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[REVIEW]: pyDeltaRCM: a flexible numerical delta model #3398

Closed whedon closed 3 years ago

whedon commented 3 years ago

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

:warning: JOSS reduced service mode :warning:

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

Status badge code:

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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

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @jhnienhuis

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @salterg

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

whedon commented 3 years ago

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 :tada:.

:warning: JOSS reduced service mode :warning:

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.

:star: Important :star:

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:

watching

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

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 commented 3 years ago 
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 commented 3 years ago 
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 commented 3 years ago

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 commented 3 years ago

@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 krbarnhart@usgs.gov).

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 commented 3 years ago

@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 commented 3 years ago

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 commented 3 years ago

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

danielskatz commented 3 years ago

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

arfon commented 3 years ago

@whedon generate pdf

whedon commented 3 years ago

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 commented 3 years ago

@whedon generate pdf

whedon commented 3 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

arfon commented 3 years ago

@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 commented 3 years ago

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

kbarnhart commented 3 years ago

@whedon add @salterg as reviewer

whedon commented 3 years ago

OK, @salterg is now a reviewer

kbarnhart commented 3 years ago

@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 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 krbarnhart@usgs.gov).

whedon commented 3 years ago

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

whedon commented 3 years ago

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

jhnienhuis commented 3 years ago

@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. image 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 commented 3 years ago

@whedon re-invite @jhnienhuis as reviewer

whedon commented 3 years ago

OK, the reviewer has been re-invited.

@jhnienhuis please accept the invite by clicking this link: https://github.com/openjournals/joss-reviews/invitations

kbarnhart commented 3 years ago

@jhnienhuis above is a new link.

A link to the paper is in one of the above comments, and we can re-build the current version anytime by writing @whedon generate pdf in a comment.

However, you also bring up a great point regarding search capabilities on the website. @arfon, do we expect search results on the website (https://joss.theoj.org/papers) to yield results if the paper is active rather than published?

arfon commented 3 years ago

However, you also bring up a great point regarding search capabilities on the website. @arfon, do we expect search results on the website (https://joss.theoj.org/papers) to yield results if the paper is active rather than published?

No, search only lists papers that are published.

kbarnhart commented 3 years ago

Thanks for that info @arfon!

@jhnienhuis looks like the search function on the website is behaving as expected.

zsylvester commented 3 years ago

Hi @kbarnhart -- it looks like I have the same problem as @jhnienhuis... Can I get re-invited (I assume I cannot re-invite myself)? Thanks!

Zoltan

kthyng commented 3 years ago

@whedon re-invite @zsylvester as reviewer

whedon commented 3 years ago

OK, the reviewer has been re-invited.

@zsylvester please accept the invite by clicking this link: https://github.com/openjournals/joss-reviews/invitations

kbarnhart commented 3 years ago

Thanks @kthyng !

kbarnhart commented 3 years ago

@zsylvester a friendly reminder to provide your review by 10 August.

@jhnienhuis @salterg thank you for providing your reviews.

@amoodie thank you for addressing the review comments as the arise.

Questions, concerns, or clarification... feel free to contact me here or at krbarnhart@usgs.gov

kbarnhart commented 3 years ago

@zsylvester @jhnienhuis @salterg thanks for providing your reviews.

@amoodie please ping me here or at krbarnhart@usgs.gov when you think you have addressed the issues raised by the reviewers, or at any point if you need input or guidance from me.

amoodie commented 3 years ago

@whedon generate pdf

whedon commented 3 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

amoodie commented 3 years ago

Hi @kbarnhart :wave:

We got great feedback from three reviewers, which mostly revolved around points of clarification within the documentation. We have responded to all of the reviewers' comments and questions in repository issues:

I've also regenerated the article proof above, which includes a minor change based on the reviews. Please let me know when you need anything from me to move forward. Thanks for considering our package in JOSS.

kbarnhart commented 3 years ago

@amoodie and co-authors: nice work addressing the reviewer's comments. I think these are great improvements to the documentation.

@zsylvester @jhnienhuis @salterg, please take a moment and revisit your reviews. If the authors have addressed your concerns, please complete your review checklists and indicate that you think the submission is ready to be accepted. If remaining issues exist, please note them in an in-repo issue.

Many thanks to each of you for contributing reviews to JOSS.

zsylvester commented 3 years ago

Hi @kbarnhart and @amoodie - I have looked at the comments on the review and it looks to me like all my questions were answered / issues addressed and the submission is ready to be accepted. I had one question that I bumped into in the meantime, while experimenting with the code; I have asked that question in the same issue / thread as the review.

kbarnhart commented 3 years ago

@zsylvester thanks for that update and for raising that other issue about grid scale dependince.

@jhnienhuis @salterg -- a friendly reminder to take a moment and revisit your reviews. If the authors have addressed your concerns, please complete your review checklists and indicate that you think the submission is ready to be accepted. If remaining issues exist, please note them in an in-repo issue.

kbarnhart commented 3 years ago

I received an email from @salterg indicating that he thinks this is ready to be published. I've checked his few remaining checkboxes.

kbarnhart commented 3 years ago

@jhnienhuis -- a friendly reminder to take a moment and revisit your reviews. If the authors have addressed your concerns, please complete your review checklists and indicate that you think the submission is ready to be accepted. If remaining issues exist, please note them in an in-repo issue.

I'll also send you this message via email.

kbarnhart commented 3 years ago

I received an email from @jhnienhuis confirming that the authors have addressed his remaining concerns and that he thinks this is ready to be accepted. I've checked off his few remaining checkboxes.

kbarnhart commented 3 years ago

@whedon check references

whedon commented 3 years ago 
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
kbarnhart commented 3 years ago

@whedon generate pdf

whedon commented 3 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

kbarnhart commented 3 years ago

@amoodie Please do the following

I can then move forward with the next stages of the JOSS process.

amoodie commented 3 years ago

@whedon generate pdf

whedon commented 3 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

amoodie commented 3 years ago

@whedon check references

whedon commented 3 years ago 
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