Julia v0.6 compatability

[CorySimon]

Am I too early to upgrade to Julia v0.6 for Bio v0.4.7?

using Bio.Intervals
Interval("chr1", 10000, 20000)

gives error:

ERROR: type String has no field data
Use `Vector{UInt8}(str)` instead.
Stacktrace:
 [1] Bio.Intervals.Interval(::String, ::Int64, ::Int64) at /Users/csimon/.julia/v0.6/Bio/src/intervals/interval.jl:34

[bicycle1885]

All functions related to Bio.Intervals have been moved to GenomicFeatures.jl, which already supports Julia 0.6 (and Julia 0.5). For a while, Bio.jl is not recommended for Julia 0.6 users but it will be rebuilt on top of more modular packages including GenomicFeatures.jl. See #425 for more details.

[tlnagy]

Since Julia 0.6 is the current stable release, I think it would be best to have a prominent warning message or something to let people know that Bio.jl is going through these large changes. It took me a while to figure out that major rearchitecting is going on and that's why running using Bio gives dozens of warnings on v0.6.

[jonathanBieler]

What's the update path ? I've been working on the master for a while and after making a few changes (e.g. BEDMetadata -> BED.Record, ...) it seems to work alright on 0.6. I'm mainly using the BAM stuff though. Is there anything else to worry about ? Will Bio.Intervals.BED keep pointing to GenomicFeatures.BED ?

[TransGirlCodes]

Will Bio.Intervals.BED keep pointing to GenomicFeatures.BED?

Yes it will will always point to GenomicFeatures.BED, Bio.jl is a meta-package and so the vast majority of its content will point to other packages.

[KarolisM]

It seems that GenomicFeatures is way ahead and in principal I failed to compile Bio.jl and GenomicFeatures because dependencies does not match: both requires diff versions of IntervalTrees...
Any tips how I could solve this issue? Thanks.

[timbitz]

The IntervalTrees.jl master branch works on Julia v0.6, just not the latest release yet I think. For now you should be able to get it with Pkg.checkout("IntervalTrees").

[bicycle1885]

Developers often forget to release the latest version because they use their latest branch on their machine.

I added a minor fix to IntervalTrees.jl (https://github.com/BioJulia/IntervalTrees.jl/pull/33) and will soon release a new version that supports Julia 0.6.

[ChrisRackauckas]

It seems there are still a lot of depwarns. Can Femtocleaner be setup and run on all of the repos, and a tag go through?

[kescobo]

Sorry... Ignore me 😕

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