[PRE REVIEW]: RiverFlowDynamics v1.0: A Landlab component for computing two-dimensional river flow dynamics

[editorialbot]

Submitting author: @angelmons (Angel Monsalve)
Repository: https://github.com/angelmons/landlab
Branch with paper.md (empty if default branch): riverFlowDynamics_dev
Version: v1.0
Editor: @cheginit
Reviewers: @mcflugen
Managing EiC: Kristen Thyng

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/67f225c623d4d1b18414572c14435c02"><img src="https://joss.theoj.org/papers/67f225c623d4d1b18414572c14435c02/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/67f225c623d4d1b18414572c14435c02/status.svg)](https://joss.theoj.org/papers/67f225c623d4d1b18414572c14435c02)

Author instructions

Thanks for submitting your paper to JOSS @angelmons. Currently, there isn't a JOSS editor assigned to your paper.

@angelmons if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). You can search the list of people that have already agreed to review and may be suitable for this submission.

Editor instructions

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[editorialbot]

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[editorialbot]

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

✅ OK DOIs

- 10.5194/esurf-5-21-2017 is OK
- 10.5194/esurf-2020-12 is OK
- 10.1016/j.geomorph.2018.08.031 is OK
- 10.1002/esp.4195 is OK
- 10.1002/2014WR016862 is OK
- 10.1002/2016JF003965 is OK
- 10.1002/esp.4635 is OK
- 10.1080/00221686.2006.9521683 is OK
- 10.1080/00221686.2006.9521684 is OK
- 10.1002/rra.1012 is OK
- 10.1061/(ASCE)0733-9429(2003)129:2(120) is OK
- 10.1029/2006WR005330 is OK
- 10.1029/97WR02387 is OK
- 10.1002/2015JF003491 is OK
- 10.1029/2006WR005172 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: 1D SEDIMENT TRANSPORT MORPHODYNAMICS with applicat...

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.90  T=1.09 s (759.4 files/s, 214531.9 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                         573          24367          51181          78148
Markdown                        78           2359              0          14676
Jupyter Notebook                94              0          33466          10993
TOML                             3            794              5           8344
Cython                          48           1089           1364           5502
TeX                              5             70              0            786
YAML                            10             89             38            561
DOS Batch                        1             29              1            212
Bourne Shell                     1             12             12             31
make                             1              4              6             12
Jinja Template                   1              5              0             10
XML                              4              0              0              8
SVG                              7              0              0              7
C/C++ Header                     1              2              4              5
reStructuredText                 1              1              0              4
HTML                             1              0              0              3
-------------------------------------------------------------------------------
SUM:                           829          28821          86077         119302
-------------------------------------------------------------------------------

Commit count by author:

  3894	Eric Hutton
  1118	Katy Barnhart
  1015	Dan Hobley
   878	Greg Tucker
   321	dependabot[bot]
   257	Jordan Adams
   256	Sai Nudurupati
   227	Nicole M Gasparini
    70	pre-commit-ci[bot]
    69	Charlie Shobe
    62	David Litwin
    59	Laurent Roberge
    49	Ronda Strauch
    44	Jenny Knuth
    43	Benjamin Campforts
    43	Sebastien Lenard
    40	Margaux Mouchene
    27	Nathan Lyons
    26	Berkan M
    18	Jeffrey Keck
    17	Allison Pfeiffer
    14	angelmons
    12	Rachel Glade
    11	Dylan Ward
    11	Giuseppecipolla95
     7	Annie Thompson
     6	Mark Piper
     2	Amanda Manaster
     2	Jay Hariharan
     2	Shelby Ahrendt
     1	(no author)
     1	Abby Langston
     1	Andy Wickert
     1	Christopher Sheehan
     1	Josh Wolpert
     1	Kristen Thyng
     1	Muneer Ahammad
     1	Sarah Lundell
     1	pankajiitkgp

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 1530

🔴 Failed to discover a Statement of need section in paper

[editorialbot]

License info:

✅ License found: MIT License (Valid open source OSI approved license)

[editorialbot]

