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[REVIEW]: Container Tree: Software to Model Container Filesystems, Packages, and Inheritance #1418

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whedon opened this issue Apr 30, 2019 · 50 comments
Closed
18 tasks done

[REVIEW]: Container Tree: Software to Model Container Filesystems, Packages, and Inheritance #1418

whedon opened this issue Apr 30, 2019 · 50 comments
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@luizirber @brainstorm
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accepted published Papers published in JOSS recommend-accept Papers recommended for acceptance in JOSS. review

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@whedon
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whedon commented Apr 30, 2019 •
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Submitting author: @vsoch (Vanessa Sochat)
Repository: https://www.github.com/singularityhub/container-tree
Version: 0.0.48
Editor: @brainstorm
Reviewer: @luizirber
Archive: 10.5281/zenodo.2853983

Status

status

Status badge code:

HTML: <a href="http://joss.theoj.org/papers/f7b46a7f922b468e535adabc2337b330"><img src="http://joss.theoj.org/papers/f7b46a7f922b468e535adabc2337b330/status.svg"></a>
Markdown: [![status](http://joss.theoj.org/papers/f7b46a7f922b468e535adabc2337b330/status.svg)](http://joss.theoj.org/papers/f7b46a7f922b468e535adabc2337b330)

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

@luizirber, 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 @brainstorm know.

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

Review checklist for @luizirber

Conflict of interest

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: Does the release version given match the GitHub release (0.0.48)?
  • Authorship: Has the submitting author (@vsoch) 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)?
@whedon whedon added the review label Apr 30, 2019
@whedon whedon mentioned this issue Apr 30, 2019
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@whedon
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whedon commented Apr 30, 2019

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

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

watching

  1. 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

@whedon
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whedon commented Apr 30, 2019 

Attempting PDF compilation. Reticulating splines etc...

@whedon
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whedon commented Apr 30, 2019

👉 Check article proof 📄 👈

@openjournals openjournals deleted a comment from whedon Apr 30, 2019
@vsoch
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vsoch commented Apr 30, 2019

@whedon generate pdf

@whedon
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whedon commented Apr 30, 2019 

Attempting PDF compilation. Reticulating splines etc...

@whedon
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whedon commented Apr 30, 2019

👉 Check article proof 📄 👈

@vsoch
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vsoch commented Apr 30, 2019

@whedon generate pdf

@whedon
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whedon commented Apr 30, 2019 

Attempting PDF compilation. Reticulating splines etc...

@whedon
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whedon commented Apr 30, 2019

👉 Check article proof 📄 👈

@vsoch
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vsoch commented Apr 30, 2019

okay, looks good! Thanks @whedon. I had some "n.d" dates that I wanted to fix up. The manuscript should be ready now. Thanks for reviewing @luizirber and overseeing @brainstorm.

@luizirber luizirber mentioned this issue May 1, 2019
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@luizirber There seem to be some unchecked boxes on the review, do you reckon this review is complete/done?

@luizirber
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luizirber commented May 5, 2019 via email

@brainstorm
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brainstorm commented May 5, 2019 via email

@vsoch
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vsoch commented May 5, 2019

Yeah @luizirber that sounds awesome!! When you come back, let us know how it was, and where PyCon 2020 will be! I found the site and I didn't realize it was closer to my neck of the woods than say, San Francisco. I totally want to go one of these years, so fingers crossed it's close by again!

@vsoch
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vsoch commented May 5, 2019

omg it's in Pittsburgh! https://pycon.blogspot.com/2019/02/pycon-2020-2021-location.html woo!

@luizirber luizirber mentioned this issue May 13, 2019
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@luizirber
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Finally back on track, sorry for the delay.

I sent some PRs for small doc fixes in the original repo, so the main items missing in the checklist are:

Automated tests

While CircleCI is set up, I didn't find any tests in the codebase. The examples are very nice, but are not automated/ran on every PR. But it seems they would be very amenable to testing, perhaps with smaller data inputs?

References

At least the PLOS ref has a DOI. Not sure about the others.

@vsoch
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vsoch commented May 13, 2019

Thanks @luizirber ! I'll get you some tests (likely tomorrow, or day after). I just responded to the PR (thank you!) and I'll see if I can update references with DOIs.

@vsoch
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vsoch commented May 14, 2019

@whedon generate pdf

@whedon
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whedon commented May 14, 2019 

Attempting PDF compilation. Reticulating splines etc...

@whedon
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whedon commented May 14, 2019

👉 Check article proof 📄 👈

@vsoch
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vsoch commented May 14, 2019

@whedon generate pdf again!

