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This library generates graph layouts using the TikZ graph layout package.

License: Other

Julia 83.73% TeX 16.27%

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tikzgraphs.jl's Issues

Unsatisfiable requirements when adding TikzGraphs

When I try to add TikzGraphs I am getting an error "Unsatisfiable requirements detected for package DataStructures [864edb3b]".

I'm using a completely fresh version of Julia 1.6 (i.e. with no other packages installed).

Here's the full terminal output:

               _
   _       _ _(_)_     |  Documentation: https://docs.julialang.org
  (_)     | (_) (_)    |
   _ _   _| |_  __ _   |  Type "?" for help, "]?" for Pkg help.
  | | | | | | |/ _` |  |
  | | |_| | | | (_| |  |  Version 1.6.0 (2021-03-24)
 _/ |\__'_|_|_|\__'_|  |  Official https://julialang.org/ release
|__/                   |

julia> using Pkg

julia> Pkg.add("TikzGraphs")
   Resolving package versions...
ERROR: Unsatisfiable requirements detected for package DataStructures [864edb3b]:
 DataStructures [864edb3b] log:
 ├─DataStructures [864edb3b] has no known versions!
 └─found to have no compatible versions left with LightGraphs [093fc24a]
   └─LightGraphs [093fc24a] log:
     ├─possible versions are: 0.13.0-1.3.5 or uninstalled
     └─restricted by compatibility requirements with TikzGraphs [b4f28e30] to versions: 0.13.1-1.3.5
       └─TikzGraphs [b4f28e30] log:
         ├─possible versions are: 0.7.0-1.1.0 or uninstalled
         └─restricted to versions * by an explicit requirement, leaving only versions 0.7.0-1.1.0
Stacktrace:
  [1] propagate_constraints!(graph::Pkg.Resolve.Graph, sources::Set{Int64}; log_events::Bool)
    @ Pkg.Resolve /Users/julia/buildbot/worker/package_macos64/build/usr/share/julia/stdlib/v1.6/Pkg/src/Resolve/graphtype.jl:1048
  [2] propagate_constraints! (repeats 2 times)
    @ /Users/julia/buildbot/worker/package_macos64/build/usr/share/julia/stdlib/v1.6/Pkg/src/Resolve/graphtype.jl:989 [inlined]
  [3] simplify_graph!(graph::Pkg.Resolve.Graph, sources::Set{Int64}; clean_graph::Bool)
    @ Pkg.Resolve /Users/julia/buildbot/worker/package_macos64/build/usr/share/julia/stdlib/v1.6/Pkg/src/Resolve/graphtype.jl:1503
  [4] simplify_graph! (repeats 2 times)
    @ /Users/julia/buildbot/worker/package_macos64/build/usr/share/julia/stdlib/v1.6/Pkg/src/Resolve/graphtype.jl:1503 [inlined]
  [5] resolve_versions!(ctx::Pkg.Types.Context, pkgs::Vector{Pkg.Types.PackageSpec})
    @ Pkg.Operations /Users/julia/buildbot/worker/package_macos64/build/usr/share/julia/stdlib/v1.6/Pkg/src/Operations.jl:404
  [6] targeted_resolve(ctx::Pkg.Types.Context, pkgs::Vector{Pkg.Types.PackageSpec}, preserve::Pkg.Types.PreserveLevel)
    @ Pkg.Operations /Users/julia/buildbot/worker/package_macos64/build/usr/share/julia/stdlib/v1.6/Pkg/src/Operations.jl:1208
  [7] tiered_resolve(ctx::Pkg.Types.Context, pkgs::Vector{Pkg.Types.PackageSpec})
    @ Pkg.Operations /Users/julia/buildbot/worker/package_macos64/build/usr/share/julia/stdlib/v1.6/Pkg/src/Operations.jl:1194
  [8] _resolve
    @ /Users/julia/buildbot/worker/package_macos64/build/usr/share/julia/stdlib/v1.6/Pkg/src/Operations.jl:1214 [inlined]
  [9] add(ctx::Pkg.Types.Context, pkgs::Vector{Pkg.Types.PackageSpec}, new_git::Vector{Base.UUID}; preserve::Pkg.Types.PreserveLevel, platform::Base.BinaryPlatforms.Platform)
    @ Pkg.Operations /Users/julia/buildbot/worker/package_macos64/build/usr/share/julia/stdlib/v1.6/Pkg/src/Operations.jl:1229
 [10] add(ctx::Pkg.Types.Context, pkgs::Vector{Pkg.Types.PackageSpec}; preserve::Pkg.Types.PreserveLevel, platform::Base.BinaryPlatforms.Platform, kwargs::Base.Iterators.Pairs{Union{}, Union{}, Tuple{}, NamedTuple{(), Tuple{}}})
    @ Pkg.API /Users/julia/buildbot/worker/package_macos64/build/usr/share/julia/stdlib/v1.6/Pkg/src/API.jl:197
 [11] add
    @ /Users/julia/buildbot/worker/package_macos64/build/usr/share/julia/stdlib/v1.6/Pkg/src/API.jl:148 [inlined]
 [12] add(pkgs::Vector{Pkg.Types.PackageSpec}; kwargs::Base.Iterators.Pairs{Union{}, Union{}, Tuple{}, NamedTuple{(), Tuple{}}})
    @ Pkg.API /Users/julia/buildbot/worker/package_macos64/build/usr/share/julia/stdlib/v1.6/Pkg/src/API.jl:73
 [13] add
    @ /Users/julia/buildbot/worker/package_macos64/build/usr/share/julia/stdlib/v1.6/Pkg/src/API.jl:72 [inlined]
 [14] #add#21
    @ /Users/julia/buildbot/worker/package_macos64/build/usr/share/julia/stdlib/v1.6/Pkg/src/API.jl:70 [inlined]
 [15] add
    @ /Users/julia/buildbot/worker/package_macos64/build/usr/share/julia/stdlib/v1.6/Pkg/src/API.jl:70 [inlined]
 [16] #add#20
    @ /Users/julia/buildbot/worker/package_macos64/build/usr/share/julia/stdlib/v1.6/Pkg/src/API.jl:69 [inlined]
 [17] add(pkg::String)
    @ Pkg.API /Users/julia/buildbot/worker/package_macos64/build/usr/share/julia/stdlib/v1.6/Pkg/src/API.jl:69
 [18] top-level scope
    @ REPL[2]:1

julia> Pkg.status()
      Status `~/.julia/environments/v1.6/Project.toml` (empty project)

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IOError: could not spawn `pdf2svg ./tmpgQGIAG/tikzpicture.pdf ./tmpgQGIAG/tikzpicture.svg`

On IJulia in Julia 0.7

plot(G)

IOError: could not spawn `pdf2svg ./tmpgQGIAG/tikzpicture.pdf ./tmpgQGIAG/tikzpicture.svg`: no such file or directory (ENOENT)

Stacktrace:
 [1] _jl_spawn(::String, ::Array{String,1}, ::Cmd, ::Tuple{Base.DevNullStream,Base.DevNullStream,Base.DevNullStream}) at ./process.jl:370
 [2] (::getfield(Base, Symbol("##499#500")){Cmd})(::Tuple{Base.DevNullStream,Base.DevNullStream,Base.DevNullStream}) at ./process.jl:512
 [3] setup_stdio(::getfield(Base, Symbol("##499#500")){Cmd}, ::Tuple{Base.DevNullStream,Base.DevNullStream,Base.DevNullStream}) at ./process.jl:493
 [4] #_spawn#498(::Nothing, ::Function, ::Cmd, ::Tuple{Base.DevNullStream,Base.DevNullStream,Base.DevNullStream}) at ./process.jl:511
 [5] #_spawn at ./none:0 [inlined]
 [6] #_spawn#504 at ./process.jl:551 [inlined]
 [7] _spawn at ./process.jl:551 [inlined]
 [8] success(::Cmd) at ./process.jl:708
 [9] save(::TikzPictures.SVG, ::TikzPictures.TikzPicture) at /Users/tomer/.julia/packages/TikzPictures/b9irC/src/TikzPictures.jl:391
 [10] save(::TikzPictures.SVG, ::TikzPictures.TikzPicture) at /Users/tomer/.julia/packages/TikzPictures/b9irC/src/TikzPictures.jl:383
 [11] show(::IOContext{Base.GenericIOBuffer{Array{UInt8,1}}}, ::MIME{Symbol("image/svg+xml")}, ::TikzPictures.TikzPicture) at /Users/tomer/.julia/packages/TikzPictures/b9irC/src/TikzPictures.jl:441
 [12] limitstringmime at /Users/tomer/.julia/packages/IJulia/0cLgR/src/inline.jl:36 [inlined]
 [13] display_mimestring(::MIME{Symbol("image/svg+xml")}, ::TikzPictures.TikzPicture) at /Users/tomer/.julia/packages/IJulia/0cLgR/src/execute_request.jl:73
 [14] display_dict(::TikzPictures.TikzPicture) at /Users/tomer/.julia/packages/IJulia/0cLgR/src/execute_request.jl:101
 [15] #invokelatest#1 at ./essentials.jl:691 [inlined]
 [16] invokelatest at ./essentials.jl:690 [inlined]
 [17] execute_request(::ZMQ.Socket, ::IJulia.Msg) at /Users/tomer/.julia/packages/IJulia/0cLgR/src/execute_request.jl:256
 [18] #invokelatest#1 at ./essentials.jl:691 [inlined]
 [19] invokelatest at ./essentials.jl:690 [inlined]
 [20] eventloop(::ZMQ.Socket) at /Users/tomer/.julia/packages/IJulia/0cLgR/src/eventloop.jl:8
 [21] (::getfield(IJulia, Symbol("##12#15")))() at ./task.jl:262

Obviously, I'm trying to plot the resulting graph from project 1 🙂!

Something wrong with using Labels + Layout

The labels are dropped when I specify a layout:

e.g.
display(TikzGraphs.plot(graph, Layouts.Spring(randomSeed=52), labels=make_string(cat(1,demand, train_load)), node_style="draw, rounded corners, fill=blue!10", node_styles=Dict(graph.vertices[end]=>"fill=green!10")))

where:
function make_string(int_array::Array{Int64})
out_array = Array{String}(length(int_array))
for i in 1:length(int_array)
out_array[i] = string(i)
end
return out_array::Array{String}
end

yields:

You'll notice the labels are just the node numbers.

could not import LaTeXStrings?

