
JOSS Documentation Open Journals Sep 28, 2021 Author and Reviewer Guides 1 About this site 3 2 Submitting a paper to JOSS 5 3 Sponsors and affiliates 7 3.1 Submitting a paper to JOSS.......................................7 3.1.1 Submission requirements....................................7 3.1.1.1 What we mean by research software.........................8 3.1.1.2 Substantial scholarly effort..............................8 3.1.1.3 Co-publication of science, methods, and software..................8 3.1.1.3.1 Other venues for reviewing and publishing software packages.......9 3.1.1.4 Should I write my own software or contribute to an existing package?........9 3.1.1.5 Questions? Open an issue to ask...........................9 3.1.2 Typical paper submission flow.................................9 3.1.3 What should my paper contain?................................9 3.1.4 Example paper and bibliography................................ 10 3.1.5 Checking that your paper compiles............................... 13 3.1.5.1 JOSS paper preview service.............................. 13 3.1.5.2 GitHub Action..................................... 14 3.1.5.3 Docker......................................... 14 3.1.6 Submitting your paper..................................... 14 3.1.7 No submission fees....................................... 14 3.1.8 Preprint Policy......................................... 14 3.1.9 Authorship........................................... 14 3.1.10 Submissions using proprietary languages/development environments............. 15 3.1.11 The review process....................................... 15 3.1.12 Confidential requests...................................... 15 3.2 Reviewing for JOSS........................................... 15 3.2.1 Guiding principles....................................... 15 3.2.2 JOSS Conflict of Interest Policy................................ 16 3.3 Review criteria.............................................. 16 3.3.1 The JOSS paper......................................... 16 3.3.2 Review items.......................................... 17 3.3.2.1 Software license.................................... 17 3.3.2.2 Substantial scholarly effort.............................. 17 3.3.2.3 Documentation.................................... 18 3.3.2.3.1 A statement of need............................. 18 i 3.3.2.3.2 Installation instructions........................... 18 3.3.2.3.3 Example usage............................... 18 3.3.2.3.4 API documentation............................. 18 3.3.2.3.5 Community guidelines........................... 18 3.3.2.4 Functionality...................................... 18 3.3.2.5 Tests.......................................... 19 3.3.3 Other considerations...................................... 19 3.3.3.1 Authorship....................................... 19 3.3.3.2 An important note about ‘novel’ software and citations of relevant work...... 19 3.3.3.3 What happens if the software I’m reviewing doesn’t meet the JOSS criteria?.... 19 3.3.3.4 What about submissions that rely upon proprietary languages/development environ- ments?......................................... 19 3.4 Review checklist............................................. 19 3.4.1 Conflict of interest....................................... 20 3.4.2 Code of Conduct........................................ 20 3.4.3 General checks......................................... 20 3.4.4 Functionality.......................................... 20 3.4.5 Documentation......................................... 20 3.4.6 Software paper......................................... 21 3.5 Editorial Guide.............................................. 21 3.5.1 Pre-review............................................ 21 3.5.1.1 How papers are assigned to editors.......................... 21 3.5.1.2 Finding reviewers................................... 22 3.5.1.3 Starting the review................................... 23 3.5.2 Review............................................. 23 3.5.2.1 Adding a new reviewer once the review has started.................. 23 3.5.3 After reviewers recommend acceptance............................ 24 3.5.4 Handling of papers published together with AAS publishing................. 24 3.5.5 Processing of rOpenSci-reviewed and accepted submissions................. 25 3.5.6 Rejecting a paper........................................ 25 3.5.6.1 Voting on papers flagged as potentially out of scope................. 25 3.5.7 Sample messages for authors and reviewers.......................... 26 3.5.7.1 Sample email to potential reviewers.......................... 26 3.5.7.2 Query scope of submission.............................. 26 3.5.7.3 GitHub invite to potential reviewers.......................... 27 3.5.7.4 Message to reviewers at the start of a review..................... 