Fix:GetCSX #303

Workflow file for this run

	name: "CI"

	on:
	push:
	branches:
	- '**'
	pull_request:
	branches:
	- "**"

	jobs:
	Dependencies:
	runs-on: ubuntu-latest
	name: "Resolve repo dependencies"

	steps:
	- name: Checkout repo
	uses: actions/checkout@v4

	- name: Resolve repo dependencies
	id: resolve-dependencies
	# writes to $GITHUB_OUTPUT file
	run: \|
	python3 $GITHUB_WORKSPACE/.github/scripts/resolve_dependent_repos.py \
	--project openEMS
	env:
	GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
	GITHUB_FORK_OWNER: ${{ github.event.pull_request.head.repo.owner.login }}

	# format a human-friendly string in the following format:
	#
	# * Checkout XXXX.git
	# (keep the "master" branch case boring to avoid information overload)
	#
	# OR:
	#
	# * Checkout XXXX.git \| PR: https://example.com/XXXX
	#
	# OR:
	#
	# * Checkout XXXX.git \| branch: feature \| http://example.com/XXXX
	- name: Format title strings
	id: format-title
	shell: python
	run: \|
	import os

	def format_title_string(var, repo, pr_url, branch):
	title = "Checkout %s.git" % repo
	if pr_url != "None":
	title += " \| PR: %s" % pr_url
	elif branch != "master":
	title += " \| branch: %s \| %s/%s/tree/%s" % (
	branch, ${{ toJSON(github.server_url) }}, repo, branch
	)
	with open(os.getenv("GITHUB_OUTPUT"), "a") as output:
	output.write("%s=%s\n" % (var, title))

	format_title_string(
	"fparser_checkout_title",
	# escape special characters (single and double quotes) in string
	# using JSON representation
	${{ toJSON(steps.resolve-dependencies.outputs.fparser_repo) }},
	${{ toJSON(steps.resolve-dependencies.outputs.fparser_pr_url) }},
	${{ toJSON(steps.resolve-dependencies.outputs.fparser_branch) }}
	)
	format_title_string(
	"CSXCAD_checkout_title",
	${{ toJSON(steps.resolve-dependencies.outputs.csxcad_repo) }},
	${{ toJSON(steps.resolve-dependencies.outputs.csxcad_pr_url) }},
	${{ toJSON(steps.resolve-dependencies.outputs.csxcad_branch) }}
	)

	# map a step output to a job output
	outputs:
	fparser_repo: ${{ steps.resolve-dependencies.outputs.fparser_repo }}
	fparser_branch: ${{ steps.resolve-dependencies.outputs.fparser_branch }}
	fparser_checkout_title: ${{ steps.format-title.outputs.fparser_checkout_title }}

	csxcad_repo: ${{ steps.resolve-dependencies.outputs.CSXCAD_repo }}
	csxcad_branch: ${{ steps.resolve-dependencies.outputs.CSXCAD_branch }}
	csxcad_checkout_title: ${{ steps.format-title.outputs.CSXCAD_checkout_title }}

	Linux:
	runs-on: ubuntu-latest
	needs: Dependencies

	defaults:
	run:
	shell: bash

	strategy:
	# Use "false" means a single failed build won't terminate other combinations
	# in the matrix. This wastes CPU time, but is an important debugging tool to
	# prevent a single broken platform from stopping the whole matrix.
	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 9"
	libc: "GNU"
	ancient: false
	docker-image: "almalinux:9"

	# Waiting for upstream packages:
	# https://bugzilla.redhat.com/show_bug.cgi?id=2374130
	# https://bugzilla.redhat.com/show_bug.cgi?id=2419727
	#
	#- name: "AlmaLinux Latest"
	# libc: "GNU"
	# ancient: false
	# docker-image: "almalinux:latest"

	- name: "Alpine"
	libc: "musl"
	ancient: false
	docker-image: "alpine:latest"

	container:
	image: ${{ matrix.os.docker-image }}
	# allow mount/netns
	options: "--cap-add CAP_SYS_ADMIN --cap-add NET_ADMIN --security-opt apparmor=unconfined"

	name: "${{ matrix.os.libc }}/Linux (${{ matrix.os.name }})"

	env:
	# Wno-error is needed because any third-party dependencies
	# like compiler version changes or even Python libraries
	# installed by pip can block the pipeline, this is not what
	# we want.
	CXXFLAGS: "-Wall -Wextra -Wno-error"

	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: Show checkout sources
	shell: sh
	run: \|
	echo "$FPARSER_CHECKOUT_TITLE"
	echo "$CSXCAD_CHECKOUT_TITLE"
	env:
	# convert template variables to shell variables to avoid arbitrary code injection
	FPARSER_CHECKOUT_TITLE: ${{ needs.Dependencies.outputs.fparser_checkout_title }}
	CSXCAD_CHECKOUT_TITLE: ${{ needs.Dependencies.outputs.csxcad_checkout_title }}

	# When checking out repos, I recommend running actions/checkout
	# as soon as possible before anything else, and in the reverse
	# order, from the project repo to its dependencies. This reduces
	# race conditions due to force pushes (they are harmless but
	# annoying).
	- if: ${{ ! matrix.os.ancient }}
	name: Checkout openEMS.git
	uses: actions/checkout@v4
	with:
	path: openEMS
	# checkout must be deep, not shallow.
	# We need tags for "git describe", otherwise build fails.
	fetch-depth: 0

