fix type errors discovered by mypyc

Author: mr-c

cwltool/cuda.py

@@ -2,6 +2,7 @@
 
 import subprocess  # nosec
 import xml.dom.minidom  # nosec
+from typing import Union
 
 from .loghandler import _logger
 from .utils import CWLObjectType
@@ -10,9 +11,9 @@
 def cuda_version_and_device_count() -> tuple[str, int]:
     """Determine the CUDA version and number of attached CUDA GPUs."""
     try:
-        out = subprocess.check_output(["nvidia-smi", "-q", "-x"])  # nosec
+        out: Union[str, bytes] = subprocess.check_output(["nvidia-smi", "-q", "-x"])  # nosec
     except Exception as e:
-        _logger.warning("Error checking CUDA version with nvidia-smi: %s", e)
+        _logger.warning("Error checking CUDA version with nvidia-smi: %s", e, exc_info=e)
         return ("", 0)
     dm = xml.dom.minidom.parseString(out)  # nosec
 
@@ -62,5 +63,5 @@ def cuda_check(cuda_req: CWLObjectType, requestCount: int) -> int:
             return 0
         return requestCount
     except Exception as e:
-        _logger.warning("Error checking CUDA requirements: %s", e)
+        _logger.warning("Error checking CUDA requirements: %s", e, exc_info=e)
         return 0

cwltool/singularity_utils.py

@@ -2,7 +2,7 @@
 
 import os
 import os.path
-from subprocess import DEVNULL, PIPE, Popen, TimeoutExpired  # nosec
+import subprocess  # nosec
 from typing import Optional
 
 _USERNS: Optional[bool] = None
@@ -14,17 +14,17 @@ def singularity_supports_userns() -> bool:
     if _USERNS is None:
         try:
             hello_image = os.path.join(os.path.dirname(__file__), "hello.simg")
-            result = Popen(  # nosec
+            result = subprocess.run(  # nosec
                 ["singularity", "exec", "--userns", hello_image, "true"],
-                stderr=PIPE,
-                stdout=DEVNULL,
-                universal_newlines=True,
-            ).communicate(timeout=60)[1]
+                capture_output=True,
+                timeout=60,
+                text=True,
+            ).stderr
             _USERNS = (
                 "No valid /bin/sh" in result
                 or "/bin/sh doesn't exist in container" in result
                 or "executable file not found in" in result
             )
-        except TimeoutExpired:
+        except subprocess.TimeoutExpired:
             _USERNS = False
     return _USERNS

cwltool/workflow_job.py

@@ -406,7 +406,7 @@ def object_from_state(
                                 ("merge_nested" if len(connections) > 1 else None),
                             ),
                         ),
-                        valueFrom=cast(str, inp.get("valueFrom")),
+                        valueFrom=cast(Optional[str], inp.get("valueFrom")),
                     ):
                         raise WorkflowException(
                             "Type mismatch between source '%s' (%s) and "