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Inspiration from Wilson et al #150

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bclaremar opened this issue Jan 22, 2025 · 7 comments
Open

Inspiration from Wilson et al #150

bclaremar opened this issue Jan 22, 2025 · 7 comments
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@LarsEklund @bclaremar

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@bclaremar
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Wilson, Greg, et al. "Good enough practices in scientific computing." PLoS computational biology 13.6 (2017): e1005510. here

I have started to look into it and feel that it will probably suggest me to add/remove material for my part.

I will probably list some thoughts that I would need input from you how to implement things
richelbilderbeek added a commit to programming-formalisms/programming_formalisms_project_summer_2025 that referenced this issue Jan 30, 2025
@richelbilderbeek
Use 'docs', after UPPMAX/programming_formalisms#150
ad67ac0
richelbilderbeek added a commit to programming-formalisms/programming_formalisms_example_project that referenced this issue Jan 30, 2025
@richelbilderbeek
Use 'docs', as recommended by UPPMAX/programming_formalisms#150
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@bclaremar
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Summary of practices

  • data management (not focus)
  • software
  • collab
  • project organization
  • tracking changes
  • manuscripts (not focus)

@bclaremar
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bclaremar commented Jan 30, 2025 •
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Software

  • explanation comment at the start of the program (also "help function" as for './program -h')
  • functions
    • names for variables and functions
  • eliminate duplication
    • libraries
    • test if you rely
  • dependencies and requirements explicit
  • program behavior by if/else (possibly arguments from outside)
  • run-all script and/or main program (also related to project organization)
  • example/test data set
  • DOI like zenodo

@bclaremar
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Collaboration

  • overview: README etc
  • to-do list/issues
  • communication strategies
  • license explicit
    • recommendations and why
  • citable

@bclaremar
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bclaremar commented Jan 30, 2025 •
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Project organization

  • proj folder/git repo
  • sub directories
    • doc, src, results, (bin)
  • run-all script and/or main program (also related to software)
  • files
    • README
  • namings

@bclaremar
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bclaremar commented Feb 5, 2025 •
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According to @LarsEklund
good tools and practices for refactoring and devel steps
focus scientific computing
lacking planning steps like requirements, analysis and design

@Lars-Uppmax
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We are discussing, how to lecture about these issues in a concise and comprehensive manner - What is good enough, or bare minimum How does not preforming formal planning effect your project.

@richelbilderbeek richelbilderbeek removed their assignment Feb 5, 2025
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I am using this paper already, hence I unassign. I am happy to see the team is adopting some of its practices 👍

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