Merge pull request #654 from borglab/feature/wrap-update

Updates to use the new version of wrap

CMakeLists.txt

@@ -62,6 +62,11 @@ add_subdirectory(CppUnitLite)
 
 # This is the new wrapper
 if(GTSAM_BUILD_PYTHON)
+    # Need to set this for the wrap package so we don't use the default value.
+    set(WRAP_PYTHON_VERSION ${GTSAM_PYTHON_VERSION}
+        CACHE STRING "The Python version to use for wrapping")
+
+    add_subdirectory(wrap)
     list(APPEND CMAKE_MODULE_PATH "${CMAKE_CURRENT_LIST_DIR}/wrap/cmake")
     add_subdirectory(python)
 endif()

cmake/GtsamMatlabWrap.cmake

@@ -240,12 +240,16 @@ function(wrap_library_internal interfaceHeader linkLibraries extraIncludeDirs ex
 
 	set(_ignore gtsam::Point2
 			gtsam::Point3)
-	add_custom_command(
+
+    # set the matlab wrapping script variable
+    set(MATLAB_WRAP_SCRIPT "${GTSAM_SOURCE_DIR}/wrap/scripts/matlab_wrap.py")
+
+    add_custom_command(
 		OUTPUT ${generated_cpp_file}
 		DEPENDS ${interfaceHeader} ${module_library_target} ${otherLibraryTargets} ${otherSourcesAndObjects}
         COMMAND
 			${PYTHON_EXECUTABLE}
-			${CMAKE_SOURCE_DIR}/wrap/matlab_wrapper.py
+			${MATLAB_WRAP_SCRIPT}
             --src ${interfaceHeader}
 			--module_name ${moduleName}
             --out ${generated_files_path}

cmake/HandlePython.cmake

@@ -1,22 +1,48 @@
 # Set Python version if either Python or MATLAB wrapper is requested.
 if(GTSAM_BUILD_PYTHON OR GTSAM_INSTALL_MATLAB_TOOLBOX)
-    if(${GTSAM_PYTHON_VERSION} STREQUAL "Default")
-        # Get info about the Python3 interpreter
-        # https://cmake.org/cmake/help/latest/module/FindPython3.html#module:FindPython3
-        find_package(Python3 COMPONENTS Interpreter Development)
+  if(${GTSAM_PYTHON_VERSION} STREQUAL "Default")
 
-        if(NOT ${Python3_FOUND})
-            message(FATAL_ERROR "Cannot find Python3 interpreter. Please install Python >= 3.6.")
-        endif()
+    if(${CMAKE_VERSION} VERSION_LESS "3.12.0")
+      # Use older version of cmake's find_python
+      find_package(PythonInterp)
+
+      if(NOT ${PYTHONINTERP_FOUND})
+        message(
+          FATAL_ERROR
+            "Cannot find Python interpreter. Please install Python >= 3.6.")
+      endif()
+
+      find_package(PythonLibs ${PYTHON_VERSION_STRING})
+
+      set(Python_VERSION_MAJOR ${PYTHON_VERSION_MAJOR})
+      set(Python_VERSION_MINOR ${PYTHON_VERSION_MINOR})
+      set(Python_EXECUTABLE ${PYTHON_EXECUTABLE})
+
+    else()
+      # Get info about the Python3 interpreter
+      # https://cmake.org/cmake/help/latest/module/FindPython3.html#module:FindPython3
+      find_package(Python3 COMPONENTS Interpreter Development)
+
+      if(NOT ${Python3_FOUND})
+        message(
+          FATAL_ERROR
+            "Cannot find Python3 interpreter. Please install Python >= 3.6.")
+      endif()
+
+      set(Python_VERSION_MAJOR ${Python3_VERSION_MAJOR})
+      set(Python_VERSION_MINOR ${Python3_VERSION_MINOR})
 
-        set(GTSAM_PYTHON_VERSION "${Python3_VERSION_MAJOR}.${Python3_VERSION_MINOR}"
-                CACHE
-                STRING
-                "The version of Python to build the wrappers against."
-                FORCE)
     endif()
+
+    set(GTSAM_PYTHON_VERSION
+        "${Python_VERSION_MAJOR}.${Python_VERSION_MINOR}"
+        CACHE STRING "The version of Python to build the wrappers against."
+              FORCE)
+
+  endif()
 endif()
 
+# Check for build of Unstable modules
 if(GTSAM_BUILD_PYTHON)
     if(GTSAM_UNSTABLE_BUILD_PYTHON)
         if (NOT GTSAM_BUILD_UNSTABLE)

python/CMakeLists.txt

@@ -4,20 +4,26 @@ if (NOT GTSAM_BUILD_PYTHON)
     return()
 endif()
 
-# Common directory for storing data/datasets stored with the package.
-# This will store the data in the Python site package directly.
-set(GTSAM_PYTHON_DATASET_DIR "./gtsam/Data")
-
 # Generate setup.py.
 file(READ "${PROJECT_SOURCE_DIR}/README.md" README_CONTENTS)
 configure_file(${PROJECT_SOURCE_DIR}/python/setup.py.in
                 ${GTSAM_PYTHON_BUILD_DIRECTORY}/setup.py)
 
-set(WRAP_USE_CUSTOM_PYTHON_LIBRARY ${GTSAM_USE_CUSTOM_PYTHON_LIBRARY})
-set(WRAP_PYTHON_VERSION ${GTSAM_PYTHON_VERSION})
+# Supply MANIFEST.in for older versions of Python
+file(COPY ${PROJECT_SOURCE_DIR}/python/MANIFEST.in
+     DESTINATION ${GTSAM_PYTHON_BUILD_DIRECTORY})
 
 include(PybindWrap)
 
+############################################################
+## Load the necessary files to compile the wrapper
+
+# Load the pybind11 code
+add_subdirectory(${PROJECT_SOURCE_DIR}/wrap/pybind11 pybind11)
+# Set the wrapping script variable
+set(PYBIND_WRAP_SCRIPT "${PROJECT_SOURCE_DIR}/wrap/scripts/pybind_wrap.py")
+############################################################
+
 add_custom_target(gtsam_header DEPENDS "${PROJECT_SOURCE_DIR}/gtsam/gtsam.i")
 add_custom_target(gtsam_unstable_header DEPENDS "${PROJECT_SOURCE_DIR}/gtsam_unstable/gtsam_unstable.i")
 
@@ -67,55 +73,68 @@ set(GTSAM_MODULE_PATH ${GTSAM_PYTHON_BUILD_DIRECTORY}/gtsam)
 create_symlinks("${CMAKE_CURRENT_SOURCE_DIR}/gtsam"
         "${GTSAM_MODULE_PATH}")
 