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

[editorialbot]

Five most similar historical JOSS papers:

pySBeLT: A Python software package for stochastic sediment transport under rarefied conditions
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Reviewers: @pfeiffea, @tdoane
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The Kestrel software for simulations of morphodynamic Earth-surface flows
Submitting author: @jakelangham
Handling editor: @crvernon (Active)
Reviewers: @mdpiper, @jatkinson1000
Similarity score: 0.6973

pyDeltaRCM: a flexible numerical delta model
Submitting author: @amoodie
Handling editor: @kbarnhart (Retired)
Reviewers: @zsylvester, @jhnienhuis, @salterg
Similarity score: 0.6973

GroundwaterDupuitPercolator: A Landlab component for groundwater flow
Submitting author: @davidlitwin
Handling editor: @kthyng (Active)
Reviewers: @dvalters, @rreinecke
Similarity score: 0.6868

⚠️ Note to editors: If these papers look like they might be a good match, click through to the review issue for that paper and invite one or more of the authors before considering asking the reviewers of these papers to review again for JOSS.

[kthyng]

Hi @angelmons and thanks for your submission! I am looking for some specific items to make sure your submission fits our requirements at a high level (not at the more detailed review level) before moving on to finding an editor or putting this on our waitlist if no relevant editors are available. I'll comment over time as I have a chance to go through them:

• OSI-approved license
• Installation instructions
• Documentation exists at all
• Tests of some sort
• Check paper (make sure compiles, read through, check for length 250-1000 words)
• Substantial scholarly effort
• Clear research application

In the meantime, please take a look at the comments above ⬆️ from the editorialbot to address any DOI, license, or paper issues if you're able (there may not be any), or suggest reviewers. For reviewers, please suggest 5 reviewers from the database listed above or your own (non-conflicted) extended network. Their github handles are most useful to receive but please don't use "@" to reference them since it will prematurely ping them.

[kthyng]

@angelmons It's been awhile since I've seen a landlab submission come through, but am I correct in thinking that the number of lines of code shown above is for all of landlab, but you are submitting on a specific module? If so, please provide more information so we can find the correct numbers for the relevant work.

[angelmons]

Hello @kthyng,
Thank you for your review and questions. I'd like to clarify that we are submitting a specific component called RiverFlowDynamics, which is integrated into the Landlab platform. You are correct that the code metrics shown above reflect the entire Landlab codebase rather than our specific component.

Regarding the submission requirements:

1. Our component is covered under Landlab's MIT license, which is OSI-approved.
2. The component is fully integrated into Landlab's official documentation system, including:
    - Detailed installation instructions as part of Landlab
    - Component-specific documentation
    - Comprehensive test suite
3. Regarding the paper:

    - It is located at: https://github.com/landlab/landlab/blob/master/joss/in_preparation/river_flow_dynamics/paper.md
    - The current word count is approximately 1150 words, which we can adjust if needed during the review process
    - The paper and code demonstrate substantial scholarly effort, representing years of research and development
    - We clearly outline the research applications and potential impact

I noticed that the editorialbot is analyzing Pfeiffer et al. (2020) NetworkSedimentTransporter component in the published folder, rather than our RiverFlowDynamics component submission located in the in_preparation folder. This may explain the discrepancy in the code metrics being reported.

Would you like me to provide any additional information about our component or clarify any specific aspects of the submission?

Regarding potential reviewers: I would suggest: zsylvester, ebgoldstein, pfeiffea, nicgaspar

[angelmons]

@angelmons It's been awhile since I've seen a landlab submission come through, but am I correct in thinking that the number of lines of code shown above is for all of landlab, but you are submitting on a specific module? If so, please provide more information so we can find the correct numbers for the relevant work.

Hello @kthyng,
I hope you're having a good week. I wanted to gently follow up on our submission and check if you need any additional information from us regarding the RiverFlowDynamics component. We're happy to provide more details or clarification if needed.

Best regards.

[kthyng]

@angelmons What I meant is where in the codebase can we find the code that is relevant to this submission so I can produce metrics for only the relevant part of the codebase?

