[REVIEW]: `repytah`: An Open-Source Python Package That Builds Aligned Hierarchies for Sequential Data Streams #5213

editorialbot · 2023-03-05T10:18:54Z

Submitting author: @kmkinnaird (Katherine M. Kinnaird)
Repository: https://github.com/smith-tinkerlab/repytah
Branch with paper.md (empty if default branch):
Version: v0.1.2
Editor: @jbytecode
Reviewers: @Rocsg, @ranzhengcode
Archive: 10.5281/zenodo.7931423

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/3a74b43826b3b3ecf4f4a56a460a4fa2/status.svg)](https://joss.theoj.org/papers/3a74b43826b3b3ecf4f4a56a460a4fa2)

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

@Rocsg & @ranzhengcode, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review.
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@editorialbot generate my checklist

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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 ✨

Checklists

📝 Checklist for @Rocsg

📝 Checklist for @ranzhengcode

The text was updated successfully, but these errors were encountered:

editorialbot · 2023-03-05T10:18:55Z

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:

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

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editorialbot · 2023-03-05T10:19:17Z

Software report:

github.com/AlDanial/cloc v 1.88  T=1.18 s (62.7 files/s, 32592.4 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
JavaScript                      11           4448           4376          16488
Python                          15            987           1466           2455
HTML                             8           1023             24           1843
CSS                              3            194             32            776
Jupyter Notebook                 6              0           2112            659
Markdown                         6            120              0            281
YAML                             4             15              6            255
reStructuredText                16            201            310            126
SVG                              1              0              0             86
TeX                              1             12              0             85
DOS Batch                        1              8              1             26
make                             1              4              7              9
TOML                             1              0              0              3
-------------------------------------------------------------------------------
SUM:                            74           7012           8334          23092
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

editorialbot · 2023-03-05T10:19:25Z

Wordcount for paper.md is 987

editorialbot · 2023-03-05T10:19:39Z

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

OK DOIs

- 10.21105/joss.03326 is OK
- 10.1109/MSP.2018.2875349 is OK
- 10.25080/Majora-7b98e3ed-003 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot · 2023-03-05T10:20:35Z

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

jbytecode · 2023-03-05T10:22:27Z

Dear Reviewers @Rocsg and @ranzhengcode

This is the review thread. Firstly, type

@editorialbot generate my checklist

to generate your own checklist. In that checklist, there are 23 check items. Whenever you complete the corresponding task, you can check off them.

Please write your comments as separate posts and do not modify your checklist descriptions.

The review process is interactive so you can always interact with the authors (@kmkinnaird ), reviewers, and the editor (me). You can also create issues and pull requests in the target repo. Please do mention this thread's URL in the issues so we can keep tracking what is going on out of our world.

Please do not hesitate to ask me about anything, anytime.

Thank you in advance!

Rocsg · 2023-03-06T09:08:08Z

Review checklist for @Rocsg

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/smith-tinkerlab/repytah?
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 (@kmkinnaird) 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?

ranzhengcode · 2023-03-06T09:53:34Z

Review checklist for @ranzhengcode

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/smith-tinkerlab/repytah?
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 (@kmkinnaird) 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?

Rocsg · 2023-03-06T10:44:46Z

👋 @jbytecode @ranzhengcode
I submitted an issue with my first round of comments, there :

smith-tinkerlab/repytah#426

Have a nice week

Romain

jbytecode · 2023-03-08T11:10:03Z

@Rocsg - thank you for your comments.

@ranzhengcode - It seems you've performed a full check in a relatively short time. thank you. could you please provide your review and thoughts here or in issues in the target repo? thank you in advance.

ranzhengcode · 2023-03-09T04:15:33Z

@jbytecode Dear jbytecode, I have completely checked and tried repytah on my computer and was able to run all instances properly according to the author's instructions. As I am not an expert in music and data processing, I don't have a more pertinent advice for authors, but I think the work is still very interesting to accept.

kmkinnaird · 2023-03-17T12:34:29Z

Thank you @Rocsg for your detailed review. We have responded in the issue that you created smith-tinkerlab/repytah#426

Thank you @ranzhengcode for your kind words. Let us know if there is anything additional that you would like us to add or if there are questions that we can answer regarding the changes made in response to @Rocsg's review

Rocsg · 2023-03-17T15:49:29Z

Hello @jbytecode . I did receive the answers and I am planning to fulfill my checklist early next week. I keep both of you in touch. I Wish you all a nice weekend.

Romain

Rocsg · 2023-04-05T08:26:41Z

@editorialbot generate pdf

editorialbot · 2023-04-05T08:27:56Z

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

jbytecode · 2023-04-07T17:42:53Z

jbytecode · 2023-04-07T17:47:27Z

@editorialbot check references

editorialbot · 2023-04-07T17:49:40Z

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

OK DOIs

- 10.21105/joss.03326 is OK
- 10.1109/MSP.2018.2875349 is OK
- 10.25080/Majora-7b98e3ed-003 is OK

MISSING DOIs

- None

INVALID DOIs

- None

jbytecode · 2023-04-07T17:49:50Z

@editorialbot generate pdf

editorialbot · 2023-04-07T17:51:08Z

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

jbytecode · 2023-04-09T10:58:24Z

@kmkinnaird - I've just sent a pull request that includes some minor changes on both the manuscript and the bibliography:

smith-tinkerlab/repytah#428

Please review the changes. If you are agreed with them, please merge.

