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.
nextstrain · Dec 26, 2023 · 61fd9f5 · 61fd9f5
1 parent ad4ed1b
commit 61fd9f5
Showing 1 changed file with 7 additions and 0 deletions.
diff --git 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 = {}