[REVIEW]: NeuralHydrology --- A Python library for Deep Learning research in hydrology

[whedon]

Submitting author: @kratzert (Frederik Kratzert)
Repository: https://github.com/neuralhydrology/neuralhydrology
Branch with paper.md (empty if default branch): paper
Version: v.1.2.3
Editor: @elbeejay
Reviewers: @ammilten, @chuckaustin, @jhamman
Archive: 10.5281/zenodo.6326394

⚠️ JOSS reduced service mode ⚠️

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/d3567e525e20638a8a27c8c6036e1bd7"><img src="https://joss.theoj.org/papers/d3567e525e20638a8a27c8c6036e1bd7/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/d3567e525e20638a8a27c8c6036e1bd7/status.svg)](https://joss.theoj.org/papers/d3567e525e20638a8a27c8c6036e1bd7)

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

@ammilten & @chuckaustin & @jhamman, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

1. Make sure you're logged in to your GitHub account
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The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @elbeejay 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 ✨

Review checklist for @ammilten

✨ Important: Please do not use the Convert to issue functionality when working through this checklist, instead, please open any new issues associated with your review in the software repository associated with the submission. ✨

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 repository url?
• 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 (@kratzert) 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

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 and who the target audience is?
• 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?

Review checklist for @chuckaustin

✨ Important: Please do not use the Convert to issue functionality when working through this checklist, instead, please open any new issues associated with your review in the software repository associated with the submission. ✨

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 repository url?
• 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 (@kratzert) 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

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 and who the target audience is?
• 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?

Review checklist for @jhamman

✨ Important: Please do not use the Convert to issue functionality when working through this checklist, instead, please open any new issues associated with your review in the software repository associated with the submission. ✨

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 repository url?
• 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 (@kratzert) 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

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 and who the target audience is?
• 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?

[whedon]

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @ammilten, @chuckaustin, @jhamman it looks like you're currently assigned to review this paper 🎉.

⚠️ JOSS reduced service mode ⚠️

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

⭐ Important ⭐

If you haven't already, you should seriously consider unsubscribing from GitHub notifications for this (https://github.com/openjournals/joss-reviews) repository. As a reviewer, you're probably currently watching this repository which means for GitHub's default behaviour you will receive notifications (emails) for all reviews 😿

To fix this do the following two things:

1. Set yourself as 'Not watching' https://github.com/openjournals/joss-reviews:

2. You may also like to change your default settings for this watching repositories in your GitHub profile here: https://github.com/settings/notifications

For a list of things I can do to help you, just type:

@whedon commands

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

@whedon generate pdf

[whedon]

PDF failed to compile for issue #4050 with the following error:

 Can't find any papers to compile :-(

[whedon]

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.21 s (692.2 files/s, 85033.4 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          60           2303           3770           5437
YAML                            18            246            217            807
reStructuredText                55            298            366            746
Jupyter Notebook                 6              0           2878            297
DOS Batch                        1              8              1             26
Markdown                         1              7              0             16
make                             1              4              7              9
-------------------------------------------------------------------------------
SUM:                           142           2866           7239           7338
-------------------------------------------------------------------------------


Statistical information for the repository '31a2108e77ad1a07e6e208aa' was
gathered on 2022/01/11.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Daniel Klotz                     2          1392            437            9.70
Frederik Kratzert               54         12028           2220           75.53
Grey Nearing                     1           259             14            1.45
Martijn Visser                   1             9             10            0.10
Martin Gauch                    32          1692            804           13.23

Below are the number of rows from each author that have survived and are still
intact in the current revision:

Author                     Rows      Stability          Age       % in comments
Daniel Klotz               1028           73.9         10.1                9.05
Frederik Kratzert          8753           72.8          3.7                9.37
Grey Nearing                199           76.8         11.7                8.54
Martijn Visser                9          100.0          8.0               22.22
Martin Gauch               1521           89.9         11.6                8.68

[elbeejay]

@ammilten, @chuckaustin, @jhamman, thanks for agreeing to review this submission to JOSS. We are currently asking reviewers to try and complete their reviews in 6 weeks.

