[REVIEW]: BasicTools: a numerical simulation toolbox #5142

editorialbot · 2023-02-09T22:27:18Z

Submitting author: @fbordeu (Felipe Bordeu)
Repository: https://gitlab.com/drti/basic-tools
Branch with paper.md (empty if default branch):
Version: v1.9.5
Editor: @diehlpk
Reviewers: @hvonwah, @sthavishtha
Archive: 10.5281/zenodo.8073764

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/69864cb5a80d1722f37e29b9335dc441"><img src="https://joss.theoj.org/papers/69864cb5a80d1722f37e29b9335dc441/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/69864cb5a80d1722f37e29b9335dc441/status.svg)](https://joss.theoj.org/papers/69864cb5a80d1722f37e29b9335dc441)

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

@hvonwah & @sthavishtha, 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 @sthavishtha

📝 Checklist for @hvonwah

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

editorialbot · 2023-02-09T22:27:20Z

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

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editorialbot · 2023-02-09T22:27:24Z

Software report:

github.com/AlDanial/cloc v 1.88  T=0.51 s (508.0 files/s, 126475.2 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                         172           9869           7759          32854
SVG                              4              3              3           5547
YAML                             8             69             79           1690
C++                             11            191            153           1186
Cython                          13            333            109           1183
C/C++ Header                    19            249            144           1100
reStructuredText                17            285            461            361
Markdown                         4            147              0            353
XML                              4             11              0            159
TeX                              1             12              0            120
JSON                             1              0              0             37
DOS Batch                        2              2              0              6
Bourne Shell                     2              0              0              4
INI                              1              0              0              3
-------------------------------------------------------------------------------
SUM:                           259          11171           8708          44603
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

editorialbot · 2023-02-09T22:27:26Z

Wordcount for paper.md is 1710

editorialbot · 2023-02-09T22:27:53Z

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

OK DOIs

- 10.1186/s40323-020-00153-6 is OK
- 10.3390/mca26010017 is OK
- 10.1051/meca/2022001 is OK
- 10.3390/fluids6100343 is OK
- 10.1007/978-3-030-92540-6_2 is OK
- 10.1515/jnum-2012-0013 is OK
- 10.11588/ans.2015.100.20553 is OK
- 10.21105/joss.01450 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot · 2023-02-09T22:28:41Z

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

sthavishtha · 2023-02-09T22:30:44Z

Review checklist for @sthavishtha

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://gitlab.com/drti/basic-tools?
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 (@fbordeu) 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?

hvonwah · 2023-02-10T09:20:56Z

Review checklist for @hvonwah

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://gitlab.com/drti/basic-tools?
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 (@fbordeu) 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?

hvonwah · 2023-02-27T10:50:09Z

https://gitlab.com/drti/basic-tools/-/issues/4

hvonwah · 2023-02-27T10:50:34Z

https://gitlab.com/drti/basic-tools/-/issues/5

diehlpk · 2023-03-09T23:10:02Z

Hi @fbordeu please have a look at the issues above.

hvonwah · 2023-03-10T08:37:22Z

https://gitlab.com/drti/basic-tools/-/issues/6

fbordeu · 2023-03-13T14:16:59Z

Hi @diehlpk we worked on the issues 4, 5, 6. Thanks for the feedback

diehlpk · 2023-03-22T01:06:25Z

Hi @hvonwah, @sthavishtha how is your review going?

hvonwah · 2023-03-22T12:38:37Z

I've reopened Issue 6 as the installation procedure still lacks details and automation in my opinion.

sthavishtha · 2023-03-22T14:47:28Z

@diehlpk thanks for asking. i will send my review comments by the end of this week.

hvonwah · 2023-03-23T13:20:16Z

Issue 7 regarding the software paper.

sthavishtha · 2023-03-27T03:04:46Z

Hi @diehlpk, my comments on the software paper are in Issue 9. Also, can you please verify comment no. 14 about the word limit?

diehlpk · 2023-03-27T14:29:33Z

@editorialbot generate pdf

editorialbot · 2023-03-27T14:31:18Z

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

sthavishtha · 2023-03-27T15:10:29Z

@editorialbot check repository

editorialbot · 2023-03-27T15:10:34Z

Software report:

github.com/AlDanial/cloc v 1.88  T=0.60 s (434.4 files/s, 107813.6 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                         172           9874           7747          32870
SVG                              4              3              3           5558
YAML                             9             81             80           1775
C/C++ Header                    19            271            146           1331
Cython                          13            333            109           1183
C++                             11            176            130           1105
reStructuredText                18            289            466            375
Markdown                         4            156              0            360
XML                              4             11              0            159
TeX                              1             12              0            120
JSON                             1              0              0             37
DOS Batch                        2              2              0              6
INI                              1              0              0              5
Bourne Shell                     2              0              0              4
-------------------------------------------------------------------------------
SUM:                           261          11208           8681          44888
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

editorialbot · 2023-03-27T15:10:36Z

Wordcount for paper.md is 1710

diehlpk · 2023-03-27T15:13:24Z

Hi @diehlpk, my comments on the software paper are in Issue 9. Also, can you please verify comment no. 14 about the word limit?

I would prefer to have the code in a file in the repo and link to the file in the paper. So the example still will work with newer versions of the code, since the code might change over time.

editorialbot · 2023-06-23T14:04:29Z

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

diehlpk · 2023-06-23T14:06:23Z

@editorialbot recommend-accept

editorialbot · 2023-06-23T14:06:24Z

Attempting dry run of processing paper acceptance...

editorialbot · 2023-06-23T14:06:31Z

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

OK DOIs

- 10.1186/s40323-020-00153-6 is OK
- 10.3390/mca26010017 is OK
- 10.1051/meca/2022001 is OK
- 10.3390/fluids6100343 is OK
- 10.1007/978-3-030-92540-6_2 is OK
- 10.1002/nme.2579 is OK
- 10.1016/S0045-7825(01)00236-5 is OK
- 10.1515/jnum-2012-0013 is OK
- 10.11588/ans.2015.100.20553 is OK
- 10.21105/joss.01450 is OK

MISSING DOIs

- None

INVALID DOIs

- None

diehlpk · 2023-06-23T14:07:06Z

@hvonwah, @sthavishtha thanks for your reviews, we could not run JOSS without you.

editorialbot · 2023-06-23T14:08:36Z

👋 @openjournals/csism-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#4338, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

danielskatz · 2023-06-23T14:52:22Z

👋 @fbordeu - I'm the track editor who will handle the rest of the processing. While proofreading the paper, I found some issues and have suggested some changes as a PR: https://gitlab.com/drti/basic-tools/-/merge_requests/13

Please merge this, or let me know what you disagree with, then we can continue the acceptance and publication process.

fbordeu · 2023-06-23T17:07:38Z

@danielskatz thanks for reading the paper. I agree with most of the changes. merging this means I have to tag a new version of the full code, do a new release and upload to zenodo with a new DOI? Or just the merge is enough so the paper alone is updated??

danielskatz · 2023-06-23T17:09:09Z

We don't need the archived repo to contain the final paper source, as the paper will be archived as part of the publication process. So the merge alone is enough, as that will enable me to generate the next version (hopefully the final one)

fbordeu · 2023-06-23T17:10:11Z

perfect

fbordeu · 2023-06-23T17:10:52Z

merge done

danielskatz · 2023-06-23T17:19:14Z

@editorialbot recommend-accept

I'll check this in the next few hours and then proceed

editorialbot · 2023-06-23T17:19:16Z

Attempting dry run of processing paper acceptance...

editorialbot · 2023-06-23T17:19:32Z

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

OK DOIs

- 10.1186/s40323-020-00153-6 is OK
- 10.3390/mca26010017 is OK
- 10.1051/meca/2022001 is OK
- 10.3390/fluids6100343 is OK
- 10.1007/978-3-030-92540-6_2 is OK
- 10.1002/nme.2579 is OK
- 10.1016/S0045-7825(01)00236-5 is OK
- 10.1515/jnum-2012-0013 is OK
- 10.11588/ans.2015.100.20553 is OK
- 10.21105/joss.01450 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot · 2023-06-23T17:21:17Z

