Convert example into a (smoke) doctest #73
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| name: Test | |
| on: | |
| pull_request: | |
| push: | |
| schedule: | |
| - cron: '0 6 * * *' | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.event_name }}-${{ github.ref_name }} | |
| cancel-in-progress: true | |
| defaults: | |
| run: | |
| # Use an interactive shell so that ~/.bashrc is sourced: | |
| shell: 'bash -eio pipefail {0}' | |
| env: | |
| # Note, that there's "turtle" as well, which is always excluded from running. | |
| PYTEST_SELECTION: "integration or usecase or slow or network" | |
| PYTEST_SELECTION_OP: "not " # so it would be "not (integration or usecase)" | |
| DATALAD_TESTS_SSH: "1" | |
| DATALAD_LOG_ENV: GIT_SSH_COMMAND | |
| # How/which git-annex we install. conda's build would be the fastest, | |
| # but it must not get ahead in PATH to not shadow travis' python | |
| _DL_ANNEX_INSTALL_SCENARIO: "miniconda=py37_23.1.0-1 --python-match minor --batch git-annex=8.20201007 -m conda" | |
| BOTO_CONFIG: /tmp/nowhere | |
| DATALAD_DATASETS_TOPURL: https://datasets-tests.datalad.org | |
| jobs: | |
| filter: | |
| runs-on: ubuntu-latest | |
| outputs: | |
| jobs: ${{ steps.jobs.outputs.matrix }} | |
| steps: | |
| - name: Check out repository | |
| uses: actions/checkout@v4 | |
| - name: Possibly filter out cron-only jobs | |
| id: jobs | |
| run: | | |
| echo 'matrix<<EOT' >> "$GITHUB_OUTPUT" | |
| if [ "${{ github.event_name == 'schedule' }}" = true ] | |
| then | |
| yq '{"include": .} | to_json' tools/ci/test-jobs.yml >> "$GITHUB_OUTPUT" | |
| else | |
| yq '{"include": [.[] | select(."cron-only" != true)]} | to_json' tools/ci/test-jobs.yml >> "$GITHUB_OUTPUT" | |
| fi | |
| echo 'EOT' >> "$GITHUB_OUTPUT" | |
| test: | |
| runs-on: ubuntu-latest | |
| needs: filter | |
| strategy: | |
| fail-fast: false | |
| matrix: ${{ fromJson(needs.filter.outputs.jobs) }} | |
| env: ${{ matrix.extra-envs }} | |
| continue-on-error: ${{ matrix.allow-failure || false }} | |
| steps: | |
| - name: Check out repository | |
| uses: actions/checkout@v4 | |
| with: | |
| # Do full clone (~10 extra seconds) to fetch all tags. | |
| # Otherwise we might be missing the tags for maint PRs | |
| # whenever those maint releases were not yet merged into master. | |
| fetch-depth: 0 | |
| - name: Set up Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Show git describe output to ensure that we did fetch all the tags | |
| run: git describe | |
| # Just in case we need to check if nfs is there etc | |
| - run: sudo lsmod | |
| - name: Install dependencies | |
| run: | | |
| # The ultimate one-liner setup for NeuroDebian repository | |
| bash <(wget -q -O- http://neuro.debian.net/_files/neurodebian-travis.sh) | |
| sudo apt-get update -qq | |
| sudo apt-get install eatmydata # to speedup some installations | |
| tools/ci/prep-travis-forssh.sh | |
| tools/ci/debians_disable_outdated_ssl_cert | |
| # Install various basic dependencies | |
| sudo eatmydata apt-get install zip pandoc p7zip-full | |
| # needed for tests of patool compression fall-back solution | |
| sudo eatmydata apt-get install xz-utils | |
| sudo eatmydata apt-get install shunit2 | |
| [ -z "$LC_ALL" ] || sudo eatmydata apt-get install locales-all | |
| - name: Configure _DL_TMPDIR before installing git-annex | |
| run: | | |
| if [[ "${_DL_TMPDIR:-}" =~ .*/sym\ link ]] | |
| then echo "Symlinking $_DL_TMPDIR" | |
| ln -s /tmp "$_DL_TMPDIR" | |
| fi | |
| if [[ "${_DL_TMPDIR:-}" =~ .*/d\ i\ r ]] | |
| then echo "mkdir $_DL_TMPDIR" | |
| mkdir -p "$_DL_TMPDIR" | |
| fi | |
| if [[ "${_DL_TMPDIR:-}" =~ .*/nfsmount ]] | |
| then echo "mkdir $_DL_TMPDIR" | |
| mkdir -p "$_DL_TMPDIR" "${_DL_TMPDIR}_" | |
| echo "/tmp/nfsmount_ localhost(rw)" | sudo bash -c 'cat - > /etc/exports' | |
| sudo apt-get install -y nfs-kernel-server | |
| sudo exportfs -a | |
| sudo mount -t nfs localhost:/tmp/nfsmount_ /tmp/nfsmount | |
| fi | |
| - name: Install custom Git from upstream | |
| if: matrix.upstream-git | |
| run: | | |
| sudo apt-get install -y gettext libcurl4-gnutls-dev | |
| source tools/ci/install-upstream-git.sh | |
| echo "$target_dir/bin-wrappers" >> "$GITHUB_PATH" | |
| - name: Install minimum Git | |
| if: matrix.minimum-git | |
