Joss-reviews: [REVIEW]: Fireworks: Reproducible Machine Learning with PyTorch

Created on 25 May 2019  ·  77Comments  ·  Source: openjournals/joss-reviews

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

Status badge code:

HTML: <a href="http://joss.theoj.org/papers/6156356281b38760548fdb14505d9ba1"><img src="http://joss.theoj.org/papers/6156356281b38760548fdb14505d9ba1/status.svg"></a>
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:

  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 @arokem know.

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

Review checklist for @dirmeier

Conflict of interest

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: 0.3.2
  • [x] Authorship: Has the submitting author (@smk508) 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)?
accepted published recommend-accept review
Source
picture whedon

All 77 comments

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 :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 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:

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

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

@whedon commands
whedon picture whedon on 25 May 2019 
Attempting PDF compilation. Reticulating splines etc...
whedon picture whedon on 25 May 2019

:point_right: Check article proof :page_facing_up: :point_left:

whedon picture whedon on 25 May 2019

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

smk508 picture smk508 on 31 May 2019

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

arokem picture arokem on 13 Jun 2019

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

dirmeier picture dirmeier on 13 Jun 2019
👍1

@whedon commands

smk508 picture smk508 on 26 Jun 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
whedon picture whedon on 26 Jun 2019

@whedon generate pdf

smk508 picture smk508 on 26 Jun 2019 
Attempting PDF compilation. Reticulating splines etc...
whedon picture whedon on 26 Jun 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 methodstrip' 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:inblock 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:incheck_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:innew'
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:inprepare'
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:ininvoke_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:instart'
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:inload'
from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in `

'

whedon picture whedon on 26 Jun 2019

@whedon generate pdf

dirmeier picture dirmeier on 2 Jul 2019 
Attempting PDF compilation. Reticulating splines etc...
whedon picture whedon on 2 Jul 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 methodstrip' 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:inblock 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:incheck_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:innew'
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:inprepare'
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:ininvoke_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:instart'
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:inload'
from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in `

'

whedon picture whedon on 2 Jul 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.

dirmeier picture dirmeier on 2 Jul 2019

@whedon generate pdf

arokem picture arokem on 4 Jul 2019 
Attempting PDF compilation. Reticulating splines etc...
whedon picture whedon on 4 Jul 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 methodstrip' 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:inblock 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:incheck_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:innew'
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:inprepare'
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:ininvoke_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:instart'
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:inload'
from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in `

'

whedon picture whedon on 4 Jul 2019

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

arokem picture arokem on 4 Jul 2019

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

kyleniemeyer picture kyleniemeyer on 4 Jul 2019
👍1

something is wrong with an orcid

danielskatz picture danielskatz on 4 Jul 2019

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

arokem picture arokem on 7 Jul 2019

Hi @arokem ,

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

smk508 picture smk508 on 8 Jul 2019

@whedon generate pdf

smk508 picture smk508 on 8 Jul 2019 
Attempting PDF compilation. Reticulating splines etc...
whedon picture whedon on 8 Jul 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:ineach'
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:ininitialize'
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:inblock 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:inparse_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:innew'
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:inprepare'
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:ininvoke_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:instart'
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:inload'
from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in `

'

whedon picture whedon on 8 Jul 2019

Ah, it looks like the affiliations block is not right. Can you change
```affiliations:
- name: Systems & Computational Biology, Albert Einstein College of Medicine

affiliations:
- name: Systems & Computational Biology, Albert Einstein College of Medicine
index: 1
```

kyleniemeyer picture kyleniemeyer on 8 Jul 2019

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

smk508 picture smk508 on 9 Jul 2019

@whedon generate pdf

smk508 picture smk508 on 9 Jul 2019 
Attempting PDF compilation. Reticulating splines etc...
whedon picture whedon on 9 Jul 2019

:point_right: Check article proof :page_facing_up: :point_left:

whedon picture whedon on 9 Jul 2019

ok it builds now

smk508 picture smk508 on 9 Jul 2019
👍1

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?

arokem picture arokem on 15 Jul 2019

@whedon generate pdf

smk508 picture smk508 on 16 Jul 2019 
Attempting PDF compilation. Reticulating splines etc...
whedon picture whedon on 16 Jul 2019

