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[REVIEW]: treemaker #1040

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whedon opened this Issue Oct 22, 2018 · 48 comments

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whedon commented Oct 22, 2018

Submitting author: @SimonGreenhill (Simon Greenhill)
Repository: https://github.com/simonGreenhill/Treemaker
Version: v1.03
Editor: @trallard
Reviewer: @RichardLitt, @deniederhut
Archive: 10.5281/zenodo.1480504

Status

status

Status badge code:

HTML: <a href="http://joss.theoj.org/papers/19eae6958062fc8a72d8a02efdaf8b23"><img src="http://joss.theoj.org/papers/19eae6958062fc8a72d8a02efdaf8b23/status.svg"></a>
Markdown: [![status](http://joss.theoj.org/papers/19eae6958062fc8a72d8a02efdaf8b23/status.svg)](http://joss.theoj.org/papers/19eae6958062fc8a72d8a02efdaf8b23)

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

@RichardLitt & @deniederhut, 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 @trallard know.

Please try and complete your review in the next two weeks

Review checklist for @RichardLitt

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 (v1.03)?
  • Authorship: Has the submitting author (@SimonGreenhill) 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)?

Review checklist for @deniederhut

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 (v1.03)?
  • Authorship: Has the submitting author (@SimonGreenhill) 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)?
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whedon commented Oct 22, 2018

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @RichardLitt, 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
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whedon commented Oct 22, 2018

Attempting PDF compilation. Reticulating splines etc...
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whedon commented Oct 22, 2018

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deniederhut commented Nov 1, 2018

@trallard the most excellent @SimonGreenhill has addressed the issues I've filed, and I believe this library is ready for inclusion in JOSS

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SimonGreenhill commented Nov 1, 2018

Thanks for the very helpful input and suggestions @deniederhut !

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SimonGreenhill commented Nov 1, 2018

@whedon generate pdf

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whedon commented Nov 1, 2018

Attempting PDF compilation. Reticulating splines etc...
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trallard commented Nov 1, 2018

Thanks @deniederhut for your time as a reviewer!

I see there are still some unchecked items from @RichardLitt 's list. I will wait until I hear from him to proceed to do some editorial checks on the submission 😄

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RichardLitt commented Nov 1, 2018

@trallard Well, @SimonGreenhill just finished doing a fantastically fast and thorough job resolving my niggling complaints. I think this is good to publish as it is now. Thanks, Simon! Cool package.

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SimonGreenhill commented Nov 1, 2018

No worries, and thanks for the helpful suggestions @RichardLitt!

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SimonGreenhill commented Nov 1, 2018

@whedon generate pdf

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whedon commented Nov 1, 2018

Attempting PDF compilation. Reticulating splines etc...
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trallard commented Nov 4, 2018

@SimonGreenhill I just checked the DOI you created for your repository and this resolves correctly. I just noticed that the DOI still points to version 1.0 of the software but this submission is on 1.03. It might be worth ensuring the versions are in sync.

I will regenerate the pdf to do some basic checks as this seems to not have worked properly (?)

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trallard commented Nov 4, 2018

@whedon generate pdf

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whedon commented Nov 4, 2018

Attempting PDF compilation. Reticulating splines etc...
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trallard commented Nov 6, 2018

@whedon generate pdf

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whedon commented Nov 6, 2018

Attempting PDF compilation. Reticulating splines etc...
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arfon commented Nov 6, 2018

@whedon generate pdf

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whedon commented Nov 6, 2018

3 similar comments
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whedon commented Nov 6, 2018

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whedon commented Nov 6, 2018

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whedon commented Nov 6, 2018

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SimonGreenhill commented Nov 7, 2018

Thanks for the enthusiasm, whedon. I've checked the proof and made a few minor tweaks.

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SimonGreenhill commented Nov 7, 2018

@whedon generate pdf

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whedon commented Nov 7, 2018

Attempting PDF compilation. Reticulating splines etc...
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whedon commented Nov 7, 2018

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SimonGreenhill commented Nov 7, 2018

Look good to me, thanks!

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trallard commented Nov 8, 2018

@SimonGreenhill gentle ping. I think this is there for acceptance but I would like to check about the DOI version. Would you be interested in uploading/sync to 1.0.3 so that the version here and the DOI versions match?
I also noticed that in Zendo the package name is Treemaker v1 you might want to edit it to remove the v1

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SimonGreenhill commented Nov 8, 2018

That makes sense, thanks! I'll get onto that shortly.

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SimonGreenhill commented Nov 8, 2018

Ok, I realised there were mismatching version numbers (1.1 and 1.03) so I've released a new version 1.2, and the Zenodo version has been updated.

I think this fixes the "Treemaker v1" issue too -- I can't see it. Could you please double-check for me, or let me know where it's still saying v1?

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trallard commented Nov 8, 2018

It all looks good to me now @SimonGreenhill

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trallard commented Nov 8, 2018

@whedon set 10.5281/zenodo.1480504 as archive

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whedon commented Nov 8, 2018

OK. 10.5281/zenodo.1480504 is the archive.

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trallard commented Nov 8, 2018

@arfon : This submission is accepted and ready to be published 🎉

@RichardLitt @deniederhut thank you very much for your time and valuable contribution to JOSS as reviewers for this submission

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SimonGreenhill commented Nov 8, 2018

Wonderful, thanks for all the input and help everyone!

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RichardLitt commented Nov 8, 2018

Thanks for the opportunity to learn more about trees. 🌲

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arfon commented Nov 8, 2018

@whedon accept

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whedon commented Nov 8, 2018

Attempting dry run of processing paper acceptance...
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whedon commented Nov 8, 2018

Check final proof 👉 openjournals/joss-papers#61

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#61, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true
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arfon commented Nov 8, 2018

@whedon accept deposit=true

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whedon commented Nov 8, 2018

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

@whedon whedon added the accepted label Nov 8, 2018

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whedon commented Nov 8, 2018

🚨🚨🚨 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#62
  2. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01040
  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...

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arfon commented Nov 8, 2018

@RichardLitt, @deniederhut - many thanks for your reviews here and to @trallard for editing this submission

@SimonGreenhill - your paper is now accepted into JOSS ⚡️🚀💥

@arfon arfon closed this Nov 8, 2018

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whedon commented Nov 8, 2018

🎉🎉🎉 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.01040/status.svg)](https://doi.org/10.21105/joss.01040)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.01040">
  <img src="http://joss.theoj.org/papers/10.21105/joss.01040/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: http://joss.theoj.org/papers/10.21105/joss.01040/status.svg
   :target: https://doi.org/10.21105/joss.01040

This is how it will look in your documentation:

DOI

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deniederhut commented Nov 8, 2018

Congrats @SimonGreenhill !!

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SimonGreenhill commented Nov 8, 2018

Awesome, thanks everyone, the review process really made this package better!

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