[REVIEW]: Pysewer: A Python Library for Sewer Network Generation in Data Scarce Regions #6430

editorialbot · 2024-02-29T12:21:46Z

Submitting author: @dbdespot (Daneish Despot)
Repository: https://git.ufz.de/despot/pysewer/
Branch with paper.md (empty if default branch):
Version: v0.1.20
Editor: @olexandr-konovalov
Reviewers: @meghnathomas, @barneydobson
Archive: 10.5281/zenodo.14355668

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/1723c806b1d23252d4642a6c1b75bb9c/status.svg)](https://joss.theoj.org/papers/1723c806b1d23252d4642a6c1b75bb9c)

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 & @simoninireland, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review.
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✨ 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 @barneydobson

The text was updated successfully, but these errors were encountered:

editorialbot · 2024-02-29T12:21:50Z

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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editorialbot · 2024-02-29T12:21:55Z

Software report:

github.com/AlDanial/cloc v 1.88  T=0.14 s (788.4 files/s, 228148.3 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
HTML                            18           1021             54           6984
TeX                             26           1021           2445           6578
SVG                              1              0              0           2671
Python                          16            526           1254           1691
JavaScript                      12            131            221            880
CSS                              4            190             35            779
XML                              8              0              0            708
Markdown                         4            148              0            340
Jupyter Notebook                 2              0           2852            189
YAML                             5             20             12            157
reStructuredText                 6             61             69             64
make                             2             22             12             50
DOS Batch                        3             17              2             49
Bourne Shell                     1              0              0              1
-------------------------------------------------------------------------------
SUM:                           108           3157           6956          21141
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

editorialbot · 2024-02-29T12:21:56Z

Wordcount for paper.md is 1967

editorialbot · 2024-02-29T12:22:16Z

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

OK DOIs

- 10.5281/zenodo.3946761 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.1109/MCSE.2007.55 is OK
- 10.5281/zenodo.5884351 is OK
- 10.3389/fenvs.2021.626634 is OK
- 10.2166/wst.2015.393 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot · 2024-02-29T12:23:38Z

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

meghnathomas · 2024-02-29T16:04:19Z

Review checklist for @meghnathomas

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

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

General checks

Repository: Is the source code for this software available at the https://git.ufz.de/despot/pysewer/?
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 (@dbdespot) 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?

simoninireland · 2024-03-04T13:39:39Z

Review checklist for @simoninireland

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

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

General checks

Repository: Is the source code for this software available at the https://git.ufz.de/despot/pysewer/?
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 (@dbdespot) 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?

meghnathomas · 2024-03-14T19:25:02Z

Hi @dbdespot! Is there any way to raise an issue with comments/questions in your repository without signing up for the UFZ GitLab service?

dbdespot · 2024-03-14T20:18:14Z

Hi @meghnathomas, I think the easiest and quickest way to do this is to add the reviewers as a "guest" role to the project. Please let me know if that's ok. If it is, please send me your email.

meghnathomas · 2024-03-14T20:20:52Z

@dbdespot that sounds good to me, thanks! My email is meghnathomas@utexas.edu

dbdespot · 2024-03-14T20:35:14Z

@meghnathomas Thanks; it turns out that I have to request the admin to add new members via email. I will try to solve this and get back to you as soon as possible. My apologies

dbdespot · 2024-03-15T14:07:35Z

Hi, @meghnathomas @simoninireland. See below regarding creating issues without signing up for the UFZ GitLab service:
The steps to gain access to UFZ GitLab as an external person are described on the GitLab Sign-In page at https://git.ufz.de/users/sign_in:
If you are an external partner(reviewer in this case):
Log in with your GitHub account first.
Then, inform your UFZ contact person (me) so I can notify the UFZ GitLab Admin to unblock your account.
So, please initially log into the UFZ GitLab with your GitHub account. Once this is done, UFZ GitLab Admin can unblock your accounts.

Please let me know how this goes.

meghnathomas · 2024-03-15T17:29:42Z

Thanks @dbdespot! I've logged in with my GitHub account.

meghnathomas · 2024-04-01T18:42:31Z

Hi @dbdespot FYI, I am still unable to access Gitlab. I have been seeing this message every time I've tried to log in the past few weeks:

Your account is pending approval from your GitLab administrator and hence blocked.

In the mean time, I would recommend setting up an alternate forum/platform where Pysewer users can publicly raise issues or questions without having to set up a Gitlab account.

ddspot · 2024-04-02T19:22:16Z

Hi @meghnathomas, sorry for the confusion. I had the impression that you could have logged in, and everything worked. I added you as a guest, and you should be able to create issues and so on now.

