Merge pull request #2141 from borglab/release/4.3a0

Release/4.3a0

Author: dellaert

.clang-format

@@ -0,0 +1 @@
+BasedOnStyle: Google

.github/ISSUE_TEMPLATE/bug-report.md

@@ -3,12 +3,12 @@ name: "Bug Report"
 about: Submit a bug report to help us improve GTSAM
 ---
 
+<!-- This is a channel to report bugs/issues, not a support channel to help install/use/debug your own code. We'd love to help, but just don't have the bandwidth. Please post questions in the GTSAM Google group (https://groups.google.com/forum/#!forum/gtsam-users) -->
+
 <!--Please only submit issues/bug reports that come with enough information to reproduce them, ideally a unit test that fails, and possible ideas on what might be wrong. -->
 
 <!-- Even better yet, fix the bug and/or documentation, add a unit test, and create a pull request! -->
 
-<!-- This is a channel to report bugs/issues, not a support channel to help install/use/debug your own code. We'd love to help, but just don't have the bandwidth. Please post questions in the GTSAM Google group (https://groups.google.com/forum/#!forum/gtsam-users) -->
-
 ## Description
 
 <!-- A clear description of the bug -->

.github/scripts/boost.sh

@@ -9,33 +9,13 @@ set -x -e
 # install TBB with _debug.so files
 function install_tbb()
 {
-  TBB_BASEURL=https://github.com/oneapi-src/oneTBB/releases/download
-  TBB_VERSION=4.4.5
-  TBB_DIR=tbb44_20160526oss
-  TBB_SAVEPATH="/tmp/tbb.tgz"
-
+  echo install_tbb
   if [ "$(uname)" == "Linux" ]; then
-    OS_SHORT="lin"
-    TBB_LIB_DIR="intel64/gcc4.4"
-    SUDO="sudo"
+    sudo apt-get -y install libtbb-dev
 
   elif [ "$(uname)" == "Darwin" ]; then
-    OS_SHORT="osx"
-    TBB_LIB_DIR=""
-    SUDO=""
-
+    brew install tbb
   fi
-
-  wget "${TBB_BASEURL}/${TBB_VERSION}/${TBB_DIR}_${OS_SHORT}.tgz" -O $TBB_SAVEPATH
-  tar -C /tmp -xf $TBB_SAVEPATH
-
-  TBBROOT=/tmp/$TBB_DIR
-  # Copy the needed files to the correct places.
-  # This works correctly for CI builds, instead of setting path variables.
-  # This is what Homebrew does to install TBB on Macs
-  $SUDO cp -R $TBBROOT/lib/$TBB_LIB_DIR/* /usr/local/lib/
-  $SUDO cp -R $TBBROOT/include/ /usr/local/include/
-
 }
 
 if [ -z ${PYTHON_VERSION+x} ]; then
@@ -56,19 +36,18 @@ function install_dependencies()
 
   export PATH=$PATH:$($PYTHON -c "import site; print(site.USER_BASE)")/bin
 
-  [ "${GTSAM_WITH_TBB:-OFF}" = "ON" ] && install_tbb
-
-  $PYTHON -m pip install -r $GITHUB_WORKSPACE/python/requirements.txt
+  if [ "${GTSAM_WITH_TBB:-OFF}" == "ON" ]; then
+    install_tbb
+  fi
 }
 
 function build()
 {
-  mkdir $GITHUB_WORKSPACE/build
-  cd $GITHUB_WORKSPACE/build
-
+  export CMAKE_GENERATOR=Ninja
   BUILD_PYBIND="ON"
-
-  cmake $GITHUB_WORKSPACE -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE} \
+  cmake $GITHUB_WORKSPACE \
+      -B build \
+      -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE} \
       -DGTSAM_BUILD_TESTS=OFF \
       -DGTSAM_BUILD_UNSTABLE=${GTSAM_BUILD_UNSTABLE:-ON} \
       -DGTSAM_USE_QUATERNIONS=OFF \
@@ -79,21 +58,28 @@ function build()
       -DGTSAM_UNSTABLE_BUILD_PYTHON=${GTSAM_BUILD_UNSTABLE:-ON} \
       -DGTSAM_PYTHON_VERSION=$PYTHON_VERSION \
       -DPYTHON_EXECUTABLE:FILEPATH=$(which $PYTHON) \
-      -DGTSAM_ALLOW_DEPRECATED_SINCE_V42=OFF \
+      -DGTSAM_ALLOW_DEPRECATED_SINCE_V43=OFF \
       -DCMAKE_INSTALL_PREFIX=$GITHUB_WORKSPACE/gtsam_install
 
