From 61fd9f53c86a7fd011802c19cde888d8f535f661 Mon Sep 17 00:00:00 2001
From: Victor Lin <13424970+victorlin@users.noreply.github.com>
Date: Tue, 26 Dec 2023 14:35:41 -0800
Subject: [PATCH] Ensure Biopython deprecation warnings are emitted

These are useful but suppressed by BCBio.GFF as of version 0.7.0. See
issue linked in changes.
---
 augur/utils.py | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/augur/utils.py b/augur/utils.py
index 2a94cc0d7..a86207e54 100644
--- a/augur/utils.py
+++ b/augur/utils.py
@@ -267,6 +267,13 @@ def _read_gff(reference, feature_names):
         If a gene is found with the name 'nuc'
     """
     from BCBio import GFF
+
+    # TODO: Remove warning filter reversal after it's addressed upstream:
+    # <https://github.com/chapmanb/bcbb/issues/140>
+    import warnings
+    from Bio import BiopythonDeprecationWarning
+    warnings.simplefilter("default", BiopythonDeprecationWarning)
+
     valid_types = ['gene', 'source', 'region']
     features = {}