Traits based sub ecosystem & `NodeAlingnedEdgeColored(Di)Graph` #107

InterdisciplinaryPhysicsTeam · 2023-01-22T17:49:22Z

Add JOSS submission badge.

Update the README

Co-Authored-By: Pietro Monticone <38562595+pitmonticone@users.noreply.github.com> Co-Authored-By: Claudio Moroni <43729990+ClaudMor@users.noreply.github.com>

Update README.md

Add v1.1 announcement posts to README and docs

TODO: write tests Co-Authored-By: Pietro Monticone <38562595+pitmonticone@users.noreply.github.com> Co-Authored-By: Claudio Moroni <43729990+ClaudMor@users.noreply.github.com>

Add example folder

TODO: - Debug precompilation up to abstractmultilayerugraph.jl - Modify abstractmultilayerdigraph.jl just as abstractmultilayerugraph.jl Co-Authored-By: Pietro Monticone <38562595+pitmonticone@users.noreply.github.com> Co-Authored-By: Claudio Moroni <43729990+ClaudMor@users.noreply.github.com>

Update "Future Developments" section in README and docs.

Co-Authored-By: Pietro Monticone <38562595+pitmonticone@users.noreply.github.com> Co-Authored-By: Claudio Moroni <43729990+ClaudMor@users.noreply.github.com>

Fix bugs in README and example

Some tests still error Co-Authored-By: Pietro Monticone <38562595+pitmonticone@users.noreply.github.com> Co-Authored-By: Claudio Moroni <43729990+ClaudMor@users.noreply.github.com>

…ltilayer graph Co-Authored-By: Pietro Monticone <38562595+pitmonticone@users.noreply.github.com> Co-Authored-By: Claudio Moroni <43729990+ClaudMor@users.noreply.github.com>

Co-Authored-By: Pietro Monticone <38562595+pitmonticone@users.noreply.github.com> Co-Authored-By: Claudio Moroni <43729990+ClaudMor@users.noreply.github.com>

1. First complete implementation of synchronized edge colored graphs 2. Working sub-ecosystem prototype mainly based on abstract types. Traits are only used to discern between directed and undirercted graphs. TODO: Test the synchronized edge colored graphs Co-Authored-By: Pietro Monticone <38562595+pitmonticone@users.noreply.github.com> Co-Authored-By: Claudio Moroni <43729990+ClaudMor@users.noreply.github.com>

Implementation of synchronized edge colored (di) graph completed Implementation of sub-ecosystem endpoints completed TODO 1. Update API.md 2. Update index.md 3. Update console printing of layers and interlayers 4. Add FAQ to readme.md & index.md 5. Clean up the code Co-Authored-By: Pietro Monticone <38562595+pitmonticone@users.noreply.github.com> Co-Authored-By: Claudio Moroni <43729990+ClaudMor@users.noreply.github.com>

Code cleaning and reordering Co-Authored-By: Pietro Monticone <38562595+pitmonticone@users.noreply.github.com> Co-Authored-By: Claudio Moroni <43729990+ClaudMor@users.noreply.github.com>

Co-Authored-By: Pietro Monticone <38562595+pitmonticone@users.noreply.github.com> Co-Authored-By: Claudio Moroni <43729990+ClaudMor@users.noreply.github.com>

github-actions

Remaining comments which cannot be posted as a review comment to avoid GitHub Rate Limit

JuliaFormatter

github-actions · 2023-01-22T17:50:58Z

src/MultilayerGraphs.jl

@@ -194,14 +205,15 @@ include("representations/abstracttensorrepresentation.jl")
 include("representations/abstractmatrixrepresentation.jl")
 include("representations/weighttensor.jl")
 include("representations/metadatatensor.jl")
-include("representations/supraweightmatrix.jl")
-include("traits.jl")
+include("representations/supraweightmatrix.jl") 


[JuliaFormatter] _{reported by reviewdog 🐶}

Suggested change

include("representations/supraweightmatrix.jl")

include("representations/supraweightmatrix.jl")

github-actions · 2023-01-22T17:50:58Z

src/MultilayerGraphs.jl

+include("special_multilayergraphs/synchronized_edge_colored/abstract_synchronized_edge_colored_graph.jl")
+include("special_multilayergraphs/synchronized_edge_colored/synchronized_edge_colored_graph.jl")
+include("special_multilayergraphs/synchronized_edge_colored/synchronized_edge_colored_di_graph.jl")


[JuliaFormatter] _{reported by reviewdog 🐶}

Suggested change

include("special_multilayergraphs/synchronized_edge_colored/abstract_synchronized_edge_colored_graph.jl")

include("special_multilayergraphs/synchronized_edge_colored/synchronized_edge_colored_graph.jl")

include("special_multilayergraphs/synchronized_edge_colored/synchronized_edge_colored_di_graph.jl")

include(

"special_multilayergraphs/synchronized_edge_colored/abstract_synchronized_edge_colored_graph.jl",

