GHA: Pin python version for osx tests

.github/workflows/test_python_cplusplus.yml

@@ -143,20 +143,27 @@ jobs:
     runs-on: macos-latest
 
     steps:
+    - name: Set up Python
+      uses: actions/setup-python@v4
+      with:
+        python-version: 3.8
+
     - uses: actions/checkout@v3
     - run: git fetch --prune --unshallow
 
     - run: echo "AMICI_DIR=$(pwd)" >> $GITHUB_ENV
     - run: echo "BNGPATH=${AMICI_DIR}/ThirdParty/BioNetGen-2.7.0" >> $GITHUB_ENV
+    # Ensure CMake is using the python version that we will use for the python tests later on
+    - run: echo "PYTHON_EXECUTABLE=${Python3_ROOT_DIR}/bin/python3" >> $GITHUB_ENV
 
     # install amici dependencies
     - name: homebrew
       run: |
         brew install hdf5 swig gcc cppcheck libomp boost \
           && brew ls -v boost \
           && brew ls -v libomp \
-          && echo LDFLAGS="-L/usr/local/lib/ -L/usr/local/Cellar/boost/1.78.0_1/lib/" >> $GITHUB_ENV \
-          && echo CPPFLAGS="-I/usr/local/Cellar/boost/1.78.0_1/include/" >> $GITHUB_ENV
+          && echo LDFLAGS="-L/usr/local/lib/ -L/usr/local/Cellar/boost/1.80.0/lib/" >> $GITHUB_ENV \
+          && echo CPPFLAGS="-I/usr/local/Cellar/boost/1.80.0/include/" >> $GITHUB_ENV
 
     - name: Build AMICI
       run: |

models/model_calvetti/model_calvetti.h

@@ -1,6 +1,6 @@
 #ifndef _amici_model_calvetti_h
 #define _amici_model_calvetti_h
-/* Generated by amiwrap (R2017b) fee0d5a069aba864a92ded7da50ae68ea7ea43cc */
+/* Generated by amiwrap (R2017b) b04ab2326fb34f3721a15806d9783ff22b6a015a */
 #include <cmath>
 #include <memory>
 #include "amici/defines.h"
@@ -70,7 +70,7 @@ class Model_model_calvetti : public amici::Model_DAE {
 
     amici::Model* clone() const override { return new Model_model_calvetti(*this); };
 
-    std::string getAmiciCommit() const override { return "fee0d5a069aba864a92ded7da50ae68ea7ea43cc"; };
+    std::string getAmiciCommit() const override { return "b04ab2326fb34f3721a15806d9783ff22b6a015a"; };
 
     void fJSparse(SUNMatrixContent_Sparse JSparse, const realtype t, const realtype *x, const realtype *p, const realtype *k, const realtype *h, const realtype cj, const realtype *dx, const realtype *w, const realtype *dwdx) override {
         JSparse_model_calvetti(JSparse, t, x, p, k, h, cj, dx, w, dwdx);

models/model_calvetti/swig/CMakeLists.txt

@@ -15,12 +15,15 @@ endif(POLICY CMP0086)
 find_package(SWIG REQUIRED)
 include(${SWIG_USE_FILE})
 
+if(DEFINED ENV{PYTHON_EXECUTABLE})
+    set(Python3_EXECUTABLE $ENV{PYTHON_EXECUTABLE})
+endif()
 if(${CMAKE_VERSION} VERSION_LESS "3.12.0")
     find_package(PythonLibs REQUIRED)
     include_directories(${PYTHON_INCLUDE_DIRS})
     set(Python3_LIBRARIES ${PYTHON_LIBRARIES})
 else()
-    find_package (Python3 COMPONENTS Development)
+    find_package(Python3 COMPONENTS Interpreter Development)
     include_directories(${Python3_INCLUDE_DIRS})
 endif()
 

models/model_dirac/model_dirac.h

@@ -1,6 +1,6 @@
 #ifndef _amici_model_dirac_h
 #define _amici_model_dirac_h
-/* Generated by amiwrap (R2017b) fee0d5a069aba864a92ded7da50ae68ea7ea43cc */
+/* Generated by amiwrap (R2017b) b04ab2326fb34f3721a15806d9783ff22b6a015a */
 #include <cmath>
 #include <memory>
 #include "amici/defines.h"
@@ -70,7 +70,7 @@ class Model_model_dirac : public amici::Model_ODE {
 
     amici::Model* clone() const override { return new Model_model_dirac(*this); };
 