In the meantime, I would look into mirroring this repo on GitHub. But for now, please let me know if you can create an issue,.

olexandr-konovalov · 2024-04-25T11:49:58Z

Hi @meghnathomas @simoninireland - how this review is going?

meghnathomas · 2024-04-29T19:12:03Z

Hi @olexandr-konovalov thank you for checking in! I just created an issue with feedback for the authors over in their repository.

dbdespot · 2024-05-13T13:35:33Z

Hi @meghnathomas, I would like to let you know that I have responded to the feedback directly on the Gitlab repo. Please note that I have made a mirror GIithub repo.

meghnathomas · 2024-06-10T03:52:06Z

Hi @olexandr-konovalov I have completed my review of this code and paper (started over here on Gitlab and continued on their Github repository). I am happy to recommend this paper for acceptance!

olexandr-konovalov · 2024-06-10T07:51:17Z

Wondereful, thank @meghnathomas! We will now wait for the 2nd review to be completed by @simoninireland

olexandr-konovalov · 2024-12-10T09:18:07Z

@kthyng I have recommended acceptance. The only technical issue is that there is a reference to a journal called "npj Clean Water" and whatever was attempted, like journal={{npj} Clean Water}, still results in it shown capitalised as Npj in the paper.

olexandr-konovalov · 2024-12-10T09:24:20Z

@dbdespot ah indeed - good to have automated checks, I've missed that while checking the PDF after the reference has been updated, sorry! Indeed page 3, line 81, broken reference to NetworkX. Please fix and make a new version and a new DOI.

dbdespot · 2024-12-10T10:15:56Z

Hi @olexandr-konovalov, here we go once more; new DOI: https://doi.org/10.5281/zenodo.14355668, version number: v0.1.20

olexandr-konovalov · 2024-12-10T11:16:33Z

@editorialbot set 10.5281/zenodo.14355668 as archive

editorialbot · 2024-12-10T11:16:36Z

Done! archive is now 10.5281/zenodo.14355668

olexandr-konovalov · 2024-12-10T11:16:58Z

@editorialbot set v0.1.20 as version

editorialbot · 2024-12-10T11:17:01Z

Done! version is now v0.1.20

olexandr-konovalov · 2024-12-10T11:17:18Z

@editorialbot generate pdf

olexandr-konovalov · 2024-12-10T11:17:41Z

@editorialbot check references

editorialbot · 2024-12-10T11:18:52Z

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

✅ OK DOIs

- 10.5281/zenodo.3946761 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.1109/MCSE.2007.55 is OK
- 10.25080/TCWV9851 is OK
- 10.5281/zenodo.5884351 is OK
- 10.3389/fenvs.2021.626634 is OK
- 10.2166/wst.2015.393 is OK
- 10.1007/BF01386390 is OK
- 10.1002/net.3230220105 is OK
- 10.1038/s41545-023-00222-4 is OK
- 10.3390/w12123337 is OK
- 10.1016/j.oneear.2023.08.005 is OK
- 10.1061/(ASCE)0733-9372(1990)116:5(927) is OK
- 10.1080/1573062X.2012.731072 is OK
- 10.1007/s11269-015-1191-8 is OK
- 10.1061/jpsea2.pseng-1358 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: Scikit-learn: Machine Learning in Python
- No DOI given, and none found for title: Rasterio: geospatial raster I/O for Python program...
- No DOI given, and none found for title: Sustainable Development Goal 6: Synthesis Report 2...
- No DOI given, and none found for title: Computer Models of Waste-Water Collection Systems

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

editorialbot · 2024-12-10T11:20:52Z

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

olexandr-konovalov · 2024-12-10T11:27:11Z

@editorialbot recommend-accept

editorialbot · 2024-12-10T11:27:13Z

Attempting dry run of processing paper acceptance...

editorialbot · 2024-12-10T11:27:47Z

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

✅ OK DOIs

- 10.5281/zenodo.3946761 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.1109/MCSE.2007.55 is OK
- 10.25080/TCWV9851 is OK
- 10.5281/zenodo.5884351 is OK
- 10.3389/fenvs.2021.626634 is OK
- 10.2166/wst.2015.393 is OK
- 10.1007/BF01386390 is OK
- 10.1002/net.3230220105 is OK
- 10.1038/s41545-023-00222-4 is OK
- 10.3390/w12123337 is OK
- 10.1016/j.oneear.2023.08.005 is OK
- 10.1061/(ASCE)0733-9372(1990)116:5(927) is OK
- 10.1080/1573062X.2012.731072 is OK
- 10.1007/s11269-015-1191-8 is OK
- 10.1061/jpsea2.pseng-1358 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: Scikit-learn: Machine Learning in Python
- No DOI given, and none found for title: Rasterio: geospatial raster I/O for Python program...
- No DOI given, and none found for title: Sustainable Development Goal 6: Synthesis Report 2...
- No DOI given, and none found for title: Computer Models of Waste-Water Collection Systems