I'm working on a solution for finding the correct paper.

[angelmons]

Hello @kthyng
Thanks for the clarification. The RiverFlowDynamics component's code and related files are distributed across the following locations in the Landlab repository:

Main Component Source Code:
https://github.com/landlab/landlab/tree/master/src/landlab/components/river_flow_dynamics
Component Tests:
https://github.com/landlab/landlab/tree/master/tests/components/river_flow_dynamics
JOSS Paper:
https://github.com/landlab/landlab/tree/master/joss/in_preparation/river_flow_dynamics
Documentation & Tutorials:
https://github.com/landlab/landlab/tree/master/docs/source/tutorials/river_flow_dynamics

The primary implementation code is in the first link (source code). This should be the most relevant directory for code metrics calculations.
Please let me know if you need any additional information about specific files or if there's anything else I can help with to move the review process forward.

[kthyng]

@angelmons Regarding the JOSS paper, can you either rename the old paper(s) (so they aren't paper.md) or make a temporary branch with only your paper in it. With either of those solutions, editorial bot should then be able to find your paper correctly.

[angelmons]

@kthyng Thank you for the suggestion. I'm happy to inform you that the Landlab repository manager has already cleaned up the JOSS folder, and now our paper is the only one remaining in the "in_preparation" directory at:

https://github.com/landlab/landlab/tree/master/joss/in_preparation/river_flow_dynamics/paper.md

The file is still named paper.md as per the repository manager's recommendation. Since it's now the only paper in the in_preparation folder, would this solve the editorial bot's paper detection issue?

[kthyng]

@editorialbot generate pdf

[editorialbot]

⚠️ An error happened when generating the pdf.

[kthyng]

@angelmons I think you are missing a comma at the end of line 35: https://github.com/landlab/landlab/blob/master/joss/in_preparation/river_flow_dynamics/paper.bib

[angelmons]

Hi @kthyng,

Thanks for catching the missing comma. To streamline the revision process, would you be willing to review the paper from my GitHub fork? It contains the exact same content as the Landlab master branch, with only the comma correction added. This would allow me to verify everything is in order before submitting an issue or pull request to the main Landlab repository.

The JOSS paper can be found here:
https://github.com/angelmons/landlab/blob/riverFlowDynamics_dev/joss/in_preparation/river_flow_dynamics

I just checked and the paper compiles all right. Please let me know

[kthyng]

Yes, we can change the repository url to yours. Alternatively would it work if you had a branch to the main repository? We have an easy way to add a branch name. Changing the url is a little more work but still ok.

[angelmons]

@kthyng Thanks! Yes, a branch will work. This is my branch:
https://github.com/angelmons/landlab/tree/riverFlowDynamics_dev
It is identical to the master branch, currently with the only exception being the missing comma.

As a summary:

Main Component Source Code:
https://github.com/angelmons/landlab/tree/riverFlowDynamics_dev/src/landlab/components/river_flow_dynamics
Component Tests:
https://github.com/angelmons/landlab/tree/riverFlowDynamics_dev/tests/components/river_flow_dynamics
JOSS Paper:
https://github.com/angelmons/landlab/tree/riverFlowDynamics_dev/joss/in_preparation/river_flow_dynamics
Documentation & Tutorials:
https://github.com/angelmons/landlab/tree/riverFlowDynamics_dev/docs/source/tutorials/river_flow_dynamics

[kthyng]

@angelmons Do you have permissions to use a branch from the main repository for landlab? If so that would be preferable, but if not we can use this fine.

[angelmons]

Hi @kthyng - Yes, I should be able to use a Landlab branch. However, I'd prefer to use my branch during the review process since each modification would require a separate review and pull request. Using my branch would allow me to consolidate all suggestions into a single pull request, streamlining the process. I am adding Landlab's coordinator so he is aware of this.

For context, my branch is identical to the main repository except for a single comma correction in one reference.

@mcflugen - FYI, JOSS is reviewing my RiverFlowDynamics component paper. I'm proposing to use my branch during the review to minimize the number of pull requests. Please let me know if you have any concerns.

