[REVIEW]: SNEWPY: A Data Pipeline from Supernova Simulations to Neutrino Signals

[whedon]

Submitting author: @JostMigenda (Jost Migenda)
Repository: https://github.com/SNEWS2/snewpy
Version: v1.1
Editor: @dfm
Reviewer: @apizzuto, @PeterDenton
Archive: 10.5281/zenodo.5719209

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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

@apizzuto & @PeterDenton, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

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Review checklist for @apizzuto

✨ Important: Please do not use the Convert to issue functionality when working through this checklist, instead, please open any new issues associated with your review in the software repository associated with the submission. ✨

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.

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• 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 (@JostMigenda) 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 @PeterDenton

✨ Important: Please do not use the Convert to issue functionality when working through this checklist, instead, please open any new issues associated with your review in the software repository associated with the submission. ✨

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 (@JostMigenda) 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. @apizzuto, @PeterDenton 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]

Wordcount for paper.md is 1075

[whedon]

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

OK DOIs

- 10.1051/0004-6361/201322068 is OK
- 10.21105/joss.02877 is OK
- 10.3847/1538-3881/aabc4f is OK
- 10.1088/1367-2630/abde33 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.1038/s41592-019-0686-2 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.48 s (157.2 files/s, 32066.6 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          26           1272           2424           3219
Jupyter Notebook                20              0           5676           1745
Markdown                        17             57              0            291
make                             1             28              6            143
reStructuredText                 7             70             67             92
TeX                              1              6              0             84
YAML                             3             16             20             84
-------------------------------------------------------------------------------
SUM:                            75           1449           8193           5658
-------------------------------------------------------------------------------


Statistical information for the repository 'c4394c8fe7f7a6e63f58999c' was
gathered on 2021/09/27.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Evan O'Connor                   19          1052            364            7.04
Jost Migenda                    50          1948           1822           18.76
Segev BenZvi                   151          7697           4154           58.96
jpkneller                       22          2454             43           12.42
mcolomermolla                    6            58             52            0.55
nuberoi                          5           365             20            1.92
thomahrens                       2            68              4            0.36

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
Evan O'Connor               102            9.7          9.6               15.69
Jim Kneller                   3          100.0          0.2               66.67
Jost Migenda               1639           84.1          0.9                8.72
Segev BenZvi               4341           56.4          7.9               18.84
Spencer Griswold              8          100.0          0.0                0.00
jpkneller                   738           30.1          7.6                9.35
mcolomermolla                10           17.2          0.3               20.00
nuberoi                      51           14.0         15.4               11.76
thomahrens                   23           33.8          2.2                4.35

[whedon]

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

[dfm]

@JostMigenda, @apizzuto, @PeterDenton – This is the review thread for the paper. All of our communications will happen here from now on. Thanks again for agreeing to participate!

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 openjournals/joss-reviews#3772 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.

[apizzuto]

Hi SNEWPY team!
Thanks for a great contribution and sorry for just getting to this now. I just read through the software paper and thought I'd leave my comments as they came up. I expect to install the code tonight and review that portion throughout the rest of this week. For the paper, overall it was great and served its purpose of introducing the software broadly to a vast audience, but here are a few minor comments:

• For the non-specialists (myself included) can you briefly describe what SNOwGLoBES does and how it is distinct from SNEWPY? From the Statement of Need section I was guessing it has to do with the neutrino lightcurve generation, but I had a hard time disentangling what it does separate from what SNEWPY does
• The SNOwGLoBES reference shows up as "Scholberg & others" while other citations have the more typical "et al."
• I'm not sure if this is something you all can fix, but in the side bar of the pdf (where the AAS partnership is mentioned), the text overlaps with the footer
• l50: Should this be "single data file" instead of "signal data file" (Edited this comment to correct the line number)

Because these are non-software related problems, I didn't create an issue for them in the SNEWPY repository.

[whedon]

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

[whedon]

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

[apizzuto]

Hi all, ran into a slight problem downloading the models. The full problem is detailed more fully in the issue that I opened at SNEWS2/snewpy#109. Sorry if it's just me misunderstanding the install directions

[JostMigenda]

Thanks for the comments on the paper, @apizzuto! Here’s a commit with changes; in particular:

• SNOwGLoBES description: Reworded a sentence to make it clear what SNOwGLoBES does.
• SNOwGLoBES reference: Changed it to “Scholberg & SNOwGLoBES Contributors”. (I think the list of contributors on GitHub is incomplete, so this is probably the best we can do?)
• Side bar: Comparing with other JOSS papers, it looks like the top of the sidebar content is aligned with the bottom of the author/institution list; so this overlap is due to the JOSS template not expecting a long author list. @dfm, is there any way to adjust this?
• “signal” vs. “single”: The files contain signal (as opposed to background) events, so “signal” is correct.

