From 5c5325605f575ed86fd36211758573991450d986 Mon Sep 17 00:00:00 2001
From: Victor Lin <13424970+victorlin@users.noreply.github.com>
Date: Tue, 21 Jan 2025 17:33:58 -0800
Subject: [PATCH] Restore ancestral functional test

This reverts "Temporarily disable failing test" (f5323beb) which should no longer fail after previous changes.
---
 ...-amino-acid-sequences-with-root-sequence.t | 31 +++++++++----------
 1 file changed, 14 insertions(+), 17 deletions(-)

diff --git a/tests/functional/ancestral/cram/infer-amino-acid-sequences-with-root-sequence.t b/tests/functional/ancestral/cram/infer-amino-acid-sequences-with-root-sequence.t
index 659f5eb29..333fb0fb0 100644
--- a/tests/functional/ancestral/cram/infer-amino-acid-sequences-with-root-sequence.t
+++ b/tests/functional/ancestral/cram/infer-amino-acid-sequences-with-root-sequence.t
@@ -8,23 +8,20 @@ assign mutations on the branch leading to the inferred root (differences between
 the "root" used as an alignment reference and the inferred most recent common
 ancestor).
 
-TODO: enable this test after Biopython 1.85 warning is properly addressed
-<https://github.com/nextstrain/augur/issues/1727>
-
-$ ${AUGUR} ancestral \
->  --tree $TESTDIR/../data/tree.nwk \
->  --alignment $TESTDIR/../data/aligned.fasta \
->  --annotation $TESTDIR/../data/zika_outgroup.gb \
->  --root-sequence $TESTDIR/../data/zika_outgroup.gb \
->  --genes ENV PRO \
->  --translations $TESTDIR/../data/aa_sequences_%GENE.fasta \
->  --seed 314159 \
->  --output-node-data "$CRAMTMP/$TESTFILE/ancestral_mutations.json" > /dev/null
+  $ ${AUGUR} ancestral \
+  >  --tree $TESTDIR/../data/tree.nwk \
+  >  --alignment $TESTDIR/../data/aligned.fasta \
+  >  --annotation $TESTDIR/../data/zika_outgroup.gb \
+  >  --root-sequence $TESTDIR/../data/zika_outgroup.gb \
+  >  --genes ENV PRO \
+  >  --translations $TESTDIR/../data/aa_sequences_%GENE.fasta \
+  >  --seed 314159 \
+  >  --output-node-data "$CRAMTMP/$TESTFILE/ancestral_mutations.json" > /dev/null
 
 Check that the reference length was correctly exported as the nuc annotation
 
-$ python3 "$TESTDIR/../../../../scripts/diff_jsons.py" \
->   --exclude-regex-paths "['seqid']" -- \
->   "$TESTDIR/../data/ancestral_mutations_with_root_sequence.json" \
->   "$CRAMTMP/$TESTFILE/ancestral_mutations.json"
-{}
+  $ python3 "$TESTDIR/../../../../scripts/diff_jsons.py" \
+  >   --exclude-regex-paths "['seqid']" -- \
+  >   "$TESTDIR/../data/ancestral_mutations_with_root_sequence.json" \
+  >   "$CRAMTMP/$TESTFILE/ancestral_mutations.json"
+  {}