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

whedon · May 25, 2019

Submitting author: @smk508 (Saad Khan)
Repository: https://github.com/kellylab/Fireworks
Version: 0.3.0
Editor: @arokem
Reviewer: @dirmeier
Archive: 10.5281/zenodo.3339548

Status

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

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Review checklist for @dirmeier

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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 (0.3.0)?
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?
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Documentation

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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 · May 25, 2019

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 😿

To fix this do the following two things:

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

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

@whedon commands

whedon · May 25, 2019

Attempting PDF compilation. Reticulating splines etc...

whedon · May 25, 2019

👉 Check article proof 📄 👈

smk508 · May 31, 2019

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

arokem · Jun 13, 2019

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

dirmeier · Jun 13, 2019

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

smk508 · Jun 26, 2019

@whedon commands

whedon · Jun 26, 2019

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 · Jun 26, 2019

@whedon generate pdf

whedon · Jun 26, 2019

Attempting PDF compilation. Reticulating splines etc...

whedon · Jun 26, 2019

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 · Jul 2, 2019

@whedon generate pdf

whedon · Jul 2, 2019

Attempting PDF compilation. Reticulating splines etc...

whedon · Jul 2, 2019

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 · Jul 2, 2019

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 · Jul 3, 2019

@whedon generate pdf

whedon · Jul 3, 2019

Attempting PDF compilation. Reticulating splines etc...

whedon · Jul 3, 2019

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 · Jul 3, 2019

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

kyleniemeyer · Jul 3, 2019

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

danielskatz · Jul 3, 2019

something is wrong with an orcid

arokem · Jul 7, 2019

@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 · Jul 8, 2019

Hi @arokem ,

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

smk508 · Jul 8, 2019

@whedon generate pdf

whedon · Jul 8, 2019

Attempting PDF compilation. Reticulating splines etc...

whedon · Jul 8, 2019

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 `

'

smk508 · Jul 9, 2019

Ok let's see if that worked. @whedon generate pdf

smk508 · Jul 9, 2019

@whedon generate pdf

whedon · Jul 9, 2019

Attempting PDF compilation. Reticulating splines etc...

whedon · Jul 9, 2019

👉 Check article proof 📄 👈

smk508 · Jul 9, 2019

ok it builds now

arokem · Jul 15, 2019

Sorry for the slowness here. One more comment: the figure caption contains the words "Figure 1". Please remove these, so that you don't get a duplication of these words in the PDF.

Also, the reference to the Paszke paper seems partial. Is there more information?

smk508 · Jul 16, 2019

@whedon generate pdf

whedon · Jul 16, 2019

Attempting PDF compilation. Reticulating splines etc...

whedon · Jul 16, 2019

👉 Check article proof 📄 👈

smk508 · Jul 16, 2019

Ok I've updated the figure caption. The Paszke reference was meant to be a reference to the Pytorch library itself and its built-in data processing modules when I was comparing them to Fireworks.

arokem · Jul 16, 2019

Gotcha. Looks like it's missing a couple of words, though.

See: https://github.com/pytorch/pytorch/blob/master/CITATION

smk508 · Jul 16, 2019

@whedon generate pdf

whedon · Jul 16, 2019

Attempting PDF compilation. Reticulating splines etc...

whedon · Jul 16, 2019

👉 Check article proof 📄 👈

smk508 · Jul 16, 2019

Oh sorry. I misunderstood what you were saying before! I fixed the typo in the citations now.

arokem · Jul 16, 2019

@whedon check references

whedon · Jul 16, 2019

Attempting to check references...

whedon · Jul 16, 2019


OK DOIs

- 10.1145/2934664 is OK
- 10.1093/bib/bbw068 is OK
- 10.1145/2934664 is OK
- 10.1007/s13218-015-0381-0 is OK
- 10.1007/bf00140399 is OK
- 10.1038/nature14539 is OK

MISSING DOIs

- https://doi.org/10.1163/1574-9347_bnp_e612900 may be missing for title: Keras

INVALID DOIs

- None

arokem · Jul 16, 2019

I think that Whedon is checking all the references in your bib file. I believe everything is in order here.

arokem · Jul 16, 2019

@smk508 : could you please create an archive of the software (e.g., using https://zenodo.org) and post the link + DOI here?

I apologize in advance for the additional delay, but I am heading out on vacation and will be back heree next week to move this ahead.

smk508 · Jul 17, 2019

Ok that sounds good. I've made an archive on zenodo by following thir instructions and added a badge to the README.
DOI: 10.5281/zenodo.3339548
URL: https://zenodo.org/badge/latestdoi/135873580

arokem · Jul 20, 2019

@whedon set 10.5281/zenodo.3339548 as archive

whedon · Jul 20, 2019

OK. 10.5281/zenodo.3339548 is the archive.

arokem · Jul 20, 2019

@openjournals/joss-eics : I believe this paper is ready for your final review

danielskatz · Jul 20, 2019

Is version 0.3.0 correct? It seems like perhaps this should be 0.3.2?

danielskatz · Jul 20, 2019

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 · Jul 20, 2019

@whedon generate pdf

whedon · Jul 20, 2019

Attempting PDF compilation. Reticulating splines etc...

whedon · Jul 20, 2019

👉 Check article proof 📄 👈

smk508 · Jul 20, 2019

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.

whedon assigned arokem May 25, 2019

whedon added the review label May 25, 2019

whedon referenced this issue May 25, 2019
Closed
[PRE REVIEW]: Fireworks: Reproducible Machine Learning with PyTorch #1422

whedon assigned dirmeier May 26, 2019

openjournals/joss-reviews

Track tasks and feature requests

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

Comments

whedon commented May 25, 2019 • edited

Status

Reviewer instructions & questions

Review checklist for @dirmeier

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

whedon assigned arokem May 25, 2019

whedon added the review label May 25, 2019

whedon referenced this issue May 25, 2019

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

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whedon commented May 25, 2019 •

edited