Thank you in advance.

kmkinnaird · 2023-04-16T20:14:23Z

I see both the Post Review Checklist and your comment above. I will complete the checklist and review the changes by May 5th.

Thank you!

editorialbot · 2023-05-13T04:30:33Z

Done! archive is now 10.5281/zenodo.7931423

jbytecode · 2023-05-13T04:31:21Z

@editorialbot check references

editorialbot · 2023-05-13T04:31:30Z

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

OK DOIs

- 10.21105/joss.03326 is OK
- 10.1109/MSP.2018.2875349 is OK
- 10.25080/Majora-7b98e3ed-003 is OK
- 10.1109/icassp.2006.1661198 is OK

MISSING DOIs

- None

INVALID DOIs

- None

jbytecode · 2023-05-13T04:32:19Z

@editorialbot generate pdf

editorialbot · 2023-05-13T04:33:33Z

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

jbytecode · 2023-05-13T04:35:56Z

@editorialbot recommend-accept

editorialbot · 2023-05-13T04:35:57Z

Attempting dry run of processing paper acceptance...

editorialbot · 2023-05-13T04:36:09Z

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

OK DOIs

- 10.21105/joss.03326 is OK
- 10.1109/MSP.2018.2875349 is OK
- 10.25080/Majora-7b98e3ed-003 is OK
- 10.1109/icassp.2006.1661198 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot · 2023-05-13T04:37:18Z

👋 @openjournals/csism-eics, this paper is ready to be accepted and published.

Check final proof 👉📄 Download article

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#4224, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

danielskatz · 2023-05-13T12:16:18Z

@kmkinnaird - I'm the track editor who will handle the final processing of your submission. I've proofread the draft, and the paper looks fine to me, but some references need work. Specifically, there are a few references that are of type article that should be of type inproceedings, such as Casey & Slaney 2006a, Casey & Slaney 2006b, Casey & Slaney 2007, and Sapp 2005. The conference name should also be written out in these cases, as it is in others already. Please fix these, then ping me here, and I'll continue the process of acceptance and publication.

kmkinnaird · 2023-05-15T11:46:26Z

@danielskatz - Thanks for your note and for introducing yourself.

I believe that I've fixed all the references to include the full conference names as well as consistent presentation for the author names. The current draft is in the main branch of the repo

One question: are the use of acronyms correct or should I remove them?

danielskatz · 2023-05-15T11:48:21Z

@editorialbot recommend-accept

editorialbot · 2023-05-15T11:48:22Z

Attempting dry run of processing paper acceptance...

editorialbot · 2023-05-15T11:48:37Z

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

OK DOIs

- 10.21105/joss.03326 is OK
- 10.1109/MSP.2018.2875349 is OK
- 10.25080/Majora-7b98e3ed-003 is OK
- 10.1109/icassp.2006.1661198 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot · 2023-05-15T11:50:17Z

👋 @openjournals/csism-eics, this paper is ready to be accepted and published.

Check final proof 👉📄 Download article

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#4225, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

danielskatz · 2023-05-15T11:52:44Z

This looks good now - thanks!

danielskatz · 2023-05-15T11:52:59Z

@editorialbot accept

editorialbot · 2023-05-15T11:53:00Z

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

editorialbot · 2023-05-15T11:55:07Z

Ensure proper citation by uploading a plain text CITATION.cff file to the default branch of your repository.

If using GitHub, a Cite this repository menu will appear in the About section, containing both APA and BibTeX formats. When exported to Zotero using a browser plugin, Zotero will automatically create an entry using the information contained in the .cff file.

You can copy the contents for your CITATION.cff file here:

