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main-ci.yml
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name: CI
on: [push]
jobs:
Lint:
runs-on: ubuntu-latest
steps:
- name: Checkout repository
uses: actions/checkout@v4
with:
lfs: 'true'
- name: Set up Python 3.12
uses: actions/setup-python@v5
with:
python-version: "3.12"
cache: "pipenv"
cache-dependency-path: |
Pipfile.lock
- name: Install pipenv and deps
run: |
python -m pip install --upgrade pipenv wheel
make deps
- name: Lint source code
run: make lint
Unit-Test:
runs-on: ubuntu-latest
needs:
- Lint
steps:
- name: Checkout repository
uses: actions/checkout@v4
with:
lfs: 'true'
- name: Set up Python 3.12
uses: actions/setup-python@v5
with:
python-version: "3.12"
cache: "pipenv"
cache-dependency-path: |
Pipfile.lock
- name: Install pipenv and deps
run: |
python -m pip install --upgrade pipenv wheel
make deps
- name: Install dependencies
run: make deps
- name: Run tests
run: make ci-unit-test
- name: Upload coverage reports to Codecov
uses: codecov/[email protected]
with:
flags: main
token: ${{ secrets.CODECOV_TOKEN }}
slug: bihealth/auto-acmg
End2End-Test:
runs-on: ubuntu-latest
needs:
- Lint
steps:
- name: Checkout repository
uses: actions/checkout@v4
with:
lfs: 'true'
- name: Set up Python 3.12
uses: actions/setup-python@v5
with:
python-version: "3.12"
cache: "pipenv"
cache-dependency-path: |
Pipfile.lock
- name: Install pipenv and deps
run: |
python -m pip install --upgrade pipenv wheel
make deps
- name: Install dependencies
run: make deps
- name: Run tests
run: make ci-e2e-test
- name: Upload coverage reports to Codecov
uses: codecov/[email protected]
with:
flags: e2e
token: ${{ secrets.CODECOV_TOKEN }}
slug: bihealth/auto-acmg
Docs:
runs-on: ubuntu-latest
steps:
- name: Checkout repository
uses: actions/checkout@v4
with:
lfs: 'true'
- name: Set up Python 3.12
uses: actions/setup-python@v5
with:
python-version: "3.12"
- name: Install docs dependencies
run: make ci-docs-deps
- name: Build documentation
run: make ci-docs
- name: Upload Sphinx log if build fails
if: failure()
uses: actions/upload-artifact@v3
with:
name: sphinx-output-log
path: docs/sphinx-output.log