[REVIEW]: SlideRule: Enabling rapid, scalable, open science for the NASA ICESat-2 mission and beyond

[editorialbot]

Submitting author: @dshean (David Shean)
Repository: https://github.com/ICESat2-SlideRule/paper
Branch with paper.md (empty if default branch): main
Version: v1.5.8
Editor: @kthyng
Reviewers: @jhkennedy, @betolink
Archive: 10.5281/zenodo.7542007

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/ddd37aab8ef5bda53725e9a262ec6cfd/status.svg)](https://joss.theoj.org/papers/ddd37aab8ef5bda53725e9a262ec6cfd)

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

@jhkennedy & @betolink, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review.
First of all you need to run this command in a separate comment to create the checklist:

@editorialbot generate my checklist

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @kthyng 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 ✨

Checklists

📝 Checklist for @jhkennedy

📝 Checklist for @betolink

[editorialbot]

Hello humans, I'm @editorialbot, a robot that can help you with some common editorial tasks.

For a list of things I can do to help you, just type:

@editorialbot commands

For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

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[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.01 s (392.5 files/s, 31795.8 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
TeX                              1             12              0            166
Markdown                         2             34              0             89
YAML                             1              1              4             18
-------------------------------------------------------------------------------
SUM:                             4             47              4            273
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gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 1969

[editorialbot]

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

OK DOIs

- 10.1016/j.rse.2019.111325 is OK
- 10.1016/j.rse.2016.12.029 is OK
- 10.1016/j.rse.2019.111352 is OK
- 10.1016/j.rse.2018.11.005 is OK
- 10.5067/ATLAS/ATL03.005 is OK
- 10.1007/s12145-020-00520-2 is OK
- 10.5281/zenodo.6717591 is OK
- 10.5281/zenodo.6917373 is OK
- 10.5281/zenodo.3665785 is OK
- 10.5281/zenodo.6697361 is OK
- 10.1016/j.srs.2020.100002 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

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

[kthyng]

👋🏼 @dshean, @jhkennedy, @betolink this is the review thread for the paper. All of our communications will happen here from now on.

As a reviewer, the first step is to create a checklist for your review by entering

@editorialbot generate my checklist

as the top of a new comment in this thread.

These checklists contain the JOSS requirements. As you go over the submission, please check any items that you feel have been satisfied. The first comment in this thread also contains 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#4982 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 reviews to be completed within about 2-4 weeks. Please let me know if any of you require some more time. We can also use EditorialBot (our bot) to set automatic reminders if you know you'll be away for a known period of time.

Please feel free to ping me (@kthyng) if you have any questions/concerns.

[jhkennedy]

Review checklist for @jhkennedy

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 https://github.com/ICESat2-SlideRule/paper?
• 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 (@dshean) 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
• Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
• Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
• Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

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, who the target audience is, and its relation to other work?
• 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?

[betolink]

Review checklist for @betolink

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 https://github.com/ICESat2-SlideRule/paper?
• 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 (@dshean) 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
• Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
• Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
• Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

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, who the target audience is, and its relation to other work?
• 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?

[jhkennedy]

@kthyng I have finished my (initial?) review of sliderule, and provided my detailed review in SlideRuleEarth/paper#2.

Overall, I am really impressed by Sliderule and all the work that has gone into it. It clearly fulfills a very valuable need in the community and does so exceedingly well. Coming in from the outside, I found the services, documentation, and code very approachable and could get up and running pretty quickly with only a few minor hitches. There are some areas of the manuscript itself that could be improved, however, so I recommend accepting this manuscript with minor revisions.

I am mostly concerned with the things in the subsection "Software paper: Quality of writing" of that issue (very bottom) which should be quick to address and would be happy to recommend accept when addressed.

[dshean]

Thanks @jhkennedy and @betolink for your detailed reviews!

We have already started preparing responses and will follow up in the discussion thread (SlideRuleEarth/sliderule#154), the issue on the paper repo (SlideRuleEarth/paper#2) and the JOSS review comment thread here.

@kthyng can you provide additional guidance on status of this review and required next steps in the JOSS review process, preferred formats, etc? A bit different than traditional academic journals, but I assume a detailed response to each comment is required here? Or are separate responses in PRs, issues, and associated github discussion sufficient?

[kthyng]

Sorry for my delay getting back to everything in the new year.

@dshean Nothing in particular needs to be said in this particular issue other than dealing with the checklist and some overall summary comments. Best is to have the discussions in the other issues and then just be sure to link them back to this issue so they can be tracked.

[kthyng]

@betolink I see that your checklist is all wrapped up! Did you have any comments to contribute, or did you open any issues that I didn't notice? What is your recommendation for the submission?

[dshean]

OK, thanks @kthyng! We will post responses here and in @betolink's discussion thread (SlideRuleEarth/sliderule#154), with links back to this one.

[dshean]

OK @kthyng, @jhkennedy and @betolink. I believe we addressed all reviewer comments in respective threads:

• JOSS review SlideRuleEarth/sliderule#154 (comment)
• @jhkennedy's review for JOSS SlideRuleEarth/paper#2 (comment)
• @jhkennedy's review for JOSS SlideRuleEarth/paper#2 (comment)

Changes to the revised paper are here: SlideRuleEarth/paper@19ac7d0. @kthyng, should we merge this into main and rebuild pdf?

Thanks again for your thorough review, and please let us know if there are any lingering items that we need to address before acceptance!

[betolink]

Hi @kthyng, I'm happy with the response I got from the SlideRule team to my questions, I anticipate there will be some follow up but overall I'm impressed by the quality of their tools and the documentation. I recommend accepting this manuscript and look forward to future work on this much needed framework for science in the cloud.

[kthyng]

Thanks @betolink!

@jhkennedy Looks like you have responses to your review to look at.

@dshean You can handle when you merge as you see fit. Currently the paper branch is set to main so you would need to merge in order for a new build to see the changes, but we could also change the branch if you'd prefer.

[dshean]

OK, thanks! If @jhkennedy does not have additional comments on the revisions, then I will merge into main.

[jhkennedy]

@kthyng and @dshean, I'm happy with the responses I got from the SlideRule team to my review and have closed the issue. While I expect we will continue a couple of conversations, I recommend accepting this manuscript and moving forward with publication as I don't think those conversations affect this manuscript.

I really enjoyed the review process (hopefully, I wasn't too thorough), and look forward to all the amazing work planned by the SlideRule team.

[kthyng]

@jhkennedy Is one checkbox intentionally left unchecked?

[jhkennedy]

@kthyng oops! I double-clicked it 😬. Should be checked now!

[kthyng]

Ok then we have both reviewers confirmed and all boxes checked! And yes discussion can certainly continue on.

@dshean I'll let you merge and regenerate the pdf — please make sure that the paper is exactly how you it should look (especially the references) since after I read through it, if I have no comments then I will accept it.

Other steps for this point for @dshean:

• After the code is merged, tag a new release for the present state and report the version back here
• Upload an archive of your code to a place like Zenodo and report back the DOI here. Please alter the metadata of the archive so that the title and author list exactly match your JOSS submission.

[dshean]

Thanks @kthyng! I merged the paper revision PR and made a few minor corrections after another final review. I think we are good to go with latest main branch in the paper repo: https://github.com/ICESat2-SlideRule/paper.

[dshean]

The reviews and paper were tagged at v1.5.8 (thanks to @jhkennedy's suggestion). Here are relevant release tags and DOIs from Zenodo for the code and docs:

https://github.com/ICESat2-SlideRule/sliderule-python/tree/v1.5.8 (https://doi.org/10.5281/zenodo.7477718)
https://github.com/ICESat2-SlideRule/sliderule/tree/v1.5.8 (https://doi.org/10.5281/zenodo.7477717)
https://github.com/ICESat2-SlideRule/sliderule-docs/tree/v1.5.8 (no Zenodo record for docs)

[dshean]

But maybe I misunderstood - do you want a release on the paper repo (no code)?

The titles for the Paper and the different code repos on Zenodo are different. I can modify the author list of the different code repos if desired.

[kthyng]

@editorialbot generate pdf

[editorialbot]

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

[kthyng]

@dshean Thanks. For this sort of review with multiple associated repositories, could you make a new, separate Zenodo archive that contains a snapshot of all the related repos? The paper repo can be included but isn't so important for archiving (since we can see the paper) but the other 3 should be included. For this combined repo please adjust the metadata.

[dshean]

Hi @kthyng.

As requested, I created a single Zenodo record containing the snapshot of the 3 repositories and the paper: https://doi.org/10.5281/zenodo.7542007. Please let me know if I should modify the description or other metadata.

I will update with final details for the paper after acceptance and publication. Thank you.

[kthyng]

Excellent! Everything is coming together.

[kthyng]

@editorialbot set 10.5281/zenodo.7542007 as archive

[editorialbot]

Done! Archive is now 10.5281/zenodo.7542007

[kthyng]

@editorialbot set v1.5.8 as version

[editorialbot]

Done! version is now v1.5.8

[kthyng]

Comments on paper:

• typo last paragraph in Summary "developent"
• Why are there question marks after the reviewer github handles in acknowledgments?

[dshean]

Thanks for catching these issues @kthyng. Fixed in SlideRuleEarth/paper@79228aa

[kthyng]

@editorialbot generate pdf

[editorialbot]

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

[kthyng]

Ok then that is everything!!

[kthyng]

@editorialbot accept

[editorialbot]

Doing it live! Attempting automated processing of paper acceptance...

[editorialbot]

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

[editorialbot]

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

[editorialbot]

🚨🚨🚨 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.04982 joss-papers#3885
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.04982
2. If everything looks good, then close this review issue.
3. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

[kthyng]

Congrats on your new publication @dshean! Many thanks to reviewers @jhkennedy and @betolink for your time, hard work, and expertise!!

[editorialbot]

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

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