[REVIEW]: AuDoLab: Automatic document labelling and1 classfication for extremely unbalanced data

[whedon]

Submitting author: @ArneTillmann (Arne Matthias Tillmann)
Repository: https://github.com/ArneTillmann/AuDoLab
Version: v1.0.7
Editor: @arfon
Reviewers: @linuxscout, @pps121
Archive: 10.5281/zenodo.5575835

⚠️ 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/ac8cf139139dbe55e00e7cc820459cee/status.svg)](https://joss.theoj.org/papers/ac8cf139139dbe55e00e7cc820459cee)

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

@linuxscout, 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 @arfon 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 @linuxscout

✨ 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 (@ArneTillmann) 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?

@linuxscout, 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 @arfon 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 @pps121

✨ 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 (@ArneTillmann) 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. @linuxscout 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]

Wordcount for paper.md is 824

[whedon]

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

OK DOIs

- 10.1162/jmlr.2003.3.4-5.993 is OK
- 10.1080/02664763.2021.1919063 is OK
- 10.1162/089976601750264965 is OK
- 10.3115/v1/W14-3110 is OK
- 10.1162/15324430260185574 is OK
- 10.21105/joss.02507 is OK
- 10.17875/gup2020-1338 is OK
- 10.13140/2.1.2393.1847 is OK
- 10.17875/gup2020-1338 is OK

MISSING DOIs

- 10.5260/cca.199178 may be a valid DOI for title: IEEE Xplore Digital Library

INVALID DOIs

- 10.5555/1953048.2078195 is INVALID

[whedon]

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.08 s (676.8 files/s, 52936.0 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          15            462            658           1030
XML                              6              0              0            213
reStructuredText                17            123             77            211
diff                             5             42             49            141
HTML                             2             15              0            134
TeX                              1             14              0            114
PowerShell                       1             49            245            104
make                             2             24              6             75
DOS Batch                        3             23              2             65
Markdown                         1             14              0             56
Jupyter Notebook                 1              0            430             40
INI                              1              4              3             16
YAML                             2              1              2             16
-------------------------------------------------------------------------------
SUM:                            57            771           1472           2215
-------------------------------------------------------------------------------


Statistical information for the repository '702fdb33409d86c5e788a30d' was
gathered on 2021/09/11.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
AFThielmann                     13           444            295            7.51
Anton Thielmann                 21          1256            449           17.33
ArneTillmann                   172          4166           2990           72.72
kantg                            3           198             40            2.42
tkneib                           1             1              1            0.02

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
AFThielmann                  81           18.2          4.4               16.05
Anton Thielmann             823           65.5          2.1                6.20
ArneTillmann               1218           29.2          2.5               17.08
kantg                        28           14.1          0.7                3.57

[whedon]

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

[arfon]

@linuxscout – 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.

Both reviewers have checklists at the top of this thread (in that first comment) with the JOSS requirements. 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/3719 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.

[ChrisW09]

Hi @linuxscout, we are very much looking forward to the review and your comments. thanks.

[arfon]

@whedon add @pps121 as reviewer

[whedon]

OK, @pps121 is now a reviewer

[arfon]

@pps121 - thanks for agreeing to review this submission for us! Please take a look at my instructions above and complete your checklist as you work through your review.

[ChrisW09]

@arfon fantastic, thank you! @linuxscout @pps121 should you have any early ideas or comments, on how to improve the paper or make things more clear, please just let us know, and we will implement them as soon as we can. thanks a lot.

[linuxscout]

I'am not assigned to this issue, to perform review, please assign me.

[ChrisW09]

@linuxscout thanks for the update! @arfon could you please help with this question "I'am not assigned to this issue, to perform the review, please assign me." thank you!

[arfon]

I'am not assigned to this issue, to perform review, please assign me.

@linuxscout – did you accept the invitation at https://github.com/openjournals/joss-reviews/invitations ?

[arfon]

@whedon re-invite @linuxscout as reviewer

[whedon]

OK, the reviewer has been re-invited.

