From b178d25664312dfc26f41d92c3e34f3fdd3f9109 Mon Sep 17 00:00:00 2001 From: Nicolas Cornu Date: Wed, 8 May 2024 13:00:48 +0200 Subject: [PATCH] Simplify CI for debugging --- .github/workflows/coverage.yml | 193 ------------- .github/workflows/docs.yml | 88 ------ .github/workflows/external.yml | 71 ----- .github/workflows/formatting.yml | 51 ---- .github/workflows/neuron-ci.yml | 455 ------------------------------- .github/workflows/release.yml | 91 ------- azure-pipelines.yml | 179 ------------ 7 files changed, 1128 deletions(-) delete mode 100644 .github/workflows/coverage.yml delete mode 100644 .github/workflows/docs.yml delete mode 100644 .github/workflows/external.yml delete mode 100644 .github/workflows/formatting.yml delete mode 100644 .github/workflows/neuron-ci.yml delete mode 100644 .github/workflows/release.yml delete mode 100644 azure-pipelines.yml diff --git a/.github/workflows/coverage.yml b/.github/workflows/coverage.yml deleted file mode 100644 index a78b6934e2..0000000000 --- a/.github/workflows/coverage.yml +++ /dev/null @@ -1,193 +0,0 @@ -name: NEURON Code Coverage - -concurrency: - # Don't cancel on master, creating a PR when a push workflow is already going will cancel the push workflow in favour of the PR workflow - group: ${{ github.workflow }}-${{ github.ref == 'refs/heads/master' && github.run_id || github.event.number && github.head_ref || github.ref_name }} - cancel-in-progress: true - -on: - merge_group: - push: - branches: - - master - - release/** - pull_request: - branches: - - master - - release/** -# TODO : https://github.com/neuronsimulator/nrn/issues/1063 -# paths-ignore: -# - '**.md' -# - '**.rst' -# - 'docs/**' - -env: - PY_MIN_VERSION: '3.8' - PY_MID_VERSION: '3.10' - PY_MAX_VERSION: '3.12' - -jobs: - coverage: - runs-on: ubuntu-22.04 - - name: Code Coverage - - timeout-minutes: 60 - - env: - DISPLAY: ${{ ':0' }} - MUSIC_INSTALL_DIR: /opt/MUSIC - MUSIC_VERSION: 1.2.0 - - steps: - - - name: Install apt packages - run: | - sudo apt-get install xfonts-100dpi build-essential doxygen lcov libboost-all-dev libopenmpi-dev libmpich-dev libx11-dev libxcomposite-dev mpich openmpi-bin gpg ninja-build flex bison libfl-dev - shell: bash - - - name: Setup Caliper profiler - run: | - git clone https://github.com/LLNL/Caliper.git - cd Caliper - mkdir build && cd build - cmake .. - make && sudo make install - - - name: Setup MUSIC@${{ env.MUSIC_VERSION }} - run: | - python3 -m venv music-venv - source music-venv/bin/activate - python3 -m pip install mpi4py "cython<3" numpy setuptools - sudo mkdir -p $MUSIC_INSTALL_DIR - sudo chown -R $USER $MUSIC_INSTALL_DIR - curl -L -o MUSIC.zip https://github.com/INCF/MUSIC/archive/refs/tags/${MUSIC_VERSION}.zip - unzip MUSIC.zip && mv MUSIC-* MUSIC && cd MUSIC - ./autogen.sh - ./configure --with-python-sys-prefix --prefix=$MUSIC_INSTALL_DIR --disable-anysource - make -j install - deactivate - working-directory: ${{runner.temp}} - - - name: Setup Xvfb - run: | - sudo apt-get install xvfb - sudo /usr/bin/Xvfb $DISPLAY -screen 0 1600x1200x24 -noreset -nolock -shmem & # run in bg - - - uses: actions/checkout@v4 - with: - fetch-depth: 2 - - - name: Clone nmodl - working-directory: ${{runner.workspace}}/nrn - run: | - git submodule update --init --recursive --force --depth 1 -- external/nmodl - - - name: Set up Python@${{ env.PY_MIN_VERSION }} - uses: actions/setup-python@v5 - with: - python-version: ${{ env.PY_MIN_VERSION }} - - - name: Install Python@${{ env.PY_MIN_VERSION }} dependencies - working-directory: ${{runner.workspace}}/nrn - run: | - python -m pip install --upgrade pip -r nrn_requirements.txt - python -m pip install --upgrade -r external/nmodl/requirements.txt - python -m pip install --upgrade -r ci_requirements.txt - - - name: Set up Python@${{ env.PY_MID_VERSION }} - uses: actions/setup-python@v5 - with: - python-version: ${{ env.PY_MID_VERSION }} - - - name: Set up Python@${{ env.PY_MAX_VERSION }} - uses: actions/setup-python@v5 - with: - python-version: ${{ env.PY_MAX_VERSION }} - - - name: Install Python@${{ env.PY_MAX_VERSION }} dependencies - working-directory: ${{runner.workspace}}/nrn - run: | - python -m pip install --upgrade pip -r nrn_requirements.txt - python -m pip install --upgrade -r external/nmodl/requirements.txt - python -m pip install --upgrade -r ci_requirements.txt - - - - name: Build & Test - id: build-test - shell: bash - working-directory: ${{runner.workspace}}/nrn - run: | - export SHELL="/bin/bash" - - # Compiler setup - export CC=gcc - export CXX=g++ - - # Python setup - export PYTHON_MIN=$(which $PYTHON_MIN_NAME); - export PYTHON_MID=$(which $PYTHON_MID_NAME); - export PYTHON_MAX=$(which $PYTHON_MAX_NAME); - - mkdir build && cd build; - - # CMake options & flags - cmake_args=(-G Ninja \ - -DCMAKE_BUILD_TYPE=Debug \ - -DCMAKE_C_COMPILER="$CC" \ - -DCMAKE_CXX_COMPILER="$CXX" \ - -DNRN_ENABLE_BACKTRACE=ON \ - -DNRN_ENABLE_CORENEURON=ON \ - -DNRN_ENABLE_COVERAGE=ON \ - -DNRN_ENABLE_INTERVIEWS=ON \ - -DNRN_ENABLE_MPI=ON \ - -DNRN_ENABLE_PERFORMANCE_TESTS=OFF \ - -DNRN_ENABLE_PROFILING=ON \ - -DNRN_ENABLE_PYTHON=ON \ - -DNRN_ENABLE_PYTHON_DYNAMIC=ON \ - -DNRN_PYTHON_DYNAMIC="${PYTHON_MIN};${PYTHON_MAX}" \ - -DNRN_PYTHON_EXTRA_FOR_TESTS=${PYTHON_MID} \ - -DNRN_ENABLE_TESTS=ON \ - -DNRN_ENABLE_MUSIC=ON \ - -DCMAKE_PREFIX_PATH="${MUSIC_INSTALL_DIR}" \ - -DMUSIC_ROOT="${MUSIC_INSTALL_DIR}") - cmake .. "${cmake_args[@]}" - # Coverage - # The Linux runners apparently have 2 cores, but jobs were being killed when we did not specify this explicitly. - # https://docs.github.com/en/actions/using-github-hosted-runners/about-github-hosted-runners#supported-runners-and-hardware-resources - # By default we get a modern version of CMake that understands --parallel. - cmake --build . --parallel 2 - cmake --build . --target cover_baseline - xvfb-run ctest --rerun-failed --output-on-failure; - for python in "${PYTHON_MIN}" "${PYTHON_MAX}" - do - echo "Using ${python}" - NEURONHOME="${PWD}/share/nrn" \ - PYTHONPATH="${PWD}/lib/python:${PYTHONPATH}" \ - PATH="${PWD}/bin:${PATH}" \ - LD_LIBRARY_PATH="${PWD}/lib:${LD_LIBRARY_PATH}" \ - DYLD_LIBRARY_PATH="${PWD}/lib:${DYLD_LIBRARY_PATH}" \ - "${python}" -c "from neuron import h; import neuron; neuron.test();neuron.test_rxd();" - done - cmake --build . --target cover_collect - cmake --build . --target cover_combine - env: - MATRIX_EVAL: "CC=gcc CXX=g++" - PYTHON_MIN_NAME: "python${{ env.PY_MIN_VERSION }}" - PYTHON_MID_NAME: "python${{ env.PY_MID_VERSION }}" - PYTHON_MAX_NAME: "python${{ env.PY_MAX_VERSION }}" - - # This step will set up an SSH connection on tmate.io for live debugging. - # To enable it, you have to: - # * add 'live-debug-coverage' to your PR title - # * push something to your PR branch (note that just re-running the pipeline disregards the title update) - - name: live debug session on failure (manual steps required, check `.github/coverage.yml`) - if: failure() && contains(github.event.pull_request.title, 'live-debug-coverage') - uses: mxschmitt/action-tmate@v3 - - - uses: codecov/codecov-action@v4 - with: - directory: ./build - fail_ci_if_error: true - verbose: true - token: ${{ secrets.CODECOV_TOKEN }} diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml deleted file mode 100644 index dffa17c6fa..0000000000 --- a/.github/workflows/docs.yml +++ /dev/null @@ -1,88 +0,0 @@ -name: NEURON Documentation - -concurrency: - # Don't cancel on master, creating a PR when a push workflow is already going will cancel the push workflow in favour of the PR workflow - group: ${{ github.workflow }}-${{ github.ref == 'refs/heads/master' && github.run_id || github.event.number && github.head_ref || github.ref_name }} - cancel-in-progress: true - -on: - merge_group: - push: - branches: - - master - - release/** - pull_request: - branches: - - master - - release/** - -env: - DEFAULT_PY_VERSION: '3.12' - -jobs: - documentation: - runs-on: ubuntu-20.04 - - name: Documentation - - timeout-minutes: 25 - - steps: - - - name: Install apt packages - run: | - sudo apt-get update --fix-missing - sudo apt-get install build-essential libopenmpi-dev libmpich-dev libx11-dev libxcomposite-dev mpich openmpi-bin - sudo apt-get install ffmpeg doxygen pandoc - shell: bash - - - name: Set up Python@${{ env.DEFAULT_PY_VERSION }} - uses: actions/setup-python@v5 - with: - python-version: ${{ env.DEFAULT_PY_VERSION }} - - - uses: actions/checkout@v4 - - - name: Install Python dependencies - working-directory: ${{runner.workspace}}/nrn - run: | - python -m pip install --upgrade pip -r nrn_requirements.txt - - - name: Install Python documentation dependencies - working-directory: ${{runner.workspace}}/nrn - run: | - python -m pip install --upgrade -r docs/docs_requirements.txt - - - name: Documentation - id: documentation - shell: bash - working-directory: ${{runner.workspace}}/nrn - run: | - echo "-------- NEURON wheel --------"; - python setup.py build_ext bdist_wheel; - neuron_wheel=dist/NEURON*.whl; - echo "-------- install wheel --------" - python -m pip install $neuron_wheel; - echo "-------- now build docs--------"; - python setup.py docs; - echo "-------- disable jekyll--------"; - pushd docs/_build; - touch .nojekyll; - echo "-------- OK to deploy! --------"; - echo "OK_TO_DEPLOY_DOCS=true" >> $GITHUB_ENV - - # This step will set up an SSH connection on tmate.io for live debugging. - # To enable it, you have to: - # * add 'live-debug-docs' to your PR title - # * push something to your PR branch (note that just re-running the pipeline disregards the title update) - - name: live debug session on failure (manual steps required, check `.github/docs.yml`) - if: failure() && contains(github.event.pull_request.title, 'live-debug-docs') - uses: mxschmitt/action-tmate@v3 - - - name: Deploy 🚀 - uses: JamesIves/github-pages-deploy-action@v4 - if: env.OK_TO_DEPLOY_DOCS == 'true' && github.ref == 'refs/heads/master' - with: - branch: gh-pages # The branch the action should deploy to. - folder: ${{runner.workspace}}/nrn/docs/_build # The folder the action should deploy. - single-commit: true #have