Merged in matt_broadway/gtsam/fix/python3cython (pull request #369)
Fix/python3cython Approved-by: Duy-Nguyen Ta <thduynguyen@gmail.com> Approved-by: Frank Dellaert <dellaert@cc.gatech.edu>release/4.3a0
matthew.broadway
Frank Dellaert
commit
0e23f77212
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@ -78,6 +78,7 @@ endif()
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option(GTSAM_INSTALL_MATLAB_TOOLBOX "Enable/Disable installation of matlab toolbox" OFF)
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option(GTSAM_INSTALL_CYTHON_TOOLBOX "Enable/Disable installation of Cython toolbox" OFF)
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option(GTSAM_BUILD_WRAP "Enable/Disable building of matlab/cython wrap utility (necessary for matlab/cython interface)" ON)
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set(GTSAM_PYTHON_VERSION "Default" CACHE STRING "The version of python to build the cython wrapper or python module for (or Default)")
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# Check / set dependent variables for MATLAB wrapper
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if((GTSAM_INSTALL_MATLAB_TOOLBOX OR GTSAM_INSTALL_CYTHON_TOOLBOX) AND NOT GTSAM_BUILD_WRAP)
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@ -554,6 +555,7 @@ endif()
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message(STATUS "Cython toolbox flags ")
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print_config_flag(${GTSAM_INSTALL_CYTHON_TOOLBOX} "Install Cython toolbox ")
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message(STATUS " Python version : ${GTSAM_PYTHON_VERSION}")
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print_config_flag(${GTSAM_BUILD_WRAP} "Build Wrap ")
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message(STATUS "===============================================================")
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@ -29,10 +29,15 @@
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# Use the Cython executable that lives next to the Python executable
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# if it is a local installation.
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find_package( PythonInterp )
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if(GTSAM_PYTHON_VERSION STREQUAL "Default")
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find_package(PythonInterp)
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else()
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find_package(PythonInterp ${GTSAM_PYTHON_VERSION} EXACT)
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endif()
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if ( PYTHONINTERP_FOUND )
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execute_process( COMMAND "${PYTHON_EXECUTABLE}" "-c"
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"import Cython; print Cython.__path__"
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"import Cython; print(Cython.__path__[0])"
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RESULT_VARIABLE RESULT
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OUTPUT_VARIABLE CYTHON_PATH
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OUTPUT_STRIP_TRAILING_WHITESPACE
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@ -51,7 +56,7 @@ endif ()
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# RESULT=0 means ok
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if ( NOT RESULT )
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execute_process( COMMAND "${PYTHON_EXECUTABLE}" "-c"
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"import Cython; print Cython.__version__"
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"import Cython; print(Cython.__version__)"
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RESULT_VARIABLE RESULT
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OUTPUT_VARIABLE CYTHON_VAR_OUTPUT
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ERROR_VARIABLE CYTHON_VAR_OUTPUT
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@ -40,9 +40,17 @@
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# Finding NumPy involves calling the Python interpreter
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if(NumPy_FIND_REQUIRED)
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if(GTSAM_PYTHON_VERSION STREQUAL "Default")
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find_package(PythonInterp REQUIRED)
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else()
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find_package(PythonInterp ${GTSAM_PYTHON_VERSION} EXACT REQUIRED)
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endif()
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else()
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if(GTSAM_PYTHON_VERSION STREQUAL "Default")
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find_package(PythonInterp)
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else()
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find_package(PythonInterp ${GTSAM_PYTHON_VERSION} EXACT)
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endif()
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endif()
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if(NOT PYTHONINTERP_FOUND)
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@ -3,8 +3,23 @@
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# in the current environment are different from the cached!
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unset(PYTHON_EXECUTABLE CACHE)
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unset(CYTHON_EXECUTABLE CACHE)
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unset(PYTHON_INCLUDE_DIR CACHE)
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unset(PYTHON_MAJOR_VERSION CACHE)
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if(GTSAM_PYTHON_VERSION STREQUAL "Default")
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find_package(PythonInterp REQUIRED)
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find_package(PythonLibs REQUIRED)
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else()
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find_package(PythonInterp ${GTSAM_PYTHON_VERSION} EXACT REQUIRED)
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find_package(PythonLibs ${GTSAM_PYTHON_VERSION} EXACT REQUIRED)
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endif()
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find_package(Cython 0.25.2 REQUIRED)
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execute_process(COMMAND "${PYTHON_EXECUTABLE}" "-c"
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"from __future__ import print_function;import sys;print(sys.version[0], end='')"
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OUTPUT_VARIABLE PYTHON_MAJOR_VERSION
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)
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# User-friendly Cython wrapping and installing function.
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# Builds a Cython module from the provided interface_header.
