From 73254a9e43038be1d7a370d951147d0a408b52f9 Mon Sep 17 00:00:00 2001
From: vyudu <vincent.duyuan@gmail.com>
Date: Fri, 22 Nov 2024 17:13:42 -0500
Subject: [PATCH] rm graphs
---
src/graphs.jl | 428 --------------------------------------------------
1 file changed, 428 deletions(-)
delete mode 100644 src/graphs.jl
diff --git a/src/graphs.jl b/src/graphs.jl
deleted file mode 100644
index 2f1fb490c4..0000000000
--- a/src/graphs.jl
+++ /dev/null
@@ -1,428 +0,0 @@
-#######################################################################
-# Contains code from Catlab.jl:
-# https://raw.githubusercontent.com/AlgebraicJulia/Catlab.jl/master/src/graphics/Graphviz.jl
-#
-# That license for that code is:
-#
-# The MIT License
-#
-# Copyright (c) 2017-2020: Evan Patterson.
-#
-# Permission is hereby granted, free of charge, to any person obtaining a copy
-# of this software and associated documentation files (the "Software"), to deal
-# in the Software without restriction, including without limitation the rights
-# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-# copies of the Software, and to permit persons to whom the Software is
-# furnished to do so, subject to the following conditions:
-#
-# The above copyright notice and this permission notice shall be included in
-# all copies or substantial portions of the Software.
-#
-# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
-# THE SOFTWARE.
-#######################################################################
-""" AST and pretty printer for Graphviz's DOT language.
-
-References:
-
-- DOT grammar: http://www.graphviz.org/doc/info/lang.html
-- DOT language guide: http://www.graphviz.org/pdf/dotguide.pdf
-"""
-
-### AST ###
-
-abstract type Expression end
-abstract type Statement <: Expression end
-
-""" AST type for Graphviz's "HTML-like" node labels.
-
-For now, the HTML content is just a string.
-"""
-struct Html
- content::String
-end
-Base.print(io::IO, html::Html) = print(io, html.content)
-
-const AttributeValue = Union{String, Html}
-const Attributes = OrderedDict{Symbol, AttributeValue}
-
-as_attributes(attrs::Attributes) = attrs
-as_attributes(d::OrderedDict) = Attributes(Symbol(k) => d[k] for k in keys(d))
-function as_attributes(d::AbstractDict)
- Attributes(Symbol(k) => d[k] for k in sort!(collect(keys(d))))
-end
-
-@with_kw_noshow struct Graph <: Expression
- name::String
- directed::Bool
- prog::String = "dot"
- stmts::Vector{Statement} = Statement[]
- graph_attrs::Attributes = Attributes()
- node_attrs::Attributes = Attributes()
- edge_attrs::Attributes = Attributes()
-end
-
-function Graph(name::String, stmts::Vector{Statement}; kw...)
- Graph(; name = name, directed = false, stmts = stmts, kw...)
-end
-function Graph(name::String, stmts::Vararg{Statement}; kw...)
- Graph(; name = name, directed = false, stmts = collect(stmts), kw...)
-end
-function Digraph(name::String, stmts::Vector{Statement}; kw...)
- Graph(; name = name, directed = true, stmts = stmts, kw...)
-end
-function Digraph(name::String, stmts::Vararg{Statement}; kw...)
- Graph(; name = name, directed = true, stmts = collect(stmts), kw...)
-end
-
-@with_kw_noshow struct Subgraph <: Statement
- name::String = "" # Subgraphs can be anonymous
- stmts::Vector{Statement} = Statement[]
- graph_attrs::Attributes = Attributes()
- node_attrs::Attributes = Attributes()
- edge_attrs::Attributes = Attributes()
-end
-
-Subgraph(stmts::Vector{Statement}; kw...) = Subgraph(; stmts = stmts, kw...)
-Subgraph(stmts::Vararg{Statement}; kw...) = Subgraph(; stmts = collect(stmts), kw...)
-function Subgraph(name::String, stmts::Vector{Statement}; kw...)
- Subgraph(; name = name, stmts = stmts, kw...)
