Merge branch 'release/4.1.1'

borglab · Dec 20, 2021 · 69a3a75 · 69a3a75
2 parents 19a9e1e + 30f4dbb
commit 69a3a75
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diff --git a/.cproject b/.cproject
diff --git a/.github/scripts/boost.sh b/.github/scripts/boost.sh
@@ -0,0 +1,18 @@
+### Script to install Boost
+BOOST_FOLDER=boost_${BOOST_VERSION//./_}
+
+# Download Boost
+wget https://boostorg.jfrog.io/artifactory/main/release/${BOOST_VERSION}/source/${BOOST_FOLDER}.tar.gz
+
+# Unzip
+tar -zxf ${BOOST_FOLDER}.tar.gz
+
+# Bootstrap
+cd ${BOOST_FOLDER}/
+./bootstrap.sh --with-libraries=serialization,filesystem,thread,system,atomic,date_time,timer,chrono,program_options,regex
+
+# Build and install
+sudo ./b2 -j$(nproc) install
+
+# Rebuild ld cache
+sudo ldconfig
diff --git a/.github/scripts/python.sh b/.github/scripts/python.sh
@@ -43,11 +43,6 @@ if [ -z ${PYTHON_VERSION+x} ]; then
     exit 127
 fi
 
-if [ -z ${WRAPPER+x} ]; then
-    echo "Please provide the wrapper to build!"
-    exit 126
-fi
-
 PYTHON="python${PYTHON_VERSION}"
 
 if [[ $(uname) == "Darwin" ]]; then
@@ -61,67 +56,33 @@ PATH=$PATH:$($PYTHON -c "import site; print(site.USER_BASE)")/bin
 
 [ "${GTSAM_WITH_TBB:-OFF}" = "ON" ] && install_tbb
 
-case $WRAPPER in
-"cython")
-    BUILD_CYTHON="ON"
-    BUILD_PYBIND="OFF"
-    TYPEDEF_POINTS_TO_VECTORS="OFF"
-
-    sudo $PYTHON -m pip install -r $GITHUB_WORKSPACE/cython/requirements.txt
-    ;;
-"pybind")
-    BUILD_CYTHON="OFF"
-    BUILD_PYBIND="ON"
-    TYPEDEF_POINTS_TO_VECTORS="ON"
-
-    sudo $PYTHON -m pip install -r $GITHUB_WORKSPACE/python/requirements.txt
-    ;;
-*)
-    exit 126
-    ;;
-esac
+
+BUILD_PYBIND="ON"
+
+sudo $PYTHON -m pip install -r $GITHUB_WORKSPACE/python/requirements.txt
 
 mkdir $GITHUB_WORKSPACE/build
 cd $GITHUB_WORKSPACE/build
 
-cmake $GITHUB_WORKSPACE -DCMAKE_BUILD_TYPE=Release \
-    -DGTSAM_BUILD_TESTS=OFF -DGTSAM_BUILD_UNSTABLE=ON \
+cmake $GITHUB_WORKSPACE -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE} \
+    -DGTSAM_BUILD_TESTS=OFF \
+    -DGTSAM_BUILD_UNSTABLE=${GTSAM_BUILD_UNSTABLE:-ON} \
     -DGTSAM_USE_QUATERNIONS=OFF \
     -DGTSAM_WITH_TBB=${GTSAM_WITH_TBB:-OFF} \
     -DGTSAM_BUILD_EXAMPLES_ALWAYS=OFF \
     -DGTSAM_BUILD_WITH_MARCH_NATIVE=OFF \
-    -DGTSAM_INSTALL_CYTHON_TOOLBOX=${BUILD_CYTHON} \
     -DGTSAM_BUILD_PYTHON=${BUILD_PYBIND} \
-    -DGTSAM_TYPEDEF_POINTS_TO_VECTORS=${TYPEDEF_POINTS_TO_VECTORS} \
+    -DGTSAM_UNSTABLE_BUILD_PYTHON=${GTSAM_BUILD_UNSTABLE:-ON} \
     -DGTSAM_PYTHON_VERSION=$PYTHON_VERSION \
     -DPYTHON_EXECUTABLE:FILEPATH=$(which $PYTHON) \
     -DGTSAM_ALLOW_DEPRECATED_SINCE_V41=OFF \
     -DCMAKE_INSTALL_PREFIX=$GITHUB_WORKSPACE/gtsam_install
 
