[refine] add tests

tests/functional/refine/cram/rooting-invalid.t

@@ -0,0 +1,22 @@
+Setup
+
+  $ source "$TESTDIR"/_setup.sh
+
+Attempt to root on a strain which is not in the tree is an error
+  $ ${AUGUR} refine \
+  >  --tree "$TESTDIR/../data/tree_raw.nwk" --metadata "$TESTDIR/../data/metadata.tsv" --alignment "$TESTDIR/../data/aligned.fasta" \
+  >  --output-tree tree.nwk --output-node-data branch_lengths.json \
+  >  --root not-in-tree > /dev/null
+  ERROR: Rooting with the provided strain name(s) failed.
+  This is probably because the following names supplied to '--root' were not found in the tree:
+      - 'not-in-tree'
+
+  [2]
+
+Check that rooting on multiple (valid) sequences + '--remove-outgroup' is an error
+  $ ${AUGUR} refine \
+  >  --tree "$TESTDIR/../data/tree_raw.nwk" --metadata "$TESTDIR/../data/metadata.tsv" --alignment "$TESTDIR/../data/aligned.fasta" \
+  >  --output-tree tree.nwk --output-node-data branch_lengths.json \
+  >  --root 'Colombia/2016/ZC204Se' 'VEN/UF_1/2016' --remove-outgroup > /dev/null
+  ERROR: --remove-outgroup is not valid when rooting on multiple strains
+  [2]

tests/functional/refine/cram/rooting-outgroup.t

@@ -0,0 +1,24 @@
+Setup
+
+  $ source "$TESTDIR"/_setup.sh
+
+Check that rooting on an outgroup strain actually works
+  $ ${AUGUR} refine \
+  >  --tree "$TESTDIR/../data/tree_raw.nwk" --metadata "$TESTDIR/../data/metadata.tsv" --alignment "$TESTDIR/../data/aligned.fasta" \
+  >  --output-tree tree1.nwk --output-node-data branch_lengths1.json \
+  >  --root 'Colombia/2016/ZC204Se' > /dev/null
+
+  $ python3 "$TESTDIR/../report-root.py" tree1.nwk
+  Tree root has a single terminal child 'Colombia/2016/ZC204Se'
+
+Check that rooting on an outgroup strain with '--remove-outgroup' does remove it 
+  $ ${AUGUR} refine \
+  >  --tree "$TESTDIR/../data/tree_raw.nwk" --metadata "$TESTDIR/../data/metadata.tsv" --alignment "$TESTDIR/../data/aligned.fasta" \
+  >  --output-tree tree2.nwk --output-node-data branch_lengths2.json \
+  >  --root 'Colombia/2016/ZC204Se' --remove-outgroup > /dev/null
+
+  $ grep 'Colombia/2016/ZC204Se' tree2.nwk
+  [1]
+
+  $ python3 "$TESTDIR/../report-root.py" tree2.nwk
+  No children of the root were terminal nodes

tests/functional/refine/report-root.py

@@ -0,0 +1,11 @@
+import sys
+from augur.utils import read_tree
+
+T = read_tree(sys.argv[1])
+root_child_tips = [c for c in T.root.clades if c.is_terminal()]
+if len(root_child_tips)==0:
+    print("No children of the root were terminal nodes")
+elif len(root_child_tips)>1:
+    print("Multiple children of the root were terminal nodes")
+else:
+    print(f"Tree root has a single terminal child {root_child_tips[0].name!r}")