[REVIEW]: GrainLearning: A Bayesian uncertainty quantification toolbox for discrete and continuum numerical models of granular materials #6338

editorialbot · 2024-02-08T22:21:01Z

Submitting author: @luisaforozco (Luisa Fernanda Orozco)
Repository: https://github.com/GrainLearning/grainLearning
Branch with paper.md (empty if default branch): joss_submission
Version: v2.0.3
Editor: @diehlpk
Reviewers: @gchure, @Haipeng-ustc
Archive: 10.5281/zenodo.11001174

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)

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

@gchure & @georgiastuart, 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 @diehlpk 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 @gchure

📝 Checklist for @georgiastuart

📝 Checklist for @Haipeng-ustc

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

editorialbot · 2024-02-08T22:21:04Z

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:

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

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editorialbot · 2024-02-08T22:21:09Z

Software report:

github.com/AlDanial/cloc v 1.88  T=0.16 s (486.8 files/s, 73370.6 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          39           1177           1756           3731
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           1783           4168           5955
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

editorialbot · 2024-02-08T22:21:11Z

Wordcount for paper.md is 718

editorialbot · 2024-02-08T22:21:11Z

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.cma.2023.116040 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

- None

editorialbot · 2024-02-08T22:22:41Z

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

gchure · 2024-02-08T22:54:37Z

Review checklist for @gchure

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/GrainLearning/grainLearning?
License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
Contribution and authorship: Has the submitting author (@luisaforozco) 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
Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

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, who the target audience is, and its relation to other work?
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?

georgiastuart · 2024-02-08T23:21:48Z

Review checklist for @georgiastuart

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/GrainLearning/grainLearning?
License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
Contribution and authorship: Has the submitting author (@luisaforozco) 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
Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

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, who the target audience is, and its relation to other work?
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?

gchure · 2024-02-15T01:13:12Z

Hi @diehlpk, I had some paper revisions come in this week that sucked up my free time. It will be at least another week or so until I get to this. Sorry to the authors for the delay!

georgiastuart · 2024-02-23T17:26:59Z

Beginning my review, sorry for the delay!!

diehlpk · 2024-02-29T01:57:57Z

Hi @gchure how is your review going?

gchure · 2024-02-29T03:56:00Z

Hi @diehlpk, I caught the flu for the past 5 days and am just coming back to life. I'll be at a conference next week and should have time in the evenings to finish it up. I'll shoot for March 8, if that is okay.

diehlpk · 2024-03-01T16:44:49Z

Hi @diehlpk, I caught the flu for the past 5 days and am just coming back to life. I'll be at a conference next week and should have time in the evenings to finish it up. I'll shoot for March 8, if that is okay.

Thanks for the update and hope you will recover soon.

gchure · 2024-03-15T00:23:17Z

Hi @diehlpk, I've finished my review. I've found the software to be in very good shape, with no substantive comments on the structure or functionality. Installation works as advertised, though it seems that building the wheel for Windows is currently failing. I don't have access to a windows machine to test installation, however, so maybe this is not an issue (@luisaforozco can maybe comment on this).

My only blocking issue is the status of the software paper (see GrainLearning-#72). I think it could use some more work to better represent the capability of the software. As the authors have very nice documentation, I don't think this should take too much effort. Once they've addressed this point, I can mark my review as complete.

Thanks for the patience -- the flu followed by APS march meeting isn't a combo I would recommend, especially if you have reviews to get to!

luisaforozco · 2024-03-15T07:49:42Z

Thanks a lot for your review @diehlpk. Regarding the building problem for windows the issue is with a dependency of tensorflow: tensorflow-io-gcs-filesystem for which the wheels for windows have been somehow forgotten or not published anymore (see issue(s) and reports via other channels). For a local installation, if the users handled the tensorflow installation on their side prior to installing GrainLearning, everything should work as intended.

diehlpk · 2024-03-15T13:10:21Z

@luisaforozco Please mention that in the documentation and I think it should be fine with the Windows installation issue.

Can you add your proposed fix to the testing system?

diehlpk · 2024-03-18T14:59:04Z

Hi @georgiastuart how is your review going?

gchure · 2024-03-19T22:10:38Z

Hi @diehlpk, I can mark my review as finished. @luisaforozco addressed all of my comments in terms of the software paper in the corresponding issue.

diehlpk · 2024-03-21T16:07:11Z

@Haipeng-ustc you need to generate the list here.

