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[REVIEW]: bíogo/ncbi: interfaces to NCBI services for the Go language #234

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whedon opened this Issue Apr 8, 2017 · 16 comments

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whedon commented Apr 8, 2017

Submitting author: @kortschak (Robert Daniel Kortschak)
Repository: https://github.com/biogo/ncbi
Version: v1.0.0
Editor: @pjotrp
Reviewer: @ngoto
Archive: 10.5281/zenodo.582354

Status

status

Status badge code:

HTML: <a href="http://joss.theoj.org/papers/f1c472b8ac1d894e12bb7bbc6e9c7e2d"><img src="http://joss.theoj.org/papers/f1c472b8ac1d894e12bb7bbc6e9c7e2d/status.svg"></a>
Markdown: [![status](http://joss.theoj.org/papers/f1c472b8ac1d894e12bb7bbc6e9c7e2d/status.svg)](http://joss.theoj.org/papers/f1c472b8ac1d894e12bb7bbc6e9c7e2d)

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)?
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whedon commented Apr 8, 2017

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

⭐️ Important ⭐️

If you haven't already, you should seriously consider unsubscribing from GitHub notifications for this (https://github.com/openjournals/joss-reviews) repository. As as reviewer, you're probably currently watching this repository which means for GitHub's default behaviour you will receive notifications (emails) for all JOSS reviews 😿

To fix this do the following two things:

  1. Set yourself as 'Not watching' https://github.com/openjournals/joss-reviews:

watching

  1. You may also like to change your default settings for this watching repositories in your GitHub profile here: https://github.com/settings/notifications

notifications

For a list of things I can do to help you, just type:

@whedon commands
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pjotrp commented Apr 8, 2017

@kortschak review has started by @ngoto who runs the bioruby project(!). @kortschak please help us by checking above boxes for us first. @ngoto, you can start ticking boxes when @kortschak says he is ready. Thanks!

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kortschak commented Apr 10, 2017

@ngoto I think this is ready for you to take a look.

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ngoto commented Apr 24, 2017

I'm sorry too late.

I'd like to run examples in README.md.
I tried to copy-and-paste code from README.md, saved and builded, but following errors:

$ go build  readme-entrez.go 
# command-line-arguments
./readme-entrez.go:38: undefined: query
$ go build readme-blast.go
can't load package: 
readme-blast.go:1:1: expected 'package', found 'const'
readme-blast.go:3:2: expected ';', found 'IDENT' tool
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kortschak commented Apr 24, 2017

Sorry. I have fixed the entrez example. That was a copy-paste error. The issue with the BLAST example is that it is not intended to be a complete runnable program; providing the harness for all that would detract from the code I have provided. I have clarified this in the preamble to that example.

Please comment at this PR.

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kortschak commented May 16, 2017

@ngoto I believe I have addressed all of your concerns.

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ngoto commented May 16, 2017

Performance: Have any performance claims of the software been confirmed?

It seems that no description about performance (only a phrase "light weight" ?). I suppose the running performance is fully depended on NCBI.

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kortschak commented May 16, 2017

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pjotrp commented May 17, 2017

Thanks @ngoto! Looks like we are pretty much done. There are no real claims on performance, so it is OK not to tick that box. If you are happy we can push for publication.

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ngoto commented May 19, 2017

Thanks. Finished. Sorry for delay.

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pjotrp commented May 20, 2017

Thank you so much @ngoto! @arfon we are ready to R&R!

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arfon commented May 22, 2017

@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.

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kortschak commented May 23, 2017

@arfon Done.

DOI

doi:10.5281/zenodo.582354

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arfon commented May 26, 2017

@whedon set 10.5281/zenodo.582354 as archive

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whedon commented May 26, 2017

OK. 10.5281/zenodo.582354 is the archive.

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arfon commented May 26, 2017

@ngoto - many thanks for your review here and thanks to @pjotrp for editing this submission

@kortschak - your paper is now accepted into JOSS and your DOI is http://dx.doi.org/10.21105/joss.00234 ⚡️🚀💥

@arfon arfon closed this May 26, 2017

@arfon arfon added the accepted label May 26, 2017

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