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Uniform code style #190

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merged 11 commits into from
Nov 21, 2022
Merged

Uniform code style #190

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af1f18f
Fix typos
aurorarossi Nov 18, 2022
b6b7797
Fix comment typo
aurorarossi Nov 18, 2022
8b5c735
Housekeeping
aurorarossi Nov 18, 2022
e19f28b
Add and remove spaces
aurorarossi Nov 19, 2022
ff60f32
Update src/dominatingset/minimal_dom_set.jl
aurorarossi Nov 20, 2022
1ee81d1
Apply JuliaFormatter and add it (+ Aqua) to testing
gdalle Nov 20, 2022
40c420a
Fix formatting fail on Windows
gdalle Nov 20, 2022
6170376
Update src/SimpleGraphs/generators/randgraphs.jl
gdalle Nov 21, 2022
30f2539
Fix contributing guidelines + add Blue style and formatting
gdalle Nov 21, 2022
ab7212e
Fix formatting bug in vf2.jl by ignoring function
gdalle Nov 21, 2022
00393ec
Fix ignore vf2.jl for formatting on Windows
gdalle Nov 21, 2022
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1 change: 1 addition & 0 deletions .JuliaFormatter.toml
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@@ -0,0 +1 @@
style = "blue"
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BlueStyle seems like the most well-established specification, whereas SciML is more recent. However JuliaFormatter cannot do it all, so we must tell contributors to adhere to the style guidelines in general. Should we add a badge to the README too?

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@simonschoelly simonschoelly Nov 20, 2022 •
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Any reason to prefer BlueStyle? (I am not yet familiar with these styles). We could also specify our own rules right?

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In any cases, most of the changes here seem to be sensible.

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I just use it because it's already well documented, so we can point contributors to the exhaustive specification by Invenia. We could make up our own rules but that would require explaining them to everyone in our docs.

Also, it's easier to contribute when you're already familiar with the style guide, which wouldn't be the case for Graphs-specific rules.

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My hot take is that the precise choice of style does not matter, as long as it's clear and easy to apply, and BlueStyle satisfies both criteria

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Maybe it makes sense to use some common style, as then people don't need to reconfigure their editor differently for every project.

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What about the default format by JuliaFormatter? Would that also be an option?

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The default format by JuliaFormatter is much less well-specified than BlueStyle. One of the perks of BlueStyle is that it also gives coherent writing advice to the contributors that cannot be enfored by a simple linter

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Maybe it makes sense to use some common style, as then people don't need to reconfigure their editor differently for every project.

Another perk of JuliaFormatter is that the formatting in the Julia extension for VSCode is based on it. And it takes into account the .JuliaFormatter.toml file at the root of the package to format each file according to the local specification (in our case style = "blue")

9 changes: 8 additions & 1 deletion Project.toml
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Expand Up @@ -16,18 +16,25 @@ SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"

[compat]
Aqua = "0.5"
ArnoldiMethod = "0.1, 0.2"
Compat = "3.40, 4"
DataStructures = "0.17, 0.18"
Documenter = "0.27"
Inflate = "0.1.3"
JuliaFormatter = "1"
SimpleTraits = "0.9"
StableRNGs = "1"
julia = "1.6"

[extras]
Aqua = "4c88cf16-eb10-579e-8560-4a9242c79595"
Base64 = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f"
DelimitedFiles = "8bb1440f-4735-579b-a4ab-409b98df4dab"
Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
JuliaFormatter = "98e50ef6-434e-11e9-1051-2b60c6c9e899"
StableRNGs = "860ef19b-820b-49d6-a774-d7a799459cd3"
Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"

[targets]
test = ["Base64", "DelimitedFiles", "StableRNGs", "Test"]
test = ["Aqua", "Base64", "DelimitedFiles", "Documenter", "JuliaFormatter", "StableRNGs", "Test"]
14 changes: 5 additions & 9 deletions benchmark/benchmarks.jl
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@@ -1,22 +1,18 @@
using BenchmarkTools
using Graphs


DIGRAPHS = Dict{String,DiGraph}(
"complete100" => complete_digraph(100),
"path500" => path_digraph(500)
"complete100" => complete_digraph(100), "path500" => path_digraph(500)
)

