Create course slides #7
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| title: Reproducibility in Scientific Computing | ||||||
| authors: Jack Franklin & Marion Weinzierl | ||||||
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| # Introduction: What is reproducibility? | ||||||
| - Reproducing results | ||||||
| - Portability | ||||||
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| # A likely scenario | ||||||
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| - You have just joined a new research group as a Student/Researcher/PI. | ||||||
| - The group use a custom pipeline/setup to perform their data analysis/simulations. | ||||||
| - You try to get the setup working on your local system/a new hpc system and... | ||||||
| It doesn't work! | ||||||
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| # Version Control | ||||||
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| - First put things into VC | ||||||
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| - Then any changes/fixes can be tracked | ||||||
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There was a problem hiding this comment. Maybe also something about better collaboration |
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| $-- Since git will be covered during the week we shouldn't need to do too much | ||||||
| $-- here. | ||||||
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| # Documentation | ||||||
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| - README | ||||||
| - User Docs | ||||||
| - Dev Docs | ||||||
| - Comments? | ||||||
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| # Dependencies | ||||||
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| - Basic documentation | ||||||
| - Project files (e.g. project.toml for python etc) | ||||||
| - System dependencies (nix/guix/docker?) | ||||||
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There was a problem hiding this comment. Add something about automatisation - creating (at least) scripts to run the simulation pipeline, produce figures etc |
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| # Testing | ||||||
| - Unit tests | ||||||
| - Integration tests | ||||||
| - Automating tests (CI etc) | ||||||
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| # FAIR Principles | ||||||
| - Findability | ||||||
| - Accessibility | ||||||
| - Interoperability | ||||||
| - Reuse | ||||||
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There was a problem hiding this comment. Notebooks and containers |
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| $-- Maybe we should look at this retrospectively, and see what elements we covered and | ||||||
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There was a problem hiding this comment. Reproducibility reviews - let new team members run the code according to documentation, and raise issues for things that are not clear/outdated. Also, point towards reprohacks and other reproducibility initiatives. |
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| $-- where we could improve on. | ||||||
| $-- Also a good way to talk about why these are good principles to start a project with | ||||||
| $-- since we can show that they avoid most/all the problems that we had to solve | ||||||
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| # Conclusion/Outlook | ||||||
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