[REVIEW]: Arabica: A Python package for exploratory analysis of text data

[editorialbot]

Submitting author: @PetrKorab (Petr Koráb)
Repository: https://github.com/PetrKorab/Arabica
Branch with paper.md (empty if default branch): main
Version: 1.7.1
Editor: @oliviaguest
Reviewers: @linuxscout, @amitkumarj441
Archive: 10.5281/zenodo.10866696

Status

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Markdown: [![status](https://joss.theoj.org/papers/c036ff8390e992855fae27db2536b3a8/status.svg)](https://joss.theoj.org/papers/c036ff8390e992855fae27db2536b3a8)

Reviewers and authors:

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Reviewer instructions & questions

@linuxscout & @amitkumarj441, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review.
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The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @oliviaguest 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 @linuxscout

📝 Checklist for @amitkumarj441

[editorialbot]

Hello humans, I'm @editorialbot, a robot that can help you with some common editorial tasks.

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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=0.14 s (536.3 files/s, 241148.5 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
JavaScript                      13           4507           4506          16694
CSS                              6            496            126           1791
Python                          13            264             59           1029
HTML                             8            317              0            905
Jupyter Notebook                 3              0            158            595
reStructuredText                17            392            340            393
Markdown                         2             65              0            200
TeX                              1             14              0            133
XHTML                            3             14              0             79
XML                              3              0              0             67
YAML                             3             12             23             38
DOS Batch                        1              8              1             26
make                             1              4              7              9
-------------------------------------------------------------------------------
SUM:                            74           6093           5220          21959
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 810

[editorialbot]

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

OK DOIs

- 10.18637/jss.v106.i02 is OK
- 10.1109/MCSE.2007.55 is OK
- 10.1609/icwsm.v8i1.14550 is OK
- 10.3389/fphys.2019.00203 is OK

MISSING DOIs

- 10.21105/joss.04886 may be a valid DOI for title: PyArabic: A Python package for Arabic text.

INVALID DOIs

- None

[editorialbot]

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

[oliviaguest]

👋 Hi @linuxscout, @amitkumarj441, thank you so much for helping out at JOSS. If you need any pointers, please feel free to look at previous reviews (which can be found by looking at published papers) and the documentation. If you need to comment on the code itself, opening an issue at the repo and then linking to it from here (to help me/others keep track) is the way to go. For comments on the paper, you can also open issues or PRs (say for typos), but those can be directly posted as replies in this issue. Thanks, and feel free to reach out if you need me. ☺️

[oliviaguest]

can you check the missing DOI @PetrKorab, please?

[linuxscout]

Review checklist for @linuxscout

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/PetrKorab/Arabica?
• License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@PetrKorab) 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
• 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.
• Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
• 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

• 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, 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?

[PetrKorab]

@oliviaguest I've added DOI for PyArabic: A Python package for Arabic text.

[amitkumarj441]

Review checklist for @amitkumarj441

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/PetrKorab/Arabica?
• License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@PetrKorab) 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
• 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.
• Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
• 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

• 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, 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?

[linuxscout]

@oliviaguest I've added DOI for PyArabic: A Python package for Arabic text.
@PetrKorab

I believe the reference to this package, PyArabic, is inappropriate for this work because PyArabic is a modest library for basic Arabic text functionality. I recommend citing more complex text processing frameworks or data visualizations.

[linuxscout]

@PetrKorab
Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
I added an issue to repo: PetrKorab/Arabica#11

[PetrKorab]

@linuxscout @oliviaguest Thanks. Should I revise the paper now ?

@oliviaguest I've added DOI for PyArabic: A Python package for Arabic text.
@PetrKorab

I believe the reference to this package, PyArabic, is inappropriate for this work because PyArabic is a modest library for basic Arabic text functionality. I recommend citing more complex text processing frameworks or data visualizations.

[linuxscout]

I give my Ok for this paper.

[linuxscout]

@linuxscout @oliviaguest Thanks. Should I revise the paper now ?

@oliviaguest I've added DOI for PyArabic: A Python package for Arabic text.
@PetrKorab

I believe the reference to this package, PyArabic, is inappropriate for this work because PyArabic is a modest library for basic Arabic text functionality. I recommend citing more complex text processing frameworks or data visualizations.

automated tests are provided and the issue is closed.

