Merge 49b4d53 into 2a6aad9

CMakeLists.txt

@@ -31,6 +31,7 @@ option(USE_PREBUILT_LLVMCLANG_PACKAGE "Use the pre-built version of the LLVMClan
 option(USE_PREBUILT_OAUTH_PACKAGE "Use the pre-built version of the OAuth package" ON)
 option(USE_PREBUILT_OPENSSL_PACKAGE "Use the pre-built version of the OpenSSL package" ON)
 option(USE_PREBUILT_PYTHON_PACKAGES_PACKAGE "Use the pre-built version of various Python packages" ON)
+option(USE_PREBUILT_PYTHONQT_PACKAGE "Use the pre-built version of the PythonQt package" ON)
 option(USE_PREBUILT_QSCINTILLA_PACKAGE "Use the pre-built version of the QScintilla package" ON)
 option(USE_PREBUILT_QWT_PACKAGE "Use the pre-built version of the Qwt package" ON)
 option(USE_PREBUILT_SUNDIALS_PACKAGE "Use the pre-built version of the SUNDIALS package" ON)
@@ -620,6 +621,13 @@ configure_file(${CMAKE_SOURCE_DIR}/res/common.qrc.in
 configure_file(${CMAKE_SOURCE_DIR}/res/i18n.qrc.in
                ${I18N_QRC_FILENAME})
 
+# The Python interface depends on Python headers, so we only include it if we
+# are using the prebuilt version of our Python and QtWebKit packages
+
+if(USE_PREBUILT_PYTHON_AND_QTWEBKIT_PACKAGES)
+    set(PYTHON_INTERFACE_FILENAME src/plugins/pythoninterface.cpp)
+endif()
+
 # Files that make up the GUI version of OpenCOR
 
 set(SOURCES
@@ -648,6 +656,7 @@ set(SOURCES
     src/plugins/plugininterface.cpp
     src/plugins/pluginmanager.cpp
     src/plugins/preferencesinterface.cpp
+    ${PYTHON_INTERFACE_FILENAME}
     src/plugins/solverinterface.cpp
     src/plugins/viewinterface.cpp
     src/plugins/windowinterface.cpp
@@ -685,6 +694,7 @@ if(WIN32)
         src/plugins/plugininfo.cpp
         src/plugins/plugininterface.cpp
         src/plugins/pluginmanager.cpp
+        ${PYTHON_INTERFACE_FILENAME}
         src/plugins/solverinterface.cpp
 
         src/windows/main.cpp
@@ -865,6 +875,7 @@ if(USE_PREBUILT_QTWEBKIT_PACKAGE)
         list(APPEND PLUGINS
             thirdParty/libSBML
             thirdParty/PythonPackages
+            thirdParty/PythonQtAPI
 
             dataStore/BioSignalMLDataStore
             dataStore/CSVDataStore
@@ -882,6 +893,9 @@ if(USE_PREBUILT_QTWEBKIT_PACKAGE)
             miscellaneous/Compiler
             miscellaneous/Core
             miscellaneous/HelpWindow
+            miscellaneous/JupyterKernel
+            miscellaneous/PythonQtConsoleWindow
+            miscellaneous/PythonShell
             miscellaneous/WebBrowserWindow
 
             organisation/FileBrowserWindow
@@ -901,6 +915,8 @@ if(USE_PREBUILT_QTWEBKIT_PACKAGE)
             support/CellMLSupport
             support/COMBINESupport
             support/PMRSupport
+            support/PythonSupport
+            support/PythonQtSupport
             support/SEDMLSupport
             support/SimulationSupport
             support/StandardSupport
@@ -958,6 +974,10 @@ if(USE_PREBUILT_QTWEBKIT_PACKAGE)
             add_definitions(-DENABLE_TEST_PLUGINS)
         endif()
 
+        # Let OpenCOR know that we want Python support
+
+        add_definitions(-DPYTHON_SUPPORT)
+
         # Let OpenCOR know about the prebuilt version of our QtWebKit package
         # being used
 
@@ -1013,6 +1033,13 @@ add_definitions(-D${CMAKE_PROJECT_NAME}_MAIN)
 
 target_compile_definitions(${CMAKE_PROJECT_NAME} PRIVATE GUI_SUPPORT)
 
