editorialbot commented 1 year ago

Submitting author: !--author-handle-->@barneydobson@crvernon<!--end-editor-- Reviewers: @cheginit, @jlarsen-usgs Archive: 10.5281/zenodo.7662569

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/9df09dbd84388e336f911bb1d55c7a87"><img src="https://joss.theoj.org/papers/9df09dbd84388e336f911bb1d55c7a87/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/9df09dbd84388e336f911bb1d55c7a87/status.svg)](https://joss.theoj.org/papers/9df09dbd84388e336f911bb1d55c7a87)

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

@cheginit & @jlarsen-usgs, 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 @crvernon 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 @cheginit

📝 Checklist for @jlarsen-usgs

editorialbot commented 1 year 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 year ago

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

OK DOIs

- 10.1088/1748-9326/abb050 is OK
- 10.1016/j.scitotenv.2021.150642 is OK
- 10.1016/j.watres.2017.09.039 is OK
- 10.3389/frwa.2021.641462 is OK
- 10.1029/2021WR030778 is OK
- 10.3389/frwa.2021.773974 is OK
- 10.1002/essoar.10511984.1 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot commented 1 year ago

Software report:

github.com/AlDanial/cloc v 1.88  T=0.30 s (198.5 files/s, 59203.8 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          34           2504           4000           6902
SVG                              2              0              1           2355
XML                              1              0             52           1534
Markdown                        16             91              0            212
JSON                             3              0              0             76
TeX                              1              6              0             75
YAML                             2              7              4             47
CSS                              1              4              3             20
-------------------------------------------------------------------------------
SUM:                            60           2612           4060          11221
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

editorialbot commented 1 year ago

Wordcount for paper.md is 448

editorialbot commented 1 year ago

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

crvernon commented 1 year ago

👋 @barneydobson @cheginit @jlarsen-usgs This is the review thread for the paper. All of our communications will happen here from now on.

Please read the "Reviewer instructions & questions" in the first comment above.

Both reviewers have checklists at the top of this thread (in that first comment) with the JOSS requirements. As you go over the submission, please check any items that you feel have been satisfied. There are also 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/4996 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 the review process to be completed within about 4-6 weeks but please make a start well ahead of this as JOSS reviews are by their nature iterative and any early feedback you may be able to provide to the author will be very helpful in meeting this schedule.

crvernon commented 1 year ago

👋 @cheginit and @jlarsen-usgs could you provide an update to how things are going? Also please let me know if you have any questions.

jlarsen-usgs commented 1 year ago

@crvernon I've blocked out time this week to complete my review. Thanks for the nudge

cheginit commented 1 year ago

Review checklist for @cheginit

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/barneydobson/wsi?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@barneydobson) 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?

jlarsen-usgs commented 1 year ago

Review checklist for @jlarsen-usgs

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/barneydobson/wsi?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@barneydobson) 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?

crvernon commented 1 year ago

👋 @cheginit and @jlarsen-usgs looks like you are making great progress! @barneydobson let me know if you have any questions!

barneydobson commented 1 year ago

Thanks @crvernon I have replied to tasks for the two review issues, to check - there's nothing else waiting for me? (Not rushing the reviewers, just want to make sure I'm not holding anything up)

crvernon commented 1 year ago

Great @barneydobson ! @cheginit and @jlarsen-usgs how are we doing on your end? Great work everyone!

cheginit commented 1 year ago

@barneydobson Thanks for taking the time to address my concerns. @crvernon In my opinion, the submission is ready for publication.

crvernon commented 1 year ago

Thanks @cheginit !

jlarsen-usgs commented 1 year ago

@crvernon, All of my review comments have been addressed. I think the submission is ready to move ahead with publication

crvernon commented 1 year ago

Thanks @jlarsen-usgs !

crvernon commented 1 year ago

@editorialbot generate pdf

editorialbot commented 1 year ago

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

crvernon commented 1 year ago

@editorialbot check references

editorialbot commented 1 year ago

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

OK DOIs

- 10.1088/1748-9326/abb050 is OK
- 10.1016/j.scitotenv.2021.150642 is OK
- 10.1016/j.watres.2017.09.039 is OK
- 10.3389/frwa.2021.641462 is OK
- 10.1029/2021WR030778 is OK
- 10.3389/frwa.2021.773974 is OK
- 10.1016/j.jenvman.2022.117045 is OK
- 10.1016/j.envsoft.2013.05.004 is OK
- 10.13031/2013.42259 is OK
- j.envsoft.2009.11.009 is OK

MISSING DOIs

- None

INVALID DOIs

- None

crvernon commented 1 year ago

@barneydobson - we are almost there! Next is just addressing the following few comments that I had for your paper and setting up the archive for your new release.

[ ] THROUGHOUT: please put a space in between the phrase and the reference. For example, "...integration framework [@Rauch:2017]." instead of "...integration framework[@Rauch:2017]."
[ ] LINE 47: missing examples "(e.g., )"
[ ] LINE 68: need to remove \bibliography from your paper.md

We want to make sure the archival has the correct metadata that JOSS requires. This includes a title that matches the paper title and a correct author list.

So here is what we have left to do:

[ ] Conduct a GitHub release of the current reviewed version of the software you now have on the main and archive the reviewed software in Zenodo or a similar service (e.g., figshare, an institutional repository)
[ ] Check the archival deposit (e.g., in Zenodo) to ensure it has the correct metadata. This includes the title (should match the paper title) and author list (make sure the list is correct and people who only made a small fix are not on it). You may also add the authors' ORCID.
[ ] Please list the DOI of the archived version here

I can then move forward with accepting the submission.

barneydobson commented 1 year ago

Thanks @crvernon , those paper changes now corrected.

