make sure s3 data is fetched beforehand #9
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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: Install AWS CLI | |
uses: unfor19/install-aws-cli-action@v1 | |
- 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 | |
# 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: Cache usecase_data | |
uses: actions/cache@v2 | |
with: | |
path: | | |
notebooks/usecase_data | |
key: usecase_data_${{ runner.os }} | |
- name: Make sure data is available | |
run: | | |
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 | |
- 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 |