[REVIEW]: QuantEcon.py: A community based Python library for quantitative economics

editorialbot commented 1 year ago

Submitting author: !--author-handle-->@jstac@sbenthall<!--end-editor-- Reviewers: @janosg, @mnwhite Archive: 10.5281/zenodo.10345102

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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

@janosg & @mnwhite, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review. First of all you need to run this command in a separate comment to create the checklist:

@editorialbot generate my checklist

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

Checklists

📝 Checklist for @janosg

📝 Checklist for @mnwhite

sbenthall commented 11 months ago

@mmcky Once you've corrected the license information in the publication, the next step is to tag a release and make an archive on Zenodo, and tell me the version number and DOI. Please read the instructions on the checklist carefully -- the title, author, and ORCIDs of the Zenodo archive need to match the paper's

mmcky commented 11 months ago

It looks like you have listed a CC-BY license on the paper, but the repository has an MIT license.

Roger that.

I think the confusion was that the paper itself was to be CC-BY -- I will look into this as the paper.md file has

[QuantEcon.py](https://github.com/quantecon/QuantEcon.py) is released under the open-source MIT License

in the actual text.

Smit-create commented 11 months ago

@editorialbot generate pdf

editorialbot commented 11 months ago

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

Smit-create commented 11 months ago

I am not exactly sure if we can configure the License text generated in the document (I still need to check more details to confirm). I think all the papers have the same License text: https://github.com/search?q=repo%3Aopenjournals%2Fjoss-papers%20%3Ccopyright-statement%3E&type=code ? For example, #5996 also has a MIT license but the paper doesn't https://joss.theoj.org/papers/10.21105/joss.05996.

Smit-create commented 11 months ago

The License in the paper is coming from JOSS side which requires a CC-BY. See: https://github.com/openjournals/joss/issues/1215#issuecomment-1513548324. So, MIT license is of QuantEcon library but CC-BY is the license of the paper. Please feel free to correct me.

mmcky commented 11 months ago

thanks @Smit-create. @sbenthall can you point me to where the license information needs to be corrected?

mmcky commented 11 months ago

[x] review references and applied minor updates to correct formatting

mmcky commented 11 months ago

@editorialbot generate pdf

editorialbot commented 11 months ago

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

mmcky commented 11 months ago

[x] this change https://github.com/QuantEcon/QuantEcon.py/commit/c939286ea984e9b325676f36540101efcaf38160 isn't flowing through to the references section so investigating.

There were duplicate entries in the bibtex file. This is now fixed.

mmcky commented 11 months ago

@sbenthall thanks for all the review and guidance.

I had another question with regards to the Zenodo upload.

Archive the release on Zenodo/figshare/etc and post the DOI here.

Should we:

upload the paper only
upload the paper + copy of the quantecon package

I am currently assuming #1 as the quantecon==0.7.1 documents the software version.

sbenthall commented 11 months ago

You know, I may be in error about the licensing issue. I apologize for the confusion; it's actually the first time I've noticed this requirement. (In the past, I haven't used the editoralbot checklist feature.)

The requirement, I believe, is that the license on the Zenodo archive is to be the same as that on the software. The paper remains CC; don't bother changing that.

The answer to your question @mmcky is actually #2. The issue is that GitHub and PyPI are not academic archives. Part of the point of JOSS is creative academic archives of software source code. So a package import is not sufficient.

I defer to @arfon or @oliviaguest on these interpretations.

danielskatz commented 11 months ago

A couple of quick comments from me as another track editor...

What we need is the software to be uploaded to the repository, so that it can be archived permanently, which neither GitHub not PyPI do - the issue is the permanence of the archive. We don't need the paper source to be in the archive, though it can, as the paper will be archived through the journal.

The license for the software can be any OSI-approved license. The license for the paper is CC-BY. The archive license should match the software license, since that's what the archive will mostly contain.

mmcky commented 11 months ago

thanks @sbenthall and @danielskatz. I appreciate the clarifications and guidance. I will get the final items on the checklist completed and then notify via this issue.

mmcky commented 11 months ago

thanks again @danielskatz and @sbenthall.

I have now setup a Zenodo record of the quantecon==0.7.1 release.

@sbenthall please let me know if you need anything further. Many thanks.

mmcky commented 10 months ago

@sbenthall can you please let me know if there is anything else required? Many thanks.

sbenthall commented 10 months ago

@editorialbot set 10.5281/zenodo.10345102 as archive

editorialbot commented 10 months ago

Done! archive is now 10.5281/zenodo.10345102

sbenthall commented 10 months ago

@editorialbot set 0.7.1 as version

editorialbot commented 10 months ago

Done! version is now 0.7.1

sbenthall commented 10 months ago

Thanks @mmcky. I believe this review is complete and the materials are in order. I recommend this submission for acceptance.