I've made a release, created an archive with the correct metadata.

With DOI: 10.5281/zenodo.7662569

crvernon commented 1 year ago

@editorialbot set 10.5281/zenodo.7662569 as archive

editorialbot commented 1 year ago

Done! Archive is now 10.5281/zenodo.7662569

crvernon commented 1 year ago

@editorialbot set 0.3_joss_reviewed as version

editorialbot commented 1 year ago

Done! version is now 0.3_joss_reviewed

crvernon commented 1 year ago

@editorialbot generate pdf

crvernon commented 1 year ago

@editorialbot check references

editorialbot commented 1 year ago

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

OK DOIs

- 10.1088/1748-9326/abb050 is OK
- 10.1016/j.scitotenv.2021.150642 is OK
- 10.1016/j.watres.2017.09.039 is OK
- 10.3389/frwa.2021.641462 is OK
- 10.1029/2021WR030778 is OK
- 10.3389/frwa.2021.773974 is OK
- 10.1016/j.jenvman.2022.117045 is OK
- 10.1016/j.envsoft.2013.05.004 is OK
- 10.13031/2013.42259 is OK
- j.envsoft.2009.11.009 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot commented 1 year ago

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

crvernon commented 1 year ago

@barneydobson I just noticed that part of the DOI is missing for the following:

Gironás, J., Roesner, L. A., Rossman, L. A., & Davis, J. (2010). A new applications manual
82 for the storm water management model(SWMM). Environmental Modelling & Software,
83 25(6), 813–814. https://doi.org/j.envsoft.2009.11.009

The DOI link should be: https://doi.org/10.1016/j.envsoft.2009.11.009

Also, do mind changing the following sentence in the "Limitations" section from:

In applications where detailed hydraulic/hydrological process representations are needed, for example, to inform the design of specific pipes, or in cases where processes are hard to quantify, for example, in representing social drivers of population growth, there are likely better tools available.

to

In applications where detailed hydraulic/hydrological process representations are needed (e.g., informing the design of specific pipes, cases where processes are hard to quantify such as representing social drivers of population growth, etc.) there are likely better tools available.

That should be the last of it. Thanks!

barneydobson commented 1 year ago

Hi @crvernon good spot there - thanks, and yep that reads more clearly.

Both now on the main repo. Do I need to make a new release or is this fine?

crvernon commented 1 year ago

@barneydobson should be all good.

crvernon commented 1 year ago

@editorialbot check references

editorialbot commented 1 year ago

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

OK DOIs

- 10.1088/1748-9326/abb050 is OK
- 10.1016/j.scitotenv.2021.150642 is OK
- 10.1016/j.watres.2017.09.039 is OK
- 10.3389/frwa.2021.641462 is OK
- 10.1029/2021WR030778 is OK
- 10.3389/frwa.2021.773974 is OK
- 10.1016/j.jenvman.2022.117045 is OK
- 10.1016/j.envsoft.2013.05.004 is OK
- 10.13031/2013.42259 is OK
- 10.1016/j.envsoft.2009.11.009 is OK

MISSING DOIs

- None

INVALID DOIs

- None

crvernon commented 1 year ago

@editorialbot generate pdf

editorialbot commented 1 year ago

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

crvernon commented 1 year ago

@barneydobson - thanks for putting together a really nice software product! Thanks to @cheginit and @jlarsen-usgs for a constructive and timely review!

I am recommending that your submission be accepted. An EIC will review this shortly and confirm final publication if all goes well.

crvernon commented 1 year ago

@editorialbot recommend-accept

editorialbot commented 1 year ago

Attempting dry run of processing paper acceptance...

editorialbot commented 1 year ago

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

OK DOIs

- 10.1088/1748-9326/abb050 is OK
- 10.1016/j.scitotenv.2021.150642 is OK
- 10.1016/j.watres.2017.09.039 is OK
- 10.3389/frwa.2021.641462 is OK
- 10.1029/2021WR030778 is OK
- 10.3389/frwa.2021.773974 is OK
- 10.1016/j.jenvman.2022.117045 is OK
- 10.1016/j.envsoft.2013.05.004 is OK
- 10.13031/2013.42259 is OK
- 10.1016/j.envsoft.2009.11.009 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot commented 1 year ago

:wave: @openjournals/ese-eics, this paper is ready to be accepted and published.

Check final proof :point_right::page_facing_up: Download article

If the paper PDF and the deposit XML files look good in https://github.com/openjournals/joss-papers/pull/3997, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

kthyng commented 1 year ago

Hi! I see the archive and version are set ✅

kthyng commented 1 year ago

Please check the capitalization in your references. You can preserve capitalization by placing {} around characters/words in your .bib file.

Also the acknowledgements for "The design of ..." look a little strange — please make sure they are coming through as you intend.

barneydobson commented 1 year ago

@kthyng Thanks for your comments there. I have updated the acknowledgements to include them as references, which I should have done from the start - hopefully you'll agree they are clearer now.

RE capitalizations, they seem OK to me (and are in curly braces in the .bib file) - is there any specific that seem wrong?

kthyng commented 1 year ago

@editorialbot generate pdf

editorialbot commented 1 year ago

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

kthyng commented 1 year ago

@barneydobson References comments:

[ ] Shrestha et al has "belgium" and the river not capitalized
[ ] Also Gironas needs a space before the acronym in the title

barneydobson commented 1 year ago

Got it - both now corrected, apologies for missing those!

openjournals / joss-reviews

[REVIEW]: Water Systems Integrated Modelling framework, WSIMOD: A Python package for integrated modelling of water quality and quantity across the water cycle #4996

Status

Reviewer instructions & questions

Checklists

Review checklist for @cheginit

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @jlarsen-usgs

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper