Remove MATLAB-specific model code

cmake/clang-tools.cmake

@@ -4,7 +4,7 @@
 execute_process(
   COMMAND
     sh -c
-    "git ls-tree -r HEAD --name-only src/*.cpp include/amici/*.h | tr '\n' ' '"
+    "git ls-tree -r HEAD --name-only src/*.cpp include/amici/*.h tests/cpp/*.h tests/cpp/unittests/*.cpp | tr '\n' ' '"
   WORKING_DIRECTORY ${CMAKE_SOURCE_DIR}
   OUTPUT_VARIABLE ALL_CXX_SOURCE_FILES)
 # ########### clang-tidy ############

include/amici/abstract_model.h

@@ -287,25 +287,6 @@ class AbstractModel {
      */
     virtual void fdx0(AmiVector& x0, AmiVector& dx0);
 
-    /**
-     * @brief Model-specific implementation of fstau (MATLAB-only, DEPRECATED)
-     * @param stau total derivative of event timepoint
-     * @param t current time
-     * @param x current state
-     * @param p parameter vector
-     * @param k constant vector
-     * @param h Heaviside vector
-     * @param tcl total abundances for conservation laws
-     * @param sx current state sensitivity
-     * @param ip sensitivity index
-     * @param ie event index
-     */
-    virtual void fstau(
-        realtype* stau, realtype t, realtype const* x, realtype const* p,
-        realtype const* k, realtype const* h, realtype const* tcl,
-        realtype const* sx, int ip, int ie
-    );
-
     /**
      * @brief Model-specific implementation of fstau
      * @param stau total derivative of event timepoint
@@ -341,25 +322,7 @@ class AbstractModel {
        realtype const* k, realtype const* h, realtype const* w);
 
     /**
-     * @brief Model-specific implementation of fdydp (MATLAB-only)
-     * @param dydp partial derivative of observables y w.r.t. model parameters p
-     * @param t current time
-     * @param x current state
-     * @param p parameter vector
-     * @param k constant vector
-     * @param h Heaviside vector
-     * @param ip parameter index w.r.t. which the derivative is requested
-     * @param w repeating elements vector
-     * @param dwdp Recurring terms in xdot, parameter derivative
-     */
-    virtual void fdydp(
-        realtype* dydp, realtype t, realtype const* x, realtype const* p,
-        realtype const* k, realtype const* h, int ip, realtype const* w,
-        realtype const* dwdp
-    );
-
-    /**
-     * @brief Model-specific implementation of fdydp (Python)
+     * @brief Model-specific implementation of fdydp
      * @param dydp partial derivative of observables y w.r.t. model parameters p
      * @param t current time
      * @param x current state
@@ -526,25 +489,7 @@ class AbstractModel {
     );
 
     /**
-     * @brief Model-specific implementation of fdeltax (MATLAB-only)
-     * @param deltax state update
-     * @param t current time
-     * @param x current state
-     * @param p parameter vector
-     * @param k constant vector
-     * @param h Heaviside vector
-     * @param ie event index
-     * @param xdot new model right hand side
-     * @param xdot_old previous model right hand side
-     */
-    virtual void fdeltax(
-        realtype* deltax, realtype t, realtype const* x, realtype const* p,
-        realtype const* k, realtype const* h, int ie, realtype const* xdot,
-        realtype const* xdot_old
-    );
-
-    /**
-     * @brief Model-specific implementation of fdeltax (Python-only)
+     * @brief Model-specific implementation of fdeltax
      * @param deltax state update
      * @param t current time
      * @param x current state
@@ -563,31 +508,7 @@ class AbstractModel {
     );
 
