Port Python bindings to Cython (#36)

* Switch to Cython bindings

* [ci] Adapt travis.yml to changes

* [ci] Prevent install directory removal

* Move wrapper functions to private pxd

* Update copyright

* Fix pickling and unit tests

* Fixes for Python 3

* [CI] Setup a Python 3.4 CI build

* Add an option to install Python bindings to user space

* Fix a few more Python 3 string issues

* Use Eigen3ToPython and SVA master

* Squashed '.travis/' changes from 7a40a28..bad6dbd

bad6dbd Allow to specify pybindgen install prefix
3f214dd Update pybindgen archive url
f13ddca Use a common script for Eigen 3.2 and 3.3
0d26976 Add a script for Eigen 3.3
027bca4 Update Eigen 3.2 version to 3.2.10
629f539 ipopt: update to 3.12.6
87f7ee7 eigen: update to 3.2.9
a0c7e47 common.sh: fix OS X environment
811fbd6 Merge pull request #31 from francois-keith/dev4
4c8a74c Hard code the path to git.exe
8c1c5f5 Build in debug.
89d0b39 Add some intermediary checks.
c2f4554 [AppVeyor] Add a method to run the unit tests.
e59a441 Correct choco install.
af4c533 Merge pull request #30 from jcarpent/master
00d90b0 Fix bug in common.sh
9da636c Merge pull request #29 from jcarpent/master
dd15db5 Use CI_BRANCH instead of TRAVIS_BRANCH
448cc3f Set DO_*_ON_BRANCH to the current branch if they are not yet defined
c5ed776 [Cppcheck] Do ccpcheck only on specified branches
3c52bd1 [Coverage] Do coverage only on specified branches
2a03b5b [AppVeyor] Support for projects with fortran subdirectory
b819e8a dependencies: add missing -qq for apt-get
9b94f1a dependencies/ipopt: install dependencies with apt
7b21446 dependencies: add script to install Ipopt from source
211e163 Merge pull request #28 from gergondet/topic/Win32
8f7b969 [Win32] Add AppVeyor support
REVERT: 7a40a28 Update submodule before building
REVERT: bc0a72e [Win32] Solve an issue in functions
REVERT: 99d898d [Win32] Add AppVeyor support

git-subtree-dir: .travis
git-subtree-split: bad6dbd29cf70e852e5e427e876390d954ca7d6b

* Fix test include path

.gitignore

@@ -1,3 +1,8 @@
 *.pyc
 *~
 .clang-format
+binding/python/build/
+binding/python/rbdyn/rbdyn.cpp
+binding/python/rbdyn/rbdyn.so
+binding/python/rbdyn/__init__.py
+binding/python/setup.py

.travis.yml

@@ -1,4 +1,4 @@
-# Copyright 2012-2016 CNRS-UM LIRMM, CNRS-AIST JRL
+# Copyright 2012-2017 CNRS-UM LIRMM, CNRS-AIST JRL
 #
 # This file is part of RBDyn.
 #
@@ -19,24 +19,29 @@ sudo: required
 dist: trusty
 language: cpp
 compiler:
-  - gcc
-  - clang
+- gcc
+- clang
 env:
   global:
-  - APT_DEPENDENCIES="doxygen doxygen-latex libboost-all-dev python-numpy"
-  - GIT_DEPENDENCIES="jrl-umi3218/SpaceVecAlg"
+  - APT_DEPENDENCIES="doxygen doxygen-latex libboost-all-dev"
+  - GIT_DEPENDENCIES="jrl-umi3218/Eigen3ToPython jrl-umi3218/SpaceVecAlg"
   - GH_USERNAME=gergondet
   - GH_REPO=jrl-umi3218/RBDyn
-  - secure: "FCe7ktcmBJWgEFsCBnG1QfIhkgNKM3uyRMS9mXiY8hfGQ9KGj/9X4qebUmfZ1ay6Rw2B22FXpRiJk2GmsHxo1RZH3f27b6F1mWz25RgJGX986k2nPChCshf5gORfMI5BKksyXFzp24sXBLcYKGz/xrOioSUY1wPJ3JZ7r7kDEV4="
+  - secure: FCe7ktcmBJWgEFsCBnG1QfIhkgNKM3uyRMS9mXiY8hfGQ9KGj/9X4qebUmfZ1ay6Rw2B22FXpRiJk2GmsHxo1RZH3f27b6F1mWz25RgJGX986k2nPChCshf5gORfMI5BKksyXFzp24sXBLcYKGz/xrOioSUY1wPJ3JZ7r7kDEV4=
+  matrix:
+    - USE_PYTHON34=false
+    - USE_PYTHON34=true
 notifications:
-  email:
-  - [email protected]
+  slack:
+    rooms:
+      secure: N2C/Q9nr/TNjVE1UIRhT7gXN6bfJCe1nH7FIMA0RrANsdGkGsJHhuJsiOs8cUE7ozRFSiZ/ewMSADqItfwwp692pI1wp2y0X8wxRMB3pmo01Owv7on6NgLHXY4Br6peCSwGem3MaywcN8QaBlPxNVXFTfGi39GDvA8szLkCGHGw=
 script: ./.travis/run build
 after_success: ./.travis/run after_success
 after_failure: ./.travis/run after_failure
 before_install:
-  - ./.travis/dependencies/eigen-3.2
-  - ./.travis/run  before_install
+- if [ $USE_PYTHON34 = true ]; then pushd .; pip install virtualenv; mkdir -p /tmp/_ci/virtualenv; virtualenv -p python3.4 3.4; source 3.4/bin/activate; popd; fi
+- ./.travis/dependencies/eigen-3.2
+- ./.travis/run  before_install
 matrix:
   allow_failures:
-    - compiler: clang
+  - compiler: clang

.travis/after_success

@@ -113,7 +113,10 @@ elif [[ ${CI_OS_NAME} = linux ]]; then
       exit 0
     fi
 
-    generate_coverage_data
+    if [[ ";${DO_COVERAGE_ON_BRANCH};" == *";${CI_BRANCH};"* ]]; then
+      generate_coverage_data
+    fi
+
     # If it's not a fork or a pull request
     if `test x${CI_REPO_SLUG} = x${GH_REPO} -a ${CI_PULL_REQUEST} = false`; then
       set_push_uri

.travis/build

@@ -15,23 +15,32 @@ build_package()
     echo "--> Building package..."
 
     cd "$build_dir"
-    cmake "$root_dir" -DCMAKE_INSTALL_PREFIX="$install_dir"	\
-      -DCMAKE_CXX_FLAGS="--coverage"				\
-      -DCMAKE_EXE_LINKER_FLAGS="--coverage"			\
-      -DCMAKE_MODULE_LINKER_FLAGS="--coverage"		\
-      ${CMAKE_ADDITIONAL_OPTIONS}
+
+    if [[ ";${DO_COVERAGE_ON_BRANCH};" == *";${CI_BRANCH};"* ]]; then
+      cmake "$root_dir" -DCMAKE_INSTALL_PREFIX="$install_dir"	\
+        -DCMAKE_CXX_FLAGS="--coverage"				\
+        -DCMAKE_EXE_LINKER_FLAGS="--coverage"			\
+        -DCMAKE_MODULE_LINKER_FLAGS="--coverage"		\
+        ${CMAKE_ADDITIONAL_OPTIONS}
+    else
+      cmake "$root_dir" -DCMAKE_INSTALL_PREFIX="$install_dir"	\
+        ${CMAKE_ADDITIONAL_OPTIONS}
+    fi
+
     ${MAKE_PREFIX} make
     make install
 
     ALLOW_TESTSUITE_FAILURE=${ALLOW_TESTSUITE_FAILURE:-false}
     make test || ${ALLOW_TESTSUITE_FAILURE}
 
-    cppcheck --quiet --enable=all \
-      -I $root_dir/src -I $root_dir/tests -I $root_dir/include \
-      -I $root_dir/tests/shared-tests \
-      -I $build_dir/include -I $install_dir/include \
-      -i $build_dir/CMakeFiles \
-      $root_dir || true
+    if [[ ";${DO_CPPCHECK_ON_BRANCH};" == *";${CI_BRANCH};"* ]]; then
+      cppcheck --quiet --enable=all \
+        -I $root_dir/src -I $root_dir/tests -I $root_dir/include \
+        -I $root_dir/tests/shared-tests \
+        -I $build_dir/include -I $install_dir/include \
+        -i $build_dir/CMakeFiles \
+        $root_dir || true
+    fi
 }
 
 # debian_build_package

.travis/common.sh

@@ -188,6 +188,10 @@ _setup_osx_env()
     export CXX=g++-4.8
     export CC=gcc-4.8
   fi
+
+  export DYLD_LIBRARY_PATH="$install_dir/lib:$DYLD_LIBRARY_PATH"
+  export LTDL_LIBRARY_PATH="$install_dir/lib:$LTDL_LIBRARY_PATH"
+  export PKG_CONFIG_PATH="$install_dir/lib/pkgconfig:$PKG_CONFIG_PATH"
 }
 
 # setup_ci_env
@@ -227,6 +231,15 @@ setup_ci_env
 export CMAKE_VERBOSE_MAKEFILE=1
 export CTEST_OUTPUT_ON_FAILURE=1
 
+# Add default DO_*_ON_BRANCH if needed
+if [ -z ${DO_COVERAGE_ON_BRANCH+x} ]; then
+  export DO_COVERAGE_ON_BRANCH=${CI_BRANCH}
+fi
+
+if [ -z ${DO_CPPCHECK_ON_BRANCH+x} ]; then
+  export DO_CPPCHECK_ON_BRANCH=${CI_BRANCH}
+fi
+
 # Create layout.
 mkdir -p "$build_dir"
 mkdir -p "$install_dir"

.travis/dependencies/eigen-3.2

@@ -2,24 +2,7 @@
 #
 # Setup Eigen 3.2
 #
-. `dirname $0`/../common.sh
+EIGEN_VERSION=3.2.10
+EIGEN_HASH=b9cd8366d4e8
 
-EIGEN_VERSION=3.2.8
-EIGEN_HASH=07105f7124f9
-
-# Checkout Eigen
-cd "$build_dir"
-wget --quiet "http://bitbucket.org/eigen/eigen/get/${EIGEN_VERSION}.tar.gz"
-tar xzf ${EIGEN_VERSION}.tar.gz
-cd "$build_dir/eigen-eigen-${EIGEN_HASH}/"
-mkdir -p "$build_dir/eigen-eigen-${EIGEN_HASH}/_build"
-cd "$build_dir/eigen-eigen-${EIGEN_HASH}/_build"
-
-# Build, make and install Eigen
-cmake .. -DCMAKE_INSTALL_PREFIX:STRING="$install_dir"
-make
-make install
-
-# Check install
-pkg-config --modversion "eigen3 >= ${EIGEN_VERSION}"
-pkg-config --cflags "eigen3 >= ${EIGEN_VERSION}"
+. `dirname $0`/eigen-common.sh $EIGEN_VERSION $EIGEN_HASH

.travis/dependencies/eigen-3.3

@@ -0,0 +1,8 @@
+#!/bin/bash
+#
+# Setup Eigen 3.3
+#
+EIGEN_VERSION=3.3.1
+EIGEN_HASH=f562a193118d
+
+. `dirname $0`/eigen-common.sh $EIGEN_VERSION $EIGEN_HASH

.travis/dependencies/eigen-common.sh

@@ -0,0 +1,25 @@
+#!/bin/bash
+#
+# Setup Eigen
+#
+. `dirname $0`/../common.sh
+
+EIGEN_VERSION=$1
+EIGEN_HASH=$2
+
+# Checkout Eigen
+cd "$build_dir"
+wget --quiet "http://bitbucket.org/eigen/eigen/get/${EIGEN_VERSION}.tar.gz"
+tar xzf ${EIGEN_VERSION}.tar.gz
+cd "$build_dir/eigen-eigen-${EIGEN_HASH}/"
+mkdir -p "$build_dir/eigen-eigen-${EIGEN_HASH}/_build"
+cd "$build_dir/eigen-eigen-${EIGEN_HASH}/_build"
+
+# Build, make and install Eigen
+cmake .. -DCMAKE_INSTALL_PREFIX:STRING="$install_dir"
+make
+make install
+
+# Check install
+pkg-config --modversion "eigen3 >= ${EIGEN_VERSION}"
+pkg-config --cflags "eigen3 >= ${EIGEN_VERSION}"

.travis/dependencies/ipopt

@@ -8,7 +8,7 @@
 ${SUDO_CMD} apt-get update -qq
 ${SUDO_CMD} apt-get install -qq libblas-dev liblapack-dev libmumps-seq-dev gfortran
 
-IPOPT_VERSION=3.12.4
+IPOPT_VERSION=3.12.6
 
 build_dir=`mktemp -d`
 trap "rm -rf -- '$build_dir'" EXIT

.travis/dependencies/pybindgen-0.16

@@ -4,16 +4,22 @@
 
 . `dirname $0`/../common.sh
 
+if [ $# -ge 1 ]; then
+  PYBINDGEN_INSTALL_PREFIX=$1
+else
+  PYBINDGEN_INSTALL_PREFIX=/usr/local
+fi
+
 # Install dependencies
 ${SUDO_CMD} apt-get install -qq gccxml python-pygccxml
 
 # Get pybindgen
 cd "$build_dir"
-wget --quiet https://pybindgen.googlecode.com/files/pybindgen-0.16.0.tar.bz2
+wget --quiet https://launchpad.net/pybindgen/trunk/0.16/+download/pybindgen-0.16.0.tar.bz2
 tar xjf pybindgen-0.16.0.tar.bz2
 cd "$build_dir/pybindgen-0.16.0/"
 
 # Configure build and install
-./waf configure
+./waf --prefix=$PYBINDGEN_INSTALL_PREFIX configure
 ./waf
 ${SUDO_CMD} ./waf install

.travis/functions.ps1

@@ -62,7 +62,7 @@ function install_choco_dependencies
 {
   ForEach($choco_dep in $Env:CHOCO_DEPENDENCIES.split(' '))
   {
-    choco install $choco_dep
+    choco install $choco_dep -y
   }
 }
 
@@ -75,13 +75,17 @@ function install_git_dependencies
     git clone -b "$git_dep_branch" "$git_dep_uri" "$git_dep"
     cd $git_dep
     git submodule update --init
+    if ($lastexitcode -ne 0){ exit $lastexitcode }
     md build
     cd build
     # For projects that use cmake_add_subfortran directory this removes sh.exe
     # from the path
     $Env:Path = $Env:Path -replace "Git","dummy"
-    cmake ../ -G "Visual Studio 14 2015 Win64" -DCMAKE_INSTALL_PREFIX="${Env:CMAKE_INSTALL_PREFIX}" -DPYTHON_BINDING=OFF -DMINGW_GFORTRAN="$env:MINGW_GFORTRAN"
-    msbuild INSTALL.vcxproj
+    cmake ../ -G "Visual Studio 14 2015 Win64" -DCMAKE_INSTALL_PREFIX="${Env:CMAKE_INSTALL_PREFIX}" -DPYTHON_BINDING=OFF -DMINGW_GFORTRAN="$env:MINGW_GFORTRAN" -DGIT="C:/Program Files/Git/cmd/git.exe"
+
+    if ($lastexitcode -ne 0){ exit $lastexitcode }
+    msbuild INSTALL.vcxproj /p:Configuration=Debug
+    if ($lastexitcode -ne 0){ exit $lastexitcode }
     # Reverse our dirty work
     $Env:Path = $Env:Path -replace "dummy","Git"
   }
@@ -97,11 +101,26 @@ function build_project
 {
   cd $Env:PROJECT_SOURCE_DIR
   git submodule update --init
+  if ($lastexitcode -ne 0){ exit $lastexitcode }
   md build
   cd build
   # See comment in dependencies regarding $Env:Path manipulation
   $Env:Path = $Env:Path -replace "Git","dummy"
-  cmake ../ -G "Visual Studio 14 2015 Win64" -DCMAKE_INSTALL_PREFIX="${Env:CMAKE_INSTALL_PREFIX}" -DPYTHON_BINDING=OFF -DMINGW_GFORTRAN="$env:MINGW_GFORTRAN"
-  msbuild INSTALL.vcxproj
+  cmake ../ -G "Visual Studio 14 2015 Win64" -DCMAKE_INSTALL_PREFIX="${Env:CMAKE_INSTALL_PREFIX}" -DPYTHON_BINDING=OFF -DMINGW_GFORTRAN="$env:MINGW_GFORTRAN" -DGIT="C:/Program Files/Git/cmd/git.exe"
+  if ($lastexitcode -ne 0){ exit $lastexitcode }
+  msbuild INSTALL.vcxproj /p:Configuration=Debug
+  if ($lastexitcode -ne 0){ exit $lastexitcode }
   $Env:Path = $Env:Path -replace "dummy","Git"
 }
+
+function test_project
+{
+  cd %PROJECT_SOURCE_DIR%/build
+  ctest -N
+  ctest --build-config Debug --exclude-regex example
+  if ($lastexitcode -ne 0)
+  {
+    type Testing/Temporary/LastTest.log
+    exit $lastexitcode
+  }
+}

CMakeLists.txt

@@ -1,4 +1,4 @@
-# Copyright 2012-2016 CNRS-UM LIRMM, CNRS-AIST JRL
+# Copyright 2012-2017 CNRS-UM LIRMM, CNRS-AIST JRL
 #
 # This file is part of RBDyn.
 #
@@ -33,7 +33,8 @@ SET(CXX_DISABLE_WERROR True)
 
 SETUP_PROJECT()
 
-option(PYTHON_BINDING "Generate python binding." OFF)
+option(PYTHON_BINDING "Generate python binding." ON)
+option(PYTHON_BINDING_USER_INSTALL "Install the Python bindings in user space" OFF)
 option(DISABLE_TESTS "Disable unit tests." OFF)
 option(BENCHMARKS "Generate benchmarks." OFF)
 
@@ -55,6 +56,8 @@ IF(MSVC)
   SET(CMAKE_MSVCIDE_RUN_PATH "\$(SolutionDir)/src/\$(Configuration)")
 ENDIF(MSVC)
 
+include_directories(${CMAKE_CURRENT_SOURCE_DIR}/src)
+
 add_subdirectory(src)
 
 if(NOT ${DISABLE_TESTS} OR ${BENCHMARKS})