The JOSS review process is entirely open and transparent, and takes place on GitHub. Review comments should be made as issues in the NeuralHydrology repository (so open up a new issue here with review comments), please link this review issue when doing so (by pasting https://github.com/openjournals/joss-reviews/issues/4050 into the review issue you create).

For reference, here are links to the JOSS documentation that may be helpful as you conduct your reviews:

JOSS Review Criteria
JOSS Review Checklist

Please feel free to ping me (@elbeejay) if you have any questions/concerns. Thanks again for agreeing to review for JOSS.

[elbeejay]

@whedon check references from branch paper

[whedon]

Attempting to check references... from custom branch paper

[elbeejay]

@whedon generate pdf from branch paper

[whedon]

Checking the BibTeX entries failed with the following error:

Failed to parse BibTeX entry: cite-key missing

[whedon]

Attempting PDF compilation from custom branch paper. Reticulating splines etc...

[whedon]

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

[elbeejay]

@kratzert - if looks like there's an issue with the bibliography file. I suspect it has to do with an "@" symbol in the citation:

"@"article{kratzert@regional,
author = {Kratzert, F. and Klotz, D. and Shalev, G. and Klambauer, G. and Hochreiter, S. and Nearing, G.},
title = {Towards learning universal, regional, and local hydrological behaviors via machine learning applied to large-sample datasets},
journal = {Hydrology and Earth System Sciences},
volume = {23},
year = {2019},
number = {12},
pages = {5089--5110},
doi = {10.5194/hess-23-5089-2019}
}

Can you remove the second "@" and update the bib file? Once you've done that please use the whedon commands like above to regenerate the paper and check the reference file.

[kratzert]

@whedon generate pdf from branch paper

[whedon]

Attempting PDF compilation from custom branch paper. Reticulating splines etc...

[whedon]

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

[kratzert]

Sorry for the spam but I just saw that we had different spellings for the same authors across different bib entries, which led to an undesired format in the reference list. I fixed this and will query whedon again to compile the manuscript. Please consider the document below for the review.

[kratzert]

@whedon generate pdf from branch paper

[whedon]

Attempting PDF compilation from custom branch paper. Reticulating splines etc...

[whedon]

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

[elbeejay]

@whedon check references from branch paper

[whedon]

Attempting to check references... from custom branch paper

[whedon]

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

OK DOIs

- 10.5194/hess-23-5089-2019 is OK
- 10.1029/2019WR026065 is OK
- 10.5194/hess-25-2045-2021 is OK
- 10.5194/hess-2021-154 is OK
- 10.5194/hess-2021-127 is OK

MISSING DOIs

- 10.2166/9781780401041 may be a valid DOI for title: Evolution of Water Supply Through the Millennia

INVALID DOIs

- https://doi.org/10.1029/2020WR028091 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1002/hyp.13805 is INVALID because of 'https://doi.org/' prefix

[kratzert]

@whedon check references from branch paper

[whedon]

Attempting to check references... from custom branch paper

[whedon]

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

OK DOIs

- 10.2166/9781780401041 is OK
- 10.5194/hess-23-5089-2019 is OK
- 10.1029/2019WR026065 is OK
- 10.5194/hess-25-2045-2021 is OK
- 10.5194/hess-2021-154 is OK
- 10.5194/hess-2021-127 is OK
- 10.1029/2020WR028091 is OK
- 10.1002/hyp.13805 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[elbeejay]

@kratzert one minor suggestion for the paper text:

• Line 19: Switch the colon to a period, or remove the capital "P" in "Pre-built" on the following line

Besides this, I think things look good. I am optimistic that this package will help accelerate deep learning acceptance/adoption in the hydrology community. After making the minor revision noted above, I need you to do a few things at this time:

• 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.

Please let me know when these steps are complete, they allow us to finalize the metadata that will be associated with the JOSS publication. Once that is done I can recommend that we accept and publish this paper.

