Bump mypy from 1.15.0 to 1.16.0

cwltool/checker.py

@@ -54,7 +54,7 @@ def check_types(
 def merge_flatten_type(src: SinkType) -> CWLOutputType:
     """Return the merge flattened type of the source type."""
     if isinstance(src, MutableSequence):
-        return [merge_flatten_type(cast(SinkType, t)) for t in src]
+        return [merge_flatten_type(t) for t in src]
     if isinstance(src, MutableMapping) and src.get("type") == "array":
         return src
     return {"items": src, "type": "array"}
@@ -94,22 +94,20 @@ def can_assign_src_to_sink(src: SinkType, sink: Optional[SinkType], strict: bool
                     if strict:
                         return False
             return True
-        return can_assign_src_to_sink(
-            cast(SinkType, src["type"]), cast(Optional[SinkType], sink["type"]), strict
-        )
+        return can_assign_src_to_sink(src["type"], sink["type"], strict)
     if isinstance(src, MutableSequence):
         if strict:
             for this_src in src:
-                if not can_assign_src_to_sink(cast(SinkType, this_src), sink):
+                if not can_assign_src_to_sink(this_src, sink):
                     return False
             return True
         for this_src in src:
-            if this_src != "null" and can_assign_src_to_sink(cast(SinkType, this_src), sink):
+            if this_src != "null" and can_assign_src_to_sink(this_src, sink):
                 return True
         return False
     if isinstance(sink, MutableSequence):
         for this_sink in sink:
-            if can_assign_src_to_sink(src, cast(SinkType, this_sink)):
+            if can_assign_src_to_sink(src, this_sink):
                 return True
         return False
     return bool(src == sink)
@@ -257,7 +255,7 @@ def static_checker(
                 )
                 + "\n"
                 + SourceLine(sink, "type").makeError(
-                    "  with sink '%s' of type %s" % (sink_name, json_dumps(sink["type"]))
+                    "  with sink '{}' of type {}".format(sink_name, json_dumps(sink["type"]))
                 )
             )
             if linkMerge is not None:

cwltool/command_line_tool.py

@@ -501,7 +501,7 @@ def _initialworkdir(self, j: Optional[JobBase], builder: Builder) -> None:
             if not isinstance(ls_evaluated, MutableSequence):
                 fail = ls_evaluated
             else:
-                ls_evaluated2 = cast(MutableSequence[Union[None, CWLOutputType]], ls_evaluated)
+                ls_evaluated2 = ls_evaluated
                 for entry in ls_evaluated2:
                     if entry == None:  # noqa
                         if classic_dirent:
@@ -1389,7 +1389,7 @@ def collect_output(
                                 "Multiple matches for output item that is a single file."
                             )
                         else:
-                            result = cast(CWLOutputType, result[0])
+                            result = result[0]
 
             if "secondaryFiles" in schema:
                 with SourceLine(schema, "secondaryFiles", WorkflowException, debug):

cwltool/cwlprov/ro.py

@@ -674,12 +674,12 @@ def _relativise_files(
 
             for val in structure.values():
                 try:
-                    self._relativise_files(cast(CWLOutputType, val))
+                    self._relativise_files(val)
                 except OSError:
                     pass
             return
 
         if isinstance(structure, MutableSequence):
             for obj in structure:
                 # Recurse and rewrite any nested File objects
-                self._relativise_files(cast(CWLOutputType, obj))
+                self._relativise_files(obj)

cwltool/main.py

@@ -304,7 +304,7 @@ def realize_input_schema(
             if isinstance(entry["type"], Mapping):
                 entry["type"] = cast(
                     CWLOutputType,
-                    realize_input_schema([cast(CWLObjectType, entry["type"])], schema_defs),
+                    realize_input_schema([entry["type"]], schema_defs),
                 )
             if entry["type"] == "array":
                 items = entry["items"] if not isinstance(entry["items"], str) else [entry["items"]]
@@ -373,7 +373,10 @@ def load_job_order(
             content_types=CWL_CONTENT_TYPES,
         )
 
-    if job_order_object is not None and "http://commonwl.org/cwltool#overrides" in job_order_object:
+    if (
+        isinstance(job_order_object, CommentedMap)
+        and "http://commonwl.org/cwltool#overrides" in job_order_object
+    ):
         ov_uri = file_uri(job_order_file or input_basedir)
         overrides_list.extend(resolve_overrides(job_order_object, ov_uri, tool_file_uri))
         del job_order_object["http://commonwl.org/cwltool#overrides"]

cwltool/pack.py

@@ -32,7 +32,7 @@ def find_run(
                 runs.add(d["run"])
                 find_run(loadref(None, d["run"]), loadref, runs)
         for s in d.values():
-            find_run(s, loadref, runs)
+            find_run(cast(Union[CWLObjectType, ResolveType], s), loadref, runs)
 
 
 def find_ids(
@@ -47,7 +47,7 @@ def find_ids(
             if i in d and isinstance(d[i], str):
                 ids.add(cast(str, d[i]))
         for s2 in d.values():
-            find_ids(cast(CWLOutputType, s2), ids)
+            find_ids(s2, ids)
 
 
 def replace_refs(d: Any, rewrite: dict[str, str], stem: str, newstem: str) -> None:
@@ -84,7 +84,7 @@ def import_embed(
 ) -> None:
     if isinstance(d, MutableSequence):
         for v in d:
-            import_embed(cast(CWLOutputType, v), seen)
+            import_embed(v, seen)
     elif isinstance(d, MutableMapping):
         for n in ("id", "name"):
             if n in d:
@@ -100,7 +100,7 @@ def import_embed(
                         break
 
         for k in sorted(d.keys()):
-            import_embed(cast(CWLOutputType, d[k]), seen)
+            import_embed(d[k], seen)
 
 
 def pack(

cwltool/process.py

@@ -444,7 +444,7 @@ def avroize_type(
                 cast(MutableSequence[CWLOutputType], field_type["items"]), name_prefix
             )
         else:
-            field_type["type"] = avroize_type(cast(CWLOutputType, field_type["type"]), name_prefix)
+            field_type["type"] = avroize_type(field_type["type"], name_prefix)
     elif field_type == "File":
         return "org.w3id.cwl.cwl.File"
     elif field_type == "Directory":
@@ -490,10 +490,10 @@ def var_spool_cwl_detector(
             r = True
     elif isinstance(obj, MutableMapping):
         for mkey, mvalue in obj.items():
-            r = var_spool_cwl_detector(cast(CWLOutputType, mvalue), obj, mkey) or r
+            r = var_spool_cwl_detector(mvalue, obj, mkey) or r
     elif isinstance(obj, MutableSequence):
         for lkey, lvalue in enumerate(obj):
-            r = var_spool_cwl_detector(cast(CWLOutputType, lvalue), obj, lkey) or r
+            r = var_spool_cwl_detector(lvalue, obj, lkey) or r
     return r
 
 

cwltool/secrets.py

@@ -2,7 +2,7 @@
 
 import uuid
 from collections.abc import MutableMapping, MutableSequence
-from typing import Optional, cast
+from typing import Optional
 
 from .utils import CWLObjectType, CWLOutputType
 
@@ -43,11 +43,11 @@ def has_secret(self, value: CWLOutputType) -> bool:
                     return True
         elif isinstance(value, MutableMapping):
             for this_value in value.values():
-                if self.has_secret(cast(CWLOutputType, this_value)):
+                if self.has_secret(this_value):
                     return True
         elif isinstance(value, MutableSequence):
             for this_value in value:
-                if self.has_secret(cast(CWLOutputType, this_value)):
+                if self.has_secret(this_value):
                     return True
         return False
 
@@ -58,7 +58,7 @@ def retrieve(self, value: CWLOutputType) -> CWLOutputType:
                 value = value.replace(key, this_value)
             return value
         elif isinstance(value, MutableMapping):
-            return {k: self.retrieve(cast(CWLOutputType, v)) for k, v in value.items()}
+            return {k: self.retrieve(v) for k, v in value.items()}
         elif isinstance(value, MutableSequence):
-            return [self.retrieve(cast(CWLOutputType, v)) for v in value]
+            return [self.retrieve(v) for v in value]
         return value

cwltool/update.py

@@ -132,7 +132,7 @@
                 new_seq[index] = update_secondaryFiles(entry)
             return new_seq
         elif isinstance(t, MutableSequence):
-            return CommentedSeq([update_secondaryFiles(cast(CWLOutputType, p)) for p in t])
+            return CommentedSeq([update_secondaryFiles(p) for p in t])
         elif isinstance(t, MutableMapping):
             return cast(MutableMapping[str, str], t)
         elif top:

mypy-requirements.txt

@@ -1,4 +1,4 @@
-mypy==1.15.0  # also update pyproject.toml
+mypy==1.16.0  # also update pyproject.toml
 ruamel.yaml>=0.16.0,<0.19
 cwl-utils>=0.32
 cwltest

pyproject.toml

@@ -2,7 +2,7 @@
 requires = [
     "setuptools>=45",
     "setuptools_scm[toml]>=8.0.4,<9",
-    "mypy==1.15.0",  # also update mypy-requirements.txt
+    "mypy==1.16.0",  # also update mypy-requirements.txt
     "types-requests",
     "types-psutil",
     "importlib_resources>=1.4;python_version<'3.9'",

setup.py

@@ -89,7 +89,7 @@ def _find_package_data(base: str, globs: list[str], root: str = "cwltool") -> li
     mypyc_targets = [x for x in all_real_pys if x not in mypyc_skiplist]
 
     # Strip out any test code
-    mypyc_targets = [x for x in mypyc_targets if not x.startswith(("tests" + os.sep))]
+    mypyc_targets = [x for x in mypyc_targets if not x.startswith("tests" + os.sep)]
 
     mypyc_targets.sort()
 

tests/test_context.py

@@ -1,14 +1,15 @@
+import logging
 import subprocess
 import sys
-import logging
 from io import StringIO
-from typing import MutableMapping, cast
+from pathlib import Path
+from typing import cast
+from collections.abc import MutableMapping
 
 from cwltool.context import RuntimeContext
 from cwltool.factory import Factory
 from cwltool.utils import CWLObjectType
 from cwltool.workflow_job import WorkflowJobStep
-from pathlib import Path
 
 from .util import get_data, needs_docker
 
@@ -49,7 +50,7 @@ def test_workflow_job_step_name_callback() -> None:
         def step_name_hook(step: WorkflowJobStep, job: CWLObjectType) -> str:
             j1 = cast(MutableMapping[str, CWLObjectType], job)
             inp = cast(MutableMapping[str, str], j1.get("revtool_input", j1.get("sorted_input")))
-            return "%s on %s" % (
+            return "{} on {}".format(
                 step.name,
                 inp.get("basename"),
             )