-    std::string getAmiciCommit() const override { return "fee0d5a069aba864a92ded7da50ae68ea7ea43cc"; };
+    std::string getAmiciCommit() const override { return "b04ab2326fb34f3721a15806d9783ff22b6a015a"; };
 
     void fJSparse(SUNMatrixContent_Sparse JSparse, const realtype t, const realtype *x, const realtype *p, const realtype *k, const realtype *h, const realtype *w, const realtype *dwdx) override {
         JSparse_model_dirac(JSparse, t, x, p, k, h, w, dwdx);

models/model_dirac/swig/CMakeLists.txt

@@ -15,12 +15,15 @@ endif(POLICY CMP0086)
 find_package(SWIG REQUIRED)
 include(${SWIG_USE_FILE})
 
+if(DEFINED ENV{PYTHON_EXECUTABLE})
+    set(Python3_EXECUTABLE $ENV{PYTHON_EXECUTABLE})
+endif()
 if(${CMAKE_VERSION} VERSION_LESS "3.12.0")
     find_package(PythonLibs REQUIRED)
     include_directories(${PYTHON_INCLUDE_DIRS})
     set(Python3_LIBRARIES ${PYTHON_LIBRARIES})
 else()
-    find_package (Python3 COMPONENTS Development)
+    find_package(Python3 COMPONENTS Interpreter Development)
     include_directories(${Python3_INCLUDE_DIRS})
 endif()
 

models/model_events/model_events.h

@@ -1,6 +1,6 @@
 #ifndef _amici_model_events_h
 #define _amici_model_events_h
-/* Generated by amiwrap (R2017b) fee0d5a069aba864a92ded7da50ae68ea7ea43cc */
+/* Generated by amiwrap (R2017b) b04ab2326fb34f3721a15806d9783ff22b6a015a */
 #include <cmath>
 #include <memory>
 #include "amici/defines.h"
@@ -84,7 +84,7 @@ class Model_model_events : public amici::Model_ODE {
 
     amici::Model* clone() const override { return new Model_model_events(*this); };
 
-    std::string getAmiciCommit() const override { return "fee0d5a069aba864a92ded7da50ae68ea7ea43cc"; };
+    std::string getAmiciCommit() const override { return "b04ab2326fb34f3721a15806d9783ff22b6a015a"; };
 
     void fJSparse(SUNMatrixContent_Sparse JSparse, const realtype t, const realtype *x, const realtype *p, const realtype *k, const realtype *h, const realtype *w, const realtype *dwdx) override {
         JSparse_model_events(JSparse, t, x, p, k, h, w, dwdx);

models/model_events/swig/CMakeLists.txt

@@ -15,12 +15,15 @@ endif(POLICY CMP0086)
 find_package(SWIG REQUIRED)
 include(${SWIG_USE_FILE})
 
+if(DEFINED ENV{PYTHON_EXECUTABLE})
+    set(Python3_EXECUTABLE $ENV{PYTHON_EXECUTABLE})
+endif()
 if(${CMAKE_VERSION} VERSION_LESS "3.12.0")
     find_package(PythonLibs REQUIRED)
     include_directories(${PYTHON_INCLUDE_DIRS})
     set(Python3_LIBRARIES ${PYTHON_LIBRARIES})
 else()
-    find_package (Python3 COMPONENTS Development)
+    find_package(Python3 COMPONENTS Interpreter Development)
     include_directories(${Python3_INCLUDE_DIRS})
 endif()
 

