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[REVIEW]: ESAT: Environmental Source Apportionment Toolkit Python package #7316

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editorialbot opened this issue Oct 4, 2024 · 72 comments
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accepted published Papers published in JOSS recommend-accept Papers recommended for acceptance in JOSS. review Track: 6 (ESE) Earth Sciences and Ecology

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editorialbot commented Oct 4, 2024

Submitting author: @deronsmith (Deron Smith)
Repository: https://github.com/quanted/esat
Branch with paper.md (empty if default branch):
Version: v2024.0.3-alpha
Editor: @mengqi-z
Reviewers: @gutabeshu, @ifoxfoot, @niravlekinwala
Archive: 10.23719/1531870

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/8d2f7f5cfcb1f2ac82acd55d5855c5ac"><img src="https://joss.theoj.org/papers/8d2f7f5cfcb1f2ac82acd55d5855c5ac/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/8d2f7f5cfcb1f2ac82acd55d5855c5ac/status.svg)](https://joss.theoj.org/papers/8d2f7f5cfcb1f2ac82acd55d5855c5ac)

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

@gutabeshu & @ifoxfoot & @niravlekinwala, 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 @mengqi-z 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 @ifoxfoot

📝 Checklist for @niravlekinwala

📝 Checklist for @gutabeshu

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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 1.90  T=6.52 s (34.1 files/s, 582999.0 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
HTML                            19           2778             78          11232
Jupyter Notebook                52              0        3753053           8504
Python                          36           1252           2138           6687
SVG                              4              0              1           2691
PO File                         45           1007              0           2284
JavaScript                      20            231            297           1894
CSS                             12            424             93           1805
CSV                              4              0              0           1454
Rust                             1             71              9            537
Markdown                         2             68              0            241
reStructuredText                18            159            260            218
YAML                             4             10              5            134
TeX                              1             11              0            116
TOML                             2             12              2             67
DOS Batch                        1              8              1             26
make                             1              4              7              9
-------------------------------------------------------------------------------
SUM:                           222           6035        3755944          37899
-------------------------------------------------------------------------------

Commit count by author:

   155	Deron Smith
    19	mikecyterski

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Paper file info:

📄 Wordcount for paper.md is 995

✅ The paper includes a Statement of need section

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License info:

✅ License found: Apache License 2.0 (Valid open source OSI approved license)

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@mengqi-z
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mengqi-z commented Oct 4, 2024

@editorialbot generate pdf

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mengqi-z commented Oct 4, 2024

👋🏼 @deronsmith, @gutabeshu, @ifoxfoot, @niravlekinwala - 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 https://github.com/openjournals/joss-reviews/issues/7316 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 (@mengqi-z) if you have any questions/concerns.

@ifoxfoot
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ifoxfoot commented Oct 4, 2024

Review checklist for @ifoxfoot

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/quanted/esat?
  • License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
  • Contribution and authorship: Has the submitting author (@deronsmith) 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?

@ifoxfoot
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ifoxfoot commented Oct 4, 2024

@editorialbot generate pdf

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@mengqi-z
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mengqi-z commented Oct 4, 2024

@openjournals/dev - The PDF is not generating correctly. Could you please help me looking into the issue? Thank you!

@gutabeshu, @ifoxfoot, @niravlekinwala @deronsmith - In the meantime, you can access the most recent PDF from the Pre-Review stage here: #7215 (comment). Apologies for the inconvenience!

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arfon commented Oct 5, 2024

@editorialbot generate pdf

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arfon commented Oct 5, 2024

@mengqi-z – the issue here is that there are two paper.md files in the repository and there must only be one. @deronsmith – could you clean this up please by removing or renaming the one that is not the JOSS paper?

@mengqi-z
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mengqi-z commented Oct 5, 2024

@arfon - Ah, I see! It turns out there is a paper.md file located under esat/docs/html/_sources/paper/. Thanks for spotting the issue!

@deronsmith
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@arfon - Ah, I see! It turns out there is a paper.md file located under esat/docs/html/_sources/paper/. Thanks for spotting the issue!

Thank you for your patience while this issue was resolved. The paper.md file in docs has been removed and the corresponding directories added to gitignore to prevent future issues.

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mengqi-z commented Oct 8, 2024

@editorialbot generate pdf

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

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ifoxfoot commented Oct 9, 2024

@editorialbot generate pdf

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

@niravlekinwala
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niravlekinwala commented Oct 20, 2024

Review checklist for @niravlekinwala

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/quanted/esat?
  • License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
  • Contribution and authorship: Has the submitting author (@deronsmith) 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?

@deronsmith
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Hi, Are there any updates on this review?
Thanks

@deronsmith
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@mengqi-z Yes, the v2024.0.3-alpha tag is good, sorry for the confusion.