	- if: ${{ ! matrix.os.ancient }}
	name: ${{ needs.Dependencies.outputs.csxcad_checkout_title }}
	uses: actions/checkout@v4
	with:
	repository: "${{ needs.Dependencies.outputs.csxcad_repo }}"
	ref: "${{ needs.Dependencies.outputs.csxcad_branch }}"
	path: CSXCAD
	# checkout must be deep, not shallow.
	# We need tags for "git describe", otherwise build fails.
	fetch-depth: 0

	- if: ${{ ! matrix.os.ancient }}
	name: ${{ needs.Dependencies.outputs.fparser_checkout_title }}
	uses: actions/checkout@v4
	with:
	repository: "${{ needs.Dependencies.outputs.fparser_repo }}"
	ref: "${{ needs.Dependencies.outputs.fparser_branch }}"
	path: fparser

	- if: ${{ matrix.os.ancient }}
	name: (legacy) Work around known problems
	run: \|
	if [ -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
	fi

	- if: ${{ matrix.os.ancient }}
	name: (legacy) Install git
	run: \|
	if [ -f /etc/centos-release ]; then
	yum install -y git
	elif grep -q "ID=ubuntu" /etc/os-release && \
	grep -q 'VERSION_ID="14.04"' /etc/os-release; then
	apt-get install -y git
	fi

	- if: ${{ matrix.os.ancient }}
	name: (legacy) Checkout openEMS.git
	run: \|
	git clone "$GITHUB_SERVER_URL/$GITHUB_REPOSITORY.git" openEMS
	cd "$GITHUB_WORKSPACE/openEMS"

	git fetch --force "$GITHUB_SERVER_URL/$GITHUB_REPOSITORY.git" "+refs/heads/:refs/remotes/origin/"
	git fetch --force "$GITHUB_SERVER_URL/$GITHUB_REPOSITORY.git" "+refs/pull//merge:refs/remotes/origin/pr/"
	git checkout "$GITHUB_SHA"

	- if: ${{ matrix.os.ancient }}
	name: (legacy) ${{ needs.Dependencies.outputs.csxcad_checkout_title }}
	run: \|
	echo "Clone $REPO.git (branch $BRANCH)"
	git clone "$GITHUB_SERVER_URL/$REPO.git"
	cd "$GITHUB_WORKSPACE/$CHECKOUT_PATH"

	git fetch --force "$GITHUB_SERVER_URL/$REPO.git" "+refs/heads/:refs/remotes/origin/"
	git fetch --force "$GITHUB_SERVER_URL/$REPO.git" "+refs/pull//merge:refs/remotes/origin/pr/"
	git checkout "$BRANCH"
	env:
	# convert template variables to shell variables to avoid arbitrary code injection
	REPO: ${{ needs.Dependencies.outputs.csxcad_repo }}
	BRANCH: ${{ needs.Dependencies.outputs.csxcad_branch }}
	CHECKOUT_PATH: CSXCAD

	- if: ${{ matrix.os.ancient }}
	name: (legacy) ${{ needs.Dependencies.outputs.fparser_checkout_title }}
	run: \|
	echo "Clone $REPO.git (branch $BRANCH)"
	git clone "$GITHUB_SERVER_URL/$REPO.git"
	cd "$GITHUB_WORKSPACE/$CHECKOUT_PATH"

	git fetch --force "$GITHUB_SERVER_URL/$REPO.git" "+refs/heads/:refs/remotes/origin/"
	git fetch --force "$GITHUB_SERVER_URL/$REPO.git" "+refs/pull//merge:refs/remotes/origin/pr/"
	git checkout "$BRANCH"
	env:
	# convert template variables to shell variables to avoid arbitrary code injection
	REPO: ${{ needs.Dependencies.outputs.fparser_repo }}
	BRANCH: ${{ needs.Dependencies.outputs.fparser_branch }}
	CHECKOUT_PATH: fparser

	- name: Install dependencies
	shell: sh
	run: \|
	cat /etc/os-release

	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 octave python3-pip \
	python3-setuptools python3-setuptools_scm \
	python3-Cython python3-numpy python3-h5py python3-matplotlib

	# only for CI/CD test builds without networks.
	dnf install -y iproute
	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 octave python3-pip \
	python3-setuptools python3-wheel python3-setuptools_scm \
	python3-Cython python3-numpy python3-h5py python3-matplotlib

	# only for CI/CD test builds without networks.
	dnf install -y iproute
	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 \
	octave \
	python3-pip \
	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 \|\| \
	apt-get install -y libvtk7-dev \|\| \
	apt-get install -y libvtk6-dev

	# only for CI/CD test builds without networks.
	apt-get install -y iproute2

	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 $GITHUB_SERVER_URL/CGAL/cgal.git --depth=1 --branch=v4.14.3
	cd cgal && mkdir build && cd build
	cmake ../ -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=$HOME/opt
	make -j`nproc` && make install

	# Must use Cython 3.0 or lower, since 3.1 uses f-string which is
	# incompatible with Python 3.4.
	pip3 install "cython<3.1"

