first cut at 0.7 compatibility #848

sbromberger · 2018-02-20T00:19:34Z

This requires the m3/where-fns branch of SimpleTraits.jl.

Current status:

Test Summary:              |  Pass  Error  Total
LightGraphs                | 28668      5  28673
  LightGraphs.SimpleGraphs |  2730          2730
  LightGraphs.LinAlg       |   336      4    340
    Graph matrices         |    45      1     46
    Spectral               |   291      3    294
  Interface                |    23            23
  Core                     |   122           122
  Operators                |   318           318
  Decomposition            |    48            48
  Distance                 |    42            42
  Transitivity             |    24            24
  Hadwick-James Cycles     |    21            21
  Cycles                   |    30            30
  Karp Minimum Cycle Mean  |    30            30
  Edit distance            |   240           240
  Connectivity             |   198      1    199
  Persistence              |    15            15
  Randgraphs               |  1270          1270
  Static graphs            |    25            25
  Small graphs             |    25            25
  Euclidean graphs         |    13            13
  A star                   |    18            18
  Bellman Ford             |    48            48
  Dijkstra                 |   441           441
  Floyd Warshall           |    21            21
  Yen                      |    72            72
  BFS                      |    75            75
  Parallel_BFS             |    25            25
  Bipartiteness            |    27            27
  DFS                      |    24            24
  Max adj visit            |    33            33
  Random walks             | 21879         21879
  Diffusion Simulation     |    57            57
  Cliques                  |    12            12
  Core periphery           |    93            93
  Label propagation        |    24            24
  Modularity               |     6             6
  Clustering               |    18            18
  Clique percolation       |     1             1
  Betweenness              |    51            51
  Closeness                |    48            48
  Degree                   |     9             9
  Katz                     |     3             3
  Pagerank                 |    54            54
  Eigenvector              |     6             6
  Stress                   |    18            18
  Radiality                |     6             6
  Utils                    |    18            18
  Kruskal                  |     6             6
  Prim                     |     6             6
  Articulation             |    24            24
  Biconnect                |     6             6
  Normalized Cut           |    29            29

Some steps for updating to sulia-v0.7 * using LightGraphs does not error * Switch to LinearAlgebra and SparseArrays std libs * Fix most of linalg tests * Add SharedArrays for distance tests to compile * Add Random and Markdown to stdlibs used * Fix connectivity tests * IntSet -> BitSet * Add DelimitedFiles stdlib for readcsv * Fix failing test

sbromberger · 2018-02-20T16:37:14Z

I've asked Mauro to tag a new version of SimpleTraits that has the where-fn fix in it. Once we have that I'll make it part of REQUIRES and will retest.

rohitvarkey · 2018-02-20T16:53:18Z

test/runtests.jl

@@ -6,6 +6,9 @@ using LinearAlgebra

 const testdir = dirname(@__FILE__)

+# we need a specific branch of SimpleTraits.jl until https://github.com/mauro3/SimpleTraits.jl/pull/51 is merged
+Pkg.checkout("m3/where-fns")


I think you need Pkg.checkout("SimpleTraits", "m3/where-fns")

sbromberger · 2018-02-20T16:58:08Z

src/LightGraphs.jl

@@ -1,15 +1,28 @@
 __precompile__(true)
 module LightGraphs

+using SharedArrays
+using Random


We will want to dedup these.

rohitvarkey · 2018-02-20T17:46:44Z

Not sure why Travis is failing. This is what I get on my local machine with julia built with the latest master and LightGraphs on this branch.

   _       _ _(_)_     |  A fresh approach to technical computing
  (_)     | (_) (_)    |  Documentation: https://docs.julialang.org
   _ _   _| |_  __ _   |  Type "?help" for help.
  | | | | | | |/ _` |  |
  | | |_| | | | (_| |  |  Version 0.7.0-DEV.4031 (2018-02-20 14:42 UTC)
 _/ |\__'_|_|_|\__'_|  |  Commit 5aa548b453* (0 days old master)
|__/                   |  x86_64-apple-darwin16.4.0

julia> Pkg.test("LightGraphs");
*....deprecations.....*
Test Summary: |  Pass  Total
LightGraphs   | 28845  28845
[ Info: LightGraphs tests passed

sbromberger · 2018-02-20T19:33:44Z

Looks like it's still not using the correct branch of SimpleTraits.

sbromberger · 2018-02-20T20:54:33Z

JuliaLang/METADATA.jl#13453

codecov · 2018-02-20T21:29:06Z

Codecov Report

Merging #848 into master will not change coverage.
The diff coverage is 100%.

