对社区中的组织和聚类结果的说明，以及用 visNetwork 包绘制交互式网络图 #110
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| on: | |
| push: | |
| branches: main | |
| pull_request: | |
| branches: main | |
| name: Book-MacOS | |
| jobs: | |
| build-deploy: | |
| runs-on: macos-13 | |
| env: | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| CMDSTAN_VERSION: "2.34.0" | |
| PANDOC_VERSION: "3.1.11" | |
| RETICULATE_PYTHON_ENV: /opt/.virtualenvs/r-tensorflow | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Install Quarto | |
| uses: quarto-dev/quarto-actions/setup@v2 | |
| with: | |
| version: 1.4.547 | |
| - uses: r-lib/actions/setup-r@v2 | |
| with: | |
| use-public-rspm: true | |
| r-version: '4.3.2' | |
| extra-repositories: 'https://mc-stan.org/r-packages https://inla.r-inla-download.org/R/stable https://grantmcdermott.r-universe.dev' | |
| - uses: r-lib/actions/setup-r-dependencies@v2 | |
| - name: Install Pandoc | |
| uses: r-lib/actions/setup-pandoc@v2 | |
| with: | |
| pandoc-version: ${{ env.PANDOC_VERSION }} | |
| - name: Install TinyTeX | |
| uses: r-lib/actions/setup-tinytex@v2 | |
| env: | |
| # install full prebuilt version | |
| TINYTEX_INSTALLER: TinyTeX | |
| - name: Setup CmdStan | |
| run: | | |
| curl -fLo cmdstan-${CMDSTAN_VERSION}.tar.gz https://github.com/stan-dev/cmdstan/releases/download/v${CMDSTAN_VERSION}/cmdstan-${CMDSTAN_VERSION}.tar.gz | |
| sudo mkdir -p /opt/cmdstan/ | |
| sudo chown -R $(whoami):staff /opt/cmdstan/ | |
| tar -xzf cmdstan-${CMDSTAN_VERSION}.tar.gz -C /opt/cmdstan/ | |
| make build -C /opt/cmdstan/cmdstan-${CMDSTAN_VERSION} | |
| rm cmdstan-${CMDSTAN_VERSION}.tar.gz | |
| - name: Install Fonts From System | |
| run: | | |
| export HOMEBREW_NO_INSTALLED_DEPENDENTS_CHECK=1 | |
| brew install optipng jags virtualenv | |
| brew install --cask xquartz | |
| brew tap homebrew/cask-fonts | |
| brew install --cask font-noto-sans-cjk-sc font-noto-serif-cjk-sc | |
| fc-list | sort | |
| - name: Setup Python | |
| run: | | |
| sudo mkdir -p /opt/.virtualenvs/r-tensorflow | |
| sudo chown -R $(whoami):staff /opt/.virtualenvs/r-tensorflow | |
| virtualenv -p /usr/bin/python3 $RETICULATE_PYTHON_ENV | |
| source $RETICULATE_PYTHON_ENV/bin/activate | |
| pip3 install -r docker/requirements.txt | |
| python -m spacy download en_core_web_sm | |
| python -m spacy download zh_core_web_sm | |
| deactivate | |
| - name: Install LaTeX packages | |
| run: | | |
| if(!require('tinytex')) install.packages('tinytex') | |
| tinytex::tlmgr_install(readLines("docker/texlive.txt")) | |
| tinytex::tl_pkgs() | |
| tikzDevice::tikzTest("m", engine = "xetex") | |
| tikzDevice::tikzTest("$\\sin(x^2/2 - y^2/4 + 3) \\cos(2 x + 1 - \\exp(y))$") | |
| shell: Rscript {0} | |
| - name: Reinstall R packages from source | |
| run: | | |
| install.packages(c("Matrix", "MatrixModels", "rjags", "lme4", "TMB", "glmmTMB"), repos = "https://cran.r-project.org/", type = "source") | |
| if(!require('remotes')) install.packages('remotes') | |
| remotes::install_github("tidyverse/ggplot2", ref = remotes::github_pull("5592")) | |
| shell: Rscript {0} | |
| - name: Render Book | |
| run: | | |
| source $RETICULATE_PYTHON_ENV/bin/activate | |
| quarto check | |
| quarto render | |
| shell: bash | |
| env: | |
| RETICULATE_PYTHON_ENV: /opt/.virtualenvs/r-tensorflow | |
| RETICULATE_PYTHON: /opt/.virtualenvs/r-tensorflow/bin/python | |
| CMDSTAN: /opt/cmdstan/cmdstan-${{ env.CMDSTAN_VERSION }} | |
| - name: Deploy to Github Pages | |
| uses: JamesIves/github-pages-deploy-action@v4 | |
| with: | |
| git-config-name: GitHub Actions | |
| git-config-email: actions@github.com | |
| branch: gh-pages | |
| folder: _book | |
| clean: true | |
| - name: Deploy book to bookdown.org | |
| if: github.event_name == 'push' | |
| env: | |
| CONNECT_API_KEY: ${{ secrets.RSC_BOOKDOWN_TOKEN }} | |
| CONTENT_ID: ${{ secrets.RSC_BOOKDOWN_APP_ID }} | |
| run: | | |
| Rscript '_deploy.R' | |
| shell: bash | |
| - name: Upload book folder for debug | |
| if: failure() | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: Upload Book | |
| path: _book |