     /**
-     * @brief Model-specific implementation of fdeltasx (MATLAB-only)
-     * @param deltasx sensitivity update
-     * @param t current time
-     * @param x current state
-     * @param p parameter vector
-     * @param k constant vector
-     * @param h Heaviside vector
-     * @param w repeating elements vector
-     * @param ip sensitivity index
-     * @param ie event index
-     * @param xdot new model right hand side
-     * @param xdot_old previous model right hand side
-     * @param sx state sensitivity
-     * @param stau event-time sensitivity
-     * @param tcl total abundances for conservation laws
-     */
-    virtual void fdeltasx(
-        realtype* deltasx, realtype t, realtype const* x, realtype const* p,
-        realtype const* k, realtype const* h, realtype const* w, int ip, int ie,
-        realtype const* xdot, realtype const* xdot_old, realtype const* sx,
-        realtype const* stau, realtype const* tcl
-    );
-
-    /**
-     * @brief Model-specific implementation of fdeltasx (Python-only)
+     * @brief Model-specific implementation of fdeltasx
      * @param deltasx sensitivity update
      * @param t current time
      * @param x current state
@@ -634,25 +555,6 @@ class AbstractModel {
         realtype const* xB, realtype const* tcl
     );
 
-    /**
-     * @brief Model-specific implementation of fdeltaxB (MATLAB-only!!)
-     * @param deltaxB adjoint state update
-     * @param t current time
-     * @param x current state
-     * @param p parameter vector
-     * @param k constant vector
-     * @param h Heaviside vector
-     * @param ie event index
-     * @param xdot new model right hand side
-     * @param xdot_old previous model right hand side
-     * @param xB current adjoint state
-     */
-    virtual void fdeltaxB(
-        realtype* deltaxB, realtype t, realtype const* x, realtype const* p,
-        realtype const* k, realtype const* h, int ie, realtype const* xdot,
-        realtype const* xdot_old, realtype const* xB
-    );
-
     /**
      * @brief Model-specific implementation of fdeltaqB
      * @param deltaqB sensitivity update
@@ -676,26 +578,6 @@ class AbstractModel {
         realtype const* x_old, realtype const* xB
     );
 
-    /**
-     * @brief Model-specific implementation of fdeltaqB (MATLAB-only!!)
-     * @param deltaqB sensitivity update
-     * @param t current time
-     * @param x current state
-     * @param p parameter vector
-     * @param k constant vector
-     * @param h Heaviside vector
-     * @param ip sensitivity index
-     * @param ie event index
-     * @param xdot new model right hand side
-     * @param xdot_old previous model right hand side
-     * @param xB adjoint state
-     */
-    virtual void fdeltaqB(
-        realtype* deltaqB, realtype t, realtype const* x, realtype const* p,
-        realtype const* k, realtype const* h, int ip, int ie,
-        realtype const* xdot, realtype const* xdot_old, realtype const* xB
-    );
-
     /**
      * @brief Model-specific implementation of fsigmay
      * @param sigmay standard deviation of measurements
@@ -1002,7 +884,7 @@ class AbstractModel {
     virtual void fdwdx_rowvals(SUNMatrixWrapper& dwdx);
 
     /**
-     * @brief Model-specific implementation of fdwdw, no w chainrule (Py)
+     * @brief Model-specific implementation of fdwdw, no w chainrule
      * @param dwdw partial derivative w wrt w
      * @param t timepoint
      * @param x Vector with the states

include/amici/model.h

@@ -72,7 +72,6 @@ enum class ModelQuantity {
     p,
     ts,
     dJydy,
-    dJydy_matlab,
     deltaqB,
     dsigmaydp,
     dsigmaydy,
@@ -1520,13 +1519,7 @@ class Model : public AbstractModel, public ModelDimensions {
     [[nodiscard]] std::vector<int> const& getReinitializationStateIdxs() const;
 
