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

editorialbot commented 1 month ago

Submitting author: !--author-handle-->@deronsmith@mengqi-z<!--end-editor-- Reviewers: @gutabeshu, @ifoxfoot, @niravlekinwala Archive: Pending

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

editorialbot commented 1 month ago

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:

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

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editorialbot commented 1 month ago

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

editorialbot commented 1 month ago

Paper file info:

📄 Wordcount for paper.md is 995

✅ The paper includes a Statement of need section

editorialbot commented 1 month ago

License info:

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

editorialbot commented 1 month ago

:warning: An error happened when generating the pdf.

mengqi-z commented 1 month ago

@editorialbot generate pdf

editorialbot commented 1 month ago

:warning: An error happened when generating the pdf.

mengqi-z commented 1 month ago

👋🏼 @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 commented 1 month ago

Review checklist for @ifoxfoot

Conflict of interest

[x] 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

[x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

[x] Repository: Is the source code for this software available at the https://github.com/quanted/esat?
[x] License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
[x] 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?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
[x] 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.
[x] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
[x] 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

[x] Installation: Does installation proceed as outlined in the documentation?
[x] Functionality: Have the functional claims of the software been confirmed?
[x] 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

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

[x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] 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?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] 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 commented 1 month ago

@editorialbot generate pdf

editorialbot commented 1 month ago

:warning: An error happened when generating the pdf.

mengqi-z commented 1 month ago

@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: https://github.com/openjournals/joss-reviews/issues/7215#issuecomment-2347314129. Apologies for the inconvenience!

arfon commented 1 month ago

@editorialbot generate pdf

editorialbot commented 1 month ago

:warning: An error happened when generating the pdf.

arfon commented 1 month ago

@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 commented 1 month ago

@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 commented 1 month ago

@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.

mengqi-z commented 1 month ago

@editorialbot generate pdf

editorialbot commented 1 month ago

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

ifoxfoot commented 1 month ago

@editorialbot generate pdf

editorialbot commented 1 month ago

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

niravlekinwala commented 1 month ago

Review checklist for @niravlekinwala

Conflict of interest

[x] 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

[x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

[x] Repository: Is the source code for this software available at the https://github.com/quanted/esat?
[x] License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
[x] 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?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
[x] 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.
[x] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
[x] 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

[x] Installation: Does installation proceed as outlined in the documentation?
[x] Functionality: Have the functional claims of the software been confirmed?
[x] 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

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

[x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] 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?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] 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 commented 3 weeks ago

Hi, Are there any updates on this review? Thanks

mengqi-z commented 3 weeks ago

@gutabeshu, @ifoxfoot, @niravlekinwala - Could you please provide a brief status update in this thread on your review progress? If you anticipate any delays, please let me know. Thanks!

ifoxfoot commented 3 weeks ago

@mengqi-z my review is complete

mengqi-z commented 3 weeks ago

@ifoxfoot - Wonderful! Thank you so much for taking the time and effort to review this submission!

gutabeshu commented 3 weeks ago

@mengqi-z I will try to complete my review over the weekend

niravlekinwala commented 3 weeks ago

@mengqi-z & @deronsmith, I apologize for the delay due to a health emergency. However, I started the review last week. While I encountered some issues installing the library, I have now figured it out and will try to complete it by November 11th (Monday).

deronsmith commented 3 weeks ago

Thank you @niravlekinwala! We will be able to push the package to pypi after a completed external review, this JOSS review will be sufficient. This is a requirement for us to release agency software and code packages.

niravlekinwala commented 2 weeks ago

@deronsmith @mengqi-z

I have completed my review. I have gone through the paper and example Jupyter notebooks and the code runs without a glitch (except for when factors are 2 & 3, @deronsmith has mentioned it as a bug on the repository page). I have raised a couple of issues on the repository's page as a suggestions for @deronsmith.

Also @mengqi-z, I have completed the checklist.

mengqi-z commented 2 weeks ago

@niravlekinwala - This is great! Thanks for the review!

deronsmith commented 1 week ago

@mengqi-z - I wanted to check in and see how the final review is progressing. Thanks.

mengqi-z commented 1 week ago

@deronsmith - Two of the three reviews are in, and we're waiting on the final one.

@gutabeshu – Just checking in to see if there’s an update on your review. Are you able to complete it soon? Thanks so much!

gutabeshu commented 1 week ago

@mengqi-z I will submit my review by Nov 16

gutabeshu commented 1 week ago

Review checklist for @gutabeshu

Conflict of interest

[x] 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

[x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

[x] Repository: Is the source code for this software available at the https://github.com/quanted/esat?
[x] License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
[x] 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?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
[x] 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.
[x] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
[x] 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

[x] Installation: Does installation proceed as outlined in the documentation?
[x] Functionality: Have the functional claims of the software been confirmed?
[x] 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

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

[x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] 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?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] 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?

gutabeshu commented 1 week ago

@mengqi-z I have completed my review. The code is well-structured, reproducible, and supported by clear documentation.

mengqi-z commented 1 week ago

@gutabeshu - Great! Thank you! I appreciate you taking the time and effort to complete your review.

@deronsmith - I’ll proofread the paper and ensure it meets JOSS standards, then follow up with you on the next steps. Thanks!

mengqi-z commented 1 week ago

@editorialbot generate pdf

mengqi-z commented 1 week ago

@editorialbot check references

editorialbot commented 1 week ago

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

editorialbot commented 1 week ago

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

mengqi-z commented 1 week ago

@editorialbot generate pdf

editorialbot commented 1 week ago

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

mengqi-z commented 1 week ago

@deronsmith - I have completed proofreading the paper and all is good. Thank you.

At this point, could you:

[ ] Double check authors and affiliations (including ORCIDs).
[ ] Make a release of the software with the latest changes from the review and post the version number here. This is the version that will be used in the JOSS paper.
[ ] Archive the released software on Zenodo or a similar service (e.g., figshare, an institutional repository).
[ ] Make sure that the archive (e.g., on Zenodo) has the correct metadata. This includes the title (which should match the paper title) and the author list (ensure the list is correct and does not include people who only made minor contributions). You may also add the authors' ORCIDs.
[ ] Make sure that the license listed for the archive is the same as the software license.
[ ] Please post the DOI of the archived version here.

I can then move forward with accepting the submission.

openjournals / joss-reviews