Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

[REVIEW]: Python Sorted Containers #1330

Closed
whedon opened this issue Mar 18, 2019 · 46 comments

Comments

Projects
None yet
5 participants
@whedon
Copy link
Collaborator

commented Mar 18, 2019

Submitting author: @grantjenks (Grant Jenks)
Repository: https://github.com/grantjenks/python-sortedcontainers
Version: v2.1.0
Editor: @jasonclark
Reviewer: @djmitche
Archive: 10.5281/zenodo.2584337

Status

status

Status badge code:

HTML: <a href="http://joss.theoj.org/papers/e8b71872eaf49e7dead39eefee7c5a21"><img src="http://joss.theoj.org/papers/e8b71872eaf49e7dead39eefee7c5a21/status.svg"></a>
Markdown: [![status](http://joss.theoj.org/papers/e8b71872eaf49e7dead39eefee7c5a21/status.svg)](http://joss.theoj.org/papers/e8b71872eaf49e7dead39eefee7c5a21)

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) 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

@djmitche, 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.theoj.org/about#reviewer_guidelines. Any questions/concerns please let @jasonclark know.

Please try and complete your review in the next two weeks

Review checklist for @djmitche

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 (v2.1.0)?
  • Authorship: Has the submitting author (@grantjenks) 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

This comment has been minimized.

Copy link
Collaborator Author

commented Mar 18, 2019

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @djmitche 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

This comment has been minimized.

Copy link
Collaborator Author

commented Mar 18, 2019

Attempting PDF compilation. Reticulating splines etc...
@whedon

This comment has been minimized.

Copy link
Collaborator Author

commented Mar 18, 2019

@djmitche djmitche self-assigned this Mar 19, 2019

@djmitche

This comment has been minimized.

Copy link

commented Mar 23, 2019

@grantjenks:

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

I don't see these bits in the repository. Have I missed them?

Typically (1) is handled with CONTRIBUTORS.md or a section in the README, and (2) and (3) are handled with GitHub issue templates.

@grantjenks

This comment has been minimized.

Copy link

commented Mar 23, 2019

There's a page for that at http://www.grantjenks.com/docs/sortedcontainers/development.html It's the second-to-last link under the User Guide section of the README. I think it covers 1-3.

@djmitche

This comment has been minimized.

Copy link

commented Mar 23, 2019

Indeed, I did miss that. That definitely covers (1), but not so much (2) and (3). It's probably a tiny thing, but just an indication that both support requests and bug reports are welcome on the github repo would be enough.

@djmitche

This comment has been minimized.

Copy link

commented Mar 23, 2019

(that's the last bit before I can check all the boxes..)

@grantjenks

This comment has been minimized.

Copy link

commented Mar 26, 2019

@djmitche I have updated the docs at Development and Support to cover (2) and (3).

There's two new sections at the top of the page: "Reporting Issues" and "Support". I've also tried to make it a bit more discoverable by updating the README's Documentation section with a Community Guide heading that links to "Development and Support". For now, I'd prefer not to use GitHub issue templates. I think the documentation provides sufficient guidelines for (2) and (3).

Thanks for the feedback and review!

One last note, you may need to reload without the cache to see the changes immediately online.

@djmitche

This comment has been minimized.

Copy link

commented Mar 26, 2019

That's fantastic :)

@djmitche

This comment has been minimized.

Copy link

commented Mar 26, 2019

@whedon commands

@whedon

This comment has been minimized.

Copy link
Collaborator Author

commented Mar 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

@djmitche

This comment has been minimized.

Copy link

commented Mar 26, 2019

@jasonclark review is complete. I think the next step is up to you?

@jasonclark

This comment has been minimized.

Copy link

commented Apr 5, 2019

@djmitche Yep. Thanks for your review.

@jasonclark

This comment has been minimized.

Copy link

commented Apr 5, 2019

@whedon generate pdf

@whedon

This comment has been minimized.

Copy link
Collaborator Author

commented Apr 5, 2019

Attempting PDF compilation. Reticulating splines etc...
@whedon

This comment has been minimized.

Copy link
Collaborator Author

commented Apr 5, 2019

@jasonclark

This comment has been minimized.

Copy link

commented Apr 5, 2019

Hi, @grantjenks. We are close to finishing this paper. There is a final step where you make an archive of the software in Zenodo and report the DOI. Can you do that and let me know the DOI here?

@grantjenks

This comment has been minimized.

Copy link

commented Apr 5, 2019

I think that's done. I believe the DOI is: 10.5281/zenodo.2584337
Here's the Zenodo link: https://zenodo.org/record/2584337
And the DOI link: https://doi.org/10.5281/zenodo.2584337

@djmitche

This comment has been minimized.

Copy link

commented Apr 13, 2019

@jasonclark is this ready to wrap up?

@grantjenks

This comment has been minimized.

Copy link

commented Apr 29, 2019

@jasonclark let me know if I can help close this out.

@djmitche djmitche removed their assignment May 12, 2019

@djmitche

This comment has been minimized.

Copy link

commented May 13, 2019

@jasonclark hey, so this keeps showing up in my "assigned" queue despite there being no action required on my part. And @whedon seems to want it that way. Can we wrap this up?

@arfon

This comment has been minimized.

Copy link
Member

commented May 18, 2019

@jasonclark hey, so this keeps showing up in my "assigned" queue despite there being no action required on my part. And @whedon seems to want it that way. Can we wrap this up?

