[PRE REVIEW]: aPhyloGeo: a multi-platform Python package for analyzing phylogenetic trees with climatic parameters #6447

editorialbot · 2024-03-06T09:42:24Z

Submitting author: @TahiriNadia (Nadia Tahiri)
Repository: https://github.com/tahiri-lab/aPhyloGeo
Branch with paper.md (empty if default branch): joss-journal
Version: v1.0.0
Editor: @fboehm
Reviewers: @annazhukova, @mmore500
Managing EiC: Kevin M. Moerman

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/6ae3cefa29ca05aa1119994549c877cb"><img src="https://joss.theoj.org/papers/6ae3cefa29ca05aa1119994549c877cb/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/6ae3cefa29ca05aa1119994549c877cb/status.svg)](https://joss.theoj.org/papers/6ae3cefa29ca05aa1119994549c877cb)

Author instructions

Thanks for submitting your paper to JOSS @TahiriNadia. Currently, there isn't a JOSS editor assigned to your paper.

@TahiriNadia if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). You can search the list of people that have already agreed to review and may be suitable for this submission.

Editor instructions

The JOSS submission bot @editorialbot is here to help you find and assign reviewers and start the main review. To find out what @editorialbot can do for you type:

@editorialbot commands

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

editorialbot · 2024-03-06T09:42:26Z

Hello human, I'm @editorialbot, a robot that can help you with some common editorial tasks.

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

@editorialbot commands

For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

@editorialbot generate pdf

editorialbot · 2024-03-06T09:42:48Z

Software report:

github.com/AlDanial/cloc v 1.90  T=0.09 s (571.3 files/s, 189848.2 lines/s)
--------------------------------------------------------------------------------
Language                      files          blank        comment           code
--------------------------------------------------------------------------------
Bourne Again Shell                2            308            722           5096
XML                               6              0              0           4149
Python                            9            491            949           1186
CSV                              12            677              0            811
Perl                              2            290            104            670
Ruby                              1             64             66            375
Markdown                          3            109              0            263
YAML                             10             15             55            205
TOML                              1              8              0             66
TeX                               1              0              0             38
DOS Batch                         2              7              6             28
PowerShell                        1              4            161             11
make                              1              3              0             10
--------------------------------------------------------------------------------
SUM:                             51           1976           2063          12908
--------------------------------------------------------------------------------

Commit count by author:

   209	Nadia Tahiri, PhD
   169	my-linh-luu
    56	Georges Marceau
    48	Nadia Tahiri
    37	slepaget
    30	cetmus
    23	db036
    23	geomarceau
    18	Elie Maalouf
    14	[email protected]
    11	Simon Lepage-Trudeau
     9	simlal
     8	Alex
     4	Wanlin Li
     2	Marc-Antoine Bélisle
     2	Mus
     2	Nadia Tahiri, Ph. D
     2	TahiriNadia
     2	jsDesm
     1	KarlP910

editorialbot · 2024-03-06T09:42:52Z

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.25080/majora-212e5952-018 is OK
- 10.25080/gerudo-f2bc6f59-00f is OK

MISSING DOIs

- 10.2307/2413638 may be a valid DOI for title: An alternating least squares approach to inferring...
- 10.1093/molbev/msl072 may be a valid DOI for title: Neighbor-joining revealed

INVALID DOIs

- None

editorialbot · 2024-03-06T09:42:57Z

Paper file info:

📄 Wordcount for paper.md is 1513

✅ The paper includes a Statement of need section

editorialbot · 2024-03-06T09:43:01Z

License info:

✅ License found: MIT License (Valid open source OSI approved license)

editorialbot · 2024-03-06T09:43:40Z

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

Kevin-Mattheus-Moerman · 2024-03-19T11:47:44Z

@editorialbot invite @fboehm as editor

editorialbot · 2024-03-19T11:47:45Z

Invitation to edit this submission sent!

