ticket/PSB-173: Create allensdk_anaconda3 image in Pika dockerhub. Modify Bamboo script #2079
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| name: ci/github-actions | |
| on: | |
| push: | |
| branches: | |
| - master | |
| pull_request: | |
| env: | |
| TEST_NWB_FILES: skip | |
| TEST_OBSERVATORY_EXPERIMENT_PLOTS_DATA: skip | |
| TEST_API_ENDPOINT: http://api.brain-map.org | |
| TEST_COMPLETE: false | |
| TEST_BAMBOO: false | |
| LIMS_DBNAME: db | |
| LIMS_PORT: 1234 | |
| LIMS_PASSWORD: password | |
| LIMS_HOST: host | |
| LIMS_USER: user | |
| MTRAIN_DBNAME: db | |
| MTRAIN_USER: user | |
| MTRAIN_HOST: host | |
| MTRAIN_PORT: 1234 | |
| MTRAIN_PASSWORD: password | |
| jobs: | |
| lint: | |
| name: Lint | |
| runs-on: "ubuntu-latest" | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: flake8 linting | |
| run: | | |
| pip install flake8 | |
| export PATH="/home/runner/.local/bin:${PATH}" | |
| git fetch origin master | |
| # `|| true` to force exit code 0 even if no files found | |
| CHANGED_PYFILES=$(git diff --name-only --diff-filter AM origin/master allensdk | grep -e ".*.py$" || true) | |
| echo "List of changed files:" | |
| echo ${CHANGED_PYFILES} | |
| flake8 ${CHANGED_PYFILES} --count | |
| allensdk: | |
| name: ${{ matrix.python-version }}, ${{ matrix.os }} | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| matrix: | |
| os: ["macos-latest", "windows-latest", "ubuntu-latest"] | |
| python-version: ["3.7", "3.8", "3.9"] | |
| fail-fast: false | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| auto-update-conda: true | |
| python-version: ${{ matrix.python-version }} | |
| activate-environment: test-env | |
| - name: Install | |
| run: | | |
| conda activate test-env | |
| pip install codecov | |
| pip install -r test_requirements.txt | |
| pip install . | |
| - name: Test | |
| run: | | |
| py.test --cov=allensdk -n 4 | |
| onprem: | |
| name: python ${{ matrix.image }} on-prem test | |
| runs-on: ["self-hosted"] | |
| strategy: | |
| matrix: | |
| image: ["allensdk_local_py38:latest"] | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: run test in docker | |
| run: | | |
| docker run \ | |
| --env-file /home/github_worker/env.list \ | |
| --mount type=bind,source=$PWD,target=/home/ghworker,bind-propagation=rshared \ | |
| --mount type=bind,source=/data/informatics/module_test_data/,target=/data/informatics/module_test_data/,bind-propagation=rshared,ro \ | |
| --mount type=bind,source=/allen/,target=/allen/,bind-propagation=rshared,ro \ | |
| --mount type=tmpfs,destination=/tmp \ | |
| --rm \ | |
| ${{ matrix.image }} \ | |
| /bin/bash -c "pip install -r requirements.txt; \ | |
| pip install -r test_requirements.txt; \ | |
| python -m pytest \ | |
| --log-level=INFO \ | |
| --capture=no \ | |
| --cov=allensdk \ | |
| --cov-config coveragerc \ | |
| --cov-report html \ | |
| --junitxml=test-reports/test.xml \ | |
| --boxed \ | |
| --numprocesses auto \ | |
| --durations=0" |