[REVIEW]: DEEPaaS API: a REST API for Machine Learning and Deep Learning models #1517

whedon · 2019-06-21T15:39:53Z

Submitting author: @alvarolopez (Álvaro López García)
Repository: https://github.com/indigo-dc/DEEPaaS
Version: 0.5.2
Editor: @trallard
Reviewer: @krother, @rougier
Archive: 10.5281/zenodo.3519350

Status

Status badge code:

HTML: <a href="http://joss.theoj.org/papers/b6c4f836a5c8573219ceb8ca23f7b00c"><img src="http://joss.theoj.org/papers/b6c4f836a5c8573219ceb8ca23f7b00c/status.svg"></a>
Markdown: [![status](http://joss.theoj.org/papers/b6c4f836a5c8573219ceb8ca23f7b00c/status.svg)](http://joss.theoj.org/papers/b6c4f836a5c8573219ceb8ca23f7b00c)

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

@dangunter & @krother & @rougier, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

Make sure you're logged in to your GitHub account
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 @trallard know.

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

Review checklist for @dangunter

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: 0.5.2
Authorship: Has the submitting author (@alvarolopez) 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 @krother

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: 0.5.2
Authorship: Has the submitting author (@alvarolopez) 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 @rougier

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: 0.5.2
Authorship: Has the submitting author (@alvarolopez) 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)?

The text was updated successfully, but these errors were encountered:

whedon · 2019-06-21T15:39:56Z

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @dangunter, @krother, @rougier it looks like you're currently assigned to review 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:

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

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 · 2019-06-21T15:39:57Z

Attempting PDF compilation. Reticulating splines etc...

whedon · 2019-06-21T15:40:14Z

👉 Check article proof 📄 👈

trallard · 2019-06-21T15:43:39Z

Hey @dangunter, @krother, @rougier thanks a lot for offering to review this submission.

Each of you have been assigned a checklist for your review, please go over the items and check them if you consider them to be satisfied.
Please use this issue for ongoing discussions. If you need to start a longer discussion or request please make an issue on the submission repo and reference it here.

If you encounter any issues or have questions, please feel free to ping me here.

Thanks again for your help 🙏🏼

trallard · 2019-07-01T07:23:38Z

@whedon remind @rougier in 2 weeks

whedon · 2019-07-01T07:23:41Z

Reminder set for @rougier in 2 weeks

trallard · 2019-07-01T07:24:38Z

Hi @krother @dangunter I am just popping by to see how the review is going and check if you need additional help

whedon · 2019-07-15T07:23:46Z

👋 @rougier, please update us on how your review is going.

rougier · 2019-07-16T05:25:21Z

Thanks for the reminder. I will try to finish by the end of the week.

rougier · 2019-07-16T05:28:45Z

@trallard Can we have a link to the paper at the top of the thread ? (I cannot find it)

trallard · 2019-07-16T21:22:54Z

@whedon generate pdf

whedon · 2019-07-16T21:22:57Z

Attempting PDF compilation. Reticulating splines etc...

whedon · 2019-07-16T21:23:20Z

👉 Check article proof 📄 👈

trallard · 2019-07-16T21:24:32Z

@rougier here is the article 👆🏼

rougier · 2019-07-17T07:03:46Z

@alvarolopez I'm trying to test your software but I have problems because of the gevent package that cannot compile v1.4.0 on my machine (OSX). Last version seems to compile ok but not the 1.4.0. Do you know through which package this dependency comes from ?

alvarolopez · 2019-07-17T08:38:00Z

@rougier this is a dependency on DEEPaaS itself, but we are depending on version 1.2.0 (actually I now realise that this can be bumped to 1.3.0).

