Port matlab test models to Python

.gitattributes

@@ -0,0 +1 @@
+tests/cpp/expected_results_py.h5 filter=lfs diff=lfs merge=lfs -text

.github/workflows/test_python_cplusplus.yml

@@ -32,6 +32,8 @@ jobs:
         python-version: ${{ matrix.python-version }}
 
     - uses: actions/checkout@v4
+      with:
+        lfs: true
     - run: git fetch --prune --unshallow
 
     - run: echo "AMICI_DIR=$(pwd)" >> $GITHUB_ENV
@@ -253,6 +255,9 @@ jobs:
         python-version: "3.11"
 
     - uses: actions/checkout@v4
+      with:
+        lfs: true
+
     - run: git fetch --prune --unshallow
 
     - name: Install dependencies
@@ -315,6 +320,8 @@ jobs:
         python-version: "3.11"
 
     - uses: actions/checkout@v4
+      with:
+        lfs: true
     - run: git fetch --prune --unshallow
 
     - name: Install dependencies

.github/workflows/test_python_ver_matrix.yml

@@ -38,6 +38,7 @@ jobs:
     - uses: actions/checkout@v4
       with:
         fetch-depth: 20
+        lfs: true
 
     - name: Install apt dependencies
       uses: ./.github/actions/install-apt-dependencies

.github/workflows/test_windows.yml

@@ -32,6 +32,8 @@ jobs:
         python-version: ${{ matrix.python-version }}
 
     - uses: actions/checkout@v4
+      with:
+        lfs: true
     - run: git fetch --prune --unshallow
 