@whedon
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whedon commented May 14, 2019 

Attempting PDF compilation. Reticulating splines etc...

@whedon
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whedon commented May 14, 2019

👉 Check article proof 📄 👈

@vsoch
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vsoch commented May 15, 2019

@luizirber I'm so glad you noticed this, because I had added the circle config to build containers without finishing the actual tests for the trees and client! I'm happy to report that I now have tests for container trees, collection trees, package trees, data export, and the command line client! All just under 1K lines of code, tested and merged: singularityhub/container-tree#44

@brainstorm I've drafted a new release for the updated version, v0.0.49, and the archive should be processing --> available via zenodo asap https://zenodo.org/account/settings/github/repository/singularityhub/container-tree#

Holy crap, I'm tired... going for a run! 🏃‍♂️

@luizirber
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Great job, @vsoch! And enjoy the run =]

@brainstorm all checked on my side, ready to go!

@brainstorm
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Cool cool, thanks everybody! @vsoch need the zenodo DOI thingie and should be Archivable, I cannot login/hack your zenodo account ;)

@vsoch
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vsoch commented May 18, 2019

This one?

https://doi.org/10.5281/zenodo.2853983

@vsoch
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vsoch commented May 18, 2019

And latest release https://github.com/singularityhub/container-tree/releases/tag/v0.0.49

@brainstorm
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@whedon set https://doi.org/10.5281/zenodo.2853983 as archive

@whedon
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whedon commented May 19, 2019

OK. 10.5281/zenodo.2853983 is the archive.

@brainstorm
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All set here too, @labarba, ready to accept/deposit 👍

@labarba
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labarba commented May 19, 2019

I'm not on duty this week.

Ping @openjournals/joss-eics

@labarba
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labarba commented May 19, 2019

@vsoch — Please edit the metadata of the Zenodo deposit (no need to get new version or new DOI) so the title and author list match the JOSS paper. You may also want to add your ORCID in the metadata.

@vsoch
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vsoch commented May 19, 2019

Ah thanks for the reminder - all fixed!

@arfon
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arfon commented May 19, 2019

@whedon accept

@whedon
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whedon commented May 19, 2019 

Attempting dry run of processing paper acceptance...

@whedon
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whedon commented May 19, 2019 


OK DOIs

- 10.5281/zenodo.2602127 is OK
- https://doi.org/10.1371/journal.pone.0188511 is OK

MISSING DOIs

- None

INVALID DOIs

- None

@whedon
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whedon commented May 19, 2019

Check final proof 👉 openjournals/joss-papers#700

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#700, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

@arfon
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arfon commented May 19, 2019

@whedon accept deposit=true

@whedon
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whedon commented May 19, 2019 

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

@whedon
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whedon commented May 19, 2019

Posted to the Twitters: https://twitter.com/JOSS_TheOJ/status/1130209744663318528

@whedon
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whedon commented May 19, 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 👉 Creating pull request for 10.21105.joss.01418 joss-papers#701
  2. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01418
  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...

@vsoch
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vsoch commented May 19, 2019

It looks like the pdf is 404, do we need to wait longer? https://www.theoj.org/joss-papers/joss.01418/10.21105.joss.01418.pdf

@vsoch
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vsoch commented May 19, 2019

Oh you know what, it's probably just github pages (this happens to me a lot!) I'll check in a few minutes.

@arfon
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arfon commented May 19, 2019

Oh you know what, it's probably just github pages (this happens to me a lot!) I'll check in a few minutes.

I've just cleared the Cloudflare cache and it's showing up for me OK. Sometimes GitHub pages is just a little slow.

@vsoch
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vsoch commented May 19, 2019

Showing up for me too! Thanks @arfon. And huge +1, GitHub pages is slow these days. Thanks to everyone for your help with this paper! 🎆

@vsoch
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vsoch commented May 19, 2019

Thanks @whedon, I think we are good and I'm ready to go party, err... keep working on other stuff, run up a hill a few times, and eat dinner :) Enjoy the rest of your robot Sunday! @arfon I can't close the issue (should I be able to?) but please feel free to do so.

@whedon
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whedon commented May 19, 2019

🎉🎉🎉 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](http://joss.theoj.org/papers/10.21105/joss.01418/status.svg)](https://doi.org/10.21105/joss.01418)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.01418">
  <img src="http://joss.theoj.org/papers/10.21105/joss.01418/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: http://joss.theoj.org/papers/10.21105/joss.01418/status.svg
   :target: https://doi.org/10.21105/joss.01418

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