JOSS and FLOSS for science: Examples for promoting open source software and science communication
- 1. JOSS and FLOSS for science: Examples for promoting open source software and science communication Patrick Diehl Center of Computation and Technology Department of Physiscs and Astronomy Louisiana State University patrickdiehl@lsu.edu June 14, 2023 Patrick Diehl (LSU) JOSS and FLOSS June 14, 2023 1 / 30
- 2. Motivation (Open source) software is essential for computational sciences For example, developing an R or Python package with some novel algorithms which are widely used by the research community is cool, but might not yet be considered for promotions, grant applications, or for awarding tenure. Bummer: NSF rejects a grant to fund the SciPy ecosystem, saying that working on it is not impactful enough. Contrary, people get credit for papers (citations) using open source software. How can we change that, and people get credit for software? Patrick Diehl (LSU) JOSS and FLOSS June 14, 2023 2 / 30
- 3. Overview 1 The Journal of Open Source Software: Developing a Software Review Community 2 Floss for Science: A podcast promoting open source software Patrick Diehl (LSU) JOSS and FLOSS June 14, 2023 3 / 30
- 4. The Journal of Open Source Software: Developing a Software Review Community Patrick Diehl (LSU) JOSS and FLOSS June 14, 2023 4 / 30
- 5. Journal of Open Source Software Developing a Software Review Community Gabriela Alessio Robles, Mikkel Meyer Andersen, Katy Barnhart, Juanjo Bazán, Sebastian Benthall, Eloisa Bentivegna, Monica Bobra, Frederick Boehm, Jed Brown, Pierre de Buyl, Patrick Diehl, Elizabeth DuPre, Vissarion Fisikopoulos, Martin Fleischmann, Dan Foreman-Mackey, Jarvis Moore Frost, Nikoleta Glynatsi, Jeff Gostick, Richard Gowers, Hugo Gruson, Olivia Guest, David Hagan, Jayaram Harihan, Chris Hartgerink, Bita Hasheminezhad, Christina Hedges, Luiz Irber, Mark A. Jensen, Prashant K. Jha, Daniel S. Katz, Vincent Knight, Rachel Kurchin, Hugo Ledoux, Christopher R. Madan, Brian McFee, Melissa Weber Mendonça, Kevin M. Moerman, Kyle Niemeyer, Juan Nunez-Iglesias, Lorena Pantano, Stefan Pfenninger, Viviane Pons, Kristina Riemer, Amy Roberts, Marie E. Rognes, Ariel Rokem, Will Rowe, Kelly Rowland, David P. Sanders, Mehmet Hakan Satman, Fabian Scheipl, Jacob Schrieber, Adi Singh, Arfon Smith, Charlotte Soneson, Øystein Sørensen, Andrew Stewart, Fabian-Robert Stöter, Yuan Tang, George K. Thiruvathukal, Kristen Thyng, Tim Tröndle, Leonardo Uieda, Chris Vernon, Marcos Vital, Lucy Whalley, Bruce E. Wilson, Frauke Wiese https://joss.theoj.org Patrick Diehl (LSU) JOSS and FLOSS June 14, 2023 5 / 30
- 6. How to better recognize software contributions? Find some way to fit software into current (paper/book-centric) system Evolve beyond one-dimensional credit model What if we just wrote papers about software? Gives us something easy to cite No changes required to existing infrastructure Publishing in existing journals raises profile of software within a community Patrick Diehl (LSU) JOSS and FLOSS June 14, 2023 6 / 30
- 7. How to better recognize software contributions? Find some way to fit software into current (paper/book-centric) system Evolve beyond one-dimensional credit model What if we just wrote papers about software? Writing another paper can be a ton of work Many journals don’t accept software papers For long-lived software packages, static authorship presents major issues Many papers about the same software may lead to citation dilution Patrick Diehl (LSU) JOSS and FLOSS June 14, 2023 6 / 30
- 8. What if we made it as easy as possible to write and publish a software paper? Embracing the hack Patrick Diehl (LSU) JOSS and FLOSS June 14, 2023 7 / 30
- 9. A developer-friendly journal* for research software packages Paper preparation (and submission) for well-documented software should take no more than an hour The primary purpose of a JOSS paper is to enable citation credit to be given to authors of research software tiny * Other (commercial) venues exist for publishing papers about software Patrick Diehl (LSU) JOSS and FLOSS June 14, 2023 8 / 30
- 10. JOSS process (https://doi.org/10.6084/m9.figshare.5147773.v2) Make software available in repository with OSI-approved license ! : https://opensource.org/licenses Author short Markdown paper: paper.md Submit to JOSS by filling out short form Editor assigns ≥2 reviewers, who review submission $ Reviewer(s) raise comments and issues following guidelines : https://joss.readthedocs.io/en/ latest/reviewer_guidelines.html Authors fix issues & Paper published & receives JOSS DOI ⚡ JOSS 10.21105/joss.##### JOSS Under review JOSS Submitted Editor accepts paper, authors archive software ✔ Editor-in-chief reviews size and scope, and assigns an editor % rejected out of scope Patrick Diehl (LSU) JOSS and FLOSS June 14, 2023 9 / 30
