Merge branch 'develop' into fix/combined-imu-cov

.github/scripts/python.sh

@@ -75,14 +75,14 @@ cmake $GITHUB_WORKSPACE -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE} \
     -DGTSAM_UNSTABLE_BUILD_PYTHON=${GTSAM_BUILD_UNSTABLE:-ON} \
     -DGTSAM_PYTHON_VERSION=$PYTHON_VERSION \
     -DPYTHON_EXECUTABLE:FILEPATH=$(which $PYTHON) \
-    -DGTSAM_ALLOW_DEPRECATED_SINCE_V41=OFF \
+    -DGTSAM_ALLOW_DEPRECATED_SINCE_V42=OFF \
     -DCMAKE_INSTALL_PREFIX=$GITHUB_WORKSPACE/gtsam_install
 
 
 # Set to 2 cores so that Actions does not error out during resource provisioning.
 make -j2 install
 
 cd $GITHUB_WORKSPACE/build/python
-$PYTHON setup.py install --user --prefix=
+$PYTHON -m pip install --user .
 cd $GITHUB_WORKSPACE/python/gtsam/tests
 $PYTHON -m unittest discover -v

.github/scripts/unix.sh

@@ -64,13 +64,14 @@ function configure()
       -DGTSAM_BUILD_UNSTABLE=${GTSAM_BUILD_UNSTABLE:-ON} \
       -DGTSAM_WITH_TBB=${GTSAM_WITH_TBB:-OFF} \
       -DGTSAM_BUILD_EXAMPLES_ALWAYS=${GTSAM_BUILD_EXAMPLES_ALWAYS:-ON} \
-      -DGTSAM_ALLOW_DEPRECATED_SINCE_V41=${GTSAM_ALLOW_DEPRECATED_SINCE_V41:-OFF} \
+      -DGTSAM_ALLOW_DEPRECATED_SINCE_V42=${GTSAM_ALLOW_DEPRECATED_SINCE_V42:-OFF} \
       -DGTSAM_USE_QUATERNIONS=${GTSAM_USE_QUATERNIONS:-OFF} \
       -DGTSAM_ROT3_EXPMAP=${GTSAM_ROT3_EXPMAP:-ON} \
       -DGTSAM_POSE3_EXPMAP=${GTSAM_POSE3_EXPMAP:-ON} \
       -DGTSAM_USE_SYSTEM_EIGEN=${GTSAM_USE_SYSTEM_EIGEN:-OFF} \
       -DGTSAM_USE_SYSTEM_METIS=${GTSAM_USE_SYSTEM_METIS:-OFF} \
       -DGTSAM_BUILD_WITH_MARCH_NATIVE=OFF \
+      -DGTSAM_SINGLE_TEST_EXE=ON \
       -DBOOST_ROOT=$BOOST_ROOT \
       -DBoost_NO_SYSTEM_PATHS=ON \
       -DBoost_ARCHITECTURE=-x64
@@ -95,7 +96,11 @@ function build ()
   configure
 
   if [ "$(uname)" == "Linux" ]; then
-    make -j$(nproc)
+    if (($(nproc) > 2)); then
+      make -j$(nproc)
+    else
+      make -j2
+    fi
   elif [ "$(uname)" == "Darwin" ]; then
     make -j$(sysctl -n hw.physicalcpu)
   fi
@@ -113,9 +118,13 @@ function test ()
 
   # Actual testing
   if [ "$(uname)" == "Linux" ]; then
-    make -j$(nproc)
+    if (($(nproc) > 2)); then
+      make -j$(nproc) check
+    else
+      make -j2 check
+    fi
   elif [ "$(uname)" == "Darwin" ]; then
-    make -j$(sysctl -n hw.physicalcpu)
+    make -j$(sysctl -n hw.physicalcpu) check
   fi
 
   finish

.github/workflows/build-linux.yml

@@ -15,7 +15,7 @@ jobs:
       BOOST_VERSION: 1.67.0
 
     strategy:
-      fail-fast: false
+      fail-fast: true
       matrix:
         # Github Actions requires a single row to be added to the build matrix.
         # See https://help.github.com/en/articles/workflow-syntax-for-github-actions.

