[REVIEW]: AutoFunc: A Python package for automating and verifying functional modeling

[whedon]

Submitting author: @AlexMikes (Alex Mikes)
Repository: https://github.com/AlexMikes/AutoFunc
Version: v0.3.1
Editor: @gkthiruvathukal
Reviewers: @cmccomb, @e-dub, @srmnitc
Archive: 10.5281/zenodo.4482795

⚠️ JOSS reduced service mode ⚠️

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Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/14f9eb408a9cb91c28332fcac1bce505/status.svg)](https://joss.theoj.org/papers/14f9eb408a9cb91c28332fcac1bce505)

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

@cmccomb & @e-dub, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

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

Review checklist for @cmccomb

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 (@AlexMikes) 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 @e-dub

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 (@AlexMikes) 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 @srmnitc

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 (@AlexMikes) 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. @cmccomb, @e-dub it looks like you're currently assigned to review this paper 🎉.

⚠️ JOSS reduced service mode ⚠️

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.

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[whedon]

Reference check summary:

OK DOIs

- 10.1115/1.1625400 is OK
- 10.1115/1.1289637 is OK
- 10.5281/zenodo.3694300 is OK

MISSING DOIs

- https://doi.org/10.1007/s00163-001-0008-3 may be missing for title: A functional basis for engineering design: Reconciling and evolving previous efforts

INVALID DOIs

- None

[whedon]

👉 Check article proof 📄 👈

[cmccomb]

@AlexMikes will you please enable issues in your repository? Once you've done so I'll put my review notes in as issues. For the time being here they are:

1. Contribution and authorship: four authors are listed on the work, but only one author has made commits in the software. How did the other authors contribute to this software?
2. Example Usage and Functionality Documentation: There are a number of (really cool!) example scripts, but the functionality in these is largely not demonstrated or discussed in the README. Could you add a list of example scripts as a way of highlighting and documenting functionality?
3. Community guidelines: no guidance on how to report issues on problems with the software, or to seek support.

[AlexMikes]

@cmccomb Thanks for being a reviewer and taking the time to give great feedback! I just enabled issues, should I reply here or after you've put your notes in the issue?

I'll work on adding documentation for the example files and community guidelines in the README.

[cmccomb]

@AlexMikes will you please enable issues in your repository? Once you've done so I'll put my review notes in as issues. For the time being here they are:

1. Contribution and authorship: four authors are listed on the work, but only one author has made commits in the software. How did the other authors contribute to this software?
2. Example Usage and Functionality Documentation: There are a number of (really cool!) example scripts, but the functionality in these is largely not demonstrated or discussed in the README. Could you add a list of example scripts as a way of highlighting and documenting functionality?
3. Community guidelines: no guidance on how to report issues on problems with the software, or to seek support.

@AlexMikes its my pleasure! Really cool piece of software. I've added the notes as issues in your repo. I believe the preference is to handle discussion there.

1. JOSS Review: Clarify contribution and authorship AlexMikes/AutoFunc#1
2. JOSS Review: Example Usage and Functionality Documentation AlexMikes/AutoFunc#2
3. JOSS Review: Community Guidelines AlexMikes/AutoFunc#3

[AlexMikes]

Thank you @cmccomb for the excellent suggestions. I have completed these and responded to the issues individually.

[cmccomb]

Thank you @cmccomb for the excellent suggestions. I have completed these and responded to the issues individually.

Thanks @AlexMikes! My review is complete, and I recommend accept, @gkthiruvathukal .

[gkthiruvathukal]

@cmccomb, This is great news.

@e-dub, Will you be able to complete your evaluation soon?

[e-dub]

@cmccomb, This is great news.

@e-dub, Will you be able to complete your evaluation soon?

I would like to start my review but am unable to edit the review checklist.
@gkthiruvathukal: could you check this for me?

[gkthiruvathukal]

@openjournals/joss-eics @e-dub is having trouble to edit the review checklist (and shows as a proper reviewer). I think we've seen this happen in the past but don't recall exactly how we resolved it.

[gkthiruvathukal]

@e-dub You can still start working on identifying issues and opening issues in the submissions project repo and linking those issues here.

[kthyng]

@whedon re-invite @e-dub as reviewer

[whedon]

OK, the reviewer has been re-invited.

@e-dub please accept the invite by clicking this link: https://github.com/openjournals/joss-reviews/invitations

[kthyng]

@e-dub See if this helps, maybe you didn't accept the invitation to review previously.

[gkthiruvathukal]

@kthyng Thanks for helping to sort this out!

@e-dub Can you let us know when you are able to complete your review?

[gkthiruvathukal]

@e-dub Just a gentle nudge to find out when we can expect your review? I know this is a busy time of year for many, including me.