	# Ubuntu 14.04's matplotlib package is ancient, install the
	# minimum version and its dependencies via pip. Note that the
	# native build uses Python 3.4 while the venv build (tested
	# later) uses Python 3.5 without these problems.
	#
	# pip's pyparsing is incompatible with Python 3.4
	apt-get install -y python3-pyparsing

	# same, newer cycler has incompatible type annotation
	pip3 install "cycler==0.10.0"
	pip3 install "matplotlib==2.1.0"
	else
	apt-get install -y libboost-all-dev
	apt-get install -y libcgal-dev
	apt-get install -y cmake
	apt-get install -y python3-setuptools-scm cython3 python3-matplotlib

	# testing Python packages in isolated venv
	apt-get install -y python3-venv
	fi
	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 py3-pip \
	py3-setuptools py3-setuptools_scm cython \
	py3-numpy py3-h5py py3-matplotlib

	# only for CI/CD test builds without networks.
	apk add iproute2
	elif [ -f /etc/centos-release ]; then
	# "(legacy) Work around known problems" must run before this step
	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 octave \
	python3-devel python3-pip \
	python3-setuptools python3-setuptools_scm python3-Cython

	# only for CI/CD test builds without networks.
	yum install -y iproute

	# 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.
	# /usr/local/include/CGAL/config.h:210:10: fatal error: boost/predef.h:
	# No such file or directory
	# We borrow a copy of Boost 1.58 from rh repo's mariadb backport package.
	yum install -y rh-mariadb101-boost-devel

	# copy rh repo's Boost to /usr/local because 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 $GITHUB_SERVER_URL/CGAL/cgal.git --depth=1 --branch=v4.14.3
	cd cgal && mkdir build && cd build
	cmake ../ -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=$HOME/opt
	make -j`nproc` && make install
	else
	echo "Unknown system!"
	exit 1
	fi

	- name: Build and install fparser
	run: \|
	cd $GITHUB_WORKSPACE/fparser
	mkdir build && cd build
	cmake ../ -DCMAKE_INSTALL_PREFIX=$HOME/opt
	make -j`nproc` && make install

	- name: Build and install CSXCAD
	run: \|
	# cmake may fail with "fatal: No names found, cannot describe anything."
	# if it happens, check if you're using a shallow clone, or if it's a GitHub
	# fork created with "Copy the master branch only". If so, you need to FULL
	# fork or clone.
	#
	# MPI may also fail, but this error is not fatal. The real error is often
	# the error above! There's no need to install MPI.
	cd $GITHUB_WORKSPACE/CSXCAD
	mkdir build && cd build
	cmake ../ -DCMAKE_INSTALL_PREFIX=$HOME/opt
	make -j`nproc` && make install

	- name: Build and install CSXCAD Python module with --no-build-isolation
	run: \|
	cd $GITHUB_WORKSPACE/CSXCAD/python
	export CSXCAD_INSTALL_PATH=$HOME/opt/

	pip_opts=( "--user" "--verbose" )
	# some systems don't have --no-build-isolation, some systems don't have
	# --break-system-packages, the oldest systems don't have both.
	if pip3 install --help \| grep -q no-build-isolation; then
	pip_opts+=( "--no-build-isolation" )
	fi
	if pip3 install --help \| grep -q break-system-packages; then
	pip_opts+=( "--break-system-packages" )
	fi
	# run in an isolated container without network, ensure
	# pip install really works without auto-downloads.
	ip netns add no-network
	ip netns exec no-network pip3 install . "${pip_opts[@]}"

	- name: Build and install openEMS
	run: \|
	# Hack: openEMS requires Boost Predef (1.55+), but CSXCAD requires CGAL, on
	# Ubuntu 14.04's libcgal-dev requires Boost 1.54. So we install Boost 1.55
	# after CSXCAD but before openEMS - this uninstalls libcgal-dev (but libcgal
	# itself is okay)
	if grep -q 'VERSION_ID="14.04"' /etc/os-release; then
	apt-get install -y boost1.55-dev
	apt-get install -y boost1.55
	fi

	cd $GITHUB_WORKSPACE/openEMS
	mkdir build && cd build
	cmake ../ -DCMAKE_INSTALL_PREFIX=$HOME/opt -DFPARSER_ROOT_DIR=$HOME/opt
	make -j`nproc` && make install

	echo "addpath('~/opt/share/openEMS/matlab')" >> ~/.octaverc
	echo "addpath('~/opt/share/CSXCAD/matlab')" >> ~/.octaverc

	- name: Build and install openEMS Python module with --no-build-isolation
	run: \|
	cd $GITHUB_WORKSPACE/openEMS/python

	# Python "exit(False)" = bash "if true"
	# Python "exit(True)" = bash "if false"
	if python3 -c "import pip; exit(int(pip.__version__.split('.')[0]) > 20)"; then
	# old pip < 21.3 (checking <= 21 here for simplicity),
	# CSXCAD needs CSXCAD_PYSRC_PATH as auto-detection is
	# not reliable.
	export CSXCAD_PYSRC_PATH=$GITHUB_WORKSPACE/CSXCAD/python/
	fi

	pip_opts=( "--user" "--verbose" )
	# some systems don't have --no-build-isolation, some systems don't have
	# --break-system-packages, the oldest systems don't have both.
	if pip3 install --help \| grep -q no-build-isolation; then
	pip_opts+=( "--no-build-isolation" )
	fi
	if pip3 install --help \| grep -q break-system-packages; then
	pip_opts+=( "--break-system-packages" )
	fi

	export CSXCAD_INSTALL_PATH=$HOME/opt/
	export OPENEMS_INSTALL_PATH=$HOME/opt/
	# run in an isolated container without network, ensure
	# pip install really works without auto-downloads.
	ip netns exec no-network pip3 install . "${pip_opts[@]}"

