Joss-reviews: [REVIEW]: bifacial_radiance: a python package for modeling bifacial solar photovoltaic systems

[whedon]

Submitting author: @shirubana (Silvana Ayala Pelaez)
Repository: https://github.com/NREL/bifacial_radiance/
Version: v0.3.3.1
Editor: @melissawm
Reviewers: @wholmgren, @dalonsoa, @usethedata
Archive: 10.5281/zenodo.3860350

Status

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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 and @usethedata 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 @wholmgren

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?
• [ ] 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 (@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

• [x] 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.
• [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 @dalonsoa

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 (@shirubana) 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 @usethedata

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 (@shirubana) 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?

[whedon]

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 :tada:.

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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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[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

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

[dalonsoa]

Acceptance-blocker due to limited/incomplete installation instructions https://github.com/NREL/bifacial_radiance/issues/190

[dalonsoa]

Not exactly an acceptance-blocker, but certainly desirable to understand how the software works https://github.com/NREL/bifacial_radiance/issues/191

[dalonsoa]

Acceptance-blocker due to missing statement of need (or more specifically, intended audience) https://github.com/NREL/bifacial_radiance/issues/192

[dalonsoa]

Not an acceptance blocker, but it will be useful for the authors to elaborate https://github.com/NREL/bifacial_radiance/issues/193

[dalonsoa]

@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.

[dalonsoa]

@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!

[melissawm]

@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!

[shirubana]

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).

[cdeline]

Yes, we’re using a BSD-3 license for the software for now and forever more.

Chris Deline
National Renewable Energy Laboratory
[phone]

From: Silvana Ayala [e-mail]
Sent: Thursday, November 7, 2019 2:05 PM
To: openjournals/joss-reviews [e-mail]
Cc: Deline, Chris [e-mail]; Mention [e-mail]
Subject: Re: [openjournals/joss-reviews] [REVIEW]: bifacial_radiance: a python package for modeling bifacial solar photovoltaic systems (#1865)

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... @cdelinehttps://github.com/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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[wholmgren]

@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.

[wholmgren]

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.

[danielskatz]

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

[melissawm]

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.

[shirubana]

@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?

[cdeline]

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.

[cdeline]

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.

[melissawm]

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!

[danielskatz]

👋 @melissawm - I'm just checking in on the progress of this review

[dalonsoa]

I'm waiting for some changes to be made in this PR https://github.com/NREL/bifacial_radiance/pull/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.

[shirubana]

sorry! I'll do this today. I hadn't realized that. ugh.

[shirubana]

@dalonsoa @danielskatz @wholmgren I have addressed all of issues and the PR comments now as well.

[dalonsoa]

I'll tick those things that have been solved... but the PR is still not passing 🤷‍♂ .

[dalonsoa]

@shirubana Installing "Radiance" (the Step 0 dependency of bifacial_radiance) is a pain. That's absolutely not your fault and there's nothing you need to do there except, maybe, asking the "Radiance" team to improve the installation pipeline.

Other than an issue I've just opened with something more of a suggestion than a requirement (https://github.com/NREL/bifacial_radiance/issues/217), this is ready to go from my side - once all check pass in the open PR.

[shirubana]

@dalonsoa @wholmgren PR passing now :)

[melissawm]

Thank you, @dalonsoa !

If you all have anything else I can help you with, feel free to let me know.

[wholmgren]

@cdeline the license is still not quite standard BSD-3. The 3rd clause contains "the United States Government, the United States Department of Energy," and the disclaimer contains "IN NO EVENT SHALL THE COPYRIGHT HOLDER, CONTRIBUTORS, UNITED STATES GOVERNMENT OR UNITED STATES DEPARTMENT OF ENERGY, NOR ANY OF THEIR EMPLOYEES..." instead of "IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS...". It's not a blocker as far as I'm concerned, but thought I should mention it here in case anyone else objects.

[wholmgren]

I'm not able to install radiance with a reasonable amount of effort on MacOS. I realize this is not really the fault of the bifacial_radiance developers, and @dalonsoa was able to get it done, so I don't feel comfortable holding up the review on my account. I recommend 1. improving the MacOS install instructions or dropping the claim of support and 2. finding another reviewer. Seems that @mikofski is already spun up on radiance and could probably do the review pretty quickly. Sorry I can't be more help.

[shirubana]

@CameronTStark you use bifacial_radiance/radiance on a mac, right? Any insights on installation issues/tricks that we should include in our instructions?

[CameronTStark]

The installer for MacOS isn't descriptive about where it installs. I tried for a bit to find it but had an easier time just choosing a location by pressing the "Change Install Location..." button in the "Installation Type" stage of the install. Then I source it in my bash/zsh_profile like so:

export PATH=$HOME/bin/radiance/bin:$PATH
export RAYPATH=$HOME/bin/radiance/lib
export MANPATH=$HOME/bin/radiance/man
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$HOME/bin/radiance/lib
export MDIR=$HOME/bin/radiance/lib

[shirubana]

@melissawm touching base on this review, what are the next steps? We have improved the documentation for installation of Radiance as much as we can with what has worked for some of our users. Are we getting another reviewer? How do we move forward?

Thank you

[melissawm]

Hello all,

Due to the problems that @wholmgren faced during installation, I believe it would be best if another reviewer could step in and continue the review. I understand in this case there is sufficient documentation for the software in question, however the installation issues stem from a dependency, and that is not under the author's control.

I would like to thank @wholmgren for his work in this review and the authors for their patience. If you have any further questions, please let me know.

[melissawm]

@mankoff, would you be willing to review this software paper for JOSS? Thanks in advance!

[melissawm]

@shirubana I would like to point out that the license file is still not a standard BSD-3 license (as previously mentioned above). Can you please check that?

[cdeline]

Hi. I’m not sure what the hold-up on the BSD-3 license is exactly. Github is not auto-detecting our license file as a BSD-3, but we are using the BSD-3 license template and this is a standard BSD-3 license. Because our organization is ‘Alliance for Sustainable Energy, LLC’ aka NREL, and we’re a federally funded national lab, we are contractually obligated to include the US Government and Department of Energy as co-copyright holders, and therefore are included explicitly anywhere the copyright holder is referenced in the legal text. Otherwise this is a bog-standard BSD-3 licence.

The reviewer (wholmgren) mentioned that this issue is not specifically a blocker. I’m not a copyright lawyer, and this isn’t something that I can just unilaterally change- this was the guidance and language given by our legal team that US government and Department of Energy need to be included because they are co-copyright holders.

Thanks-

Chris Deline
National Renewable Energy Laboratory
[phone]

From: Melissa Weber Mendonça [e-mail]
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Cc: Deline, Chris [e-mail]; Mention [e-mail]
Subject: Re: [openjournals/joss-reviews] [REVIEW]: bifacial_radiance: a python package for modeling bifacial solar photovoltaic systems (#1865)

@shirubanahttps://github.com/shirubana I would like to point out that the license file is still not a standard BSD-3 license (as previously mentioned above). Can you please check that?

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[melissawm]

@cdeline thanks for the clarification. I believe in this case, this is ok. I'm sorry as I'm not familiar with the US government licensing terms.

I'll wait for a few more days and if we don't get an answer I'll ask another reviewer to complete the review.

[shirubana]

Awesome! Thank you Chris and @melissawm Looking forward to getting the review process unstuck and finished 💃

[shirubana]

@melissawm updates on the review process? :) ty

[melissawm]

@shirubana do you have any suggestions for reviewers from the potential reviewer's list for JOSS?

[shirubana]

I remember there was a list to reviewers and their expretise but I can't find them

[melissawm]

Here it is.

[shirubana]

Sorry, now I dropped the ball. u_u

Based on prioritizing Python as language, having done more than 1 reviews in the past year and not being currently overwhelmed with research, and having some kind of atmospheric, energy, or optics experience: andreas-h, dhhagan, cmccomb, dhhagan, yxqd, sarats, usethedata, mikaem, leouieda

[melissawm]

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

[melissawm]

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

[cmccomb]

Hi @melissawm! This is a busy time of year for me. I would not be able to review it very quickly :(

[arfon]

Dear authors and reviewers

We wanted to notify you that in light of the current COVID-19 pandemic, JOSS has decided to suspend submission of new manuscripts and to handle existing manuscripts (such as this one) on a "best efforts basis". We understand that you may need to attend to more pressing issues than completing a review or updating a repository in response to a review. If this is the case, a quick note indicating that you need to put a "pause" on your involvement with a review would be appreciated but is not required.

Thanks in advance for your understanding.

_Arfon Smith, Editor in Chief, on behalf of the JOSS editorial team._

[shirubana]

Hello @arfon, we would still like to proceed if possible with this manuscript as best as we can. Our first reviewer @dalonsoa gave us much great feedback and we implemented all of it, but we've been stuck first with installation issues of Radiance raytrace software (not ours - we've documented as best we can from other users) and with getting another reviewer. We've put a lot of effort in this package, tutorials and associated material, as well as into the improvements for the JOSS journal and all of these efforts will continue -- this tool is very useful in our field. We've had many publications in the past based on this software and more forthcoming so, it would be great to have an official way such as JOSS for us and others to cite it, since we've found it's an issue that we have that many users don't know how to properly cite our package and refer to it. Please advise how to best move forward!

