Prevent spurious warnings from causing test failure.

The `test_annotate_file` command may fail because the `annotate` command
may emit some unexpected warnings on STDERR about invalid CURIEs, even
if there are no errors and the expected output is normally produced on
STDOUT.

This commit amends the test so that it ignores any 'WARNING:' line in
the STDERR stream produced by the `annotate` command.

closes #795.

tests/test_cli.py

@@ -1522,7 +1522,7 @@ def test_annotate_file(self):
             ],
         )
         print("STDERR", result.stdout)
-        err = result.stderr
+        err = "\n".join([line for line in result.stderr.split("\n") if not line.startswith("WARNING")])
         self.assertEqual("", err)
         self.assertEqual(0, result.exit_code)
         with open(outfile) as stream: