Fix error 'expected replacement of "find_package(HDF5 1.8 "' #12
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| name: "CI" | |
| on: | |
| push: | |
| branches: | |
| - master | |
| - CI_testing | |
| pull_request: | |
| branches: | |
| - master | |
| jobs: | |
| Linux: | |
| runs-on: ubuntu-latest | |
| defaults: | |
| run: | |
| shell: bash | |
| strategy: | |
| # Use "false" means a single failed build won't terminate other combinations | |
| # in the matrix. This wastes CPU time, so it's meant for debugging only. | |
| fail-fast: false | |
| matrix: | |
| os: | |
| # name: OS name (only a name for humans to read). | |
| # libc: userland libc, "GNU" or "musl" | |
| # (only a name for humans to read) | |
| # ancient: true or false. | |
| # true: incompatible with GitHub's actions/checkout due to | |
| # node.js compatibility problem. Manual git checkout | |
| # required. | |
| # false: use standard GitHub's actions/checkout. | |
| # docker-image: string, image on DockerHub to use | |
| - name: "CentOS 7" | |
| libc: "GNU" | |
| ancient: true | |
| docker-image: "centos:7" | |
| - name: "Ubuntu 14.04" | |
| libc: "GNU" | |
| ancient: true | |
| docker-image: "ubuntu:14.04" | |
| - name: "Debian oldoldstable" | |
| libc: "GNU" | |
| ancient: false | |
| docker-image: "debian:oldoldstable" | |
| - name: "Debian oldstable" | |
| libc: "GNU" | |
| ancient: false | |
| docker-image: "debian:oldstable" | |
| - name: "Debian" | |
| libc: "GNU" | |
| ancient: false | |
| docker-image: "debian:latest" | |
| - name: "Ubuntu" | |
| libc: "GNU" | |
| ancient: false | |
| docker-image: "ubuntu:latest" | |
| - name: "Fedora" | |
| libc: "GNU" | |
| ancient: false | |
| docker-image: "fedora:latest" | |
| - name: "AlmaLinux 8" | |
| libc: "GNU" | |
| ancient: false | |
| docker-image: "almalinux:8" | |
| - name: "AlmaLinux Latest" | |
| libc: "GNU" | |
| ancient: false | |
| docker-image: "almalinux:latest" | |
| # GUI is not supported on Alpine as VTK is built without Qt | |
| - name: "Alpine, No GUI" | |
| libc: "musl" | |
| ancient: false | |
| docker-image: "alpine:latest" | |
| container: | |
| image: ${{ matrix.os.docker-image }} | |
| name: "${{ matrix.os.libc }}/Linux (${{ matrix.os.name }})" | |
| steps: | |
| - name: Check for dockerenv file | |
| # bash is not installed on Alpine at this point | |
| shell: sh | |
| run: (ls /.dockerenv && echo Found dockerenv) || exit 1 | |
| - name: Install dependencies | |
| shell: sh | |
| run: | | |
| cat /etc/os-release | |
| touch ~/.bash_profile | |
| echo 'export CXXFLAGS="-std=c++11"' >> ~/.bash_profile | |
| if grep -q "ID=fedora" /etc/os-release; then | |
| dnf install -y git | |
| dnf install -y gcc gcc-c++ cmake git boost-devel tinyxml-devel vtk-devel hdf5-devel \ | |
| CGAL-devel vtk-qt octave python3-Cython python3-h5py \ | |
| python3-matplotlib | |
| elif grep -q 'ID="almalinux"' /etc/os-release; then | |
| dnf install -y epel-release | |
| dnf config-manager --set-enabled powertools || dnf config-manager --set-enabled crb | |
| dnf install -y git | |
| dnf install -y gcc gcc-c++ cmake git boost-devel tinyxml-devel vtk-devel hdf5-devel \ | |
| CGAL-devel vtk-qt octave python3-Cython python3-h5py \ | |
| python3-matplotlib | |
| elif grep -q "ID=debian" /etc/os-release || grep -q "ID=ubuntu" /etc/os-release; then | |
| # retry failed downloads 3 times | |
| echo 'Acquire::Retries "3";' > /etc/apt/apt.conf.d/80-retries | |
| apt-get update | |
| apt-get install -y build-essential git \ | |
| libhdf5-dev libtinyxml-dev \ | |
| qtbase5-dev octave \ | |
| python3-setuptools python3-numpy \ | |
| python3-matplotlib python3-h5py | |
| # VTK9 or VTK7, at least one must succeed (depending on Debian version) | |
| # VTK9, VTK7, or VTK6, at least one must succeed (depending on Debian version) | |
| apt-get install -y libvtk9-dev libvtk9-qt-dev || \ | |
| apt-get install -y libvtk7-dev libvtk7-qt-dev || \ | |
| apt-get install -y libvtk6-dev | |
| # libvtk6-qt-dev is not used on Ubuntu 14.04 | |
| if grep -q 'VERSION_ID="14.04"' /etc/os-release; then | |
| # Ubuntu 14.04 has CMake 2 by default, but we require CMake 3 | |
| apt-get install -y cmake3 | |
| # Ubuntu 14.04 ships Boost 1.54 and is required by libcgal-dev, | |
| # but we need Boost 1.55, so we install Boost 1.55 first, then | |
| # install CGAL from source. | |
| apt-get install -y boost1.55 boost1.55-dev | |
| # CGAL v4.14.3 was old enough to be compatible with GCC 4.8. Otherwise, | |
| # you get: The compiler feature "cxx_decltype_auto" is not known | |
| # to CXX compiler "GNU" version 4.8.5. | |
| apt-get install -y libgmp-dev libmpfr-dev | |
| git clone $GITHUB_SERVER_URL/CGAL/cgal.git --depth=1 --branch=v4.14.3 | |
| cd cgal && mkdir build && cd build | |
| cmake ../ && make && make install | |
| # Ubuntu 14.04's cython3 package is ancient, install via pip instead | |
| apt-get install -y python3-pip | |
| pip3 install cython | |
| else | |
| apt-get install -y libboost-all-dev | |
| apt-get install -y libcgal-dev | |
| apt-get install -y cmake | |
| apt-get install -y cython3 | |
| fi | |
| # old Debian | |
| apt-get install -y libqt4-dev || (echo Qt4 not installed) | |
| elif grep -q "ID=alpine" /etc/os-release; then | |
| apk add bash \ | |
| build-base gmp-dev mpfr-dev git cmake \ | |
| boost-dev tinyxml-dev hdf5-dev cgal-dev vtk-dev \ | |
| octave \ | |
| python3-dev cython \ | |
| py3-setuptools \ | |
| py3-matplotlib py3-numpy py3-h5py | |
| elif [ -f /etc/centos-release ]; then | |
| # IPv6 on GitHub Actions is broken, causing random network failures | |
| # if a CDN rosolves to IPv6. | |
| echo "ip_resolve=4" >> /etc/yum.conf | |
| # CentOS repos are EOL and desupported | |
| sed -i 's|^mirrorlist|#mirrorlist|g; s|^#baseurl|baseurl|g; s|mirror.centos.org|vault.centos.org|g' \ | |
| /etc/yum.repos.d/CentOS-Base.repo | |
| yum install -y centos-release-scl || true | |
| sed -i 's|^mirrorlist|#mirrorlist|g; s|^#baseurl|baseurl|g; | |
| s|^# baseurl|baseurl|g; s|mirror.centos.org|vault.centos.org|g' \ | |
| /etc/yum.repos.d/CentOS-SCLo-scl.repo \ | |
| /etc/yum.repos.d/CentOS-SCLo-scl-rh.repo | |
| cat /etc/yum.repos.d/CentOS-SCLo-scl.repo | |
| cat /etc/yum.repos.d/CentOS-SCLo-scl-rh.repo | |
| yum install -y epel-release | |
| yum install -y git | |
| yum install -y gcc gcc-c++ gmp-devel mpfr-devel \ | |
| cmake3 git tinyxml-devel vtk-devel hdf5-devel \ | |
| vtk-qt octave python3-pip python3-devel python3-Cython | |
| # use cmake3 instead of default cmake2 | |
| alternatives --install /usr/local/bin/cmake cmake /usr/bin/cmake3 99 | |
| # To upgrade GCC, one can use GCC 7 from centos-release-scl, required by CGAL. | |
| # Even GCC 10+ is provided. | |
| # Not used for now, since openEMS is still compatible with GCC 4.8! But we may | |
| # need it in the future. | |
| # yum install -y devtoolset-7-gcc devtoolset-7-gcc-c++ | |
| # alternatives --install /usr/local/bin/gcc gcc /opt/rh/devtoolset-7/root/usr/bin/gcc 99 | |
| # alternatives --install /usr/local/bin/g++ g++ /opt/rh/devtoolset-7/root/usr/bin/g++ 99 | |
| # boost-predef is only available on Boost 1.55 and later. | |
| # We borrow a copy of Boost 1.58 from rh repo's mariadb backport package. | |
| # /usr/local/include/CGAL/config.h:210:10: fatal error: boost/predef.h: No such | |
| # file or directory # include <boost/predef.h> | |
| yum install -y rh-mariadb101-boost-devel | |
| # CMake doesn't support CPATH | |
| ln -s /opt/rh/rh-mariadb101/root/usr/include/boost /usr/local/include/boost | |
| mkdir /usr/local/lib64 && cd /usr/local/lib64 | |
| for i in /opt/rh/rh-mariadb101/root/usr/lib64/libboost*; do | |
| ln -s $i /usr/local/lib64/ | |
| done | |
| # setup.py is broken on CentOS 7, installing openEMS shows: | |
| # error: Couldn't find a setup script in /tmp/easy_install-8fl5smm_/numpy-2.2.0.tar.gz | |
| # Error: Process completed with exit code 1. | |
| pip3 install numpy h5py matplotlib --user | |
| # not package on CentOS | |
| # CGAL v4.14.3 was old enough to be compatible with GCC 4.8. Otherwise, | |
| # you get: The compiler feature "cxx_decltype_auto" is not known | |
| # to CXX compiler "GNU" version 4.8.5. | |
| git clone $GITHUB_SERVER_URL/CGAL/cgal.git --depth=1 --branch=v4.14.3 | |
| cd cgal && mkdir build && cd build | |
| cmake ../ && make && make install | |
| else | |
| echo "Unknown system!" | |
| exit 1 | |
| fi | |
| - if: ${{ ! matrix.os.ancient }} | |
| name: Checkout openEMS-Project.git | |
| uses: actions/checkout@v4 | |
| with: | |
| path: openEMS-Project | |
| submodules: recursive | |
| # checkout must be deep, not shallow. | |
| # We need tags for "git describe", otherwise build fails. | |
| fetch-depth: 0 | |
| - if: ${{ matrix.os.ancient }} | |
| name: Checkout openEMS-Project.git (legacy system only) | |
| run: | | |
| echo "Clone $GITHUB_REF_NAME from $GITHUB_SERVER_URL/$GITHUB_REPOSITORY.git" | |
| git clone -b $GITHUB_REF_NAME --recursive $GITHUB_SERVER_URL/$GITHUB_REPOSITORY.git openEMS-Project | |
| cd $GITHUB_WORKSPACE/openEMS-Project | |
| - name: Build and install openEMS | |
| run: | | |
| source ~/.bash_profile | |
| cd $GITHUB_WORKSPACE/openEMS-Project | |
| # GUI is not supported on Alpine as VTK is built without Qt | |
| if grep -q "ID=alpine" /etc/os-release; then | |
| gui_opt="--disable-GUI" | |
| else | |
| gui_opt="" | |
| fi | |
| if ./update_openEMS.sh ~/opt --python $gui_opt; then | |
| cat build_*.log | |
| else | |
| cat build_*.log | |
| exit 1 | |
| fi | |
| echo "addpath('~/opt/share/openEMS/matlab')" >> ~/.octaverc | |
| echo "addpath('~/opt/share/CSXCAD/matlab')" >> ~/.octaverc | |
| - name: Smoketest Octave execution | |
| run: | | |
| cd $GITHUB_WORKSPACE/openEMS-Project/openEMS/.github/smoketests/octave | |
| octave MSL_NotchFilter.m | |
| - name: Smoketest Python execution | |
| run: | | |
| source ~/.bash_profile | |
| cd $GITHUB_WORKSPACE/openEMS-Project/openEMS/.github/smoketests/python | |
| python3 MSL_NotchFilter.py | |
| macOS: | |
| name: "macOS (ARM, latest)" | |
| runs-on: macos-latest | |
| steps: | |
| - name: Install dependencies | |
| run: | | |
| echo 'export CXXFLAGS="-std=c++11"' >> ~/.zprofile | |
| brew install cmake boost tinyxml hdf5 cgal vtk python3 octave | |
| # cython is keg-only, which means it was not symlinked into /opt/homebrew, | |
| # because this formula is mainly used internally by other formulae. | |
| # Users are advised to use `pip` to install cython. | |
| # | |
| # So Python will NOT be able to find cython from "site-package", nor | |
| # will the shell finds a cython executable from "bin" | |
| # | |
| # But then, `pip` can't be used directly due to PEP 668, which asks us | |
| # to install cython via the system's package manager, buh Howebrew does | |
| # not provide a fully-function package (unless you hack the symlinks | |
| # manually). | |
| # | |
| # So, the real solution is creating a virtualenv specifically for openEMS | |
