🚧 Efficiency upgraded (not fully tested yet).

CHANGELOG.md

@@ -9,7 +9,7 @@
   to transfer input to correct blueprint constructors
 - Blueprints typically have different types based on their inputs.
 
-  ```julia
+  ```julia-repl
   julia> Species
   Species (component for <internals>, expandable from:
     Names: raw species names,
@@ -32,7 +32,7 @@
 - Equivalent `get_*` and `set_*!` methods may still exist
   but they are no longer exposed or recommended:
   use direct property accesses instead.
-  ```julia
+  ```julia-repl
   julia> m = Model(Species(3))
   julia> m.species.number # (no more `.n_species` or `get_n_species(m)`)
   3
@@ -48,14 +48,17 @@
     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`.
+
 
 ## New features
 
 - Model properties available with `<tab>`-completion within the REPL.
 
 - Every blueprint *brought* by another is available as a brought field
   to be either *embedded*, *implied* or *unbrought*:
-  ```julia
+  ```julia-repl
   julia> fw = Foodweb.Matrix([0 0; 1 0]) # Implied (brought if missing).
   blueprint for <Foodweb>: Matrix {
     A: 1 trophic link,
@@ -80,26 +83,33 @@
 - 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
+  ```julia-repl
   julia> m = Model(fw, BodyMass(2));
          m.M[1] *= 10;
          m.M == [20, 2]
   true
   ```
 
 - Values are checked prior to expansion:
-  ```julia
+  ```julia-repl
   julia> m = Model(fw, Efficiency(1.5))
-  TODO
+  ERROR: Blueprint value cannot be expanded:
+    Not a value within [0, 1]: e = 1.5.
   ```
 
 - Efficiency from a matrix implies a Foodweb.
-  ```julia
+  ```julia-repl
   julia> e = 0.5;
-         m = Model(fw, Efficiency([
+         m = Model(Efficiency([
             0 e e
             0 0 e
             e 0 0
-         ]))
-  TODO
+         ]));
+         has_component(m, Foodweb)
+  true
+  julia> m.A
+  3×3 EcologicalNetworksDynamics.TrophicMatrix:
+   0  1  1
+   0  0  1
+   1  0  0
   ```

src/GraphDataInputs/convert.jl

@@ -260,6 +260,23 @@ graphdataconvert(::Type{Adjacency{<:Any,T}}, input::Adjacency{Int64,T}) where {T
 graphdataconvert(::Type{BinAdjacency{<:Any}}, input::BinAdjacency{Symbol}) = input
 graphdataconvert(::Type{BinAdjacency{<:Any}}, input::BinAdjacency{Int64}) = input
 
+#-------------------------------------------------------------------------------------------
+# Extract binary maps/adjacency from regular ones.
+function graphdataconvert(::Type{BinMap}, input::Map{I}) where {I}
+    res = BinMap{I}()
+    for (k, _) in input
+        push!(res, k)
+    end
+    res
+end
+function graphdataconvert(::Type{BinAdjacency{<:Any}}, input::Adjacency{I}) where {I}
+    res = BinAdjacency{I}()
+    for (i, sub) in input
+        res[i] = graphdataconvert(BinMap, sub)
+    end
+    res
+end
+
 #-------------------------------------------------------------------------------------------
 # Conversion helpers.
 
@@ -366,7 +383,7 @@ function _tographdata(vsym, var, targets)
                 argerr("Error while attempting to convert \
                         '$vsym' to $Target \
                         (details further down the stacktrace). \
-                        Received $(repr(var))::$(typeof(var)).")
+                        Received $(repr(var)) ::$(typeof(var)).")
             end
         end
     end

src/components/body_mass.jl

@@ -119,7 +119,7 @@ end
 
 # Basic query.
 @expose_data nodes begin
-    property(body_masses, M)
+    property(body_mass, M)
     depends(BodyMass)
     @species_index
     ref(raw -> raw._foodweb.M)

src/components/efficiency.jl

@@ -27,14 +27,14 @@ F.implied_blueprint_for(bp::Raw, ::_Foodweb) = Foodweb(bp.e .!= 0)
 @blueprint Raw "matrix"
 export Raw
 
