Joss-reviews: [REVIEW]: tcherry: Learning the structure of tcherry trees

[whedon]

Submitting author: @katrinekirkeby (Katrine Kirkeby)
Repository: https://github.com/nvihrs14/tcherry
Version: 0.1.1
Editor: @jasonclark
Reviewer: @kellieotto, @dhhagan
Archive: 10.5281/zenodo.3340382

Status

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Markdown: [![status](http://joss.theoj.org/papers/b8118cb7ec7b0fd7bf93ae41dbcc65ea/status.svg)](http://joss.theoj.org/papers/b8118cb7ec7b0fd7bf93ae41dbcc65ea)

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

@kellieotto, 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 @jasonclark know.

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

Review checklist for @kellieotto

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 (0.1.1)?
• [x] Authorship: Has the submitting author (@katrinekirkeby) 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 @dhhagan

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 (0.1.1)?
• [x] Authorship: Has the submitting author (@katrinekirkeby) 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. @kellieotto 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:

[jasonclark]

@kellieotto Can you carry out the review this week? Thanks!

[kellieotto]

Yes, thank you for the reminder!

On Jun 9, 2019, at 1:53 PM, Jason A. Clark [e-mail] wrote:

@kellieotto Can you carry out the review this week? Thanks!

—
You are receiving this because you were mentioned.
Reply to this email directly, view it on GitHub, or mute the thread.

[kellieotto]

@jasonclark @katrinekirkeby The package looks good on the whole but needs minor revisions. I've detailed them in the issues referenced above. Please tag me when they're done and I will take another look.

[katrinekirkeby]

@kellieotto Thank you for reviewing this packages. We have now tried to solved the missing issues, but regarding the issue about gramma we are not quite sure what you mean since we are not native english speakers, could you please clarify what the issues are

[kellieotto]

Thanks for making those changes so quickly @katrinekirkeby. Everything looks good now. I made some very minor grammar edits to the paper in the issue here: https://github.com/nvihrs14/tcherry/issues/4

Please ping me once the changes are made so I can approve the submission!

[katrinekirkeby]

@kellieotto I have now fixed the grammar edits

[kellieotto]

Looks good! @jasonclark I recommend this package for acceptance.

[arfon]

:wave: @dhhagan - please complete your review when you get a chance.

[dhhagan]

Hey @arfon I'm trying to complete the review now, but it appears the invite to the repository/issue didn't work and I can't seem to update the checkboxes above. Is there something I'm missing..?

[arfon]

@dhhagan - you'll need to accept this invite (shown at the top of this page) https://github.com/openjournals/joss-reviews/invitations

[dhhagan]

@arfon For some reason, it keeps saying that it can't find the invitation and won't let me accept.

[arfon]

@arfon For some reason, it keeps saying that it can't find the invitation and won't let me accept.

Hrm. Can you try again now?

[dhhagan]

@arfon That worked! Should have the review done within 24h.

[dhhagan]

Hey @arfon Sorry to bother you again, but for some reason when I logged on this morning, I no longer had access - not sure what's going on with GitHub...

[arfon]

@dhhagan - I'm so sorry for the trouble we've caused you here. You've actually helped me uncover a bug in our infrastructure. This should be fixed in https://github.com/openjournals/joss/commit/16230e01a4fdafc7a9df4f894b8f4a0dc46909b7 but you will have to accept the invite (hopefully for the last time!) again.

[dhhagan]

Hey @arfon and @katrinekirkeby I have completed most of the review - I opened up a couple of issues on the github repository - if you can address those, I will approve ASAP!

[arfon]

Hey @arfon and @katrinekirkeby I have completed most of the review - I opened up a couple of issues on the github repository - if you can address those, I will approve ASAP!

Excellent, thanks @dhhagan. @katrinekirkeby - please take a look at these issues and let us know when you have done so.

[katrinekirkeby]

Hey @arfon and @katrinekirkeby I have completed most of the review - I opened up a couple of issues on the github repository - if you can address those, I will approve ASAP!

Hello @dhhagan regarding the issue about the names, it is a choice we made because we think the name should say what the function is made for. Regarding the issue about contributions we have stated in the readme that the packages is a part of our Masters thesis, and because of that we don’t will be adding further functions, but we will answer questions over mail

[dhhagan]

Okay then - I think it's done. I've checked off the last box.

[arfon]

@katrinekirkeby - At this point could you make a new release of this software that includes the changes that have resulted from this review. Then, please make an archive of the software in Zenodo/figshare/other service and update this thread with the DOI of the archive? For the Zenodo/figshare archive, please make sure that:

• The title of the archive is the same as the JOSS paper title
• That the authors of the archive are the same as the JOSS paper authors

I can then move forward with accepting the submission.

[arfon]

I've just emailed the submitting author to ask them to return to this submission soon.

[katrinekirkeby]

I've just emailed the submitting author to ask them to return to this submission soon.

Sorry for the late answer, somehow the emails ended up in my spam box. I'm not quite sure how to make an archive of the software in Zenodo/figshare/other service, but I have created a new release of the software and made a new release on GitHub where this number is under the tags version: e472a7a

[mikldk]

@katrinekirkeby See e.g. https://genr.eu/wp/cite/ (or some other guide) on how to do that. It is only a few steps.

[katrinekirkeby]

@katrinekirkeby - At this point could you make a new release of this software that includes the changes that have resulted from this review. Then, please make an archive of the software in Zenodo/figshare/other service and update this thread with the DOI of the archive? For the Zenodo/figshare archive, please make sure that:

• The title of the archive is the same as the JOSS paper title
• That the authors of the archive are the same as the JOSS paper authors

I can then move forward with accepting the submission.

Hi @arfon.
The DOI of the zenodo archive is: 10.5281/zenodo.3340382.

[arfon]

@whedon set 10.5281/zenodo.3340382 as archive

[whedon]

OK. 10.5281/zenodo.3340382 is the archive.

[arfon]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/845

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/845, 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]

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

[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/846
2. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01480
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]

@kellieotto, @dhhagan - many thanks for your reviews here and to @jasonclark for editing this submission.

@katrinekirkeby - your paper is now accepted into JOSS :zap::rocket::boom:

[whedon]

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

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