add default seqrepo path #689
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| 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 | |
| Check-OpenAPI-Schema: | |
| 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: Dump OpenAPI Schema | |
| run: make ci-dump-openapi | |
| - name: Check for OpenAPI schema changes | |
| run: | | |
| diff openapi.yaml ci-openapi.yaml | |
| shell: bash -euo pipefail {0} | |
| 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 | |