[REVIEW]: Fireworks: Reproducible Machine Learning with PyTorch #1478

whedon · 2019-05-25T20:34:38Z

Submitting author: @smk508 (Saad Khan)
Repository: https://github.com/kellylab/Fireworks
Version: 0.3.2
Editor: @arokem
Reviewer: @dirmeier
Archive: 10.5281/zenodo.3339548

Status

Status badge code:

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Markdown: [![status](http://joss.theoj.org/papers/6156356281b38760548fdb14505d9ba1/status.svg)](http://joss.theoj.org/papers/6156356281b38760548fdb14505d9ba1)

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

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

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The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @arokem know.

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

Review checklist for @dirmeier

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: 0.3.2
Authorship: Has the submitting author (@smk508) 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 · 2019-05-25T20:34:41Z

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

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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 😿

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@whedon commands

whedon · 2019-05-25T20:34:42Z

Attempting PDF compilation. Reticulating splines etc...

whedon · 2019-05-25T20:35:05Z

👉 Check article proof 📄 👈

smk508 · 2019-05-31T20:56:26Z

Hi @dirmeier . Do you have any updates on this review or any questions?

arokem · 2019-06-13T06:16:17Z

Hello @dirmeier! Have you had a chance to take a look?

dirmeier · 2019-06-13T07:22:41Z

Yeah, the review is in the repo's issue tracker..

smk508 · 2019-06-26T21:30:37Z

@whedon commands

whedon · 2019-06-26T21:30:40Z

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

smk508 · 2019-06-26T21:30:59Z

@whedon generate pdf

whedon · 2019-06-26T21:31:02Z

Attempting PDF compilation. Reticulating splines etc...

whedon · 2019-06-26T21:31:09Z

PDF failed to compile for issue #1478 with the following error:

/app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-18b9a37e7f54/lib/whedon/orcid_validator.rb:12:in initialize': undefined method strip' for nil:NilClass (NoMethodError)
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-18b9a37e7f54/lib/whedon.rb:123:in new' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-18b9a37e7f54/lib/whedon.rb:123:in block in check_orcids'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-18b9a37e7f54/lib/whedon.rb:121:in each' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-18b9a37e7f54/lib/whedon.rb:121:in check_orcids'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-18b9a37e7f54/lib/whedon.rb:81:in initialize' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-18b9a37e7f54/lib/whedon/processor.rb:36:in new'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-18b9a37e7f54/lib/whedon/processor.rb:36:in set_paper' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-18b9a37e7f54/bin/whedon:55:in prepare'
from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/command.rb:27:in run' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/invocation.rb:126:in invoke_command'
from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor.rb:387:in dispatch' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/base.rb:466:in start'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-18b9a37e7f54/bin/whedon:116:in <top (required)>' from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in load'
from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in `

'

dirmeier · 2019-07-02T08:45:53Z

@whedon generate pdf

whedon · 2019-07-02T08:45:56Z

Attempting PDF compilation. Reticulating splines etc...

whedon · 2019-07-02T08:46:07Z

PDF failed to compile for issue #1478 with the following error:

/app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-85c572552d68/lib/whedon/orcid_validator.rb:12:in initialize': undefined method strip' for nil:NilClass (NoMethodError)
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-85c572552d68/lib/whedon.rb:123:in new' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-85c572552d68/lib/whedon.rb:123:in block in check_orcids'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-85c572552d68/lib/whedon.rb:121:in each' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-85c572552d68/lib/whedon.rb:121:in check_orcids'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-85c572552d68/lib/whedon.rb:81:in initialize' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-85c572552d68/lib/whedon/processor.rb:36:in new'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-85c572552d68/lib/whedon/processor.rb:36:in set_paper' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-85c572552d68/bin/whedon:55:in prepare'
from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/command.rb:27:in run' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/invocation.rb:126:in invoke_command'
from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor.rb:387:in dispatch' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/base.rb:466:in start'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-85c572552d68/bin/whedon:116:in <top (required)>' from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in load'
from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in `

'

dirmeier · 2019-07-02T08:50:18Z

Hey @arokem ,
I think once we fix the error above we are done with the review. I am not sure what is failing here, the md file seems fine.

arokem · 2019-07-03T23:02:50Z

@whedon generate pdf

whedon · 2019-07-03T23:02:52Z

Attempting PDF compilation. Reticulating splines etc...

whedon · 2019-07-03T23:02:57Z

PDF failed to compile for issue #1478 with the following error:

/app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-85c572552d68/lib/whedon/orcid_validator.rb:12:in initialize': undefined method strip' for nil:NilClass (NoMethodError)
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-85c572552d68/lib/whedon.rb:123:in new' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-85c572552d68/lib/whedon.rb:123:in block in check_orcids'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-85c572552d68/lib/whedon.rb:121:in each' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-85c572552d68/lib/whedon.rb:121:in check_orcids'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-85c572552d68/lib/whedon.rb:81:in initialize' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-85c572552d68/lib/whedon/processor.rb:36:in new'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-85c572552d68/lib/whedon/processor.rb:36:in set_paper' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-85c572552d68/bin/whedon:55:in prepare'
from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/command.rb:27:in run' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/invocation.rb:126:in invoke_command'
from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor.rb:387:in dispatch' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/base.rb:466:in start'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-85c572552d68/bin/whedon:116:in <top (required)>' from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in load'
from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in `

'

arokem · 2019-07-03T23:09:46Z

@openjournals/joss-eics : does anyone know what this error means? I am failing to debug this just by looking at the markdown.

