Merge remote-tracking branch 'upstream/develop' into develop

Author: PeterCalifano

.github/copilot-instructions.md

@@ -0,0 +1,9 @@
+For reviewing PRs:
+* All functions in header files should have doxygen-style API docs
+* Use /// for single-line comments rather than /** */
+* Use meaningful variable names, e.g. `measurement` not `msm`, avoid abbreviations.
+* Flag overly complex or long/functions: break up in smaller functions
+* On Windows it is necessary to explicitly export all functions from the library which should be externally accessible. To do this, include the macro `GTSAM_EXPORT` in your class or function definition.
+* If we add a C++ function to a `.i` file to expose it to the wrapper, we must ensure that the parameter names match exactly between the declaration in the header file and the declaration in the `.i`. Similarly, if we change any parameter names in a wrapped function in a header file, or change any parameter names in a `.i` file, we must change the corresponding function in the other file to reflect those changes.
+* Classes are Uppercase, methods and functions lowerMixedCase.
+* Apart from those naming conventions, we adopt Google C++ style.

.github/scripts/python.sh

@@ -45,6 +45,16 @@ function build()
 {
   export CMAKE_GENERATOR=Ninja
   BUILD_PYBIND="ON"
+
+  # Add Boost hints on Windows
+  BOOST_CMAKE_ARGS=""
+  if [[ "$OSTYPE" == "msys" || "$OSTYPE" == "win32" || "$OSTYPE" == "cygwin" ]]; then
+    if [ -n "${BOOST_ROOT}" ]; then
+     BOOST_ROOT_UNIX=$(echo "$BOOST_ROOT" | sed 's/\\/\//g')
+     BOOST_CMAKE_ARGS="-DBOOST_ROOT=${BOOST_ROOT_UNIX} -DBOOST_INCLUDEDIR=${BOOST_ROOT_UNIX}/include -DBOOST_LIBRARYDIR=${BOOST_ROOT_UNIX}/lib"
+    fi
+  fi
+
   cmake $GITHUB_WORKSPACE \
       -B build \
       -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE} \
@@ -58,9 +68,11 @@ function build()
       -DGTSAM_UNSTABLE_BUILD_PYTHON=${GTSAM_BUILD_UNSTABLE:-ON} \
       -DGTSAM_PYTHON_VERSION=$PYTHON_VERSION \
       -DPYTHON_EXECUTABLE:FILEPATH=$(which $PYTHON) \
+      -DGTSAM_USE_BOOST_FEATURES=ON \
+      -DGTSAM_ENABLE_BOOST_SERIALIZATION=ON \
       -DGTSAM_ALLOW_DEPRECATED_SINCE_V43=OFF \
-      -DCMAKE_INSTALL_PREFIX=$GITHUB_WORKSPACE/gtsam_install
-
+      -DCMAKE_INSTALL_PREFIX=$GITHUB_WORKSPACE/gtsam_install \
+      $BOOST_CMAKE_ARGS
 
   # Set to 2 cores so that Actions does not error out during resource provisioning.
   cmake --build build -j2

.github/scripts/python_wheels/cibw_before_all.sh

@@ -16,7 +16,7 @@ if [ "$(uname)" == "Linux" ]; then
     # manylinux2014 is based on CentOS 7, so use yum to install dependencies
     yum install -y wget doxygen
 elif [ "$(uname)" == "Darwin" ]; then
-    brew install cmake doxygen
+    brew install doxygen
 
     # If MACOSX_DEPLOYMENT_TARGET is not explicitly set, default to the version of the host system.
     if [[ -z "${MACOSX_DEPLOYMENT_TARGET}" ]]; then

.github/scripts/python_wheels/cleanup_gtsam_develop.sh

@@ -33,7 +33,7 @@ echo "         of 'gtsam-develop' on PyPI for user '$PYPI_USER'."
 echo "         This cannot be undone."
 echo "-----------------------------------------------------------------------"
 read -rp "Proceed? [y/N]: " REPLY
-REPLY=${REPLY,,}   # to lowercase
+REPLY=$(echo "$REPLY" | tr '[:upper:]' '[:lower:]')   # to lowercase
 [[ "$REPLY" != "y" && "$REPLY" != "yes" ]] && { echo "Aborted."; exit 0; }
 
 echo "Running pypi_cleanup for user '$PYPI_USER'..."

