flake8 inspired fixes

Author: mr-c

cwltool/builder.py

@@ -89,17 +89,17 @@ def formatSubclassOf(
 
     uriRefFmt = URIRef(fmt)
 
-    for s, p, o in ontology.triples((uriRefFmt, RDFS.subClassOf, None)):
+    for _s, _p, o in ontology.triples((uriRefFmt, RDFS.subClassOf, None)):
         # Find parent classes of `fmt` and search upward
         if formatSubclassOf(o, cls, ontology, visited):
             return True
 
-    for s, p, o in ontology.triples((uriRefFmt, OWL.equivalentClass, None)):
+    for _s, _p, o in ontology.triples((uriRefFmt, OWL.equivalentClass, None)):
         # Find equivalent classes of `fmt` and search horizontally
         if formatSubclassOf(o, cls, ontology, visited):
             return True
 
-    for s, p, o in ontology.triples((None, OWL.equivalentClass, uriRefFmt)):
+    for s, _p, _o in ontology.triples((None, OWL.equivalentClass, uriRefFmt)):
         # Find equivalent classes of `fmt` and search horizontally
         if formatSubclassOf(s, cls, ontology, visited):
             return True

cwltool/command_line_tool.py

@@ -1146,7 +1146,7 @@ def collect_output(
                                     )
                                 ]
                             )
-                        except (OSError, IOError) as e:
+                        except (OSError) as e:
                             _logger.warning(str(e))
                         except Exception:
                             _logger.error(

cwltool/cwlrdf.py

@@ -138,7 +138,7 @@ def dot_without_parameters(g: Graph, stdout: Union[TextIO, StreamWriter]) -> Non
     )
 
     currentwf = None  # type: Optional[str]
-    for wf, step, run, runtype in qres:
+    for wf, step, _run, runtype in qres:
         if step not in dotname:
             dotname[step] = lastpart(step)
 

cwltool/job.py

@@ -867,7 +867,7 @@ def docker_monitor(
             try:
                 with open(cidfile) as cidhandle:
                     cid = cidhandle.readline().strip()
-            except (OSError, IOError):
+            except (OSError):
                 cid = None
         max_mem = psutil.virtual_memory().total
         tmp_dir, tmp_prefix = os.path.split(tmpdir_prefix)

cwltool/main.py

@@ -876,7 +876,7 @@ def main(
 
         if not args.workflow:
             if os.path.isfile("CWLFile"):
-                setattr(args, "workflow", "CWLFile")
+                args.workflow = "CWLFile"
             else:
                 _logger.error("CWL document required, no input file was provided")
                 arg_parser().print_help()

cwltool/mpi.py

@@ -1,7 +1,7 @@
 import os
 import re
 import inspect
-from typing import List, Type, TypeVar, MutableMapping, Mapping, Union
+from typing import List, Type, TypeVar, Optional, MutableMapping, Mapping, Union
 from ruamel import yaml
 
 
@@ -16,10 +16,10 @@ def __init__(
         runner: str = "mpirun",
         nproc_flag: str = "-n",
         default_nproc: Union[int, str] = 1,
-        extra_flags: List[str] = [],
-        env_pass: List[str] = [],
-        env_pass_regex: List[str] = [],
-        env_set: Mapping[str, str] = {},
+        extra_flags: Optional[List[str]] = None,
+        env_pass: Optional[List[str]] = None,
+        env_pass_regex: Optional[List[str]] = None,
+        env_set: Optional[Mapping[str, str]] = None,
     ) -> None:
         """
         Initialize from the argument mapping.
@@ -38,10 +38,10 @@ def __init__(
         self.runner = runner
         self.nproc_flag = nproc_flag
         self.default_nproc = int(default_nproc)
-        self.extra_flags = extra_flags
-        self.env_pass = env_pass
-        self.env_pass_regex = env_pass_regex
-        self.env_set = env_set
+        self.extra_flags = extra_flags or []
+        self.env_pass = env_pass or []
+        self.env_pass_regex = env_pass_regex or []
+        self.env_set = env_set or {}
 
     @classmethod
     def load(cls: Type[MpiConfigT], config_file_name: str) -> MpiConfigT:

cwltool/provenance_profile.py

@@ -45,6 +45,7 @@
     versionstring,
 )
 from .workflow_job import WorkflowJob
+from .job import CommandLineJob, JobBase
 
 if TYPE_CHECKING:
     from .provenance import ResearchObject
@@ -258,8 +259,8 @@ def record_process_start(
         elif not hasattr(job, "workflow"):
             # commandline tool execution as part of workflow
             name = ""
-            if hasattr(job, "name"):
-                name = getattr(job, "name")
+            if isinstance(job, (CommandLineJob, JobBase, WorkflowJob)):
+                name = job.name
             process_name = urllib.parse.quote(name, safe=":/,#")
             process_run_id = self.start_process(process_name, datetime.datetime.now())
         return process_run_id

cwltool/singularity.py

@@ -155,7 +155,7 @@ def get_image(
         if is_version_2_6() and "SINGULARITY_PULLFOLDER" in os.environ:
             targets.append(os.environ["SINGULARITY_PULLFOLDER"])
         for target in targets:
-            for dirpath, subdirs, files in os.walk(target):
+            for dirpath, _subdirs, files in os.walk(target):
                 for entry in files:
                     if entry in candidates:
                         path = os.path.join(dirpath, entry)