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Susan Vanderplas
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Updates via chatgpt
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‎.github/workflows/main.yml‎

Lines changed: 54 additions & 17 deletions
Original file line numberDiff line numberDiff line change
@@ -1,9 +1,9 @@
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name: Render and deploy Quarto files
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on:
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push:
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pull_request:
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6-
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jobs:
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build:
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runs-on: ubuntu-latest
@@ -16,40 +16,77 @@ jobs:
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GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
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GH_PAT: ${{ secrets.GH_PAT }}
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GITHUB_PAT: ${{ secrets.GH_PAT }}
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RENV_CACHE: ~/.cache/renv
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PIP_CACHE: ~/.cache/pip
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steps:
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- name: Checkout repository
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uses: actions/checkout@v4
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# Prepare cache directories so they always exist
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- name: Set up Docker Buildx
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uses: docker/setup-buildx-action@v3
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# Make sure caches exist even on first run
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- name: Prepare cache dirs
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run: |
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mkdir -p ~/.cache/pip
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mkdir -p ~/.cache/renv
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mkdir -p ~/.local/share/renv
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# Cache Python packages
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- name: Cache pip packages
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- name: Cache pip (downloads/wheels)
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uses: actions/cache@v4
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with:
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path: ~/.cache/pip
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key: ${{ runner.os }}-pip-${{ hashFiles('setup/requirements.txt') }}
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restore-keys: |
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${{ runner.os }}-pip-
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# Cache R packages from renv
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- name: Cache R packages
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- name: Cache renv (global cache, not project folder)
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uses: actions/cache@v4
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with:
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path: renv
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key: ${{ runner.os }}-renv-${{ hashFiles('renv.lock') }}
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path: ~/.local/share/renv
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key: ${{ runner.os }}-renv-${{ hashFiles('setup/renv.lock') }}
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restore-keys: |
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${{ runner.os }}-renv-
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# Build Docker image
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- name: Build Docker image
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run: docker build -t local/quarto-reticulate:latest .
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- name: Build Docker image with layer cache
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uses: docker/build-push-action@v6
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with:
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context: .
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file: ./Dockerfile
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push: false
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tags: local/quarto-reticulate:latest
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cache-from: type=gha
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cache-to: type=gha,mode=max
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# Run Docker container (optional test)
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- name: Test build inside container
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run: docker run --rm local/quarto-reticulate:latest
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# Run inside the container against the mounted repo
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- name: Render & publish with cached renv/pip
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run: |
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docker run --rm \
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-v "${{ github.workspace }}:/project" \
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-v "${HOME}/.local/share/renv:/root/.local/share/renv" \
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-v "${HOME}/.cache/pip:/root/.cache/pip" \
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-e RENV_PATHS_CACHE=/root/.local/share/renv \
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-e PIP_CACHE_DIR=/root/.cache/pip \
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-e NEWSAPI_KEY="${{ secrets.NEWSAPI_KEY }}" \
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-e GH_APP_ID="${{ secrets.GH_APP_ID }}" \
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-e GH_APP_SECRET="${{ secrets.GH_APP_SECRET }}" \
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-e GH_PAT_DEMO="${{ secrets.GH_PAT_DEMO }}" \
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-e GITHUB_TOKEN="${{ secrets.GITHUB_TOKEN }}" \
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-e GH_PAT="${{ secrets.GH_PAT }}" \
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-e GITHUB_PAT="${{ secrets.GH_PAT }}" \
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local/quarto-reticulate:latest \
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/bin/sh -c '
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set -e
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# R deps from renv in setup/
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if [ -f "/project/renv.lock" ]; then
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Rscript -e "renv::restore(project = '/project', prompt = FALSE)"
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fi
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# Python deps
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if [ -f "/project/setup/requirements.txt" ]; then
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python3 -m venv /root/.virtualenvs/venv
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/root/.virtualenvs/venv/bin/pip install --upgrade pip
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/root/.virtualenvs/venv/bin/pip install --cache-dir ${PIP_CACHE_DIR} -r /project/setup/requirements.txt
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export PATH=/root/.virtualenvs/venv/bin:$PATH
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fi
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# Quarto
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cd /project
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quarto render && quarto publish
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'

