search

BioJulia / GenomicFeatures.jl

Tools for genomic features in Julia.
Other
32 stars 13 forks source link

Plans for julia 1.0? #14

Closed phaverty closed 6 years ago

phaverty commented 6 years ago

Are there plans to get GenomicFeatures ready for julia 1.0? How can I help?

TransGirlCodes commented 6 years ago

Hey @phaverty, there's a branch (creatively) called "updates", which has a few commits ahead of master already, including appveyor and travis changes to julia v0.7 / v1.0. This "updates" branch has an associated PR here: https://github.com/BioJulia/GenomicFeatures.jl/pull/15.

The plan is to apply changes until everything builds and tests fine. You can either apply changes directly to the "updates" branch if you like, or use it as a base for your own PRs.

TransGirlCodes commented 6 years ago

It might be better to PR against "updates" just incase any squashes of commits and the like involving force pushes occurs, I've already done one commit squash.

phaverty commented 6 years ago

Excellent, thanks. I'll set aside some evening coding time to see what I can do.

Pete

Peter M. Haverty, Ph.D. Genentech, Inc. phaverty@gene.com

On Thu, Aug 23, 2018 at 9:54 AM, Ben J. Ward notifications@github.com wrote:

It might be better to PR against "updates" just incase any squashes of commits and the like involving force pushes occurs.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/BioJulia/GenomicFeatures.jl/issues/14#issuecomment-415490067, or mute the thread https://github.com/notifications/unsubscribe-auth/AH02K3GamzNzF2ERuG3DK4F9mqnhj7-Tks5uTt47gaJpZM4WJ1uv .

TransGirlCodes commented 6 years ago

Awesome :)

Also I’ve just noticed that before GenomicFeatures can be upgraded, we need to have a 0.7/1.0 release for BGZFStreams first as it’s a dependency, so there’s a want for updates contributions there as well :)

On 23 Aug 2018, at 18:07, Peter Haverty notifications@github.com wrote:

Excellent, thanks. I'll set aside some evening coding time to see what I can do.

Pete

Peter M. Haverty, Ph.D. Genentech, Inc. phaverty@gene.com

On Thu, Aug 23, 2018 at 9:54 AM, Ben J. Ward notifications@github.com wrote:

It might be better to PR against "updates" just incase any squashes of commits and the like involving force pushes occurs.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/BioJulia/GenomicFeatures.jl/issues/14#issuecomment-415490067, or mute the thread https://github.com/notifications/unsubscribe-auth/AH02K3GamzNzF2ERuG3DK4F9mqnhj7-Tks5uTt47gaJpZM4WJ1uv .

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/BioJulia/GenomicFeatures.jl/issues/14#issuecomment-415495190, or mute the thread https://github.com/notifications/unsubscribe-auth/ADPejVZUAkL8ogEoGF_aB81Is7y59BsKks5uTuFCgaJpZM4WJ1uv.

phaverty commented 6 years ago

I saw that BioSequences released their version for 1.0. BGZFStreams looks like it is ready to go. I don't really know anything about the compression domain, but if it's just modernizing syntax, I can help.

Pete

Peter M. Haverty, Ph.D. Genentech, Inc. phaverty@gene.com

On Thu, Aug 23, 2018 at 10:10 AM, Ben J. Ward notifications@github.com wrote:

Awesome :)

Also I’ve just noticed that before GenomicFeatures can be upgraded, we need to have a 0.7/1.0 release for BGZFStreams first as it’s a dependency, so there’s a want for updates contributions there as well :)

On 23 Aug 2018, at 18:07, Peter Haverty notifications@github.com wrote:

Excellent, thanks. I'll set aside some evening coding time to see what I can do.

Pete

Peter M. Haverty, Ph.D. Genentech, Inc. phaverty@gene.com

On Thu, Aug 23, 2018 at 9:54 AM, Ben J. Ward notifications@github.com wrote:

It might be better to PR against "updates" just incase any squashes of commits and the like involving force pushes occurs.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/BioJulia/GenomicFeatures.jl/issues/14# issuecomment-415490067, or mute the thread https://github.com/notifications/unsubscribe-auth/ AH02K3GamzNzF2ERuG3DK4F9mqnhj7-Tks5uTt47gaJpZM4WJ1uv .

— You are receiving this because you commented. Reply to this email directly, view it on GitHub < https://github.com/BioJulia/GenomicFeatures.jl/issues/14# issuecomment-415495190>, or mute the thread https://github.com/ notifications/unsubscribe-auth/ADPejVZUAkL8ogEoGF_ aB81Is7y59BsKks5uTuFCgaJpZM4WJ1uv.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/BioJulia/GenomicFeatures.jl/issues/14#issuecomment-415496196, or mute the thread https://github.com/notifications/unsubscribe-auth/AH02K1AvRgbsfquqE4PTcatnVG3XaZuHks5uTuHogaJpZM4WJ1uv .

TransGirlCodes commented 6 years ago

@phaverty So it does! The errors I saw must have been due to the non 1.0 version of BGZFStreams being used.

TransGirlCodes commented 6 years ago

@phaverty The next release should fix this as a result of the two PRs Dan and myself done did. It has made way into METADATA so I'll close this.

phaverty commented 6 years ago

Fantastic! Sorry I wasn't more help. I'll keep an eye out for a place to contribute in the future.