.github/workflows/build-special.yml

@@ -110,7 +110,7 @@ jobs:
       - name: Set Allow Deprecated Flag
         if: matrix.flag == 'deprecated'
         run: |
-          echo "GTSAM_ALLOW_DEPRECATED_SINCE_V41=ON" >> $GITHUB_ENV
+          echo "GTSAM_ALLOW_DEPRECATED_SINCE_V42=ON" >> $GITHUB_ENV
           echo "Allow deprecated since version 4.1"
 
       - name: Set Use Quaternions Flag

.github/workflows/build-windows.yml

@@ -26,7 +26,11 @@ jobs:
             windows-2019-cl,
           ]
 
-        build_type: [Debug, Release]
+        build_type: [
+            Debug,
+            #TODO(Varun) The release build takes over 2.5 hours, need to figure out why.
+            # Release
+          ]
         build_unstable: [ON]
         include:
           #TODO This build fails, need to understand why.
@@ -44,7 +48,9 @@ jobs:
       - name: Install Dependencies
         shell: powershell
         run: |
-          Invoke-Expression (New-Object System.Net.WebClient).DownloadString('https://get.scoop.sh')
+          iwr -useb get.scoop.sh -outfile 'install_scoop.ps1'
+          .\install_scoop.ps1 -RunAsAdmin
+
           scoop install cmake --global  # So we don't get issues with CMP0074 policy
           scoop install ninja --global
 
@@ -90,13 +96,33 @@ jobs:
       - name: Checkout
         uses: actions/checkout@v2
 
-      - name: Build
+      - name: Configuration
         run: |
           cmake -E remove_directory build
           cmake -B build -S . -DGTSAM_BUILD_EXAMPLES_ALWAYS=OFF -DBOOST_ROOT="${env:BOOST_ROOT}" -DBOOST_INCLUDEDIR="${env:BOOST_ROOT}\boost\include" -DBOOST_LIBRARYDIR="${env:BOOST_ROOT}\lib"
-          cmake --build build --config ${{ matrix.build_type }} --target gtsam
-          cmake --build build --config ${{ matrix.build_type }} --target gtsam_unstable
-          cmake --build build --config ${{ matrix.build_type }} --target wrap
-          cmake --build build --config ${{ matrix.build_type }} --target check.base
-          cmake --build build --config ${{ matrix.build_type }} --target check.base_unstable
-          cmake --build build --config ${{ matrix.build_type }} --target check.linear
+
+      - name: Build
+        run: |
+          # Since Visual Studio is a multi-generator, we need to use --config
+          # https://stackoverflow.com/a/24470998/1236990
+          cmake --build build -j 4 --config ${{ matrix.build_type }} --target gtsam
+          cmake --build build -j 4 --config ${{ matrix.build_type }} --target gtsam_unstable
+          cmake --build build -j 4 --config ${{ matrix.build_type }} --target wrap
+
+          # Run GTSAM tests
+          cmake --build build -j 4 --config ${{ matrix.build_type }} --target check.base
+          cmake --build build -j 4 --config ${{ matrix.build_type }} --target check.basis
+          cmake --build build -j 4 --config ${{ matrix.build_type }} --target check.discrete
+          #cmake --build build -j 4 --config ${{ matrix.build_type }} --target check.geometry
+          cmake --build build -j 4 --config ${{ matrix.build_type }} --target check.inference
+          cmake --build build -j 4 --config ${{ matrix.build_type }} --target check.linear
+          cmake --build build -j 4 --config ${{ matrix.build_type }} --target check.navigation
+          #cmake --build build -j 4 --config ${{ matrix.build_type }} --target check.nonlinear
+          #cmake --build build -j 4 --config ${{ matrix.build_type }} --target check.sam
+          cmake --build build -j 4 --config ${{ matrix.build_type }} --target check.sfm
+          #cmake --build build -j 4 --config ${{ matrix.build_type }} --target check.slam
+          cmake --build build -j 4 --config ${{ matrix.build_type }} --target check.symbolic
+
+          # Run GTSAM_UNSTABLE tests
+          #cmake --build build -j 4 --config ${{ matrix.build_type }} --target check.base_unstable
+          

