Reproducible Research: a container approach

Description

This repository provides a hands-on introduction to reproducible research using modern computational tools. It demonstrates best practices for creating, sharing, and maintaining reproducible scientific workflows, with a focus on Jupyter, VS Code, Docker, and Binder. The included materials guide users through setting up interactive environments, building and running containers, and generating shareable documentation and slides. Whether you are a researcher, educator, or student, this project helps you understand and apply reproducibility principles in your own computational work.
Key features include:

• Interactive Jupyter and VS Code environments via Docker and Binder
• Step-by-step instructions for building and running containers
• Automated documentation and slide generation
• Examples and templates for reproducible workflows
• Support for collaborative development and sharing

Explore the resources to learn how to make your research transparent, repeatable, and easy to share.

Slides

Test the environment in Binder

Binder is a playground environment where you can test the environment and code. All the changes will disappear when the Tabs are closed.

1. Right click on the Binder badge below and then Open Link in New Tab

   

2. When the Jupyter Lab interface is displayed, click on the VS Code icon.

3. Make some changes in the slides, for example, in ./docs/source/_sections/fundamentals.rst (optional).

4. Render the html slides, open a new terminal and run

   cd docs
   make revealjs

   The html slides will be saved in ./build/revealjs/index.html

5. Render the pdf slides, run

   make pdfslides

   Then the slides in pdf format will be in ./build/latex/slides.pdf which can be opened via the Jupyter Lab interface.

6. To inspect changes immediately run

   make autobuild

   in the pop up window click on Open in browser. Any changes in the slides will be reflected after refreshin the tab.

Installation

Within a particular ecosystem, there may be a common way of installing things, such as using Yarn, NuGet, or Homebrew. However, consider the possibility that whoever is reading your README is a novice and would like more guidance. Listing specific steps helps remove ambiguity and gets people to using your project as quickly as possible. If it only runs in a specific context like a particular programming language version or operating system or has dependencies that have to be installed manually, also add a Requirements subsection.

Build the docker container

cd docker
docker build -t jupyter-vscode:1.0 .

or

docker build --network=host -t jupyter-vscode:1.0 .

Run the container

docker run -it --rm -p 8888:8888 -v "${PWD}":/home/jovyan jupyter-vscode:1.0

or

docker run -it --rm \
  -p 8888:8888 \
  --user root \
  -e NB_USER=root \
  -e NB_UID=0 \
  -e NB_GID=0 \
  -v ~/.ssh:/home/jovyan/.ssh:ro \
  -v ~/.gitconfig:/home/jovyan/.gitconfig:ro \
  -v "${PWD}":/home/jovyan/work \
  jupyter-vscode:1.0

Usage

Visit the link provided in the terminal

...
        http://127.0.0.1:8888/lab?token=9cc59e2fa3b64f29d857332aa41cc5fc3463b8319b513406

Click on VS Code.

Build documentation

Open a terminal Menu->Terminal->New Terminal and move to the docs folder

  cd docs

Build the html slides

  make revealjs

Build the pdf slides (make sure you run the above command)

  make pdfslides

Rebuild automatically (useful during continuous file changes)

  make autobuild

and follow the link on the terminal ctrl + click

Support

Tell people where they can go to for help. It can be any combination of an issue tracker, a chat room, an email address, etc.

Roadmap

If you have ideas for releases in the future, it is a good idea to list them in the README.

Contributing

State if you are open to contributions and what your requirements are for accepting them.

For people who want to make changes to your project, it's helpful to have some documentation on how to get started. Perhaps there is a script that they should run or some environment variables that they need to set. Make these steps explicit. These instructions could also be useful to your future self.

You can also document commands to lint the code or run tests. These steps help to ensure high code quality and reduce the likelihood that the changes inadvertently break something. Having instructions for running tests is especially helpful if it requires external setup, such as starting a Selenium server for testing in a browser.

Authors and acknowledgment

Show your appreciation to those who have contributed to the project.

License

For open source projects, say how it is licensed.

Project status

In progress