a single commit on the deployment branch instead of maintaining the full history diff --git a/.github/workflows/external.yml b/.github/workflows/external.yml deleted file mode 100644 index ab06e55459..0000000000 --- a/.github/workflows/external.yml +++ /dev/null @@ -1,71 +0,0 @@ -name: External CIs - -concurrency: - # Don't cancel on master, creating a PR when a push workflow is already going will cancel the push workflow in favour of the PR workflow - group: ${{ github.workflow }}-${{ github.ref == 'refs/heads/master' && github.run_id || github.event.number && github.head_ref || github.ref_name }} - cancel-in-progress: true - -on: - pull_request: - types: [ labeled ] -env: - PR_URL: ${{ github.event.pull_request.html_url }} - GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} - -jobs: - get-last-azure-url: - runs-on: ubuntu-latest - if: ${{ github.event.label.name == 'nrn-modeldb-ci-nightly' }} - outputs: - azure_drop_url: ${{ steps.drop.outputs.azure_drop_url }} - pr_azure_sha: ${{ steps.drop.outputs.pr_azure_sha }} - steps: - - id: drop - run: | - # use jq to get the last Azure drop URL from the PR and the SHA1 from the same body - export pr_json=$(gh pr view $PR_URL --json comments -q 'last(.comments[] .body | capture(".*(?[0-9a-f]{40}).*?(?https://dev.azure.com/neuronsimulator/.*=zip)"))') - if [ -z "$pr_json" ]; then - echo "Unable to retrieve AZURE drop url and SHA from comments!" - exit 1 - fi - # use jq to get pr_azure_sha and azure_drop_url from the json - export azure_drop_url=$(echo $pr_json | jq -r .azure_drop_url) - export pr_azure_sha=$(echo $pr_json | jq -r .pr_azure_sha) - echo azure_drop_url=$azure_drop_url >> $GITHUB_OUTPUT - echo pr_azure_sha=$pr_azure_sha >> $GITHUB_OUTPUT - - - id: remove-label - if: always() - run: | - # remove the label - gh pr edit $PR_URL --remove-label nrn-modeldb-ci-nightly - # if we encounter an error in last github action step, add a comment - if [ ${{ steps.drop.outcome }} == 'failure' ]; then - gh pr comment $PR_URL --body "Unable to retrieve AZURE drop url from comments!" - else - gh pr comment $PR_URL --body "NEURON ModelDB CI: launching for ${pr_azure_sha} via its [drop url]($azure_drop_url)" - fi - env: - pr_azure_sha: ${{ steps.drop.outputs.pr_azure_sha }} - azure_drop_url: ${{ steps.drop.outputs.azure_drop_url }} - - nrn-modeldb-ci: - needs: get-last-azure-url - uses: neuronsimulator/nrn-modeldb-ci/.github/workflows/nrn-modeldb-ci.yaml@master - with: - neuron_v1: ${{needs.get-last-azure-url.outputs.azure_drop_url}} - neuron_v2: neuron-nightly - - pr-update: - needs: - - nrn-modeldb-ci - - get-last-azure-url - runs-on: ubuntu-latest - steps: - - run: | - gh pr comment $PR_URL --body "NEURON ModelDB CI: ${pr_azure_sha} -> download reports [from here](${ARTIFACTS_URL})" - name: Post NEURON ModelDB CI Artifact URL - if: always() || cancelled() - env: - ARTIFACTS_URL: ${{ github.server_url }}/${{ github.repository }}/actions/runs/${{ github.run_id }} - pr_azure_sha: ${{ needs.get-last-azure-url.outputs.pr_azure_sha }} diff --git a/.github/workflows/formatting.yml b/.github/workflows/formatting.yml deleted file mode 100644 index 434bef743d..0000000000 --- a/.github/workflows/formatting.yml +++ /dev/null @@ -1,51 +0,0 @@ -name: Check formatting - -concurrency: - # Don't cancel on master, creating a PR when a push workflow is already going will cancel the push workflow in favour of the PR workflow - group: ${{ github.workflow }}-${{ github.ref == 'refs/heads/master' && github.run_id || github.event.number && github.head_ref || github.ref_name }} - cancel-in-progress: true - -on: - merge_group: - push: - branches: - - release/** - pull_request: - branches: - - master - - release/** - -jobs: - all: - name: C/C++, CMake and Python - runs-on: ubuntu-22.04 - timeout-minutes: 5 - steps: - - uses: actions/checkout@v4 - - name: Update submodule - working-directory: ${{runner.workspace}}/nrn - run: git submodule update --init external/coding-conventions - - name: Check formatting - working-directory: ${{runner.workspace}}/nrn - run: external/coding-conventions/bin/format -v --dry-run - - # If formatting fails, apply formatting and push changes. - # This will trigger another workflow run, which will cancel the current one. - - name: Apply formatting - working-directory: ${{runner.workspace}}/nrn - if: failure() && github.event_name == 'pull_request' - run: | - # Checkout PR - gh pr checkout ${{ github.event.pull_request.number }} - - # Apply formatting - external/coding-conventions/bin/format -v - - # Commit & push changes - git config --global user.name "github-actions[bot]" - git config --global user.email "41898282+github-actions[bot]@users.noreply.github.com" - git add -u :/ - git commit -a -m "Fix formatting" - git push - env: - GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} diff --git a/.github/workflows/neuron-ci.yml b/.github/workflows/neuron-ci.yml deleted file mode 100644 index f702b71872..0000000000 --- a/.github/workflows/neuron-ci.yml +++ /dev/null @@ -1,455 +0,0 @@ -name: NEURON CI - -concurrency: - # Don't cancel on master, creating a PR when a push workflow is already going will cancel the push workflow in favour of the PR workflow - group: ${{ github.workflow }}-${{ github.ref == 'refs/heads/master' && github.run_id || github.event.number && github.head_ref || github.ref_name }} - cancel-in-progress: true - -on: - merge_group: - push: - branches: - # If nothing else, this is important for the ccache logic below... - - master - - release/** - pull_request: - branches: - - master - - release/** -# TODO : https://github.com/neuronsimulator/nrn/issues/1063 -# paths-ignore: -# - '**.md' -# - '**.rst' -# - 'docs/**' - - -jobs: - ci: - runs-on: ${{ matrix.os }} - - name: ${{ matrix.os }} - ${{ matrix.config.build_mode }} (${{ matrix.config.cmake_option }}${{ matrix.config.config_options }}${{ matrix.config.matrix_eval }}${{ matrix.config.sanitizer }}) - - timeout-minutes: 75 - - env: - INSTALL_DIR: install - SDK_ROOT: $(xcrun --sdk macosx --show-sdk-path) - SKIP_WHEELHOUSE_REPAIR: true - BUILD_TYPE: Release - DESIRED_CMAKE_VERSION: 3.17 - DYNAMIC_PYTHON_CMAKE_VERSION: 3.18 - PY_MIN_VERSION: ${{ matrix.config.python_min_version || '3.8' }} - PY_MAX_VERSION: ${{ matrix.config.python_max_version || '3.12' }} - MUSIC_INSTALL_DIR: /opt/MUSIC - MUSIC_VERSION: 1.2.1 - - strategy: - matrix: - os: [ macOS-12, ubuntu-20.04] - config: - - { matrix_eval : "CC=gcc-9 CXX=g++-9", build_mode: "setuptools"} - - { matrix_eval : "CC=gcc-10 CXX=g++-10", build_mode: "cmake", music: ON} - - { matrix_eval : "CC=gcc-10 CXX=g++-10", build_mode: "cmake", python_dynamic: ON} - - { matrix_eval : "CC=gcc-9 CXX=g++-9" , build_mode: "cmake", cmake_option: "-DNRN_ENABLE_CORENEURON=ON"} - - { matrix_eval : "CC=gcc-9 CXX=g++-9", build_mode: "cmake", cmake_option: "-DNRN_ENABLE_MPI=OFF -DNRN_ENABLE_INTERVIEWS=OFF -DNRN_ENABLE_CORENEURON=ON"} - - { matrix_eval : "CC=gcc-10 CXX=g++-10", build_mode: "cmake", cmake_option: "-DNRN_ENABLE_PYTHON=OFF -DNRN_ENABLE_RX3D=OFF -DNRN_ENABLE_CORENEURON=ON"} - include: - - os: ubuntu-22.04 - config: - build_mode: cmake - cmake_option: -DNRN_ENABLE_CORENEURON=ON - -DNRN_ENABLE_INTERVIEWS=OFF -DNMODL_SANITIZERS=undefined - flag_warnings: ON - sanitizer: undefined - - os: ubuntu-22.04 - config: - build_mode: cmake - # TODO: CoreNEURON is only LeakSanitizer-clean if we disable MPI - cmake_option: -DNRN_ENABLE_CORENEURON=ON - -DNRN_ENABLE_INTERVIEWS=OFF -DNMODL_SANITIZERS=address - # TODO: address-leak is the dream, but there are many problems, - # including external ones from the MPI implementations - sanitizer: address - - os: ubuntu-22.04 - config: - build_mode: cmake - # Cannot use a non-instrumented OpenMP with TSan, and we don't - # have a TSan-instrumented OpenMP runtime available. - # TODO: debug RX3D + TSan - cmake_option: -DNRN_ENABLE_CORENEURON=ON -DNRN_ENABLE_MPI=OFF - -DCORENRN_ENABLE_OPENMP=OFF -DNRN_ENABLE_RX3D=OFF - sanitizer: thread - - os: macOS-13 - config: - build_mode: cmake - # TODO: investigate rxd test timeouts in this build and re-enable them - cmake_option: -DNRN_ENABLE_CORENEURON=ON -DNRN_ENABLE_INTERVIEWS=OFF - -DNRN_ENABLE_RX3D=OFF -DNMODL_SANITIZERS=address - sanitizer: address - fail-fast: false - - 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.os == 'ubuntu-22.04' - - - name: Setup cmake - uses: jwlawson/actions-setup-cmake@v2 - with: - cmake-version : ${{(matrix.config.python_dynamic || matrix.config.build_mode == 'setuptools') && env.DYNAMIC_PYTHON_CMAKE_VERSION || env.DESIRED_CMAKE_VERSION}} - - - name: Install homebrew packages - if: startsWith(matrix.os, 'macOS') - run: | - # Unlink and re-link to prevent errors when GitHub macOS runner images - # install Python outside of brew; See actions/setup-python#577 and BlueBrain/libsonata/pull/317 - brew list -1 | grep python | while read formula; do brew unlink $formula; brew link --overwrite $formula; done - brew install ccache coreutils doxygen flex bison mpich ninja xz autoconf automake libtool - # We use both for dynamic mpi in nrn - brew unlink mpich - brew install openmpi - brew install --cask xquartz - echo "$(brew --prefix)/opt/flex/bin:$(brew --prefix)/opt/bison/bin" >> $GITHUB_PATH - # Core https://docs.github.com/en/actions/using-github-hosted-runners/about-github-hosted-runners/about-github-hosted-runners#standard-github-hosted-runners-for-public-repositories - if [[ "${{matrix.os}}" == "macOS-13" ]]; then - echo CMAKE_BUILD_PARALLEL_LEVEL=4 >> $GITHUB_ENV - echo CTEST_PARALLEL_LEVEL=4 >> $GITHUB_ENV - else - echo CMAKE_BUILD_PARALLEL_LEVEL=3 >> $GITHUB_ENV - echo CTEST_PARALLEL_LEVEL=3 >> $GITHUB_ENV - fi - echo CI_OS_NAME=osx >> $GITHUB_ENV - shell: bash - - - name: Install apt packages - if: startsWith(matrix.os, 'ubuntu') - run: | - sudo apt-get install build-essential ccache libopenmpi-dev \ - libmpich-dev libx11-dev libxcomposite-dev mpich ninja-build \ - openmpi-bin flex libfl-dev bison - # The sanitizer builds use ubuntu 22.04 - if [[ "${{matrix.os}}" == "ubuntu-20.04" ]]; then - sudo apt-get install g++-7 g++-8 - fi - # Core