Bump github/codeql-action from 3.25.15 to 3.28.0 #5849

Workflow file for this run

.github/workflows/nestbuildmatrix.yml at 757e7b9

	#
	# detailed syntax defined in
	# https://docs.github.com/en/actions/learn-github-actions/workflow-syntax-for-github-actions
	#
	name: "NEST CI"

	on: [push, pull_request]

	jobs:
	clang-format:
	runs-on: "ubuntu-22.04"
	env:
	CLANG_REQUIRE_VERSION: 17.0.4
	CLANG_FORMAT_FILE: ".clang-format"
	steps:
	- name: Harden Runner
	uses: step-security/harden-runner@91182cccc01eb5e619899d80e4e971d6181294a7 # v2.10.1
	with:
	egress-policy: audit
	disable-telemetry: true

	- name: "Checkout repository content"
	uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4.1.7
	with:
	fetch-depth: 0

	- name: "Install dependencies"
	run: \|
	python -m pip install --force-reinstall clang-format==${{ env.CLANG_REQUIRE_VERSION }}

	- name: "Run clang-format..."
	run: \|
	files=$(find . $ -iname ".h" -o -iname ".c" -o -iname ".cc" -o -iname ".cpp" $ -not -path "./thirdparty/*")
	diff -u <(cat ${files}) <(clang-format ${files})

	cppcheck:
	runs-on: "ubuntu-22.04"
	steps:
	- name: Harden Runner
	uses: step-security/harden-runner@91182cccc01eb5e619899d80e4e971d6181294a7 # v2.10.1
	with:
	egress-policy: audit
	disable-telemetry: true

	- name: "Checkout repository content"
	uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4.1.7
	with:
	fetch-depth: 0

	- name: "Install Linux system dependencies"
	run: \|
	sudo apt-get update
	sudo apt-get install cppcheck

	- name: "Run cppcheck..."
	run: \|
	cppcheck --enable=all --language=c++ --std=c++17 -i sli/ --suppressions-list=.cppcheck_suppressions ./

	rstcheck:
	runs-on: "ubuntu-22.04"
	steps:
	- name: Harden Runner
	uses: step-security/harden-runner@91182cccc01eb5e619899d80e4e971d6181294a7 # v2.10.1
	with:
	egress-policy: audit
	disable-telemetry: true

	- name: "Checkout repository content"
	uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4.1.7
	with:
	fetch-depth: 0

	- name: "Set up Python 3.x"
	uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5.2.0
	with:
	python-version: "3.10"

	- name: "Install dependencies"
	run: \|
	pip install rstcheck

	- name: "Run rstcheck..."
	run: \|
	rstcheck -r doc/

	vale:
	runs-on: "ubuntu-22.04"
	steps:
	- name: Harden Runner
	uses: step-security/harden-runner@91182cccc01eb5e619899d80e4e971d6181294a7 # v2.10.1
	with:
	egress-policy: audit
	disable-telemetry: true

	- name: "Checkout repository content"
	uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4.1.7
	with:
	fetch-depth: 0

	- name: "Set up Python 3.x"
	uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5.2.0
	with:
	python-version: "3.10"

	- name: "Install dependencies"
	run: \|
	sudo apt update
	sudo apt install python3-docutils
	wget --progress=dot:mega 'https://github.com/errata-ai/vale/releases/download/v2.26.0/vale_2.26.0_Linux_64-bit.tar.gz'
	echo '956577b214ce3db8fb11483f99a183cf65673e3bd47423c6d4ebe37f085cadc7 vale_2.26.0_Linux_64-bit.tar.gz' \| sha256sum -c
	tar -xzf 'vale_2.26.0_Linux_64-bit.tar.gz'

	- name: "Run vale..."
	run: \|
	./vale -v
	./vale doc

	copyright_headers:
	runs-on: "ubuntu-22.04"
	steps:
	- name: Harden Runner
	uses: step-security/harden-runner@91182cccc01eb5e619899d80e4e971d6181294a7 # v2.10.1
	with:
	egress-policy: audit
	disable-telemetry: true

	- name: "Checkout repository content"
	uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4.1.7
	with:
	fetch-depth: 0

	- name: "Set up Python 3.x"
	uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5.2.0
	with:
	python-version: "3.10"

	- name: "Install dependencies"
	run: \|
	pip install pydocstyle

	- name: "Check copyright headers..."
	run: \|
	python build_support/check_copyright_headers.py

	unused_names:
	runs-on: "ubuntu-22.04"
	steps:
	- name: Harden Runner
	uses: step-security/harden-runner@91182cccc01eb5e619899d80e4e971d6181294a7 # v2.10.1
	with:
	egress-policy: audit
	disable-telemetry: true

	- name: "Checkout repository content"
	uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4.1.7
	with:
	fetch-depth: 0

	- name: "Set up Python 3.x"
	uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5.2.0
	with:
	python-version: "3.10"

	- name: "Check for unused nest::names..."
	run: \|
	python build_support/check_unused_names.py

	forbidden_types:
	runs-on: "ubuntu-22.04"
	steps:
	- name: Harden Runner
	uses: step-security/harden-runner@91182cccc01eb5e619899d80e4e971d6181294a7 # v2.10.1
	with:
	egress-policy: audit
	disable-telemetry: true

	- name: "Checkout repository content"
	uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4.1.7
	with:
	fetch-depth: 0

	- name: "Check for forbidden types..."
	run: \|
	./build_support/check_forbidden_types.sh

	lychee_IGNORED:
	runs-on: "ubuntu-22.04"
	steps:
	- name: Harden Runner
	uses: step-security/harden-runner@91182cccc01eb5e619899d80e4e971d6181294a7 # v2.10.1
	with:
	egress-policy: audit
	disable-telemetry: true

	- name: "Checkout repository content"
	uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4.1.7
	with:
	fetch-depth: 0

	- name: "Install dependencies"
	run: \|
	wget --progress=dot:mega 'https://github.com/lycheeverse/lychee/releases/download/v0.8.2/lychee-v0.8.2-x86_64-unknown-linux-gnu.tar.gz'
	echo '12c27c9b6d551aea9178080d27de75ed26125b130722153399259432f723e606 lychee-v0.8.2-x86_64-unknown-linux-gnu.tar.gz' \| sha256sum -c
	tar -xzf 'lychee-v0.8.2-x86_64-unknown-linux-gnu.tar.gz'

	- name: "Run lychee..."
	continue-on-error: true
	run: "pwd; ls -l; ./lychee build_support/ doc/{.txt,.md,htmldoc} examples/ lib* models/ nest* pynest/ testsuite/ *.md"
	# TODO: doc/auto_examples and doc/models need to be added here, but exists only after a `make html`
	env:
	GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

	pydocstyle:
	runs-on: "ubuntu-22.04"
	steps:
	- name: Harden Runner
	uses: step-security/harden-runner@91182cccc01eb5e619899d80e4e971d6181294a7 # v2.10.1
	with:
	egress-policy: audit
	disable-telemetry: true

	- name: "Checkout repository content"
	uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4.1.7
	with:
	fetch-depth: 0

	- name: "Set up Python 3.x"
	uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5.2.0
	with:
	python-version: "3.10"

	- name: "Install dependencies"
	run: \|
	pip install pydocstyle

	- name: "Run pydocstyle..."
	run: \|
	pydocstyle pynest/

	mypy:
	runs-on: "ubuntu-22.04"
	steps:
	- name: Harden Runner
	uses: step-security/harden-runner@91182cccc01eb5e619899d80e4e971d6181294a7 # v2.10.1
	with:
	egress-policy: audit
	disable-telemetry: true

	- name: "Checkout repository content"
	uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4.1.7
	with:
	fetch-depth: 0

	- name: "Set up Python 3.x"
	uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5.2.0
	with:
	python-version: "3.10"

	- name: "Install dependencies"
	run: \|
	pip install mypy matplotlib numpy scipy data-science-types

	- name: "Run mypy..."
	run: \|
	mypy pynest/

	# pytest-linux:
	# runs-on: "ubuntu-22.04"
	# needs: [build_linux]
	# env:
	# NEST_VPATH: "build"
	# NEST_RESULT: "result"

	# strategy:
	# fail-fast: true
	# matrix:
	# os: ["ubuntu-22.04"]
	# cpp_compiler: ["gcc"]

	# # available use flags (all default to "OFF"):
	# use:
	# - "boost, optimize, warning" # formerly "minimal"
	# # - "openmp, python, gsl, ltdl, boost, optimize, warning" # formerly "openmp_only"
	# # - "mpi, python, gsl, ltdl, boost, optimize, warning" # formerly "mpi_only"
	# # - "openmp, mpi, python, gsl, ltdl, boost, sionlib, libneurosim, optimize, warning" # formerly "full"

	# steps:
	# - name: "Download binary artifacts"
	# uses: actions/download-artifact@v3
	# with:
	# name: "build-${{ matrix.os }}-${{ matrix.cpp_compiler }}-${{ matrix.use }}"

	# - name: "Set up Python 3.x"
	# uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5.2.0
	# with:
	# python-version: "3.10"

	# - name: "Install dependencies"
	# run: \|
	# pip install pytest pytest-cov pytest-doctestplus

	# - name: "Run pytest..."
	# run: \|
	# pwd
	# ls -lisa
	# cd "$NEST_VPATH"
	# pwd
	# ls -lisa
	# pytest testsuite/pytests/

	# pytest-mac:
	# runs-on: "macos-latest"
	# needs: [build_macos]
	# steps:
	# - name: "Checkout repository content"
	# uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4.1.7
	# with:
	# fetch-depth: 0

	# - name: "Set up Python 3.x"
	# uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5.2.0
	# with:
	# python-version: "3.10"

	# - name: "Install dependencies"
	# run: \|
	# pip install pytest pytest-cov pytest-doctestplus

	# - name: "Run pytest..."
	# run: \|
	# pytest pynest/

	pylint:
	runs-on: "ubuntu-22.04"
	steps:
	- name: Harden Runner
	uses: step-security/harden-runner@91182cccc01eb5e619899d80e4e971d6181294a7 # v2.10.1
	with:
	egress-policy: audit
	disable-telemetry: true

	- name: "Checkout repository content"
	uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4.1.7
	with:
	fetch-depth: 0

	- name: "Set up Python 3.x"
	uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5.2.0
	with:
	python-version: "3.10"

	- name: "Install dependencies"
	run: \|
	pip install pylint

	- name: "Run pylint..."
	run: \|
	pylint --jobs=$(nproc) pynest/ testsuite/pytests/.py testsuite/regressiontests/.py

	isort:
	runs-on: "ubuntu-20.04"
	steps:
	- name: "Checkout repository content"
	uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4.1.7
	with:
	fetch-depth: 0

	- name: "Run isort..."
	uses: isort/isort-action@f14e57e1d457956c45a19c05a89cccdf087846e5 # 1.1.0
	with:
	configuration: --profile=black --thirdparty="nest" --check-only --diff

	black:
	runs-on: "ubuntu-22.04"
	steps:
	- name: Harden Runner
	uses: step-security/harden-runner@91182cccc01eb5e619899d80e4e971d6181294a7 # v2.10.1
	with:
	egress-policy: audit
	disable-telemetry: true

	- name: "Checkout repository content"
	uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4.1.7
	with:
	fetch-depth: 0

	- name: "Run black..."
	uses: psf/black@d9ad09a32b0e0481bb4fef548d35b7a49cc03c5d # 23.12.0
	with:
	jupyter: true

	flake8:
	runs-on: "ubuntu-22.04"
	steps:
	- name: Harden Runner
	uses: step-security/harden-runner@91182cccc01eb5e619899d80e4e971d6181294a7 # v2.10.1
	with:
	egress-policy: audit
	disable-telemetry: true

