[PRE REVIEW]: GrainLearning: A Bayesian uncertainty quantification toolbox for discrete and continuum numerical models of granular materials

[editorialbot]

Submitting author: !--author-handle-->@luisaforozco<!--end-author-handle-- (Luisa Fernanda Orozco) Repository: https://github.com/GrainLearning/grainLearning Branch with paper.md (empty if default branch): joss_submission Version: v2.0.2 Editor: !--editor-->@diehlpk<!--end-editor-- Reviewers: @gchure, @georgiastuart, @Haipeng-ustc Managing EiC: Kevin M. Moerman

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/95be80cfca49cdb6a1850f1460a47d10"><img src="https://joss.theoj.org/papers/95be80cfca49cdb6a1850f1460a47d10/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/95be80cfca49cdb6a1850f1460a47d10/status.svg)](https://joss.theoj.org/papers/95be80cfca49cdb6a1850f1460a47d10)

Author instructions

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

@luisaforozco 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

The JOSS submission bot @editorialbot is here to help you find and assign reviewers and start the main review. To find out what @editorialbot can do for you type:

@editorialbot commands

[editorialbot]

Hello human, 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]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.12 s (657.8 files/s, 100347.3 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          39           1232           1806           3772
YAML                            14             35             14            854
reStructuredText                10            409            689            514
Markdown                         7            140              2            386
Jupyter Notebook                 3              0           1688            174
TeX                              1              0              0            164
JSON                             1              0              0             45
TOML                             1              4              0             45
DOS Batch                        1              8              1             26
make                             1              4              7              9
Bourne Shell                     1              6             11              7
-------------------------------------------------------------------------------
SUM:                            79           1838           4218           5996
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 718

[editorialbot]

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

OK DOIs

- 10.1016/j.cma.2019.01.027 is OK
- 10.1007/s10035-017-0781-y is OK
- 10.1016/j.compgeo.2021.104491 is OK
- 10.1016/j.powtec.2021.11.044 is OK
- 10.1016/j.compgeo.2023.105957 is OK
- 10.23967/c.particles.2023.015 is OK
- 10.5281/zenodo.8352544 is OK
- 10.1016/J.APT.2018.03.001 is OK
- 10.1016/j.powtec.2011.03.023 is OK
- 10.1016/J.POWTEC.2021.07.048 is OK
- 10.1016/j.powtec.2016.01.003 is OK

MISSING DOIs

- None

INVALID DOIs

- https://doi.org/10.1016/j.cma.2023.116040 is INVALID because of 'https://doi.org/' prefix

[editorialbot]

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

[editorialbot]

Five most similar historical JOSS papers:

UnlockNN: Uncertainty quantification for neural network models of chemical systems Submitting author: @a-ws-m Handling editor: @osorensen (Active) Reviewers: @TahiriNadia, @pmeier, @Het-Shah Similarity score: 0.8235

GrainSizeTools: a Python script for grain size analysis and paleopiezometry based on grain size Submitting author: @marcoalopez Handling editor: @lheagy (Retired) Reviewers: @lheagy, @jsta Similarity score: 0.8231

GB code: A grain boundary generation code Submitting author: @https://github.com/oekosheri Handling editor: @labarba (Retired) Reviewers: @vyasr, @trallard Similarity score: 0.8231

MCSD: A MATLAB Tool for Monte-Carlo Simulations of Diffusion in biological Tissues Submitting author: @davidnsousa Handling editor: @Kevin-Mattheus-Moerman (Active) Reviewers: @nnadeau, @mwacaan Similarity score: 0.8198

NetworkSedimentTransporter: A Landlab component for bed material transport through river networks Submitting author: @pfeiffea Handling editor: @kthyng (Active) Reviewers: @zsylvester, @ebgoldstein Similarity score: 0.8185

⚠️ 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.

[Kevin-Mattheus-Moerman]

@editorialbot invite @diehlpk as editor

[editorialbot]

Invitation to edit this submission sent!

[diehlpk]

@editorialbot add @diehlpk as editor

[editorialbot]

Assigned! @diehlpk is now the editor

[diehlpk]

I can edit the paper, but can only start at the end of next week.

