[REVIEW]: scikit-fem: A Python package for finite element assembly

[whedon]

Submitting author: @kinnala (Tom Gustafsson)
Repository: https://github.com/kinnala/scikit-fem
Version: 2.0.0
Editor: @meg-simula
Reviewer: @thelfer, @AnjaliSandip
Archive: 10.5281/zenodo.3994106

⚠️ JOSS reduced service mode ⚠️

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Status

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Markdown: [![status](https://joss.theoj.org/papers/4120aba1525403e6d0972f4270d7b61e/status.svg)](https://joss.theoj.org/papers/4120aba1525403e6d0972f4270d7b61e)

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

@thelfer & @AnjaliSandip, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

1. Make sure you're logged in to your GitHub account
2. Be sure to accept the invite at this URL: https://github.com/openjournals/joss-reviews/invitations

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @meg-simula know.

✨ Please try and complete your review in the next six weeks ✨

Review checklist for @thelfer

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 repository url?
• 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 (@kinnala) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

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: Do the authors clearly state 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?

Review checklist for @AnjaliSandip

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 repository url?
• 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 (@kinnala) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

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: Do the authors clearly state 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?

[whedon]

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @thelfer, @AnjaliSandip it looks like you're currently assigned to review this paper 🎉.

⚠️ JOSS reduced service mode ⚠️

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

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[whedon]

Reference check summary:

OK DOIs

- 10.5281/zenodo.1173115 is OK
- 10.11588/ans.2015.100.20553 is OK
- 10.1145/2998441 is OK
- 10.1007/s10444-019-09666-0 is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.1149/osf.io/67ckj is OK
- 10.21914/anziamj.v60i0.14058 is OK
- 10.4171/PM/2016 is OK
- 10.1137/19M1246869 is OK
- 10.5281/zenodo.3862391 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

👉 Check article proof 📄 👈

[AnjaliSandip]

Hello,

This is my first time reviewing for JOSS. In regards to the checklist, do I select the boxes (if the paper meets that criterion) in the checklist under my name listed in this thread?

Thanks for any information you can provide.

Anjali

[danielskatz]

Yes, that's correct. If you have any problem doing so, be sure you have accepted the invite at this URL: https://github.com/openjournals/joss-reviews/invitations

[AnjaliSandip]

Thanks for letting me know!

…

On Sun, Jun 21, 2020 at 11:56 AM Daniel S. Katz ***@***.***> wrote: Yes, that's correct. If you have any problem doing so, be sure you have accepted the invite at this URL: https://github.com/openjournals/joss-reviews/invitations — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#2369 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AOQK52FAAHO535MKGIVKCFDRXY3STANCNFSM4ODA2YQA> .

[AnjaliSandip]

I have completed the review. I have a few comments on the unchecked boxes, do I post it in this thread or elsewhere?

[kinnala]

From above:

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.

Feel free to use our issue tracker if you feel it's appropriate.

[AnjaliSandip]

I have posted the comments here: kinnala/scikit-fem#422

[thelfer]

@meg-simula Sorry for the time I spent on the review.

@kinnala I posted some comments and general remarks on the paper here: kinnala/scikit-fem#426.

[meg-simula]

@thelfer @kinnala Just checking in here - could you update us on the status of the review and response to the reviewers' comments?

[meg-simula]

/ooo July 28 until August 10

[ooo]

👍 Marked @meg-simula as OOO from Tuesday, July 28th 2020 to Monday, August 10th 2020. 📆

[kinnala]

I have implemented a majority of the requested changes to the project README and other documentation; with the most significant effort being the introduction of a gallery of examples (https://scikit-fem.readthedocs.io/en/latest/listofexamples.html).

Next I'll focus on improving the paper itself which consist mainly of adding references and extending the discussion on the limits of the code's features. I hope to finish my work on the improvements by the end of the next week at the latest.

[meg-simula]

Ok, thanks for the update!

…

On Tue, 28 Jul 2020 at 16:32, Tom Gustafsson ***@***.***> wrote: I have implemented a majority of the requested changes to the project README and other documentation; with the most significant effort being the introduction of a gallery of examples ( https://scikit-fem.readthedocs.io/en/latest/listofexamples.html). Next I'll focus on improving the paper itself which consist mainly of adding references and extending the discussion on the limits of the code's features. I hope to finish my work on the improvements by the end of the next week at the latest. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#2369 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAFPESRELXC4BUVFQ3EVHY3R53OO5ANCNFSM4ODA2YQA> .

[thelfer]

Waiting for @kinnala updates. Seems well underway

[kinnala]

@whedon generate pdf

[whedon]

👉 Check article proof 📄 👈

[kinnala]

@whedon generate pdf

[whedon]

👉 Check article proof 📄 👈

[kinnala]

We thank both reviewers for their valuable feedback. The submission has been now updated based on the feedback. Below are specific answers to the comments; hopefully we were able to address everything.

Answers to @AnjaliSandip

For someone who does not have a background in finite elements, they may not understand what basis functions or weak formulation means.

We added a reference to the FEniCS book which explains these concepts very well.

The performance claim in vague: “Despite being fully interpreted, the code has a reasonably good performance.” If the author could be more specific (quantifiable), it would help the reviewer in making a judgement.

We added a benchmark to the README just below the given quote. The benchmark compares time spent on assembly and on linear solve.

Answers to @thelfer

In the paper we added a paragraph discussing the various points mentioned by @thelfer (nonuniform coefficients, boundary conditions, nonlinear problems, fields at quadrature points, parallel computing, and so on).

The library do provide a way to handle Dirichlet boundary conditions by elimination. This shall be at least mentioned

Done.

For example, is the mesh connectivity clearly described (how the unknowns are numbered)?

Mesh connectivity is now covered in the package documentation:
https://scikit-fem.readthedocs.io/en/latest/bcs.html

The authors shall describe how the library could be used in non linear cases.

It is now mentioned in the paper that nonlinear iterations should be implemented by the user and that we provide tools and examples for doing that.

Can non uniform coefficients be handled ?

Yes. It is now mentioned also in the paper.

The authors claims that the assembly, while made in pure python, is "fast enough" ? This shall be made more explicit. Do the authors mean that the assembly takes a negligible time compared to the resolution of the resulting linear system ?

There is now a performance benchmark in the beginning of the README which hopefully clarifies this.

The authors claims that more than 30 examples illustrate the use of the library. I did not find any page that summarises those examples.

We added a page to the documentation which summarizes the examples: https://scikit-fem.readthedocs.io/en/latest/listofexamples.html

With which package have the figures been generated ?

Modified the caption to include this information.

The description of the second example is very sparse.

Added the governing equation and clarified the meaning of the figure colors in the caption.p

Some examples depends on external packages which are not installed with scikit-fem. An appropriate list of dependencies would be appreciated.

README has now has instructions on installing the test dependencies that allow running all examples.

UFL offers functional spaces at quadrature points. This functional spaces are relevant when dealing with non linear constitutive equations in solid mechanics. Is there anything similar in scikit-fem ?

We support assembling weak forms with arbitrary fields/values at the quadrature points. This is now mentioned in the paper also.

Would it work in MPI-like processes ? Do you plan any extension of the package in that matter or is it out of its scope ?

Paper now clarifies our thinking on the distributed computing. While it's out of scope for scikit-fem, we can see it used as a building block in some kind of specific parallel computations.

[thelfer]

@meg-simula, @kinnala I am quite satisfied by those answers. I think I can finish the review by the end of the week.

[ooo]

👋 Hey @thelfer...

Letting you know, @meg-simula is currently OOO until Monday, August 10th 2020. ❤️

[AnjaliSandip]

The feedback provided by the author to my question was sufficient.

