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BioJulia / Bio.jl

[DEPRECATED] Bioinformatics and Computational Biology Infrastructure for Julia
http://biojulia.dev
MIT License
261 stars 63 forks source link

Release Bio.jl 0.4 #320

Closed bicycle1885 closed 8 years ago

bicycle1885 commented 8 years ago

We've added so many new features since Bio.jl 0.3, so I believe it's time to release a new minor version for users. Hopefully, I'd like to do that on this weekend, but if you have anything that should be addressed immediately please let us know here. I have time to focus on this project for a few days this week.

kdm9 commented 8 years ago

:+1:

I'd say at least #255 and #295 are worth waiting for.

bicycle1885 commented 8 years ago

Yes, but I'd like to step forward to the next phase of my project as soon as possible. We can release Bio.jl 0.5 at any moment after 0.4.

kdm9 commented 8 years ago

Go for it then mate!

bicycle1885 commented 8 years ago

And, as you already notice, I'm going to send a series of patches to improve the performance and usability as much as possible before release. These are mostly trivial stuffs so I may merge these things before getting approval from you but please feel free to add comments or open issues about them.

bicycle1885 commented 8 years ago

FYI: Julia 0.5 RC4 has been released (https://groups.google.com/forum/#!topic/julia-users/_33iQxEEx6Q), which is supposed to be the last release candidate before Julia 0.5. So, the release of it must be very soon!

bicycle1885 commented 8 years ago

Once CI tests pass on https://github.com/BioJulia/Bio.jl/commit/658d40f7d9c4dc39e427b4706db6e610aa3080d3 I will create a new branch release-0.4 and tag a new release v0.4.0.

sbromberger commented 8 years ago

Congratulations on the release of 0.4! Please let us over at LightGraphs know if you need anything from us - we're working with several of the bigger packages to make sure we're meeting needs.

bicycle1885 commented 8 years ago

@sbromberger Thank you! LightGraphs.jl is one of the greatest packages I've ever used. We'll continue to use it and the range will expand to gene networks, ontologies, and more!

bicycle1885 commented 8 years ago

Released Bio.jl 0.4. Thank you all!

TransGirlCodes commented 8 years ago

@sbromberger Yes thank you so much, as you know we're already building Phylogenetics functionality in Bio.jl with LightGraphs after several iterations of Phylo LightGraphs is definitely the best way to store phylogenetic network structures, and bioinformatics and genome assembly is a field chock full of graph use :)

sbromberger commented 8 years ago

I'm really glad it's meeting your needs. We're always open to suggestions and feedback - feel free to open an issue any time.

One heads-up - if you guys are testing for Julia 0.5, please make sure to check out the compat-0.5 branch of LG - we've got some pretty hefty changes in there. Nothing API-breaking, but it'd be good to get performance feedback from folks who are using it for advanced work (like you).