Move version functions from utils to __version__ module

Also stop using AugurException in node file parsing. It doesn't add any
information over RuntimeError.

augur/__version__.py

@@ -1 +1,23 @@
 __version__ = '9.0.0'
+
+
+def is_augur_version_compatible(version):
+    """
+    Checks if the provided **version** is the same major version
+    as the currently running version of augur.
+
+    Parameters
+    ----------
+    version : str
+        version to check against the current version
+
+    Returns
+    -------
+    Bool
+
+    """
+    import packaging.version
+
+    current_version = packaging.version.parse(__version__)
+    this_version = packaging.version.parse(version)
+    return this_version.release[0] == current_version.release[0]

augur/util_support/node_data_file.py

@@ -1,8 +1,7 @@
 import json
 
-from augur.utils import AugurException  # TODO use something more meaningful
-from augur.utils import get_augur_version
-from augur.utils import is_augur_version_compatible
+from augur.__version__ import __version__
+from augur.__version__ import is_augur_version_compatible
 from augur.validate import validate_json, ValidateError, load_json_schema
 
 
@@ -59,21 +58,21 @@ def validate(self):
                     self.fname,
                 )
             except ValidateError as err:
-                raise AugurException(
+                raise RuntimeError(
                     f"{self.fname} contains an `annotations` attribute of an invalid JSON format. Was it "
                     "produced by different version of augur the one you are currently using "
-                    f" ({get_augur_version()})? Please check the program that produced that JSON file."
+                    f" ({__version__})? Please check the program that produced that JSON file."
                 ) from err
 
         if not isinstance(self.nodes, dict):
-            raise AugurException(
+            raise RuntimeError(
                 f"`nodes` value in {self.fname} is not a dictionary. Please check the formatting of this JSON!"
             )
 
         if self.is_generated_by_incompatible_augur:
-            raise AugurException(
+            raise RuntimeError(
                 f"Augur version incompatibility detected: the JSON {self.fname} was generated by "
                 f"{self.generated_by}, which is incompatible with the current augur version "
-                f"({get_augur_version()}). We suggest you rerun the pipeline using the current version of "
+                f"({__version__}). We suggest you rerun the pipeline using the current version of "
                 "augur."
             )

augur/utils.py

@@ -12,11 +12,11 @@
 from pkg_resources import resource_stream
 from io import TextIOWrapper
 from .__version__ import __version__
-import packaging.version as packaging_version
 
 from augur.util_support.color_parser import ColorParser
 from augur.util_support.date_disambiguator import DateDisambiguator
 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
 
 
@@ -156,11 +156,8 @@ def read_tree(fname, min_terminals=3):
     return T
 
 
-
 def read_node_data(fnames, tree=None):
-    import augur
-    return augur.util_support.node_data_reader.NodeDataReader(fnames, tree).read()
-    #return NodeDataReader(fnames, tree).read()
+    return NodeDataReader(fnames, tree).read()
 
 
 def write_json(data, file_name, indent=(None if os.environ.get("AUGUR_MINIFY_JSON") else 2), include_version=True):
@@ -572,25 +569,6 @@ def get_augur_version():
     return __version__
 
 
-def is_augur_version_compatible(version):
-    """
-    Checks if the provided **version** is the same major version
-    as the currently running version of augur.
-
-    Parameters
-    ----------
-    version : str
-        version to check against the current version
-
-    Returns
-    -------
-    Bool
-
-    """
-    current_version = packaging_version.parse(get_augur_version())
-    this_version = packaging_version.parse(version)
-    return this_version.release[0] == current_version.release[0]
-
 def read_bed_file(bed_file):
     """Read a BED file and return a list of excluded sites.
 

tests/util_support/test_node_data_file.py

@@ -1,6 +1,6 @@
 import json
 
-from augur.utils import AugurException
+from augur.__version__ import __version__
 from augur.util_support.node_data_file import NodeDataFile
 
 import pytest
@@ -35,17 +35,17 @@ def test_items(self, build_node_data_file):
     def test_validate_valid(self, build_node_data_file):
         # Implied assertion that no exceptions are raised
         build_node_data_file(
-            """
-            {
-                "annotations": { "a": { "start": 5 } },
-                "generated_by": { "program": "augur", "version": "9.0.0" },
-                "nodes": { "a": 5 }
-            }
+            f"""
+            {{
+                "annotations": {{ "a": {{ "start": 5 }} }},
+                "generated_by": {{ "program": "augur", "version": "{__version__}" }},
+                "nodes": {{ "a": 5 }}
+            }}
             """
         )
 
     def test_validate_invalid_annotation(self, build_node_data_file):
-        with pytest.raises(AugurException, match="annotations.*invalid JSON format"):
+        with pytest.raises(RuntimeError, match="annotations.*invalid JSON format"):
             build_node_data_file(
                 """
                 {
@@ -56,11 +56,11 @@ def test_validate_invalid_annotation(self, build_node_data_file):
             )
 
     def test_validate_nodes_not_dict(self, build_node_data_file):
-        with pytest.raises(AugurException, match="is not a dictionary"):
+        with pytest.raises(RuntimeError, match="is not a dictionary"):
             build_node_data_file('{ "nodes": "hhh" }')
 
     def test_validate_incompatible_augur_version(self, build_node_data_file):
-        with pytest.raises(AugurException, match="incompatibility detected"):
+        with pytest.raises(RuntimeError, match="incompatibility detected"):
             build_node_data_file(
                 """
                 {