	- name: "Checkout repository content"
	uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4.1.7
	with:
	fetch-depth: 0

	- name: "Set up Python 3.x"
	uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5.2.0
	with:
	python-version: "3.10"

	- name: "Install dependencies"
	run: \|
	pip install flake8

	- name: "Run flake8..."
	run: \|
	flake8 .

	sphinx-rtd:
	# as close as possible to the Readthedocs setup (system install cmake, pip install -r doc/requirements.txt)
	runs-on: "ubuntu-22.04"
	needs: [pydocstyle, rstcheck, vale]
	steps:
	- name: Harden Runner
	uses: step-security/harden-runner@91182cccc01eb5e619899d80e4e971d6181294a7 # v2.10.1
	with:
	egress-policy: audit
	disable-telemetry: true

	- name: "Checkout repository content"
	uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4.1.7
	with:
	fetch-depth: 0

	- name: "Set up Python 3.x"
	uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5.2.0
	with:
	# Using 3.8 because Read the docs does not work with higher versions.
	# See also: https://github.com/nest/nest-simulator/pull/2744
	python-version: "3.10"

	- name: "Install dependencies"
	run: \|
	sudo apt update
	pip install -r doc/requirements.txt
	# The pandoc executable, which is required, cannot be installed via pip see: https://stackoverflow.com/a/71585691
	sudo apt install pandoc

	- name: "Test-build documentation"
	run: \|
	mkdir -pv build
	cd build
	cmake -Dwith-userdoc=ON -DCMAKE_INSTALL_PREFIX=../install ..
	make docs \|& tee sphinx-output.log

	- name: Upload artifacts
	uses: actions/upload-artifact@0b2256b8c012f0828dc542b3febcab082c67f72b # v4.3.4
	with:
	name: "sphinx-rtd output"
	path: \|
	build/sphinx-output.log
	build/doc/_build/html/

	sphinx-conda:
	# as close as possible to the suggested user docs build in the documentation
	runs-on: "ubuntu-22.04"
	if: false
	needs: [pydocstyle, rstcheck, vale]
	steps:
	- name: Harden Runner
	uses: step-security/harden-runner@91182cccc01eb5e619899d80e4e971d6181294a7 # v2.10.1
	with:
	egress-policy: audit
	disable-telemetry: true

	- name: "Checkout repository content"
	uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4.1.7
	with:
	fetch-depth: 0

	- name: Install Conda
	uses: conda-incubator/setup-miniconda@a4260408e20b96e80095f42ff7f1a15b27dd94ca # v3.0.4
	with:
	auto-update-conda: true
	python-version: "3.10"

	- name: Install conda dependencies
	shell: bash -l {0}
	run: \|
	conda info
	conda env create -p conda

	- name: "Test-build documentation"
	shell: bash -l {0}
	run: \|
	conda activate conda/
	mkdir -pv build
	cd build
	cmake -DCMAKE_INSTALL_PREFIX=../install ..
	make html \|& tee sphinx-output.log

	- name: Upload artifacts
	uses: actions/upload-artifact@0b2256b8c012f0828dc542b3febcab082c67f72b # v4.3.4
	with:
	path: \|
	build/sphinx-output.log
	build/doc/_build/html/

	build_linux:
	if: ${{ !contains(github.event.head_commit.message, 'ci skip') }}
	runs-on: ${{ matrix.os }}
	needs: [clang-format, mypy, copyright_headers, unused_names, forbidden_types, pylint, isort, black, flake8]
	env:
	CXX_FLAGS: "-pedantic -Wextra -Woverloaded-virtual -Wno-unknown-pragmas"
	NEST_VPATH: "build"
	NEST_RESULT: "result"

	strategy:
	fail-fast: false
	matrix:
	os: ["ubuntu-22.04"]
	cpp_compiler: ["gcc"]

