[REVIEW]: Augmenty: A Python Library for Structured Text Augmentation

[editorialbot]

Submitting author: @KennethEnevoldsen (Kenneth C. Enevoldsen)
Repository: https://github.com/KennethEnevoldsen/augmenty
Branch with paper.md (empty if default branch):
Version: joss
Editor: @arfon
Reviewers: @sap218, @wdduncan
Archive: 10.5281/zenodo.11002422

Status

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Reviewers and authors:

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Reviewer instructions & questions

@sap218 & @wdduncan, 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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✨ 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 @sap218

📝 Checklist for @wdduncan

[editorialbot]

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[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.14 s (853.9 files/s, 71243.5 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          75            736           1042           2736
Markdown                        12           1080              0           1667
JSON                             3              0              0            415
YAML                             8             44             20            318
TeX                              1              2              0            194
reStructuredText                13            151            134            173
TOML                             1             10              4            163
Jupyter Notebook                 2              0            668             82
make                             1              8              0             31
-------------------------------------------------------------------------------
SUM:                           116           2031           1868           5779
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 1040

[editorialbot]

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

[editorialbot]

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

OK DOIs

- 10.18653/v1/2020.acl-main.442 is OK
- 10.18653/v1/D19-1670 is OK
- 10.5281/zenodo.1212303 is OK
- 10.18653/v1/2021.naacl-demos.6 is OK
- 10.18653/v1/2023.latechclfl-1.13 is OK
- 10.3115/v1/D14-1162 is OK

MISSING DOIs

- 10.21437/interspeech.2019-2680 may be a valid DOI for title: SpecAugment: A Simple Data Augmentation Method for Automatic Speech Recognition
- 10.1007/978-3-030-57321-8_21 may be a valid DOI for title: Improving short text classification through global augmentation methods
- 10.18653/v1/2020.emnlp-demos.16 may be a valid DOI for title: TextAttack: A Framework for Adversarial Attacks, Data Augmentation, and Adversarial Training in NLP

INVALID DOIs

- None

[arfon]

@sap218, @wdduncan This is the review thread for the paper. All of our communications will happen here from now on.

Please read the "Reviewer instructions & questions" in the first comment above. Please create your checklist typing:

@editorialbot generate my checklist

As you go over the submission, please check any items that you feel have been satisfied. There are also links to the JOSS reviewer guidelines.

The JOSS review is different from most other journals. Our goal is to work with the authors to help them meet our criteria instead of merely passing judgment on the submission. As such, the reviewers are encouraged to submit issues and pull requests on the software repository. When doing so, please mention https://github.com/openjournals/joss-reviews/issues/6370 so that a link is created to this thread (and I can keep an eye on what is happening). Please also feel free to comment and ask questions on this thread. In my experience, it is better to post comments/questions/suggestions as you come across them instead of waiting until you've reviewed the entire package.

We aim for the review process to be completed within about 4-6 weeks but please make a start well ahead of this as JOSS reviews are by their nature iterative and any early feedback you may be able to provide to the author will be very helpful in meeting this schedule.

[sap218]

Review checklist for @sap218

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/KennethEnevoldsen/augmenty?
• 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 (@KennethEnevoldsen) 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?

[sap218]

Hi all! Happy to have started this review - looking great and I've successfully ran the "Simple Example" from the repo.

Whilst I am looking into the code, I have some initial comments about the Paper:

• Needs a little introduction to text augmentation itself - e.g. "Text augmentation is creating pseudo/AI-generated text" etc. just to give the reader a little more context
• Fix references: spaCy [honnibal_efficient_2020] line 12/41, & NLTK [bird2009natural] line 64 & ref on line 66
• On line 22 you have "natural language processing (NLP)" but you can move this to line 7 and instead use the abbreviation NLP from that point onward
• On line 21 "used for both training more robust models and for evaluating the ability of the models to handle pertubations" this is actually repeated from line 6
• Moreover, I would like if Summary to focus more on Augmenty and keep Statement of Need about other packages
• I would like Statement of Need to end on the introduction to Augmenty (so it flows nicely to Features and Functions) and so move the final paragraph (lines 46-52) to before the introduction of Augmenty

Some little things I wanted to mention - I appreciate that the author acknowledges the contributors & the documentation is very good and thorough!