.gitignore

@@ -3,6 +3,7 @@
 .idea
 *.pyc
 *.DS_Store
+*.swp
 /examples/Data/dubrovnik-3-7-pre-rewritten.txt
 /examples/Data/pose2example-rewritten.txt
 /examples/Data/pose3example-rewritten.txt
@@ -16,3 +17,4 @@
 # for QtCreator:
 CMakeLists.txt.user*
 xcode/
+/Dockerfile

CMakeLists.txt

@@ -1,4 +1,3 @@
-project(GTSAM CXX C)
 cmake_minimum_required(VERSION 3.0)
 
 # new feature to Cmake Version > 2.8.12
@@ -9,12 +8,23 @@ endif()
 
 # Set the version number for the library
 set (GTSAM_VERSION_MAJOR 4)
-set (GTSAM_VERSION_MINOR 1)
+set (GTSAM_VERSION_MINOR 2)
 set (GTSAM_VERSION_PATCH 0)
+set (GTSAM_PRERELEASE_VERSION "a6")
 math (EXPR GTSAM_VERSION_NUMERIC "10000 * ${GTSAM_VERSION_MAJOR} + 100 * ${GTSAM_VERSION_MINOR} + ${GTSAM_VERSION_PATCH}")
-set (GTSAM_VERSION_STRING "${GTSAM_VERSION_MAJOR}.${GTSAM_VERSION_MINOR}.${GTSAM_VERSION_PATCH}")
 
-set (CMAKE_PROJECT_VERSION ${GTSAM_VERSION_STRING})
+if (${GTSAM_VERSION_PATCH} EQUAL 0)
+    set (GTSAM_VERSION_STRING "${GTSAM_VERSION_MAJOR}.${GTSAM_VERSION_MINOR}${GTSAM_PRERELEASE_VERSION}")
+else()
+    set (GTSAM_VERSION_STRING "${GTSAM_VERSION_MAJOR}.${GTSAM_VERSION_MINOR}.${GTSAM_VERSION_PATCH}${GTSAM_PRERELEASE_VERSION}")
+endif()
+
+project(GTSAM
+        LANGUAGES CXX C
+        VERSION "${GTSAM_VERSION_MAJOR}.${GTSAM_VERSION_MINOR}.${GTSAM_VERSION_PATCH}")
+
+message(STATUS "GTSAM Version: ${GTSAM_VERSION_STRING}")
+
 set (CMAKE_PROJECT_VERSION_MAJOR ${GTSAM_VERSION_MAJOR})
 set (CMAKE_PROJECT_VERSION_MINOR ${GTSAM_VERSION_MINOR})
 set (CMAKE_PROJECT_VERSION_PATCH ${GTSAM_VERSION_PATCH})
@@ -87,6 +97,13 @@ if(GTSAM_BUILD_PYTHON OR GTSAM_INSTALL_MATLAB_TOOLBOX)
         CACHE STRING "The Python version to use for wrapping")
     # Set the include directory for matlab.h
     set(GTWRAP_INCLUDE_NAME "wrap")
+
+    # Copy matlab.h to the correct folder.
+    configure_file(${PROJECT_SOURCE_DIR}/wrap/matlab.h
+               ${PROJECT_BINARY_DIR}/wrap/matlab.h COPYONLY)
+    # Add the include directories so that matlab.h can be found
+    include_directories("${PROJECT_BINARY_DIR}" "${GTSAM_EIGEN_INCLUDE_FOR_BUILD}")
+
     add_subdirectory(wrap)
     list(APPEND CMAKE_MODULE_PATH "${CMAKE_CURRENT_LIST_DIR}/wrap/cmake")
 endif()
@@ -105,6 +122,11 @@ endif()
 GtsamMakeConfigFile(GTSAM "${CMAKE_CURRENT_SOURCE_DIR}/gtsam_extra.cmake.in")
 export(TARGETS ${GTSAM_EXPORTED_TARGETS} FILE GTSAM-exports.cmake)
 
+if (GTSAM_BUILD_UNSTABLE)
+    GtsamMakeConfigFile(GTSAM_UNSTABLE "${CMAKE_CURRENT_SOURCE_DIR}/gtsam_extra.cmake.in")
+    export(TARGETS ${GTSAM_UNSTABLE_EXPORTED_TARGETS} FILE GTSAM_UNSTABLE-exports.cmake)
+endif()
+
 # Check for doxygen availability - optional dependency
 find_package(Doxygen)
 

DEVELOP.md

@@ -15,7 +15,7 @@ For example:
 ```cpp
 class GTSAM_EXPORT MyClass { ... };
 
-GTSAM_EXPORT myFunction();
+GTSAM_EXPORT return_type myFunction();
 ```
 
 More details [here](Using-GTSAM-EXPORT.md).

