Add tutorial on modules and files

docs/make.jl

@@ -22,7 +22,8 @@ makedocs(;
         "Virtual Plant Laboratory" => "index.md",
         "Manual" => [
             "Julia" => ["Julia basic concepts" => "manual/Julia/Julia.md",
-                        "Multiple dispatch and composition" => "manual/Julia/Objects.md"
+                        "Multiple dispatch and composition" => "manual/Julia/Objects.md",
+                        "Modules and files" => "manual/Julia/Modules.md"
                         ],
             "Dynamic graph creation and manipulation" => "manual/Graphs.md",
             "Geometry primitives" => "manual/Geometry/Primitives.md",

docs/src/manual/Julia/Modules.md

@@ -0,0 +1,163 @@
+# [Modules and files](@id manual_modules)
+
+In this document we will learn how VPL code can be organized into files and modules.
+
+## Files
+
+Julia code can be organized into files, which are plain text files with a `.jl` extension.
+A file can contain multiple functions, types, and variables. We can load the code from a
+file using the `include` function. For example, if we have a file named `my_functions.jl`
+that contains the following code, we can load this file into the current Julia session using:
+
+```julia
+include("my_functions.jl")
+```
+
+This will simply execute the code in the file, so it is equivalent to copying and pasting
+the code into the current session.
+
+When developing a VPL model you want to be able to makes changes to the code and run it without
+having to restart the Julia session. For functions this is not really an issue but redefinition
+of types (`struct` or `mutable struct`) is not allowed in Julia within the same session. To
+bypass this we need to use the following strategy:
+
+- Make sure that the package `Revise.jl` is installed and loaded.
+- Use `includet` instead of `include` to load files.
+- Place all type definitions and global variables inside one or more modules.
+
+This means that, when building a typical VPL model, you should include at least one module
+to host the type definitions for the different organs in your model. Of course, for large
+models you may want to consider splitting your code into multiple files and modules
+to keep it organized and manageable.
+
+Note that there are alternative ways to bypass the type redefinition issue, such as using the
+[`ProtoStruct.jl`](https://github.com/BeastyBlacksmith/ProtoStruct.jl) package.
+
+## Modules
+
+In Julia, a module is a collection of related functions, types, and variables that can be
+grouped together to form a namespace. Modules help in organizing code and avoiding name
+clashes. A module can be defined using the `module` keyword, and it can export specific
+functions or types to make them available outside the module.
+
+For example, the following code defines a simple module named `MyModule` that exports a function
+`my_function`:
+
+```julia
+module MyModule
+
+export my_function
+
+function my_function(x)
+    return x + 1
+end
+
+end
+```
+
+We can refer to the name of the module as `.MyModule` where the `.` indicates that it is a
+local module defined in the current scope (Julia packages also defined modules, but they are
+not prefixed with a `.`).
+
+```julia
+using .MyModule
+result = my_function(5)  # This will return 6
+```
+
+Modules can also be nested, allowing for better organization of code. For example, we can define
+a module `OuterModule` that contains another module `InnerModule`:
+
+```julia
+module OuterModule
+    module InnerModule
+        export inner_function
+        function inner_function(x)
+            return x * 2
+        end
+    end  # End of InnerModule
+    export outer_function
+    function outer_function(x)
+        return x + 2
+    end
+end  # End of OuterModule
+```
+
+We can use the nested module as follows (not that `.` is used to separated nested modules):
+
+```julia
+using .OuterModule.InnerModule
+result_inner = inner_function(3)  # This will return 6
+using .OuterModule
+result_outer = outer_function(3)  # This will return 5
+```
+
+The keyword `using` will make available all exported functions and types from the module,
+while `import` will only make the module available without importing its exported functions
+or types. This allows for more control over what is imported into the current namespace but
+we need to prefix each function or type with the module name to use it:
+
+```julia
+import .OuterModule.InnerModule
+result_inner = OuterModule.InnerModule.inner_function(3)  # This will return 6
+result_outer = OuterModule.outer_function(3)  # This will return 5
+```
+
+If the name of the module is too long or cumbersome, we can use the `as` keyword to
+create an alias for the module:
+
+```julia
+using .OuterModule.InnerModule as Inner # Now Inner refers to OuterModule.InnerModule
+result_inner = Inner.inner_function(3)  # This will return 6
+```
+
+Also, we can import specific functions or types from a module using the `import` keyword:
+
+```julia
+import .OuterModule.InnerModule: inner_function
+result_inner = inner_function(3)  # This will return 6
+```
+
+A Julia source file can contain multiple modules, but a module can only be defined within a
+single source file.
+
+### Defining methods for existing functions
+
+If you want to add a method to an existing function so that it works with a new type (e.g.,
+the `feed!` methods that are used in VPL to generate geometry), you need to define the
+method by prefixing the function name with the module name where the function is defined.
+As you will see in the tutorials, this means we define `feed!` methods as follows:
+
+```julia
+function VirtualPlantLab.feed!(turtle::Turtle,, ...)
+    # Implementation of the method
+end
+```
+
+It is important to do this to make sure that we are creating a method for the `feed!` function
+even if you used `using VirtualPlantLab`.
+
+## How to organize your code
+
+VPL models can become quite complex, depending on how much functionality is added. There is
+no correct way to organize your code into multiples files and modules but it helps to think
+for a bit why do we even want to do this (i.e., as said before, you probably want to have
+at least one modules for your organ types but you could write an entire model in a single
+file, as in the tutorials in this website).
+
+We generally want to have multiple files to make sure that, when we are editing a particular
+aspect of the code, we visit as few files as possible. The reason for this is that it is
+always easier to search within a single file and to jump up and down in the code than to
+switch files (though searching across files is also possible in most editors).
+
+We also want to have multiple files if we expect to reuse some of the code for other models
+or simpler version of our current model. This touches on the issue of modularity, whereby
+we want to organized different parts of the code that can be reused in different contexts.
+
+Regarding modules, the main reason for their use (besides what was described earlier about
+types) is to avoid clashes between function names and global variables. This is very much
+related to the issue of modularity, as we want to be able to reuse code without worrying
+about having to rename functions or variables inside the code (i.e., a module helps build
+the abstraction of a *black box* that can be used without knowing its internal details).
+This may never be required in small models (or even in large models that are not meant
+to be reused), so just use your own judgement to decide how to organize your code based on
+your specific needs.