Remove loading of images

Author: AleMorales

docs/src/howto/Materials.md

@@ -89,22 +89,16 @@ should scale with the absorptance of the tile.
 α = 1.0 .- τ .- ρ
 pl = scatter(α, irradiance, ylabel = "Irradiance", xlabel = "Absorptance", legend = false)
 Plots.abline!(pl, 1.0, 0.0)
-savefig(pl, "absorptance_vs_irradiance.png") ## hide
 ```
 
-![](absorptance_vs_irradiance.png)
-
 Finally, let's scale the colors of each triangle by the irradiance absorbed by each triangle
 assuming different shades of green and let's visualize them by turning of the shader in the
 renderer to get the exact colors we specify.
 
 ```julia
 tile.colors = RGB.(0.0, α, 0.0)
 sc = Scene(g)
-pl = render(sc, wireframe = true, shading = GLMakie.NoShading)
-GLMakie.save("tile.png", pl) ## hide
-
-#![](tile.png)
+render(sc, wireframe = true, shading = GLMakie.NoShading)
 ```
 
 ---

docs/src/tutorials/from_tree_forest/forest.md

@@ -181,21 +181,15 @@ relative growth rate:
 ```julia
 growths = rand(LogNormal(-2, 0.3), 10, 10)
 histogram(vec(growths))
-savefig("growths.png") ## hide
 ```
 
-![](growths.png)
-
 And for the budbreak parameter:
 
 ```julia
 budbreaks = rand(Beta(2.0, 10), 10, 10)
 histogram(vec(budbreaks))
-savefig("budbreaks.png") ## hide
 ```
 
-![](budbreaks.png)
-
 Now we can create our forest by calling the `create_tree` function we defined earlier
 with the correct inputs per tree:
 
@@ -226,23 +220,17 @@ And we can render the forest with the function `render` as in the binary tree
 example but passing the whole forest at once
 
 ```julia
-pl = render(Scene(newforest))
-GLMakie.save("newforest1.png", pl) ## hide
+render(Scene(newforest))
 ```
 
-![](newforest1.png)
-
 If we iterate 4 more iterations we will start seeing the different individuals
 diverging in size due to the differences in growth rates
 
 ```julia
 newforest = [simulate(tree, getInternode, 15) for tree in newforest];
-pl = render(Scene(newforest))
-GLMakie.save("newforest2.png", pl) ## hide
+render(Scene(newforest))
 ```
 
-![](newforest2.png)
-
 ## Multithreaded simulation
 
 In the previous section, the simulation of growth was done sequentially, one tree
@@ -258,12 +246,9 @@ newforest = deepcopy(forest)
 @threads for i in 1:length(forest)
     newforest[i] = simulate(forest[i], getInternode, 6)
 end
-pl = render(Scene(newforest, parallel = true))
-GLMakie.save("newforest3.png", pl) ## hide
+render(Scene(newforest, parallel = true))
 ```
 
-![](newforest3.png)
-
 An alternative way to perform the simulation is to have an outer loop for each timestep and an internal loop over the different trees. Although this approach is not required for this simple model, most FSP models will probably need such a scheme as growth of each individual plant will depend on competition for resources with neighbouring plants. In this case, this approach would look as follows:
 
 ```julia
@@ -273,12 +258,9 @@ for step in 1:15
         newforest[i] = simulate(newforest[i], getInternode, 1)
     end
 end
-pl = render(Scene(newforest, parallel = true))
-GLMakie.save("newforest4.png", pl) ## hide
+render(Scene(newforest, parallel = true))
 ```
 
-![](newforest4.png)
-
 # Customizing the scene
 
 Here we are going to customize the scene of our simulation by adding a horizontal tile represting soil and
@@ -318,12 +300,9 @@ Howver, it may be distracting for the visualization. It turns out that we can tu
 `axes = false`:
 
 ```julia
-pl = render(scene, axes = false)
-GLMakie.save("newforest5.png", pl) ## hide
+render(scene, axes = false)
 ```
 
