[REVIEW]: pyDeltaRCM: a flexible numerical delta model

[whedon]

Submitting author: @amoodie (Andrew Moodie)
Repository: https://github.com/DeltaRCM/pyDeltaRCM
Version: v2.0.3
Editor: @kbarnhart
Reviewers: @zsylvester, @jhnienhuis, @salterg
Archive: 10.5281/zenodo.5259060

⚠️ 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/b5415fded71aee0c364eb7e3f9ca17fd"><img src="https://joss.theoj.org/papers/b5415fded71aee0c364eb7e3f9ca17fd/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/b5415fded71aee0c364eb7e3f9ca17fd/status.svg)](https://joss.theoj.org/papers/b5415fded71aee0c364eb7e3f9ca17fd)

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

@zsylvester & @jhnienhuis, 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
2. Be sure to accept the invite at this URL: https://github.com/openjournals/joss-reviews/invitations

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @kbarnhart 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 @zsylvester

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 (@amoodie) 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 @jhnienhuis

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 (@amoodie) 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 @salterg

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. #3510

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 (@amoodie) 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. @zsylvester, @jhnienhuis 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]

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

OK DOIs

- 10.5194/esurf-3-67-2015 is OK
- 10.5194/esurf-3-87-2015 is OK
- 10.2110/pec.05.83.0011 is OK
- 10.1002/2015JF003653 is OK
- 10.1002/2016GL070519 is OK
- 10.1029/2019GL082792 is OK
- 10.1029/2018GL079405 is OK
- 10.1029/2020JF005706 is OK
- 10.1016/j.earscirev.2016.06.016 is OK
- 10.1038/s41467-020-18531-4 is OK
- 10.1146/annurev-marine-120709-142856 is OK
- 10.21105/joss.02317 is OK
- 10.1145/2833157.2833162 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.1109/MCSE.2007.55 is OK
- 10.1038/s41592-019-0686-2 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.19 s (538.7 files/s, 102400.9 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          50           3127           3412           8659
reStructuredText                37            948            937            801
YAML                             4             23              4            324
TeX                              1             16              0            172
Pascal                           1             77              0            154
CSS                              1             19              7             86
SVG                              2              1              1             76
Markdown                         1             22              0             69
DOS Batch                        1              8              1             26
make                             1             12              7             17
HTML                             1              2              0              2
-------------------------------------------------------------------------------
SUM:                           100           4255           4369          10386
-------------------------------------------------------------------------------


Statistical information for the repository '621f60900dd49b1b8cb1345a' was
gathered on 2021/06/23.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Andrew Moodie                  200         14492           8071           41.60
Eric Barefoot                   44          2707           2493            9.59
JayH                            61          3255           1346            8.48
Mariela Perignon                29          4632           1634           11.55
Mark Piper                       6            28             28            0.10
amoodie                         98          5677           2739           15.52
deltarcm-helper                  4           409            309            1.32
jay                             24          3494           2921           11.83

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
Andrew Moodie             12411           85.6          4.7               11.92
Eric Barefoot               475           17.5         16.6                5.47
Mariela Perignon            167            3.6         23.0                3.59
Mark Piper                    9           32.1         57.1                0.00
deltarcm-helper             104           25.4         13.7               34.62
jayh                       2032          100.0          5.0               11.71

[whedon]

PDF failed to compile for issue #3398 with the following error:

 Error producing PDF.
! Illegal parameter number in definition of \@xs@arg@i.
<to be read again> 
                   q
l.350 }

Looks like we failed to compile the PDF

[kbarnhart]

@zsylvester, @jhnienhuis - thanks for agreeing to review this submission to JOSS. In the prior comments there is a checklist that you can use to guide you through your review.

We have an automatic reminder set up in two weeks to ask you how the review is going. At present we request that reviewers complete their reviews within 6 weeks. JOSS is trying to be mindful of changes people have experienced due to COVID-19.

As you work through your review, if there are any issues that come up, please make an issue in the pyDeltaRCM repository, and link to this issue (paste openjournals/joss-reviews/issues/3398 into the issue you create). That way most of the discussion can occur on in-repo issues.

If you have any questions, please let me know (tag me here or email [email protected]).

I plan to find a third reviewer for this submission and will manually edit this page to provide them a checklist once they have been identified.

[kbarnhart]

@amoodie could you see about the PDF compilation error? If you can't figure it out, let me know and I can tag one of the whedon experts on the JOSS editorial team to help out.

[amoodie]

Hi @kbarnhart, I've looked into that error, but have not identified any leads to explain it. The paper compiles on the preview service without issue, and so I do think we need the help of an expert.

Thanks reviewers for your time, and looking forward to your feedback.

[kbarnhart]

@arfon any recommendations on addressing this PDF compile error (or who else I should ping about it).

[danielskatz]

@kbarnhart - for things like this ping @openjournals/dev (though it may still be @arfon who replies)

[arfon]

@whedon generate pdf

[whedon]

PDF failed to compile for issue #3398 with the following error:

 Error producing PDF.
! Illegal parameter number in definition of \@xs@arg@i.
<to be read again> 
                   q
l.350 }

Looks like we failed to compile the PDF

[arfon]

@whedon generate pdf

[whedon]

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

[arfon]

@kbarnhart – well that was a new one for me 😸. It turns out the URL you have in your JOSS bio https://www.usgs.gov/staff-profiles/katherine-barnhart?qt-staff_profile_science_products=3#qt-staff_profile_science_products was causing some issues with the paper compilation (as we link to editors in the JOSS paper). For now I've changed it to https://www.usgs.gov/staff-profiles/katherine-barnhart which seems to redirect to https://www.usgs.gov/staff-profiles/katherine-barnhart?qt-staff_profile_science_products=3#qt-staff_profile_science_products anyway but I'll need to look into fixing this in the LaTeX template.

[kbarnhart]

Wow! Thanks for figuring that out @arfon. 🎉 🎉 I did just update that URL recently.

[kbarnhart]

@whedon add @salterg as reviewer

[whedon]

OK, @salterg is now a reviewer

[kbarnhart]

@salterg - thanks for agreeing to review this submission to JOSS. In the prior comments there is a checklist that you can use to guide you through your review.

We have an automatic reminder set up to ask you how the review is going. At present we request that reviewers complete their reviews within 6 weeks (August 10, 2021). JOSS is trying to be mindful of changes people have experienced due to COVID-19.

As you work through your review, if there are any issues that come up, please make an issue in the pyDeltaRCM repository, and link to this issue (paste /issues/3398 into the issue you create). That way most of the discussion can occur on in-repo issues.

If you have any questions, please let me know (tag me here or email [email protected]).

[whedon]

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

[whedon]

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

[jhnienhuis]

@kbarnhart,

thanks again for inviting me to this review. Its been fun exploring github and python!

I noticed two small things:

1. I noticed this link is expired. do I need to accept anything still?
   Be sure to accept the invite at this URL: https://github.com/openjournals/joss-reviews/invitations

2. I tried to find the paper pdf on the JOSS webpage because I could not find it anywhere on github. I eventually found it, but by doing that also noticed the search function doesn't really work properly.
   
   for example, when i search for "@amoodie" or pydeltarcm is doesn't find the pdf of this manuscript: https://joss.theoj.org/papers/search?q=pydeltarcm

Perhaps you can forward this to the appropriate webpage developer?

Best,
Jaap

[kbarnhart]

@whedon re-invite @jhnienhuis as reviewer

[kbarnhart]

@whedon set v2.0.3 as version

[whedon]

OK. v2.0.3 is the version.

[kbarnhart]

@whedon set 10.5281/zenodo.5259060 as archive

[whedon]

OK. 10.5281/zenodo.5259060 is the archive.

[kbarnhart]

@whedon recommend-accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

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

OK DOIs

- 10.5194/esurf-3-67-2015 is OK
- 10.5194/esurf-3-87-2015 is OK
- 10.2110/pec.05.83.0011 is OK
- 10.1002/2015JF003653 is OK
- 10.1002/2016GL070519 is OK
- 10.1029/2019GL082792 is OK
- 10.1029/2018GL079405 is OK
- 10.1029/2020JF005706 is OK
- 10.1016/j.earscirev.2016.06.016 is OK
- 10.1038/s41467-020-18531-4 is OK
- 10.1146/annurev-marine-120709-142856 is OK
- 10.21105/joss.02317 is OK
- 10.1145/2833157.2833162 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.1109/MCSE.2007.55 is OK
- 10.1038/s41592-019-0686-2 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

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

Check final proof 👉 openjournals/joss-papers#2537

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#2537, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

[kbarnhart]

@amoodie and co-authors: I've now recommended that this submission be accepted. One of the @openjournals/joss-eics will handle the final steps of this process. Congratulations on a valuable contribution. Many thanks to reviewers @zsylvester, @jhnienhuis, @salterg for your thoughtful and constructive reviews.

[amoodie]

🎉 wahoo! Thanks Katy, and to Zoltán, Jaap, and Gerard for your helpful reviews!

[danielskatz]

Hi - I'll be working on this as the AEiC this week.

I have one minor comment:

• On page 2, the fact that parallel is broken across lines is awkward. Perhaps this text could be rephrased so that this doesn't happen?

Otherwise, I think this is ready to publish

[amoodie]

Hi Daniel, I can work on revising the text to try and prevent that line break. After I make the change, do you need me to make a new release and re-upload to Zenodo for archive?

[danielskatz]

No, if the change is just to the paper, it's fine - the archive is of the software, since the paper is archived as part of the journal's process when published.

[amoodie]

@whedon generate pdf

[whedon]

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

[amoodie]

@danielskatz, okay, I think that this minor change seems to have pushed the parallel to the next line and prevented the break 👍

[danielskatz]

@whedon accept deposit=true

[whedon]

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

[whedon]

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

[whedon]

🚨🚨🚨 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.03398 joss-papers#2540
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.03398
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...

[danielskatz]

Congratulations to @amoodie (Andrew Moodie) and co-authors!!

And thanks to @kbarnhart for editing, and to @zsylvester, @jhnienhuis, and @salterg for reviewing!
We couldn't do this without you!

[whedon]

🎉🎉🎉 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.03398/status.svg)](https://doi.org/10.21105/joss.03398)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.03398">
  <img src="https://joss.theoj.org/papers/10.21105/joss.03398/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.03398/status.svg
   :target: https://doi.org/10.21105/joss.03398

This is how it will look in your documentation:

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