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Merged
dweindl merged 1 commit into from
Dec 16, 2025
Merged

Refactor names and ids #3110

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26 changes: 14 additions & 12 deletions include/amici/model.h
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Original file line number Diff line number Diff line change
Expand Up @@ -11,6 +11,8 @@
#include "amici/sundials_matrix_wrapper.h"

#include <map>
#include <span>
#include <string_view>
#include <vector>

namespace amici {
Expand Down Expand Up @@ -618,7 +620,7 @@ class Model : public AbstractModel, public ModelDimensions {
*
* @return The parameter names
*/
virtual std::vector<std::string> get_free_parameter_names() const;
virtual std::span<std::string_view const> get_free_parameter_names() const;

/**
* @brief Report whether the model has state names set.
Expand All @@ -633,14 +635,14 @@ class Model : public AbstractModel, public ModelDimensions {
*
* @return State names
*/
virtual std::vector<std::string> get_state_names() const;
virtual std::span<std::string_view const> get_state_names() const;

/**
* @brief Get names of the solver states.
*
* @return State names
*/
virtual std::vector<std::string> get_state_names_solver() const;
virtual std::span<std::string_view const> get_state_names_solver() const;

/**
* @brief Report whether the model has fixed parameter names set.
Expand All @@ -655,7 +657,7 @@ class Model : public AbstractModel, public ModelDimensions {
*
* @return Fixed parameter names
*/
virtual std::vector<std::string> get_fixed_parameter_names() const;
virtual std::span<std::string_view const> get_fixed_parameter_names() const;

/**
* @brief Report whether the model has observable names set.
Expand All @@ -670,7 +672,7 @@ class Model : public AbstractModel, public ModelDimensions {
*
* @return Observable names
*/
virtual std::vector<std::string> get_observable_names() const;
virtual std::span<std::string_view const> get_observable_names() const;

/**
* @brief Report whether the model has expression names set.
Expand All @@ -685,7 +687,7 @@ class Model : public AbstractModel, public ModelDimensions {
*
* @return Expression names
*/
virtual std::vector<std::string> get_expression_names() const;
virtual std::span<std::string_view const> get_expression_names() const;

/**
* @brief Report whether the model has parameter IDs set.
Expand All @@ -700,7 +702,7 @@ class Model : public AbstractModel, public ModelDimensions {
*
* @return Parameter IDs
*/
virtual std::vector<std::string> get_free_parameter_ids() const;
virtual std::span<std::string_view const> get_free_parameter_ids() const;

/**
* @brief Report whether the model has state IDs set.
Expand All @@ -715,14 +717,14 @@ class Model : public AbstractModel, public ModelDimensions {
*
* @return State IDs
*/
virtual std::vector<std::string> get_state_ids() const;
virtual std::span<std::string_view const> get_state_ids() const;

/**
* @brief Get IDs of the solver states.
*
* @return State IDs
*/
virtual std::vector<std::string> get_state_ids_solver() const;
virtual std::span<std::string_view const> get_state_ids_solver() const;

/**
* @brief Report whether the model has fixed parameter IDs set.
Expand All @@ -737,7 +739,7 @@ class Model : public AbstractModel, public ModelDimensions {
*
* @return Fixed parameter IDs
*/
virtual std::vector<std::string> get_fixed_parameter_ids() const;
virtual std::span<std::string_view const> get_fixed_parameter_ids() const;

/**
* @brief Report whether the model has observable IDs set.
Expand All @@ -752,7 +754,7 @@ class Model : public AbstractModel, public ModelDimensions {
*
* @return Observable IDs
*/
virtual std::vector<std::string> get_observable_ids() const;
virtual std::span<std::string_view const> get_observable_ids() const;

/**
* @brief Report whether the model has expression IDs set.
Expand All @@ -767,7 +769,7 @@ class Model : public AbstractModel, public ModelDimensions {
*
* @return Expression IDs
*/
virtual std::vector<std::string> get_expression_ids() const;
virtual std::span<std::string_view const> get_expression_ids() const;

/**
* @brief Checks whether the defined noise model is Gaussian, i.e., the nllh
Expand Down
5 changes: 5 additions & 0 deletions models/model_calvetti_py/CMakeLists.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,11 @@
cmake_minimum_required(VERSION 3.22)
cmake_policy(VERSION 3.22...3.31)

# We aren't using C++20 modules, so disable scanning for them to avoid
# clang-scan-deps-notfound errors.
# See also https://discourse.cmake.org/t/cmake-3-28-cmake-cxx-compiler-clang-scan-deps-notfound-not-found/9244/3
set(CMAKE_CXX_SCAN_FOR_MODULES OFF)

project(model_calvetti_py)

message(STATUS "CMAKE_CURRENT_SOURCE_DIR: ${CMAKE_CURRENT_SOURCE_DIR}")
Expand Down
39 changes: 29 additions & 10 deletions models/model_calvetti_py/model_calvetti_py.cpp
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Original file line number Diff line number Diff line change
@@ -1,15 +1,16 @@
#include <amici/defines.h>
#include <array>
#include <string_view>

namespace amici::model_model_calvetti_py {

// clang-format off

std::array<const char*, 0> free_parameter_names = {
extern const std::array<std::string_view const, 0> free_parameter_names = {

};

std::array<const char*, 6> fixed_parameter_names = {
extern const std::array<std::string_view const, 6> fixed_parameter_names = {
"V1ss", // k[0]
"R1ss", // k[1]
"V2ss", // k[2]
Expand All @@ -18,7 +19,7 @@ std::array<const char*, 6> fixed_parameter_names = {
"R3ss", // k[5]
};

std::array<const char*, 6> state_names = {
extern const std::array<std::string_view const, 6> state_names = {
"V1", // x_rdata[0]
"V2", // x_rdata[1]
"V3", // x_rdata[2]
Expand All @@ -27,7 +28,16 @@ std::array<const char*, 6> state_names = {
"f3", // x_rdata[5]
};

std::array<const char*, 6> observable_names = {
extern const std::array<std::string_view const, 6> state_names_solver = {
"V1", // x_solver[0]
"V2", // x_solver[1]
"V3", // x_solver[2]
"f1", // x_solver[3]
"f2", // x_solver[4]
"f3", // x_solver[5]
};

extern const std::array<std::string_view const, 6> observable_names = {
"y0", // y[0]
"y1", // y[1]
"y2", // y[2]
Expand All @@ -45,7 +55,7 @@ ObservableScaling::lin, // y[4]
ObservableScaling::lin, // y[5]
};

std::array<const char*, 16> expression_names = {
extern const std::array<std::string_view const, 16> expression_names = {
"C1ss", // w[0]
"C2ss", // w[1]
"C3ss", // w[2]
Expand All @@ -64,11 +74,11 @@ std::array<const char*, 16> expression_names = {
"rate_of_V3", // w[15]
};

std::array<const char*, 0> free_parameter_ids = {
extern const std::array<std::string_view const, 0> free_parameter_ids = {

};

std::array<const char*, 6> fixed_parameter_ids = {
extern const std::array<std::string_view const, 6> fixed_parameter_ids = {
"V1ss", // k[0]
"R1ss", // k[1]
"V2ss", // k[2]
Expand All @@ -77,7 +87,7 @@ std::array<const char*, 6> fixed_parameter_ids = {
"R3ss", // k[5]
};

std::array<const char*, 6> state_ids = {
extern const std::array<std::string_view const, 6> state_ids = {
"V1", // x_rdata[0]
"V2", // x_rdata[1]
"V3", // x_rdata[2]
Expand All @@ -86,7 +96,16 @@ std::array<const char*, 6> state_ids = {
"f3", // x_rdata[5]
};

std::array<const char*, 6> observable_ids = {
extern const std::array<std::string_view const, 6> state_ids_solver = {
"V1", // x_solver[0]
"V2", // x_solver[1]
"V3", // x_solver[2]
"f1", // x_solver[3]
"f2", // x_solver[4]
"f3", // x_solver[5]
};

extern const std::array<std::string_view const, 6> observable_ids = {
"obs_V1", // y[0]
"obs_V2", // y[1]
"obs_V3", // y[2]
Expand All @@ -95,7 +114,7 @@ std::array<const char*, 6> observable_ids = {
"obs_f2", // y[5]
};

std::array<const char*, 16> expression_ids = {
extern const std::array<std::string_view const, 16> expression_ids = {
"C1ss", // w[0]
"C2ss", // w[1]
"C3ss", // w[2]
Expand Down
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