[REVIEW]: Xenomapper - short read mapping in a mixed species context about joss-reviews HOT 14 CLOSED

✋ I am reviewing this

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/ cc @openjournals/joss-reviewers - would anyone be willing to review this submission?

If you would like to review this submission then please comment on this thread so that others know you're doing a review (so as not to duplicate effort). Something as simple as :hand: I am reviewing this will suffice.

Reviewer instructions

• Please work through the checklist at the start of this issue.
• If you need any further guidance/clarification take a look at the reviewer guidelines here http://joss.theoj.org/about#reviewer_guidelines
• Please make a publication recommendation at the end of your review

Any questions, please ask for help by commenting on this issue! 🚀

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General checks

all checked

Functionality

all checked

• I confirmed the functionality using code from the test suite

Documentation

some checked

Missing:

• Example Usage: There is no example usage or command to run the software using some of the sample data included. Recommendation: Add a 'Example usage' section with step-by-step commands to run Xenomapper with files from xenomapper/tests/data as input and explanation of each problem solved. More than a single example would be great to have examples of some of the multiple features.
• Community guidelines: There is no mention on how to contribute, report bugs or get support. Recommendation: Add a 'How to contribute' section with at least a brief statement encouraging posible contributors to help pointing them to open a new github issue. Even better would be to link to a CONTRIBUTING.md file with extended instructions. Add also comments on how to report a problem (opening an issue should be OK) and seek support (ideas: mailing list, contact email, github issue with a specific tag).

Software paper:

all checked

• Authors and statement of needs OK
• All DOIs verified

Nice-to-have improvements:

• License file is included in the repository, but users need to open it to know what is the actual license used. I'd recommend adding a mention in the readme file. Just something like "Licensed under GPL v3" would be useful.
• Tests are included and Travis is configured, so that point is clearly checked. But It would be good if instructions on how to run the tests locally are clearly stated in the README. Actually the command to do it (python3 -m xenomapper.tests.test_all) is there, but under the Alternate Installation section.

Recommendation:

I recommend publication after some minor revisions: usage examples and contributing instructions should be added to the documentation.

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I recommend publication after some minor revisions: usage examples and contributing instructions should be added to the documentation.

Many thanks for the review @xuanxu. @genomematt - please let us know when you've addressed @xuanxu's comments and we can move forward.

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@xuanxu @afron - updated version addressing review comments pushed. Examples are still a bit sparse but I will continue to add to them. Data access issues with most of the worked examples I already have so I will need to hunt up some more datasets. I really want these to be runnable notebooks. I also added an extra affiliation line to reflect my dual appointment to the paper.md

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👍 thanks @genomematt!
I've checked both points and I consider this publication-ready now.

A small doubt, @arfon & @genomematt: the archive link in this issue and the "DOI for current release" link in the "How to cite Xenomapper" section both still point to version 1.0.0. Probably a new DOI should be created for the current 1.0.1 version and have both links updated before paper is published.

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Ok @arfon and @xuanxu I have made an updated release with a new zenodo id 10.5281/zenodo.51798 but this is in the whedon part of the submission not the paper.md so I can't see a way for me to edit it.

Updated the how to cite to reflect JOSS, and the Zenodo badge updates automatically (links to current version not a fixed DOI).

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All checked!

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Thanks @xuanxu
@arfon PDF will need regenerating. Look forward to being official! Where do I sign up as a reviewer and evangelist?

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Thanks @xuanxu for the review.

@arfon PDF will need regenerating.

👍 - yes, it's regenerated and should be correct at https://github.com/openjournals/joss-papers/blob/master/joss.00018/10.21105.joss.00018.pdf

@genomematt - your DOI will be http://dx.doi.org/10.21105/joss.00018 but the Crossref system seems to be a little backed up right now (this paper is pretty far back in the queue).

Where do I sign up as a reviewer and evangelist?

I'd be happy to add you to the @openjournals/joss-reviewers team if that sounds good?

🎉

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@arfon Only the second affiliation comes up on the PDF. I will raise a bug.

Yes, add me to @openjournals/joss-reviewers

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Yes, add me to @openjournals/joss-reviewers

Excellent, thanks! You should have received an invite to join the team.

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@genomematt - the DOI is now live: http://dx.doi.org/10.21105/joss.00018

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🎉

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