-F.early_check(bp::Raw) = check_edges(bp.e, check)
+F.early_check(bp::Raw) = check_edges(check, bp.e)
 check(e, ref = nothing) =
     check_value(e -> 0 <= e <= 1, e, ref, :e, "Not a value within [0, 1]")
 
 function F.late_check(raw, bp::Raw)
     (; e) = bp
     A = @ref raw.trophic.matrix
-    @check_template e A :trophic_links
+    @check_template e A "trophic links"
 end
 
 F.expand!(raw, bp::Raw) = expand!(raw, bp.e)
@@ -65,16 +65,19 @@ mutable struct Adjacency <: Blueprint
     foodweb::Brought(Foodweb)
     Adjacency(e, foodweb = _Foodweb) = new(@tographdata(e, Adjacency{Float64}), foodweb)
 end
-F.implied_blueprint_for(bp::Adjacency, ::_Foodweb) = Foodweb(refs(bp.e))
+function F.implied_blueprint_for(bp::Adjacency, ::_Foodweb)
+    (; e) = bp
+    Foodweb(@tographdata e Adjacency{:bin})
+end
 @blueprint Adjacency "[predactor => [prey => efficiency]] adjacency list"
 export Adjacency
 
-F.early_check(bp::Adjacency) = check_edges(bp.e, check)
+F.early_check(bp::Adjacency) = check_edges(check, bp.e)
 function F.late_check(raw, bp::Adjacency)
     (; e) = bp
     index = @ref raw.species.index
     A = @ref raw.trophic.matrix
-    @check_list_refs e :trophic_link index template(A)
+    @check_list_refs e "trophic link" index template(A)
 end
 
 function F.expand!(raw, bp::Adjacency)
@@ -124,12 +127,17 @@ export Efficiency
 
 function (::_Efficiency)(e; kwargs...)
 
-    e = @tographdata e {Symbol, SparseMatrix, Adjacency}{Float64}
+    e = @tographdata e {Symbol, Scalar, SparseMatrix, Adjacency}{Float64}
     @check_if_symbol e (:Miele2019,)
+    @kwargs_helpers kwargs
 
     if e == :Miele2019
-        Efficiency.Miele2019(; kwargs...)
-    elseif e isa SparseMatrix
+        return Efficiency.Miele2019(; kwargs...)
+    end
+
+    no_unused_arguments()
+
+    if e isa SparseMatrix
         Efficiency.Raw(e)
     elseif e isa Real
         Efficiency.Flat(e)

src/components/growth_rate.jl

@@ -112,7 +112,7 @@ end
 
 function F.expand!(raw, bp::Allometric)
     M = @ref raw.M
-    mc = @ref raw.metabolic_classes
+    mc = @ref raw.metabolic_class
     prods = @ref raw.producers.mask
     r = sparse_nodes_allometry(bp.allometry, prods, M, mc)
     expand!(raw, r)
@@ -154,7 +154,7 @@ function F.expand!(raw, bp::Temperature)
     (; E_a) = bp
     T = @get raw.T
     M = @ref raw.M
-    mc = @ref raw.metabolic_classes
+    mc = @ref raw.metabolic_class
     prods = @ref raw.producers.mask
     r = sparse_nodes_allometry(bp.allometry, prods, M, mc; E_a, T)
     expand!(raw, r)
@@ -203,7 +203,7 @@ end
     get(GrowthRates{Float64}, sparse, "producer")
     template(raw -> @ref raw.producers.mask)
     write!((raw, rhs::Real, i) -> begin
-        GrowthRate_.check(rhs)
+        GrowthRate_.check(rhs, i)
         rhs = Float64(rhs)
         raw.biorates.r[i] = rhs
         rhs

src/components/macros_keywords.jl

@@ -4,6 +4,7 @@ if (false)
     #! format: off
     (
     local
+        A,
         E,
         Scalar,
         V,

src/components/metabolic_class.jl

@@ -154,7 +154,7 @@ end
 
 # Basic query.
 @expose_data nodes begin
-    property(metabolic_classes)
+    property(metabolic_class)
     depends(MetabolicClass)
     @species_index
     ref_cached(raw -> Symbol.(raw._foodweb.metabolic_class)) # Legacy reverse conversion.
@@ -170,5 +170,5 @@ end
 