+# We can't compile Python interface code until after the Python headers are in
+# place
+
+if(NOT "${PYTHON_DEPENDENCIES}" STREQUAL "")
+    add_dependencies(${CMAKE_PROJECT_NAME} ${PYTHON_DEPENDENCIES})
+endif()
+
 set_target_properties(${CMAKE_PROJECT_NAME} PROPERTIES
     OUTPUT_NAME ${CMAKE_PROJECT_NAME}
     LINK_FLAGS "${LINK_FLAGS_PROPERTIES}"
@@ -1023,6 +1050,7 @@ configure_clang_and_clang_tidy(${CMAKE_PROJECT_NAME})
 if(WIN32)
     target_link_libraries(${CMAKE_PROJECT_NAME}
         ${Qt5Core_QTMAIN_LIBRARIES}
+        ${PYTHON_LIBRARY}
     )
 endif()
 
@@ -1032,6 +1060,16 @@ foreach(REQUIRED_QT_MODULE ${REQUIRED_QT_MODULES})
     )
 endforeach()
 
+# Under Linux, the Python package needs linking directly to the executable as
+# otherwise extension DSOs (which are loaded using dlopen()) can't find symbols
+# (see https://www.akkadia.org/drepper/dsohowto.pdf for details)
+
+if(NOT WIN32 AND NOT APPLE)
+    include_directories(${PYTHON_INCLUDE_DIR})
+    target_link_libraries(${CMAKE_PROJECT_NAME} ${PYTHON_LIBRARY})
+    add_dependencies(${CMAKE_PROJECT_NAME} PythonPlugin)
+endif()
+
 # Build the CLI version of OpenCOR (Windows specific)
 # Note: when it comes to WINDOWS_CLI_PROJECT_NAME, we used to have it set to
 #       ${CMAKE_PROJECT_NAME}.com, but Ninja found a duplicate rule (from a copy
@@ -1045,6 +1083,17 @@ if(WIN32)
         ${WINDOWS_CLI_RESOURCES}
     )
 
+    # We can't compile Python interface code until after the Python headers are
+    # in place
+
+    if(NOT "${PYTHON_DEPENDENCIES}" STREQUAL "")
+        add_dependencies(${WINDOWS_CLI_PROJECT_NAME} ${PYTHON_DEPENDENCIES})
+    endif()
+
+    target_link_libraries(${WINDOWS_CLI_PROJECT_NAME}
+        ${PYTHON_LIBRARY}
+    )
+
     set_target_properties(${WINDOWS_CLI_PROJECT_NAME} PROPERTIES
         LINK_FLAGS "${LINK_FLAGS_PROPERTIES}"
     )
@@ -1267,6 +1316,28 @@ if(WIN32)
     windows_deploy_qt_plugin(sqldrivers qsqlite)
     windows_deploy_qt_plugin(styles qwindowsvistastyle)
 
+    # Python runtime libraries and utilities
+
+    INSTALL(DIRECTORY ${PROJECT_BUILD_DIR}/Python
+            DESTINATION .)
+
+    # Scripts to setup and run Python and Jupyter
+
+    set(RUN_PYTHON_FILENAME "${PROJECT_BUILD_DIR}/run_python.bat")
+    configure_file(${CMAKE_SOURCE_DIR}/distrib/windows/run_python.bat.in
+                   ${RUN_PYTHON_FILENAME})
+
+    install(FILES ${CMAKE_SOURCE_DIR}/distrib/windows/IPython.bat
+                  ${CMAKE_SOURCE_DIR}/distrib/windows/JupyterLab.bat
+                  ${CMAKE_SOURCE_DIR}/distrib/windows/Notebook.bat
+                  ${CMAKE_SOURCE_DIR}/distrib/windows/run_jupyter.bat
+                  ${CMAKE_SOURCE_DIR}/distrib/windows/set_python_path.bat
+                  ${RUN_PYTHON_FILENAME}
+            DESTINATION .)
+
+    install(FILES ${CMAKE_SOURCE_DIR}/distrib/windows/start_jupyter.py
+            DESTINATION ./Python/Scripts)
+
     # Batch and VBScript files to run OpenCOR (useful when downloading a ZIPped
     # version of OpenCOR)
 
