[REVIEW]: bíogo/hts: high throughput sequence handling for the Go language

[whedon]

Submitting author: kortschak (Robert Daniel Kortschak)
Repository: https://github.com/biogo/hts
Version: v1.0.0
Editor: @pjotrp
Reviewer: @sb10
Archive: 10.5281/zenodo.268032

Status

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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) 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 questions

Conflict of interest

• As the reviewer I confirm that there are no conflicts of interest for me to review this work (such as being a major contributor to the software).

General checks

• Repository: Is the source code for this software available at the repository url?
• License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• Version: Does the release version given match the GitHub release (v1.0.0)?
• Authorship: Has the submitting author (kortschak) made major contributions to the software?

Functionality

• Installation: Does installation proceed as outlined in the documentation?
• Functionality: Have the functional claims of the software been confirmed?
• Performance: Have any performance claims of the software been confirmed?

Documentation

• A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
• Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
• Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g. API method documentation)?
• Automated tests: Are there automated tests or manual steps described so that the function of the software can be verified?
• 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

• Authors: Does the paper.md file include a list of authors with their affiliations?
• A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• References: Do all archival references that should have a DOI list one (e.g. papers, datasets, software)?

[whedon]

Hello human, I'm @whedon. I'm here to help you with some common editorial tasks for JOSS. @sb10 it looks like you're currently assigned as the reviewer for this paper 🎉.

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[sb10]

@whedon commands

[whedon]

Here are some things you can ask me to do:

# List all of Whedon's capabilities
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This is all quite new. Please make sure you check the top of the issue after running a @whedon command (you might also need to refresh the page to see the issue update).

[sb10]

v1.0.1 passes all of the reviewer questions and I'm satisfied with it.

[pjotrp]

Thank you @sb10 for the review. @arfon I think we can proceed with acceptance.

[arfon]

Thank you @sb10 for the review. @arfon I think we can proceed with acceptance.

Great. Thanks @pjotrp and thanks to @sb10 for completing the review ⚡

@kortschak - At this point could you make an archive of the reviewed software in Zenodo/figshare/other service and update this thread with the DOI of the archive? I can then move forward with accepting the submission.

[kortschak]

Thank you.

[arfon]

@whedon set 10.5281/zenodo.268032 as archive

[whedon]

OK. 10.5281/zenodo.268032 is the archive.

[arfon]

@kortschak - could you please move the references in https://github.com/biogo/hts/blob/master/paper/paper.md to a separate paper.bib file and then reference them from your paper.md file. You can see an example of how to do this here: https://github.com/arfon/fidgit/tree/master/paper

[kortschak]

@arfon Done.

[arfon]

Many thanks @pjotrp for editing this submission and @sb10 for the review ✨

@kortschak - your paper is now accepted into JOSS and your DOI is http://dx.doi.org/10.21105/joss.00168 ⚡️ 🚀 💥