Thank you

Silvana Ayala

[arfon]

Hi @shirubana, incase my message wasn't clear - we still plan to review this submission, I'm just asking for you patience with reviewers and editors who may be dealing with other matters during this time.

[shirubana]

Ahh! Sorry didn't get it thanks for the clarification. Of course, Patience hat on :D

[melissawm]

Hello @shirubana I'm so sorry we haven't been able to find a third reviewer, but I'll keep looking.

[melissawm]

@usethedata would you be willing to review this software paper for JOSS? At this time, we understand the disruptions caused by the COVID-19 pandemic so if you are willing to do it (even if it takes more time than usual) we would greatly appreciate it if you could mention it here. Thanks!

[usethedata]

@melissawm Give me a couple of days to get through the chaos. I'm a line manager, and I'm in the midst of getting my group configured for 100% remote work. But I should be able to start on this by the end of the week.

[melissawm]

@usethedata thank you so much, I'll assign you as a reviewer but feel free to start your review when you are ready (as per the message above by Arfon, JOSS is currently working on a "best effort basis").

[melissawm]

@whedon add @usethedata as reviewer

[whedon]

OK, @usethedata is now a reviewer

[usethedata]

Checking in. It took me longer to get through some chaos in my world. I'm starting in on my review.

[usethedata]

@whedon generate pdf

[whedon]

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

[usethedata]

This is not, IMO, a conflict of interest. However, I am documenting it here for transparency. I work at Oak Ridge National Laboratory, and I am therefore an employee of UT-Battelle, which is a 50/50 joint venture between the University of Tennessee and Battelle Memorial Institute. The authors are at the National Renewable Energy Laboratory, which is another of the US Department of Energy labs, and are presumably employees of the Alliance for Sustainable Energy. ASE is a joint venture between MRI Global and Battelle Memorial Institute. Battelle Memorial Institute, therefore, has a financial interest in the legal entities which employ me and which employ the authors. However, that is not a controlling interest in either entity. The authors and I are, for legal and practical purposes, employed by separate legal entities, which happen to share a common partial owner. I am not aware of any other connections between me and the authors of this work.

[usethedata]

I've finally completed my review. I found one minor documentation problem, which appears to be fixed in the repository. I was able to successfully install and use the system on Mac OS Catalina. Apologies for the delay, but the work from home situation means I have way more meetings, it seems.

[melissawm]

Thank you, @usethedata !

@shirubana can you create an archive for this and report the DOI on this issue?

[shirubana]

sorry, confused. what? @melissawm

[melissawm]

Since the review is complete, we can go forward with the review workflow. According to the review guide,

Upon successful completion of the review, authors will make a tagged release of the software, and deposit a copy of the repository with a data-archiving service such as Zenodo or figshare, get a DOI for the archive, and update the review issue thread with the version number and DOI.

When you get a chance to do that, let me know so I can proofread the manuscript and we can proceed. Thanks!

[arfon]

👋 @shirubana - have you managed to complete the steps that @melissawm asked of you a few weeks ago? JOSS is now open again for submissions and we're actively trying to wrap up existing reviews.

[kyleniemeyer]

Hi @shirubana, just checking in again.

[shirubana]

@arfon @kyleniemeyer @melissawm thanks for reminding me! OMG so close,. Here is the Zenodo number: 10.5281/zenodo.3860350

[kyleniemeyer]

Thanks @shirubana, can you change the title to match the paper's title?

[shirubana]

@kyleniemeyer change the title of what?

[kyleniemeyer]

@shirubana the title and authors for the Zenodo archive should match the paper; actually, it looks like you need to edit the author list as well. (You can edit these things for an existing archive without changing the DOI)

[shirubana]

Sweet, I think I just did that. I moved the other contributors to contributors and left the author list as in the paper, and changed the title. Hope it's good! Thank you! @kyleniemeyer

[kyleniemeyer]

@whedon set 10.5281/zenodo.3860350 as archive

[whedon]

OK. 10.5281/zenodo.3860350 is the archive.

[kyleniemeyer]

@whedon generate pdf

[whedon]

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

[shirubana]

@kyleniemeyer, there is an image that does not want to render properly on the proof for some reason. I think @melissawm was going to help us investigate, I tried various ways of typing the Markdown to have it show it but could't make it work... any suggestions?

[kyleniemeyer]

@shirubana yeah, I noticed this as well. I will see if I can figure it out now, and if not reach out to the dev team.

[kyleniemeyer]

@shirubana I think the issue is that you are using HTML commands for the image, rather than Markdown image commands. Can you replace

<figure>
    <img src='https://github.com/NREL/bifacial_radiance/blob/master/paper/Alderman.PNG' />
    <figcaption> Visualization of a bifacial photovoltaic array generated through bifacial_radiance. Courtesy of J. Alderman. </figcaption>
</figure>

![Visualization of a bifacial photovoltaic array generated through bifacial_radiance. Courtesy of J. Alderman.\label{fig:visualization}](Alderman.PNG)

If you want to reference the figure in the text, you can do so with \autoref{fig: visualization}

[shirubana]

@whedon generate pdf

[whedon]

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

[shirubana]

@whedon generate pdf

[shirubana]

@kyleniemeyer thanks for the tip. it works well now 👍

[whedon]

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

[shirubana]

@whedon generate pdf

[whedon]

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

[shirubana]

I had to add a dash between my two last names so it would put both at the footer of the page :)

It looks beautiful now.

[kyleniemeyer]

@shirubana just a few final edits to the text:

• in the 4th paragraph ("bifacial_radiance was first coded in ..."), the last sentence uses the references as nouns but uses the usual parenthetical citation. Could you remove the square brackets? For reference, these are the different citation commands and their results:

- `@author:2001`  ->  "Author et al. (2001)"
- `[@author:2001]` -> "(Author et al., 2001)"
- `[@author1:2001; @author2:2001]` -> "(Author1 et al., 2001; Author2 et al., 2002)"

• please add a period after Stein's middle initial in the Stein2019b reference; I think this is why the in-text references are doing "J. S. Stein et al. 2019" and "Stein et al. 2019" (the compiler thinks that they are different people due to the inconsistent period after middle initial)
• in the 5th paragraph ("bifacial_radiance has been used in numerous studies..."), one of the references needs a semicolon rather than a comma: [@PVSyst, @SAM]
• You can remove the final sentence that includes a citation to the GitHub repo, since the link to the source code is given on the first page for all JOSS articles

[shirubana]

@kyleniemeyer it's been updated! Thank you for being so thorough.

[kyleniemeyer]

@whedon generate pdf

[whedon]

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

[kyleniemeyer]

@shirubana almost there! It looks like that reference actually has either a missing or incorrect citation: in [@PVSyst; @SAM], there does not appear to be a corresponding item for PVSyst in your bib file.

[shirubana]

@whedon generate pdf

[whedon]

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

[shirubana]

@whedon generate pdf

[whedon]

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

[shirubana]

@kyleniemeyer done! I tried to put my lastname in brackets like in the bib { } but the footer didn't recognize that :( So I guess I have to stay with the dash in between. Oh well. Everything else is updated though :)

[kyleniemeyer]

@openjournals/dev @arfon I thought we could handle double barrel (but no hyphen) last names—is that not the case?

[arfon]

@openjournals/dev @arfon I thought we could handle double barrel (but no hyphen) last names—is that not the case?

We can, but we have to handle this manually. Let me know if this is needed here.

[shirubana]

@whedon generate pdf

[whedon]

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

[shirubana]

@arfon that would be very appreciated. Right now the last name reads "Pelaez" instead of "Ayala Pelaez" on the footer :)

[arfon]

@arfon that would be very appreciated. Right now the last name reads "Pelaez" instead of "Ayala Pelaez" on the footer :)

Sure thing. I'll fix this once the paper is accepted as it's a manual process.

[kyleniemeyer]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

Reference check summary:

OK DOIs

- 10.1109/JPHOTOV.2018.2819676 is OK
- 10.1109/JPHOTOV.2018.2877000 is OK
- 10.1109/JPHOTOV.2019.2892872 is OK
- 10.1109/JPHOTOV.2019.2924394 is OK
- 10.5281/zenodo.1401378 is OK
- 10.1145/192161.192286 is OK
- 10.1109/PVSC.2017.8366263 is OK

MISSING DOIs

- https://doi.org/10.1002/pip.3259 may be missing for title: Estimating and parameterizing mismatch power loss in bifacial photovoltaic systems
- https://doi.org/10.1109/pvsc.2017.8366704 may be missing for title: View Factor Model and Validation for Bifacial PV and Diffuse Shade on Single-Axis Trackers.
- https://doi.org/10.2172/1440404 may be missing for title: System Advisor Model (SAM) General Description (Version 2017.9.5

INVALID DOIs

- https://doi.org/10.21105/joss.00884 is INVALID because of 'https://doi.org/' prefix

[whedon]

: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/1470

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/1470, 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 @shirubana sorry, looks like I missed a few issues in the references:

• remove the "https://doi.org/" from the DOI for the Holmgren 2018 reference
• remove the extraneous \url{...} from the Deline 2017 reference, since the DOI link is in another place
• The Anoma 2017 paper is missing the DOI
• The Deline 2019b reference should include the journal and DOI (it looks to be in press now)
• it looks like the SAM reference has a DOI that should be added: 10.2172/1440404
• Also, please look over the references—there are a number that are missing curly brackets around words to enforce capitalization

[shirubana]

@whedon generate pdf

[whedon]

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

[kyleniemeyer]

@shirubana looks good, thanks!

[kyleniemeyer]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

Reference check summary:

OK DOIs

- 10.1109/JPHOTOV.2018.2819676 is OK
- 10.1109/JPHOTOV.2018.2877000 is OK
- 10.1109/JPHOTOV.2019.2892872 is OK
- 10.1109/JPHOTOV.2019.2924394 is OK
- 10.11578/dc.20180530.16 is OK
- 10.4229/EUPVSEC20192019-5DO.3.4 is OK
- 10.1002/pip.3259 is OK
- 10.5281/zenodo.1401378 is OK
- 10.1145/192161.192286 is OK
- 10.21105/joss.00884 is OK
- 10.1109/PVSC.2017.8366704 is OK
- 10.2172/1440404 is OK
- 10.1109/PVSC.2017.8366263 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

: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/1473

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/1473, 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]

Hey @arfon, this is now ready to publish—do you handle the name fix before or after the final step?

[shirubana]

hold on need to push two more small reference updates! trying to add a DOI for a poster 2 mins

[shirubana]

ok now we're good :)

[shirubana]

@whedon generate pdf

[whedon]

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

[shirubana]

I liked.... hmmm one of the titles disapeared.

[shirubana]

@whedon generate pdf

[whedon]

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

[shirubana]

@whedon generate pdf

[whedon]

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

[shirubana]

@kyleniemeyer ok I'm good , all references have DOI if they have them now.

[kyleniemeyer]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

Reference check summary:

OK DOIs

- 10.1109/JPHOTOV.2018.2819676 is OK
- 10.1109/JPHOTOV.2018.2877000 is OK
- 10.1109/JPHOTOV.2019.2892872 is OK
- 10.1109/JPHOTOV.2019.2924394 is OK
- 10.11578/dc.20180530.16 is OK
- 10.4229/EUPVSEC20192019-5DO.3.4 is OK
- 10.1002/pip.3259 is OK
- 10.5281/zenodo.1401378 is OK
- 10.1145/192161.192286 is OK
- 10.21105/joss.00884 is OK
- 10.1109/PVSC.2017.8366704 is OK
- 10.4229/35thEUPVSEC20182018-6CV.2.19 is OK
- 10.2172/1440404 is OK
- 10.1109/PVSC.2017.8366263 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

: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/1474

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/1474, 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]

@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:

1. Check final PDF and Crossref metadata that was deposited :point_right: https://github.com/openjournals/joss-papers/pull/1475
2. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01865
3. If everything looks good, then close this review issue.

4. Party like you just published a paper! 🎉🌈🦄💃👻🤘

   Any issues? notify your editorial technical team...

[kyleniemeyer]

Hey @arfon, this is now ready for the name fix, both in the paper footer and the citation on the landing page.

[kyleniemeyer]

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

Many thanks to @wholmgren, @dalonsoa, and @usethedata for reviewing this, and @melissawm for editing.

[melissawm]

Thank you all for working on this, especially @kyleniemeyer for taking over since I was unavailable. Congratulations @shirubana !

[shirubana]

thank you for this! everyone!!!! this is really great :)

[shirubana]

@arfon if you get a chance to update the last name on the footer and webpage --- to "Ayala Pelaez" instead of just Pelaez :) t

[arfon]

@arfon if you get a chance to update the last name on the footer and webpage --- to "Ayala Pelaez" instead of just Pelaez :) t

Sure thing. I can do that - I might not be able to get to this until tomorrow though sorry.

[arfon]

@shirubana - this should be updated now although the PDF may take a while to update as it's cached.

[whedon]

: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.01865/status.svg)](https://doi.org/10.21105/joss.01865)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.01865">
  <img src="https://joss.theoj.org/papers/10.21105/joss.01865/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.01865/status.svg
   :target: https://doi.org/10.21105/joss.01865

This is how it will look in your documentation:

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