@@ -1299,6 +1370,12 @@ if(WIN32)
             \\\${UnregisterExtension} \\\".cellml\\\" \\\"CellML File\\\"
             System::Call \\\"Shell32::SHChangeNotify(i 0x08000000, i 0, i 0, i 0)\\\"
         ")
+
+        # Update Python scripts to refer to our installed Python
+
+        set(CPACK_NSIS_EXTRA_INSTALL_COMMANDS
+           "${CPACK_NSIS_EXTRA_INSTALL_COMMANDS} Exec '\\\"\\\$INSTDIR\\\\Python\\\\bin\\\\python.exe\\\" \\\"\\\$INSTDIR\\\\Python\\\\Scripts\\\\set_python_path.py\\\" \\\"\\\$INSTDIR\\\\Python\\\" -s'
+        ")
     endif()
 elseif(APPLE)
     # Select PackageMaker and ZIP as the packagers on macOS
@@ -1317,6 +1394,29 @@ elseif(APPLE)
     install(TARGETS ${CMAKE_PROJECT_NAME} BUNDLE
             DESTINATION .)
 
+    # Shell scripts to setup and run Python and Jupyter
+
+    set(RUN_JUPYTER_FILENAME ${PROJECT_BUILD_DIR}/run_jupyter.sh)
+    configure_file(${CMAKE_SOURCE_DIR}/distrib/macos/run_jupyter.sh.in
+                   ${RUN_JUPYTER_FILENAME} @ONLY)
+
+    set(RUN_PYTHON_FILENAME ${PROJECT_BUILD_DIR}/run_python.sh)
+    configure_file(${CMAKE_SOURCE_DIR}/distrib/macos/run_python.sh.in
+                   ${RUN_PYTHON_FILENAME} @ONLY)
+
+    set(SET_PYTHON_PATH_FILENAME ${PROJECT_BUILD_DIR}/set_python_path.sh)
+    configure_file(${CMAKE_SOURCE_DIR}/distrib/macos/set_python_path.sh.in
+                   ${SET_PYTHON_PATH_FILENAME} @ONLY)
+
+    install(FILES ${CMAKE_SOURCE_DIR}/distrib/macos/ipython.sh
+                  ${CMAKE_SOURCE_DIR}/distrib/macos/jupyterlab.sh
+                  ${CMAKE_SOURCE_DIR}/distrib/macos/notebook.sh
+                  ${RUN_JUPYTER_FILENAME}
+                  ${RUN_PYTHON_FILENAME}
+                  ${SET_PYTHON_PATH_FILENAME}
+            DESTINATION .
+            PERMISSIONS OWNER_READ OWNER_WRITE OWNER_EXECUTE GROUP_READ GROUP_EXECUTE WORLD_READ WORLD_EXECUTE)
+
     # Shell script to run OpenCOR (useful when downloading a ZIPped version of
     # OpenCOR)
 
@@ -1384,6 +1484,28 @@ else()
     linux_deploy_qt_plugin(sqldrivers qsqlite)
     linux_deploy_qt_plugin(xcbglintegrations qxcb-egl-integration qxcb-glx-integration)
 
+
+    # Python runtime libraries and utilities
+
+    INSTALL(DIRECTORY ${PROJECT_BUILD_DIR}/python
+            DESTINATION .
+            USE_SOURCE_PERMISSIONS)
+
+    # Shell scripts to setup and run Python and Jupyter
+
+    set(RUN_PYTHON_FILENAME ${PROJECT_BUILD_DIR}/run_python.sh)
+    configure_file(${CMAKE_SOURCE_DIR}/distrib/linux/run_python.sh.in
+                   ${RUN_PYTHON_FILENAME} @ONLY)
+
+    install(FILES ${CMAKE_SOURCE_DIR}/distrib/linux/ipython.sh
+                  ${CMAKE_SOURCE_DIR}/distrib/linux/jupyterlab.sh
+                  ${CMAKE_SOURCE_DIR}/distrib/linux/notebook.sh
+                  ${CMAKE_SOURCE_DIR}/distrib/linux/run_jupyter.sh
+                  ${CMAKE_SOURCE_DIR}/distrib/linux/set_python_path.sh
+                  ${RUN_PYTHON_FILENAME}
+            DESTINATION .
+            PERMISSIONS OWNER_READ OWNER_WRITE OWNER_EXECUTE GROUP_READ GROUP_EXECUTE WORLD_READ WORLD_EXECUTE)
+
     # Shell script to run OpenCOR
 
     set(SH_FILENAME ${PROJECT_BUILD_DIR}/${CMAKE_PROJECT_NAME}.sh)

cmake/common.cmake

@@ -138,6 +138,10 @@ macro(build_documentation DOCUMENTATION_NAME)
                                                    ${PROJECT_BUILD_DIR}/doc/${DOCUMENTATION_NAME}
         )
 
