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use Requires.jl to remove direct dependency on PyCall.jl
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Stuart Daines committed May 6, 2022
1 parent ef5cba5 commit 3766cdd
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6 changes: 3 additions & 3 deletions Project.toml
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
name = "PALEOmodel"
uuid = "bf7b4fbe-ccb1-42c5-83c2-e6e9378b660c"
authors = ["Stuart Daines <[email protected]>"]
version = "0.14.3"
version = "0.14.4"

[deps]
DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
Expand All @@ -15,8 +15,8 @@ Logging = "56ddb016-857b-54e1-b83d-db4d58db5568"
NLsolve = "2774e3e8-f4cf-5e23-947b-6d7e65073b56"
PALEOboxes = "804b410e-d900-4b2a-9ecd-f5a06d4c1fd4"
Printf = "de0858da-6303-5e67-8744-51eddeeeb8d7"
PyCall = "438e738f-606a-5dbb-bf0a-cddfbfd45ab0"
RecipesBase = "3cdcf5f2-1ef4-517c-9805-6587b60abb01"
Requires = "ae029012-a4dd-5104-9daa-d747884805df"
Revise = "295af30f-e4ad-537b-8983-00126c2a3abe"
SciMLBase = "0bca4576-84f4-4d90-8ffe-ffa030f20462"
SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
Expand All @@ -36,8 +36,8 @@ Infiltrator = "1.0"
JLD2 = "0.4"
NLsolve = "4.5"
PALEOboxes = "0.15, 0.16, 0.17"
PyCall = "1.92"
RecipesBase = "1.2"
Requires = "1.0"
Revise = "3.1"
SciMLBase = "1.29"
SparseDiffTools = "1.13"
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211 changes: 4 additions & 207 deletions src/ReactionNetwork.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -5,9 +5,8 @@ Functions to analyize a PALEOboxes.Model that contains a reaction network
"""
module ReactionNetwork

using PyCall
import Printf

import Requires
import PALEOboxes as PB
import PALEOmodel

Expand Down Expand Up @@ -266,212 +265,10 @@ function show_ratesummaries(ratesummaries; select_species=[])
return nothing
end

"""
show_network_rate_nodes(model::PB.Model, domainname, output [, outputrec] [, indices] [.rate_thresh=0.0]) -> graph
Display reaction network as a `pydot` `graph`, including nodes for reactions.
NB: requires the Python `pydot` package. See <https://github.com/JuliaPy/PyCall.jl>,
and the docstring for `pyimport_conda`. Assuming that a conda-based Python is being used,
julia> using PyCall
julia> pyimport_conda("pydot", "pydot")
will download and install the Python package.
"""
function show_network_rate_nodes(
model::PB.Model, domainname, output;
outputrec=length(output.domains[domainname]),
indices=nothing,
rate_thresh=0.0,
species_root_only=true
)

rate_totals = get_rates(model, output, domainname;
outputrec=outputrec,
indices=indices)

rate_max = 0.0
for (rname, r) in rate_totals
rate_max = max(rate_max, r)
end

# species_ratevars = get_all_species_ratevars(model, domainname)

ratesummaries = get_all_species_ratesummaries(
model, output, domainname,
outputrec=outputrec,
indices=indices,
species_root_only=species_root_only
)

pydot = pyimport_conda("pydot", "pydot")
graph = pydot.Dot("Reactions", graph_type="digraph", bgcolor="white", layout="dot", rank="same", splines="line")

for (species, ratesummary) in ratesummaries

node = pydot.Node(species, label=species)
graph.add_node(node)

net = ratesummary.net
if abs(net) >= rate_thresh
node = pydot.Node(species*"_net", label=string(abs(net)), shape="diamond")
graph.add_node(node)
if net > 0
from, to = species, species*"_net"
else
from, to = species*"_net", species
end
net_norm = abs(net)/rate_max
edge = pydot.Edge(
from, to,
color="black",
weight=Int(floor(100*net_norm))+1,
penwidth=max(1.0, 20.0*net_norm)
)
graph.add_edge(edge)
end
end