-end
-function Subgraph(name::String, stmts::Vararg{Statement}; kw...)
- Subgraph(; name = name, stmts = collect(stmts), kw...)
-end
-
-struct Node <: Statement
- name::String
- attrs::Attributes
-end
-Node(name::String, attrs::AbstractDict) = Node(name, as_attributes(attrs))
-Node(name::String; attrs...) = Node(name, attrs)
-
-struct NodeID <: Expression
- name::String
- port::String
- anchor::String
- NodeID(name::String, port::String = "", anchor::String = "") = new(name, port, anchor)
-end
-
-struct Edge <: Statement
- path::Vector{NodeID}
- attrs::Attributes
-end
-Edge(path::Vector{NodeID}, attrs::AbstractDict) = Edge(path, as_attributes(attrs))
-Edge(path::Vector{NodeID}; attrs...) = Edge(path, attrs)
-Edge(path::Vararg{NodeID}; attrs...) = Edge(collect(path), attrs)
-Edge(path::Vector{String}, attrs::AbstractDict) = Edge(map(NodeID, path), attrs)
-Edge(path::Vector{String}; attrs...) = Edge(map(NodeID, path), attrs)
-Edge(path::Vararg{String}; attrs...) = Edge(map(NodeID, collect(path)), attrs)
-
-### Bindings ###
-
-""" Run a Graphviz program.
-
-Invokes Graphviz through its command-line interface. If the `Graphviz_jll`
-package is installed and loaded, it is used; otherwise, Graphviz must be
-installed on the local system.
-
-For bindings to the Graphviz C API, see the the package
-[GraphViz.jl](https://github.com/Keno/GraphViz.jl). At the time of this writing,
-GraphViz.jl is unmaintained.
-"""
-function run_graphviz(io::IO, graph::Graph; prog::Union{String, Nothing} = nothing,
- format::String = "json0")
- if isnothing(prog)
- prog = graph.prog
- end
- @assert prog in ("dot", "neato", "fdp", "sfdp", "twopi", "circo")
- if USE_GV_JLL[]
- fun = getfield(Graphviz_jll, Symbol(prog))
- fun() do exe
- open(`$exe -T$format`, io, write = true) do gv
- pprint(gv, graph)
- end
- end
- else
- open(`$prog -T$format`, io, write = true) do gv
- pprint(gv, graph)
- end
- end
-end
-function run_graphviz(graph::Graph; kw...)
- io = IOBuffer()
- run_graphviz(io, graph; kw...)
- seekstart(io)
-end
-
-function Base.show(io::IO, ::MIME"image/svg+xml", graph::Graph)
- run_graphviz(io, graph, format = "svg")
-end
-
-### Pretty-print ###
-
-""" Pretty-print the Graphviz expression.
-"""
-pprint(expr::Expression) = pprint(stdout, expr)
-pprint(io::IO, expr::Expression) = pprint(io, expr, 0)
-
-function pprint(io::IO, graph::Graph, n::Int)
- indent(io, n)
- print(io, graph.directed ? "digraph " : "graph ")
- print(io, graph.name)
- println(io, " {")
- pprint_attrs(io, graph.graph_attrs, n + 2; pre = "graph", post = ";\n")
- pprint_attrs(io, graph.node_attrs, n + 2; pre = "node", post = ";\n")
- pprint_attrs(io, graph.edge_attrs, n + 2; pre = "edge", post = ";\n")
- for stmt in graph.stmts
- pprint(io, stmt, n + 2, directed = graph.directed)
- println(io)
- end
- indent(io, n)
- println(io, "}")
-end
-
-function pprint(io::IO, subgraph::Subgraph, n::Int; directed::Bool = false)
- indent(io, n)
- if isempty(subgraph.name)
- println(io, "{")
- else
- print(io, "subgraph ")
- print(io, subgraph.name)
- println(io, " {")
- end
- pprint_attrs(io, subgraph.graph_attrs, n + 2; pre = "graph", post = ";\n")
- pprint_attrs(io, subgraph.node_attrs, n + 2; pre = "node", post = ";\n")
- pprint_attrs(io, subgraph.edge_attrs, n + 2; pre = "edge", post = ";\n")
- for stmt in subgraph.stmts