…

On Sun, Aug 2, 2020 at 12:45 AM ooo[bot] ***@***.***> wrote: 👋 Hey @thelfer <https://github.com/thelfer>... Letting you know, @meg-simula is currently OOO until Monday, August 10th 2020 <#2313 (comment)>. ❤️ — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#2369 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AOQK52FNOJPYYQKWLC2JLTLR6T4OPANCNFSM4ODA2YQA> .

[meg-simula]

@kinnala This looks very nice, well done.

• Two very minor grammatical comments: please replace (i) "FEM" by "the FEM" in the second paragraph and (ii) "examples on" by "examples by" at the top of page 2.

Next, could you please:

• Make a tagged release of your software, and list the version tag of the archived version here.
• Archive the reviewed software in Zenodo or a similar service (e.g., figshare, an institutional repository)
• Check the archival deposit (e.g., in Zenodo) has the correct metadata. This includes the title (should match the paper title) and author list (make sure the list is correct and people who only made a small fix are not on it). You may also add the authors' ORCID.
• Please list the DOI of the archived version here.

I can then move forward with accepting the submission.

[kinnala]

@whedon generate pdf

[whedon]

👉 Check article proof 📄 👈

[kinnala]

Thanks @meg-simula . Hopefully I did the fixes correctly.

The tagged release happens to be 2.0.0. The major version increment does not signify other than that we happened to remove some (undocumented) features deprecated already 6 months ago while waiting for the review to finish, and hence semantic versioning mandates such an increment.

Here is the Zenodo archive: https://zenodo.org/record/3994106#.Xz-AhHX7Tb1

The corresponding DOI is: 10.5281/zenodo.3994106

Edit: In case you are wondering what the backwards-incompatible changes are, here is the related commit: kinnala/scikit-fem@5d07cad Simply put, we had an alternative syntax for defining the forms since 0.1.0 that we deprecated in 1.0.0 and now removed completely in 2.0.0. This syntax has not been used in the documentation since 1.0.0 so it does not concern this review.

[meg-simula]

@whedon set 10.5281/zenodo.3994106 as archive

[whedon]

OK. 10.5281/zenodo.3994106 is the archive.

[meg-simula]

@whedon set 2.0.0 as version

[whedon]

OK. 2.0.0 is the version.

[meg-simula]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

Reference check summary:

OK DOIs

- 10.5281/zenodo.1173115 is OK
- 10.1007/978-3-642-23099-8 is OK
- 10.11588/ans.2015.100.20553 is OK
- 10.1145/2998441 is OK
- 10.1007/s10444-019-09666-0 is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.1149/osf.io/67ckj is OK
- 10.21914/anziamj.v60i0.14058 is OK
- 10.4171/PM/2016 is OK
- 10.1137/19M1246869 is OK
- 10.5281/zenodo.3862391 is OK
- 10.1016/B978-012387582-2/50038-1 is OK
- 10.1109/MCSE.2007.55 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

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

Check final proof 👉 openjournals/joss-papers#1654

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#1654, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

[arfon]

@whedon accept deposit=true

[whedon]

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

[whedon]

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

[whedon]

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

Here's what you must now do:

0. Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.02369 joss-papers#1658
1. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.02369
2. If everything looks good, then close this review issue.
3. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

[arfon]

@thelfer, @AnjaliSandip - many thanks for your reviews here and to @meg-simula for editing this submission ✨

@kinnala - your paper is now accepted into JOSS ⚡🚀💥

Finally, it seems like Crossref is having some issues today and the DOI registrations aren't working right now. When https://doi.org/10.21105/joss.02369 starts resolving I will close this issue.

[whedon]

🎉🎉🎉 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.02369/status.svg)](https://doi.org/10.21105/joss.02369)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.02369">
  <img src="https://joss.theoj.org/papers/10.21105/joss.02369/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.02369/status.svg
   :target: https://doi.org/10.21105/joss.02369

This is how it will look in your documentation:

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