Happy to check these things off when addressed - please let me know if you have any questions (hope it all makes sense)
Will continue with the review this week! :)

[KennethEnevoldsen]

Thanks for the suggestions @sap218 I have fixed 1, 2, 3, 6.

re. 4) it is a summary so some degree of duplication is expected. If you feel it is a big problem I will reformulate the sentence, but I don't see it as problematic.

re. 5) I believe the summary should include both the relevant context as well as the package. If you have specific information you would like added to the summary I would be more than happy to rewrite it. Statement of needs is structured such that existing augmentation libraries are contrasted with augmenty, I believe this is the best way to highlight both the need for the package, but also what it tried to solve and what it does not.

[KennethEnevoldsen]

@editorialbot generate pdf

[editorialbot]

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

[KennethEnevoldsen]

@editorialbot generate pdf

[editorialbot]

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

[sap218]

Hi @KennethEnevoldsen thank you for addressing my comments! I think the paper flows much better and I appreciate your comments on 4 & 5 - I've ticked off these points from my review checklist :)

One minor last thing, on line 67 ref needs fixing (pennington-etal-2014-glove)

[sap218]

1. In Documentation "Installation instructions: Is there a clearly-stated list of dependencies?" I might be missing this but I can't find these dependencies easily?
2. In Documentation "Functionality documentation" I am happy with your documentation! This isn't necessary to change but the table on page "Overview of Augmenters" is a little difficult to navigate for me - perhaps font is too big or you could move description into same column as Augmenter name - but again you don't need to change this if you wish to keep it as is :)

[wdduncan]

I've started reviewing. So far here is what I've done using python 3.11.8 and pip version 24.0. I am running code on an a MacBook Pro with an Apple M1 Max processor and 64GB of RAM; OSX version Sonoma 14.3.1.

• created a virtual environment with python -m venv
• installed using pip install augmenty
  • when I try to install using pip install augmenty[all], it fails with zsh: no matches found: augmenty[all]. any ideas why?
• run make test -> this fails with error make: *** [test] Abort trap: 6. perhaps a memory error?
• it would helpful if the instructions included instructions about downloading spacy models; e.g. I had run python -m spacy download en_core_web_sm to get en_core_web_sm. also, I am not an expert using spacy, but to get your github code to run, I had to load en_core_web_sm using:

import en_core_web_sm 
nlp = en_core_web_sm.load()

• when I run:

for doc in augmenty.docs(docs, augmenter=entity_augmenter, nlp=nlp):
    print(doc)

it fails with error NameError: name 'docs' is not defined.

am I using the correct version of python?

[KennethEnevoldsen]

Hi @sap218

1. the pyproject.toml specified all the required dependencies. The pyproject.toml is a more recent alternative to setup.py and setup.cfg (I believe it is the recommended format)

2. I agree the table could be better. Currently, there is sadly not a lot of support for tables in the sphinx ecosystem. I will see if I can make it clearer though.

[KennethEnevoldsen]

Hi @wdduncan

1. When running on zsh I believe you need to write pip install "augmenty[all]" (I will change to documentation to match)
2. to run the make test you will have to install it using make install, this installs the development dependencies as well. I have tried to make this more clear in the contributing.md.
3. I agree that it should be clear that it needs to be downloaded. I have added a comment:

import spacy
import augmenty

nlp = spacy.load("en_core_web_md")
# if not installed run: python -m spacy download en_core_web_md

docs = nlp.pipe(["Augmenty is a great tool for text augmentation"])

entity_augmenter = augmenty.load("ents_replace_v1", 
                                 ent_dict = {"ORG": [["spaCy"], ["spaCy", "Universe"]]}, level=1)

for doc in augmenty.docs(docs, augmenter=entity_augmenter, nlp=nlp):
    print(doc)

3.1) You shouldn't need to use this syntax. However, that seems to be a spacy issue. If you only have issues with it when installing augmenty let me know. (I suspect it might be spacy assuming something about your paths)

4. I believe you need to run the following line:

docs = nlp.pipe(["Augmenty is a great tool for text augmentation"])

If this step failed it could suggest an error in your spacy pipeline installation.

[sap218]

Hi @KennethEnevoldsen

1. Thanks for letting me know! I've ticked off this item (Installation instructions: Is there a clearly-stated list of dependencies?)
2. I appreciate this - no worries if you can't come to a solution as I do think the table does the job well 😃

I should be completed with my review at the end of this week/next week (functionality and automated tests are left)

[arfon]

👋 @wdduncan – it looks like you've not started your review yet. Do you think you might be able to complete it in the next couple of weeks?