https://docs.github.com/en/actions/using-github-hosted-runners/about-github-hosted-runners/about-github-hosted-runners#standard-github-hosted-runners-for-public-repositories - echo CMAKE_BUILD_PARALLEL_LEVEL=4 >> $GITHUB_ENV - echo CTEST_PARALLEL_LEVEL=4 >> $GITHUB_ENV - echo CI_OS_NAME=linux >> $GITHUB_ENV - shell: bash - - - uses: actions/checkout@v4 - with: - fetch-depth: 2 - - - name: Clone nmodl - working-directory: ${{runner.workspace}}/nrn - run: | - git submodule update --init --recursive --force --depth 1 -- external/nmodl - - - name: Set up Python@${{ env.PY_MIN_VERSION }} - if: ${{matrix.config.python_dynamic == 'ON'}} - uses: actions/setup-python@v5 - with: - python-version: ${{ env.PY_MIN_VERSION }} - - - name: Install Python@${{ env.PY_MIN_VERSION }} dependencies - if: ${{ matrix.config.python_dynamic == 'ON' }} - working-directory: ${{runner.workspace}}/nrn - run: | - python -m pip install --upgrade pip -r nrn_requirements.txt - python -m pip install --upgrade -r external/nmodl/requirements.txt - python -m pip install --upgrade -r ci_requirements.txt - - - name: Set up Python@${{ env.PY_MAX_VERSION }} - uses: actions/setup-python@v5 - with: - python-version: ${{ env.PY_MAX_VERSION }} - - - name: Install Python@${{ env.PY_MAX_VERSION }} dependencies - working-directory: ${{runner.workspace}}/nrn - run: | - python -m pip install --upgrade pip -r nrn_requirements.txt - python -m pip install --upgrade -r external/nmodl/requirements.txt - python -m pip install --upgrade -r ci_requirements.txt - - - name: Install a new automake - # A new automake is needed for python 3.12 because it generate a python script - # called py-compile and the original one is not supporting this version of python - # Once ubuntu got a newer version of automake we can remove this part. - if: matrix.config.music == 'ON' && startsWith(matrix.os, 'ubuntu') - run: | - curl -L -o automake.tar.xz https://ftp.gnu.org/gnu/automake/automake-1.16.5.tar.xz - tar -xf automake.tar.xz - cd automake-1.16.5/ - ./configure --prefix=/usr/ - make -j - sudo make -j install - automake --version - working-directory: ${{runner.temp}} - - - name: Setup MUSIC@${{ env.MUSIC_VERSION }} - if: matrix.config.music == 'ON' - run: | - python3 -m venv music-venv - source music-venv/bin/activate - python3 -m pip install mpi4py "cython<3" numpy setuptools - sudo mkdir -p $MUSIC_INSTALL_DIR - sudo chown -R $USER $MUSIC_INSTALL_DIR - curl -L -o MUSIC.zip https://github.com/INCF/MUSIC/archive/refs/tags/${MUSIC_VERSION}.zip - unzip MUSIC.zip && mv MUSIC-* MUSIC && cd MUSIC - ./autogen.sh - # on some systems MPI library detection fails, provide exact flags/compilers - ./configure --with-python-sys-prefix --prefix=$MUSIC_INSTALL_DIR --disable-anysource MPI_CXXFLAGS="-g -O3" MPI_CFLAGS="-g -O3" MPI_LDFLAGS=" " CC=mpicc CXX=mpicxx - make -j install - deactivate - working-directory: ${{runner.temp}} - - - name: Register gcc 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: Hash config dictionary - run: | - cat << EOF > matrix.json - ${{toJSON(matrix.config)}} - EOF - echo matrix.config JSON: - cat matrix.json - echo ----- - - - name: Restore compiler cache - uses: actions/cache@v4 - with: - path: ${{runner.workspace}}/ccache - save-always: true - key: ${{matrix.os}}-${{hashfiles('matrix.json')}}-${{github.ref}}-${{github.sha}} - restore-keys: | - ${{matrix.os}}-${{hashfiles('matrix.json')}}-${{github.ref}}- - ${{matrix.os}}-${{hashfiles('matrix.json')}}- - - - name: Build and Test - id: build-test - shell: bash - working-directory: ${{runner.workspace}}/nrn - run: | - # OS related - if [ "$RUNNER_OS" == "Linux" ]; then - export ${MATRIX_EVAL}; - export SHELL="/bin/bash" - else - export CXX=${CXX:-g++}; - export CC=${CC:-gcc}; - fi - if [ "$RUNNER_OS" == "macOS" ]; then - # TODO - this is a workaround that was implemented for Azure being reported as getting stuck. - # However it does not get stuck: neuron module not found and script goes to interpreter, seeming stuck. - # This needs to be addressed and SKIP_EMBEDED_PYTHON_TEST logic removed everywhere. - export SKIP_EMBEDED_PYTHON_TEST="true" - # long TMPDIR path on MacOS can results into runtime failures with OpenMPI - # Set shorter path as discussed in https://github.com/open-mpi/ompi/issues/8510 - export TMPDIR=/tmp/$GITHUB_JOB - mkdir -p $TMPDIR - fi - - # Python setup - export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python/ - # Python setup - export PYTHON_MIN=$(command -v $PYTHON_MIN_NAME); - export PYTHON_MAX=$(command -v $PYTHON_MAX_NAME); - export PYTHON=$PYTHON_MAX - if [ "$RUNNER_OS" == "macOS" ]; then - # Python is not installed as a framework, so we need to writ 'backend: TkAgg' to `matplotlibrc`. - # Since we are in a virtual environment, we cannot use `$HOME/matplotlibrc` - # The following solution is generic and relies on `matplotlib.__file__` to know where to append backend setup. - $PYTHON -c "import os,matplotlib; f =open(os.path.join(os.path.dirname(matplotlib.