fixes most depwarns as of 20180529 #895

sbromberger · 2018-05-30T05:19:50Z

Also closes #872.

sbromberger · 2018-05-30T05:43:43Z

Passes on -5258, but not on current travis nightly. Will wait and retest.

codecov · 2018-05-30T18:48:19Z

Codecov Report

Merging #895 into master will decrease coverage by <.01%.
The diff coverage is 100%.

@@            Coverage Diff             @@
##           master     #895      +/-   ##
==========================================
- Coverage   99.69%   99.69%   -0.01%     
==========================================
  Files          60       60              
  Lines        2281     2279       -2     
==========================================
- Hits         2274     2272       -2     
  Misses          7        7

sbromberger · 2018-05-30T19:35:13Z

Tests are passing locally as well as here. Ready for review and merge.

cc @jpfairbanks @juliohm @slyles1001 @somil55

iamed2 · 2018-05-30T20:23:28Z

src/linalg/graphmatrices.jl

@@ -30,13 +30,13 @@ abstract type Laplacian{T} <: GraphMatrix{T} end
 The standard adjacency matrix.
 """
 struct CombinatorialAdjacency{T,S,V} <: Adjacency{T}
-	A::S
-	D::V
+    	A::S


Something weird appears to have happened with indentation in this file and a couple others

It's vscode doing auto-formatting on save. The indentation looks fine to me. Is there something specific you're seeing?

Oh, wait. I see the issue. It looks like this file was tabbed originally, but my editor uses 4 spaces. Let me fix.

It was clearer in the full diff view on Github as it highlighted the spaces as new and the tabs as old

juliohm · 2018-05-30T23:12:49Z

Thanks @sbromberger for the fixes. Is it correct to say that all the changes fit in the 3 categories:

Adding package prefixes to function calls like LinearAlgebra.issymmetric
Replacing using with import
Indentation and code style changes like <: becomes <: with blank space?

I am approving anyways 👍

juliohm

Syntax changes and fixes for Julia v0.7. All seem reasonable to me, my eye didn't catch anything strange.

sbromberger · 2018-05-30T23:15:47Z

@juliohm - yes. The formatting changes are a side effect of vscode and autolint. You have the other two explicit goals correct.

Thanks for the quick review.

sbromberger · 2018-05-30T23:21:52Z

Cc @StefanKarpinski since you might be interested in the net effects of this approach.

* 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

* fixes most depwarns as of 20180529 * graphmatrices problems * remove tabs * tabs, again

* 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

* fixes most depwarns as of 20180529 * graphmatrices problems * remove tabs * tabs, again

sbromberger force-pushed the sbromberger/fix-0.7-depwarns branch 3 times, most recently from c3497c6 to 0846587 Compare May 30, 2018 05:30

fixes most depwarns as of 20180529

e713643

sbromberger force-pushed the sbromberger/fix-0.7-depwarns branch from 0846587 to e713643 Compare May 30, 2018 05:42

graphmatrices problems

646c007

iamed2 reviewed May 30, 2018

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sbromberger added 2 commits May 30, 2018 14:24

remove tabs

164e654

tabs, again

7fb3df4

juliohm approved these changes May 30, 2018

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jpfairbanks self-requested a review June 1, 2018 02:11

jpfairbanks approved these changes Jun 1, 2018

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sbromberger merged commit 8cc1626 into master Jun 1, 2018

sbromberger deleted the sbromberger/fix-0.7-depwarns branch June 1, 2018 05:54

This was referenced Jun 1, 2018

Broadcasting warning in v0.13.0+ #892

Closed

back to using for nonextended functions #898

Merged

sbromberger added a commit that referenced this pull request Jun 5, 2018

fixes most depwarns as of 20180529 (#895)

666ace4

* fixes most depwarns as of 20180529 * graphmatrices problems * remove tabs * tabs, again

SohamTamba pushed a commit to SohamTamba/LightGraphs.jl that referenced this pull request Jun 25, 2018

fixes most depwarns as of 20180529 (sbromberger#895)

eb89254

* fixes most depwarns as of 20180529 * graphmatrices problems * remove tabs * tabs, again

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fixes most depwarns as of 20180529 #895

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fixes most depwarns as of 20180529 #895

fixes most depwarns as of 20180529 #895

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