Avoid venvs see quarto-dev/quarto#809 (comment) and geocompx#107

Author: Robinlovelace

rocker-rpy/Dockerfile

@@ -5,12 +5,10 @@ FROM ghcr.io/geocompx/minimal
 # - 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/*
 
@@ -22,19 +20,17 @@ RUN ln -sf /usr/bin/python3 /usr/bin/python
 # The '-f' flag forces the creation of the symbolic link, overwriting any existing file.
 RUN ln -sf /usr/bin/pip3 /usr/bin/pip
 
-# 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
-
-# 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/')"
+
+# Set the environment variable for Quarto to use the system Python 3.
+# The `which python3` command finds the path of the globally installed executable.
+ENV QUARTO_PYTHON=/usr/bin/python
+
+# Install project requirements globally using the system's pip3.
+# We use `pip3` to ensure we are using the package manager for Python 3.
+# The `--break-system-packages` flag is added to override the security feature.
+# The `--ignore-installed` flag is added to prevent pip from trying to uninstall
+# packages that are managed by the system.
+RUN pip3 install --no-cache-dir --break-system-packages --ignore-installed -r https://github.com/geocompx/geocompy/raw/refs/heads/main/requirements.txt