[luisaforozco]

Hello, other potential reviewers, from the list of JOSS reviewers:

• jwbuurlage
• a-ws-m
• gchure
• Haipeng-ustc
• georgiastuart
• prmiles

[diehlpk]

Hi @jwbuurlage do you have time to review that paper?

[diehlpk]

Hi @a-ws-m do you have time to review that paper?

[diehlpk]

Hi @prmiles do you have time to review this paper?

[diehlpk]

Hi @gchure do you have time to review this paper?

[diehlpk]

Hi @Haipeng-ustc do you have time to review this paper?

[diehlpk]

Hi @georgiastuart do you have time to review this paper?

[georgiastuart]

I think I can review in a week or two.

[gchure]

Hi @diehlpk, happy to review, though it may be two weeks to complete.

[diehlpk]

@editorialbot add @gchure as reviewer

[editorialbot]

@gchure added to the reviewers list!

[diehlpk]

@editorialbot add @georgiastuart as reviewer

[editorialbot]

@georgiastuart added to the reviewers list!

[diehlpk]

@editorialbot start review

[editorialbot]

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/6338.

[Haipeng-ustc]

I'm happy to be one of the reviewers. It'll take me around two weeks to finish it.

[diehlpk]

@editorialbot add @Haipeng-ustc as reviewer

[editorialbot]

@Haipeng-ustc added to the reviewers list!

[Haipeng-ustc]

In my review of this repo, I found it is a well-developed software. The installation process works smoothly, although I didn't test on Windows. The code quality is good, and the tutorial provided makes it accessible to its users. Furthermore, the unit test suite is very developed as well. Overall, "GrainLearning" represents a decent package for its related research. I recommend it highly for its utility and design.

[diehlpk]

@editorialbot commands

[editorialbot]

Hello @diehlpk, here are the things you can ask me to do:

# List all available commands
@editorialbot commands

# Add to this issue's reviewers list
@editorialbot add @username as reviewer

# Remove from this issue's reviewers list
@editorialbot remove @username from reviewers

# Get a list of all editors's GitHub handles
@editorialbot list editors

# Assign a user as the editor of this submission
@editorialbot assign @username as editor

# Remove the editor assigned to this submission
@editorialbot remove editor

# Remind an author, a reviewer or the editor to return to a review after a 
# certain period of time (supported units days and weeks)
@editorialbot remind @reviewer in 2 weeks

# Adds a checklist for the reviewer using this command
@editorialbot generate my checklist

# Set a value for version
@editorialbot set v1.0.0 as version

# Set a value for branch
@editorialbot set joss-paper as branch

# Set a value for repository
@editorialbot set https://github.com/organization/repo as repository

# Set a value for the archive DOI
@editorialbot set set 10.5281/zenodo.6861996 as archive

# Mention the EiCs for the correct track
@editorialbot ping track-eic

# Run checks and provide information on the repository and the paper file
@editorialbot check repository

# Check the references of the paper for missing DOIs
@editorialbot check references

# Generates the pdf paper
@editorialbot generate pdf

# Recommends the submission for acceptance
@editorialbot recommend-accept

# Generates a LaTeX preprint file
@editorialbot generate preprint

# Flag submission with questionable scope
@editorialbot query scope

# Get a link to the complete list of reviewers
@editorialbot list reviewers

# Creates a post-review checklist with editor and authors tasks
@editorialbot create post-review checklist

# Open the review issue
@editorialbot start review

[diehlpk]

In my review of this repo, I found it is a well-developed software. The installation process works smoothly, although I didn't test on Windows. The code quality is good, and the tutorial provided makes it accessible to its users. Furthermore, the unit test suite is very developed as well. Overall, "GrainLearning" represents a decent package for its related research. I recommend it highly for its utility and design.

@Haipeng-ustc could you please run @editorialbot generate my checklist and check the appropriate boxes?

[Haipeng-ustc]

@editorialbot generate my checklist

[editorialbot]

Checklists can only be created once the review has started in the review issue