[REVIEW]: MatDL: A Lightweight Deep Learning Library in MATLAB

whedon commented 7 years ago

Submitting author: @haythamfayek (Haytham Fayek) Repository: https://github.com/haythamfayek/MatDL Version: v0.8.0 Editor: @cMadan Reviewer: @nirum Archive: 10.5281/zenodo.1042860

Status

Status badge code:

HTML: <a href="http://joss.theoj.org/papers/fa33e01459843ac8a5b781b1bd0c3250"><img src="http://joss.theoj.org/papers/fa33e01459843ac8a5b781b1bd0c3250/status.svg"></a>
Markdown: [![status](http://joss.theoj.org/papers/fa33e01459843ac8a5b781b1bd0c3250/status.svg)](http://joss.theoj.org/papers/fa33e01459843ac8a5b781b1bd0c3250)

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) 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 questions

@nirum, please carry out your review in this issue by updating the checklist below (please make sure you're logged in to GitHub). The reviewer guidelines are available here: http://joss.theoj.org/about#reviewer_guidelines. Any questions/concerns please let @cmadan know.

Conflict of interest

[x] 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

[x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

[x] Repository: Is the source code for this software available at the repository url?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] Version: Does the release version given match the GitHub release (v0.7.0)?
[x] Authorship: Has the submitting author (@haythamfayek) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

Functionality

[x] Installation: Does installation proceed as outlined in the documentation?
[x] Functionality: Have the functional claims of the software been confirmed?
[x] 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

[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
[x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
[x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
[x] Automated tests: Are there automated tests or manual steps described so that the function of the software can be verified?
[x] 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

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

whedon commented 7 years ago

Hello human, I'm @whedon. I'm here to help you with some common editorial tasks for JOSS. @nirum it looks like you're currently assigned as the reviewer for this paper :tada:.

:star: Important :star:

If you haven't already, you should seriously consider unsubscribing from GitHub notifications for this (https://github.com/openjournals/joss-reviews) repository. As as reviewer, you're probably currently watching this repository which means for GitHub's default behaviour you will receive notifications (emails) for all JOSS reviews 😿

To fix this do the following two things:

Set yourself as 'Not watching' https://github.com/openjournals/joss-reviews:

watching

You may also like to change your default settings for this watching repositories in your GitHub profile here: https://github.com/settings/notifications

notifications

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

@whedon commands

cMadan commented 6 years ago

@nirum, let me know if you have any questions about the review process :)

nirum commented 6 years ago

Will do! I'm working on the review, will likely need a few more days :)

cMadan commented 6 years ago

@nirum, no worries, thanks for the update!

haythamfayek commented 6 years ago

Ping @cMadan @nirum :)

nirum commented 6 years ago

Apologies I’ve been swamped with other work—but I am planning on getting to this by the end of the week!

On Oct 25, 2017, at 10:44 AM, Haytham Fayek notifications@github.com wrote:

Ping @cMadan @nirum :)

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or mute the thread.

nirum commented 6 years ago

Hi @cMadan,

I have installed and verified @haythamfayek's code. It looks very good! There are a couple of minor issues I made over on his main repo. One those are addressed, then this has my approval!

Thanks for being so patient--sorry about the delay! Niru

nirum commented 6 years ago

p.s. here's my CNN training on MNIST 😃

nirum commented 6 years ago

One other comment--there aren't tests that can be run--but there is gradient checking code, and a number of pre-specified architectures. I would encourage @haythamfayek to include some tests for his code (perhaps there are some ideas to be harvested from this post), but I don't think that this is a blocking issue.

cMadan commented 6 years ago

Thanks for the thorough review, @nirum!

haythamfayek commented 6 years ago

Thanks @nirum for your time and feedback. I addressed both issues you raised: haythamfayek/MatDL#1 and haythamfayek/MatDL#2.

nirum commented 6 years ago

Looks great! This has my approval. @cMadan, can you advise on the next steps?

cMadan commented 6 years ago

@haythamfayek, I just need you to archive the current code on a service like Zenodo or figshare (and provide me with the DOI) and we'll be all set!

haythamfayek commented 6 years ago

Hi @cMadan

Here is the DOI from Zenodo:

There is now a version mismatch from the above. The submitted version is 0.7 vs the archived version is 0.8. How can I amend that?

nirum commented 6 years ago

I updated this issue with the new version. In case you reference the version in the paper.md file, edit it there too--I think that's all you have to do.

arfon commented 6 years ago

@whedon set 10.5281/zenodo.1042860 as archive

whedon commented 6 years ago

OK. 10.5281/zenodo.1042860 is the archive.

arfon commented 6 years ago

@nirum - many thanks for your review and to @cMadan for editing this submission ✨

@haythamfayek - your paper is now accepted into JOSS and your DOI is https://doi.org/10.21105/joss.00413 ⚡️ 🚀 💥

haythamfayek commented 6 years ago

Thanks @cMadan @nirum @arfon! This is fantastic 💥

@arfon - the last line in the pdf has a link that overflows into the margin and out of the pdf. Is there anything that can be done about it?

arfon commented 6 years ago

@arfon - the last line in the pdf has a link that overflows into the margin and out of the pdf. Is there anything that can be done about it?

Huh, yeah, something weird going on in the LaTeX template we use to produce the PDF. A couple of thoughts:

The word 'GitHub' in that sentence already links to the GitHub repository in the PDF so perhaps we don't need the URL called out separately too.
JOSS papers by default link to the software repository already (see the left-hand column) so this entire sentence could be considered redundant?

haythamfayek commented 6 years ago

@arfon - I am happy to remove the link from paper.md (Will that auto recompile?) but the links will continue to overflow in other documents as well. We can add the breaklinks option to the hyperref package to allow multi-line links. Would you like me to submit a pull request?

arfon commented 6 years ago

Would you like me to submit a pull request?

Yes please do. I'll recompile the paper once you've made the change to the LaTeX template.

openjournals / joss-reviews