🚧 Upgrade toplevel simulation utils.

src/EcologicalNetworksDynamics.jl

@@ -6,8 +6,8 @@ using OrderedCollections
 using SparseArrays
 using Graphs
 
-imap = Iterators.map
-ifilter = Iterators.filter
+const imap = Iterators.map
+const ifilter = Iterators.filter
 iid(it) = imap(identity, it) # Useful to not leak refs.
 
 #-------------------------------------------------------------------------------------------
@@ -96,13 +96,12 @@ include("./expose_data.jl")
 # connecting them to the internals via the framework.
 include("./components/main.jl")
 
-# HERE: now that all components have been upgraded, upgrade the following!
 # Additional exposed utils built on top of components and methods.
 include("./default_model.jl")
 include("./nontrophic_layers.jl")
-#  include("./simulate.jl")
-#  include("./topology.jl")
-#  include("./diversity.jl")
+include("./simulate.jl")
+include("./topology.jl")
+include("./diversity.jl")
 
 # Avoid Revise interruptions when redefining methods and properties.
 Framework.REVISING = true

src/basic_topology_queries.jl

@@ -13,7 +13,7 @@ function n_live_species(g::Topology)
     check_species(g)
     U.n_nodes(g, :species)
 end
-n_live_species(m::InnerParms; kwargs...) = n_live_species(get_topology(m; kwargs...))
+n_live_species(raw::Internal; kwargs...) = n_live_species(get_topology(raw; kwargs...))
 @method n_live_species depends(Species)
 n_live_species(sol::Solution; kwargs...) = n_live_species(get_topology(sol; kwargs...))
 export n_live_species
@@ -30,7 +30,7 @@ function n_live_nutrients(g::Topology)
     check_nutrients(g)
     U.n_nodes(g, :nutrients)
 end
-n_live_nutrients(m::InnerParms; kwargs...) = n_live_nutrients(get_topology(m; kwargs...))
+n_live_nutrients(raw::Internal; kwargs...) = n_live_nutrients(get_topology(raw; kwargs...))
 @method n_live_nutrients depends(Nutrients.Nodes)
 n_live_nutrients(sol::Solution; kwargs...) = n_live_nutrients(get_topology(sol; kwargs...))
 export n_live_nutrients
@@ -50,8 +50,8 @@ Number of live producers within the topology after simulation.
 See [`topology`](@ref).
 ⚠*: Assumes consistent indices from the same model: will be removed in a future version.
 """
-n_live_producers(m::InnerParms; kwargs...) =
-    n_live_producers(get_topology(m; kwargs...), m.producers_indices)
+n_live_producers(raw::Internal; kwargs...) =
+    n_live_producers(get_topology(raw; kwargs...), raw.producers_indices)
 @method n_live_producers depends(Foodweb)
 n_live_producers(sol::Solution; kwargs...) =
     n_live_producers(get_topology(sol; kwargs...), get_model(sol).producers_indices)
@@ -75,8 +75,8 @@ Number of live consumers within the topology after simulation.
 See [`topology`](@ref).
 ⚠*: Assumes consistent indices from the same model: will be removed in a future version.
 """
-n_live_consumers(m::InnerParms; kwargs...) =
-    n_live_consumers(get_topology(m; kwargs...), m.consumers_indices)
+n_live_consumers(raw::Internal; kwargs...) =
+    n_live_consumers(get_topology(raw; kwargs...), raw.consumers_indices)
 @method n_live_consumers depends(Foodweb)
 n_live_consumers(sol::Solution; kwargs...) =
     n_live_consumers(get_topology(sol; kwargs...), get_model(sol).consumers_indices)
@@ -100,8 +100,8 @@ Number of live preys within the topology after simulation.
 See [`topology`](@ref).
 ⚠*: Assumes consistent indices from the same model: will be removed in a future version.
 """
-n_live_preys(m::InnerParms; kwargs...) =
-    n_live_preys(get_topology(m; kwargs...), m.preys_indices)
+n_live_preys(raw::Internal; kwargs...) =
+    n_live_preys(get_topology(raw; kwargs...), raw.preys_indices)
 @method n_live_preys depends(Foodweb)
 n_live_preys(sol::Solution; kwargs...) =
     n_live_preys(get_topology(sol; kwargs...), get_model(sol).preys_indices)
@@ -125,8 +125,8 @@ Number of live tops within the topology after simulation.
 See [`topology`](@ref).
 ⚠*: Assumes consistent indices from the same model: will be removed in a future version.
 """
-n_live_tops(m::InnerParms; kwargs...) =