- pprint(io, stmt, n + 2, directed = directed)
- println(io)
- end
- indent(io, n)
- print(io, "}")
-end
-
-function pprint(io::IO, node::Node, n::Int; directed::Bool = false)
- indent(io, n)
- print(io, node.name)
- pprint_attrs(io, node.attrs)
- print(io, ";")
-end
-
-function pprint(io::IO, node::NodeID, n::Int)
- print(io, node.name)
- if !isempty(node.port)
- print(io, ":")
- print(io, node.port)
- end
- if !isempty(node.anchor)
- print(io, ":")
- print(io, node.anchor)
- end
-end
-
-function pprint(io::IO, edge::Edge, n::Int; directed::Bool = false)
- indent(io, n)
- for (i, node) in enumerate(edge.path)
- if i > 1
- print(io, directed ? " -> " : " -- ")
- end
- pprint(io, node, n)
- end
- pprint_attrs(io, edge.attrs)
- print(io, ";")
-end
-
-function pprint_attrs(io::IO, attrs::Attributes, n::Int = 0;
- pre::String = "", post::String = "")
- if !isempty(attrs)
- indent(io, n)
- print(io, pre)
- print(io, " [")
- for (i, (key, value)) in enumerate(attrs)
- if (i > 1)
- print(io, ",")
- end
- print(io, key)
- print(io, "=")
- print(io, value isa Html ? "<" : "\"")
- print(io, value)
- print(io, value isa Html ? ">" : "\"")
- end
- print(io, "]")
- print(io, post)
- end
-end
-
-indent(io::IO, n::Int) = print(io, " "^n)
-
-#######################################################################
-# following is adapted from Petri.jl
-# https://github.com/mehalter/Petri.jl
-#######################################################################
-
-const graph_attrs = Attributes(:rankdir => "LR")
-const node_attrs = Attributes(:shape => "plain", :style => "filled", :color => "white")
-const edge_attrs = Attributes(:splines => "splines")
-
-function edgify(δ, i, reverse::Bool)
- attr = Attributes()
- return map(δ) do p
- val = String(getname(p[1]))
- weight = "$(p[2])"
- attr = Attributes(:label => weight, :labelfontsize => "6")
- return Edge(reverse ? ["rx_$i", "$val"] :
- ["$val", "rx_$i"], attr)
- end
-end
-
-# make distinguished edge based on rate constant
-function edgifyrates(rxs, specs)
- es = Edge[]
- for (i, rx) in enumerate(rxs)
- deps = rx.rate isa Number ? Any[] : get_variables(rx.rate, specs)
- for dep in deps
- val = String(getname(dep))
- attr = Attributes(:color => "#d91111", :style => "dashed")
- e = Edge(["$val", "rx_$i"], attr)
- push!(es, e)
- end
- end
- es
-end
-
-# create edges from one reaction complex to another reaction complex
-function edgifycomplex(δ, attr)
- return map(δ) do p
- return Edge([p[1], p[2]], attr)
- end
-end
-
-# modify vector of string of complexes into graphviz compatible strings
-function modifystrcomp(strcomp::Vector{String})
- for i in 1:length(strcomp)
- # cannot allow (t) as per graphviz
- if occursin("(t)", strcomp[i])
- strcomp[i] = replace(strcomp[i], "(t)" => "")
- end
- # prettify NUll with ∅
- if occursin("0", strcomp[i])
- strcomp[i] = replace(strcomp[i], "0" => "∅")
- end
- end
- strcomp = "<" .* strcomp .* ">"
-end
-
-### Public-facing API ###
-
-"""
- complexgraph(rn::ReactionSystem; complexdata=reactioncomplexes(rn))
-
-Creates a Graphviz graph of the [`ReactionComplex`](@ref)s in `rn`. Reactions
-correspond to arrows and reaction complexes to blue circles.
-
-Notes:
-- Black arrows from complexes to complexes indicate reactions whose rate is a
- parameter or a `Number`. i.e. `k, A --> B`.