CITATION.cff

cff-version: "1.2.0"
authors:
- family-names: Jia
  given-names: Chenhui
- family-names: Carpenter
  given-names: Lizette
- family-names: Tran
  given-names: Thu
- family-names: Liu
  given-names: Amanda Y.
- family-names: Yeutseyeva
  given-names: Sasha
- family-names: Tapal
  given-names: Marium
  orcid: "https://orcid.org/0000-0001-5093-6462"
- family-names: Wang
  given-names: Yingke
- family-names: Zhao
  given-names: Zoie Kexin
- family-names: Moody
  given-names: Jordan
- family-names: Nava
  given-names: Denise
- family-names: Donaher
  given-names: Eleanor
- family-names: Jiang
  given-names: Lillian Yushu
- family-names: Bruncati
  given-names: Ben
- family-names: Kinnaird
  given-names: Katherine M.
  orcid: "https://orcid.org/0000-0002-0435-8996"
contact:
- family-names: Kinnaird
  given-names: Katherine M.
  orcid: "https://orcid.org/0000-0002-0435-8996"
doi: 10.5281/zenodo.7931423
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Jia
    given-names: Chenhui
  - family-names: Carpenter
    given-names: Lizette
  - family-names: Tran
    given-names: Thu
  - family-names: Liu
    given-names: Amanda Y.
  - family-names: Yeutseyeva
    given-names: Sasha
  - family-names: Tapal
    given-names: Marium
    orcid: "https://orcid.org/0000-0001-5093-6462"
  - family-names: Wang
    given-names: Yingke
  - family-names: Zhao
    given-names: Zoie Kexin
  - family-names: Moody
    given-names: Jordan
  - family-names: Nava
    given-names: Denise
  - family-names: Donaher
    given-names: Eleanor
  - family-names: Jiang
    given-names: Lillian Yushu
  - family-names: Bruncati
    given-names: Ben
  - family-names: Kinnaird
    given-names: Katherine M.
    orcid: "https://orcid.org/0000-0002-0435-8996"
  date-published: 2023-05-15
  doi: 10.21105/joss.05213
  issn: 2475-9066
  issue: 85
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 5213
  title: "repytah: An Open-Source Python Package for Building Aligned
    Hierarchies for Sequential Data"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.05213"
  volume: 8
title: "`repytah`: An Open-Source Python Package for Building Aligned
  Hierarchies for Sequential Data"

If the repository is not hosted on GitHub, a .cff file can still be uploaded to set your preferred citation. Users will be able to manually copy and paste the citation.

Find more information on .cff files here and here.

editorialbot · 2023-05-15T11:55:19Z

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

editorialbot · 2023-05-15T11:55:20Z

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

editorialbot · 2023-05-15T11:55:21Z

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.05213 joss-papers#4226
Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.05213
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

danielskatz · 2023-05-15T12:02:27Z

Congratulations to @kmkinnaird (Katherine M. Kinnaird) and co-authors!!

And thanks to @Rocsg and @ranzhengcode for reviewing, and to @jbytecode for editing!
We couldn't do this without your volunteering

(I'll also note that the DOI doesn't resolve, and it normally should by now - I'll leave this open until it is working.)

kmkinnaird · 2023-05-15T12:08:36Z

Thank you @Rocsg, @ranzhengcode, @jbytecode, and @danielskatz for all your work during this reviewing process. It was a really great reviewing experience!

danielskatz · 2023-05-15T13:45:23Z

the DOI is now resolving for me - thanks again to everyone!

editorialbot · 2023-05-15T13:45:25Z

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

If you would like to include a link to your paper from your README use the following code snippets:

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</a>

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   :target: https://doi.org/10.21105/joss.05213

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editorialbot added Python review TeX Track: 7 (CSISM) Computer science, Information Science, and Mathematics labels Mar 5, 2023

editorialbot assigned jbytecode Mar 5, 2023

editorialbot mentioned this issue Mar 5, 2023

[PRE REVIEW]: repytah: An Open-Source Python Package That Builds Aligned Hierarchies for Sequential Data Streams #5166

Closed

Rocsg mentioned this issue Mar 6, 2023

First review / Rocsg smith-tinkerlab/repytah#426

Closed

jbytecode mentioned this issue Apr 9, 2023

Update paper and bibliography smith-tinkerlab/repytah#428

Merged

editorialbot added the recommend-accept Papers recommended for acceptance in JOSS. label May 13, 2023

editorialbot added accepted published Papers published in JOSS labels May 15, 2023

danielskatz closed this as completed May 15, 2023

[REVIEW]: repytah: An Open-Source Python Package That Builds Aligned Hierarchies for Sequential Data Streams #5213

[REVIEW]: repytah: An Open-Source Python Package That Builds Aligned Hierarchies for Sequential Data Streams #5213

Comments

editorialbot commented Mar 5, 2023 • edited Loading

Status

Reviewer instructions & questions

Checklists

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Rocsg commented Mar 6, 2023 • edited Loading

Review checklist for @Rocsg

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

ranzhengcode commented Mar 6, 2023 • edited Loading

Review checklist for @ranzhengcode

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Rocsg commented Mar 6, 2023

jbytecode commented Mar 8, 2023

ranzhengcode commented Mar 9, 2023

kmkinnaird commented Mar 17, 2023

Rocsg commented Mar 17, 2023

Rocsg commented Apr 5, 2023

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jbytecode commented Apr 7, 2023 • edited Loading

Post-Review Checklist for Editor and Authors

Additional Author Tasks After Review is Complete

Editor Tasks Prior to Acceptance

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kmkinnaird commented Apr 16, 2023

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danielskatz commented May 15, 2023

kmkinnaird commented May 15, 2023

danielskatz commented May 15, 2023

editorialbot commented May 15, 2023

[REVIEW]: `repytah`: An Open-Source Python Package That Builds Aligned Hierarchies for Sequential Data Streams #5213

[REVIEW]: `repytah`: An Open-Source Python Package That Builds Aligned Hierarchies for Sequential Data Streams #5213

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