search

openjournals / joss-reviews

Reviews for the Journal of Open Source Software
Creative Commons Zero v1.0 Universal
721 stars 38 forks source link

[REVIEW]: fishStan: Hierarchical Bayesian models for fisheries #3444

Closed whedon closed 2 years ago

whedon commented 3 years ago

Submitting author: !--author-handle-->@rerickson-usgs<!--end-author-handle-- (Richard Erickson) Repository: https://code.usgs.gov/umesc/quant-ecology/fishstan/ Branch with paper.md (empty if default branch): Version: v2.0.0 Editor: !--editor-->@marcosvital<!--end-editor-- Reviewers: @MikeKaller, @Cole-Monnahan-NOAA Archive: 10.5066/P9TT3ILO

:warning: JOSS reduced service mode :warning:

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/34bd0a9673510f204ee01fe1536b2196"><img src="https://joss.theoj.org/papers/34bd0a9673510f204ee01fe1536b2196/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/34bd0a9673510f204ee01fe1536b2196/status.svg)](https://joss.theoj.org/papers/34bd0a9673510f204ee01fe1536b2196)

Reviewers and authors:

Please avoid lengthy details of difficulties in the review thread. Instead, please create a new issue in the target repository and link to those issues (especially acceptance-blockers) by leaving comments in the review thread below. (For completists: if the target issue tracker is also on GitHub, linking the review thread in the issue or vice versa will create corresponding breadcrumb trails in the link target.)

Reviewer instructions & questions

@BrandonEdwards & @MikeKaller, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

  1. Make sure you're logged in to your GitHub account
  2. Be sure to accept the invite at this URL: https://github.com/openjournals/joss-reviews/invitations

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @marcosvital know.

✨ Please start on your review when you are able, and be sure to complete your review in the next six weeks, at the very latest ✨

Review checklist for @MikeKaller

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @Cole-Monnahan-NOAA

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

editorialbot commented 2 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

marcosvital commented 2 years ago

@editorialbot set 10.5066/P9TT3ILO as archive

editorialbot commented 2 years ago

Done! Archive is now 10.5066/P9TT3ILO

marcosvital commented 2 years ago

@editorialbot set v2.0.0 as version

editorialbot commented 2 years ago

Done! version is now v2.0.0

marcosvital commented 2 years ago

@editorialbot recommend-accept

editorialbot commented 2 years ago 
Attempting dry run of processing paper acceptance...
editorialbot commented 2 years ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1016/j.fishres.2015.03.009 is OK
- 10.1201/9781315371986 is OK
- 10.1002/nafm.10515 is OK
- 10.1002/nafm.10515 is OK
- 10.5066/P9IAOZ8G is OK
- 10.3996/JFWM-20-070 is OK
- 10.5066/P9Q6SUML is OK

MISSING DOIs

- None

INVALID DOIs

- None
editorialbot commented 2 years ago

:wave: @openjournals/joss-eics, this paper is ready to be accepted and published.

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/3039

If the paper PDF and the deposit XML files look good in https://github.com/openjournals/joss-papers/pull/3039, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

Kevin-Mattheus-Moerman commented 2 years ago

@rerickson-usgs I have proofread the paper and it seems to be in order. Below are some minor comments to address/consider:

I also have a concern about the archived version and DOI http://doi.org/10.5066/P9TT3ILO. Usually we use ZENODO to archive software as it has a clear commitment for long-term storage. If I follow the above DOI it points to: https://code.usgs.gov/umesc/quant-ecology/fishstan/-/tree/2.0, which seems to be GitLab repository and the page for the version tagged as 2.0. Usually though such versions on a repository can be edited/deleted, and therefore this does not seem to be a stable long term storage. Can you please how the DOI was created and if http://code.usgs.gov/ is committed to long term storage similar to ZENODO?

raerickson commented 2 years ago

@Kevin-Mattheus-Moerman thank you for the proofing.

  1. I have added "United States of America" to our affiliations and "Oneonta, NY" to the second affiliation. I also removed the zip code.
  2. I added a citation for JAGS and Stan.

The DOI is issued by my agency, the USGS. We are required by US policy and law to post our source code to a *.gov webpage. code. As an agency, we have Trusted Digital repository pages, listed here, but USGS has not yet obtained that status for our software page (code.usgs.gov). USGS Software Policy is listed here.

I am working my my admin people to move the DOI to point towards the repo rather than the release tag. (This was one of our first DOIs for software at my center).

raerickson commented 2 years ago

@Kevin-Mattheus-Moerman the doi now points to the repo

Kevin-Mattheus-Moerman commented 2 years ago

@editorialbot generate pdf

editorialbot commented 2 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

Kevin-Mattheus-Moerman commented 2 years ago

@raerickson thanks for amending those affiliation descriptions. About the DOI. I am afraid pointing to the repository is "even worse" (since the repository version is always in flux). The point of archiving the software is such that a non-changing permanent record is maintained of the software. So it should be a static snapshot of the reviewed software and it should be stored permanently. Next the DOI should point to this static/stable long term storage version. It seems like your US government website is not set up for that? If not, I suggest the following. Download the reviewed software (v2.0.0) and upload it to ZENODO. Here is an example of such an archived version for a recent JOSS pubication: https://zenodo.org/record/6341565. Note for the ZENODO record the title, and the author list, should match the paper. You make sure you fill in all this meta-data, including the license type, accurately. Once this is completed please report back here with the ZENODO DOI. Thanks.

raerickson commented 2 years ago

@Kevin-Mattheus-Moerman I have moved the DOI back to the version 2.0 tag https://doi.org/10.5066/P9TT3ILO

The tag is immutable and cannot be changed. The code.usgs.gov page should be stable in the long term. The USGS considers software releases to code.usgs.gov to a formal product type, similar to our data releases on sciencebase.gov, our agencies maps, or our different types of reports.

I am not allowed to create a ZENDO archive because it is not a US Government authorized cloud service.

raerickson commented 2 years ago

@Kevin-Mattheus-Moerman Also, thank you for your patience in working through this!

raerickson commented 2 years ago

@Kevin-Mattheus-Moerman as a bump, any thoughts about this?

arfon commented 2 years ago

@raerickson – JOSS has a strong preference for a service with archiving in it's mission. As such, I've made an archive of the software myself with Zenodo here: 10.5281/zenodo.6373008

In preparing this archive, I noticed a (possibly) bigger challenge, this software is not actually licensed with an OSI-approved license (https://code.usgs.gov/umesc/quant-ecology/fishstan/-/blob/master/LICENSE.md). I'm sorry for not spotting this sooner @raerickson, but CC-0 is not OSI-approved, and as such isn't allowed in JOSS.

I understand that there are reasons US government funded work has guidance for being shared as CC-0, but for other submissions from other US agencies, the authors have been allowed to dual license their submissions.

Calling @kbarnhart and @jedbrown who I believe may have some expertise/experience to share here.

kbarnhart commented 2 years ago

@raerickson this is the best publicly available guidance I've found on what licenses are permitted and/or encouraged for USGS-authored software releases. I've pasted the key text below. In short, of the three licenses listed, only CC0 1.0 is not on the list of OSI approved licenses. In addition, I think that the text could reasonably be interpreted to allow an open-source license other than the three listed.

All software developed by the USGS should by default use an open-source license (put a "LICENSE.md" file in the project root of your repository). Below are license options to consider:

The Creative Commons (CC0) license may be used (currently CC0 1.0) when an official license declaration is required or appropriate to include. This assumes the software is either completely original, or using other software also with the CC0 license. This license places the work as completely as possible in the public domain so that it is free for others to build upon, enhance, or reuse, should work for most USGS software.

"MIT/X11" is an option when governing jurisdictions do not recognize the public domain dedication (e.g. outside the U.S.). Outside the United States, we are not required to release the source unencumbered (though MIT/X11 is probably the least encumbered, open-source license).

The Unlicense (unlicense.org) may be used to opt out of copyright altogether.

raerickson commented 2 years ago

@arfon and @kbarnhart Thank you both of you for helping!

I changed switched to an Unlicense.

I added a sentence to manuscript

An archived version of the package exists on Zenodo (10.5281/zenodo.6373008).

Please let me know if you need me to do anything else.

danielskatz commented 2 years ago

@raerickson - I'm the AEiC on duty this week, so I'm going to do a final proofread/check now

danielskatz commented 2 years ago

@editorialbot recommend-accept

editorialbot commented 2 years ago 
Attempting dry run of processing paper acceptance...
editorialbot commented 2 years ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.18637/jss.v076.i01 is OK
- 10.1016/j.fishres.2015.03.009 is OK
- 10.1201/9781315371986 is OK
- 10.1002/nafm.10515 is OK
- 10.1002/nafm.10515 is OK
- 10.5066/P9IAOZ8G is OK
- 10.3996/JFWM-20-070 is OK
- 10.5066/P9Q6SUML is OK

MISSING DOIs

- None

INVALID DOIs

- None
editorialbot commented 2 years ago

:wave: @openjournals/joss-eics, this paper is ready to be accepted and published.

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/3073

If the paper PDF and the deposit XML files look good in https://github.com/openjournals/joss-papers/pull/3073, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

danielskatz commented 2 years ago

@editorialbot accept

editorialbot commented 2 years ago 
Doing it live! Attempting automated processing of paper acceptance...
editorialbot commented 2 years ago

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

editorialbot commented 2 years ago

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

  1. Check final PDF and Crossref metadata that was deposited :point_right: https://github.com/openjournals/joss-papers/pull/3074
  2. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.03444
  3. If everything looks good, then close this review issue.
  4. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

danielskatz commented 2 years ago

Congratulations to @rerickson-usgs @raerickson and co-authors

And thanks to @MikeKaller and @Cole-Monnahan-NOAA for reviewing, and @marcosvital for editing! We couldn't do this without you

editorialbot commented 2 years ago

:tada::tada::tada: Congratulations on your paper acceptance! :tada::tada::tada:

If you would like to include a link to your paper from your README use the following code snippets:

Markdown:
[![DOI](https://joss.theoj.org/papers/10.21105/joss.03444/status.svg)](https://doi.org/10.21105/joss.03444)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.03444">
  <img src="https://joss.theoj.org/papers/10.21105/joss.03444/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.03444/status.svg
   :target: https://doi.org/10.21105/joss.03444

This is how it will look in your documentation:

DOI

We need your help!

The Journal of Open Source Software is a community-run journal and relies upon volunteer effort. If you'd like to support us please consider doing either one (or both) of the the following: