Update API and Tutorials for better workflow

Author: AleMorales

Project.toml

@@ -9,6 +9,7 @@ PlantGeomPrimitives = "7eef3cc5-4580-4ff0-8f6f-933507db6664"
 PlantGeomTurtle = "7d6e2781-1c99-4c66-97ec-106669f3e96e"
 PlantGraphs = "615ad455-9aac-4340-9247-71ef610f781a"
 PlantRayTracer = "78485975-e4aa-407d-b3bb-ded5a4265d05"
+PlantSimEngine = "9a576370-710b-4269-adf9-4f603a9c6423"
 PlantViz = "358bd95d-d12c-439f-94b7-04b17e500c7f"
 SkyDomes = "1838625c-7cf7-40c6-898b-904883e4b556"
 
@@ -18,6 +19,7 @@ PlantGeomPrimitives = "0.0.2"
 PlantGeomTurtle = "0.0.3"
 PlantGraphs = "0.0.2"
 PlantRayTracer = "0.0.4"
+PlantSimEngine = "^0.8"
 PlantViz = "0.0.4"
 SkyDomes = "0.1.3"
 julia = "1.9"

docs/Project.toml

@@ -5,6 +5,7 @@ PlantGeomPrimitives = "7eef3cc5-4580-4ff0-8f6f-933507db6664"
 PlantGeomTurtle = "7d6e2781-1c99-4c66-97ec-106669f3e96e"
 PlantGraphs = "615ad455-9aac-4340-9247-71ef610f781a"
 PlantRayTracer = "78485975-e4aa-407d-b3bb-ded5a4265d05"
+PlantSimEngine = "9a576370-710b-4269-adf9-4f603a9c6423"
 PlantViz = "358bd95d-d12c-439f-94b7-04b17e500c7f"
 SkyDomes = "1838625c-7cf7-40c6-898b-904883e4b556"
 VPLDocs = "19246b20-85cd-4f94-a989-28bb6828320f"

docs/make.jl

@@ -1,10 +1,10 @@
 using VPLDocs
 using Documenter
-import PlantGraphs, PlantGeomPrimitives, PlantGeomTurtle, PlantRayTracer, PlantViz, SkyDomes, Ecophys
+import PlantGraphs, PlantGeomPrimitives, PlantGeomTurtle, PlantRayTracer, PlantViz, SkyDomes, Ecophys, PlantSimEngine
 
 makedocs(;
     doctest = false,
-    modules=[VPLDocs, PlantGraphs, PlantGeomPrimitives, PlantGeomTurtle, PlantRayTracer, PlantViz, SkyDomes, Ecophys],
+    modules = [VPLDocs, PlantGraphs, PlantGeomPrimitives, PlantGeomTurtle, PlantRayTracer, PlantViz, SkyDomes, Ecophys, PlantSimEngine],
     authors="Alejandro Morales <alejandro.moralessierra@wur.nl> and contributors",
     repo="https://github.com/VirtualPlantLab/VPLDocs/blob/{commit}{path}#{line}",
     sitename="Virtual Plant Laboratory",
@@ -26,14 +26,14 @@ makedocs(;
             "3D visualization" => "manual/Visualization.md"
         ],
         "Tutorials" => [
-            "Algae growth" => "tutorials/Algae/Algae.md",
-            "The Koch snowflake" => "tutorials/Snowflakes/Snowflakes.md",
-            "Tree" => "tutorials/Tree/Tree.md",
-            "Forest" => "tutorials/Forest/Forest.md",
-            "Growth forest" => "tutorials/GrowthForest/GrowthForest.md",
-            "Ray-traced forest" => "tutorials/RaytracedForest/RaytracedForest.md",
-            "Context sensitive rules" => "tutorials/Context/Context.md",
-            "Relational queries" => "tutorials/RelationalQueries/RelationalQueries.md"
+            "Algae growth" => "tutorials/algae.md",
+            "The Koch snowflake" => "tutorials/snowflakes.md",
+            "Tree" => "tutorials/tree.md",
+            "Forest" => "tutorials/forest.md",
+            "Growth forest" => "tutorials/growthforest.md",
+            "Ray-traced forest" => "tutorials/raytracedforest.md",
+            "Context sensitive rules" => "tutorials/context.md",
+            "Relational queries" => "tutorials/relationalqueries.md"
         ],
         "How-to guides" => [
             "Setting up a grid cloner" => "howto/GridCloner.md"
@@ -47,18 +47,18 @@ makedocs(;
         ],
         "VPLVerse" => [
             "SkyDomes" => [
-                "SkyDomes package" => "SkyDomes/index.md",
-                "SkyDomes API" => "SkyDomes/API.md"
+                "SkyDomes package" => "VPLVerse/SkyDomes/index.md",
+                "SkyDomes API" => "VPLVerse/SkyDomes/API.md"
             ],
             "Ecophys" => [
-                "Ecophys package" => "Ecophys/index.md",
-                "Photosynthesis API" => "Ecophys/photosynthesis.md"
+                "Ecophys package" => "VPLVerse/Ecophys/index.md",
+                "Photosynthesis API" => "VPLVerse/Ecophys/photosynthesis.md"
             ],
             "PlantSimEngine" => [
-                "PlantSimEngine package" => "PlantSimEngine/index.md"
+                "PlantSimEngine package" => "VPLVerse/PlantSimEngine/index.md"
             ],
             "PlantBioPhysics" => [
-                "PlantBioPhysics package" => "PlantBioPhysics/index.md"
+                "PlantBioPhysics package" => "VPLVerse/PlantBioPhysics/index.md"
             ]
         ],
         "Developers" => [

docs/src/Ecophys/photosynthesis.md

@@ -0,0 +1,24 @@
+
+# Photosynthesis
+
+```@meta
+CurrentModule = Ecophys.Photosynthesis
+```
+
+## Public API
+
+```@autodocs
+Modules = [Photosynthesis]
+Public = true
+Private = false
+```
+
+## Private
+
+Private functions, types or constants from `Photosynthesis`. These are not exported, so you need to prefix the function name with `PlantGeomPrimitives.` to access them. Also bear in mind that these are not part of the public API, so they may change without notice.
+
+```@autodocs
+Modules = [Photosynthesis]
+Public = false
+Private = true
+```

docs/src/PlantSimEngine/index.md

@@ -0,0 +1,23 @@
+# PlantSimEngine
+
+The documentation for PlantSimEngine.jl is hosted in its own [website](https://virtualplantlab.github.io/PlantSimEngine.jl/stable/). Public and private API is documented below:
+
+```@meta
+CurrentModule = PlantSimEngine
+```
+## API documentation
+
+```@autodocs
+Modules = [PlantSimEngine]
+Private = false
+```
+
+## Un-exported
+
+Private functions, types or constants from `PlantSimEngine`. These are not exported, so you need to use `PlantSimEngine.` to access them (*e.g.* `PlantSimEngine.DataFormat`).
+
+```@autodocs
+Modules = [PlantSimEngine]
+Public = false
+Private = true
+```