	- name: Smoketest Octave execution
	run: \|
	cd $GITHUB_WORKSPACE/openEMS/.github/smoketests/octave
	octave MSL_NotchFilter.m

	- name: Smoketest Python execution
	run: \|
	cd $GITHUB_WORKSPACE/openEMS/.github/smoketests/python
	python3 -c "import CSXCAD; print(CSXCAD.__version__)"
	python3 -c "import openEMS; print(openEMS.__version__)"
	python3 MSL_NotchFilter.py

	- name: Create Python venv and install dependencies
	run: \|
	cd ~/

	if grep -q "ID=ubuntu" /etc/os-release && \
	grep -q 'VERSION_ID="14.04"' /etc/os-release; then
	# Use Python 3.5 instead of the default Python 3.4 because
	# 3.5 is the latest available version on Ubuntu 14.04, and
	# also because Python 3.5 is the first Python that supported
	# type annotation, while Python 3.4 is locked out from most
	# modern packages.
	apt-get install -y curl python3.5-dev

	# Ubuntu 14.04 is ancient, and the python3.5-venv package is
	# broken. So the best approach is to install a bare Python 3.5
	# interpreter from apt, and bootstrapping pip ourselves.
	python3.5 -m venv ~/venv --without-pip
	curl -O https://bootstrap.pypa.io/pip/3.5/get-pip.py
	source ~/venv/bin/activate
	python3.5 get-pip.py
	else
	python3 -m venv ~/venv
	source ~/venv/bin/activate
	fi

	pip install --upgrade pip

	if [ -f /etc/centos-release ]; then
	pip3 install "cython<3.1"
	fi

	- name: Build and install CSXCAD Python module in venv
	run: \|
	source ~/venv/bin/activate
	cd $GITHUB_WORKSPACE/CSXCAD/python
	export CSXCAD_INSTALL_PATH="$HOME/opt"
	pip3 install . --verbose

	- name: Build and install openEMS Python module in venv
	run: \|
	source ~/venv/bin/activate
	cd $GITHUB_WORKSPACE/openEMS/python

	# Python "exit(False)" = bash "if true"
	# Python "exit(True)" = bash "if false"
	if python3 -c "import pip; exit(int(pip.__version__.split('.')[0]) > 20)"; then
	# old pip < 21.3 (checking <= 21 here for simplicity),
	# CSXCAD needs CSXCAD_PYSRC_PATH as auto-detection is
	# not reliable.
	export CSXCAD_PYSRC_PATH=$GITHUB_WORKSPACE/CSXCAD/python/
	fi

	export CSXCAD_INSTALL_PATH="$HOME/opt"
	export OPENEMS_INSTALL_PATH="$HOME/opt"
	pip3 install . --verbose

	- name: Smoketest Python execution in venv
	run: \|
	source ~/venv/bin/activate
	cd $GITHUB_WORKSPACE/openEMS/.github/smoketests/python
	python3 -c "import CSXCAD; print(CSXCAD.__version__)"
	python3 -c "import openEMS; print(openEMS.__version__)"
	python3 MSL_NotchFilter.py

	macOS:
	name: "macOS (ARM, latest)"

	runs-on: macos-latest
	needs: Dependencies

	steps:
	- name: Show checkout sources
	run: \|
	echo "$FPARSER_CHECKOUT_TITLE"
	echo "$CSXCAD_CHECKOUT_TITLE"
	env:
	# convert template variables to shell variables to avoid arbitrary code injection
	FPARSER_CHECKOUT_TITLE: ${{ needs.Dependencies.outputs.fparser_checkout_title }}
	CSXCAD_CHECKOUT_TITLE: ${{ needs.Dependencies.outputs.csxcad_checkout_title }}

	# When checking out repos, I recommend running actions/checkout
	# as soon as possible before anything else, and in the reverse
	# order, from the project repo to its dependencies. This reduces
	# race conditions due to force pushes (they are harmless but
	# annoying).
	- name: Checkout openEMS.git
	uses: actions/checkout@v4
	with:
	path: openEMS
	# checkout must be deep, not shallow.
	# We need tags for "git describe", otherwise build fails.
	fetch-depth: 0

	- name: ${{ needs.Dependencies.outputs.csxcad_checkout_title }}
	uses: actions/checkout@v4
	with:
	repository: "${{ needs.Dependencies.outputs.csxcad_repo }}"
	ref: "${{ needs.Dependencies.outputs.csxcad_branch }}"
	path: CSXCAD
	# checkout must be deep, not shallow.
	# We need tags for "git describe", otherwise build fails.
	fetch-depth: 0

