Refactor de_export.py, extract C++ function info to cxx_functions.py (#…

…2321)

Move everything related to information on C++ model functions to a separate module.

Related to #2306.

No changes in functionality.

python/sdist/amici/_codegen/cxx_functions.py

@@ -0,0 +1,385 @@
+"""Info about C++ functions in the generated model code."""
+from __future__ import annotations
+
+from dataclasses import dataclass
+
+
+@dataclass
+class _FunctionInfo:
+    """Information on a model-specific generated C++ function
+
+    :ivar ode_arguments: argument list of the ODE function.
+        input variables should be ``const``.
+    :ivar dae_arguments: argument list of the DAE function, if different from
+        ODE function. input variables should be ``const``.
+    :ivar return_type: the return type of the function
+    :ivar assume_pow_positivity:
+        identifies the functions on which ``assume_pow_positivity`` will have
+        an effect when specified during model generation. generally these are
+        functions that are used for solving the ODE, where negative values may
+        negatively affect convergence of the integration algorithm
+    :ivar sparse:
+        specifies whether the result of this function will be stored in sparse
+        format. sparse format means that the function will only return an
+        array of nonzero values and not a full matrix.
+    :ivar generate_body:
+        indicates whether a model-specific implementation is to be generated
+    :ivar body:
+        the actual function body. will be filled later
+    """
+
+    ode_arguments: str = ""
+    dae_arguments: str = ""
+    return_type: str = "void"
+    assume_pow_positivity: bool = False
+    sparse: bool = False
+    generate_body: bool = True
+    body: str = ""
+
+    def arguments(self, ode: bool = True) -> str:
+        """Get the arguments for the ODE or DAE function"""
+        if ode or not self.dae_arguments:
+            return self.ode_arguments
+        return self.dae_arguments
+
+
+# Information on a model-specific generated C++ function
+# prototype for generated C++ functions, keys are the names of functions
+functions = {
+    "Jy": _FunctionInfo(
+        "realtype *Jy, const int iy, const realtype *p, "
+        "const realtype *k, const realtype *y, const realtype *sigmay, "
+        "const realtype *my"
+    ),
+    "dJydsigma": _FunctionInfo(
+        "realtype *dJydsigma, const int iy, const realtype *p, "
+        "const realtype *k, const realtype *y, const realtype *sigmay, "
+        "const realtype *my"
+    ),
+    "dJydy": _FunctionInfo(
+        "realtype *dJydy, const int iy, const realtype *p, "
+        "const realtype *k, const realtype *y, "
+        "const realtype *sigmay, const realtype *my",
+        sparse=True,
+    ),
+    "Jz": _FunctionInfo(
+        "realtype *Jz, const int iz, const realtype *p, const realtype *k, "
+        "const realtype *z, const realtype *sigmaz, const realtype *mz"
+    ),
+    "dJzdsigma": _FunctionInfo(
+        "realtype *dJzdsigma, const int iz, const realtype *p, "
+        "const realtype *k, const realtype *z, const realtype *sigmaz, "
+        "const realtype *mz"
+    ),
+    "dJzdz": _FunctionInfo(
+        "realtype *dJzdz, const int iz, const realtype *p, "
+        "const realtype *k, const realtype *z, const realtype *sigmaz, "
+        "const double *mz",
+    ),
+    "Jrz": _FunctionInfo(
+        "realtype *Jrz, const int iz, const realtype *p, "
+        "const realtype *k, const realtype *rz, const realtype *sigmaz"
+    ),
+    "dJrzdsigma": _FunctionInfo(
+        "realtype *dJrzdsigma, const int iz, const realtype *p, "
+        "const realtype *k, const realtype *rz, const realtype *sigmaz"
+    ),
+    "dJrzdz": _FunctionInfo(
+        "realtype *dJrzdz, const int iz, const realtype *p, "
+        "const realtype *k, const realtype *rz, const realtype *sigmaz",
+    ),