-- Red dashed arrows from complexes to complexes indicate reactions whose rate
- depends on species. i.e. `k*C, A --> B` for `C` a species.
-- Requires the Graphviz jll to be installed, or Graphviz to be installed and
- commandline accessible.
-"""
-function complexgraph(rn::ReactionSystem; complexdata = reactioncomplexes(rn))
- rxs = reactions(rn)
- specs = species(rn)
- complexes, B = complexdata
- fun = rcel -> specs[rcel.speciesid] * rcel.speciesstoich
- compfun(rc) = rc == Catalyst.ReactionComplex{Int64}[] ? 0 : sum(fun, rc)
-
- strcomp = [string(compfun(rc)) for rc in complexes]
-
- newstrcomp = modifystrcomp(strcomp)
- compnodes = [Node(str, Attributes(:shape => "circle", :color => "#6C9AC3"))
- for str in newstrcomp]
-
- edges = []
- for (i, r) in enumerate(rxs)
- subcomp = newstrcomp[argmin(@view B[:, i])]
- prodcomp = newstrcomp[argmax(@view B[:, i])]
- deps = get_variables(r.rate, specs)
- if deps != Any[]
- attr = Attributes(:color => "#d91111", :style => "dashed")
- push!(edges, edgifycomplex(zip([subcomp], [prodcomp]), attr))
- else
- attr = Attributes()
- push!(edges, edgifycomplex(zip([subcomp], [prodcomp]), attr))
- end
- end
- stmts2 = Vector{Statement}()
- append!(stmts2, compnodes)
- append!(stmts2, collect(Iterators.flatten(edges)))
- g = Digraph("G", stmts2; graph_attrs = graph_attrs, node_attrs = node_attrs,
- edge_attrs = edge_attrs)
- return g
-end
-
-"""
- Graph(rn::ReactionSystem)
-
-Converts a [`ReactionSystem`](@ref) into a Graphviz graph.
-Reactions correspond to small green circles, and species to blue circles.
-
-Notes:
-- Black arrows from species to reactions indicate reactants, and are labelled
- with their input stoichiometry.
-- Black arrows from reactions to species indicate products, and are labelled
- with their output stoichiometry.
-- Red arrows from species to reactions indicate that species is used within the
- rate expression. For example, in the reaction `k*A, B --> C`, there would be a
- red arrow from `A` to the reaction node. In `k*A, A+B --> C`, there would be
- red and black arrows from `A` to the reaction node.
-- Requires the Graphviz jll to be installed, or Graphviz to be installed and
- commandline accessible.
-"""
-function Graph(rn::ReactionSystem)
- rxs = reactions(rn)
- specs = species(rn)
- statenodes = [Node(string(getname(s)),
- Attributes(:shape => "circle", :color => "#6C9AC3")) for s in specs]
- transnodes = [Node(string("rx_$i"),
- Attributes(:shape => "point", :color => "#E28F41", :width => ".1"))
- for (i, r) in enumerate(rxs)]
-
- stmts = vcat(statenodes, transnodes)
- edges = map(enumerate(rxs)) do (i, r)
- vcat(edgify(zip(r.substrates, r.substoich), i, false),
- edgify(zip(r.products, r.prodstoich), i, true))
- end
- es = edgifyrates(rxs, specs)
- (!isempty(es)) && push!(edges, es)
-
- stmts2 = Vector{Statement}()
- append!(stmts2, stmts)
- append!(stmts2, collect(Iterators.flatten(edges)))
- g = Digraph("G", stmts2; graph_attrs = graph_attrs, node_attrs = node_attrs,
- edge_attrs = edge_attrs)
- return g
-end
-
-"""
- savegraph(g::Graph, fname, fmt="png")
-
-Given a `Graph` generated by [`Graph`](@ref), save the graph to the file with
-name `fname` and extension `fmt`.
-
-Notes:
-- `fmt="png"` is the default output format.
-- Requires the Graphviz jll to be installed, or Graphviz to be installed and commandline accessible.
-"""
-function savegraph(g::Graph, fname, fmt = "png")
- open(fname, "w") do io
- run_graphviz(io, g, format = fmt)
- end
- nothing
-end