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[REVIEW]: bifacial_radiance: a python package for modeling bifacial solar photovoltaic systems #1865

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whedon opened this issue Nov 5, 2019 · 22 comments
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@whedon whedon commented Nov 5, 2019 •
edited by wholmgren

Submitting author: @shirubana (Silvana Ayala Pelaez)
Repository: https://github.com/NREL/bifacial_radiance/
Version: v0.3.3.1
Editor: @melissawm
Reviewer: @wholmgren, @dalonsoa
Archive: Pending

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/b018890e2ab7ddf723d37b17e308e273"><img src="https://joss.theoj.org/papers/b018890e2ab7ddf723d37b17e308e273/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/b018890e2ab7ddf723d37b17e308e273/status.svg)](https://joss.theoj.org/papers/b018890e2ab7ddf723d37b17e308e273)

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

@wholmgren & @dalonsoa, 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 @wholmgren

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

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 (@shirubana) 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 @dalonsoa

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

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 (@shirubana) 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 whedon added the review label Nov 5, 2019
@whedon whedon mentioned this issue Nov 5, 2019
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@whedon whedon commented Nov 5, 2019

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @wholmgren, @dalonsoa 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:

watching

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

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
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@whedon whedon commented Nov 5, 2019 

Attempting PDF compilation. Reticulating splines etc...
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@whedon whedon commented Nov 5, 2019

👉 Check article proof 📄 👈

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@dalonsoa dalonsoa commented Nov 6, 2019

Acceptance-blocker due to limited/incomplete installation instructions NREL/bifacial_radiance#190
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@dalonsoa dalonsoa commented Nov 6, 2019

Not exactly an acceptance-blocker, but certainly desirable to understand how the software works NREL/bifacial_radiance#191
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@dalonsoa dalonsoa commented Nov 6, 2019

Acceptance-blocker due to missing statement of need (or more specifically, intended audience) NREL/bifacial_radiance#192
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@dalonsoa dalonsoa commented Nov 6, 2019

Not an acceptance blocker, but it will be useful for the authors to elaborate NREL/bifacial_radiance#193
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@dalonsoa dalonsoa commented Nov 7, 2019 •
edited

@melissawm It seems there’s a figure missing in the Software Paper. It is present in the repository and it appears when showing the markdown file of the paper in GitHub but it is not rendered when creating the PDF. I'm not sure of the reason for that.
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@dalonsoa dalonsoa commented Nov 7, 2019

@melissawm The license of the software is BSD-3-Clause, clearly stated in the corresponding file, but in the DOI 10.11578/dc.20180530.16 it appears as BSD 2-clause "Simplified" License. I am not sure if it will necessary to consolidate the license in both places or, if not possible, to add a note somewhere indicating when the license was changed from one to the other. Or it it matters at all!
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@melissawm melissawm commented Nov 7, 2019 •
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@melissawm The license of the software is BSD-3-Clause, clearly stated in the corresponding file, but in the DOI 10.11578/dc.20180530.16 it appears as BSD 2-clause "Simplified" License. I am not sure if it will necessary to consolidate the license in both places or, if not possible, to add a note somewhere indicating when the license was changed from one to the other. Or it it matters at all!

I think it does matter, yes. Sorry for not catching this before. @shirubana could you clarify?

I'll check about the picture. Thanks!
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@shirubana shirubana commented Nov 7, 2019

Well the DOI paper was published in 2017 when we started and it seems we changed the license to BSD-3 1 year ago, as per the github history of the file... @cdeline can you confirm if BSD-3 is what we will go on forever now and/or if we need to consolidate?

I think a simple solution would be to write a note of the switch on the documentation (maybe on the updates, package overview and/or contribution guidelines).
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@cdeline cdeline commented Nov 7, 2019

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@wholmgren wholmgren commented Nov 7, 2019

@melissawm the COI policy states:

In addition, your recent (past year) association with the same organization of a submitter is a COI, for example, being employed at the same institution.

@shirubana was a graduate student at my organization, University of Arizona, from 2012- Dec 2018. So there is 1-2 month overlap over the past year. But, the COI policy also states as an example of when a waiver can be granted:

Or if you and a submitter are both employed by the same very large organization but in different units without any knowledge of each other.

We knew of each other but very rarely interacted. Different departments, siloed research programs.

I wouldn't have any problem providing an impartial review of this paper.
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@wholmgren wholmgren commented Nov 7, 2019

Also on the subject of the license, it includes this NREL specific language:

NOTICE: This software was developed at least in part by Alliance for Sustainable
Energy, LLC (“Alliance”) under Contract No. DE-AC36-08GO28308 with the U.S.
Department of Energy and the U.S. Government retains for itself and others acting
on its behalf a nonexclusive, paid-up, irrevocable worldwide license in the software
to reproduce, prepare derivative works, distribute copies to the public, perform
publicly and display publicly, and to permit others to do so.

Does this violate the requirement "Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?" My own opinion is "no" but seems like a question for the editors.
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@danielskatz danielskatz commented Nov 7, 2019

@wholmgren - the conflict you describe is weak enough that it can be waived, but thank you for making this possible issue transparent.
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@melissawm melissawm commented Nov 12, 2019

Thank you all for your patience while I was checking this. As far as the change in licensing, a note in the documentation would be ok.

However, as far as the NOTICE mentioned above by @wholmgren , the best solution would be to remove it from the licence file (mantaining it a pure BSD 3 license) and adding this note somewhere in the project (for example, in the README).

@shirubana do you think this is feasible?

Please let me know if you have further questions or comments.
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@shirubana shirubana commented Nov 12, 2019

@cdeline would this option of using the README instead of the License file to have the sponsoring/DOE acknowledgment work to satisfy NREL's legal stuff?
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@cdeline cdeline commented Nov 13, 2019

Hi everybody! I'm investigating these two points with the legal team here at NREL, but for everyone's information, a LICENSE file wasn't added until v0.2.3 on 11/14/2018, and it was initiated as a BSD-3 license, and has remained the same since then. So, I believe the DOI entry is incorrect and should probably be updated - there are a couple of other inaccuracies there including that we were supported by the CEC.
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@cdeline cdeline commented Nov 18, 2019

Hi all, i've been given approval by NREL legal to replace LICENSE.txt with a stock BSD-3 from the OSI webpage. I'm merging that in Master now.
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@melissawm melissawm commented Nov 19, 2019

Thank you, @cdeline and @shirubana!

@wholmgren and @dalonsoa this means the review can resume as normal. If you have any further questions, don't hesitate to ask!
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@danielskatz danielskatz commented Dec 5, 2019

👋 @melissawm - I'm just checking in on the progress of this review
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@dalonsoa dalonsoa commented Dec 5, 2019

I'm waiting for some changes to be made in this PR NREL/bifacial_radiance#199 before I can tick all the remaining boxes in the review. It seems that the PR is not passing all checks for now, so no sure what is the status of the review.
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