Merge de7f698 into fc03a45

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)
@@ -625,6 +626,13 @@ 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
@@ -653,6 +661,7 @@ 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
@@ -690,6 +699,7 @@ 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
@@ -870,6 +880,7 @@ if(USE_PREBUILT_QTWEBKIT_PACKAGE)
         list(APPEND PLUGINS
             thirdParty/libSBML
             thirdParty/PythonPackages
+            thirdParty/PythonQtAPI
 
             dataStore/BioSignalMLDataStore
             dataStore/CSVDataStore
@@ -887,6 +898,9 @@ if(USE_PREBUILT_QTWEBKIT_PACKAGE)
             miscellaneous/Compiler
             miscellaneous/Core
             miscellaneous/HelpWindow
+            miscellaneous/JupyterKernel
+            miscellaneous/PythonConsoleWindow
+            miscellaneous/PythonShell
             miscellaneous/WebBrowserWindow
 
             organisation/FileBrowserWindow
@@ -906,6 +920,8 @@ if(USE_PREBUILT_QTWEBKIT_PACKAGE)
             support/CellMLSupport
             support/COMBINESupport
             support/PMRSupport
+            support/PythonSupport
+            support/PythonQtSupport
             support/SEDMLSupport
             support/SimulationSupport
             support/StandardSupport
@@ -963,6 +979,10 @@ 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
 
@@ -1028,6 +1048,7 @@ configure_clang_and_clang_tidy(${CMAKE_PROJECT_NAME})
 if(WIN32)
     target_link_libraries(${CMAKE_PROJECT_NAME}
         ${Qt5Core_QTMAIN_LIBRARIES}
+        ${PYTHON_LIBRARY}
     )
 endif()
 
@@ -1037,6 +1058,29 @@ foreach(REQUIRED_QT_MODULE ${REQUIRED_QT_MODULES})
     )
 endforeach()
 
+# 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} ${PYTHON_DEPENDENCIES})
+endif()
+
+# On Linux, our Python package needs to be directly linked to OpenCOR otherwise
+# Python extension DSOs can't find symbols
+# Note: this is because the lookup scope changes for DSOs that are loaded
+#       using dlopen()...
+#       (See https://www.akkadia.org/drepper/dsohowto.pdf)
+
+if(NOT WIN32 AND NOT APPLE)
+    include_directories(${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
 #       ${CMAKE_PROJECT_NAME}.com, but Ninja found a duplicate rule (from a copy
@@ -1059,7 +1103,12 @@ if(WIN32)
     target_link_libraries(${WINDOWS_CLI_PROJECT_NAME}
         Qt5::Core
         Qt5::Network
+        ${PYTHON_LIBRARY}
     )
+
+    if(NOT "${PYTHON_DEPENDENCIES}" STREQUAL "")
+        add_dependencies(${WINDOWS_CLI_PROJECT_NAME} ${PYTHON_DEPENDENCIES})
+    endif()
 endif()
 
 # Some post-processing specific stuff
@@ -1285,6 +1334,40 @@ if(WIN32)
     install(FILES ${VBS_FILENAME}
             DESTINATION .)
 