GRAPHS = Dict{String,Graph}(
"complete100" => complete_graph(100),
"tutte" => smallgraph(:tutte),
"path500" => path_graph(500)
"complete100" => complete_graph(100),
"tutte" => smallgraph(:tutte),
"path500" => path_graph(500),
)


suite = BenchmarkGroup()
include("core.jl")


tune!(suite);
results = run(suite, verbose = true, seconds = 10)
results = run(suite; verbose=true, seconds=10)
46 changes: 23 additions & 23 deletions benchmark/centrality.jl
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@@ -1,26 +1,26 @@

@benchgroup "centrality" begin
@benchgroup "graphs" begin
for (name, g) in GRAPHS
@bench "$(name): degree" Graphs.degree_centrality($g)
@bench "$(name): closeness" Graphs.closeness_centrality($g)
if nv(g) < 1000
@bench "$(name): betweenness" Graphs.betweenness_centrality($g)
@bench "$(name): katz" Graphs.katz_centrality($g)
end
end
end #graphs
@benchgroup "digraphs" begin
for (name, g) in DIGRAPHS
@bench "$(name): degree" Graphs.degree_centrality($g)
@bench "$(name): closeness" Graphs.closeness_centrality($g)
if nv(g) < 1000
@bench "$(name): betweenness" Graphs.betweenness_centrality($g)
@bench "$(name): katz" Graphs.katz_centrality($g)
end
if nv(g) < 500
@bench "$(name): pagerank" Graphs.pagerank($g)
end
end
end # digraphs
@benchgroup "graphs" begin
for (name, g) in GRAPHS
@bench "$(name): degree" Graphs.degree_centrality($g)
@bench "$(name): closeness" Graphs.closeness_centrality($g)
if nv(g) < 1000
@bench "$(name): betweenness" Graphs.betweenness_centrality($g)
@bench "$(name): katz" Graphs.katz_centrality($g)
end
end
end # graphs
@benchgroup "digraphs" begin
for (name, g) in DIGRAPHS
@bench "$(name): degree" Graphs.degree_centrality($g)
@bench "$(name): closeness" Graphs.closeness_centrality($g)
if nv(g) < 1000
@bench "$(name): betweenness" Graphs.betweenness_centrality($g)
@bench "$(name): katz" Graphs.katz_centrality($g)
end
if nv(g) < 500
@bench "$(name): pagerank" Graphs.pagerank($g)
end
end
end # digraphs
end # centrality
22 changes: 12 additions & 10 deletions benchmark/connectivity.jl
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@@ -1,12 +1,14 @@
@benchgroup "connectivity" begin
@benchgroup "digraphs" begin
for (name, g) in DIGRAPHS
@bench "$(name): strongly_connected_components" Graphs.strongly_connected_components($g)
end
end # digraphs
@benchgroup "graphs" begin
for (name, g) in GRAPHS
@bench "$(name): connected_components" Graphs.connected_components($g)
end
end # graphs
@benchgroup "digraphs" begin
for (name, g) in DIGRAPHS
@bench "$(name): strongly_connected_components" Graphs.strongly_connected_components(
$g
)
end
end # digraphs
@benchgroup "graphs" begin
for (name, g) in GRAPHS
@bench "$(name): connected_components" Graphs.connected_components($g)
end
end # graphs
end # connectivity
13 changes: 6 additions & 7 deletions benchmark/core.jl
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suite["core"] = BenchmarkGroup(["nv", "edges", "has_edge"])


# nv
suite["core"]["nv"] = BenchmarkGroup(["graphs", "digraphs"])
suite["core"]["nv"]["graphs"] = @benchmarkable [nv(g) for (n,g) in $GRAPHS]
suite["core"]["nv"]["digraphs"] = @benchmarkable [nv(g) for (n,g) in $DIGRAPHS]
suite["core"]["nv"]["graphs"] = @benchmarkable [nv(g) for (n, g) in $GRAPHS]
suite["core"]["nv"]["digraphs"] = @benchmarkable [nv(g) for (n, g) in $DIGRAPHS]