[mcflugen]

@angelmons, @kthyng I'm happy to help however I can.

@angelmons, your idea of working from a branch on your fork sounds reasonable to me, if that works for @kthyng.

[mcflugen]

@kthyng Would it make sense for me to be a reviewer of this submission? If so, and you need reviewers, I could do that.

[editorialbot]

Paper file info:

⚠️ Wordcount for paper.md is 1220

✅ The paper includes a Statement of need section

[editorialbot]

License info:

✅ License found: MIT License (Valid open source OSI approved license)

[kthyng]

Here is what I found running cloc on the component code specifically:

Since tests and docs are on top of this 1000 LOC, I think it passes substantial scholarly effort.

[kthyng]

@angelmons paper comments:

• the references aren't working currently
• Please check the capitalization in your references. You can preserve capitalization by placing {} around characters/words in your .bib file.
• Please reduce to length of your paper to up to about 1000 words. Paper format information here: https://joss.readthedocs.io/en/latest/paper.html. You can check paper length (and a few other items) with the command @editorialbot check repository though note it needs to be the first item in a comment to run correctly. Currently it's 1220 words.

[kthyng]

@cheginit Can you edit this paper? Just waiting on a few paper changes and should be good to go.

[kthyng]

@editorialbot invite @cheginit as editor

[editorialbot]

Invitation to edit this submission sent!

[cheginit]

@kthyng Yes, I can edit this.

[cheginit]

@editorialbot assign @cheginit as editor

[editorialbot]

Assigned! @cheginit is now the editor

[angelmons]

@editorialbot generate pdf

[angelmons]

@editorialbot check repository

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.98  T=1.22 s (699.3 files/s, 208751.0 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                         573          24368          51181          78153
Text                            20             84              0          19342
Markdown                        78           2367             34          14651
Jupyter Notebook                94              0          33466          10993
TOML                             3            794              5           8344
Cython                          48           1089           1364           5502
TeX                              5             76              0            843
YAML                            11             91             39            598
DOS Batch                        1             29              1            212
Bourne Shell                     1             12             12             31
make                             1              4              6             12
Jinja Template                   1              5              0             10
XML                              4              0              0              8
SVG                              7              0              0              7
C/C++ Header                     1              2              4              5
reStructuredText                 1              1              0              4
HTML                             1              0              0              3
-------------------------------------------------------------------------------
SUM:                           850          28922          86112         138718
-------------------------------------------------------------------------------

Commit count by author:

  3923	Eric Hutton
  1118	Katy Barnhart
  1015	Dan Hobley
   878	Greg Tucker
   321	dependabot[bot]
   257	Jordan Adams
   256	Sai Nudurupati
   227	Nicole M Gasparini
    76	pre-commit-ci[bot]
    69	Charlie Shobe
    62	David Litwin
    59	Laurent Roberge
    49	Ronda Strauch
    44	Jenny Knuth
    43	Benjamin Campforts
    43	Sebastien Lenard
    40	Margaux Mouchene
    32	angelmons
    27	Nathan Lyons
    26	Berkan M
    18	Jeffrey Keck
    17	Allison Pfeiffer
    12	Rachel Glade
    11	Dylan Ward
    11	Giuseppecipolla95
     7	Annie Thompson
     6	Mark Piper
     2	Amanda Manaster
     2	Jay Hariharan
     2	Shelby Ahrendt
     1	(no author)
     1	Abby Langston
     1	Andy Wickert
     1	Christopher Sheehan
     1	Josh Wolpert
     1	Kristen Thyng
     1	Muneer Ahammad
     1	Sarah Lundell
     1	pankajiitkgp

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 863

✅ The paper includes a Statement of need section

[editorialbot]

License info:

✅ License found: MIT License (Valid open source OSI approved license)

[editorialbot]

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

[editorialbot]

Five most similar historical JOSS papers:

pyDeltaRCM: a flexible numerical delta model
Submitting author: @amoodie
Handling editor: @kbarnhart (Retired)
Reviewers: @zsylvester, @jhnienhuis, @salterg
Similarity score: 0.7575

