utils: remove read_metadata and supporting file

Previous commits removed all references to this function, and it has been fully replaced by io.read_metadata.

augur/utils.py

@@ -15,7 +15,6 @@
 from augur.io import open_file
 
 from augur.util_support.color_parser import ColorParser
-from augur.util_support.metadata_file import MetadataFile
 from augur.util_support.node_data_reader import NodeDataReader
 from augur.util_support.shell_command_runner import ShellCommandRunner
 
@@ -64,10 +63,6 @@ def get_json_name(args, default=None):
             raise ValueError("Please specify a name for the JSON file containing the results.")
 
 
-def read_metadata(fname, query=None, as_data_frame=False):
-    return MetadataFile(fname, query, as_data_frame).read()
-
-
 class InvalidTreeError(Exception):
     """Represents an error loading a phylogenetic tree from a filename.
     """

tests/test_utils.py

@@ -4,7 +4,6 @@
 import pytest
 
 from augur import utils
-from test_filter import write_metadata
 
 class TestUtils:
     @pytest.mark.parametrize("extension", ["bed","BED"])
@@ -90,18 +89,3 @@ def test_read_strains(self, tmpdir):
         strains = utils.read_strains(strains1, strains2)
         assert len(strains) == 3
         assert "strain1" in strains
-
-    def test_read_metadata(self, tmpdir):
-        meta_fn = write_metadata(tmpdir, (("strain","location","quality"),
-                                          ("SEQ_1","colorado","good"),
-                                          ("SEQ_2","colorado","bad"),
-                                          ("SEQ_3","nevada","good")))
-        utils.read_metadata(meta_fn, as_data_frame=True)
-        # duplicates SEQ_1 raises ValueError
-        meta_fn = write_metadata(tmpdir, (("strain","location","quality"),
-                                          ("SEQ_1","colorado","good"),
-                                          ("SEQ_1","colorado","bad"),
-                                          ("SEQ_3","nevada","good")))
-        with pytest.raises(ValueError) as e_info:
-            utils.read_metadata(meta_fn, as_data_frame=True)
-        assert str(e_info.value) == "Duplicated strain in metadata: SEQ_1"