converted qmd from cellchat #8
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| name: CellChat Signaling Workflow | |
| on: | |
| push: | |
| branches: [main] | |
| paths: | |
| - '05_signaling/cellchat.qmd' | |
| pull_request: | |
| branches: [main] | |
| paths: | |
| - '05_signaling/cellchat.qmd' | |
| workflow_dispatch: | |
| jobs: | |
| r-cellchat: | |
| runs-on: ubuntu-22.04 | |
| env: | |
| RENV_PATHS_ROOT: ~/.local/share/renv | |
| steps: | |
| - name: Checkout code | |
| uses: actions/checkout@v4 | |
| - name: Install pandoc | |
| run: sudo apt-get update && sudo apt-get install -y pandoc | |
| - name: Set up R | |
| uses: r-lib/actions/setup-r@v2 | |
| - name: Install system dependencies for R packages | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get install -y build-essential cmake libcurl4-openssl-dev libssl-dev libxml2-dev libgit2-dev libmagick++-dev libharfbuzz-dev libfribidi-dev libglpk-dev | |
| shell: bash | |
| - name: Set up Python with conda | |
| uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| python-version: 3.9 | |
| auto-update-conda: true | |
| - name: Create and activate conda environment and install UMAP | |
| run: | | |
| conda env remove -n cellchat_env -y 2>/dev/null || true | |
| conda create -n cellchat_env python=3.9 -y | |
| source "$(conda info --base)/etc/profile.d/conda.sh" | |
| conda activate cellchat_env | |
| pip install --no-cache-dir umap-learn | |
| shell: bash | |
| - name: Cache R packages (renv) | |
| uses: actions/cache@v4 | |
| with: | |
| path: ${{ env.RENV_PATHS_ROOT }} | |
| key: ${{ runner.os }}-renv-${{ hashFiles('05_signaling/renv.lock') }} | |
| restore-keys: | | |
| ${{ runner.os }}-renv- | |
| - name: Set repositories | |
| run: Rscript ubuntu.R | |
| - name: Restore environment from renv.lock | |
| run: | | |
| install.packages("renv", repos = "https://cloud.r-project.org") | |
| renv::restore(prompt = FALSE, lockfile = "05_signaling/renv.lock") | |
| shell: Rscript {0} | |
| - name: Install Quarto via conda (conda-forge) | |
| run: | | |
| # Use the existing conda installation to install quarto so we don't rely on the GitHub release URL | |
| source "$(conda info --base)/etc/profile.d/conda.sh" | |
| conda activate cellchat_env | |
| conda install -y -c conda-forge quarto | |
| quarto --version || true | |
| shell: bash | |
| - name: Render CellChat QMD | |
| id: render_qmd | |
| run: | | |
| source "$(conda info --base)/etc/profile.d/conda.sh" | |
| conda activate cellchat_env | |
| # Ensure reticulate uses the conda env Python (set explicit env var so R->reticulate picks it up) | |
| export RETICULATE_PYTHON=$(which python) | |
| echo "RETICULATE_PYTHON=$RETICULATE_PYTHON" | |
| cd 05_signaling | |
| quarto render cellchat.qmd | |
| shell: bash | |
| - name: Deploy HTML to gh-pages | |
| if: success() | |
| run: | | |
| git config --global user.name "github-actions[bot]" | |
| git config --global user.email "github-actions[bot]@users.noreply.github.com" | |
| git fetch origin gh-pages || git checkout --orphan gh-pages | |
| git switch gh-pages || git checkout -b gh-pages | |
| git add 05_signaling/cellchat.html | |
| git commit -m "Deploy cellchat.html [skip ci]" || echo "No changes to commit" | |
| git push origin gh-pages | |
| shell: bash | |