-    n_live_tops(get_topology(m; kwargs...), m.tops_indices)
+n_live_tops(raw::Internal; kwargs...) =
+    n_live_tops(get_topology(raw; kwargs...), raw.tops_indices)
 @method n_live_tops depends(Foodweb)
 n_live_tops(sol::Solution; kwargs...) =
     n_live_tops(get_topology(sol; kwargs...), get_model(sol).tops_indices)
@@ -159,7 +159,7 @@ function live_species(g::Topology)
         U.node_rel_index(g, abs, sp).rel
     end
 end
-live_species(m::InnerParms; kwargs...) = live_species(get_topology(m; kwargs...))
+live_species(raw::Internal; kwargs...) = live_species(get_topology(raw; kwargs...))
 @method live_species depends(Species)
 live_species(sol::Solution; kwargs...) = live_species(get_topology(sol; kwargs...))
 export live_species
@@ -179,7 +179,7 @@ function live_nutrients(g::Topology)
         U.node_rel_index(g, abs, sp).rel
     end
 end
-live_nutrients(m::InnerParms; kwargs...) = live_nutrients(get_topology(m; kwargs...))
+live_nutrients(raw::Internal; kwargs...) = live_nutrients(get_topology(raw; kwargs...))
 @method live_nutrients depends(Nutrients.Nodes)
 live_nutrients(sol::Solution; kwargs...) = live_nutrients(get_topology(sol; kwargs...))
 export live_nutrients
@@ -202,7 +202,7 @@ function trophic_adjacency(g::Topology)
     check_trophic(g)
     U.outgoing_adjacency_labels(g, :species, :trophic, :species)
 end
-trophic_adjacency(m::InnerParms; kwargs...) = trophic_adjacency(get_topology(m; kwargs...))
+trophic_adjacency(raw::Internal; kwargs...) = trophic_adjacency(get_topology(raw; kwargs...))
 @method trophic_adjacency depends(Foodweb)
 trophic_adjacency(sol::Solution; kwargs...) =
     trophic_adjacency(get_topology(sol; kwargs...))
@@ -218,8 +218,8 @@ Iterate over relative indices of live producer species after simulation.
 See [`topology`](@ref).
 ⚠*: Assumes consistent indices from the same model: will be removed in a future version.
 """
-live_producers(m::InnerParms; kwargs...) =
-    live_producers(get_topology(m; kwargs...), m.producers_indices)
+live_producers(raw::Internal; kwargs...) =
+    live_producers(get_topology(raw; kwargs...), raw.producers_indices)
 @method live_producers depends(Foodweb)
 live_producers(sol::Solution; kwargs...) =
     live_producers(get_topology(sol; kwargs...), get_model(sol).producers_indices)
@@ -244,8 +244,8 @@ Iterate over relative indices of live consumer species after simulation.
 See [`topology`](@ref).
 ⚠*: Assumes consistent indices from the same model: will be removed in a future version.
 """
-live_consumers(m::InnerParms; kwargs...) =
-    live_consumers(get_topology(m; kwargs...), m.consumers_indices)
+live_consumers(raw::Internal; kwargs...) =
+    live_consumers(get_topology(raw; kwargs...), raw.consumers_indices)
 @method live_consumers depends(Foodweb)
 live_consumers(sol::Solution; kwargs...) =
     live_consumers(get_topology(sol; kwargs...), get_model(sol).consumers_indices)
@@ -270,8 +270,8 @@ Iterate over relative indices of live prey species after simulation.
 See [`topology`](@ref).
 ⚠*: Assumes consistent indices from the same model: will be removed in a future version.
 """
-live_preys(m::InnerParms; kwargs...) =
-    live_preys(get_topology(m; kwargs...), m.preys_indices)
+live_preys(raw::Internal; kwargs...) =
+    live_preys(get_topology(raw; kwargs...), raw.preys_indices)
 @method live_preys depends(Foodweb)
 live_preys(sol::Solution; kwargs...) =
     live_preys(get_topology(sol; kwargs...), get_model(sol).preys_indices)
@@ -296,7 +296,7 @@ Iterate over relative indices of live top species after simulation.
 See [`topology`](@ref).
 ⚠*: Assumes consistent indices from the same model: will be removed in a future version.
 """
-live_tops(m::InnerParms; kwargs...) = live_tops(get_topology(m; kwargs...), m.tops_indices)
+live_tops(raw::Internal; kwargs...) = live_tops(get_topology(raw; kwargs...), raw.tops_indices)
 @method live_tops depends(Foodweb)
 live_tops(sol::Solution; kwargs...) =
     live_tops(get_topology(sol; kwargs...), get_model(sol).tops_indices)