[oliviaguest]

@linuxscout thank you so much. ☺️

[PetrKorab]

@oliviaguest Hi, may I ask what's the current status of the submission? ☺️

[oliviaguest]

I believe @amitkumarj441 has not completed the checklist yet?

[amitkumarj441]

@oliviaguest Thanks for the reminder. I have been reviewing this codebase earlier in mid Feb but kind of busy with other commitments and due to no notifications, It just slipped from my schedule. I will send my reviews soon.

[amitkumarj441]

@editorialbot check references

[editorialbot]

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

OK DOIs

- 10.18637/jss.v106.i02 is OK
- 10.1109/MCSE.2007.55 is OK
- 10.1609/icwsm.v8i1.14550 is OK
- 10.3389/fphys.2019.00203 is OK
- 10.21105/joss.04886 is OK

MISSING DOIs

- No DOI given, and none found for title: Cleantext—An open-source python package to clean r...
- No DOI given, and none found for title: FinVADER: VADER sentiment classifier updated with ...
- No DOI given, and none found for title: Optimal data classification for choropleth maps
- No DOI given, and none found for title: Jenkspy- Compute Natural Breaks (Fisher-Jenks algo...
- No DOI given, and none found for title: NLTK: The Natural Language Toolkit
- No DOI given, and none found for title: Python for data analysis
- No DOI given, and none found for title: NETWORK: Stata module to perform network meta-anal...
- No DOI given, and none found for title: texthero — Text preprocessing, representation and ...
- No DOI given, and none found for title: Textblob - Simple, Pythonic text processing. Senti...
- No DOI given, and none found for title: The Grammar of Graphics

INVALID DOIs

- None

[oliviaguest]

@amitkumarj441 what's a sensible ETA for your review? ☺️

[amitkumarj441]

I was able to run the python tests without any issue and most of the functionalities in the examples work well, though, I suggest checking the compatibility among the dependencies, such as the requirement for installing this should be at least Python 3.8.x. However, it is Python 3.9 in setup.py, I suggest fixing python_requires=>3.9. Also, I suggest an instruction for a source installation as pip install Arabica and given the version of this package upon installation is 1.7.7, you should fix it here . On another note, you should make use of Makefile to have an automated tests.

@PetrKorab I suggest fixing the missing DOIs as well.

[amitkumarj441]

@editorialbot check references

[editorialbot]

⚠️ An error happened when generating the pdf.

[oliviaguest]

@PetrKorab I didn't mean that and in fact that might be a bug? Please fix that too.

What I mean is, see these:

Unlike the current packages to perform meta-analysis ((White, 2017); (Mikolajewicz & Komarova, 2019); (Balduzzi et al., 2023)), the package leverages text mining methods for

While some existing text-processing packages (e.g. (Zerrouki, 2022)) focus on a specific

They do need to have double brackets. I can show you how to fix this if you do not know how, but please fix the compilaton bugs first?

[PetrKorab]

@editorialbot check references

[editorialbot]

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

OK DOIs

- 10.18637/jss.v106.i02 is OK
- 10.1109/MCSE.2007.55 is OK
- 10.1609/icwsm.v8i1.14550 is OK
- 10.48550/arXiv.cs/0205028 is OK
- 10.3389/fphys.2019.00203 is OK
- 10.21105/joss.04886 is OK
- 10.1007/0-387-28695-0 is OK

MISSING DOIs

- No DOI given, and none found for title: Cleantext—An open-source python package to clean r...
- No DOI given, and none found for title: FinVADER: VADER sentiment classifier updated with ...
- No DOI given, and none found for title: Optimal data classification for choropleth maps
- No DOI given, and none found for title: Jenkspy- Compute Natural Breaks Fisher-Jenks algor...
- No DOI given, and none found for title: Python for data analysis
- No DOI given, and none found for title: NETWORK: Stata module to perform network meta-anal...
- No DOI given, and none found for title: texthero — Text preprocessing, representation and ...
- No DOI given, and none found for title: Textblob - Simple, Pythonic text processing. Senti...

INVALID DOIs

- None

[PetrKorab]

@editorialbot generate pdf

[editorialbot]

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

[PetrKorab]

@oliviaguest I made these updates, thanks.

[oliviaguest]

@PetrKorab OK, I think I will do a PR to explain. Perhaps it's just that you have not seen this type of citation format previously.

[oliviaguest]

Let me know if this is clear: PetrKorab/Arabica#12 and/or just merge it. Thanks. What else is left to do?