	# available use flags (all default to "OFF"):
	# openmp, mpi, python, gsl, ltdl, boost, sionlib, libneurosim, optimize, warning, userdoc, music
	use:
	- "boost, optimize, warning"
	- "openmp, python, gsl, ltdl, boost, optimize, warning"
	- "mpi, python, gsl, ltdl, boost, optimize, warning"
	- "openmp, mpi, python, gsl, ltdl, boost, hdf5, sionlib, libneurosim, optimize, warning, music"

	steps:
	- name: Harden Runner
	uses: step-security/harden-runner@91182cccc01eb5e619899d80e4e971d6181294a7 # v2.10.1
	with:
	egress-policy: audit
	disable-telemetry: true

	- name: "Checkout repository content"
	uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4.1.7
	with:
	fetch-depth: 0

	- name: "Set up Python 3.x"
	uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5.2.0
	with:
	python-version: "3.10"

	- name: "Restore apt cache"
	uses: actions/cache@0c45773b623bea8c8e75f6c82b208c3cf94ea4f9 # v4.0.2
	env:
	cache-name: "apt-cache"
	with:
	path: \|
	!/var/cache/apt/archives/lock
	!/var/cache/apt/archives/partial
	/var/cache/apt
	key: ${{ runner.os }}-system-${{ env.cache-name }}-${{ hashFiles('**/environment.yml') }}
	restore-keys: \|
	${{ runner.os }}-system-${{ env.cache-name }}-
	${{ runner.os }}-system-

	- name: "Install Linux system dependencies"
	run: \|
	sudo apt-get update
	# https://github.com/actions/virtual-environments/blob/main/images/linux/Ubuntu2004-README.md
	sudo apt-get install ccache
	sudo apt-get install libltdl-dev libreadline6-dev libncurses5-dev libgsl0-dev python3-all-dev jq libpcre3 libpcre3-dev
	sudo apt-get install tcl8.6 tcl8.6-dev tk8.6-dev
	# Install MPI dependencies regardless of whether we compile NEST with or without MPI, so the installation of MPI4Py works
	sudo apt-get install openmpi-bin libopenmpi-dev
	sudo apt-get install libboost-filesystem-dev libboost-regex-dev libboost-wave-dev libboost-python-dev libboost-program-options-dev libboost-test-dev
	sudo apt-get install pkg-config
	sudo ldconfig

	- name: "Install GSL system dependencies"
	if: "${{ contains(matrix.use, 'gsl') }}"
	run: \|
	sudo apt-get install libgsl0-dev

	- name: "Install HDF5 system dependencies"
	if: "${{ contains(matrix.use, 'hdf5') }}"
	run: \|
	sudo apt-get install libhdf5-dev

	- name: "Restore ccache"
	# Using CCache to re-use compiled objects from prior runs that have the same
	# source (hashed), compiler (mtime+size) and compile flags.
	env:
	cache-name: "ccache"
	uses: actions/cache@0c45773b623bea8c8e75f6c82b208c3cf94ea4f9 # v4.0.2
	with:
	path: \|
	$HOME/.ccache
	.ccache
	/home/runner/.ccache
	key: ${{ runner.os }}-${{ env.cache-name }}-${{ matrix.cpp_compiler }}-${{ matrix.NEST_BUILD_TYPE }}
	restore-keys: \|
	${{ runner.os }}-${{ env.cache-name }}-${{ matrix.cpp_compiler }}-${{ matrix.NEST_BUILD_TYPE }}
	${{ runner.os }}-${{ env.cache-name }}-${{ matrix.cpp_compiler }}
	${{ runner.os }}-${{ env.cache-name }}
	${{ runner.os }}

	- name: "Restore pip cache"
	env:
	cache-name: "pip-cache"
	uses: actions/cache@0c45773b623bea8c8e75f6c82b208c3cf94ea4f9 # v4.0.2
	with:
	path: \|
	/opt/hostedtoolcache/Python/*/site-packages/
	$HOME/.cache/pip
	key: ${{ runner.os }}-python-${{ env.cache-name }}-${{ hashFiles('**/requirements.txt') }}
	restore-keys: \|
	${{ runner.os }}-python-${{ env.cache-name }}-
	${{ runner.os }}-python-

	- name: "Install Python dependencies"
	run: \|
	python -m pip install --upgrade pip setuptools
	python -c "import setuptools; print('package location:', setuptools.__file__)"
	python -m pip install --force-reinstall --upgrade scipy 'junitparser>=2' numpy pytest pytest-timeout pytest-xdist cython matplotlib terminaltables pandoc pandas
	# Install mpi4py regardless of whether we compile NEST with or without MPI, so regressiontests/issue-1703.py will run in both cases
	python -m pip install --force-reinstall --upgrade mpi4py
	test \! -e "=2" # assert junitparser is correctly quoted and '>' is not interpreted as shell redirect
	python -c "import pytest; print('package location:', pytest.__file__)"
	pip list

	- name: "Install h5py"
	if: "${{ contains(matrix.use, 'hdf5') }}"
	run: \|
	python -m pip install --force-reinstall --upgrade --no-binary=h5py h5py

	- name: "Install MUSIC"
	if: "${{ contains(matrix.use, 'music') }}"
	run: \|
	chmod +x build_support/install_music.sh
	./build_support/install_music.sh

	- name: "Install SIONlib"
	if: "${{ contains(matrix.use, 'sionlib') }}"
	run: \|
	chmod +x build_support/install_sionlib.sh
	./build_support/install_sionlib.sh

	- name: "Install LibNeurosim – WARNING WARNING NO PROPER PYTHON INSTALL!"
	if: "${{ contains(matrix.use, 'libneurosim') }}"
	run: \|
	chmod +x build_support/install_csa-libneurosim.sh
	PYLIB_DIR="$(python3 -c "import sysconfig; print(sysconfig.get_path('include'))" \| sed 's/include/lib/')"
	./build_support/install_csa-libneurosim.sh $PYLIB_DIR

	- name: "Configure NEST build"
	env:
	CMAKE_C_COMPILER_LAUNCHER: ccache
	CMAKE_CXX_COMPILER_LAUNCHER: ccache
	run: \|
	mkdir -p "$NEST_VPATH/reports" "$NEST_RESULT"

	if [ "$xNEST_BUILD_COMPILER" = "CLANG" ]; then
	export CC=clang-11
	export CXX=clang++-11
	fi
	export CXX_FLAGS="-pedantic -Wextra -Wno-unknown-pragmas -D_GLIBCXX_ASSERTIONS"

	cd "$NEST_VPATH"
	cmake \
	-DCMAKE_INSTALL_PREFIX="$NEST_RESULT" \
	-DCMAKE_CXX_FLAGS="$CXX_FLAGS" \
	-Dwith-optimize=${{ contains(matrix.use, 'optimize') && 'ON' \|\| 'OFF' }} \
	-Dwith-warning=${{ contains(matrix.use, 'warning') && 'ON' \|\| 'OFF' }} \
	-Dwith-boost=${{ contains(matrix.use, 'boost') && 'ON' \|\| 'OFF' }} \
	-Dwith-openmp=${{ contains(matrix.use, 'openmp') && 'ON' \|\| 'OFF' }} \
	-Dwith-mpi=${{ contains(matrix.use, 'mpi') && 'ON' \|\| 'OFF' }} \
	-Dwith-python=${{ contains(matrix.use, 'python') && 'ON' \|\| 'OFF' }} \
	-Dwith-gsl=${{ contains(matrix.use, 'gsl') && 'ON' \|\| 'OFF' }} \
	-Dwith-ltdl=${{ contains(matrix.use, 'ltdl') && 'ON' \|\| 'OFF' }} \
	-Dwith-readline=${{ contains(matrix.use, 'readline') && 'ON' \|\| 'OFF' }} \
	-Dwith-hdf5=${{ contains(matrix.use, 'hdf5') && 'ON' \|\| 'OFF' }} \
	-Dwith-sionlib=${{ contains(matrix.use, 'sionlib') && '$HOME/.cache/sionlib.install' \|\| 'OFF' }} \
	-Dwith-libneurosim=${{ contains(matrix.use, 'libneurosim') && '$HOME/.cache/libneurosim.install' \|\| 'OFF' }} \
	-Dwith-music=${{ contains(matrix.use, 'music') && '$HOME/.cache/music.install' \|\| 'OFF' }} \
	..

