[REVIEW]: Adaptive numerical simulations with Trixi.jl: A case study of Julia for scientific computing

whedon commented 3 years ago

Submitting author: !--author-handle-->@ranocha@carstenbauer<!--end-editor-- Reviewers: @johnfgibson, @simonbyrne Archive:

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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

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

Make sure you're logged in to your GitHub account
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 @carstenbauer 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 ✨

Review checklist for @johnfgibson

Conflict of interest

[x] As the reviewer I confirm that I have read the JuliaCon conflict of interest policy and that there are no conflicts of interest for me to review this work.

Code of Conduct

[x] I confirm that I read and will adhere to the JuliaCon code of conduct.

General checks

[x] Repository: Is the source code for this software available at the repository url?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] Authorship: Has the submitting author (@ranocha) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

Functionality

[x] Installation: Does installation proceed as outlined in the documentation?
[x] 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

[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
[x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
[x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
[x] Automated tests: Are there automated tests or manual steps described so that the function of the software can be verified?
[x] 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

Paper format

[x] Authors: Does the paper.tex file include a list of authors with their affiliations?
[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?
[ ] Page limit: Is the page limit for full papers respected by the submitted document?

Content

[x] Context: is the scientific context motivating the work correctly presented?
[x] Methodology: is the approach taken in the work justified, presented with enough details and reference to reproduce it?
[x] Results: are the results presented and compared to approaches with similar goals?

Review checklist for @simonbyrne

Conflict of interest
[x] As the reviewer I confirm that I have read the JuliaCon conflict of interest policy and that there are no conflicts of interest for me to review this work.

Code of Conduct

[x] I confirm that I read and will adhere to the JuliaCon code of conduct.

General checks

[x] Repository: Is the source code for this software available at the repository url?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] Authorship: Has the submitting author (@ranocha) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

Functionality

[x] Installation: Does installation proceed as outlined in the documentation?
[x] Functionality: Have the functional claims of the software been confirmed?
[x] 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

[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
[x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
[x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
[x] Automated tests: Are there automated tests or manual steps described so that the function of the software can be verified?
[x] 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

Paper format

[x] Authors: Does the paper.tex file include a list of authors with their affiliations?
[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?
[x] Page limit: Is the page limit for full papers respected by the submitted document?

Content

[x] Context: is the scientific context motivating the work correctly presented?
[x] Methodology: is the approach taken in the work justified, presented with enough details and reference to reproduce it?
[x] Results: are the results presented and compared to approaches with similar goals?

whedon commented 2 years ago

Attempting PDF compilation from custom branch hr/convince_whedon. Reticulating splines etc...

whedon commented 2 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

ranocha commented 2 years ago

@whedon generate pdf from branch hr/convince_whedon

whedon commented 2 years ago

Attempting PDF compilation from custom branch hr/convince_whedon. Reticulating splines etc...

whedon commented 2 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

ranocha commented 2 years ago

@whedon generate pdf from branch hr/convince_whedon

whedon commented 2 years ago

Attempting PDF compilation from custom branch hr/convince_whedon. Reticulating splines etc...

whedon commented 2 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

ranocha commented 2 years ago

@whedon generate pdf from branch hr/convince_whedon

whedon commented 2 years ago

Attempting PDF compilation from custom branch hr/convince_whedon. Reticulating splines etc...

whedon commented 2 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

ranocha commented 2 years ago

@whedon generate pdf from branch hr/convince_whedon

whedon commented 2 years ago

Attempting PDF compilation from custom branch hr/convince_whedon. Reticulating splines etc...

whedon commented 2 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

ranocha commented 2 years ago

@whedon generate pdf from branch hr/convince_whedon

whedon commented 2 years ago

Attempting PDF compilation from custom branch hr/convince_whedon. Reticulating splines etc...

whedon commented 2 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

ranocha commented 2 years ago

@whedon generate pdf from branch hr/convince_whedon

whedon commented 2 years ago

Attempting PDF compilation from custom branch hr/convince_whedon. Reticulating splines etc...

whedon commented 2 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

ranocha commented 2 years ago

@whedon generate pdf from branch hr/convince_whedon

whedon commented 2 years ago

Attempting PDF compilation from custom branch hr/convince_whedon. Reticulating splines etc...

whedon commented 2 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

ranocha commented 2 years ago

@whedon generate pdf from branch hr/convince_whedon

whedon commented 2 years ago

Attempting PDF compilation from custom branch hr/convince_whedon. Reticulating splines etc...

whedon commented 2 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

ranocha commented 2 years ago

@whedon generate pdf from branch hr/convince_whedon

whedon commented 2 years ago

Attempting PDF compilation from custom branch hr/convince_whedon. Reticulating splines etc...

whedon commented 2 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

ranocha commented 2 years ago

@whedon generate pdf from branch hr/convince_whedon

whedon commented 2 years ago

Attempting PDF compilation from custom branch hr/convince_whedon. Reticulating splines etc...

whedon commented 2 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

ranocha commented 2 years ago

@whedon generate pdf from branch hr/convince_whedon

whedon commented 2 years ago

Attempting PDF compilation from custom branch hr/convince_whedon. Reticulating splines etc...

whedon commented 2 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

ranocha commented 2 years ago

@whedon generate pdf from branch hr/convince_whedon

whedon commented 2 years ago

Attempting PDF compilation from custom branch hr/convince_whedon. Reticulating splines etc...

whedon commented 2 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

ranocha commented 2 years ago

@whedon generate pdf from branch hr/convince_whedon

whedon commented 2 years ago

Attempting PDF compilation from custom branch hr/convince_whedon. Reticulating splines etc...

whedon commented 2 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

ranocha commented 2 years ago

@whedon generate pdf

whedon commented 2 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

ranocha commented 2 years ago

After two hours of annoying debugging, I found and fixed the issue: The old LaTeX installation of whedon has a bug in the subcaption package/setup. The labels of subfigures are too big by default, even bigger than the main captions of figures. See https://github.com/trixi-framework/paper-2021-juliacon/pull/25 for details.

@carstenbauer The current draft complies with the page limit (10 pages). Is there anything else we should do?

carstenbauer commented 2 years ago

Glad that you could fix the issue!

Is there anything else we should do?

No, looks good to me! Will try to publish it soon! 🎊 🙂

carstenbauer commented 2 years ago

@whedon check references

whedon commented 2 years ago

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

OK DOIs

- 10.5281/zenodo.5201484 is OK
- 10.1016/j.jcp.2021.110467 is OK
- 10.1007/s42967-021-00148-z is OK
- 10.1137/141000671 is OK
- 10.5334/jors.151 is OK
- 10.21105/jcon.00068 is OK
- 10.21105/joss.03454 is OK
- 10.1137/15M1020575 is OK
- 10.1109/HPTCDL.2014.10 is OK
- 10.21105/joss.03053 is OK
- 10.21105/joss.02520 is OK
- 10.21105/joss.02018 is OK
- 10.1016/j.camwa.2020.05.004 is OK
- 10.1016/j.jcp.2020.109844 is OK
- 10.1137/100791634 is OK
- 10.1038/467753a is OK
- 10.1093/biostatistics/kxq028 is OK
- 10.1109/TPDS.2018.2872064 is OK
- 10.1093/mnras/stu114 is OK
- 10.1007/978-0-387-72067-8 is OK
- 10.1007/978-90-481-2261-5 is OK
- 10.1090/S0025-5718-1987-0890255-3 is OK
- 10.1137/S003614290240069X is OK
- 10.1016/j.jcp.2013.06.014 is OK
- 10.1007/s10915-017-0618-1 is OK
- 10.1016/j.jcp.2017.05.025 is OK
- 10.1016/S0021-9991(03)00168-2 is OK
- 10.1137/18M1209234 is OK
- 10.1142/9789814313193_0004 is OK
- 10.18419/opus-3895 is OK
- 10.1016/j.jcp.2018.06.027 is OK
- 10.1007/b79761 is OK
- 10.1016/j.jcp.2004.08.020 is OK
- 10.1007/978-3-030-39647-3_42 is OK
- 10.1016/j.jcp.2016.09.013 is OK
- 10.18419/opus-3788 is OK
- 10.1109/PMBS51919.2020.00008 is OK
- 10.1145/2464996.2465020 is OK
- 10.1145/2807591.2807623 is OK

MISSING DOIs

- 10.1007/s42967-021-00159-w may be a valid DOI for title: Optimized Runge-Kutta Methods with Automatic Step Size Control for Compressible Computational Fluid Dynamics

INVALID DOIs

- None

carstenbauer commented 2 years ago

@ranocha Can you check / fix the missing DOI. Should be https://doi.org/10.1007/s42967-021-00159-w as whedon reported.

ranocha commented 2 years ago

Fixed, thanks for the ping (the paper was published in the meantime, we cited only the preprint before)

ranocha commented 2 years ago

@whedon check references

JuliaCon / proceedings-review