Replace install_python.sh, see quarto-dev/quarto#809 (comment) and geocompx#107

Author: Robinlovelace

rocker-rpy/Dockerfile

@@ -1,19 +1,40 @@
+# Use the specified base image
 FROM ghcr.io/geocompx/minimal
 
-# Use Python already provisioned by the base image virtualenv (/opt/venv).
-# Do not reinstall Python; ensure the venv python is preferred and 'python' exists.
-RUN /rocker_scripts/install_python.sh
+# Install core Python 3 packages and other dependencies.
+# - python3-dev: Headers needed to compile certain Python packages with C extensions.
+# - python3-pip: The package installer for Python 3, installed globally.
+# - swig: Used for wrapping C/C++ libraries for Python.
+# - python3-venv: The module to create virtual environments.
+RUN apt-get update && apt-get install -y --no-install-recommends \
+    python3 \
+    python3-dev \
+    python3-pip \
+    python3-venv \
+    swig && \
+    rm -rf /var/lib/apt/lists/*
 
-# Prefer the venv python and put its bin on PATH so reticulate picks it up.
-ENV RETICULATE_PYTHON=/opt/venv/bin/python
-ENV PATH=/opt/venv/bin:${PATH}
+# Create a symbolic link so the 'python' command defaults to 'python3'
+# The '-f' flag forces the creation of the symbolic link, overwriting any existing file.
+RUN ln -sf /usr/bin/python3 /usr/bin/python
 
-# Override the python symlink to use the venv Python (not system Python)
-RUN ln -sf /opt/venv/bin/python /usr/bin/python
-RUN ln -sf /opt/venv/bin/python /bin/python 
+# Create a symbolic link so the 'pip' command defaults to 'pip3'
+# The '-f' flag forces the creation of the symbolic link, overwriting any existing file.
+RUN ln -sf /usr/bin/pip3 /usr/bin/pip
 
-# Set version of Python that Quarto will use:
+# Create a Python virtual environment to avoid system package conflicts.
+RUN python3 -m venv /opt/venv
+
+# Set the environment variable for Quarto to use the virtual environment's Python.
 ENV QUARTO_PYTHON=/opt/venv/bin/python
 
-# Optionally install project requirements into the existing venv if desired:
-RUN /opt/venv/bin/pip install -r https://github.com/geocompx/geocompy/raw/refs/heads/main/requirements.txt
+# Add the virtual environment's bin directory to the PATH.
+ENV PATH="/opt/venv/bin:$PATH"
+
+# Install project requirements into the virtual environment.
+# This avoids all system package conflicts.
+RUN pip install --no-cache-dir -r https://github.com/geocompx/geocompy/raw/refs/heads/main/requirements.txt
+
+# Install reticulate R package to enable R-Python interoperability
+# This step remains the same as it is a separate R installation.
+RUN R -e "install.packages('reticulate', repos='https://cloud.r-project.org/')"