Fix render and publish step

Author: Susan Vanderplas

.github/workflows/main.yml

@@ -57,7 +57,7 @@ jobs:
           cache-to: type=gha,mode=max
 
       # Run inside the container against the mounted repo
-      - name: Render & publish with cached renv/pip
+      - name: Render & publish
         run: |
           docker run --rm \
             -v "${{ github.workspace }}:/project" \
@@ -75,18 +75,34 @@ jobs:
             local/quarto-reticulate:latest \
             /bin/sh -c '
               set -e
-              # R deps from renv in setup/
+
+              echo "=== Checking renv cache path ==="
+              ls -lah ${RENV_PATHS_CACHE} || echo "renv cache dir not found"
+
+              echo "=== Checking pip cache path ==="
+              ls -lah ${PIP_CACHE_DIR} || echo "pip cache dir not found"
+
+              echo "=== Package count in renv cache before restore ==="
+              Rscript -e "cat(length(list.files(Sys.getenv('RENV_PATHS_CACHE'), recursive=TRUE)), 'packages in cache\n')"
+
+              # Restore R packages from project root
               if [ -f "/project/renv.lock" ]; then
+                echo "=== Restoring R packages with renv ==="
                 Rscript -e "renv::restore(project = '/project', prompt = FALSE)"
               fi
-              # Python deps
-              if [ -f "/project/setup/requirements.txt" ]; then
+
+              echo "=== Package count in renv cache after restore ==="
+              Rscript -e "cat(length(list.files(Sys.getenv('RENV_PATHS_CACHE'), recursive=TRUE)), 'packages in cache\n')"
+
+              # Restore Python packages
+              if [ -f "/project/requirements.txt" ]; then
+                echo "=== Restoring Python packages ==="
                 python3 -m venv /root/.virtualenvs/venv
                 /root/.virtualenvs/venv/bin/pip install --upgrade pip
-                /root/.virtualenvs/venv/bin/pip install --cache-dir ${PIP_CACHE_DIR} -r /project/setup/requirements.txt
+                /root/.virtualenvs/venv/bin/pip install --cache-dir ${PIP_CACHE_DIR} -r /project/requirements.txt
                 export PATH=/root/.virtualenvs/venv/bin:$PATH
               fi
-              # Quarto
+
+              # Render + publish
               cd /project
-              quarto render && quarto publish
-            '
+              quarto render && quarto publish

Dockerfile

@@ -1,12 +1,10 @@
-# Fast, sane base with R + tools
 FROM rocker/verse:4.5
 
 ENV DEBIAN_FRONTEND=noninteractive
-# Default cache locations (can be overridden at runtime)
 ENV RENV_PATHS_CACHE=/root/.local/share/renv \
     PIP_CACHE_DIR=/root/.cache/pip
 
-# --- Layer 1: OS deps (cacheable)
+# --- Layer 1: OS deps (cacheable with BuildKit)
 RUN --mount=type=cache,target=/var/cache/apt \
     --mount=type=cache,target=/var/lib/apt \
     apt-get update && apt-get install -y --no-install-recommends \
@@ -19,7 +17,7 @@ RUN --mount=type=cache,target=/var/cache/apt \
       curl gnupg ca-certificates \
     && rm -rf /var/lib/apt/lists/*
 
-# --- Layer 2: GitHub CLI (optional)
+# --- Layer 2: GitHub CLI
 RUN curl -fsSL https://cli.github.com/packages/githubcli-archive-keyring.gpg \
       | dd of=/usr/share/keyrings/githubcli-archive-keyring.gpg && \
     chmod go+r /usr/share/keyrings/githubcli-archive-keyring.gpg && \
@@ -28,21 +26,18 @@ RUN curl -fsSL https://cli.github.com/packages/githubcli-archive-keyring.gpg \
     apt-get update && apt-get install -y gh && \
     rm -rf /var/lib/apt/lists/*
 
-# --- Layer 3: Quarto
+# --- Layer 3: Quarto CLI
 RUN curl -fsSL https://quarto.org/download/latest/quarto-linux-amd64.deb -o /tmp/quarto.deb && \
     apt-get update && apt-get install -y /tmp/quarto.deb && rm -f /tmp/quarto.deb && \
     rm -rf /var/lib/apt/lists/*
 
-# --- Layer 4: TinyTeX (LaTeX)
+# --- Layer 4: TinyTeX
 RUN Rscript -e "install.packages('tinytex', repos='https://cloud.r-project.org'); tinytex::install_tinytex()"
 
-# Optional: a couple of helper R packages used during checks
-RUN Rscript -e "install.packages(c('digest'), repos='https://cloud.r-project.org')"
-
-# Ensure cache dirs always exist (first-run safe)
+# Ensure cache dirs exist
 RUN mkdir -p ${RENV_PATHS_CACHE} ${PIP_CACHE_DIR} /root/.virtualenvs
 
 WORKDIR /project
 
-# Default command: render then publish
+# Default command: render and publish
 CMD ["/bin/sh","-c","quarto render && quarto publish"]