Add graph

EarthSciML · Jul 19, 2023 · 992f6c5 · 992f6c5
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commit 992f6c5
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Showing 3 changed files with 31 additions and 14 deletions.
diff --git a/.github/workflows/deploy.yml b/.github/workflows/deploy.yml
@@ -23,7 +23,7 @@ jobs:
     - name: Install Julia
       uses: julia-actions/setup-julia@v1
       with:
-        version: 1.5
+        version: 1.9
     # NOTE
     #   The steps below ensure that NodeJS and Franklin are loaded then it
     #   installs highlight.js which is needed for the prerendering step

diff --git a/Project.toml b/Project.toml
@@ -1,4 +1,5 @@
 [deps]
+CairoMakie = "13f3f980-e62b-5c42-98c6-ff1f3baf88f0"
 Dates = "ade2ca70-3891-5945-98fb-dc099432e06a"
 DifferentialEquations = "0c46a032-eb83-5123-abaf-570d42b7fbaa"
 Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f"
@@ -7,8 +8,10 @@ EarthSciData = "a293c155-435f-439d-9c11-a083b6b47337"
 EarthSciMLBase = "e53f1632-a13c-4728-9402-0c66d48804b0"
 Franklin = "713c75ef-9fc9-4b05-94a9-213340da978e"
 GasChem = "58070593-4751-4c87-a5d1-63807d11d76c"
+GraphMakie = "1ecd5474-83a3-4783-bb4f-06765db800d2"
 LaTeXStrings = "b964fa9f-0449-5b57-a5c2-d3ea65f4040f"
 Latexify = "23fbe1c1-3f47-55db-b15f-69d7ec21a316"
+MetaGraphsNext = "fa8bd995-216d-47f1-8a91-f3b68fbeb377"
 MethodOfLines = "94925ecb-adb7-4558-8ed8-f975c56a0bf4"
 ModelingToolkit = "961ee093-0014-501f-94e3-6117800e7a78"
 NodeJS = "2bd173c7-0d6d-553b-b6af-13a54713934c"

diff --git a/tutorials/example.md b/tutorials/example.md
@@ -18,12 +18,13 @@ tags = ["syntax", "code"]
 using EarthSciData, EarthSciMLBase, GasChem,
     DomainSets, ModelingToolkit, MethodOfLines, 
     DifferentialEquations, Dates, Distributions,
-    Latexify, Plots, SciMLBase
+    Latexify, Plots, SciMLBase,
+    CairoMakie, GraphMakie, MetaGraphsNext
 
 @parameters t lev lon lat
 model = SuperFast(t)
 ls = latexify(model.rxn_sys) # TODO: Change to model.rxn_sys
-print(replace(ls.s, "\require{mhchem}" => "")) # hide
+print(replace(ls.s, raw"\require{mhchem}" => "")) # hide
 ```
 
 This is what `ls` looks like:
@@ -46,11 +47,13 @@ prob = ODEProblem(structural_simplify(get_mtk(model_ode)), [], (start, finish),
 sol = solve(prob, TRBDF2(), saveat=1800.0)
 
 # Plot result.
-ticks = Dates.datetime2unix.([Dates.DateTime(2022, 5, 1), Dates.DateTime(2022, 5, 2), Dates.DateTime(2022, 5, 3)])
+ticks = Dates.datetime2unix.([Dates.DateTime(2022, 5, 1), Dates.DateTime(2022, 5, 2), 
+    Dates.DateTime(2022, 5, 3)])
 tickstrings = Dates.format.(Dates.unix2datetime.(ticks), "m-d-yy")
-plot(sol,ylims=(0,15),xlabel="Date", ylabel="Concentration (ppb)", ylabelfontsize=9, xlabelfontsize=9, 
+Plots.plot(sol,ylims=(0,30),xlabel="Date", ylabel="Concentration (ppb)", 
+    ylabelfontsize=9, xlabelfontsize=9, 
     xticks=(ticks, tickstrings), legend=:outertopright, size=(500, 310))
-savefig(joinpath(@OUTPUT, "ode.svg")) # hide
+Plots.savefig(joinpath(@OUTPUT, "ode.svg")) # hide
 ```
 
 \textoutput{./code/ex2}
@@ -94,7 +97,7 @@ SciMLBase.observed(sol::SciMLBase.AbstractTimeseriesSolution, sym, i::Colon) = z
 \textoutput{./code/ex4}
 
 ## Figure 4
-```julia:./code/ex5
+```julia:./code/ex5a
 domain = DomainInfo(
     partialderivatives_lonlat2xymeters,
     constIC(1.0f0, t ∈ Interval(start, finish)),
@@ -105,12 +108,23 @@ geos = GEOSFP("0.25x0.3125_NA", t; coord_defaults = Dict(:lat => 34.0, :lev => 1
 model = SuperFast(t) + FastJX(t) + domain +
     Emissions(t, -118.2, 0.2)+ Advection() + geos
 
+g = graph(model)
+
+f, ax, p = graphplot(g; ilabels=labels(g))
+hidedecorations!(ax); hidespines!(ax); ax.aspect = DataAspect()
+
+save(joinpath(@OUTPUT, "graph.svg"), f) # hide
+```
+\output{./code/ex5a}
+\fig{graph}
+
+```julia:./code/ex5b
 discretization = MOLFiniteDifference([lon => 50], t, approx_order=2)
 prob = discretize(get_mtk(model), discretization)
 sol = solve(prob, TRBDF2(), saveat=3600.0)
 ```
 
-\textoutput{./code/ex5}
+\output{./code/ex5b}
 
 ## Supplemental plotting code
 ```julia:./code/ex6
@@ -124,20 +138,20 @@ sol_no = sol[superfast₊NO(t, lon)]
 sol_no2 = sol[superfast₊NO2(t, lon)]
 
 using LaTeXStrings
-plot(
-    heatmap(discrete_t, discrete_lon[1:end], sol_isop[:, 1:end]', 
+Plots.plot(
+    Plots.heatmap(discrete_t, discrete_lon[1:end], sol_isop[:, 1:end]', 
         xticks=(ticks, tickstrings), 
         ylabel="Longitude (°)", title="Isoprene", titlefontsize=12,
         margin=0Plots.mm,
         size=(600, 400), dpi=300),
-    heatmap(discrete_t, discrete_lon[1:end], sol_no[:, 1:end]', 
+    Plots.heatmap(discrete_t, discrete_lon[1:end], sol_no[:, 1:end]', 
         xticks=(ticks, tickstrings), title="NO", titlefontsize=12),
-    heatmap(discrete_t, discrete_lon[1:end], sol_no2[:, 1:end]', 
+    Plots.heatmap(discrete_t, discrete_lon[1:end], sol_no2[:, 1:end]', 
         xticks=(ticks, tickstrings), xlabel="Date", title=L"\textrm{NO_2}"),
-    heatmap(discrete_t, discrete_lon[1:end], sol_o3[:, 1:end]',colorbar_title="Concentration (ppb)",
+    Plots.heatmap(discrete_t, discrete_lon[1:end], sol_o3[:, 1:end]',colorbar_title="Concentration (ppb)",
         xticks=(ticks, tickstrings), title=L"\textrm{O_3}", titlefontsize=12),
 )
-savefig(joinpath(@OUTPUT, "pde.svg"))
+Plots.savefig(joinpath(@OUTPUT, "pde.svg"))
 ```
 
 \textoutput{./code/ex6}