     /**
-     * @brief getter for dxdotdp (matlab generated)
-     * @return dxdotdp
-     */
-    [[nodiscard]] AmiVectorArray const& get_dxdotdp() const;
-
-    /**
-     * @brief getter for dxdotdp (python generated)
+     * @brief getter for dxdotdp
      * @return dxdotdp
      */
     [[nodiscard]] SUNMatrixWrapper const& get_dxdotdp_full() const;

include/amici/model_dae.h

@@ -46,7 +46,6 @@ class Model_DAE : public Model {
               events
           ) {
         SUNContext sunctx = derived_state_.sunctx_;
-        derived_state_.M_ = SUNMatrixWrapper(nx_solver, nx_solver, sunctx);
         auto const M_nnz = static_cast<sunindextype>(
             std::reduce(idlist.begin(), idlist.end())
         );

include/amici/model_dimensions.h

@@ -54,8 +54,6 @@ struct ModelDimensions {
      * @param nnz Number of nonzero elements in Jacobian
      * @param ubw Upper matrix bandwidth in the Jacobian
      * @param lbw Lower matrix bandwidth in the Jacobian
-     * @param pythonGenerated Flag indicating model creation from Matlab or
-     * Python
      * @param ndxdotdp_explicit Number of nonzero elements in `dxdotdp_explicit`
      * @param ndxdotdx_explicit Number of nonzero elements in `dxdotdx_explicit`
      * @param w_recursion_depth Recursion depth of fw
@@ -69,8 +67,8 @@ struct ModelDimensions {
         int const ndwdw, int const ndxdotdw, std::vector<int> ndJydy,
         int const ndxrdatadxsolver, int const ndxrdatadtcl,
         int const ndtotal_cldx_rdata, int const nnz, int const ubw,
-        int const lbw, bool pythonGenerated = false, int ndxdotdp_explicit = 0,
-        int ndxdotdx_explicit = 0, int w_recursion_depth = 0
+        int const lbw, int ndxdotdp_explicit = 0, int ndxdotdx_explicit = 0,
+        int w_recursion_depth = 0
     )
         : nx_rdata(nx_rdata)
         , nxtrue_rdata(nxtrue_rdata)
@@ -99,7 +97,6 @@ struct ModelDimensions {
         , nJ(nJ)
         , ubw(ubw)
         , lbw(lbw)
-        , pythonGenerated(pythonGenerated)
         , ndxdotdp_explicit(ndxdotdp_explicit)
         , ndxdotdx_explicit(ndxdotdx_explicit)
         , w_recursion_depth(w_recursion_depth) {
@@ -243,9 +240,6 @@ struct ModelDimensions {
     /** Lower bandwidth of the Jacobian */
     int lbw{0};
 
-    /** Flag indicating model creation from Matlab or Python */
-    bool pythonGenerated = false;
-
     /** Number of nonzero elements in `dxdotdx_explicit` */
     int ndxdotdp_explicit = 0;
 

include/amici/model_ode.h

@@ -280,24 +280,7 @@ class Model_ODE : public Model {
 
   protected:
     /**
-     * @brief Model specific implementation for fJSparse (Matlab)
-     * @param JSparse Matrix to which the Jacobian will be written
-     * @param t timepoint
-     * @param x Vector with the states
-     * @param p parameter vector
-     * @param k constants vector
-     * @param h Heaviside vector
-     * @param w vector with helper variables
-     * @param dwdx derivative of w wrt x
-     **/
-    virtual void fJSparse(
-        SUNMatrixContent_Sparse JSparse, realtype t, realtype const* x,
-        realtype const* p, realtype const* k, realtype const* h,
-        realtype const* w, realtype const* dwdx
-    );
-
-    /**
-     * @brief Model specific implementation for fJSparse, data only (Py)
+     * @brief Model specific implementation for fJSparse, data only
      * @param JSparse Matrix to which the Jacobian will be written
      * @param t timepoint
      * @param x Vector with the states
@@ -355,28 +338,8 @@ class Model_ODE : public Model {
         realtype const* k, realtype const* h, realtype const* w
     ) = 0;
 
