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Merge pull request #58 from NeurodataWithoutBorders/fix_docs_image #93

Merge pull request #58 from NeurodataWithoutBorders/fix_docs_image

Merge pull request #58 from NeurodataWithoutBorders/fix_docs_image #93

Workflow file for this run

name: Run tests
on:
push:
branches:
- main
pull_request:
branches:
- main
workflow_dispatch:
jobs:
test:
defaults:
run:
shell: bash
concurrency:
group: ${{ github.workflow }}-${{ github.ref }}-${{ matrix.os }}
cancel-in-progress: true
strategy:
fail-fast: false
matrix:
os: [macos-latest, ubuntu-latest]
runs-on: ${{ matrix.os }}
steps:
- name: Checkout repository
uses: actions/checkout@v4
- name: Install dependencies - ubuntu
if: matrix.os == 'ubuntu-latest'
run: |
sudo apt-get update
sudo apt-get install -y libhdf5-dev libboost-all-dev
git clone https://github.com/catchorg/Catch2.git
cd Catch2
git checkout "v3.5.3"
cmake -Bbuild -H. -DBUILD_TESTING=OFF
sudo cmake --build build/ --target install
- name: Install dependencies - macos
if: matrix.os == 'macos-latest'
run: brew install hdf5 boost catch2
- name: Configure
shell: pwsh
run: cmake "--preset=ci-$("${{ matrix.os }}".split("-")[0])"
- name: Build
run: cmake --build build --config Release -j 2
- name: Install
run: cmake --install build --config Release --prefix prefix
- name: Test
working-directory: build
run: ctest --output-on-failure --no-tests=error -C Release -j 2
- name: Upload artifacts
uses: actions/upload-artifact@v3
with:
name: test-files-${{ matrix.os }}
path: |
build/tests/data/*.nwb
sanitize:
needs: test
runs-on: ubuntu-latest
steps:
- name: Checkout repository
uses: actions/checkout@v4
- name: Install dependencies
run: |
sudo apt-get update
sudo apt-get install -y libhdf5-dev libboost-all-dev
git clone https://github.com/catchorg/Catch2.git
cd Catch2
git checkout "v3.5.3"
cmake -Bbuild -H. -DBUILD_TESTING=OFF
sudo cmake --build build/ --target install
- name: Configure
run: cmake --preset=ci-sanitize
- name: Build
run: cmake --build build/sanitize -j 2
- name: Test
working-directory: build/sanitize
env:
ASAN_OPTIONS: "strict_string_checks=1:\
detect_stack_use_after_return=1:\
check_initialization_order=1:\
strict_init_order=1:\
detect_leaks=1:\
halt_on_error=1"
UBSAN_OPTIONS: "print_stacktrace=1:\
halt_on_error=1"
run: ctest --output-on-failure --no-tests=error -j 2
validate:
needs: [test, sanitize]
defaults:
run:
shell: bash
concurrency:
group: ${{ github.workflow }}-${{ github.ref }}-${{ matrix.os }}
cancel-in-progress: true
strategy:
fail-fast: false
matrix:
os: [macos-latest, ubuntu-latest]
runs-on: ${{ matrix.os }}
steps:
- name: Download test files
uses: actions/download-artifact@v3
with:
name: test-files-${{ matrix.os }}
path: nwb_files
- name: Set up Python
uses: actions/setup-python@v5
with:
python-version: '3.12'
- name: Install pynwb and run validation
run: |
python -m pip install --upgrade pip
python -m pip install nwbinspector
nwbinspector nwb_files --threshold BEST_PRACTICE_VIOLATION