[REVIEW]: EPyT-C: A Python package for water quality modeling in water distribution systems

editorialbot commented 3 months ago

Submitting author: !--author-handle-->@SWIL-IITK@cheginit<!--end-editor-- Reviewers: @meghnathomas, @samhatchett Archive: Pending

Status

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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

@meghnathomas & @samhatchett, 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 @cheginit 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 @meghnathomas

📝 Checklist for @samhatchett

editorialbot commented 3 months ago

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editorialbot commented 3 months ago

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

OK DOIs

- 10.1061/(ASCE)EE.1943-7870.0001918 is OK
- 10.3390/w14101665 is OK
- 10.1016/j.jenvman.2022.115817 is OK
- 10.1061/(ASCE)0733-9496(2002)128:5(334) is OK

MISSING DOIs

- No DOI given, and none found for title: EPANET 2.0 User Manual
- No DOI given, and none found for title: EPANET 2.2 User Manual, Report EPA/600/R-20/133
- No DOI given, and none found for title: EPANET Multi-Species Extension User’s Manual
- No DOI given, and none found for title:  National Primary Drinking Water Regulations: Stag...

INVALID DOIs

- None

editorialbot commented 3 months ago

Software report:

github.com/AlDanial/cloc v 1.90  T=0.09 s (867.2 files/s, 248504.0 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
HTML                            14            693             42           5684
Python                          16            398           1556           3849
SVG                              1              0              0           2671
JavaScript                      12            131            221            880
CSS                              4            190             35            780
Markdown                         4            123              0            307
Jupyter Notebook                15              0           4237            173
YAML                             4             19             21             96
TeX                              1              7              0             69
reStructuredText                 4             27             43             38
DOS Batch                        1              8              1             26
make                             1              4              7              9
TOML                             1              0              0              6
-------------------------------------------------------------------------------
SUM:                            78           1600           6163          14588
-------------------------------------------------------------------------------

Commit count by author:

    98  g-jaykrishnan
    87  Smart Water Infrastructure Laboratory, IIT Kanpur
    36  G Jaykrishnan

editorialbot commented 3 months ago

Paper file info:

📄 Wordcount for paper.md is 2255

✅ The paper includes a Statement of need section

editorialbot commented 3 months ago

License info:

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

editorialbot commented 3 months ago

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

cheginit commented 3 months ago

👋🏼 @SWIL-IITK, @meghnathomas, and @samhatchett, this is the review thread for the paper. All of our communications will happen here from now on.

As a reviewer, the first step, as mentioned in the first comment of this issue, 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#6885 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 notify me 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 don't hesitate to ping me (@cheginit) if you have any questions/concerns.

meghnathomas commented 3 months ago

Review checklist for @meghnathomas

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/SWIL-IITK/EPyT-C?
[x] 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 (@SWIL-IITK) 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
[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.
[ ] 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

[ ] 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?

cheginit commented 3 months ago

👋🏼 @samhatchett, a friendly reminder for this review.

cheginit commented 2 months ago

👋🏼 @meghnathomas, please update us on how the review is going.

meghnathomas commented 2 months ago

Thanks for checking in @cheginit ! I started my review over in https://github.com/SWIL-IITK/EPyT-C/issues/7

cheginit commented 2 months ago

@meghnathomas Awesome, thanks for the update!

cheginit commented 2 months ago

👋🏼 @SWIL-IITK Please update us on your progress addressing issues raised by the reviewers.

cheginit commented 2 months ago

👋🏼 @samhatchett, Please let me know if you'll be able to start reviewing this submission soon. I reached out via email, but unfortunately I haven't heard back from you.

cheginit commented 1 month ago

@SWIL-IITK, after reviewing the feedback from our reviewers and conducting my own analysis, I've identified several key issues that need to be addressed before we can proceed with the review:

Scholarly effort: A reviewer has pointed out to me via email that the submission "ineffectively reproduces work that has already been long understood in the field and presents cases that are already well-documented in existing software." This raises concerns about the contribution of your work. In JOSS documents under the "Substantial Scholarly Effort" section, we state that:

JOSS publishes articles about software that represent substantial scholarly effort on the part of the authors. Your software should be a significant contribution to the available open source software that either enables some new research challenges to be addressed or makes addressing research challenges significantly better (e.g., faster, easier, simpler).

Unaddressed Issues: The issue opened by @meghnathomas on July 9 (https://github.com/SWIL-IITK/EPyT-C/issues/7) has not received any response. This issue highlights problems including example notebooks not running as expected.
Demonstration of Contributions: Considering the first issue, more comprehensive example notebooks are needed to clearly demonstrate the significant contributions of your submission.

To move forward with your submission, please provide the following:

[ ] A plan detailing how you will address the reviewer's feedback regarding your contributions.
[ ] A response to @meghnathomas's issue, including a timeline for resolving the reported problems.
[ ] A proposal for additional example notebooks that will effectively showcase the contributions of your software package.
[ ] A tentative timeline for implementing these improvements.

Please submit your plan and timeline as a reply to this comment within the next two weeks. This will help us assess the viability of your submission moving forward. We look forward to your response and are committed to working with you to improve your submission to meet JOSS standards.

cheginit commented 2 weeks ago

@SWIL-IITK, since I haven't heard from you after three weeks from my previous comment, unfortunately, we cannot continue with your submission in its current form. Please feel free to make the suggested changes, as laid out in my previous comment, at your own pace and resubmit your software package.

@meghnathomas and @samhatchett, I appreciate your time and effort in reviewing this submission and providing constructive feedback.

@kthyng, Unfortunately, we are unable to proceed with the review of this submission. It requires substantial changes and the author did not respond to my requests for providing a timeline to address the issues in a timely manner.

kthyng commented 2 weeks ago

@editorialbot reject

editorialbot commented 2 weeks ago

Paper rejected.

SWIL-IITK commented 2 weeks ago

@cheginit Sorry, the previous email about the timeline went to my spam folder. I just didn't know. We are working on the edits offline. Can you please give us a week more time? I am really sorry about this!

SWIL-IITK commented 2 weeks ago

@kthyng is this possible?

kthyng commented 2 weeks ago

@SWIL-IITK Ah, a miscommunication. Considering we hadn't heard from you on the reviewer issue several months ago nor the message above, we figured you had abandoned this submission. In lieu of restarting this submission, I propose that you address the issues in detail from @cheginit's comment, then resubmit after you've taken all the time necessary to do so. We recognize that this will probably take a substantial amount of time and there is no hurry to resubmit. Thank you.

openjournals / joss-reviews