feat: add new covid_symptom__nlp_results_term_exists task #810
Workflow file for this run
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name: CI | |
on: | |
pull_request: | |
push: | |
branches: | |
- main | |
paths-ignore: | |
- 'docs/**' | |
- '*.md' | |
# The goal here is to cancel older workflows when a PR is updated (because it's pointless work) | |
concurrency: | |
group: ${{ github.workflow }}-${{ github.head_ref || github.ref_name }} | |
cancel-in-progress: true | |
jobs: | |
unittest: | |
name: unit tests | |
runs-on: ubuntu-22.04 | |
strategy: | |
matrix: | |
# while we are still private, don't go crazy with the Python versions as they eat up CI minutes | |
python-version: ["3.10"] | |
steps: | |
- uses: actions/checkout@v3 | |
- name: Set up Python ${{ matrix.python-version }} | |
uses: actions/setup-python@v4 | |
with: | |
python-version: ${{ matrix.python-version }} | |
- name: Install dependencies | |
run: | | |
python -m pip install --upgrade pip | |
pip install pytest | |
pip install .[tests] | |
- name: Check out MS tool | |
uses: actions/checkout@v3 | |
with: | |
repository: microsoft/Tools-for-Health-Data-Anonymization | |
path: mstool | |
- name: Build MS tool | |
run: | | |
sudo apt-get update | |
sudo apt-get install dotnet6 | |
dotnet publish \ | |
--runtime=linux-x64 \ | |
--configuration=Release \ | |
-p:PublishSingleFile=true \ | |
--output=$HOME/.local/bin \ | |
mstool/FHIR/src/Microsoft.Health.Fhir.Anonymizer.R4.CommandLineTool | |
- name: Test with pytest | |
run: | | |
python -m pytest | |
lint: | |
runs-on: ubuntu-22.04 | |
steps: | |
- uses: actions/checkout@v3 | |
- name: Install linters | |
# black is synced with the .pre-commit-hooks version | |
run: | | |
python -m pip install --upgrade pip | |
pip install bandit[toml] pycodestyle pylint black==22.12.0 | |
- name: Run pycodestyle | |
run: | | |
pycodestyle --max-line-length=120 . | |
- name: Run pylint | |
if: success() || failure() # still run pylint if above checks fail | |
run: | | |
pylint cumulus_etl tests | |
- name: Run bandit | |
if: success() || failure() # still run bandit if above checks fail | |
run: | | |
bandit -c pyproject.toml -r . | |
- name: Run black | |
if: success() || failure() # still run black if above checks fails | |
run: | | |
black --check --verbose --line-length 120 . |