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Tests

Tests #5790

Workflow file for this run

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