Checklist¶
- Choose the most appropriate method for your project for capturing your computational environment
- Capture your computational environment
- Share your captured computational environment along with your results/analysis
What to Learn Next¶
We recommend reading the chapter on Code Testing, and then the chapter on Continuous integration. Note that the chapter on Version Control is a prerequisite for the chapter on continuous integration. The Open Research chapter also contains further information on sharing research reproducibly.
Further Reading¶
The Docker documentation contains a lot of information about containers in general.
Bibliography¶
semantic versioning Creative Commons - CC BY 3.0
A. Brinckman, et al., Computing environments for reproducibility: Capturing the “Whole Tale”, Future Generation Computer Systems (2018), https://doi.org/10.1016/j.future.2017.12.029 Attribution 4.0 International (CC BY 4.0)
Paper presenting singularity CC0 1.0 Universal (CC0 1.0)
Paper presenting singularity CC0 1.0 Universal (CC0 1.0)
Package Managers Attribution-ShareAlike 4.0 International (CC BY-SA 4.0)
Talk by Will Furnass on Conda Attribution-NonCommercial-ShareAlike 4.0 International
Binder illustration Permission to use granted by Juliette Taka, Logilab and the OpenDreamKit project.
What is docker? CC BY-SA 4.0
What are containers? CC BY-SA 4.0
Docker carpentry Creative Commons Attribution 4.0
Geohackweek tutorial Creative Commons Attribution 3.0 Unported
Nüst, D., Sochat, V., Marwick, B., Eglen, S., Head, T., Hirst, T., & Evans, B. (2020, November 10). Ten simple rules for writing Dockerfiles for reproducible data science, https://doi.org/10.1371/journal.pcbi.1008316 Creative Commons Attribution 4.0 International
- Kurtzer, G. M., Sochat, V., & Bauer, M. W. (2017). Singularity: Scientific containers for mobility of compute. PLOS ONE, 12(5), e0177459. 10.1371/journal.pone.0177459