[REVIEW]: NIMPHS: Numerous Instruments to Manipulate and Post-process Hydraulic Simulations #4868

editorialbot · 2022-10-20T13:28:08Z

Submitting author: @Failxxx (Félix Olart)
Repository: https://github.com/Artelia/NIMPHS
Branch with paper.md (empty if default branch): paper
Version: v0.4.3
Editor: @hugoledoux
Reviewers: @vbassn, @liberostelios
Archive: 10.5281/zenodo.7696769

Status

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Markdown: [![status](https://joss.theoj.org/papers/63596babdb26138c6eb1886b094c00ad/status.svg)](https://joss.theoj.org/papers/63596babdb26138c6eb1886b094c00ad)

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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

@bnase & @liberostelios, 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 @liberostelios

📝 Checklist for @bnase

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

editorialbot · 2022-10-20T13:28:11Z

Hello humans, I'm @editorialbot, a robot that can help you with some common editorial tasks.

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editorialbot · 2022-10-20T13:28:15Z

Software report:

github.com/AlDanial/cloc v 1.88  T=0.16 s (861.3 files/s, 99910.1 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          91           2911           3220           6983
reStructuredText                19            407            329            432
JSON                             3              0              0            393
Markdown                         6            169              0            352
YAML                             8             46              0            277
TeX                              1             13              0            159
DOS Batch                        1              8              1             26
make                             1              8              9             14
CSS                              1              1              0              6
SVG                              2              0              0              6
INI                              1              0              0              3
XML                              2              0              0              2
-------------------------------------------------------------------------------
SUM:                           136           3563           3559           8653
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gitinspector failed to run statistical information for the repository

editorialbot · 2022-10-20T13:28:17Z

Wordcount for paper.md is 882

editorialbot · 2022-10-20T13:28:38Z

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

OK DOIs

- 10.21105/joss.01450 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.3744/JNAOE.2009.1.2.089 is OK
- 10.1109/SITIS.2008.39 is OK
- 10.1016/b978-012387582-2/50038-1 is OK
- 10.1145/2833157.2833162 is OK
- 10.1145/2487228.2487235 is OK
- 10.1109/TVCG.2016.2599041 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot · 2022-10-20T13:30:22Z

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

Failxxx · 2022-11-19T19:58:54Z

Hello. Do you need more information to start reviewing?

bnase · 2022-11-20T12:51:37Z

@Failxxx @hugoledoux I have fallen a bit behind with the review process due to the usual deadlines, but I will finish it by next weekend! I think it's 6 weeks so I will be in time!

liberostelios · 2022-11-24T20:42:23Z

@Failxxx @hugoledoux Apologies for the delay. It has been quite a busy period. I'll proceed with the review asap (at least before the end of next week).

liberostelios · 2022-12-05T07:05:57Z

Review checklist for @liberostelios

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/Artelia/NIMPHS?
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 (@Failxxx) 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?

liberostelios · 2022-12-05T07:43:25Z

This is a great piece of software! Very nice @Failxxx!

Everything seems very well documented, from a software engineering point of view. The documentation is concise and clear, it made me understand the tool's purpose and way of working. The dev documentation is top notch, as well. Testing is present and everything is automated so that it can be run with minimal effort.

I can only give a small suggestion for improvement with respect to the installation process (made an issue about it here).

From my standpoint, I suggest that this gets accepted. Again, congratulations @Failxxx for the fine work! 👌

bnase · 2022-12-09T10:54:35Z

Review checklist for @bnase

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/Artelia/NIMPHS?
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 (@Failxxx) 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?

bnase · 2022-12-09T10:56:11Z

@Failxxx I have concluded my review. Sorry for the delay! Thanks to @hugoledoux for his trust. I have two minor (install and support) issues and I will open two issues about it! Other than it works flawlessly!

Failxxx · 2022-12-09T15:27:14Z

Thank you very much @liberostelios and @bnase for your reviews. I will work on the issues you pointed out as soon as I can :)

Failxxx · 2022-12-12T17:45:13Z

Hello @hugoledoux. Once the checklists are completed, is there something I should do? Any information to provide? Thank you.

hugoledoux · 2022-12-23T12:14:52Z

sorry for the delay @Failxxx .

You mentioned 2w ago that you would work on the issues raised, but have you fixed those? I don't see any commits. I think concerning the installation it would be good to improve before we publish.

I went over the paper and made a few corrections: Artelia/NIMPHS#16 please accept it.

hugoledoux · 2022-12-23T12:15:59Z

@editorialbot generate pdf

editorialbot · 2022-12-23T12:17:13Z

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

hugoledoux · 2022-12-23T12:27:09Z

@editorialbot check references

Failxxx · 2022-12-23T12:27:09Z

sorry for the delay @Failxxx . You mentioned 2w ago that you would work on the issues raised, but have you fixed those? I don't see any commits.

No problem. Indeed I did not have the time to work on those yet. Is it mandatory for now? I don't think I will have the time by the end of the next week.

editorialbot · 2022-12-23T12:28:21Z

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

OK DOIs

- 10.21105/joss.01450 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.3744/JNAOE.2009.1.2.089 is OK
- 10.1109/SITIS.2008.39 is OK
- 10.1016/b978-012387582-2/50038-1 is OK
- 10.1145/2833157.2833162 is OK
- 10.1145/2487228.2487235 is OK
- 10.1109/TVCG.2016.2599041 is OK

MISSING DOIs

- None

INVALID DOIs

- None

hugoledoux · 2022-12-23T13:06:31Z

Now certainly not mandatory, but if you could beginning of January then that would be great (I'm off next week).