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mengqi-z commented Dec 3, 2024

@editorialbot set v2024.0.3-alpha as version

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Done! version is now v2024.0.3-alpha

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mengqi-z commented Dec 3, 2024

@editorialbot set 10.23719/1531870 as archive

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Done! archive is now 10.23719/1531870

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mengqi-z commented Dec 3, 2024

@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

- 10.5194/amt-15-6051-2022 is OK
- 10.1016/j.scitotenv.2015.01.022 is OK
- 10.1109/TPAMI.2008.277 is OK
- 10.1007/s13201-019-0938-4 is OK
- 10.3390/ijerph18168268 is OK
- 10.1002/env.3170050203 is OK
- 10.1080/10618600.1999.10474853 is OK
- 10.5194/amt-7-781-2014 is OK
- 10.1186/1471-2105-7-175 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: Semi-NMF and Weighted Semi-NMF Algorithms Comparis...
- No DOI given, and none found for title: Positive Matrix Factorization Model for Environmen...

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

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👋 @openjournals/ese-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#6208, 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 3, 2024
@mengqi-z
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mengqi-z commented Dec 3, 2024

@deronsmith – I’ve recommended your submission for acceptance. Thanks so much for submitting to JOSS! From here, our Editor-in-Chief will step in to do some final checks before the paper can be officially accepted and published. Congrats and great job!

@gutabeshu, @ifoxfoot, @niravlekinwala – Huge thanks to all of you for reviewing this paper! It’s been great working with you during this process, and I really appreciate your thoughtful feedback. I look forward to seeing your reviews for JOSS in the future!

@deronsmith
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@mengqi-z Thank you for coordinating everything, and thank you reviewers for all your work. Much appreciated!

@kthyng
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kthyng commented Dec 6, 2024

Hi! I'll take over now as Track Associate Editor in Chief to do some final submission editing checks. After these checks are complete, I will publish your submission!

  • Are checklists all checked off?
  • Check that version was updated and make sure the version from JOSS matches github and Zenodo.
  • Check that software archive exists, has been input to JOSS, and title and author list match JOSS paper (or purposefully do not).
  • Check paper.

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kthyng commented Dec 6, 2024

Please check the capitalization in your references. You can preserve capitalization by placing {} around characters/words in your .bib file. For example "china" and "south korea" are not capitalized but please check for others.

@deronsmith
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@kthyng Thank you for catching those reference formatting inconsistencies. I have updated the bib to maintain all capitalizations, based upon source formatting and proper nouns, with merge b2f7cc7.

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kthyng commented Dec 10, 2024

@editorialbot generate pdf

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

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kthyng commented Dec 10, 2024

Ok everything looks ready to go!

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kthyng commented Dec 10, 2024

@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: Smith
  given-names: Deron
  orcid: "https://orcid.org/0009-0009-4015-5270"
- family-names: Cyterski
  given-names: Michael
  orcid: "https://orcid.org/0000-0002-8630-873X"
- family-names: Johnston
  given-names: John M
  orcid: "https://orcid.org/0000-0002-5886-7876"
- family-names: Wolfe
  given-names: Kurt
  orcid: "https://orcid.org/0009-0009-4679-5922"
- family-names: Parmar
  given-names: Rajbir
  orcid: "https://orcid.org/0009-0005-2221-0433"
doi: 10.23719/1531870
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Smith
    given-names: Deron
    orcid: "https://orcid.org/0009-0009-4015-5270"
  - family-names: Cyterski
    given-names: Michael
    orcid: "https://orcid.org/0000-0002-8630-873X"
  - family-names: Johnston
    given-names: John M
    orcid: "https://orcid.org/0000-0002-5886-7876"
  - family-names: Wolfe
    given-names: Kurt
    orcid: "https://orcid.org/0009-0009-4679-5922"
  - family-names: Parmar
    given-names: Rajbir
    orcid: "https://orcid.org/0009-0005-2221-0433"
  date-published: 2024-12-10
  doi: 10.21105/joss.07316
  issn: 2475-9066
  issue: 104
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 7316
  title: "ESAT: Environmental Source Apportionment Toolkit Python
    package"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.07316"
  volume: 9
title: "ESAT: Environmental Source Apportionment Toolkit Python package"

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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🦋🦋🦋 👉 Bluesky post 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.07316 joss-papers#6246
  2. Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.07316
  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 Dec 10, 2024
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kthyng commented Dec 10, 2024

Congratulations on your new publication @deronsmith! Many thanks to editor @mengqi-z and to reviewers @gutabeshu, @ifoxfoot, and @niravlekinwala for your time, hard work, and expertise!! JOSS wouldn't be able to function nor succeed without your efforts.

Note we have a new tool for reviewers! You can go to https://joss.theoj.org/papers/reviewed_by/@your-github-username to see the JOSS submissions you have reviewed, and you can also copy a badge there with the number of your JOSS reviews.

@deronsmith If you'd like to join JOSS as a reviewer, please sign up at https://reviewers.joss.theoj.org/join!

@kthyng kthyng closed this as completed Dec 10, 2024
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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.07316/status.svg)](https://doi.org/10.21105/joss.07316)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.07316">
  <img src="https://joss.theoj.org/papers/10.21105/joss.07316/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.07316/status.svg
   :target: https://doi.org/10.21105/joss.07316

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:

@deronsmith
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Thank you @kthyng, and again thank you @mengqi-z and reviewers for all your work and assistance on this submission.

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