Merged with upstream/develop

CMakeLists.txt

@@ -78,6 +78,7 @@ endif()
 option(GTSAM_INSTALL_MATLAB_TOOLBOX      "Enable/Disable installation of matlab toolbox"  OFF)
 option(GTSAM_INSTALL_CYTHON_TOOLBOX      "Enable/Disable installation of Cython toolbox"  OFF)
 option(GTSAM_BUILD_WRAP                  "Enable/Disable building of matlab/cython wrap utility (necessary for matlab/cython interface)" ON)
+set(GTSAM_PYTHON_VERSION "Default" CACHE STRING "The version of python to build the cython wrapper or python module for (or Default)")
 
 # Check / set dependent variables for MATLAB wrapper
 if((GTSAM_INSTALL_MATLAB_TOOLBOX OR GTSAM_INSTALL_CYTHON_TOOLBOX) AND NOT GTSAM_BUILD_WRAP)
@@ -554,6 +555,7 @@ endif()
 
 message(STATUS "Cython toolbox flags                                      ")
 print_config_flag(${GTSAM_INSTALL_CYTHON_TOOLBOX}      "Install Cython toolbox         ")
+message(STATUS "  Python version                 : ${GTSAM_PYTHON_VERSION}")
 print_config_flag(${GTSAM_BUILD_WRAP}                  "Build Wrap                     ")
 message(STATUS "===============================================================")
 

cmake/FindCython.cmake

@@ -29,10 +29,15 @@
 
 # Use the Cython executable that lives next to the Python executable
 # if it is a local installation.
-find_package( PythonInterp )
+if(GTSAM_PYTHON_VERSION STREQUAL "Default")
+  find_package(PythonInterp)
+else()
+  find_package(PythonInterp ${GTSAM_PYTHON_VERSION} EXACT)
+endif()
+
 if ( PYTHONINTERP_FOUND )
   execute_process( COMMAND "${PYTHON_EXECUTABLE}" "-c"
-      "import Cython; print Cython.__path__"
+      "import Cython; print(Cython.__path__[0])"
       RESULT_VARIABLE RESULT
       OUTPUT_VARIABLE CYTHON_PATH
       OUTPUT_STRIP_TRAILING_WHITESPACE
@@ -51,7 +56,7 @@ endif ()
 # RESULT=0 means ok
 if ( NOT RESULT )
   execute_process( COMMAND "${PYTHON_EXECUTABLE}" "-c"
-      "import Cython; print Cython.__version__"
+      "import Cython; print(Cython.__version__)"
       RESULT_VARIABLE RESULT
       OUTPUT_VARIABLE CYTHON_VAR_OUTPUT
       ERROR_VARIABLE CYTHON_VAR_OUTPUT

cmake/FindNumPy.cmake

@@ -40,9 +40,17 @@
 
 # Finding NumPy involves calling the Python interpreter
 if(NumPy_FIND_REQUIRED)
+  if(GTSAM_PYTHON_VERSION STREQUAL "Default")
     find_package(PythonInterp REQUIRED)
+  else()
+      find_package(PythonInterp ${GTSAM_PYTHON_VERSION} EXACT REQUIRED)
+  endif()
 else()
+  if(GTSAM_PYTHON_VERSION STREQUAL "Default")
     find_package(PythonInterp)
+  else()
+    find_package(PythonInterp ${GTSAM_PYTHON_VERSION} EXACT)
+  endif()
 endif()
 
 if(NOT PYTHONINTERP_FOUND)

cmake/GtsamCythonWrap.cmake

@@ -3,8 +3,23 @@
 # in the current environment are different from the cached!
 unset(PYTHON_EXECUTABLE CACHE)
 unset(CYTHON_EXECUTABLE CACHE)
+unset(PYTHON_INCLUDE_DIR CACHE)
+unset(PYTHON_MAJOR_VERSION CACHE)
+
+if(GTSAM_PYTHON_VERSION STREQUAL "Default")
+  find_package(PythonInterp REQUIRED)
+  find_package(PythonLibs REQUIRED)
+else()
+  find_package(PythonInterp ${GTSAM_PYTHON_VERSION} EXACT REQUIRED)
+  find_package(PythonLibs ${GTSAM_PYTHON_VERSION} EXACT REQUIRED)
+endif()
 find_package(Cython 0.25.2 REQUIRED)
 
+execute_process(COMMAND "${PYTHON_EXECUTABLE}" "-c"
+    "from __future__ import print_function;import sys;print(sys.version[0], end='')"
+    OUTPUT_VARIABLE PYTHON_MAJOR_VERSION
+)
+
 # User-friendly Cython wrapping and installing function.
 # Builds a Cython module from the provided interface_header.
 # For example, for the interface header gtsam.h,
@@ -29,12 +44,12 @@ endfunction()
 
 function(set_up_required_cython_packages)
   # Set up building of cython module
-  find_package(PythonLibs 2.7 REQUIRED)
   include_directories(${PYTHON_INCLUDE_DIRS})
   find_package(NumPy REQUIRED)
   include_directories(${NUMPY_INCLUDE_DIRS})
 endfunction()
 