 
   # Set to 2 cores so that Actions does not error out during resource provisioning.
-  make -j2 install
+  cmake --build build -j2
 
-  cd $GITHUB_WORKSPACE/build/python
-  $PYTHON -m pip install --user .
+  cmake --build build --target python-install
 }
 
 function test()
 {
   cd $GITHUB_WORKSPACE/python/gtsam/tests
   $PYTHON -m unittest discover -v
+  cd $GITHUB_WORKSPACE
+
+  cd $GITHUB_WORKSPACE/python/gtsam_unstable/tests
+  $PYTHON -m unittest discover -v
+  cd $GITHUB_WORKSPACE
+
+  # cmake --build build --target python-test
+  # cmake --build build --target python-test-unstable
 }
 
 # select between build or test

.github/scripts/python.sh

@@ -0,0 +1,10 @@
+#!/bin/bash
+
+# This script calls cibuildwheel to build the wheels for the project. It is used in the build-cibw.yml workflow in .github/workflows.
+# Note that the build/python directory contains the wrapper module built for the specified Python version.
+
+set -e
+set -x
+
+python -m pip install cibuildwheel
+python -m cibuildwheel build/python --output-dir wheelhouse

.github/scripts/python_wheels/build_wheels.sh

@@ -0,0 +1,97 @@
+#!/bin/bash
+
+# This script is invoked prior to building the wheels with cibuildwheel. It is used in the build-cibw.yml workflow in .github/workflows.
+# It installs the necessary dependencies and builds the wrapper module for the specified Python version.
+
+set -e
+set -x
+
+PYTHON_VERSION="$1"
+PROJECT_DIR="$2"
+ARCH=$(uname -m)
+
+export PYTHON="python${PYTHON_VERSION}"
+
+if [ "$(uname)" == "Linux" ]; then
+    # manylinux2014 is based on CentOS 7, so use yum to install dependencies
+    yum install -y wget doxygen
+elif [ "$(uname)" == "Darwin" ]; then
+    brew install cmake doxygen
+
+    # If MACOSX_DEPLOYMENT_TARGET is not explicitly set, default to the version of the host system.
+    if [[ -z "${MACOSX_DEPLOYMENT_TARGET}" ]]; then
+        export MACOSX_DEPLOYMENT_TARGET="$(sw_vers -productVersion | cut -d '.' -f 1-2)"
+    fi
+fi
+
+# Install Boost from source
+wget https://archives.boost.io/release/1.87.0/source/boost_1_87_0.tar.gz --quiet
+tar -xzf boost_1_87_0.tar.gz
+cd boost_1_87_0
+
+BOOST_PREFIX="$HOME/opt/boost"
+./bootstrap.sh --prefix=${BOOST_PREFIX}
+
+if [ "$(uname)" == "Linux" ]; then
+    ./b2 install --prefix=${BOOST_PREFIX} --with=all -d0
+elif [ "$(uname)" == "Darwin" ]; then
+    ./b2 install --prefix=${BOOST_PREFIX} --with=all -d0 \
+        cxxflags="-mmacosx-version-min=${MACOSX_DEPLOYMENT_TARGET}" \
+        linkflags="-mmacosx-version-min=${MACOSX_DEPLOYMENT_TARGET}"
+fi
+cd ..
+
+# Export paths so CMake or build system can find Boost
+export BOOST_ROOT="${BOOST_PREFIX}"
+export BOOST_INCLUDEDIR="${BOOST_PREFIX}/include"
+export BOOST_LIBRARYDIR="${BOOST_PREFIX}/lib"
+
+# Ensure runtime linker can find Boost libraries
+export LD_LIBRARY_PATH="${BOOST_LIBRARYDIR}:$LD_LIBRARY_PATH" # For Linux
