Fix initially blank mutations #188
Workflow file for this run
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| name: Tests | |
| on: | |
| pull_request: | |
| push: | |
| branches: [main, test] | |
| permissions: | |
| contents: read | |
| issues: write | |
| pull-requests: write | |
| jobs: | |
| pre-commit: | |
| name: Lint | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Cancel Previous Runs | |
| uses: styfle/[email protected] | |
| with: | |
| access_token: ${{ github.token }} | |
| - uses: actions/checkout@v3 | |
| - uses: actions/setup-python@v4 | |
| with: | |
| python-version: '3.11' | |
| - uses: pre-commit/[email protected] | |
| test: | |
| name: Python | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| python: [ "3.11" ] | |
| os: [ ubuntu-latest, ] | |
| defaults: | |
| run: | |
| shell: bash | |
| steps: | |
| - name: Cancel Previous Runs | |
| uses: styfle/[email protected] | |
| with: | |
| access_token: ${{ github.token }} | |
| - name: Checkout | |
| uses: actions/checkout@v3 | |
| - uses: actions/setup-python@v4 | |
| with: | |
| python-version: '3.11' | |
| cache: 'pip' | |
| - name: Install deps | |
| run: pip install -r requirements.txt | |
| - name: Tests with numba | |
| run: coverage run --source=tsbrowse -m pytest -x tests | |
| - name: Tests with coverage (no numba) | |
| run: TSBROWSE_DISABLE_NUMBA=1 coverage run --source=tsbrowse -m pytest -x tests | |
| - name: Create Screenshot | |
| run: | | |
| msp simulate --length 1000 --recombination-rate 0.01 --mutation-rate 0.01 100 out.trees | |
| python -m tsbrowse preprocess out.trees | |
| python -m tsbrowse screenshot out.tsbrowse mutations | |
| python -m tsbrowse screenshot out.tsbrowse edges | |
| python -m tsbrowse screenshot out.tsbrowse nodes | |
| - name: Upload Screenshot Artifact | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: screenshots | |
| path: "*.png" | |
| - name: Post Screenshots to PR | |
| if: github.event_name == 'pull_request' | |
| uses: actions/github-script@v6 | |
| with: | |
| script: | | |
| const fs = require('fs'); | |
| const path = process.env.GITHUB_WORKSPACE; | |
| const screenshotDir = path; | |
| const imageFiles = fs.readdirSync(screenshotDir).filter(file => file.endsWith('.png')); | |
| if (imageFiles.length > 0) { | |
| let imagesMarkdown = ''; | |
| for (const file of imageFiles) { | |
| const filePath = `${screenshotDir}/${file}`; | |
| const imageData = fs.readFileSync(filePath, { encoding: 'base64' }); | |
| imagesMarkdown += `\n`; | |
| } | |
| const body = `<details><summary>PR Screenshots</summary>\n${imagesMarkdown}\n</details>`; | |
| await github.rest.issues.createComment({ | |
| issue_number: context.issue.number, | |
| owner: context.repo.owner, | |
| repo: context.repo.repo, | |
| body: body | |
| }); | |
| } | |
| - name: Upload coverage | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| run: | | |
| coveralls --service=github |