Ocellaris: a DG FEM solver for free-surface flows
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Similarity score: 0.7429

pyflowline: a mesh-independent river network generator for hydrologic models
Submitting author: @changliao1025
Handling editor: @observingClouds (Active)
Reviewers: @smchartrand, @andres-patrignani
Similarity score: 0.7399

NetworkSedimentTransporter: A Landlab component for bed material transport through river networks
Submitting author: @pfeiffea
Handling editor: @kthyng (Active)
Reviewers: @zsylvester, @ebgoldstein
Similarity score: 0.7351

The Kestrel software for simulations of morphodynamic Earth-surface flows
Submitting author: @jakelangham
Handling editor: @crvernon (Active)
Reviewers: @mdpiper, @jatkinson1000
Similarity score: 0.7282

⚠️ Note to editors: If these papers look like they might be a good match, click through to the review issue for that paper and invite one or more of the authors before considering asking the reviewers of these papers to review again for JOSS.

[angelmons]

@editorialbot generate pdf

[editorialbot]

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

[editorialbot]

Five most similar historical JOSS papers:

pyDeltaRCM: a flexible numerical delta model
Submitting author: @amoodie
Handling editor: @kbarnhart (Retired)
Reviewers: @zsylvester, @jhnienhuis, @salterg
Similarity score: 0.7529

Ocellaris: a DG FEM solver for free-surface flows
Submitting author: @TormodLandet
Handling editor: @labarba (Retired)
Reviewers: @inducer, @piyueh
Similarity score: 0.7428

pyflowline: a mesh-independent river network generator for hydrologic models
Submitting author: @changliao1025
Handling editor: @observingClouds (Active)
Reviewers: @smchartrand, @andres-patrignani
Similarity score: 0.7396

The Kestrel software for simulations of morphodynamic Earth-surface flows
Submitting author: @jakelangham
Handling editor: @crvernon (Active)
Reviewers: @mdpiper, @jatkinson1000
Similarity score: 0.7337

NetworkSedimentTransporter: A Landlab component for bed material transport through river networks
Submitting author: @pfeiffea
Handling editor: @kthyng (Active)
Reviewers: @zsylvester, @ebgoldstein
Similarity score: 0.7292

⚠️ Note to editors: If these papers look like they might be a good match, click through to the review issue for that paper and invite one or more of the authors before considering asking the reviewers of these papers to review again for JOSS.

[angelmons]

Hi @kthyng and @cheginit, I have addressed the issues you raised:

Fixed the capitalization in references using {} brackets
Reduced the paper length to under 1000 words
Corrected the citation formats

Let me know if there are any other comments or adjustments needed. I'll be happy to address them as soon as possible.

[cheginit]

@angelmons Thanks for addressing the issues. I will be editing your submission. To begin, please provide a list of GitHub handles of potential reviewers without using @ to prevent premature pinging. In addition to people in your own network, you can use JOSS's search tool.

[angelmons]

@cheginit

Potential reviewers for this paper are: mdpiper, mcflugen, nicgaspar, pfeiffea, zsylvester, ebgoldstein

[cheginit]

👋🏼 @mdpiper, @mcflugen, and @nicgaspar, Would you like to review this submission to the Journal for Open Source Software? Our reviews are checklist-driven and openly conducted on GitHub over a timeline of 4–6 weeks. Because the process is much more iterative and interactive than a traditional paper review, we would ask you to start within the next 2 weeks. Here are reviewer guidelines for reference: joss.readthedocs.io/en/latest/reviewer_guidelines.html

Thanks for your consideration.

[mcflugen]

Would you like to review this submission to the Journal for Open Source Software?

@cheginit Sure!

[cheginit]

@mcflugen Thanks for agreeing to review this submission, appreciate it! When I find other reviewers, I will create a new issue with instructions for the review.

[cheginit]

@editorialbot add @mcflugen as reviewer

[editorialbot]

@mcflugen added to the reviewers list!