Setup

Chapter 3. Getting from a machine with nothing installed to one that can run every build in the book.

Clone and install

git clone https://github.com/nexagenlabs/claude-code-for-scientists.git
cd claude-code-for-scientists
python -m venv .venv
source .venv/bin/activate        # Windows: .venv\Scripts\activate
pip install -r requirements.txt

Check it worked

python check_setup.py

It changes nothing. It reports on your Python version, the three libraries the analysis chapters use, whether Claude Code is on your path and answering, whether git is present, whether you are standing in a sensible directory and whether you can write to it.

A failure stops the next chapter working. A warning does not.

On Windows

Use python rather than python3. On many Windows installations python3 resolves to a Microsoft Store stub and fails with a message that looks like a broken install and is not one.

If it cannot find Claude Code

The commonest first-run failure is that the program installed correctly and your shell cannot see it yet. Open a new terminal before anything else. If it still cannot be found, the install directory is not on your PATH, and Chapter 3 covers adding it.