+    # Python runtime libraries and utilities
+
+    install(DIRECTORY ${PROJECT_BUILD_DIR}/Python
+            DESTINATION .)
+
+    # Batch files to setup and run Python and Jupyter
+
+    set(JUPYTER_CONSOLE_FILENAME "${PROJECT_BUILD_DIR}/jupyterconsole.bat")
+    set(RUN_PYTHON_FILENAME "${PROJECT_BUILD_DIR}/runpython.bat")
+
+    configure_file(${PLATFORM_DISTRIB_DIR}/jupyterconsole.bat.in ${JUPYTER_CONSOLE_FILENAME})
+    copy_file_to_build_dir(DIRECT ${PLATFORM_DISTRIB_DIR} . jupyterlab.bat)
+    copy_file_to_build_dir(DIRECT ${PLATFORM_DISTRIB_DIR} . jupyterlab.vbs)
+    copy_file_to_build_dir(DIRECT ${PLATFORM_DISTRIB_DIR} . jupyternotebook.bat)
+    copy_file_to_build_dir(DIRECT ${PLATFORM_DISTRIB_DIR} . jupyternotebook.vbs)
+    copy_file_to_build_dir(DIRECT ${PLATFORM_DISTRIB_DIR} . runjupyter.bat)
+    configure_file(${PLATFORM_DISTRIB_DIR}/runpython.bat.in ${RUN_PYTHON_FILENAME})
+    copy_file_to_build_dir(DIRECT ${PLATFORM_DISTRIB_DIR} . setpythonpath.bat)
+
+    install(FILES ${JUPYTER_CONSOLE_FILENAME}
+                  ${PLATFORM_DISTRIB_DIR}/jupyterlab.bat
+                  ${PLATFORM_DISTRIB_DIR}/jupyterlab.vbs
+                  ${PLATFORM_DISTRIB_DIR}/jupyternotebook.bat
+                  ${PLATFORM_DISTRIB_DIR}/jupyternotebook.vbs
+                  ${PLATFORM_DISTRIB_DIR}/runjupyter.bat
+                  ${RUN_PYTHON_FILENAME}
+                  ${PLATFORM_DISTRIB_DIR}/setpythonpath.bat
+            DESTINATION .)
+
+    copy_file_to_build_dir(DIRECT ${PLATFORM_DISTRIB_DIR} ./Python/Scripts start_jupyter.py)
+
+    install(FILES ${PLATFORM_DISTRIB_DIR}/start_jupyter.py
+            DESTINATION ./Python/Scripts)
+
     # File type association
     # Note: the calls to SHChangeNotify are to ensure that Windows refreshes
     #       file icons (so that it is clear to the user that an extension has
@@ -1301,6 +1384,12 @@ if(WIN32)
             \\\${UnregisterExtension} \\\".cellml\\\" \\\"CellML File\\\"
             System::Call \\\"Shell32::SHChangeNotify(i 0x08000000, i 0, i 0, i 0)\\\"
         ")
+
+        # Update Python scripts to refer to our installed Python
+
+        set(CPACK_NSIS_EXTRA_INSTALL_COMMANDS
+           "${CPACK_NSIS_EXTRA_INSTALL_COMMANDS} Exec '\\\"\\\$INSTDIR\\\\Python\\\\bin\\\\python.exe\\\" \\\"\\\$INSTDIR\\\\Python\\\\Scripts\\\\setpythonpath.py\\\" \\\"\\\$INSTDIR\\\\Python\\\" -s'
+        ")
     endif()
 elseif(APPLE)
     # Select PackageMaker and ZIP as the packagers on macOS
@@ -1330,6 +1419,29 @@ elseif(APPLE)
             DESTINATION .
             RENAME ${CMAKE_PROJECT_NAME}
             PERMISSIONS OWNER_READ OWNER_WRITE OWNER_EXECUTE GROUP_READ GROUP_EXECUTE WORLD_READ WORLD_EXECUTE)
+
+    # Shell scripts to setup and run Python and Jupyter
+
+    set(JUPYTER_CONSOLE_FILENAME ${PROJECT_BUILD_DIR}/jupyterconsole)
+    set(RUN_JUPYTER_FILENAME ${PROJECT_BUILD_DIR}/runjupyter)
+    set(RUN_PYTHON_FILENAME ${PROJECT_BUILD_DIR}/runpython)
+    set(SET_PYTHON_PATH_FILENAME ${PROJECT_BUILD_DIR}/setpythonpath)
+
+    configure_file(${PLATFORM_DISTRIB_DIR}/jupyterconsole.in ${JUPYTER_CONSOLE_FILENAME} @ONLY)
+    copy_file_to_build_dir(DIRECT ${PLATFORM_DISTRIB_DIR} . jupyterlab)
+    copy_file_to_build_dir(DIRECT ${PLATFORM_DISTRIB_DIR} . jupyternotebook)
+    configure_file(${PLATFORM_DISTRIB_DIR}/runjupyter.in ${RUN_JUPYTER_FILENAME} @ONLY)
+    configure_file(${PLATFORM_DISTRIB_DIR}/runpython.in ${RUN_PYTHON_FILENAME} @ONLY)
+    configure_file(${PLATFORM_DISTRIB_DIR}/setpythonpath.in ${SET_PYTHON_PATH_FILENAME} @ONLY)
+
+    install(FILES ${JUPYTER_CONSOLE_FILENAME}
+                  ${PLATFORM_DISTRIB_DIR}/jupyterlab
+                  ${PLATFORM_DISTRIB_DIR}/jupyternotebook
+                  ${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)
 else()
     # Select TGZ as the packager on Linux
 
