Joss-reviews: [REVIEW]: treemaker

[whedon]

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 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

• [x] As the reviewer I confirm that I have read the JOSS conflict of interest policy and that there are no conflicts of interest for me to review this work.

Code of Conduct

• [x] I confirm that I read and will adhere to the JOSS 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: Does the release version given match the GitHub release (v1.03)?
• [x] Authorship: Has the submitting author (@SimonGreenhill) 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)?

Review checklist for @deniederhut

Conflict of interest

• [x] As the reviewer I confirm that I have read the JOSS conflict of interest policy and that there are no conflicts of interest for me to review this work.

Code of Conduct

• [x] I confirm that I read and will adhere to the JOSS 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: Does the release version given match the GitHub release (v1.03)?
• [x] Authorship: Has the submitting author (@SimonGreenhill) 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)?

[whedon]

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 :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:

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

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

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

@whedon commands

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

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

[deniederhut]

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

[SimonGreenhill]

Thanks for the very helpful input and suggestions @deniederhut !

[SimonGreenhill]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[trallard]

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 😄

[RichardLitt]

@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.

[SimonGreenhill]

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

[SimonGreenhill]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[trallard]

@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 (?)

[trallard]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[trallard]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[arfon]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

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

[whedon]

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

[whedon]

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

[whedon]

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

[whedon]

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

[SimonGreenhill]

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

[SimonGreenhill]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

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

[SimonGreenhill]

Look good to me, thanks!

[trallard]

@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

[SimonGreenhill]

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

[SimonGreenhill]

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?

[trallard]

It all looks good to me now @SimonGreenhill

[trallard]

@whedon set 10.5281/zenodo.1480504 as archive

[whedon]

OK. 10.5281/zenodo.1480504 is the archive.

[trallard]

@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

[SimonGreenhill]

Wonderful, thanks for all the input and help everyone!

[RichardLitt]

Thanks for the opportunity to learn more about trees. 🌲

[arfon]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/61

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

[arfon]

@whedon accept deposit=true

[whedon]

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

[whedon]

🚨🚨🚨 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/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...

[arfon]

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

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

[whedon]

: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.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:

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:

• Volunteering to review for us sometime in the future. You can add your name to the reviewer list here: http://joss.theoj.org/reviewer-signup.html
• Making a small donation to support our running costs here: https://www.flipcause.com/secure/cause_pdetails/Mjk3Nzk=

[deniederhut]

Congrats @SimonGreenhill !!

[SimonGreenhill]

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