Thank you to all the authors for their patience with the process. Thank you @janosg and @mnwhite for your reviews. Thanks to the editorial team for weighing in.

sbenthall commented 10 months ago

@editorialbot recommend-accept

editorialbot commented 10 months ago

Attempting dry run of processing paper acceptance...

editorialbot commented 10 months ago

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

Check final proof :point_right::page_facing_up: Download article

If the paper PDF and the deposit XML files look good in https://github.com/openjournals/joss-papers/pull/4853, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

editorialbot commented 10 months ago

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.11650/twjm/1500405875 is OK
- 10.1002/anac.200410015 is OK
- 10.1007/s10589-010-9329-3 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.1016/0165-1765(86)90168-0 is OK
- 10.2307/j.ctv14163jx.16 is OK

MISSING DOIs

- None

INVALID DOIs

- None

jstac commented 10 months ago

Hi @sbenthall , happy new year and thanks again for your help in shepharding this paper through!

Just quickly: one of the junior coauthors is applying for a scholarship and it would be very helpful if this was published on the main site. Is there a timeline? (I'm writing a recommendation letter for him so if you can let me know I'll adjust it accordingly.)

Thanks in advance.

oliviaguest commented 10 months ago

@editorialbot recommend-accept

editorialbot commented 10 months ago

Attempting dry run of processing paper acceptance...

editorialbot commented 10 months ago

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.11650/twjm/1500405875 is OK
- 10.1002/anac.200410015 is OK
- 10.1007/s10589-010-9329-3 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.1016/0165-1765(86)90168-0 is OK
- 10.2307/j.ctv14163jx.16 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot commented 10 months ago

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

Check final proof :point_right::page_facing_up: Download article

If the paper PDF and the deposit XML files look good in https://github.com/openjournals/joss-papers/pull/4874, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

oliviaguest commented 10 months ago

@editorialbot accept

editorialbot commented 10 months ago

Doing it live! Attempting automated processing of paper acceptance...

editorialbot commented 10 months ago

Ensure proper citation by uploading a plain text CITATION.cff file to the default branch of your repository.

If using GitHub, a Cite this repository menu will appear in the About section, containing both APA and BibTeX formats. When exported to Zotero using a browser plugin, Zotero will automatically create an entry using the information contained in the .cff file.

You can copy the contents for your CITATION.cff file here:

CITATION.cff

``` cff-version: "1.2.0" authors: - family-names: Batista given-names: Quentin - family-names: Coleman given-names: Chase - family-names: Furusawa given-names: Yuya - family-names: Hu given-names: Shu - family-names: Lunagariya given-names: Smit - family-names: Lyon given-names: Spencer - family-names: McKay given-names: Matthew - family-names: Oyama given-names: Daisuke - family-names: Sargent given-names: Thomas J. - family-names: Shi given-names: Zejin - family-names: Stachurski given-names: John - family-names: Winant given-names: Pablo - family-names: Watkins given-names: Natasha - family-names: Yang given-names: Ziyue - family-names: Zhang given-names: Hengcheng doi: 10.5281/zenodo.10345102 message: If you use this software, please cite our article in the Journal of Open Source Software. preferred-citation: authors: - family-names: Batista given-names: Quentin - family-names: Coleman given-names: Chase - family-names: Furusawa given-names: Yuya - family-names: Hu given-names: Shu - family-names: Lunagariya given-names: Smit - family-names: Lyon given-names: Spencer - family-names: McKay given-names: Matthew - family-names: Oyama given-names: Daisuke - family-names: Sargent given-names: Thomas J. - family-names: Shi given-names: Zejin - family-names: Stachurski given-names: John - family-names: Winant given-names: Pablo - family-names: Watkins given-names: Natasha - family-names: Yang given-names: Ziyue - family-names: Zhang given-names: Hengcheng date-published: 2024-01-06 doi: 10.21105/joss.05585 issn: 2475-9066 issue: 93 journal: Journal of Open Source Software publisher: name: Open Journals start: 5585 title: "QuantEcon.py: A community based Python library for quantitative economics" type: article url: "https://joss.theoj.org/papers/10.21105/joss.05585" volume: 9 title: "QuantEcon.py: A community based Python library for quantitative economics" ```

If the repository is not hosted on GitHub, a .cff file can still be uploaded to set your preferred citation. Users will be able to manually copy and paste the citation.

Find more information on .cff files here and here.

editorialbot commented 10 months ago

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

editorialbot commented 10 months ago

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

Here's what you must now do:

Check final PDF and Crossref metadata that was deposited :point_right: https://github.com/openjournals/joss-papers/pull/4878
Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.05585
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

oliviaguest commented 10 months ago

@jstac do you want to have your orcids added here?

oliviaguest commented 10 months ago

Hi @sbenthall , happy new year and thanks again for your help in shepharding this paper through!

Just quickly: one of the junior coauthors is applying for a scholarship and it would be very helpful if this was published on the main site. Is there a timeline? (I'm writing a recommendation letter for him so if you can let me know I'll adjust it accordingly.)

Thanks in advance.

You can definitely use the DOI to refer to this now, if needed, see above. Apologies for slow reply; Xmas, new year, etc. Good luck with the application.

oliviaguest commented 9 months ago

Huge thanks to the reviewers @janosg, @mnwhite and editor @sbenthall! ✨ JOSS appreciates your work and effort. ✨ Also, big congratulations to the authors! 🥳 🍾

editorialbot commented 9 months ago

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