Merge pull request #26 from nossleinad/message-type-declaration

Be consistent with message type declaration

Author: nossleinad

src/core/algorithms/ancestors.jl

@@ -29,7 +29,7 @@ function depth_first_reconstruction(
     run_fel_up = true,
     run_fel_down = true,
     partition_list = 1:length(tree.message),
-    node_message_dict = Dict{FelNode,Vector{Partition}}(),
+    node_message_dict = Dict{FelNode,Vector{<:Partition}}(),
 )
     if run_fel_up
         felsenstein!(tree, model_func, partition_list = partition_list)
@@ -56,7 +56,7 @@ function depth_first_reconstruction(
     run_fel_up = true,
     run_fel_down = true,
     partition_list = 1:length(tree.message),
-    node_message_dict = Dict{FelNode,Vector{Partition}}(),
+    node_message_dict = Dict{FelNode,Vector{<:Partition}}(),
 )
     depth_first_reconstruction(
         tree,
@@ -76,7 +76,7 @@ function depth_first_reconstruction(
     run_fel_up = true,
     run_fel_down = true,
     partition_list = 1:length(tree.message),
-    node_message_dict = Dict{FelNode,Vector{Partition}}(),
+    node_message_dict = Dict{FelNode,Vector{<:Partition}}(),
 )
     depth_first_reconstruction(
         tree,
@@ -91,7 +91,7 @@ end
 
 #For marginal reconstructions
 function reconstruct_marginal_node!(
-    node_message_dict::Dict{FelNode,Vector{Partition}},
+    node_message_dict::Dict{FelNode,Vector{<:Partition}},
     node::FelNode,
     model_array::Vector{<:BranchModel},
     partition_list,
@@ -109,7 +109,7 @@ end
 
 export marginal_state_dict
 """
-    marginal_state_dict(tree::FelNode, model; partition_list = 1:length(tree.message), node_message_dict = Dict{FelNode,Vector{Partition}}())
+    marginal_state_dict(tree::FelNode, model; partition_list = 1:length(tree.message), node_message_dict = Dict{FelNode,Vector{<:Partition}}())
 
 Takes in a tree and a model (which can be a single model, an array of models, or a function that maps FelNode->Array{<:BranchModel}), and
 returns a dictionary mapping nodes to their marginal reconstructions (ie. P(state|all observations,model)). A subset of partitions can be specified by partition_list,
@@ -119,7 +119,7 @@ function marginal_state_dict(
     tree::FelNode,
     model;
     partition_list = 1:length(tree.message),
-    node_message_dict = Dict{FelNode,Vector{Partition}}(),
+    node_message_dict = Dict{FelNode,Vector{<:Partition}}(),
 )
     return depth_first_reconstruction(
         tree,
@@ -133,7 +133,7 @@ end
 #For joint max reconstructions
 export dependent_reconstruction!
 function dependent_reconstruction!(
-    node_message_dict::Dict{FelNode,Vector{Partition}},
+    node_message_dict::Dict{FelNode,Vector{<:Partition}},
     node::FelNode,
     model_array::Vector{<:BranchModel},
     partition_list;
@@ -173,7 +173,7 @@ reconstruct_cascading_max_node!(node_message_dict, node, model_array, partition_
     )
 export cascading_max_state_dict
 """
-    cascading_max_state_dict(tree::FelNode, model; partition_list = 1:length(tree.message), node_message_dict = Dict{FelNode,Vector{Partition}}())
+    cascading_max_state_dict(tree::FelNode, model; partition_list = 1:length(tree.message), node_message_dict = Dict{FelNode,Vector{<:Partition}}())
 
 Takes in a tree and a model (which can be a single model, an array of models, or a function that maps FelNode->Array{<:BranchModel}), and
 returns a dictionary mapping nodes to their inferred ancestors under the following scheme: the state that maximizes the marginal likelihood is selected at the root,
@@ -184,7 +184,7 @@ function cascading_max_state_dict(
     tree::FelNode,
     model;
     partition_list = 1:length(tree.message),
-    node_message_dict = Dict{FelNode,Vector{Partition}}(),
+    node_message_dict = Dict{FelNode,Vector{<:Partition}}(),
 )
     return depth_first_reconstruction(
         tree,
@@ -206,7 +206,7 @@ conditioned_sample_node!(node_message_dict, node, model_array, partition_list) =
     )
 export endpoint_conditioned_sample_state_dict
 """
-    endpoint_conditioned_sample_state_dict(tree::FelNode, model; partition_list = 1:length(tree.message), node_message_dict = Dict{FelNode,Vector{Partition}}())
+    endpoint_conditioned_sample_state_dict(tree::FelNode, model; partition_list = 1:length(tree.message), node_message_dict = Dict{FelNode,Vector{<:Partition}}())
 