‎Dockerfile‎

Lines changed: 32 additions & 61 deletions
Original file line numberDiff line numberDiff line change
@@ -1,77 +1,48 @@
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# Base image
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FROM rocker/verse:latest
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# Fast, sane base with R + tools
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FROM rocker/verse:4.5
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# Set environment variables so renv/pip use them
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ENV R_CACHE=/root/.cache/R/
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ENV RENV_CACHE=/root/.cache/R/renv/
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ENV PIP_CACHE=/root/.cache/pip
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# Install Python
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RUN apt-get update && apt-get install -y \
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python3 python3-pip python3-venv python3-dev\
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&& rm -rf /var/lib/apt/lists/*
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# Install system dependencies
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RUN apt-get update && apt-get upgrade -y && \
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apt-get install -y --no-install-recommends \
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make build-essential libssl-dev zlib1g-dev libbz2-dev libreadline-dev \
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libsqlite3-dev curl libncursesw5-dev xz-utils tk-dev libxml2-dev \
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libxmlsec1-dev libffi-dev liblzma-dev \
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ENV DEBIAN_FRONTEND=noninteractive
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# Default cache locations (can be overridden at runtime)
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ENV RENV_PATHS_CACHE=/root/.local/share/renv \
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PIP_CACHE_DIR=/root/.cache/pip
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# --- Layer 1: OS deps (cacheable)
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RUN --mount=type=cache,target=/var/cache/apt \
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--mount=type=cache,target=/var/lib/apt \
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apt-get update && apt-get install -y --no-install-recommends \
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python3 python3-pip python3-venv python3-dev \
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libcurl4-openssl-dev libssl-dev libxml2-dev \
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libtesseract-dev libpoppler-cpp-dev tesseract-ocr \
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libleptonica-dev libpng-dev libjpeg-dev libtiff-dev imagemagick \
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gdal-bin libgdal-dev libsecret-1-dev \
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default-jdk openjdk-11-jdk \
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libleptonica-dev libpng-dev libjpeg-dev libtiff-dev \
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imagemagick gdal-bin libgdal-dev libsecret-1-dev \
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libglpk-dev libudunits2-dev \
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gnupg software-properties-common
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curl gnupg ca-certificates \
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&& rm -rf /var/lib/apt/lists/*
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# Install GitHub CLI
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RUN curl -fsSL https://cli.github.com/packages/githubcli-archive-keyring.gpg | \
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dd of=/usr/share/keyrings/githubcli-archive-keyring.gpg && \
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# --- Layer 2: GitHub CLI (optional)
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RUN curl -fsSL https://cli.github.com/packages/githubcli-archive-keyring.gpg \
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| dd of=/usr/share/keyrings/githubcli-archive-keyring.gpg && \
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chmod go+r /usr/share/keyrings/githubcli-archive-keyring.gpg && \
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echo "deb [arch=$(dpkg --print-architecture) signed-by=/usr/share/keyrings/githubcli-archive-keyring.gpg] https://cli.github.com/packages stable main" \
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> /etc/apt/sources.list.d/github-cli.list && \
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apt-get update && apt-get install -y gh && \
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rm -rf /var/lib/apt/lists/*
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# Install Quarto CLI separately
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RUN curl -fsSL https://quarto.org/download/latest/quarto-linux-amd64.deb -o quarto.deb && \
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apt-get update && apt-get install -y ./quarto.deb && \
39-
rm quarto.deb
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41-
# Environment variables
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ENV JAVA_HOME="/usr/lib/jvm/java-11-openjdk-amd64/"
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ENV PATH=/root/.pyenv/bin:$PATH
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ENV VENV_PATH="/root/.virtualenvs/venv"
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ENV REQ_FILE="/project/setup/requirements.txt"
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ENV DEBIAN_FRONTEND=noninteractive
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# Make sure these exist
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# RUN mkdir -p ${RENV_CACHE} ${PIP_CACHE}
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51-
# Install tinytex system-wide (for LaTeX support)
52-
RUN --mount=type=cache,target=${R_CACHE} Rscript -e "install.packages('tinytex'); tinytex::install_tinytex(force=T)"
53-
54-
# Install minimal R packages for system-level support
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RUN --mount=type=cache,target=${R_CACHE} Rscript -e "install.packages(c('digest','devtools','renv','reticulate','yaml'))"
31+
# --- Layer 3: Quarto
32+
RUN curl -fsSL https://quarto.org/download/latest/quarto-linux-amd64.deb -o /tmp/quarto.deb && \
33+
apt-get update && apt-get install -y /tmp/quarto.deb && rm -f /tmp/quarto.deb && \
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rm -rf /var/lib/apt/lists/*
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57-
# Copy renv.lock and renv directory for layer caching, install R dependencies via renv
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COPY renv.lock /project/renv.lock
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COPY renv /project/renv
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# --- Layer 4: TinyTeX (LaTeX)
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RUN Rscript -e "install.packages('tinytex', repos='https://cloud.r-project.org'); tinytex::install_tinytex()"
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# Restore R deps from renv.lock using persistent cache
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RUN --mount=type=cache,target=${R_CACHE} Rscript -e 'renv::restore(lockfile = "/project/renv.lock", prompt = FALSE)'
39+
# Optional: a couple of helper R packages used during checks
40+
RUN Rscript -e "install.packages(c('digest'), repos='https://cloud.r-project.org')"
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# Copy Python requirements file if exists (cached separately)
65-
COPY setup/requirements.txt ${REQ_FILE}
66-
RUN --mount=type=cache,target=${PIP_CACHE} python3 -m venv /root/.virtualenvs/venv && \
67-
"${VENV_PATH}/bin/pip" install --cache-dir "${PIP_CACHE}" -r "${REQ_FILE}"
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# Ensure cache dirs always exist (first-run safe)
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RUN mkdir -p ${RENV_PATHS_CACHE} ${PIP_CACHE_DIR} /root/.virtualenvs
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# Copy the rest of the project
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COPY . /project
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WORKDIR /project
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# Verify Environment
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RUN Rscript -e "renv::status();renv::diagnostics();devtools::session_info();reticulate::py_config()"
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76-
# Default command
77-
CMD ["/bin/sh", "-c", "quarto render && quarto publish"]
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# Default command: render then publish
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CMD ["/bin/sh","-c","quarto render && quarto publish"]

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