Maybe this is an issue with my environment?

[ Info: Precompiling TikzGraphs [b4f28e30-c73f-5eaf-a395-8a9db949a742]
WARNING: could not import LaTeXStrings.@L_mstr into TikzPictures

Switch to Graphs.jl instead of LightGraphs.jl

Since LightGraphs.jl seized development, which is now being continued at Graphs.jl, it might be better to make TikzGraphs.jl depend on Graphs.jl, in order to use Graphs.jl along with TikzGraphs.jl in other projects.

Documentation link does not work

Error 503 first byte timeout

first byte timeout

Guru Mediation:

Details: cache-bma7031-BMA 1481631868 1664798385

Varnish cache server

LaTeX error

A trivial graph with

g = DiGraph(2)
add_edge!(g, 1, 2)
t = TikzGraphs.plot(g)
TikzPictures.save(TEX("tpic"), t)

creates a tex file that produces an error when processed with lualatex (so save(SVG(...)), etc., produce the same error):

! Argument of \next has an extra }.                                                                                                    
<inserted text>                                                                                                                        
\par                                                                                                                                   
l.11 \ProvidesFileRCS{pgfsys-luatex.def}

This is with the latest texlive (2021) on Debian 10.

META not seeing v0.5.1

Pkg.update() doesn't seem to be pulling in v0.5.1 which has the precompile flag enabled and depwarns removed. It's breaking travis on downstream packages that use precompilation. Can we update meta? or should I try to work around it?

Undirected Graphs have edge arrows

using TikzGraphs
using LightGraphs
g = Graph(4)
add_edge!(g, 1, 2)
add_edge!(g, 2, 3)
TikzGraphs.plot(g)

Undirected graphs are currently plotted with arrows.

Error saving as SVG

`#` character in graph labels causes LaTeX error

The # character inside a graph label seems to get interpreted as a LaTeX parameter marker, which causes a LaTeX error. Here's a minimal example:

using LightGraphs
using TikzGraphs

g = DiGraph(2)
add_edge!(g, 1, 2)
TikzGraphs.plot(g, ["foo#", "bar"])

which produces:

! Illegal parameter number in definition of \pgfutil@reserved@a.
<to be read again> 
"
l.15 }
    ;
Error saving as SVG
LaTeX error

System info

julia> versioninfo()
Julia Version 0.5.0
Commit 3c9d753 (2016-09-19 18:14 UTC)
Platform Info:
  System: Darwin (x86_64-apple-darwin13.4.0)
  CPU: Intel(R) Core(TM) i7-2860QM CPU @ 2.50GHz
  WORD_SIZE: 64
  BLAS: libopenblas (USE64BITINT DYNAMIC_ARCH NO_AFFINITY Sandybridge)
  LAPACK: libopenblas64_
  LIBM: libopenlibm
  LLVM: libLLVM-3.7.1 (ORCJIT, sandybridge)

julia> Pkg.installed("TikzGraphs")
v"0.3.0"

julia> run(`latex --version`)
pdfTeX 3.14159265-2.6-1.40.16 (TeX Live 2015)
kpathsea version 6.2.1
Copyright 2015 Peter Breitenlohner (eTeX)/Han The Thanh (pdfTeX).
There is NO warranty.  Redistribution of this software is
covered by the terms of both the pdfTeX copyright and
the Lesser GNU General Public License.
For more information about these matters, see the file
named COPYING and the pdfTeX source.
Primary author of pdfTeX: Peter Breitenlohner (eTeX)/Han The Thanh (pdfTeX).
Compiled with libpng 1.6.17; using libpng 1.6.17
Compiled with zlib 1.2.8; using zlib 1.2.8
Compiled with xpdf version 3.04

1.2.1 patch to sync up with Graphs.jl?

Hi,

Thanks for maintaining the package. I was trying to go through the notebook tutorial here and was getting errors on the most basic example.

Here's the simplest MWE possible:

using Graphs, TikzGraphs
TikzGraphs.plot(DiGraph(1))

Which gave me

ERROR: MethodError: no method matching plot(::SimpleDiGraph{Int64})
Closest candidates are:
  plot(::Any, ::TikzGraphs.Layouts.Layout) at /home/renatogeh/.julia/packages/TikzGraphs/tob6G/src/TikzGraphs.jl:44
  plot(::Any, ::TikzGraphs.Layouts.Layout, ::Vector{T}; args...) where T<:AbstractString at /home/renatogeh/.julia/packages/TikzGraphs/tob6G/src/TikzGraphs.jl:44
  plot(::Any, ::Vector{T}; args...) where T<:AbstractString at /home/renatogeh/.julia/packages/TikzGraphs/tob6G/src/TikzGraphs.jl:45
  ...
Stacktrace:
 [1] top-level scope
   @ REPL[2]:1

With all latest versions:

Julia: 1.6.3
Graphs: 1.4.1
TikzGraphs: 1.2.0

My first guess was that it was not recognizing SimpleDiGraph{Int64} as an AbstractGraph for some reason. Indeed, if I pass a Layout the function goes through fine.

TikzGraphs.plot(DiGraph(1), Layouts.Spring())

But complains about something else.

