[REVIEW]: Mechkit: A continuum mechanics toolkit in Python #4389

editorialbot · 2022-05-11T19:39:24Z

Submitting author: @JulianKarlBauer (Julian Karl Bauer)
Repository: https://github.com/JulianKarlBauer/mechkit
Branch with paper.md (empty if default branch): paper
Version: v0.4.0
Editor: @Kevin-Mattheus-Moerman
Reviewers: @nicoguaro, @likask, @lizarett
Archive: 10.5281/zenodo.7185691

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/5bc306fb511a596eb25e2032a39b4baa/status.svg)](https://joss.theoj.org/papers/5bc306fb511a596eb25e2032a39b4baa)

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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

@nicoguaro & @likask & @lizarett, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review.
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✨ 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 @nicoguaro

📝 Checklist for @likask

📝 Checklist for @lizarett

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

editorialbot · 2022-05-11T19:39:25Z

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 · 2022-05-11T19:39:26Z

Software report:

github.com/AlDanial/cloc v 1.88  T=0.09 s (770.0 files/s, 148370.7 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
SVG                              3              3              3           3679
Python                          24           1021           1385           2969
YAML                             6             22             10            460
TeX                              3             42             19            457
Markdown                         9             67              0            235
make                             2             35             13            188
Jupyter Notebook                 6              0           1683            179
reStructuredText                13             74            121             52
-------------------------------------------------------------------------------
SUM:                            66           1264           3234           8219
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

editorialbot · 2022-05-11T19:39:28Z

Wordcount for paper.md is 821

editorialbot · 2022-05-11T19:39:31Z

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

OK DOIs

- 10.1177/10812865211057602 is OK
- 10.1016/0020-7225(84)90090-9 is OK
- 10.1007/978-3-319-19566-7 is OK
- 10.1007/978-1-4757-1275-9 is OK
- 10.1093/qjmam/43.1.15 is OK
- 10.1016/0022-5096(92)90029-2 is OK
- 10.1088/978-0-7503-1454-1 is OK
- 10.5281/zenodo.4679756 is OK
- 10.5281/zenodo.1173115 is OK
- 10.5281/zenodo.5938012 is OK
- 10.5281/zenodo.5564818 is OK

MISSING DOIs

- 10.1016/0020-7225(70)90024-8 may be a valid DOI for title: A note on the decomposition of tensors into traceless symmetric tensors
- 10.1122/1.549945 may be a valid DOI for title: The use of tensors to describe and predict fiber orientation in short fiber composites

INVALID DOIs

- None

editorialbot · 2022-05-11T19:40:32Z

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

Kevin-Mattheus-Moerman · 2022-05-12T08:20:36Z

@JulianKarlBauer can you check those potentially missing DOI's ☝️ ?

@editorialbot

@editorialbot in openjournals/joss-reviews#4389 (comment)

JulianKarlBauer · 2022-05-12T12:52:41Z

@editorialbot generate pdf

editorialbot · 2022-05-12T12:53:59Z

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

JulianKarlBauer · 2022-05-12T12:56:17Z

@JulianKarlBauer can you check those potentially missing DOI's point_up ?

Thank you for pointing this out! I added the missing DOIs and regenerated the pdf.

Kevin-Mattheus-Moerman · 2022-05-12T14:53:09Z

@editorialbot check references

editorialbot · 2022-05-12T14:53:12Z

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

OK DOIs

- 10.1177/10812865211057602 is OK
- 10.1016/0020-7225(84)90090-9 is OK
- 10.1007/978-3-319-19566-7 is OK
- 10.1007/978-1-4757-1275-9 is OK
- 10.1093/qjmam/43.1.15 is OK
- 10.1016/0022-5096(92)90029-2 is OK
- 10.1088/978-0-7503-1454-1 is OK
- 10.1122/1.549945 is OK
- 10.5281/zenodo.4679756 is OK
- 10.5281/zenodo.1173115 is OK
- 10.5281/zenodo.5938012 is OK
- 10.5281/zenodo.5564818 is OK

MISSING DOIs

- None

INVALID DOIs

- https://doi.org/10.1016/0020-7225(70)90024-8 is INVALID because of 'https://doi.org/' prefix

Kevin-Mattheus-Moerman · 2022-05-12T14:53:54Z

@JulianKarlBauer nearly there, note the invalid one ☝️, fyi you can also run @editorialbot check references.

