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

[editorialbot]

Submitting author: @deronsmith (Deron Smith)
Repository: https://github.com/quanted/esat
Branch with paper.md (empty if default branch):
Version: 2024.0.2
Editor: @mengqi-z
Reviewers: @gutabeshu, @ifoxfoot, @niravlekinwala
Managing EiC: Kristen Thyng

Status

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Markdown: [![status](https://joss.theoj.org/papers/8d2f7f5cfcb1f2ac82acd55d5855c5ac/status.svg)](https://joss.theoj.org/papers/8d2f7f5cfcb1f2ac82acd55d5855c5ac)

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[editorialbot]

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

✅ OK DOIs

- 10.5194/amt-15-6051-2022 is OK
- 10.1007/s13201-019-0938-4 is OK
- 10.3390/ijerph18168268 is OK
- 10.1002/env.3170050203 is OK
- 10.5194/amt-7-781-2014 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

- 10.1016/j.scitotenv.2015.01.022 may be a valid DOI for title: Methods for estimating uncertainty in PMF solution...
- 10.1109/tpami.2008.277 may be a valid DOI for title: Convex and semi-nonnegative matrix factorizations
- 10.2307/1390831 may be a valid DOI for title: The multilinear engine—a table-driven, least squar...
- 10.1186/1471-2105-7-175 may be a valid DOI for title: LS-NMF: a modified non-negative matrix factorizati...

❌ INVALID DOIs

- None

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.90  T=6.16 s (26.6 files/s, 614553.1 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Jupyter Notebook                50              0        3749619           8141
HTML                            21            746             63           7304
Python                          37           1262           2138           6763
SVG                              1              0              0           2671
JavaScript                      15            231            292           1890
CSS                              7            424             74           1723
CSV                              4              0              0           1454
Rust                             1             71              9            537
Markdown                         2             66              0            225
reStructuredText                17            146            236            202
YAML                             4             10              5            134
TeX                              1             11              0            112
TOML                             2             12              2             67
DOS Batch                        1              8              1             26
make                             1              4              7              9
-------------------------------------------------------------------------------
SUM:                           164           2991        3752446          31258
-------------------------------------------------------------------------------

Commit count by author:

   150	Deron Smith
    19	mikecyterski

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 1046

✅ The paper includes a Statement of need section

[editorialbot]

License info:

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

[editorialbot]

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

[editorialbot]

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[kthyng]

Hi @deronsmith and thanks for your submission! I am looking for some specific items to make sure your submission fits our requirements at a high level (not at the more detailed review level) before moving on to finding an editor or putting this on our waitlist if no relevant editors are available. I'll comment over time as I have a chance to go through them:

• OSI-approved license
• Installation instructions
• Documentation exists at all
• Tests of some sort
• Check paper (make sure compiles, read through, check for length 250-1000 words)
• Substantial scholarly effort
• Clear research application

In the meantime, please take a look at the comments above ⬆️ from the editorialbot to address any DOI, license, or paper issues if you're able (there may not be any), or suggest reviewers. For reviewers, please suggest 5 reviewers from the database listed above or your own (non-conflicted) extended network. Their github handles are most useful to receive but please don't use "@" to reference them since it will prematurely ping them.

[deronsmith]

Hi @kthyng, thank you for this information. I have gone ahead and addressed the missing doi and reduced the paper word count to under 1000 (pushed to the main branch). I will review the database of reviewers for potential options and get back to you with that information.

[kthyng]

@editorialbot generate pdf

[editorialbot]

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

[editorialbot]

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[kthyng]

@deronsmith

• have you thought about putting your notebooks into your docs? That would be nice for users!
• I see PyPI is in your plan for the future — would be great to have that as part of the JOSS review process.

[kthyng]

@mengqi-z Could you edit this submission?

[kthyng]

@editorialbot invite @mengqi-z as editor

[editorialbot]

Invitation to edit this submission sent!

[mengqi-z]

@editorialbot assign me as editor

[editorialbot]

Assigned! @mengqi-z is now the editor

[deronsmith]

@kthyng @mengqi-z

@deronsmith

• have you thought about putting your notebooks into your docs? That would be nice for users!
• I see PyPI is in your plan for the future — would be great to have that as part of the JOSS review process.

Absolutely, I'll move a few of the more polished workflow notebooks into the docs.

The EPA's QA policy requires an external peer review prior to code or software release, so we were planning on pushing to pypi once we have the JOSS review completed (assuming we successfully publish through JOSS). But I believe the prebuilt wheels are available to logged in Github user's by looking at the 'Build and Publish Wheel' workflow.

[deronsmith]

I had actually linked to the two primary notebooks in the README, which is also shown in the documentation readme page https://quanted.github.io/esat/README.html

[mengqi-z]

👋 @eldemet @acocac @KatyJMiles @MoLi7 - Would any of you be interested and available to review this submission for JOSS? The review process is straightforward, handled through GitHub issues, and follows a checklist-driven approach: https://joss.readthedocs.io/en/latest/review_criteria.html

If you're unable to review, any recommendations for other potential reviewers with relevant expertise would also be greatly appreciated. Thank you!

[kthyng]

@deronsmith Excellent, thank you!

[mengqi-z]

👋@Zeitsperre @nanhung @katmratliff @ZiyiHuang0708 - Would any of you be willing o review this submission to JOSS? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html

[mengqi-z]

👋 @ethanwhite @laura-hyesung-yang - Would any of you be available to review a submission for JOSS? Given your background, I believe you'd be a great fit to review this paper.

JOSS uses a checklist-driven review process, which you can find here: https://joss.readthedocs.io/en/latest/review_criteria.html

If you're unable to review, any recommendations for other potential reviewers with relevant expertise would also be greatly appreciated. Thank you!

[mengqi-z]

@editorialbot add @gutabeshu as reviewer

[editorialbot]

@gutabeshu added to the reviewers list!

[mengqi-z]

👋 @nickrsan @ifoxfoot - Would you be willing to review this submission for JOSS? JOSS uses a checklist-driven review process, which you can find here: https://joss.readthedocs.io/en/latest/review_criteria.html

[mengqi-z]

👋 @ibarraespinosa @purushottamkar @niravlekinwala - Would any of you be interested in reviewing this submission for JOSS?
JOSS uses a checklist-driven review process, which you can find here: https://joss.readthedocs.io/en/latest/review_criteria.html

[nickrsan]

Hi @mengqi-z - I'm sorry but I have to decline at this time. It looks like a great submission though!

[mengqi-z]

@nickrsan - No problem at all. Thanks for letting me know!

[ifoxfoot]

Hi @mengqi-z I am available to review this submission

[niravlekinwala]

Hi @mengqi-z, I am also available to review the submission.

[mengqi-z]

@editorialbot add @ifoxfoot as reviewer

[editorialbot]

@ifoxfoot added to the reviewers list!

[mengqi-z]

@editorialbot add @niravlekinwala as reviewer

[editorialbot]

@niravlekinwala added to the reviewers list!

[mengqi-z]

@gutabeshu, @ifoxfoot, @niravlekinwala - Thank you very much for agreeing to review this submission. I will now close this Pre-Review issue and start the review process.

[mengqi-z]

@editorialbot start review

[editorialbot]

OK, I've started the review over in #7316.