[REVIEW]: Fast k-medoids Clustering in Rust and Python

whedon commented 2 years ago

Submitting author: !--author-handle-->@kno10@mikldk<!--end-editor-- Reviewers: @timClicks, @TahiriNadia Archive: 10.5281/zenodo.6802320

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Review checklist for @timClicks

✨ 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

[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.

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General checks

[x] Repository: Is the source code for this software available at the repository url?
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[x] Contribution and authorship: Has the submitting author (@kno10) 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: 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?
[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 @TahiriNadia

✨ 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

[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 (@kno10) 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] #4344
[x] Functionality: Have the functional claims of the software been confirmed?
[x] #4346

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] #4349
[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] #4348
[x] #4347
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] #4345

whedon commented 2 years ago

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @timClicks, @TahiriNadia it looks like you're currently assigned to review this paper :tada:.

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whedon commented 2 years ago

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.06 s (186.4 files/s, 18247.1 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                           2             85            206            211
Rust                             1              9             77            174
Markdown                         2             29              0             64
reStructuredText                 1             48             34             57
TOML                             2              4              0             40
YAML                             2              4              1             29
make                             1              1              0              4
-------------------------------------------------------------------------------
SUM:                            11            180            318            579
-------------------------------------------------------------------------------

Statistical information for the repository 'c55cad42f8224e43fd62b6df' was
gathered on 2022/02/19.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Erich Schubert                   8           596             94          100.00

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
Erich Schubert              502           84.2          1.4                8.57

whedon commented 2 years ago

PDF failed to compile for issue #4183 with the following error:

 Can't find any papers to compile :-(

mikldk commented 2 years ago

@whedon generate pdf from branch JOSS-draft

whedon commented 2 years ago

Attempting PDF compilation from custom branch JOSS-draft. Reticulating splines etc...

whedon commented 2 years ago

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

mikldk commented 2 years ago

@whedon check references from branch JOSS-draft

whedon commented 2 years ago

Attempting to check references... from custom branch JOSS-draft

whedon commented 2 years ago

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

OK DOIs

- 10.1002/9780470316801.ch2 is OK
- 10.1137/0137041 is OK
- 10.1007/978-3-030-32047-8_16 is OK
- 10.1016/j.is.2021.101804 is OK
- 10.21105/joss.01230 is OK
- 10.1287/opre.16.5.955 is OK
- 10.1111/j.1538-4632.1979.tb00674.x is OK
- 10.1007/s10852-005-9022-1 is OK
- 10.1147/sj.22.0129 is OK
- 10.1016/j.eswa.2008.01.039 is OK
- 10.1093/bioinformatics/btp163 is OK

MISSING DOIs

- None

INVALID DOIs

- None

mikldk commented 2 years ago

@timClicks, @TahiriNadia: Thanks for agreeing to review.

Please note that both the repos should be reviewed (https://github.com/openjournals/joss-reviews/issues/4096#issuecomment-1020333611):

The engine: https://github.com/kno10/rust-kmedoids
Python interface: https://github.com/kno10/python-kmedoids

Please carry out your review in this issue by updating the checklist above and giving feedback in this issue. The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. If possible create issues (and cross-reference) in the submission's repository to avoid too specific discussions in this review thread.

If you have any questions or concerns please let me know.

@kno10: As you see both repos will be reviewed. This also means that when the repos are ready, you will have to prepare a combined archive (e.g. zenodo.org) of both repositories.

mikldk commented 2 years ago

@timClicks, @TahiriNadia, can you please give a brief status of your review? This is not to rush you, merely to give me an impression of the progress and time-frame.

mikldk commented 2 years ago

@timClicks, @TahiriNadia, can you please give a brief status of your review? This is not to rush you, merely to give me an impression of the progress and time-frame.

mikldk commented 2 years ago

@timClicks, @TahiriNadia, can you please give a brief status of your review? This is not to rush you, merely to give me an impression of the progress and time-frame.

mikldk commented 2 years ago

@timClicks, @TahiriNadia, can you please give a brief status of your review? This is not to rush you, merely to give me an impression of the progress and time-frame.

timClicks commented 2 years ago

I will try to have my review completed this week. Sorry for the lack of communication!

TahiriNadia commented 2 years ago

I will definitely give a brief overview of my review. Sorry too, this is my first time writing a review on JOSS and I don't know how it works.

mikldk commented 2 years ago

I will definitely give a brief overview of my review. Sorry too, this is my first time writing a review on JOSS and I don't know how it works.

Thanks. No worries. Let me know if there is anything I can help you with.

TahiriNadia commented 2 years ago

@whedon generate pdf

editorialbot commented 2 years ago

My name is now @editorialbot

TahiriNadia commented 2 years ago

@editorialbot generate pdf

editorialbot commented 2 years ago

:warning: An error happened when generating the pdf. Paper file not found.

TahiriNadia commented 2 years ago

@editorialbot check references from branch JOSS-draft

editorialbot commented 2 years ago

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

OK DOIs

- 10.1002/9780470316801.ch2 is OK
- 10.1137/0137041 is OK
- 10.1007/978-3-030-32047-8_16 is OK
- 10.1016/j.is.2021.101804 is OK
- 10.21105/joss.01230 is OK
- 10.1287/opre.16.5.955 is OK
- 10.1111/j.1538-4632.1979.tb00674.x is OK
- 10.1007/s10852-005-9022-1 is OK
- 10.1147/sj.22.0129 is OK
- 10.1016/j.eswa.2008.01.039 is OK
- 10.1093/bioinformatics/btp163 is OK

MISSING DOIs

- None

INVALID DOIs

- None

mikldk commented 2 years ago

@editorialbot set JOSS-draft as branch

editorialbot commented 2 years ago

Done! branch is now JOSS-draft

mikldk commented 2 years ago

@editorialbot check references

editorialbot commented 2 years ago

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

OK DOIs

- 10.1002/9780470316801.ch2 is OK
- 10.1137/0137041 is OK
- 10.1007/978-3-030-32047-8_16 is OK
- 10.1016/j.is.2021.101804 is OK
- 10.21105/joss.01230 is OK
- 10.1287/opre.16.5.955 is OK
- 10.1111/j.1538-4632.1979.tb00674.x is OK
- 10.1007/s10852-005-9022-1 is OK
- 10.1147/sj.22.0129 is OK
- 10.1016/j.eswa.2008.01.039 is OK
- 10.1093/bioinformatics/btp163 is OK

MISSING DOIs

- Errored finding suggestions for Clustering by means of medoids, please try later
- Errored finding suggestions for BanditPAM: Almost Linear Time k-medoids Clustering via Multi-Armed Bandits, please try later

INVALID DOIs

- None

mikldk commented 2 years ago

@timClicks, @TahiriNadia: Can you please give a brief status of your review? This is not to rush you, merely to give me an impression of the progress and time-frame.

kno10 commented 2 years ago

Hi, no updates in a month - any progress? @timClicks @TahiriNadia @mikldk

timClicks commented 2 years ago

Sorry about the lack of contact from me! I will finish the review within 24h

timClicks commented 2 years ago

@editorialbot generate pdf

editorialbot commented 2 years ago

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

timClicks commented 2 years ago

Re performance claims - the paper only claims to be faster than the upstream Java implementation. I don't think that the paper should be refused because it hasn't been benchmarked against all k-medoids/PAM implementations. Accordingly, I have marked the item as satisfied in my review.

