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Workflows

This is a list of workflows configured in the JOSS papers repo that are triggered by the editorial bot.

Accept

This workflow is triggered by the @editorialbot accept command.

Repository and paper info

This workflow is triggered by the @editorialbot check repository command, and is also triggered automatically when a new review or pre preview issue is created.

  • It uses the repository-and-paper-checks action to run checks on the submitted software repository and paper file

  • It labels the issue with the more used languages of the software repository

  • Then post back comments with info on the software authors and file types, on the license of the submitted software and on the length of the paper file and the presence of a Statement of need section in it

Compile pdf

This workflow is triggered by the @editorialbot generate pdf command.

  • First it uses the paper action to compile the pdf

  • Using the upload-files action it pushes the paper.pdf file to a branch in the papers repo

  • And finally posts a comment to the original review issue with links to view and download the pdf file

Preprint

This workflow is triggered by the @editorialbot generate preprint command.

  • First it uses the preprint action to generate a LaTeX file suitable to send to preprint archives and saves it as an artefact with a 24h expiration date.

  • Then it posts a comment to the original review issue with a link to the the page where the preprint file is located

Re-accept

This workflow is triggered by the @editorialbot reaccept command.

Recommend acceptance

This workflow is triggered by the @editorialbot recommend-accept command.

  • It uses the paper action to compile the pdf and generate XML metadata files

  • The files are uploaded to a branch in the papers repo using the upload-files action

  • And a pull request is open (using the pull-request action) so the files can be easily inspected

  • Then the metadata files are validated with the validate-metadata-files action

  • If no problems are found with the files, a comment is posted to the original review issue with links to view the files and the issue is labeled as recommend-accept, otherwise a link to any error found is posted in a comment in the review issue

Check bibtex references

This workflow is triggered by the @editorialbot check references command, and is also triggered automatically when a new review or pre preview issue is created.

  • It uses the check-references action to check the validity of the DOIs listed in the .bibfile containing the bibliographic references of a paper submitted for review.

  • It posts an error comment if no .bib file is found

  • It posts a comment to the original issue with a list of valid/invalid/missing DOIs

Retract paper

This workflow is meant to be triggered manually. It requires as input the review issue number of the paper to be retracted and the URL of the markdown file containing the retraction notice text. It can be run in draft or in final mode.

  • It uses the retraction action to compile the pdf, generate XML metadata files and optionally accept the retracion notice.

  • Draft mode will generate a zip with pdf, jats and crossref files for the retraction notice and save it as an artefact with a 24h expiration date.

  • Final mode will also merge the files into the joss-papers repository and deposit the retraction with JOSS and with Crossref.

Secrets

For the workflows to work some values are added to the repo settings in the actions secrets section:

To allow the bot to interact with the JOSS reviews and JOSS site:

BOT_TOKEN
JOSS_SECRET

For Crossref depositing:

CROSSREF_USERNAME
CROSSREF_PASSWORD

To post to Mastodon:

MASTODON_ACCESS_TOKEN
MASTODON_INSTANCE_URL
MASTODON_USER

To post to Twitter:

TWITTER_ACCESS_TOKEN
TWITTER_ACCESS_TOKEN_SECRET
TWITTER_CONSUMER_KEY
TWITTER_CONSUMER_SECRET