[REVIEW]: Pynteny: a Python package to perform synteny-aware, profile HMM-based searches in sequence databases

[editorialbot]

Submitting author: @Robaina (Dr. Semidán Robaina Estévez)
Repository: https://github.com/Robaina/Pynteny
Branch with paper.md (empty if default branch):
Version: v1.1.0
Editor: @Kevin-Mattheus-Moerman
Reviewers: @Kevin-Mattheus-Moerman
Archive: 10.5281/zenodo.7750666

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/d6265f4aba18fd5e15b7ddce5909b06c"><img src="https://joss.theoj.org/papers/d6265f4aba18fd5e15b7ddce5909b06c/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/d6265f4aba18fd5e15b7ddce5909b06c/status.svg)](https://joss.theoj.org/papers/d6265f4aba18fd5e15b7ddce5909b06c)

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

@Kevin-Mattheus-Moerman, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review.
First of all you need to run this command in a separate comment to create the checklist:

@editorialbot generate my checklist

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @Kevin-Mattheus-Moerman 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 ✨

Checklists

@Kevin-Mattheus-Moerman, please create your checklist typing: @editorialbot generate my checklist

[editorialbot]

Hello humans, 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]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.06 s (823.5 files/s, 118463.0 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          16            498            807           2439
Markdown                        12            225              0            476
YAML                            11             35             16            311
TeX                              1             13              0            197
Jupyter Notebook                 4              0           1720            184
TOML                             1              3              0             47
Dockerfile                       2              5             12             28
JSON                             2              5              0             28
-------------------------------------------------------------------------------
SUM:                            49            784           2555           3710
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 1038

[editorialbot]

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

OK DOIs

- 10.1093/nar/gkt263 is OK
- 10.1186/s12859-019-2996-x is OK
- 10.1186/1471-2105-11-431 is OK
- 10.1038/nbt1004-1315 is OK
- 10.1186/1471-2105-11-119 is OK
- 10.1093/nar/gkr1293 is OK
- 10.1101/2021.06.03.446950 is OK
- 10.1093/bioinformatics/btab007 is OK
- 10.1126/science.1153917 is OK
- 10.1093/bioinformatics/btq413 is OK
- 10.7554/eLife.78526 is OK
- 10.1093/nar/gkaa1105 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[Kevin-Mattheus-Moerman]

This submission relates to this PyOpenSci review: pyOpenSci/software-submission#67

[Kevin-Mattheus-Moerman]

@editorialbot generate pdf

[editorialbot]

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

[editorialbot]

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

[Kevin-Mattheus-Moerman]

@editorialbot set v1.1.0 as version

[editorialbot]

Done! version is now v1.1.0

[Kevin-Mattheus-Moerman]

@editorialbot set 10.5281/zenodo.7750666 as archive

[editorialbot]

Done! Archive is now 10.5281/zenodo.7750666

[Kevin-Mattheus-Moerman]

Post-Review Checklist for Editor and Authors

Additional Author Tasks After Review is Complete

• Double check authors and affiliations (including ORCIDs)
• Make a release of the software with the latest changes from the review and post the version number here. This is the version that will be used in the JOSS paper.
• Archive the release on Zenodo/figshare/etc and post the DOI here.
• Make sure that the title and author list (including ORCIDs) in the archive match those in the JOSS paper.
• Make sure that the license listed for the archive is the same as the software license.

Editor Tasks Prior to Acceptance

• Read the text of the paper and offer comments/corrections (as either a list or a PR)
• Check the references in the paper for corrections (e.g. capitalization)
• Check that the archive title, author list, version tag, and the license are correct
• Set archive DOI with @editorialbot set <DOI here> as archive
• Set version with @editorialbot set <version here> as version
• Double check rendering of paper with @editorialbot generate pdf
• Specifically check the references with @editorialbot check references and ask author(s) to update as needed
• Recommend acceptance with @editorialbot recommend-accept

[Kevin-Mattheus-Moerman]

@Robaina I am the AEiC for JOSS to process this submission. Note I left some boxes unticked ☝️. The main things are to get the title, authors set, and the license to match between the software/paper and the archive. Can you make these changes to the archive and let me know when you are done?

[Robaina]

Hi @Kevin-Mattheus-Moerman, thank you for processing this submission. I think I have now completed the requested updates: https://doi.org/10.5281/zenodo.7048684

[Kevin-Mattheus-Moerman]

@editorialbot recommend-accept

[editorialbot]

Attempting dry run of processing paper acceptance...

[editorialbot]

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

OK DOIs

- 10.1093/nar/gkt263 is OK
- 10.1186/s12859-019-2996-x is OK
- 10.1186/1471-2105-11-431 is OK
- 10.1038/nbt1004-1315 is OK
- 10.1186/1471-2105-11-119 is OK
- 10.1093/nar/gkr1293 is OK
- 10.1101/2021.06.03.446950 is OK
- 10.1093/bioinformatics/btab007 is OK
- 10.1126/science.1153917 is OK
- 10.1093/bioinformatics/btq413 is OK
- 10.7554/eLife.78526 is OK
- 10.1093/nar/gkaa1105 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

👋 @openjournals/bcm-eics, this paper is ready to be accepted and published.

Check final proof 👉📄 Download article

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#4068, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[Kevin-Mattheus-Moerman]

@editorialbot accept

[editorialbot]

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

[editorialbot]

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

[editorialbot]

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

[editorialbot]

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

Here's what you must now do:

0. Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.05289 joss-papers#4069
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.05289
2. If everything looks good, then close this review issue.
3. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

[Kevin-Mattheus-Moerman]

@Robaina, congratulations on this JOSS publication!

[editorialbot]

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

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HTML:
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  <img src="https://joss.theoj.org/papers/10.21105/joss.05289/status.svg" alt="DOI badge" >
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reStructuredText:
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   :target: https://doi.org/10.21105/joss.05289

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[Robaina]

@Robaina, congratulations on this JOSS publication!

Awesome! thank you @Kevin-Mattheus-Moerman !