Merge branch 'develop' into NavState-LieGroup

.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-linux.yml

@@ -31,7 +31,7 @@ jobs:
           ubuntu-22.04-clang-14,
         ]
 
-        build_type: [Release]
+        build_type: [Debug, Release]
         build_unstable: [ON]
         include:
           - name: ubuntu-20.04-gcc-9

.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

@@ -1,30 +1,22 @@
 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)
 set (GTSAM_VERSION_PATCH 0)
 set (GTSAM_PRERELEASE_VERSION "a0")
 math (EXPR GTSAM_VERSION_NUMERIC "10000 * ${GTSAM_VERSION_MAJOR} + 100 * ${GTSAM_VERSION_MINOR} + ${GTSAM_VERSION_PATCH}")
 
-if (${GTSAM_VERSION_PATCH} EQUAL 0)
-    set (GTSAM_VERSION_STRING "${GTSAM_VERSION_MAJOR}.${GTSAM_VERSION_MINOR}${GTSAM_PRERELEASE_VERSION}")
+if ("${GTSAM_PRERELEASE_VERSION}" STREQUAL "")
+    set (GTSAM_VERSION_STRING "${GTSAM_VERSION_MAJOR}.${GTSAM_VERSION_MINOR}.${GTSAM_VERSION_PATCH}")
 else()
-    set (GTSAM_VERSION_STRING "${GTSAM_VERSION_MAJOR}.${GTSAM_VERSION_MINOR}.${GTSAM_VERSION_PATCH}${GTSAM_PRERELEASE_VERSION}")
+    set (GTSAM_VERSION_STRING "${GTSAM_VERSION_MAJOR}.${GTSAM_VERSION_MINOR}${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 ${GTSAM_VERSION_PATCH})
@@ -44,20 +36,20 @@ set(CMAKE_MODULE_PATH "${CMAKE_MODULE_PATH}" "${CMAKE_CURRENT_SOURCE_DIR}/cmake"
 include(GtsamMakeConfigFile)
 include(GNUInstallDirs)
 
-# Load build type flags and default to Debug mode
-include(GtsamBuildTypes)
-
-# Use macros for creating tests/timing scripts
-include(GtsamTesting)
-include(GtsamPrinting)
-
 # guard against in-source builds
 if(${GTSAM_SOURCE_DIR} STREQUAL ${GTSAM_BINARY_DIR})
   message(FATAL_ERROR "In-source builds not allowed. Please make a new directory (called a build directory) and run CMake from there. You may need to remove CMakeCache.txt. ")
 endif()
 
 include(cmake/HandleGeneralOptions.cmake)   # CMake build options
 
+# Load build type flags and default to Debug mode
+include(GtsamBuildTypes)
+
+# Use macros for creating tests/timing scripts
+include(GtsamTesting)
+include(GtsamPrinting)
+
 ############### Decide on BOOST ######################################
 # Enable or disable serialization with GTSAM_ENABLE_BOOST_SERIALIZATION
 option(GTSAM_ENABLE_BOOST_SERIALIZATION "Enable Boost serialization" ON)
@@ -80,6 +72,7 @@ include(cmake/HandleCCache.cmake)           # ccache
 include(cmake/HandleCPack.cmake)            # CPack
 include(cmake/HandleEigen.cmake)            # Eigen3
 include(cmake/HandleMetis.cmake)            # metis
+include(cmake/HandleCephes.cmake)           # cephes
 include(cmake/HandleMKL.cmake)              # MKL
 include(cmake/HandleOpenMP.cmake)           # OpenMP
 include(cmake/HandlePerfTools.cmake)        # Google perftools

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.

README.md

@@ -4,7 +4,7 @@
 
 **As of January 2023, the `develop` branch is officially in "Pre 4.3" mode. We envision several API-breaking changes as we switch to C++17 and away from boost.**
 
-In addition, features deprecated in 4.2 will be removed. Please use the last [4.2a8 release](https://github.com/borglab/gtsam/releases/tag/4.2a8) if you need those features. However, most are easily converted and can be tracked down (in 4.2) by disabling the cmake flag `GTSAM_ALLOW_DEPRECATED_SINCE_V42`.
+In addition, features deprecated in 4.2 will be removed. Please use the stable [4.2 release](https://github.com/borglab/gtsam/releases/tag/4.2) if you need those features. However, most are easily converted and can be tracked down (in 4.2) by disabling the cmake flag `GTSAM_ALLOW_DEPRECATED_SINCE_V42`.
 
