# Interacting with Whedon¶

Whedon or @whedon on GitHub, is our editorial bot that interacts with authors, reviewers, and editors on JOSS reviews.

@whedon can do a bunch of different things. If you want to ask @whedon what it can do, simply type the following in a JOSS review or pre-review issue:

@whedon commands


This will return an output something like this (the exact response depends upon whether or not you’re an editor):

# List all of Whedon's capabilities
@whedon commands

# Assign a GitHub user as the sole reviewer of this submission

# Add a GitHub user to the reviewers of this submission

# Remove a GitHub user from the reviewers of this submission

# List of editor GitHub usernames
@whedon list editors

# List of reviewers together with programming language preferences and domain expertise
@whedon list reviewers

# Change editorial assignment

# Set the software archive DOI at the top of the issue e.g.
@whedon set 10.0000/zenodo.00000 as archive

# Set the software version at the top of the issue e.g.
@whedon set v1.0.1 as version

# Open the review issue
@whedon start review

# Compile the paper
@whedon generate pdf

# Compile the paper from alternative branch
@whedon generate pdf from branch custom-branch-name

# Remind an author or reviewer to return to a review after a
# certain period of time (supported units days and weeks)
@whedon remind @reviewer in 2 weeks

# Ask Whedon to accept the paper and deposit with Crossref
@whedon accept

# Ask Whedon to check the references for missing DOIs
@whedon check references


## Author commands¶

A subset of the Whedon commands are available to authors (and reviewers):

### Compiling papers¶

When a pre-review or review issue is opened, @whedon will try to compile the JOSS paper by looking for a paper.md file in the repository specified when the paper was submitted.

If it can’t find the paper.md file it will say as much in the review issue. If it can’t compile the paper (i.e. there’s some kind of Pandoc error), it will try and report that error back in the thread too.

Note

If you want to see what command @whedon is running when compiling the JOSS paper, take a look at the code here.

Anyone can ask @whedon to compile the paper again (e.g. after a change has been made). To do this simply comment on the review thread as follows:

@whedon generate pdf


#### Compiling papers from a non-default branch¶

By default, Whedon will look for papers in the default git branch. If you want to compile a paper from a non-default branch, this can be done as follows:

@whedon generate pdf from branch custom-branch-name


### Finding reviewers¶

Sometimes submitting authors suggest people the think might be appropriate to review their submission. If you want the link to the current list of JOSS reviewers, type the following in the review thread:

@whedon list reviewers


## Editorial commands¶

Most of @whedon’s functionality can only be used by the journal editors.

### Assigning an editor¶

Editors can either assign themselves or other editors as the editor of a submission as follows:

@whedon assign @editorname as editor


Reviewers should be assigned by using the following commands:

# Assign a GitHub user as the sole reviewer of this submission

# Add a GitHub user to the reviewers of this submission

# Remove a GitHub user from the reviewers of this submission


Note

The assign command clobbers all reviewer assignments. If you want to add an additional reviewer use the add command.

### Starting the review¶

Once the reviewer(s) and editor have been assigned in the pre-review issue, the editor starts the review with:

@whedon start review


Important

If a reviewer recants their commitment or is unresponsive, editors can remove them with the command @whedon remove @username as reviewer. You can also add new reviewers in the REVIEW issue, but in this case, you need to manually add a review checklist for them by editing the issue body.

### Reminding reviewers and authors¶

Whedon can reminders authors and reviewers after a specified amount of time to return to the review issue. Reminders can only be set by editors, and only for REVIEW issues. For example:

# Remind the reviewer in two weeks to return to the review
@whedon remind @reviewer in two weeks

# Remind the reviewer in five days to return to the review
@whedon remind @reviewer in five days

# Remind the author in two weeks to return to the review
@whedon remind @author in two weeks


Note

Most units of times are understood by Whedon e.g. hour/hours/day/days/week/weeks.

Important

For reviewers, the reminder will only be triggered if the reviewer’s review is outstanding (i.e. outstanding checkboxes).

### Setting the software archive¶

When a submission is accepted, we ask that the authors create an archive (on Zenodo, figshare, or other) and post the archive DOI in the REVIEW issue. The editor should add the accepted label on the issue and ask @whedon to add the archive to the issue as follows:

@whedon set 10.0000/zenodo.00000 as archive


### Changing the software version¶

Sometimes the version of the software changes as a consequence of the review process. To update the version of the software do the following:

@whedon set v1.0.1 as version


## Accepting a paper (dry run)¶

Whedon can accept a paper from the review issue. This includes generating the final paper PDF, Crossref metedata, and depositing this metadata with the Crossref API.

JOSS topic editors can ask for the final proofs to be created by Whedon with the following command:

@whedon accept


On issuing this command, Whedon will also check the references of the paper for any missing DOIs. This command can be triggered separately:

### Check references¶

@whedon check references


Note

Whedon can verify that DOIs resolve, but cannot verify that the DOI associated with a paper is actually correct. In addition, DOI suggestions from Whedon are just that - i.e. they may not be correct.

## Accepting a paper (for real)¶

If everything looks good with the draft proofs from the @whedon accept command, JOSS editors-in-chief can take the additional step of actually accepting the JOSS paper with the following command:

@whedon accept deposit=true


Note

This command is only available to the JOSS editor-in-chief, or associate editor-in-chiefs.