From 96b0c048229a33b34ff5242bc1a284787b48dd00 Mon Sep 17 00:00:00 2001
From: Cornelius Roemer <cornelius.roemer@gmail.com>
Date: Wed, 17 Jul 2024 14:28:50 +0200
Subject: [PATCH] chore(tree): use new, preferred iqtree option names (those
 mentioned by `iqtree2 -h`)

---
 augur/tree.py           | 8 ++++----
 tests/functional/tree.t | 4 ++--
 2 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/augur/tree.py b/augur/tree.py
index bd39cd624..cbef80840 100644
--- a/augur/tree.py
+++ b/augur/tree.py
@@ -28,9 +28,9 @@
     # For compat with older versions of iqtree, we avoid the newish -fast
     # option alias and instead spell out its component parts:
     #
-    #     -ninit 2
+    #     --ninit 2
     #     -n 2
-    #     -me 0.05
+    #     --epsilon 0.05
     #
     # This may need to be updated in the future if we want to stay in lock-step
     # with -fast, although there's probably no particular reason we have to.
@@ -38,8 +38,8 @@
     #   https://github.com/Cibiv/IQ-TREE/blob/44753aba/utils/tools.cpp#L2926-L2936
     # Increasing threads (-T) can cause IQtree to run longer, hence use AUTO by default
     # -T AUTO makes IQtree chose the optimal number of threads
-    # -redo prevents IQtree errors when a run was aborted and restarted
-    "iqtree": "-ninit 2 -n 2 -me 0.05 -T AUTO -redo",
+    # --redo prevents IQtree errors when a run was aborted and restarted
+    "iqtree": "--ninit 2 -n 2 --epsilon 0.05 -T AUTO --redo",
 }
 
 # IQ-TREE only; see usage below
diff --git a/tests/functional/tree.t b/tests/functional/tree.t
index eb4ae191f..fa6aede14 100644
--- a/tests/functional/tree.t
+++ b/tests/functional/tree.t
@@ -40,7 +40,7 @@ Build a tree, augmenting existing default arguments with custom arguments.
   $ ${AUGUR} tree \
   >  --method iqtree \
   >  --alignment tree/aligned.fasta \
-  >  --tree-builder-args="-czb" \
+  >  --tree-builder-args="--polytomy" \
   >  --output "$TMP/tree_raw.nwk" > /dev/null
 
 Build a tree, replacing existing default arguments with custom arguments.
@@ -49,7 +49,7 @@ Since the following custom arguments are incompatible with the default IQ-TREE a
   $ ${AUGUR} tree \
   >  --method iqtree \
   >  --alignment tree/full_aligned.fasta \
-  >  --tree-builder-args="-czb -bb 1000 -bnni -redo" \
+  >  --tree-builder-args="--polytomy -bb 1000 -bnni --redo" \
   >  --override-default-args \
   >  --output "$TMP/tree_raw.nwk" > /dev/null