[REVIEW]: RayFlare: flexible optical modelling of solar cells

[whedon]

Submitting author: @phoebe-p (Phoebe Pearce)
Repository: https://github.com/qpv-research-group/rayflare
Version: v1.0.0
Editor: @arfon
Reviewer: @kanderso-nrel, @EricaEgg
Archive: 10.5281/zenodo.5526536

⚠️ JOSS reduced service mode ⚠️

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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

@kanderso-nrel & @EricaEgg, 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
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The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @arfon know.

✨ Please start on your review when you are able, and be sure to complete your review in the next six weeks, at the very latest ✨

Review checklist for @kanderso-nrel

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 (@phoebe-p) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

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: Does the paper have a section titled 'Statement of Need' that clearly states 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 @EricaEgg

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 (@phoebe-p) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

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: Does the paper have a section titled 'Statement of Need' that clearly states 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. @kanderso-nrel, @EricaEgg 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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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:

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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]

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.16 s (448.8 files/s, 92145.3 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          40           2246            770           5128
Jupyter Notebook                13              1           2649           2276
CSS                              1             84             39            541
reStructuredText                11            132            103            259
YAML                             1             13              3             57
DOS Batch                        1              8              1             26
Markdown                         1              3              0             12
make                             1              4              7              9
SVG                              1              0              0              1
-------------------------------------------------------------------------------
SUM:                            70           2491           3572           8309
-------------------------------------------------------------------------------


Statistical information for the repository 'd9a84c89ff36743409856460' was
gathered on 2021/07/08.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Phoebe                           3           761             39            1.11
Phoebe Pearce                   35          3031           1621            6.46
phoebe-p                       196         33654          32872           92.43

Below are the number of rows from each author that have survived and are still
intact in the current revision:

Author                     Rows      Stability          Age       % in comments
Phoebe Pearce               700           23.1         10.2                9.71
phoebe-p                   7444           22.1          9.6                5.05

[arfon]

@whedon generate pdf from branch paper

[whedon]

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

[whedon]

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

[arfon]

@kanderso-nrel, @EricaEgg - This is the review thread for the paper. All of our communications will happen here from now on.

Please read the "Reviewer instructions & questions" in the first comment above.

Both reviewers have checklists at the top of this thread (in that first comment) with the JOSS requirements. As you go over the submission, please check any items that you feel have been satisfied. There are also links to the JOSS reviewer guidelines.

The JOSS review is different from most other journals. Our goal is to work with the authors to help them meet our criteria instead of merely passing judgment on the submission. As such, the reviewers are encouraged to submit issues and pull requests on the software repository. When doing so, please mention #3460 so that a link is created to this thread (and I can keep an eye on what is happening). Please also feel free to comment and ask questions on this thread. In my experience, it is better to post comments/questions/suggestions as you come across them instead of waiting until you've reviewed the entire package.

We aim for the review process to be completed within about 4-6 weeks but please make a start well ahead of this as JOSS reviews are by their nature iterative and any early feedback you may be able to provide to the author will be very helpful in meeting this schedule.

[whedon]

👋 @EricaEgg, please update us on how your review is going (this is an automated reminder).

[whedon]

👋 @kanderso-nrel, please update us on how your review is going (this is an automated reminder).

[EricaEgg]

Hi, So sorry for the delay. I need a new invitation to the repository. My link seems to have expired. Thanks, Erica

…

On Thu, Jul 22, 2021 at 1:48 AM whedon ***@***.***> wrote: 👋 @EricaEgg <https://github.com/EricaEgg>, please update us on how your review is going (this is an automated reminder). — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#3460 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ALCPASWEYYZKPM2Q3GNJQRLTY7LN5ANCNFSM5AAI4K4Q> .

-- *Erica Eggleton* she/her/hers PhD Candidate Schwartz Research Group <https://uwemilab.github.io/> Department of Chemical Engineering <https://www.cheme.washington.edu/> University of Washington

[danielskatz]

@whedon re-invite @EricaEgg as reviewer

[whedon]

OK, the reviewer has been re-invited.