)

include(

"special_multilayergraphs/synchronized_edge_colored/synchronized_edge_colored_graph.jl"

)

include(

"special_multilayergraphs/synchronized_edge_colored/synchronized_edge_colored_di_graph.jl",

)

github-actions · 2023-01-22T17:50:58Z

src/abstractmultilayergraph.jl

+# General MultilayerGraph Utilities
+fadjlist(mg::AbstractMultilayerGraph) = mg.fadjlist
+
+


[JuliaFormatter] _{reported by reviewdog 🐶}

Suggested change

github-actions · 2023-01-22T17:50:58Z

src/abstractmultilayergraph.jl

 """
-function add_node!(mg::AbstractMultilayerGraph, n::Node)
+function _add_node!(mg::AbstractMultilayerGraph, n::Node; add_vertex_to_layers::Union{Vector{Symbol}, Symbol} = Symbol[])


[JuliaFormatter] _{reported by reviewdog 🐶}

Suggested change

function _add_node!(mg::AbstractMultilayerGraph, n::Node; add_vertex_to_layers::Union{Vector{Symbol}, Symbol} = Symbol[])

function _add_node!(

mg::AbstractMultilayerGraph,

n::Node;

add_vertex_to_layers::Union{Vector{Symbol},Symbol}=Symbol[],

)

github-actions · 2023-01-22T17:50:59Z

src/abstractmultilayergraph.jl

+            _add_vertex!(mg, MV(n, layer_name))
+        end
+    end
+


[JuliaFormatter] _{reported by reviewdog 🐶}

Suggested change

github-actions · 2023-01-22T17:51:02Z

src/directed.jl

+        @debug "An edge between $(src(me)) and $(dst(me)) already exists"  
+        return false
+    end
+


[JuliaFormatter] _{reported by reviewdog 🐶}

Suggested change

github-actions · 2023-01-22T17:51:03Z

src/directed.jl

+    return true
+end
+
+


[JuliaFormatter] _{reported by reviewdog 🐶}

Suggested change

github-actions · 2023-01-22T17:51:03Z

src/directed.jl

+"""
+@traitfn function _rem_edge!(
+    mg::M, src::MultilayerVertex, dst::MultilayerVertex
+) where {M<:AbstractMultilayerGraph; IsDirected{M}}


[JuliaFormatter] _{reported by reviewdog 🐶}

Suggested change

) where {M<:AbstractMultilayerGraph; IsDirected{M}}

) where {M <: AbstractMultilayerGraph; IsDirected{M}}

github-actions · 2023-01-22T17:51:03Z

src/directed.jl

+    return true
+end
+
+


[JuliaFormatter] _{reported by reviewdog 🐶}

Suggested change

github-actions · 2023-01-22T17:51:03Z

src/directed.jl

    mg::M, src::MultilayerVertex, dst::MultilayerVertex, weight::U
-) where {T,U,M<:AbstractMultilayerDiGraph{T,U}}
+) where {T,U,M<:AbstractMultilayerGraph{T,U}; IsDirected{M}}


[JuliaFormatter] _{reported by reviewdog 🐶}

Suggested change

) where {T,U,M<:AbstractMultilayerGraph{T,U}; IsDirected{M}}

) where {T,U,M<:AbstractMultilayerGraph{T,U};IsDirected{M}}

coveralls · 2023-01-22T17:56:17Z

Pull Request Test Coverage Report for Build 3980839972

Warning: This coverage report may be inaccurate.

This pull request's base commit is no longer the HEAD commit of its target branch. This means it includes changes from outside the original pull request, including, potentially, unrelated coverage changes.

For more information on this, see Tracking coverage changes with pull request builds.
To avoid this issue with future PRs, see these Recommended CI Configurations.
For a quick fix, rebase this PR at GitHub. Your next report should be accurate.

Details

174 of 191 (91.1%) changed or added relevant lines in 9 files are covered.
144 unchanged lines in 6 files lost coverage.
Overall coverage increased (+0.2%) to 83.498%

Changes Missing Coverage	Covered Lines	Changed/Added Lines	%
src/utilities.jl	2	3	66.67%
src/abstractmultilayergraph.jl	28	32	87.5%
src/directed.jl	69	74	93.24%
src/undirected.jl	54	61	88.52%

Files with Coverage Reduction	New Missed Lines	%
src/multilayerdigraph.jl	1	89.58%
src/multilayergraph.jl	3	91.49%
src/subgraphs/abstractsubgraph.jl	21	71.43%
src/utilities.jl	34	77.33%
src/abstractmultilayergraph.jl	41	88.07%
src/subgraphs/layer.jl	44	75.81%

Totals
Change from base Build 3940940912:	0.2%
Covered Lines:	1695
Relevant Lines:	2030

💛 - Coveralls

codecov · 2023-01-22T17:56:29Z

Codecov Report

Merging #107 (c9a6b2d) into main (94e0a7a) will increase coverage by 0.09%.
The diff coverage is 89.69%.

