[REVIEW]: Ngesh: a Python library for synthetic phylogenetic data

whedon commented 3 years ago

Submitting author: @tresoldi (Tiago Tresoldi) Repository: https://github.com/tresoldi/ngesh Version: 1.0 Editor: @majensen Reviewer: @DavidNickle, @rvosa Archive: 10.5281/zenodo.5552605

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Status

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Markdown: [![status](https://joss.theoj.org/papers/33b21b92804433dd0f5e61bacc323130/status.svg)](https://joss.theoj.org/papers/33b21b92804433dd0f5e61bacc323130)

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

@DavidNickle & @rvosa, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

Make sure you're logged in to your GitHub account
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 @majensen know.

✨ Please start on your review when you are able, and be sure to complete your review in the next six weeks, at the very latest ✨

Review checklist for @DavidNickle

Conflict of interest

[x] I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

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] Contribution and authorship: Has the submitting author (@tresoldi) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

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 functionality 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] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] A statement of need: Does the paper have a section titled 'Statement of Need' that clearly states what problems the software is designed to solve and who the target audience is?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

Review checklist for @rvosa

Conflict of interest

[x] I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

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] Contribution and authorship: Has the submitting author (@tresoldi) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

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 functionality 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] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] A statement of need: Does the paper have a section titled 'Statement of Need' that clearly states what problems the software is designed to solve and who the target audience is?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

majensen commented 3 years ago

@whedon set version as 1.0

whedon commented 3 years ago

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

@whedon commands

majensen commented 3 years ago

@whedon set 1.0 as version

whedon commented 3 years ago

OK. 1.0 is the version.

majensen commented 3 years ago

@whedon set 10.5281/zenodo.5552605 as archive

whedon commented 3 years ago

OK. 10.5281/zenodo.5552605 is the archive.

majensen commented 3 years ago

@whedon recommend accept

whedon commented 3 years ago

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

@whedon commands

majensen commented 3 years ago

@whedon recommend-accept

whedon commented 3 years ago

Attempting dry run of processing paper acceptance...

whedon commented 3 years ago

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

OK DOIs

- 10.1038/sdata.2018.205 is OK
- 10.2307/2333730 is OK
- 10.1126/science.283.5406.1310 is OK
- 10.32942/osf.io/e3xnr is OK
- 10.1093/sysbio/syr029 is OK
- 10.1093/molbev/msw046 is OK
- 10.1126/science.1219669 is OK
- 10.16993/baj.h is OK
- 10.1093/bioinformatics/btu181 is OK
- 10.1093/bioinformatics/bty633 is OK
- 10.1371/journal.pone.0180908 is OK
- 10.1371/journal.pcbi.1006650 is OK

MISSING DOIs

- None

INVALID DOIs

- None

whedon commented 3 years ago

:wave: @openjournals/joss-eics, this paper is ready to be accepted and published.

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/2648

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/2648, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

kyleniemeyer commented 3 years ago

Hi @tresoldi! I am just doing some final checks before accepting. I noticed some very minor issues in the paper, could you fix these and let me know in here?

second paragraph: please add commas after "e.g."
Bailey: John Wiley & Soins -> John Wiley & Sons

tresoldi commented 3 years ago

@whedon generate pdf

whedon commented 3 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

tresoldi commented 3 years ago

Hi @kyleniemeyer ! Thanks for catching those, they are now fixed.

kyleniemeyer commented 3 years ago

@whedon accept deposit=true

whedon commented 3 years ago

Doing it live! Attempting automated processing of paper acceptance...

whedon commented 3 years ago

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

whedon commented 3 years ago

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

Check final PDF and Crossref metadata that was deposited :point_right: https://github.com/openjournals/joss-papers/pull/2654
Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.03173
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

tresoldi commented 3 years ago

Great! Thank you everybody! :smiley:

tresoldi commented 3 years ago

It seems I can't close the issue, I guess there is one last thing I need to bother you, @majensen

kyleniemeyer commented 3 years ago

@tresoldi I am waiting for the PDF to show up before closing the issue.

kyleniemeyer commented 3 years ago

... which it looks like is now working!

whedon commented 3 years ago

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

If you would like to include a link to your paper from your README use the following code snippets:

Markdown:
[![DOI](https://joss.theoj.org/papers/10.21105/joss.03173/status.svg)](https://doi.org/10.21105/joss.03173)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.03173">
  <img src="https://joss.theoj.org/papers/10.21105/joss.03173/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.03173/status.svg
   :target: https://doi.org/10.21105/joss.03173

This is how it will look in your documentation:

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majensen commented 3 years ago

@tresoldi congratulations! Thanks very much to @DavidNickle and @rvosa for your reviews.

tresoldi commented 3 years ago

Thanks again for all the support, @majensen , and @DavidNickle and @rvosa for the review work. :)

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