Comments (17)
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This is a nifty piece of software, combining a snappy algorithm with a pleasant Python API, and a model for good packaging and programmer/developer-friendly documentation (including working demo code, executable documentation, and a command-line tool!).
In the process of reviewing, I've opened a number of issues on the sourmash package itself, but I've only linked to this ticket on those issues that I feel should be resolved before a JOSS acceptance.
I recommend acceptance (after minor revisions).
As an afterword (and a comment to the Editors): Minting a new Zenodo snapshot & DOI before reviewing seems like wasted effort, since (I would hope) nearly all reviewers are going to request changes (even if minor) that will require a new Zenodo snapshot.
Can reviewers bless a particular tag or revision in the target repo, and have authors or JOSS take the zenodo snapshot/doi after the review process is complete?
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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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Hi @jkahn thx - note that I just updated master with a bug fix (and a test for the bug :) for a bug discovered yesterday.
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I am not a copyright lawyer, but I don't think the text given in the release is exactly what the BSD 3-clause would say. For one thing, the Regents of the U of C and the MSU are mentioned the LICENSE
file, but only the RofUofC in the header. (I understand that @ctb has probably moved from one to the other, looking at @dib-lab .
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updated the checklist so that there are unchecked boxes corresponding to the open questions.
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Hi @jkahn Thanks for all your comments - many excellent improvements resulted. I think this is ready for review once again!
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Note, the latest version is 0.9.4, https://github.com/dib-lab/sourmash/releases/tag/v0.9.4, and zenodo etc should be updated soon
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Pending these two concerns (both resolved by a little bit more attention to onboarding new developers), I'm satisfied that my concerns have been addressed and recommend the package re-mint and be accepted.
I want to address my one continuing gripe: I don't love that the test code is mixed in (closed, wontfix) among the shipped code (in a public-facing library, this could open an entirely new attack surface) but I don't think it's a release-blocking offense, especially in a research package.
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Pending these two concerns (both resolved by a little bit more attention to onboarding new developers), I'm satisfied that my concerns have been addressed and recommend the package re-mint and be accepted.
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OK, I've made the changes and @luizirber has checked them twice :).
Am I correct in thinking that I should proceed by cutting a new release (v1.0) and then putting the zenodo link in here? That's it, yes? (Reading author guidelines)
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Am I correct in thinking that I should proceed by cutting a new release (v1.0) and then putting the zenodo link in here? That's it, yes? (Reading author guidelines)
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sgtm! congratulations!
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sourmash 1.0 now up!
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thanks for all your hard work @jkahn!
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Many thanks again for the review @jkahn!
@ctb your paper is now accepted in JOSS. Your DOI is http://dx.doi.org/10.21105/joss.00027
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