models/model_jakstat_adjoint/model_jakstat_adjoint.h

@@ -1,6 +1,6 @@
 #ifndef _amici_model_jakstat_adjoint_h
 #define _amici_model_jakstat_adjoint_h
-/* Generated by amiwrap (R2017b) fee0d5a069aba864a92ded7da50ae68ea7ea43cc */
+/* Generated by amiwrap (R2017b) b04ab2326fb34f3721a15806d9783ff22b6a015a */
 #include <cmath>
 #include <memory>
 #include "amici/defines.h"
@@ -73,7 +73,7 @@ class Model_model_jakstat_adjoint : public amici::Model_ODE {
 
     amici::Model* clone() const override { return new Model_model_jakstat_adjoint(*this); };
 
-    std::string getAmiciCommit() const override { return "fee0d5a069aba864a92ded7da50ae68ea7ea43cc"; };
+    std::string getAmiciCommit() const override { return "b04ab2326fb34f3721a15806d9783ff22b6a015a"; };
 
     void fJSparse(SUNMatrixContent_Sparse JSparse, const realtype t, const realtype *x, const realtype *p, const realtype *k, const realtype *h, const realtype *w, const realtype *dwdx) override {
         JSparse_model_jakstat_adjoint(JSparse, t, x, p, k, h, w, dwdx);

models/model_jakstat_adjoint/swig/CMakeLists.txt

@@ -15,12 +15,15 @@ endif(POLICY CMP0086)
 find_package(SWIG REQUIRED)
 include(${SWIG_USE_FILE})
 
+if(DEFINED ENV{PYTHON_EXECUTABLE})
+    set(Python3_EXECUTABLE $ENV{PYTHON_EXECUTABLE})
+endif()
 if(${CMAKE_VERSION} VERSION_LESS "3.12.0")
     find_package(PythonLibs REQUIRED)
     include_directories(${PYTHON_INCLUDE_DIRS})
     set(Python3_LIBRARIES ${PYTHON_LIBRARIES})
 else()
-    find_package (Python3 COMPONENTS Development)
+    find_package(Python3 COMPONENTS Interpreter Development)
     include_directories(${Python3_INCLUDE_DIRS})
 endif()
 

models/model_jakstat_adjoint_o2/model_jakstat_adjoint_o2.h

@@ -1,6 +1,6 @@
 #ifndef _amici_model_jakstat_adjoint_o2_h
 #define _amici_model_jakstat_adjoint_o2_h
-/* Generated by amiwrap (R2017b) fee0d5a069aba864a92ded7da50ae68ea7ea43cc */
+/* Generated by amiwrap (R2017b) b04ab2326fb34f3721a15806d9783ff22b6a015a */
 #include <cmath>
 #include <memory>
 #include "amici/defines.h"
@@ -73,7 +73,7 @@ class Model_model_jakstat_adjoint_o2 : public amici::Model_ODE {
 
     amici::Model* clone() const override { return new Model_model_jakstat_adjoint_o2(*this); };
 
-    std::string getAmiciCommit() const override { return "fee0d5a069aba864a92ded7da50ae68ea7ea43cc"; };
+    std::string getAmiciCommit() const override { return "b04ab2326fb34f3721a15806d9783ff22b6a015a"; };
 
     void fJSparse(SUNMatrixContent_Sparse JSparse, const realtype t, const realtype *x, const realtype *p, const realtype *k, const realtype *h, const realtype *w, const realtype *dwdx) override {
         JSparse_model_jakstat_adjoint_o2(JSparse, t, x, p, k, h, w, dwdx);

models/model_jakstat_adjoint_o2/swig/CMakeLists.txt

@@ -15,12 +15,15 @@ endif(POLICY CMP0086)
 find_package(SWIG REQUIRED)
 include(${SWIG_USE_FILE})
 