+        # Make our local target depend on having Python fully installed
+
+        add_dependencies(${DOCUMENTATION_BUILD} ${PYTHON_DEPENDENCIES})
+
         # Make our local target depend on our project build target and make our
         # documentation build target depend on our local target
 
@@ -188,6 +192,7 @@ macro(add_plugin PLUGIN_NAME)
         SYSTEM_BINARIES
         DEPENDS_ON
         TESTS
+        BYPRODUCTS
     )
 
     cmake_parse_arguments(ARG "${OPTIONS}" "${ONE_VALUE_KEYWORDS}" "${MULTI_VALUE_KEYWORDS}" ${ARGN})
@@ -276,22 +281,28 @@ macro(add_plugin PLUGIN_NAME)
         )
     endforeach()
 
-    # External binaries
-
-    if(NOT "${ARG_EXTERNAL_BINARIES_DIR}" STREQUAL "")
-        # Create a custom target for copying binaries
+    IF((NOT "${ARG_EXTERNAL_BINARIES_DIR}" STREQUAL "")
+    OR (    NOT "${ARG_EXTERNAL_DESTINATION_DIR}" STREQUAL ""
+        AND NOT "${ARG_EXTERNAL_SOURCE_DIR}" STREQUAL ""))
+        # Create a custom target for installing files
         # Note: this is to prevent Ninja from getting confused with circular
         #       references...
+        # Note: we use this target in the PythonQtAPI build script when setting
+        #       the PYTHON_DEPENDENCIES list
 
-        set(COPY_EXTERNAL_BINARIES_TARGET "COPY_${PROJECT_NAME}_EXTERNAL_BINARIES")
+        SET(INSTALL_EXTERNAL_FILES_TARGET "${PROJECT_NAME}_INSTALL_EXTERNAL_FILES")
 
-        add_custom_target(${COPY_EXTERNAL_BINARIES_TARGET})
-        add_dependencies(${PROJECT_NAME} ${COPY_EXTERNAL_BINARIES_TARGET})
+        ADD_CUSTOM_TARGET(${INSTALL_EXTERNAL_FILES_TARGET})
+        ADD_DEPENDENCIES(${PROJECT_NAME} ${INSTALL_EXTERNAL_FILES_TARGET})
 
-        if(NOT "${ARG_DEPENDS_ON}" STREQUAL "")
-            add_dependencies(${COPY_EXTERNAL_BINARIES_TARGET} ${ARG_DEPENDS_ON})
-        endif()
+        IF(NOT "${ARG_DEPENDS_ON}" STREQUAL "")
+            ADD_DEPENDENCIES(${INSTALL_EXTERNAL_FILES_TARGET} ${ARG_DEPENDS_ON})
+        ENDIF()
+    ENDIF()
+
+    # External binaries
 
+    if(NOT "${ARG_EXTERNAL_BINARIES_DIR}" STREQUAL "")
         foreach(ARG_EXTERNAL_BINARY ${ARG_EXTERNAL_BINARIES})
             # Make sure that the external binary exists
 
@@ -304,7 +315,7 @@ macro(add_plugin PLUGIN_NAME)
                AND "${ARG_DEPENDS_ON}" STREQUAL "")
                 set(COPY_TARGET DIRECT)
             else()
-                set(COPY_TARGET ${COPY_EXTERNAL_BINARIES_TARGET})
+                set(COPY_TARGET ${INSTALL_EXTERNAL_FILES_TARGET})
             endif()
 