+
 # Convert pyx to cpp by executing cython
 # This is the first step to compile cython from the command line
 # as described at: http://cython.readthedocs.io/en/latest/src/reference/compilation.html
@@ -52,7 +67,7 @@ function(pyx_to_cpp target pyx_file generated_cpp include_dirs)
   add_custom_command(
     OUTPUT ${generated_cpp}
     COMMAND
-      ${CYTHON_EXECUTABLE} -X boundscheck=False -v --fast-fail --cplus ${includes_for_cython} ${pyx_file} -o ${generated_cpp}
+    ${CYTHON_EXECUTABLE} -X boundscheck=False -v --fast-fail --cplus -${PYTHON_MAJOR_VERSION} ${includes_for_cython} ${pyx_file} -o ${generated_cpp}
     VERBATIM)
   add_custom_target(${target} ALL DEPENDS ${generated_cpp})
 endfunction()

cython/CMakeLists.txt

@@ -19,7 +19,7 @@ if (GTSAM_INSTALL_CYTHON_TOOLBOX)
   # wrap gtsam_unstable
   if(GTSAM_BUILD_UNSTABLE)
     add_custom_target(gtsam_unstable_header DEPENDS "../gtsam_unstable/gtsam_unstable.h")
-    set(GTSAM_UNSTABLE_IMPORT "from gtsam_unstable import *")
+    set(GTSAM_UNSTABLE_IMPORT "from .gtsam_unstable import *")
     wrap_and_install_library_cython("../gtsam_unstable/gtsam_unstable.h" # interface_header
                                     "from gtsam.gtsam cimport *"                  # extra imports
                                     "${GTSAM_CYTHON_INSTALL_PATH}/gtsam_unstable" # install path

cython/README.md

@@ -2,20 +2,22 @@ This is the Cython/Python wrapper around the GTSAM C++ library.
 
 INSTALL
 =======
+- 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.
+    - If the interpreter is inside an environment (such as an anaconda environment or virtualenv environment) then the environment should be active while building gtsam.
 - This wrapper needs Cython(>=0.25.2), backports_abc>=0.5, and numpy. These can be installed as follows:
 
 ```bash
  pip install -r <gtsam_folder>/cython/requirements.txt
 ```
 
-- For compatiblity with gtsam's Eigen version, it contains its own cloned version of [Eigency](https://github.com/wouterboomsma/eigency.git),
+- For compatibility with gtsam's Eigen version, it contains its own cloned version of [Eigency](https://github.com/wouterboomsma/eigency.git),
 named **gtsam_eigency**, to interface between C++'s Eigen and Python's numpy.
 
-- Build and install gtsam using cmake with GTSAM_INSTALL_CYTHON_TOOLBOX enabled.
+- Build and install gtsam using cmake with `GTSAM_INSTALL_CYTHON_TOOLBOX` enabled.
-The wrapped module will be installed to GTSAM_CYTHON_INSTALL_PATH, which is
+The wrapped module will be installed to `GTSAM_CYTHON_INSTALL_PATH`, which is
-by default: <your CMAKE_INSTALL_PREFIX>/cython
+by default: `<your CMAKE_INSTALL_PREFIX>/cython`
 
-- Modify your PYTHONPATH to include the GTSAM_CYTHON_INSTALL_PATH:
+- Modify your `PYTHONPATH` to include the `GTSAM_CYTHON_INSTALL_PATH`:
 ```bash
 export PYTHONPATH=$PYTHONPATH:<GTSAM_CYTHON_INSTALL_PATH>
 ```

cython/gtsam/__init__.py.in

@@ -1,2 +1,2 @@
-from gtsam import *
+from .gtsam import *
 ${GTSAM_UNSTABLE_IMPORT}

wrap/Module.cpp

@@ -394,14 +394,18 @@ void Module::emit_cython_pxd(FileWriter& pxdFile) const {
 
 /* ************************************************************************* */
 void Module::emit_cython_pyx(FileWriter& pyxFile) const {
+  // directives...
+  // allow str to automatically coerce to std::string and back (for python3)
+  pyxFile.oss << "# cython: c_string_type=str, c_string_encoding=ascii\n\n";
+
   // headers...
   string pxdHeader = name;
   pyxFile.oss << "cimport numpy as np\n"
                  "import numpy as npp\n"
                  "cimport " << pxdHeader << "\n"
-                 "from "<< pxdHeader << " cimport shared_ptr\n"
+                 "from ."<< pxdHeader << " cimport shared_ptr\n"
-                 "from "<< pxdHeader << " cimport dynamic_pointer_cast\n"
+                 "from ."<< pxdHeader << " cimport dynamic_pointer_cast\n"
-                 "from "<< pxdHeader << " cimport make_shared\n";
+                 "from ."<< pxdHeader << " cimport make_shared\n";
 
   pyxFile.oss << "# C helper function that copies all arguments into a positional list.\n"
                  "cdef list process_args(list keywords, tuple args, dict kwargs):\n"

wrap/tests/expected-cython/geometry.pyx

@@ -1,9 +1,11 @@
+# cython: c_string_type=str, c_string_encoding=ascii
+
 cimport numpy as np
 import numpy as npp
 cimport geometry
-from geometry cimport shared_ptr
+from .geometry cimport shared_ptr
-from geometry cimport dynamic_pointer_cast
+from .geometry cimport dynamic_pointer_cast
-from geometry cimport make_shared
+from .geometry cimport make_shared
 # C helper function that copies all arguments into a positional list.
 cdef list process_args(list keywords, tuple args, dict kwargs):
    cdef str keyword