Pybind11 manual bindings (#499)

* Manual binding for minimal set of  aikido components

* Update readme

* Fix typo

* Add Skeleton, MetaSkeleton, WorldInteractiveMarkerViewer, TSRMarker, World, ConcreteManipulator, CollisionFree to pybind11

* update python binding install guide

* update pybinding for conda-managed python

* remove swp file

* Update README.md

* Skeleton code for aikidopy using pybind11 (#528)

.ci/install_linux_catkin.sh

@@ -9,3 +9,26 @@ cp -r "${TRAVIS_BUILD_DIR}" src
 if [ $BUILD_NAME = TRUSTY_FULL_DEBUG ]; then
   sudo apt-get install -y clang-format-3.8
 fi
+
+if [ "$BUILD_AIKIDOPY" = "ON" ]; then
+  $SUDO apt-get -y install python3-dev python3-numpy
+  $SUDO apt-get -y install python3-pip -y
+  $SUDO pip3 install pytest -U
+
+  if [ $(lsb_release -sc) = "trusty" ] || [ $(lsb_release -sc) = "xenial" ] || [ $(lsb_release -sc) = "bionic" ]; then
+    git clone https://github.com/pybind/pybind11 -b 'v2.3.0' --single-branch --depth 1
+    cd pybind11
+    mkdir build
+    cd build
+    cmake .. -DCMAKE_BUILD_TYPE=Release -DPYBIND11_TEST=OFF
+    make -j4
+    $SUDO make install
+    cd ../..
+  elif [ $(lsb_release -sc) = "cosmic" ] || [ $(lsb_release -sc) = "disco" ]; then
+    $SUDO apt-get -y install pybind11-dev python3 libpython3-dev python3-pytest \
+      python3-distutils
+  else
+    echo -e "$(lsb_release -sc) is not supported."
+    exit 1
+  fi
+fi

.ci/script_catkin.sh

@@ -17,6 +17,13 @@ if [ $BUILD_NAME = TRUSTY_FULL_DEBUG ]; then
   ./scripts/internal-run.sh catkin build --no-status --no-deps -p 1 -i --make-args check-format -- aikido
 fi
 
+# Build aikidopy and pytest
+if [ $BUILD_AIKIDOPY = ON ]; then
+  ./scripts/internal-run.sh catkin build --no-status --no-deps -p 1 -i --cmake-args -DCMAKE_BUILD_TYPE=$BUILD_TYPE -DTREAT_WARNINGS_AS_ERRORS=OFF -DCODECOV=OFF --make-args aikidopy -- aikido
+  ./scripts/internal-run.sh make -C build/aikido pytest
+  exit 0
+fi
+
 # Manually build Aikido's tests; they are not built automatically because it is not a Catkin package.
 if [ $BUILD_NAME = TRUSTY_FULL_DEBUG ]; then
   ./scripts/internal-run.sh catkin build --no-status --no-deps -p 1 -i --cmake-args -DCMAKE_BUILD_TYPE=$BUILD_TYPE -DTREAT_WARNINGS_AS_ERRORS=ON -DCODECOV=ON --make-args tests -- aikido

.ci/script_cmake.sh

@@ -6,6 +6,13 @@ unset -f cd; # Disable rvm override of cd (see https://github.com/travis-ci/trav
 
 mkdir build
 cd build
-cmake -DCMAKE_BUILD_TYPE=${BUILD_TYPE} -DTREAT_WARNINGS_AS_ERRORS=ON ..
-make -j4 tests
-make test
+
+if [ $BUILD_AIKIDOPY = ON ]; then
+  cmake -DCMAKE_BUILD_TYPE=${BUILD_TYPE} -DTREAT_WARNINGS_AS_ERRORS=ON -DBUILD_AIKIDOPY=ON ..
+  make -j4 aikidopy
+  make pytest
+else
+  cmake -DCMAKE_BUILD_TYPE=${BUILD_TYPE} -DTREAT_WARNINGS_AS_ERRORS=ON ..
+  make -j4 tests
+  make test
+fi

