alternative aws download #10
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| on: | |
| pull_request: | |
| push: | |
| branches: main | |
| name: Publish | |
| jobs: | |
| build-deploy: | |
| runs-on: ubuntu-latest | |
| permissions: | |
| contents: write | |
| steps: | |
| - name: Check out repository | |
| uses: actions/checkout@v4 | |
| - name: Set up specific version of Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: '3.12' | |
| - name: Install R | |
| uses: r-lib/actions/setup-r@v2 | |
| - name: Set up Quarto | |
| uses: quarto-dev/quarto-actions/setup@v2 | |
| # - name: Install AWS CLI | |
| # uses: unfor19/install-aws-cli-action@v1 | |
| - name: Cache usecase_data | |
| uses: actions/cache@v2 | |
| with: | |
| path: | | |
| notebooks/usecase_data | |
| key: usecase_data_${{ runner.os }} | |
| - name: Make sure data is available | |
| run: | | |
| if [[ ! -f notebooks/usecase_data/sc_counts_reannotated_with_counts.h5ad ]]; then | |
| wget https://openproblems-bio.s3.amazonaws.com/public/neurips-2023-competition/sc_counts_reannotated_with_counts.h5ad \ | |
| -O notebooks/usecase_data/sc_counts_reannotated_with_counts.h5ad | |
| fi | |
| # aws s3 cp \ | |
| # --no-sign-request \ | |
| # s3://openproblems-bio/public/neurips-2023-competition/sc_counts_reannotated_with_counts.h5ad \ | |
| # notebooks/usecase_data/sc_counts_reannotated_with_counts.h5ad | |
| # attempt with pixi: | |
| # - name: Install pixi | |
| # run: curl -fsSL https://pixi.sh/install.sh | bash | |
| # - name: Cache several folders | |
| # uses: actions/cache@v2 | |
| # with: | |
| # path: | | |
| # _freeze | |
| # .pixi | |
| # key: pixi_${{ runner.os }} | |
| # - name: Set up dependencies | |
| # run: pixi install -e dev | |
| # - name: Render slides | |
| # run: pixi run render_slides | |
| # attempt with renv | |
| - name: Set up renv | |
| uses: r-lib/actions/setup-renv@v2 | |
| - name: Cache _freeze | |
| uses: actions/cache@v2 | |
| with: | |
| path: | | |
| _freeze | |
| key: renv_${{ runner.os }} | |
| - name: Render slides | |
| run: | | |
| source renv/python/virtualenvs/renv-python-3.12/bin/activate | |
| quarto render | |
| - name: Deploy 🚀 | |
| if: github.event_name != 'pull_request' | |
| uses: JamesIves/github-pages-deploy-action@v4 | |
| with: | |
| folder: _book | |
| branch: gh-pages | |
| force: false | |
| clean-exclude: pr-preview/ | |
| - name: Deploy preview | |
| if: github.event_name == 'pull_request' | |
| uses: rossjrw/pr-preview-action@v1 | |
| with: | |
| source-dir: _book | |
| preview-branch: gh-pages | |
| umbrella-dir: pr-preview | |
| action: auto |