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Graph data structures with multiple heterogeneous metadata for Graphs.jl.

Home Page: https://juliagraphs.org/MetaGraphs.jl/

License: Other

Julia 100.00%

graph graphs metadata juliagraphs datastructures data-structures hacktoberfest

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gjunqueira-sys binary-eater abraunst filchristou mroavi gabriel-fallen henrik-wolf josbert1

metagraphs.jl's Issues

link to docs is broken

The GitHub Pages link to the documentation returns a 404 error.

LightGraphs is not compatible anymore

MetaGraphs was working with LightGraphs.jl before but this isn't the case anymore.

julia> using LightGraphs, MetaGraphs
julia> g = DiGraph(5)
julia> G = MetaDiGraph(g)
ERROR: MethodError: no method matching Graphs.SimpleGraphs.SimpleDiGraph(::SimpleDiGraph{Int64})
Closest candidates are:
  Graphs.SimpleGraphs.SimpleDiGraph() ...

[Port] Extend `rem_vertices!` to `MetaGraph`

See sbromberger/MetaGraphs.jl#104

Similar to Julia's Base.get would be nice to have get_prop(mgr::AbstractMetaGraph, v, defaultvalue), get_prop(mgr::AbstractMetaGraph, n1, n2, defaultvalue) and so on.
The implementation should be super easy. Just checking with has_prop and act appropriately.
Personally I would find that useful. Other opinions ?

Error messages with `MetaGraph`, `vertices`, and `edges`

Hi
I get a number of problems with MetaGraphs.

The MetaGraph function of MetaGraphs does not convert a SimpleGraph to a MetaGraph. The error message refers to LightGraphs, which I uninstalled (rm LightGraphs) before adding Graphs.
The vertices function works on a SimpleGraph and does not on a MetaGraph -> no method matching...
The edges function works on a SimpleGraph and does not on a MetaGraph -> edges function not implemented

Any help is welcome.
Laurent
PS: I am a biologist not very well skilled at Julia and programing in general.

julia> using Graphs, MetaGraphs, DataFrames, GraphDataFrameBridge

julia> g=complete_graph(3)
{3, 3} undirected simple Int64 graph

julia> mg=MetaGraphs.MetaGraph(g)
ERROR: MethodError: no method matching LightGraphs.SimpleGraphs.SimpleGraph(::SimpleGraph{Int64})
Closest candidates are:
  LightGraphs.SimpleGraphs.SimpleGraph(::Any, ::Array{Vector{T}, 1}) where T at C:\Users\Laurent\.julia\packages\LightGraphs\IgJif\src\SimpleGraphs\simplegraph.jl:18
  LightGraphs.SimpleGraphs.SimpleGraph() at C:\Users\Laurent\.julia\packages\LightGraphs\IgJif\src\SimpleGraphs\simplegraph.jl:50
  LightGraphs.SimpleGraphs.SimpleGraph(::MetaGraph) at C:\Users\Laurent\.julia\packages\MetaGraphs\UlMik\src\metagraph.jl:50
  ...
Stacktrace:
 [1] MetaGraph(x::SimpleGraph{Int64}, weightfield::Symbol, defaultweight::Float64)
   @ MetaGraphs ~\.julia\packages\MetaGraphs\UlMik\src\metagraph.jl:14
 [2] MetaGraph(x::SimpleGraph{Int64})
   @ MetaGraphs ~\.julia\packages\MetaGraphs\UlMik\src\metagraph.jl:26
 [3] top-level scope
   @ REPL[20]:1

julia> df = DataFrame(src=["g1", "g2", "g3"], dst=["g2", "g3", "g1"], weight=[1, 1 ,1])
3×3 DataFrame
 Row │ src     dst     weight
     │ String  String  Int64
─────┼────────────────────────
   1 │ g1      g2           1
   2 │ g2      g3           1
   3 │ g3      g1           1

julia> mg=GraphDataFrameBridge.MetaGraph(df, :src, :dst, weight=:weight)
{3, 3} undirected Int64 metagraph with Float64 weights defined by :weight (default weight 1.0)

julia> vertices(mg)
ERROR: MethodError: no method matching vertices(::MetaGraph{Int64, Float64})
Closest candidates are:
  vertices(::Graphs.SimpleGraphs.AbstractSimpleGraph) at C:\Users\Laurent\.julia\packages\Graphs\Mih78\src\SimpleGraphs\SimpleGraphs.jl:58
  vertices(::AbstractGraph) at C:\Users\Laurent\.julia\packages\Graphs\Mih78\src\interface.jl:181
Stacktrace:
 [1] top-level scope
   @ REPL[23]:1

julia> vertices(g)
Base.OneTo(3)

julia> edges(mg)
ERROR: method edges not implemented.
Stacktrace:
 [1] _NI(m::String)
   @ Graphs ~\.julia\packages\Graphs\Mih78\src\interface.jl:16
 [2] edges(g::MetaGraph{Int64, Float64})
   @ Graphs ~\.julia\packages\Graphs\Mih78\src\interface.jl:207
 [3] top-level scope
   @ REPL[25]:1

julia> edges(g)
SimpleEdgeIter 3

[Port] Property of edge lost when going from `MetaDiGraph` with inversed edge direction to `MetaGraph`

See sbromberger/MetaGraphs.jl#109

[Port] Replace inner metadata `Dict`s with `NamedTuple`s

See sbromberger/MetaGraphs.jl#46

[Port] Method to check whether an index exists (`has_indexing_prop`)

See sbromberger/MetaGraphs.jl#99

[Port] Multi-threading with MetaGraphs

See sbromberger/MetaGraphs.jl#98

[Port] MGFormat persistence broken

See sbromberger/MetaGraphs.jl#85

[Port] How to update vertex / node color in a loop

See sbromberger/MetaGraphs.jl#93

[Port] Roadmap to 1.0?

