From 1b1912ffe6e912c1fd7ce74d14b54eeb885d89eb Mon Sep 17 00:00:00 2001
From: Marco Molari <mmolari91@gmail.com>
Date: Wed, 12 Jul 2023 15:46:21 +0200
Subject: [PATCH 1/2] fix: marginalize variable name

---
 src/marginalize.jl | 20 ++++++++++----------
 1 file changed, 10 insertions(+), 10 deletions(-)

diff --git a/src/marginalize.jl b/src/marginalize.jl
index cc7f6132..6f8a3bdf 100644
--- a/src/marginalize.jl
+++ b/src/marginalize.jl
@@ -70,27 +70,27 @@ Marginalize = Command(
             pairs = [(n₁, n₂) for n₁ in names for n₂ in names if n₁ < n₂]
 
             Threads.@threads for (name₁, name₂) in pairs
-                G = Graphs.copy_graph(graph)
-                Graphs.keeponly!(G, name₁, name₂)
+                Γ = Graphs.copy_graph(graph)
+                Graphs.keeponly!(Γ, name₁, name₂)
                 if reduce
                     changed = true
                     while changed
-                        l = length(G.block)
-                        Graphs.deparalog!(G)
-                        Graphs.detransitive!(G)
-                        changed = l != length(G.block)
+                        l = length(Γ.block)
+                        Graphs.deparalog!(Γ)
+                        Graphs.detransitive!(Γ)
+                        changed = l != length(Γ.block)
                     end
                 else
-                    Graphs.detransitive!(G)
+                    Graphs.detransitive!(Γ)
                 end
 
                 # recompute positions
-                Graphs.finalize!(G)
+                Graphs.finalize!(Γ)
 
-                test_flag && verify(graph, G)
+                test_flag && verify(graph, Γ)
 
                 open("$(output)/$(name₁)-$(name₂).json", "w") do io
-                    marshal(io, G; fmt = :json)
+                    marshal(io, Γ; fmt = :json)
                 end
             end
         end

From b312fd01632d3a4160125c4bca9026f1bd9822ac Mon Sep 17 00:00:00 2001
From: Marco Molari <mmolari91@gmail.com>
Date: Wed, 12 Jul 2023 15:50:58 +0200
Subject: [PATCH 2/2] chore: changelog

---
 CHANGELOG.md | 4 ++++
 Project.toml | 2 +-
 2 files changed, 5 insertions(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 330eef6f..968beec7 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,5 +1,9 @@
 # PanGraph Changelog
 
+## v0.7.1
+
+- minor fix for multi-threaded marginalize, see [#58](https://github.com/neherlab/pangraph/pull/58).
+
 ## v0.7.0
 
 - fasta input files are checked for duplicated records, and white lines between records are tolerated, see [#55](https://github.com/neherlab/pangraph/pull/55).
diff --git a/Project.toml b/Project.toml
index 171bc211..8e4f73e2 100644
--- a/Project.toml
+++ b/Project.toml
@@ -1,7 +1,7 @@
 name = "PanGraph"
 uuid = "0f9f61ca-f32c-45e1-b3bc-00138f4f8814"
 authors = ["Nicholas Noll <nbnoll@eml.cc>"]
-version = "0.7.0"
+version = "0.7.1"
 
 [deps]
 Dates = "ade2ca70-3891-5945-98fb-dc099432e06a"