Refactor names and ids

Refactor name and ID handling as preparation for #3107.

* Store IDs/names in const string_view array and only pass around spans to avoid always constructing new vectors
* Store solver state IDs/names arrays instead of creating them dynamically, to be compatible with the previous point
* Update tests accordingly
* Add the respective typemaps
* Regenerate test models

Author: dweindl

include/amici/model.h

@@ -11,6 +11,8 @@
 #include "amici/sundials_matrix_wrapper.h"
 
 #include <map>
+#include <span>
+#include <string_view>
 #include <vector>
 
 namespace amici {
@@ -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.
@@ -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.
@@ -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.
@@ -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.
@@ -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.
@@ -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.
@@ -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.
@@ -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.
@@ -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.
@@ -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

models/model_calvetti_py/CMakeLists.txt

@@ -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}")

models/model_calvetti_py/model_calvetti_py.cpp

@@ -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]
@@ -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]
@@ -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]
@@ -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]
@@ -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]
@@ -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]
@@ -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]
@@ -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]