@ extern std::array<const char*, 0> fixed_parameter_names;
extern std::array<const char*, 2> state_names;
extern std::array<const char*, 1> observable_names;
extern std::array<const ObservableScaling, 1> observable_scalings;
extern std::array<const char*, 1> expression_names;
extern std::array<const char*, 0> expression_names;
extern std::array<const char*, 4> free_parameter_ids;
extern std::array<const char*, 0> fixed_parameter_ids;
extern std::array<const char*, 2> state_ids;
extern std::array<const char*, 1> observable_ids;
extern std::array<const char*, 1> expression_ids;
extern std::array<const char*, 0> expression_ids;
extern std::array<int, 2> state_idxs_solver;

extern void Jy_model_dirac_py(realtype *Jy, const int iy, const realtype *p, const realtype *k, const realtype *y, const realtype *sigmay, const realtype *my);
Expand Down Expand Up @@ -125,7 +125,7 @@ class Model_model_dirac_py : public amici::Model_ODE {
.ne = 1,
.ne_solver = 0,
.nspl = 0,
.nw = 1,
.nw = 0,
.ndwdx = 0,
.ndwdp = 0,
.ndwdw = 0,
Expand Down Expand Up @@ -544,7 +544,7 @@ class Model_model_dirac_py : public amici::Model_ODE {
* @return AMICI git commit hash
*/
std::string get_amici_commit() const override {
return "63f2e78a186ee722a79b0da2797e0c116ec81065";
return "c4a395b6462dc1f26ad1472e6b2fa71fe0d54382";
}

bool has_quadratic_llh() const override {
Expand Down
1 change: 0 additions & 1 deletion models/model_dirac_py/w.h
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1 change: 0 additions & 1 deletion models/model_dirac_py/xdot.cpp
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Expand Up @@ -5,7 +5,6 @@
#include "x.h"
#include "p.h"
#include "h.h"
#include "w.h"
#include "xdot.h"

namespace amici {
Expand Down
1 change: 0 additions & 1 deletion models/model_events_py/CMakeLists.txt
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Expand Up @@ -104,7 +104,6 @@ stau.cpp
stau.h
sx.h
sx0_fixedParameters.cpp
w.h
wrapfunctions.cpp
wrapfunctions.h
x.h
Expand Down
1 change: 0 additions & 1 deletion models/model_events_py/deltaqB.cpp
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Expand Up @@ -6,7 +6,6 @@
#include "p.h"
#include "k.h"
#include "h.h"
#include "w.h"
#include "xdot.h"
#include "xdot_old.h"
#include "x_old.h"
Expand Down
1 change: 0 additions & 1 deletion models/model_events_py/deltaxB.cpp
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Expand Up @@ -6,7 +6,6 @@
#include "p.h"
#include "k.h"
#include "h.h"
#include "w.h"
#include "xdot.h"
#include "xdot_old.h"
#include "x_old.h"
Expand Down
1 change: 0 additions & 1 deletion models/model_events_py/dxdotdp_explicit.cpp
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Expand Up @@ -49,7 +49,6 @@ void dxdotdp_explicit_rowvals_model_events_py(SUNMatrixWrapper &dxdotdp_explicit
#include "p.h"
#include "k.h"
#include "h.h"
#include "w.h"
#include "dxdotdp_explicit.h"

namespace amici {
Expand Down
1 change: 0 additions & 1 deletion models/model_events_py/dxdotdx_explicit.cpp
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Expand Up @@ -49,7 +49,6 @@ void dxdotdx_explicit_rowvals_model_events_py(SUNMatrixWrapper &dxdotdx_explicit
#include "p.h"
#include "k.h"
#include "h.h"
#include "w.h"
#include "dxdotdx_explicit.h"

namespace amici {
Expand Down
8 changes: 4 additions & 4 deletions models/model_events_py/model_events_py.cpp
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Expand Up @@ -33,8 +33,8 @@ std::array<const ObservableScaling, 1> observable_scalings = {
ObservableScaling::lin, // y[0]
};

std::array<const char*, 1> expression_names = {
"flux_r0", // w[0]
std::array<const char*, 0> expression_names = {

};

std::array<const char*, 4> free_parameter_ids = {
Expand All @@ -61,8 +61,8 @@ std::array<const char*, 1> observable_ids = {
"y1", // y[0]
};

std::array<const char*, 1> expression_ids = {
"flux_r0", // w[0]
std::array<const char*, 0> expression_ids = {

};

std::array<int, 3> state_idxs_solver = {
Expand Down
8 changes: 4 additions & 4 deletions models/model_events_py/model_events_py.h
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Expand Up @@ -19,12 +19,12 @@ extern std::array<const char*, 4> fixed_parameter_names;
extern std::array<const char*, 3> state_names;
extern std::array<const char*, 1> observable_names;
extern std::array<const ObservableScaling, 1> observable_scalings;
extern std::array<const char*, 1> expression_names;
extern std::array<const char*, 0> expression_names;
extern std::array<const char*, 4> free_parameter_ids;
extern std::array<const char*, 4> fixed_parameter_ids;
extern std::array<const char*, 3> state_ids;
extern std::array<const char*, 1> observable_ids;
extern std::array<const char*, 1> expression_ids;
extern std::array<const char*, 0> expression_ids;
extern std::array<int, 3> state_idxs_solver;

