[REVIEW]: SuchTree : A Python library for fast, thread-safe computations on phylogenetic trees #678

whedon · 2018-04-16T17:37:32Z

Submitting author: @ryneches (Russell Y. Neches)
Repository: https://github.com/ryneches/SuchTree
Version: 0.6
Editor: @karthik
Reviewer: @giraola
Archive: 10.5281/zenodo.1294297

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General checks

Repository: Is the source code for this software available at the repository url?
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Version: Does the release version given match the GitHub release (0.6)?
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Functionality

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Documentation

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Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
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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)?

The text was updated successfully, but these errors were encountered:

whedon · 2018-04-16T17:37:34Z

Hello human, I'm @whedon. I'm here to help you with some common editorial tasks. @giraola it looks like you're currently assigned as the reviewer for this paper 🎉.

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whedon · 2018-04-16T17:37:35Z

Attempting PDF compilation. Reticulating splines etc...

whedon · 2018-04-16T17:37:53Z

--> Check article proof 📄 <--

ryneches · 2018-04-27T23:32:43Z

Article proof looks good to me, aside from missing a reference for FastTree. D'oh.

giraola · 2018-04-28T21:37:06Z

@ryneches please add DOIs to all references listed in the manuscript.

ryneches · 2018-04-30T23:24:24Z

Done. I also added references for FastTree. Hmm... do I ask @whedon to make a new proof?

karthik · 2018-05-01T01:23:28Z

@whedon generate pdf

whedon · 2018-05-01T01:23:30Z

Attempting PDF compilation. Reticulating splines etc...

whedon · 2018-05-01T01:24:06Z

--> Check article proof 📄 <--

ryneches · 2018-05-01T01:45:46Z

@whedon generate pdf

whedon · 2018-05-01T01:45:49Z

Attempting PDF compilation. Reticulating splines etc...

whedon · 2018-05-01T01:46:18Z

--> Check article proof 📄 <--

ryneches · 2018-05-01T02:36:44Z

Hmm. I'm not happy with the way the references are getting formatted. Multiple references look weird, and BibTeX is doing that thing where it turns repeated author lists into a long dash. :-/

Is there a formatting guide? I'm not so familiar with the MarkDown to LaTeX way of doing things.

arfon · 2018-05-03T14:10:05Z

Hmm. I'm not happy with the way the references are getting formatted. Multiple references look weird, and BibTeX is doing that thing where it turns repeated author lists into a long dash. :-/

This is the standard style for our bibliography - it's because the author list of the second paper is the same as the one above it.

ryneches · 2018-05-07T23:02:20Z

Ah, OK. I've always thought looks weird.

ryneches · 2018-05-17T23:57:31Z

What's next?

arfon · 2018-05-18T14:45:41Z

What's next?

I think we're waiting for @giraola to finish their review?

giraola · 2018-05-18T14:51:44Z

Hi @arfon @ryneches, sorry for the delay, I will complete it within the following two of days...

giraola · 2018-05-18T15:06:26Z

@ryneches please add installation guidelines and list SuchTree dependencies in the readme file.

ryneches · 2018-05-20T09:44:11Z

Added.

ryneches · 2018-06-01T01:26:55Z

Anything else?

giraola · 2018-06-12T17:01:18Z

@ryneches I just completed the revision. Sorry for this delay.

arfon · 2018-06-15T19:59:19Z

@karthik - I think this paper is good to accept?

karthik · 2018-06-19T22:58:10Z

@arfon Yes, definitely. I communicated with Russel before I left for my trip and am just returning to editorial duties. Will finish this up asap.

karthik · 2018-06-19T22:59:10Z

@ryneches So sorry for the delay. This is good to go and thanks for your patience!
🙏

Now, can you deposit the software on Zenodo and post a DOI here so we can complete the final steps towards acceptance?

ryneches · 2018-06-20T23:47:20Z

All right! After a little tidying up, here's the Zenodo DOI :

https://doi.org/10.5281/zenodo.1294297

karthik · 2018-06-22T04:39:46Z

@whedon set 10.5281/zenodo.1294297 as archive

whedon · 2018-06-22T04:39:49Z

OK. 10.5281/zenodo.1294297 is the archive.

karthik · 2018-06-22T04:40:11Z

@whedon generate pdf

whedon · 2018-06-22T04:40:13Z

Attempting PDF compilation. Reticulating splines etc...

whedon · 2018-06-22T04:40:40Z

--> Check article proof 📄 <--

karthik · 2018-06-22T04:42:15Z

@ryneches Congrats on your paper being accepted! 🎉
@arfon will do a couple more steps to finalize your paper.

arfon · 2018-06-22T10:36:55Z

@ryneches - I made a small fix to one of your bibtex entries which wasn't working in ryneches/SuchTree#14

@giraola - many thanks for your review here and to @karthik for editing this submission ✨

@ryneches - your paper is now accepted into JOSS and your DOI is https://doi.org/10.21105/joss.00678 ⚡ 🚀 💥

whedon · 2018-06-22T10:36:59Z

🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

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whedon assigned karthik Apr 16, 2018

whedon added the review label Apr 16, 2018

whedon mentioned this issue Apr 16, 2018

[PRE REVIEW]: SuchTree : A Python library for fast, thread-safe computations on phylogenetic trees #666

Closed

arfon added the accepted label Jun 22, 2018

arfon closed this as completed Jun 22, 2018

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

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[REVIEW]: SuchTree : A Python library for fast, thread-safe computations on phylogenetic trees #678

[REVIEW]: SuchTree : A Python library for fast, thread-safe computations on phylogenetic trees #678

whedon commented Apr 16, 2018 •

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[REVIEW]: SuchTree : A Python library for fast, thread-safe computations on phylogenetic trees #678

[REVIEW]: SuchTree : A Python library for fast, thread-safe computations on phylogenetic trees #678

Comments

whedon commented Apr 16, 2018 • edited

Status

Reviewer instructions & questions

Review checklist for @giraola

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

whedon commented Apr 16, 2018

whedon commented Apr 16, 2018

whedon commented Apr 16, 2018

ryneches commented Apr 27, 2018 • edited

giraola commented Apr 28, 2018

ryneches commented Apr 30, 2018

karthik commented May 1, 2018

whedon commented May 1, 2018

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ryneches commented May 20, 2018 • edited

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