src/simulate.jl

@@ -8,7 +8,7 @@ const Solution = AbstractODESolution
 # because a reference to the original model needs to be forwarded down to the internals
 # to save a copy next to the results,
 # and the @method macro misses the feature of providing this reference yet.
-function _simulate(model::InnerParms, u0, tmax::Real; kwargs...)
+function _simulate(raw::Internal, u0, tmax::Real; kwargs...)
     # Depart from the legacy Internal defaults.
     @kwargs_helpers kwargs
 
@@ -28,11 +28,11 @@ function _simulate(model::InnerParms, u0, tmax::Real; kwargs...)
     verbose = take_or!(:show_extinction_events, false)
 
     # No TerminateSteadyState.
-    extc = extinction_callback(model, extinction_threshold; verbose)
+    extc = extinction_callback(raw, extinction_threshold; verbose)
     callback = take_or!(:callbacks, Internals.CallbackSet(extc))
 
     out = Internals.simulate(
-        model,
+        raw,
         u0;
         tmax,
         extinction_threshold,
@@ -42,7 +42,7 @@ function _simulate(model::InnerParms, u0, tmax::Real; kwargs...)
     )
 
     deg_top && show_degenerated_biomass_graph_properties(
-        model,
+        raw,
         out.u[end][get_species_indices(out)],
         deg_top_arg,
     )
@@ -79,7 +79,8 @@ export simulate
 include("./solution_queries.jl")
 
 # Re-expose from internals so it works with the new API.
-extinction_callback(m, thr; verbose = false) = Internals.ExtinctionCallback(thr, m, verbose)
+extinction_callback(raw::Internal, thr; verbose = false) =
+    Internals.ExtinctionCallback(thr, raw, verbose)
 export extinction_callback
 @method extinction_callback depends(
     FunctionalResponse,
@@ -89,8 +90,8 @@ export extinction_callback
 )
 
 # Collect topology diagnostics after simulation and decide whether to display them or not.
-function show_degenerated_biomass_graph_properties(model::InnerParms, biomass, arg)
-    g = get_topology(model; without_species = biomass .<= 0.0)
+function show_degenerated_biomass_graph_properties(raw::Internal, biomass, arg)
+    g = get_topology(raw; without_species = biomass .<= 0.0)
     diagnostics = []
     # Consume iterator to return lengths without collecting allocated yielded values.
     function count(it)
@@ -100,8 +101,8 @@ function show_degenerated_biomass_graph_properties(model::InnerParms, biomass, a
         end
         res
     end
-    pi = model.producers_indices
-    ci = model.consumers_indices
+    pi = @get raw.producers.indices
+    ci = @get raw.consumers.indices
     for comp in disconnected_components(g)
         sp = live_species(comp)
         prods = live_producers(comp, pi)
@@ -126,7 +127,7 @@ function show_degenerated_biomass_graph_properties(model::InnerParms, biomass, a
         else
             m *= " contains degenerated species nodes:\n"
         end
-        vec(i_species) = "[$(join_elided(model.species_label.(sort(i_species)), ", "))]"
+        vec(i_species) = "[$(join_elided(raw.species_label.(sort(i_species)), ", "))]"
         for (sp, prods, cons, ip, sc) in diagnostics
             n_sp, n_prods, n_cons, n_ip, n_sc = length.((sp, prods, cons, ip, sc))
             m *= "Connected component with $n_sp species:\n"

src/solution_queries.jl

@@ -20,7 +20,7 @@ Retrieve the correct indices to extract species-related data from simulation out
 """
 function get_species_indices(sol::Solution)
     m = get_model(sol)
-    1:(m.n_species)
+    1:(m.species.number)
 end
 export get_species_indices
 
