first cut at fixing deprecations / errors on 0.6 #536

sbromberger · 2017-03-08T08:20:38Z

Branch sbromberger/compat-0.6 is designed to work on Julia 0.6. So far all tests pass, though there are deprecations in graphmatrices, randgraphs, and persistence (the latter two dealing with produce/consume stuff.)

codecov-io · 2017-03-10T03:32:18Z

Codecov Report

Merging #536 into master will increase coverage by 0.62%.
The diff coverage is 100%.

@@            Coverage Diff             @@
##           master     #536      +/-   ##
==========================================
+ Coverage   99.13%   99.75%   +0.62%     
==========================================
  Files          57       57              
  Lines        2898     2902       +4     
==========================================
+ Hits         2873     2895      +22     
+ Misses         25        7      -18

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sbromberger · 2017-03-10T15:41:39Z

@jpfairbanks for some reason, spectral.jl is now failing tests. I didn't do anything specific to it; just merged some other code from master in to keep this branch up to date. I tried lowering the tolerance from 1e-8 to 1e-5 but that didn't seem to do it. I also tried changing the approx function. I may have to revert that. Any ideas?

Specifically: https://travis-ci.org/JuliaGraphs/LightGraphs.jl/builds/209615638#L1033-L1035

jpfairbanks · 2017-03-10T23:22:59Z

Does this need julialang master?
I get errors on Version 0.6.0-dev.1393

INFO: Precompiling module LightGraphs.
ERROR: LoadError: LoadError: syntax: invalid type signature
 in include_from_node1(::String) at ./loading.jl:532
 in include(::String) at ./sysimg.jl:14
 in include_from_node1(::String) at ./loading.jl:532
 in include(::String) at ./sysimg.jl:14
 in anonymous at ./<missing>:2
 in eval(::Module, ::Any) at ./boot.jl:236
 in process_options(::Base.JLOptions) at ./client.jl:248
 in _start() at ./client.jl:335
while loading /home/.julia/v0.6/LightGraphs/src/core.jl, in expression starting on line 1
while loading /home/.julia/v0.6/LightGraphs/src/LightGraphs.jl, in expression starting on line 134
ERROR: Failed to precompile LightGraphs to /home/.julia/lib/v0.6/LightGraphs.ji.
 in compilecache(::String) at ./loading.jl:672
 in require(::Symbol) at ./loading.jl:453

sbromberger · 2017-03-10T23:27:10Z

I'm pretty sure it needs -alpha.

jpfairbanks · 2017-03-11T02:02:04Z

I built master as of today and it worked.

There are some deprecation warnings about inner constructors, which I think are tied to changes made in the following commit.
JuliaLang/julia@0190b3a

jpfairbanks · 2017-03-11T02:04:44Z

Well tests failed with GZip.jl@master:

running /home/.julia/v0.6/LightGraphs/test/persistence/persistence.jl ...
ERROR: LoadError: LoadError: UndefVarError: readall not defined
Stacktrace:
 [1] loadgraphml_mult(::GZip.GZipStream)

sbromberger · 2017-03-11T02:05:05Z

Yup. These are the combinatorial laplacian and friends.

sbromberger · 2017-03-11T02:13:47Z

It was working for me as of yesterday's build. :(

jpfairbanks · 2017-03-11T19:21:01Z

So readall got renamed to readstring. I will put a commit on this branch to fix that.

What happened to Tasks and produce/consume?

[TODO]: turn this test back on before 0.6 release!

The inner constructor form: ```julia function NormalizedAdjacency(adjmat::CombinatorialAdjacency) sf = adjmat.D.^(-1/2) return new(adjmat, sf) end end ``` is replaced by ```julia function NormalizedAdjacency{T}(adjmat::CombinatorialAdjacency{T}) sf = adjmat.D.^(-1/2) return NormalizedAdjacency(adjmat, sf) end ``` This deprecates the calling convention: NormalizedAdjacency{Float64}(adjmat) in favor of NormalizedAdjacency(adjmat) which is much cleaner. The {Float64} parameter was needed because the NormalizedAdjacency(CombinatorialAdjacency{Int}(a)) needed to be of type Float64. This promotion choice was exposed to the caller instead of being made automatically. Now if you want to construct a NormalizedAdjacency{Float64} from a CombinatorialAdjacency{Int} you will have to use the default constructor and do the conversion by hand.

