[REVIEW]: py_SBeLT: A Python software package for stochastic sediment transport under rarefied conditions #4282

editorialbot · 2022-03-29T16:21:27Z

Submitting author: @szwiep (Sarah Zwiep)
Repository: https://github.com/szwiep/py_SBeLT
Branch with paper.md (empty if default branch):
Version: v1.0.2
Editor: @kbarnhart
Reviewers: @pfeiffea, @tdoane
Archive: 10.6084/m9.figshare.19967552.v3

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/d7b9cc16b87e8875ec7115a22e1413fe/status.svg)](https://joss.theoj.org/papers/d7b9cc16b87e8875ec7115a22e1413fe)

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

@pfeiffea & @tdoane, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review.
First of all you need to run this command in a separate comment to create the checklist:

@editorialbot generate my checklist

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 ✨

Checklists

📝 Checklist for @tdoane

📝 Checklist for @pfeiffea

The text was updated successfully, but these errors were encountered:

editorialbot · 2022-03-29T16:21:29Z

Hello humans, I'm @editorialbot, a robot that can help you with some common editorial tasks.

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

@editorialbot commands

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

@editorialbot generate pdf

editorialbot · 2022-03-29T16:21:32Z

Software report:

github.com/AlDanial/cloc v 1.88  T=0.15 s (177.5 files/s, 92229.5 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
HTML                             5            989              0           7950
Python                           7            491            913           1348
Markdown                         9            167              0            468
TeX                              1             15              0            180
Jupyter Notebook                 2              0            839             80
YAML                             2              5             30             38
-------------------------------------------------------------------------------
SUM:                            26           1667           1782          10064
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

editorialbot · 2022-03-29T16:21:33Z

Wordcount for paper.md is 1219

editorialbot · 2022-03-29T16:21:43Z

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

OK DOIs

- 10.1103/PhysRevE.74.011302 is OK
- 10.1017/S0022112007008774 is OK
- 10.1029/2009JF001260 is OK
- 10.1080/00221686.2019.1702594 is OK
- 10.14288/1.0349138 is OK
- 10.1002/2015JF003552 is OK
- 10.1029/2012JF002352 is OK
- 10.1002/2016JF003833 is OK
- 10.5194/esurf-9-629-2021 is OK
- 10.5194/esurf-6-1089-2018 is OK
- 10.1061/9780784408148.ch03 is OK
- 10.1029/2012JF002353 is OK
- 10.1002/2014RG000474 is OK
- 10.1029/2019WR025116 is OK

MISSING DOIs

- None

INVALID DOIs

- None

kbarnhart · 2022-03-29T16:22:01Z

@editorialbot set v1.0.1 as version

editorialbot · 2022-03-29T16:22:02Z

Done! version is now v1.0.1

editorialbot · 2022-03-29T16:23:47Z

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

kbarnhart · 2022-03-29T16:29:32Z

👋🏼 @pfeiffea @tdoane this is the review thread for the paper. All of our communications about this review will happen here from now on.

At the top of the thread is a comment with key information about the review process. Please read it carefully. If you have issues as you go about your review, let me know, and I'll provide guidance and assistance.

The JOSS review is different from most other journals. Our goal is to work with the authors to help them meet our criteria instead of merely passing judgment on the submission. As such, the reviewers are encouraged to submit issues and pull requests on the software repository. When doing so, please mention openjournals/joss-reviews/issues/4282 so that a link is created to this thread (and I can keep an eye on what is happening). Please also feel free to comment and ask questions on this thread. In my experience, it is better to post comments/questions/suggestions as you come across them instead of waiting until you've reviewed the entire package.

I'll set an automatic reminder for four weeks from now.

Please feel free to ping me (@krbarnhart or krbarnhart@usgs.gov) if you have any questions/concerns.

