Merge branch 'develop' into feature/point_cloud_generator

.dockerignore

@@ -0,0 +1,23 @@
+
+# Note:
+#   - libpointmatch cmake install require that the README.md file exist in the docker image
+#   - libpointmatcher-CI doc related step require that .svg, .png and .md be copied in the docker image
+
+# Graphic/image related
+*.svg
+*.svgz
+*.png
+*.drawio
+
+# Text related
+*.pdf
+
+# Files
+
+
+# Directories
+drawio/*
+visual/*
+
+# IDE
+.run/*

.github/workflows/build-python.yaml

@@ -0,0 +1,321 @@
+name: Compile python package
+
+on:
+  push:
+    branches: [master, feature/github-release]
+    tags:
+      - '[0-9]+.[0-9]+.[0-9]+'
+  pull_request:
+    branches: [master, develop]
+  workflow_dispatch:
+
+env:
+  BOOST_MAJOR_VERSION: '1'
+  BOOST_MINOR_VERSION: '80'
+  BOOST_PATCH_VERSION: '0'
+  LIBNABO_VERSION: '1.0.7'
+  PYBIND11_VERSION: 'v2.10.2'
+  BOOST_INSTALL_PATH: ${{ github.workspace }}/.tmp/boost/install
+  BOOST_SRC_DIR: ${{ github.workspace }}/.tmp/boost
+  LIBNABO_INSTALL_PATH: ${{ github.workspace }}/.tmp/libnabo-build/install
+  LIBNABO_SRC_DIR: ${{ github.workspace }}/.tmp/libnabo
+  PYBIND11_INSTALL_PATH: ${{ github.workspace }}/.tmp/pybind11-build/install
+  PYBIND11_SRC_DIR: ${{ github.workspace }}/.tmp/pybind11
+  PYTHON_WHEEL_DIR: ${{ github.workspace }}/.tmp/python-wheel
+  VCPKG_DEFAULT_BINARY_CACHE: '${{ github.workspace }}/.tmp/bin-cache'
+  CMAKE_BUILD_PARALLEL_LEVEL: 2
+  BUILD_DIR: ${{ github.workspace }}/build
+
+jobs:
+  compile-python-package:
+    strategy:
+      fail-fast: false
+      matrix:
+        python_version: ['3.8', '3.9', '3.10', '3.11']
+        os: 
+          # - windows-2019 cannot compile on Windows
+          # (!) TODO: The workflow contains code for Windows building, but we cannot compile it with MS MPI. Changes in the source code are needed.
+
+          - ubuntu-20.04
+
+    permissions:
+      contents: write
+
+    runs-on: ${{ matrix.os }}
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Make temp dir
+        run: mkdir ${{ github.workspace }}/.tmp
+
+      - name: Init base env variable on Linux
+        if: ${{ runner.os == 'Linux' }}
+        run: |
+          echo "BOOST_DIR=boost_${{ env.BOOST_MAJOR_VERSION }}_${{ env.BOOST_MINOR_VERSION }}_${{ env.BOOST_PATCH_VERSION }}" >> $GITHUB_ENV
+          echo "BOOST_VERSION=${{ env.BOOST_MAJOR_VERSION }}.${{ env.BOOST_MINOR_VERSION }}.${{ env.BOOST_PATCH_VERSION }}" >> $GITHUB_ENV
+ 
+      - name: Init env variable on Linux
+        if: ${{ runner.os == 'Linux' }}
+        run: | 
+          echo "BOOST_ARCHIVE_NAME=${{ env.BOOST_DIR }}.7z" >> $GITHUB_ENV
+
+      - name: Init base env variable on Windows
+        if: ${{ runner.os == 'Windows' }}
+        run: |
+          echo "BOOST_DIR=boost_${{ env.BOOST_MAJOR_VERSION }}_${{ env.BOOST_MINOR_VERSION }}_${{ env.BOOST_PATCH_VERSION }}" | Out-File -FilePath $env:GITHUB_ENV -Append
+          echo "BOOST_VERSION=${{ env.BOOST_MAJOR_VERSION }}.${{ env.BOOST_MINOR_VERSION }}.${{ env.BOOST_PATCH_VERSION }}" | Out-File -FilePath $env:GITHUB_ENV -Append
+ 
+      - name: Init env variable on Windows
+        if: ${{ runner.os == 'Windows' }}
+        run: | 
+          echo "BOOST_ARCHIVE_NAME=${{ env.BOOST_DIR }}.zip" | Out-File -FilePath $env:GITHUB_ENV -Append
+      
+      - name: Cache boost
+        id: cache-boost
+        if: ${{ runner.os  == 'Linux' }}
+        uses: actions/cache@v3
+        with:
+          path: ${{ env.BOOST_INSTALL_PATH }}