- 11. JOSS - Review Checklist Agree to Conflict of Interest & Code of Conduct General checks: repository URL, license, contribution and authorship Functionality: installation, functional claims, performance Documentation: statement of need, installation instructions, example usage, functionality documentation, automated tests, community guidelines Software paper: summary, statement of need, state of the field, quality of writing, references Patrick Diehl (LSU) JOSS and FLOSS June 14, 2023 10 / 30
- 12. JOSS - Review Checklist Details Definition of each check-in JOSS documentation: https://joss.readthedocs.io/en/latest/review_criteria.html The editor helps the reviewer and author come to agreement and some criteria have guidance Installation API documentation Community guidelines Automated testing Patrick Diehl (LSU) JOSS and FLOSS June 14, 2023 11 / 30
- 13. JOSS - Review Checklist Details Installation : The software is simple to install, and follows established distribution and dependency management approaches for the language being used : A list of dependencies to install, together with some kind of script to handle their installation (e.g., a Makefile) (not acceptable): Dependencies are unclear, and/or installation process lacks automation Patrick Diehl (LSU) JOSS and FLOSS June 14, 2023 12 / 30
- 14. JOSS - Review Checklist Details API Documentation : All functions/methods are documented including example inputs and outputs : Core API functionality is documented (not acceptable): API is undocumented Patrick Diehl (LSU) JOSS and FLOSS June 14, 2023 13 / 30
- 15. JOSS - Review Checklist Details Installation : The software is simple to install, and follows established distribution and dependency management approaches for the language being used : A list of dependencies to install, together with some kind of script to handle their installation (e.g., a Makefile) (not acceptable): Dependencies are unclear, and/or installation process lacks automation Patrick Diehl (LSU) JOSS and FLOSS June 14, 2023 14 / 30
- 16. JOSS - Review Checklist Details Automated Tests : An automated test suite hooked up to continuous integration (GitHub Actions, Circle CI, or similar) : Documented manual steps that can be followed to objectively check the expected functionality of the software (e.g., a sample input file to assert behavior) (not acceptable): No way for you, the reviewer, to objectively assess whether the software works Patrick Diehl (LSU) JOSS and FLOSS June 14, 2023 15 / 30
- 17. JOSS as a Community Cultures change based on rules and incentives JOSS practices have influenced reviewers and developers in terms of what’s good and what’s minimally acceptable Similar to rOpenSci’s influence in the R community JOSS provides rules, and at a high-level, tries to nudge incentives Accepted software = accepted paper If software was cited directly, JOSS papers wouldn’t be needed, but JOSS reviews and JOSS community would still have great value Patrick Diehl (LSU) JOSS and FLOSS June 14, 2023 16 / 30
- 18. Bot-based process using GitHub: @editorialbot Interacts with authors, reviewers, and editors in review ‘issues’ on GitHub Compiles papers (Pandoc) Conducts automated ‘healthchecks’ for incoming submissions (e.g. license checks, search for missing DOIs) Sends automated reminders Deposits metadata and and registers DOIs with Crossref Patrick Diehl (LSU) JOSS and FLOSS June 14, 2023 17 / 30
- 19. Some data on most cited papers More data: http://www.theoj.org/joss-analytics/joss-submission-analytics.html Patrick Diehl (LSU) JOSS and FLOSS June 14, 2023 18 / 30
- 20. Some data on published papers More data: http://www.theoj.org/joss-analytics/joss-submission-analytics.html Patrick Diehl (LSU) JOSS and FLOSS June 14, 2023 19 / 30
- 21. Conclusion JOSS is a collaboration between author, editor and reviewer Please submit your software package and get credit for your work! Slides based on: https://doi.org/10.5281/zenodo.6305241 Guest Post — The Evolving Role of Scientific Editing: https://scholarlykitchen.sspnet.org/2021/09/23/guest-post-the-evolving-role-of-scientific-editing/ Patrick Diehl (LSU) JOSS and FLOSS June 14, 2023 20 / 30
- 22. Floss for Science: A podcast promoting open source software Patrick Diehl (LSU) JOSS and FLOSS June 14, 2023 21 / 30