 # Display.
 function F.shortline(io::IO, model::Model, ::_MetabolicClass)
-    print(io, "Metabolic classes: [$(join_elided(model.metabolic_classes, ", "))]")
+    print(io, "Metabolic classes: [$(join_elided(model.metabolic_class, ", "))]")
 end

src/dedicate_framework_to_model.jl

@@ -185,6 +185,16 @@ function F.display_blueprint_field_short(
     end
     print(io, "{$(join_elided(it, ", "; repr = false))}")
 end
+function F.display_blueprint_field_short(
+    io::IO,
+    map::@GraphData(Adjacency{T}),
+    bp::Blueprint,
+) where {T}
+    it = imap(map) do (k, v)
+        "$k: $(sprint(F.display_blueprint_field_short, v, bp))"
+    end
+    print(io, "{$(join_elided(it, ", "; repr = false))}")
+end
 
 F.display_blueprint_field_long(io::IO, v, bp::Blueprint) =
     F.display_blueprint_field_short(io, v, bp)

src/graph_views.jl

@@ -189,30 +189,45 @@ function check_sparse_index(
     item = item_name(v)
     level = level_name(v)
     n = length(index)
-    valids = valid_refs(v, template, labels)
-    refs, vrefs = if isnothing(labels)
-        ("index $index", "indices")
+    refs = if isnothing(labels)
+        "index $(inline(index))"
     else
-        ("label$(n > 1 : "s" : "") $labels ($index)", "labels")
+        "label$(n > 1 : "s" : "") $labels ($index)"
     end
     throw(
         ViewError(
             typeof(v),
-            "Invalid $item $refs to write $level data. Valid $vrefs $valids",
+            "Invalid $item $refs to write $level data. " *
+            valid_refs_phrase(v, template, labels),
         ),
     )
 end
-valid_refs(_, template::Vector, ::Nothing) =
-    "are " * join_elided(findnz(template)[1], ", ", " and "; max = 100)
-valid_refs(_, template::Matrix, ::Nothing) =
-    "are " *
-    join_elided((ij for ij in zip(findnz(template)[1:2]...)), ", ", " and "; max = 50)
-function valid_refs(v, template::Vector, ::Any)
-    valids = valid_refs(v, template, nothing)
-    "are " * join_elided((l for (l, i) in v._index if i in valids), ", ", " and "; max = 10)
+
+function valid_refs_phrase(v, template, labels)
+    valids = collect(valid_refs(v, template, labels))
+    if isempty(valids)
+        "There is no valid $(vref(labels)) for this template."
+    elseif length(valids) == 1
+        "The only valid $(vref(labels)) for this template is $(first(valids))."
+    else
+        max = isnothing(labels) ? (template isa AbstractVector ? 100 : 50) : 10
+        "Valid $(vrefs(labels)) for this template \
+         are $(join_elided(valids, ", ", " and "; max))"
+    end
+end
+valid_refs_phrase(_, template::AbstractMatrix, ::Nothing) =
+    "Valid indices must comply to the following template:\n\
+     $(repr(MIME("text/plain"), template))"
+vref(::Nothing) = "index"
+vrefs(::Nothing) = "indices"
+vref(::Any) = "label"
+vrefs(::Any) = "labels"
+valid_refs(_, template::AbstractVector, ::Nothing) = findnz(template)[1]
+valid_refs(_, template::AbstractMatrix, ::Nothing) = zip(findnz(template)[1:2]...)
+function valid_refs(v, template::AbstractVector, ::Any)
+    valids = Set(valid_refs(v, template, nothing))
+    (l for (l, i) in v._index if i in valids)
 end
-valid_refs(_, template::Matrix, ::Any) =
-    " must comply to the following template:\n$(repr(MIME("text/plain"), template))"
 
 
 #-------------------------------------------------------------------------------------------