Update API of tutorials

Author: AleMorales

docs/src/tutorials/from_tree_forest/forest.md

@@ -5,7 +5,7 @@ Alejandro Morales and Ana Ernst
 Centre for Crop Systems Analysis - Wageningen University
 
 > ## TL;DR
-> Similar in functionality to [Tree](https://virtualplantlab.com/dev/tutorials/from_tree_forest/tree/) tutorial with separate graphs for each tree 
+> Similar in functionality to [Tree](https://virtualplantlab.com/dev/tutorials/from_tree_forest/tree/) tutorial with separate graphs for each tree
 > - Modify tree parameters for each tree
 > - Multithreaded simulation (grow trees in parallel)
 > - Scene customization (e.g., add soil)
@@ -61,7 +61,7 @@ function VirtualPlantLab.feed!(turtle::Turtle, i::TreeTypes.Internode, data)
     # Rotate turtle around the head to implement elliptical phyllotaxis
     rh!(turtle, data.phyllotaxis)
     HollowCylinder!(turtle, length = i.length, height = i.length/15, width = i.length/15,
-                move = true, color = RGB(0.5,0.4,0.0))
+                move = true, colors = RGB(0.5,0.4,0.0))
     return nothing
 end
 ````
@@ -74,7 +74,7 @@ function VirtualPlantLab.feed!(turtle::Turtle, l::TreeTypes.Leaf, data)
     ra!(turtle, -data.leaf_angle)
     # Generate the leaf
     Ellipse!(turtle, length = l.length, width = l.width, move = false,
-             color = RGB(0.2,0.6,0.2))
+             colors = RGB(0.2,0.6,0.2))
     # Rotate turtle back to original direction
     ra!(turtle, data.leaf_angle)
     return nothing
@@ -293,7 +293,7 @@ VirtualPlantLab.translate!(soil, Vec(0.0, 10.5, 0.0))
 We can now add the `soil` to the `scene` object with the `add!` function.
 