Haipeng-ustc · 2024-03-22T22:03:11Z

@editorialbot generate my checklist

editorialbot · 2024-03-22T22:03:12Z

@Haipeng-ustc I can't do that because you are not a reviewer

diehlpk · 2024-03-25T17:33:35Z

@Haipeng-ustc please try again.

diehlpk · 2024-03-28T21:23:35Z

Hi @georgiastuart how is your review going?

diehlpk · 2024-04-25T16:22:26Z

@editorialbot generate pdf

editorialbot · 2024-04-25T16:23:38Z

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

diehlpk · 2024-04-25T16:26:45Z

@editorialbot recommend-accept

editorialbot · 2024-04-25T16:26:47Z

Attempting dry run of processing paper acceptance...

editorialbot · 2024-04-25T16:27:25Z

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.cma.2023.116040 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

- No DOI given, and none found for title: Machine learning in the calibration process of dis...

INVALID DOIs

- None

editorialbot · 2024-04-25T16:28:36Z

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

Check final proof 👉📄 Download article

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#5277, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

Kevin-Mattheus-Moerman · 2024-05-01T20:04:25Z

@luisaforozco as AEiC for JOSS I will now help to process this submission for acceptance in JOSS. I have checked this review, your repository, the archive link, and the paper. Most seems in order, however the below are some points that require your attention:

Consider adding the town/city for the first and second affiliation.
Please spell out AU as Australia in the last your.
gaussian and bayesian should start with a capital letter.

luisaforozco · 2024-05-02T06:36:29Z

@Kevin-Mattheus-Moerman thanks for the comments! I've made the requested changes to the text.

@luisaforozco as AEiC for JOSS I will now help to process this submission for acceptance in JOSS. I have checked this review, your repository, the archive link, and the paper. Most seems in order, however the below are some points that require your attention:

Consider adding the town/city for the first and second affiliation.

Please spell out AU as Australia in the last your.

gaussian and bayesian should start with a capital letter.

Kevin-Mattheus-Moerman · 2024-05-02T06:46:39Z

@editorialbot generate pdf

editorialbot · 2024-05-02T06:48:04Z

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

Kevin-Mattheus-Moerman · 2024-05-02T07:26:01Z

@editorialbot accept

editorialbot · 2024-05-02T07:26:03Z

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

editorialbot · 2024-05-02T07:32:45Z

Ensure proper citation by uploading a plain text CITATION.cff file to the default branch of your repository.

If using GitHub, a Cite this repository menu will appear in the About section, containing both APA and BibTeX formats. When exported to Zotero using a browser plugin, Zotero will automatically create an entry using the information contained in the .cff file.

You can copy the contents for your CITATION.cff file here:

CITATION.cff

cff-version: "1.2.0"
authors:
- family-names: Cheng
  given-names: Hongyang
  orcid: "https://orcid.org/0000-0001-7652-8600"
- family-names: Orozco
  given-names: Luisa
  orcid: "https://orcid.org/0000-0002-9153-650X"
- family-names: Lubbe
  given-names: Retief
- family-names: Jansen
  given-names: Aron
  orcid: "https://orcid.org/0000-0002-4764-9347"
- family-names: Hartmann
  given-names: Philipp
  orcid: "https://orcid.org/0000-0002-2524-8024"
- family-names: Thoeni
  given-names: Klaus
  orcid: "https://orcid.org/0000-0001-7351-7447"
contact:
- family-names: Orozco
  given-names: Luisa
  orcid: "https://orcid.org/0000-0002-9153-650X"
doi: 10.5281/zenodo.11001174
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Cheng
    given-names: Hongyang
    orcid: "https://orcid.org/0000-0001-7652-8600"
  - family-names: Orozco
    given-names: Luisa
    orcid: "https://orcid.org/0000-0002-9153-650X"
  - family-names: Lubbe
    given-names: Retief
  - family-names: Jansen
    given-names: Aron
    orcid: "https://orcid.org/0000-0002-4764-9347"
  - family-names: Hartmann
    given-names: Philipp
    orcid: "https://orcid.org/0000-0002-2524-8024"
  - family-names: Thoeni
    given-names: Klaus
    orcid: "https://orcid.org/0000-0001-7351-7447"
  date-published: 2024-05-02
  doi: 10.21105/joss.06338
  issn: 2475-9066
  issue: 97
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 6338
  title: "GrainLearning: A Bayesian uncertainty quantification toolbox
    for discrete and continuum numerical models of granular materials"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.06338"
  volume: 9
title: "GrainLearning: A Bayesian uncertainty quantification toolbox for
  discrete and continuum numerical models of granular materials"

If the repository is not hosted on GitHub, a .cff file can still be uploaded to set your preferred citation. Users will be able to manually copy and paste the citation.

Find more information on .cff files here and here.

editorialbot · 2024-05-02T07:32:48Z

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

editorialbot · 2024-05-02T07:32:49Z

🚨🚨🚨 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.06338 joss-papers#5294
Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.06338
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

Kevin-Mattheus-Moerman · 2024-05-03T07:07:36Z

@luisaforozco congratulations on this JOSS publication!!!

Thanks for editing @diehlpk !!

And a special thank you to the reviewers: @gchure, @Haipeng-ustc !!!

editorialbot · 2024-05-03T07:07:38Z

🎉🎉🎉 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.06338/status.svg)](https://doi.org/10.21105/joss.06338)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.06338">
  <img src="https://joss.theoj.org/papers/10.21105/joss.06338/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.06338/status.svg
   :target: https://doi.org/10.21105/joss.06338

This is how it will look in your documentation:

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luisaforozco · 2024-05-08T12:59:55Z

Dear @Kevin-Mattheus-Moerman, a co-author noticed that there was an error in the acknowledgements:
“~~The last author~~ H. Cheng would like to thank the Netherlands eScience Center for the funding provided under grant number NLESC.OEC.2021.032.”

I've updated the paper.md accordingly, is it possible to update the published paper?
Thanks!

Kevin-Mattheus-Moerman · 2024-05-08T13:03:25Z

@editorialbot generate pdf

editorialbot · 2024-05-08T13:04:54Z

⚠️ An error happened when generating the pdf.

Kevin-Mattheus-Moerman · 2024-05-08T13:09:06Z

@openjournals/dev not sure what to make of this error? Could you advise and perhaps process the re-accept? Thanks!

Kevin-Mattheus-Moerman · 2024-05-08T13:27:34Z

@luisaforozco we should be able to reaccept (and fix that acknowledgement) once the paper compilation is working. As this one is accepted it is not on our radar as clearly as the "in process" papers, so do ping me if this doesn't get resolved shortly.

xuanxu · 2024-05-08T13:28:21Z

The draft generation fails because the paper has already been accepted. You can run the reaccept command directly.

Kevin-Mattheus-Moerman · 2024-05-08T18:52:13Z

@editorialbot reaccept

editorialbot · 2024-05-08T18:52:14Z

Rebuilding paper!

editorialbot · 2024-05-08T18:54:02Z

🌈 Paper updated!

New PDF and metadata files 👉 openjournals/joss-papers#5331

editorialbot added Jupyter Notebook Python review TeX Track: 2 (BCM) Biomedical Engineering, Biosciences, Chemistry, and Materials labels Feb 8, 2024

editorialbot assigned diehlpk Feb 8, 2024

editorialbot mentioned this issue Feb 8, 2024

[PRE REVIEW]: GrainLearning: A Bayesian uncertainty quantification toolbox for discrete and continuum numerical models of granular materials #6225

Closed

gchure mentioned this issue Mar 5, 2024

JOSS Review: Paper Comments GrainLearning/grainLearning#72

Closed

editorialbot added the recommend-accept Papers recommended for acceptance in JOSS. label Apr 25, 2024

editorialbot added accepted published Papers published in JOSS labels May 2, 2024

Kevin-Mattheus-Moerman closed this as completed May 3, 2024

[REVIEW]: GrainLearning: A Bayesian uncertainty quantification toolbox for discrete and continuum numerical models of granular materials #6338

[REVIEW]: GrainLearning: A Bayesian uncertainty quantification toolbox for discrete and continuum numerical models of granular materials #6338

Comments

editorialbot commented Feb 8, 2024 • edited

Status

Reviewer instructions & questions

Checklists

editorialbot commented Feb 8, 2024

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gchure commented Feb 8, 2024 • edited

Review checklist for @gchure

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

georgiastuart commented Feb 8, 2024 • edited

Review checklist for @georgiastuart

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

gchure commented Feb 15, 2024

georgiastuart commented Feb 23, 2024

diehlpk commented Feb 29, 2024

gchure commented Feb 29, 2024

diehlpk commented Mar 1, 2024

gchure commented Mar 15, 2024

luisaforozco commented Mar 15, 2024

diehlpk commented Mar 15, 2024 • edited

diehlpk commented Mar 18, 2024

gchure commented Mar 19, 2024

diehlpk commented Mar 21, 2024

Haipeng-ustc commented Mar 22, 2024

editorialbot commented Mar 22, 2024

diehlpk commented Mar 25, 2024

diehlpk commented Mar 28, 2024

diehlpk commented Apr 25, 2024

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diehlpk commented Apr 25, 2024

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Kevin-Mattheus-Moerman commented May 1, 2024 • edited

luisaforozco commented May 2, 2024

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luisaforozco commented May 8, 2024

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Kevin-Mattheus-Moerman commented May 8, 2024

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xuanxu commented May 8, 2024

Kevin-Mattheus-Moerman commented May 8, 2024

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editorialbot commented Feb 8, 2024 •

edited

gchure commented Feb 8, 2024 •

edited

georgiastuart commented Feb 8, 2024 •

edited

diehlpk commented Mar 15, 2024 •

edited

Kevin-Mattheus-Moerman commented May 1, 2024 •

edited