.travis.yml

@@ -83,6 +83,25 @@ matrix:
         - USE_CATKIN=OFF
       services: docker
 
+    - os: linux
+      env:
+        - BUILD_NAME=BIONIC_CATKIN_FULL_RELEASE_AIKIDOPY
+        - DOCKER_FILE="ubuntu-bionic"
+        - BUILD_TYPE=Release
+        - CATKIN_CONFIG_OPTIONS="-DCMAKE_BUILD_TYPE=Release -DTREAT_WARNINGS_AS_ERRORS=ON -DBUILD_AIKIDOPY=ON"
+        - USE_CATKIN=ON
+        - BUILD_AIKIDOPY=ON
+      services: docker
+
+    - os: linux
+      env:
+        - BUILD_NAME=BIONIC_CMAKE_RELEASE_AIKIDOPY
+        - DOCKER_FILE="ubuntu-bionic"
+        - BUILD_TYPE=Release
+        - USE_CATKIN=OFF
+        - BUILD_AIKIDOPY=ON
+      services: docker
+
     - os: osx
       osx_image: xcode11
       compiler: clang
@@ -150,6 +169,14 @@ matrix:
         - USE_CATKIN=ON
       services: docker
 
+    - os: osx
+      osx_image: xcode11
+      compiler: clang
+      env:
+        - BUILD_NAME=XCODE11_CMAKE_RELEASE
+        - BUILD_TYPE=Release
+        - USE_CATKIN=OFF
+
 before_install:
   - if [ -n "$DOCKER_FILE" ]; then
       docker build -t "$DOCKER_FILE" -f ".ci/docker/$DOCKER_FILE" .;

CMakeLists.txt

@@ -36,6 +36,11 @@ set(CONFIG_INSTALL_DIR "${LIBRARY_INSTALL_DIR}/${PROJECT_NAME}/cmake")
 option(CODECOV "Enable codecov support" OFF)
 option(DOWNLOAD_TAGFILES "Download Doxygen tagfiles for dependencies" OFF)
 option(TREAT_WARNINGS_AS_ERRORS "Treat warnings as errors" OFF)
+option(BUILD_AIKIDOPY "Build aikidopy (the python binding)" OFF)
+
+if(BUILD_AIKIDOPY)
+  set(BUILD_SHARED_LIBS OFF)
+endif()
 
 #==============================================================================
 # codecov Setup
@@ -134,6 +139,8 @@ add_custom_target(headers SOURCES ${aikido_headers})
 
 add_subdirectory("src")
 
+add_subdirectory("python")
+
 enable_testing()
 add_subdirectory("tests" EXCLUDE_FROM_ALL)
 

include/aikido/robot.hpp

@@ -0,0 +1,7 @@
+#include "robot/ConcreteManipulator.hpp"
+#include "robot/ConcreteRobot.hpp"
+#include "robot/GrabMetadata.hpp"
+#include "robot/Hand.hpp"
+#include "robot/Manipulator.hpp"
+#include "robot/Robot.hpp"
+#include "robot/util.hpp"

include/aikido/rviz.hpp

@@ -1,10 +1,10 @@
 #include "rviz/BodyNodeMarker.hpp"
 #include "rviz/FrameMarker.hpp"
 #include "rviz/InteractiveMarkerViewer.hpp"
+#include "rviz/pointers.hpp"
 #include "rviz/ResourceServer.hpp"
+#include "rviz/shape_conversions.hpp"
 #include "rviz/ShapeFrameMarker.hpp"
 #include "rviz/SkeletonMarker.hpp"
-#include "rviz/SmartPointers.hpp"
 #include "rviz/TSRMarker.hpp"
 #include "rviz/WorldInteractiveMarkerViewer.hpp"
-#include "rviz/shape_conversions.hpp"

python/CMakeLists.txt

@@ -0,0 +1,4 @@
+set(AIKIDOPY_BUILD_DIR "${CMAKE_CURRENT_BINARY_DIR}/aikidopy")
+
+add_subdirectory(aikidopy)
+add_subdirectory(tests)