 ## What is GTSAM?
 

cmake/GtsamBuildTypes.cmake

@@ -55,9 +55,6 @@ if(NOT CMAKE_BUILD_TYPE AND NOT MSVC AND NOT XCODE_VERSION)
       "Choose the type of build, options are: None Debug Release Timing Profiling RelWithDebInfo." FORCE)
 endif()
 
-# Add option for using build type postfixes to allow installing multiple build modes
-option(GTSAM_BUILD_TYPE_POSTFIXES        "Enable/Disable appending the build type to the name of compiled libraries" ON)
-
 # Define all cache variables, to be populated below depending on the OS/compiler:
 set(GTSAM_COMPILE_OPTIONS_PRIVATE        "" CACHE INTERNAL "(Do not edit) Private compiler flags for all build configurations." FORCE)
 set(GTSAM_COMPILE_OPTIONS_PUBLIC         "" CACHE INTERNAL "(Do not edit) Public compiler flags (exported to user projects) for all build configurations."  FORCE)
@@ -82,6 +79,13 @@ set(GTSAM_COMPILE_DEFINITIONS_PRIVATE_RELWITHDEBINFO  "NDEBUG" CACHE STRING "(Us
 set(GTSAM_COMPILE_DEFINITIONS_PRIVATE_RELEASE         "NDEBUG" CACHE STRING "(User editable) Private preprocessor macros for Release configuration.")
 set(GTSAM_COMPILE_DEFINITIONS_PRIVATE_PROFILING       "NDEBUG" CACHE STRING "(User editable) Private preprocessor macros for Profiling configuration.")
 set(GTSAM_COMPILE_DEFINITIONS_PRIVATE_TIMING          "NDEBUG;ENABLE_TIMING" CACHE STRING "(User editable) Private preprocessor macros for Timing configuration.")
+
+mark_as_advanced(GTSAM_COMPILE_DEFINITIONS_PRIVATE_DEBUG)
+mark_as_advanced(GTSAM_COMPILE_DEFINITIONS_PRIVATE_RELWITHDEBINFO)
+mark_as_advanced(GTSAM_COMPILE_DEFINITIONS_PRIVATE_RELEASE)
+mark_as_advanced(GTSAM_COMPILE_DEFINITIONS_PRIVATE_PROFILING)
+mark_as_advanced(GTSAM_COMPILE_DEFINITIONS_PRIVATE_TIMING)
+
 if(MSVC)
   # Common to all configurations:
   list_append_cache(GTSAM_COMPILE_DEFINITIONS_PRIVATE
@@ -143,6 +147,13 @@ else()
   set(GTSAM_COMPILE_OPTIONS_PRIVATE_TIMING          -g -O3  CACHE STRING "(User editable) Private compiler flags for Timing configuration.")
 endif()
 
+mark_as_advanced(GTSAM_COMPILE_OPTIONS_PRIVATE_COMMON)
+mark_as_advanced(GTSAM_COMPILE_OPTIONS_PRIVATE_DEBUG)
+mark_as_advanced(GTSAM_COMPILE_OPTIONS_PRIVATE_RELWITHDEBINFO)
+mark_as_advanced(GTSAM_COMPILE_OPTIONS_PRIVATE_RELEASE)
+mark_as_advanced(GTSAM_COMPILE_OPTIONS_PRIVATE_PROFILING)
+mark_as_advanced(GTSAM_COMPILE_OPTIONS_PRIVATE_TIMING)
+
 # Enable C++17:
 if (NOT CMAKE_VERSION VERSION_LESS 3.8)
     set(GTSAM_COMPILE_FEATURES_PUBLIC "cxx_std_17" CACHE STRING "CMake compile features property for all gtsam targets.")
@@ -198,7 +209,6 @@ if(${CMAKE_CXX_COMPILER_ID} STREQUAL "Clang")
 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!)" OFF)
   if(GTSAM_BUILD_WITH_MARCH_NATIVE)
     # Check if Apple OS and compiler is [Apple]Clang
     if(APPLE AND (${CMAKE_CXX_COMPILER_ID} MATCHES "^(Apple)?Clang$"))