.github/scripts/unix.sh

@@ -8,33 +8,13 @@
 set -e   # Make sure any error makes the script to return an error code
 set -x   # echo
 
-# install TBB with _debug.so files
-function install_tbb()
-{
-  echo install_tbb  
-  if [ "$(uname)" == "Linux" ]; then
-    sudo apt-get -y install libtbb-dev
-
-  elif [ "$(uname)" == "Darwin" ]; then
-    brew install tbb
-  fi
-}
 
 # common tasks before either build or test
 function configure()
 {
   # delete old build
   rm -rf build
 
-  if [ "${GTSAM_WITH_TBB:-OFF}" == "ON" ]; then
-    install_tbb
-  fi
-
-  if [ ! -z "$GCC_VERSION" ]; then
-    export CC=gcc-$GCC_VERSION
-    export CXX=g++-$GCC_VERSION
-  fi
-
   # GTSAM_BUILD_WITH_MARCH_NATIVE=OFF: to avoid crashes in builder VMs
   # CMAKE_CXX_FLAGS="-w": Suppress warnings to avoid IO latency in CI logs
   export CMAKE_GENERATOR=Ninja
@@ -52,10 +32,11 @@ function configure()
       -DGTSAM_POSE3_EXPMAP=${GTSAM_POSE3_EXPMAP:-ON} \
       -DGTSAM_USE_SYSTEM_EIGEN=${GTSAM_USE_SYSTEM_EIGEN:-OFF} \
       -DGTSAM_USE_SYSTEM_METIS=${GTSAM_USE_SYSTEM_METIS:-OFF} \
-      -DGTSAM_USE_BOOST_FEATURES=${GTSAM_USE_BOOST_FEATURES:-ON} \
-      -DGTSAM_ENABLE_BOOST_SERIALIZATION=${GTSAM_ENABLE_BOOST_SERIALIZATION:-ON} \
+      -DGTSAM_USE_BOOST_FEATURES=${GTSAM_USE_BOOST_FEATURES:-OFF} \
+      -DGTSAM_ENABLE_BOOST_SERIALIZATION=${GTSAM_ENABLE_BOOST_SERIALIZATION:-OFF} \
       -DGTSAM_BUILD_WITH_MARCH_NATIVE=OFF \
-      -DGTSAM_SINGLE_TEST_EXE=OFF
+      -DGTSAM_SINGLE_TEST_EXE=${GTSAM_SINGLE_TEST_EXE:-OFF} \
+      -DGTSAM_ENABLE_GEOGRAPHICLIB=${GTSAM_ENABLE_GEOGRAPHICLIB:-OFF}
 }
 
 

.github/workflows/build-linux.yml

@@ -6,9 +6,10 @@ on:
       - "**.md"
       - "**.ipynb"
       - "myst.yml"
+      
 
-# Every time you make a push to your PR, it cancel immediately the previous checks,
-# and start a new one. The other runner will be available more quickly to your PR.
+# Cancels any in-progress workflow runs for the same PR when a new push is made,
+# allowing the runner to become available more quickly for the latest changes.
 concurrency:
   group: ${{ github.workflow }}-${{ github.head_ref || github.run_id }}
   cancel-in-progress: true
@@ -17,13 +18,13 @@ jobs:
   build:
     name: ${{ matrix.name }} ${{ matrix.build_type }}
     runs-on: ${{ matrix.os }}
-
-    env:
-      CTEST_OUTPUT_ON_FAILURE: ON
-      CTEST_PARALLEL_LEVEL: 2
-      CMAKE_BUILD_TYPE: ${{ matrix.build_type }}
-      GTSAM_BUILD_UNSTABLE: ${{ matrix.build_unstable }}
-
+    container:
+      image: borglab/gtsam-ci:${{ matrix.os }}-${{ matrix.compiler }}-${{ matrix.version }}
+      env:
+        CMAKE_BUILD_TYPE: ${{ matrix.build_type }}
+        GTSAM_BUILD_UNSTABLE: ${{ matrix.build_unstable }}
+      volumes:
+        - ${{ github.workspace }}:/gtsam
     strategy:
       fail-fast: true
       matrix:
@@ -35,6 +36,8 @@ jobs:
             ubuntu-22.04-clang-11,
             ubuntu-24.04-gcc-14,
             ubuntu-24.04-clang-16,
+            ubuntu-24.04-clang-16-boost,
+            ubuntu-24.04-clang-16-geographiclib,
           ]
 
         build_type: [Debug, Release]
@@ -60,40 +63,38 @@ jobs:
             compiler: clang
             version: "16"
 