-make -j$(nproc) install &
-
-while ps -p $! > /dev/null
-do
-  sleep 60
-  now=$(date +%s)
-  printf "%d seconds have elapsed\n" $(( (now - start) ))
-done
-
-case $WRAPPER in
-"cython")
-    cd $GITHUB_WORKSPACE/build/cython
-    $PYTHON setup.py install --user --prefix=
-    cd $GITHUB_WORKSPACE/build/cython/gtsam/tests
-    $PYTHON -m unittest discover
-    ;;
-"pybind")
-    cd $GITHUB_WORKSPACE/build/python
-    $PYTHON setup.py install --user --prefix=
-    cd $GITHUB_WORKSPACE/python/gtsam/tests
-    $PYTHON -m unittest discover
-    ;;
-*)
-    echo "THIS SHOULD NEVER HAPPEN!"
-    exit 125
-    ;;
-esac
+
+# 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=
+cd $GITHUB_WORKSPACE/python/gtsam/tests
+$PYTHON -m unittest discover -v
diff --git a/.github/scripts/unix.sh b/.github/scripts/unix.sh
@@ -66,6 +66,10 @@ function configure()
       -DGTSAM_BUILD_EXAMPLES_ALWAYS=${GTSAM_BUILD_EXAMPLES_ALWAYS:-ON} \
       -DGTSAM_ALLOW_DEPRECATED_SINCE_V41=${GTSAM_ALLOW_DEPRECATED_SINCE_V41:-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=${GTSAM_USE_SYSTEM_METIS:-OFF} \
       -DGTSAM_BUILD_WITH_MARCH_NATIVE=OFF \
       -DBOOST_ROOT=$BOOST_ROOT \
       -DBoost_NO_SYSTEM_PATHS=ON \
@@ -90,7 +94,11 @@ function build ()
 
   configure
 
-  make -j2
+  if [ "$(uname)" == "Linux" ]; then
+    make -j$(nproc)
+  elif [ "$(uname)" == "Darwin" ]; then
+    make -j$(sysctl -n hw.physicalcpu)
+  fi
 
   finish
 }
@@ -103,8 +111,12 @@ function test ()
 
   configure
 
-  # Actual build:
-  make -j2 check
+  # Actual testing
+  if [ "$(uname)" == "Linux" ]; then
+    make -j$(nproc) check
+  elif [ "$(uname)" == "Darwin" ]; then
+    make -j$(sysctl -n hw.physicalcpu) check
+  fi
 
   finish
 }

diff --git a/.github/workflows/build-linux.yml b/.github/workflows/build-linux.yml
@@ -12,6 +12,7 @@ jobs:
       CTEST_PARALLEL_LEVEL: 2
       CMAKE_BUILD_TYPE: ${{ matrix.build_type }}
       GTSAM_BUILD_UNSTABLE: ${{ matrix.build_unstable }}
+      BOOST_VERSION: 1.67.0
 
     strategy:
       fail-fast: false
@@ -44,35 +45,38 @@ jobs:
 