 ````julia
-VirtualPlantLab.add!(scene, mesh = soil, color = RGB(1,1,0))
+VirtualPlantLab.add!(scene, mesh = soil, colors = RGB(1,1,0))
 ````
 
 We can now render the scene that combines the random forest of binary trees and a yellow soil. Notice that
@@ -321,4 +321,3 @@ export_scene(scene = output, filename = "nice_trees.png")
 ---
 
 *This page was generated using [Literate.jl](https://github.com/fredrikekre/Literate.jl).*
-

docs/src/tutorials/from_tree_forest/growthforest.md

@@ -8,10 +8,10 @@ Centre for Crop Systems Analysis - Wageningen University
 > Now we want to implement a more extended functionality of our [Forest]()!
 > - Growth rules, based on information stored in organs (dimensions, carbon assimilation)
 > - Update dimensions in function of assimilation
-> - Compute sink strength 
+> - Compute sink strength
 > - Merge Scenes
 > - Generate forest on grid and retrieve canopy-level data (e.g., LAI)
-> 
+>
 
 In this example we extend the binary forest example to have more complex, time-
 dependent development and growth based on carbon allocation. For simplicity, the
@@ -111,7 +111,7 @@ function VirtualPlantLab.feed!(turtle::Turtle, i::TreeTypes.Internode, vars)
     # Rotate turtle around the head to implement elliptical phyllotaxis
     rh!(turtle, vars.phyllotaxis)
     HollowCylinder!(turtle, length = i.length, height = i.width, width = i.width,
-                move = true, color = RGB(0.5,0.4,0.0))
+                move = true, colors = RGB(0.5,0.4,0.0))
     return nothing
 end
 
@@ -121,7 +121,7 @@ function VirtualPlantLab.feed!(turtle::Turtle, l::TreeTypes.Leaf, vars)
     ra!(turtle, -vars.leaf_angle)
     # Generate the leaf
     Ellipse!(turtle, length = l.length, width = l.width, move = false,
-             color = RGB(0.2,0.6,0.2))
+             colors = RGB(0.2,0.6,0.2))
     # Rotate turtle back to original direction
     ra!(turtle, vars.leaf_angle)
     return nothing
@@ -400,7 +400,7 @@ Base.@kwdef struct Soil <: VirtualPlantLab.Node
     width::Float64
 end
 function VirtualPlantLab.feed!(turtle::Turtle, s::Soil, vars)
-    Rectangle!(turtle, length = s.length, width = s.width, color = RGB(255/255, 236/255, 179/255))
+    Rectangle!(turtle, length = s.length, width = s.width, colors = RGB(255/255, 236/255, 179/255))
 end
 soil_graph = RA(-90.0) + T(Vec(0.0, 10.0, 0.0)) + # Moves into position
              Soil(length = 20.0, width = 20.0) # Draws the soil tile
@@ -459,4 +459,3 @@ get_LAI(forest)
 ---
 
 *This page was generated using [Literate.jl](https://github.com/fredrikekre/Literate.jl).*
-

docs/src/tutorials/from_tree_forest/raytracedforest.md

@@ -10,8 +10,8 @@ Centre for Crop Systems Analysis - Wageningen University
 > - Create sky for specific conditions and locations using [SkyDomes](https://virtualplantlab.com/dev/VPLVerse/SkyDomes/)
 > - Layer different types of radiation in sky domes (e.g., direct and diffuse)
 > - Combine graph and sky with a ray-tracer
-> - Compute growth and biomass production according to PAR interception and RUE 
-> 
+> - Compute growth and biomass production according to PAR interception and RUE
+>
 
 In this example we extend the [Growth Forest](https://virtualplantlab.com/dev/tutorials/from_tree_forest/growthforest/) model to include PAR interception and radiation use efficiency to compute the daily growth rate.
 
@@ -107,7 +107,7 @@ function VirtualPlantLab.feed!(turtle::Turtle, i::TreeTypes.Internode, data)
     # Rotate turtle around the head to implement elliptical phyllotaxis
     rh!(turtle, data.phyllotaxis)
     HollowCylinder!(turtle, length = i.length, height = i.width, width = i.width,
-                move = true, color = RGB(0.5,0.4,0.0), material = i.material)
+                move = true, colors = RGB(0.5,0.4,0.0), materials = i.material)
     return nothing
 end
 
@@ -117,7 +117,7 @@ function VirtualPlantLab.feed!(turtle::Turtle, l::TreeTypes.Leaf, data)
     ra!(turtle, -data.leaf_angle)
     # Generate the leaf
     Ellipse!(turtle, length = l.length, width = l.width, move = false,
-             color = RGB(0.2,0.6,0.2), material = l.material)
+             colors = RGB(0.2,0.6,0.2), materials = l.material)
     # Rotate turtle back to original direction
     ra!(turtle, data.leaf_angle)
     return nothing
@@ -227,7 +227,7 @@ function create_scene(forest)
     # Add a soil surface
     soil = create_soil()
     soil_material = Lambertian(τ = 0.0, ρ = 0.21)
-    add!(scene, mesh = soil, material = soil_material)
+    add!(scene, mesh = soil, materials = soil_material)
     # Return the scene
     return scene
 end
@@ -558,7 +558,7 @@ Base.@kwdef struct Soil <: VirtualPlantLab.Node
     width::Float64
 end
 function VirtualPlantLab.feed!(turtle::Turtle, s::Soil, data)
-    Rectangle!(turtle, length = s.length, width = s.width, color = RGB(255/255, 236/255, 179/255))
+    Rectangle!(turtle, length = s.length, width = s.width, colors = RGB(255/255, 236/255, 179/255))
 end
 soil_graph = RA(-90.0) + T(Vec(0.0, 10.0, 0.0)) + ## Moves into position
              Soil(length = 20.0, width = 20.0) ## Draws the soil tile
@@ -598,4 +598,3 @@ end
 ---
 
 *This page was generated using [Literate.jl](https://github.com/fredrikekre/Literate.jl).*
-

docs/src/tutorials/from_tree_forest/tree.md

@@ -73,7 +73,7 @@ function VirtualPlantLab.feed!(turtle::Turtle, i::TreeTypes.Internode, vars)
     # Rotate turtle around the head to implement elliptical phyllotaxis
     rh!(turtle, vars.phyllotaxis)
     HollowCylinder!(turtle, length = i.length, height = i.length/15, width = i.length/15,
-                move = true, color = RGB(0.5,0.4,0.0))
+                move = true, colors = RGB(0.5,0.4,0.0))
     return nothing
 end
 
@@ -83,7 +83,7 @@ function VirtualPlantLab.feed!(turtle::Turtle, l::TreeTypes.Leaf, vars)
     ra!(turtle, -vars.leaf_angle)
     # Generate the leaf
     Ellipse!(turtle, length = l.length, width = l.width, move = false,
-             color = RGB(0.2,0.6,0.2))
+             colors = RGB(0.2,0.6,0.2))
     # Rotate turtle back to original direction
     ra!(turtle, vars.leaf_angle)
     return nothing
@@ -202,4 +202,3 @@ render(Scene(newtree))
 ---
 
 *This page was generated using [Literate.jl](https://github.com/fredrikekre/Literate.jl).*
-

docs/src/tutorials/getting_started/snowflakes.md

@@ -7,7 +7,7 @@ Centre for Crop Systems Analysis - Wageningen University
 > ### TL;DR
 > - Define parameter for graph nodes
 > - Define methods for VirtualPlantLab.feed! functions
-> - Create [Scenes](https://virtualplantlab.com/dev/manual/Geometry/Turtle/#Scenes) 
+> - Create [Scenes](https://virtualplantlab.com/dev/manual/Geometry/Turtle/#Scenes)
 > - [Visualization](https://virtualplantlab.com/dev/manual/Visualization/) of 'Graph' with render()
 >
 
@@ -118,7 +118,7 @@ to generate random colors.
 function VirtualPlantLab.feed!(turtle::Turtle, e::sn.E, vars)
     HollowCylinder!(turtle, length = e.length, width = e.length/10,
                     height = e.length/10, move = true,
-                    color = RGB(rand(), rand(), rand()))
+                    colors = RGB(rand(), rand(), rand()))
     return nothing
 end
 ````
@@ -215,4 +215,3 @@ render(Scene(Cesaro), axes = false)
 ---
 
 *This page was generated using [Literate.jl](https://github.com/fredrikekre/Literate.jl).*
-