Chapter on toolboxes

[mloning]

Detailed description

This issue is a place to discuss matters relating to the writing of the chapter on the importance of framework toolboxes such as scikit-learn for reproducible science.

Table of contents

A few ideas:

• toolboxes help ensure that key parts of research code are co-developed, and unit and field tested by the wider research community
• they facilitate transparency and checkability of research code (clear abstractions, common interfaces, etc.)
• they promote appropriate workflows
• they facilitate readability

Resources

• links in with concerns about research software quality (see https://github.com/alan-turing-institute/tps-project-management/issues/22):
• https://www.bcs.org/more/about-us/press-office/press-releases/computer-coding-in-scientific-research-must-be-professionalised-to-restore-trust-bcs
• https://society-rse.org/covid-software-statement/
• http://amid.fish/reproducing-deep-rl
• https://arxiv.org/ftp/arxiv/papers/1810/1810.04570.pdf
• https://indico.ijclab.in2p3.fr/event/2914/contributions/6476/subcontributions/168/attachments/6033/7158/Likhomanenko_REP_paper.pdf

Thanks to @malvikasharan for suggesting some useful resources

Discussion points/related issues

• builds upon section on open-source software (open leadership principles), but would be more specific on toolboxes

Current status

This chapter is empty. If anyone would like to make a start they are more than welcome to do so.

• [x] Write chapter outline
• [ ] Add material to the chapter
• [ ] Combine materials into a readable chapter
• [ ] Proofread
• [ ] Request reviews
• [ ] Address reviews
• [ ] Merge to master branch.

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[srishti-nema]

Hey @mloning , I am already writing a chapter on reviewing pull requests under the Collaborating on GitHub/Gitlab chapter. I will create a PR by Monday. Let me know if any of that helps in accomplishing some of the tasks mentioned above.

[mloning]

I've opened a PR with a rough draft of the content, still work in progress.

Could we add help-wanted label? I'm actually not aware of any literature that discusses the important of data science toolboxes for reproducible research, but I'm sure there are resources out there. Any pointer would be much appreciated!

[mloning]

Hi all, I've worked on a PR #1233 but won't have time to finish it. I'm happy to help/review if anyone wants to work on this.