[REVIEW]: Persistable: persistent and stable clustering

editorialbot commented 1 year ago

Submitting author: !--author-handle-->@LuisScoccola@rkurchin<!--end-editor-- Reviewers: @lmcinnes, @AP6YC Archive: 10.5281/zenodo.7697173

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/63d612cd4730c3aa708e3a47eb2c50f3/status.svg)](https://joss.theoj.org/papers/63d612cd4730c3aa708e3a47eb2c50f3)

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

@lmcinnes & @AP6YC, 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 @rkurchin 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 @AP6YC

📝 Checklist for @lmcinnes

editorialbot commented 1 year ago

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:

@editorialbot generate pdf

editorialbot commented 1 year ago

Checking the BibTeX entries failed with the following error:

Failed to parse BibTeX entry: cite-key missing

editorialbot commented 1 year ago

Software report:

github.com/AlDanial/cloc v 1.88  T=0.14 s (249.2 files/s, 57751.9 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                           8            304            271           2558
Cython                           7            519            809           1508
reStructuredText                 6            194            169            428
TeX                              1             19              0            184
Markdown                         2             73              0            162
CSS                              1             42             20            158
YAML                             4             14              4            113
Jupyter Notebook                 2              0            272             37
JSON                             1              0              0             15
TOML                             1              0              0              7
SVG                              1              0              0              1
-------------------------------------------------------------------------------
SUM:                            34           1165           1545           5171
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

editorialbot commented 1 year ago

Wordcount for paper.md is 998

editorialbot commented 1 year ago

Failed to discover a Statement of need section in paper

editorialbot commented 1 year ago

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

rkurchin commented 1 year ago

@LuisScoccola, it looks like you may have a typo in a citation somewhere that's borking the BibTeX checker, take a look at that when you can since those checks will eventually have to pass to accept the submission.

LuisScoccola commented 1 year ago

@editorialbot generate pdf

editorialbot commented 1 year ago

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

LuisScoccola commented 1 year ago

@editorialbot commands

editorialbot commented 1 year ago

Hello @LuisScoccola, here are the things you can ask me to do:


# List all available commands
@editorialbot commands

# Get a list of all editors's GitHub handles
@editorialbot list editors

# Check the references of the paper for missing DOIs
@editorialbot check references

# Perform checks on the repository
@editorialbot check repository

# Adds a checklist for the reviewer using this command
@editorialbot generate my checklist

# Set a value for branch
@editorialbot set joss-paper as branch

# Generates the pdf paper
@editorialbot generate pdf

# Generates a LaTeX preprint file
@editorialbot generate preprint

# Get a link to the complete list of reviewers
@editorialbot list reviewers

LuisScoccola commented 1 year ago

@editorialbot check references

editorialbot commented 1 year ago

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

OK DOIs

- 10.1007/978-3-642-37456-2_14 is OK
- 10.1109/ICDMW.2017.12 is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.1145/3068335 is OK
- 10.1145/2535927 is OK
- 10.1137/20M1388425 is OK
- 10.48550/ARXIV.1512.00180 is OK

MISSING DOIs

- 10.21105/joss.00205 may be a valid DOI for title: hdbscan: Hierarchical density based clustering.

INVALID DOIs

- None

LuisScoccola commented 1 year ago

@editorialbot check references

editorialbot commented 1 year ago

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

OK DOIs

- 10.1007/978-3-642-37456-2_14 is OK
- 10.1109/ICDMW.2017.12 is OK
- 10.21105/joss.00205 is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.1145/3068335 is OK
- 10.1145/2535927 is OK
- 10.1137/20M1388425 is OK
- 10.48550/ARXIV.1512.00180 is OK

MISSING DOIs

- None

INVALID DOIs

- None

LuisScoccola commented 1 year ago

@rkurchin Thank you for pointing out the bibtex issue. I think I have fixed it. Please let me know if there is anything that I should look into.

rkurchin commented 1 year ago

Happy New Year, everyone! Hope everyone had a great holiday. Just a friendly reminder for reviewers @lmcinnes and @AP6YC to get reviews started and let me know if you have any questions about the process. :)

rkurchin commented 1 year ago

Hi again, checking in once more with @lmcinnes and @AP6YC about reviewing – if you need any guidance about getting started, don't hesitate to ask!

AP6YC commented 1 year ago

Hi @rkurchin, sorry for the delay. I will get my checklist started below and begin my review.

AP6YC commented 1 year ago

Review checklist for @AP6YC

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 https://github.com/LuisScoccola/persistable?
[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 (@LuisScoccola) 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
[x] 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.
[x] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
[x] 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

[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: 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?
[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?

lmcinnes commented 1 year ago

Review checklist for @lmcinnes

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 https://github.com/LuisScoccola/persistable?
[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 (@LuisScoccola) 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
[x] 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.
[x] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
[x] 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

[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: 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?
[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?

rkurchin commented 1 year ago

Hi reviewers @AP6YC and @lmcinnes, just checking in on your review progress! Reminder that as you progress through your checklist, if you encounter any issues, feel free to file in the source repo. If you do so, mention (i.e. link to) this review so I can easily track progress. Thanks!

lmcinnes commented 1 year ago

Sorry, I was having installation issues (on my end from my environment manager; not the package), and set it aside for a little while.

I have a couple of minor issues that I'll file imminently, but mostly it looks good to me.

LuisScoccola commented 1 year ago

@lmcinnes thanks a lot for your feedback! I have tried to address the issues. Please let me know if I have missed anything.

lmcinnes commented 1 year ago

Thanks Luis, it all looks good to me now. Thanks forgetting the changes made so swiftly.

@rkurchin I am done the review, all the boxes are checked, and it looks good to go from me. Is there anything more I need to do at this stage?

rkurchin commented 1 year ago

@lmcinnes, nope, thanks very much! Now we're just waiting on the other review from @AP6YC!

AP6YC commented 1 year ago

I am overall happy with the contributions of the package, and I would like to congratulate the authors and programmers for making such useful and relevant software. The authors should feel proud of their work.

I apologize for the delay, but I have nearly completed my review, contingent on only a few points. I have provided two non-blocking issues on the repo in the form of questions and suggestions, and I have one minor blocking issue for improving the API reference. In short, I have a suggestion for the improvement of the API index that I would like addressed (with hopefully minimal time required of the authors) and two questions that may be long-term changes, which is why I do not wish for them to be addressed before my approval.

These issues are:

Non-blocking (not necessary to complete my review):

Blocking (small suggestions that I would like implemented or explained):

https://github.com/LuisScoccola/persistable/issues/33

LuisScoccola commented 1 year ago

Thank you for the feedback @AP6YC ! I have tried to address the last issue.

rkurchin commented 1 year ago

Hi @AP6YC, just checking in if you're happy for this to be published at this point? If so, can you check the last box on your checklist and let us know in a comment?

AP6YC commented 1 year ago

@rkurchin I sincerely apologize for this latest delay, but I am indeed satisfied with the latest changes; they correctly and successfully address the last issue, and I am happy for this to be published. Great work and congratulations to all the authors/programmers of the project.

rkurchin commented 1 year ago

Great, thanks everyone! Authors, I'll do an editorial pass over the manuscript and send any comments shortly. In the meantime, the next steps for you are:

Merge any and all changes from this review into your main branch and issue a new version tag. (If you want to merge in the paper, you may, but it is not required that the actual manuscript live into the repo in perpetuity since JOSS will host it and you can simply add a badge link or whatever you like. But the actual changes to software and docs do need to be merged!)
Create a DOI for the contents of the repo at the same commit corresponding to that version tag, e.g. using figshare or Zenodo. Please make sure that the metadata (version number, title, author list, etc.) match those of your manuscript.
Post a comment here with the version number and DOI.

rkurchin commented 1 year ago

@editorialbot check references

editorialbot commented 1 year ago

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

OK DOIs

- 10.1007/978-3-642-37456-2_14 is OK
- 10.1109/ICDMW.2017.12 is OK
- 10.21105/joss.00205 is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.1145/3068335 is OK
- 10.1145/2535927 is OK
- 10.1137/20M1388425 is OK
- 10.48550/ARXIV.1512.00180 is OK

MISSING DOIs

- None

INVALID DOIs

- None

rkurchin commented 1 year ago

@editorialbot generate pdf

rkurchin commented 1 year ago

@editorialbot generate pdf

xuanxu commented 1 year ago

@editorialbot generate pdf

editorialbot commented 1 year ago

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

LuisScoccola commented 1 year ago

@rkurchin Here's the DOI created with Zenodo: 10.5281/zenodo.7697173, and here is the corresponding website https://zenodo.org/record/7697173. The reviewers' comments have been incorporated in version 0.4.0, which is the one the DOI points to. Please let me know if there's anything I have missed.

rkurchin commented 1 year ago

@editorialbot set 10.5281/zenodo.7697173 as archive

editorialbot commented 1 year ago

Done! Archive is now 10.5281/zenodo.7697173

rkurchin commented 1 year ago

@editorialbot set 0.4.0 as version

editorialbot commented 1 year ago

Done! version is now 0.4.0

rkurchin commented 1 year ago

Some very minor editorial suggestions:

line 13-14: hyphenate "high-performance"
31: remove comma after "data"
36: hyphenate "high-performance"
38: this sentence reads slightly better to me with a "that" instead of the "which" (in which case you should also remove the comma before)
39: remove comma after "threshold"
52: I would change the "2" to "two" unless "2-parameter" is a standard phrasing

Otherwise, this looks good!

LuisScoccola commented 1 year ago

@rkurchin Thank you for the feedback! I have implemented the suggestions except for the one about line 52, since it is indeed standard phrasing.

rkurchin commented 1 year ago

@editorialbot generate pdf

editorialbot commented 1 year ago

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

rkurchin commented 1 year ago

@editorialbot recommend-accept

editorialbot commented 1 year ago

Attempting dry run of processing paper acceptance...

editorialbot commented 1 year ago

:wave: @openjournals/dsais-eics, this paper is ready to be accepted and published.

Check final proof :point_right::page_facing_up: Download article

If the paper PDF and the deposit XML files look good in https://github.com/openjournals/joss-papers/pull/4031, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

editorialbot commented 1 year ago

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

OK DOIs

- 10.1007/978-3-642-37456-2_14 is OK
- 10.1109/ICDMW.2017.12 is OK
- 10.21105/joss.00205 is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.1145/3068335 is OK
- 10.1145/2535927 is OK
- 10.1137/20M1388425 is OK
- 10.48550/ARXIV.1512.00180 is OK

MISSING DOIs

- None

INVALID DOIs

- None

openjournals / joss-reviews