+          key: ${{ runner.os }}-boost-cache-${{ env.BOOST_VERSION }}-python-${{ matrix.python_version }}
+
+      - name: Cache libnabo
+        id: cache-libnabo
+        uses: actions/cache@v3
+        with:
+          path: ${{ env.LIBNABO_INSTALL_PATH }}
+          key: ${{ runner.os }}-libnabo-cache-${{ env.LIBNABO_VERSION }}
+
+      - name: Cache binary vcpkg
+        if: ${{ runner.os  == 'Windows' }}
+        id: cache-vcpkg
+        uses: actions/cache@v3
+        with:
+          path: ${{ env.VCPKG_DEFAULT_BINARY_CACHE }}
+          key: ${{ runner.os }}-vcpkg-cache-${{ matrix.python_version }}
+
+      - name: Cache pybind11
+        id: cache-pybind11
+        uses: actions/cache@v3
+        with:
+          path: ${{ env.PYBIND11_INSTALL_PATH }}
+          key: ${{ runner.os }}-pybind11-cache--${{ env.PYBIND11_VERSION }}-python-${{ matrix.python_version }}
+
+      - name: Make dirs on Linux
+        if: ${{ runner.os  == 'Linux' }}
+        run: |
+          mkdir -p ${{ env.BOOST_SRC_DIR }}
+          mkdir -p ${{ env.LIBNABO_SRC_DIR }}
+          mkdir -p ${{ env.PYBIND11_SRC_DIR }}
+          mkdir -p ${{ env.BOOST_INSTALL_PATH }}
+          mkdir -p ${{ env.PYBIND11_INSTALL_PATH }}
+          mkdir -p ${{ env.LIBNABO_INSTALL_PATH }}
+          mkdir -p ${{ env.VCPKG_DEFAULT_BINARY_CACHE }}
+
+      - name: Make dirs on Windows
+        if: ${{ runner.os == 'Windows' }}
+        run: |
+          mkdir -Force ${{ env.BOOST_SRC_DIR }}
+          mkdir -Force ${{ env.LIBNABO_SRC_DIR }}
+          mkdir -Force ${{ env.PYBIND11_SRC_DIR }}
+          mkdir -Force ${{ env.BOOST_INSTALL_PATH }}
+          mkdir -Force ${{ env.PYBIND11_INSTALL_PATH }}
+          mkdir -Force ${{ env.LIBNABO_INSTALL_PATH }}
+          mkdir -Force ${{ env.VCPKG_DEFAULT_BINARY_CACHE }}
+
+      - name: Install dependencies on Linux
+        if: ${{ runner.os  == 'Linux' }}
+        run: |
+          sudo apt update
+          sudo apt install -y --no-install-recommends g++ \
+            gcc \
+            make \
+            libeigen3-dev \
+            ninja-build \
+            catch \
+            libomp-dev \
+            wget
+
+      - name: Install MS MPI
+        if: ${{ runner.os == 'Windows' }}
+        working-directory: ${{ runner.temp }}
+        run: |
+          Invoke-WebRequest https://download.microsoft.com/download/a/5/2/a5207ca5-1203-491a-8fb8-906fd68ae623/msmpisetup.exe  -OutFile ./msmpisetup.exe
+          Start-Process -Wait -FilePath ./msmpisetup.exe  -ArgumentList "-unattend","-log","./log.txt" -NoNewWindow
+          cat ./log.txt
+
+      - name: Set up Python ${{ matrix.python_version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python_version }}
+          cache: 'pip'
+
+      - name: Install required dependencies for Python
+        run: |
+          python -m pip install -U 'pip>=23.0'
+          pip install 'numpy>=1.20' wheel 'setuptools>=61.0' 'build~=0.10'
+      
+      - name: Install dependencies on Windows
+        if: ${{ runner.os == 'Windows' }}
+        run: |
+          vcpkg install eigen3:x64-windows-static `
+                libopenmpt:x64-windows `
+                boost-mpi:x64-windows-static `
+                boost-thread:x64-windows-static `
+                boost-filesystem:x64-windows-static `
+                boost-system:x64-windows-static `
+                boost-program-options:x64-windows-static `
