Closed Robaina closed 1 year ago
ok wonderful @Robaina @arianesasso will followup with next steps. so appreciative of all of the back and forth on this review. Essentially we just need to get an Ok from both reviewers that the changes to your package have satisfied their requests in the review... and then there are a few closing steps and we can send you on your way to JOSS! more soon...
Thanks for looking into this issue @Robaina and thanks for your support @lwasser!
@c-thoben thank YOU for being such a wonderful reviewer and for supporting open source!!
hi everyone! i just wanted to check in @Batalex @c-thoben has everything in your reviews been completed at this point? i just want to understand where we are in the review !
Yup, it is all good on my side. I could not have asked for a more reactive & understanding submitter 🙌
For me also everything is fine :)
Thank you @Batalex. Likewise, you far exceeded my expectations in your review. Incredibly supportive and collaborative. From now on using ruff --fix
in all my projects 😆
Thank you so much for your time and great review @c-thoben, and for helping me identify and solve Pynteny's installation problems!
ok next steps! @Robaina @Batalex @c-thoben please followup here by taking our post review survey. We greatly appreciate your time in doing. Your input improves our overall process (Alex if this survey feels super redundant to you please tell me as i know you've taken some of our other surveys). i welcome all input.
🎉 Pynteny has been approved by pyOpenSci! Thank you @Robaina for submitting pyteny and many thanks to @Batalex @c-thoben for reviewing this package! 😸 NOTE: I have to say this was an extraordinary review over all. @NickleDave you also really did a wonderful job in getting this review together early on. All aspects of this review went exactly as i would hope a pyOpenSci review would go!! We want our reviews to be a conversation that supports maintainers in improving their package! And i really think this was achieved here. So thank you ALL for being a tremendous team in this review.
There are a few things left to do to wrap up this submission after you've taken the post review survey!
@Robaina please do the following:
[![pyOpenSci](https://tinyurl.com/y22nb8up)](https://github.com/pyOpenSci/software-review/issues/issue-number)
.<tag> all-contributors please add @robaina for code, review
@lwasser
I couldn't determine any contributions to add, did you specify any contributions? Please make sure to use valid contribution names.
I've put up a pull request to add @ALL! :tada:
I've put up a pull request to add @badge! :tada:
I've put up a pull request to add @robaina! :tada:
I've put up a pull request to add @package! :tada:
I couldn't determine any contributions to add, did you specify any contributions? Please make sure to use valid contribution names.
Could not find the user feedback
on github.
Weird, seems like the all-contribs bot got triggered even though we didn't tag it?
I closed all these PRs except for the one that added @Robaina which I went ahead and merged. The reviewers will still need to be added.
@NickleDave you also really did a wonderful job in getting this review together early on.
It was really easy to work with @Robaina who has been really responsive to feedback and who has now evolved pynteny
into a full-fledged package, happy to be a part of the review
Weird, seems like the all-contribs bot got triggered even though we didn't tag it?
I closed all these PRs except for the one that added @Robaina which I went ahead and merged. The reviewers will still need to be added.
woah -- i just saw that. i guess i will have to link to instructions in our guide book 🙈 sorry y'all! i didn't think the bot worked like that
@NickleDave you also really did a wonderful job in getting this review together early on.
It was really easy to work with @Robaina who has been really responsive to feedback and who has now evolved
pynteny
into a full-fledged package, happy to be a part of the review
Thank you so much for your help during the pre-review @NickleDave!
Thank you so much you all! I think I have completed all the required checks from my side. Please, review my PR to include Pynteny in the database. Not sure I completed the fields correctly.
As a final note. I have to say that I have enjoyed this review process. You have been tremendously supportive. Feedback has been always constructive to better the package. I wished these kinds of open reviews were the norm in Science...
It is really great to know you enjoyed the process! I think we all did 😄 . Now, for the last steps regarding JOSS:
Please read their paper.md file requirements, and make sure that the paper is in your repo.
Then, follow the instructions here: submitting the package to JOSS.
Now, you don't need to go through another review 🙂 : You should just tag the JOSS issue with our issue.
Great! will check paper format and submit it in the following days. Thank you @arianesasso !
Closing this now that we're pyOS-approved and joss-approved! Great review y'all
Submitting Author: Semidán Robaina (@Robaina) All current maintainers: @Robaina Package Name: Pynteny One-Line Description of Package: Query sequence database by HMMs arranged in predefined synteny structure Repository Link: https://github.com/Robaina/Pynteny Version submitted: v0.0.5 Editor: @arianesasso Reviewer 1: @Batalex Reviewer 2: @c-thoben
JOSS DOI:
Version accepted: 1.0.0
Date accepted (month-day-year): 03-10-2023
Archive:
Description
Pynteny is Python tool to search for synteny blocks in (prokaryotic) sequence data through HMMs of the ORFs of interest and HMMER. By leveraging genomic context information, Pynteny can be employed to decrease the uncertainty of functional annotation of unlabelled sequence data due to the effect of paralogs. Pynteny can be accessed (i) through the command line, (ii) as a Python module, or (iii) as a (locally served) web application.
Scope
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Explain how and why the package falls under these categories (briefly, 1-2 sentences). Please note any areas you are unsure of:
Pynteny's main objective is to provide a means to query NGS (unannotated) sequence databases, such as metagenomic/metatranscriptomic datasets using syntenic blocks (i.e. spatial arrangements of genes) rather than single target genes/protein domains. In this sense, I would classify Pynteny within Data Extraction.
Pynteny was designed to be used by researchers working with large, unannotated sequence databases, such as those typically encountered in metagenomic analyses. It can be accessed through a command line interface or easily integrated into pipelines as a Python package. Pynteny can also be used through a graphical interface running locally in the browser, which is more suitable for educational purposes.
To the extent of my knowledge, there isn't any Python package that provides the functionality provided by Pynteny.
@tag
the editor you contacted: https://github.com/pyOpenSci/software-review/issues/65Technical checks
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I had submitted this package for publication at JOSS prior to pyOpenSci. The submission is currently under consideration for scope in this issue: https://github.com/openjournals/joss-reviews/issues/4978
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