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

[editorialbot]

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

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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.

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[editorialbot]

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
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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
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SUM:                             51           1976           2063          12908
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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	francis.lewis07@gmail.com
    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]

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]

Paper file info:

📄 Wordcount for paper.md is 1513

✅ The paper includes a Statement of need section

[editorialbot]

License info:

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

[editorialbot]

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

[Kevin-Mattheus-Moerman]

@editorialbot invite @fboehm as editor

[editorialbot]

Invitation to edit this submission sent!

[fboehm]

@editorialbot assign me as editor

[editorialbot]

Assigned! @fboehm is now the editor

[fboehm]

@editorialbot invite @fboehm as editor

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

[fboehm]

@editorialbot generate pdf

[editorialbot]

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

[fboehm]

@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]

@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!

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

[fboehm]

@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]

@editorialbot generate pdf

[editorialbot]

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

[TahiriNadia]

@editorialbot generate pdf

[editorialbot]

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

[TahiriNadia]

@editorialbot generate pdf

[editorialbot]

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

[AgustinPardo]

@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]

@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]

@editorialbot generate pdf

[fboehm]

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]

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

[fboehm]

@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]

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]

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]

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]

@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]

@editorialbot generate pdf

[editorialbot]

⚠️ An error happened when generating the pdf.

[TahiriNadia]

@editorialbot generate pdf

[editorialbot]

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

[TahiriNadia]

@editorialbot check references

[editorialbot]

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]

@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]

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

[annazhukova]

@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!

1. Jeronymo Dalapicolla (https://github.com/jdalapicolla)
2. Agustin Pardo (https://github.com/AgustinPardo/)
3. Anna Zhukova (https://github.com/annazhukova)
4. 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]

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

[fboehm]

@editorialbot add @annazhukova as reviewer

[editorialbot]

@annazhukova added to the reviewers list!

[fboehm]

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

[fboehm]

@editorialbot add @mmore500 as reviewer

[editorialbot]

@mmore500 added to the reviewers list!

[fboehm]

@editorialbot begin review

[editorialbot]

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

@editorialbot commands

[fboehm]

@editorialbot start review

[editorialbot]

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