[REVIEW]: Flint: a simulator for biological and physiological models in ordinary and stochastic differential equations

whedon commented 4 years ago

Submitting author: @tabe (Takeshi Abe) Repository: https://github.com/flintproject/Flint Version: Flint-2.4.0RC1-JOSS Editor: @majensen Reviewers: @mstimberg, @dawbarton Archive: 10.5281/zenodo.4017040

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Status

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Markdown: [![status](https://joss.theoj.org/papers/ba63c7df89b7f27f5d8003bc42cdf5e5/status.svg)](https://joss.theoj.org/papers/ba63c7df89b7f27f5d8003bc42cdf5e5)

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

@mstimberg & @dawbarton, 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 @majensen know.

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

Review checklist for @dawbarton

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 (@tabe) 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 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 @mstimberg

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 (@tabe) 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 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?

tabe commented 4 years ago

@majensen, uploaded an archive to Zenodo: https://doi.org/10.5281/zenodo.4017040 I hope this works for you.

majensen commented 4 years ago

@whedon set Flint-2.4.0RC1-JOSS as version

whedon commented 4 years ago

OK. Flint-2.4.0RC1-JOSS is the version.

majensen commented 4 years ago

@whedon set 10.5281/zenodo.4017040 as archive

whedon commented 4 years ago

OK. 10.5281/zenodo.4017040 is the archive.

majensen commented 4 years ago

@whedon accept

whedon commented 4 years ago

Attempting dry run of processing paper acceptance...

whedon commented 4 years ago

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

OK DOIs

- 10.3389/fphys.2015.00251 is OK
- 10.14326/abe.3.50 is OK
- 10.1109/SAINT.2012.40 is OK
- 10.1016/j.pbiomolbio.2004.01.004 is OK
- 10.1093/bioinformatics/btg015 is OK
- 10.3389/fphys.2010.00164 is OK
- 10.1093/bioinformatics/btl485 is OK
- 10.1126/science.290.5495.1358 is OK
- 10.1073/pnas.0406841102 is OK
- 10.1016/j.imr.2015.12.004 is OK

MISSING DOIs

- None

INVALID DOIs

- None

whedon commented 4 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/1713

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/1713, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

danielskatz commented 4 years ago

👋 @tabe - this looks good, and I'm working on the final processing. Can you merge https://github.com/flintproject/Flint/pull/24, which has some minor changes to the paper? Also, I think the SUNDIALS TOMS paper should have 10.1145/1089014.1089020 added as the DOI.

tabe commented 4 years ago

Dear @danielskatz,

👋 @tabe - this looks good, and I'm working on the final processing. Can you merge flintproject/Flint#24, which has some minor changes to the paper?

Done.

Also, I think the SUNDIALS TOMS paper should have 10.1145/1089014.1089020 added as the DOI.

Added at https://github.com/flintproject/Flint/commit/c90b99a53b3930b1e46d570e79e3e6f3d39c9b6e.

danielskatz commented 4 years ago

@whedon generate pdf

whedon commented 4 years ago

:point_right: Check article proof :page_facing_up: :point_left:

danielskatz commented 4 years ago

@whedon accept

whedon commented 4 years ago

Attempting dry run of processing paper acceptance...

whedon commented 4 years ago

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

OK DOIs

- 10.3389/fphys.2015.00251 is OK
- 10.14326/abe.3.50 is OK
- 10.1109/SAINT.2012.40 is OK
- 10.1137/S0036144500378302 is OK
- 10.1016/j.pbiomolbio.2004.01.004 is OK
- 10.1093/bioinformatics/btg015 is OK
- 10.1145/1089014.1089020 is OK
- 10.3389/fphys.2010.00164 is OK
- 10.1093/bioinformatics/btl485 is OK
- 10.1126/science.290.5495.1358 is OK
- 10.1073/pnas.0406841102 is OK
- 10.1016/j.imr.2015.12.004 is OK

MISSING DOIs

- None

INVALID DOIs

- None

whedon commented 4 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/1717

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/1717, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

danielskatz commented 4 years ago

@whedon accept deposit=true

whedon commented 4 years ago

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

whedon commented 4 years ago

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

whedon commented 4 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/1718
Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.02331
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

danielskatz commented 4 years ago

Thanks to @mstimberg, @dawbarton for reviewing, and @majensen for editing!

And congratulations to @tabe (Takeshi Abe) and co-author!!

whedon commented 4 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.02331/status.svg)](https://doi.org/10.21105/joss.02331)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.02331">
  <img src="https://joss.theoj.org/papers/10.21105/joss.02331/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.02331/status.svg
   :target: https://doi.org/10.21105/joss.02331

This is how it will look in your documentation:

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