# iterate edges
function iter_edges(g::AbstractGraph)
Expand All @@ -16,8 +15,8 @@ function iter_edges(g::AbstractGraph)
end

suite["core"]["edges"] = BenchmarkGroup(["graphs", "digraphs"])
suite["core"]["edges"]["graphs"] = @benchmarkable [iter_edges(g) for (n,g) in $GRAPHS]
suite["core"]["edges"]["digraphs"] = @benchmarkable [iter_edges(g) for (n,g) in $DIGRAPHS]
suite["core"]["edges"]["graphs"] = @benchmarkable [iter_edges(g) for (n, g) in $GRAPHS]
suite["core"]["edges"]["digraphs"] = @benchmarkable [iter_edges(g) for (n, g) in $DIGRAPHS]

# has edge
function all_has_edge(g::AbstractGraph)
Expand All @@ -34,5 +33,5 @@ function all_has_edge(g::AbstractGraph)
end

suite["core"]["has_edge"] = BenchmarkGroup(["graphs", "digraphs"])
suite["core"]["has_edge"]["graphs"] = @benchmark [all_has_edge(g) for (n,g) in $GRAPHS]
suite["core"]["has_edge"]["digraphs"] = @benchmark [all_has_edge(g) for (n,g) in $DIGRAPHS]
suite["core"]["has_edge"]["graphs"] = @benchmark [all_has_edge(g) for (n, g) in $GRAPHS]
suite["core"]["has_edge"]["digraphs"] = @benchmark [all_has_edge(g) for (n, g) in $DIGRAPHS]
10 changes: 5 additions & 5 deletions benchmark/edges.jl
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Expand Up @@ -32,9 +32,9 @@ end

n = 10000
@benchgroup "edges" begin
@bench "$(n): fille" fille($n)
@bench "$(n): fillp" fillp($n)
a, b = fille(n), fillp(n)
@bench "$(n): tsume" tsum($a)
@bench "$(n): tsump" tsum($b)
@bench "$(n): fille" fille($n)
@bench "$(n): fillp" fillp($n)
a, b = fille(n), fillp(n)
@bench "$(n): tsume" tsum($a)
@bench "$(n): tsump" tsum($b)
end # edges
4 changes: 2 additions & 2 deletions benchmark/insertions.jl
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@@ -1,4 +1,4 @@
@benchgroup "insertions" begin
n = 10000
@bench "ER Generation" g = SimpleGraph($n, 16 * $n)
n = 10000
@bench "ER Generation" g = SimpleGraph($n, 16 * $n)
end
5 changes: 2 additions & 3 deletions benchmark/parallel/egonets.jl
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Expand Up @@ -22,7 +22,6 @@ using BenchmarkTools
return a
end


function mapvertices(f, g::Graph)
n = nv(g)
a = zeros(Int, n)
Expand All @@ -43,13 +42,13 @@ using BenchmarkTools

function comparison(f, g)
println("Mulithreaded on $(Threads.nthreads())")
b1 = @benchmark mapvertices($f, $g)
b1 = @benchmark mapvertices($f, $g)
println(b1)

println("singlethreaded")
b2 = @benchmark mapvertices_single($f, $g)
println(b2)
println("done")
return println("done")
end

nv_ = 10000
Expand Down
24 changes: 12 additions & 12 deletions benchmark/traversals.jl
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@@ -1,14 +1,14 @@
@benchgroup "traversals" begin
@benchgroup "graphs" begin
for (name, g) in GRAPHS
@bench "$(name): bfs_tree" Graphs.bfs_tree($g, 1)
@bench "$(name): dfs_tree" Graphs.dfs_tree($g, 1)
end
end # graphs
@benchgroup "digraphs" begin
for (name, g) in DIGRAPHS
@bench "$(name): bfs_tree" Graphs.bfs_tree($g, 1)
@bench "$(name): dfs_tree" Graphs.dfs_tree($g, 1)
end
end # digraphs
@benchgroup "graphs" begin
for (name, g) in GRAPHS
@bench "$(name): bfs_tree" Graphs.bfs_tree($g, 1)
@bench "$(name): dfs_tree" Graphs.dfs_tree($g, 1)
end
end # graphs
@benchgroup "digraphs" begin
for (name, g) in DIGRAPHS
@bench "$(name): bfs_tree" Graphs.bfs_tree($g, 1)
@bench "$(name): dfs_tree" Graphs.dfs_tree($g, 1)
end
end # digraphs
end # traversals
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