[REVIEW]: Integrated hydrologic model development and postprocessing for GSFLOW using pyGSFLOW

[whedon]

Submitting author: @jlarsen-usgs (Joshua Larsen)
Repository: https://github.com/pygsflow/pygsflow.git
Branch with paper.md (empty if default branch):
Version: 1.0.2
Editor: @crvernon
Reviewers: @thurber, @mdbartos, @mdbartos
Archive: 10.5281/zenodo.6468426

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Markdown: [![status](https://joss.theoj.org/papers/d3989e65aedcc241930001cd32ba3a92/status.svg)](https://joss.theoj.org/papers/d3989e65aedcc241930001cd32ba3a92)

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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.)

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

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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 ✨

Review checklist for @thurber

✨ 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 (@jlarsen-usgs) 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 @mdbartos

✨ 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 (@jlarsen-usgs) 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. @thurber, @mdbartos 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]

Wordcount for paper.md is 1529

[whedon]

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

OK DOIs

- 10.1111/gwat.12413 is OK
- 10.5066/F7BK19FH is OK
- 10.1016/j.jhydrol.2016.03.026 is OK
- 10.1016/j.envsoft.2018.07.020 is OK
- 10.3133/tm6A16 is OK
- 10.1109/MCSE.2007.55 is OK
- 10.3233/978-1-61499-649-1-87 is OK
- 10.3133/tm6A55 is OK
- 10.13140/2.1.2741.9202 is OK
- 10.3133/tm6B7 is OK
- 10.5194/gmd-11-4755-2018 is OK
- 10.3133/tm6A37 is OK
- 10.3133/tm6A45 is OK
- 10.1016/J.ENVSOFT.2019.01.006 is OK
- 10.3133/sir20145052 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.26 s (351.2 files/s, 121230.2 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          60           1985           2648           6741
JSON                             2              7              0           1506
Visual Basic                     4              1              0           1286
Jupyter Notebook                 9              0          15586            586
Markdown                         7            141              0            464
TeX                              1             16              0            231
YAML                             4             19             11            136
XML                              3              0              0             42
reStructuredText                 1              2              0              6
-------------------------------------------------------------------------------
SUM:                            91           2171          18245          10998
-------------------------------------------------------------------------------


Statistical information for the repository '9d3c4197ae169fff697d827c' was
gathered on 2021/10/26.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Ayman Alzraiee                  10           741             51            4.29
Joshua Larsen                  145         13802           3673           94.68
ayman_alzraiee                   3             0             35            0.19
aymanalz                         3           140             11            0.82
jlarsen-usgs                     1             2              2            0.02

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
Ayman Alzraiee              479           64.6         28.5                9.19
Joshua Larsen             10812           78.3         11.4                6.45
aymanalz                     83           59.3          9.5                6.02

[whedon]

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

[crvernon]

👋 @jlarsen-usgs @thurber @mdbartos - the review takes place in this issue.

[crvernon]

❗ Also, please don't forget to add a link to this review issue in any issues or pull requests you may generate in the https://github.com/pygsflow/pygsflow repository. This will help everyone have a single point of reference.

[crvernon]

📣 Mid-week rally! Looks like @thurber has started providing feedback to @jlarsen-usgs. Let's keep things rolling towards a successful review!

👋 @mdbartos - please update me to your progress thus far and don't hesitate to reach out if you have any questions.

👏 Keep up the good work!

[whedon]

👋 @thurber, please update us on how your review is going (this is an automated reminder).

[whedon]

👋 @mdbartos, please update us on how your review is going (this is an automated reminder).

[jlarsen-usgs]

review from @thurber is linked to

pygsflow/pygsflow#12

[crvernon]

📣 Mid-week rally! Looks like issues are cycling with @thurber and @jlarsen-usgs. Let's keep things rolling towards a successful review!

👋 @mdbartos - Please let me know if you are unable to participate in this review at this time. If you are still willing, could you reply here with an expected time of completion? Thanks!

[mdbartos]

@crvernon Can I get permissions to edit my checklist? Thx.

[mdbartos]

Could I get another invite? I still don't have permissions to edit the checklist.

[crvernon]

@whedon add @mdbartos as reviewer

[editorialbot]

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

Check final proof 👉 openjournals/joss-papers#3139

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#3139, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[jlarsen-usgs]

@crvernon

I just read through the proof and found a typo that should be corrected before final acceptance and publication. "gsflow_coef" should be "gwflow_coef". I'll correct this right now.

[jlarsen-usgs]

@crvernon

Fixed the typos on my end. Sorry about the last minute update.

[crvernon]

@jlarsen-usgs - no problem, please create a new release with the fix and post the new version and DOI here. Then I will assign them accordingly.

[jlarsen-usgs]

@crvernon - created a new release in github and posted the new version to zenodo 10.5281/zenodo.6468426

[crvernon]

@editorialbot set 10.5281/zenodo.6468426 as archive

[editorialbot]

Done! Archive is now 10.5281/zenodo.6468426

[arfon]

@editorialbot recommend-accept

[editorialbot]

Attempting dry run of processing paper acceptance...

[editorialbot]

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

OK DOIs

- 10.1111/gwat.12413 is OK
- 10.5066/F7BK19FH is OK
- 10.1061/(ASCE)WR.1943-5452.0000034 is OK
- 10.4324/9780203798942 is OK
- 10.1016/j.jhydrol.2016.03.026 is OK
- 10.1016/j.envsoft.2018.07.020 is OK
- 10.1007/s11269-017-1714-6 is OK
- 10.3133/tm6A16 is OK
- 10.1109/MCSE.2007.55 is OK
- 10.3233/978-1-61499-649-1-87 is OK
- 10.5066/P9NPZ5AD is OK
- 10.3133/tm6A55 is OK
- 10.3133/sir20105249 is OK
- 10.1111/j.1574-0862.2008.00336.x is OK
- 10.13140/2.1.2741.9202 is OK
- 10.3133/tm6B7 is OK
- 10.1126/sciadv.1500323 is OK
- 10.5194/gmd-11-4755-2018 is OK
- 10.3133/tm6A37 is OK
- 10.3133/tm6A45 is OK
- 10.5066/F7P55KJN is OK
- 10.3133/sir20145166 is OK
- 10.1016/J.ENVSOFT.2019.01.006 is OK
- 10.3133/sir20145052 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

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

Check final proof 👉 openjournals/joss-papers#3150

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#3150, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[arfon]

@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.03852 joss-papers#3152
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.03852
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...

[arfon]

@thurber, @mdbartos, @mdbartos – many thanks for your reviews here and to @crvernon for editing this submission! JOSS relies upon the volunteer effort of people like you and we simply wouldn't be able to do this without you ✨

@jlarsen-usgs – your paper is now accepted and published in JOSS ⚡🚀💥

[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:

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[![DOI](https://joss.theoj.org/papers/10.21105/joss.03852/status.svg)](https://doi.org/10.21105/joss.03852)

HTML:
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  <img src="https://joss.theoj.org/papers/10.21105/joss.03852/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.03852/status.svg
   :target: https://doi.org/10.21105/joss.03852

This is how it will look in your documentation:

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The Journal of Open Source Software is a community-run journal and relies upon volunteer effort. If you'd like to support us please consider doing either one (or both) of the the following:

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[jlarsen-usgs]

Thank you for your helpful reviews @thurber, @mdbartos, and @crvernon!

[jlarsen-usgs]

@arfon

Hello, the doi link for the paper https://joss.theoj.org/papers/10.21105/joss.03852 is showing a 404 not found message from github pages. The pdf download is available however.

[crvernon]

@jlarsen-usgs should be live now