 Takes in a tree and a model (which can be a single model, an array of models, or a function that maps FelNode->Array{<:BranchModel}), and draws samples under the model
 conditions on the leaf observations. These samples are stored in the node_message_dict, which is returned. A subset of partitions can be specified by partition_list, and a
@@ -216,7 +216,7 @@ function endpoint_conditioned_sample_state_dict(
     tree::FelNode,
     model;
     partition_list = 1:length(tree.message),
-    node_message_dict = Dict{FelNode,Vector{Partition}}(),
+    node_message_dict = Dict{FelNode,Vector{<:Partition}}(),
 )
     return depth_first_reconstruction(
         tree,

src/core/algorithms/branchlength_optim.jl

@@ -1,7 +1,7 @@
 #Model list should be a list of P matrices.
 function branch_LL_up(
     bl::Real,
-    temp_message::Vector{Partition},
+    temp_message::Vector{<:Partition},
     node::FelNode,
     model_list::Vector{<:BranchModel},
     partition_list,
@@ -22,8 +22,8 @@ end
 #I need to add a version of this that takes a generic optimizer function and uses that instead of golden_section_maximize on just the branchlength.
 #This is for cases where the user stores node-level parameters and wants to optimize them.
 function branchlength_optim!(
-    temp_message::Vector{Partition},
-    message_to_set::Vector{Partition},
+    temp_message::Vector{<:Partition},
+    message_to_set::Vector{<:Partition},
     node::FelNode,
     models,
     partition_list,

src/core/algorithms/nni_optim.jl

@@ -1,8 +1,8 @@
 
 
 function nni_optim!(
-    temp_message::Vector{Partition},
-    message_to_set::Vector{Partition},
+    temp_message::Vector{<:Partition},
+    message_to_set::Vector{<:Partition},
     node::FelNode,
     models,
     partition_list;
@@ -72,8 +72,8 @@ end
 
 #Unsure if this is the best choice to handle the model,models, and model_func stuff.
 function nni_optim!(
-    temp_message::Vector{Partition},
-    message_to_set::Vector{Partition},
+    temp_message::Vector{<:Partition},
+    message_to_set::Vector{<:Partition},
     node::FelNode,
     models::Vector{<:BranchModel},
     partition_list;
@@ -89,8 +89,8 @@ function nni_optim!(
     )
 end
 function nni_optim!(
-    temp_message::Vector{Partition},
-    message_to_set::Vector{Partition},
+    temp_message::Vector{<:Partition},
+    message_to_set::Vector{<:Partition},
     node::FelNode,
     model::BranchModel,
     partition_list;

src/models/models.jl

@@ -48,6 +48,7 @@ function partition_from_template(partition_template::T) where {T <: DiscretePart
 end
 =#
 
+#Note: not enforcing a return type causes some unnecesarry conversions
 copy_message(msg::Vector{<:Partition}) = [copy_partition(x) for x in msg]
 
 #This is a function shared for all models - perhaps move this elsewhere

test/message_type_stability.jl

@@ -0,0 +1,17 @@
+begin
+    # Single partition example
+    tree = sim_tree(n = 10)
+    GAA_partition = GappyAminoAcidPartition(5)
+    AA_freqs = [1 / GAA_partition.states for _ = 1:GAA_partition.states]
+    GAA_partition.state .= AA_freqs
+    internal_message_init!(tree, GAA_partition)
+    Q = gappy_Q_from_symmetric_rate_matrix(WAGmatrix, 1.0, AA_freqs)
+    model = DiagonalizedCTMC(Q)
+    sample_down!(tree, model)
+    felsenstein!(tree, model)
+
+    # These would previously break since Vector{GappyAminoAcidPartition} is not <: Vector{Partition}, for example.
+    branchlength_optim!(tree, model)
+    marginal_state_dict(tree, model)
+    nni_optim!(tree, model)
+end

test/runtests.jl

@@ -26,4 +26,8 @@ using Test
         include("partition_selection.jl")
     end
 
+    @testset "message_type_stability" begin
+        include("message_type_stability.jl")
+    end
+
 end