Distinct Blueprints/Components type hierarchies.

This deep refactoring of the Framework addresses and fixes #139.
It fixes the semantics of the components library
(*e.g.* `OmegaFromRawEdges` and `OmegaFromAllometry`
are *not* two separate components)
while making it more flexible and future-proof.

Take this opportunity to tick the numerous additional Framework `TODO`s,
contributing to polishing the whole library API experience.

Summarize changes in a fresh `CHANGELOG.md`, suggesting to issue v0.2.x.

Author: iago-lito

CHANGELOG.md

@@ -1,3 +1,231 @@
+# Version 0.2.x
+
+## Breaking changes (minor)
+
+- Components and blueprints are now two separate type hierachies.
+  ```julia-repl
+  julia> Foodweb # The component.
+  Foodweb (component for <internals>, expandable from:
+    Matrix: boolean matrix of trophic links,
+    Adjacency: adjacency list of trophic links,
+  )
+  julia> typeof(Foodweb)
+  <Foodweb> (component type EcologicalNetworksDynamics._Foodweb)
+
+  julia> fw = Foodweb.Adjacency([:a => :b]) # A blueprint for this component.
+  blueprint for <Foodweb>: Adjacency {
+    A: {a: {b}},
+    species: <implied blueprint for <Species>>,
+  }
+  julia> typeof(fw)
+  Foodweb_.Adjacency (blueprint type for System{<internals>})
+  julia> fw isa Foodweb
+  false
+  julia> fw isa Foodweb.Adjacency
+  true
+  ```
+
+- Components are singletons types
+  whose fields are blueprint types expanding into themselves.
+  ```julia
+  Species        # The component.
+  Species.Names  # A blueprint to expand from a list of names.
+  Species.Number # A blueprint to expand from a species count.
+  ```
+
+- Components can be directly called
+  to transfer input to correct blueprint constructors
+  ```julia-repl
+  julia> Species(5) isa Species.Number
+  true
+  julia> Species(["a", "b", "c"]) isa Species.Names
+  true
+  ```
+
+  This comes with minor incompatible changes
+  to the available set of blueprint constructor methods.
+  For instance the redundant form
+  `BodyMass(M = [1, 2])` is not supported anymore,
+  but `BodyMass([1, 2])` does the same
+  and `BodyMass(Z = 1.5)` still works as expected.
+
+- Model properties are now typically namespaced to ease future extensions.
+  Equivalent `get_*` and `set_*!` methods may still exist
+  but they are no longer exposed or recommended:
+  use direct property accesses instead.
+  ```julia-repl
+  julia> m = Model(Foodweb([:a => [:b, :c]]));
+  julia> m.species # The namespace.
+  Property space for '<internals>': .species
+    .index
+    .richness
+    .label
+    .names
+    .number
+  julia> m.species.number # (no more `m.n_species` or `get_n_species(m)`)
+  3
+
+  julia> m.trophic # Another namespace.
+  Property space for '<internals>': .trophic
+    .levels
+    .n_links
+    .matrix
+    .herbivory_matrix
+    .carnivory_matrix
+    .A
+  julia> m.trophic.matrix
+  3×3 EcologicalNetworksDynamics.TrophicMatrix:
+   0  1  1
+   0  0  0
+   0  0  0
+  ```
+
+- Some property names have changed. The following list is not exhaustive,
+  but new names can easily be discovered using REPL autocompletion
+  or the `properties(m)` and `properties(m.prop)` methods:
+  - `model.trophic_links` becomes `model.trophic.matrix`,
+    because it does yield a matrix and not some collection of "links".
+    The alias `model.A` is still available.
+  - Likewise,
+    `model.herbivorous_links` becomes `model.trophic.herbivory_matrix` *etc.*
+  - Akward plurals like `model.body_masses` and `model.metabolic_classes`
+    become `model.body_mass` and `model.metabolic_class`.
+
+- Julia allows linear indexing into 2D structures,
+  but the package chooses instead to consider this a semantic flaw:
+  ```julia-repl
+  julia> m = Model(
+             Foodweb([:a => [:b, :c], :b => [:c, :d]]),
+             Efficiency(:Miele2019; e_herbivorous = .1, e_carnivorous = .2),
+         );
+         m.e[5]
