editorialbot commented 2 years ago

Submitting author: !--author-handle-->@dunnkers@diehlpk<!--end-editor-- Reviewers: @mcasl, @estefaniatalavera Archive: 10.5281/zenodo.7343417

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/d850aeb67247318aeef735d5eca95c1c/status.svg)](https://joss.theoj.org/papers/d850aeb67247318aeef735d5eca95c1c)

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:

@editorialbot generate my checklist

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 commented 2 years 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 2 years ago

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 commented 2 years ago

Wordcount for paper.md is 1376

editorialbot commented 2 years ago

Failed to discover a valid open source license

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:

editorialbot commented 2 years ago

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 commented 2 years ago

@editorialbot check repository from branch master

editorialbot commented 2 years ago

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 commented 2 years ago

Failed to discover a Statement of need section in paper

dunnkers commented 2 years ago

@editorialbot generate pdf

(should now discover Statement of need)

dunnkers 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:

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:

mcasl commented 2 years ago

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 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:

mcasl commented 2 years ago

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 commented 2 years ago

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 commented 2 years ago

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 commented 2 years ago

@editorialbot commands

editorialbot commented 2 years ago

Hello @mcasl, 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

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

mcasl commented 2 years ago

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 commented 2 years ago

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

dunnkers commented 2 years ago

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

diehlpk commented 2 years ago

@dunnkers how are things going?

dunnkers commented 2 years ago

@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 commented 2 years ago

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:

👉📄 Download article proof https://raw.githubusercontent.com/openjournals/joss-papers/joss.04611/joss.04611/10.21105.joss.04611.pdf 📄 View article proof on GitHub https://github.com/openjournals/joss-papers/blob/joss.04611/joss.04611/10.21105.joss.04611.pdf 📄 👈

— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/4611#issuecomment-1224243707, or unsubscribe https://github.com/notifications/unsubscribe-auth/ACR5ZWCMCPQIW5PBP5LBDC3V2TVUJANCNFSM54WI6XXA. You are receiving this because you were mentioned.

dunnkers commented 2 years ago

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 commented 1 year ago

Hi @estefaniatalavera could you change your email address?

How is your review going?

estefaniatalavera commented 1 year ago

@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.

diehlpk commented 1 year ago

@dunnkers Please have a look at the above comments.

diehlpk commented 1 year ago

@mcasl can you have please a look at the new changes?

diehlpk commented 1 year ago

@estefaniatalavera can you please run @editorialbot generate my checklist to generate your checklist?

estefaniatalavera commented 1 year ago

Review checklist for @estefaniatalavera

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/dunnkers/fseval?
[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 (@dunnkers) 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?

estefaniatalavera 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:

dunnkers commented 1 year ago

Dear @estefaniatalavera @mcasl @diehlpk, I worked hard to process more feedback. These are some of the changes on the repo side of things (package and documentation):

[x] Installation instructions were improved (https://github.com/dunnkers/fseval/pull/81)
[x] 2 new recipes to better illustrate the "essential components of the library"
- [x] analyzing algorithm stability (https://github.com/dunnkers/fseval/pull/83)
- [x] running fseval on AWS (https://github.com/dunnkers/fseval/pull/86)
[x] Pipeline schematic was updated on the website (https://github.com/dunnkers/fseval/pull/88)

For the paper, I have an open PR here:

[x] Improve paper (https://github.com/dunnkers/fseval/pull/85)

Which is to be shortly reviewed by my peer-submitters.

That said, we have been (and are actively) working on processing the feedback of both @mcasl and @estefaniatalavera.

Update:

[x] Added Developer guidelines for contributing (https://github.com/dunnkers/fseval/pull/89)
[x] Paper reviewed by peer-submitters & merged into paper

dunnkers 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:

diehlpk commented 1 year ago

@estefaniatalavera and @mcasl could you please have a look at the changes @dunnkers made?

dunnkers commented 1 year ago

Update: added a recipe called "Comparing Feature Selectors", explaining how to run a benchmark of bigger size and analyse the results in a Jupyter-notebook style explanation. Shows the experiment results using both a table and a plot.

( https://github.com/dunnkers/fseval/pull/90 )

diehlpk commented 1 year ago

@estefaniatalavera and @mcasl could you please have a look at the changes @dunnkers made?

estefaniatalavera commented 1 year ago

@dunnkers you mentioned that you were waiting by your peer-submitters, to review the updated version of the paper. Could you confirm if this has already happened?

dunnkers commented 1 year ago

@dunnkers you mentioned that you were waiting by your peer-submitters, to review the updated version of the paper. Could you confirm if this has already happened?

Hi @estefaniatalavera. Yes this has happened (mentioned at the bottom of this comment ✅). Cheers! 🌞

diehlpk commented 1 year ago

@estefaniatalavera and @mcasl could you please have a look at the changes @dunnkers made?

estefaniatalavera 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:

estefaniatalavera commented 1 year ago

@diehlpk I am satisfied with the current status of the project. How can I proceed to suggest acceptance of this work?

diehlpk commented 1 year ago

@diehlpk I am satisfied with the current status of the project. How can I proceed to suggest acceptance of this work?

By checking all items in your checklist and letting me know in the comments.

diehlpk commented 1 year ago

@mcasl how is your review going?

openjournals / joss-reviews

[REVIEW]: fseval: A Benchmarking Framework for Feature Selection and Feature Ranking Algorithms #4611

Status

Reviewer instructions & questions

Checklists

Review checklist for @mcasl

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @estefaniatalavera

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper