In codecheckers/codecheck: Helper Functions for CODECHECK Project

Installing the package

The latest version of the package can be installed using:

remotes::install_github("codecheckers/codecheck")

Pre-requisites for being a CODECHECKER>

1. Member of the github codecheckers community.
2. Have a Zenodo account.
3. Experience with R Markdown and R is helpful, but not essential.

Clone the project

Clone the project that you wish to check into codecheckers/ organisation.

Get a certificate number

Go onto https://github.com/codecheckers/register and add an issue for the new paper to reproduce. Check the other issues for the highest used certificate number, and claim the next one by adding it to an issue comment and adding the tag "id assigned". Certificate numbers are simply YYYY-NNN where YYYY is the date and NNN is a 3 digit number that starts at 001 and increases by 1 each time.

Write a codecheck certificate

In the top-level of the repo to replicate ("the root"), start R and run the following to generate several template files. These will then need to be committed into the repo.

require(codecheck)
create_codecheck_files()

These create several files that need to be edited for the codecheck process:

1. codecheck.yml contains the metadata for the reproduction. If the author or someone else has already created it, double-check if all required information is provided - see the specification.
2. codecheck/codecheck.Rmd is a suggested R Markdown script to edit, along with Makefile and codecheck-preamble.sty to help compile the PDF.
3. codecheck/zenodo-codecheck.R for help in loading the certificate to Zenodo along with the corresponding metadata.

There is also a Makefile so that make within the codecheck folder will rebuild codecheck.pdf.

Completing the metadata file codecheck.yml

The codecheck.yml file contains all the relevant metadata for the certificate. Simply edit it to your needs, bearing in mind the specification comments at https://codecheck.org.uk/spec/config/latest.

Submitting the certificate to Zenodo

There is no requirement to use the following code to generate the record on Zenodo -- if you prefer to do it manually, that is fine. However, we encourage codecheckers to use this API as it will save time and ensure that certificates have similar structure.

You will first need a zenodo account and to generate a token to use the API. This token can be generated from https://zenodo.org/account/settings/applications/tokens/new/. The token should not be stored in your R script, but should be typed in or read from a local file and stored in the variable my_token in the file codecheck/codecheck-zenodo.R.

The metadata contained in codecheck.yml is uploaded using some helper functions from the codecheck package. To start with, you can create a new empty record on Zenodo using get_zenodo_record() and then store the resulting URL in codecheck.yml. The rest of the metadata can remain as before.

Once you are ready, upload the certificate itself using the function set_zenodo_certificate(). Whilst the zenodo record is in draft form, you can delete files from the website, and then re-add them using the API.

Once you have uploaded the certificate and checked the metadata, you can then publish the record.

Archive your repo onto zenodo so that we have a backup

close issue on register repo and update register html pages.

codecheckers/codecheck documentation built on Dec. 6, 2024, 7:38 p.m.