BioJulia / Libz.jl

Fast, flexible zlib bindings.
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Fix Julia 0.7 deprecations. #61

Closed GunnarFarneback closed 6 years ago

GunnarFarneback commented 6 years ago

Fix remaining Julia 0.7 deprecations.

GunnarFarneback commented 6 years ago

I mixed up my work a bit here, this PR is far from complete. In fact all the big type and where fixes are missing. However, those will cause Julia 0.5 to break even worse in CI. I'm guessing there's no real intention to keep supporting 0.5 on master and that it can be dropped from testing.

(I'm aware that this package is semi-deprecated but it's still in the dependency chain of other packages and would be good to have it running cleanly when Julia 1.0 comes.)

codecov-io commented 6 years ago

Codecov Report

Merging #61 into master will increase coverage by 0.87%. The diff coverage is 100%.

Impacted file tree graph

@@            Coverage Diff             @@
##           master      #61      +/-   ##
==========================================
+ Coverage   85.11%   85.99%   +0.87%     
==========================================
  Files           6        6              
  Lines         262      257       -5     
==========================================
- Hits          223      221       -2     
+ Misses         39       36       -3
Impacted Files Coverage Δ
src/sink.jl 88% <ø> (+0.82%) :arrow_up:
src/source.jl 89.55% <ø> (+2.05%) :arrow_up:
src/lowlevel.jl 86.58% <ø> (ø) :arrow_up:
src/state.jl 40% <100%> (+15%) :arrow_up:

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GunnarFarneback commented 6 years ago

Good to go from my point of view now.

TransGirlCodes commented 6 years ago

This looks great to me @GunnarFarneback, thanks for taking the trouble! :)

GunnarFarneback commented 6 years ago

Thanks for the prompt merge. However, the new release doesn't seem to make it into METADATA. Is attobot not watching this package?

TransGirlCodes commented 6 years ago

@GunnarFarneback I'll double check and if not I'll make sure it gets triggered.

TransGirlCodes commented 6 years ago

There it goes!

GunnarFarneback commented 6 years ago

Hm, JuliaCIBot finds (indirectly) that BGZFStreams works with Libz 0.2.4 but not with 0.3.0. It turns out that 0.2.4 was made from a branch and not from master, so the changes in 0.3.0 are larger than could be expected. Anyhow, the apparent problems with BGZFStreams are easy enough to solve (#63) but I don't know if there are other dangers lurking that caused earlier releases to be made from a branch.

GunnarFarneback commented 6 years ago

Checking the commit histories of master and the release-0.2 branch, it looks like the only controversial commit is 15f0644a91d20ef4469b00f529e6816fb5a6e7bd (Add support for raw deflate streams.) I've extended #63 with backwards compatibility for all functions touched by that commit, regardless of the likelihood that they would ever be called externally. If this package had long-term development plans they should rather be deprecation warnings, alternatively the raw support should be implemented differently, but here I think it is okay.

The main alternative to #63 would be to revert the raw support entirely, but I think that would be unnecessarily disruptive in case people are actively using the master branch.