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[REVIEW]: Basix: a runtime finite element basis evaluation library #3982
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Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @tisaac, @wence- it looks like you're currently assigned to review this paper 🎉. 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. ⭐ Important ⭐ If you haven't already, you should seriously consider unsubscribing from GitHub notifications for this (https://github.com/openjournals/joss-reviews) repository. As a reviewer, you're probably currently watching this repository which means for GitHub's default behaviour you will receive notifications (emails) for all reviews 😿 To fix this do the following two things:
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Hi @tisaac @wence-, 👋 Welcome to JOSS and thanks for agreeing to review! The comments from @whedon above outline the review process, which takes place in this thread (possibly with issues filed in the Basix repository). I'll be watching this thread if you have any questions. The JOSS review is different from most other journals. Our goal is to work with the authors to help them meet our criteria instead of merely passing judgment on the submission. As such, the reviewers are encouraged to submit issues and pull requests on the software repository. When doing so, please mention this issue so that a link is created to this thread (and I can keep an eye on what is happening). Please also feel free to comment and ask questions on this thread. In my experience, it is better to post comments/questions/suggestions as you come across them instead of waiting until you've reviewed the entire package. We aim for reviews to be completed within a month or so. Please let me know if you require some more time. We can also use Whedon (our bot) to set automatic reminders if you know you'll be away for a known period of time. Please feel free to ping me (@jedbrown) if you have any questions/concerns. |
👋 @tisaac, please update us on how your review is going (this is an automated reminder). |
👋 @wence-, please update us on how your review is going (this is an automated reminder). |
Installation issues on first pass review
(Will update this issue with more comments as I proceed). |
@whedon generate pdf |
We fixed a few typos in the paper, so I'm re-generating it |
Slowly, but I have no commitments from close of play Friday, so next week? |
First off, many apologies to both the authors and JOSS for taking such a long time to review here. I had already taken a long time, but a break between jobs where I thought I would get this done needed to be more handsoff than I had anticipated. So I am only now getting round to cleaning the slate. That said, here are my comments on this paper/submission. From a software/documentation point of view, I have no real qualms. The two minor installation issues I mentioned above were swiftly fixed. One very minor thing is that the frontpage of the docs doesn't do quite a job at summarising the point of basix as the top of the README on the github project page. Replicating this information by hand is probably a bad idea but perhaps it can be incorporated programmatically in future docs builds (I don't think this is a sufficient issue to requiring fixing for the paper, but can open an issue to track it if that is normal policy). From the paper point of view, I think that the survey of related software is a little bit weak. I agree that most finite element libraries do not separate the element library from the rest of the software (and hence there are often not publications specifically about tabulation), however, it would be useful to provide a short summary of alternate approaches and how that in
I agree that you don't want to recreate too much from the longer arxiv paper, but I think the paper would be improved by a little bit of discussion here. One thing that I think should probably be addressed is whether there is a development track towards efficient high-order finite elements that expose structure (typically tensor-product of some kind), or if this is a direction the library intends to go at all. I see there is an open issue on the interpolation part of this. Thanks! |
I will finish my review by next Thursday, apologies for the delay |
@jedbrown Was my invitation revoked? |
Ah, you can use the new system now. Please comment with the one line command
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Review checklist for @tisaacConflict of interest
Code of Conduct
General checks
Functionality
Documentation
Software paper
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@wence- Thanks for your comments. We've made some changes to the paper, I'll rebuild it here once the CI has finished running and I've merged it.
I've made the docs builder copy this info when building the website docs (FEniCS/basix#484)
Thanks for the suggested references, this was very helpful. We've added us much information as we can about other libraries based on what they've written in papers and docs (see changes in FEniCS/basix#481).
We've added a little bit more to the paragraph on this (see changes in FEniCS/basix#481)
We've added a paragraph on this (see changes in FEniCS/basix#481) |
@whedon generate pdf |
My name is now @editorialbot |
@wence- yep! |
Wonderful! I just notice one minor copy edit.
remove second of "the" or say "Most of Basix's functionality" After making this change, could you:
I can then move forward with accepting the submission. |
@wence- and @tisaac: Thanks for reviewing this! @jedbrown. The release tag is |
@editorialbot set joss as version |
Done! version is now joss |
@editorialbot set 10.6084/m9.figshare.19794268.v1 as archive |
Done! Archive is now 10.6084/m9.figshare.19794268.v1 |
@editorialbot recommend-accept |
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Element doi: [facet 'pattern'] The value is not accepted by the pattern '10\.[0-9]{4,9}/.{1,200}'. |
Looks like one of the references in the paper has an extra set of curly braces around the DOI, which is causing an issue. FEniCS/basix#511 will hopefully fix this |
Thanks for diagnosing. |
@jedbrown Correction is merged so it should be ready for another attempt now |
@editorialbot recommend-accept |
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👋 @openjournals/joss-eics, this paper is ready to be accepted and published. Check final proof 👉 openjournals/joss-papers#3223 If the paper PDF and the deposit XML files look good in openjournals/joss-papers#3223, then you can now move forward with accepting the submission by compiling again with the command |
@editorialbot accept |
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Submitting author: @mscroggs (Matthew Scroggs)
Repository: https://github.com/FEniCS/basix
Branch with paper.md (empty if default branch):
Version: joss
Editor: @jedbrown
Reviewers: @tisaac, @wence-
Archive: 10.6084/m9.figshare.19794268.v1
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