[oliviaguest]

Check that the archive title, author list, version tag, and the license are correct

[oliviaguest]

OK, so once that PR is dealt with can you make sure the version is OK? I see pypi has 1.7.7 but above is 1.7.1, which is right for JOSS? Otherwise, we're good to go. 😊

[PetrKorab]

@oliviaguest Many thanks for the explanation. Yes, I came from the Economics field where the citation system is a bit different. For JOSS, 1.7.7 is correct. Thanks ! :)

[oliviaguest]

@editorialbot recommend-accept

[editorialbot]

Attempting dry run of processing paper acceptance...

[editorialbot]

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

OK DOIs

- 10.18637/jss.v106.i02 is OK
- 10.1109/MCSE.2007.55 is OK
- 10.1609/icwsm.v8i1.14550 is OK
- 10.48550/arXiv.cs/0205028 is OK
- 10.3389/fphys.2019.00203 is OK
- 10.21105/joss.04886 is OK
- 10.1007/0-387-28695-0 is OK

MISSING DOIs

- No DOI given, and none found for title: Cleantext—An open-source python package to clean r...
- No DOI given, and none found for title: FinVADER: VADER sentiment classifier updated with ...
- No DOI given, and none found for title: Optimal data classification for choropleth maps
- No DOI given, and none found for title: Jenkspy- Compute Natural Breaks Fisher-Jenks algor...
- No DOI given, and none found for title: Python for data analysis
- No DOI given, and none found for title: NETWORK: Stata module to perform network meta-anal...
- No DOI given, and none found for title: texthero — Text preprocessing, representation and ...
- No DOI given, and none found for title: Textblob - Simple, Pythonic text processing. Senti...

INVALID DOIs

- None

[editorialbot]

👋 @openjournals/sbcs-eics, this paper is ready to be accepted and published.

Check final proof 👉📄 Download article

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#5306, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[oliviaguest]

@editorialbot accept

[editorialbot]

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

[editorialbot]

Ensure proper citation by uploading a plain text CITATION.cff file to the default branch of your repository.

If using GitHub, a Cite this repository menu will appear in the About section, containing both APA and BibTeX formats. When exported to Zotero using a browser plugin, Zotero will automatically create an entry using the information contained in the .cff file.

You can copy the contents for your CITATION.cff file here:

CITATION.cff

cff-version: "1.2.0"
authors:
- family-names: Koráb
  given-names: Petr
  orcid: "https://orcid.org/0000-0003-2513-8981"
- family-names: Poměnková
  given-names: Jitka
  orcid: "https://orcid.org/0000-0002-8060-0086"
contact:
- family-names: Koráb
  given-names: Petr
  orcid: "https://orcid.org/0000-0003-2513-8981"
doi: 10.5281/zenodo.10866696
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Koráb
    given-names: Petr
    orcid: "https://orcid.org/0000-0003-2513-8981"
  - family-names: Poměnková
    given-names: Jitka
    orcid: "https://orcid.org/0000-0002-8060-0086"
  date-published: 2024-05-05
  doi: 10.21105/joss.06186
  issn: 2475-9066
  issue: 97
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 6186
  title: "Arabica: A Python package for exploratory analysis of text
    data"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.06186"
  volume: 9
title: "Arabica: A Python package for exploratory analysis of text data"

If the repository is not hosted on GitHub, a .cff file can still be uploaded to set your preferred citation. Users will be able to manually copy and paste the citation.

Find more information on .cff files here and here.

[editorialbot]

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

[editorialbot]

🚨🚨🚨 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.06186 joss-papers#5307
1. Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.06186
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...

[oliviaguest]

Huge thanks to the reviewers (@linuxscout, @amitkumarj441)! ✨ JOSS appreciates your work and effort. ✨ Also, big congratulations to the author(s), @PetrKorab! 🥳 🍾

[editorialbot]

🎉🎉🎉 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.06186/status.svg)](https://doi.org/10.21105/joss.06186)

HTML:
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  <img src="https://joss.theoj.org/papers/10.21105/joss.06186/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.06186/status.svg
   :target: https://doi.org/10.21105/joss.06186

This is how it will look in your documentation:

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[PetrKorab]

@oliviaguest @linuxscout @amitkumarj441
Many thanks for your time 👋 I will update README and will also gladly serve as a reviewer.