python/README.md

@@ -0,0 +1,55 @@
+# aikidopy
+
+This folder contains manual bindings for aikidopy using pybind11. The installation guide have been tested on
+- sudo apt installed Python 2.7 and Python 3.4.
+- anaconda managed Python 3.6
+
+0. If you use system installed Python, ensure you have `python2.7-dev` or `python3-dev` correspondingly. Run `$ sudo apt-get install python3-dev` to obtain it.
+
+
+1. Install [pybind11](https://github.com/pybind/pybind11.git) **from source** following these [instructions](https://pybind11.readthedocs.io/en/master/basics.html#compiling-the-test-cases). (Need version >= 2.2.0).
+
+```
+$ git clone https://github.com/pybind/pybind11.git
+$ cd pybind11
+$ mkdir build
+$ cd build
+$ cmake ..
+$ make -j 4
+```
+
+- For system managed python: `$ sudo make install`;
+- For anaconda: `$ pip install -e .`.
+
+You should be able to load `pybind11` in your python.
+
+```
+$ python
+>>> import pybind11
+```
+
+2. Build aikido and source the setup file.
+```
+$ catkin build aikido
+$ source workspace/devel/setup.bash
+```
+
+3. Create a folder `workspace/src/aikido/python/build` (instead of `workspace/src/aikido/build`). Build and install the python binding, passing the desired python version using `-DAIKIDOPY_PYTHON_VERSION`.
+
+```
+$ cd build
+$ cmake .. -DAIKIDOPY_PYTHON_VERSION=2.7 # or 3.4, 3.6 etc
+$ make -j
+$ sudo make install
+```
+
+Read the output of `sudo make install` and ensure that `aikidopy.so` get installed in the python library path (i.e. `/usr/lib/python2.7/dist-packages/aikidopy.so` or `anaconda3/envs/YOUR_ENV/lib/python3.6/site-packages/aikidopy.so`).
+
+4. Try loading.
+```
+$ python
+>>> import aikidopy
+```
+
+## Tips
+- If you have multiple python environment, ensure that `which python` and the python version you passed to cmake refers to the same python.

python/aikidopy/CMakeLists.txt

@@ -0,0 +1,101 @@
+cmake_minimum_required(VERSION 2.8.12)
+
+if(NOT AIKIDOPY_PYTHON_VERSION)
+  set(AIKIDOPY_PYTHON_VERSION 3.4 CACHE STRING "Choose the target Python version (e.g., 3.4, 2.7)" FORCE)
+endif()
+
+find_package(PythonInterp ${AIKIDOPY_PYTHON_VERSION} REQUIRED)
+execute_process(COMMAND ${PYTHON_EXECUTABLE} -c
+  "from distutils.sysconfig import get_python_lib;\
+  print(get_python_lib(plat_specific=True, prefix=''))"
+  OUTPUT_VARIABLE PYTHON_SITE_PACKAGES
+  OUTPUT_STRIP_TRAILING_WHITESPACE
+)
+if(NOT PythonInterp_FOUND)
+  message(STATUS "BUILD_PYTHON is ON, but failed to find PythonInterp. "
+    "Disabling aikidopy."
+  )
+  return()
+endif()
+
+find_package(PythonLibs ${AIKIDOPY_PYTHON_VERSION} QUIET)
+if(NOT PythonLibs_FOUND)
+  message(STATUS "BUILD_AIKIDOPY is ON, but failed to find PythonLibs. "
+    "Disabling aikidopy."
+  )
+  return()
+endif()
+
+# Find pybind11
+# Needs to set PYBIND11_PYTHON_VERSION before finding pybind11
+set(PYBIND11_PYTHON_VERSION ${AIKIDOPY_PYTHON_VERSION})
+find_package(pybind11 2.2.0 QUIET)
+if(NOT pybind11_FOUND)
+  message(STATUS "BUILD_PYTHON is ON, but failed to find pybind11 >= "
+    "2.2.0. Disabling aikidopy."
+  )
+  return()
+endif()
+
+#================================================================================
+# Dependencies
+#
+
+#================================================================================
+
+file(GLOB_RECURSE aikidopy_headers "*.h" "*.hpp")
+file(GLOB_RECURSE aikidopy_sources "*.cpp")
+
+# Build a Python extension module:
+# pybind11_add_module(<name> [MODULE | SHARED] [EXCLUDE_FROM_ALL]
+#                     [NO_EXTRAS] [SYSTEM] [THIN_LTO] source1 [source2 ...])
+#
+pybind11_add_module(aikidopy
+  MODULE
+    ${aikidopy_headers}
+    ${aikidopy_sources}
+)
+
+target_include_directories(aikidopy
+  SYSTEM PUBLIC
+    ${PYTHON_INCLUDE_DIRS}
+    ${pybind11_INCLUDE_DIRS}
+  PRIVATE
+    ${CMAKE_CURRENT_SOURCE_DIR}
+)
+
+target_link_libraries(aikidopy
+  PUBLIC
+    aikido_common
+    aikido_constraint
+    aikido_control
+    aikido_distance
+    aikido_io
+    aikido_planner
+    aikido_robot
+    aikido_statespace
+    aikido_trajectory
+    ${PYTHON_LIBRARIES}
+)
+if(TARGET aikido_control_ros)
+  target_link_libraries(aikidopy PUBLIC aikido_control_ros)
+endif()
+if(TARGET aikido_perception)
+  target_link_libraries(aikidopy PUBLIC aikido_perception)
+endif()
+if(TARGET aikido_rviz)
+  target_link_libraries(aikidopy PUBLIC aikido_rviz)
+endif()
+
+set_target_properties(aikidopy
+  PROPERTIES
+    PREFIX ""
+    SUFFIX ".so"  # python uses '.so' extension even on macOS
+    DEBUG_POSTFIX ""
+)
+
+install(TARGETS aikidopy
+  LIBRARY DESTINATION "${PYTHON_SITE_PACKAGES}"
+)
+
+clang_format_add_sources(${aikidopy_headers} ${aikidopy_sources})