+if(DEFINED ENV{PYTHON_EXECUTABLE})
+    set(Python3_EXECUTABLE $ENV{PYTHON_EXECUTABLE})
+endif()
 if(${CMAKE_VERSION} VERSION_LESS "3.12.0")
     find_package(PythonLibs REQUIRED)
     include_directories(${PYTHON_INCLUDE_DIRS})
     set(Python3_LIBRARIES ${PYTHON_LIBRARIES})
 else()
-    find_package (Python3 COMPONENTS Development)
+    find_package(Python3 COMPONENTS Interpreter Development)
     include_directories(${Python3_INCLUDE_DIRS})
 endif()
 

models/model_nested_events/model_nested_events.h

@@ -1,6 +1,6 @@
 #ifndef _amici_model_nested_events_h
 #define _amici_model_nested_events_h
-/* Generated by amiwrap (R2017b) fee0d5a069aba864a92ded7da50ae68ea7ea43cc */
+/* Generated by amiwrap (R2017b) b04ab2326fb34f3721a15806d9783ff22b6a015a */
 #include <cmath>
 #include <memory>
 #include "amici/defines.h"
@@ -73,7 +73,7 @@ class Model_model_nested_events : public amici::Model_ODE {
 
     amici::Model* clone() const override { return new Model_model_nested_events(*this); };
 
-    std::string getAmiciCommit() const override { return "fee0d5a069aba864a92ded7da50ae68ea7ea43cc"; };
+    std::string getAmiciCommit() const override { return "b04ab2326fb34f3721a15806d9783ff22b6a015a"; };
 
     void fJSparse(SUNMatrixContent_Sparse JSparse, const realtype t, const realtype *x, const realtype *p, const realtype *k, const realtype *h, const realtype *w, const realtype *dwdx) override {
         JSparse_model_nested_events(JSparse, t, x, p, k, h, w, dwdx);

models/model_nested_events/swig/CMakeLists.txt

@@ -15,12 +15,15 @@ endif(POLICY CMP0086)
 find_package(SWIG REQUIRED)
 include(${SWIG_USE_FILE})
 
+if(DEFINED ENV{PYTHON_EXECUTABLE})
+    set(Python3_EXECUTABLE $ENV{PYTHON_EXECUTABLE})
+endif()
 if(${CMAKE_VERSION} VERSION_LESS "3.12.0")
     find_package(PythonLibs REQUIRED)
     include_directories(${PYTHON_INCLUDE_DIRS})
     set(Python3_LIBRARIES ${PYTHON_LIBRARIES})
 else()
-    find_package (Python3 COMPONENTS Development)
+    find_package(Python3 COMPONENTS Interpreter Development)
     include_directories(${Python3_INCLUDE_DIRS})
 endif()
 

models/model_neuron/model_neuron.h

@@ -1,6 +1,6 @@
 #ifndef _amici_model_neuron_h
 #define _amici_model_neuron_h
-/* Generated by amiwrap (R2017b) fee0d5a069aba864a92ded7da50ae68ea7ea43cc */
+/* Generated by amiwrap (R2017b) b04ab2326fb34f3721a15806d9783ff22b6a015a */
 #include <cmath>
 #include <memory>
 #include "amici/defines.h"
@@ -87,7 +87,7 @@ class Model_model_neuron : public amici::Model_ODE {
 
     amici::Model* clone() const override { return new Model_model_neuron(*this); };
 
-    std::string getAmiciCommit() const override { return "fee0d5a069aba864a92ded7da50ae68ea7ea43cc"; };
+    std::string getAmiciCommit() const override { return "b04ab2326fb34f3721a15806d9783ff22b6a015a"; };
 
     void fJSparse(SUNMatrixContent_Sparse JSparse, const realtype t, const realtype *x, const realtype *p, const realtype *k, const realtype *h, const realtype *w, const realtype *dwdx) override {
         JSparse_model_neuron(JSparse, t, x, p, k, h, w, dwdx);

models/model_neuron/swig/CMakeLists.txt

@@ -15,12 +15,15 @@ endif(POLICY CMP0086)
 find_package(SWIG REQUIRED)
 include(${SWIG_USE_FILE})
 
