upgrade to mypy 0.971

Author: mr-c

cwl_utils/cwl_normalizer.py

@@ -83,9 +83,7 @@ def run(args: argparse.Namespace) -> int:
         add_lc_filename(result, document)
         version = result.get("cwlVersion", None)
         if version in ("draft-3", "cwl:draft-3", "v1.0", "v1.1"):
-            result = cwlupgrader.upgrade_document(
-                result, False, False, args.dir, imports
-            )
+            result = cwlupgrader.upgrade_document(result, args.dir, imports=imports)
         else:
             _logger.error(
                 "Sorry, %s in %s is not a supported CWL version by this tool.",

cwl_utils/graph_split.py

@@ -11,7 +11,7 @@
 import argparse
 import json
 import os
-from typing import Any, IO, MutableMapping, Set, Union, cast
+from typing import IO, Any, MutableMapping, Set, Union, cast
 
 from cwlformat.formatter import stringify_dict
 from ruamel import yaml

cwl_utils/pack.py

@@ -18,12 +18,25 @@
 import sys
 import urllib.parse
 import urllib.request
-from typing import Any, Dict, ItemsView, List, Optional, Tuple, cast
+from typing import (
+    TYPE_CHECKING,
+    Any,
+    Dict,
+    ItemsView,
+    List,
+    Optional,
+    Tuple,
+    Union,
+    cast,
+)
 
 from packaging import version
 
 from cwl_utils import schemadef, utils
 
+if TYPE_CHECKING:
+    from _collections_abc import dict_items
+
 logger = logging.getLogger(__name__)
 
 
@@ -167,7 +180,7 @@ def resolve_schemadefs(
 
 def resolve_imports(cwl: Any, base_url: urllib.parse.ParseResult) -> Any:
     if isinstance(cwl, dict):
-        itr = cwl.items()
+        itr: Union["dict_items[Any, Any]", ItemsView[Any, Any]] = cwl.items()
     elif isinstance(cwl, list):
         itr = cast(ItemsView[Any, Any], [(n, v) for n, v in enumerate(cwl)])
     else:

cwl_utils/sandboxjs.py

@@ -97,12 +97,13 @@ def __init__(
         self.have_node_slim: bool = have_node_slim
         self.minimum_node_version_str: str = minimum_node_version_str
         self.process_finished_str: str = process_finished_str
-        self.processes_to_kill = (
-            collections.deque()
-        )  # type: Deque[subprocess.Popen[str]]
+        self.processes_to_kill: Deque[subprocess.Popen[str]] = collections.deque()
 
     def __del__(self) -> None:
-        kill_processes(self.processes_to_kill)
+        try:
+            kill_processes(self.processes_to_kill)
+        except TypeError:
+            pass
 
     def check_js_threshold_version(self, working_alias: str) -> bool:
         """

cwl_utils/utils.py

@@ -51,8 +51,7 @@ def _is_github_symbolic_link(base_url: urllib.parse.ParseResult, contents: str)
 
 def bytes2str_in_dicts(
     inp: Union[MutableMapping[str, Any], MutableSequence[Any], Any],
-):
-    # type: (...) -> Union[str, MutableSequence[Any], MutableMapping[str, Any]]
+) -> Union[str, MutableSequence[Any], MutableMapping[str, Any]]:
     """
     Convert any present byte string to unicode string, inplace.
 
@@ -79,9 +78,7 @@ def bytes2str_in_dicts(
     return inp
 
 
-def kill_processes(
-    processes_to_kill,  # type: Deque[subprocess.Popen[str]]
-) -> None:
+def kill_processes(processes_to_kill: Deque[subprocess.Popen[str]]) -> None:
     while processes_to_kill:
         process = processes_to_kill.popleft()
         if isinstance(process.args, MutableSequence):

mypy-requirements.txt

@@ -1,4 +1,4 @@
-mypy==0.910
+mypy==0.971
 typing_extensions
 types-requests
 types-setuptools>==57.4.0

requirements.txt

@@ -1,4 +1,4 @@
-cwl-upgrader >= 1.2
+cwl-upgrader >= 1.2.3
 packaging
 requests
 schema-salad >= 8.2, < 9

tests/load_cwl_by_path.py

@@ -2,7 +2,6 @@
 # SPDX-License-Identifier: Apache-2.0
 from pathlib import Path
 
-
 from cwl_utils.parser import load_document_by_uri, save
 
 # File Input - This is the only thing you will need to adjust or take in as an input to your function:

tests/test_parser.py

@@ -73,7 +73,7 @@ def test_latest_parser() -> None:
     uri = Path(TEST_v1_2_CWL).as_uri()
     with open(TEST_v1_2_CWL) as cwl_h:
         yaml_obj12 = yaml.main.round_trip_load(cwl_h, preserve_quotes=True)
-    latest_cwl_obj = latest.load_document_by_yaml(yaml_obj12, uri)  # type: ignore
+    latest_cwl_obj = latest.load_document_by_yaml(yaml_obj12, uri)
     assert latest_cwl_obj.cwlVersion == "v1.2"