+    "root": _FunctionInfo(
+        "realtype *root, const realtype t, const realtype *x, "
+        "const realtype *p, const realtype *k, const realtype *h, "
+        "const realtype *tcl"
+    ),
+    "dwdp": _FunctionInfo(
+        "realtype *dwdp, const realtype t, const realtype *x, "
+        "const realtype *p, const realtype *k, const realtype *h, "
+        "const realtype *w, const realtype *tcl, const realtype *dtcldp, "
+        "const realtype *spl, const realtype *sspl, bool include_static",
+        assume_pow_positivity=True,
+        sparse=True,
+    ),
+    "dwdx": _FunctionInfo(
+        "realtype *dwdx, const realtype t, const realtype *x, "
+        "const realtype *p, const realtype *k, const realtype *h, "
+        "const realtype *w, const realtype *tcl, const realtype *spl, "
+        "bool include_static",
+        assume_pow_positivity=True,
+        sparse=True,
+    ),
+    "create_splines": _FunctionInfo(
+        "const realtype *p, const realtype *k",
+        return_type="std::vector<HermiteSpline>",
+    ),
+    "spl": _FunctionInfo(generate_body=False),
+    "sspl": _FunctionInfo(generate_body=False),
+    "spline_values": _FunctionInfo(
+        "const realtype *p, const realtype *k", generate_body=False
+    ),
+    "spline_slopes": _FunctionInfo(
+        "const realtype *p, const realtype *k", generate_body=False
+    ),
+    "dspline_valuesdp": _FunctionInfo(
+        "realtype *dspline_valuesdp, const realtype *p, const realtype *k, "
+        "const int ip"
+    ),
+    "dspline_slopesdp": _FunctionInfo(
+        "realtype *dspline_slopesdp, const realtype *p, const realtype *k, "
+        "const int ip"
+    ),
+    "dwdw": _FunctionInfo(
+        "realtype *dwdw, const realtype t, const realtype *x, "
+        "const realtype *p, const realtype *k, const realtype *h, "
+        "const realtype *w, const realtype *tcl, bool include_static",
+        assume_pow_positivity=True,
+        sparse=True,
+    ),
+    "dxdotdw": _FunctionInfo(
+        "realtype *dxdotdw, const realtype t, const realtype *x, "
+        "const realtype *p, const realtype *k, const realtype *h, "
+        "const realtype *w",
+        "realtype *dxdotdw, const realtype t, const realtype *x, "
+        "const realtype *p, const realtype *k, const realtype *h, "
+        "const realtype *dx, const realtype *w",
+        assume_pow_positivity=True,
+        sparse=True,
+    ),
+    "dxdotdx_explicit": _FunctionInfo(
+        "realtype *dxdotdx_explicit, const realtype t, "
+        "const realtype *x, const realtype *p, const realtype *k, "
+        "const realtype *h, const realtype *w",
+        "realtype *dxdotdx_explicit, const realtype t, "
+        "const realtype *x, const realtype *p, const realtype *k, "
+        "const realtype *h, const realtype *dx, const realtype *w",
+        assume_pow_positivity=True,
+        sparse=True,
+    ),
+    "dxdotdp_explicit": _FunctionInfo(
+        "realtype *dxdotdp_explicit, const realtype t, "
+        "const realtype *x, const realtype *p, const realtype *k, "
+        "const realtype *h, const realtype *w",
+        "realtype *dxdotdp_explicit, const realtype t, "
+        "const realtype *x, const realtype *p, const realtype *k, "
+        "const realtype *h, const realtype *dx, const realtype *w",
+        assume_pow_positivity=True,
+        sparse=True,
+    ),
+    "dydx": _FunctionInfo(
+        "realtype *dydx, const realtype t, const realtype *x, "
+        "const realtype *p, const realtype *k, const realtype *h, "
+        "const realtype *w, const realtype *dwdx",
+    ),
+    "dydp": _FunctionInfo(
+        "realtype *dydp, const realtype t, const realtype *x, "
+        "const realtype *p, const realtype *k, const realtype *h, "
+        "const int ip, const realtype *w, const realtype *tcl, "
+        "const realtype *dtcldp, const realtype *spl, const realtype *sspl"