@linuxscout please accept the invite by clicking this link: https://github.com/openjournals/joss-reviews/invitations

[linuxscout]

ok, thanks.

[linuxscout]

Hi,
I finished the review.

[ChrisW09]

@linuxscout thanks a lot for being that quick with the review. We really appreciated your comments and the fast review process!

[ChrisW09]

@pps121 we are already looking forward to your comments. Please let us know if anything is unclear :) thanks!

[ChrisW09]

@whedon generate pdf

[whedon]

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

[ChrisW09]

@arfon Thank you. I checked the DOI suggestion for "IEEE Xplore. (2020). IEEE Xplore Digital Library. https://ieeexplore.ieee.org/Xplore/home. jsp." This is a website, so that we cannot cite a DOI.

I removed the invalid DOI for the paper below and confirmed that the paper has no DOI.

Pedregosa, F., Varoquaux, G., Gramfort, A., Michel, V., Thirion, B., Grisel, O., Blondel, M., Prettenhofer, P., Weiss, R., Dubourg, V., Vanderplas, J., Passos, A., Cournapeau, D., Brucher, M., Perrot, M., & Duchesnay, E. (2011). Scikit-learn: Machine learning in Python. Journal of Machine Learning Research, 12, 2825–2830.

Is this okay?

@ArneTillmann will do the merges asap.

[ArneTillmann]

done

[ArneTillmann]

Thank you @arfon!

[ChrisW09]

@arfon Please let us know if everything is okay now. Otherwise, we will implement any requested changes asap. We would also like to thank you for this great review process!

[arfon]

@whedon recommend-accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

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

OK DOIs

- 10.1162/jmlr.2003.3.4-5.993 is OK
- 10.1080/02664763.2021.1919063 is OK
- 10.1162/089976601750264965 is OK
- 10.3115/v1/W14-3110 is OK
- 10.1162/15324430260185574 is OK
- 10.21105/joss.02507 is OK
- 10.17875/gup2020-1338 is OK
- 10.13140/2.1.2393.1847 is OK
- 10.17875/gup2020-1338 is OK
- 10.17875/gup2021-1608 is OK
- 10.1007/978-3-030-76620-7_23 is OK

MISSING DOIs

- 10.5260/cca.199178 may be a valid DOI for title: IEEE Xplore Digital Library

INVALID DOIs

- None

[whedon]

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

Check final proof 👉 openjournals/joss-papers#2693

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#2693, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

[arfon]

@whedon accept deposit=true

[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.03719 joss-papers#2694
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.03719
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...

[ChrisW09]

@arfon Thank you! Somehow there is an error such that the PDF is not shown on the JOSS website?

[arfon]

It's showing for me now – sometimes the caching takes a few minutes to update the PDFs.

[arfon]

@linuxscout, @pps121 – many thanks for your reviews here! JOSS relies upon the volunteer effort of people like you and we simply wouldn't be able to do this without you ✨

@ArneTillmann @ChrisW09 – your paper is now accepted and published in JOSS ⚡🚀💥

[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.03719/status.svg)](https://doi.org/10.21105/joss.03719)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.03719">
  <img src="https://joss.theoj.org/papers/10.21105/joss.03719/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.03719/status.svg
   :target: https://doi.org/10.21105/joss.03719

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

[ChrisW09]

@arfon @linuxscout @pps121 thank you again very much for your help and support!

[ChrisW09]

@arfon Somehow I still cannot see the PDF on the JOSS website. @ArneTillmann Can you see the PDF? thanks

.

[ArneTillmann]

@arfon @pps121 @linuxscout thank you all very much for the help and constructive feedback.
Nothing but the best to all of you!

[arfon]

@arfon Somehow I still cannot see the PDF on the JOSS website. @ArneTillmann Can you see the PDF? thanks

@ChrisW09 – this is almost certainly your browser caching the old GitHub Pages response. I assure you this will automatically fix itself over the coming hours (and doesn't affect new visitors to the paper page)

[ChrisW09]

@arfon now it works well. thanks a lot :)