Merge branch 'develop' into matlab-update

.github/scripts/python.sh

@@ -39,8 +39,6 @@ function install_dependencies()
   if [ "${GTSAM_WITH_TBB:-OFF}" == "ON" ]; then
     install_tbb
   fi
-
-  $PYTHON -m pip install -r $GITHUB_WORKSPACE/python/requirements.txt
 }
 
 function build()

.github/workflows/build-python.yml

@@ -109,10 +109,13 @@ jobs:
         with:
           swap-size-gb: 6
 
-      - name: Install Dependencies
+      - name: Install System Dependencies
         run: |
           bash .github/scripts/python.sh -d
 
+      - name: Install Python Dependencies
+        run: python$PYTHON_VERSION -m pip install -r python/dev_requirements.txt
+
       - name: Build
         run: |
           bash .github/scripts/python.sh -b

.github/workflows/build-windows.yml

@@ -150,7 +150,10 @@ jobs:
           # cmake --build build -j4 --config ${{ matrix.build_type }} --target check.dynamics_unstable
           # Compile. Fail with exception
           # cmake --build build -j4 --config ${{ matrix.build_type }} --target check.nonlinear_unstable
-          # Compilation error
+          # Compile. Fail with exception
           # cmake --build build -j4 --config ${{ matrix.build_type }} --target check.slam_unstable
-          # Compilation error
+          # Compile. Fail with exception
           # cmake --build build -j4 --config ${{ matrix.build_type }} --target check.partition
+
+          # Run all tests
+          # cmake --build build -j1 --config ${{ matrix.build_type }} --target check

CMakeLists.txt

@@ -1,11 +1,5 @@
 cmake_minimum_required(VERSION 3.0)
 
-# new feature to Cmake Version > 2.8.12
-# Mac ONLY. Define Relative Path on Mac OS
-if(NOT DEFINED CMAKE_MACOSX_RPATH)
-  set(CMAKE_MACOSX_RPATH 0)
-endif()
-
 # Set the version number for the library
 set (GTSAM_VERSION_MAJOR 4)
 set (GTSAM_VERSION_MINOR 3)

INSTALL.md

@@ -182,7 +182,7 @@ Here are some tips to get the best possible performance out of GTSAM.
     optimization by 30-50%. Please note that this may not be true for very small 
     problems where the overhead of dispatching work to multiple threads outweighs
     the benefit. We recommend that you benchmark your problem with/without TBB.
-3. Add `-march=native` to `GTSAM_CMAKE_CXX_FLAGS`. A performance gain of
+3. Use `GTSAM_BUILD_WITH_MARCH_NATIVE`. A performance gain of
     25-30% can be expected on modern processors. Note that this affects the portability
     of your executable. It may not run when copied to another system with older/different
     processor architecture.

docker/ubuntu-gtsam-python/Dockerfile

@@ -6,9 +6,6 @@ FROM borglab/ubuntu-gtsam:bionic
 # Install pip
 RUN apt-get install -y python3-pip python3-dev
 
-# Install python wrapper requirements
-RUN python3 -m pip install -U -r /usr/src/gtsam/python/requirements.txt
-
 # Run cmake again, now with python toolbox on
 WORKDIR /usr/src/gtsam/build
 RUN cmake \

gtsam/base/serialization.h

@@ -17,6 +17,7 @@
  * @date Feb 7, 2012
  */
 
+#ifdef GTSAM_ENABLE_BOOST_SERIALIZATION
 #pragma once
 
 #include <Eigen/Core>
@@ -270,3 +271,4 @@ void deserializeBinary(const std::string& serialized, T& output,
 ///@}
 
 }  // namespace gtsam
+#endif

gtsam/discrete/AlgebraicDecisionTree.h

@@ -36,7 +36,7 @@ namespace gtsam {
    * @ingroup discrete
    */
   template <typename L>
-  class GTSAM_EXPORT AlgebraicDecisionTree : public DecisionTree<L, double> {
+  class AlgebraicDecisionTree : public DecisionTree<L, double> {
     /**
      * @brief Default method used by `labelFormatter` or `valueFormatter` when
      * printing.

