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[REVIEW]: QuantEcon.py: A community based Python library for quantitative economics #5585

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editorialbot opened this issue Jun 22, 2023 · 90 comments
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accepted Makefile published Papers published in JOSS Python recommend-accept Papers recommended for acceptance in JOSS. review TeX Track: 4 (SBCS) Social, Behavioral, and Cognitive Sciences

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editorialbot commented Jun 22, 2023

Submitting author: @jstac (John Stachurski)
Repository: https://github.com/QuantEcon/QuantEcon.py
Branch with paper.md (empty if default branch): joss_paper
Version: 0.7.1
Editor: @sbenthall
Reviewers: @janosg, @mnwhite
Archive: 10.5281/zenodo.10345102

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/55e166343438f3a075ed40504b7bb394"><img src="https://joss.theoj.org/papers/55e166343438f3a075ed40504b7bb394/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/55e166343438f3a075ed40504b7bb394/status.svg)](https://joss.theoj.org/papers/55e166343438f3a075ed40504b7bb394)

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

@editorialbot editorialbot added review TeX Track: 4 (SBCS) Social, Behavioral, and Cognitive Sciences labels Jun 22, 2023
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Hello humans, I'm @editorialbot, a robot that can help you with some common editorial tasks.

For a list of things I can do to help you, just type:

@editorialbot commands

For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

@editorialbot generate pdf

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Software report:

github.com/AlDanial/cloc v 1.88  T=0.25 s (939.2 files/s, 119069.2 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                         152           5877           9408          12165
Markdown                         5            209              0            736
DOS Batch                        2             31              1            218
TeX                              1             22              0            196
make                             2             32              7            169
YAML                             5             32             41            159
reStructuredText                66             76            315            143
TOML                             1              8              0             62
INI                              1              0              0              3
Bourne Shell                     1              3              4              2
-------------------------------------------------------------------------------
SUM:                           236           6290           9776          13853
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

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Wordcount for paper.md is 2221

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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

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👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

@sbenthall
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👋🏼 @jstac @janosg @mnwhite this is the review thread for the paper. All of our communications will happen here from now on.

As a reviewer, the first step is to create a checklist for your review by entering

@editorialbot generate my checklist

as the top of a new comment in this thread.

These checklists contain the JOSS requirements. As you go over the submission, please check any items that you feel have been satisfied. The first comment in this thread also contains links to the JOSS reviewer guidelines.

The JOSS review is different from most other journals. Our goal is to work with the authors to help them meet our criteria instead of merely passing judgment on the submission. As such, the reviewers are encouraged to submit issues and pull requests on the software repository. When doing so, please mention openjournals/joss-reviews#5585 so that a link is created to this thread (and I can keep an eye on what is happening). Please also feel free to comment and ask questions on this thread. In my experience, it is better to post comments/questions/suggestions as you come across them instead of waiting until you've reviewed the entire package.

We aim for reviews to be completed within about 2-4 weeks. Please let me know if any of you require some more time. We can also use EditorialBot (our bot) to set automatic reminders if you know you'll be away for a known period of time.

Please feel free to ping me (@sbenthall) if you have any questions/concerns.

@janosg
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janosg commented Jul 5, 2023

Review checklist for @janosg

Conflict of interest

  • I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

General checks

  • Repository: Is the source code for this software available at the https://github.com/QuantEcon/QuantEcon.py?
  • License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
  • Contribution and authorship: Has the submitting author (@jstac) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
  • Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
  • Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
  • Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
  • Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

Functionality

  • Installation: Does installation proceed as outlined in the documentation?
  • Functionality: Have the functional claims of the software been confirmed?
  • Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

  • A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
  • Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
  • Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
  • Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
  • Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
  • Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

  • Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
  • A statement of need: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
  • State of the field: Do the authors describe how this software compares to other commonly-used packages?
  • Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
  • References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

@mmcky
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mmcky commented Jul 12, 2023

@janosg thank you for the issues and review. Greatly appreciated. I think I have now addressed both comments linked above. I have also opened this discussion to see if we can make improvements through a more direct example gallery. Currently examples are provided across our lecture series and in the QuantEcon.py documentation docstrings.