cmake/GtsamTesting.cmake

@@ -42,7 +42,7 @@ endmacro()
 # GTSAM_BUILD_EXAMPLES_ALWAYS is enabled.  They may also be built with 'make examples'.
 #
 # Usage example:
-#   gtsamAddExamplesGlob("*.cpp" "BrokenExample.cpp" "gtsam;GeographicLib")
+#   gtsamAddExamplesGlob("*.cpp" "BrokenExample.cpp" "gtsam;GeographicLib" ON)
 #
 # Arguments:
 #   globPatterns:  The list of files or glob patterns from which to create examples, with
@@ -51,8 +51,9 @@ endmacro()
 #   excludedFiles: A list of files or globs to exclude, e.g. "C*.cpp;BrokenExample.cpp".  Pass
 #                  an empty string "" if nothing needs to be excluded.
 #   linkLibraries: The list of libraries to link to.
-macro(gtsamAddExamplesGlob globPatterns excludedFiles linkLibraries)
-	gtsamAddExesGlob_impl("${globPatterns}" "${excludedFiles}" "${linkLibraries}" "examples" ${GTSAM_BUILD_EXAMPLES_ALWAYS})
+#   buildWithAll: Build examples with `make` and/or `make all`
+macro(gtsamAddExamplesGlob globPatterns excludedFiles linkLibraries buildWithAll)
+	gtsamAddExesGlob_impl("${globPatterns}" "${excludedFiles}" "${linkLibraries}" "examples" ${buildWithAll})
 endmacro()
 
 
@@ -76,8 +77,9 @@ endmacro()
 #   excludedFiles: A list of files or globs to exclude, e.g. "C*.cpp;BrokenExample.cpp".  Pass
 #                  an empty string "" if nothing needs to be excluded.
 #   linkLibraries: The list of libraries to link to.
-macro(gtsamAddTimingGlob globPatterns excludedFiles linkLibraries)
-	gtsamAddExesGlob_impl("${globPatterns}" "${excludedFiles}" "${linkLibraries}" "timing" ${GTSAM_BUILD_TIMING_ALWAYS})
+#   buildWithAll: Build examples with `make` and/or `make all`
+macro(gtsamAddTimingGlob globPatterns excludedFiles linkLibraries buildWithAll)
+	gtsamAddExesGlob_impl("${globPatterns}" "${excludedFiles}" "${linkLibraries}" "timing" ${buildWithAll})
 endmacro()
 
 
@@ -86,9 +88,8 @@ endmacro()
 # Build macros for using tests
 enable_testing()
 
-option(GTSAM_BUILD_TESTS                 "Enable/Disable building of tests"          ON)
-option(GTSAM_BUILD_EXAMPLES_ALWAYS       "Build examples with 'make all' (build with 'make examples' if not)"       ON)
-option(GTSAM_BUILD_TIMING_ALWAYS         "Build timing scripts with 'make all' (build with 'make timing' if not"    OFF)
+#TODO(Varun) Move to HandlePrintConfiguration.cmake. This will require additional changes.
+option(GTSAM_BUILD_TESTS                 "Enable/Disable building of tests"          ON)	
 
 # Add option for combining unit tests
 if(MSVC OR XCODE_VERSION)
@@ -123,6 +124,7 @@ add_custom_target(timing)
 # Implementations of this file's macros:
 
 macro(gtsamAddTestsGlob_impl groupName globPatterns excludedFiles linkLibraries)
+	#TODO(Varun) Building of tests should not depend on global gtsam flag
 	if(GTSAM_BUILD_TESTS)
 		# Add group target if it doesn't already exist
 		if(NOT TARGET check.${groupName})