@@ -32,7 +32,7 @@ Retrieve the correct indices to extract nutrients-related data from simulation o
 function get_nutrients_indices(sol::Solution)
     m = get_model(sol)
     N = m.n_nutrients
-    S = m.n_species
+    S = m.species.number
     (S+1):(S+N)
 end
 export get_nutrients_indices

src/topology.jl

@@ -5,8 +5,6 @@
 # Convenience local aliases.
 const T = Topologies
 const U = Topologies.Unchecked
-const imap = Iterators.map
-const ifilter = Iterators.filter
 
 """
     get_topology(model::Model; without_species = [], without_nutrients = [])
@@ -17,20 +15,20 @@ When called on a static model, nodes can be explicitly removed during extraction
 When called on a simulation result, extinct nodes are automatically removed
 with extra arguments passed to [`extinctions`](@ref).
 """
-function get_topology(model::InnerParms; without_species = [], without_nutrients = [])
+function get_topology(raw::Internal; without_species = [], without_nutrients = [])
     @tographdata! without_species K{:bin}
     @tographdata! without_nutrients K{:bin}
-    g = deepcopy(model._topology)
+    g = deepcopy(raw._topology)
     removes = []
     if !isempty(without_species)
         check_species(g)
-        spi = model.species_index
+        spi = @ref raw.species.index
         @check_refs_if_list without_species "species" spi
         push!(removes, (:species, without_species, spi))
     end
     if !isempty(without_nutrients)
         check_nutrients(g)
-        nti = model.nutrients_index
+        nti = raw.nutrients_index
         @check_refs_if_list without_nutrients "nutrients" nti
         push!(removes, (:nutrients, without_nutrients, nti))
     end
@@ -45,7 +43,7 @@ function get_topology(model::InnerParms; without_species = [], without_nutrients
     end
     g
 end
-@method get_topology depends() read_as(topology)
+@method get_topology{Internal} depends() read_as(topology)
 
 function get_topology(sol::Solution; kwargs...)
     m = get_model(sol)
@@ -96,8 +94,8 @@ See [`topology`](@ref).
 
   - ⚠ : Assumes consistent indices from the same model: will be removed in a future version.
 """
-isolated_producers(m::InnerParms; kwargs...) =
-    isolated_producers(get_topology(m; kwargs...), m.producers_indices)
+isolated_producers(raw::Internal; kwargs...) =
+    isolated_producers(get_topology(raw; kwargs...), raw.producers_indices)
 @method isolated_producers depends(Foodweb)
 
 isolated_producers(sol::Solution; kwargs...) =
@@ -132,8 +130,8 @@ See [`topology`](@ref).
 
   - ⚠ : Assumes consistent indices from the same model: will be removed in a future version.
 """
-starving_consumers(m::InnerParms; kwargs...) =
-    starving_consumers(get_topology(m; kwargs...), m.producers_indices, m.consumers_indices)
+starving_consumers(raw::Internal; kwargs...) =
+    starving_consumers(get_topology(raw; kwargs...), raw.producers_indices, raw.consumers_indices)
 @method starving_consumers depends(Foodweb)
 
 function starving_consumers(sol::Solution; kwargs...)

test/user/06-basic_pipelines.jl

@@ -103,7 +103,7 @@ end
     m = default_model(
         Foodweb([1 => 2, 2 => 3]),
         # Add one facilitation interaction randomly.
-        FacilitationLayer(; A = (L = 1,)),
+        Facilitation.Layer(; A = (L = 1,)),
     )
 
     sol = simulate(m, 0.5, 500)

test/user/runtests.jl

@@ -17,7 +17,8 @@ only = [
     #  "./02-graphviews.jl"
     #  "./03-components.jl"
     #  "./04-exposed_data.jl"
-    "./05-default_model.jl"
+    #  "./05-default_model.jl"
+    "06-basic_pipelines.jl"
 ] # Unless some files are specified here, in which case only run these.
 if isempty(only)
     folder = dirname(@__FILE__)