	- name: ${{ needs.Dependencies.outputs.fparser_checkout_title }}
	uses: actions/checkout@v4
	with:
	repository: "${{ needs.Dependencies.outputs.fparser_repo }}"
	ref: "${{ needs.Dependencies.outputs.fparser_branch }}"
	path: fparser

	- name: Install dependencies
	run: \|
	touch ~/.zprofile # set environment variables here
	echo 'export CXXFLAGS="-Wall -Wextra -Wno-error"' >> ~/.zprofile

	# already installed on the CI/CD system, disable to avoid warning fatigue
	# brew install python3 cmake
	brew install boost hdf5 cgal vtk octave \
	python-setuptools cython numpy python-matplotlib

	echo "export NCPUS=$(python3 -c 'import os; print(os.cpu_count())')" >> ~/.zprofile
	source ~/.zprofile

	# TinyXML has been disabled by Homebrew at it's unmaintained
	# since 2011, TinyXML2 is not API-compatible. As a stop-gap,
	# build from source.
	#
	# -L: follow redirect, REQUIRED!
	curl -L https://sourceforge.net/projects/tinyxml/files/tinyxml/2.6.2/tinyxml_2_6_2.tar.gz -o tinyxml-2.6.2.tar.gz
	tar -xf tinyxml-2.6.2.tar.gz
	cd tinyxml

	# The first patch enforces use of stl strings, rather than a custom string type.
	# The second patch is a fix for incorrect encoding of elements with special characters
	# The third and fourth patches are security fixes.
	#
	# -L: follow redirect, REQUIRED!
	# -O: save to disk with an automatic file name.
	curl -L -O "https://raw.githubusercontent.com/alpinelinux/aports/b1ff376e83eb49c0127b039b3684eccdf9a60694/community/tinyxml/tinyxml-2.6.2-defineSTL.patch"
	curl -L -O "https://raw.githubusercontent.com/alpinelinux/aports/b1ff376e83eb49c0127b039b3684eccdf9a60694/community/tinyxml/tinyxml-2.6.1-entity.patch"
	curl -L -O "https://raw.githubusercontent.com/alpinelinux/aports/b1ff376e83eb49c0127b039b3684eccdf9a60694/community/tinyxml/CVE-2021-42260.patch"
	curl -L -O "https://raw.githubusercontent.com/alpinelinux/aports/b1ff376e83eb49c0127b039b3684eccdf9a60694/community/tinyxml/CVE-2023-34194.patch"

	# The final patch adds a CMakeLists.txt file to build a shared library and provide an install target
	# submitted upstream as https://sourceforge.net/p/tinyxml/patches/66/
	curl -L -O "https://gist.githubusercontent.com/scpeters/6325123/raw/cfb079be67997cb19a1aee60449714a1dedefed5/tinyxml_CMakeLists.patch"

	patch -p1 < tinyxml-2.6.2-defineSTL.patch
	patch -p1 < tinyxml-2.6.1-entity.patch
	patch -p1 < CVE-2021-42260.patch
	patch -p1 < CVE-2023-34194.patch

	# You know something is truly deprecated when the patch itself needs
	# patching! In CMake 4, 3.10 is deprecated and 3.5 has been removed.
	# use 3.0...3.10 so all of these versions are acceptable as min. version.
	# (CMake 2 is dropped since openEMS already requires CMake 3, and also
	# because CMake 2 is too old that it's not even documented anymore)
	#
	# https://cmake.org/cmake/help/latest/command/cmake_minimum_required.html
	sed -i -e "s/cmake_minimum_required(VERSION 2.4.6)/cmake_minimum_required(VERSION 3.0...3.10)/" \
	tinyxml_CMakeLists.patch # -e is not optional in BSD sed
	patch -p1 < tinyxml_CMakeLists.patch

	mkdir build && cd build
	cmake ../ -DCMAKE_INSTALL_PREFIX=$HOME/opt
	make -j$NCPUS && make install

	- name: Build and install fparser
	run: \|
	source ~/.zprofile
	cd $GITHUB_WORKSPACE/fparser
	mkdir build && cd build
	cmake ../ -DCMAKE_INSTALL_PREFIX=$HOME/opt
	make -j$NCPUS && make install

	- name: Build and install CSXCAD
	run: \|
	# cmake may fail with "fatal: No names found, cannot describe anything."
	# if it happens, check if you're using a shallow clone, or if it's a GitHub
	# fork created with "Copy the master branch only". If so, you need to FULL
	# fork or clone.
	#
	# MPI may also fail, but this error is not fatal. The real error is often
	# the error above! There's no need to install MPI.
	source ~/.zprofile
	cd $GITHUB_WORKSPACE/CSXCAD
	mkdir build && cd build
	cmake ../ -DCMAKE_INSTALL_PREFIX=$HOME/opt
	make -j$NCPUS && make install

	- name: Build and install CSXCAD Python module with --no-build-isolation
	run: \|
	source ~/.zprofile
	cd $GITHUB_WORKSPACE/CSXCAD/python
	export CSXCAD_INSTALL_PATH=$HOME/opt/
	pip3 install . --user --break-system-packages --no-build-isolation --verbose