+          - name: ubuntu-24.04-clang-16-boost
+            os: ubuntu-24.04
+            compiler: clang
+            version: "16"
+
+          - name: ubuntu-24.04-clang-16-geographiclib
+            os: ubuntu-24.04
+            compiler: clang
+            version: "16"
+
+        exclude:
+          - name: ubuntu-24.04-clang-16-boost
+            build_type: Debug
+          - name: ubuntu-24.04-clang-16-geographiclib
+            build_type: Debug
+
     steps:
       - name: Checkout
         uses: actions/checkout@v4
 
-      - name: Install Dependencies
+      - name: Set Boost Environment (Conditional)
+        if : contains(matrix.name, 'boost') && matrix.build_type == 'Release'
         run: |
-          # LLVM (clang) 9/14 is not in Bionic's repositories so we add the official LLVM repository.
-          if [ "${{ matrix.compiler }}" = "clang" ]; then
-            # (ipv4|ha).pool.sks-keyservers.net is the SKS GPG global keyserver pool
-            # ipv4 avoids potential timeouts because of crappy IPv6 infrastructure
-            # 15CF4D18AF4F7421 is the GPG key for the LLVM apt repository
-            # This key is not in the keystore by default for Ubuntu so we need to add it.
-            LLVM_KEY=15CF4D18AF4F7421
-            gpg --keyserver keyserver.ubuntu.com --recv-key $LLVM_KEY || gpg --keyserver hkp://keyserver.ubuntu.com:80 --recv-key $LLVM_KEY
-            gpg -a --export $LLVM_KEY | sudo apt-key add -
-            sudo add-apt-repository "deb http://apt.llvm.org/bionic/ llvm-toolchain-bionic-9 main"
-          fi
-
-          sudo apt-get -y update
-          sudo apt-get -y install cmake build-essential pkg-config libpython3-dev python3-numpy libicu-dev ninja-build
-
-          if [ "${{ matrix.compiler }}" = "gcc" ]; then
-            sudo apt-get install -y g++-${{ matrix.version }} g++-${{ matrix.version }}-multilib
-            echo "CC=gcc-${{ matrix.version }}" >> $GITHUB_ENV
-            echo "CXX=g++-${{ matrix.version }}" >> $GITHUB_ENV
-          else
-            sudo apt-get install -y clang-${{ matrix.version }} g++-multilib
-            echo "CC=clang-${{ matrix.version }}" >> $GITHUB_ENV
-            echo "CXX=clang++-${{ matrix.version }}" >> $GITHUB_ENV
-          fi
-
-      - name: Install Boost
+          echo "GTSAM_USE_BOOST_FEATURES=ON" >> $GITHUB_ENV
+          echo "GTSAM_ENABLE_BOOST_SERIALIZATION=ON" >> $GITHUB_ENV
+          echo "Using Boost features."
+      
+      - name: Set GeographicLib Environment (Conditional)
+        if: contains(matrix.name, 'geographiclib') && matrix.build_type == 'Release'
         run: |
-          sudo apt-get -y install libboost-all-dev
+          echo "GTSAM_ENABLE_GEOGRAPHICLIB=ON" >> $GITHUB_ENV
 
       - name: Build and Test
-        run: bash .github/scripts/unix.sh -t
+        run: |
+          .github/scripts/unix.sh -t

.github/workflows/build-macos.yml

@@ -6,8 +6,8 @@ on:
       - '**.md'
       - '**.ipynb' 
       - 'myst.yml'
-# Every time you make a push to your PR, it cancel immediately the previous checks, 
-# and start a new one. The other runner will be available more quickly to your PR. 
+# Cancels any in-progress workflow runs for the same PR when a new push is made,
+# allowing the runner to become available more quickly for the latest changes.
 concurrency:
   group: ${{ github.workflow }}-${{ github.head_ref || github.run_id }}
   cancel-in-progress: true
@@ -22,6 +22,7 @@ jobs:
       CTEST_PARALLEL_LEVEL: 2
       CMAKE_BUILD_TYPE: ${{ matrix.build_type }}
       GTSAM_BUILD_UNSTABLE: ${{ matrix.build_unstable }}
+      GTSAM_ALLOW_DEPRECATED_SINCE_V43: OFF
 
     strategy:
       fail-fast: true
@@ -31,6 +32,8 @@ jobs:
         name: [
           macos-13-xcode-14.2,
           macos-14-xcode-15.4,
+          macos-14-xcode-15.4-boost,
+          macos-14-xcode-15.4-geographiclib,
         ]
 
         build_type: [Debug, Release]
@@ -46,16 +49,46 @@ jobs:
             compiler: xcode
             version: "15.4"
 