- 23. Floss for Science A podcast promoting open source software FLOSS for Science is a podcast with the goal of showcasing free, libre and open source software uses in science. We want to highlight how FLOSS empowers researchers and enables them to produce high quality research. So far 32 episodes published, however, we did a break during the pandemic Credits to David Brassard my co-host, who started the podcast with me in January 2018. Patrick Diehl (LSU) JOSS and FLOSS June 14, 2023 22 / 30
- 24. Some selected episodes Patrick Diehl (LSU) JOSS and FLOSS June 14, 2023 23 / 30
- 25. Open source software for production Low-cost hardware is readily available The software components required for high quality audio production are available with open source licenses under Linux It is strongly recommended to record every participant on individual audio tracks to adjust their audio level separately The setup to record a podcast with all participants on a single track will be significantly easier to prepare and manage, but we chose to go with a multitrack setup for high audio quality Patrick Diehl (LSU) JOSS and FLOSS June 14, 2023 24 / 30
- 26. Open source software for production Portable hardware setup for podcast recording : Behringer UMC404HD audio interface ($180) Up to 4 local participants One Shure SM58 for each local participants Samson q2u USB microphone for remote participants ($70) Other class-compliant audio interfaces and microphones are available One computer serves as a central node for the remote and local recording General use computers are plenty sufficient Recording for FFS was performed on either a Thinkpad W530 or a Thinkpad X260 The computer will need stable network connectivity A multichannel headphone amplifier ($35) is strongly suggested to give audio feedback for all local participants and improve their posture while recording Patrick Diehl (LSU) JOSS and FLOSS June 14, 2023 25 / 30
- 27. Open source software for production General software Jitsi.meet VOIP software for remote participants The only requirement for the participants is a webRTC compatible web browser Chromium Separate Jitsi.meet instances on different tabs Firefox did not allow to split the audio from different tabs into multiple channels Linux All packages are available in Ubuntu from the main or third-party repositories Any Linux distribution can be made to work Ubuntu Studio is an easy all-in-one solution for beginners Real time or low latency kernel are suggested but not absolutely required for less demanding recording situations such as podcast recording Patrick Diehl (LSU) JOSS and FLOSS June 14, 2023 26 / 30
- 28. Open source software for production Audio software JACK (will eventualy be replaced by PipeWire for an easier setup) JACK Audio Connection Kit Linux low latency audio stack Allow special routing between different sources and sinks A JACK session manager and routing software (for graphical routing) Multiple combination/alternatives Cadence Ubuntu Studio Controls Qjackctl Catia Patchage Patrick Diehl (LSU) JOSS and FLOSS June 14, 2023 27 / 30
- 29. Open source software for production Audio software Ardour Multitrack audio recorder and editor Plugin host (denoise, gate, compressor, limiter, etc.) CALF plugins Decent and easy to use audio plugins Gate, Compressor, Limiter... Other software and services Mediafile hosting on Archive.org Website hosting on Github-pages Jeckyl static generated website Audio leveling with Auphonic online (non-free software) Patrick Diehl (LSU) JOSS and FLOSS June 14, 2023 28 / 30
- 30. Lessons learned Surprising Was quite easy to find people willing to be interviewed, A professional graphic designer volunteered helping with the artwork Some episodes had over 600 listeners Challenges Was sometimes difficult to schedule interviews, e.g. time zones, working hours. High quality audio is important, however, editing took much time out of David’s resources. Funding is needed for editing, however, we want to avoid advertisement or sponsoring Patrick Diehl (LSU) JOSS and FLOSS June 14, 2023 29 / 30
- 31. Conclusion Benefits JOSS is one opportunity to get credit for software development FLOSS was a good opportunity for science communication Challenges Obtain funding for the promotion of open-source and science communication: JOSS is funded by NumFocus, e.g. server, DOI. However, all editors and reviewers are volunteers. FLOSS was funded by the hosts with their private money. Recording, Editing, and Graphic Design were done by volunteers. More work is needed to get funding and credits for software development. This work is licensed under a Creative Commons “Attribution-NonCommercial-ShareAlike 3.0 Un- ported” license. Patrick Diehl (LSU) JOSS and FLOSS June 14, 2023 30 / 30