__file__), 'mpl-data/matplotlibrc'),'a'); f.write('backend: TkAgg');f.close();" - fi; - - # Some logging - echo $LANG - echo $LC_ALL - python3 -c 'import os,sys; os.set_blocking(sys.stdout.fileno(), True)' - cmake --version - - # different builds with CMake - if [[ "$BUILD_MODE" == "cmake" ]]; then - cmake_args=(-G Ninja) - # Sanitizer-specific setup - if [[ -n "${{matrix.config.sanitizer}}" ]]; then - if [ "$RUNNER_OS" == "Linux" ]; then - if [[ "${{matrix.config.sanitizer}}" == "thread" ]]; then - # GitHub/ubuntu-22.04 + clang-14 seems to have problems with TSan. - # Vanilla 22.04 + clang-16 from apt.llvm.org seemed to work. - # Use gcc-12 instead, as GitHub/ubuntu-22.04 already has it. - CC=$(command -v gcc-12) - CXX=$(command -v g++-12) - else - CC=$(command -v clang-14) - CXX=$(command -v clang++-14) - symbolizer_path="$(readlink -f "$(command -v llvm-symbolizer-14)")" - cmake_args+=(-DLLVM_SYMBOLIZER_PATH="${symbolizer_path}") - fi - fi - cmake_args+=(-DCMAKE_BUILD_TYPE=Custom \ - -DCMAKE_C_FLAGS="-O1 -g" \ - -DCMAKE_CXX_FLAGS="-O1 -g" \ - -DNRN_SANITIZERS=$(echo ${{matrix.config.sanitizer}} | sed -e 's/-/,/g')) - fi - cmake_args+=(-DCMAKE_C_COMPILER="${CC}" \ - -DCMAKE_C_COMPILER_LAUNCHER=ccache \ - -DCMAKE_CXX_COMPILER="${CXX}" \ - -DCMAKE_CXX_COMPILER_LAUNCHER=ccache \ - -DCMAKE_INSTALL_PREFIX="${INSTALL_DIR}" \ - -DNRN_ENABLE_TESTS=ON \ - -DNRN_ENABLE_PERFORMANCE_TESTS=OFF \ - ${{matrix.config.cmake_option}}) - if [[ "$NRN_ENABLE_PYTHON_DYNAMIC" == "ON" ]]; then - cmake_args+=(-DNRN_ENABLE_PYTHON=ON \ - -DNRN_ENABLE_PYTHON_DYNAMIC=ON \ - -DNRN_PYTHON_DYNAMIC="${PYTHON_MIN};${PYTHON_MAX}" \ - -DNRN_ENABLE_CORENEURON=ON) - else - cmake_args+=(-DPYTHON_EXECUTABLE="${PYTHON}") - fi - if [[ "$NRN_ENABLE_MUSIC" == "ON" ]]; then - cmake_args+=(-DNRN_ENABLE_MUSIC=ON \ - -DCMAKE_PREFIX_PATH=${MUSIC_INSTALL_DIR} \ - -DMUSIC_ROOT=${MUSIC_INSTALL_DIR}) - fi - # Enable more warnings in the builds whose compiler warnings we - # highlight in the GitHub UI - if [[ "${{matrix.config.flag_warnings}}" == "ON" ]]; then - cmake_args+=(-DNRN_EXTRA_CXX_FLAGS="-Wall \ - -Wno-char-subscripts \ - -Wno-unknown-pragmas \ - -Wno-unused-variable \ - -Wno-unused-function \ - -Wno-unused-but-set-variable \ - -Wno-reorder \ - -Wno-sign-compare" \ - -DNRN_EXTRA_MECH_CXX_FLAGS="-Wno-sometimes-uninitialized \ - -Wno-missing-braces") - fi - mkdir build && cd build - echo "Building with: ${cmake_args[@]}" - cmake .. "${cmake_args[@]}" - if ccache --version | grep -E '^ccache version 4\.(4|4\.1)$' - then - echo "------- Disable ccache direct mode -------" - # https://github.com/ccache/ccache/issues/935 - export CCACHE_NODIRECT=1 - fi - ccache -z - # Older versions don't support -v (verbose) - ccache -vs 2>/dev/null || ccache -s - cmake --build . --parallel - ccache -vs 2>/dev/null || ccache -s - if [ "$RUNNER_OS" == "macOS" ] - then - mkdir -p src/nrnpython - echo $'[install]\nprefix='>src/nrnpython/setup.cfg; - fi - if [[ "$NRN_ENABLE_PYTHON_DYNAMIC" == "ON" ]]; then - echo "--RUNNING BASIC TESTS FROM BUILD DIR--" - for python in "${PYTHON_MIN}" "${PYTHON_MAX}" - do - echo "Using ${python}" - NEURONHOME="${PWD}/share/nrn" \ - PYTHONPATH="${PWD}/lib/python" \ - PATH="${PWD}/bin" \ - LD_LIBRARY_PATH="${PWD}/lib:${LD_LIBRARY_PATH}" \ - DYLD_LIBRARY_PATH="${PWD}/lib:${DYLD_LIBRARY_PATH}" \ - "${python}" -c "from neuron import h; import neuron; neuron.test()" - done - fi - ctest --output-on-failure - cmake --build . --target install - export PATH="${INSTALL_DIR}/bin:${PATH}" - if [[ -f "${INSTALL_DIR}/bin/nrn-enable-sanitizer" ]]; then - echo --- bin/nrn-enable-sanitizer --- - cat bin/nrn-enable-sanitizer - echo --- - nrn_enable_sanitizer=${INSTALL_DIR}/bin/nrn-enable-sanitizer - nrn_enable_sanitizer_preload_python="${nrn_enable_sanitizer} --preload python" - else - echo nrn-enable-sanitizer not found, not using it - fi - elif [[ "$BUILD_MODE" == "setuptools" ]]; then - ./packaging/python/build_wheels.bash CI; - fi; - if [[ -z "${nrn_enable_sanitizer_preload_python}" ]]; then - nrn_enable_sanitizer_preload_python="${PYTHON}" - fi - - # basic test for cmake when python is not disabled - if [[ "$BUILD_MODE" == "cmake" && ! "${cmake_args[*]}" =~ "NRN_ENABLE_PYTHON=OFF" ]]; then - ${nrn_enable_sanitizer_preload_python} --version && ${nrn_enable_sanitizer_preload_python} -c 'import neuron; neuron.test()' - fi; - - # test neurondemo with cmake - if [[ "$BUILD_MODE" != "setuptools" ]]; then - ${nrn_enable_sanitizer} neurondemo -nogui -c 'demo(4)' -c 'run()' -c 'quit()' - fi; - - # with cmake dynamic check python_min and python_max together - if [[ "$BUILD_MODE" == "cmake" && "$NRN_ENABLE_PYTHON_DYNAMIC" == "ON" ]]; then - ${nrn_enable_sanitizer_preload_python} -c 'import neuron; neuron.test()' - $PYTHON_MIN -c 'import neuron; neuron.test()' - fi; - - # run rxd tests manually if rxd is enabled *and CoreNEURON is - # disabled -- otherwise hh-related tests fail - if [[ "$BUILD_MODE" == "cmake" \ - && ! "${cmake_args[*]}" =~ "NRN_ENABLE_RX3D=OFF" \ - && ! "${cmake_args[*]}" =~ "NRN_ENABLE_CORENEURON=ON" ]]; then - ${nrn_enable_sanitizer_preload_python} ../share/lib/python/neuron/rxdtests/run_all.py - fi; - - if [ "$BUILD_MODE" == "setuptools" ]; then - neuron_wheel=wheelhouse/NEURON*.whl; - # test with virtual environment - ./packaging/python/test_wheels.sh $PYTHON $neuron_wheel - # test with global installation - ./packaging/python/test_wheels.sh $PYTHON $neuron_wheel false - fi; - env: - BUILD_MODE: ${{ matrix.config.build_mode }} - CCACHE_BASEDIR: ${{runner.workspace}}/nrn - CCACHE_DIR: ${{runner.workspace}}/ccache - NRN_ENABLE_PYTHON_DYNAMIC : ${{ matrix.config.python_dynamic }} - NRN_ENABLE_MUSIC: ${{ matrix.config.music }} - PYTHON_MIN_NAME: "python${{ env.PY_MIN_VERSION }}" - PYTHON_MAX_NAME: "python${{ env.PY_MAX_VERSION }}" - INSTALL_DIR : ${{ runner.workspace }}/install - MATRIX_EVAL: ${{ matrix.config.matrix_eval }} - - # This step will set up an SSH connection on tmate.io for live debugging. - # To enable it, you have to: - # * add 'live-debug-ci' to your PR title - # * push something to your PR branch (note that just re-running the pipeline disregards the title update) - - name: live debug session on failure (manual steps required, check `.github/neuron-ci.yml`) - if: failure() && contains(github.event.pull_request.title, 'live-debug-ci') - uses: mxschmitt/action-tmate@v3 - - # see https://github.com/orgs/community/discussions/26822 - final: - name: Final CI - needs: [ci] - if: ${{ always() }} - runs-on: ubuntu-latest - steps: - - name: Check ci matrix all done - if: >- - ${{ - contains(needs.*.result, 'failure') - || contains(needs.*.result, 'cancelled') - || contains(needs.*.result, 'skipped') - }} - run: exit 1 diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml deleted file mode 100644 index 3ba15345b3..0000000000 --- a/.github/workflows/release.yml +++ /dev/null @@ -1,91 +0,0 @@ -name: NEURON Release - -on: - workflow_dispatch: - inputs: - rel_branch: - description: 'Release branch/commit' - default: 'release/x.y' - required: true - rel_tag: - description: 'Release version (tag name)' - default: 'x.y.z' - required: true - -env: - GH_REPO: ${{ github.server_url }}/${{ github.repository }} - REL_TAG: ${{ github.event.inputs.rel_tag }} - REL_BRANCH: ${{ github.event.inputs.rel_branch }} - -jobs: - tag-n-release: - runs-on: ubuntu-latest - name: tag-n-release ${{ github.event.inputs.rel_tag }} (${{ github.event.inputs.rel_branch }}) - outputs: - release_url: ${{ steps.create_release.outputs.upload_url }} - rel_tag: ${{ env.REL_TAG }} - steps: - - uses: actions/checkout@v4 - name: Checkout branch ${{ env.REL_BRANCH }} - with: - ref: ${{ env.REL_BRANCH }} - - - name: Create and upload tag ${{ env.REL_TAG }} - run: | - git config user.name github-actions - git config user.email github-actions@github.com - git tag -a $REL_TAG -m "${REL_TAG}" - git push origin $REL_TAG - env: - GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} - working-directory: ${{runner.workspace}}/nrn - - - name: Create Release - id: create_release - uses: ncipollo/release-action@v1 - env: - GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} - with: - tag: ${{ env.REL_TAG }} - name: Release ${{ env.REL_TAG }} - prerelease: true - - nrn-full-src-package: - runs-on: ubuntu-latest - needs: tag-n-release - steps: - - name: Checkout feature-rich code - run: | - git clone --depth=1 --shallow-submodules --recurse-submodules $GH_REPO -b $REL_TAG --single-branch - cd nrn - LOCAL_TAG=`git tag` - if [ $REL_TAG != $LOCAL_TAG ]; then - echo "Wrong tag downloaded!" - exit 1 - else - git log --oneline - fi - - - name: Make nrnversion.h - run: | - mkdir build && cd build - cmake -DNRN_ENABLE_PYTHON=OFF -DNRN_ENABLE_RX3D=OFF -DNRN_ENABLE_MPI=OFF -DNRN_ENABLE_INTERVIEWS=OFF ../nrn - make nrnversion_h VERBOSE=1 - - - name: Create nrn-full-src-package - id: tar - run: | - tar -czvf nrn-full-src-package-${REL_TAG}.tar.gz nrn - echo "asset_file=nrn-full-src-package-${REL_TAG}.tar.gz" >> $GITHUB_OUTPUT - - - name: Upload nrn-full-src-package to release - run: | - gh release upload ${{ needs.tag-n-release.outputs.rel_tag }} ${{ steps.tar.outputs.asset_file }} - env: - GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} - - windows-installer: - needs: tag-n-release - uses: neuronsimulator/nrn/.github/workflows/windows.yml@master - with: - tag: ${{ needs.tag-n-release.outputs.rel_tag }} diff --git a/azure-pipelines.yml b/azure-pipelines.yml deleted file mode 100644 index b7dd958f4a..0000000000 --- a/azure-pipelines.yml +++ /dev/null @@ -1,179 +0,0 @@ -#============================================================================= -# Azure Pipeline settings -#============================================================================= - -# Nightly build master for pypi upload -schedules: -- cron: "0 0 * * *" - branches: - include: - - master - always: true - -# Auto cancel old PR builds -pr: - autoCancel: true -# TODO : https://github.com/neuronsimulator/nrn/issues/1063 -# paths: -# exclude: -# - docs -# - README.md - -# Trigger build for certain branches only -trigger: -- master -- release/* - -stages: - - stage: BuildTestDeploy - jobs: - - - job: 'ManyLinuxWheels' - timeoutInMinutes: 45 - pool: - vmImage: 'ubuntu-20.04' - strategy: - matrix: - Python38: - python.version: '3.8' - Python39: - python.version: '3.9' - Python310: - python.version: '3.10' - Python311: - python.version: '3.11' - Python312: - python.version: '3.12' - steps: - - # Secure files documentation: - # https://docs.microsoft.com/en-us/azure/devops/pipelines/library/secure-files?view=azure-devops - # NOTE: when uploading new secure files, access must be permitted from the Azure pipeline interface (check message there) - - task: DownloadSecureFile@1 - name: mpt_headersSF - displayName: 'Download mpt_headers secure file' - inputs: - secureFile: 'mpt_headears.2.21.tar.gz' - - # Note that mpt headers must be mounted in the docker imager under `/nrnwheel/mpt` - # This path is checked by `packaging/python/build_wheels.bash` when run in the image. - - script: | - sudo mkdir -p /opt/nrnwheel/mpt - sudo tar -zxf $(mpt_headersSF.secureFilePath) --directory /opt/nrnwheel/mpt - docker run --rm \ - -w /root/nrn \ - -v $PWD:/root/nrn \ - -v /opt/nrnwheel/mpt:/nrnwheel/mpt \ - -e NEURON_NIGHTLY_TAG \ - -e NRN_NIGHTLY_UPLOAD \ - -e NRN_RELEASE_UPLOAD \ - -e SETUPTOOLS_SCM_PRETEND_VERSION \ - -e NRN_BUILD_FOR_UPLOAD=1 \ - 'neuronsimulator/neuron_wheel:latest-x86_64' \ - packaging/python/build_wheels.bash linux $(python.version) coreneuron - displayName: 'Building ManyLinux Wheel' - - - script: | - sudo apt update - sudo apt install -y mpich openmpi-bin libopenmpi-dev libmpich-dev - displayName: 'Install Test System Depdendencies' - - - template: ci/azure-wheel-test-upload.yml - - - # Jobs to build OSX wheels natively - - job: 'MacOSWheels' - timeoutInMinutes: 60 - pool: - vmImage: 'macOS-12' - strategy: - matrix: - Python38: - python.version: '3.8' - python.org.version: '3.8.9' - python.installer.name: 'macosx10.9.pkg' - Python39: - python.version: '3.9' - python.org.version: '3.9.13' - python.installer.name: 'macos11.pkg' - Python310: - python.version: '3.10' - python.org.version: '3.10.11' - python.installer.name: 'macos11.pkg' - Python311: - python.version: '3.11' - python.org.version: '3.11.7' - python.installer.name: 'macos11.pkg' - Python312: - python.version: '3.12' - python.org.version: '3.12.0' - python.installer.name: 'macos11.pkg' - - steps: - - - script: | - installer=python-$(python.org.version)-$(python.installer.name) - url=https://www.python.org/ftp/python/$(python.org.version)/$installer - curl $url -o $installer - sudo installer -pkg $installer -target / - displayName: 'Install Python from python.org' - - - script: | - brew install --cask xquartz - brew install flex bison mpich - brew unlink mpich && brew install openmpi - cmake --version - # see https://github.com/BlueBrain/CoreNeuron/issues/817, uninstall libomp until we fix this - # as we are building wheels, we shouldn't enable OpenMP here anyway - brew uninstall --ignore-dependencies libomp || echo "libomp doesn't exist" - displayName: 'Install OSX System Dependencies' - - # readline has been manually built with ncurses and MACOSX_DEPLOYMENT_TARGET=10.9 and stored as secure file on Azure. - # See `packaging/python/Dockerfile` for build instructions. - # - # Secure files documentation: - # https://docs.microsoft.com/en-us/azure/devops/pipelines/library/secure-files?view=azure-devops - # NOTE: when uploading new secure files, access must be permitted from the Azure pipeline interface (check message there) - - task: DownloadSecureFile@1 - name: readlineSF - displayName: 'Download readline secure file' - inputs: - secureFile: 'readline7.0-ncurses6.4.tar.gz' - - # 10.14 is required for full C++17 support according to - # https://cibuildwheel.readthedocs.io/en/stable/cpp_standards, but it - # seems that 10.15 is actually needed for std::filesystem::path. - - script: | - export MACOSX_DEPLOYMENT_TARGET=10.15 - export PATH=/usr/local/opt/flex/bin:/usr/local/opt/bison/bin:$PATH - export SDKROOT=$(xcrun --sdk macosx --show-sdk-path) - export NRN_BUILD_FOR_UPLOAD=1 - sudo mkdir /opt/nrnwheel - sudo tar -zxf $(readlineSF.secureFilePath) --directory /opt/nrnwheel/ - packaging/python/build_wheels.bash osx $(python.version) coreneuron - displayName: 'Build MacOS Wheel' - - - template: ci/azure-wheel-test-upload.yml - - - - stage: Final - jobs: - - job: AzureDropURL - pool: - vmImage: 'ubuntu-20.04' - condition: eq(variables['Build.Reason'], 'PullRequest') - steps: - - checkout: none - - script: | - export AZURE_DROP_URL=`curl -v 'https://dev.azure.com/neuronsimulator/nrn/_apis/build/builds/$(Build.BuildId)/artifacts?artifactName=drop' | jq -r '.resource.downloadUrl'` - echo "Setting dropurl to $AZURE_DROP_URL" - echo "##vso[task.setvariable variable=dropurl]$AZURE_DROP_URL" - displayName: 'Resolve Azure drop URL' - - - task: GitHubComment@0 - continueOnError: true - inputs: - gitHubConnection: 'neuronsimulator' - repositoryName: '$(Build.Repository.Name)' - comment: | - ✔️ $(system.pullRequest.sourceCommitId) -> [Azure artifacts URL]($(dropurl))