@janosg
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janosg commented Jul 12, 2023

Thanks @mmcky. I added a suggestion to your discussion but that is not a prerequisite for acceptance.

quantecon.py is a great package and it was a pleasure to review it!

@sbenthall my review is complete.

@sbenthall
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Thank you @janosg !

@sbenthall
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Hello @mnwhite , this submission is still waiting for your review.
Please let me know if you have any questions about the process.

@mnwhite
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mnwhite commented Jul 21, 2023 via email

@mnwhite
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mnwhite commented Jul 26, 2023

Review checklist for @mnwhite

Conflict of interest

  • I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

General checks

  • Repository: Is the source code for this software available at the https://github.com/QuantEcon/QuantEcon.py?
  • License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
  • Contribution and authorship: Has the submitting author (@jstac) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
  • Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
  • Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
  • Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
  • Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

Functionality

  • Installation: Does installation proceed as outlined in the documentation?
  • Functionality: Have the functional claims of the software been confirmed?
  • Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

  • A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
  • Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
  • Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
  • Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
  • Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
  • Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

  • Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
  • A statement of need: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
  • State of the field: Do the authors describe how this software compares to other commonly-used packages?
  • Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
  • References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

@arfon
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arfon commented Oct 1, 2023

@mnwhite – how are you getting on here. Do you think you might be able to complete your review in the next week or so?

@mnwhite
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mnwhite commented Oct 1, 2023 via email

@jstac
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jstac commented Oct 30, 2023

@arfon @sbenthall Is there a target date for the first round referee process? Please let us know if we can help expedite by providing more information.

@mnwhite
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mnwhite commented Oct 30, 2023 via email

@jstac
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jstac commented Oct 30, 2023

No problem @mnwhite, I've been in your shoes and I remember what it was like. We're looking forward to your review when you're ready to submit.

@jstac
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jstac commented Nov 21, 2023

@mnwhite Sorry to keep pinging you but it would help some of the young people listed as coauthors. Hopefully it won't take too long.

@mnwhite
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mnwhite commented Nov 21, 2023 via email

@mnwhite
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mnwhite commented Nov 25, 2023

@jstac @sbenthall I finally, finally, finally got around to this. I am so sorry this took so long and kept slipping.

John: Are you in Canberra? If so, cookies (etc) will be sent to your office.

@mmcky
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mmcky commented Dec 7, 2023

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
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mmcky commented Dec 11, 2023

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
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mmcky commented Dec 18, 2023

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

@sbenthall
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@editorialbot set 10.5281/zenodo.10345102 as archive

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Done! archive is now 10.5281/zenodo.10345102

@sbenthall
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@editorialbot set 0.7.1 as version

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Done! version is now 0.7.1

@sbenthall
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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
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@editorialbot recommend-accept

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Attempting dry run of processing paper acceptance...

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

Check final proof 👉📄 Download article

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

@editorialbot editorialbot added the recommend-accept Papers recommended for acceptance in JOSS. label Dec 18, 2023
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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
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jstac commented Jan 3, 2024

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
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@editorialbot recommend-accept

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Attempting dry run of processing paper acceptance...

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

Check final proof 👉📄 Download article

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

@oliviaguest
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@editorialbot accept

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

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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.

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🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

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🚨🚨🚨 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 👉 Creating pull request for 10.21105.joss.05585 joss-papers#4878
  2. Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.05585
  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...

@editorialbot editorialbot added accepted published Papers published in JOSS labels Jan 6, 2024
@oliviaguest
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@jstac do you want to have your orcids added here?

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

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🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

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.05585/status.svg)](https://doi.org/10.21105/joss.05585)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.05585">
  <img src="https://joss.theoj.org/papers/10.21105/joss.05585/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.05585/status.svg
   :target: https://doi.org/10.21105/joss.05585

This is how it will look in your documentation:

DOI

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