What error are you obtaining?

rougier · 2019-07-18T10:05:27Z

Lots of warnings and errors which make it difficult to track the actual error. Among them:

  src/gevent/libev/gevent.corecext.c:30182:21: error: no member named 'exc_type' in 'struct _ts'
      *type = tstate->exc_type;
              ~~~~~~  ^
  src/gevent/libev/gevent.corecext.c:30183:22: error: no member named 'exc_value' in 'struct _ts'; did you mean 'curexc_value'?
      *value = tstate->exc_value;
                       ^~~~~~~~~

alvarolopez · 2019-07-23T12:12:11Z

@Rouger I have fixed this issue, related with an old pinned dependency version and Python3. Version 0.5.0 should work.

rougier · 2019-07-24T08:31:34Z

I confirm it fixed my problem.

rougier · 2019-07-24T08:39:52Z

@alvarolopez I think you're missing some DOI in the references of your paper. Also, I did not find any way to test the package. Would you that be possible to have a step by step description of a minimal test to run?

trallard · 2019-08-25T16:37:54Z

Thanks all for the reviews.
@dangunter, @krother can I have an estimated date for this review to be completed? it has been going on for a while and we'd like to move it forwards

alvarolopez · 2019-09-04T11:02:42Z

Hi @rougier, catching up after summer break.

I will correct the DOIs as soon as possible.

Regarding the instructions to run the API is to use the "make develop" command, documented here I reckon that docs must be updated properly, with more detailed information. Currently there is more information on how to run it in the project-wide documentation here.

If you want to test a real model that is integrated with the API, you can have a loot at here.

trallard · 2019-09-16T10:09:04Z

Hi folks, just checking in to see how is the review moving? @alvarolopez

alvarolopez · 2019-09-16T11:50:33Z

@trallard I've fixed the missing DOI in several publications, under the paper branch.

alvarolopez · 2019-10-25T17:02:54Z

@kthyng 🤦‍♂️ yes indeed. I forgot to create the release for that version.

kthyng · 2019-10-25T20:35:11Z

@whedon accept

whedon · 2019-10-25T20:35:14Z

No archive DOI set. Exiting...

kthyng · 2019-10-25T20:35:30Z

Oh right

kthyng · 2019-10-25T20:36:07Z

@whedon set 10.5281/zenodo.3519350 as archive

whedon · 2019-10-25T20:36:11Z

OK. 10.5281/zenodo.3519350 is the archive.

kthyng · 2019-10-25T20:36:14Z

@whedon accept

whedon · 2019-10-25T20:36:17Z

Attempting dry run of processing paper acceptance...

whedon · 2019-10-25T20:36:38Z


OK DOIs

- 10.1007/s10462-018-09679-z is OK
- 10.1126/science.1110411 is OK
- 10.1016/j.dss.2012.05.045 is OK

MISSING DOIs

- None

INVALID DOIs

- None

whedon · 2019-10-25T20:36:52Z

Check final proof 👉 openjournals/joss-papers#1055

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#1055, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

kthyng · 2019-10-25T20:37:43Z

@whedon accept deposit=true

whedon · 2019-10-25T20:37:45Z

Doing it live! Attempting automated processing of paper acceptance...

whedon · 2019-10-25T20:38:29Z

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

whedon · 2019-10-25T20:38:30Z

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.01517 joss-papers#1056
Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01517
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? notify your editorial technical team...

kthyng · 2019-10-25T20:42:11Z

Congrats @alvarolopez on your new paper!!

Many thanks to @krother and @rougier for your time and expertise reviewing, and to @trallard for editing!

kthyng · 2019-10-25T20:42:45Z

@arfon I just realized that the final paper still lists as a reviewer someone who ended up not participated but is still listed. Can we remove them?

arfon · 2019-10-26T11:20:43Z

@arfon I just realized that the final paper still lists as a reviewer someone who ended up not participated but is still listed. Can we remove them?

Sure thing, I can fix that.

arfon · 2019-10-26T11:22:24Z

OK done!

alvarolopez · 2019-10-28T08:16:58Z

@trallard @kthyng @krother @rougier thanks for taking care of the whole process.

@arfon: I just realized that my surname and name are not correctly identified. My name is "Álvaro" and surname is "López García" (i.e. I have two surnames). Can this be fixed?

Many thanks in advance.

arfon · 2019-10-28T12:14:45Z

@arfon: I just realized that my surname and name are not correctly identified. My name is "Álvaro" and surname is "López García" (i.e. I have two surnames). Can this be fixed?

