Joss-reviews: [REVIEW]: Ripserer.jl: flexible and efficient persistent homology computation in Julia

[whedon]

Submitting author: @mtsch (Matija Čufar)
Repository: https://github.com/mtsch/Ripserer.jl
Version: v0.15.2
Editor: @VivianePons
Reviewer: @juliohm, @sauln
Archive: 10.5281/zenodo.4081109

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Reviewers and authors:

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Reviewer instructions & questions

@juliohm & @sauln, 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 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 @juliohm

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

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 @sauln

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

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. @juliohm, @sauln it looks like you're currently assigned to review this paper :tada:.

:warning: JOSS reduced service mode :warning:

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

@whedon generate pdf

[whedon]

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

OK DOIs

- 10.1007/978-3-319-64185-0_11 is OK
- 10.1137/15M1031151 is OK
- 10.1038/ncomms15396 is OK
- 10.1145/3350755.3400244 is OK
- 10.4230/LIPIcs.SoCG.2016.71 is OK
- 10.21105/joss.00925 is OK
- 10.1137/141000671 is OK

MISSING DOIs

- 10.1090/conm/453/08802 may be a valid DOI for title: Persistent homology-a survey

INVALID DOIs

- None

[whedon]

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

[mtsch]

I fixed the missing DOI.

[mtsch]

@whedon generate pdf

[whedon]

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

[juliohm]

I love to review submissions such as this, really well-written, to the point, and a great piece of software! Thanks @mtsch for this amazing work. I only have one minor comment that I already shared as a GitHub issue yesterday about the related Julia packages you recently added to the docs: https://mtsch.github.io/Ripserer.jl/dev/related-work/

Do you think that these should also be listed in the JOSS paper or at least cited in the list of references? I noticed that you cited the major alternatives from other languages, but perhaps it would be a good idea to list related work in Julia.

[mtsch]

Thanks for the kind words!

I added a short paragraph listing Julia packages. I also added citation for Julia and a reference to a Ripser fork I forgot to include.

[mtsch]

@whedon generate pdf

[whedon]

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

[juliohm]

I am happy to approve the submission. Everything is checked on my side :100:

[VivianePons]

Thank you very much @juliohm for reviewing so efficiently! @sauln let me know when you are done and do not hesitate to ask questions / make comments to the author, also you can take your time ;) The other reviewer was particularly quick!

[VivianePons]

Hi @sauln I haven't heard of you in a while and nothing has been udptaed on the review, are you still on board?

[sauln]

Hi Sorry @VivianePons It's still on my radar but have been swamped the last few weeks. I'll try to either finish it up this weekend, or bow out.

[VivianePons]

If you need some time, it's ok. I just need to know we are still on track

[VivianePons]

Hi @sauln I see that you haven't finished it up as you were planning (which is ok) but I'm hoping that you haven't bowed out. If you have, please let me know!

[sauln]

@VivianePons, I have completed my review. As @juliohm expressed, this project was a pleasure to review. I am only sorry it took me so long to complete it. The documentation is best in class, the library interface is remarkably clean and intuitive, and the testing appears more exhaustive than any other TDA library I've seen.

I am happy to accept this submission to JOSS 🥇

[mtsch]

@juliohm and @sauln thanks again for taking the time to review!

[VivianePons]

@whedon generate pdf

[whedon]

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

[VivianePons]

@whedon check references

[whedon]

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

OK DOIs

- 10.1007/978-3-319-64185-0_11 is OK
- 10.1137/15M1031151 is OK
- 10.1090/conm/453/08802 is OK
- 10.1038/ncomms15396 is OK
- 10.1145/3350755.3400244 is OK
- 10.4230/LIPIcs.SoCG.2016.71 is OK
- 10.21105/joss.00925 is OK
- 10.1137/141000671 is OK
- 10.3390/a13010019 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[VivianePons]

@mtsch I see you give many arXiv references in the bibliography. the arXiv number is always given but the actual link is present only in some ref. Could you put the link on all of them, that makes it easier for the reader to follow the ref!

Once this is done, I need you to make an archive (on Zenodo, or figshare, or other) and give the doi.

Thank you very much!

[mtsch]

@whedon generate pdf

[whedon]

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

[mtsch]

@VivianePons all references have links now. I made an archive on Zenodo. Here is a link.

[VivianePons]

Thanks, could you update the meta information of the Zenodo archive so that it has the same title as the paper and complete author name, thank you!

[mtsch]

Done.

[VivianePons]

@whedon set v0.15.2 as version

[whedon]

OK. v0.15.2 is the version.

[VivianePons]

@whedon set 10.5281/zenodo.4081109 as archive

[whedon]

OK. 10.5281/zenodo.4081109 is the archive.

[VivianePons]

Thank you all for the great work! The paper and software have received many praises, it is pleasure to accept it into JOSS, thank you @mtsch for the work and thank you @juliohm and @sauln for the reviews :)

[VivianePons]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[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/1826

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/1826, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.
@whedon accept deposit=true

[whedon]

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

OK DOIs

- 10.1007/978-3-319-64185-0_11 is OK
- 10.1137/15M1031151 is OK
- 10.1090/conm/453/08802 is OK
- 10.1038/ncomms15396 is OK
- 10.1145/3350755.3400244 is OK
- 10.4230/LIPIcs.SoCG.2016.71 is OK
- 10.21105/joss.00925 is OK
- 10.1137/141000671 is OK
- 10.3390/a13010019 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[mtsch]

@VivianePons thank you for editing! Submitting to this paper was an awesome experience!

[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/1827
2. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.02614
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]

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

Many thanks to @juliohm and @sauln for reviewing this, and @VivianePons for editing.

[whedon]

:tada::tada::tada: Congratulations on your paper acceptance! :tada::tada::tada:

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