INSTALL.md

@@ -13,7 +13,7 @@ $ make install
 ## Important Installation Notes
 
 1. GTSAM requires the following libraries to be installed on your system:
-    - BOOST version 1.65 or greater (install through Linux repositories or MacPorts). Please see [Boost Notes](#boost-notes).
+    - BOOST version 1.65 or greater (install through Linux repositories or MacPorts). Please see [Boost Notes](#boost-notes) for version recommendations based on your compiler.
 
     - Cmake version 3.0 or higher
     - Support for XCode 4.3 command line tools on Mac requires CMake 2.8.8 or higher
@@ -72,7 +72,7 @@ execute commands as follows for an out-of-source build:
 Versions of Boost prior to 1.65 have a known bug that prevents proper "deep" serialization of objects, which means that objects encapsulated inside other objects don't get serialized.
 This is particularly seen when using `clang` as the C++ compiler.
 
-For this reason we require Boost>=1.65, and recommend installing it through alternative channels when it is not available through your operating system's primary package manager.
+For this reason we recommend Boost>=1.65, and recommend installing it through alternative channels when it is not available through your operating system's primary package manager.
 
 ## Known Issues
 

README.md

@@ -2,9 +2,9 @@
 
 **Important Note**
 
-As of August 1 2020, the `develop` branch is officially in "Pre 4.1" mode, and features deprecated in 4.0 have been removed. Please use the last [4.0.3 release](https://github.com/borglab/gtsam/releases/tag/4.0.3) if you need those features. 
+As of Dec 2021, the `develop` branch is officially in "Pre 4.2" mode. A great new feature we will be adding in 4.2 is *hybrid inference* a la DCSLAM (Kevin Doherty et al) and we envision several API-breaking changes will happen in the discrete folder.
 
-However, most are easily converted and can be tracked down (in 4.0.3) by disabling the cmake flag `GTSAM_ALLOW_DEPRECATED_SINCE_V4`.
+In addition, features deprecated in 4.1 will be removed. Please use the last [4.1.1 release](https://github.com/borglab/gtsam/releases/tag/4.1.1) if you need those features. However, most (not all, unfortunately) are easily converted and can be tracked down (in 4.1.1) by disabling the cmake flag `GTSAM_ALLOW_DEPRECATED_SINCE_V42`.
 
 ## What is GTSAM?
 
@@ -57,7 +57,7 @@ GTSAM 4 introduces several new features, most notably Expressions and a Python t
 
 GTSAM 4 also deprecated some legacy functionality and wrongly named methods. If you are on a 4.0.X release, you can define the flag `GTSAM_ALLOW_DEPRECATED_SINCE_V4` to use the deprecated methods.
 
-GTSAM 4.1 added a new pybind wrapper, and **removed** the deprecated functionality. There is a flag `GTSAM_ALLOW_DEPRECATED_SINCE_V41` for newly deprecated methods since the 4.1 release, which is on by default, allowing anyone to just pull version 4.1 and compile.
+GTSAM 4.1 added a new pybind wrapper, and **removed** the deprecated functionality. There is a flag `GTSAM_ALLOW_DEPRECATED_SINCE_V42` for newly deprecated methods since the 4.1 release, which is on by default, allowing anyone to just pull version 4.1 and compile.
 
 
 ## Wrappers

Using-GTSAM-EXPORT.md

@@ -8,6 +8,7 @@ To create a DLL in windows, the `GTSAM_EXPORT` keyword has been created and need
     * At least one of the functions inside that class is declared in a .cpp file and not just the .h file.
     * You can `GTSAM_EXPORT` any class it inherits from as well.  (Note that this implictly requires the class does not derive from a "header-only" class.  Note that Eigen is a "header-only" library, so if your class derives from Eigen, _do not_ use `GTSAM_EXPORT` in the class definition!) 
 3.  If you have defined a class using `GTSAM_EXPORT`, do not use `GTSAM_EXPORT` in any of its individual function declarations.  (Note that you _can_ put `GTSAM_EXPORT` in the definition of individual functions within a class as long as you don't put `GTSAM_EXPORT` in the class definition.)
+4. For template specializations, you need to add `GTSAM_EXPORT` to each individual specialization.
 