Thank you for contributing a review to JOSS.

tdoane · 2022-04-05T19:05:38Z

Review checklist for @tdoane

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 https://github.com/szwiep/py_SBeLT?
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 (@szwiep) 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?

szwiep · 2022-04-05T20:48:33Z

Hi all, I forgot to include the updated paper.md in the pre-review revisions. I realized my mistake and just pushed it to the main branch now. Hopefully this doesn't cause any difficulties. @kbarnhart should I re-generate the pdf?

kbarnhart · 2022-04-05T21:01:03Z

@szwiep yes, at any time you can re-generate the PDF.

kbarnhart · 2022-04-05T21:01:07Z

@editorialbot generate pdf

editorialbot · 2022-04-05T21:02:23Z

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

pfeiffea · 2022-04-12T22:05:08Z

@editorialbot generate my checklist

kbarnhart · 2022-04-12T23:27:11Z

@editorialbot remind @pfeiffea in two weeks

editorialbot · 2022-04-12T23:27:12Z

Reminder set for @pfeiffea in two weeks

kbarnhart · 2022-04-12T23:27:27Z

@editorialbot remind @tdoane in two weeks

editorialbot · 2022-04-12T23:27:27Z

Reminder set for @tdoane in two weeks

pfeiffea · 2022-04-13T17:30:14Z

@kbarnhart I'm having a clueless moment... any idea why the @ editorial bot didn't generate my checklist, above?

kbarnhart · 2022-04-13T21:20:30Z

@pfeiffea no clue why. I made one for you by hand.

@arfon - Flagging that editorialbot didn't make a checklist for @pfeiffea when we expected it would.

pfeiffea · 2022-04-21T22:41:16Z

@kbarnhart thanks for doing that-- and then I realized that I could have just copied @tdoane 's. In any case, I can't check boxes on yours, and when I tried again just now it worked. Shrug.

Review checklist for @pfeiffea

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 https://github.com/szwiep/py_SBeLT?
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 (@szwiep) 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?

pfeiffea · 2022-04-22T22:37:13Z

First off, well done @szwiep (and @smchartrand). This is a very well organized, well documented bit of software. It is a simple and elegant little tool. My edits are relatively minor. I have a few lingering “to-dos” on my review checklist, which I’ll deal with in the coming days.

Basic Usage Notebook:

This is an excellent notebook. It is not verbose, but gives me a great sense for how to use and interpret results of pySBeLT.
Minor suggestion: It would be great to add the default parameters to the “parameters and running” table.

Data Storage Notebook:

Accessing Final Metrics section you’re missing a “.hdf5” at the end of the file name in the 2nd and 3rd to last code blocks. Make sure to restart the kernel and clear all outputs (or run all) in your final submission. The version up on your repo currently shows that you’ve re-run cells several times without restarting.

Manuscript:

Ln 12: I’d suggest editing to “… a function of local water flow conditions and the grain size distribution of the bed material.”
Ln 12-14: The sentence that starts “A predictive approach…” seems like your opportunity to succinctly state the gap pySBeELT is trying to fill. But, as written, it feels a bit muddled (“the approach introduces challenges”). Do you mean something like “This standard approach to modeling bedload transport obscures(? Neglects?) the mechanistic reality of sediment transport: the bed material flux is the integrated transport of individual stochastic particle motions.”
Ln 17: Instead of “examine connections”, how about “reveal the relationship” or “illustrate the relationship” (the user will be the one examining, the tool will make the examination possible)?
Ln 38: “motivated by a..” suggests that your work was motivated by some specific earlier published work. If so, cite. Or maybe “pySBeLT takes a birth-death….. approach to modeling bedload transport”.
Ln 46: set_diam should have quotes around it, right? ‘set_diam’
Ln 51-54: I think these last two sentences should be combined or re-ordered.
Figure 1. Add a flow direction arrow.
Figure 2. The lower panel is too small to read. Add the units of particle flux to the y axis of the upper plot.

