nuest/ten-simple-rules-dockerfiles repository overview

⁠Ten Simple Rules for Writing Dockerfiles for Reproducible Data Science

The manuscript is published as a preprint: https://osf.io/fsd7t⁠

We welcome your feedback, e.g., by opening issues on this repository or with OSF annotations⁠. We especially welcome your help by creating strong illustrating examples, see issue #4⁠.

Ten Simple Rules Collection on PLOS⁠

Current draft as PDF⁠

⁠Author contributions

DN conceived the idea and contributed to conceptualisation, methodology, and writing - original draft, review & editing, and validation. VS contributed to conceptualisation, methodology, and writing - original draft, and review & editing. BM contributed to writing – review & editing. SJE contributed to conceptualisation, writing – review & editing, and validation. THe contributed to conceptualisation. THi contributed to writing – review & editing. BDE contributed to conceptualisation, writing – review & editing, visualisation, and validation. This articles was written collaboratively on GitHub, where contributions in form of text or discussions comments⁠ are documented: https://github.com/nuest/ten-simple-rules-dockerfiles/⁠.

⁠Run container for editing the document

First, build the container. It will install the dependencies that you need for compiling the LaTex.

docker build -t ten-simple-rules-dockerfiles .

Then run it! You'll need to set a password to login with user "rstudio."

PASSWORD=simple
docker run --rm -it -p 8787:8787 -e PASSWORD=$PASSWORD -v $(pwd):/home/rstudio/ten-simple-rules-dockerfiles ten-simple-rules-dockerfiles

Open http://localhost:8787⁠ to get to RStudio, log in, and navigate to the directory ~/ten-simple-rules-dockerfiles to open the Rmd file and start editing. Use the "Knit" button to render the PDF. The first rendering takes a bit longer, because required LaTeX packages must be installed.

See more options in the Rocker docs⁠.

⁠Run container for building the PDF

See the end of the Dockerfile for instructions.

⁠Useful snippets

• Get all author's GitHub handles:

  cat *.Rmd | grep ' # https://github.com/' | sed 's|    # https://github.com/|@|'
  

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• Get all author's emails:

  cat *.Rmd | grep 'email:' | sed 's|    email: ||'
  

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• [Work in progress!] Get a .docx file out of the Rmd so one can compare versions and generate marked-up copies of changes:

  # https://github.com/davidgohel/officedown
  library("officedown")
  rmarkdown::render("ten-simple-rules-dockerfiles.Rmd", output_format = officedown::rdocx_document(), output_file = "tsrd.docx")
  
  # https://noamross.github.io/redoc/articles/mixed-workflows-with-redoc.html
  library("redoc")
  rmarkdown::render("ten-simple-rules-dockerfiles.Rmd", output_format = redoc::redoc(), output_file = "tsrd.docx")
  

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• Compare with latexdiff

  # get a specific version of the text file
  wget -O submission.v2.tex https://raw.githubusercontent.com/nuest/ten-simple-rules-dockerfiles/submission.v2/ten-simple-rules-dockerfiles.tex
  # compare it with current version
  latexdiff --graphics-markup=2 submission.v2.tex ten-simple-rules-dockerfiles.tex > diff.tex
  # render diff.tex with RStudio
  

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⁠License

This manuscript is published under a Creative Commons Attribution 4.0 International⁠ (CC BY 4.0) license, see file LICENSE.md⁠.