BioJulia / IntervalTrees.jl

A data structure for efficient manipulation of sets of intervals
MIT License
44 stars 17 forks source link

Fix deprecations #43

Closed bicycle1885 closed 6 years ago

bicycle1885 commented 6 years ago

This fixes deprecations. Fixing performance will be done in another pull request if needed.

codecov-io commented 6 years ago

Codecov Report

Merging #43 into master will increase coverage by 0.01%. The diff coverage is 100%.

Impacted file tree graph

@@            Coverage Diff             @@
##           master      #43      +/-   ##
==========================================
+ Coverage   97.66%   97.68%   +0.01%     
==========================================
  Files           3        3              
  Lines         600      604       +4     
==========================================
+ Hits          586      590       +4     
  Misses         14       14
Impacted Files Coverage Δ
src/slice.jl 94.87% <ø> (-0.26%) :arrow_down:
src/map.jl 100% <100%> (ø) :arrow_up:
src/IntervalTrees.jl 97.71% <100%> (+0.02%) :arrow_up:

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bicycle1885 commented 6 years ago

No performance degradation have been detected (actually, it gets faster!). I'd like to tag a new release from master if @BenJWard says okay.

~/w/IntervalTrees (master|…) $ julia benchmark.jl
Julia Version 0.7.0
Commit a4cb80f3ed (2018-08-08 06:46 UTC)
Platform Info:
  OS: macOS (x86_64-apple-darwin14.5.0)
  CPU: Intel(R) Core(TM) i5-6267U CPU @ 2.90GHz
  WORD_SIZE: 64
  LIBM: libopenlibm
  LLVM: libLLVM-6.0.0 (ORCJIT, skylake)
Environment:
  JULIA_PROJECT = @.
  JULIA_SHELL = /bin/bash
random query
  0.584057 seconds (2.67 M allocations: 107.485 MiB, 11.46% gc time)
  0.126999 seconds (1.49 M allocations: 45.381 MiB, 3.50% gc time)
  0.121476 seconds (1.49 M allocations: 45.381 MiB, 1.47% gc time)
  0.123130 seconds (1.49 M allocations: 45.381 MiB, 1.84% gc time)
  0.131035 seconds (1.49 M allocations: 45.381 MiB, 1.36% gc time)
~/w/IntervalTrees (master|…) $
~/w/IntervalTrees (master|…) $ /usr/local/bin/julia benchmark.jl
Julia Version 0.6.2
Commit d386e40c17 (2017-12-13 18:08 UTC)
Platform Info:
  OS: macOS (x86_64-apple-darwin14.5.0)
  CPU: Intel(R) Core(TM) i5-6267U CPU @ 2.90GHz
  WORD_SIZE: 64
  BLAS: libopenblas (USE64BITINT DYNAMIC_ARCH NO_AFFINITY Haswell)
  LAPACK: libopenblas64_
  LIBM: libopenlibm
  LLVM: libLLVM-3.9.1 (ORCJIT, skylake)
random query
  0.403435 seconds (1.71 M allocations: 56.540 MiB, 2.94% gc time)
  0.206816 seconds (1.56 M allocations: 47.478 MiB, 3.96% gc time)
  0.186784 seconds (1.56 M allocations: 47.478 MiB, 0.72% gc time)
  0.178138 seconds (1.56 M allocations: 47.478 MiB, 0.81% gc time)
  0.198571 seconds (1.56 M allocations: 47.478 MiB, 0.79% gc time)
TransGirlCodes commented 6 years ago

This probably should have been merged into the version-1.0 branch, as that's where other 0.7 changes by Sambit were merged, I was going to update project files on that branch and then release for 0.7.

TransGirlCodes commented 6 years ago

We can rebase version-1.0 and then do the release from there.

bicycle1885 commented 6 years ago

version-1.0 has been merged into master, so this is effectively built on top of version-1.0.

TransGirlCodes commented 6 years ago

Ah I didn't see that. Ok, I have some project files to add I haven't commited yet but have in my workspace, like Documenter.jl docs and such, I'd like to add those so they are included in the release, if that's ok. I'll work on that now.

bicycle1885 commented 6 years ago

Great. Please do that and then tag a new release if you are ready. I have nothing to add anymore.