Fix citation issues:
? in Wainwright 2014 and Wu 2019
Some first names or initials included in the in-text citations.

THEORY.md

Entrainment section, second paragraph has some odd number typos interspersed in the text. Take a look.
@kbarnhart should this section be a part of the paper? It seems to me that it describes both the rationale and function of the model, so maybe? Or is it better to keep separate?

smchartrand · 2022-04-24T03:56:19Z

Thanks @pfeiffea. These are all super helpful suggestions. We appreciate your time and energy reviewing our submission.

kbarnhart · 2022-04-26T22:14:30Z

@pfeiffea many thanks for your review! 🎉

Regarding your question:

@kbarnhart should this section be a part of the paper? It seems to me that it describes both the rationale and function of the model, so maybe? Or is it better to keep separate?

I tend to recommend that theory lives with the main documentation (here, the file theory.md) rather than in the paper because the theory is then more closely tied with what a typical user is looking at when they are learning to use the software. In contrast, the paper would contain the type of information that a potential user might use to determine if this software could solve their problem.

I agree with you that in this case, the theory.md file includes both rationale and function (e.g., discussion of results of model testing). A more traditional theory document would probably just have the rationale and mathematical description. A second document might discuss how the theory interacts with the implementation (e.g., the discussion of how discretization interacts with entrainment "This means particle entrainment is treated as independent events between the 'num_subregions' (see README.md and paper.md) and between each iteration.")

If either you (@pfeiffea) or @tdoane found that it was hard to "see" the theory as described by "theory.md", then it may be worth recommending to @szwiep and co-authors to revise. If not, I think that it is fine as it is.

editorialbot · 2022-04-26T23:27:14Z

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

danielskatz · 2022-06-03T17:39:30Z

I'm sorry, but I'm going to request that you change the title - in my opinion, "a software" is not grammatically correct. Can you change it to "a software package" or "a software library" or "software" (without the "a" first)?

danielskatz · 2022-06-03T17:40:49Z

also, I see "bed load" and "bedload" in different parts of the paper. Can you choose one and use it consistently?

danielskatz · 2022-06-03T17:42:06Z

Once these two issues are fixed, the paper looks ready to go to me

smchartrand · 2022-06-03T18:02:01Z

Apologies. I will take care of both of these issues in the next hour.

smchartrand · 2022-06-03T18:14:17Z

@danielskatz

For the title, how about: py_SBeLT: Python model for stochastic sediment transport under rarefied conditions?

I am glad you raised this issues. I am hesitant to use "package", and now "software" since it is really a numerical model. Thoughts?

danielskatz · 2022-06-03T18:16:37Z

"A Python model" sounds better grammatically to me, though I think the model is implemented in software, so I could see reasons to state this is software too, particularly as a JOSS paper.

smchartrand · 2022-06-03T18:22:34Z

Okay. I will use: "A Python software package...."
Sound good?

danielskatz · 2022-06-03T18:27:29Z

yes, thanks

smchartrand · 2022-06-03T18:29:57Z

I will also correct the title in the archived repository at figshare.

I have made the corrections to the use of bedload, and have opted for "bed load". And I have changed the title. The paper is ready.

smchartrand · 2022-06-03T18:32:34Z

@danielskatz

Updated DOI for figshare archive: https://doi.org/10.6084/m9.figshare.19967552.v3

danielskatz · 2022-06-03T18:46:03Z

@editorialbot set 10.6084/m9.figshare.19967552.v3 as archive

editorialbot · 2022-06-03T18:46:05Z

Done! Archive is now 10.6084/m9.figshare.19967552.v3

danielskatz · 2022-06-03T18:46:36Z

@editorialbot recommend-accept

editorialbot · 2022-06-03T18:46:37Z

Attempting dry run of processing paper acceptance...