Sorry about that @alvarolopez. That should be fixed now. If the PDF on the JOSS site is still looking out of date it might take a while to refresh as there's caching in place.

whedon · 2019-10-28T12:14:49Z

🎉🎉🎉 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.01517/status.svg)](https://doi.org/10.21105/joss.01517)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.01517">
  <img src="https://joss.theoj.org/papers/10.21105/joss.01517/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.01517/status.svg
   :target: https://doi.org/10.21105/joss.01517

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

kthyng · 2019-10-28T14:11:44Z

Thanks @arfon! Sorry for all the after-changes.

alvarolopez · 2019-10-28T15:00:04Z

@arfon, many thanks!

whedon assigned trallard Jun 21, 2019

whedon added the review label Jun 21, 2019

whedon mentioned this issue Jun 21, 2019

[PRE REVIEW]: DEEPaaS API: a REST API for Machine Learning and Deep Learning models #1403

Closed

whedon assigned dangunter, krother and rougier Jun 22, 2019

whedon added the accepted label Oct 25, 2019

arfon closed this as completed Oct 28, 2019

whedon added published Papers published in JOSS recommend-accept Papers recommended for acceptance in JOSS. labels Mar 2, 2020

whedon unassigned dangunter Mar 2, 2020

editorialbot mentioned this issue Sep 28, 2023

[PRE REVIEW]: StockAIT : Python Machine Learning Framework for Stock Artificial Intelligence Trader #5890

Closed

editorialbot mentioned this issue Dec 26, 2023

[PRE REVIEW]: Deep-Waste: An app that manages household waste using deep learning #6166

Closed

[REVIEW]: DEEPaaS API: a REST API for Machine Learning and Deep Learning models #1517

[REVIEW]: DEEPaaS API: a REST API for Machine Learning and Deep Learning models #1517

Comments

whedon commented Jun 21, 2019 • edited by arfon Loading

Status

Reviewer instructions & questions

Review checklist for @dangunter

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @krother

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @rougier

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

whedon commented Jun 21, 2019

whedon commented Jun 21, 2019

whedon commented Jun 21, 2019

trallard commented Jun 21, 2019

trallard commented Jul 1, 2019

whedon commented Jul 1, 2019

trallard commented Jul 1, 2019

whedon commented Jul 15, 2019

rougier commented Jul 16, 2019

rougier commented Jul 16, 2019

trallard commented Jul 16, 2019

whedon commented Jul 16, 2019

whedon commented Jul 16, 2019

trallard commented Jul 16, 2019

rougier commented Jul 17, 2019

alvarolopez commented Jul 17, 2019

rougier commented Jul 18, 2019

alvarolopez commented Jul 23, 2019

rougier commented Jul 24, 2019

rougier commented Jul 24, 2019

trallard commented Aug 25, 2019

alvarolopez commented Sep 4, 2019 • edited Loading

trallard commented Sep 16, 2019

alvarolopez commented Sep 16, 2019

alvarolopez commented Oct 25, 2019

kthyng commented Oct 25, 2019

whedon commented Oct 25, 2019

kthyng commented Oct 25, 2019

kthyng commented Oct 25, 2019

whedon commented Oct 25, 2019

kthyng commented Oct 25, 2019

whedon commented Oct 25, 2019

whedon commented Oct 25, 2019

whedon commented Oct 25, 2019

kthyng commented Oct 25, 2019

whedon commented Oct 25, 2019

whedon commented Oct 25, 2019

whedon commented Oct 25, 2019

kthyng commented Oct 25, 2019

kthyng commented Oct 25, 2019

arfon commented Oct 26, 2019

arfon commented Oct 26, 2019

alvarolopez commented Oct 28, 2019

arfon commented Oct 28, 2019

whedon commented Oct 28, 2019

kthyng commented Oct 28, 2019

alvarolopez commented Oct 28, 2019

whedon commented Jun 21, 2019 •

edited by arfon

Loading

alvarolopez commented Sep 4, 2019 •

edited

Loading