[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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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

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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

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Reviewer instructions & questions

Review checklist for @giraola

Conflict of interest

Code of Conduct

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Functionality

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Software paper

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