gtsam/linear/SubgraphBuilder.h

@@ -182,7 +182,7 @@ GaussianFactorGraph buildFactorSubgraph(const GaussianFactorGraph &gfg,
 
 /** Split the graph into a subgraph and the remaining edges. 
  * Note that the remaining factorgraph has null factors. */
-std::pair<GaussianFactorGraph, GaussianFactorGraph> splitFactorGraph(
+std::pair<GaussianFactorGraph, GaussianFactorGraph> GTSAM_EXPORT splitFactorGraph(
     const GaussianFactorGraph &factorGraph, const Subgraph &subgraph);
 
 }  // namespace gtsam

gtsam/nonlinear/NonlinearFactor.h

@@ -46,7 +46,7 @@ namespace gtsam {
  * Had to use the static_cast of a nullptr, because the compiler is not able to
  * deduce the type of the nullptr when expanding the evaluateError templates.
  */
-#define OptionalNone static_cast<Matrix*>(nullptr)
+#define OptionalNone static_cast<gtsam::Matrix*>(nullptr)
 
 /** This typedef will be used everywhere boost::optional<Matrix&> reference was used
  * previously. This is used to indicate that the Jacobian is optional. In the future

gtsam/sfm/TranslationRecovery.h

@@ -48,7 +48,7 @@ namespace gtsam {
 // where s is an arbitrary scale that can be supplied, default 1.0. Hence, two
 // versions are supplied below corresponding to whether we have initial values
 // or not.
-class TranslationRecovery {
+class GTSAM_EXPORT TranslationRecovery {
  public:
   using KeyPair = std::pair<Key, Key>;
   using TranslationEdges = std::vector<BinaryMeasurement<Unit3>>;

gtsam_unstable/geometry/Event.h

@@ -34,7 +34,7 @@ namespace gtsam {
  * SLAM, where we have "time of arrival" measurements at a set of sensors. The
  * TOA functor below provides a measurement function for those applications.
  */
-class Event {
+class GTSAM_UNSTABLE_EXPORT Event {
   double time_;      ///< Time event was generated
   Point3 location_;  ///< Location at time event was generated
 
@@ -62,10 +62,10 @@ class Event {
   }
 
   /** print with optional string */
-  GTSAM_UNSTABLE_EXPORT void print(const std::string& s = "") const;
+  void print(const std::string& s = "") const;
 
   /** equals with an tolerance */
-  GTSAM_UNSTABLE_EXPORT bool equals(const Event& other,
+  bool equals(const Event& other,
                                     double tol = 1e-9) const;
 
   /// Updates a with tangent space delta

gtsam_unstable/partition/GenericGraph.h

@@ -14,6 +14,7 @@
 #include <stdexcept>
 #include <string>
 #include <memory>
+#include <gtsam_unstable/dllexport.h>
 
 #include "PartitionWorkSpace.h"
 
@@ -49,7 +50,7 @@ namespace gtsam { namespace partition {
   typedef std::vector<sharedGenericFactor2D> GenericGraph2D;
 
   /** merge nodes in DSF using constraints captured by the given graph */
-  std::list<std::vector<size_t> > findIslands(const GenericGraph2D& graph, const std::vector<size_t>& keys, WorkSpace& workspace,
+  std::list<std::vector<size_t> > GTSAM_UNSTABLE_EXPORT findIslands(const GenericGraph2D& graph, const std::vector<size_t>& keys, WorkSpace& workspace,
       const int minNrConstraintsPerCamera, const int minNrConstraintsPerLandmark);
 
   /** eliminate the sensors from generic graph */
@@ -97,11 +98,11 @@ namespace gtsam { namespace partition {
   typedef std::vector<sharedGenericFactor3D> GenericGraph3D;
 