cmake/HandleCephes.cmake

@@ -0,0 +1,19 @@
+# ##############################################################################
+# Cephes library
+
+# For both system or bundle version, a cmake target "cephes-gtsam-if" is defined
+# (interface library)
+
+
+add_subdirectory(${GTSAM_SOURCE_DIR}/gtsam/3rdparty/cephes)
+
+list(APPEND GTSAM_EXPORTED_TARGETS cephes-gtsam)
+
+add_library(cephes-gtsam-if INTERFACE)
+target_link_libraries(cephes-gtsam-if INTERFACE cephes-gtsam)
+
+list(APPEND GTSAM_EXPORTED_TARGETS cephes-gtsam-if)
+install(
+  TARGETS cephes-gtsam-if
+  EXPORT GTSAM-exports
+  ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR})

cmake/HandleGeneralOptions.cmake

@@ -8,6 +8,18 @@ else()
     set(GTSAM_UNSTABLE_AVAILABLE 0)
 endif()
 
+### GtsamTesting related options
+option(GTSAM_BUILD_EXAMPLES_ALWAYS       "Build examples with 'make all' (build with 'make examples' if not)"       ON)
+option(GTSAM_BUILD_TIMING_ALWAYS         "Build timing scripts with 'make all' (build with 'make timing' if not"    OFF)
+###
+
+# Add option for using build type postfixes to allow installing multiple build modes
+option(GTSAM_BUILD_TYPE_POSTFIXES        "Enable/Disable appending the build type to the name of compiled libraries" ON)
+
+if (NOT MSVC)
+    option(GTSAM_BUILD_WITH_MARCH_NATIVE  "Enable/Disable building with all instructions supported by native architecture (binary may not be portable!)" OFF)
+endif()
+
 # Configurable Options
 if(GTSAM_UNSTABLE_AVAILABLE)
     option(GTSAM_BUILD_UNSTABLE              "Enable/Disable libgtsam_unstable"          ON)
@@ -19,6 +31,7 @@ option(GTSAM_FORCE_STATIC_LIB               "Force gtsam to be a static library,
 option(GTSAM_USE_QUATERNIONS                "Enable/Disable using an internal Quaternion representation for rotations instead of rotation matrices. If enable, Rot3::EXPMAP is enforced by default." OFF)
 option(GTSAM_POSE3_EXPMAP                   "Enable/Disable using Pose3::EXPMAP as the default mode. If disabled, Pose3::FIRST_ORDER will be used." ON)
 option(GTSAM_ROT3_EXPMAP                    "Ignore if GTSAM_USE_QUATERNIONS is OFF (Rot3::EXPMAP by default). Otherwise, enable Rot3::EXPMAP, or if disabled, use Rot3::CAYLEY." ON)
+option(GTSAM_DT_MERGING                     "Enable/Disable merging of equal leaf nodes in DecisionTrees. This leads to significant speed up and memory savings." ON)
 option(GTSAM_ENABLE_CONSISTENCY_CHECKS      "Enable/Disable expensive consistency checks" OFF)
 option(GTSAM_ENABLE_MEMORY_SANITIZER        "Enable/Disable memory sanitizer" OFF)
 option(GTSAM_WITH_TBB                       "Use Intel Threaded Building Blocks (TBB) if available" ON)

cmake/HandlePrintConfiguration.cmake

@@ -90,6 +90,7 @@ print_enabled_config(${GTSAM_ENABLE_CONSISTENCY_CHECKS}   "Runtime consistency c
 print_enabled_config(${GTSAM_ENABLE_MEMORY_SANITIZER}     "Build with Memory Sanitizer     ")
 print_enabled_config(${GTSAM_ROT3_EXPMAP}                 "Rot3 retract is full ExpMap     ")
 print_enabled_config(${GTSAM_POSE3_EXPMAP}                "Pose3 retract is full ExpMap    ")
+print_enabled_config(${GTSAM_DT_MERGING}                  "Enable branch merging in DecisionTree")
 print_enabled_config(${GTSAM_ALLOW_DEPRECATED_SINCE_V43}  "Allow features deprecated in GTSAM 4.3")
 print_enabled_config(${GTSAM_SUPPORT_NESTED_DISSECTION}   "Metis-based Nested Dissection   ")
 print_enabled_config(${GTSAM_TANGENT_PREINTEGRATION}      "Use tangent-space preintegration")