	- name: Build and install openEMS
	run: \|
	source ~/.zprofile
	cd $GITHUB_WORKSPACE/openEMS
	mkdir build && cd build
	cmake ../ -DCMAKE_INSTALL_PREFIX=$HOME/opt -DFPARSER_ROOT_DIR=$HOME/opt
	make -j$NCPUS && make install

	echo "addpath('~/opt/share/openEMS/matlab')" >> ~/.octaverc
	echo "addpath('~/opt/share/CSXCAD/matlab')" >> ~/.octaverc

	- name: Build and install openEMS Python module with --no-build-isolation
	run: \|
	source ~/.zprofile
	cd $GITHUB_WORKSPACE/openEMS/python
	export CSXCAD_INSTALL_PATH=$HOME/opt/
	export OPENEMS_INSTALL_PATH=$HOME/opt/
	pip3 install . --user --break-system-packages --no-build-isolation --verbose

	- name: Smoketest Octave execution
	run: \|
	cd $GITHUB_WORKSPACE/openEMS/.github/smoketests/octave
	octave MSL_NotchFilter.m

	- name: Smoketest Python execution
	run: \|
	cd $GITHUB_WORKSPACE/openEMS/.github/smoketests/python
	python3 -c "import CSXCAD; print(CSXCAD.__version__)"
	python3 -c "import openEMS; print(openEMS.__version__)"
	python3 MSL_NotchFilter.py

	- name: Create Python venv and install dependencies
	run: \|
	# remove Python dependencies to see if venv really works
	pip3 uninstall -y CSXCAD openEMS --break-system-packages
	brew remove python-setuptools cython numpy python-matplotlib

	python3 -m venv ~/venv
	source ~/venv/bin/activate
	pip3 install --upgrade pip

	- name: Build and install CSXCAD Python module in venv
	run: \|
	source ~/venv/bin/activate
	cd $GITHUB_WORKSPACE/CSXCAD/python
	export CSXCAD_INSTALL_PATH="$HOME/opt"
	pip3 install . --verbose

	- name: Build and install openEMS Python module in venv
	run: \|
	source ~/venv/bin/activate
	cd $GITHUB_WORKSPACE/openEMS/python
	export CSXCAD_INSTALL_PATH="$HOME/opt"
	export OPENEMS_INSTALL_PATH="$HOME/opt"
	pip3 install . --verbose

	- name: Smoketest Python execution in venv
	run: \|
	source ~/venv/bin/activate
	cd $GITHUB_WORKSPACE/openEMS/.github/smoketests/python
	python3 -c "import CSXCAD; print(CSXCAD.__version__)"
	python3 -c "import openEMS; print(openEMS.__version__)"
	python3 MSL_NotchFilter.py

	FreeBSD:
	runs-on: ubuntu-latest
	needs: Dependencies

	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: Show checkout sources
	run: \|
	echo "$FPARSER_CHECKOUT_TITLE"
	echo "$CSXCAD_CHECKOUT_TITLE"
	env:
	# convert template variables to shell variables to avoid arbitrary code injection
	FPARSER_CHECKOUT_TITLE: ${{ needs.Dependencies.outputs.fparser_checkout_title }}
	CSXCAD_CHECKOUT_TITLE: ${{ needs.Dependencies.outputs.csxcad_checkout_title }}

	# When checking out repos, I recommend running actions/checkout
	# as soon as possible before anything else, and in the reverse
	# order, from the project repo to its dependencies. This reduces
	# race conditions due to force pushes (they are harmless but
	# annoying).
	- name: Checkout openEMS.git
	uses: actions/checkout@v4
	with:
	path: openEMS
	# checkout must be deep, not shallow.
	# We need tags for "git describe", otherwise build fails.
	fetch-depth: 0

	- name: ${{ needs.Dependencies.outputs.csxcad_checkout_title }}
	uses: actions/checkout@v4
	with:
	repository: "${{ needs.Dependencies.outputs.csxcad_repo }}"
	ref: "${{ needs.Dependencies.outputs.csxcad_branch }}"
	path: CSXCAD
	# checkout must be deep, not shallow.
	# We need tags for "git describe", otherwise build fails.
	fetch-depth: 0

	- name: ${{ needs.Dependencies.outputs.fparser_checkout_title }}
	uses: actions/checkout@v4
	with:
	repository: "${{ needs.Dependencies.outputs.fparser_repo }}"
	ref: "${{ needs.Dependencies.outputs.fparser_branch }}"
	path: fparser

	- 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 cmake git boost-libs tinyxml vtk9 hdf5 cgal octave python3 \
	py311-pip \
	py311-setuptools py311-wheel py311-setuptools-scm \
	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-"

	export CXXFLAGS="-Wall -Wextra -Wno-error"
	export NCPUS=$(python3 -c 'import os; print(os.cpu_count())')

	echo "Build and install fparser..."
	cd $GITHUB_WORKSPACE/fparser
	mkdir build && cd build
	cmake ../ -DCMAKE_INSTALL_PREFIX=$HOME/opt
	make -j$NCPUS && make install

	echo "Build and install CSXCAD..."
	# cmake may fail with "fatal: No names found, cannot describe anything."
	# if it happens, check if you're using a shallow clone, or if it's a GitHub
	# fork created with "Copy the master branch only". If so, you need to FULL
	# fork or clone.
	#
	# MPI may also fail, but this error is not fatal. The real error is often
	# the error above! There's no need to install MPI.
	cd $GITHUB_WORKSPACE/CSXCAD
	mkdir build && cd build
	cmake ../ -DCMAKE_INSTALL_PREFIX=$HOME/opt
	make -j$NCPUS && make install

