README.md

Register of CODECHECK certificates

See the register online at https://codecheck.org.uk/register/.

Editing the register

The main register file is a simple CSV file, register.csv which connects the pieces published elsewhere to create a complete metadata set for each CODECHECK. The CSV file should not unneedingly replicate information from elsewhere, especially from the CODECHECK configuration files (i.e., codecheck.yml). Here are some possible values or rules for the specific columns in the file:

• Certificate: the certificate number
• Repository: qualified reference to the repository where the codecheck.yml file can be retrieved; the file must be in the project "root"; supported types and examples:
  • github:: for referencing a GitHub repository using org/name, e.g., github::codecheckers/Piccolo-2020 from codecheckers organisation
  • osf:: for referencing an OSF project using the project identifier, e.g., osf::ZTC7M
• Type: type of the check, e.g., solicited as part of peer review in a journal or conference, or initiated from the community; possible values:
  • community = check initiated independently by community members and following the CODECHECK community workflow guide; may be qualified further, e.g., for preprints as community (preprint)
  • journal (<journal abbreviation>) = check conducted as part of a peer review process with a scientific journal, including a reference to the check in the published article; the journal abbreviation uses the ISO 4 standard name for the journal, using common capitalization and omitting full stops, for example J Geogr Syst or GigaScience (find the correct name via Wikipedia or the journal website)
  • conference (<conf name>) = check conducted as part of a peer review process at a scientific conference, e.g., conference (AGILEGIS)
• Issue: number of the issue in the register project where the CODECHECK is managed (informative mostly, not for metadata retrieval)

To update the register, simply edit the register.csv file and submit the change. A GitHub Action will apply the process outlined below for manual rendering to update the different representations of the register, including the website, in case the main register file changes.

Note: The GitHub action requieres a PAT token to be added, because the default per-action-run token is not used by the R code that renders the package. See the docs about manual rendering below for details.

Deposit/archive

This repository is archived manually, in regular intervals, on Zenodo using the GitHub-Zenodo-Integration. To deposit a new version on Zenodo, create a new release following the naming scheme of previous releases. Then, go to the new record and manually make the following changes:

• add the record to the CODECHECK community (if not already included)
• change the record type to "Dataset"
• update the ORCIDs and affiliations of authors
• set the license to "Open Data Commons Attribution License"
• update the Desription text (see previous records)
• add https://codecheck.org.uk/register/ as a related identifier with "is new version of this upload"

Files in this repository

• register.csv: the main file to edit to put a new certificate into the register
• Makefile: common commands for managing the register
• Dockerfile: Dockerfile for building and image to use in the GitHub action; needs to be build and pushed to Docker Hub
• docs/register.md: Markdown table of the register with additional metadata for checks
• docs/register.json and docs/featured.json: JSON file with additional metadata for checks, whereas the "featured" file only contains the last ten codechecks; use for integration of CODECHECK metadata in third party services, APIs, etc.; public links: https://codecheck.org.uk/register/register.json and https://codecheck.org.uk/register/featured.json
• docs/index.html: HTML rendering of the extended register

The above files are human-readable and machine-readable representations based on the register and metadata from the codecheck.yml files.

Do not edit any file in the docs directory by hand! Edit only register.csv.

Manual register rendering and checking

The representations above can also be generated manually using the following command from the codecheck R package:

# R -q -e "remotes::install_github('codecheckers/codecheck')"

R -q -e "codecheck::register_render(); warnings()"

You can also check the configuration files with

R -q -e "codecheck::register_check(); warnings()"

and clear the cache (in case you made a recent change to an online repo) with R -q -e "codecheck::register_clear_cache()".

To fix problems with hitting the GitHub API rate limit on local register management, go to your PAT page and save a PAT in the environment variable GITHUB_PAT to the file .Renviron next to this README file. Alternatively, you may log into your GitHub account locally using the GitHub CLI (gh).

License

The data in this repository is published under a Open Data Commons Attribution License (ODC-BY).

The code and documentation in this repository is published under the MIT License.

See file LICENSE for details.

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