-    /**
-     * @brief Model specific implementation of fdxdotdp, with w chainrule
-     * (Matlab)
-     * @param dxdotdp partial derivative xdot wrt p
-     * @param t timepoint
-     * @param x Vector with the states
-     * @param p parameter vector
-     * @param k constants vector
-     * @param h Heaviside vector
-     * @param ip parameter index
-     * @param w vector with helper variables
-     * @param dwdp derivative of w wrt p
-     */
-    virtual void fdxdotdp(
-        realtype* dxdotdp, realtype t, realtype const* x, realtype const* p,
-        realtype const* k, realtype const* h, int ip, realtype const* w,
-        realtype const* dwdp
-    );
-
     /**
      * @brief Model specific implementation of fdxdotdp_explicit, no w chainrule
-     * (Py)
      * @param dxdotdp_explicit partial derivative xdot wrt p
      * @param t timepoint
      * @param x Vector with the states

include/amici/model_state.h

@@ -93,7 +93,6 @@ struct ModelStateDerived {
         , dxdotdw_(other.dxdotdw_)
         , dwdx_(other.dwdx_)
         , dwdp_(other.dwdp_)
-        , M_(other.M_)
         , MSparse_(other.MSparse_)
         , dfdx_(other.dfdx_)
         , dxdotdp_full(other.dxdotdp_full)
@@ -106,7 +105,6 @@ struct ModelStateDerived {
         , dtotal_cldx_rdata(other.dtotal_cldx_rdata)
         , dxdotdp(other.dxdotdp)
         , dJydy_(other.dJydy_)
-        , dJydy_matlab_(other.dJydy_matlab_)
         , dJydsigma_(other.dJydsigma_)
         , dJydx_(other.dJydx_)
         , dJydp_(other.dJydp_)
@@ -152,7 +150,6 @@ struct ModelStateDerived {
         dxdotdw_.set_ctx(sunctx_);
         dwdx_.set_ctx(sunctx_);
         dwdp_.set_ctx(sunctx_);
-        M_.set_ctx(sunctx_);
         MSparse_.set_ctx(sunctx_);
         dfdx_.set_ctx(sunctx_);
         dxdotdp_full.set_ctx(sunctx_);
@@ -210,13 +207,6 @@ struct ModelStateDerived {
     /** Sparse dwdp temporary storage (dimension: `nw` x `np`, nnz: `ndwdp`) */
     SUNMatrixWrapper dwdp_;
 
-    /**
-     * Dense Mass matrix (dimension: `nx_solver` x `nx_solver`)
-     *
-     * MATLAB-generated-only, DEPRECATED.
-     */
-    SUNMatrixWrapper M_;
-
     /**
      * Sparse Mass matrix, Python-generated-only
      *
@@ -296,12 +286,6 @@ struct ModelStateDerived {
      */
     std::vector<SUNMatrixWrapper> dJydy_;
 
-    /** Observable derivative of data likelihood, only used if
-     * `pythonGenerated` == `false` (dimension `nJ` x `ny` x `nytrue` ,
-     * row-major)
-     */
-    std::vector<realtype> dJydy_matlab_;
-
     /** Observable sigma derivative of data likelihood
      * (dimension nJ x ny x nytrue, row-major)
      */

include/amici/serialization.h

@@ -149,7 +149,6 @@ void serialize(Archive& ar, amici::Model& m, unsigned int const /*version*/) {
     ar & m.sx0data_;
     ar & m.nmaxevent_;
     ar & m.state_is_non_negative_;
-    ar & m.pythonGenerated;
     ar & m.min_sigma_;
     ar & m.sigma_res_;
     ar & m.steadystate_computation_mode_;

models/model_calvetti_py/model_calvetti_py.h

@@ -138,7 +138,6 @@ class Model_model_calvetti_py : public amici::Model_DAE {
                   0,                                       // nnz
                   6,                                 // ubw
                   6,                                 // lbw
-                  true,                                    // pythonGenerated
                   0,                   // ndxdotdp_explicit
                   5,                   // ndxdotdx_explicit
                   2                    // w_recursion_depth
@@ -558,7 +557,7 @@ class Model_model_calvetti_py : public amici::Model_DAE {
      * @return AMICI git commit hash
      */
     std::string getAmiciCommit() const override {
-        return "b12c68a7a02f1cbd33de59d47cbc0c4d77d30d6f";
+        return "dcbbae0f8e9b52afd7ab8b4b7a046da36b907139";
     }
 
     bool hasQuadraticLLH() const override {