[wdduncan]

@editorialbot generate my checklist

[arfon]

@editorialbot generate pdf

[editorialbot]

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

[arfon]

@KennethEnevoldsen – can you please merge this PR please? KennethEnevoldsen/augmenty#224

It also looks like we're very close to being done here. I will circle back here next week, but in the meantime, please give your own paper a final read to check for any potential typos etc.

After that, could you make a new release of this software that includes the changes that have resulted from this review. Then, please make an archive of the software in Zenodo/figshare/other service and update this thread with the DOI of the archive? For the Zenodo/figshare archive, please make sure that:

• The title of the archive is the same as the JOSS paper title
• That the authors of the archive are the same as the JOSS paper authors
• I can then move forward with accepting the submission.

[KennethEnevoldsen]

Thanks, @arfon, I believe all of the things are now done:

• Read through the paper and correct any issues I found
• Create a release at https://zenodo.org/records/11002422
  • with the name of the publication
  • with the same authors as the publication

[arfon]

@editorialbot set 10.5281/zenodo.11002423 as archive

[editorialbot]

Done! archive is now 10.5281/zenodo.11002423

[arfon]

@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

- 10.18653/v1/2020.acl-main.442 is OK
- 10.18653/v1/D19-1670 is OK
- 10.5281/zenodo.1212303 is OK
- 10.18653/v1/2021.naacl-demos.6 is OK
- 10.18653/v1/2023.latechclfl-1.13 is OK
- 10.3115/v1/D14-1162 is OK

MISSING DOIs

- No DOI given, and none found for title: The effectiveness of data augmentation in image cl...
- 10.21437/interspeech.2019-2680 may be a valid DOI for title: SpecAugment: A Simple Data Augmentation Method for...
- No DOI given, and none found for title: ScandEval: A Benchmark for Scandinavian Natural La...
- No DOI given, and none found for title: hetpandya/textgenie
- 10.1007/978-3-030-57321-8_21 may be a valid DOI for title: Improving short text classification through global...
- 10.18653/v1/2020.emnlp-demos.16 may be a valid DOI for title: TextAttack: A Framework for Adversarial Attacks, D...
- No DOI given, and none found for title: Natural language processing with Python. O’Reilly ...
- No DOI given, and none found for title: WordNet: A Lexical Database for English
- No DOI given, and none found for title: DaDebias/genda-lens
- No DOI given, and none found for title: DaCy: A Unified Framework for Danish NLP

INVALID DOIs

- None

[editorialbot]

👋 @openjournals/dsais-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#5264, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[KennethEnevoldsen]

The proof looks good on my end

[crvernon]

@editorialbot set joss as version

[editorialbot]

Done! version is now joss

[crvernon]

@editorialbot set 10.5281/zenodo.11002422 as archive

[editorialbot]

Done! archive is now 10.5281/zenodo.11002422

[crvernon]

👋 @KennethEnevoldsen - one last thing before we accept...

Could you edit your metadata for the license stated in this archive https://zenodo.org/records/11002422 to match what is used by your package?

No need to do another release, you can just edit the existing record on Zenodo.

Let me know when this is done and I'll move forward with accepting the submission for publications. Thanks!

[KennethEnevoldsen]

@crvernon I have updated the license to match

[crvernon]

@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.

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cff-version: "1.2.0"
authors:
- family-names: Enevoldsen
  given-names: Kenneth
  orcid: "https://orcid.org/0000-0001-8733-0966"
doi: 10.5281/zenodo.11002422
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Enevoldsen
    given-names: Kenneth
    orcid: "https://orcid.org/0000-0001-8733-0966"
  date-published: 2024-04-27
  doi: 10.21105/joss.06370
  issn: 2475-9066
  issue: 96
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 6370
  title: "Augmenty: A Python Library for Structured Text Augmentation"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.06370"
  volume: 9
title: "Augmenty: A Python Library for Structured Text Augmentation"

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[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.06370 joss-papers#5282
1. Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.06370
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...

[crvernon]

Congratulations on your new publication @KennethEnevoldsen! Many thanks to @arfon and to reviewers @sap218 and @wdduncan for your time, hard work, and expertise!! JOSS wouldn't be able to function nor succeed without your efforts.

[editorialbot]

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

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[KennethEnevoldsen]

Thanks @crvernon, @arfon and the reviewers @wdduncan and @sap218 - very happy about the feedback always a good experience to publish with joss