   /** merge nodes in DSF using constraints captured by the given graph */
-  std::list<std::vector<size_t> > findIslands(const GenericGraph3D& graph, const std::vector<size_t>& keys, WorkSpace& workspace,
+  std::list<std::vector<size_t> > GTSAM_UNSTABLE_EXPORT findIslands(const GenericGraph3D& graph, const std::vector<size_t>& keys, WorkSpace& workspace,
       const size_t minNrConstraintsPerCamera, const size_t minNrConstraintsPerLandmark);
 
   /** eliminate the sensors from generic graph */
-  void reduceGenericGraph(const GenericGraph3D& graph, const std::vector<size_t>& cameraKeys,  const std::vector<size_t>& landmarkKeys,
+  void GTSAM_UNSTABLE_EXPORT reduceGenericGraph(const GenericGraph3D& graph, const std::vector<size_t>& cameraKeys,  const std::vector<size_t>& landmarkKeys,
       const std::vector<int>& dictionary,  GenericGraph3D& reducedGraph);
 
   /** check whether the 3D graph is singular (under constrained) */

gtsam_unstable/partition/tests/CMakeLists.txt

@@ -1,6 +1,6 @@
 set(ignore_test "testNestedDissection.cpp")
 
-if (NOT GTSAM_USE_BOOST_FEATURES)
+if (NOT GTSAM_USE_BOOST_FEATURES OR MSVC)
 	list(APPEND ignore_test "testFindSeparator.cpp")
 endif()
 

gtsam_unstable/slam/ProjectionFactorPPPC.h

@@ -32,7 +32,7 @@ namespace gtsam {
    * @ingroup slam
    */
 template <class POSE, class LANDMARK, class CALIBRATION = Cal3_S2>
-class GTSAM_UNSTABLE_EXPORT ProjectionFactorPPPC
+class ProjectionFactorPPPC
     : public NoiseModelFactorN<POSE, POSE, LANDMARK, CALIBRATION> {
  protected:
   Point2 measured_;  ///< 2D measurement

gtsam_unstable/slam/SmartProjectionPoseFactorRollingShutter.h

@@ -42,7 +42,7 @@ namespace gtsam {
  * @ingroup slam
  */
 template <class CAMERA>
-class GTSAM_UNSTABLE_EXPORT SmartProjectionPoseFactorRollingShutter
+class SmartProjectionPoseFactorRollingShutter
     : public SmartProjectionFactor<CAMERA> {
  private:
   typedef SmartProjectionFactor<CAMERA> Base;

gtsam_unstable/slam/tests/testSmartStereoProjectionPoseFactor.cpp

@@ -1441,14 +1441,14 @@ TEST( SmartStereoProjectionPoseFactor, HessianWithRotationNonDegenerate ) {
   std::shared_ptr<GaussianFactor> hessianFactorRotTran =
       smartFactor->linearize(tranValues);
 
-  // Hessian is invariant to rotations and translations in the degenerate case
-  EXPECT(
-      assert_equal(hessianFactor->information(),
+  double error;
 #ifdef GTSAM_USE_EIGEN_MKL
-          hessianFactorRotTran->information(), 1e-5));
+  error = 1e-5;
 #else
-          hessianFactorRotTran->information(), 1e-6));
+  error = 1e-6;
 #endif
+  // Hessian is invariant to rotations and translations in the degenerate case
+  EXPECT(assert_equal(hessianFactor->information(), hessianFactorRotTran->information(), error));
 }
 
 /* ************************************************************************* */

python/CMakeLists.txt

@@ -1,3 +1,4 @@
+set(PROJECT_PYTHON_SOURCE_DIR ${PROJECT_SOURCE_DIR}/python)
 set(GTSAM_PYTHON_BUILD_DIRECTORY ${PROJECT_BINARY_DIR}/python)
 
 if (NOT GTSAM_BUILD_PYTHON)
@@ -6,11 +7,11 @@ endif()
 