+    ),
+    "dzdx": _FunctionInfo(
+        "realtype *dzdx, const int ie, const realtype t, "
+        "const realtype *x, const realtype *p, const realtype *k, "
+        "const realtype *h",
+    ),
+    "dzdp": _FunctionInfo(
+        "realtype *dzdp, const int ie, const realtype t, "
+        "const realtype *x, const realtype *p, const realtype *k, "
+        "const realtype *h, const int ip",
+    ),
+    "drzdx": _FunctionInfo(
+        "realtype *drzdx, const int ie, const realtype t, "
+        "const realtype *x, const realtype *p, const realtype *k, "
+        "const realtype *h",
+    ),
+    "drzdp": _FunctionInfo(
+        "realtype *drzdp, const int ie, const realtype t, "
+        "const realtype *x, const realtype *p, const realtype *k, "
+        "const realtype *h, const int ip",
+    ),
+    "dsigmaydy": _FunctionInfo(
+        "realtype *dsigmaydy, const realtype t, const realtype *p, "
+        "const realtype *k, const realtype *y"
+    ),
+    "dsigmaydp": _FunctionInfo(
+        "realtype *dsigmaydp, const realtype t, const realtype *p, "
+        "const realtype *k, const realtype *y, const int ip",
+    ),
+    "sigmay": _FunctionInfo(
+        "realtype *sigmay, const realtype t, const realtype *p, "
+        "const realtype *k, const realtype *y",
+    ),
+    "dsigmazdp": _FunctionInfo(
+        "realtype *dsigmazdp, const realtype t, const realtype *p,"
+        " const realtype *k, const int ip",
+    ),
+    "sigmaz": _FunctionInfo(
+        "realtype *sigmaz, const realtype t, const realtype *p, "
+        "const realtype *k",
+    ),
+    "sroot": _FunctionInfo(
+        "realtype *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, "
+        "const realtype *tcl",
+        generate_body=False,
+    ),
+    "drootdt": _FunctionInfo(generate_body=False),
+    "drootdt_total": _FunctionInfo(generate_body=False),
+    "drootdp": _FunctionInfo(generate_body=False),
+    "drootdx": _FunctionInfo(generate_body=False),
+    "stau": _FunctionInfo(
+        "realtype *stau, const realtype t, const realtype *x, "
+        "const realtype *p, const realtype *k, const realtype *h, "
+        "const realtype *tcl, const realtype *sx, const int ip, "
+        "const int ie"
+    ),
+    "deltax": _FunctionInfo(
+        "double *deltax, const realtype t, const realtype *x, "
+        "const realtype *p, const realtype *k, const realtype *h, "
+        "const int ie, const realtype *xdot, const realtype *xdot_old"
+    ),
+    "ddeltaxdx": _FunctionInfo(generate_body=False),
+    "ddeltaxdt": _FunctionInfo(generate_body=False),
+    "ddeltaxdp": _FunctionInfo(generate_body=False),
+    "deltasx": _FunctionInfo(
+        "realtype *deltasx, const realtype t, const realtype *x, "
+        "const realtype *p, const realtype *k, const realtype *h, "
+        "const realtype *w, const int ip, const int ie, "
+        "const realtype *xdot, const realtype *xdot_old, "
+        "const realtype *sx, const realtype *stau, const realtype *tcl"
+    ),
+    "w": _FunctionInfo(
+        "realtype *w, const realtype t, const realtype *x, "
+        "const realtype *p, const realtype *k, "
+        "const realtype *h, const realtype *tcl, const realtype *spl, "
+        "bool include_static",
+        assume_pow_positivity=True,
+    ),
+    "x0": _FunctionInfo(
+        "realtype *x0, const realtype t, const realtype *p, "
+        "const realtype *k"
+    ),
+    "x0_fixedParameters": _FunctionInfo(
+        "realtype *x0_fixedParameters, const realtype t, "
+        "const realtype *p, const realtype *k, "
+        "gsl::span<const int> reinitialization_state_idxs",
+    ),
+    "sx0": _FunctionInfo(
+        "realtype *sx0, const realtype t, const realtype *x, "
+        "const realtype *p, const realtype *k, const int ip",
+    ),
+    "sx0_fixedParameters": _FunctionInfo(
+        "realtype *sx0_fixedParameters, const realtype t, "