     steps:
       - name: Checkout
-        uses: actions/checkout@master
-      - name: Install (Linux)
-        if: runner.os == 'Linux'
+        uses: actions/checkout@v2
+
+      - name: Install Dependencies
         run: |
-          # LLVM 9 is not in Bionic's repositories so we add the official LLVM repository.
+          # LLVM (clang) 9 is not in Bionic's repositories so we add the official LLVM repository.
           if [ "${{ matrix.compiler }}" = "clang" ] && [ "${{ matrix.version }}" = "9" ]; 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 install cmake build-essential pkg-config libpython-dev python-numpy
-          
-          echo "::set-env name=BOOST_ROOT::$(echo $BOOST_ROOT_1_69_0)"
-          echo "::set-env name=LD_LIBRARY_PATH::$(echo $BOOST_ROOT_1_69_0/lib)"
-          
+          sudo apt-get -y install cmake build-essential pkg-config libpython-dev python-numpy libicu-dev
+
           if [ "${{ matrix.compiler }}" = "gcc" ]; then
             sudo apt-get install -y g++-${{ matrix.version }} g++-${{ matrix.version }}-multilib
-            echo "::set-env name=CC::gcc-${{ matrix.version }}"
-            echo "::set-env name=CXX::g++-${{ matrix.version }}"
+            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 "::set-env name=CC::clang-${{ matrix.version }}"
-            echo "::set-env name=CXX::clang++-${{ matrix.version }}"
+            echo "CC=clang-${{ matrix.version }}" >> $GITHUB_ENV
+            echo "CXX=clang++-${{ matrix.version }}" >> $GITHUB_ENV
           fi
-      - name: Check Boost version
-        if: runner.os == 'Linux'
-        run: |
-          echo "BOOST_ROOT = $BOOST_ROOT"
-      - name: Build and Test (Linux)
-        if: runner.os == 'Linux'
+
+      - name: Install Boost
         run: |
-          bash .github/scripts/unix.sh -t
+          bash .github/scripts/boost.sh
+
+      - name: Build and Test
+        run: bash .github/scripts/unix.sh -t
diff --git a/.github/workflows/build-macos.yml b/.github/workflows/build-macos.yml
@@ -12,6 +12,7 @@ jobs:
       CTEST_PARALLEL_LEVEL: 2
       CMAKE_BUILD_TYPE: ${{ matrix.build_type }}
       GTSAM_BUILD_UNSTABLE: ${{ matrix.build_unstable }}
+
     strategy:
       fail-fast: false
       matrix:
@@ -31,21 +32,20 @@ jobs:
 
     steps:
       - name: Checkout
-        uses: actions/checkout@master
-      - name: Install (macOS)
-        if: runner.os == 'macOS'
+        uses: actions/checkout@v2
+
+      - name: Install Dependencies
         run: |
-          brew install cmake ninja boost
+          brew install cmake ninja
+          brew install boost
           if [ "${{ matrix.compiler }}" = "gcc" ]; then
             brew install gcc@${{ matrix.version }}
-            echo "::set-env name=CC::gcc-${{ matrix.version }}"
-            echo "::set-env name=CXX::g++-${{ matrix.version }}"
+            echo "CC=gcc-${{ matrix.version }}" >> $GITHUB_ENV
+            echo "CXX=g++-${{ matrix.version }}" >> $GITHUB_ENV
           else
             sudo xcode-select -switch /Applications/Xcode_${{ matrix.version }}.app
-            echo "::set-env name=CC::clang"
-            echo "::set-env name=CXX::clang++"
+            echo "CC=clang" >> $GITHUB_ENV
+            echo "CXX=clang++" >> $GITHUB_ENV
           fi
-      - name: Build and Test (macOS)
-        if: runner.os == 'macOS'
-        run: |
-          bash .github/scripts/unix.sh -t
+      - name: Build and Test
+        run: bash .github/scripts/unix.sh -t
diff --git a/.github/workflows/build-python.yml b/.github/workflows/build-python.yml
@@ -12,39 +12,45 @@ jobs:
       CTEST_PARALLEL_LEVEL: 2
       CMAKE_BUILD_TYPE: ${{ matrix.build_type }}
       PYTHON_VERSION: ${{ matrix.python_version }}
-      WRAPPER: ${{ matrix.wrapper }}
+
     strategy:
       fail-fast: false
       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.
         name: [
           ubuntu-18.04-gcc-5,
-          # ubuntu-18.04-gcc-9,  # TODO Disabled for now because of timeouts
+          ubuntu-18.04-gcc-9,
           ubuntu-18.04-clang-9,
           macOS-10.15-xcode-11.3.1,
           ubuntu-18.04-gcc-5-tbb,
         ]
 
         build_type: [Debug, Release]
         python_version: [3]
-        wrapper: [pybind]
         include:
           - name: ubuntu-18.04-gcc-5
             os: ubuntu-18.04
             compiler: gcc
             version: "5"
 