| run: | | |
| sudo apt-get install -y gettext libcurl4-gnutls-dev | |
| tools/ci/install-minimum-git.sh | |
| echo "$PWD/git-src/bin-wrappers" >> "$GITHUB_PATH" | |
| - name: Install git-annex | |
| run: | | |
| pip install datalad-installer | |
| eval datalad-installer --sudo ok -E new.env ${_DL_ANNEX_INSTALL_SCENARIO} | |
| # Append new.env to ~/.bashrc instead of $GITHUB_OUTPUT because it | |
| # can include `source` and `conda activate` commands that are invalid | |
| # for the latter; this also necessitates using an interactive shell | |
| # for the workflow. | |
| cat new.env >> ~/.bashrc | |
| - name: Install Python dependencies | |
| run: | | |
| pip install --upgrade pip | |
| pip install codecov | |
| pip install -r requirements-devel.txt | |
| - name: Configure Git | |
| run: | | |
| git config --global user.email "[email protected]" | |
| git config --global user.name "GitHub Almighty" | |
| # We do `sudo pip install` below, and versioneer needs to run git. | |
| # Recent git needs to be made certain it is safe to do | |
| sudo git config --global --add safe.directory $PWD | |
| - name: Configure sudoers | |
| # So we could test under sudo -E with PATH pointing to installed | |
| # location | |
| run: sudo sed -i -e 's/^Defaults.*secure_path.*$//' /etc/sudoers | |
| # TODO: remove - should not be needed | |
| - name: Git-annex workaround for NFS mounts | |
| run: | | |
| if [[ "${_DL_TMPDIR:-}" =~ .*/nfsmount ]] | |
| then sudo git config --system annex.pidlock true | |
| fi | |
| # Now it should be safe to point TMPDIR to a "tricky" setup just for the | |
| # purpose of testing | |
| - name: Point TMPDIR to "tricky" setup | |
| run: | | |
| if [ -n "${_DL_TMPDIR:-}" ] | |
| then echo TMPDIR="${_DL_TMPDIR}" >> "$GITHUB_ENV" | |
| fi | |
| - name: Test installation for user | |
| run: sudo pip install --user . | |
| - name: Report WTF information using system-wide installed version | |
| run: | | |
| datalad wtf | |
| python -m pip freeze | |
| - name: Run tests | |
| run: | | |
| PYTEST_OPTS=( -v ) | |
| # If we requested to run only not slow (typically <10sec) tests, fail | |
| # if a test takes 3x more than that - it needs to get @slow or | |
| # @turtle annotation | |
| if echo "$PYTEST_SELECTION_OP($PYTEST_SELECTION)" | grep -q "^not.*slow" | |
| then | |
| PYTEST_OPTS=( "${PYTEST_OPTS[@]}" --doctest-modules --durations=0 --durations-min=5 --fail-slow 60 ) | |
| export DATALAD_TESTS_SETUP_TESTREPOS=1 | |
| fi | |
| mkdir -p __testhome__ | |
| cd __testhome__ | |
| # Note: adding --log-cli-level=INFO would result in | |
| # DATALAD_LOG_TARGET=/dev/null being not in effect, dumping too many | |
| # logs. | |
| set -x | |
| http_proxy= | |
| PATH=$PWD/../tools/coverage-bin:$PATH | |
| $PYTEST_WRAPPER python \ | |
| -m pytest "${PYTEST_OPTS[@]}" \ | |
| -c ../tox.ini \ | |
| -n 2 \ | |
| -m "${PYTEST_SELECTION:+$PYTEST_SELECTION_OP($PYTEST_SELECTION) and }not(turtle)" \ | |
| --doctest-modules \ | |
| --cov=datalad \ | |
| --cov-report=xml \ | |
| --pyargs ${TESTS_TO_PERFORM:-datalad} | |
| # Makes it only more difficult to comprehend the failing output. Enable | |
| # only when necessary for a particular debugging. | |
| - name: Dump debug info | |
| #if: "failure()" # Enabled | |
| if: "failure() && false" # Disabled | |
| run: | | |
| if [ ! -z "$DATALAD_TESTS_NONETWORK" ] | |
| then sudo route add -net 0.0.0.0 netmask 0.0.0.0 dev lo | |
| fi | |
| DATALAD_LOG_LEVEL=DEBUG \ | |
| $PYTEST_WRAPPER `which pytest` \ | |
| -s -v --doctest-modules --cov datalad --log-cli-level=DEBUG | |
| if [ ! -z "$DATALAD_TESTS_NONETWORK" ] | |
| then sudo route del -net 0.0.0.0 netmask 0.0.0.0 dev lo | |
| fi | |
| # cron jobs test more and then PRs will be falling behind since they | |
| # would not trigger some codepaths. So submit coverage only from | |
| # non-cron jobs, but report for all | |
| - name: Report coverage | |
| run: | | |
| python -m coverage debug sys | |
| python -m coverage report | |
| working-directory: __testhome__ | |
| - name: Upload coverage to Codecov | |
| if: github.event_name != 'schedule' | |
| uses: codecov/codecov-action@v5 | |
| with: | |
| directory: __testhome__ | |
| fail_ci_if_error: false | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| # vim:set et sts=2: |