black 2025 reformat

Author: mr-c

cwl_utils/cwl_v1_0_expression_refactor.py

@@ -49,7 +49,7 @@ def escape_expression_field(contents: str) -> str:
 
 
 def clean_type_ids(
-    cwltype: Union[cwl.ArraySchema, cwl.InputRecordSchema]
+    cwltype: Union[cwl.ArraySchema, cwl.InputRecordSchema],
 ) -> Union[cwl.ArraySchema, cwl.InputRecordSchema]:
     """Simplify type identifiers."""
     result = copy.deepcopy(cwltype)
@@ -427,7 +427,7 @@ def get_input_for_id(
 def find_expressionLib(
     processes: Sequence[
         Union[cwl.CommandLineTool, cwl.Workflow, cwl.ExpressionTool, cwl.WorkflowStep]
-    ]
+    ],
 ) -> Optional[list[str]]:
     """
     Return the expressionLib from the highest priority InlineJavascriptRequirement.

cwl_utils/cwl_v1_1_expression_refactor.py

@@ -49,7 +49,7 @@ def escape_expression_field(contents: str) -> str:
 
 
 def clean_type_ids(
-    cwltype: Union[cwl.ArraySchema, cwl.InputRecordSchema]
+    cwltype: Union[cwl.ArraySchema, cwl.InputRecordSchema],
 ) -> Union[cwl.ArraySchema, cwl.InputRecordSchema]:
     """Simplify type identifiers."""
     result = copy.deepcopy(cwltype)
@@ -425,7 +425,7 @@ def get_input_for_id(
 def find_expressionLib(
     processes: Sequence[
         Union[cwl.CommandLineTool, cwl.Workflow, cwl.ExpressionTool, cwl.WorkflowStep]
-    ]
+    ],
 ) -> Optional[list[str]]:
     """
     Return the expressionLib from the highest priority InlineJavascriptRequirement.

cwl_utils/cwl_v1_2_expression_refactor.py

@@ -49,7 +49,7 @@ def escape_expression_field(contents: str) -> str:
 
 
 def clean_type_ids(
-    cwltype: Union[cwl.ArraySchema, cwl.InputRecordSchema]
+    cwltype: Union[cwl.ArraySchema, cwl.InputRecordSchema],
 ) -> Union[cwl.ArraySchema, cwl.InputRecordSchema]:
     """Simplify type identifiers."""
     result = copy.deepcopy(cwltype)
@@ -425,7 +425,7 @@ def get_input_for_id(
 def find_expressionLib(
     processes: Sequence[
         Union[cwl.CommandLineTool, cwl.Workflow, cwl.ExpressionTool, cwl.WorkflowStep]
-    ]
+    ],
 ) -> Optional[list[str]]:
     """
     Return the expressionLib from the highest priority InlineJavascriptRequirement.

cwl_utils/inputs_schema_gen.py

@@ -5,13 +5,14 @@
 
 """Generate JSON Schema from CWL inputs object."""
 import argparse
+import json
 import logging
 import sys
-import json
 from copy import deepcopy
 from pathlib import Path
-from typing import Any, List, Union, Dict, Optional
+from typing import Any, Dict, List, Optional, Union
 from urllib.parse import urlparse
+
 import requests
 
 # Get typeguard from extensions if we're running in python3.8
@@ -22,25 +23,25 @@
 
 from cwl_utils.loghandler import _logger as _cwlutilslogger
 from cwl_utils.parser import (
-    load_document_by_uri,
+    CommandLineTool,
+    Directory,
+    File,
+    InputArraySchema,
     InputArraySchemaTypes,
+    InputEnumSchema,
     InputEnumSchemaTypes,
-    InputRecordSchemaTypes,
-    File,
-    Directory,
-    WorkflowInputParameter,
     InputRecordSchema,
-    InputEnumSchema,
-    InputArraySchema,
+    InputRecordSchemaTypes,
     Workflow,
-    CommandLineTool,
+    WorkflowInputParameter,
+    load_document_by_uri,
 )
 from cwl_utils.utils import (
-    sanitise_schema_field,
-    is_uri,
-    to_pascal_case,
     get_value_from_uri,
     is_local_uri,
+    is_uri,
+    sanitise_schema_field,
+    to_pascal_case,
 )
 
 _logger = logging.getLogger("cwl-inputs-schema-gen")  # pylint: disable=invalid-name

cwl_utils/utils.py

@@ -6,12 +6,12 @@
 import sys
 import urllib.error
 import urllib.parse
-from urllib.parse import urlparse
 import urllib.request
 from collections.abc import MutableMapping, MutableSequence
 from copy import deepcopy
 from io import StringIO
-from typing import Any, Optional, Union, Dict, List
+from typing import Any, Dict, List, Optional, Union
+from urllib.parse import urlparse
 
 from ruamel.yaml.main import YAML
 from ruamel.yaml.parser import ParserError
@@ -24,8 +24,8 @@
 from cwl_utils.parser import InputRecordSchemaTypes
 
 # Load as 1.2 files
-from cwl_utils.parser.cwl_v1_2 import InputEnumSchema as InputEnumSchemaV1_2
 from cwl_utils.parser.cwl_v1_2 import InputArraySchema as InputArraySchemaV1_2
+from cwl_utils.parser.cwl_v1_2 import InputEnumSchema as InputEnumSchemaV1_2
 
 fast_yaml = YAML(typ="safe")
 
@@ -260,7 +260,7 @@ def to_pascal_case(name: str) -> str:
 
 
 def sanitise_schema_field(
-    schema_field_item: Union[Dict[str, Any], str]
+    schema_field_item: Union[Dict[str, Any], str],
 ) -> Union[Dict[str, Any], str]:
     """
     Schemas need to be resolved before converted to JSON properties.

tests/test_inputs_schema_gen.py

@@ -2,15 +2,16 @@
 """Tests for cwl-inputs-schema-gen."""
 from pathlib import Path
 from typing import Dict
+
 import pytest
 import requests
-from jsonschema.exceptions import ValidationError, SchemaError
+from jsonschema.exceptions import SchemaError, ValidationError
 from jsonschema.validators import validate
 from ruamel.yaml import YAML
 
 from cwl_utils.inputs_schema_gen import cwl_to_jsonschema
-from cwl_utils.parser import load_document_by_uri
 from cwl_utils.loghandler import _logger as _cwlutilslogger
+from cwl_utils.parser import load_document_by_uri
 
 TEST_ROOT_URL = (
     "https://raw.githubusercontent.com/common-workflow-language/cwl-v1.2/main/tests"