+export REPAIR_LIBRARY_PATH="${BOOST_LIBRARYDIR}:$DYLD_LIBRARY_PATH" # For macOS, REPAIR_LIBRARY_PATH is used by delocate
+
+if [ "$(uname)" == "Darwin" ]; then
+    # Explicitly add rpath to Boost dylibs so delocate can find them
+    for dylib in ${BOOST_LIBRARYDIR}/*.dylib; do
+        install_name_tool -add_rpath "@loader_path" "$dylib"
+    done
+fi
+
+$(which $PYTHON) -m pip install -r $PROJECT_DIR/python/dev_requirements.txt
+
+# Remove build/cache files that were generated on host
+rm -rf $PROJECT_DIR/build
+rm -rf CMakeCache.txt CMakeFiles
+
+# Build the Python wrapper module
+cmake $PROJECT_DIR \
+    -B build \
+    -DCMAKE_BUILD_TYPE=${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_BUILD_PYTHON=ON \
+    -DGTSAM_UNSTABLE_BUILD_PYTHON=${GTSAM_BUILD_UNSTABLE:-ON} \
+    -DGTSAM_PYTHON_VERSION=$PYTHON_VERSION \
+    -DPYTHON_EXECUTABLE:FILEPATH=$(which $PYTHON) \
+    -DGTSAM_ALLOW_DEPRECATED_SINCE_V43=OFF \
+    -DCMAKE_INSTALL_PREFIX=$PROJECT_DIR/gtsam_install \
+    -DGTSAM_GENERATE_DOC_XML=1 \
+    -DGTWRAP_ADD_DOCSTRINGS=ON
+
+# Generate Doxygen XML documentation
+doxygen build/doc/Doxyfile
+
+# Install the Python wrapper module and generate Python stubs
+cd $PROJECT_DIR/build/python
+if [ "$(uname)" == "Linux" ]; then
+    make -j $(nproc) install
+    make -j $(nproc) python-stubs
+elif [ "$(uname)" == "Darwin" ]; then
+    make -j $(sysctl -n hw.logicalcpu) install
+    make -j $(sysctl -n hw.logicalcpu) python-stubs
+fi
+

.github/scripts/python_wheels/cibw_before_all.sh

@@ -0,0 +1,46 @@
+#!/usr/bin/env bash
+
+# This script deletes all but the most recent release from the gtsam-develop project on PyPI
+# and can be used if the project size exceeds the PyPI limit of 10 GB. The user must have
+# owner or maintainer privileges on the project.
+
+set -euo pipefail
+
+usage() {
+  cat <<EOF
+Usage: $(basename "$0") <pypi_username>
+
+Deletes all but the most recent release from the gtsam-develop project on PyPI.
+You must supply the PyPI user name that has owner or maintainer privileges on
+the project. THIS OPERATION IS PERMANENT.
+
+Examples
+  $ $(basename "$0") yambati3
+  $ $(basename "$0")        # will prompt for user name
+EOF
+}
+
+if [[ $# -ge 1 ]]; then
+  PYPI_USER="$1"
+else
+  read -rp "Enter your PyPI user name: " PYPI_USER
+  [[ -z "$PYPI_USER" ]] && { echo "No user name supplied."; usage; exit 1; }
+fi
+
+echo "-----------------------------------------------------------------------"
+echo "WARNING: This WILL permanently delete all but the most recent release"
+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
+[[ "$REPLY" != "y" && "$REPLY" != "yes" ]] && { echo "Aborted."; exit 0; }
+
+echo "Running pypi_cleanup for user '$PYPI_USER'..."
+python3 -m pypi_cleanup.__init__ \
+        -p gtsam-develop \
+        --leave-most-recent-only \
+        --do-it \
+        -u "$PYPI_USER"
+
+echo "Done."