Sorry @djmitche - Whedon periodically tries to fix assignments on review issues but it looks like it's been a little over-keen here.

@grantjenks - I've just emailed Jason a reminder. If we don't hear back from him in the next day or so then I'll finish up this submission for him.

@arfon

This comment has been minimized.

Copy link
Member

commented May 21, 2019

@whedon set 10.5281/zenodo.2584337 as archive

@whedon

This comment has been minimized.

Copy link
Collaborator Author

commented May 21, 2019

OK. 10.5281/zenodo.2584337 is the archive.

@arfon

This comment has been minimized.

Copy link
Member

commented May 21, 2019

@whedon accept

@whedon

This comment has been minimized.

Copy link
Collaborator Author

commented May 21, 2019

Attempting dry run of processing paper acceptance...
@whedon

This comment has been minimized.

Copy link
Collaborator Author

commented May 21, 2019


OK DOIs

- 10.1051/0004-6361/201322068 is OK
- 10.3847/1538-3881/aabc4f is OK
- 10.5281/zenodo.2584337 is OK

MISSING DOIs

- https://doi.org/10.1109/sp.2016.17 may be missing for title: SoK: (State of) The Art of War: Offensive Techniques in Binary Analysis
- https://doi.org/10.25080/majora-7b98e3ed-013 may be missing for title: Dask: Parallel Computation with Blocked algorithms and Task Scheduling

INVALID DOIs

- None
@whedon

This comment has been minimized.

Copy link
Collaborator Author

commented May 21, 2019

Check final proof 👉 openjournals/joss-papers#708

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#708, 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

This comment has been minimized.

Copy link
Member

commented May 21, 2019

👋 @grantjenks - a couple of final changes to the paper:

  • Could you remove the last sentence about the Zenodo archive? We link to the archive directly from the paper already so this is superfluous.
  • When you're mentioning projects (e.g. Astropy, Dask etc.) could you cite those packages in the paper? You can read how to do that here. Also, note the Dask paper needs a DOI added to it.
@grantjenks

This comment has been minimized.

Copy link

commented Jun 3, 2019

@whedon generate pdf

@whedon

This comment has been minimized.

Copy link
Collaborator Author

commented Jun 3, 2019

Attempting PDF compilation. Reticulating splines etc...
@whedon

This comment has been minimized.

Copy link
Collaborator Author

commented Jun 3, 2019

@grantjenks

This comment has been minimized.

Copy link

commented Jun 3, 2019

@arfon Update:

  1. I removed the last sentence and verified the article proof still includes the DOI.
  2. I found the Dask Distributed DOI and included it.
  3. I cited the projects in the paper based on your reference. I wasn't sure how the text would be rendered. Looks like it included just the year. I think that's OK but let me know if there's a better rendering.
  4. Everyone in the bibliography now has a reference from the paper except astropy:2013. Should I remove that entry from paper.bib?

I'm excited to wrap this up today, if possible.

@arfon

This comment has been minimized.

Copy link
Member

commented Jun 3, 2019

@whedon generate pdf

@whedon

This comment has been minimized.

Copy link
Collaborator Author

commented Jun 3, 2019

Attempting PDF compilation. Reticulating splines etc...
@whedon

This comment has been minimized.

Copy link
Collaborator Author

commented Jun 3, 2019

@arfon

This comment has been minimized.

Copy link
Member

commented Jun 3, 2019

👍 thanks. This looks good @grantjenks

@arfon

This comment has been minimized.

Copy link
Member

commented Jun 3, 2019

@whedon accept

@whedon

This comment has been minimized.

Copy link
Collaborator Author

commented Jun 3, 2019

Attempting dry run of processing paper acceptance...
@whedon

This comment has been minimized.

Copy link
Collaborator Author

commented Jun 3, 2019


OK DOIs

- 10.1051/0004-6361/201322068 is OK
- 10.3847/1538-3881/aabc4f is OK
- 10.25080/Majora-7b98e3ed-013 is OK
- 10.5281/zenodo.2584337 is OK

MISSING DOIs

- https://doi.org/10.1109/sp.2016.17 may be missing for title: SoK: (State of) The Art of War: Offensive Techniques in Binary Analysis

INVALID DOIs

- None
@whedon

This comment has been minimized.

Copy link
Collaborator Author

commented Jun 3, 2019

Check final proof 👉 openjournals/joss-papers#732

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#732, 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

This comment has been minimized.

Copy link
Member

commented Jun 3, 2019

@whedon accept deposit=true

@whedon

This comment has been minimized.

Copy link
Collaborator Author

commented Jun 3, 2019

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

@whedon whedon added the accepted label Jun 3, 2019

@whedon

This comment has been minimized.

Copy link
Collaborator Author

commented Jun 3, 2019

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

@whedon

This comment has been minimized.

Copy link
Collaborator Author

commented Jun 3, 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 👉 openjournals/joss-papers#733
  2. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01330
  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...

@djmitche djmitche closed this Jun 10, 2019

@whedon

This comment has been minimized.

Copy link
Collaborator Author

commented Jun 10, 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.01330/status.svg)](https://doi.org/10.21105/joss.01330)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.01330">
  <img src="http://joss.theoj.org/papers/10.21105/joss.01330/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: http://joss.theoj.org/papers/10.21105/joss.01330/status.svg
   :target: https://doi.org/10.21105/joss.01330

This is how it will look in your documentation:

DOI

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:

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
You can’t perform that action at this time.