👋 @openjournals/csism-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#4339, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

danielskatz · 2023-06-23T17:50:18Z

@editorialbot accept

editorialbot · 2023-06-23T17:50:20Z

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

editorialbot · 2023-06-23T17:52:08Z

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: Bordeu
  given-names: Felipe
  orcid: "https://orcid.org/0000-0002-0640-5485"
- family-names: Casenave
  given-names: Fabien
  orcid: "https://orcid.org/0000-0002-8810-9128"
- family-names: Cortial
  given-names: Julien
  orcid: "https://orcid.org/0000-0002-7181-9561"
contact:
- family-names: Bordeu
  given-names: Felipe
  orcid: "https://orcid.org/0000-0002-0640-5485"
doi: 10.5281/zenodo.8073764
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Bordeu
    given-names: Felipe
    orcid: "https://orcid.org/0000-0002-0640-5485"
  - family-names: Casenave
    given-names: Fabien
    orcid: "https://orcid.org/0000-0002-8810-9128"
  - family-names: Cortial
    given-names: Julien
    orcid: "https://orcid.org/0000-0002-7181-9561"
  date-published: 2023-06-23
  doi: 10.21105/joss.05142
  issn: 2475-9066
  issue: 86
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 5142
  title: "BasicTools: a numerical simulation toolbox"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.05142"
  volume: 8
title: "BasicTools: a numerical simulation toolbox"

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 · 2023-06-23T17:52:14Z

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

editorialbot · 2023-06-23T17:52:15Z

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

editorialbot · 2023-06-23T17:52:15Z

🚨🚨🚨 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.05142 joss-papers#4340
Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.05142
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

danielskatz · 2023-06-23T18:14:51Z

Congratulations to @fbordeu (Felipe Bordeu) and co-authors on your publication!!

And thanks to @hvonwah and @sthavishtha for reviewing, and to @diehlpk for editing!
We rely on volunteers and really appreciate your help in making this possible

editorialbot · 2023-06-23T18:14:53Z

🎉🎉🎉 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:
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HTML:
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  <img src="https://joss.theoj.org/papers/10.21105/joss.05142/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.05142/status.svg
   :target: https://doi.org/10.21105/joss.05142

This is how it will look in your documentation:

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fbordeu · 2023-06-24T06:15:46Z

@danielskatz thanks for the good news!! thanks to the reviewers @sthavishtha and especially @hvonwah for the work done. It took some time to do the full review but the quality of the paper and de software documentation was significantly increased. I think the work done will make an appreciable impact to the visibility of BasicTools. Finally thanks @diehlpk for all the support and keeping this issue alive.

editorialbot added Batchfile C++ Python review Track: 7 (CSISM) Computer science, Information Science, and Mathematics labels Feb 9, 2023

editorialbot assigned diehlpk Feb 9, 2023

editorialbot mentioned this issue Feb 9, 2023

[PRE REVIEW]: BasicTools: a numerical simulation toolbox #5134

Closed

editorialbot added the recommend-accept Papers recommended for acceptance in JOSS. label Jun 23, 2023

editorialbot added accepted published Papers published in JOSS labels Jun 23, 2023

danielskatz closed this as completed Jun 23, 2023

editorialbot mentioned this issue Aug 21, 2024

[PRE REVIEW]: GridapSolvers.jl: Scalable multiphysics finite element solvers in Julia #7126

Closed

editorialbot mentioned this issue Sep 27, 2024

[PRE REVIEW]: pyMechT: A Python package for mechanics of soft tissues #7295

Open

[REVIEW]: BasicTools: a numerical simulation toolbox #5142

[REVIEW]: BasicTools: a numerical simulation toolbox #5142

Comments

editorialbot commented Feb 9, 2023 • edited Loading

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Reviewer instructions & questions

Checklists

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sthavishtha commented Feb 9, 2023 • edited Loading

Review checklist for @sthavishtha

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

hvonwah commented Feb 10, 2023 • edited Loading

Review checklist for @hvonwah

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

hvonwah commented Feb 27, 2023

hvonwah commented Feb 27, 2023

diehlpk commented Mar 9, 2023

hvonwah commented Mar 10, 2023

fbordeu commented Mar 13, 2023

diehlpk commented Mar 22, 2023

hvonwah commented Mar 22, 2023 • edited Loading

sthavishtha commented Mar 22, 2023

hvonwah commented Mar 23, 2023

sthavishtha commented Mar 27, 2023

diehlpk commented Mar 27, 2023

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danielskatz commented Jun 23, 2023

fbordeu commented Jun 23, 2023

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fbordeu commented Jun 24, 2023

editorialbot commented Feb 9, 2023 •

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