27 3.5.7.5 Message to authors at the end of a review....................... 27 3.5.7.6............................................. 27 3.5.8 Overview of editorial process.................................. 27 3.5.9 Visualization of editorial flow................................. 29 3.5.10 Expectations on JOSS editors.................................. 30 3.5.10.1 Responding to editorial assignments......................... 30 3.5.10.2 Continued attention to assigned submissions..................... 30 3.5.11 Out of office........................................... 30 3.5.12 Editorial buddy......................................... 30 3.5.13 Managing notifications..................................... 31 3.5.13.1 Things you should do when joining the editorial team................ 31 3.6 Interacting with Whedon......................................... 32 3.6.1 Author commands....................................... 33 3.6.1.1 Compiling papers................................... 33 3.6.1.1.1 Compiling papers from a non-default branch................ 34 3.6.1.2 Finding reviewers................................... 34 3.6.2 Editorial commands....................................... 34 3.6.2.1 Assigning an editor.................................. 34 ii 3.6.2.2 Inviting an editor................................... 34 3.6.2.3 Adding and removing reviewers............................ 34 3.6.2.4 Starting the review................................... 35 3.6.2.5 Reminding reviewers and authors........................... 35 3.6.2.6 Setting the software archive.............................. 35 3.6.2.7 Changing the software version............................ 36 3.6.3 Accepting a paper (dry run)................................... 36 3.6.3.1 Check references................................... 36 3.6.4 Accepting a paper (for real)................................... 36 3.7 Installing the JOSS application..................................... 36 3.7.1 Setting up a local development environment.......................... 37 3.7.2 Deploying your JOSS application............................... 37 3.7.3 Making modifications to launch your own site......................... 38 3.7.3.1 Modifying your site configuration........................... 38 3.7.3.1.1 Updating your application database..................... 39 3.7.3.2 Modifying your site contents............................. 39 3.7.4 Deploying your Whedon-API Application........................... 39 3.7.5 Modifying your Whedon-API deployment........................... 40 3.7.5.1 Modifying your Whedon-API configuration..................... 40 iii iv JOSS Documentation The Journal of Open Source Software (JOSS) is a developer friendly journal for research software packages. JOSS is an academic journal (ISSN 2475-9066) with a formal peer-review process that is designed to improve the quality of the software submitted. Upon acceptance into JOSS, we mint a CrossRef DOI for your paper and we list it on the JOSS website. Author and Reviewer Guides 1 JOSS Documentation 2 Author and Reviewer Guides CHAPTER 1 About this site This site contains documentation for authors interested in submitting to JOSS, reviewers who have generously volun- teered their time to review submissions, and editors who manage the JOSS editorial process. If you’re interested in learning more about JOSS, you might want to read: • Our announcement blog post describing some of the motivations for starting a new journal • The paper in Computing in Science and Engineering introducing JOSS • The paper in PeerJ CS describing the first year of JOSS • The about page on the main JOSS site 3 JOSS Documentation 4 Chapter 1. About this site CHAPTER 2 Submitting a paper to JOSS If you’d like to submit a paper to JOSS, please read the author submission guidelines in the Submitting a paper to JOSS section. 5 JOSS Documentation 6 Chapter 2. Submitting a paper to JOSS CHAPTER 3 Sponsors and affiliates JOSS is a proud affiliate of the Open Source Initiative. As such, we are committed to public support for open source software and the role OSI plays therein. In addition, Open Journals (the parent entity behind JOSS) is a NumFOCUS- sponsored project. 3.1 Submitting a paper to JOSS If you’ve already developed a fully featured research code, released it under an OSI-approved license, and written good documentation and tests, then we expect that it should take perhaps an hour or two to prepare and submit your paper to JOSS. But please read these instructions carefully for a streamlined submission. 3.1.1 Submission requirements • The software must be open source as per the OSI definition. • The software must have an obvious research application. • You must be a major contributor to the software
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