kyleniemeyer · 2019-07-03T23:17:06Z

I would try removing the empty orcid: field for the second author, I think whedon gets confused by that

danielskatz · 2019-07-03T23:17:10Z

something is wrong with an orcid

arokem · 2019-07-07T20:45:35Z

@smk508 : I implemented @kyleniemeyer's suggestion here: kellylab/Fireworks#75. If you merge that, we can take a look and see what remains to complete the review of this paper.

smk508 · 2019-07-08T16:18:03Z

Hi @arokem ,

Sorry I was on vacation for the weekend so I didn't see this. I've merged the PR.

smk508 · 2019-07-08T16:18:33Z

@whedon generate pdf

whedon · 2019-07-08T16:18:36Z

Attempting PDF compilation. Reticulating splines etc...

whedon · 2019-07-08T16:18:44Z

PDF failed to compile for issue #1478 with the following error:

/app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-85c572552d68/lib/whedon/author.rb:58:in block in build_affiliation_string': Problem with affiliations for Saad Khan, perhaps the affiliations index need quoting? (RuntimeError) from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-85c572552d68/lib/whedon/author.rb:57:in each'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-85c572552d68/lib/whedon/author.rb:57:in build_affiliation_string' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-85c572552d68/lib/whedon/author.rb:17:in initialize'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-85c572552d68/lib/whedon.rb:141:in new' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-85c572552d68/lib/whedon.rb:141:in block in parse_authors'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-85c572552d68/lib/whedon.rb:138:in each' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-85c572552d68/lib/whedon.rb:138:in parse_authors'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-85c572552d68/lib/whedon.rb:84:in initialize' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-85c572552d68/lib/whedon/processor.rb:36:in new'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-85c572552d68/lib/whedon/processor.rb:36:in set_paper' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-85c572552d68/bin/whedon:55:in prepare'
from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/command.rb:27:in run' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/invocation.rb:126:in invoke_command'
from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor.rb:387:in dispatch' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/base.rb:466:in start'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-85c572552d68/bin/whedon:116:in <top (required)>' from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in load'
from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in `

'

danielskatz · 2019-07-20T21:28:11Z

Also, I don't think Kubeflow is a journal, so in paper.bib:
@misc{kubeflow_2019, title={Kubeflow}, howpublished={https://www.kubeflow.org/}, journal={Kubeflow}, year={2019}, month={Jan}
}
should probably be:
@misc{kubeflow_2019, title={Kubeflow}, howpublished={https://www.kubeflow.org/}, year={2019}, month={Jan}
}

smk508 · 2019-07-20T23:37:57Z

@whedon generate pdf

whedon · 2019-07-20T23:38:00Z

Attempting PDF compilation. Reticulating splines etc...

whedon · 2019-07-20T23:38:40Z

👉 Check article proof 📄 👈

smk508 · 2019-07-20T23:40:21Z

Ok I've updated the kubeflow citation in paper.bib. The current version is 0.3.2, yes. I don't know how to change the top post in this thread to say 0.3.2.

danielskatz · 2019-07-21T13:24:45Z

@whedon set 0.3.2 as version

whedon · 2019-07-21T13:24:48Z

OK. 0.3.2 is the version.

danielskatz · 2019-07-21T13:26:30Z

@whedon accept

whedon · 2019-07-21T13:26:33Z

Attempting dry run of processing paper acceptance...

whedon · 2019-07-21T13:27:13Z

Check final proof 👉 openjournals/joss-papers#849

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#849, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

danielskatz · 2019-07-21T13:36:43Z

sorry, I see a few more small things in the bib - can we try with kellylab/Fireworks#76 ?

smk508 · 2019-07-21T14:28:00Z

@whedon generate pdf

whedon · 2019-07-21T14:28:02Z

Attempting PDF compilation. Reticulating splines etc...

smk508 · 2019-07-21T14:28:07Z

Ok I merged the PR

whedon · 2019-07-21T14:28:43Z

👉 Check article proof 📄 👈

danielskatz · 2019-07-21T14:32:33Z

@whedon accept

whedon · 2019-07-21T14:32:36Z

Attempting dry run of processing paper acceptance...

whedon · 2019-07-21T14:33:11Z

Check final proof 👉 openjournals/joss-papers#850

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#850, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

danielskatz · 2019-07-21T14:34:15Z

@whedon accept deposit=true

whedon · 2019-07-21T14:34:18Z

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

whedon · 2019-07-21T14:35:02Z

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

whedon · 2019-07-21T14:35:03Z

🚨🚨🚨 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.01478 joss-papers#851
Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01478
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? notify your editorial technical team...

smk508 · 2019-07-21T14:36:47Z

Thanks!

danielskatz · 2019-07-21T14:39:09Z

Thanks to @dirmeier for reviewing and @arokem for editing!

whedon · 2019-07-21T14:39:12Z

🎉🎉🎉 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:
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HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.01478">
  <img src="http://joss.theoj.org/papers/10.21105/joss.01478/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: http://joss.theoj.org/papers/10.21105/joss.01478/status.svg
   :target: https://doi.org/10.21105/joss.01478

This is how it will look in your documentation:

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whedon assigned arokem May 25, 2019

whedon added the review label May 25, 2019

whedon mentioned this issue May 25, 2019

[PRE REVIEW]: Fireworks: Reproducible Machine Learning with PyTorch #1422

Closed

whedon assigned dirmeier May 26, 2019

whedon added the accepted label Jul 21, 2019

danielskatz closed this as completed Jul 21, 2019

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

editorialbot mentioned this issue Sep 28, 2023

[PRE REVIEW]: Learning from Crowds with Crowd-Kit #5898

Closed

[REVIEW]: Fireworks: Reproducible Machine Learning with PyTorch #1478

[REVIEW]: Fireworks: Reproducible Machine Learning with PyTorch #1478

Comments

whedon commented May 25, 2019 • edited Loading

Status

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Review checklist for @dirmeier

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General checks

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