From 891e4876db68917ce095af6505c532165a3c7fc0 Mon Sep 17 00:00:00 2001
From: Niema Moshiri <niemamoshiri@gmail.com>
Date: Fri, 3 May 2024 09:58:56 -0700
Subject: [PATCH] Forgot to delete debugging line

---
 global.json                                | 2 +-
 plugins/mutation_rates/common_treeswift.py | 1 -
 2 files changed, 1 insertion(+), 2 deletions(-)

diff --git a/global.json b/global.json
index b7a1681..1fecfef 100644
--- a/global.json
+++ b/global.json
@@ -1,5 +1,5 @@
 {
-    "VERSION": "1.0.2",
+    "VERSION": "1.0.3",
     "CONFIG_KEYS": ["Contact Network", "Transmission Network", "Sample Times", "Viral Phylogeny (Transmissions)", "Viral Phylogeny (Seeds)", "Mutation Rates", "Ancestral Sequence", "Sequence Evolution"],
     "DESC": {
         "Contact Network": "The <b style='color:red;'>Contact Network</b> graph model describes all social interactions:<ul><li>Nodes represent individuals in the population</li><li>Edges represent all interactions across which the pathogen can transmit</li><li>Currently, FAVITES-Lite only supports static (i.e., unchanging) contact networks</li></ul>",
diff --git a/plugins/mutation_rates/common_treeswift.py b/plugins/mutation_rates/common_treeswift.py
index e22a179..d0ac6c5 100644
--- a/plugins/mutation_rates/common_treeswift.py
+++ b/plugins/mutation_rates/common_treeswift.py
@@ -216,7 +216,6 @@ def treeswift_truncnorm(params, out_fn, config, GLOBAL, verbose=True):
     tree = read_tree_newick(out_fn['viral_phylogeny_time'])
     nodes = [node for node in tree.traverse_preorder() if node.edge_length is not None]
     rates = truncnorm_rvs(loc=mu, scale=sigma, a_min=a_min, b_max=b_max, size=len(nodes))
-    print('\n'.join(str(r) for r in rates)); exit() # TODO
     for i in range(len(nodes)):
         nodes[i].edge_length *= rates[i]
     tree.write_tree_newick(out_fn['viral_phylogeny_mut'])