python/aikidopy/aikidopy.cpp

@@ -0,0 +1,37 @@
+#include <pybind11/pybind11.h>
+
+namespace py = pybind11;
+
+namespace aikido {
+namespace python {
+
+void eigen_geometry(py::module& m);
+
+void aikidopy_common(py::module& m);
+void aikidopy_statespace(py::module& m);
+void aikidopy_constraint(py::module& m);
+void aikidopy_planner(py::module& m);
+void aikidopy_robot(py::module& m);
+#ifdef AIKIDO_HAS_RVIZ
+void aikidopy_rviz(py::module& m);
+#endif // AIKIDO_HAS_RVIZ
+
+PYBIND11_MODULE(aikidopy, m)
+{
+  py::module::import("numpy");
+
+  m.doc() = "aikidopy is a Python library for solving robotic motion planning "
+      "and decision making problems.";
+
+  aikidopy_common(m);
+  aikidopy_statespace(m);
+  aikidopy_constraint(m);
+  aikidopy_planner(m);
+  aikidopy_robot(m);
+#ifdef AIKIDO_HAS_RVIZ
+  aikidopy_rviz(m);
+#endif // AIKIDO_HAS_RVIZ
+}
+
+} // namespace python
+} // namespace aikido

python/aikidopy/common/module.cpp

@@ -0,0 +1,14 @@
+#include <pybind11/pybind11.h>
+
+namespace py = pybind11;
+
+namespace aikido {
+namespace python {
+
+void aikidopy_common(py::module& m)
+{
+  auto sm = m.def_submodule("common");
+}
+
+} // namespace python
+} // namespace aikido

python/aikidopy/constraint/dart/CollisionFree.cpp

@@ -0,0 +1,16 @@
+#include <pybind11/pybind11.h>
+#include <aikido/constraint.hpp>
+#include <aikido/constraint/dart/CollisionFree.hpp>
+
+namespace py = pybind11;
+
+namespace aikido {
+namespace python {
+
+void CollisionFree(py::module& m)
+{
+  py::class_<aikido::constraint::dart::CollisionFree, std::shared_ptr<aikido::constraint::dart::CollisionFree>>(m, "CollisionFree");
+}
+
+} // namespace python
+} // namespace aikido