Fix for finite differences. #3303
Workflow file for this run
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| name: NMODL CI | |
| concurrency: | |
| group: ${{ github.workflow }}#${{ github.ref }} | |
| cancel-in-progress: true | |
| on: | |
| push: | |
| branches: | |
| - master | |
| - release/** | |
| pull_request: | |
| branches: | |
| - master | |
| - release/** | |
| env: | |
| PYTHON_VERSION: 3.8 | |
| DESIRED_CMAKE_VERSION: 3.15.0 | |
| jobs: | |
| ci: | |
| runs-on: ${{matrix.config.os}} | |
| name: ${{toJson(matrix.config)}} | |
| strategy: | |
| matrix: | |
| include: | |
| - config: | |
| os: ubuntu-20.04 | |
| - config: | |
| flag_warnings: ON | |
| glibc_asserts: ON | |
| os: ubuntu-22.04 | |
| - config: | |
| os: macos-13 | |
| - config: | |
| os: macos-14 | |
| - config: | |
| os: windows-latest | |
| # TODO: might be interesting to add the thread sanitizer too | |
| - config: | |
| os: ubuntu-22.04 | |
| # Hyphens here will be replaced with commas before the value is | |
| # passed to NMODL_SANITIZERS | |
| sanitizer: address-leak | |
| - config: | |
| os: ubuntu-22.04 | |
| enable_usecases: On | |
| update_references: On | |
| - config: | |
| flag_warnings: ON | |
| os: ubuntu-22.04 | |
| sanitizer: undefined | |
| fail-fast: true | |
| steps: | |
| - name: Fix kernel mmap rnd bits | |
| # Asan in llvm 14 provided in ubuntu 22.04 is incompatible with | |
| # high-entropy ASLR in much newer kernels that GitHub runners are | |
| # using leading to random crashes: https://reviews.llvm.org/D148280 | |
| run: sudo sysctl vm.mmap_rnd_bits=28 | |
| if: matrix.config.os == 'ubuntu-22.04' | |
| - name: Setup cmake | |
| uses: jwlawson/actions-setup-cmake@v2 | |
| with: | |
| cmake-version: ${{ env.DESIRED_CMAKE_VERSION }} | |
| - name: Install homebrew packages | |
| if: startsWith(matrix.config.os, 'macOS') | |
| run: | | |
| brew install [email protected] || true | |
| brew link --overwrite [email protected] | |
| brew install ccache coreutils bison boost flex ninja | |
| echo /usr/local/opt/flex/bin:/usr/local/opt/bison/bin:/opt/homebrew/opt/flex/bin:/opt/homebrew/opt/bison/bin >> $GITHUB_PATH | |
| # Taken from https://docs.github.com/en/actions/using-github-hosted-runners/about-github-hosted-runners#supported-runners-and-hardware-resources | |
| echo CMAKE_BUILD_PARALLEL_LEVEL=3 >> $GITHUB_ENV | |
| shell: bash | |
| - name: Install apt packages | |
| if: startsWith(matrix.config.os, 'ubuntu') | |
| run: | | |
| sudo apt-get install bison ccache flex libfl-dev ninja-build python3-dev python3-pip | |
| # Taken from https://docs.github.com/en/actions/using-github-hosted-runners/about-github-hosted-runners#supported-runners-and-hardware-resources | |
| echo CMAKE_BUILD_PARALLEL_LEVEL=2 >> $GITHUB_ENV | |
| shell: bash | |
| - name: Install choco packages | |
| if: startsWith(matrix.config.os, 'windows') | |
| run: | | |
| choco install winflexbison3 | |
| - name: Configure VS Toolchain (Windows) | |
| if: startsWith(matrix.config.os, 'windows') | |
| uses: ilammy/msvc-dev-cmd@v1 | |
| - name: Set up Python3 | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ env.PYTHON_VERSION }} | |
| - uses: actions/checkout@v4 | |
| - name: Install Python3 dependencies | |
| working-directory: ${{runner.workspace}}/nmodl | |
| run: | | |
| python3 -m pip install -U pip setuptools | |