editorialbot · 2022-06-03T18:46:41Z

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

OK DOIs

- 10.1103/PhysRevE.74.011302 is OK
- 10.1017/S0022112007008774 is OK
- 10.1029/2009JF001260 is OK
- 10.1080/00221686.2019.1702594 is OK
- 10.14288/1.0349138 is OK
- 10.1002/2015JF003552 is OK
- 10.1029/2012JF002352 is OK
- 10.1002/2016JF003833 is OK
- 10.5194/esurf-9-629-2021 is OK
- 10.5194/esurf-6-1089-2018 is OK
- 10.1061/9780784408148.ch03 is OK
- 10.1029/2012JF002353 is OK
- 10.1002/2014RG000474 is OK
- 10.1029/2019WR025116 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot · 2022-06-03T18:47:48Z

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

Check final proof 👉 openjournals/joss-papers#3267

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#3267, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

danielskatz · 2022-06-03T18:49:21Z

@editorialbot accept

editorialbot · 2022-06-03T18:49:22Z

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

editorialbot · 2022-06-03T18:51:11Z

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

editorialbot · 2022-06-03T18:51:12Z

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.04282 joss-papers#3268
Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.04282
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

danielskatz · 2022-06-03T18:56:47Z

Congratulations to @szwiep and @smchartrand!!

And thanks to @pfeiffea and @tdoane for reviewing, and to @kbarnhart for editing!
We couldn't do this without you

editorialbot · 2022-06-03T18:56:49Z

🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

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reStructuredText:
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szwiep · 2022-06-03T19:07:17Z

How exciting! Thank you again @kbarnhart, @tdoane, @pfeiffea, and @danielskatz for your efforts. I learned a lot, and the model was definitely improved, by participating in this process. What a great experience.

editorialbot added Python review TeX labels Mar 29, 2022

editorialbot assigned kbarnhart Mar 29, 2022

editorialbot mentioned this issue Mar 29, 2022

[PRE REVIEW]: py_SBeLT: A Python software for stochastic sediment transport under rarefied conditions #4091

Closed

danielskatz changed the title ~~[REVIEW]: py_SBeLT: A Python software for stochastic sediment transport under rarefied conditions~~ [REVIEW]: py_SBeLT: A Python software package for stochastic sediment transport under rarefied conditions Jun 3, 2022

editorialbot added accepted published Papers published in JOSS labels Jun 3, 2022

danielskatz closed this as completed Jun 3, 2022

editorialbot mentioned this issue Oct 1, 2023

[PRE REVIEW]: Stokesian Dynamics in Python #5907

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editorialbot mentioned this issue Jan 12, 2024

[PRE REVIEW]: statemodify: a Python framework to facilitate accessible exploratory modeling for discovering drought vulnerabilities #6223

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editorialbot mentioned this issue Dec 11, 2024

[PRE REVIEW]: RiverFlowDynamics v1.0: A Landlab component for computing two-dimensional river flow dynamics #7585

Open

[REVIEW]: py_SBeLT: A Python software package for stochastic sediment transport under rarefied conditions #4282

[REVIEW]: py_SBeLT: A Python software package for stochastic sediment transport under rarefied conditions #4282

Comments

editorialbot commented Mar 29, 2022 • edited Loading

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tdoane commented Apr 5, 2022 • edited Loading

Review checklist for @tdoane

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

szwiep commented Apr 5, 2022

kbarnhart commented Apr 5, 2022

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pfeiffea commented Apr 13, 2022

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pfeiffea commented Apr 21, 2022 • edited Loading

Review checklist for @pfeiffea

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

pfeiffea commented Apr 22, 2022 • edited Loading

Basic Usage Notebook:

Data Storage Notebook:

Manuscript:

THEORY.md

smchartrand commented Apr 24, 2022

kbarnhart commented Apr 26, 2022

editorialbot commented Apr 26, 2022

danielskatz commented Jun 3, 2022

danielskatz commented Jun 3, 2022

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smchartrand commented Jun 3, 2022

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