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Add line number to error message #5746

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Add line number to error message

Add line number to error message #5746

Workflow file for this run

.github/workflows/nestbuildmatrix.yml at 27ea8bf
#
# 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_*/