🛠️ SofHarDevOps4BioMedEng:

Hands-on Workshop on Software and Hardware Developer Operations for Biomedical Engineers

Workshop

Aims

The aim of this workshop is to provide an introduction to the GitHub toolkits to manage the development of software and hardware projects for biomedical engineers.

Audience

This workshop is targeted to persons with little to none experience with GitHub tools. However, intermediate and advance users might also find the topics of interests.

Dates and times

22 to 26 August 2022! (Exact days to be confirmed)

Instructor(s)

Miguel, etc

Prerequisites

• Create GitHub account: https://github.com/
• Terminal applications: Git BASH for windows users and a terminal for mac and Linux users.
• Setting up Setting up SSH keys
• Clone this repo:

mkdir -p $HOME/repositories/ && cd $HOME/repositories/ ## suggested path
git clone git@github.com:KCL-BMEIS/SofHarDevOps4BioMedEng.git

Content

1. Introduction to GitHub

   • Version control
   • Git
     • The Good
     • The Bad
   • The concepts
     • Commits
     • Graphs
     • Branches / Tags
     • Detaching
     • Conflicts
     • Rebasing
     • Merging
     • Cherry picking

2. Project management

   • Project
   • Milestones
   • Labels
   • Discussions
   • Wikis
   • repository forks and what they are for (ie. allowing outside users to propose PRs without being collaborators on the original repo)

3. Continous Integration

   • Actions
   • doing code releases through Github and
   • triggering actions to do deployment (eg. uploading to PyPI for Python),
   • other continuous integration tasks such as testing before PRs can be accepted

4. Standards

   • Software Testing and validation (IEC 62305)
   • Medical Device Software (IEC 60601)
   • Good machine learning practices by FDA

5. Exercises

   • doing PRs in Github and what the protocol for that should be for a small team,
   • PRs between forks,

6. Software/Hardware projects

   • Version control for CAD files (pcbs, stls, others)
   • Markdown
   • CHANGELOGs
   • Jupyter notebook features
   • Jupyterlab
   • Projects combining software/hardware
     • https://github.com/nasa-jpl/open-source-rover
     • https://github.com/NVIDIA-AI-IOT/jetbot

References

• GitAhead to visualise what's going on and prevent some patterns of error
• Git cheat sheet: https://education.github.com/git-cheat-sheet-education.pdf : a quick and easy to reference document on the most common git commands. [by RS]
• Git "choose your own adventure": http://sethrobertson.github.io/GitFixUm/fixup.html. Essentially it asks a series of questions and then tells you the combination of git commands to fix whatever you need. I find it useful when you have done something particularly stupid (say pushed to remote when you did not mean to). [by RS]
• Tutorials
  • https://lab.github.com/githubtraining/first-day-on-github
  • https://lab.github.com/githubtraining/introduction-to-github
  • https://lab.github.com/githubtraining/first-day-on-github
  • http://sethrobertson.github.io/GitFixUm/fixup.html
• Onshape and gihub: https://forum.onshape.com/discussion/14327/making-onshape-document-available-on-github
• GitFlow concepts (https://www.atlassian.com/git/tutorials/comparing-workflows/gitflow-workflow) [by EK]

Reproducibility, replicability and trust in science 2022

Abstract

See submitted abstract

References

https://coursesandconferences.wellcomeconnectingscience.org/event/reproducibility-replicability-and-trust-in-science-20220907