[REVIEW]: eigentools: A Python package for studying differential eigenvalue problems with an emphasis on robustness

whedon commented 3 years ago

Submitting author: @jsoishi (Jeffrey S. Oishi) Repository: https://github.com/DedalusProject/eigentools Version: 2.2106 Editor: @dpsanders Reviewer: @ketch, @caropen Archive: 10.5281/zenodo.4968601

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Markdown: [![status](https://joss.theoj.org/papers/c7fac08ba47b750d49799a2aac4e80a6/status.svg)](https://joss.theoj.org/papers/c7fac08ba47b750d49799a2aac4e80a6)

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

@ketch & @caropen, 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 @dpsanders 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 @ketch

Conflict of interest

[x] 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

[x] I confirm that I read and will adhere to the JOSS 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] Contribution and authorship: Has the submitting author (@jsoishi) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

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: 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?
[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 functionality 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

Software paper

[x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[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] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] 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 @caropen

Conflict of interest

[x] 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

[x] I confirm that I read and will adhere to the JOSS 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] Contribution and authorship: Has the submitting author (@jsoishi) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

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: 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?
[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 functionality 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

Software paper

[x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[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] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] 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 commented 3 years ago

https://zenodo.org/record/4968601#.YMpIOJpKirQ doesn't look like an archive DOI.

dpsanders commented 3 years ago

@whedon set https://doi.org/10.5281/zenodo.4968601 as archive

whedon commented 3 years ago

OK. 10.5281/zenodo.4968601 is the archive.

dpsanders commented 3 years ago

@whedon recommend-accept

whedon commented 3 years ago

Attempting dry run of processing paper acceptance...

whedon commented 3 years ago

PDF failed to compile for issue #3079 with the following error:

 Can't find any papers to compile :-(

dpsanders commented 3 years ago

@whedon generate pdf from branch joss_paper

whedon commented 3 years ago

Attempting PDF compilation from custom branch joss_paper. Reticulating splines etc...

whedon commented 3 years ago

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

dpsanders commented 3 years ago

@whedon recommend-accept

whedon commented 3 years ago

Attempting dry run of processing paper acceptance...

whedon commented 3 years ago

PDF failed to compile for issue #3079 with the following error:

 Can't find any papers to compile :-(

dpsanders commented 3 years ago

@whedon recommend-accept from branch joss_paper

whedon commented 3 years ago

Attempting dry run of processing paper acceptance...

whedon commented 3 years ago

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

OK DOIs

- 10.1126/science.261.5121.578 is OK
- 10.1137/0153002 is OK
- 10.1103/PhysRevResearch.2.023068 is OK
- 10.3847/1538-4357/aa6ff6 is OK
- 10.3847/1538-4357/aa6ff1 is OK
- 10.1137/15M1055012 is OK
- 10.1063/1.4934378 is OK
- 10.1103/PhysRevFluids.2.083501 is OK
- 10.3847/1538-4357/aaff61 is OK
- 10.1098/rspa.2019.0622 is OK

MISSING DOIs

- 10.3847/1538-4357/abcd9b may be a valid DOI for title: Stratified and vertically-shearing streaming instabilities in protoplanetary disks

INVALID DOIs

- https://doi.org/10.1016/j.aop.2015.02.031 is INVALID because of 'https://doi.org/' prefix

whedon commented 3 years ago

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

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/2399

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/2399, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true from branch joss_paper

dpsanders commented 3 years ago

@jsoishi: Could you please check the issues with the DOIs signalled above. Thanks!

jsoishi commented 3 years ago

@dpsanders I've done so. Thanks

On Sun, Jun 20, 2021 at 7:45 PM David P. Sanders @.***> wrote:

@jsoishi https://github.com/jsoishi: Could you please check the issues with the DOIs signalled above. Thanks!

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/3079#issuecomment-864629766, or unsubscribe https://github.com/notifications/unsubscribe-auth/AA7SHYOJFO5MNULAR2OPAMTTTZ4SJANCNFSM4YPGFCIQ .

kyleniemeyer commented 3 years ago

@whedon generate pdf from branch joss_paper

whedon commented 3 years ago

Attempting PDF compilation from custom branch joss_paper. Reticulating splines etc...

whedon commented 3 years ago

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

kyleniemeyer commented 3 years ago

Hi @jsoishi, I'm doing some final checks before publishing. Thanks for fixing those DOI issues. I still see one minor issue with the Lin reference: the journal name is missing. Can you please add that? Otherwise, this looks good to go.

jsoishi commented 3 years ago

Hi @kyleniemeyer, thanks for catching that. I've pushed to the joss_paper branch with a fix for that just now.

kyleniemeyer commented 3 years ago

@whedon generate pdf from branch joss_paper

whedon commented 3 years ago

Attempting PDF compilation from custom branch joss_paper. Reticulating splines etc...

whedon commented 3 years ago

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

kyleniemeyer commented 3 years ago

@whedon accept deposit=true from branch joss_paper

whedon commented 3 years ago

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

whedon commented 3 years ago

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

whedon commented 3 years ago

🚨🚨🚨 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 :point_right: https://github.com/openjournals/joss-papers/pull/2409
Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.03079
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

kyleniemeyer commented 3 years ago

Congratulations @jsoishi on your article's publication in JOSS!

Many thanks to @ketch and @caropen for reviewing this, and @dpsanders for editing.

whedon commented 3 years ago

:tada::tada::tada: Congratulations on your paper acceptance! :tada::tada::tada:

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.03079/status.svg)](https://doi.org/10.21105/joss.03079)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.03079">
  <img src="https://joss.theoj.org/papers/10.21105/joss.03079/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.03079/status.svg
   :target: https://doi.org/10.21105/joss.03079

This is how it will look in your documentation:

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dpsanders commented 3 years ago

Congratulations on the paper, @jsoishi! Many thanks to @ketch and @caropen for your reviews, and to @kyleniemeyer for editorial help.

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