+if(DEFINED ENV{PYTHON_EXECUTABLE})
+    set(Python3_EXECUTABLE $ENV{PYTHON_EXECUTABLE})
+endif()
 if(${CMAKE_VERSION} VERSION_LESS "3.12.0")
     find_package(PythonLibs REQUIRED)
     include_directories(${PYTHON_INCLUDE_DIRS})
     set(Python3_LIBRARIES ${PYTHON_LIBRARIES})
 else()
-    find_package (Python3 COMPONENTS Development)
+    find_package(Python3 COMPONENTS Interpreter Development)
     include_directories(${Python3_INCLUDE_DIRS})
 endif()
 

models/model_neuron_o2/model_neuron_o2.h

@@ -1,6 +1,6 @@
 #ifndef _amici_model_neuron_o2_h
 #define _amici_model_neuron_o2_h
-/* Generated by amiwrap (R2017b) fee0d5a069aba864a92ded7da50ae68ea7ea43cc */
+/* Generated by amiwrap (R2017b) b04ab2326fb34f3721a15806d9783ff22b6a015a */
 #include <cmath>
 #include <memory>
 #include "amici/defines.h"
@@ -89,7 +89,7 @@ class Model_model_neuron_o2 : public amici::Model_ODE {
 
     amici::Model* clone() const override { return new Model_model_neuron_o2(*this); };
 
-    std::string getAmiciCommit() const override { return "fee0d5a069aba864a92ded7da50ae68ea7ea43cc"; };
+    std::string getAmiciCommit() const override { return "b04ab2326fb34f3721a15806d9783ff22b6a015a"; };
 
     void fJSparse(SUNMatrixContent_Sparse JSparse, const realtype t, const realtype *x, const realtype *p, const realtype *k, const realtype *h, const realtype *w, const realtype *dwdx) override {
         JSparse_model_neuron_o2(JSparse, t, x, p, k, h, w, dwdx);

models/model_neuron_o2/swig/CMakeLists.txt

@@ -15,12 +15,15 @@ endif(POLICY CMP0086)
 find_package(SWIG REQUIRED)
 include(${SWIG_USE_FILE})
 
+if(DEFINED ENV{PYTHON_EXECUTABLE})
+    set(Python3_EXECUTABLE $ENV{PYTHON_EXECUTABLE})
+endif()
 if(${CMAKE_VERSION} VERSION_LESS "3.12.0")
     find_package(PythonLibs REQUIRED)
     include_directories(${PYTHON_INCLUDE_DIRS})
     set(Python3_LIBRARIES ${PYTHON_LIBRARIES})
 else()
-    find_package (Python3 COMPONENTS Development)
+    find_package(Python3 COMPONENTS Interpreter Development)
     include_directories(${Python3_INCLUDE_DIRS})
 endif()
 

models/model_robertson/model_robertson.h

@@ -1,6 +1,6 @@
 #ifndef _amici_model_robertson_h
 #define _amici_model_robertson_h
-/* Generated by amiwrap (R2017b) fee0d5a069aba864a92ded7da50ae68ea7ea43cc */
+/* Generated by amiwrap (R2017b) b04ab2326fb34f3721a15806d9783ff22b6a015a */
 #include <cmath>
 #include <memory>
 #include "amici/defines.h"
@@ -71,7 +71,7 @@ class Model_model_robertson : public amici::Model_DAE {
 
     amici::Model* clone() const override { return new Model_model_robertson(*this); };
 
-    std::string getAmiciCommit() const override { return "fee0d5a069aba864a92ded7da50ae68ea7ea43cc"; };
+    std::string getAmiciCommit() const override { return "b04ab2326fb34f3721a15806d9783ff22b6a015a"; };
 
     void fJSparse(SUNMatrixContent_Sparse JSparse, const realtype t, const realtype *x, const realtype *p, const realtype *k, const realtype *h, const realtype cj, const realtype *dx, const realtype *w, const realtype *dwdx) override {
         JSparse_model_robertson(JSparse, t, x, p, k, h, cj, dx, w, dwdx);

models/model_robertson/swig/CMakeLists.txt

@@ -15,12 +15,15 @@ endif(POLICY CMP0086)
 find_package(SWIG REQUIRED)
 include(${SWIG_USE_FILE})
 
