[REVIEW]: Feature-engine: A Python package for feature engineering for machine learning

[whedon]

Submitting author: @solegalli (Soledad)
Repository: https://github.com/feature-engine/feature_engine
Version: v1.1.2
Editor: @osorensen
Reviewers: @Jose-Augusto-C-M, @papachristoumarios, @bobturneruk
Archive: 10.5281/zenodo.5515531

⚠️ JOSS reduced service mode ⚠️

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/cb8978d632aabe0bff7c3c3d7f72c419/status.svg)](https://joss.theoj.org/papers/cb8978d632aabe0bff7c3c3d7f72c419)

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

@Jose-Augusto-C-M & @papachristoumarios & @bobturneruk, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

1. Make sure you're logged in to your GitHub account
2. Be sure to accept the invite at this URL: https://github.com/openjournals/joss-reviews/invitations

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

Review checklist for @Jose-Augusto-C-M

✨ 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

• 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 repository url?
• 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 (@solegalli) 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.
• 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 and who the target audience is?
• 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?

Review checklist for @papachristoumarios

✨ 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

• 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 repository url?
• 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 (@solegalli) 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.
• 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 and who the target audience is?
• 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?

Review checklist for @bobturneruk

✨ 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

• 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 repository url?
• 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 (@solegalli) 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.
• 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 and who the target audience is?
• 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?

[whedon]

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @Jose-Augusto-C-M, @papachristoumarios, @bobturneruk it looks like you're currently assigned to review this paper 🎉.

⚠️ JOSS reduced service mode ⚠️

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

⭐ Important ⭐

If you haven't already, you should seriously consider unsubscribing from GitHub notifications for this (https://github.com/openjournals/joss-reviews) repository. As a reviewer, you're probably currently watching this repository which means for GitHub's default behaviour you will receive notifications (emails) for all reviews 😿

To fix this do the following two things:

1. Set yourself as 'Not watching' https://github.com/openjournals/joss-reviews:

2. You may also like to change your default settings for this watching repositories in your GitHub profile here: https://github.com/settings/notifications

For a list of things I can do to help you, just type:

@whedon commands

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

@whedon generate pdf

[whedon]

PDF failed to compile for issue #3642 with the following error:

 Can't find any papers to compile :-(

[whedon]

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.20 s (1025.2 files/s, 122989.2 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                         118           3806           5560           9397
reStructuredText                72           1496           2056           1400
Markdown                         6             88              0            242
YAML                             2             17             10            152
INI                              2             22              0             62
CSS                              1              5              0             15
make                             1              4              6             10
HTML                             1              1              0              3
-------------------------------------------------------------------------------
SUM:                           203           5439           7632          11281
-------------------------------------------------------------------------------


Statistical information for the repository '2c0619004a54ff6f5a5497c6' was
gathered on 2021/08/21.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Andrew Tan                       1             3              5            0.02
Arthur Cabral                    1             1              1            0.00
Ashok kumar                      2             3              3            0.01
ChristopherGS                    1            65            323            0.89
Gleb Levitskiy                   1            36              8            0.10
Indy Navarro Vidal               1            84             46            0.30
Karthik Kothareddy               2           145             10            0.36
Kishan Manani                    2             2              2            0.01
Michał Gromiec                   3           718             10            1.67
Miguel Trejo Marrufo             2           655             72            1.67
NicoGalli                        1           393             58            1.04
Nodar Okroshiashvili             1            41             50            0.21
Sana Ben Driss                   2           827              2            1.91
Soledad Galli                   35         24112          11757           82.50
Surya Krishnamurthy              2           233              3            0.54
Tejash Shah                      1           243              4            0.57
hectorpatino                     1           396              1            0.91
piecot                           1             1              1            0.00
pradumna123                      1           224              0            0.52
solegalli                        1          2937              0            6.76

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
Andrew Tan                    3          100.0          3.2                0.00
Ashok kumar                   1           33.3          7.9                0.00
ChristopherGS                 1            1.5         20.6              100.00
Indy Navarro Vidal           84          100.0          3.9                0.00
Michał Gromiec               18            2.5         12.0               11.11
Miguel Trejo Marrufo        655          100.0          0.8                8.85
NicoGalli                   289           73.5          9.3               12.80
Nodar Okroshiashvili         41          100.0          9.3                0.00
Sana Ben Driss              534           64.6          8.9               16.29
Soledad Galli             16622           68.9          7.3                9.29
hectorpatino                313           79.0          3.4                7.67
pradumna123                 202           90.2          6.8                7.92

[osorensen]

@whedon generate pdf from branch paper

[whedon]

Attempting PDF compilation from custom branch paper. Reticulating splines etc...

[whedon]

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

[papachristoumarios]

@osorensen My review is complete via the checklist above. Briefly, I liked the paper and the functionality it provides on a data scientist's pipeline. The software is widely used, well-structured and passes all the quality criteria outlined by the JOSS guidelines.

Finally, as a request for future work I have opened an issue (feature-engine/feature_engine#302) requesting a data imputation method and data generation methods.

[osorensen]

Thanks a lot for your work, @papachristoumarios!

[osorensen]

@whedon generate pdf from branch paper

[whedon]

Attempting PDF compilation from custom branch paper. Reticulating splines etc...

[whedon]

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

[whedon]

👋 @Jose-Augusto-C-M, please update us on how your review is going (this is an automated reminder).

[whedon]

👋 @bobturneruk, please update us on how your review is going (this is an automated reminder).

[Jose-Augusto-C-M]

Hello, I can´t update the checklist, I think that my invitation link expired.

[osorensen]

Thanks for letting us know @Jose-Augusto-C-M. Does nothing happen if you try to click the check boxes? Could you please give it a try with a different browser? If that doesn't work I'll ask for help.

[osorensen]

@whedon add @Jose-Augusto-C-M as reviewer

[whedon]

OK, @Jose-Augusto-C-M is now a reviewer

[bobturneruk]

👋 @bobturneruk, please update us on how your review is going (this is an automated reminder).

Thanks @whedon. Started looking at the COI statement on Friday.

[kthyng]

Ok great, thanks. One more thing: please update the title and author list of the Zenodo archive metadata so they exactly match the JOSS paper.

[kthyng]

@whedon set 10.5281/zenodo.5515531 as archive

[whedon]

OK. 10.5281/zenodo.5515531 is the archive.

[kthyng]

@whedon set v1.1.2 as version

[whedon]

OK. v1.1.2 is the version.

[solegalli]

Ok great, thanks. One more thing: please update the title and author list of the Zenodo archive metadata so they exactly match the JOSS paper.

I am not sure I understand what I need to do. Should I delete all the other authors from zenodo?

[solegalli]

Ok, I think I got it. It is updated now.

[kthyng]

Presumably the people listed made minor contributions to the software at some point and were auto-included by Zenodo. If on the other hand they were authors of the software, they should be included as co-authors to the paper itself.

[solegalli]

Thank you!. It's been updated.

We discussed the authorship in the pre-review PR :)

[kthyng]

@whedon accept deposit=true

[whedon]

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

[whedon]

PDF failed to compile for issue #3642 with the following error:

 Can't find any papers to compile :-(

[kthyng]

@whedon accept deposit=true from branch paper

[whedon]

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

[whedon]

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

[whedon]

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

Here's what you must now do:

0. Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.03642 joss-papers#2603
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.03642
2. If everything looks good, then close this review issue.
3. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

[kthyng]

@openjournals/dev it's been awhile and the DOI page is still not resolving.. any ideas?

[kthyng]

@openjournals/dev This is still not resolving for me — strange!

[kthyng]

@openjournals/dev, @arfon I'm going to stop checking this after today so I wanted to get one more ping in. The DOI is not resolving for me, 2 days later.

[arfon]

@openjournals/dev, @arfon I'm going to stop checking this after today so I wanted to get one more ping in. The DOI is not resolving for me, 2 days later.

I re-deposited the metadata. Not sure what was going on here but the DOI is resolving now.

[whedon]

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

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

Markdown:
[![DOI](https://joss.theoj.org/papers/10.21105/joss.03642/status.svg)](https://doi.org/10.21105/joss.03642)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.03642">
  <img src="https://joss.theoj.org/papers/10.21105/joss.03642/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.03642/status.svg
   :target: https://doi.org/10.21105/joss.03642

This is how it will look in your documentation:

We need your help!

Journal of Open Source Software is a community-run journal and relies upon volunteer effort. If you'd like to support us please consider doing either one (or both) of the the following:

• Volunteering to review for us sometime in the future. You can add your name to the reviewer list here: https://joss.theoj.org/reviewer-signup.html
• Making a small donation to support our running costs here: https://numfocus.org/donate-to-joss

[arfon]

@Jose-Augusto-C-M, @papachristoumarios, @bobturneruk – many thanks for your reviews here and to @osorensen for editing this submission! JOSS relies upon the volunteer effort of people like you and we simply wouldn't be able to do this without you ✨

@solegalli – your paper is now accepted and published in JOSS ⚡🚀💥