Move AugurError from utils to new file errors.py

This reduces complexity and chance of circular imports in utils.

augur/__init__.py

@@ -11,8 +11,9 @@
 from textwrap import dedent
 from types import SimpleNamespace
 
+from .errors import AugurError
 from .io import print_err
-from .utils import AugurError, first_line
+from .utils import first_line
 
 recursion_limit = os.environ.get("AUGUR_RECURSION_LIMIT")
 if recursion_limit:

augur/errors.py

@@ -0,0 +1,2 @@
+class AugurError(Exception):
+    pass

augur/filter.py

@@ -18,9 +18,10 @@
 from typing import Collection
 
 from .dates import numeric_date, numeric_date_type, SUPPORTED_DATE_HELP_TEXT, is_date_ambiguous, get_numerical_dates
+from .errors import AugurError
 from .index import index_sequences, index_vcf
 from .io import open_file, read_metadata, read_sequences, write_sequences
-from .utils import AugurError, is_vcf as filename_is_vcf, read_vcf, read_strains, run_shell_command, shquote
+from .utils import is_vcf as filename_is_vcf, read_vcf, read_strains, run_shell_command, shquote
 
 comment_char = '#'
 

augur/parse.py

@@ -6,7 +6,7 @@
 
 from .io import open_file, read_sequences, write_sequences
 from .dates import get_numerical_date_from_value
-from .utils import AugurError
+from .errors import AugurError
 
 forbidden_characters = str.maketrans(
     {' ': None,

augur/util_support/node_data_file.py

@@ -2,7 +2,7 @@
 
 from augur.__version__ import __version__
 from augur.__version__ import is_augur_version_compatible
-from augur.utils import AugurError
+from augur.errors import AugurError
 from augur.validate import validate_json, ValidateError, load_json_schema
 
 

augur/utils.py

@@ -15,10 +15,6 @@
 from augur.io import open_file
 
 
-class AugurError(Exception):
-    pass
-
-
 def is_vcf(filename):
     """Convenience method to check if a file is a vcf file.
 

tests/util_support/test_node_data_file.py

@@ -1,7 +1,7 @@
 import json
 
 from augur.__version__ import __version__
-from augur.utils import AugurError
+from augur.errors import AugurError
 from augur.util_support.node_data_file import NodeDataFile
 
 import pytest