ERROR: MethodError: no method matching vertices(::SimpleDiGraph{Int64})
Closest candidates are:
  vertices(::LightGraphs.SimpleGraphs.AbstractSimpleGraph) at /home/renatogeh/.julia/packages/LightGraphs/IgJif/src/SimpleGraphs/SimpleGraphs.jl:58
  vertices(::LightGraphs.AbstractGraph) at /home/renatogeh/.julia/packages/LightGraphs/IgJif/src/interface.jl:181
Stacktrace:
 [1] plot(g::SimpleDiGraph{Int64}, layout::TikzGraphs.Layouts.Spring)
   @ TikzGraphs ~/.julia/packages/TikzGraphs/tob6G/src/TikzGraphs.jl:44
 [2] top-level scope
   @ REPL[2]:1

What's weird about this is that vertices is calling LightGraphs, and not Graphs.jl. After some digging around, I found out that the latest version (v1.2.0) of TikzGraphs is not yet synced with the latest docs.

An easy fix would be to simply send out a v1.2.1 patch so that we get the updated Project.toml, fixing this issue. This way new users won't get confused for not getting the most basic example running in their machines. What do you think?

Thanks

How to resize inline graphs in ipynb?

Is there any easy way to do this with TikzGraphs graphs?

Nodes are amalgamated if they have the same label

I am trying to draw a syntax tree where different nodes have the same label.
Those nodes seem to get amalgamated into one.

Error tagging new release

The URL of this package does not match that stored in METADATA.jl.
cc: @Shushman

Allow set options for \graph

Currently, the keyword options is for begin{tikzpiture}[options...]. It should be useful to allow set options for \graph [options]. For example, we can set the common styles for nodes and edges here. This is also they how TikzGraphs set the options for layout.

TikzGraphs.plot doesn't work on Jupyter notebook (Julia 1.0)

Even with

dev TikzPictures
dev TikzGraphs

Jupyter code:

using TikzGraphs
using LightGraphs
g = DiGraph(4)
add_edge!(g, 1, 2)
add_edge!(g, 2, 3)
TikzGraphs.plot(g)
using TikzGraphs
using LightGraphs
g = DiGraph(4)
add_edge!(g, 1, 2)
add_edge!(g, 2, 3)
TikzGraphs.plot(g)

Error message:

MethodError: no method matching replace(::String, ::String, ::String)
Closest candidates are:
  replace(::String, !Matched::Pair{#s55,B} where B where #s55<:AbstractChar; count) at strings/util.jl:414
  replace(::String, !Matched::Pair{#s52,B} where B where #s52<:Union{Tuple{Vararg{AbstractChar,N} where N}, Set{#s49} where #s49<:AbstractChar, AbstractArray{#s50,1} where #s50<:AbstractChar}; count) at strings/util.jl:419
  replace(::String, !Matched::Pair; count) at strings/util.jl:423
  ...

Stacktrace:
 [1] show(::IOContext{Base.GenericIOBuffer{Array{UInt8,1}}}, ::MIME{Symbol("image/svg+xml")}, ::TikzPictures.TikzPicture) at /home/wangnan/store/workspace/julia/TikzPictures/src/TikzPictures.jl:327
 [2] limitstringmime(::MIME{Symbol("image/svg+xml")}, ::TikzPictures.TikzPicture) at /home/wangnan/.julia/packages/IJulia/iMVN2/src/inline.jl:36
 [3] display_dict(::TikzPictures.TikzPicture) at /home/wangnan/.julia/packages/IJulia/iMVN2/src/execute_request.jl:38
 [4] #invokelatest#1 at ./essentials.jl:686 [inlined]
 [5] invokelatest at ./essentials.jl:685 [inlined]
 [6] execute_request(::ZMQ.Socket, ::IJulia.Msg) at /home/wangnan/.julia/packages/IJulia/iMVN2/src/execute_request.jl:207
 [7] #invokelatest#1 at ./essentials.jl:686 [inlined]
 [8] invokelatest at ./essentials.jl:685 [inlined]
 [9] eventloop(::ZMQ.Socket) at /home/wangnan/.julia/packages/IJulia/iMVN2/src/eventloop.jl:8
 [10] (::getfield(IJulia, Symbol("##15#18")))() at ./task.jl:259

Input node co-ordinates

Hi. It would be nice to have the functionality to include a dictionary containing the x and y coordinates of the nodes such that they can be placed as desired. Thanks!

SystemError: mktempdir: Permission denied

When I am trying to run the example code

using TikzGraphs
using LightGraphs
g = DiGraph(4)
add_edge!(g, 1, 2)
add_edge!(g, 2, 3)
TikzGraphs.plot(g)

in a Jupyter notebook, I met the following error:

SystemError: mktempdir: Permission denied

Stacktrace:
 [1] #systemerror#39(::Nothing, ::Function, ::Symbol, ::Bool) at ./error.jl:106
 [2] systemerror at ./error.jl:106 [inlined]
 [3] mktempdir(::String) at ./file.jl:501
 [4] _mktempdir at /Users/qz/.julia/packages/TikzPictures/b9irC/src/TikzPictures.jl:195 [inlined]
 [5] save(::TikzPictures.SVG, ::TikzPictures.TikzPicture) at /Users/qz/.julia/packages/TikzPictures/b9irC/src/TikzPictures.jl:354
 [6] show(::IOContext{Base.GenericIOBuffer{Array{UInt8,1}}}, ::MIME{Symbol("image/svg+xml")}, ::TikzPictures.TikzPicture) at /Users/qz/.julia/packages/TikzPictures/b9irC/src/TikzPictures.jl:441
 [7] limitstringmime at /Users/qz/.julia/packages/IJulia/4VL8h/src/inline.jl:36 [inlined]
 [8] display_dict(::TikzPictures.TikzPicture) at /Users/qz/.julia/packages/IJulia/4VL8h/src/execute_request.jl:39
 [9] #invokelatest#1 at ./essentials.jl:686 [inlined]
 [10] invokelatest at ./essentials.jl:685 [inlined]
 [11] execute_request(::ZMQ.Socket, ::IJulia.Msg) at /Users/qz/.julia/packages/IJulia/4VL8h/src/execute_request.jl:197
 [12] #invokelatest#1 at ./essentials.jl:686 [inlined]
 [13] invokelatest at ./essentials.jl:685 [inlined]
 [14] eventloop(::ZMQ.Socket) at /Users/qz/.julia/packages/IJulia/4VL8h/src/eventloop.jl:8
 [15] (::getfield(IJulia, Symbol("##12#15")))() at ./task.jl:259

However, I can execute mktempdir directly in Julia:

julia> mktempdir()
"/var/folders/hx/79tr9k0x27b_z93pl1pyspbw0000gn/T/tmpF5waul"

My system is

System Version: macOS 10.13.6 (17G2307)
Kernel Version: Darwin 17.7.0

My Julia version is 1.0.0, the deps are: TikzGraphs v1.0.0, and LightGraphs v1.1.0. My MacTeX version is 2018.0417.

Installing TeX tools on Ubuntu

I was following https://github.com/sisl/BayesNets.jl/blob/master/doc/BayesNets.ipynb (great tutorial btw) and ran into trouble getting the figures running.

I needed texlive-luatex, texlive-pictures, and texlive-xetex to get the figures generated. Just leaving this here in case anyone else finds it useful.

No Directory Available Error

I got this error trying to use TikzGraphs, not sure how to remedy it.

Error saving as SVG
could not spawn lualatex --enable-write18 --output-directory=. tikzpicture: no such file or directory (ENOENT)

This is my code:
using LightGraphs
using TikzGraphs
g = Grid([5,5])
TikzGraphs.plot(g)

Self loop nodes

Hello,
Is it possible to draw a node with a self loop? How would one proceed?

I tried the following:

using LightGraphs
g = SimpleDiGraph(2)
add_edge!(g, (2, 1))
add_edge!(g, (1,1))
TikzGraphs.plot(g, node_styles=Dict(1=>"loop below"))

The arrow corresponding to the edge (1,1) seems to be there but is poorly formatted.

Heads-up: LightGraphs and Julia 0.6

Hi all,

LightGraphs is preparing for a fairly large upgrade with Julia 0.6, and I wanted to make you aware of what we're doing. Very few things are breaking, but there will be some potential performance improvements that you might be able to take advantage of.

In a nutshell: we're abstracting Graph and DiGraph, renaming them to SimpleGraph and SimpleDiGraph*, and parameterizing vertex indices to <: Integer. This will allow you to create, e.g., SimpleGraph{UInt8}s that will be much more space-efficient if you have graphs that are < 256 vertices.

*While we plan on more abstractions (e.g., for weighted graphs) in the future, for now Graph and DiGraph will continue to work and will continue to default to SimpleGraph, and the default parameterization for both Simple(Di)Graphs and (Di)Graphs will be Int.

Feel free to review the (very long) WIP at sbromberger/LightGraphs.jl#541 - your feedback would be greatly appreciated.

Phylogenetic Trees

Hi,

I just discovered this really cool package!
I was wondering if there were any plan to support the phylogenetic tree layout?

Thanks!

Travis failure

Need to figure out why it is failing on travis. It seems to work on the Ubuntu, Windows, and MacOS machines in our lab.

HEADS UP: Breaking change in LightGraphs API

Sorry if this is not relevant to your use of LightGraphs, but I wanted to make sure you’re aware of a change in the API for the induced_subgraph() function.

Starting in LightGraphs 0.7.1, induced_subgraph() will, in addition to the subgraph itself, return a mapping of the original vertex indices to the new ones. This will require code changes to ignore the new return value if you’re using this function.

If you’re using the getindex version of induced_subgraph (that is, g[1:5]), there will be no change.

Feel free to close this out if it’s not applicable to your use of LightGraphs. Thanks!

Drawing FFNN and RNN

Hello,

I am trying to draw a simple FFNN and a simple RNN.
In order to show the input layer of the FFNN how can I insert edges that are directed to nodes? And for the RNN part is it possible to draw reflexive edges ?

B.R.

Imcompatible with dark-mode Pluto

It seems the background of a graph figure is transparent. Therefore, it is nearly invisible in the dark-mode Pluto cell.

Latex Error: `Package pgfkeys Error:`

Hello,

I just installed the package and I get an eror when Trying to run

using TikzGraphs
g = DiGraph(4)
add_edge!(g, 1, 2)
add_edge!(g, 2, 3)
TikzGraphs.plot(g)

I get

! Package pgfkeys Error: I do not know the key '/tikz/hyper/.forward to' and I 
am going to ignore it. Perhaps you misspelled it.