             # Copy the external binary to its destination directory, so we can
@@ -376,9 +387,10 @@ macro(add_plugin PLUGIN_NAME)
 
         # Copy the entire source directory to the destination
 
-        add_custom_command(TARGET ${PROJECT_NAME} POST_BUILD
+        add_custom_command(TARGET ${INSTALL_EXTERNAL_FILES_TARGET}
                            COMMAND ${CMAKE_COMMAND} -E copy_directory ${ARG_EXTERNAL_SOURCE_DIR}
-                                                                      ${ARG_EXTERNAL_DESTINATION_DIR})
+                                                                      ${ARG_EXTERNAL_DESTINATION_DIR}
+                           BYPRODUCTS ${ARG_BYPRODUCTS})
     endif()
 
     # System binaries

distrib/linux/application.sh.in

@@ -1,3 +1,5 @@
 #!/bin/sh
 
-bin/${CMAKE_PROJECT_NAME} $*
+OPENCOR_DIR="$(cd "$(dirname "$0")"; pwd)"
+
+${OPENCOR_DIR}/bin/@CMAKE_PROJECT_NAME@ $*

distrib/linux/ipython.sh

@@ -0,0 +1,9 @@
+#!/bin/sh
+
+# Get the script's directory, which should be OpenCOR's base directory
+
+OPENCOR_DIR="$(cd "$(dirname "$0")"; pwd)"
+
+# Start an IPython console attached to an OpenCOR kernel
+
+${OPENCOR_DIR}/run_jupyter.sh console --kernel OpenCOR $*

distrib/linux/jupyterlab.sh

@@ -0,0 +1,9 @@
+#!/bin/sh
+
+# Get the script's directory, which should be OpenCOR's base directory
+
+OPENCOR_DIR="$(cd "$(dirname "$0")"; pwd)"
+
+# Start Jupyter Lab
+
+${OPENCOR_DIR}/run_jupyter.sh lab --ip 127.0.0.1 $*

distrib/linux/notebook.sh

@@ -0,0 +1,9 @@
+#!/bin/sh
+
+# Get the script's directory, which should be OpenCOR's base directory
+
+OPENCOR_DIR="$(cd "$(dirname "$0")"; pwd)"
+
+# Start Jupyter notebook
+
+${OPENCOR_DIR}/run_jupyter.sh notebook --ip 127.0.0.1 $*

distrib/linux/run_jupyter.sh

@@ -0,0 +1,17 @@
+#!/bin/sh
+
+# Get the script's directory, which should be OpenCOR's base directory
+
+OPENCOR_DIR="$(cd "$(dirname "$0")"; pwd)"
+
+# Make sure the path to Python is correct before starting Jupyter
+
+${OPENCOR_DIR}/set_python_path.sh
+
+# Make sure we can find the OpenCOR application to run as a Jupyter kernel
+
+export PATH=${OPENCOR_DIR}:$PATH
+
+# Start Jupyter
+
+${OPENCOR_DIR}/python/bin/jupyter $*

distrib/linux/run_python.sh.in

@@ -0,0 +1,13 @@
+#!/bin/sh
+
+# Get the script's directory, which should be OpenCOR's base directory
+
+OPENCOR_DIR="$(cd "$(dirname "$0")"; pwd)"
+
+# Make sure the path to Python is correct before starting Jupyter
+
+${OPENCOR_DIR}/set_python_path.sh
+
+# Start the OpenCOR plugin that runs Python code
+
+${OPENCOR_DIR}/bin/@CMAKE_PROJECT_NAME@ -c Python $*

distrib/linux/set_python_path.sh

@@ -0,0 +1,9 @@
+#!/bin/sh
+
+# Get the script's directory, which should be OpenCOR's base directory
+
+OPENCOR_DIR="$(cd "$(dirname "$0")"; pwd)"
+
+# Make sure the path to Python is correct
+
+${OPENCOR_DIR}/python/bin/python ${OPENCOR_DIR}/python/bin/set_python_path.py ${OPENCOR_DIR}/python -s

distrib/macos/application.sh.in

@@ -1,3 +1,5 @@
 #!/bin/sh
 
-${CMAKE_PROJECT_NAME}.app/Contents/MacOS/${CMAKE_PROJECT_NAME} $*
+OPENCOR_DIR="$(cd "$(dirname "$0")"; pwd)"
+
+${OPENCOR_DIR}/@CMAKE_PROJECT_NAME@.app/Contents/MacOS/@CMAKE_PROJECT_NAME@ $*