Binder @ OSIP2019

This is the master hackmd for the OSIP2019 session on Binder. All other materials
should be linked from here.

👋 You can (and should) edit this document. To edit click on the pen symbol at the top left.

⸮? Please ask questions and to help us all remember them add them to this document.

📽 Slides: https://hackmd.io/@jVeyrAXKRpWC3e6Q9Evo6g/binder-osip2019#/

Detailed Plan

• 14.00h Start
• 14.01h Slide show
  • https://hackmd.io/@jVeyrAXKRpWC3e6Q9Evo6g/binder-osip2019
• 14.20h Why the environment matters
  • https://github.com/alan-turing-institute/the-turing-way/blob/master/workshops/boost-research-reproducibility-binder/paired_examples.md
• 14.42h Zero to Binder
  • Zero to Binder guide
  • If you want to repeat the exercise or need to look up something when you get home checkout Zero to Binder guide without instructor. It is the same workshop with additional notes.
• 15.45h Wrap up
  • questions that came up and their resolution
  • Take home points
    • data ✅
    • code ✅
    • environment ✅
    • Project Binder builds tools that automate community best practices
      • (Hopefully) you just keep doing what you were doing already
      • Reduces time and effort needed for sharing
      • Even a professor can do research again!
• 16.00h ☀️☕️🍫 Coffee 🍫☕️☀️
• 16.30h Plan for the next two hours
  • work on your own project
    • This is the thing. you should start with
    • See if you can get a (subset) of one of your research projects up and running on mybinder.org
  • Jupyter book
    • Create a (text)book where each page is a notebook that can be run
    • https://jupyter.org/jupyter-book/intro.html
  • Online courses
    • You can use Binder to power online courses
    • A great tool made in response to the problems at DataCamp https://github.com/ines/spacy-course
  • holepunch or "Binder with R"
    • A tool to make it easier to get your R
    • https://karthik.github.io/holepunch/
    • https://www.rostrum.blog/2019/08/25/holepunch-drake/
  • advanced Binder'ing
    • There are a lot of things you can customise about your Binder
    • https://repo2docker.readthedocs.io/en/latest/config_files.html#configuration-files
    • Examples of things you can do https://github.com/binder-examples/
  • Running repo2docker locally
    • Useful for situations where your code isn't public yet or you need more computational resources
    • https://repo2docker.readthedocs.io/en/latest/install.html
  • reproducibility can start small
    • don't need a whole repo, Gist works as well
• 16.40h form groups
• 16.45h start work!
• 17.45h Show and tell
  • show off what you tried
• 18.15h Wrap up
• 18.30h The End 🎉

Getting Help

🚨 During the workshop ask your question at the end of this HackMD or in person

This section is for you if you want to get help or learn more later on.

You can find Tim on twitter: twitter.com/betatim

You can find the Binder project in these places. We are

• forum: https://discourse.jupyter.org/
• chat: https://gitter.im/jupyterhub/binder
• GitHub:
  • we are super happy for new people to help out!
  • not just code!! Graphics, documentation, outreach, bugs, helping other users, …
  • (if you are new to open-source we can help mentor you)
  • https://github.com/jupyter/repo2docker
  • https://github.com/jupyterhub/binderhub

The Turing Way Project:

• https://the-turing-way.netlify.com/introduction/introduction
• GitHub: https://github.com/alan-turing-institute/the-turing-way

Questions

For exercise 3 (https://github.com/alan-turing-institute/CompEnv-Ex3) the second link doesn't work? Why?

• The answer is that there is a typo in one of the links. Where it says branch-a at the top the link actually goes to https://github.com/alan-turing-institute/CompEnv-Ex3/tree/branch-1 (branch-1) but it should be https://github.com/alan-turing-institute/CompEnv-Ex3/tree/branch-a

Can I let Binder create a Docker image with my repo and download that image to use locally?

• You can't download the image from mybinder.org but you can use the tool that mybinder.org uses to build the image locally: https://repo2docker.readthedocs.io/

Is there a good way to generate a requirements.txt?

• run pip freeze to create your requirements.txt.
• use Pipenv to manage your environments, the Pipfile generated can be used
  to generate the environment.

Can I use aws cli from mybinder.org?