cmake/README.html

@@ -47,9 +47,9 @@ <h2>GtsamTesting</h2>
 </code></pre>
 </li>
 <li>
-<p><code>gtsamAddExamplesGlob(globPatterns excludedFiles linkLibraries)</code> Add scripts that will serve as examples of how to use the library.  A list of files or glob patterns is specified, and one executable will be created for each matching .cpp file.  These executables will not be installed.  They are build with 'make all' if GTSAM_BUILD_EXAMPLES_ALWAYS is enabled.  They may also be built with 'make examples'.</p>
+<p><code>gtsamAddExamplesGlob(globPatterns excludedFiles linkLibraries buildWithAll)</code> Add scripts that will serve as examples of how to use the library.  A list of files or glob patterns is specified, and one executable will be created for each matching .cpp file.  These executables will not be installed.  They are build with 'make all' if GTSAM_BUILD_EXAMPLES_ALWAYS is enabled.  They may also be built with 'make examples'.</p>
 <p>Usage example:</p>
-<pre><code>gtsamAddExamplesGlob("*.cpp" "BrokenExample.cpp" "gtsam;GeographicLib")
+<pre><code>gtsamAddExamplesGlob("*.cpp" "BrokenExample.cpp" "gtsam;GeographicLib" ON)
 </code></pre>
 <p>Arguments:</p>
 <pre><code>globPatterns:  The list of files or glob patterns from which to create unit tests, with
@@ -58,6 +58,7 @@ <h2>GtsamTesting</h2>
 excludedFiles: A list of files or globs to exclude, e.g. "C*.cpp;BrokenExample.cpp".  Pass
                an empty string "" if nothing needs to be excluded.
 linkLibraries: The list of libraries to link to.
+buildWithAll: Build examples with `make` and/or `make all`
 </code></pre>
 </li>
 </ul>

cmake/README.md

@@ -52,11 +52,11 @@ Defines two useful functions for creating CTest unit tests.  Also immediately cr
                        Pass an empty string "" if nothing needs to be excluded.
         linkLibraries: The list of libraries to link to in addition to CppUnitLite.
 
-*   `gtsamAddExamplesGlob(globPatterns excludedFiles linkLibraries)` Add scripts that will serve as examples of how to use the library.  A list of files or glob patterns is specified, and one executable will be created for each matching .cpp file.  These executables will not be installed.  They are build with 'make all' if GTSAM_BUILD_EXAMPLES_ALWAYS is enabled.  They may also be built with 'make examples'.
+*   `gtsamAddExamplesGlob(globPatterns excludedFiles linkLibraries buildWithAll)` Add scripts that will serve as examples of how to use the library.  A list of files or glob patterns is specified, and one executable will be created for each matching .cpp file.  These executables will not be installed.  They are build with 'make all' if GTSAM_BUILD_EXAMPLES_ALWAYS is enabled.  They may also be built with 'make examples'.
 
     Usage example:
 
-        gtsamAddExamplesGlob("*.cpp" "BrokenExample.cpp" "gtsam;GeographicLib")
+        gtsamAddExamplesGlob("*.cpp" "BrokenExample.cpp" "gtsam;GeographicLib" ON)
 
     Arguments:
 
@@ -66,6 +66,7 @@ Defines two useful functions for creating CTest unit tests.  Also immediately cr
         excludedFiles: A list of files or globs to exclude, e.g. "C*.cpp;BrokenExample.cpp".  Pass
                        an empty string "" if nothing needs to be excluded.
         linkLibraries: The list of libraries to link to.
+        buildWithAll: Build examples with `make` and/or `make all`
 
 ## GtsamMakeConfigFile
 

doc/CMakeLists.txt

@@ -56,7 +56,7 @@ if (GTSAM_BUILD_DOCS)
     if (GTSAM_BUILD_UNSTABLE)
         list(APPEND doc_subdirs ${gtsam_unstable_doc_subdirs})
     endif()
-    if (GTSAM_BUILD_EXAMPLES)
+    if (GTSAM_BUILD_EXAMPLES_ALWAYS)
         list(APPEND doc_subdirs examples)
     endif()