Update umap #39
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| name: Update umap | |
| on: | |
| schedule: | |
| - cron: '0 0 * * 2' # every Tuesday at midnight | |
| workflow_dispatch: | |
| inputs: null | |
| jobs: | |
| update_umap: | |
| strategy: | |
| matrix: | |
| python-version: [ "3.10", "3.13" ] | |
| os: [ ubuntu-latest ] # can't use macOS when using service containers or container jobs | |
| runs-on: ${{ matrix.os }} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install uv | |
| uv pip install torch --index-url https://download.pytorch.org/whl/cpu --system | |
| uv pip install bedboss --system | |
| # uv pip install git+https://github.com/databio/bedboss.git@umap_model#egg=bedboss --system | |
| - name: Update umap | |
| run: | | |
| bedboss --version | |
| bedboss download-umap --config config.yaml --output-file umap/hg38_umap.json | |
| env: | |
| POSTGRES_HOST: ${{ secrets.POSTGRES_HOST }} | |
| POSTGRES_PASSWORD: ${{ secrets.POSTGRES_PASSWORD }} | |
| POSTGRES_USER: ${{ secrets.POSTGRES_USER }} | |
| QDRANT_HOST: ${{ secrets.QDRANT_HOST }} | |
| QDRANT_API_KEY: ${{ secrets.QDRANT_API_KEY }} | |
| AWS_ENDPOINT_URL: ${{ secrets.AWS_ENDPOINT_URL }} | |
| AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }} | |
| AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }} | |
| - name: Add to huggingface repo | |
| run: | | |
| pip install huggingface_hub | |
| python upload_hf.py umap | |
| env: | |
| HF_TOKEN: ${{ secrets.HF_TOKEN }} | |
| # - name: Commit report | |
| # run: | | |
| # git config --global user.name 'Oleksandr Khoroshevskyi' | |
| # git config --global user.email 'khoroshevskyi@users.noreply.github.com' | |
| # git add -A | |
| # git commit -m "Automated update of number of files" | |
| # git push |