Mess with python a bit?

Author: Susan Vanderplas

.github/workflows/main.yml

@@ -66,7 +66,6 @@ jobs:
             -v "${HOME}/.cache/pip:/root/.cache/pip" \
             -e RENV_PATHS_CACHE=/root/.local/share/renv \
             -e PIP_CACHE_DIR=/root/.cache/pip \
-            -e QUARTO_PYTHON="venv" \
             -e NEWSAPI_KEY="${{ secrets.NEWSAPI_KEY }}" \
             -e GH_APP_ID="${{ secrets.GH_APP_ID }}" \
             -e GH_APP_SECRET="${{ secrets.GH_APP_SECRET }}" \
@@ -96,17 +95,13 @@ jobs:
               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
+              # Restore Python packages into baked-in venv
               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 ${PIP_CACHE_DIR} -r /project/requirements.txt
-                export PATH=/root/.virtualenvs/venv/bin:$PATH
-                source /root/.virtualenvs/venv/bin/activate
+                echo "=== Restoring Python packages into baked-in venv ==="
+                /opt/venv/bin/pip install --cache-dir ${PIP_CACHE_DIR} -r /project/requirements.txt
               fi
 
               # Render + publish
               cd /project
               quarto render && quarto publish
-              ' --verbose
+              ' --verbose

Dockerfile

@@ -47,6 +47,30 @@ RUN curl -fsSL https://quarto.org/download/latest/quarto-linux-amd64.deb -o /tmp
 # --- Layer 4: TinyTeX
 RUN Rscript -e "tinytex::install_tinytex(force=T)"
 
+# --- Layer 5: python
+# Install Python and venv support
+RUN apt-get update && \
+    apt-get install -y python3 python3-venv python3-pip && \
+    apt-get clean && rm -rf /var/lib/apt/lists/*
+
+# Create a dedicated virtual environment
+ENV VENV_PATH=/opt/venv
+RUN python3 -m venv $VENV_PATH
+
+# Make sure pip is up to date and install common build tools
+RUN $VENV_PATH/bin/pip install --upgrade pip setuptools wheel
+
+# Register venv globally for R/reticulate and Quarto
+ENV PATH="$VENV_PATH/bin:$PATH"
+ENV RETICULATE_PYTHON=$VENV_PATH/bin/python
+ENV QUARTO_PYTHON=$VENV_PATH/bin/python
+
+# Pre-install Jupyter kernel so Quarto sees it, and populate with dependencies
+RUN $VENV_PATH/bin/pip install ipykernel && \
+    $VENV_PATH/bin/python -m ipykernel install --prefix=/usr/local --name=venv --display-name "Python (venv)" \
+    $VENV_PATH/bin/pip install -r /project/requirements.txt
+
+
 # Ensure cache dirs exist
 RUN mkdir -p ${RENV_PATHS_CACHE} ${PIP_CACHE_DIR} /root/.virtualenvs