ENH: organize - show files with conflicts requiring adding _obj- #5789
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| name: Tests | |
| on: | |
| push: | |
| branches: | |
| - master | |
| pull_request: | |
| schedule: | |
| - cron: '0 6 * * *' | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.event_name }}-${{ github.ref_name }} | |
| cancel-in-progress: true | |
| defaults: | |
| run: | |
| shell: bash | |
| jobs: | |
| test: | |
| runs-on: ${{ matrix.os }} | |
| env: | |
| NO_ET: 1 | |
| DANDI_ALLOW_LOCALHOST_URLS: "1" | |
| DANDI_PAGINATION_DISABLE_FALLBACK: "1" | |
| DANDI_TESTS_PERSIST_DOCKER_COMPOSE: "1" | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: | |
| - windows-2019 | |
| - ubuntu-latest | |
| - macos-latest | |
| python: | |
| - 3.8 | |
| - 3.9 | |
| - '3.10' # Needs quotes so YAML doesn't think it's 3.1 | |
| - '3.11' | |
| - '3.12' | |
| mode: | |
| - normal | |
| include: | |
| - os: ubuntu-latest | |
| python: 3.8 | |
| mode: dandi-api | |
| - os: ubuntu-latest | |
| python: 3.8 | |
| mode: dev-deps | |
| - os: ubuntu-latest | |
| python: 3.8 | |
| mode: nfs | |
| steps: | |
| - name: Set up environment | |
| uses: actions/checkout@v4 | |
| with: | |
| # Fetch all commits so that versioneer will return something compatible | |
| # with semantic-version | |
| fetch-depth: 0 | |
| - name: Set up Python ${{ matrix.python }} | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python }} | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip wheel | |
| pip install ".[extras,test]" | |
| - name: Install dev versions of select dependencies | |
| if: matrix.mode == 'dev-deps' | |
| run: | | |
| pip install git+https://github.com/jaraco/keyring | |
| pip install git+https://github.com/NeurodataWithoutBorders/nwbinspector | |
| pip install git+https://github.com/NeurodataWithoutBorders/pynwb | |
| pip install git+https://github.com/hdmf-dev/hdmf | |
| - name: Create NFS filesystem | |
| if: matrix.mode == 'nfs' | |
| run: | | |
| mkdir /tmp/nfsmount_ /tmp/nfsmount | |
| mkdir /tmp/nfsmount_/tmp /tmp/nfsmount_/home | |
| echo "/tmp/nfsmount_ localhost(rw)" | sudo tee /etc/exports | |
| sudo apt-get install -y nfs-kernel-server | |
| sudo exportfs -a | |
| sudo mount -t nfs localhost:/tmp/nfsmount_ /tmp/nfsmount | |
| echo TMPDIR=/tmp/nfsmount/tmp >> "$GITHUB_ENV" | |
| echo HOME=/tmp/nfsmount/home >> "$GITHUB_ENV" | |
| echo DANDI_DEVEL_INSTRUMENT_REQUESTS_SUPERLEN=1 >> "$GITHUB_ENV" | |
| - name: Use scheduled test configuration | |
| if: github.event_name == 'schedule' | |
| run: echo PYTEST_ADDOPTS=--scheduled >> "$GITHUB_ENV" | |
| - name: Run all tests | |
| if: matrix.mode != 'dandi-api' | |
| run: | | |
| python -m pytest -s -v --cov=dandi --cov-report=xml dandi | |
| - name: Smoke test example code in docs | |
| if: matrix.mode != 'dandi-api' && github.event_name == 'schedule' | |
| run: | | |
| set -ex | |
| cd docs/source/examples | |
| for f in *.py | |
| do python "$f" | |
| done | |
| - name: Run Dandi API tests only | |
| if: matrix.mode == 'dandi-api' | |
| run: | | |
| export DANDI_TESTS_AUDIT_CSV=/tmp/audit.csv | |
| python -m pytest -s -v --cov=dandi --cov-report=xml --dandi-api dandi | |
| if [ ! -e /tmp/audit.csv ] | |
| then echo Audit file not created | |
| exit 1 | |
| fi | |
| lines="$(wc -l /tmp/audit.csv | awk '{print $1}')" | |
| if [ "$lines" -lt 100 ] | |
| then echo Audit file shorter than expected - only "$lines" lines | |
| exit 1 | |
| fi | |
| - name: Dump Docker Compose logs | |
| if: failure() && startsWith(matrix.os, 'ubuntu') | |
| run: | | |
| docker compose \ | |
| -f dandi/tests/data/dandiarchive-docker/docker-compose.yml \ | |
| logs --timestamps | |
| - name: Shut down Docker Compose | |
| if: startsWith(matrix.os, 'ubuntu') | |
| run: | | |
| docker compose \ | |
| -f dandi/tests/data/dandiarchive-docker/docker-compose.yml \ | |
| down -v | |
| - name: Upload coverage to Codecov | |
| uses: codecov/codecov-action@v4 | |
| with: | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| file: ./coverage.xml | |
| flags: unittests | |
| # name: codecov-umbrella | |
| # yml: ./codecov.yml | |
| fail_ci_if_error: false |