-          # TODO Disabled for now because of timeouts
-          # - name: ubuntu-18.04-gcc-9
-          #   os: ubuntu-18.04
-          #   compiler: gcc
-          #   version: "9"
+          - name: ubuntu-18.04-gcc-9
+            os: ubuntu-18.04
+            compiler: gcc
+            version: "9"
+
+          - name: ubuntu-18.04-clang-9
+            os: ubuntu-18.04
+            compiler: clang
+            version: "9"
 
+          # NOTE temporarily added this as it is a required check.
           - name: ubuntu-18.04-clang-9
             os: ubuntu-18.04
             compiler: clang
             version: "9"
+            build_type: Debug
+            python_version: "3"
 
           - name: macOS-10.15-xcode-11.3.1
             os: macOS-10.15
@@ -59,44 +65,52 @@ jobs:
 
     steps:
       - name: Checkout
-        uses: actions/checkout@master
+        uses: actions/checkout@v2
       - name: Install (Linux)
         if: runner.os == 'Linux'
         run: |
-          # LLVM 9 is not in Bionic's repositories so we add the official LLVM repository.
           if [ "${{ matrix.compiler }}" = "clang" ] && [ "${{ matrix.version }}" = "9" ]; 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 install cmake build-essential pkg-config libpython-dev python-numpy libboost-all-dev
+          sudo apt-get -y install cmake build-essential pkg-config libpython-dev python-numpy libboost-all-dev
           
           if [ "${{ matrix.compiler }}" = "gcc" ]; then
             sudo apt-get install -y g++-${{ matrix.version }} g++-${{ matrix.version }}-multilib
-            echo "::set-env name=CC::gcc-${{ matrix.version }}"
-            echo "::set-env name=CXX::g++-${{ matrix.version }}"
+            echo "CC=gcc-${{ matrix.version }}" >> $GITHUB_ENV
+            echo "CXX=g++-${{ matrix.version }}" >> $GITHUB_ENV
           else
             sudo apt-get install -y clang-${{ matrix.version }} g++-multilib
-            echo "::set-env name=CC::clang-${{ matrix.version }}"
-            echo "::set-env name=CXX::clang++-${{ matrix.version }}"
+            echo "CC=clang-${{ matrix.version }}" >> $GITHUB_ENV
+            echo "CXX=clang++-${{ matrix.version }}" >> $GITHUB_ENV
           fi
       - name: Install (macOS)
         if: runner.os == 'macOS'
         run: |
-          brew install cmake ninja boost
+          brew tap ProfFan/robotics
+          brew install cmake ninja
+          brew install boost
           if [ "${{ matrix.compiler }}" = "gcc" ]; then
             brew install gcc@${{ matrix.version }}
-            echo "::set-env name=CC::gcc-${{ matrix.version }}"
-            echo "::set-env name=CXX::g++-${{ matrix.version }}"
+            echo "CC=gcc-${{ matrix.version }}" >> $GITHUB_ENV
+            echo "CXX=g++-${{ matrix.version }}" >> $GITHUB_ENV
           else
             sudo xcode-select -switch /Applications/Xcode_${{ matrix.version }}.app
-            echo "::set-env name=CC::clang"
-            echo "::set-env name=CXX::clang++"
+            echo "CC=clang" >> $GITHUB_ENV
+            echo "CXX=clang++" >> $GITHUB_ENV
           fi
       - name: Set GTSAM_WITH_TBB Flag
         if: matrix.flag == 'tbb'
         run: |
-          echo "::set-env name=GTSAM_WITH_TBB::ON"
+          echo "GTSAM_WITH_TBB=ON" >> $GITHUB_ENV
           echo "GTSAM Uses TBB"
       - name: Build (Linux)
         if: runner.os == 'Linux'
@@ -105,4 +119,4 @@ jobs:
       - name: Build (macOS)
         if: runner.os == 'macOS'
         run: |
-          bash .github/scripts/python.sh
+          bash .github/scripts/python.sh