Run JuliaFormatter.format()

README.md

@@ -175,7 +175,7 @@ CellML specification allows for models spanning multiple XML files. In these mod
 ```julia
 ml = CellModel("models/noble_1962/Noble_1962.cellml")
 prob = ODEProblem(ml, tspan)
-sol = solve(prob, dtmax=0.5)
+sol = solve(prob, dtmax = 0.5)
 ```
 
 Note that the syntax is exactly the same as before. However, the list of the imported files are printed during `CellModel` generation:
@@ -195,7 +195,7 @@ Note that the syntax is exactly the same as before. However, the list of the imp
 Same as before, we can plot the output as
 
 ```julia
-plot(sol, idxs=2)
+plot(sol, idxs = 2)
 ```
 
 ![](docs/src/assets/noble_1962.png)

docs/make.jl

@@ -4,30 +4,30 @@ cp("./docs/Manifest.toml", "./docs/src/assets/Manifest.toml", force = true)
 cp("./docs/Project.toml", "./docs/src/assets/Project.toml", force = true)
 
 mathengine = MathJax3(Dict(:loader => Dict("load" => ["[tex]/require", "[tex]/mathtools"]),
-                           :tex => Dict("inlineMath" => [["\$", "\$"], ["\\(", "\\)"]],
-                                        "packages" => [
-                                            "base",
-                                            "ams",
-                                            "autoload",
-                                            "mathtools",
-                                            "require",
-                                        ])))
+    :tex => Dict("inlineMath" => [["\$", "\$"], ["\\(", "\\)"]],
+        "packages" => [
+            "base",
+            "ams",
+            "autoload",
+            "mathtools",
+            "require"
+        ])))
 
 makedocs(sitename = "CellMLToolkit.jl",
-         authors = "Chris Rackauckas",
-         modules = Module[],
-         clean = true, doctest = false, linkcheck = true,
-         linkcheck_ignore = [
-             "https://journals.physiology.org/doi/full/10.1152/ajpheart.00794.2003",
-         ],
-         format = Documenter.HTML(;assets = ["assets/favicon.ico"],
-                                  mathengine,
-                                  canonical = "https://docs.sciml.ai/CellMLToolkit/stable/",
-                                  prettyurls = (get(ENV, "CI", nothing) == "true")),
-         pages = [
-             "Home" => "index.md",
-             "Tutorial" => "tutorial.md",
-         ])
+    authors = "Chris Rackauckas",
+    modules = Module[],
+    clean = true, doctest = false, linkcheck = true,
+    linkcheck_ignore = [
+        "https://journals.physiology.org/doi/full/10.1152/ajpheart.00794.2003"
+    ],
+    format = Documenter.HTML(; assets = ["assets/favicon.ico"],
+        mathengine,
+        canonical = "https://docs.sciml.ai/CellMLToolkit/stable/",
+        prettyurls = (get(ENV, "CI", nothing) == "true")),
+    pages = [
+        "Home" => "index.md",
+        "Tutorial" => "tutorial.md"
+    ])
 
 deploydocs(repo = "github.com/SciML/CellMLToolkit.jl.git";
-           push_preview = true)
+    push_preview = true)

docs/src/index.md

@@ -106,4 +106,4 @@ file and the
 [project]($link_project)
 file.
 """)
-```
+```

src/CellMLToolkit.jl

@@ -45,8 +45,8 @@ import ModelingToolkit.ODEProblem
     ODEProblem constructs an ODEProblem from a CellModel
 """
 function ODEProblem(ml::CellModel, tspan;
-                    jac = false, level = 1, p = last.(list_params(ml)),
-                    u0 = last.(list_states(ml)))
+        jac = false, level = 1, p = last.(list_params(ml)),
+        u0 = last.(list_states(ml)))
     ODEProblem(ml.sys, u0, tspan, p; jac = jac)
 end
 

src/accessors.jl

@@ -138,15 +138,17 @@ end
 function list_encapsulation(doc, comp)
     name = string(nameof(comp))
     ns = cellml_ns(doc)
-    groups = parentnode.(findall("//x:group/x:relationship_ref[@relationship='encapsulation']",
-                                 root(doc), ["x" => ns]))
+    groups = parentnode.(findall(
+        "//x:group/x:relationship_ref[@relationship='encapsulation']",
+        root(doc), ["x" => ns]))
     if isempty(groups)  # CellML ver 2.0
-        return findall("//x:encapsulation//x:component_ref[@component='$name']//x:component_ref",
-                       root(doc), ["x" => ns])
+        return findall(
+            "//x:encapsulation//x:component_ref[@component='$name']//x:component_ref",
+            root(doc), ["x" => ns])
     else                # CellML ver 1.0 and 1.1
         for g in groups
             nodes = findall(".//x:component_ref[@component='$name']//x:component_ref", g,
-                            ["x" => ns])
+                ["x" => ns])
             if !isempty(nodes)
                 return nodes
             end

src/components.jl

@@ -227,9 +227,9 @@ function process_components(doc::Document; simplify = true)
     post_sub = post_substitution(doc, systems)
 
     sys = ODESystem(translate_connections(doc, systems, class),
-                    get_ivₚ(doc),
-                    systems = collect(values(systems)),
-                    name = gensym(:cellml))
+        get_ivₚ(doc),
+        systems = collect(values(systems)),
+        name = gensym(:cellml))
 
     if simplify
         sys = structural_simplify(sys)
@@ -252,7 +252,7 @@ end
 """
 function subsystems(doc::Document, class)
     Dict{Symbol, ODESystem}(to_symbol(comp) => process_component(doc, comp, class)
-                            for comp in components(doc))
+    for comp in components(doc))
 end
 
 """