+          - name: macos-14-xcode-15.4-boost
+            os: macos-14
+            compiler: xcode
+            version: "15.4"
+
+          - name: macos-14-xcode-15.4-geographiclib
+            os: macos-14
+            compiler: xcode
+            version: "15.4"
+
+        exclude:
+          - name: macos-14-xcode-15.4-boost
+            build_type: Debug
+          - name: macos-14-xcode-15.4-geographiclib
+            build_type: Debug
+
     steps:
       - name: Checkout
         uses: actions/checkout@v4
 
       - name: Install Dependencies
         run: |
-          brew install cmake ninja
-          brew install boost
+          brew upgrade cmake --quiet || brew install cmake --quiet
+          brew upgrade ninja --quiet || brew install ninja --quiet
           sudo xcode-select -switch /Applications/Xcode.app
           echo "CC=clang" >> $GITHUB_ENV
           echo "CXX=clang++" >> $GITHUB_ENV
+
+      - name: Install Boost
+        if: contains(matrix.name, 'boost') && matrix.build_type == 'Release'
+        run: |
+          brew upgrade boost --quiet || brew install boost --quiet
+          echo "GTSAM_USE_BOOST_FEATURES=ON" >> $GITHUB_ENV
+          echo "GTSAM_ENABLE_BOOST_SERIALIZATION=ON" >> $GITHUB_ENV
+
+      - name: Install GeographicLib
+        if: contains(matrix.name, 'geographiclib') && matrix.build_type == 'Release'
+        run: |
+          brew upgrade geographiclib --quiet || brew install geographiclib --quiet
+          echo "GTSAM_ENABLE_GEOGRAPHICLIB=ON" >> $GITHUB_ENV
+
       - name: Build and Test
         run: bash .github/scripts/unix.sh -t

.github/workflows/build-python.yml

@@ -3,7 +3,19 @@ name: Python CI
 # Since this is a required check, specify paths-ignore in the check-paths job
 # instead of under 'pull_request:'. Otherwise, the check is still required but
 # never runs, and a maintainer must bypass the check in order to merge the PR.
-on: [pull_request]
+on:
+  push:
+    branches:
+      - develop
+    paths-ignore:
+      - '**.md'
+      - '**.ipynb'
+      - 'myst.yml'
+  pull_request:
+    paths-ignore:
+      - '**.md'
+      - '**.ipynb'
+      - 'myst.yml'
 
 # Every time you make a push to your PR, it cancel immediately the previous checks,
 # and start a new one. The other runner will be available more quickly to your PR.
@@ -18,11 +30,13 @@ jobs:
     outputs:
       should_run: ${{ steps.filter.outputs.relevant_changes }}
     steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
       - name: Check modified files
         id: filter
         uses: dorny/paths-filter@v3
         with:
-          predicate-quantifier: "every" # If any changed file matches every filter, proceed with build
           filters: |
             relevant_changes:
               - '!**.md'
@@ -44,6 +58,7 @@ jobs:
       PYTHON_VERSION: ${{ matrix.python_version }}
       BOOST_VERSION: 1.72.0
       BOOST_EXE: boost_1_72_0-msvc-14.2
+      GTSAM_ALLOW_DEPRECATED_SINCE_V43: OFF
 
     strategy:
       fail-fast: true
@@ -120,9 +135,17 @@ jobs:
       - name: Install (macOS)
         if: runner.os == 'macOS'
         run: |
-          brew tap ProfFan/robotics
-          brew install cmake ninja
-          brew install boost
+          brew update
+          # Avoid reinstalling cmake when a pinned/local tap version is preinstalled on the runner.
+          if brew list cmake >/dev/null 2>&1; then
+            echo "cmake already installed"
+            cmake --version
+          else
+            brew install cmake
+          fi
+          # Install ninja and boost only if missing
+          brew list ninja >/dev/null 2>&1 || brew install ninja
+          brew list boost >/dev/null 2>&1 || brew install boost
           sudo xcode-select -switch /Applications/Xcode.app
           echo "CC=clang" >> $GITHUB_ENV
           echo "CXX=clang++" >> $GITHUB_ENV