Finding new packages and docs


#1

It looks like the Bio.jl documentation and such is moving from https://github.com/BioJulia to https://biojulia.net/. I that right? Some cross-links and explanation would be very helpful. The “not for use with Julia 0.6” warning on the old site could lead a lazier user to give up on Bio.jl. I was very excited to see the newer packages at biojulia.net, but I only found that site by accident. Apologies in advance if I’m just late to the game.


#2

The BioJulia website and docs are at https://biojulia.net and the code is hosted on GitHub at https://github.com/BioJulia.

A while ago BioJulia decided to move from one large package (Bio.jl) to a series of separate packages (BioSequences.jl etc). Bio.jl would then re-export all the individual packages so a user could deal with a single dependency if they like.

The separate packages are generally stable on Julia v0.6 and are used commonly. The Bio.jl package isn’t yet stabilised, hence the warning.

I agree this situation is not immediately obvious, perhaps we could change the warning at https://github.com/BioJulia/Bio.jl to indicate that the individual packages are stable on v0.6 and that BioJulia as a whole is very much an active project.

Hopefully we should have it in a more stable state soon; stabilisation of Julia after v1.0 will certainly help. Currently it is primarily @Ward9250 putting in the work on the organisational front, an often thankless task.


#3

Thanks for the explanation. I’m glad to hear that things are still moving forward.


#4

Also, these links might help you find some new packages?

// sorry the search feature is a little weak :frowning:


#5

Excellent. I always thought the julia package listing needed categories. Great to see that someone has done that!


#6

Can’t take too much credit for that :stuck_out_tongue:

// it’s pulled from @svaksha’s curated decibans


#7

Thanks for the credit @djsegal :smiley:


#9

Hopefully this clears things up a bit on the readme, thanks for the input @phaverty.


#10

It’s just anecdotal, but I’ve been using Bio.jl intensively on v.06 (only a subset of features though) and I’ve never add an issue with it. It’s very well made imo.


#11

Yeah, I’m pretty sure the decision to shift to federated packages was made after 0.6, so it still works. It’s just that new developments are not happening in that repo - if you only look there you would not see all of the exciting new features :smiley:


#12

The decision to shift was made during the julia v0.5 -> v0.6 transition, I don’t think it’s reliably stable on julia v0.6 (see https://github.com/BioJulia/Bio.jl/issues/480 and https://github.com/BioJulia/Bio.jl/issues/425). If it is we should get the autobuild working and tag a release.

Still, great that it works for people! Not going to complain about that :smile:.


#13

Bio.jl is getting some love and a release before JuliaCon.
(So are some other packages too).

It’s going to get less confusing for new users and explorers as to exactly what Bio.jl is and where the other packages are.