The Bennett Institute's skeleton notebook environment

Getting started with this skeleton project

This is a skeleton project for creating a reproducible, cross-platform analysis notebook, using Docker.

Developers and analysts using this skeleton for new development should refer to DEVELOPERS.md for instructions on getting started. Update this README.md so it is a suitable introduction to your project.

Running Jupyter Lab

You will need to have installed Git and Docker, please see the INSTALLATION_GUIDE.md for further details.

Windows and Linux users should double-click the jupyter-lab file. Users on macOS should double-click jupyter-lab-mac-os instead.

Note: if double-clicking the jupyter-lab file opens the file in VS Code, you should instead right-click on the file and open it with Git for Windows.

This will build a Docker image with all software requirements installed, start a new Jupyter Lab server, and then provide a link to access this server.

The first time you run this command it may take some time to download and install the necessary software. Subsequent runs should be much faster.

Note: if running the command fails with:

docker: Error response from daemon: user declined directory sharing C:\path\to\directory

you should open the Docker dashboard, and then under Settings -> Resources -> FileSharing, add the appropriate path.

Once the server starts you should see the URL needed to access it, followed by some lines of Jupyter log output, for example:

 -> Connect to notebook with URL:

        http://localhost:59169/?token=C1atgmXc9IJGXCZy

    Tip: to open in browser, triple-click the URL, right-click, choose "Open"

[I 2024-08-08 13:13:18.953 ServerApp] jupyter_lsp | extension was successfully linked.
[I 2024-08-08 13:13:18.959 ServerApp] jupyter_server_terminals | extension was successfully linked.
[I 2024-08-08 13:13:18.969 ServerApp] jupyterlab | extension was successfully linked.
...
[I 2024-08-08 13:13:19.471 ServerApp] Serving notebooks from local directory: /workspace
[I 2024-08-08 13:13:19.472 ServerApp] Jupyter Server 2.14.0 is running at:
[I 2024-08-08 13:13:19.472 ServerApp] http://localhost:59169/?token=C1atgmXc9IJGXCZy
[I 2024-08-08 13:13:19.472 ServerApp]     http://127.0.0.1:59169/lab?token=...
[I 2024-08-08 13:13:19.472 ServerApp] Use Control-C to stop this server and shut down all kernels.

How to cite

XXX Please change to either a paper (if published) or the repo. You may find it helpful to use Zenodo DOI (see DEVELOPERS.md for further information)