See sbromberger/MetaGraphs.jl#106

save/load not working?

I thought this should work, but it doesn't:

using Graphs
using MetaGraphs

g = path_graph(5)
mg = MetaGraph(g, 3.0)
set_prop!(mg, :description, "This is a metagraph.")

savegraph("/tmp/test_graph.lg", mg)

mg1 = loadgraph("/tmp/test_graph.lg")

ERROR: LoadError: BoundsError: attempt to access 2-element Vector{SubString{String}} at index [3]
Stacktrace:
  [1] getindex
    @ ./array.jl:861 [inlined]
  [2] indexed_iterate
    @ ./tuple.jl:90 [inlined]
  [3] _parse_header(s::SubString{String})
    @ Graphs ~/.julia/packages/Graphs/zrMoC/src/persistence/lg.jl:62
  [4] loadlg(io::IOStream, gname::String)
    @ Graphs ~/.julia/packages/Graphs/zrMoC/src/persistence/lg.jl:104
  [5] loadgraph
    @ ~/.julia/packages/Graphs/zrMoC/src/persistence/lg.jl:147 [inlined]
  [6] #120
    @ ~/.julia/packages/Graphs/zrMoC/src/persistence/common.jl:15 [inlined]
  [7] open(::Graphs.var"#120#121"{String, LGFormat}, ::String, ::Vararg{String}; kwargs::Base.Pairs{Symbol, Union{}, Tuple{}, NamedTuple{(), Tuple{}}})
    @ Base ./io.jl:330
  [8] open
    @ ./io.jl:328 [inlined]
  [9] loadgraph
    @ ~/.julia/packages/Graphs/zrMoC/src/persistence/common.jl:14 [inlined]
 [10] loadgraph(fn::String)
    @ Graphs ~/.julia/packages/Graphs/zrMoC/src/persistence/common.jl:18
 [11] top-level scope
    @ untitled-55510ba3fa4677b8db7457446bdad39a:10

Is it something to do with the compressed format - savegraph(.. ... metagraph ... , compress=false) doesn't work either?

Using Graphs v1.7.0, MetaGraphs v0.7.1, Julia 1.7.

[Port] Weight matrix error in the function `dijkstra_shortest_paths()`

See sbromberger/MetaGraphs.jl#103

MetaGraph's GitHub Pages documentation returns a 404.

The link to MetaGraph's documentation appears to be broken.

[Port] `set_prop!` returns `Set{Symbol}` if an indexing property is being set

See sbromberger/MetaGraphs.jl#115

MetaGraph does not accept SimpleGraph properly

using LightGraphs, MetaGraphs
g = LightGraphs.SimpleGraphs.grid([5, 24])
MetaGraph(g)

crashes with

ERROR: LoadError: MethodError: no method matching Graphs.SimpleGraphs.SimpleGraph(::SimpleGraph{Int64})
Closest candidates are:
  Graphs.SimpleGraphs.SimpleGraph(::Any, ::Array{Vector{T}, 1}) where T at C:\Users\racinsky\.julia\packages\Graphs\Mih78\src\SimpleGraphs\simplegraph.jl:18
  Graphs.SimpleGraphs.SimpleGraph() at C:\Users\racinsky\.julia\packages\Graphs\Mih78\src\SimpleGraphs\simplegraph.jl:50
  Graphs.SimpleGraphs.SimpleGraph(::Graphs.SimpleGraphs.SimpleGraph) at C:\Users\racinsky\.julia\packages\Graphs\Mih78\src\SimpleGraphs\simplegraph.jl:115
  ...
Stacktrace:
 [1] MetaGraph(x::SimpleGraph{Int64}, weightfield::Symbol, defaultweight::Float64)
   @ MetaGraphs C:\Users\racinsky\.julia\packages\MetaGraphs\bffKb\src\metagraph.jl:14
 [2] MetaGraph(x::SimpleGraph{Int64})
   @ MetaGraphs C:\Users\racinsky\.julia\packages\MetaGraphs\bffKb\src\metagraph.jl:26
 [3] top-level scope
   @ c:\Projects\others\advent_of_code_2021\loading_data.jl:545
in expression starting at c:\Projects\others\advent_of_code_2021\loading_data.jl:545

that's because without parameters it does not dispatch to https://github.com/JuliaGraphs/MetaGraphs.jl/blob/master/src/metagraph.jl#L36.

[Port] We shouldn't be allowed to `set_indexing_prop!` on nonexistent vertices

See sbromberger/MetaGraphs.jl#74

[Port] Catlab contains some GraphViz code we could use

See sbromberger/MetaGraphs.jl#66

How to cite

Hi all, been enjoying using MetaGraphs in my research. What's the best way to cite this work in a publication (academic paper)?

[Port] `clear_props!` type-unstable

See sbromberger/MetaGraphs.jl#89

Register package

[Port] `rem_prop!` and `clear_props!` on vertex leaves dangling `metaindex`

See sbromberger/MetaGraphs.jl#75

[Port] Disallow construction of `MetaGraph` from directed graph?

See sbromberger/MetaGraphs.jl#118

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