	echo "Build and install CSXCAD Python module with --no-build-isolation..."
	cd $GITHUB_WORKSPACE/CSXCAD/python
	export CSXCAD_INSTALL_PATH=$HOME/opt/
	pip install . --user --break-system-packages --no-build-isolation --verbose

	echo "Build and install openEMS..."
	cd $GITHUB_WORKSPACE/openEMS
	mkdir build && cd build
	cmake ../ -DCMAKE_INSTALL_PREFIX=$HOME/opt -DFPARSER_ROOT_DIR=$HOME/opt
	make -j$NCPUS && make install

	echo "addpath('~/opt/share/openEMS/matlab')" >> ~/.octaverc
	echo "addpath('~/opt/share/CSXCAD/matlab')" >> ~/.octaverc

	echo "Build and install openEMS Python module with --no-build-isolation..."
	cd $GITHUB_WORKSPACE/openEMS/python
	export CSXCAD_INSTALL_PATH=$HOME/opt/
	export OPENEMS_INSTALL_PATH=$HOME/opt/
	pip install . --user --break-system-packages --no-build-isolation --verbose

	echo "Smoketest Octave execution..."
	cd $GITHUB_WORKSPACE/openEMS/.github/smoketests/octave/
	octave MSL_NotchFilter.m

	echo "Smoketest Python execution..."
	cd $GITHUB_WORKSPACE/openEMS/.github/smoketests/python
	python3 -c "import CSXCAD; print(CSXCAD.__version__)"
	python3 -c "import openEMS; print(openEMS.__version__)"
	python3 MSL_NotchFilter.py

	echo "Create Python venv and install dependencies..."
	# remove Python dependencies to see if venv really works
	pip uninstall -y CSXCAD openEMS --break-system-packages
	sudo pkg remove -y py311-pip \
	py311-setuptools py311-wheel py311-setuptools-scm \
	py311-cython3 py311-numpy py311-h5py py311-matplotlib
	python3 -m venv ~/venv
	. ~/venv/bin/activate
	pip install --upgrade pip

	echo "Build and install CSXCAD Python module in venv..."
	cd $GITHUB_WORKSPACE/CSXCAD/python
	export CSXCAD_INSTALL_PATH="$HOME/opt"
	pip install . --verbose

	echo "Build and install openEMS Python module in venv..."
	cd $GITHUB_WORKSPACE/openEMS/python
	export CSXCAD_INSTALL_PATH="$HOME/opt"
	export OPENEMS_INSTALL_PATH="$HOME/opt"
	pip install . --verbose

	echo "Smoketest Python execution in venv..."
	cd $GITHUB_WORKSPACE/openEMS/.github/smoketests/python
	python3 -c "import CSXCAD; print(CSXCAD.__version__)"
	python3 -c "import openEMS; print(openEMS.__version__)"
	python3 MSL_NotchFilter.py

	Windows:
	runs-on: windows-latest
	needs: Dependencies

	strategy:
	# Use "false" means a single failed build won't terminate other combinations
	# in the matrix. This wastes CPU time, but is an important debugging tool to
	# prevent a single broken platform from stopping the whole matrix.
	fail-fast: false

	matrix:
	toolchain:
	# name: toonchain name (only a name for humans to read).
	# CC, CXX: C/C++ compiler, environment variables
	- name: "MSVC"
	CC: "cl"
	CXX: "cl"

	- name: "clang-cl"
	CC: "clang-cl"
	CXX: "clang-cl"

	env:
	VS_ROOT_DIR: "C:/Program Files/Microsoft Visual Studio/2022/Enterprise/"
	CC: "${{ matrix.toolchain.CC }}"
	CXX: "${{ matrix.toolchain.CXX }}"
	CFLAGS: "/D_WIN32_WINNT=0x0601"
	CXXFLAGS: "/D_WIN32_WINNT=0x0601"

	VCPKG_CACHE_PATH: "${{ github.workspace }}/vcpkg-cache/"
	VCPKG_BINARY_CACHE_PATH: "${{ github.workspace }}/vcpkg-cache/binary"
	VCPKG_BINARY_SOURCES: "clear;files,${{ github.workspace }}/vcpkg-cache/binary,readwrite"
	VCPKG_ASSET_CACHE_PATH: "${{ github.workspace }}/vcpkg-cache/asset"
	X_VCPKG_ASSET_SOURCES: "x-azurl,file://${{ github.workspace }}/vcpkg-cache/asset,readwrite"

	name: "Windows (${{ matrix.toolchain.name }}, latest)"

	steps:
	- name: Show checkout sources
	run: \|
	echo "$env:FPARSER_CHECKOUT_TITLE"
	echo "$env:CSXCAD_CHECKOUT_TITLE"
	env:
	# convert template variables to shell variables to avoid arbitrary code injection
	FPARSER_CHECKOUT_TITLE: ${{ needs.Dependencies.outputs.fparser_checkout_title }}
	CSXCAD_CHECKOUT_TITLE: ${{ needs.Dependencies.outputs.csxcad_checkout_title }}