| python3 -m pip install --user -r requirements.txt | |
| - name: Install neuron-nightly | |
| if: ${{matrix.config.enable_usecases == 'On'}} | |
| run: | | |
| python3 -m pip install neuron-nightly | |
| - name: Register compiler warning problem matcher | |
| if: ${{matrix.config.flag_warnings == 'ON'}} | |
| run: echo "::add-matcher::.github/problem-matchers/gcc.json" | |
| - name: Register sanitizer problem matcher | |
| if: ${{matrix.config.sanitizer}} | |
| run: echo "::add-matcher::.github/problem-matchers/${{matrix.config.sanitizer}}.json" | |
| - name: Configure Windows | |
| if: startsWith(matrix.config.os, 'windows') | |
| run: | | |
| cmake -S . -B build -DFLEX_INCLUDE_PATH=C:/ProgramData/chocolatey/lib/winflexbison3/tools -DBUILD_SHARED_LIBS=OFF | |
| - name: Configure Linux/MacOS | |
| if: ${{ !startsWith(matrix.config.os, 'windows') }} | |
| shell: bash | |
| working-directory: ${{runner.workspace}}/nmodl | |
| run: | | |
| echo "------- Configure -------" | |
| cmake_args=(-G Ninja | |
| -DPYTHON_EXECUTABLE=$(which python3) \ | |
| -DCMAKE_INSTALL_PREFIX=$INSTALL_DIR) | |
| if [[ -n "${{matrix.config.flag_warnings}}" ]]; then | |
| cmake_args+=(-DNMODL_EXTRA_CXX_FLAGS="-Wall \ | |
| -Wno-reorder \ | |
| -Wno-unknown-pragmas \ | |
| -Wno-sign-compare \ | |
| -Wno-overloaded-virtual") | |
| fi | |
| if [[ -n "${{matrix.config.enable_usecases}}" ]]; then | |
| cmake_args+=(-DNMODL_ENABLE_USECASES=${{matrix.config.enable_usecases}}) | |
| fi | |
| if [[ -n "${{matrix.config.sanitizer}}" ]]; then | |
| cmake_args+=(-DCMAKE_BUILD_TYPE=Custom \ | |
| -DCMAKE_CXX_FLAGS="-O1 -g" \ | |
| -DNMODL_SANITIZERS=$(echo ${{matrix.config.sanitizer}} | sed -e 's/-/,/g')) | |
| CXX=$(command -v clang++-14) | |
| else | |
| CXX=${CXX:-g++} | |
| if [[ -n "${{matrix.config.glibc_asserts}}" ]]; then | |
| cmake_args+=(-DCMAKE_BUILD_TYPE=Debug \ | |
| -DCMAKE_CXX_FLAGS=-D_GLIBCXX_DEBUG) | |
| fi | |
| fi | |
| cmake_args+=(-DCMAKE_CXX_COMPILER=${CXX} \ | |
| -DCMAKE_CXX_COMPILER_LAUNCHER=ccache) | |
| cmake_args+=(-DNMODL_ENABLE_BACKWARD=On) | |
| cmake -B build -S . "${cmake_args[@]}" | |
| env: | |
| INSTALL_DIR: ${{ runner.workspace }}/install | |
| - name: Dump config dictionary | |
| if: ${{ !startsWith(matrix.config.os, 'windows') }} | |
| run: | | |
| cat << EOF > matrix.json | |
| ${{toJSON(matrix.config)}} | |
| EOF | |
| echo matrix.config JSON: | |
| cat matrix.json | |
| echo ----- | |
| - name: Restore compiler cache | |
| if: ${{ !startsWith(matrix.config.os, 'windows') }} | |
| uses: actions/cache@v4 | |
| with: | |
| path: | | |
| ${{runner.workspace}}/ccache | |
| key: ${{hashfiles('matrix.json')}}-${{github.ref}}-${{github.sha}} | |
| restore-keys: | | |
| ${{hashfiles('matrix.json')}}-${{github.ref}}- | |
| ${{hashfiles('matrix.json')}}- | |
| save-always: true | |
| - name: Build Windows | |
| if: startsWith(matrix.config.os, 'windows') | |
| run: | | |
| cmake --build build --verbose | |
| - name: Build Linux/MacOS | |
| if: ${{ !startsWith(matrix.config.os, 'windows') }} | |
| shell: bash | |
| working-directory: ${{runner.workspace}}/nmodl | |
| env: | |
| CCACHE_BASEDIR: ${{runner.workspace}}/nmodl | |
| CCACHE_DIR: ${{runner.workspace}}/ccache | |
| PYTHONMALLOC: malloc | |
| run: | | |
| if ccache --version | grep -E '^ccache version 4\.(4|4\.1)$' | |
| then | |