Then the submission will be ready to be accepted, all the rest was there and nicely done. Rarely seen reviewers so enthusiastic about a submission, so well done 👍

Joyeux Noël 🎄

hugoledoux · 2022-12-23T13:07:25Z

and heads-up: I put a PR above after editing the comment, you might have missed it: Artelia/NIMPHS#16

Failxxx · 2023-01-25T07:47:53Z

Hello. Here is an update :

I merged your suggestions @hugoledoux in Some small corrections Artelia/NIMPHS#16
We are currently discussing about the following issue opened by @liberostelios: Mac support Artelia/NIMPHS#15. I try to really understand what the issue is.
The last issue will need more work. However, since this it is about an improvement, the add-on can still be installed and used normally. I will only be able to add suggested information in the installation process soon. I am working on a solution to better the process but this is not as easy as I thought haha. I will share my ideas and findings in the issue: Improve installation process Artelia/NIMPHS#14

editorialbot · 2023-02-28T06:53:33Z

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

editorialbot · 2023-02-28T06:54:29Z

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

OK DOIs

- 10.21105/joss.01450 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.3744/JNAOE.2009.1.2.089 is OK
- 10.1109/SITIS.2008.39 is OK
- 10.1016/b978-012387582-2/50038-1 is OK
- 10.1145/2833157.2833162 is OK
- 10.1145/2487228.2487235 is OK
- 10.1109/TVCG.2016.2599041 is OK

MISSING DOIs

- None

INVALID DOIs

- None

hugoledoux · 2023-02-28T13:52:43Z

@Failxxx congrats the reviewers recommend acceptance!

At this point could you:

Accept my PR with some minor fixes: Some some fixes Artelia/NIMPHS#21
Make a tagged release of your software, and list the version tag of the archived version here.
Archive the reviewed software in Zenodo or a similar service (e.g., figshare, an institutional repository)
Check the archival deposit (e.g., in Zenodo) 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 recommending acceptance of the submission.

Failxxx · 2023-03-03T17:35:44Z

Here are the requested information @hugoledoux:

Tagged release: https://github.com/Artelia/NIMPHS/releases/tag/v0.4.3.
Archived software on Zenodo: https://zenodo.org/record/7696769.
I confirm that the archival deposit has the right metadata.
DOI of the archived version: 10.5281/zenodo.7696769

Thank you!

hugoledoux · 2023-03-13T07:51:17Z

@editorialbot generate pdf

hugoledoux · 2023-03-13T07:51:23Z

@editorialbot check references

editorialbot · 2023-03-13T07:52:09Z

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

OK DOIs

- 10.21105/joss.01450 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.3744/JNAOE.2009.1.2.089 is OK
- 10.1109/SITIS.2008.39 is OK
- 10.1016/b978-012387582-2/50038-1 is OK
- 10.1145/2833157.2833162 is OK
- 10.1145/2487228.2487235 is OK
- 10.1109/TVCG.2016.2599041 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot · 2023-03-13T07:52:56Z

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

hugoledoux · 2023-03-13T07:55:51Z

@editorialbot set 10.5281/zenodo.7696769 as archive

editorialbot · 2023-03-13T07:55:54Z

Done! Archive is now 10.5281/zenodo.7696769

hugoledoux · 2023-03-13T07:56:13Z

@editorialbot set v0.4.3 as version

editorialbot · 2023-03-13T07:56:16Z

Done! version is now v0.4.3

hugoledoux · 2023-03-13T07:56:26Z

@editorialbot recommend-accept

editorialbot · 2023-03-13T07:56:27Z

Attempting dry run of processing paper acceptance...

editorialbot · 2023-03-13T07:57:11Z

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

OK DOIs

- 10.21105/joss.01450 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.3744/JNAOE.2009.1.2.089 is OK
- 10.1109/SITIS.2008.39 is OK
- 10.1016/b978-012387582-2/50038-1 is OK
- 10.1145/2833157.2833162 is OK
- 10.1145/2487228.2487235 is OK
- 10.1109/TVCG.2016.2599041 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot · 2023-03-13T07:58:06Z

👋 @openjournals/pe-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#4049, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

kyleniemeyer · 2023-03-13T12:05:23Z

@editorialbot accept

editorialbot · 2023-03-13T12:05:25Z

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

editorialbot · 2023-03-13T12:07:54Z

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

editorialbot · 2023-03-13T12:07:56Z

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

editorialbot · 2023-03-13T12:07:57Z

🚨🚨🚨 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.04868 joss-papers#4050
Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.04868
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

kyleniemeyer · 2023-03-13T12:39:22Z

Congratulations @Failxxx on your article's publication in JOSS!

Many thanks to @vbassn and @liberostelios for reviewing this, and @hugoledoux for editing.

editorialbot · 2023-03-13T12:39:24Z

🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

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[PRE REVIEW]: NIMPHS: Numerous Instruments to Manipulate and Post-process Hydraulic Simulations #4786

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[REVIEW]: NIMPHS: Numerous Instruments to Manipulate and Post-process Hydraulic Simulations #4868

[REVIEW]: NIMPHS: Numerous Instruments to Manipulate and Post-process Hydraulic Simulations #4868

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Failxxx commented Nov 19, 2022

bnase commented Nov 20, 2022

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Review checklist for @liberostelios

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

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Review checklist for @bnase

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

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