[REVIEW]: TX2: Transformer eXplainability and eXploration

[whedon]

Submitting author: @WildfireXIII (Nathan Martindale)
Repository: https://github.com/ORNL/tx2
Version: v1.0.0
Editor: @fabian-s
Reviewers: @assenmacher-mat, @deniederhut
Archive: 10.5281/zenodo.5796089

⚠️ JOSS reduced service mode ⚠️

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Markdown: [![status](https://joss.theoj.org/papers/b7c161917e5a31af052a597bf98f0e94/status.svg)](https://joss.theoj.org/papers/b7c161917e5a31af052a597bf98f0e94)

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

@assenmacher-mat & @sara-02, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

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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 ✨

Review checklist for @assenmacher-mat

✨ 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 (@WildfireXIII) 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 @deniederhut

✨ 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 (@WildfireXIII) 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. @assenmacher-mat, @sara-02 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.

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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:

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

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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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[whedon]

Wordcount for paper.md is 1341

[whedon]

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.20 s (299.4 files/s, 146974.3 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
JavaScript                      15           2516           2689           9868
HTML                            12           1495             36           2909
SVG                              1              0              0           2671
Python                           9            402            512           1630
CSS                              5            183             36            734
Jupyter Notebook                 2              0           2621            302
Markdown                         5             69              0            177
reStructuredText                 8            121            152            164
TeX                              1             17              0             96
DOS Batch                        1              8              1             26
make                             1              4              7              9
-------------------------------------------------------------------------------
SUM:                            60           4815           6054          18586
-------------------------------------------------------------------------------


Statistical information for the repository 'faa95a716c4f24951fd7338d' was
gathered on 2021/08/24.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Martindale, Nathan               7          2146             68           12.25
Nathan Martindale               16         15697            158           87.75

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
Martindale, Nathan        17617          820.9          0.5               17.03

[whedon]

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

[whedon]

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

OK DOIs

- 10.18653/v1/P19-3007 is OK
- 10.1145/3366424.3383542 is OK

MISSING DOIs

- 10.18653/v1/2020.emnlp-demos.15 may be a valid DOI for title: The Language Interpretability Tool: Extensible, Interactive Visualizations and Analysis for NLP Models

INVALID DOIs

- None

[fabian-s]

👋🏼 @WildfireXIII @assenmacher-mat @sara-02, this is the review thread for the paper. All of our communications will happen here from now on.

Both reviewers have checklists at the top of this thread 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 openjournals/joss-reviews#REVIEW_NUMBER 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 reviews to be completed within about 2-4 weeks. Please let me know if any of you require some more time. We can also use Whedon (our bot) to set automatic reminders if you know you'll be away for a known period of time.

Please feel free to ping me (@fabian-s) if you have any questions/concerns.

[whedon]

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

[whedon]

👋 @sara-02, please update us on how your review is going (this is an automated reminder).

[assenmacher-mat]

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

still struggling a little bit with the runtime on my cpu machine, but everythin seems to work. Should be done by the end of this week.

[assenmacher-mat]

Two small issues:

• Maybe there should also be an explicit manual on how exactly install pytoch w/o gpu
• Regarding the point I haven't marked (see above): I could not find any comment regarding this

[fabian-s]

@WildfireXIII : please add a CONTRIBUTING.md file or similar to your repo, as pointed out by @assenmacher-mat

[fabian-s]

@sara-02 please update us on how your review is going, as you know JOSS aims for quick turnaround times.

[stewartsl]

@WildfireXIII : please add a CONTRIBUTING.md file or similar to your repo, as pointed out by @assenmacher-mat

@fabian-s please note that there is currently a contributing.MD file in master tx2 contributing. does this sufficiently address your concern?

[fabian-s]

@fabian-s please note that there is currently a contributing.MD file in master tx2 contributing. does this sufficiently address your concern?

sure, that seems sufficient.

[WarmCyan]

Hey, I haven't heard anything in a while, so I just wanted to check what the status on this review was, and if there's anything else needed from me so far.

[fabian-s]

@sara-02 please do update us on how this review is going, as you know JOSS aims for quick turnaround times and we are waiting for your review to proceed.

[fabian-s]

@sara-02 ping

[fabian-s]

@WildfireXIII very sorry for the delay, @sara-02 is not reacting to my e-mails or messages.
I'll find someone else for the 2nd review.

[fabian-s]

hi @ahurriyetoglu @RichardLitt @deniederhut @linuxscout -- would one of you be willing and able to review this submission for JOSS within the next 2 weeks?

[RichardLitt]

Bit out of my wheelhouse. Sorry!

[deniederhut]

Hey @fabian-s yeah I should have some time to take a look at this late next week. Would you mind asking whedon to remind me? Thanks

[fabian-s]

thanks, @deniederhut!

[fabian-s]

@whedon add @deniederhut as reviewer

[whedon]

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

[whedon]

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

OK DOIs

- 10.18653/v1/2020.emnlp-demos.15 is OK
- 10.21105/joss.00861 is OK
- 10.18653/v1/P19-3007 is OK
- 10.1145/3366424.3383542 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[fabian-s]

Great, ty @WildfireXIII !

At this point could you:

• Make a tagged release of your software, and list the version tag of the archived version here.
• Archive the reviewed software in Zenodo or a similar service (e.g., figshare, an institutional repository)
• Check the archival deposit (e.g., in Zenodo) has the correct metadata. This includes the title (should match the paper title) and author list (make sure the list is correct and people who only made a small fix are not on it). You may also add the authors' ORCID.
• Please list the DOI of the archived version here.

I can then move forward with accepting the submission.
I don't think your DOEcode entry counts as an "archival deposit" in our sense of the word since it just points to the GH repo in general, not a specific tagged commit in the repo.

[WarmCyan]

Release tag: v1.0.0
Zenodo DOI: 10.5281/zenodo.5796089

[fabian-s]

@whedon set 10.5281/zenodo.5796089 as archive

[whedon]

OK. 10.5281/zenodo.5796089 is the archive.

[fabian-s]

@whedon set v1.0.0 as version

[whedon]

OK. v1.0.0 is the version.

[fabian-s]

@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

- 10.18653/v1/2020.emnlp-demos.15 is OK
- 10.21105/joss.00861 is OK
- 10.18653/v1/P19-3007 is OK
- 10.1145/3366424.3383542 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

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

Check final proof 👉 openjournals/joss-papers#2841

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#2841, 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.03652 joss-papers#2842
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.03652
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...

[arfon]

@assenmacher-mat, @deniederhut – many thanks for your reviews here and to @fabian-s 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 ✨

@WildfireXIII – 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.03652/status.svg)](https://doi.org/10.21105/joss.03652)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.03652">
  <img src="https://joss.theoj.org/papers/10.21105/joss.03652/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.03652/status.svg
   :target: https://doi.org/10.21105/joss.03652

This is how it will look in your documentation:

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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
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[WarmCyan]

Thanks everyone!

[deniederhut]

🎉 congratulations!