fboehm · 2024-03-20T17:38:30Z

@editorialbot assign me as editor

editorialbot · 2024-03-20T17:38:34Z

Assigned! @fboehm is now the editor

fboehm · 2024-03-20T17:39:37Z

@editorialbot invite @fboehm as editor

Thank you, @Kevin-Mattheus-Moerman ! I'm excited to edit this submission

fboehm · 2024-03-21T01:57:18Z

@editorialbot generate pdf

editorialbot · 2024-03-21T01:58:48Z

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

fboehm · 2024-03-21T02:02:45Z

@TahiriNadia - can you recommend four or five individuals who might like to review this submission? They don't need to be listed in the joss reviewer list. Please feel free to list their names and github usernames in a comment. Thank you!

TahiriNadia · 2024-03-22T10:05:36Z

@TahiriNadia - can you recommend four or five individuals who might like to review this submission? They don't need to be listed in the joss reviewer list. Please feel free to list their names and github usernames in a comment. Thank you!

Jeronymo Dalapicolla (https://github.com/jdalapicolla)
Agustin Pardo (https://github.com/AgustinPardo/)
Anna Zhukova (https://github.com/annazhukova)
Fredericle Moine (https://github.com/fredericlemoine)

fboehm · 2024-03-23T18:38:20Z

@jdalapicolla @AgustinPardo @annazhukova @fredericlemoine - would you be willing to review this submission for JOSS? JOSS reviews are checklist-driven. If you agree to review, you would need to assess whether the package meets each of a number of criteria. For those where it currently doesn't meet the criteria, we would ask that you offer suggestions to the authors on how to improve the existing submission. Thank you for considering this invitation!

TahiriNadia · 2024-03-26T22:20:31Z

@editorialbot generate pdf

editorialbot · 2024-03-26T22:21:04Z

⚠️ An error happened when generating the pdf. Problem with affiliations for Georges Marceau, perhaps the affiliations index need quoting?.

TahiriNadia · 2024-03-26T22:37:18Z

@editorialbot generate pdf

editorialbot · 2024-03-26T22:38:53Z

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

TahiriNadia · 2024-03-27T20:22:15Z

@editorialbot generate pdf

editorialbot · 2024-03-27T20:23:35Z

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

AgustinPardo · 2024-03-27T23:47:03Z

@jdalapicolla @AgustinPardo @annazhukova @fredericlemoine - would you be willing to review this submission for JOSS? JOSS reviews are checklist-driven. If you agree to review, you would need to assess whether the package meets each of a number of criteria. For those where it currently doesn't meet the criteria, we would ask that you offer suggestions to the authors on how to improve the existing submission. Thank you for considering this invitation!

Hello, thanks for taking me into account.
What is the review criteria of the assessment?
Out of curiosity, where did you get my username, where did you meet me?

fboehm · 2024-03-28T02:28:53Z

@AgustinPardo thank you for the reply! My name is Fred, and I invited you to review at the suggestion of @TahiriNadia . I'm not sure how they know you or your work; I'll ask them to reply, too. The criteria, in general, involve assessing the quality of the software. There also is a very short manuscript that accompanies the software. For example, you would be asked to install the software package and see if it performs as advertised. If it contains unit tests, you would want to look at those.

I will try to remember to point you to the exact checklist tomorrow . I don't have it at my fingertips right now.

Thank you again for the consideration 😊

fboehm · 2024-03-28T18:38:45Z

@editorialbot generate pdf

fboehm · 2024-03-28T18:39:08Z

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.25080/majora-212e5952-018 is OK
- 10.25080/gerudo-f2bc6f59-00f is OK

MISSING DOIs

- 10.2307/2413638 may be a valid DOI for title: An alternating least squares approach to inferring...
- 10.1093/molbev/msl072 may be a valid DOI for title: Neighbor-joining revealed

INVALID DOIs

- None

@TahiriNadia - please feel free to fix the dois, if possible.

editorialbot · 2024-03-28T18:40:01Z

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

fboehm · 2024-03-28T18:41:24Z

@mmore500 - I'd like to invite you to review this submission for JOSS. It seems like your research experience and previous JOSS publication make you a good fit for this. Thank you for considering the invitation!

mmore500 · 2024-03-29T04:43:59Z

Thank you for the invitation! I'll be available after April 10 (big deadline) and would be happy to review then. Let me know if that time frame would be suitable!

TahiriNadia · 2024-03-29T05:37:47Z

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.25080/majora-212e5952-018 is OK
- 10.25080/gerudo-f2bc6f59-00f is OK

MISSING DOIs

- 10.2307/2413638 may be a valid DOI for title: An alternating least squares approach to inferring...
- 10.1093/molbev/msl072 may be a valid DOI for title: Neighbor-joining revealed

INVALID DOIs

- None

@TahiriNadia - please feel free to fix the dois, if possible.

For sure. Thanks @fboehm.

editorialbot · 2024-03-29T05:51:16Z

Checking the BibTeX entries failed with the following error:

Lexical or syntactical errors: 

@article{robinson1981comparisontitle={Comparison of phylogenetic trees},author={Robinson, David F and Foulds, Leslie R},journal={Mathematical biosciences},volume={53},number={1-2},pages={131--147},year={1981},publisher={Elsevier},doi=10.1016/0025-5564(

TahiriNadia · 2024-03-29T05:51:38Z

@TahiriNadia - do you know of other individuals who might be suitable reviewers? If so, please list, as you did last time, their information. You might also want to consult the JOSS reviewer database to find reviewers.

Perfect. I'll take a look. Thank you.

TahiriNadia · 2024-03-29T05:51:50Z

@editorialbot generate pdf

editorialbot · 2024-03-29T05:52:57Z

⚠️ An error happened when generating the pdf.

TahiriNadia · 2024-03-29T05:57:04Z

@editorialbot generate pdf

editorialbot · 2024-03-29T05:58:23Z

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

TahiriNadia · 2024-03-29T05:58:30Z

@editorialbot check references

editorialbot · 2024-03-29T05:58:49Z

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.25080/majora-212e5952-018 is OK
- 10.2307/2413638 is OK
- 10.25080/gerudo-f2bc6f59-00f is OK
- 10.1093/molbev/msl072 is OK
- 10.1016/0025-5564(81)90043-2 is OK

MISSING DOIs

- None

INVALID DOIs

- None

TahiriNadia · 2024-03-29T07:06:53Z

@TahiriNadia - can you recommend four or five individuals who might like to review this submission? They don't need to be listed in the joss reviewer list. Please feel free to list their names and github usernames in a comment. Thank you!

I noticed on the JOSS list that Tyler Chafin (https://github.com/tkchafin) could be a great fit for this topic.

Some other reviewers:

Will Pearse (https://github.com/willpearse)
Katy Brown (https://github.com/KatyBrown)
Benjamin Lee (https://github.com/benjamin-lee)

AgustinPardo · 2024-03-29T19:30:39Z

Claudio Schuster (https://github.com/CDSchuster) @CDSchuster

annazhukova · 2024-04-02T08:50:23Z

@TahiriNadia - can you recommend four or five individuals who might like to review this submission? They don't need to be listed in the joss reviewer list. Please feel free to list their names and github usernames in a comment. Thank you!

Jeronymo Dalapicolla (https://github.com/jdalapicolla)

Agustin Pardo (https://github.com/AgustinPardo/)

Anna Zhukova (https://github.com/annazhukova)

Fredericle Moine (https://github.com/fredericlemoine)

Thank you for considering me as a reviewer! I have several deadlines piling up at the moment, unfortunately. But if producing a review by ~April 26 will be not too long of a delay, I will be glad to review.

fboehm · 2024-04-03T13:37:28Z

THank you, @annazhukova ! Yes, completing an initial review in late April works for us. I'll add you as a reviewer now.

fboehm · 2024-04-03T13:37:41Z

@editorialbot add @annazhukova as reviewer

editorialbot · 2024-04-03T13:38:17Z

@annazhukova added to the reviewers list!

fboehm · 2024-04-03T13:39:09Z

Thank you @mmore500 ! Yes, we'd love to have you as a reviewer after your deadline. I'll add you now.

fboehm · 2024-04-03T13:39:23Z

@editorialbot add @mmore500 as reviewer

editorialbot · 2024-04-03T13:39:29Z

@mmore500 added to the reviewers list!

fboehm · 2024-04-03T13:39:35Z

@editorialbot begin review

editorialbot · 2024-04-03T13:39:46Z

I'm sorry human, I don't understand that. You can see what commands I support by typing:

@editorialbot commands

fboehm · 2024-04-03T13:40:01Z

@editorialbot start review

editorialbot · 2024-04-03T13:40:06Z

OK, I've started the review over in #6579.

editorialbot added pre-review Track: 2 (BCM) Biomedical Engineering, Biosciences, Chemistry, and Materials labels Mar 6, 2024

editorialbot added Shell Python Perl labels Mar 6, 2024

editorialbot assigned fboehm Mar 20, 2024

editorialbot assigned annazhukova Apr 3, 2024

editorialbot assigned mmore500 Apr 3, 2024

editorialbot closed this as completed Apr 3, 2024

[PRE REVIEW]: aPhyloGeo: a multi-platform Python package for analyzing phylogenetic trees with climatic parameters #6447

[PRE REVIEW]: aPhyloGeo: a multi-platform Python package for analyzing phylogenetic trees with climatic parameters #6447

Comments

editorialbot commented Mar 6, 2024 • edited Loading

Status

editorialbot commented Mar 6, 2024

editorialbot commented Mar 6, 2024

editorialbot commented Mar 6, 2024

editorialbot commented Mar 6, 2024

editorialbot commented Mar 6, 2024

editorialbot commented Mar 6, 2024

Kevin-Mattheus-Moerman commented Mar 19, 2024

editorialbot commented Mar 19, 2024

fboehm commented Mar 20, 2024

editorialbot commented Mar 20, 2024

fboehm commented Mar 20, 2024

fboehm commented Mar 21, 2024

editorialbot commented Mar 21, 2024

fboehm commented Mar 21, 2024

TahiriNadia commented Mar 22, 2024

fboehm commented Mar 23, 2024

TahiriNadia commented Mar 26, 2024

editorialbot commented Mar 26, 2024

TahiriNadia commented Mar 26, 2024

editorialbot commented Mar 26, 2024

TahiriNadia commented Mar 27, 2024

editorialbot commented Mar 27, 2024

AgustinPardo commented Mar 27, 2024

fboehm commented Mar 28, 2024

fboehm commented Mar 28, 2024

fboehm commented Mar 28, 2024

editorialbot commented Mar 28, 2024

fboehm commented Mar 28, 2024

mmore500 commented Mar 29, 2024

TahiriNadia commented Mar 29, 2024

editorialbot commented Mar 29, 2024

TahiriNadia commented Mar 29, 2024

TahiriNadia commented Mar 29, 2024

editorialbot commented Mar 29, 2024

TahiriNadia commented Mar 29, 2024

editorialbot commented Mar 29, 2024

TahiriNadia commented Mar 29, 2024

editorialbot commented Mar 29, 2024

TahiriNadia commented Mar 29, 2024

AgustinPardo commented Mar 29, 2024

annazhukova commented Apr 2, 2024

fboehm commented Apr 3, 2024

fboehm commented Apr 3, 2024

editorialbot commented Apr 3, 2024

fboehm commented Apr 3, 2024

fboehm commented Apr 3, 2024

editorialbot commented Apr 3, 2024

fboehm commented Apr 3, 2024

editorialbot commented Apr 3, 2024

fboehm commented Apr 3, 2024

editorialbot commented Apr 3, 2024

editorialbot commented Mar 6, 2024 •

edited

Loading