chore(tree): use new, preferred iqtree option names (those mentioned by iqtree2 -h)

Author: corneliusroemer

augur/tree.py

@@ -28,18 +28,18 @@
     # 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.
     # Refer to the handling of -fast in utils/tools.cpp:
     #   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

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