+  ERROR: View error (EcologicalNetworksDynamics.EfficiencyRates):
+  Edges data are 2-dimensional:
+  cannot access trophic link data values with 1 index: [5].
+  ```
+
+## New features
+
+- Colored console display.
+  ```julia-repl
+  julia> NutrientIntake() # (won't work in a .md file: try in your REPL)
+  blueprint for <NutrientIntake>: NutrientIntake_ {
+    r: <embedded blueprint for <GrowthRate>: Allometric {
+      allometry: Allometry(p: (a: 1.0, b: -0.25), i: (), e: ()),
+    }>,
+    nodes: <embedded blueprint for <Nodes>: PerProducer {
+      n: 1,
+    }>,
+    turnover: <embedded blueprint for <Turnover>: Flat {
+      t: 0.25,
+    }>,
+    supply: <embedded blueprint for <Supply>: Flat {
+      s: 4.0,
+    }>,
+    concentration: <embedded blueprint for <Concentration>: Flat {
+      c: 0.5,
+    }>,
+    half_saturation: <embedded blueprint for <HalfSaturation>: Flat {
+      h: 0.15,
+    }>,
+  }
+  ```
+
+- Model properties available with `<tab>`-completion within the REPL.
+  ```julia-repl
+  julia> m = Model(Foodweb([:a => [:b, :c]]));
+  julia> m.trop|<tab> # -> m.trophic|
+  julia> m.trophic.|<tab>
+  A                 carnivory_matrix
+  herbivory_matrix  levels
+  matrix            n_links
+  ```
+
+- Every blueprint *brought* by another is available as a brought field
+  to be either *embedded*, *implied* or *unbrought*:
+  ```julia-repl
+  julia> fw = Foodweb.Matrix([0 0; 1 0]) # Implied (brought if missing).
+  blueprint for <Foodweb>: Matrix {
+    A: 1 trophic link,
+    species: <implied blueprint for <Species>>,
+  }
+  julia> fw.species = [:a, :b]; # Embedded (brought, erroring if already present).
+         fw
+  blueprint for <Foodweb>: Matrix {
+    A: 1 trophic link,
+    species: <embedded blueprint for <Species>: Names {
+      names: [:a, :b],
+    }>,
+  }
+  julia> fw.species = nothing; # Unbrought (error if missing).
+         fw
+  blueprint for <Foodweb>: Matrix {
+    A: 1 trophic link,
+    species: <no blueprint brought>,
+  }
+  ```
+
+- Every "leaf" "geometrical" model property *i.e.* a property whose futher
+  model topology does not depend on or is not planned to depend on
+  is now writeable.
+  ```julia-repl
+  julia> m = Model(fw, BodyMass(2));
+         m.M[1] *= 10;
+         m.M == [20, 2]
+  true
+  ```
+
+- Values are checked prior to expansion:
+  ```julia-repl
+  julia> m = Model(fw, Efficiency(1.5))
+  ERROR: Blueprint value cannot be expanded:
+    Not a value within [0, 1]: e = 1.5.
+  ```
+
+- Efficiency from a matrix implies a Foodweb.
+  ```julia-repl
+  julia> e = 0.5;
+         m = Model(Efficiency([
+            0 e e
+            0 0 e
+            e 0 0
+         ]));
+         has_component(m, Foodweb)
+  true
+  julia> m.A
+  3×3 EcologicalNetworksDynamics.TrophicMatrix:
+   0  1  1
+   0  0  1
+   1  0  0
+  ```
+
+- Aggregated blueprints expansion is now clever enough
+  to not error if two brought blueprints would bring the same component:
+  ```julia-repl
+  julia> base = Model(
+             Foodweb([:a => :b]),
+             BodyMass(1),
+             MetabolicClass(:all_invertebrates),
+         )
+         ni = NutrientIntake(nodes = 2; supply = [1, 2], turnover = [1, 2]);
+         # 3 different specifications of Nutrients.Nodes.
+  julia> ni.nodes
+  <embedded blueprint for <Nutrients.Nodes>: Number {
+    n: 2,
+  }>
+  julia> ni.supply.nutrients
+  <implied blueprint for <Nutrients.Nodes>>
+  julia> ni.turnover.nutrients
+  <implied blueprint for <Nutrients.Nodes>>
+  julia> base + ni; # But this still works fine.
+  ```
+
+- Aggregated blueprints expansion is now clever enough
+  to correctly figure a correct expansion order among brought blueprints:
+  ```julia-repl
+  julia> ni = NutrientIntake(; turnover = [1, 2]);
+  julia> base + ni; # `ni.turnover.nutrients` is expanded before `ni.supply`.
+  ```
 # v0.2.1
 
 🚨 Quick patch to fix [#171]: