workshop-computational-reproducibility
Material for the workshop 'Best Practices for Writing Reproducible Code'
https://github.com/utrechtuniversity/workshop-computational-reproducibility
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Repository
Material for the workshop 'Best Practices for Writing Reproducible Code'
Basic Info
- Host: GitHub
- Owner: UtrechtUniversity
- License: other
- Language: SCSS
- Default Branch: main
- Homepage: https://utrechtuniversity.github.io/workshop-computational-reproducibility/
- Size: 17.1 MB
Statistics
- Stars: 11
- Watchers: 5
- Forks: 13
- Open Issues: 19
- Releases: 1
Metadata Files
README.md
Best Practices for Writing Reproducible Code
If you are looking at a GitHub README, please note that the course book and the slides are available via the course website.
Ensuring your research is reproducible can be a difficult task. Scripting your analysis is a start, but this in and of itself is no guarantee that you, or someone else, can faithfully repeat your work at a later stage. In this workshop, we will help you not only to make your work reproducible, but also to increase the efficiency of your workflow. We do this by teaching you a few good programming habits: how to set up a good project structure, how to code and comment well, and how to document your code so that it can be used by others. We will furthermore introduce you to Git and GitHub, which are essential tools in managing and publishing code. Reproducibility requires extra effort, but we will focus on teaching you skills that will save you much more time in the long run than they cost to implement.
Preparation
If you are attending this workshop, you can prepare a few things so we can hit the ground running! We have more details on this page.
Schedule
Day 1
| Time | Activity | |-------:|----------| | 9:00 | Welcome & introduction)| | 9:30 | Project setup & version control with git | | 10:45 | Questions & discussion | | 11:00 | Break | | 11:15 | Code quality | | 12:45 | Questions & discussion | | 13:00 | End |
Day 2
| Time | Activity | |-------:|----------| | 9:00 | Code quality discussion | | 9:15 | Documentation | | 10:45 | Questions & discussion | | 11:00 | Break | | 11:15 | Accessibility & reproducibility | | 12:15 | Reproduction of projects | | 13:00 | End |
External resources, recommended reading, and developer inspiration
- Software Development Guide by the Netherlands eScience Center
- The Turing Way: a guide to reproducible data science by the Turing Institute
- Software Carpentry lessons
- Pro GIT
- Good Enough Practices in Scientific Computing
License
All workshop material is licensed under a Creative Commons Attribution 4.0 International License. View the license here.
History and acknowledgements
This course was developed at Utrecht University, supported by the Open Science Community Utrecht (OSCU) and Research Data Management (RDM) support.
Workshop development is being coordinated by Neha Moopen, and the course received contributions from (in alphabetical order):
Owner
- Name: Utrecht University
- Login: UtrechtUniversity
- Kind: organization
- Email: info.rdm@uu.nl
- Location: Utrecht, The Netherlands
- Website: https://www.uu.nl
- Repositories: 85
- Profile: https://github.com/UtrechtUniversity
The central place for managing code and software for Utrecht University researchers and employees
Citation (CITATION.cff)
cff-version: 1.2.0
title: Workshop Best Practices for Writing Reproducible Code
message: 'If you reuse our materials, please cite us!'
type: software
authors:
- given-names: Research Data Management Support
affiliation: Utrecht University
email: info.rdm@uu.nl
identifiers:
- type: doi
value: 10.5281/zenodo.8167841
description: The concept DOI for the collection of these materials.
repository-code: >-
https://github.com/UtrechtUniversity/workshop-computational-reproducibility
url: 'https://uu.nl/rdm'
abstract: >
This repository contains the materials for the two-day
workshop 'Best Practices in Writing Reproducible Code',
organized by Research Data Management Support at Utrecht
University, the Netherlands.
keywords:
- reproducibility
- open science
- programming
- dependency
- documentation
- version control
- reusability
- robustness
- workshop
license: CC-BY-4.0
version: 2023.07.21
date-released: '2023-07-21'
GitHub Events
Total
- Issues event: 7
- Watch event: 1
- Delete event: 9
- Issue comment event: 5
- Push event: 71
- Pull request review comment event: 28
- Pull request review event: 17
- Pull request event: 20
- Create event: 9
Last Year
- Issues event: 7
- Watch event: 1
- Delete event: 9
- Issue comment event: 5
- Push event: 71
- Pull request review comment event: 28
- Pull request review event: 17
- Pull request event: 20
- Create event: 9
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 53
- Total pull requests: 35
- Average time to close issues: over 1 year
- Average time to close pull requests: 13 days
- Total issue authors: 9
- Total pull request authors: 7
- Average comments per issue: 0.6
- Average comments per pull request: 0.23
- Merged pull requests: 27
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 6
- Pull requests: 14
- Average time to close issues: about 6 hours
- Average time to close pull requests: 3 days
- Issue authors: 3
- Pull request authors: 3
- Average comments per issue: 0.0
- Average comments per pull request: 0.36
- Merged pull requests: 10
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- bvreede (19)
- nehamoopen (18)
- chStaiger (6)
- jelletreep (4)
- laurensstoop (1)
- javimangal (1)
- jurra (1)
- hanneoberman (1)
- SanderKeulers (1)
Pull Request Authors
- jelletreep (17)
- chStaiger (9)
- bvreede (5)
- hanneoberman (3)
- DorienHuijser (3)
- parisa-zahedi (2)
- nehamoopen (1)
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Dependencies
- knitr * suggests
- rmarkdown * suggests
- testthat >= 2.1.0 suggests