@editorialbot

@editorialbot in openjournals/joss-reviews#4389 (comment)

JulianKarlBauer · 2022-05-12T15:26:23Z

@editorialbot check references

editorialbot · 2022-05-12T15:26:27Z

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

OK DOIs

- 10.1177/10812865211057602 is OK
- 10.1016/0020-7225(84)90090-9 is OK
- 10.1007/978-3-319-19566-7 is OK
- 10.1007/978-1-4757-1275-9 is OK
- 10.1093/qjmam/43.1.15 is OK
- 10.1016/0022-5096(92)90029-2 is OK
- 10.1088/978-0-7503-1454-1 is OK
- 10.1016/0020-7225(70)90024-8 is OK
- 10.1122/1.549945 is OK
- 10.5281/zenodo.4679756 is OK
- 10.5281/zenodo.1173115 is OK
- 10.5281/zenodo.5938012 is OK
- 10.5281/zenodo.5564818 is OK

MISSING DOIs

- None

INVALID DOIs

- None

Kevin-Mattheus-Moerman · 2022-05-12T15:38:47Z

@nicoguaro, @likask, @lizarett this is where the review takes place. You can each call @editorialbot generate my checklist here to create your check list. Let me know if you have any question.

nicoguaro · 2022-05-23T15:10:51Z

Review checklist for @nicoguaro

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/JulianKarlBauer/mechkit?
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 (@JulianKarlBauer) 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?

nicoguaro · 2022-05-23T17:46:13Z

I have done a first pass on the package. I have some comments:

I don't see a clear statement of need on the README or docs.
There isn't an API section on the docs. My guess is that it is already there in the different sections that appear on ReadTheDocs.
There isn't a section or file specifying how to contribute to the project.

I will resume the review after these comments have been addressed.

JulianKarlBauer · 2022-05-25T08:39:20Z

Hi @nicoguaro
thank you very much for starting your review!
Please let me address the points of concern.

* There isn't a section or file specifying how to contribute to the project.

Thank you, indeed a file CONTRIBUTING.md only had been added to the paper-branch, which had been used to create the paper draft and prepare the review. I merged the paper-branch into master and will keep both identical side by side. As I specified the paper-branch during submission to JOSS, I'll keep it alive till the end of the review.

* I don't see a clear statement of need on the README or docs.

This is true, I copied the "Statement of need" from the paper to the landing page of the docs. Personally I think that the README.md should not contain a statement of need, this is why I added it to the docs. Is this ok for you?
(see b8052796ed936d32b8ace1160bea27f5cc596458)

* There isn't an API section on the docs. My guess is that it is already there in the different sections that appear on ReadTheDocs.

I added headings to the different parts of the documentation now looking like:

Is this ok from your point of view?

Thank you again for starting the review and the valuable feedback!

Kevin-Mattheus-Moerman · 2022-05-26T08:16:24Z

@likask, @lizarett thanks for your help with this review. Can you please provide an update on progress? Thanks.

Kevin-Mattheus-Moerman · 2022-06-01T11:37:17Z

@likask, @lizarett thanks for your help with this review. Can you please provide an update on progress? Thanks.

nicoguaro · 2022-06-07T16:52:42Z

Is this ok from your point of view?

It is better. Although, I would add an API section in the left menu bar to group all the different modules.

Regarding the paper, I don't see any mention of similar packages. I do not know if there are any besides SymPy's module (not so similar) and continuum_mechanics (disclaimer, I am the author).

JulianKarlBauer · 2022-06-07T19:10:24Z

Is this ok from your point of view?

It is better. Although, I would add an API section in the left menu bar to group all the different modules.

Thanks, I'll fight with Sphinx to clean the lean toctree.

Regarding the paper, I don't see any mention of similar packages. I do not know if there are any besides SymPy's module (not so similar) and continuum_mechanics (disclaimer, I am the author).

Thank you for mentioning these packages which also refer to continuum mechanics. However, the tasks accomplished by these packages are quite varying. This is probably caused by the fact that the phrase continuum mechanics describes a high-level topic. As far as I know, no packages similar to mechkit exist. This is the reason, why I did not list others.

SymPy's module implements beam-theory and therefore should refer to "structural mechanics" instead of continuum mechanics. Continuum_mechanics is a great package for a rather specific selection of continuum mechanics topics, like mechkit. But as far as I see, no common tasks are solved.

Kevin-Mattheus-Moerman · 2022-06-08T08:13:02Z

@likask, @lizarett can you please update us on review progress? Thanks again for your help!

