Running the code in this book requires the following:
- Python dependencies, which can be installed with
pip, a package manager or a Docker container (see below) - An integrated development environment (IDE) such as VS Code (running locally or on Codespaces/other host) or Jupyter Notebook for running and exploring the Python code interactively
- Quarto, which is used to generate the book
GitHub Codespaces minimise set-up costs by providing access to a modern IDE (VS Code) plus dependencies in your browser. This can save time on package installation. Codespaces allow you to make and commit changes, providing a way to test changes and contribute fixes in an instant.
To run the book in Codespaces, click on the link below.
Open in GitHub Codespaces
You should see something like this, the result of running all the code in the book by opening the terminal (e.g. with the command Ctrl+J) and entering the following command:
quarto preview
If you can install Docker this is likely to be the quickest way to reproduce the contents of this book. To do this from within VS Code:
- Install Microsoft’s official Dev Container extension
- Open the folder containing the repo in VS Code and click on the ‘Reopen in container’ button that should appear, as shown below (you need to have Docker installed on your computer for this to work)
Edit the code in the containerised instance of VS Code that will appear 🎉
See details below for other ways to get the dependencies and reproduce the book.
Use pip to install the dependencies as follows, after cloning the repo
and opening a terminal in the root folder of the repo.
First we’ll set-up a virtual environment to install the dependencies in:
# Create a virtual environment called geocompy
python -m venv geocompy
# Activate the virtual environment
source geocompy/bin/activateThen install the dependencies (with the optional
python -m
prefix specifying the Python version):
# Install dependencies from the requirements.txt file
python -m pip install -r requirements.txtYou can also install packages individually, e.g.:
pip install jupyter-bookDeactivate the virtual environment when you’re done:
deactivateThe environment.yml file contains a list of
dependencies that can be installed with a package manager such as
conda, mamba or micromamba. The instructions below are for
micromamba
but should work for any package manager.
# For Linux, the default shell is bash:
curl -L micro.mamba.pm/install.sh | bash
# For macOS, the default shell is zsh:
curl -L micro.mamba.pm/install.sh | zshAfter answering the questions, install dependencies with the following command:
micromamba env create -f environment.ymlActivate the environment as follows:
micromamba activate geocompyInstall kernel, this will allow you to select the environment in vscode or IPython as follows:
python -m ipykernel install --userYou can now reproduce the book (requires quarto to be installed):
micromamba run -n geocompy quarto previewVS Code’s quarto.quarto plugin can Python code in the chunks in the
.qmd files in this book interactively.
However, you can also run any of the chapters in a Jupyter Notebook, e.g. as follows:
cd ipynb
# jupyter notebook . # open a notebook showing all chapters
jupyter notebook 02-spatial-data.ipynbYou should see something like this:
See documentation on running and developing Python code in a Jupyter notebook at docs.jupyter.org.
If you’re interested in how to auto-generate and run the .py and .ipynb files from the .qmd files, see below.
The Python scripts and IPython notebook files stored in the code and ipynb folders are generated from the .qmd files. To regenerate them, you can use the following commands, to generate .ipynb and .py files for local versions of Chapter 2, for example:
quarto convert 02-spatial-data.qmd # generate .ipynb file
jupytext --to py *.ipynb # generate .py files .ipynb filesDo this for all chapters with the following bash script in the repo:
./convert.shWe have set-up a GitHub Action to do this automatically: every commit message that contains the text string ‘convert’ will create and push updated .ipynb and .py files.
Running the code chunks in the .qmd files in an IDE such as VSCode or directly with quarto is the main way code in this book is designed to be run interactively, but you can also execute the .py and .ipynb files directly. To run the code for chapter 2, for example, you can run one of the following commands from your system shell:
python code/chapters/02-spatial-data.py # currently requires manual intervention to complete, see #71
ipython ipynb/02-spatial-data.ipynb # currently requires manual intervention to complete, see #71
bash ./run-code.sh # run all .python filesWe pin package versions in the environment.yml and requirements.txt files to ensure reproducibility.
To update the requirements.txt run the following:
python -m pip install pur
pur -r requirements.txt
python -m pip install -r requirements.txtTo update the environment.yml file in the same way based on your newly
installed packages, run the following:
micromamba list export > environment.yml
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