+# Common directory for data/datasets stored with the package.
+# This will store the data in the Python site package directly.
+file(COPY "${GTSAM_SOURCE_DIR}/examples/Data" DESTINATION "${GTSAM_MODULE_PATH}")
+
+# Add gtsam as a dependency to the install target
+set(GTSAM_PYTHON_DEPENDENCIES gtsam_py)
+
+
 if(GTSAM_UNSTABLE_BUILD_PYTHON)
-set(ignore
-        gtsam::Point2
-        gtsam::Point3
-        gtsam::LieVector
-        gtsam::LieMatrix
-        gtsam::ISAM2ThresholdMapValue
-        gtsam::FactorIndices
-        gtsam::FactorIndexSet
-        gtsam::BetweenFactorPose3s
-        gtsam::Point2Vector
-        gtsam::Pose3Vector
-        gtsam::KeyVector
-        gtsam::FixedLagSmootherKeyTimestampMapValue
-        gtsam::BinaryMeasurementsUnit3
-        gtsam::CameraSetCal3_S2
-        gtsam::CameraSetCal3Bundler
-        gtsam::KeyPairDoubleMap)
-
-pybind_wrap(gtsam_unstable_py # target
-        ${PROJECT_SOURCE_DIR}/gtsam_unstable/gtsam_unstable.i # interface_header
-        "gtsam_unstable.cpp" # generated_cpp
-        "gtsam_unstable" # module_name
-        "gtsam" # top_namespace
-        "${ignore}" # ignore_classes
-        ${PROJECT_SOURCE_DIR}/python/gtsam_unstable/gtsam_unstable.tpl
-        gtsam_unstable # libs
-        "gtsam_unstable;gtsam_unstable_header" # dependencies
-        ON # use_boost
-        )
-
-set_target_properties(gtsam_unstable_py PROPERTIES
-        INSTALL_RPATH "${CMAKE_INSTALL_PREFIX}/lib"
-        INSTALL_RPATH_USE_LINK_PATH TRUE
-        OUTPUT_NAME "gtsam_unstable"
-        LIBRARY_OUTPUT_DIRECTORY "${GTSAM_PYTHON_BUILD_DIRECTORY}/gtsam_unstable"
-        DEBUG_POSTFIX "" # Otherwise you will have a wrong name
-        RELWITHDEBINFO_POSTFIX "" # Otherwise you will have a wrong name
-        )
-
-set(GTSAM_UNSTABLE_MODULE_PATH ${GTSAM_PYTHON_BUILD_DIRECTORY}/gtsam_unstable)
+    set(ignore
+            gtsam::Point2
+            gtsam::Point3
+            gtsam::LieVector
+            gtsam::LieMatrix
+            gtsam::ISAM2ThresholdMapValue
+            gtsam::FactorIndices
+            gtsam::FactorIndexSet
+            gtsam::BetweenFactorPose3s
+            gtsam::Point2Vector
+            gtsam::Pose3Vector
+            gtsam::KeyVector
+            gtsam::FixedLagSmootherKeyTimestampMapValue
+            gtsam::BinaryMeasurementsUnit3
+            gtsam::CameraSetCal3_S2
+            gtsam::CameraSetCal3Bundler
+            gtsam::KeyPairDoubleMap)
+
+    pybind_wrap(gtsam_unstable_py # target
+            ${PROJECT_SOURCE_DIR}/gtsam_unstable/gtsam_unstable.i # interface_header
+            "gtsam_unstable.cpp" # generated_cpp
+            "gtsam_unstable" # module_name
+            "gtsam" # top_namespace
+            "${ignore}" # ignore_classes
+            ${PROJECT_SOURCE_DIR}/python/gtsam_unstable/gtsam_unstable.tpl
+            gtsam_unstable # libs
+            "gtsam_unstable;gtsam_unstable_header" # dependencies
+            ON # use_boost
+            )
+
+    set_target_properties(gtsam_unstable_py PROPERTIES
+            INSTALL_RPATH "${CMAKE_INSTALL_PREFIX}/lib"
+            INSTALL_RPATH_USE_LINK_PATH TRUE
+            OUTPUT_NAME "gtsam_unstable"
+            LIBRARY_OUTPUT_DIRECTORY "${GTSAM_PYTHON_BUILD_DIRECTORY}/gtsam_unstable"
+            DEBUG_POSTFIX "" # Otherwise you will have a wrong name
+            RELWITHDEBINFO_POSTFIX "" # Otherwise you will have a wrong name
+            )
+
+    set(GTSAM_UNSTABLE_MODULE_PATH ${GTSAM_PYTHON_BUILD_DIRECTORY}/gtsam_unstable)
+
+    # Symlink all tests .py files to build folder.
+    create_symlinks("${CMAKE_CURRENT_SOURCE_DIR}/gtsam_unstable"
+            "${GTSAM_UNSTABLE_MODULE_PATH}")
+
+    # Add gtsam_unstable to the install target
+    list(APPEND GTSAM_PYTHON_DEPENDENCIES gtsam_unstable_py)
 
-# Symlink all tests .py files to build folder.
-create_symlinks("${CMAKE_CURRENT_SOURCE_DIR}/gtsam_unstable"
-        "${GTSAM_UNSTABLE_MODULE_PATH}")
 endif()
 
+# Add custom target so we can install with `make python-install`
 set(GTSAM_PYTHON_INSTALL_TARGET python-install)
 add_custom_target(${GTSAM_PYTHON_INSTALL_TARGET}
         COMMAND ${PYTHON_EXECUTABLE} ${GTSAM_PYTHON_BUILD_DIRECTORY}/setup.py install
-        DEPENDS gtsam_py gtsam_unstable_py
+        DEPENDS ${GTSAM_PYTHON_DEPENDENCIES}
         WORKING_DIRECTORY ${GTSAM_PYTHON_BUILD_DIRECTORY})

python/MANIFEST.in

@@ -0,0 +1 @@
+recursive-include gtsam/Data *

python/setup.py.in

@@ -1,6 +1,4 @@
-import glob
-import os
-import sys
+"""Setup file to install the GTSAM package."""
 