See the pgfkeys package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
                                                  
l.71 ...appendtoforwardinglist{/tikz/,/tikz/graphs/}
                                                  
Error saving as SVG
LaTeX error

The error suggests Latex problems. Nevertheless I use LaTeX regularly.

My Latex info:

pdflatex --version
pdfTeX 3.14159265-2.6-1.40.16 (TeX Live 2015/Debian)
kpathsea version 6.2.1
Copyright 2015 Peter Breitenlohner (eTeX)/Han The Thanh (pdfTeX).
There is NO warranty.  Redistribution of this software is
covered by the terms of both the pdfTeX copyright and
the Lesser GNU General Public License.
For more information about these matters, see the file
named COPYING and the pdfTeX source.
Primary author of pdfTeX: Peter Breitenlohner (eTeX)/Han The Thanh (pdfTeX).
Compiled with libpng 1.6.17; using libpng 1.6.17
Compiled with zlib 1.2.8; using zlib 1.2.8
Compiled with poppler version 0.41.0

My system is running an ubuntu with the following details:

Pkg.versioninfo()
Julia Version 0.6.2
Commit d386e40c17 (2017-12-13 18:08 UTC)
Platform Info:
  OS: Linux (x86_64-pc-linux-gnu)
  CPU: Intel(R) Core(TM) i7-4600U CPU @ 2.10GHz
  WORD_SIZE: 64
  BLAS: libopenblas (USE64BITINT DYNAMIC_ARCH NO_AFFINITY Haswell)
  LAPACK: libopenblas64_
  LIBM: libopenlibm
  LLVM: libLLVM-3.9.1 (ORCJIT, haswell)

I would appreciate any hint to solve this.
Thank you

I should add That I've tried it in macOS and it works, but on my ubuntu machine I cannot make it work.
In the documentation you could add brew install pdf2svg for mac users.

TikZ graphs on texlive 2018

The most recent version of PGF on texlive 2018 leads to this failure:

! Package pgf Error: Graph drawing library 'layered' not found.

See the pgf package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
                                                  
l.7 \usegdlibrary{layered}
                        
LaTeX error

Stacktrace:
 [1] error(::String) at .\error.jl:33
 [2] save(::TikzPictures.SVG, ::TikzPictures.TikzPicture) at C:\Users\Mykel\.julia\packages\TikzPictures\b9irC\src\TikzPictures.jl:387
 [3] show(::IOContext{Base.GenericIOBuffer{Array{UInt8,1}}}, ::MIME{Symbol("image/svg+xml")}, ::TikzPictures.TikzPicture) at C:\Users\Mykel\.julia\packages\TikzPictures\b9irC\src\TikzPictures.jl:441
 [4] limitstringmime at C:\Users\Mykel\.julia\packages\IJulia\0cLgR\src\inline.jl:36 [inlined]
 [5] display_mimestring(::MIME{Symbol("image/svg+xml")}, ::TikzPictures.TikzPicture) at C:\Users\Mykel\.julia\packages\IJulia\0cLgR\src\execute_request.jl:73
 [6] display_dict(::TikzPictures.TikzPicture) at C:\Users\Mykel\.julia\packages\IJulia\0cLgR\src\execute_request.jl:101
 [7] #invokelatest#1 at .\essentials.jl:686 [inlined]
 [8] invokelatest at .\essentials.jl:685 [inlined]
 [9] execute_request(::ZMQ.Socket, ::IJulia.Msg) at C:\Users\Mykel\.julia\packages\IJulia\0cLgR\src\execute_request.jl:256
 [10] #invokelatest#1 at .\essentials.jl:686 [inlined]
 [11] invokelatest at .\essentials.jl:685 [inlined]
 [12] eventloop(::ZMQ.Socket) at C:\Users\Mykel\.julia\packages\IJulia\0cLgR\src\eventloop.jl:8
 [13] (::getfield(IJulia, Symbol("##12#15")))() at .\task.jl:259

LaTeX env takes forever to install in Travis and breaks.

Lualatex takes ~20 min to install when running a travis test.
It then fails with lualatex -v not being able to run.

Tree Graph has crossing edges

I have a relative big tree graph but not overly complicated (around 75 nodes).
A tree is always a planar graph, so it should be able to be plotted without crossing edges.
Is there a trick to make it look like a normal tree graph?

Remove support for Graphs.jl

With BayesNets.jl no longer using Graphs.jl (it uses LightGraphs.jl instead) and Graphs.jl becoming unmaintained (see discussion), it seems like we should just drop support for Graphs.jl.

