[REVIEW]: fseval: A Benchmarking Framework for Feature Selection and Feature Ranking Algorithms

[editorialbot]

Submitting author: @dunnkers (Jeroen Gerard Sebastiaan Overschie) Repository: https://github.com/dunnkers/fseval Branch with paper.md (empty if default branch): paper Version: v3.0.2 Editor: @diehlpk Reviewers: @mcasl, @estefaniatalavera Archive: Pending

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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

@mcasl & @estefaniatalavera, 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:

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

📝 Checklist for @estefaniatalavera

[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:

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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]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.09 s (42.7 files/s, 4799.5 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
TeX                              1             16              0            204
Markdown                         1             28              0            178
YAML                             1              1              4             18
SVG                              1              0              0              1
-------------------------------------------------------------------------------
SUM:                             4             45              4            401
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 1376

[editorialbot]

Failed to discover a valid open source license

[editorialbot]

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

[editorialbot]

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

OK DOIs

- 10.1016/j.eswa.2015.07.007 is OK
- 10.1109/ICCV.2015.478 is OK
- 10.1109/TPAMI.2005.159 is OK
- 10.1007/10968987_3 is OK
- 10.1145/2641190.2641198 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[dunnkers]

@editorialbot check repository from branch master

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.21 s (931.8 files/s, 38979.6 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          81           1024            658           3096
Markdown                        19            437              0           1227
YAML                            67             14             10            639
SVG                             10              6              1            495
JavaScript                       7             32             36            343
JSON                             7              0              0             98
CSS                              4             11             10             60
TypeScript                       1              5              2             34
Dockerfile                       1              1              0              2
-------------------------------------------------------------------------------
SUM:                           197           1530            717           5994
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

[editorialbot]

Failed to discover a Statement of need section in paper

[dunnkers]

@editorialbot generate pdf

(should now discover Statement of need)

[dunnkers]

@editorialbot generate pdf

[editorialbot]

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

[editorialbot]

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

[mcasl]

Review checklist for @mcasl

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/dunnkers/fseval?
• ✅ 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 (@dunnkers) 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

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.

• ✅ 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?

• ✅ Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).

• ✅ 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?

[diehlpk]

@editorialbot generate pdf

[editorialbot]

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

[mcasl]

The ‘Software Paper’ section of my checklist shows that “State of the field” and “References” need improvement. I failed to discover the state of the field in the paper, and thus, while completing that section, the references will need to be update to reflect the new additions to the paper

[mcasl]

The “Documentation” section of my checklist shows that a “Statement of need” is missing. The target audience is covered in the motivation section of the documentation, but the description of the problems the software is designed to solve is weak.

[mcasl]

The “Documentation” section of my checklist shows that the “Installation instructions” need improvement. Though there is a requeriments.txt file to automatically install the dependencies, the documentation fails to explicitly describe these dependencies.

[mcasl]

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[mcasl]

The checklist shows that “Functionality documentation” needs improvement. Though the methods’ documentation reflects the parameters, results and a succinct explanation of what they do, more time has to be devoted to the documentation to clearly explain the new user the elements of the library and how to use them.

[diehlpk]

Hi @dunnkers, please have a look at the comments above.

[dunnkers]

Hi @mcasl thanks for the review and @diehlpk thanks for notifying me - I am going to have a look.

[diehlpk]

@dunnkers how are things going?

[dunnkers]

@dunnkers how are things going?

Hi @diehlpk. I just merged https://github.com/dunnkers/fseval/pull/81 and am working on https://github.com/dunnkers/fseval/pull/83, making improvements where necessary. So it's in-progress.

[estefaniatalavera]

Hello,

Can you please change the contact email to the one from my new employer? The old one has been deactivated.

@.*** @.***>

Thank you! Best regards, Estefania

—————————————————————————— Dr. Estefanía Talavera | Assistant Professor Data Management and Biometrics | University of Twente Zilverling room 4098 https://estefaniatalavera.github.io/ https://estefaniatalavera.github.io/ | https://people.utwente.nl/e.talaveramartinez https://people.utwente.nl/e.talaveramartinez

On 23 Aug 2022, at 17:35, The Open Journals editorial robot @.*** @.***>> wrote:

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[dunnkers]

Dear @estefaniatalavera , you will have to update your email address yourself in your own GitHub settings here:

https://docs.github.com/en/account-and-profile/setting-up-and-managing-your-personal-account-on-github/managing-email-preferences/adding-an-email-address-to-your-github-account

Thanks :)

[diehlpk]

Hi @estefaniatalavera could you change your email address?

How is your review going?

[estefaniatalavera]

@dunnkers @diehlpk

This is a useful package for the community. I would suggest the following improvement to the document:

• The first sentence of the statement of need mentions that FS and FR are extensively researched topics within machine learning, but the reference you include is from 2003. Aren’t there more recent works that present an overview of this field?
• If this is the first of such tools, clearly state it. If not, include a comparison with such other tools.
• If page limit allows it, this document would be more efficient into attracting new users by describing terminology and technology used. For instance, terms and concepts such as dataset adapters, bootstrap, AWS, among others could be described. Hydra was correctly presented.
• The document does not use numbering for the sections but they are referenced like that. You should fix that. For instance, you refer to section 3.2 in dataset adapters.
• The “Analyze algorithm stability” is mentioned but not described.
• I suggest you use the images equally in both the paper and documentation website.
• I miss a section on how the results look like and how they can be visualised or interpreted by the user of such package.

Improvements documentation website:

• Use verbs in present form. For example, in https://dunnkers.com/fseval/docs/the-pipeline/ pipeline step 4.