+                boost-date-time:x64-windows-static `
+                boost-chrono:x64-windows-static `
+                boost-regex[icu]:x64-windows-static `
+                boost-assign:x64-windows-static `
+                boost-timer:x64-windows-static `
+                --clean-after-build
+
+      - name: Download boost ${{ env.BOOST_VERSION }} on Linux
+        if: ${{ steps.cache-boost.outputs.cache-hit != 'true' &&  runner.os == 'Linux' }}
+        working-directory: ${{ env.BOOST_SRC_DIR }}
+        run: |
+          wget --no-verbose https://boostorg.jfrog.io/artifactory/main/release/${{ env.BOOST_VERSION }}/source/${{ env.BOOST_ARCHIVE_NAME }}
+          7z -y x ${{ env.BOOST_ARCHIVE_NAME }}
+          rm ${{ env.BOOST_ARCHIVE_NAME }}
+
+      - name: Configure static boost on Linux
+        if: ${{ steps.cache-boost.outputs.cache-hit != 'true' && runner.os == 'Linux' }}
+        working-directory: ${{ env.BOOST_SRC_DIR }}/${{ env.BOOST_DIR }}
+        run: |
+          ./bootstrap.sh --with-libraries=thread,filesystem,system,program_options,date_time,chrono --with-icu --prefix=${{ env.BOOST_INSTALL_PATH }}
+          ./b2 cxxflags=-fPIC cflags=-fPIC link=static install
+
+      - name: Download source code libnabo ${{ env.LIBNABO_VERSION }}
+        if: steps.cache-libnabo.outputs.cache-hit != 'true'
+        working-directory: ${{ env.LIBNABO_SRC_DIR }}
+        run: |
+          git clone -b ${{ env.LIBNABO_VERSION }} --single-branch https://github.com/ethz-asl/libnabo.git
+
+      - name: Install libnabo ${{ env.LIBNABO_VERSION }} on Windows
+        if: ${{ steps.cache-libnabo.outputs.cache-hit != 'true' && runner.os == 'Windows' }}
+        working-directory: ${{ env.LIBNABO_SRC_DIR }}
+        run: |
+          cd libnabo
+          cmake -A x64 `
+            -DCMAKE_TOOLCHAIN_FILE="$env:VCPKG_INSTALLATION_ROOT/scripts/buildsystems/vcpkg.cmake" `
+            -DCMAKE_INSTALL_PREFIX=${{ env.LIBNABO_INSTALL_PATH }} `
+            -DCMAKE_BUILD_TYPE=RelWithDebInfo `
+            -DUSE_OPEN_MP:BOOL=ON `
+            -S . -B ./build
+          cmake --build ./build --target install
+          cd -
+          rm -r ./libnabo/build
+
+      - name: Install libnabo ${{ env.LIBNABO_VERSION }} on Linux
+        if: ${{ steps.cache-libnabo.outputs.cache-hit != 'true' && runner.os == 'Linux' }}
+        working-directory: ${{ env.LIBNABO_SRC_DIR }}
+        run: |
+          cd libnabo
+          cmake -GNinja \
+            -DBOOST_ROOT=${{ env.BOOST_INSTALL_PATH }} \
+            -DCMAKE_INSTALL_PREFIX=${{ env.LIBNABO_INSTALL_PATH }} \
+            -DCMAKE_BUILD_TYPE=RelWithDebInfo \
+            -DUSE_OPEN_MP:BOOL=ON \
+            -S . -B ./build
+          cmake --build ./build --target install
+          cd -
+          rm -r ./libnabo/build
+
+      - name: Download source code pybind11 ${{ env.PYBIND11_VERSION }}
+        if: steps.cache-pybind11.outputs.cache-hit != 'true'
+        working-directory: ${{ env.PYBIND11_SRC_DIR }}
+        run: |
+          git clone -b ${{ env.PYBIND11_VERSION }} --single-branch https://github.com/pybind/pybind11.git
+
+      
+      - name: Install pybind11 ${{ env.PYBIND11_VERSION }} on Linux
+        working-directory:  ${{ env.PYBIND11_SRC_DIR }}
+        if: ${{ steps.cache-pybind11.outputs.cache-hit != 'true' && runner.os == 'Linux' }}
+        run: |
+          cd pybind11
+          cmake -GNinja \
+            -DCMAKE_INSTALL_PREFIX=${{ env.PYBIND11_INSTALL_PATH }} \
+            -DCMAKE_BUILD_TYPE=RelWithDebInfo \
+            -DPYBIND11_TEST:BOOL=OFF \
+            -S . -B ./build
+          cmake --build ./build --target install
+          rm -r ./build
+      
+      - name: Install pybind11 ${{ env.PYBIND11_VERSION }} on Windows
+        working-directory:  ${{ env.PYBIND11_SRC_DIR }}
+        if: ${{ steps.cache-pybind11.outputs.cache-hit != 'true' && runner.os == 'Windows' }}
+        run: |
+          cd pybind11
+          cmake -A x64 `
+            -DCMAKE_TOOLCHAIN_FILE="$env:VCPKG_INSTALLATION_ROOT/scripts/buildsystems/vcpkg.cmake" `
+            -DCMAKE_INSTALL_PREFIX=${{ env.PYBIND11_INSTALL_PATH }} `
+            -DCMAKE_BUILD_TYPE=RelWithDebInfo `
+            -DPYBIND11_TEST:BOOL=OFF `
+            -S . -B ./build
+          cmake --build ./build --target install
+          rm -r ./build
+
+      - name: Compile libpointmatcher on Linux
+        if: runner.os == 'Linux'
+        run: |
+          cmake \
+            -DBOOST_ROOT:PATH=${{ env.BOOST_INSTALL_PATH }} \
+            -DLIBNABO_INSTALL_DIR=${{ env.LIBNABO_INSTALL_PATH }} \
+            -Dpybind11_DIR=${{ env.PYBIND11_INSTALL_PATH }}/share/cmake/pybind11 \
+            -DBUILD_PYTHON_MODULE:BOOL=ON \
+            -DUSE_OPEN_MP:BOOL=ON \
+            -DBoost_USE_STATIC_LIBS:BOOL=ON \
+            -DCMAKE_BUILD_TYPE=RelWithDebInfo \
+            -S . -B ${{ env.BUILD_DIR }}
+          sudo cmake --build ${{ env.BUILD_DIR }} --target install
+
+      - name: Compile libpointmatcher on Windows
+        if: runner.os == 'Windows'
+        env:
+          PYTHON_PACKAGE_NAME: pypointmatcher
+        run: |
+          cmake -A x64 `
+            -DCMAKE_TOOLCHAIN_FILE:FILEPATH="$env:VCPKG_INSTALLATION_ROOT/scripts/buildsystems/vcpkg.cmake" `
+            -DLIBNABO_INSTALL_DIR:PATH="${{ env.LIBNABO_INSTALL_PATH }}" `
+            -Dpybind11_DIR:PATH="${{ env.PYBIND11_INSTALL_PATH }}/share/cmake/pybind11" `
+            -DBUILD_PYTHON_MODULE:BOOL=ON `
+            -DBoost_USE_STATIC_LIBS:BOOL=ON `
+            -DPYTHON_INSTALL_TARGET:PATH="./python/${{ env.PYTHON_PACKAGE_NAME }}" `
+            -DVCPKG_TARGET_TRIPLET="x64-windows-static" `
+            -DUSE_OPEN_MP:BOOL=ON `
+            -DCMAKE_BUILD_TYPE="RelWithDebInfo" `
+            -S . -B ${{ env.BUILD_DIR }}
+          cmake --build ${{ env.BUILD_DIR }} --target install
+      
+      - name: Build python wheel
+        working-directory: ./python
+        run: |
+          python -m build --wheel --no-isolation --outdir ${{ env.PYTHON_WHEEL_DIR }}
+
+      - name: Install package
+        working-directory: ./python
+        run: |
+          pip install ${{ env.PYTHON_WHEEL_DIR }}/*.whl
+      
+      - name: Test import
+        working-directory: ${{ runner.temp }}
+        run: python -c "from pypointmatcher import *"
+
+      - name: Upload python wheel
+        uses: actions/upload-artifact@v3
+        with:
+          name: libpointmatcher python ${{ matrix.python_version }} wheel
+          path: ${{ env.PYTHON_WHEEL_DIR }}/*.whl
+          if-no-files-found: error
+          retention-days: 10
+
+      - uses: ncipollo/release-action@v1
+        if: github.ref_type == 'tag'
+        with:
+          artifacts: "${{ env.PYTHON_WHEEL_DIR }}/*.whl"
+          prerelease: true
+          allowUpdates: true
+          generateReleaseNotes: true
+

.gitignore

@@ -5,3 +5,6 @@
 *.cur_trans
 build
 .ipynb_checkpoints/
+
+dist/
+*.so