From e0b3d735902626e44a6f4a9f365a7586962e0c2d Mon Sep 17 00:00:00 2001
From: Alexey Stukalov <astukalov@seer.bio>
Date: Sun, 19 Mar 2023 19:58:11 -0700
Subject: [PATCH 1/3] affprop(): add temp diagnostic output

---
 src/affprop.jl | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/src/affprop.jl b/src/affprop.jl
index e8ea51d3..b2088325 100644
--- a/src/affprop.jl
+++ b/src/affprop.jl
@@ -118,13 +118,17 @@ function _affinityprop(S::AbstractMatrix{T},
 
     # extract exemplars and assignments
     exemplars = _afp_extract_exemplars(A, R)
+    if isempty(exemplars)
+        @show A R
+    end
+    @assert !isempty(exemplars)
     assignments, counts = _afp_get_assignments(S, exemplars)
 
     if displevel >= 1
         if converged
-            println("Affinity propagation converged with $t iterations: $(length(exemplars)) exemplars.")
+            @info "Affinity propagation converged with $t iterations: $(length(exemplars)) exemplars."
         else
-            println("Affinity propagation terminated without convergence after $t iterations: $(length(exemplars)) exemplars.")
+            @warn "Affinity propagation terminated without convergence after $t iterations: $(length(exemplars)) exemplars."
         end
     end
 

From 95c97142f8af7e4e98ac83e34bac19865f38e61b Mon Sep 17 00:00:00 2001
From: Alexey Stukalov <astukalov@gmail.com>
Date: Wed, 26 Jul 2023 01:23:33 -0700
Subject: [PATCH 2/3] _asp_get_assignments(): simplify

---
 src/affprop.jl | 10 ++++------
 1 file changed, 4 insertions(+), 6 deletions(-)

diff --git a/src/affprop.jl b/src/affprop.jl
index b2088325..113b46a2 100644
--- a/src/affprop.jl
+++ b/src/affprop.jl
@@ -254,7 +254,6 @@ function _afp_get_assignments(S::AbstractMatrix, exemplars::Vector{Int})
     k = length(exemplars)
     Se = S[:, exemplars]
     a = Vector{Int}(undef, n)
-    cnts = zeros(Int, k)
     for i = 1:n
         p = 1
         v = Se[i,1]
@@ -267,11 +266,10 @@ function _afp_get_assignments(S::AbstractMatrix, exemplars::Vector{Int})
         end
         a[i] = p
     end
-    for i = 1:k
-        a[exemplars[i]] = i
-    end
-    for i = 1:n
-        @inbounds cnts[a[i]] += 1
+    a[exemplars] = eachindex(exemplars)
+    cnts = zeros(Int, k)
+    for aa in a
+        @inbounds cnts[aa] += 1
     end
     return (a, cnts)
 end

From 48dded19b56277fc9f2e6f91d972d3213f737355 Mon Sep 17 00:00:00 2001
From: Alexey Stukalov <astukalov@gmail.com>
Date: Wed, 26 Jul 2023 01:24:34 -0700
Subject: [PATCH 3/3] affprop: fix test matrix

---
 test/affprop.jl | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/test/affprop.jl b/test/affprop.jl
index 7e94027f..d51c3382 100644
--- a/test/affprop.jl
+++ b/test/affprop.jl
@@ -16,9 +16,11 @@ include("test_helpers.jl")
         @test_throws ArgumentError affinityprop(randn(2, 2), tol=0.0)
         @test_throws ArgumentError affinityprop(randn(2, 2), damp=-0.1)
         @test_throws ArgumentError affinityprop(randn(2, 2), damp=1.0)
-        @test affinityprop(randn(2, 2), damp=0.5, tol=0.5) isa AffinityPropResult
+        x = randn(2, 4)
+        S = -pairwise(Euclidean(), x, x, dims=2)
+        @test affinityprop(S, damp=0.5, tol=0.5) isa AffinityPropResult
         for disp in keys(Clustering.DisplayLevels)
-            @test affinityprop(randn(2, 2), tol=0.1, display=disp) isa AffinityPropResult
+            @test affinityprop(S, tol=0.1, display=disp) isa AffinityPropResult
         end
     end