[REVIEW]: OpenOA: An Open-Source Codebase For Operational Analysis of Wind Farms

[whedon]

Submitting author: @jordanperr (Jordan Perr-Sauer)
Repository: https://github.com/NREL/OpenOA
Version: v2.1
Editor: @sjpfenninger
Reviewers: @gschivley, @brynpickering
Archive: 10.5281/zenodo.4549876

Status

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Markdown: [![status](https://joss.theoj.org/papers/d635ef3c3784d49f6e81e07a0b35ff6b/status.svg)](https://joss.theoj.org/papers/d635ef3c3784d49f6e81e07a0b35ff6b)

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

@gschivley, 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 two weeks ✨

Review checklist for @gschivley

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 (@jordanperr) 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 @brynpickering

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

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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 😿

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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

- 10.1088/1742-6596/1037/5/052021 is OK

MISSING DOIs

- https://doi.org/10.1088/1742-6596/1037/6/062009 may be missing for title: Understanding Biases in Pre-Construction Estimates

INVALID DOIs

- None

[whedon]

👉 Check article proof 📄 👈

[sjpfenninger]

@whedon add @coroa as reviewer

[whedon]

OK, @coroa is now a reviewer

[gschivley]

@sjpfenninger how strict is JOSS about requiring OSI approved licenses? It looks like the authors use a modified version of the BSD 3-clause. There are very minor changes to wording in the original 3 clauses, plus an extra clause:

3. The entire corresponding source code of any redistribution, with or without modification, by a research entity,
   including but not limited to any contracting manager/operator of a United States National Laboratory, any
   institution of higher learning, and any non-profit organization, must be made publicly available under this license
   for as long as the redistribution is made available by the research entity.

[danielskatz]

We are very strict about this! We will not publish this submission with a modified license

[gschivley]

Thanks @danielskatz. Does that include minor modifications to the original clauses like those below?

1. Redistributions of source code must retain the above copyright notice, the above government rights notice, this list of conditions and the following disclaimer.

The name of the copyright holder, contributors, the United States Government, the United States Department of Energy, or any of their employees may not be used to endorse or promote products derived from this software without specific prior written permission.

NREL has other repos that use a standard BSD 3-Clause so I would think they should be able to change this one, I just want to be clear on exactly how strict JOSS is about deviations in wording.

[danielskatz]

No deviations in wording are allowed. Any deviation is a different (and thus non-OSI-approved) license.

[jordanperr]

@danielskatz @gschivley - I will bring this up with our team and see if we can accommodate this request. I imagine this license issue may have come up in the past for JOSS if they've published any work that was funded by the US government.

[danielskatz]

In other cases that I remember, labs have found a way to use a standard license.

[arfon]

@jordanperr - this is one example of another project making the change to a standard license (DoE/LBL funded work): #1370

[jordanperr]

@gschivley - Great news! I was able to change the license to a standard BSD license. This change has been merged in to the master branch of the OpenOA repository.

[gschivley]

Great! Hopefully I'll have a chance to try installation this weekend.

In the meantime, I noticed a number of authors on the paper who don't show up as contributors. Can you confirm that all authors contributed to the work, even if they didn't make commits to the repo?

[jordanperr]

Yes. I tried to make this author list a most complete reflection of the NREL team. Some of those authors may only have contributed in the past, using an internal git server, or they have been a guiding force in planning or architecture of the software.

[jordanperr]

Updated spelling of an author's name and added another author to the paper.
@whedon generate pdf from branch joss-review

[danielskatz]

requests to @whedon have to be at the start of a comment

[danielskatz]

@whedon generate pdf from branch joss-review

[whedon]

Attempting PDF compilation from custom branch joss-review. Reticulating splines etc...

[whedon]

👉 Check article proof 📄 👈

[sjpfenninger]

@coroa Just checking to see this hasn't dropped off your radar!

[kthyng]

(@sjpfenninger not trying to step on any toes but just to help out the handling editors since people have been pretty busy lately)

[kthyng]

@whedon set v2.1 as version

[whedon]

OK. v2.1 is the version.

[kthyng]

@jordanperr I read through your paper and it looks good pending some corrections you can check out in this PR.

[kthyng]

@whedon generate pdf from branch main

[whedon]

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

[whedon]

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

[kthyng]

@whedon set 10.5281/zenodo.4549876 as archive

[whedon]

OK. 10.5281/zenodo.4549876 is the archive.

[kthyng]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

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

OK DOIs

- 10.1088/1742-6596/1037/6/062009 is OK
- 10.5194/wes-5-1435-2020 is OK
- 10.25080/Majora-92bf1922-00a is OK
- 10.1109/mcse.2007.55 is OK
- 10.11578/dc.20181023.1 is OK
- 10.1088/1742-6596/1037/5/052021 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#2114

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#2114, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

[kthyng]

@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.02171 joss-papers#2115
1. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.02171
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...

[kthyng]

Congratulations on your new publication to @jordanperr and team!! Many thanks to editor @sjpfenninger and reviewers @gschivley and @brynpickering — we couldn't make JOSS happen without your time and expertise!! 🎉

[whedon]

🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

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[sjpfenninger]

@kthyng Many thanks for stepping in and of course no issue at all! @jordanperr Many thanks for your patience during this very long and drawn-out process. I am very happy with the result and I hope so are you!