	# When checking out repos, I recommend running actions/checkout
	# as soon as possible before anything else, and in the reverse
	# order, from the project repo to its dependencies. This reduces
	# race conditions due to force pushes (they are harmless but
	# annoying).
	- name: Checkout openEMS.git
	uses: actions/checkout@v4
	with:
	path: openEMS
	# checkout must be deep, not shallow.
	# We need tags for "git describe", otherwise build fails.
	fetch-depth: 0

	- name: ${{ needs.Dependencies.outputs.csxcad_checkout_title }}
	uses: actions/checkout@v4
	with:
	repository: "${{ needs.Dependencies.outputs.csxcad_repo }}"
	ref: "${{ needs.Dependencies.outputs.csxcad_branch }}"
	path: CSXCAD
	# checkout must be deep, not shallow.
	# We need tags for "git describe", otherwise build fails.
	fetch-depth: 0

	- name: ${{ needs.Dependencies.outputs.fparser_checkout_title }}
	uses: actions/checkout@v4
	with:
	repository: "${{ needs.Dependencies.outputs.fparser_repo }}"
	ref: "${{ needs.Dependencies.outputs.fparser_branch }}"
	path: fparser

	# It doesn't really work, because MSVC itself doesn't support long path.
	# But for future-proofing (it does work for clang).
	- name: Enable long paths
	run: \|
	New-ItemProperty -Path "HKLM:/SYSTEM/CurrentControlSet/Control/FileSystem" `
	-Name "LongPathsEnabled" -Value 1 -PropertyType DWORD -Force

	- name: Create vcpkg cache directories
	run: \|
	mkdir -p "$env:VCPKG_CACHE_PATH"
	mkdir -p "$env:VCPKG_BINARY_CACHE_PATH"
	mkdir -p "$env:VCPKG_ASSET_CACHE_PATH"

	- name: Restore vcpkg cache
	uses: actions/cache/restore@v5
	with:
	path: ${{ env.VCPKG_CACHE_PATH }}
	# almost always nonexistent
	key: "Windows - ${{ matrix.toolchain.name }} - ${{ github.sha }}"
	# use GitHub's fallback feature to pick the latest cache with this prefix
	restore-keys: \|
	Windows - ${{ matrix.toolchain.name }}

	- name: Build and install fparser
	run: \|
	& "$env:VS_ROOT_DIR/Common7/Tools/Launch-VsDevShell.ps1" -Arch amd64 -HostArch amd64

	cd "$env:GITHUB_WORKSPACE/fparser"
	mkdir build && cd build
	cmake ../ -GNinja -DCMAKE_WINDOWS_EXPORT_ALL_SYMBOLS=ON `
	-DCMAKE_BUILD_TYPE=Release `
	-DCMAKE_INSTALL_PREFIX="$HOME/opt"

	cmake --build ./ --parallel
	cmake --install ./ --parallel 8

	- name: Build and install CSXCAD
	run: \|
	& "$env:VS_ROOT_DIR/Common7/Tools/Launch-VsDevShell.ps1" -Arch amd64 -HostArch amd64

	cd "$env:GITHUB_WORKSPACE/CSXCAD"
	mkdir build && cd build
	cmake ../ -GNinja `
	-DCMAKE_BUILD_TYPE=Release `
	-DCMAKE_INSTALL_PREFIX="$HOME/opt" `
	-DFPARSER_ROOT_DIR="$HOME/opt" `
	-DCMAKE_TOOLCHAIN_FILE="$env:VCPKG_ROOT/scripts/buildsystems/vcpkg.cmake" `
	-DVCPKG_HOST_TRIPLET="x64-windows-release" `
	-DVCPKG_TARGET_TRIPLET="x64-windows-release"

	cmake --build ./ --parallel
	cmake --install ./ --parallel 8

	- name: Build and install openEMS
	run: \|
	& "$env:VS_ROOT_DIR/Common7/Tools/Launch-VsDevShell.ps1" -Arch amd64 -HostArch amd64

	cd "$env:GITHUB_WORKSPACE/openEMS"
	mkdir build && cd build
	cmake ../ -GNinja `
	-DCMAKE_BUILD_TYPE=Release `
	-DCMAKE_INSTALL_PREFIX="$HOME/opt" `
	-DFPARSER_ROOT_DIR="$HOME/opt" `
	-DCSXCAD_ROOT_DIR="$HOME/opt" `
	-DCMAKE_TOOLCHAIN_FILE="$env:VCPKG_ROOT/scripts/buildsystems/vcpkg.cmake" `
	-DVCPKG_HOST_TRIPLET="x64-windows-release" `
	-DVCPKG_TARGET_TRIPLET="x64-windows-release"

	cmake --build ./ --parallel
	cmake --install ./ --parallel 8

	- name: Save vcpkg cache
	if: always() # save even after a build failure.
	uses: actions/cache/save@v5
	with:
	path: ${{ env.VCPKG_CACHE_PATH }}
	# GitHub cache is immutable and can't be overwritten
	# save a new cache key every time
	key: Windows - ${{ matrix.toolchain.name }} - ${{ github.sha }}

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Fix:GetCSX #303

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Fix:GetCSX #303

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