+        "const realtype *x0, const realtype *p, const realtype *k, "
+        "const int ip, gsl::span<const int> reinitialization_state_idxs",
+    ),
+    "xdot": _FunctionInfo(
+        "realtype *xdot, const realtype t, const realtype *x, "
+        "const realtype *p, const realtype *k, const realtype *h, "
+        "const realtype *w",
+        "realtype *xdot, const realtype t, const realtype *x, "
+        "const realtype *p, const realtype *k, const realtype *h, "
+        "const realtype *dx, const realtype *w",
+        assume_pow_positivity=True,
+    ),
+    "xdot_old": _FunctionInfo(generate_body=False),
+    "y": _FunctionInfo(
+        "realtype *y, const realtype t, const realtype *x, "
+        "const realtype *p, const realtype *k, "
+        "const realtype *h, const realtype *w",
+    ),
+    "x_rdata": _FunctionInfo(
+        "realtype *x_rdata, const realtype *x, const realtype *tcl, "
+        "const realtype *p, const realtype *k"
+    ),
+    "total_cl": _FunctionInfo(
+        "realtype *total_cl, const realtype *x_rdata, "
+        "const realtype *p, const realtype *k"
+    ),
+    "dtotal_cldp": _FunctionInfo(
+        "realtype *dtotal_cldp, const realtype *x_rdata, "
+        "const realtype *p, const realtype *k, const int ip"
+    ),
+    "dtotal_cldx_rdata": _FunctionInfo(
+        "realtype *dtotal_cldx_rdata, const realtype *x_rdata, "
+        "const realtype *p, const realtype *k, const realtype *tcl",
+        sparse=True,
+    ),
+    "x_solver": _FunctionInfo("realtype *x_solver, const realtype *x_rdata"),
+    "dx_rdatadx_solver": _FunctionInfo(
+        "realtype *dx_rdatadx_solver, const realtype *x, "
+        "const realtype *tcl, const realtype *p, const realtype *k",
+        sparse=True,
+    ),
+    "dx_rdatadp": _FunctionInfo(
+        "realtype *dx_rdatadp, const realtype *x, "
+        "const realtype *tcl, const realtype *p, const realtype *k, "
+        "const int ip"
+    ),
+    "dx_rdatadtcl": _FunctionInfo(
+        "realtype *dx_rdatadtcl, const realtype *x, "
+        "const realtype *tcl, const realtype *p, const realtype *k",
+        sparse=True,
+    ),
+    "z": _FunctionInfo(
+        "realtype *z, const int ie, const realtype t, const realtype *x, "
+        "const realtype *p, const realtype *k, const realtype *h"
+    ),
+    "rz": _FunctionInfo(
+        "realtype *rz, const int ie, const realtype t, const realtype *x, "
+        "const realtype *p, const realtype *k, const realtype *h"
+    ),
+}
+
+#: list of sparse functions
+sparse_functions = [
+    func_name for func_name, func_info in functions.items() if func_info.sparse
+]
+
+#: list of nobody functions
+nobody_functions = [
+    func_name
+    for func_name, func_info in functions.items()
+    if not func_info.generate_body
+]
+
+#: list of sensitivity functions
+sensi_functions = [
+    func_name
+    for func_name, func_info in functions.items()
+    if "const int ip" in func_info.arguments()
+]
+
+#: list of sparse sensitivity functions
+sparse_sensi_functions = [
+    func_name
+    for func_name, func_info in functions.items()
+    if "const int ip" not in func_info.arguments()
+    and func_name.endswith("dp")
+    or func_name.endswith("dp_explicit")
+]
+
+#: list of event functions
+event_functions = [
+    func_name
+    for func_name, func_info in functions.items()
+    if "const int ie" in func_info.arguments()
+    and "const int ip" not in func_info.arguments()
+]
+
+#: list of event sensitivity functions
+event_sensi_functions = [
+    func_name
+    for func_name, func_info in functions.items()
+    if "const int ie" in func_info.arguments()
+    and "const int ip" in func_info.arguments()
+]
+
+#: list of multiobs functions
+multiobs_functions = [
+    func_name
+    for func_name, func_info in functions.items()
+    if "const int iy" in func_info.arguments()
+    or "const int iz" in func_info.arguments()
+]