     - shell: bash

models/model_calvetti_py/.gitignore

@@ -0,0 +1 @@
+**

models/model_calvetti_py/CMakeLists.txt

@@ -0,0 +1,151 @@
+# Build AMICI model
+cmake_minimum_required(VERSION 3.22)
+cmake_policy(VERSION 3.22...3.31)
+
+project(model_calvetti_py)
+
+set(CMAKE_CXX_STANDARD 17)
+set(CMAKE_CXX_STANDARD_REQUIRED ON)
+set(CMAKE_POSITION_INDEPENDENT_CODE ON)
+
+include(CheckCXXCompilerFlag)
+set(MY_CXX_FLAGS -Wall -Wno-unused-function -Wno-unused-variable)
+if(CMAKE_CXX_COMPILER_ID STREQUAL "GNU")
+  list(APPEND MY_CXX_FLAGS -Wno-unused-but-set-variable)
+endif()
+foreach(flag ${MY_CXX_FLAGS})
+  unset(CUR_FLAG_SUPPORTED CACHE)
+  check_cxx_compiler_flag(${flag} CUR_FLAG_SUPPORTED)
+  if(${CUR_FLAG_SUPPORTED})
+    string(APPEND CMAKE_CXX_FLAGS " ${flag}")
+  endif()
+endforeach()
+
+if(DEFINED ENV{AMICI_CXXFLAGS})
+  message(STATUS "Appending flags from AMICI_CXXFLAGS: $ENV{AMICI_CXXFLAGS}")
+  add_compile_options("$ENV{AMICI_CXXFLAGS}")
+endif()
+if(DEFINED ENV{AMICI_LDFLAGS})
+  message(STATUS "Appending flags from AMICI_LDFLAGS: $ENV{AMICI_LDFLAGS}")
+  link_libraries("$ENV{AMICI_LDFLAGS}")
+endif()
+
+find_package(Amici 0.33.0 REQUIRED HINTS
+             ${CMAKE_CURRENT_LIST_DIR}/../../build)
+message(STATUS "Found AMICI ${Amici_DIR}")
+set_target_properties(Upstream::amici PROPERTIES
+    MAP_IMPORTED_CONFIG_RELWITHDEBINFO RelWithDebInfo;Release;
+    MAP_IMPORTED_CONFIG_RELEASE Release
+    MAP_IMPORTED_CONFIG_DEBUG Debug;RelWithDebInfo;)
+
+# Debug build?
+if("$ENV{ENABLE_AMICI_DEBUGGING}" OR "$ENV{ENABLE_GCOV_COVERAGE}")
+  add_compile_options(-UNDEBUG)
+  if(MSVC)
+    add_compile_options(-DEBUG)
+  else()
+    add_compile_options(-O0 -g)
+  endif()
+endif()
+
+# coverage options
+if($ENV{ENABLE_GCOV_COVERAGE})
+  string(APPEND CMAKE_CXX_FLAGS_DEBUG " --coverage")
+  string(APPEND CMAKE_EXE_LINKER_FLAGS_DEBUG " --coverage")
+endif()
+
+set(MODEL_DIR ${CMAKE_CURRENT_LIST_DIR})
+
+set(SRC_LIST_LIB Jy.cpp 
+Jy.h 
+create_splines.cpp 
+dJydsigma.cpp 
+dJydy.cpp 
+dJydy.h 
+dwdw.cpp 
+dwdw.h 
+dwdx.cpp 
+dwdx.h 
+dx.h 
+dxdotdw.cpp 
+dxdotdw.h 
+dxdotdx_explicit.cpp 
+dxdotdx_explicit.h 
+dydx.cpp 
+h.h 
+k.h 
+model_calvetti_py.cpp 
+model_calvetti_py.h 
+my.h 
+root.cpp 
+sigmay.cpp 
+sigmay.h 
+sx.h 
+w.cpp 
+w.h 
+wrapfunctions.cpp 
+wrapfunctions.h 
+x.h 
+x0.cpp 
+x0_fixedParameters.cpp 
+xB.h 
+x_old.h 
+x_rdata.cpp 
+x_rdata.h 
+x_solver.cpp 
+x_solver.h 
+xdot.cpp 
+xdot.h 
+xdot_old.h 
+y.cpp 
+y.h  ${MODEL_DIR}/wrapfunctions.cpp)
+
+add_library(${PROJECT_NAME} ${SRC_LIST_LIB})
+
+# ${PROJECT_NAME} might already be "model"
+if(NOT TARGET model)
+    add_library(model ALIAS ${PROJECT_NAME})
+endif()
+
+# Some special functions require boost
+#
+# TODO: set some flag during code generation whether the given model requires
+# boost. for now, try to find it, add include directories and link against it.
+# let the compiler/linker error if it is required but not found
+find_package(Boost)
+
+target_include_directories(${PROJECT_NAME} PUBLIC "${CMAKE_CURRENT_SOURCE_DIR}")
+
+target_link_libraries(
+  ${PROJECT_NAME}
+  PUBLIC Upstream::amici
+  PRIVATE $<$<BOOL:${Boost_FOUND}>:Boost::boost>)
+
+if(NOT "${AMICI_PYTHON_BUILD_EXT_ONLY}")
+  set(SRC_LIST_EXE main.cpp)
+  add_executable(simulate_${PROJECT_NAME} ${SRC_LIST_EXE})
+  target_link_libraries(simulate_${PROJECT_NAME} ${PROJECT_NAME})
+endif()
+
+# SWIG
+option(ENABLE_SWIG "Build swig/python library?" ON)
+if(ENABLE_SWIG)
+  add_subdirectory(swig)
+endif()
+
+# <Export cmake configuration>
+include(GNUInstallDirs)
+install(
+  TARGETS ${PROJECT_NAME}
+  EXPORT ${PROJECT_NAME}Targets
+  ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR}
+  LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}
+  RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR}
+  INCLUDES
+  DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}
+  PUBLIC_HEADER DESTINATION ${CMAKE_INSTALL_INCLUDEDIR})
+export(
+  EXPORT ${PROJECT_NAME}Targets
+  FILE ${PROJECT_NAME}Config.cmake
+  NAMESPACE Upstream::)
+# </Export cmake configuration>

