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
• Introduce point of exercises: Get hands dirty, no time to do all, so do not worry, all have solutions and can be done on own time
• Schedule
• Materials
  • Slides
    • [] Remove what is covered in Exercises
  • Exercises
    • Test for timing
    • Solutions
  • Rest of materials
  • Extra slides "what we did not talk about"
    • Containers
    • Testing
• connect materials to HPC
• add collaborative git?
• 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)
• Zenodo

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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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Preparation instructions

• GitHub account
• Sphinx?

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Schedule

14.30 - 14.35 context break 5 min
14.35 - 14.50 Why are we talking about this + example intro 15 min
14.50 - 15.10 Version control 20 min
15.10 - 15.30 Exercise I 20 min (GitHub)
15.30 - 15.50 Reproducibility 20 min
15.50 - 16.10 Break 20 min
16.10 - 16.30 Documentation 20 min
16.30 - 16.50 Exercise II 20 min (ReadMe + Sphinx)
16.50 - 17.00 Sharing and reusing 10 min
17.00 - 17.20 Exercise III 20 min (own org, Derivative work, Licensing situation)
17.20 - 17.30 wrapup 10 min

Exercise sessions

Exercise I (20 min)

• Version control

Git-1: Turn a project to a Git repo and share it
Git-2: Contribute to the example repository
Git-3: Archaeology using Git annotate (“blame”)

Exercise II (20 min)

• Documentation

Documentation-1: Comments
TODO: Documentation-2: ReadMe
Documentation-3a: Sphinx
Documentation-3b: Add more content to your example Sphinx documentation

Exercise III (20 min)

Sharing-1: Licensing
Sharing-2: CITATION.cff and Zenodo sandbox
Sharing-3: What constitutes derivative work?
Sharing-4: Licensing situations

Mini exercises

• Example project

• Reproducibility

Reproducibility-1: Time-capsule of dependencies