CODECHECK bundle

The CODECHECK bundle is not formally specified, as its contents are largely at the discretion of the codechecker. Unlike the CODECHECK configuration file, which has a more formal specification. Therefore, this page acts as a guidance for codecheckers and may evolve over time.

The CODECHECK bundle includes all files that the codechecker used to conduct the CODECHECK. This may include a copy of the author’s files, and any additional files that the codechecker created to assisst them in their CODECHECK.

Computing environment documentation

• Binder’s REES specification, for example by creating one or several of the following files or tools:
  • Dockerfile
  • Binder
  • environment.yml
  • requirements.txt
  • DESCRIPTION file (R package)
• virtual environments (Python)
• package renv (R)
• Dockerfile and Docker image, see Ten simple rules for writing Dockerfiles for reproducible data science
• …

Codecheck certificate with computational notebooks

Computational notebooks such as R Markdown (Rmd), Jupyter, or Quarto have very nice features that are helpful for writing a CODECHECK certificate.

• Literate programming and code chunks (hidden, visible) with nice looking and mostly hastle free PDF output (using tinytex)
• You can configure document metadata, e.g. the title or subtitle, anywhere in the document, so you can choose to configure them only in the codecheck.yml, see this example
• You can capture the metadata of the computing environment in an automatically generated colophon that lists installed packages and session information (using sessionInfo() or devtools::session_info() in R), see for example this one in the template from rrtools by Ben Marwick, or a reproducibility receipt, see this code example, which adds git repository information and information about external libraries to the session information

We provide templates for R Markdown and Jupyter notebooks in an R package and a Python project:

• R package codecheck with Rmd templates and functions to validate metadata and upload the certificate to Zenodo
• Python project codecheck-py with a Jupyter notebook template and functions to validate

In the future, a CODECHECK assistant could be helpful - share your ideas an wishes in the project repository.