[kratzert]

Hi @kratzert, it looks like those last few issues have been resolved. I wanted to follow up on some of the discussion that happened in issue 77 - it sounded like you and @chuckaustin agreed that it would be useful to expand the documentation in response to some of the questions raised in that issue. Do you plan on making those changes to the documentation prior to publication? I see that the issue was closed, so this is by no means a requirement for publication, but I figured I would ask first.

Thanks

Hi @elbeejay,

I will try to make the changes today yes, definitely plan to add them prior to the publication (tagged release), since it is not a lot of work. Also thanks for the typo, I will make sure that is fixed. I will come back to you as soon as I have everything done.

[kratzert]

@kratzert one minor suggestion for the paper text:

* Line 19: Switch the colon to a period, or remove the capital "P" in "Pre-built" on the following line

Besides this, I think things look good. I am optimistic that this package will help accelerate deep learning acceptance/adoption in the hydrology community. After making the minor revision noted above, I need you to do a few things at this time:

* [ ]  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.

Please let me know when these steps are complete, they allow us to finalize the metadata that will be associated with the JOSS publication. Once that is done I can recommend that we accept and publish this paper.

• Link to tagged version: https://github.com/neuralhydrology/neuralhydrology/releases/tag/v.1.2.3
• Link to archived software: https://zenodo.org/record/6326394
• Checked all authors names, added ORCID ids
• DOI: https://doi.org/10.5281/zenodo.6326394

The paper is also updated with the typo fix.

Anything else you need?

[elbeejay]

@editorialbot set v.1.2.3 as version

[editorialbot]

Done! version is now v.1.2.3

[elbeejay]

@editorialbot set 10.5281/zenodo.6326394 as archive

[editorialbot]

Done! archive is now 10.5281/zenodo.6326394

[elbeejay]

Anything else you need?

@kratzert that is it, thank you for taking care of those last items. I wanted to thank the folks that peer-reviewed this submission once again as well - so thank you to @jhamman, @ammilten, and @chuckaustin.

At this time I will be recommending that we accept and publish this submission in JOSS. The paper and metadata will get one final review by an Editor-in-Chief prior to publication.

[elbeejay]

@editorialbot recommend-accept

[editorialbot]

Attempting dry run of processing paper acceptance...

[editorialbot]

👋 @openjournals/joss-eics, this paper is ready to be accepted and published.

Check final proof 👉 openjournals/joss-papers#3023

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#3023, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[kratzert]

@kratzert that is it, thank you for taking care of those last items. I wanted to thank the folks that peer-reviewed this submission once again as well - so thank you to @jhamman, @ammilten, and @chuckaustin.

Also thank you from my side for taking care of the entire review process @elbeejay and @jhamman, @ammilten and @chuckaustin for reviewing our package and providing useful feedback!

At this time I will be recommending that we accept and publish this submission in JOSS. The paper and metadata will get one final review by an Editor-in-Chief prior to publication.

Juhu 🎉

[kyleniemeyer]

Hi @kratzert, I made a small PR with some formatting fixes to the paper: neuralhydrology/neuralhydrology#79

Could you merge this? Then I can publish the paper.

[kratzert]

Hi @kratzert, I made a small PR with some formatting fixes to the paper: neuralhydrology/neuralhydrology#79

Could you merge this? Then I can publish the paper.

Done. Thanks for the fixes.

[kyleniemeyer]

@editorialbot accept

[editorialbot]

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

[editorialbot]

🐦🐦🐦 👉 Tweet 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.04050 joss-papers#3024
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.04050
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...

[kyleniemeyer]

Congratulations @kratzert on your article's publication in JOSS!
Many thanks to @ammilten, @chuckaustin, and @jhamman for reviewing this, and @elbeejay for editing.

[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.04050/status.svg)](https://doi.org/10.21105/joss.04050)

HTML:
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  <img src="https://joss.theoj.org/papers/10.21105/joss.04050/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.04050/status.svg
   :target: https://doi.org/10.21105/joss.04050

This is how it will look in your documentation:

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