| # usage. | |
| # | |
| # TODO: completely update openEMS documentation and scripts to enable and | |
| # teach users about virtualenv | |
| python3 -m venv $HOME/opt | |
| $HOME/opt/bin/pip3 install setuptools cython numpy h5py matplotlib | |
| - name: Checkout openEMS.git | |
| uses: actions/checkout@v4 | |
| with: | |
| path: openEMS-Project | |
| submodules: recursive | |
| # checkout must be deep, not shallow. | |
| # We need tags for "git describe", otherwise build fails. | |
| fetch-depth: 0 | |
| - name: Build and install openEMS | |
| run: | | |
| source ~/.zprofile | |
| cd $GITHUB_WORKSPACE/openEMS-Project | |
| # needed by Python modules | |
| source $HOME/opt/bin/activate # activate venv | |
| export PATH="$HOME/opt/bin:${PATH}" | |
| export CXXFLAGS="-std=c++11 -I$HOME/opt/include -I/opt/homebrew/include" | |
| export LDFLAGS="-L$HOME/opt/lib -L/opt/homebrew/lib" | |
| if ./update_openEMS.sh ~/opt --python; then | |
| cat build_*.log | |
| else | |
| cat build_*.log | |
| exit 1 | |
| fi | |
| echo "addpath('~/opt/share/openEMS/matlab')" >> ~/.octaverc | |
| echo "addpath('~/opt/share/CSXCAD/matlab')" >> ~/.octaverc | |
| - name: Smoketest Octave execution | |
| run: | | |
| cd $GITHUB_WORKSPACE/openEMS-Project/openEMS/.github/smoketests/octave | |
| octave MSL_NotchFilter.m | |
| - name: Smoketest Python execution | |
| run: | | |
| cd $GITHUB_WORKSPACE/openEMS-Project/openEMS/.github/smoketests/python | |
| $HOME/opt/bin/python3 MSL_NotchFilter.py | |
| FreeBSD: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| machine: | |
| - name: "FreeBSD 14.2" | |
| os: freebsd | |
| arch: x86-64 | |
| version: '14.2' | |
| # macOS already tests ARM for us, so disable the slow ARM emulator | |
| # for now | |
| #- name: "FreeBSD 14.2 (ARM emulator)" | |
| # os: freebsd | |
| # arch: arm64 | |
| # version: '14.2' | |
| name: "${{ matrix.machine.name }}" | |
| steps: | |
| - name: Checkout repo | |
| uses: actions/checkout@v4 | |
| - name: Test in FreeBSD ${{ matrix.machine.version }} ${{ matrix.machine.arch }} | |
| uses: cross-platform-actions/action@v0.26.0 | |
| with: | |
| cpu_count: 4 | |
| architecture: ${{ matrix.machine.arch }} | |
| operating_system: ${{ matrix.machine.os }} | |
| version: ${{ matrix.machine.version }} | |
| run: | | |
| echo "Install dependencies..." | |
| sudo pkg install -y bash cmake git boost-libs tinyxml vtk9 hdf5 cgal octave \ | |
| qt5 python3 \ | |
| py311-cython3 py311-numpy py311-h5py py311-matplotlib | |
| # prefix must match FreeBSD's default python | |
| # version. FreeBSD 14.2 uses Python 3.11 so | |
| # use "py311-" | |
| echo "Clone $GITHUB_REF_NAME from $GITHUB_SERVER_URL/$GITHUB_REPOSITORY.git" | |
| cd ~/ | |
| git clone -b $GITHUB_REF_NAME --recursive $GITHUB_SERVER_URL/$GITHUB_REPOSITORY.git openEMS-Project | |
| echo "Build and install openEMS..." | |
| # needed by Python modules | |
| export CFLAGS="-I$HOME/opt/include -I/usr/local/include" | |
| export CXXFLAGS="-I$HOME/opt/include -I/usr/local/include" | |
| export LDFLAGS="-L$HOME/opt/lib -L/usr/local/lib" | |
| cd ~/openEMS-Project | |
| if bash ./update_openEMS.sh ~/opt --python; then | |
| cat build_*.log | |
| else | |
| cat build_*.log | |
| exit 1 | |
| fi | |
| echo "addpath('~/opt/share/openEMS/matlab')" >> ~/.octaverc | |
| echo "addpath('~/opt/share/CSXCAD/matlab')" >> ~/.octaverc | |
| echo "Smoketest Octave execution..." | |
| cd ~/openEMS-Project/openEMS/.github/smoketests/octave/ | |
| octave MSL_NotchFilter.m | |
| echo "Smoketest Python execution..." | |
| cd ~/openEMS-Project/openEMS/.github/smoketests/python | |
| python3 MSL_NotchFilter.py |