Closed whedon closed 7 years ago
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 :tada:.
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@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!
@ngoto I think this is ready for you to take a look.
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
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.
@ngoto I believe I have addressed all of your concerns.
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.
We make no claims about performance since the vast majority of computational effort is made by the NCBI servers or the local BLAST executable.
I don't believe that syntactic weight constitutes performance, but I guess that could be assessed by comparison of exported function count or SLOC with other similar suites.
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.
Thanks. Finished. Sorry for delay.
Thank you so much @ngoto! @arfon we are ready to R&R!
@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.
@whedon set 10.5281/zenodo.582354 as archive
OK. 10.5281/zenodo.582354 is the archive.
@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 ⚡️:rocket:💥
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
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