Rmdawn: (de)construct, convert, and render R Markdown (IN SCOPE)

[marskar]

Submitting Author: Name (@marskar)
Repository Link: https://github.com/marskar/rmdawn
Documentation Link: https://marskar.github.io/rmdawn/
PyPI Link: https://pypi.org/project/rmdawn/

---

• Paste the full DESCRIPTION file inside a code block below:

The Rmdawn Python package allows you to 
- (de)construct,
- convert, and 
- render
R Markdown (Rmd) files.

The Rmdawn Python package consists of 6 shell commands and functions:

- rmdawn, which concatenates input files to generate an Rmd file.
- rmdusk, which extracts 
    - a YAML file, 
    - Python or R scripts and 
    - Markdown (md) files from Rmd files.
- rmdtor, which converts Rmd files into R scripts using knitr::purl.
- rtormd, which converts R scripts into Rmd files using knitr::spin.
- render, which creates rendered versions of R scripts or Rmd files into 
    - HTML, 
    - PDF, 
    - Word, and 
    - other output file formats.
- catren, which combines the functionality of 
    - rmdawn and 
    - render to generate an Rmd file from source files and then create an output file.

All Rmdawn functions and commands, 
except for rmdawn and rmdusk, rely on the rpy2 Python library.
The command line interface relies on the click Python library.

Scope

• Please indicate which category or categories this package falls under:

  • Data retrieval
  • Data extraction
  • Data munging
  • Data deposition
  • Data visualization
  • Reproducibility
  • Geospatial
  • Education
  • Unsure/Other (explain below)

• Explain how and why the package falls under these categories (briefly, 1-2 sentences). Please note any areas you are unsure of:

R markdown is important for reproducibility, because it facilitates literate programming, the combination of code and text. This way, descriptions of methods and results can be adjacent to the code used to obtain the results.
I frequently use R markdown for my work and I want to make it easier for the students in the Python classes I teach to use R markdown. With Rmdawn, anyone can create R markdown files from simple source files, or extract source files from R markdown files. This can promote the modularity principle without sacrificing the benefits of literate programming or the convenience of a single file with all code, text, and output for the project.

• Who is the target audience and what are scientific applications of this package?

The target audience is anyone who uses R markdown. This package may help teachers and researchers to improve the efficiency of their R markdown workflows. The package aims to be useful for both R users and non-users. The rmdawn and rmdusk do not even require R to be installed! I imagine teachers and researchers writing markdown and code files and then using rmdawn to creating R markdown files to share with their students and colleagues.

• Are there other Python packages that accomplish the same thing? If so, how does yours differ?

Related packages include:

• notedown

Notedown can all convert Jupyter notebooks into markdown and R markdown files. Rmdawn is different, because it can take a more modular approach to file conversion by extracting the contents of each code chunk into a separate file (chunk -> file) or using a source file to create each code chunk (file -> chunk).

• Any other questions or issues we should be aware of?:

P.S. Have feedback/comments about our review process? Leave a comment here

[mbjoseph]

@marskar this looks like this would be in-scope for us! I will be the handling editor for Rmdawn.

I'll close this presubmission issue, and you can open a new submission issue using the "Submit Software for Review" template whenever you are ready. Let me know if you have any questions!

[lwasser]

hey @marskar just checking in here -- are you still interested in us reviewing rmdawn? if so, please open a new software submission issue here and we can get the review process going with @mbjoseph as editor.

[marskar]

Great! Yes, I will prepare the submission. Thanks!

[lwasser]

Hey @marskar checking in on this submission again! Would you still like to submit it for review ?it just needs a formal submission so we can move it forward.

[lwasser]

closing this given no activity in over a year!