run-tests.yml

name: Tests

on:
  workflow_dispatch:
  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-2022
          - windows-latest
          - ubuntu-latest
          - macos-latest  # M1 architecture
          - macos-15-intel  # non-M1 architecture
        python:
          - '3.10'  # Needs quotes so YAML doesn't think it's 3.1
          - '3.11'
          - '3.12'
          - '3.13'
        mode:
          - normal
        vendored_dandiapi:
          # Allow vendor information for the dandi-api instance to default to
          #   the default values specified in
          #   dandi/tests/data/dandiarchive-docker/docker-compose.yml
          - default
        include:
          - os: ubuntu-latest
            python: '3.10'
            mode: dandi-api
          - os: ubuntu-latest
            python: '3.10'
            mode: dandi-api
            vendored_dandiapi: ember-dandi
            instance_name: EMBER-DANDI
            instance_identifier: 'RRID:SCR_026700'
            doi_prefix: '10.82754'
          - os: ubuntu-latest
            python: 3.13
            mode: obolibrary-only
          - os: ubuntu-latest
            python: '3.10'
            mode: dev-deps
          - os: ubuntu-latest
            python: 3.13
            mode: dev-deps
          - os: ubuntu-latest
            python: '3.10'
            mode: nfs

    steps:
    - name: Set up environment
      uses: actions/checkout@v6
      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@v6
      with:
        python-version: ${{ matrix.python }}

    - name: Install dependencies
      run: |
        python -m pip install --upgrade pip wheel
        pip install ".[extras,test]"

    # Set only if matrix.instance_name is defined
    - name: Set DANDI_TESTS_INSTANCE_NAME
      if: ${{ matrix.instance_name }}
      run: echo "DANDI_TESTS_INSTANCE_NAME=${{ matrix.instance_name }}" >> "$GITHUB_ENV"

    # Set only if matrix.instance_identifier is defined
    - name: Set DANDI_TESTS_INSTANCE_IDENTIFIER
      if: ${{ matrix.instance_identifier }}
      run: echo "DANDI_TESTS_INSTANCE_IDENTIFIER=${{ matrix.instance_identifier }}" >> "$GITHUB_ENV"

    # Set only if matrix.doi_prefix is defined
    - name: Set DANDI_TESTS_DOI_PREFIX
      if: ${{ matrix.doi_prefix }}
      run: echo "DANDI_TESTS_DOI_PREFIX=${{ matrix.doi_prefix }}" >> "$GITHUB_ENV"

    - 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 \
            git+https://github.com/hdmf-dev/hdmf \
            git+https://github.com/hdmf-dev/hdmf-zarr

    - 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 except those involving obolibrary
      if: matrix.mode != 'dandi-api' && matrix.mode != 'obolibrary-only'
      run: |
        python -m pytest -s -v -m "not obolibrary" --cov=dandi --cov-report=xml dandi

    - name: Run only tests related to obolibrary
      if: matrix.mode == 'obolibrary-only'
      run: |
        python -m pytest -s -v -m obolibrary 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@v6
      with:
        token: ${{ secrets.CODECOV_TOKEN }}
        files: ./coverage.xml
        flags: unittests
        # name: codecov-umbrella
        # yml: ./codecov.yml
        fail_ci_if_error: false