extern void Jy_model_events_py(realtype *Jy, const int iy, const realtype *p, const realtype *k, const realtype *y, const realtype *sigmay, const realtype *my);
Expand Down Expand Up @@ -125,7 +125,7 @@ class Model_model_events_py : public amici::Model_ODE {
.ne = 6,
.ne_solver = 2,
.nspl = 0,
.nw = 1,
.nw = 0,
.ndwdx = 0,
.ndwdp = 0,
.ndwdw = 0,
Expand Down Expand Up @@ -579,7 +579,7 @@ class Model_model_events_py : public amici::Model_ODE {
* @return AMICI git commit hash
*/
std::string get_amici_commit() const override {
return "63f2e78a186ee722a79b0da2797e0c116ec81065";
return "c4a395b6462dc1f26ad1472e6b2fa71fe0d54382";
}

bool has_quadratic_llh() const override {
Expand Down
1 change: 0 additions & 1 deletion models/model_events_py/w.h
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1 change: 0 additions & 1 deletion models/model_events_py/xdot.cpp
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Expand Up @@ -6,7 +6,6 @@
#include "p.h"
#include "k.h"
#include "h.h"
#include "w.h"
#include "xdot.h"

namespace amici {
Expand Down
4 changes: 2 additions & 2 deletions models/model_jakstat_adjoint_py/dxdotdw.cpp
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Expand Up @@ -7,8 +7,8 @@
namespace amici {
namespace model_model_jakstat_adjoint_py {

static constexpr std::array<sunindextype, 3> dxdotdw_colptrs_model_jakstat_adjoint_py_ = {
0, 2, 2
static constexpr std::array<sunindextype, 2> dxdotdw_colptrs_model_jakstat_adjoint_py_ = {
0, 2
};

void dxdotdw_colptrs_model_jakstat_adjoint_py(SUNMatrixWrapper &dxdotdw){
Expand Down
6 changes: 2 additions & 4 deletions models/model_jakstat_adjoint_py/model_jakstat_adjoint_py.cpp
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Expand Up @@ -54,9 +54,8 @@ ObservableScaling::lin, // y[1]
ObservableScaling::lin, // y[2]
};

std::array<const char*, 2> expression_names = {
std::array<const char*, 1> expression_names = {
"u", // w[0]
"flux_r0", // w[1]
};

std::array<const char*, 17> free_parameter_ids = {
Expand Down Expand Up @@ -102,9 +101,8 @@ std::array<const char*, 3> observable_ids = {
"obs_spline", // y[2]
};

std::array<const char*, 2> expression_ids = {
std::array<const char*, 1> expression_ids = {
"u", // w[0]
"flux_r0", // w[1]
};

std::array<int, 9> state_idxs_solver = {
Expand Down
8 changes: 4 additions & 4 deletions models/model_jakstat_adjoint_py/model_jakstat_adjoint_py.h
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Expand Up @@ -19,12 +19,12 @@ extern std::array<const char*, 2> fixed_parameter_names;
extern std::array<const char*, 9> state_names;
extern std::array<const char*, 3> observable_names;
extern std::array<const ObservableScaling, 3> observable_scalings;
extern std::array<const char*, 2> expression_names;
extern std::array<const char*, 1> expression_names;
extern std::array<const char*, 17> free_parameter_ids;
extern std::array<const char*, 2> fixed_parameter_ids;
extern std::array<const char*, 9> state_ids;
extern std::array<const char*, 3> observable_ids;
extern std::array<const char*, 2> expression_ids;
extern std::array<const char*, 1> expression_ids;
extern std::array<int, 9> state_idxs_solver;

extern void Jy_model_jakstat_adjoint_py(realtype *Jy, const int iy, const realtype *p, const realtype *k, const realtype *y, const realtype *sigmay, const realtype *my);
Expand Down Expand Up @@ -125,7 +125,7 @@ class Model_model_jakstat_adjoint_py : public amici::Model_ODE {
.ne = 0,
.ne_solver = 0,
.nspl = 1,
.nw = 2,
.nw = 1,
.ndwdx = 0,
.ndwdp = 5,
.ndwdw = 0,
Expand Down Expand Up @@ -552,7 +552,7 @@ class Model_model_jakstat_adjoint_py : public amici::Model_ODE {
* @return AMICI git commit hash
*/
std::string get_amici_commit() const override {
return "63f2e78a186ee722a79b0da2797e0c116ec81065";
return "c4a395b6462dc1f26ad1472e6b2fa71fe0d54382";
}

bool has_quadratic_llh() const override {
Expand Down
1 change: 0 additions & 1 deletion models/model_jakstat_adjoint_py/w.h
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@@ -1,2 +1 @@
#define u w[0]
#define flux_r0 w[1]
1 change: 0 additions & 1 deletion models/model_nested_events_py/CMakeLists.txt
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Expand Up @@ -90,7 +90,6 @@ stau.cpp
stau.h
sx.h
sx0.cpp
w.h
wrapfunctions.cpp
wrapfunctions.h
x.h
Expand Down
1 change: 0 additions & 1 deletion models/model_nested_events_py/deltaqB.cpp
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Expand Up @@ -5,7 +5,6 @@
#include "x.h"
#include "p.h"
#include "h.h"
#include "w.h"
#include "xdot.h"
#include "xdot_old.h"
#include "x_old.h"
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1 change: 0 additions & 1 deletion models/model_nested_events_py/deltaxB.cpp
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Expand Up @@ -5,7 +5,6 @@
#include "x.h"
#include "p.h"
#include "h.h"
#include "w.h"
#include "xdot.h"
#include "xdot_old.h"
#include "x_old.h"
Expand Down
1 change: 0 additions & 1 deletion models/model_nested_events_py/dxdotdp_explicit.cpp
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Expand Up @@ -48,7 +48,6 @@ void dxdotdp_explicit_rowvals_model_nested_events_py(SUNMatrixWrapper &dxdotdp_e
#include "x.h"
#include "p.h"
#include "h.h"
#include "w.h"
#include "dxdotdp_explicit.h"

namespace amici {
Expand Down
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