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

[kandersolar]

@arfon I'm not sure the LICENSE.txt is acceptable as I don't think it matches the official GPLv3 text. But I'm not a lawyer, can you take a look from JOSS's perspective? Also @phoebe-p I notice that setup.py says the package is licensed LGPL rather than GPL, I suppose that should be made consistent: https://github.com/qpv-research-group/rayflare/blob/devel/setup.py#L74

[danielskatz]

The author should take a look at the "How to apply this license" section of https://choosealicense.com/licenses/gpl-3.0/

[phoebe-p]

@kanderso-nrel I have just had a look at the 'How to Apply These Terms to Your New Programs' section of Daniel's link, and as far as I can tell the text I have in LICENSE.txt is the same as what is given there, though it is missing contact information as suggested and I do not currently have the license or a pointer to it in every individual file or terminal output, as is suggested by this section. I could add these things, have a copyright thing on every file is probably a good idea. Is there another version of this text/something else I am missing here?

Thanks for pointing out the inconsistency with setup.py, I will change that (I want to use GPL, not LGPL)!

[kandersolar]

Oh interesting @phoebe-p. I had the impression that the LICENSE.txt is supposed to contain the full license text (several hundred lines long in the case of GPL) rather than that abbreviated notice. My interpretation is that the abbreviated notice is intended for the top of source files, and when it says "You should have received a copy of the GNU General Public License along with this program", the source code file is the "program" and LICENSE.txt is the "copy" of the GPL that goes along with the source code. But I'm very much not a lawyer, thus the appeal to JOSS for guidance :)

[phoebe-p]

From some more research on the GNU website, it seems that it is indeed recommended you distribute a copy of the full license text with the software, so I will add this, since I see no reason not to. Either way, the 'How to apply this' section is clear that I am supposed to put a copyright notice at the start of every file, so I will also add that.

[phoebe-p]

@whedon generate pdf

[whedon]

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

[phoebe-p]

License issue has been fixed/updated; I've changed setup.py, added a full copy of the license in addition to the shorter statement, and added a copyright statement to each file.

[kandersolar]

I've completed the reviewer checklist and am happy to recommend this ms for acceptance. Note that I do not consider qpv-research-group/rayflare#32 to be a blocker for this review. Please let me know if you need anything else from me.

Thanks @phoebe-p for this useful contribution to the PV community!

[phoebe-p]

@EricaEgg do you have any comments /issues so far?

[EricaEgg]

@EricaEgg do you have any comments /issues so far?

Hi @phoebe-p , thanks for checking in! Sorry for the delay on this. I have been running into problems installing S4 correctly. I was hesitant to open an issue, since it is not an issue with rayflare, itself. However, it has made it impossible to run the examples. I went ahead and posted an issue on the rayflare repo now. Thank you!

[EricaEgg]

I have completed the checklist and support this work. I currently have an open issue , but this is related to the installation of S4, which is not required for rayflare. I am able to run all examples that do not perform RCWA calculations/use S4. Therefore I do not think this should prevent the acceptance of this work, but is instead an issue that can be worked out over time. Thank you @phoebe-p!

[phoebe-p]

@arfon, what are next steps now that the checklist is completed?

[arfon]

@phoebe – 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.

[phoebe-p]

Ok, I have made a new release version which is v1.0.1. Zenodo archive DOI with that release is 10.5281/zenodo.5526536

[arfon]

@whedon set 10.5281/zenodo.5526536 as archive

[whedon]

OK. 10.5281/zenodo.5526536 is the archive.

[arfon]

@whedon recommend-accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

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

OK DOIs

- 10.1117/12.2550136 is OK
- 10.1007/s10825-018-1171-3 is OK
- 10.1109/PVSC40753.2019.8980868 is OK
- 10.1016/j.cpc.2012.04.026 is OK
- 10.1109/JPHOTOV.2017.2669640 is OK
- 10.1364/OE.23.00A502 is OK
- 10.1364/OE.23.0A1720 is OK
- 10.1016/j.solmat.2019.110051 is OK
- 10.1038/s41560-019-0444-9 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#2612

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#2612, 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.03460 joss-papers#2613
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.03460
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]

@kanderso-nrel, @EricaEgg – many thanks for your reviews here! JOSS relies upon the volunteer effort of people like you and we simply wouldn't be able to do this without you ✨

@phoebe-p – your paper is now accepted and published in JOSS ⚡🚀💥

[whedon]

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

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