I’ll look at the issue in a bit.

[dfm]

@dfm, is there any way to adjust this?

Good question! For now, let's just roll with the ugly formatting if that's ok and I'll work on tweaking the layout before publication.

[apizzuto]

@whedon commands

[whedon]

Here are some things you can ask me to do:

# List Whedon's capabilities
@whedon commands

# List of editor GitHub usernames
@whedon list editors

# List of reviewers together with programming language preferences and domain expertise
@whedon list reviewers

EDITORIAL TASKS

# Compile the paper
@whedon generate pdf

# Compile the paper from alternative branch
@whedon generate pdf from branch custom-branch-name

# Ask Whedon to check the references for missing DOIs
@whedon check references

# Ask Whedon to check repository statistics for the submitted software
@whedon check repository

[apizzuto]

@whedon generate pdf

[whedon]

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

[apizzuto]

Hi @JostMigenda, thanks for the tweaks to the paper and looking into the install issue. My installation is working now and I checked off everything for the paper in my checklist. I'll work through the examples in the next few days.

[apizzuto]

I just had a look at all of the notebooks, and first and foremost, after running through them I have to say I'm really impressed with all of the notebooks and all of the examples that you provided. I had a good time running through all of the different model notebooks and seeing what SNEWPY can do.
However, I ran into a couple of small problems with some of the notebooks, and I had a request for the organization of the notebooks. These are all outlined in the issue I just opened (SNEWS2/snewpy#113).

I think that I'm close to finishing up my review, but just to keep everyone in the loop – I still want to (1) read through the rest of the API docs to make sure everything looks good, (2) briefly take a glance at the code to make sure all of the functionality claims are verified (although after looking at the notebooks I think it's safe to say that they are) and (3) take a glance at the testing suite

[dfm]

@JostMigenda Awesome - thanks for the summary! Give me a few days to do some final checks and edits, then I'll have a couple of small tasks for you before publication.

@PeterDenton @apizzuto: thank you both for your reviews!! I really appreciate the time and expertise that you donated to this process.

[dfm]

@JostMigenda: Thanks for your patience. I've checked in about the formatting issue with the manuscript and we're actually just going to fix that in post production, so for now, we're going to proceed with the final processing. Here are the steps that I'll need from you:

1. Take one last read through the manuscript to make sure that you're happy with it (it's harder to make changes later!), especially the author names and affiliations. I've taken a pass and it looks good to me!
2. Increment the version number of the software and report that version number back here.
3. Create an archived release of that version of the software (using Zenodo or something similar). Please make sure that the metadata (title and author list) exactly match the paper. Then report the DOI of the release back to this thread.

Thanks!

[JostMigenda]

@dfm I’ve tagged a new version (v1.1) and archived it to Zenodo (DOI:10.5281/zenodo.5719209). The metadata that’s automatically generated by GitHub isn’t correct; I’ll contact a co-author who has permissions to edit that and will respond here as soon as that’s fixed.

[dfm]

@whedon set v1.1 as version

[whedon]

OK. v1.1 is the version.

[dfm]

@whedon set 10.5281/zenodo.5719209 as archive

[whedon]

OK. 10.5281/zenodo.5719209 is the archive.

[dfm]

@JostMigenda thanks! Just ping me once they have had a chance to update it and I'll get us wrapped up.

[JostMigenda]

@dfm We've updated the Zenodo metadata; so go ahead whenever you're ready! 😊

[dfm]

@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

- 10.1051/0004-6361/201322068 is OK
- 10.21105/joss.02877 is OK
- 10.3847/1538-3881/aabc4f is OK
- 10.1088/1367-2630/abde33 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.1038/s41592-019-0686-2 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#2767

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#2767, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

[dfm]

This has now been handed off to the EiCs for the final processing, and they may have some remaining edits before publication. But, in the meantime, thanks @JostMigenda, @PeterDenton, and @apizzuto for participating in this process!!

👋 ping @arfon re formatting issues

[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.03772 joss-papers#2770
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.03772
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]

@apizzuto, @PeterDenton – many thanks for your reviews here and to @dfm for editing this submission! JOSS relies upon the volunteer effort of people like you and we simply wouldn't be able to do this without you ✨

@JostMigenda – your paper is now accepted and published in JOSS ⚡🚀💥

[whedon]

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

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