Python for Malaria Modellers

MINTverse is written in Python because the machine-learning libraries it is built on are written in Python. You can keep the rest of your work in R, and the models are still reachable, but only from a Python session. If you already write Python and work in virtual environments, go straight to Getting Started.

Most of the trouble an R user has with Python is not the language. It is that a package can install successfully and then fail to import. The interpreter that ran pip and the interpreter that ran the script were not the same one. R avoids this by keeping a single shared library. Python cannot, because Python projects routinely need conflicting versions of the same package. The setup below is arranged to prevent that.

• What is Python? — indexing, methods, imports, and where R differs.
• Python tools — pip, virtual environments, and uv.
• Installing Python — uv, or the platform route.
• Working in VS Code — the editor, the interpreter, and the interactive window.
• Environments and packages — .venv, uv sync, and diagnosing a failed import.
• Notebooks — .ipynb, kernels, and execution order.