+if(DEFINED ENV{PYTHON_EXECUTABLE})
+    set(Python3_EXECUTABLE $ENV{PYTHON_EXECUTABLE})
+endif()
 if(${CMAKE_VERSION} VERSION_LESS "3.12.0")
     find_package(PythonLibs REQUIRED)
     include_directories(${PYTHON_INCLUDE_DIRS})
     set(Python3_LIBRARIES ${PYTHON_LIBRARIES})
 else()
-    find_package (Python3 COMPONENTS Development)
+    find_package(Python3 COMPONENTS Interpreter Development)
     include_directories(${Python3_INCLUDE_DIRS})
 endif()
 

models/model_steadystate/model_steadystate.h

@@ -1,6 +1,6 @@
 #ifndef _amici_model_steadystate_h
 #define _amici_model_steadystate_h
-/* Generated by amiwrap (R2017b) fee0d5a069aba864a92ded7da50ae68ea7ea43cc */
+/* Generated by amiwrap (R2017b) b04ab2326fb34f3721a15806d9783ff22b6a015a */
 #include <cmath>
 #include <memory>
 #include "amici/defines.h"
@@ -70,7 +70,7 @@ class Model_model_steadystate : public amici::Model_ODE {
 
     amici::Model* clone() const override { return new Model_model_steadystate(*this); };
 
-    std::string getAmiciCommit() const override { return "fee0d5a069aba864a92ded7da50ae68ea7ea43cc"; };
+    std::string getAmiciCommit() const override { return "b04ab2326fb34f3721a15806d9783ff22b6a015a"; };
 
     void fJSparse(SUNMatrixContent_Sparse JSparse, const realtype t, const realtype *x, const realtype *p, const realtype *k, const realtype *h, const realtype *w, const realtype *dwdx) override {
         JSparse_model_steadystate(JSparse, t, x, p, k, h, w, dwdx);

models/model_steadystate/swig/CMakeLists.txt

@@ -15,12 +15,15 @@ endif(POLICY CMP0086)
 find_package(SWIG REQUIRED)
 include(${SWIG_USE_FILE})
 
+if(DEFINED ENV{PYTHON_EXECUTABLE})
+    set(Python3_EXECUTABLE $ENV{PYTHON_EXECUTABLE})
+endif()
 if(${CMAKE_VERSION} VERSION_LESS "3.12.0")
     find_package(PythonLibs REQUIRED)
     include_directories(${PYTHON_INCLUDE_DIRS})
     set(Python3_LIBRARIES ${PYTHON_LIBRARIES})
 else()
-    find_package (Python3 COMPONENTS Development)
+    find_package(Python3 COMPONENTS Interpreter Development)
     include_directories(${Python3_INCLUDE_DIRS})
 endif()
 

python/CMakeLists.txt

@@ -1,11 +1,10 @@
+if(DEFINED ENV{PYTHON_EXECUTABLE})
+    set(Python3_EXECUTABLE $ENV{PYTHON_EXECUTABLE})
+endif()
 if(${CMAKE_VERSION} VERSION_LESS "3.12.0")
-    if(DEFINED ENV{PYTHON_EXECUTABLE})
-        set( PYTHON_EXECUTABLE $ENV{PYTHON_EXECUTABLE} )
-    endif()
     find_package(PythonInterp 3.8 REQUIRED)
-    set(Python3_EXECUTABLE ${PYTHON_EXECUTABLE})
 else()
-    find_package (Python3 COMPONENTS Interpreter)
+    find_package(Python3 COMPONENTS Interpreter)
 endif()