actually check that the warning was raised instead of surpressing it

Tests/test_SeqIO_PdbIO.py

@@ -18,6 +18,7 @@
         "Install NumPy if you want to use PDB formats with SeqIO.")
 
 from Bio import SeqIO
+from Bio import BiopythonWarning
 from Bio.PDB.PDBExceptions import PDBConstructionWarning
 
 
@@ -95,6 +96,7 @@ def test_atom_read(self):
                          'KALGPGATLEEMMTACQG')
         with warnings.catch_warnings():
             warnings.simplefilter("ignore", PDBConstructionWarning)
+            warnings.simplefilter("ignore", BiopythonWarning)
             chain = SeqIO.read('PDB/a_structure.pdb', 'pdb-atom')
         self.assertEqual(chain.id, '????:A')
         self.assertEqual(chain.annotations['chain'], 'A')
@@ -103,13 +105,13 @@ def test_atom_read(self):
     def test_atom_noheader(self):
         """Parse a PDB with no HEADER line."""
 
-        with warnings.catch_warnings():
-            warnings.simplefilter('ignore', PDBConstructionWarning)
-            warnings.simplefilter('ignore', UserWarning)
-            chains = list(SeqIO.parse('PDB/1LCD.pdb', 'pdb-atom'))
+        with warnings.catch_warnings(record=True) as warning_list:
+            warnings.simplefilter('always')
+            # Trigger the warning.
+            chains = list(SeqIO.parse('PDB/a_structure.pdb', 'pdb-atom'))
 
-        self.assertEqual(len(chains), 1)
-        self.assertEqual(str(chains[0].seq), 'MKPVTLYDVAEYAGVSYQTVSRVVNQASHVSAKTREKVEAAMAELNYIPNR')
+        # Verify that the warning was raised
+        self.assertEqual(warning_list[0].category, BiopythonWarning)
 
 
 if __name__ == "__main__":