jpfairbanks · 2017-03-12T01:02:46Z

The next step is to replace produce/consume with channels.

channels deprecate produce, consume and task iteration JuliaLang/julia#19841
nonbacktracking operator
merge benchmarks
test for regressions

Fixes deprecation warnings introduced in: JuliaLang/julia#19841 Changes an API interface: -function Graph(nvg::Int, neg::Int, edgestream::Task) +function Graph(nvg::Int, neg::Int, edgestream::Channel) Iteration over Tasks is deprecated so now we iterate over the Channel.

sbromberger · 2017-03-13T00:50:34Z

(@jpfairbanks - I edited your list above.)

sbromberger · 2017-03-18T00:20:33Z

Where is the channels code? (Why is this checked off?)

jpfairbanks · 2017-03-18T13:23:31Z

I thought I made a branch with my commits that should be a part of this PR, but I can't find it.

sbromberger · 2017-03-18T20:51:30Z

I thought I made a branch with my commits that should be a part of this PR, but I can't find it.

I thought I saw it too, and I was going to steal it. Could you (re)write it?

…hs/LightGraphs.jl into sbromberger/compat-0.6

jpfairbanks · 2017-03-19T15:19:00Z

This commit 017137a has my channels stuff. It is in this PR

sbromberger · 2017-03-19T18:05:58Z

OK, I got it (cherry picked into abstractions). I'm going to close this out since I think the plan is to make the abstractions branch the "official" 0.6 release.

first cut at fixing deprecations / errors on 0.6

7b6c697

sbromberger added breaking change non-deprecable change. work in progress (DO NOT MERGE) used for proofs-of-concept and other code that is ready for review but not ready for merging labels Mar 8, 2017

sbromberger assigned sbromberger and jpfairbanks Mar 8, 2017

sbromberger and others added 3 commits March 8, 2017 08:58

pick #537

977dcd7

Merge branch 'master' into sbromberger/compat-0.6

76a8917

v0.6-

3190615

sbromberger force-pushed the sbromberger/compat-0.6 branch from 82cdb67 to 3190615 Compare March 9, 2017 21:21

Merge branch 'master' into sbromberger/compat-0.6

f29e87a

tuples

42daf7c

sbromberger force-pushed the sbromberger/compat-0.6 branch from a72350c to 567b4f8 Compare March 10, 2017 05:12

sbromberger force-pushed the sbromberger/compat-0.6 branch from 567b4f8 to 42daf7c Compare March 10, 2017 15:45

Pair and Tuple constructors

4756181

sbromberger mentioned this pull request Mar 10, 2017

updates for 0.6 #518

Closed

jpfairbanks added 3 commits March 11, 2017 14:34

replace readall with readstring

e8e2cff

@test_skip nonbacktracking test temporarily

10d957b

[TODO]: turn this test back on before 0.6 release!

sbromberger added 5 commits March 13, 2017 08:25

Merge branch 'master' into sbromberger/compat-0.6

d95252b

testset

5deb114

Base.full moved to top

8ebd3ae

added base.linalg

73053dd

Pair and Tuple constructors

ef8c221

sbromberger force-pushed the sbromberger/compat-0.6 branch from 73053dd to ef8c221 Compare March 17, 2017 22:36

Merge branch 'sbromberger/compat-0.6' of https://github.com/JuliaGrap…

1406f0e

…hs/LightGraphs.jl into sbromberger/compat-0.6

sbromberger closed this Mar 19, 2017

sbromberger deleted the sbromberger/compat-0.6 branch March 29, 2017 17:33

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first cut at fixing deprecations / errors on 0.6 #536

first cut at fixing deprecations / errors on 0.6 #536

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first cut at fixing deprecations / errors on 0.6 #536

first cut at fixing deprecations / errors on 0.6 #536

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