-![](newforest5.png)
-
 We may also want to save a screenshot of the scene. For this, we need to store the output of the `render` function.
 We can then resize the window rendering the scene, move around, zoom, etc. When we have a perspective that we like,
 we can run the `save_scene` function on the object returned from `render`. The argument `resolution` can be adjusted in both

docs/src/tutorials/from_tree_forest/growthforest.md

@@ -245,17 +245,11 @@ sink_strength(leaf, vars) = leaf.age > vars.leaf_expansion ? 0.0 :
                             pdf(leaf.sink, leaf.age/vars.leaf_expansion)/100.0
 plot(0:1:50, x -> sink_strength(TreeTypes.Leaf(age = x), TreeTypes.treeparams()),
      xlabel = "Age", ylabel = "Sink strength", label = "Leaf")
-savefig("leaf_sink_strength.png") ## hide
-
-#![](leaf_sink_strength.png)
 
 sink_strength(int) = pdf(int.sink, int.age)
 plot!(0:1:50, x -> sink_strength(TreeTypes.Internode(age = x)), label = "Internode")
-savefig("internode_sink_strength.png") ## hide
 ```
 
-#![](internode_sink_strength.png)
-
 Now we need a function that updates the biomass of the tree, allocates it to the
 different organs and updates the dimensions of said organs. For simplicity,
 we create the functions `leaves()` and `internodes()` that will apply the queries
@@ -363,13 +357,9 @@ orientation and RGR:
 ```julia
 RGRs = rand(Normal(0.3,0.01), 10, 10)
 histogram(vec(RGRs))
-savefig("RGRs.png") ## hide
-#![](RGRs.png)
 
 orientations = [rand()*360.0 for i = 1:2.0:20.0, j = 1:2.0:20.0]
 histogram(vec(orientations))
-savefig("orientations.png") ## hide
-#![](orientations.png)
 
 origins = [Vec(i,j,0) for i = 1:2.0:20.0, j = 1:2.0:20.0];
 nothing #hide
@@ -419,12 +409,9 @@ 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
 soil = Scene(Graph(axiom = soil_graph));
-pl = render(soil, axes = false)
-GLMakie.save("soil.png", pl) ## hide
+render(soil, axes = false)
 ```
 
-![](soil.png)
-
 And the following function renders the entire scene (notice that we need to
 use `display()` to force the rendering of the scene when called within a loop
 or a function):
@@ -464,12 +451,9 @@ render_forest(forest, soil)
 for i in 1:50
     daily_step!(forest)
 end
-pl = render_forest(forest, soil)
-GLMakie.save("forest.png", pl) ## hide
+render_forest(forest, soil)
 ```
 
-![](forest.png)
-
 And compute the leaf area index:
 
 ```julia

docs/src/tutorials/from_tree_forest/raytracedforest.md

@@ -391,19 +391,11 @@ sink_strength(leaf, vars) = leaf.age > vars.leaf_expansion ? 0.0 :
                             pdf(leaf.sink, leaf.age/vars.leaf_expansion)/100.0
 plot(0:1:50, x -> sink_strength(TreeTypes.Leaf(age = x), TreeTypes.treeparams()),
      xlabel = "Age", ylabel = "Sink strength", label = "Leaf")
-savefig("leaf_sink_strength.png") ## hide
-```
-
-![](leaf_sink_strength.png)
 
-```julia
 sink_strength(int) = pdf(int.sink, int.age)
 plot!(0:1:50, x -> sink_strength(TreeTypes.Leaf(age = x)), label = "Internode")
-savefig("internode_sink_strength.png") ## hide
 ```
 
-![](internode_sink_strength.png)
-
 Now we need a function that updates the biomass of the tree, allocates it to the
 different organs and updates the dimensions of said organs. For simplicity,
 we create the functions `leaves()` and `internodes()` that will apply the queries
@@ -514,12 +506,10 @@ orientation and RUE:
 ```julia
 RUEs = rand(Normal(1.5,0.2), 10, 10)
 histogram(vec(RUEs))
-savefig("RUEs.png") ## hide
-#![](RUEs.png)
+
 orientations = [rand()*360.0 for i = 1:2.0:20.0, j = 1:2.0:20.0]
 histogram(vec(orientations))
-savefig("orientations.png") ## hide
-#![](orientations.png)
+
 origins = [Vec(i,j,0) for i = 1:2.0:20.0, j = 1:2.0:20.0];
 nothing #hide
 ```
@@ -568,12 +558,9 @@ 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
 soil = Scene(Graph(axiom = soil_graph));
-pl = render(soil, axes = false)
-GLMakie.save("soil.png", pl) ## hide
+render(soil, axes = false)
 ```
 
-![](soil.png)
-
 And the following function renders the entire scene (notice that we need to
 use `display()` to force the rendering of the scene when called within a loop
 or a function):
@@ -598,17 +585,11 @@ for i in 1:20
     println("Day $i")
     daily_step!(forest, i + start)
     if mod(i, 5) == 0
-        pl = render_forest(forest, soil)
-        GLMakie.save("forest$i.png", pl) ## hide
+        render_forest(forest, soil)
     end
 end
 ```
 
-![](forest5.png)
-![](forest10.png)
-![](forest15.png)
-![](forest20.png)
-
 ---
 
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