[REVIEW]: Effluent - A python package for modelling effluent discharge

[editorialbot]

Submitting author: @pnsaevik (Pål Næverlid Sævik)
Repository: https://github.com/pnsaevik/effluent
Branch with paper.md (empty if default branch):
Version: 1.3
Editor: @kthyng
Reviewers: @castelao, @bastorer
Archive: 10.5281/zenodo.8333370

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/9e755d60196949d66ddbf2d803a74460"><img src="https://joss.theoj.org/papers/9e755d60196949d66ddbf2d803a74460/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/9e755d60196949d66ddbf2d803a74460/status.svg)](https://joss.theoj.org/papers/9e755d60196949d66ddbf2d803a74460)

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

@castelao & @bastorer, 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 @kthyng 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 @castelao

📝 Checklist for @bastorer

[editorialbot]

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:

@editorialbot commands

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

@editorialbot generate pdf

[editorialbot]

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

OK DOIs

- 10.1023/A:1025583110842 is OK
- 10.1016/j.envsoft.2003.08.018 is OK
- 10.1007/978-1-4615-0407-8 is OK
- 10.1016/j.ocemod.2004.08.002 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.04 s (1221.4 files/s, 101733.5 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          16            383            167           1500
reStructuredText                16            469            767            376
TOML                             8             14             21            155
Markdown                         3             40              0             99
YAML                             3             10             14             82
TeX                              1              5              0             63
DOS Batch                        1              8              1             26
CSS                              1              3              0             19
make                             1              4              7              9
INI                              1              0              0              6
-------------------------------------------------------------------------------
SUM:                            51            936            977           2335
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 255

[editorialbot]

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

[kthyng]

Hi @castelao, @bastorer — this is the place for the review itself. Please make issues on the software repo as needed, and otherwise you can use the checklist to drive your review, and put updates in here as we go. Thanks and let me know if you have any questions!

[castelao]

Review checklist for @castelao

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://github.com/pnsaevik/effluent?
• License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@pnsaevik) 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?

[pnsaevik]

I wasn't aware of the citation syntax required in paper.md. Have fixed it now.

[bastorer]

@editorialbot generate pdf

[editorialbot]

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

[kthyng]

@castelao @bastorer @pnsaevik Looks like everyone has been up to other things this summer (like me!). Will you have time to work on this review this week?

[castelao]

I can next week. Thanks for checking.

[bastorer]

Hi @kthyng . @pnsaevik mentioned being on holidays until August (in this issue pnsaevik/effluent#26). I asked them to send me a ping where they're back and ready to resume :-)

[kthyng]

@bastorer Ah, thanks. Summer is pretty spotty for a lot of us!

[kthyng]

Looks like we are back to moving along. Let me know if any issues are holding people up that I can help with!

[castelao]

For the record, I made a few comments and suggestions to @pnsaevik early in the summer (BTW @pnsaevik was very positive and proactive, even for modifications that wouldn't be strictly required), but I forgot to add links to here. Those modifications and discussions can be found as closed PRs in the effluent repository.

[pnsaevik]

@bastorer has not responded to my requests for three weeks, but I assume he has been busy. But as he suggested only minor edits, the review process is almost finished I hope.

[bastorer]

@editorialbot generate pdf

[editorialbot]

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

[bastorer]

Review checklist for @bastorer

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://github.com/pnsaevik/effluent?
• License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@pnsaevik) 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?

[kthyng]

Post-Review Checklist for Editor and Authors

Additional Author Tasks After Review is Complete

• 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 release on Zenodo/figshare/etc and post the DOI here.
• Make sure that the title and author list (including ORCIDs) in the archive match those in the JOSS paper.
• Make sure that the license listed for the archive is the same as the software license.

Editor Tasks Prior to Acceptance

• Read the text of the paper and offer comments/corrections (as either a list or a PR)
• Check the references in the paper for corrections (e.g. capitalization)
• Check that the archive title, author list, version tag, and the license are correct
• Set archive DOI with @editorialbot set <DOI here> as archive
• Set version with @editorialbot set <version here> as version
• Double check rendering of paper with @editorialbot generate pdf
• Specifically check the references with @editorialbot check references and ask author(s) to update as needed
• Recommend acceptance with @editorialbot recommend-accept

[kthyng]

@pnsaevik Please copy and paste the author checklist above so you can use it to guide your next steps; let me know if you have any questions.

[castelao]

Congrats @pnsaevik !

[pnsaevik]

Thanks @castelao and @bastorer for helpful suggestions and comments throughout the review process!

[pnsaevik]

Additional Author Tasks After Review is Complete

• 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 release on Zenodo/figshare/etc and post the DOI here.
• Make sure that the title and author list (including ORCIDs) in the archive match those in the JOSS paper.
• Make sure that the license listed for the archive is the same as the software license.

[pnsaevik]

Hi @kthyng,

The Zenodo doi is 10.5281/zenodo.8333370. The license and title was added automatically from GitHub, but it was wrong, so I had to change it manually. Zenodo still shows the auto-generated title when I access the record without being logged in, but hopefully it will resolve itself when the cache refreshes eventually.

The official version number with all the latest changes incorporated, is 1.3. It's also published on PyPI here: https://pypi.org/project/effluent/

The most recent version of the documentation is also online, at https://effluent.readthedocs.io/

[castelao]

@pnsaevik , you can control Zenodo's DOI metadata with a .zenodo.json file. Here an example. Note that this would only affect the next release.

[pnsaevik]

Thanks for the tip, I didn't know that!

[kthyng]

@editorialbot generate pdf

[editorialbot]

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

[kthyng]

@editorialbot set 1.3 as version

[editorialbot]

Done! version is now 1.3

[kthyng]

A comment on your paper @pnsaevik:
The citation on line 14 should be inline instead of parenthetical.

[kthyng]

@editorialbot set 10.5281/zenodo.8333370 as archive

[editorialbot]

Done! archive is now 10.5281/zenodo.8333370

[kthyng]

@editorialbot check references

[editorialbot]

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

OK DOIs

- 10.1023/A:1025583110842 is OK
- 10.1016/j.envsoft.2003.08.018 is OK
- 10.1007/978-1-4615-0407-8 is OK
- 10.1016/j.ocemod.2004.08.002 is OK
- 10.1016/j.desal.2011.11.037 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[pnsaevik]

A comment on your paper @pnsaevik: The citation on line 14 should be inline instead of parenthetical.

Thanks. I've fixed the issue in v1.3.2 (and added a zenodo metadata file as well). But it's probably not worth re-iterating the process since nothing else is changed.

[kthyng]

@editorialbot generate pdf

[editorialbot]

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

[kthyng]

@editorialbot accept

[editorialbot]

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

[editorialbot]

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: Sævik
  given-names: Pål Næverlid
  orcid: "https://orcid.org/0000-0002-7301-2008"
doi: 10.5281/zenodo.8333370
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Sævik
    given-names: Pål Næverlid
    orcid: "https://orcid.org/0000-0002-7301-2008"
  date-published: 2023-09-13
  doi: 10.21105/joss.05554
  issn: 2475-9066
  issue: 89
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 5554
  title: "Effluent: A Python package for modelling effluent discharge"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.05554"
  volume: 8
title: "Effluent: A Python package for modelling effluent discharge"

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]

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

[editorialbot]

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

Here's what you must now do:

0. Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.05554 joss-papers#4566
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.05554
2. If everything looks good, then close this review issue.
3. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

[kthyng]

Congrats on your new publication @pnsaevik! Many thanks to reviewers @castelao and @bastorer for your time, hard work, and expertise!!

[editorialbot]

🎉🎉🎉 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.05554/status.svg)](https://doi.org/10.21105/joss.05554)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.05554">
  <img src="https://joss.theoj.org/papers/10.21105/joss.05554/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.05554/status.svg
   :target: https://doi.org/10.21105/joss.05554

This is how it will look in your documentation:

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