 # Generate setup.py.
 file(READ "${PROJECT_SOURCE_DIR}/README.md" README_CONTENTS)
-configure_file(${PROJECT_SOURCE_DIR}/python/setup.py.in
+configure_file(${PROJECT_PYTHON_SOURCE_DIR}/setup.py.in
                 ${GTSAM_PYTHON_BUILD_DIRECTORY}/setup.py)
 
 # Supply MANIFEST.in for older versions of Python
-file(COPY ${PROJECT_SOURCE_DIR}/python/MANIFEST.in
+file(COPY ${PROJECT_PYTHON_SOURCE_DIR}/MANIFEST.in
      DESTINATION ${GTSAM_PYTHON_BUILD_DIRECTORY})
 
 set(WRAP_BUILD_TYPE_POSTFIXES ${GTSAM_BUILD_TYPE_POSTFIXES})
@@ -99,7 +100,7 @@ pybind_wrap(${GTSAM_PYTHON_TARGET} # target
             "gtsam" # module_name
             "gtsam" # top_namespace
             "${ignore}" # ignore_classes
-            ${PROJECT_SOURCE_DIR}/python/gtsam/gtsam.tpl
+            ${PROJECT_PYTHON_SOURCE_DIR}/gtsam/gtsam.tpl
             gtsam # libs
             "gtsam;gtsam_header" # dependencies
             ${GTSAM_ENABLE_BOOST_SERIALIZATION} # use_boost_serialization
@@ -178,7 +179,7 @@ if(GTSAM_UNSTABLE_BUILD_PYTHON)
             "gtsam_unstable" # module_name
             "gtsam" # top_namespace
             "${ignore}" # ignore_classes
-            ${PROJECT_SOURCE_DIR}/python/gtsam_unstable/gtsam_unstable.tpl
+            ${PROJECT_PYTHON_SOURCE_DIR}/gtsam_unstable/gtsam_unstable.tpl
             gtsam_unstable # libs
             "gtsam_unstable;gtsam_unstable_header" # dependencies
             ${GTSAM_ENABLE_BOOST_SERIALIZATION} # use_boost_serialization

python/README.md

@@ -16,7 +16,7 @@ For instructions on updating the version of the [wrap library](https://github.co
 - This wrapper needs `pyparsing(>=2.4.2)`, and `numpy(>=1.11.0)`. These can be installed as follows:
 
   ```bash
-  pip install -r <gtsam_folder>/python/requirements.txt
+  pip install -r <gtsam_folder>/python/dev_requirements.txt
   ```
 
 ## Install

python/dev_requirements.txt

@@ -0,0 +1,2 @@
+-r requirements.txt
+pyparsing>=2.4.2

python/requirements.txt

@@ -1,2 +1 @@
 numpy>=1.11.0
-pyparsing>=2.4.2

python/setup.py.in

@@ -1,19 +1,17 @@
 """Setup file to install the GTSAM package."""
 
-try:
-    from setuptools import setup, find_packages
-except ImportError:
-    from distutils.core import setup, find_packages
+from setuptools import setup, find_namespace_packages
 
-packages = find_packages(where=".")
+packages = find_namespace_packages(
+    where=".",
+    exclude=('build', 'build.*', 'CMakeFiles', 'CMakeFiles.*',
+             'gtsam.notebooks', '*.preamble', '*.specializations', 'dist'))
 print("PACKAGES: ", packages)
 
 package_data = {
     '': [
         "./*.so",
-        "./*.dll",
-        "Data/*"  # Add the data files to the package
-        "Data/**/*"  # Add the data files in subdirectories
+        "./*.dll"
     ]
 }
 
@@ -41,7 +39,6 @@ setup(
         'Operating System :: Microsoft :: Windows',
         'Operating System :: POSIX',
         'License :: OSI Approved :: BSD License',
-        'Programming Language :: Python :: 2',
         'Programming Language :: Python :: 3',
     ],
     packages=packages,