CodeRefinery at PDC summer school 2025

old materials:

• Last year materials: https://coderefinery.github.io/research-software-engineering
• Slides: https://cicero.xyz/v3/remark/0.14.0/github.com/coderefinery/research-software-engineering/main/presentation.md/

WIP materials: https://samumantha.github.io/research-software-engineering/

PDC Summer school webpage: https://www.pdc.kth.se/summer-school/2025

Timing: 14:30-17:30 (- few minutes in beginning and 15 min break in middle)

Mix of lecture and hands-on!
- working with neighbor?

Plan

• Samantha does lecture
• Johan assistant, asking questions and supporting answering of tricky questions
• Short break in beginning
• Longer break in middle
• 2 larger exercise sessions
• people run on own laptop (fallback: Dardel)
• Reconnect Tue 15.7
• Johan on vacation: 21.7-3.8

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Meeting notes

16.7 Johan, Samantha

• learners do not have any project work
• more exercises than time, mark as optional
• slides vs materials -> Samantha still undecided :/ but materials will stay availabe even if slides will be used for the presentation
• main exercises for the lesson: git & documentation
• "Let's bring us all to same level" instead of "this will be boring for some of you"
• dependency management for compiled languages ? (compiling etc is being discussed on Fri before by Johan)
  • cmake: non-intrusive, separate machinery, define order in which to execute files to compile + buildtime and runtime availability, constraints are defined (between x and y), scans computer for availability: if not available it throws an error (for non-optional)
  • Johan will add a brief info box on that

during PASC25: Johan, Alessandra, Parasuram, Samantha
People should understand:

• licensing as a concept
• collaborative coding
• documentation
• short on git
• testing as a concept (within a minute)
• packaging (no containers)

7.3 Johan, Samantha

• Plan: co-teaching
• We decided to go with slides
• And limit the content to really fit the timeframe, keep other stuff as extra reading material
  • eg the course has no immediate need for containers
• Johan to discuss with Allessandra what are the most important aspects of this lecture + hands-on to see what to focus on
• After that another meeting to split the content "who does what" and then start preparing

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To do

• Installation & setup instructions (to be sent before summer school) -> link to CR install instructions from material
• Schedule
• Materials
• Zenodo
• exercises + solutions
• connect materials to HPC
• add collaborative git?
• add sharing?
• wrap up - what is needed when?
• Johan add something on reproducibility for compiled languages
• Note box in reproducibility: Module versioning (default often the latest version, often but not always stable)

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Parts

• Why we are here talking about RSE
  • PDC flagship codes will be presented (Gromacs, Veloxchem and neko) -> exemplary projects for implementation of what is taught here; all sizes!
• Introduction of the example project
  • Share the link to the example repository
    Ask questions:
    • Would you know what to do with that?
    • What would you wish for?
    • Could you run it?
      -> link to lessons!
• Version control
• Documentation
  • connect to Sphinx of lesson material
  • link to gromacs: https://manual.gromacs.org/current/index.html
  • show it's textbased
• Reproducibile dependencies and environments
  • Focus on concept
• Sharing (licensing and publishing)
• (Testing)
• (Automation and reproducible workflows)
• When what is needed

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Exercises (to be updated)

• Why we are here talking about RSE
  • x
• Introduction of the example project
  • make it run?
• Version control
  • Git-1: Turn your project to a Git repo and share it
  • Git-2: Create a new branch and a new commit
  • Git-3: Archaeology using Git annotate (“blame”)
• Documentation
  • Documentation-1: Improve the README of your project
  • Documentation-2: In-code documentation
• Reproducibile dependencies and environments
  • Reproducibility-1: Time-capsule of dependencies
  • Reproducibility-2: Time-travel with containers
  • Reproducibility-3: Build a container and run it on a cluster
  • Reproducibility-4: Building a container on GitHub and running it on a cluster
  • Reproducibility-5: Building a container on a cluster
• (Testing)
  • Testing-1: Design an end-to-end test
  • Testing-2: Add a unit test
• (Automation and reproducible workflows)
• Sharing (licensing and publishing)
  • Sharing-1: Add a license file to your project
  • Sharing-2: CITATION.cff and Zenodo sandbox
  • Sharing-3: What constitutes derivative work?
  • Sharing-4: Licensing situations

Schedule

14.30 - 14.40 context break
14.40 - 14.50 Why are we talking about this
14.50 - 15.10 Version control
15.10 - 15.30 Exercises
15.30 - 15.20 Reproducible dependencies
xx - xx
16.00 - 16.20 Break
16.20 - xx Documentation
xx - xx Exercises
xx - 17.15
17.15 - 17.30 wrapup