TahiriNadia commented 2 years ago

I put my comment on this document via PR. My major comment is about the package installation, it gives me a lot of errors. I asked the authors to correct this point by managing a requirements file. However, the idea of the paper is original and very relevant since it compares the best-known classification algorithms (i.e. kmedoids) in different programming languages (i.e. java, python, Rust, C++) and in classical python libraries (i.e. biopython, sklearn_extra, pyclustering). This paper will be of great interest to the scientific community, as the task of classification is ubiquitous in various spheres of society (imaging, marketing, linguistics and others). Speed is often a critical element, especially when performing simulations of large-scale projects. Along with better documentation of how to install, a user guide and finally a requirements file, I highly recommend this article.

timClicks commented 2 years ago

Re "a statement of need" The authors describe high performance + ease of use as their motivations. This satisfies the requirements within the Documentation section of the review, but unfortunately not the Software Paper section. It requires a paragraph entitled "Statement of Need". I have submitted an issue in the Python repository.

Re Community Guidelines I could not find contributor documentation when I looked. I have submitted an issue in the Python repository along with some example wording.

timClicks commented 2 years ago

My major comment is about the package installation, it gives me a lot of errors.

Installation worked flawlessly for me today.

TahiriNadia commented 2 years ago

My major comment is about the package installation, it gives me a lot of errors.

Installation worked flawlessly for me today.

I'm trying it now and I confirm that it's OK for me too.

TahiriNadia commented 2 years ago

I put my comment on this document via PR. My major comment is about the package installation, it gives me a lot of errors. I asked the authors to correct this point by managing a requirements file. However, the idea of the paper is original and very relevant since it compares the best-known classification algorithms (i.e. kmedoids) in different programming languages (i.e. java, python, Rust, C++) and in classical python libraries (i.e. biopython, sklearn_extra, by clustering). This paper will be of great interest to the scientific community, as the task of classification is ubiquitous in various spheres of society (imaging, marketing, linguistics and others). Speed is often a critical element, especially when performing simulations of large-scale projects. Along with better documentation of how to install, a user guide, and finally a requirements file, I highly recommend this article. => FIX by @kno10

mikldk commented 2 years ago

@TahiriNadia: Can you confirm that you have finished the review and recommend that this paper is now published?

@timClicks: Thanks for specifying the remaining items for @kno10

larslenssen commented 2 years ago

Hi @timClicks, we benchmarked the performance against different implementations of kmedoids in different languages:

TahiriNadia commented 2 years ago

@TahiriNadia: Can you confirm that you have finished the review and recommend that this paper is now published?

@mikldk: Yes, I confirm that everything is finished on my side and I recommend that this paper be published.

larslenssen commented 2 years ago

@mikldk and @timClicks: We have finished the remaining items

kno10 commented 2 years ago

to see the added statement of need: @editorialbot generate pdf

mikldk commented 2 years ago

@kno10 @lale1009: Thanks. I'll wait on @timClicks have the time to check the items.

timClicks commented 2 years ago

@editorialbot generate pdf

editorialbot commented 2 years ago

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

timClicks commented 2 years ago

@mikldk I recommend this paper for publication.

@kno10 @lale1009 Please accept my apologies for the repeated delays.

mikldk commented 2 years ago

@timClicks, @TahiriNadia: Thanks for your reviews.

@kno10:

Please have a final read though of the paper, checking language etc.
Have a final check of the proofs with @editorialbot generate pdf
In general, be sure that all versions are correct and that the repo is in the state that should be published.
Please make a tagged release and archive (e.g. with Zenodo) as described here, and report the version number and archive DOI in this thread. Please verify that the archive deposit has the correct metadata (title and author list), or edit these if that is not the case.

kno10 commented 2 years ago

@mikldk: I have archived a snapshot of the Rust and Python parts version 0.3.3 at Zenodo as: Schubert, Erich, & Lenssen, Lars. (2022). Fast k-medoids Clustering in Rust and Python (0.3.3). Zenodo. https://doi.org/10.5281/zenodo.6802320 The version number is 0.3.3 (some small bug fixes were integrated, and the package is now automatically built for more architectures to make it easier to install). I do not have further changes to the paper itself.

mikldk commented 2 years ago

@editorialbot set v0.3.3 as version

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