Doesn't seem to work on Julia v1.0

Error message upon building:

Updating registry at `~/.julia/registries/General`
  Updating git-repo `https://github.com/JuliaRegistries/General.git`
ERROR: MethodError: no method matching haskey(::Nothing, ::String)
Closest candidates are:
  haskey(::Base.Iterators.Pairs, ::Any) at iterators.jl:247
  haskey(::Dict, ::Any) at dict.jl:546
  haskey(::Base.ImmutableDict, ::Any) at dict.jl:731
  ...
Stacktrace:
 [1] _get_deps!(::Pkg.Types.Context, ::Array{Pkg.Types.PackageSpec,1}, ::Array{Base.UUID,1}) at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.0/Pkg/src/API.jl:396
 [2] #build#55(::Base.Iterators.Pairs{Union{},Union{},Tuple{},NamedTuple{(),Tuple{}}}, ::Function, ::Pkg.Types.Context, ::Array{Pkg.Types.PackageSpec,1}) at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.0/Pkg/src/API.jl:434
 [3] build at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.0/Pkg/src/API.jl:411 [inlined]
 [4] do_build!(::Dict{Symbol,Any}, ::Array{Pkg.Types.PackageSpec,1}, ::Dict{Symbol,Any}) at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.0/Pkg/src/REPLMode.jl:601
 [5] #invokelatest#1(::Base.Iterators.Pairs{Union{},Union{},Tuple{},NamedTuple{(),Tuple{}}}, ::Function, ::Any, ::Any, ::Vararg{Any,N} where N) at ./essentials.jl:686
 [6] invokelatest(::Any, ::Any, ::Vararg{Any,N} where N) at ./essentials.jl:685
 [7] do_cmd!(::Pkg.REPLMode.PkgCommand, ::REPL.LineEditREPL) at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.0/Pkg/src/REPLMode.jl:542
 [8] #do_cmd#30(::Bool, ::Function, ::REPL.LineEditREPL, ::String) at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.0/Pkg/src/REPLMode.jl:507
 [9] do_cmd at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.0/Pkg/src/REPLMode.jl:503 [inlined]
 [10] (::getfield(Pkg.REPLMode, Symbol("##41#44")){REPL.LineEditREPL,REPL.LineEdit.Prompt})(::REPL.LineEdit.MIState, ::Base.GenericIOBuffer{Array{UInt8,1}}, ::Bool) at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.0/Pkg/src/REPLMode.jl:842
 [11] #invokelatest#1 at ./essentials.jl:686 [inlined]
 [12] invokelatest at ./essentials.jl:685 [inlined]
 [13] run_interface(::REPL.Terminals.TextTerminal, ::REPL.LineEdit.ModalInterface, ::REPL.LineEdit.MIState) at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.0/REPL/src/LineEdit.jl:2261
 [14] run_frontend(::REPL.LineEditREPL, ::REPL.REPLBackendRef) at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.0/REPL/src/REPL.jl:1029
 [15] run_repl(::REPL.AbstractREPL, ::Any) at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.0/REPL/src/REPL.jl:191
 [16] (::getfield(Base, Symbol("##720#722")){Bool,Bool,Bool,Bool})(::Module) at ./logging.jl:311
 [17] #invokelatest#1 at ./essentials.jl:686 [inlined]
 [18] invokelatest at ./essentials.jl:685 [inlined]
 [19] macro expansion at ./logging.jl:308 [inlined]
 [20] run_main_repl(::Bool, ::Bool, ::Bool, ::Bool, ::Bool) at ./client.jl:330
 [21] exec_options(::Base.JLOptions) at ./client.jl:242
 [22] _start() at ./client.jl:421

Non-unique labels

Non-unique labels no not result in the correct graph:

g = DiGraph(3)
add_edge!(g, 1, 2)
add_edge!(g, 1, 3)
TikzGraphs.plot(g, ["+", "a", "a"])

This can certainly be bypassed with pure Tikz; not sure whether the graphs package would support something like this. We could throw a warning if it cannot be solved.

Error saving as SVG

PDFPlots works but TikzGraphs doesn't; I get this inscrutable error message.

using LightGraphs
g = DiGraph(4)
add_edge!(g, 1, 2)
add_edge!(g, 2, 3)
TikzGraphs.plot(g)

! Undefined control sequence.
l.1793 \__msg_kernel_new:nnnn
                            { xparse } { bad-arg-spec }
Error saving as SVG
LaTeX error

Using inside of VSCode

Hi,

I'm trying to use the package to visualize some graphs using the Julia REPL in VSCode. I tried running the simple example in the docs and got the following error:

julia> using TikzGraphs

julia> using LightGraphs

julia> g = DiGraph(4)
{4, 0} directed simple Int64 graph

julia> add_edge!(g, 1, 2)
true

julia> add_edge!(g, 2, 3)
true

julia> TikzGraphs.plot(g)
Error showing value of type TikzPictures.TikzPicture:
ERROR: IOError: could not spawn `lualatex --enable-write18 --output-directory=./jl_sKcDvq ./jl_sKcDvq/tikzpicture.tex`: no such file or directory (ENOENT)
Stacktrace:
  [1] _spawn_primitive(file::String, cmd::Cmd, stdio::Vector{Any}) 
    @ Base .\process.jl:99
  [2] #637
    @ .\process.jl:112 [inlined]
  [3] setup_stdios(f::Base.var"#637#638"{Cmd}, stdios::Vector{Any})
    @ Base .\process.jl:196
  [4] _spawn
    @ .\process.jl:111 [inlined]
  [5] _spawn
    @ .\process.jl:106 [inlined]
  [6] success(cmd::Cmd)
    @ Base .\process.jl:496
  [7] _mkTempPdf(tp::TikzPictures.TikzPicture, temp_dir::String, temp_filename::String; dvi::Bool) 
    @ TikzPictures C:\Users\UB01382\.julia\packages\TikzPictures\nU7Cj\src\svg.jl:82
  [8] _mkTempPdf
    @ C:\Users\UB01382\.julia\packages\TikzPictures\nU7Cj\src\svg.jl:74 [inlined]
  [9] _mkTempSvg(backend::TikzPictures.PopplerBackend, tp::TikzPictures.TikzPicture, temp_dir::String, temp_filename::String)
    @ TikzPictures C:\Users\UB01382\.julia\packages\TikzPictures\nU7Cj\src\svg.jl:37
 [10] _mkTempSvg(tp::TikzPictures.TikzPicture, temp_dir::String, temp_filename::String)
    @ TikzPictures C:\Users\UB01382\.julia\packages\TikzPictures\nU7Cj\src\svg.jl:51
 [11] (::TikzPictures.var"#21#22"{TikzPictures.TikzPicture, String})()
    @ TikzPictures C:\Users\UB01382\.julia\packages\TikzPictures\nU7Cj\src\TikzPictures.jl:368
 [12] cd(f::TikzPictures.var"#21#22"{TikzPictures.TikzPicture, String}, dir::String)
    @ Base.Filesystem .\file.jl:95
 [13] save(f::TikzPictures.SVG, tp::TikzPictures.TikzPicture)
    @ TikzPictures C:\Users\UB01382\.julia\packages\TikzPictures\nU7Cj\src\TikzPictures.jl:361
 [14] show(f::IOBuffer, #unused#::MIME{Symbol("image/svg+xml")}, tp::TikzPictures.TikzPicture)     
    @ TikzPictures C:\Users\UB01382\.julia\packages\TikzPictures\nU7Cj\src\TikzPictures.jl:396     
 [15] display(d::VSCodeServer.InlineDisplay, m::MIME{Symbol("image/svg+xml")}, x::TikzPictures.TikzPicture)
    @ VSCodeServer c:\Users\UB01382\.vscode\extensions\julialang.language-julia-1.2.7\scripts\packages\VSCodeServer\src\display.jl:0
 [16] display(d::VSCodeServer.InlineDisplay, mime::String, x::Any)
    @ Base.Multimedia .\multimedia.jl:216
 [17] display(d::VSCodeServer.InlineDisplay, x::TikzPictures.TikzPicture)
    @ VSCodeServer c:\Users\UB01382\.vscode\extensions\julialang.language-julia-1.2.7\scripts\packages\VSCodeServer\src\display.jl:108
 [18] display(x::Any)
    @ Base.Multimedia .\multimedia.jl:328
 [19] #invokelatest#2
    @ .\essentials.jl:708 [inlined]
 [20] invokelatest
    @ .\essentials.jl:706 [inlined]
 [21] print_response(errio::IO, response::Any, show_value::Bool, have_color::Bool, specialdisplay::Union{Nothing, AbstractDisplay})
    @ REPL C:\buildbot\worker\package_win64\build\usr\share\julia\stdlib\v1.6\REPL\src\REPL.jl:247 
 [22] (::REPL.var"#40#41"{REPL.LineEditREPL, Pair{Any, Bool}, Bool, Bool})(io::Any)
    @ REPL C:\buildbot\worker\package_win64\build\usr\share\julia\stdlib\v1.6\REPL\src\REPL.jl:231 
 [23] with_repl_linfo(f::Any, repl::REPL.LineEditREPL)
    @ REPL C:\buildbot\worker\package_win64\build\usr\share\julia\stdlib\v1.6\REPL\src\REPL.jl:462 
 [24] print_response(repl::REPL.AbstractREPL, response::Any, show_value::Bool, have_color::Bool)   
    @ REPL C:\buildbot\worker\package_win64\build\usr\share\julia\stdlib\v1.6\REPL\src\REPL.jl:229 
 [25] (::REPL.var"#do_respond#61"{Bool, Bool, REPL.var"#72#82"{REPL.LineEditREPL, REPL.REPLHistoryProvider}, REPL.LineEditREPL, REPL.LineEdit.Prompt})(s::REPL.LineEdit.MIState, buf::Any, ok::Bool)
    @ REPL C:\buildbot\worker\package_win64\build\usr\share\julia\stdlib\v1.6\REPL\src\REPL.jl:798 
 [26] #invokelatest#2
    @ .\essentials.jl:708 [inlined]
 [27] invokelatest
    @ .\essentials.jl:706 [inlined]
 [28] run_interface(terminal::REPL.Terminals.TextTerminal, m::REPL.LineEdit.ModalInterface, s::REPL.LineEdit.MIState)
    @ REPL.LineEdit C:\buildbot\worker\package_win64\build\usr\share\julia\stdlib\v1.6\REPL\src\LineEdit.jl:2441
 [29] run_frontend(repl::REPL.LineEditREPL, backend::REPL.REPLBackendRef)
    @ REPL C:\buildbot\worker\package_win64\build\usr\share\julia\stdlib\v1.6\REPL\src\REPL.jl:1126 [30] (::REPL.var"#44#49"{REPL.LineEditREPL, REPL.REPLBackendRef})()
    @ REPL .\task.jl:411

However, I can run this inside a Julia terminal.

Any idea why this is happening?

Julia v1.6.1
TikzGraphs v1.1.0