holepunch
github/karthik/holepunch
Reproducible Notebooks with
- x - x - bit.ly/rmedicine2020
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Now
Future
Over time
Dependencies change
Datasets become
unavailable
APIs break
Two solutions
Carefully document your dependencies
Create a container with the exact versions of packages used in your analysis
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Research compendia
Gentleman and Temple Lang, 2004
...We introduce the concept of a compendium as both a container for the different elements that make up the document and its computations (i.e. text, code, data, ...), and as a means for distributing, managing and updating the collection.
The R package structure is great way to organize and share as a compendium!
Compendia need a minimal DESCRIPTION file
devtools::install_deps()
Binder
Binder is an open source project that is designed to make it really easy to share analyses that are in notebooks.
mybinder.org
Binder
mybinder.org
Any web browser
Exact versions of dependencies already installed
Your code is ready to run
How do you get your project binder ready with holepunch?
/karthik/holepunch
The workflow
Load holepunch
Write { description, Dockerfile}
Add badge to readme
Push to GitHub
Build Docker image on Binder
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Write a DESCRIPTION file
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Add a Dockerfile
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Generate a badge
Build Binder
🖐️ Commit and push to GitHub 🖐️
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write_dockerfile()
generate_badge()
build_binder()
write_compendium_ description()
🖐️ Commit and push to GitHub 🖐️
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Limitations
1 gb ram
Times out after 10 mins of inactivity
You still have to figure out how to read in data
karthik.github.io/holepunch/
bit.ly/rmedicine2020