Kevin-Mattheus-Moerman · 2022-10-08T07:33:51Z

@JulianKarlBauer I read your paper and have two remaining very minor points:

Please add city names to all affiliations
For several ... , exist but mainly... it looks like the comma should go after exist (but feel free to disagree)

openjournals/joss-reviews#4389 (comment)

JulianKarlBauer · 2022-10-09T17:55:52Z

Please add city names to all affiliations
For several ... , exist but mainly... it looks like the comma should go after exist (but feel free to disagree)

@Kevin-Mattheus-Moerman Thank you! Fixed both.

JulianKarlBauer · 2022-10-09T17:56:03Z

@editorialbot generate pdf

editorialbot · 2022-10-09T17:57:31Z

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

Kevin-Mattheus-Moerman · 2022-10-10T12:23:17Z

@JulianKarlBauer Great, looks like we are good to proceed. At this point can you please:

Archive a copy of the reviewed work on ZENODO. We recommend that you do so for a newly minted/tagged release, however this is up to you. Some find these automated steps useful: https://docs.github.com/en/repositories/archiving-a-github-repository/referencing-and-citing-content
Once the archive is created please check if the title and the author names match those of the paper. You may need to manually edit your archive entry to change the title/author entries. You can also check if you can have it refer to the license properly (or leave it as Other(Open) since the archived content contains the license too). Next you may wish to add author ORCID information too. The most important things though are the title and author list.
Once the above is complete please report back here with the archive DOI and which version tag we should use, i.e. are we still at v0.3.9 or have you created a new release.

Thanks.

JulianKarlBauer · 2022-10-11T13:47:54Z

@Kevin-Mattheus-Moerman
Perfect, thank you for the detailed instructions.
I created release v0.4.0 with DOI https://zenodo.org/record/7185691
and manually edited the title, author, license and added a funding note.

Kevin-Mattheus-Moerman · 2022-10-11T16:30:05Z

@editorialbot set v0.4.0 as version

editorialbot · 2022-10-11T16:30:07Z

Done! version is now v0.4.0

Kevin-Mattheus-Moerman · 2022-10-11T16:30:57Z

@editorialbot set 10.5281/zenodo.7185691 as archive

editorialbot · 2022-10-11T16:30:59Z

Done! Archive is now 10.5281/zenodo.7185691

Kevin-Mattheus-Moerman · 2022-10-11T16:32:19Z

@JulianKarlBauer Looks like we are all set. 🚀

Kevin-Mattheus-Moerman · 2022-10-11T16:32:29Z

@editorialbot recommend-accept

editorialbot · 2022-10-11T16:32:31Z

Attempting dry run of processing paper acceptance...

editorialbot · 2022-10-11T16:33:43Z

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

OK DOIs

- 10.1177/10812865211057602 is OK
- 10.1016/0020-7225(84)90090-9 is OK
- 10.1007/978-3-319-19566-7 is OK
- 10.1007/978-1-4757-1275-9 is OK
- 10.1093/qjmam/43.1.15 is OK
- 10.1016/0022-5096(92)90029-2 is OK
- 10.1088/978-0-7503-1454-1 is OK
- 10.1016/0020-7225(70)90024-8 is OK
- 10.1122/1.549945 is OK
- 10.5281/zenodo.4679756 is OK
- 10.5281/zenodo.1173115 is OK
- 10.5281/zenodo.5938012 is OK
- 10.5281/zenodo.5564818 is OK
- 10.21468/SciPostPhysLectNotes.5 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot · 2022-10-11T16:34:00Z

👋 @openjournals/joss-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#3607, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

Kevin-Mattheus-Moerman · 2022-10-11T16:35:13Z

@editorialbot accept

editorialbot · 2022-10-11T16:35:15Z

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

editorialbot · 2022-10-11T16:37:11Z

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

editorialbot · 2022-10-11T16:37:12Z

🚨🚨🚨 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.04389 joss-papers#3608
Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.04389
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

kthyng · 2022-10-11T22:18:07Z

Congratulations on your new publication to @JulianKarlBauer! Many thanks to editor @Kevin-Mattheus-Moerman and reviewers @nicoguaro, @likask, and @lizarett for your time, hard work, and expertise!!

editorialbot · 2022-10-11T22:18:09Z

🎉🎉🎉 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.04389/status.svg)](https://doi.org/10.21105/joss.04389)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.04389">
  <img src="https://joss.theoj.org/papers/10.21105/joss.04389/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.04389/status.svg
   :target: https://doi.org/10.21105/joss.04389

This is how it will look in your documentation:

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JulianKarlBauer · 2022-10-12T06:58:03Z

(: thanks for the great experience of publishing in JOSS.
Thank you @Kevin-Mattheus-Moerman for your efforts in moderation!
Thanks to the reviewers @nicoguaro @likask @lizarett for your valuable suggestions and dedication and thank you @kthyng for finalizing the process.

editorialbot added Python review TeX labels May 11, 2022

editorialbot assigned Kevin-Mattheus-Moerman May 11, 2022

editorialbot mentioned this issue May 11, 2022

[PRE REVIEW]: Mechkit: A continuum mechanics toolkit in Python #4267

Closed

JulianKarlBauer added a commit to JulianKarlBauer/mechkit that referenced this issue May 12, 2022

Add missing DOIs following editorialbot

cbbffbe

@editorialbot in openjournals/joss-reviews#4389 (comment)

JulianKarlBauer added a commit to JulianKarlBauer/mechkit that referenced this issue May 12, 2022

Fix DOI, remove prefix

781da1f

@editorialbot in openjournals/joss-reviews#4389 (comment)

JulianKarlBauer added a commit to JulianKarlBauer/mechkit that referenced this issue Oct 9, 2022

Add city names in affiliation

975dbf0

openjournals/joss-reviews#4389 (comment)

JulianKarlBauer added a commit to JulianKarlBauer/mechkit that referenced this issue Oct 9, 2022

Fix comma

d75ea74

openjournals/joss-reviews#4389 (comment)

JulianKarlBauer mentioned this issue Oct 9, 2022

Paper JulianKarlBauer/mechkit#57

Merged

editorialbot added the recommend-accept Papers recommended for acceptance in JOSS. label Oct 11, 2022

editorialbot added accepted published Papers published in JOSS labels Oct 11, 2022

kthyng closed this as completed Oct 11, 2022

Kevin-Mattheus-Moerman mentioned this issue Mar 22, 2023

[PRE REVIEW]: SarcGraph: A Python package for automated segmentation, tracking and analysis of sarcomeres in hiPSC-CMs #5228

Closed

[REVIEW]: Mechkit: A continuum mechanics toolkit in Python #4389

[REVIEW]: Mechkit: A continuum mechanics toolkit in Python #4389

Comments

editorialbot commented May 11, 2022 • edited

Status

Reviewer instructions & questions

Checklists

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Kevin-Mattheus-Moerman commented May 12, 2022 • edited

JulianKarlBauer commented May 12, 2022

editorialbot commented May 12, 2022

JulianKarlBauer commented May 12, 2022

Kevin-Mattheus-Moerman commented May 12, 2022

editorialbot commented May 12, 2022

Kevin-Mattheus-Moerman commented May 12, 2022 • edited

JulianKarlBauer commented May 12, 2022

editorialbot commented May 12, 2022

Kevin-Mattheus-Moerman commented May 12, 2022

nicoguaro commented May 23, 2022 • edited

Review checklist for @nicoguaro

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

nicoguaro commented May 23, 2022

JulianKarlBauer commented May 25, 2022 • edited

Kevin-Mattheus-Moerman commented May 26, 2022

Kevin-Mattheus-Moerman commented Jun 1, 2022

nicoguaro commented Jun 7, 2022

JulianKarlBauer commented Jun 7, 2022

Kevin-Mattheus-Moerman commented Jun 8, 2022

Kevin-Mattheus-Moerman commented Oct 8, 2022 • edited

JulianKarlBauer commented Oct 9, 2022

JulianKarlBauer commented Oct 9, 2022

editorialbot commented Oct 9, 2022

Kevin-Mattheus-Moerman commented Oct 10, 2022 • edited

JulianKarlBauer commented Oct 11, 2022

Kevin-Mattheus-Moerman commented Oct 11, 2022

editorialbot commented Oct 11, 2022

Kevin-Mattheus-Moerman commented Oct 11, 2022

editorialbot commented Oct 11, 2022

Kevin-Mattheus-Moerman commented Oct 11, 2022

Kevin-Mattheus-Moerman commented Oct 11, 2022

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editorialbot commented Oct 11, 2022

Kevin-Mattheus-Moerman commented Oct 11, 2022

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kthyng commented Oct 11, 2022

editorialbot commented Oct 11, 2022

JulianKarlBauer commented Oct 12, 2022

editorialbot commented May 11, 2022 •

edited

Kevin-Mattheus-Moerman commented May 12, 2022 •

edited

Kevin-Mattheus-Moerman commented May 12, 2022 •

edited

nicoguaro commented May 23, 2022 •

edited

JulianKarlBauer commented May 25, 2022 •

edited

Kevin-Mattheus-Moerman commented Oct 8, 2022 •

edited

Kevin-Mattheus-Moerman commented Oct 10, 2022 •

edited