[gkthiruvathukal]

@e-dub ?

[kthyng]

@gkthiruvathukal Unless you can track down an email address for @e-dub to try another contact venue, this may be a good time to find a replacement reviewer.

[AlexMikes]

Thanks, @gkthiruvathukal and @kthyng

Let me know if I can do anything to help move this along

[gkthiruvathukal]

@kthyng Yes, I'll try to get someone else before the weekend. I've been dealing with a rather intense phase at work. I almost went into "out of office" mode as I thought I could work through this.

@AlexMikes What could help is to suggest more reviewers. I think I've tried all of your initial suggestions. Let me know if you have any others in mind from our reviewer list.

[AlexMikes]

I suggest @trallard as an additional reviewer

[gkthiruvathukal]

@AlexMikes I am ready to move toward acceptance. Please do the following:

• Make a tagged release of your software, and list the version tag of the archived version here.
• Archive the reviewed software in Zenodo
• Check the Zenodo deposit has the correct metadata, this includes the title (should match the paper title) and author list (make sure the list is correct and people who only made a small fix are not on it); you may also add the authors' ORCID.
• List the Zenodo DOI of the archived version here.

[AlexMikes]

@gkthiruvathukal this is great news, thank you for all of your work in this process!

• Make a tagged release of your software, and list the version tag of the archived version here.
  v0.3.1
• Archive the reviewed software in Zenodo
• Check the Zenodo deposit has the correct metadata, this includes the title (should match the paper title) and author list (make sure the list is correct and people who only made a small fix are not on it); you may also add the authors' ORCID.
• List the Zenodo DOI of the archived version here.
  10.5281/zenodo.4482795

[gkthiruvathukal]

@whedon set 10.5281/zenodo.4482795 as archive

[whedon]

OK. 10.5281/zenodo.4482795 is the archive.

[gkthiruvathukal]

@whedon set v0.3.1 as version

[whedon]

OK. v0.3.1 is the version.

[gkthiruvathukal]

@whedon generate pdf

[whedon]

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

[gkthiruvathukal]

@AlexMikes My pleasure. Thank you, too! for all of your work and patience with us during COVID-19. I'm moving to acceptance now!

[gkthiruvathukal]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

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

OK DOIs

- 10.1115/1.1625400 is OK
- 10.1115/1.1289637 is OK
- 10.1007/s00163-001-0008-3 is OK
- 10.5281/zenodo.3694300 is OK

MISSING DOIs

- None

INVALID DOIs

- https://doi.org/10.1115/DETC2020-22495 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1115/DETC2020-22346 is INVALID because of 'https://doi.org/' prefix

[whedon]

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

Check final proof 👉 openjournals/joss-papers#2066

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#2066, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

[kyleniemeyer]

Hi @AlexMikes, I'm doing some final checks before publishing - there are just a few small changes needed in the paper:

• We require a brief Statement of Need section that illustrates the research purpose of the software (part of our required paper elements, normally checked for automatically by whedon). You can likely reuse some of the text in your summary, but add this section header.
• in your reference for the software, it looks like your name is missing a space (the author field should be Alex Mikes instead of AlexMikes)
• in the two 2020 ASME IDETC references (edmonds2020_2 and mikes2020), you need to remove the https://doi.org/ from the DOI fields

Please let me know when you've made these changes, and then I will publish the paper. There's no need to re-deposit into Zenodo, since we archive the paper itself. Thanks!

[AlexMikes]

Thanks, @kyleniemeyer, I have made these changes. Let me know if you need anything else from me.

[kyleniemeyer]

@whedon generate pdf

[whedon]

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

[kyleniemeyer]

👍 @AlexMikes, looks good.

[kyleniemeyer]

@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.02362 joss-papers#2072
1. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.02362
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...

[kyleniemeyer]

Congrats @AlexMikes on your article's publication in JOSS!

Many thanks to @cmccomb and @srmnitc for reviewing this submission, and @gkthiruvathukal for editing it.

[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.02362/status.svg)](https://doi.org/10.21105/joss.02362)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.02362">
  <img src="https://joss.theoj.org/papers/10.21105/joss.02362/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.02362/status.svg
   :target: https://doi.org/10.21105/joss.02362

This is how it will look in your documentation:

We need your help!

Journal of Open Source Software is a community-run journal and relies upon volunteer effort. If you'd like to support us please consider doing either one (or both) of the the following:

• Volunteering to review for us sometime in the future. You can add your name to the reviewer list here: https://joss.theoj.org/reviewer-signup.html
• Making a small donation to support our running costs here: https://numfocus.org/donate-to-joss

[AlexMikes]

Thanks @kyleniemeyer! Thanks again @gkthiruvathukal for leading this and @cmccomb and @srmnitc for reviewing and helping to improve it!