models/model_calvetti_py/Jy.cpp

@@ -0,0 +1,40 @@
+#include "amici/symbolic_functions.h"
+#include "amici/defines.h"
+#include "sundials/sundials_types.h"
+
+#include <gsl/gsl-lite.hpp>
+#include <algorithm>
+
+#include "k.h"
+#include "y.h"
+#include "sigmay.h"
+#include "my.h"
+
+namespace amici {
+namespace model_model_calvetti_py {
+
+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){
+    switch(iy) {
+        case 0:
+            Jy[0] = 0.5*std::log(2*amici::pi*std::pow(sigma_obs_V1, 2)) + 0.5*std::pow(-mobs_V1 + obs_V1, 2)/std::pow(sigma_obs_V1, 2);
+            break;
+        case 1:
+            Jy[0] = 0.5*std::log(2*amici::pi*std::pow(sigma_obs_V2, 2)) + 0.5*std::pow(-mobs_V2 + obs_V2, 2)/std::pow(sigma_obs_V2, 2);
+            break;
+        case 2:
+            Jy[0] = 0.5*std::log(2*amici::pi*std::pow(sigma_obs_V3, 2)) + 0.5*std::pow(-mobs_V3 + obs_V3, 2)/std::pow(sigma_obs_V3, 2);
+            break;
+        case 3:
+            Jy[0] = 0.5*std::log(2*amici::pi*std::pow(sigma_obs_f0, 2)) + 0.5*std::pow(-mobs_f0 + obs_f0, 2)/std::pow(sigma_obs_f0, 2);
+            break;
+        case 4:
+            Jy[0] = 0.5*std::log(2*amici::pi*std::pow(sigma_obs_f1, 2)) + 0.5*std::pow(-mobs_f1 + obs_f1, 2)/std::pow(sigma_obs_f1, 2);
+            break;
+        case 5:
+            Jy[0] = 0.5*std::log(2*amici::pi*std::pow(sigma_obs_f2, 2)) + 0.5*std::pow(-mobs_f2 + obs_f2, 2)/std::pow(sigma_obs_f2, 2);
+            break;
+    }
+}
+
+} // namespace model_model_calvetti_py
+} // namespace amici

models/model_calvetti_py/Jy.h

@@ -0,0 +1,6 @@
+#define Jy0 Jy[0]
+#define Jy1 Jy[1]
+#define Jy2 Jy[2]
+#define Jy3 Jy[3]
+#define Jy4 Jy[4]
+#define Jy5 Jy[5]

models/model_calvetti_py/MANIFEST.in

@@ -0,0 +1,3 @@
+include *.cpp *.h
+include CMakeLists.txt
+recursive-include swig/ *

models/model_calvetti_py/create_splines.cpp

@@ -0,0 +1,20 @@
+#include "amici/symbolic_functions.h"
+#include "amici/defines.h"
+#include "sundials/sundials_types.h"
+
+#include <gsl/gsl-lite.hpp>
+#include <algorithm>
+
+#include "amici/splinefunctions.h"
+#include <vector>
+#include "k.h"
+
+namespace amici {
+namespace model_model_calvetti_py {
+
+std::vector<HermiteSpline> create_splines_model_calvetti_py(const realtype *p, const realtype *k){
+    return {};
+}
+
+} // namespace model_model_calvetti_py
+} // namespace amici

models/model_calvetti_py/dJydsigma.cpp

@@ -0,0 +1,40 @@
+#include "amici/symbolic_functions.h"
+#include "amici/defines.h"
+#include "sundials/sundials_types.h"
+
+#include <gsl/gsl-lite.hpp>
+#include <algorithm>
+
+#include "k.h"
+#include "y.h"
+#include "sigmay.h"
+#include "my.h"
+
+namespace amici {
+namespace model_model_calvetti_py {
+
+void dJydsigma_model_calvetti_py(realtype *dJydsigma, const int iy, const realtype *p, const realtype *k, const realtype *y, const realtype *sigmay, const realtype *my){
+    switch(iy) {
+        case 0:
+            dJydsigma[0] = 1.0/sigma_obs_V1 - 1.0*std::pow(-mobs_V1 + obs_V1, 2)/std::pow(sigma_obs_V1, 3);
+            break;
+        case 1:
+            dJydsigma[1] = 1.0/sigma_obs_V2 - 1.0*std::pow(-mobs_V2 + obs_V2, 2)/std::pow(sigma_obs_V2, 3);
+            break;
+        case 2:
+            dJydsigma[2] = 1.0/sigma_obs_V3 - 1.0*std::pow(-mobs_V3 + obs_V3, 2)/std::pow(sigma_obs_V3, 3);
+            break;
+        case 3:
+            dJydsigma[3] = 1.0/sigma_obs_f0 - 1.0*std::pow(-mobs_f0 + obs_f0, 2)/std::pow(sigma_obs_f0, 3);
+            break;
+        case 4:
+            dJydsigma[4] = 1.0/sigma_obs_f1 - 1.0*std::pow(-mobs_f1 + obs_f1, 2)/std::pow(sigma_obs_f1, 3);
+            break;
+        case 5:
+            dJydsigma[5] = 1.0/sigma_obs_f2 - 1.0*std::pow(-mobs_f2 + obs_f2, 2)/std::pow(sigma_obs_f2, 3);
+            break;
+    }
+}
+
+} // namespace model_model_calvetti_py
+} // namespace amici