Setup guide

This guide gets you ready to run the course notebooks in VS Code using a conda‑forge environment managed with mamba.

Install Miniforge

• Go to https://conda-forge.org/download/.
• Download the Miniforge installer for your OS and CPU.
• Run the installer with defaults.

Install VS Code

• Download and install from https://code.visualstudio.com/.

Download the course materials

• Direct download (recommended): https://github.com/yoavram/ModelsPopBiol/archive/refs/heads/master.zip
  • Unzip and note the folder path (e.g., ~/Downloads/ModelsPopBiol-master).
• If you prefer git, clone https://github.com/yoavram/ModelsPopBiol (not covered here).

Open the course folder in VS Code

• Start VS Code in the course folder: File → Open Folder… → select the course folder.

Install the Python extension for VS Code

• Open VS Code → Extensions → search Python (by Microsoft) → Install.
• Reference: https://code.visualstudio.com/docs/python/python-quick-start

Install the Jupyter extension for VS Code

• Extensions → search Jupyter (by Microsoft) → Install.
• Reference: https://code.visualstudio.com/docs/datascience/jupyter-notebooks

Create the course environment from the VS Code terminal

• In VS Code: Terminal → New Terminal. Confirm the terminal path is the course folder (the one containing environment.yaml).
• Run:

  mamba env create -f environment.yaml
  conda activate modelspopbio
  

• If mamba is unavailable, install it with conda install -n base -c conda-forge mamba or run conda env create -f environment.yaml instead.

Open the notebooks and select the kernel

• Open index.ipynb in VS Code.
• In the notebook editor, set the kernel to the course environment:
  • Click the kernel picker at the top right → choose the interpreter named modelspopbio.

Quick test

In a notebook cell, run:

import numpy
print(numpy.__version__)

You should see version number without errors.

Enable GitHub Copilot in VS Code

• Apply or sign in at https://education.github.com/pack to get Copilot Pro for free.
• Set up GitHub Copilot in VS Code: https://code.visualstudio.com/docs/copilot/setup