 try:
     from setuptools import setup, find_packages
@@ -10,19 +8,17 @@ except ImportError:
 packages = find_packages(where=".")
 print("PACKAGES: ", packages)
 
-data_path = '${GTSAM_SOURCE_DIR}/examples/Data/'
-data_files_and_directories = glob.glob(data_path + '**', recursive=True)
-data_files = [x for x in data_files_and_directories if not os.path.isdir(x)]
-
 package_data = {
     '': [
-        './*.so',
-        './*.dll',
+        "./*.so",
+        "./*.dll",
+        "Data/*"  # Add the data files to the package
+        "Data/**/*"  # Add the data files in subdirectories
     ]
 }
 
 # Cleaner to read in the contents rather than copy them over.
-readme_contents = open("${PROJECT_SOURCE_DIR}/README.md").read()
+readme_contents = open("${GTSAM_SOURCE_DIR}/README.md").read()
 
 setup(
     name='gtsam',
@@ -49,9 +45,9 @@ setup(
         'Programming Language :: Python :: 3',
     ],
     packages=packages,
+    include_package_data=True,
     package_data=package_data,
-    data_files=[('${GTSAM_PYTHON_DATASET_DIR}', data_files),],
     test_suite="gtsam.tests",
-    install_requires=["numpy"],
+    install_requires=open("${GTSAM_SOURCE_DIR}/python/requirements.txt").readlines(),
     zip_safe=False,
 )

wrap/.gitignore

@@ -1,2 +1,5 @@
 __pycache__/
 .vscode/
+*build*
+*dist*
+*.egg-info

wrap/CMakeLists.txt

@@ -0,0 +1,55 @@
+cmake_minimum_required(VERSION 3.9)
+
+# Set the project name and version
+project(GTwrap VERSION 1.0)
+
+# ##############################################################################
+# General configuration
+
+set(WRAP_PYTHON_VERSION
+    "Default"
+    CACHE STRING "The Python version to use for wrapping")
+
+include(${CMAKE_CURRENT_SOURCE_DIR}/cmake/GtwrapUtils.cmake)
+gtwrap_get_python_version(${WRAP_PYTHON_VERSION})
+
+# ##############################################################################
+# Install the CMake file to be used by other projects
+if(WIN32 AND NOT CYGWIN)
+  set(SCRIPT_INSTALL_DIR "${CMAKE_INSTALL_PREFIX}/CMake")
+else()
+  set(SCRIPT_INSTALL_DIR "${CMAKE_INSTALL_PREFIX}/lib/cmake")
+endif()
+
+# Install scripts to the standard CMake script directory.
+install(FILES cmake/gtwrapConfig.cmake cmake/PybindWrap.cmake
+              cmake/GtwrapUtils.cmake
+        DESTINATION "${SCRIPT_INSTALL_DIR}/gtwrap")
+
+# Install wrapping scripts as binaries to `CMAKE_INSTALL_PREFIX/bin` so they can
+# be invoked for wrapping.
+install(PROGRAMS scripts/pybind_wrap.py scripts/matlab_wrap.py TYPE BIN)
+
+# Install pybind11 directory to `CMAKE_INSTALL_PREFIX/lib/pybind11` This will
+# allow the gtwrapConfig.cmake file to load it later.
+install(DIRECTORY pybind11 TYPE LIB)
+
+# ##############################################################################
+# Install the Python package
+find_package(
+  Python ${WRAP_PYTHON_VERSION}
+  COMPONENTS Interpreter
+  REQUIRED)
+
+# Detect virtualenv and set Pip args accordingly
+# https://www.scivision.dev/cmake-install-python-package/
+if(DEFINED ENV{VIRTUAL_ENV} OR DEFINED ENV{CONDA_PREFIX})
+  set(_pip_args)
+else()
+  set(_pip_args "--user")
+endif()
+#TODO add correct flags for virtualenv
+
+# Finally install the gtwrap python package.
+execute_process(COMMAND ${Python_EXECUTABLE} -m pip install . ${_pip_args}
+                WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR})

wrap/LICENSE

@@ -0,0 +1,13 @@
+Copyright (c) 2010, Georgia Tech Research Corporation
+Atlanta, Georgia 30332-0415
+All Rights Reserved
+
+Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.