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

editorialbot · 2024-12-10T11:29:54Z

👋 @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#6243, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

olexandr-konovalov · 2024-12-10T11:40:18Z

Wonderful - thanks @dbdespot! This is now passed over to @openjournals/ese-eics team.

kthyng · 2024-12-10T16:33:07Z

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.

kthyng · 2024-12-10T16:40:13Z

Looks good to go!

kthyng · 2024-12-10T16:40:18Z

@editorialbot accept

editorialbot · 2024-12-10T16:40:22Z

Doing it live! Attempting automated processing of paper acceptance...

editorialbot · 2024-12-10T16:48:16Z

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: Sanne
  given-names: Moritz
- family-names: Khurelbaatar
  given-names: Ganbaatar
  orcid: "https://orcid.org/0000-0002-2430-1612"
- family-names: Despot
  given-names: Daneish
  orcid: "https://orcid.org/0000-0002-8980-5651"
- family-names: Afferden
  given-names: Manfred
  name-particle: van
- family-names: Friesen
  given-names: Jan
  orcid: "https://orcid.org/0000-0003-0454-0437"
contact:
- family-names: Despot
  given-names: Daneish
  orcid: "https://orcid.org/0000-0002-8980-5651"
doi: 10.5281/zenodo.14355668
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Sanne
    given-names: Moritz
  - family-names: Khurelbaatar
    given-names: Ganbaatar
    orcid: "https://orcid.org/0000-0002-2430-1612"
  - family-names: Despot
    given-names: Daneish
    orcid: "https://orcid.org/0000-0002-8980-5651"
  - family-names: Afferden
    given-names: Manfred
    name-particle: van
  - family-names: Friesen
    given-names: Jan
    orcid: "https://orcid.org/0000-0003-0454-0437"
  date-published: 2024-12-10
  doi: 10.21105/joss.06430
  issn: 2475-9066
  issue: 104
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 6430
  title: "Pysewer: A Python Library for Sewer Network Generation in Data
    Scarce Regions"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.06430"
  volume: 9
title: "Pysewer: A Python Library for Sewer Network Generation in Data
  Scarce Regions"

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.

editorialbot · 2024-12-10T16:48:20Z

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

editorialbot · 2024-12-10T16:48:21Z

🦋🦋🦋 👉 Bluesky post for this paper 👈 🦋🦋🦋

editorialbot · 2024-12-10T16:48:22Z

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.06430 joss-papers#6247
Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.06430
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

kthyng · 2024-12-10T16:59:22Z

Congratulations on your new publication @dbdespot! Many thanks to editor @olexandr-konovalov and to reviewers @meghnathomas and @barneydobson 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.

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

editorialbot · 2024-12-10T16:59:27Z

🎉🎉🎉 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.06430/status.svg)](https://doi.org/10.21105/joss.06430)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.06430">
  <img src="https://joss.theoj.org/papers/10.21105/joss.06430/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.06430/status.svg
   :target: https://doi.org/10.21105/joss.06430

This is how it will look in your documentation:

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editorialbot added Batchfile Jupyter Notebook review Shell Track: 6 (ESE) Earth Sciences and Ecology waitlisted Submissions in the JOSS backlog due to reduced service mode. labels Feb 29, 2024

editorialbot assigned olexandr-konovalov Feb 29, 2024

editorialbot mentioned this issue Feb 29, 2024

[PRE REVIEW]: Pysewer: A Python Library for Sewer Network Generation in Data Scarce Regions #6006

Closed

editorialbot added Python TeX labels Feb 29, 2024

editorialbot added the recommend-accept Papers recommended for acceptance in JOSS. label Dec 10, 2024

editorialbot added accepted published Papers published in JOSS labels Dec 10, 2024

kthyng closed this as completed Dec 10, 2024

[REVIEW]: Pysewer: A Python Library for Sewer Network Generation in Data Scarce Regions #6430

[REVIEW]: Pysewer: A Python Library for Sewer Network Generation in Data Scarce Regions #6430

Comments

editorialbot commented Feb 29, 2024 • edited Loading

Status

Reviewer instructions & questions

Checklists

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meghnathomas commented Feb 29, 2024 • edited Loading

Review checklist for @meghnathomas

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

simoninireland commented Mar 4, 2024 • edited Loading

Review checklist for @simoninireland

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

meghnathomas commented Mar 14, 2024 • edited Loading

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kthyng commented Dec 10, 2024

editorialbot commented Dec 10, 2024

editorialbot commented Feb 29, 2024 •

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meghnathomas commented Feb 29, 2024 •

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simoninireland commented Mar 4, 2024 •

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meghnathomas commented Mar 14, 2024 •

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meghnathomas commented Mar 15, 2024 •

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kthyng commented Dec 10, 2024 •

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