Merge pull request #921: Move AugurError to new errors.py, replace Ru…

…ntimeError

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, is_vcf as filename_is_vcf, write_vcf
-from .utils import AugurError, read_strains
+from .utils import read_strains
 
 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

@@ -2,6 +2,7 @@
 
 from augur.__version__ import __version__
 from augur.__version__ import is_augur_version_compatible
+from augur.errors import AugurError
 from augur.validate import validate_json, ValidateError, load_json_schema
 
 
@@ -58,19 +59,19 @@ def validate(self):
                     self.fname,
                 )
             except ValidateError as err:
-                raise RuntimeError(
+                raise AugurError(
                     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" ({__version__})? Please check the program that produced that JSON file."
                 ) from err
 
         if not isinstance(self.nodes, dict):
-            raise RuntimeError(
+            raise AugurError(
                 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 RuntimeError(
+            raise AugurError(
                 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"({__version__}). We suggest you rerun the pipeline using the current version of "

augur/utils.py

@@ -18,11 +18,6 @@
 from augur.util_support.node_data_reader import NodeDataReader
 
 
-class AugurError(Exception):
-    pass
-
-
-
 def get_json_name(args, default=None):
     if args.output_node_data:
         return args.output_node_data

tests/util_support/test_node_data_file.py

@@ -1,6 +1,7 @@
 import json
 
 from augur.__version__ import __version__
+from augur.errors import AugurError
 from augur.util_support.node_data_file import NodeDataFile
 
 import pytest
@@ -45,7 +46,7 @@ def test_validate_valid(self, build_node_data_file):
         )
 
     def test_validate_invalid_annotation(self, build_node_data_file):
-        with pytest.raises(RuntimeError, match="annotations.*invalid JSON format"):
+        with pytest.raises(AugurError, match="annotations.*invalid JSON format"):
             build_node_data_file(
                 """
                 {
@@ -56,11 +57,11 @@ def test_validate_invalid_annotation(self, build_node_data_file):
             )
 
     def test_validate_nodes_not_dict(self, build_node_data_file):
-        with pytest.raises(RuntimeError, match="is not a dictionary"):
+        with pytest.raises(AugurError, 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(RuntimeError, match="incompatibility detected"):
+        with pytest.raises(AugurError, match="incompatibility detected"):
             build_node_data_file(
                 """
                 {