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# For example, for the interface header gtsam.h,
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@ -29,12 +44,12 @@ endfunction()
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function(set_up_required_cython_packages)
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# Set up building of cython module
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find_package(PythonLibs 2.7 REQUIRED)
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include_directories(${PYTHON_INCLUDE_DIRS})
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find_package(NumPy REQUIRED)
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include_directories(${NUMPY_INCLUDE_DIRS})
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endfunction()
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# Convert pyx to cpp by executing cython
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# This is the first step to compile cython from the command line
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# as described at: http://cython.readthedocs.io/en/latest/src/reference/compilation.html
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@ -52,7 +67,7 @@ function(pyx_to_cpp target pyx_file generated_cpp include_dirs)
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add_custom_command(
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OUTPUT ${generated_cpp}
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COMMAND
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${CYTHON_EXECUTABLE} -X boundscheck=False -v --fast-fail --cplus ${includes_for_cython} ${pyx_file} -o ${generated_cpp}
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${CYTHON_EXECUTABLE} -X boundscheck=False -v --fast-fail --cplus -${PYTHON_MAJOR_VERSION} ${includes_for_cython} ${pyx_file} -o ${generated_cpp}
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VERBATIM)
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add_custom_target(${target} ALL DEPENDS ${generated_cpp})
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endfunction()
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@ -19,7 +19,7 @@ if (GTSAM_INSTALL_CYTHON_TOOLBOX)
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# wrap gtsam_unstable
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if(GTSAM_BUILD_UNSTABLE)
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add_custom_target(gtsam_unstable_header DEPENDS "../gtsam_unstable/gtsam_unstable.h")
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set(GTSAM_UNSTABLE_IMPORT "from gtsam_unstable import *")
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set(GTSAM_UNSTABLE_IMPORT "from .gtsam_unstable import *")
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wrap_and_install_library_cython("../gtsam_unstable/gtsam_unstable.h" # interface_header
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"from gtsam.gtsam cimport *" # extra imports
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"${GTSAM_CYTHON_INSTALL_PATH}/gtsam" # install path
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@ -2,20 +2,22 @@ This is the Cython/Python wrapper around the GTSAM C++ library.
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INSTALL
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=======
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- if you want to build the gtsam python library for a specific python version (eg 2.7), use the `-DGTSAM_PYTHON_VERSION=2.7` option when running `cmake` otherwise the default interpreter will be used.
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- If the interpreter is inside an environment (such as an anaconda environment or virtualenv environment) then the environment should be active while building gtsam.
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- This wrapper needs Cython(>=0.25.2), backports_abc>=0.5, and numpy. These can be installed as follows:
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```bash
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pip install -r <gtsam_folder>/cython/requirements.txt
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```
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- For compatiblity with gtsam's Eigen version, it contains its own cloned version of [Eigency](https://github.com/wouterboomsma/eigency.git),
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- For compatibility with gtsam's Eigen version, it contains its own cloned version of [Eigency](https://github.com/wouterboomsma/eigency.git),
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named **gtsam_eigency**, to interface between C++'s Eigen and Python's numpy.
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- Build and install gtsam using cmake with GTSAM_INSTALL_CYTHON_TOOLBOX enabled.
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The wrapped module will be installed to GTSAM_CYTHON_INSTALL_PATH, which is
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by default: <your CMAKE_INSTALL_PREFIX>/cython
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- Build and install gtsam using cmake with `GTSAM_INSTALL_CYTHON_TOOLBOX` enabled.
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The wrapped module will be installed to `GTSAM_CYTHON_INSTALL_PATH`, which is
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by default: `<your CMAKE_INSTALL_PREFIX>/cython`
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- Modify your PYTHONPATH to include the GTSAM_CYTHON_INSTALL_PATH:
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- Modify your `PYTHONPATH` to include the `GTSAM_CYTHON_INSTALL_PATH`:
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```bash
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export PYTHONPATH=$PYTHONPATH:<GTSAM_CYTHON_INSTALL_PATH>
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```
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@ -1,2 +1,2 @@
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from gtsam import *
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from .gtsam import *
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${GTSAM_UNSTABLE_IMPORT}
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@ -394,14 +394,18 @@ void Module::emit_cython_pxd(FileWriter& pxdFile) const {
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/* ************************************************************************* */
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void Module::emit_cython_pyx(FileWriter& pyxFile) const {
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// directives...
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// allow str to automatically coerce to std::string and back (for python3)
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pyxFile.oss << "# cython: c_string_type=str, c_string_encoding=ascii\n\n";
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// headers...
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string pxdHeader = name;
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pyxFile.oss << "cimport numpy as np\n"
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"import numpy as npp\n"
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"cimport " << pxdHeader << "\n"
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"from "<< pxdHeader << " cimport shared_ptr\n"
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"from "<< pxdHeader << " cimport dynamic_pointer_cast\n"
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"from "<< pxdHeader << " cimport make_shared\n";
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"from ."<< pxdHeader << " cimport shared_ptr\n"
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"from ."<< pxdHeader << " cimport dynamic_pointer_cast\n"
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"from ."<< pxdHeader << " cimport make_shared\n";
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pyxFile.oss << "# C helper function that copies all arguments into a positional list.\n"
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"cdef list process_args(list keywords, tuple args, dict kwargs):\n"
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@ -1,9 +1,11 @@
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# cython: c_string_type=str, c_string_encoding=ascii
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cimport numpy as np
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import numpy as npp
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cimport geometry
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from geometry cimport shared_ptr
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from geometry cimport dynamic_pointer_cast
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from geometry cimport make_shared
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from .geometry cimport shared_ptr
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from .geometry cimport dynamic_pointer_cast
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from .geometry cimport make_shared
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# C helper function that copies all arguments into a positional list.
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cdef list process_args(list keywords, tuple args, dict kwargs):
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cdef str keyword
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