 ## When is GTSAM_EXPORT being used incorrectly
 Unfortunately, using `GTSAM_EXPORT` incorrectly often does not cause a compiler or linker error in the library that is being compiled, but only when you try to use that DLL in a different library.  For example, an error in `gtsam/base` will often show up when compiling the `check_base_program` or the MATLAB wrapper, but not when compiling/linking gtsam itself.  The most common errors will say something like:
@@ -29,7 +30,7 @@ Rule #1 doesn't seem very bad, until you combine it with rule #2
 
 ***Compiler Rule #2*** Anything declared in a header file is not included in a DLL.
 
-When these two rules are combined, you get some very confusing results.  For example, a class which is completely defined in a header (e.g. LieMatrix) cannot use `GTSAM_EXPORT` in its definition.  If LieMatrix is defined with `GTSAM_EXPORT`, then the compiler _must_ find LieMatrix in a DLL.  Because LieMatrix is a header-only class, however, it can't find it, leading to a very confusing "I can't find this symbol" type of error.  Note that the linker says it can't find the symbol even though the compiler found the header file that completely defines the class.
+When these two rules are combined, you get some very confusing results.  For example, a class which is completely defined in a header (e.g. Foo) cannot use `GTSAM_EXPORT` in its definition.  If Foo is defined with `GTSAM_EXPORT`, then the compiler _must_ find Foo in a DLL.  Because Foo is a header-only class, however, it can't find it, leading to a very confusing "I can't find this symbol" type of error.  Note that the linker says it can't find the symbol even though the compiler found the header file that completely defines the class.
 
 Also note that when a class that you want to export inherits from another class that is not exportable, this can cause significant issues.  According to this [MSVC Warning page](https://docs.microsoft.com/en-us/cpp/error-messages/compiler-warnings/compiler-warning-level-2-c4275?view=vs-2019), it may not strictly be a rule, but we have seen several linker errors when a class that is defined with `GTSAM_EXPORT` extended an Eigen class.  In general, it appears that any inheritance of non-exportable class by an exportable class is a bad idea.
 

cmake/GtsamBuildTypes.cmake

@@ -93,6 +93,10 @@ if(MSVC)
 	/wd4267 # warning C4267: 'initializing': conversion from 'size_t' to 'int', possible loss of data
   )
 
+  add_compile_options(/wd4005)
+  add_compile_options(/wd4101)
+  add_compile_options(/wd4834)
+
 endif()
 
 # Other (non-preprocessor macros) compiler flags:
@@ -187,7 +191,7 @@ endif()
 
 if (NOT MSVC)
   option(GTSAM_BUILD_WITH_MARCH_NATIVE  "Enable/Disable building with all instructions supported by native architecture (binary may not be portable!)" ON)
-  if(GTSAM_BUILD_WITH_MARCH_NATIVE)
+  if(GTSAM_BUILD_WITH_MARCH_NATIVE AND (APPLE AND NOT CMAKE_SYSTEM_PROCESSOR STREQUAL "arm64"))
     # Add as public flag so all dependant projects also use it, as required
     # by Eigen to avid crashes due to SIMD vectorization:
     list_append_cache(GTSAM_COMPILE_OPTIONS_PUBLIC "-march=native")

cmake/GtsamMakeConfigFile.cmake

@@ -27,6 +27,8 @@ function(GtsamMakeConfigFile PACKAGE_NAME)
 	# here.
 	if(NOT DEFINED ${PACKAGE_NAME}_VERSION AND DEFINED ${PACKAGE_NAME}_VERSION_STRING)
 		set(${PACKAGE_NAME}_VERSION ${${PACKAGE_NAME}_VERSION_STRING})
+	elseif(NOT DEFINED ${PACKAGE_NAME}_VERSION_STRING)
+		set(${PACKAGE_NAME}_VERSION ${GTSAM_VERSION_STRING})
 	endif()
 
 	# Version file