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publish.yml
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name: Quarto Publish
on:
push:
branches: [ master ]
pull_request:
branches: [ master ]
jobs:
build-deploy:
container:
image: bioconductor/bioconductor_docker:devel
runs-on: ubuntu-latest
permissions:
contents: write
steps:
- name: Check out repository
uses: actions/checkout@v4
- name: Install rsync
run: |
sudo apt-get update
sudo apt-get install -y rsync
# - name: Install curl
# run: |
# sudo apt-get install libcurl4-openssl-dev
# - name: Setup Quarto
# uses: quarto-dev/quarto-actions/setup@v2
# with:
# tinytex: true
- name: Setup Quarto
run: |
wget https://github.com/quarto-dev/quarto-cli/releases/download/v1.5.43/quarto-1.5.43-linux-amd64.deb && \
dpkg -i quarto-1.5.43-linux-amd64.deb && \
rm quarto-1.5.43-linux-amd64.deb
- name: Setup tinytex
run: quarto install tinytex
# - name: Setup Python
# uses: actions/setup-python@v4
# with:
# python-version: '3.9'
# cache: 'pip'
- name: Install Python dependencies
run: pip install -r requirements.txt
# - name: Setup R
# uses: r-lib/actions/setup-r@v2
# with:
# r-version: '4.4.0'
- name: Set directories
run: |
echo "R_PKG_DIR=${R_HOME}/site-library" >> $GITHUB_ENV
- name: Restore the package directory
uses: actions/cache@v3
with:
path: ${{ env.R_PKG_DIR }}
key: check-packages
- name: Install R packages
run: Rscript rpackages.R
# build SQLite from source, because I need 3.35<=
- name: Download SQLite3
run: |
wget https://www.sqlite.org/2024/sqlite-autoconf-3450300.tar.gz
tar -xvf sqlite-autoconf-3450300.tar.gz
- name: Install SQLite3
run: |
cd sqlite-autoconf-3450300
./configure
make
sudo make install
export PATH="/usr/local/lib:$PATH"
cd ..
- name: Quarto render
run: |
quarto render --execute --to html --output-dir ./build
env:
LD_LIBRARY_PATH: /usr/local/lib
- name: Create nojekyll
run: touch ./build/.nojekyll
- name: GH Pages Deployment
# if: github.ref == 'refs/heads/master'
uses: JamesIves/github-pages-deploy-action@v4
with:
branch: gh-pages # The branch the action should deploy to.
folder: ./build
clean: true # Automatically remove deleted files from the deploy branch