[REVIEW]: sourmash: a library for MinHash sketching of DNA about joss-reviews HOT 17 CLOSED

✋ I am reviewing this submission. I should have a review by end of week; likely sooner.

from joss-reviews.

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?

from joss-reviews.

/ 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! 🚀

from joss-reviews.

Hi @jkahn thx - note that I just updated master with a bug fix (and a test for the bug :) for a bug discovered yesterday.

from joss-reviews.

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 .

from joss-reviews.

updated the checklist so that there are unchecked boxes corresponding to the open questions.

from joss-reviews.

from joss-reviews.

Hi @jkahn Thanks for all your comments - many excellent improvements resulted. I think this is ready for review once again!

from joss-reviews.

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

from joss-reviews.

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.

from joss-reviews.

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.

👍 thanks @jkahn. @ctb - please let me know when you've made these changes.

from joss-reviews.

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)

from joss-reviews.

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)

👍 yes please @ctb

from joss-reviews.

sgtm! congratulations!

from joss-reviews.

sourmash 1.0 now up!

from joss-reviews.

thanks for all your hard work @jkahn!

from joss-reviews.

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 🎉 🚀 💥

from joss-reviews.