@@          Coverage Diff          @@
##           master   #848   +/-   ##
=====================================
  Coverage     100%   100%           
=====================================
  Files          59     59           
  Lines        3001   3001           
=====================================
  Hits         3001   3001

sbromberger · 2018-02-20T21:41:05Z

OK, so: should we merge this now, or try to get rid of some of these deprecations first?

If we merge now, we'll need to cut a final 0.6-compatible version beforehand. This will allow us to use FemtoCleaner on the master branch.

rohitvarkey · 2018-02-21T04:16:56Z

I tried setting up FemtoCleaner locally to try and remove deprecations on this branch but had lots of issues with Homebrew etc.

Considering that, I think the approach of cutting a final 0.6 release, merging this PR and then running FemtoCleaner on master is probably the best way of removing the deprecations and getting LG completely ready for 0.7.

sbromberger · 2018-02-21T05:30:15Z

https://github.com/JuliaGraphs/LightGraphs.jl/releases/tag/v0.12.0

JuliaLang/METADATA.jl#13458

rohitvarkey · 2018-02-21T16:12:33Z

Hmm. Seems like Pkg isn't finding the correct version of SimpleTraits. Could this be cause SimpleTraits is set as julia 0.7 and not julia 0.7- in METADATA?

sbromberger · 2018-02-21T16:39:43Z

Could this be cause SimpleTraits is set as julia 0.7 and not julia 0.7- in METADATA?

I'll bet that's it.

Ref: mauro3/SimpleTraits.jl#52

(edited again): tests won't pass until SimpleTraits v0.7.1 is merged (JuliaLang/METADATA.jl#13470).

rohitvarkey · 2018-02-22T11:18:44Z

Now that the METADATA PR is merged, let's try Travis again? 🤞

sbromberger · 2018-02-22T18:01:31Z

OK, tests pass. I'm going to merge this into master.

* removed flow algorithms (sbromberger#815) * fixes sbromberger#820, plus tests (sbromberger#821) * change show() for empty graphs (ref JuliaGraphs/MetaGraphs.jl#20 (comment)) (sbromberger#822) * Pull request clique_percolation.jl (sbromberger#826) clique percolation is a method of uncovering the overlapping community structure of complex networks in nature and society * add src/community/clique_percolation.jl * tests in file test/community/clique_percolation.jl * cites the original clique percolation paper * for undirected graphs only using traitfn * in_ / out_ -> in / out (sbromberger#830) * (in,out)_neighbors -> (in,out)neighbors * all_neighbors -> allneighbors * Pull request clique_percolation.jl (sbromberger#826) clique percolation is a method of uncovering the overlapping community structure of complex networks in nature and society * add src/community/clique_percolation.jl * tests in file test/community/clique_percolation.jl * cites the original clique percolation paper * for undirected graphs only using traitfn * revert allneighbors * expected_degree_graph (Chung-Lu model) (sbromberger#832) * Expected degree random graph generator implemented, including tests * algorithm corrected * Missing seed corrected in expected_degree_graph * expected_degree_graph! implemented * Added return in function, comment with references removed, references in docs added (expected_degree_graph) * Update randgraphs.jl minor doc update * Update randgraphs.jl * Fixing problems with MST Kruskal's on SimpleWeightedGraphs (sbromberger#835) * Update kruskal.jl * Update prim.jl * Update kruskal.jl * Update kruskal.jl * Update prim.jl * Update kruskal.jl * Update prim.jl * Update kruskal.jl * Update prim.jl * reverting changes * Revert "reverting changes" This reverts commit ac1760b. * Revert "Update prim.jl" This reverts commit 677f6fa. * Revert "Update kruskal.jl" This reverts commit a0e9c47. * Revert "Update prim.jl" This reverts commit 793bac4. * Revert "Update kruskal.jl" This reverts commit 6114e16. * Revert "Update prim.jl" This reverts commit 551f1e6. * Revert "Update kruskal.jl" This reverts commit 941005e. * Revert "Update kruskal.jl" This reverts commit a404514. * Revert "Update prim.jl" This reverts commit 2d43a60. * Revert "Update kruskal.jl" This reverts commit 4577920. * fix problems with SimpleWeightedGraphs * fix problems with SimpleWeightedGraphs * fix problems with SimpleWeightedGraphs * bipartite_map on 2-order graphs fixed. Added proper tests. Fixed test connected to bipartite_map (sbromberger#836) * Correct pre-allocation of memory in Prim's MST (sbromberger#839) * Improve Kruskal's MST by optimizing Union-Find (sbromberger#843) * add missing backtick (sbromberger#846) * Add greedy_color for Graph Coloring (sbromberger#844) * Add greedy_color for Graph Coloring * Improve Kruskal's MST by optimizing Union-Find (sbromberger#843) * Update README.md * Update README.md * first cut at 0.7 compatibility (sbromberger#848) * using LightGraphs does not error * Switch to LinearAlgebra and SparseArrays std libs * Fix most of linalg tests * Add SharedArrays for distance tests to compile * Add Random and Markdown to stdlibs used * Fix connectivity tests * IntSet -> BitSet * Add DelimitedFiles stdlib for readcsv * Fix failing test * first cut * Use mauro/SimpleTraits.jl/m3/where-fns in tests * Fix SimpleTraits checkout (sbromberger#851) * Move up SimpleTraits checkout (sbromberger#852) * Update runtests.jl * Update REQUIRE * Update REQUIRE * femtocleaner with additional depwarn fixes (sbromberger#856) fix deprecation warnings based on local femtocleaner run * use equalto in degeneracy.jl (sbromberger#858) * fix depwarns in linalg submodule (sbromberger#860) * update linalg/spectral to fix deprecations * fix depwarns in graphmatrices * fixes doc deprecation warnings (sbromberger#861) * fixes doc deprecation warnings * adding Base64 to runtests * Update README.md * remove add/remove vertex/edge from core, minor bug fix (sbromberger#862) * remove add/remove vertex/edge from core, minor bug fix * fix tests * export add/rem vertex * remove long-term deprecation warnings (sbromberger#863) * uninitialized -> undef, blkdiag -> blockdiag, and removed import of d… (sbromberger#865) * uninitialized -> undef, blkdiag -> blockdiag, and removed import of deprecated functions from LG to LinAlg * test coverage for digraph eltype * removes equalto (sbromberger#867) * optional sorting algorithm for gdistances (sbromberger#868) add the ability to pass RadixSort to gdistances! * update url and mention directed graphs explicilty (sbromberger#837) * update url and mention directed graphs explicilty * Update graphtypes.md * Update graphtypes.md fixed references. * Speed improvements for function transitiveclosure! (sbromberger#870) * Speed improvements for function transitiveclosure! Instead of checking for all paths i -> k and k -> j for a given vertex k we only iterate over the in- and outneighbours of k. * Merged some conditionals into a single statement * Cache efficient Floyd Warshall (sbromberger#873) * Update floyd-warshall.jl * Cache efficient Floyd Warshall * fixed an error where smallgraph(:frucht) had 20 vertices instead of 12 (sbromberger#878) * Delete .Rhistory * Added function transitivereduction (sbromberger#877) * added function transitivereduction * Update transitivity.jl docstring formatting * Fixed some tests && added testdigraphs for all tests * Johnson Shortest Path for Sparse Graphs (sbromberger#884) * Johnson Shortest Path for Sparse Graphs Johnson Shortest Path for Sparse Graphs * Improved memory efficiency if distmx is mutable * Improved memory efficiency for parallel implementation * Update index.md * Added constructors to create graphs from a vector or an iterator of edges (sbromberger#880) * Added constructors to create SimpleGraphs and SimpleDiGraphs from a vector or an iterator of edges * Added constructors to create SimpleGraphs and SimpleDiGraphs from a vector or an iterator of edges * Slyles1001/892 (sbromberger#894) * comments are your friend * Most of LightGraphs warnings are fixed * Delete HITS.jl * Slyles1001/872 (sbromberger#891) * DataStructures fixed * missed heappop!, now it tests clean * spaces * Update LightGraphs.jl * Update runtests.jl * fixes most depwarns as of 20180529 (sbromberger#895) * fixes most depwarns as of 20180529 * graphmatrices problems * remove tabs * tabs, again * Update CONTRIBUTING.md (sbromberger#897) * Improve Kruskal and use in-built disjoint set data structure (sbromberger#896) * Improve Kruskal and use in-built disjoint set data structure * Update kruskal.jl Changes requested by @somil55

* using LightGraphs does not error * Switch to LinearAlgebra and SparseArrays std libs * Fix most of linalg tests * Add SharedArrays for distance tests to compile * Add Random and Markdown to stdlibs used * Fix connectivity tests * IntSet -> BitSet * Add DelimitedFiles stdlib for readcsv * Fix failing test * first cut * Use mauro/SimpleTraits.jl/m3/where-fns in tests * Fix SimpleTraits checkout (#851) * Move up SimpleTraits checkout (#852) * Update runtests.jl * Update REQUIRE * Update REQUIRE

* ignore coverage file * merge master (#2) * removed flow algorithms (#815) * fixes #820, plus tests (#821) * change show() for empty graphs (ref JuliaGraphs/MetaGraphs.jl#20 (comment)) (#822) * Pull request clique_percolation.jl (#826) clique percolation is a method of uncovering the overlapping community structure of complex networks in nature and society * add src/community/clique_percolation.jl * tests in file test/community/clique_percolation.jl * cites the original clique percolation paper * for undirected graphs only using traitfn * in_ / out_ -> in / out (#830) * (in,out)_neighbors -> (in,out)neighbors * all_neighbors -> allneighbors * Pull request clique_percolation.jl (#826) clique percolation is a method of uncovering the overlapping community structure of complex networks in nature and society * add src/community/clique_percolation.jl * tests in file test/community/clique_percolation.jl * cites the original clique percolation paper * for undirected graphs only using traitfn * revert allneighbors * expected_degree_graph (Chung-Lu model) (#832) * Expected degree random graph generator implemented, including tests * algorithm corrected * Missing seed corrected in expected_degree_graph * expected_degree_graph! implemented * Added return in function, comment with references removed, references in docs added (expected_degree_graph) * Update randgraphs.jl minor doc update * Update randgraphs.jl * Fixing problems with MST Kruskal's on SimpleWeightedGraphs (#835) * Update kruskal.jl * Update prim.jl * Update kruskal.jl * Update kruskal.jl * Update prim.jl * Update kruskal.jl * Update prim.jl * Update kruskal.jl * Update prim.jl * reverting changes * Revert "reverting changes" This reverts commit ac1760b. * Revert "Update prim.jl" This reverts commit 677f6fa. * Revert "Update kruskal.jl" This reverts commit a0e9c47. * Revert "Update prim.jl" This reverts commit 793bac4. * Revert "Update kruskal.jl" This reverts commit 6114e16. * Revert "Update prim.jl" This reverts commit 551f1e6. * Revert "Update kruskal.jl" This reverts commit 941005e. * Revert "Update kruskal.jl" This reverts commit a404514. * Revert "Update prim.jl" This reverts commit 2d43a60. * Revert "Update kruskal.jl" This reverts commit 4577920. * fix problems with SimpleWeightedGraphs * fix problems with SimpleWeightedGraphs * fix problems with SimpleWeightedGraphs * bipartite_map on 2-order graphs fixed. Added proper tests. Fixed test connected to bipartite_map (#836) * Correct pre-allocation of memory in Prim's MST (#839) * Improve Kruskal's MST by optimizing Union-Find (#843) * add missing backtick (#846) * Add greedy_color for Graph Coloring (#844) * Add greedy_color for Graph Coloring * Improve Kruskal's MST by optimizing Union-Find (#843) * Update README.md * Update README.md * first cut at 0.7 compatibility (#848) * using LightGraphs does not error * Switch to LinearAlgebra and SparseArrays std libs * Fix most of linalg tests * Add SharedArrays for distance tests to compile * Add Random and Markdown to stdlibs used * Fix connectivity tests * IntSet -> BitSet * Add DelimitedFiles stdlib for readcsv * Fix failing test * first cut * Use mauro/SimpleTraits.jl/m3/where-fns in tests * Fix SimpleTraits checkout (#851) * Move up SimpleTraits checkout (#852) * Update runtests.jl * Update REQUIRE * Update REQUIRE * femtocleaner with additional depwarn fixes (#856) fix deprecation warnings based on local femtocleaner run * use equalto in degeneracy.jl (#858) * fix depwarns in linalg submodule (#860) * update linalg/spectral to fix deprecations * fix depwarns in graphmatrices * fixes doc deprecation warnings (#861) * fixes doc deprecation warnings * adding Base64 to runtests * Update README.md * remove add/remove vertex/edge from core, minor bug fix (#862) * remove add/remove vertex/edge from core, minor bug fix * fix tests * export add/rem vertex * remove long-term deprecation warnings (#863) * uninitialized -> undef, blkdiag -> blockdiag, and removed import of d… (#865) * uninitialized -> undef, blkdiag -> blockdiag, and removed import of deprecated functions from LG to LinAlg * test coverage for digraph eltype * removes equalto (#867) * optional sorting algorithm for gdistances (#868) add the ability to pass RadixSort to gdistances! * update url and mention directed graphs explicilty (#837) * update url and mention directed graphs explicilty * Update graphtypes.md * Update graphtypes.md fixed references. * Speed improvements for function transitiveclosure! (#870) * Speed improvements for function transitiveclosure! Instead of checking for all paths i -> k and k -> j for a given vertex k we only iterate over the in- and outneighbours of k. * Merged some conditionals into a single statement * Cache efficient Floyd Warshall (#873) * Update floyd-warshall.jl * Cache efficient Floyd Warshall * fixed an error where smallgraph(:frucht) had 20 vertices instead of 12 (#878) * Delete .Rhistory * Added function transitivereduction (#877) * added function transitivereduction * Update transitivity.jl docstring formatting * Fixed some tests && added testdigraphs for all tests * Johnson Shortest Path for Sparse Graphs (#884) * Johnson Shortest Path for Sparse Graphs Johnson Shortest Path for Sparse Graphs * Improved memory efficiency if distmx is mutable * Improved memory efficiency for parallel implementation * Update index.md * Added constructors to create graphs from a vector or an iterator of edges (#880) * Added constructors to create SimpleGraphs and SimpleDiGraphs from a vector or an iterator of edges * Added constructors to create SimpleGraphs and SimpleDiGraphs from a vector or an iterator of edges * Slyles1001/892 (#894) * comments are your friend * Most of LightGraphs warnings are fixed * Delete HITS.jl * Slyles1001/872 (#891) * DataStructures fixed * missed heappop!, now it tests clean * spaces * Update LightGraphs.jl * Update runtests.jl * fixes most depwarns as of 20180529 (#895) * fixes most depwarns as of 20180529 * graphmatrices problems * remove tabs * tabs, again * Update CONTRIBUTING.md (#897) * Improve Kruskal and use in-built disjoint set data structure (#896) * Improve Kruskal and use in-built disjoint set data structure * Update kruskal.jl Changes requested by @somil55 * updated syntax for iterator protocol * fixed iterator, broken inference

rohitvarkey and others added 10 commits February 14, 2018 02:06

using LightGraphs does not error

40a3f39

Switch to LinearAlgebra and SparseArrays std libs

2b2000f

Fix most of linalg tests

efb5601

Add SharedArrays for distance tests to compile

a7739e2

Add Random and Markdown to stdlibs used

cbd600d

Fix connectivity tests

322a108

IntSet -> BitSet

201e878

Add DelimitedFiles stdlib for readcsv

a73c69c

Fix failing test

96cfbf7

first cut

ac9bad4

sbromberger force-pushed the sbromberger/zero-dot-seven branch from ffd3d7f to ac9bad4 Compare February 20, 2018 15:57

Merge branch 'master' into sbromberger/zero-dot-seven

421cf2e

jpfairbanks mentioned this pull request Feb 20, 2018

WIP: Getting LightGraphs 0.7 ready #842

Closed

3 tasks

sbromberger mentioned this pull request Feb 20, 2018

Convert traitfns to use where-syntax mauro3/SimpleTraits.jl#46

Closed

sbromberger and others added 2 commits February 20, 2018 08:27

Merge branch 'master' into 0.7

c4c4f93

Use mauro/SimpleTraits.jl/m3/where-fns in tests

b8a3ea8

rohitvarkey reviewed Feb 20, 2018

View reviewed changes

Fix SimpleTraits checkout (#851)

c455f26

sbromberger commented Feb 20, 2018

View reviewed changes

Move up SimpleTraits checkout (#852)

e8150ea

sbromberger mentioned this pull request Feb 21, 2018

fix deprecations #810

Closed

sbromberger added 3 commits February 20, 2018 21:44

Merge branch 'master' into sbromberger/zero-dot-seven

dc031e5

Update runtests.jl

7de7eea

Update REQUIRE

5ad7dd6

rohitvarkey mentioned this pull request Feb 21, 2018

Tag SimpleTraits.jl v0.7.0 JuliaLang/METADATA.jl#13453

Merged

Update REQUIRE

0571e37

sbromberger mentioned this pull request Feb 21, 2018

Version info as we move to 0.7 compatibility #854

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jpfairbanks approved these changes Feb 22, 2018

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sbromberger merged commit b419c0f into master Feb 22, 2018

sbromberger deleted the sbromberger/zero-dot-seven branch June 5, 2018 03:24

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first cut at 0.7 compatibility #848

first cut at 0.7 compatibility #848

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first cut at 0.7 compatibility #848

first cut at 0.7 compatibility #848

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