:point_right: Check article proof :page_facing_up: :point_left:

whedon picture whedon on 16 Jul 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.

smk508 picture smk508 on 16 Jul 2019

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

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

arokem picture arokem on 16 Jul 2019

@whedon generate pdf

smk508 picture smk508 on 16 Jul 2019 
Attempting PDF compilation. Reticulating splines etc...
whedon picture whedon on 16 Jul 2019

:point_right: Check article proof :page_facing_up: :point_left:

whedon picture whedon on 16 Jul 2019

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

smk508 picture smk508 on 16 Jul 2019

@whedon check references

arokem picture arokem on 17 Jul 2019 
Attempting to check references...
whedon picture whedon on 17 Jul 2019

```Reference check summary:

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

INVALID DOIs

  • None
    ```
whedon picture whedon on 17 Jul 2019

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

arokem picture arokem on 17 Jul 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.

arokem picture arokem on 17 Jul 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

smk508 picture smk508 on 17 Jul 2019

@whedon set 10.5281/zenodo.3339548 as archive

arokem picture arokem on 20 Jul 2019

OK. 10.5281/zenodo.3339548 is the archive.

whedon picture whedon on 20 Jul 2019

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

arokem picture arokem on 20 Jul 2019

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

danielskatz picture danielskatz on 20 Jul 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}
}

danielskatz picture danielskatz on 20 Jul 2019

@whedon generate pdf

smk508 picture smk508 on 21 Jul 2019 
Attempting PDF compilation. Reticulating splines etc...
whedon picture whedon on 21 Jul 2019

:point_right: Check article proof :page_facing_up: :point_left:

whedon picture whedon on 21 Jul 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.

smk508 picture smk508 on 21 Jul 2019

@whedon set 0.3.2 as version

danielskatz picture danielskatz on 21 Jul 2019

OK. 0.3.2 is the version.

whedon picture whedon on 21 Jul 2019

@whedon accept

danielskatz picture danielskatz on 21 Jul 2019 
Attempting dry run of processing paper acceptance...
whedon picture whedon on 21 Jul 2019

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/849

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/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

whedon picture whedon on 21 Jul 2019

sorry, I see a few more small things in the bib - can we try with https://github.com/kellylab/Fireworks/pull/76 ?

danielskatz picture danielskatz on 21 Jul 2019

@whedon generate pdf

smk508 picture smk508 on 21 Jul 2019 
Attempting PDF compilation. Reticulating splines etc...
whedon picture whedon on 21 Jul 2019

Ok I merged the PR

smk508 picture smk508 on 21 Jul 2019

:point_right: Check article proof :page_facing_up: :point_left:

whedon picture whedon on 21 Jul 2019

@whedon accept

danielskatz picture danielskatz on 21 Jul 2019 
Attempting dry run of processing paper acceptance...
whedon picture whedon on 21 Jul 2019

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/850

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/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

whedon picture whedon on 21 Jul 2019

@whedon accept deposit=true

danielskatz picture danielskatz on 21 Jul 2019 
Doing it live! Attempting automated processing of paper acceptance...
whedon picture whedon on 21 Jul 2019

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

whedon picture whedon on 21 Jul 2019

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

Here's what you must now do:

  1. Check final PDF and Crossref metadata that was deposited :point_right: https://github.com/openjournals/joss-papers/pull/851
  2. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01478
  3. If everything looks good, then close this review issue.

  4. Party like you just published a paper! 🎉🌈🦄💃👻🤘

    Any issues? notify your editorial technical team...

whedon picture whedon on 21 Jul 2019

Thanks!

smk508 picture smk508 on 21 Jul 2019

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

danielskatz picture danielskatz on 21 Jul 2019

:tada::tada::tada: Congratulations on your paper acceptance! :tada::tada::tada:

If you would like to include a link to your paper from your README use the following code snippets:

Markdown:
[![DOI](http://joss.theoj.org/papers/10.21105/joss.01478/status.svg)](https://doi.org/10.21105/joss.01478)

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:

DOI

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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:

whedon picture whedon on 21 Jul 2019
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