@@ -1395,6 +1507,33 @@ else()
             DESTINATION .
             RENAME ${CMAKE_PROJECT_NAME}
             PERMISSIONS OWNER_READ OWNER_WRITE OWNER_EXECUTE GROUP_READ GROUP_EXECUTE WORLD_READ WORLD_EXECUTE)
+
+    # 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(JUPYTER_CONSOLE_FILENAME ${PROJECT_BUILD_DIR}/jupyterconsole)
+    set(RUN_PYTHON_FILENAME ${PROJECT_BUILD_DIR}/runpython)
+
+    configure_file(${PLATFORM_DISTRIB_DIR}/jupyterconsole.in ${JUPYTER_CONSOLE_FILENAME} @ONLY)
+    copy_file_to_build_dir(DIRECT ${PLATFORM_DISTRIB_DIR} . jupyterlab)
+    copy_file_to_build_dir(DIRECT ${PLATFORM_DISTRIB_DIR} . jupyternotebook)
+    copy_file_to_build_dir(DIRECT ${PLATFORM_DISTRIB_DIR} . runjupyter)
+    configure_file(${PLATFORM_DISTRIB_DIR}/runpython.in ${RUN_PYTHON_FILENAME} @ONLY)
+    copy_file_to_build_dir(DIRECT ${PLATFORM_DISTRIB_DIR} . setpythonpath)
+
+    install(FILES ${JUPYTER_CONSOLE_FILENAME}
+                  ${PLATFORM_DISTRIB_DIR}/jupyterlab
+                  ${PLATFORM_DISTRIB_DIR}/jupyternotebook
+                  ${PLATFORM_DISTRIB_DIR}/runjupyter
+                  ${RUN_PYTHON_FILENAME}
+                  ${PLATFORM_DISTRIB_DIR}/setpythonpath
+            DESTINATION .
+            PERMISSIONS OWNER_READ OWNER_WRITE OWNER_EXECUTE GROUP_READ GROUP_EXECUTE WORLD_READ WORLD_EXECUTE)
 endif()
 
 # Specify the package file name, depending on whether we are generating a

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
 
@@ -187,6 +191,7 @@ macro(add_plugin PLUGIN_NAME)
         EXTERNAL_BINARIES
         SYSTEM_BINARIES
         DEPENDS_ON
+        BYPRODUCTS
         TESTS
     )
 
@@ -277,8 +282,10 @@ macro(add_plugin PLUGIN_NAME)
     endforeach()
 
     # Create a custom target for copying external binaries
-    # Note: this is to prevent Ninja from getting confused with circular
-    #       references...
+    # Note #1: this is to prevent Ninja from getting confused with circular
+    #          references...
+    # Note #2: we use this target in the PythonQtAPI build script when setting
+    #          the PYTHON_DEPENDENCIES list...
 
     if(   NOT "${ARG_EXTERNAL_BINARIES_DIR}" STREQUAL ""
        OR (    NOT "${ARG_EXTERNAL_SOURCE_DIR}" STREQUAL ""
@@ -381,7 +388,8 @@ macro(add_plugin PLUGIN_NAME)
 
         add_custom_command(TARGET ${COPY_EXTERNAL_BINARIES_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/jupyterconsole.in

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

distrib/linux/jupyterlab

@@ -0,0 +1,5 @@
+#!/bin/sh
+
+appDir="$(cd "$(dirname "$0")"; pwd)"
+
+${appDir}/runjupyter lab --ip 127.0.0.1 $*

distrib/linux/jupyternotebook

@@ -0,0 +1,5 @@
+#!/bin/sh
+
+appDir="$(cd "$(dirname "$0")"; pwd)"
+
+${appDir}/runjupyter notebook --ip 127.0.0.1 $*

distrib/linux/runjupyter

@@ -0,0 +1,9 @@
+#!/bin/sh
+
+appDir="$(cd "$(dirname "$0")"; pwd)"
+
+${appDir}/setpythonpath
+
+export PATH=${appDir}:$PATH
+
+${appDir}/python/bin/jupyter $*

distrib/linux/runpython.in

@@ -0,0 +1,7 @@
+#!/bin/sh
+
+appDir="$(cd "$(dirname "$0")"; pwd)"
+
+${appDir}/setpythonpath
+
+${appDir}/bin/@CMAKE_PROJECT_NAME@ -c Python $*

distrib/linux/setpythonpath

@@ -0,0 +1,5 @@
+#!/bin/sh
+
+appDir="$(cd "$(dirname "$0")"; pwd)"
+
+${appDir}/python/bin/python ${appDir}/python/bin/setpythonpath.py ${appDir}/python -s

distrib/macos/jupyterconsole.in

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

distrib/macos/jupyterlab

@@ -0,0 +1,5 @@
+#!/bin/sh
+
+appDir="$(cd "$(dirname "$0")"; pwd)"
+
+${appDir}/runjupyter lab --ip 127.0.0.1 $*

distrib/macos/jupyternotebook

@@ -0,0 +1,5 @@
+#!/bin/sh
+
+appDir="$(cd "$(dirname "$0")"; pwd)"
+
+${appDir}/runjupyter notebook --ip 127.0.0.1 $*

distrib/macos/runjupyter.in

@@ -0,0 +1,9 @@
+#!/bin/sh
+
+appDir="$(cd "$(dirname "$0")"; pwd)"
+
+${appDir}/setpythonpath
+
+export PATH=${appDir}:$PATH
+
+${appDir}/@CMAKE_PROJECT_NAME@.app/Contents/Frameworks/Python/bin/jupyter $*

distrib/macos/runpython.in

@@ -0,0 +1,7 @@
+#!/bin/sh
+
+appDir="$(cd "$(dirname "$0")"; pwd)"
+
+${appDir}/setpythonpath
+
+${appDir}/@CMAKE_PROJECT_NAME@.app/Contents/MacOS/@CMAKE_PROJECT_NAME@ -c Python $*

distrib/macos/setpythonpath.in

@@ -0,0 +1,8 @@
+#!/bin/sh
+
+appDir="$(cd "$(dirname "$0")"; pwd)"
+
+${appDir}/@CMAKE_PROJECT_NAME@.app/Contents/Frameworks/Python/bin/python           \
+${appDir}/@CMAKE_PROJECT_NAME@.app/Contents/Frameworks/Python/bin/setpythonpath.py \
+${appDir}/@CMAKE_PROJECT_NAME@.app/Contents/Frameworks/Python                      \
+-s

distrib/windows/jupyterconsole.bat.in

@@ -0,0 +1,7 @@
+@ECHO OFF
+
+TITLE Running the Jupyter Lab environment...
+
+SET appDir=%~dp0
+
+CALL "%appDir%runjupyter.bat" console --kernel ${CMAKE_PROJECT_NAME} %*

distrib/windows/jupyterlab.bat

@@ -0,0 +1,7 @@
+@ECHO OFF
+
+TITLE Running the Jupyter Lab environment...
+
+SET appDir=%~dp0
+
+CALL "%appDir%runjupyter.bat" lab --ip 127.0.0.1 %*