[REVIEW]: Delira: A High-Level Framework for Deep Learning in Medical Image Analysis

[whedon]

Submitting author: @haarburger (Christoph Haarburger)
Repository: https://github.com/justusschock/delira
Version: v0.3.2
Editor: @mbobra
Reviewer: @PingjunChen, @acolum
Archive: 10.5281/zenodo.3247307

Status

Status badge code:

HTML: <a href="http://joss.theoj.org/papers/744634c556aa17cdc2f41f6387b1975d"><img src="http://joss.theoj.org/papers/744634c556aa17cdc2f41f6387b1975d/status.svg"></a>
Markdown: [![status](http://joss.theoj.org/papers/744634c556aa17cdc2f41f6387b1975d/status.svg)](http://joss.theoj.org/papers/744634c556aa17cdc2f41f6387b1975d)

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

@PingjunChen & @acolum, 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 @mbobra know.

✨ Please try and complete your review in the next two weeks ✨

Review checklist for @PingjunChen

Conflict of interest

• As the reviewer I confirm that I have read the JOSS conflict of interest policy and that there are no conflicts of interest for me to review this work.

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?
• Version: Does the release version given match the GitHub release (v0.3.2)?
• Authorship: Has the submitting author (@haarburger) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

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 function 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

• Authors: Does the paper.md file include a list of authors with their affiliations?
• A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

Review checklist for @acolum

Conflict of interest

• As the reviewer I confirm that I have read the JOSS conflict of interest policy and that there are no conflicts of interest for me to review this work.

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?
• Version: Does the release version given match the GitHub release (v0.3.2)?
• Authorship: Has the submitting author (@haarburger) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

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 function 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

• Authors: Does the paper.md file include a list of authors with their affiliations?
• A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

[whedon]

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @PingjunChen, it looks like you're currently assigned as the reviewer for this paper 🎉.

⭐ 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

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

👉 Check article proof 📄 👈

[mbobra]

Sorry about Whedon's comment, @acolum! You are a reviewer, too ☀️

[PingjunChen]

@haarburger please add DOI to references if exist. Also, the current reference format looks not standard.

[haarburger]

@whedon commands

[whedon]

Here are some things you can ask me to do:

# List Whedon's capabilities
@whedon commands

# List of editor GitHub usernames
@whedon list editors

# List of reviewers together with programming language preferences and domain expertise
@whedon list reviewers

EDITORIAL TASKS

# Compile the paper
@whedon generate pdf

# Compile the paper from alternative branch
@whedon generate pdf from branch custom-branch-name

# Ask Whedon to check the references for missing DOIs
@whedon check references

[haarburger]

@whedon generate pdf from branch reformat-paper-refs

[whedon]

Attempting PDF compilation from custom branch reformat-paper-refs. Reticulating splines etc...

[whedon]

👉 Check article proof 📄 👈

[haarburger]

@PingjunChen, unfortunately none of the references has a DOI. Please let me know if you have further suggestions on how to improve the reference format.

[PingjunChen]

@haarburger Thanks, now the reference format should be fine.

I have some difficulty to understand the installation on the backend. Take tensorflow as an example, does pip install delira[tf] mean pip install delira tf? But in PyPI, tf is not tensorflow . Please give more explicit installation instructions.

Because of the complexity of this framework, I need more time to check the functionalities and tests.

[haarburger]

@PingjunChen the pip command is supposed to be used exactly as stated in our readme. Maybe this explanation about the syntax is helpful. It means that we want to install the tensorflow/pytorch backend as an extra.

[PingjunChen]

@haarburger The link you provide helps me understand the usage of the square bracket. Although for deep learning people, tf defaults to tensorflow, and you also give tensorflow link to tf. Nevertheless, I still suggest changing tf to tensorflow, at least in the Installation part. The main reason is to avoid ambiguity, as tf is already used by https://pypi.org/project/tf in PyPI.

[acolum]

I'm finished with my review and am recommending this for publication. @haarburger I just wanted to commend you and your team for a job well done writing and documenting this package. This is one of the best JOSS submissions I've reviewed.

[PingjunChen]

@mbobra Just a reminder that we have finished the review. Overall, this package has rich features for deep learning model training, data preparation, visualization, etc. In addition, the documentation is well-written with iPython notebook examples for classification, segmentation, and GAN applications. I recommend accepting for publication.

[haarburger]

Thank you @PingjunChen and @acolum for your quick reviews 👍

[mbobra]

@openjournals/joss-eics This submission is ready to be accepted! 🚀

[arfon]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

👉 Check article proof 📄 👈

[arfon]

@haarburger - At this point could you make an archive of the reviewed software in Zenodo/figshare/other service and update this thread with the DOI of the archive? Please make sure that the title of the Zenodo archive and authors match the authors of the paper here.

Once you've done this, I can then move forward with accepting the submission.

[labarba]

I think the software also needs a new tagged release with the latest changes?

[arfon]

I think the software also needs a new tagged release with the latest changes?

Oh yes. Please do that too when making the Zenodo archive!

[haarburger]

We'd like to add a few bugfixes and minor improvements to the new tag. I'll let you know when these changes are merged and tagged and the Zenodo archive is created.

[haarburger]

@labarba, @arfon we've finally tagged our repository and uploaded v0.4.0 to Zenodo at 10.5281/zenodo.3247307

[arfon]

@whedon set 10.5281/zenodo.3247307 as archive

[whedon]

OK. 10.5281/zenodo.3247307 is the archive.

[arfon]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

OK DOIs

- None

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

Check final proof 👉 openjournals/joss-papers#764

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#764, 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.01488 joss-papers#765
1. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01488
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]

@PingjunChen, @acolum - many thanks for your reviews and to @mbobra for editing this submission ✨

@haarburger - your paper is now accepted into 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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reStructuredText:
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