	- name: "Add GCC problem matcher"
	run: \|
	echo "::add-matcher::gcc_problem_matcher.json"

	- name: "Build NEST"
	run: \|
	cd "$NEST_VPATH"
	env
	make VERBOSE=1

	- name: "Remove GCC problem matcher"
	run: \|
	echo "::remove-matcher owner=gcc-problem-matcher::"

	- name: "Install NEST"
	run: \|
	cd "$NEST_VPATH"
	make install

	- name: "Initialize Matplotlibrc"
	run: \|
	# initialize matplotlib backend
	mkdir -p $HOME/.matplotlib
	echo "backend : svg" > $HOME/.matplotlib/matplotlibrc

	- name: "Run NEST testsuite"
	env:
	DO_TESTS_SKIP_TEST_REQUIRING_MANY_CORES: ${{ contains(matrix.use, 'mpi') && contains(matrix.use, 'openmp') }}
	run: \|
	pwd
	cd "$NEST_VPATH"
	chmod -v u+x ${NEST_RESULT}/share/nest/testsuite/do_tests.sh
	make VERBOSE=1 installcheck

	- name: "Upload install and test results"
	uses: actions/upload-artifact@0b2256b8c012f0828dc542b3febcab082c67f72b # v4.3.4
	if: always()
	with:
	name: "build-logs-${{ matrix.os }}-${{ matrix.cpp_compiler }}-${{ matrix.use }}"
	path: \|
	build/install_manifest.txt
	build/test_report_*/

	build_macos:
	if: ${{ !contains(github.event.head_commit.message, 'ci skip') }}
	runs-on: ${{ matrix.os }}
	needs: [clang-format, mypy, copyright_headers, unused_names, forbidden_types, pylint, isort, black, flake8]
	env:
	CXX_FLAGS: "-pedantic -Wextra -Woverloaded-virtual -Wno-unknown-pragmas"
	NEST_VPATH: "build"
	NEST_RESULT: "result"

	strategy:
	fail-fast: false
	matrix:
	os: [macos-latest]
	cpp_compiler: ["clang"]

	# available use flags (all default to "OFF"):
	# openmp, mpi, python, gsl, ltdl, boost, hdf5, sionlib, libneurosim, optimize, warning, userdoc, music
	use:
	- "openmp, mpi, python, gsl, ltdl, boost, hdf5, optimize, warning"

	steps:
	- name: Harden Runner
	uses: step-security/harden-runner@91182cccc01eb5e619899d80e4e971d6181294a7 # v2.10.1
	with:
	egress-policy: audit
	disable-telemetry: true

	- name: "Checkout repository content"
	uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4.1.7
	with:
	fetch-depth: 0

	- name: "Set up Python 3.x"
	uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5.2.0
	with:
	python-version: 3.12

	- name: "Install MacOS system dependencies"
	run: \|
	brew install coreutils gsl open-mpi libomp automake autoconf libtool boost hdf5

	- name: "Restore pip cache"
	env:
	cache-name: "pip-cache"
	uses: actions/cache@0c45773b623bea8c8e75f6c82b208c3cf94ea4f9 # v4.0.2
	with:
	path: \|
	/opt/hostedtoolcache/Python/*/site-packages/
	$HOME/.cache/pip
	key: ${{ runner.os }}-python-${{ env.cache-name }}-${{ hashFiles('**/requirements.txt') }}
	restore-keys: \|
	${{ runner.os }}-python-${{ env.cache-name }}-
	${{ runner.os }}-python-