@@            Coverage Diff             @@
##             main     #107      +/-   ##
==========================================
+ Coverage   83.32%   83.42%   +0.09%     
==========================================
  Files          30       32       +2     
  Lines        2015     2057      +42     
==========================================
+ Hits         1679     1716      +37     
- Misses        336      341       +5

Impacted Files	Coverage Δ
src/graphs_extensions/graphs_extensions.jl	`100.00% <ø> (ø)`
src/graphs_extensions/metagraphs.jl	`60.00% <ø> (-1.54%)`	⬇️
src/graphs_extensions/simplevaluegraphs.jl	`64.86% <ø> (+1.70%)`	⬆️
src/graphs_extensions/simpleweightedgraphs.jl	`84.61% <ø> (+6.04%)`	⬆️
src/subgraphs/abstractsubgraph.jl	`72.41% <ø> (ø)`
src/utilities.jl	`77.33% <0.00%> (-0.70%)`	⬇️
...olored/abstract_node_aligned_edge_colored_graph.jl	`80.00% <80.00%> (ø)`
src/multilayerdigraph.jl	`88.46% <87.50%> (-2.24%)`	⬇️
src/multilayergraph.jl	`90.19% <87.50%> (+1.18%)`	⬆️
src/undirected.jl	`96.39% <89.23%> (ø)`
... and 10 more

Help us with your feedback. Take ten seconds to tell us how you rate us. Have a feature suggestion? Share it here.

- Rename new graph - Fix APis (to be completed) Co-Authored-By: Pietro Monticone <38562595+pitmonticone@users.noreply.github.com> Co-Authored-By: Claudio Moroni <43729990+ClaudMor@users.noreply.github.com>

Co-Authored-By: Pietro Monticone <38562595+pitmonticone@users.noreply.github.com> Co-Authored-By: Claudio Moroni <43729990+ClaudMor@users.noreply.github.com>

github-actions · 2023-01-24T10:05:52Z

docs/make.jl

+    if f isa Function
+        for method in methods
+            tv, decls, file, line = arg_decl_parts(m)
+


[JuliaFormatter] _{reported by reviewdog 🐶}

Suggested change

Co-Authored-By: Pietro Monticone <38562595+pitmonticone@users.noreply.github.com> Co-Authored-By: Claudio Moroni <43729990+ClaudMor@users.noreply.github.com>

pitmonticone

LGTM now.

ClaudMor

Will update docs in main branch.

pitmonticone and others added 20 commits January 7, 2023 22:43

Merge pull request #70 from JuliaGraphs/main

5b8bb7a

Add JOSS submission badge.

Merge pull request #71 from JuliaGraphs/main

190ad00

Update the README

Update

58c98c2

Co-Authored-By: Pietro Monticone <38562595+pitmonticone@users.noreply.github.com> Co-Authored-By: Claudio Moroni <43729990+ClaudMor@users.noreply.github.com>

Merge pull request #75 from JuliaGraphs/main

784fc1a

Update README.md

Merge pull request #77 from JuliaGraphs/main

0f80113

Add v1.1 announcement posts to README and docs

Implement Multiplex(Di)Graph

1d28cc5

TODO: write tests Co-Authored-By: Pietro Monticone <38562595+pitmonticone@users.noreply.github.com> Co-Authored-By: Claudio Moroni <43729990+ClaudMor@users.noreply.github.com>

Merge pull request #80 from JuliaGraphs/main

6c6bfb5

Add example folder

Merge pull request #99 from JuliaGraphs/main

65d99e8

Update "Future Developments" section in README and docs.

