[REVIEW]: tfaip - a Generic and Powerful Research Framework for Deep Learning based on Tensorflow

[whedon]

Submitting author: @ChWick (Christoph Wick)
Repository: https://github.com/Planet-AI-GmbH/tfaip
Version: v1.1.0
Editor: @arfon
Reviewer: @levimcclenny, @Het-Shah
Archive: 10.5281/zenodo.5011366

⚠️ JOSS reduced service mode ⚠️

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Status

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Markdown: [![status](https://joss.theoj.org/papers/ec226548a533905bcf0f87e71d60208a/status.svg)](https://joss.theoj.org/papers/ec226548a533905bcf0f87e71d60208a)

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

@levimcclenny & @Het-Shah, 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 @levimcclenny

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 (@ChWick) 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 @Het-Shah

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 (@ChWick) 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. @levimcclenny, @Het-Shah 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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[whedon]

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.19 s (1082.8 files/s, 91706.3 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                         166           2406           4403           8184
reStructuredText                24            446            379            673
Markdown                         7             98              0            358
TeX                              1              6              0             94
YAML                             3             14             13             64
DOS Batch                        1              8              1             26
make                             1              4              7              9
-------------------------------------------------------------------------------
SUM:                           203           2982           4803           9408
-------------------------------------------------------------------------------


Statistical information for the repository '7339204651bab0024b3730a9' was
gathered on 2021/05/20.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
C. Wick                         37         29912          14144           99.95
jochen                           3            20              3            0.05

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
C. Wick                   15785           52.8          2.4               28.81

[whedon]

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

OK DOIs

- 10.1145/2939672.2945397 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

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

[arfon]

@levimcclenny, @Het-Shah – 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/3297 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.

[levimcclenny]

I'm trying to accept the invite to edit the checklist but its saying "invite expired" - Any idea?

Thanks!

[arfon]

@whedon re-invite @levimcclenny as reviewer

[whedon]

OK, the reviewer has been re-invited.

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

[arfon]

I'm trying to accept the invite to edit the checklist but its saying "invite expired" - Any idea?

Weird. Could you try clicking the invite link above now?

[Het-Shah]

I have opened an issue in the tfaip repository. I believe this is a great addition to the journal. However, I had some concerns that are mentioned in the issue.

[levimcclenny]

I also commented on the issue opened by @Het-Shah. I think it's a good paper as well. A few minor things but overall well-written and the documentation is really professional. Would like to see more accessible examples though. Other comments are on the repo.

[Het-Shah]

@whedon generate pdf

[whedon]

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

[Het-Shah]

I am satisfied with the changes that are made. I believe the submission is ready to be accepted!

[arfon]

@levimcclenny - it looks like there are still a couple of checkboxes unchecked for your review. Would you still like to see changes here from the author to address these items?

[levimcclenny]

@arfon i good with it!

[whedon]

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

[levimcclenny]

Apologies for the delay - looks good!

[arfon]

@ChWick – I've found a small issue with your paper here that makes it a little more readable: Planet-AI-GmbH/tfaip#4

Also, I find the current 'Statement of Need' section rather confusing to read. This section should clearly state for the reader why this software is needed, what problems it uniquely solves (or solves better than other tools) etc. Some comments on this section:

This sentence seems out of context?

An application of tfaip resolves recurrent obstacles of research and development in an elegant and robust way.

Are you saying that other tools don't enable this?

A complete scenario including the graph (e.g., the network architecture), the training (e.g., the optimizer or learning rate schedule),...

This next paragraph again is lacking clarity. Is tfaip unique at being able to describe the 'complete scenario'? What is hard about how current tools do this and how is tfaip solving these problems?

tfaip provides a simple API to deploy a scenario. The corresponding module will automatically apply pre-processing, infer the trained model, and optionally transform the output by a post-processing pipeline.

Again, for the next paragraph, what is the value-add here compared to other tools or challenges data practitioners currently face?

[danielskatz]

@ChWick - Any update on the above?

[ChWick]

@danielskatz I was on vacation. I will deal with this hopefully this, at most next week. Thanks @afron for the additional, valuable remarks!

[ChWick]

@whedon generate pdf

[whedon]

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

[ChWick]

@arfon Thank you very much for this comment! We agree that this section required some modification which I guess is also in the interest of the other two reviewers!
We completely rewrote the section in order to clarify but also highlight the "Need" of tfaip. Please let us know if you have additional remarks.

Please also see Planet-AI-GmbH/tfaip#4.

[arfon]

@whedon generate pdf

[whedon]

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

[arfon]

@whedon generate pdf

[whedon]

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

[arfon]

@ChWick – I made a final few changes here: Planet-AI-GmbH/tfaip#6

[ChWick]

@whedon generate pdf
@arfon I merged your PR, thank you again!

[whedon]

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

[arfon]

@ChWick - At this point 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.

[ChWick]

@arfon The DOI is 10.5281/zenodo.5011366 (see also https://zenodo.org/record/5011366)

[arfon]

@whedon set 10.5281/zenodo.5011366 as archive

[whedon]

OK. 10.5281/zenodo.5011366 is the archive.

[arfon]

@whedon recommend-accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

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

Check final proof 👉 openjournals/joss-papers#2401

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#2401, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

[whedon]

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

OK DOIs

- 10.1145/2939672.2945397 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[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.03297 joss-papers#2403
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.03297
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]

@levimcclenny, @Het-Shah – many thanks for your reviews here. JOSS relies upon the volunteer efforts of people like you and we simply wouldn't be able to do this without you ✨

@ChWick – 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:

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HTML:
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  <img src="https://joss.theoj.org/papers/10.21105/joss.03297/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.03297/status.svg
   :target: https://doi.org/10.21105/joss.03297

This is how it will look in your documentation:

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[ChWick]

@levimcclenny @Het-Shah @arfon Thank you all for your efforts!

[Het-Shah]

Congratulations @ChWick and to all your colleagues for the acceptance! 🎉