[REVIEW]: MF2: A Collection of Multi-Fidelity Benchmark Functions in Python

[whedon]

Submitting author: @sjvrijn (Sander van Rijn)
Repository: https://github.com/sjvrijn/mf2
Version: v2020.8.0
Editor: @melissawm
Reviewers: @torressa, @zbeekman
Archive: 10.5281/zenodo.3998591

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/2575e93fc693c5c3bfa8736c60c35398"><img src="https://joss.theoj.org/papers/2575e93fc693c5c3bfa8736c60c35398/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/2575e93fc693c5c3bfa8736c60c35398/status.svg)](https://joss.theoj.org/papers/2575e93fc693c5c3bfa8736c60c35398)

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

@petroniocandido, @torressa 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 @melissawm know.

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

Review checklist for @petroniocandido

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 (@sjvrijn) 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 @zbeekman

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 (@sjvrijn) 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 @torressa

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 (@sjvrijn) 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. @petroniocandido it looks like you're currently assigned to review this paper 🎉.

⭐ 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:

1. Set yourself as 'Not watching' https://github.com/openjournals/joss-reviews:

2. You may also like to change your default settings for this watching repositories in your GitHub profile here: https://github.com/settings/notifications

For a list of things I can do to help you, just type:

@whedon commands

For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

@whedon generate pdf

[whedon]

Reference check summary:

OK DOIs

- 10.1007/s00158-014-1213-9 is OK
- 10.1007/s00158-014-1209-5 is OK
- 10.5281/zenodo.2594848 is OK
- 10.1098/rspa.2007.1900 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

👉 Check article proof 📄 👈

[danielskatz]

👋 @melissawm - Hi, can you let me know what's going on with this submission. In particular, I only see one reviewer, rather than the required two.

[petroniocandido]

wave @melissawm - Hi, can you let me know what's going on with this submission. In particular, I only see one reviewer, rather than the required two.

Hi @melissawm... Two unforeseen events happened with me and my pregnant wife and took me a long time to solve. I am deeply sorry and I will try to finish the review as soon as possible.

[melissawm]

@danielskatz I'm so sorry, I think I misread the conversation in the pre-review. Can I add new reviewers now?

[danielskatz]

Yes, please do

[melissawm]

Hello @jgoldfar, would you be willing/available to review this software paper for JOSS? Thank you

[sjvrijn]

Hi @melissawm here's the list of potential reviewers again if you're having trouble finding a second one:

• benjamin-lee
• torressa
• jmadera
• zbeekman
• lucashn
• tupi
• sarats

And hi @petroniocandido! 👋 Hope everything is fine again with you and your wife! If you've found/noticed anything at all, please let me know! I'm itching to improve my project based on the feedback 😃

[melissawm]

Hello, @torressa! Would you be willing/available to review this software paper for JOSS?

[torressa]

Hi @melissawm! I'd love to! Looks like a really interesting review.
I'll reserve some time next weekend.

[melissawm]

@whedon add @toressa as reviewer

[whedon]

OK, @toressa is now a reviewer

[melissawm]

@whedon remove @toressa as reviewer

[whedon]

OK, @toressa is no longer a reviewer

[melissawm]

@whedon add @torressa as reviewer

[arfon]

@sjvrijn - I made a couple of minor changes in sjvrijn/mf2#8 to your paper.

At this point could you make a new release of this software that includes the changes that have resulted from this review. Then, please make an archive of the software in Zenodo/figshare/other service and update this thread with the DOI of the archive? For the Zenodo/figshare archive, please make sure that:

• The title of the archive is the same as the JOSS paper title
• That the authors of the archive are the same as the JOSS paper authors

I can then move forward with accepting the submission.

[sjvrijn]

Hi @arfon I've published version v2020.8.0, the zenodo DOI is 10.5281/zenodo.3998591

[arfon]

@whedon set 10.5281/zenodo.3998591 as archive

[whedon]

OK. 10.5281/zenodo.3998591 is the archive.

[arfon]

@whedon set v2020.8.0 as version

[whedon]

OK. v2020.8.0 is the version.

[arfon]

@whedon remove @petroniocandido as reviewer

[whedon]

OK, @petroniocandido is no longer a reviewer

[arfon]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

Reference check summary:

OK DOIs

- 10.1007/s00158-014-1213-9 is OK
- 10.1007/s00158-014-1209-5 is OK
- 10.5281/zenodo.2594848 is OK
- 10.1098/rspa.2007.1900 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#1666

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#1666, 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.02049 joss-papers#1667
1. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.02049
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]

@torressa, @zbeekman - many thanks for your reviews and to @melissawm for editing this submission ✨

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

[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.02049/status.svg)](https://doi.org/10.21105/joss.02049)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.02049">
  <img src="https://joss.theoj.org/papers/10.21105/joss.02049/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.02049/status.svg
   :target: https://doi.org/10.21105/joss.02049

This is how it will look in your documentation:

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