	- name: "Install Python dependencies"
	run: \|
	python -m pip install --upgrade pip setuptools
	python -c "import setuptools; print('package location:', setuptools.__file__)"
	python -m pip install --force-reinstall --upgrade scipy 'junitparser>=2' numpy pytest pytest-timeout pytest-xdist mpi4py h5py cython matplotlib terminaltables pandoc pandas
	test \! -e "=2" # assert junitparser is correctly quoted and '>' is not interpreted as shell redirect
	python -c "import pytest; print('package location:', pytest.__file__)"
	pip list

	- name: "Configure NEST build"
	run: \|
	mkdir -p "$NEST_VPATH/reports" "$NEST_RESULT"

	cd "$NEST_VPATH"
	cmake \
	-DCMAKE_INSTALL_PREFIX="$NEST_RESULT" \
	-DCMAKE_CXX_FLAGS="$CXX_FLAGS" \
	-Dwith-optimize=${{ contains(matrix.use, 'optimize') && 'ON' \|\| 'OFF' }} \
	-Dwith-warning=${{ contains(matrix.use, 'warning') && 'ON' \|\| 'OFF' }} \
	-Dwith-boost=${{ contains(matrix.use, 'boost') && 'ON' \|\| 'OFF' }} \
	-Dwith-openmp=${{ contains(matrix.use, 'openmp') && 'ON' \|\| 'OFF' }} \
	${{ contains(matrix.use, 'openmp') && '-DOpenMP_ROOT=$(brew --prefix libomp)' }} \
	-Dwith-mpi=${{ contains(matrix.use, 'mpi') && 'ON' \|\| 'OFF' }} \
	-Dwith-python=${{ contains(matrix.use, 'python') && 'ON' \|\| 'OFF' }} \
	-Dwith-gsl=${{ contains(matrix.use, 'gsl') && 'ON' \|\| 'OFF' }} \
	-Dwith-ltdl=${{ contains(matrix.use, 'ltdl') && 'ON' \|\| 'OFF' }} \
	-Dwith-readline=${{ contains(matrix.use, 'readline') && 'ON' \|\| 'OFF' }} \
	-Dwith-hdf5=${{ contains(matrix.use, 'hdf5') && 'ON' \|\| 'OFF' }} \
	-Dwith-sionlib=${{ contains(matrix.use, 'sionlib') && '$HOME/.cache/sionlib.install' \|\| 'OFF' }} \
	-Dwith-libneurosim=${{ contains(matrix.use, 'libneurosim') && '$HOME/.cache/libneurosim.install' \|\| 'OFF' }} \
	-Dwith-music=${{ contains(matrix.use, 'music') && '$HOME/.cache/music.install' \|\| 'OFF' }} \
	..

	- name: "Add GCC problem matcher"
	run: \|
	echo "::add-matcher::gcc_problem_matcher.json"

	- name: "Build NEST"
	run: \|
	cd "$NEST_VPATH"
	env
	make VERBOSE=1

	- name: "Remove GCC problem matcher"
	run: \|
	echo "::remove-matcher owner=gcc-problem-matcher::"

	- name: "Install NEST"
	run: \|
	cd "$NEST_VPATH"
	make install

	- name: "Initialize Matplotlibrc"
	run: \|
	# initialize matplotlib backend
	mkdir -p $HOME/.matplotlib
	echo "backend : svg" > $HOME/.matplotlib/matplotlibrc

	- name: "Run NEST testsuite"
	run: \|
	pwd
	cd "$NEST_VPATH"
	chmod -v u+x ${NEST_RESULT}/share/nest/testsuite/do_tests.sh
	make VERBOSE=1 installcheck

	- name: "Upload install and test results"
	uses: actions/upload-artifact@0b2256b8c012f0828dc542b3febcab082c67f72b # v4.3.4
	if: ${{ always() }}
	with:
	name: "${{ matrix.NEST_BUILD_TYPE }}-build-logs-${{ matrix.os }}-${{ matrix.cpp_compiler }}"
	path: \|
	build/install_manifest.txt
	build/test_report_*/

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Bump github/codeql-action from 3.25.15 to 3.28.0 #5849

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Bump github/codeql-action from 3.25.15 to 3.28.0 #5849

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