Fix tests

b769596

Co-Authored-By: Pietro Monticone <38562595+pitmonticone@users.noreply.github.com> Co-Authored-By: Claudio Moroni <43729990+ClaudMor@users.noreply.github.com>

Revert to SimpleTraits

f219a60

Co-Authored-By: Pietro Monticone <38562595+pitmonticone@users.noreply.github.com> Co-Authored-By: Claudio Moroni <43729990+ClaudMor@users.noreply.github.com>

Merge pull request #101 from JuliaGraphs/main

f67d948

Fix bugs in README and example

update

9df566e

Some tests still error Co-Authored-By: Pietro Monticone <38562595+pitmonticone@users.noreply.github.com> Co-Authored-By: Claudio Moroni <43729990+ClaudMor@users.noreply.github.com>

Restructure API, begin implementation of synchronized edge colored mu…

2915992

…ltilayer graph Co-Authored-By: Pietro Monticone <38562595+pitmonticone@users.noreply.github.com> Co-Authored-By: Claudio Moroni <43729990+ClaudMor@users.noreply.github.com>

update

62c5011

Co-Authored-By: Pietro Monticone <38562595+pitmonticone@users.noreply.github.com> Co-Authored-By: Claudio Moroni <43729990+ClaudMor@users.noreply.github.com>

Update abstractsynchronizededgecolored.jl

7556cdb

Co-Authored-By: Pietro Monticone <38562595+pitmonticone@users.noreply.github.com> Co-Authored-By: Claudio Moroni <43729990+ClaudMor@users.noreply.github.com>

Update

0c06802

Code cleaning and reordering Co-Authored-By: Pietro Monticone <38562595+pitmonticone@users.noreply.github.com> Co-Authored-By: Claudio Moroni <43729990+ClaudMor@users.noreply.github.com>

Eliminate multiplex graphs (moved to multiplex_graphs branch)

1fc488f

Co-Authored-By: Pietro Monticone <38562595+pitmonticone@users.noreply.github.com> Co-Authored-By: Claudio Moroni <43729990+ClaudMor@users.noreply.github.com>

InterdisciplinaryPhysicsTeam requested review from ClaudMor and pitmonticone January 22, 2023 17:49

InterdisciplinaryPhysicsTeam added the enhancement New feature or request. label Jan 22, 2023

github-actions bot reviewed Jan 22, 2023

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InterdisciplinaryPhysicsTeam and others added 3 commits January 23, 2023 00:29

Update

b71be25

- Rename new graph - Fix APis (to be completed) Co-Authored-By: Pietro Monticone <38562595+pitmonticone@users.noreply.github.com> Co-Authored-By: Claudio Moroni <43729990+ClaudMor@users.noreply.github.com>

format src and test

41de4ee

Co-Authored-By: Pietro Monticone <38562595+pitmonticone@users.noreply.github.com> Co-Authored-By: Claudio Moroni <43729990+ClaudMor@users.noreply.github.com>

Update docs

72110d2

Co-Authored-By: Pietro Monticone <38562595+pitmonticone@users.noreply.github.com> Co-Authored-By: Claudio Moroni <43729990+ClaudMor@users.noreply.github.com>

github-actions bot reviewed Jan 24, 2023

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InterdisciplinaryPhysicsTeam and others added 2 commits January 24, 2023 11:42

Update make.jl

33d35d0

Co-Authored-By: Pietro Monticone <38562595+pitmonticone@users.noreply.github.com> Co-Authored-By: Claudio Moroni <43729990+ClaudMor@users.noreply.github.com>

Update API_organized.md

c9a6b2d

Co-Authored-By: Pietro Monticone <38562595+pitmonticone@users.noreply.github.com> Co-Authored-By: Claudio Moroni <43729990+ClaudMor@users.noreply.github.com>

pitmonticone approved these changes Jan 24, 2023

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ClaudMor approved these changes Jan 24, 2023

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InterdisciplinaryPhysicsTeam merged commit 364692e into main Jan 24, 2023

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Traits based sub ecosystem & `NodeAlingnedEdgeColored(Di)Graph` #107

Traits based sub ecosystem & `NodeAlingnedEdgeColored(Di)Graph` #107

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	include("representations/supraweightmatrix.jl")
	include("representations/supraweightmatrix.jl")

		# General MultilayerGraph Utilities
		fadjlist(mg::AbstractMultilayerGraph) = mg.fadjlist

	) where {M<:AbstractMultilayerGraph; IsDirected{M}}
	) where {M <: AbstractMultilayerGraph; IsDirected{M}}

	) where {T,U,M<:AbstractMultilayerGraph{T,U}; IsDirected{M}}
	) where {T,U,M<:AbstractMultilayerGraph{T,U};IsDirected{M}}

Traits based sub ecosystem & NodeAlingnedEdgeColored(Di)Graph #107

Traits based sub ecosystem & NodeAlingnedEdgeColored(Di)Graph #107

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coveralls commented Jan 22, 2023 • edited Loading

Pull Request Test Coverage Report for Build 3980839972

Warning: This coverage report may be inaccurate.

Details

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Traits based sub ecosystem & `NodeAlingnedEdgeColored(Di)Graph` #107

Traits based sub ecosystem & `NodeAlingnedEdgeColored(Di)Graph` #107

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