From dd43585aef8e913b14a01116ba71531cf9da933e Mon Sep 17 00:00:00 2001
From: Marius <marius.neubert@gmail.com>
Date: Fri, 27 Sep 2024 19:09:02 +0200
Subject: [PATCH] Changed type of root_distribution entries to QQ in all
 models. Made tests more elaborate. Changed testing for graphs so that false
 negatives are avoided.

---
 .../src/PhylogeneticModels.jl                 |  6 ++--
 .../AlgebraicStatistics/test/runtests.jl      | 32 +++++++++++++------
 2 files changed, 25 insertions(+), 13 deletions(-)

diff --git a/experimental/AlgebraicStatistics/src/PhylogeneticModels.jl b/experimental/AlgebraicStatistics/src/PhylogeneticModels.jl
index db852ff54d47..dd21b0b410b6 100644
--- a/experimental/AlgebraicStatistics/src/PhylogeneticModels.jl
+++ b/experimental/AlgebraicStatistics/src/PhylogeneticModels.jl
@@ -247,7 +247,7 @@ function cavender_farris_neyman_model(graph::Graph{Directed})
   ne = n_edges(graph)
   R, list_a, list_b = polynomial_ring(QQ, :a => 1:ne, :b => 1:ne; cached=false)
   
-  root_distr = repeat([1//ns], outer = ns)
+  root_distr = repeat([QQ(1,ns)], outer = ns)
   edgs = sort_edges(graph)
   matrices = Dict{Edge, MatElem}(e => matrix(R, [
     a b 
@@ -332,7 +332,7 @@ function kimura2_model(graph::Graph{Directed})
   ne = n_edges(graph)
   R, list_a, list_b, list_c = polynomial_ring(QQ, :a => 1:ne, :b => 1:ne, :c => 1:ne; cached=false)
   
-  root_distr = repeat([1//ns], outer = ns)
+  root_distr = repeat([QQ(1,ns)], outer = ns)
   edgs = sort_edges(graph)
   matrices = Dict{Edge, MatElem}(e => matrix(R, [
     a b c b
@@ -375,7 +375,7 @@ function kimura3_model(graph::Graph{Directed})
   ne = n_edges(graph)
   R, list_a, list_b , list_c, list_d= polynomial_ring(QQ, :a => 1:ne, :b => 1:ne, :c => 1:ne, :d => 1:ne; cached=false)
   
-  root_distr = repeat([1//ns], outer = ns)
+  root_distr = repeat([QQ(1,ns)], outer = ns)
   edgs = sort_edges(graph)
   matrices = Dict{Edge, MatElem}(e => matrix(R, [
     a b c d
diff --git a/experimental/AlgebraicStatistics/test/runtests.jl b/experimental/AlgebraicStatistics/test/runtests.jl
index 228f0cb929b0..6eaa95ca0a0b 100644
--- a/experimental/AlgebraicStatistics/test/runtests.jl
+++ b/experimental/AlgebraicStatistics/test/runtests.jl
@@ -16,6 +16,7 @@ end
 @testset "Graphical Models tests" begin
 
   tree = graph_from_edges(Directed,[[4,1],[4,2],[4,3]])
+  group_based_components = [number_states, probability_ring, root_distribution, transition_matrices, fourier_ring, fourier_parameters, group_of_model]
 
   @testset "cavender_farris_neyman_model" begin
     model = cavender_farris_neyman_model(tree)         
@@ -43,8 +44,10 @@ end
     # serialization working? 
     mktempdir() do path 
       test_save_load_roundtrip(path, model) do loaded
-        @test model == loaded
-        @test probability_map(model) == probability_map(loaded) 
+        for component in group_based_components
+          @test component(model) == component(loaded)
+          @test incidence_matrix(graph(model)) == incidence_matrix(graph(loaded))
+        end
       end
     end
   end
@@ -76,8 +79,10 @@ end
     # serialization working? 
     mktempdir() do path 
       test_save_load_roundtrip(path, model) do loaded
-        @test model == loaded
-        @test probability_map(model) == probability_map(loaded) 
+        for component in group_based_components
+          @test component(model) == component(loaded)
+          @test incidence_matrix(graph(model)) == incidence_matrix(graph(loaded))
+        end
       end
     end
   end
@@ -109,8 +114,10 @@ end
     # serialization working? 
     mktempdir() do path 
       test_save_load_roundtrip(path, model) do loaded
-        @test model == loaded
-        @test probability_map(model) == probability_map(loaded) 
+        for component in group_based_components
+          @test component(model) == component(loaded)
+          @test incidence_matrix(graph(model)) == incidence_matrix(graph(loaded))
+        end
       end
     end
   end
@@ -142,8 +149,10 @@ end
     # serialization working? 
     mktempdir() do path 
       test_save_load_roundtrip(path, model) do loaded
-        @test model == loaded
-        @test probability_map(model) == probability_map(loaded) 
+        for component in group_based_components
+          @test component(model) == component(loaded)
+          @test incidence_matrix(graph(model)) == incidence_matrix(graph(loaded))
+        end
       end
     end
   end
@@ -166,10 +175,13 @@ end
     # generators of the polynomial ring
     @test length(gens(model.prob_ring)) == 148 
     # serialization working? 
+    gmm_components = [number_states, probability_ring, root_distribution, transition_matrices]
     mktempdir() do path 
       test_save_load_roundtrip(path, model) do loaded
-        @test model == loaded
-        @test probability_map(model) == probability_map(loaded) 
+        for component in gmm_components
+          @test component(model) == component(loaded)
+          @test incidence_matrix(graph(model)) == incidence_matrix(graph(loaded))
+        end
       end
     end
   end