dom = PB.get_domain(model, domainname)

colourlist = ["green", "black", "blue"]
rate_idx = 1
for rj in dom.reactions
rvs = PB.get_rate_stoichiometry(rj)
if !isnothing(rvs)


for (ratevarname, processname, stoichvec) in rvs
if abs(rate_totals[ratevarname]) >= rate_thresh
if processname == "photolysis"
colour="red"
else
colour=colourlist[mod(rate_idx, length(colourlist))+1]
end

rate_norm = abs(rate_totals[ratevarname])/rate_max
node = pydot.Node(ratevarname, shape="box", color=colour)
graph.add_node(node)
for (speciesname, stoich) in stoichvec
if species_root_only
speciesname = get_species_root(speciesname)
end
if stoich*rate_totals[ratevarname] > 0
from, to = ratevarname, speciesname
else
from, to = speciesname, ratevarname
end
if stoich != 0
rate_stoich_norm = rate_norm * abs(stoich)
edge = pydot.Edge(
from, to,
color=colour,
weight=Int(floor(100*rate_stoich_norm))+1,
penwidth=max(1.0, 20.0*rate_stoich_norm),
)
graph.add_edge(edge)
end
end
rate_idx += 1
end
end
end
end

return graph
end


function display_svg(graph)
output_graphviz_svg = graph.create_svg()
display("image/svg+xml", output_graphviz_svg)
end

#=
function show_network(model::PB.Model, domainname, output;
outputrec=length(output.domains[domainname]),
indices=nothing,
rate_thresh=0.0)
rate_totals = get_rates(model, output, domainname;
outputrec=outputrec,
indices=indices)
rate_max = 0.0
for (rname, r) in rate_totals
rate_max = max(rate_max, r)
end
species_ratevars = get_all_species_ratevars(model, domainname)
pydot = pyimport_conda("pydot", "pydot")
graph = pydot.Dot("Reactions", graph_type="digraph", bgcolor="white", layout="dot", splines="line")
for (species, rates) in species_ratevars
node = pydot.Node(species, label=species)
graph.add_node(node)
end
dom = PB.get_domain(model, domainname)
rate_idx = 1
for rj in dom.reactions
rvs = PB.get_rate_stoichiometry(rj)
if !isnothing(rvs)
for (ratevarname, processname, stoichvec) in rvs
if rate_totals[ratevarname] >= rate_thresh
rate_norm= rate_totals[ratevarname]/rate_max
reactants = []
products = []
for (speciesname, stoich) in stoichvec
if stoich < 0
push!(reactants, speciesname)
end
if stoich > 0
push!(products, speciesname)
end
end
for r in reactants
for p in products
edge = pydot.Edge(r, p, color="blue", weight=Int(floor(100*rate_norm)), penwidth=max(1.0, 20.0*rate_norm))
graph.add_edge(edge)
end
end
rate_idx += 1
end
end
end
end
return graph
end
=#

"""
test_pydot()

Test python pydot package and graphviz command-line tools installed and working
"""
function test_pydot()
pydot = pyimport_conda("pydot", "pydot")
graph = pydot.Dot("my_graph", graph_type="graph", bgcolor="white")
my_node = pydot.Node("a", label="Foo")
graph.add_node(my_node)
graph.add_node(pydot.Node("b", shape="circle"))
my_edge = pydot.Edge("a", "b", color="blue")
graph.add_edge(my_edge)

output_graphviz_svg = graph.create_svg()
display("image/svg+xml", output_graphviz_svg)

return graph
function __init__()
# If PyCall is available, include additional functions using Python pydot.
Requires.@require PyCall="438e738f-606a-5dbb-bf0a-cddfbfd45ab0" include("ReactionNetworkVis.jl")
end

end # module
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