| echo "------- Disable ccache direct mode -------" | |
| # https://github.com/ccache/ccache/issues/935 | |
| export CCACHE_NODIRECT=1 | |
| fi | |
| echo "------- Building -------" | |
| ccache -z | |
| # Older versions don't support -v (verbose) | |
| ccache -vs 2>/dev/null || ccache -s | |
| cmake --build build --verbose | |
| ccache -vs 2>/dev/null || ccache -s | |
| - name: Test | |
| shell: bash | |
| working-directory: ${{runner.workspace}}/nmodl/build | |
| env: | |
| PYTHONMALLOC: malloc | |
| run: | | |
| ctest --output-on-failure --parallel 4 | |
| - name: Install | |
| shell: bash | |
| working-directory: ${{runner.workspace}}/nmodl | |
| run: | | |
| cmake --install build | |
| - name: Update references | |
| if: matrix.config.update_references == 'On' | |
| shell: bash | |
| working-directory: ${{runner.workspace}}/nmodl/test/usecases | |
| run : | | |
| export PATH="${INSTALL_DIR}/bin:${PATH}" | |
| export PYTHONPATH="${INSTALL_DIR}/lib:${PYTHONPATH}" | |
| for d in */ | |
| do | |
| ./generate_references.py nmodl "$d" "$OUTPUT_DIR/$d" | |
| done | |
| cd $OUTPUT_DIR | |
| tar cf ../references.tar * | |
| env: | |
| INSTALL_DIR: ${{ runner.workspace }}/install | |
| OUTPUT_DIR: ${{ runner.workspace }}/references | |
| - uses: actions/upload-artifact@v4 | |
| if: matrix.config.update_references == 'On' | |
| with: | |
| name: references | |
| path: ${{runner.workspace}}/references.tar | |
| - uses: actions/upload-artifact@v4 | |
| with: | |
| name: ctest-results-${{hashfiles('matrix.json')}} | |
| path: ${{runner.workspace}}/nmodl/build/Testing/*/Test.xml | |
| # This step will set up an SSH connection on tmate.io for live debugging. | |
| # To enable it, you have to: | |
| # * add 'live-debug-tests' to your PR title | |
| # * push something to your PR branch (note that just re-running disregards the title update) | |
| - name: live debug session on failure (manual steps required, check `nmodl-ci.yml`) | |
| if: failure() && contains(github.event.pull_request.title, 'live-debug-tests') | |
| uses: mxschmitt/action-tmate@v3 | |
| timeout-minutes: 60 | |
| commit-references: | |
| runs-on: ubuntu-latest | |
| needs: ci | |
| steps: | |
| - uses: actions/download-artifact@v4 | |
| with: | |
| name: references | |
| path: ${{runner.workspace}}/ | |
| - name: Check out nmodl-references | |
| uses: actions/checkout@v4 | |
| with: | |
| repository: BlueBrain/nmodl-references | |
| token: ${{ secrets.NMODL_REFERENCES_ACCESS_TOKEN }} | |
| - name: Update references | |
| run: | | |
| git config user.name "GitHub Actions Bot" | |
| git config user.email "<>" | |
| # If not a PR, then `pr_number` is the branch name. | |
| if [[ ${{ github.event_name }} == "pull_request" ]] | |
| then | |
| pr_number="$(echo ${GITHUB_REF_NAME} | sed "s/^\([0-9]*\)\/merge/\1/")" | |
| nmodl_desc=https://github.com/BlueBrain/nmodl/pull/${pr_number} | |
| branch="nmodl-${pr_number}" | |
| else | |
| nmodl_desc="nmodl@${GITHUB_SHA}" | |
| branch="main" | |
| fi | |
| git fetch | |
| git checkout ${branch} 2>/dev/null || git checkout -b ${branch} | |
| for d in */ | |
| do | |
| rm -rf "$d" | |
| done | |
| tar xf ${{ runner.workspace }}/references.tar | |
| git add . | |
| git commit --allow-empty -m "References for '${nmodl_desc}'." | |
| git push 2>/dev/null || git push --set-upstream origin ${branch} | |