remove unused imports, vars

Author: mr-c

cwltool/__init__.py

@@ -1,5 +1,3 @@
 """Reference implementation of the CWL standards."""
-import sys
-import warnings
 
 __author__ = "[email protected]"

cwltool/builder.py

@@ -1,7 +1,6 @@
 import copy
 import logging
 import math
-import os
 from typing import (
     IO,
     Any,
@@ -231,7 +230,9 @@ def bind_input(
             lead_pos = []
 
         bindings = []  # type: List[MutableMapping[str, Union[str, List[int]]]]
-        binding = {}  # type: Union[MutableMapping[str, Union[str, List[int]]], CommentedMap]
+        binding = (
+            {}
+        )  # type: Union[MutableMapping[str, Union[str, List[int]]], CommentedMap]
         value_from_expression = False
         if "inputBinding" in schema and isinstance(
             schema["inputBinding"], MutableMapping
@@ -484,7 +485,9 @@ def addsf(
         # Position to front of the sort key
         if binding:
             for bi in bindings:
-                bi["position"] = cast(List[int], binding["position"]) + cast(List[int], bi["position"])
+                bi["position"] = cast(List[int], binding["position"]) + cast(
+                    List[int], bi["position"]
+                )
             bindings.append(binding)
 
         return bindings

cwltool/context.py

@@ -1,7 +1,7 @@
 """Shared context objects that replace use of kwargs."""
 import copy
 import threading
-from typing import Any, Callable, Dict, Iterable, List, MutableMapping, Optional, Type
+from typing import Any, Callable, Dict, Iterable, List, MutableMapping, Optional
 
 # move to a regular typing import when Python 3.3-3.6 is no longer supported
 from ruamel.yaml.comments import CommentedMap

cwltool/cwlrdf.py

@@ -1,5 +1,5 @@
 import urllib
-from typing import IO, Any, Dict, MutableMapping, Optional, cast
+from typing import IO, Any, Dict, Optional, cast
 
 from rdflib import Graph
 from ruamel.yaml.comments import CommentedMap

cwltool/docker.py

@@ -19,7 +19,6 @@
 from .context import RuntimeContext
 from .docker_id import docker_vm_id
 from .errors import WorkflowException
-from .expression import JSON
 from .job import ContainerCommandLineJob
 from .loghandler import _logger
 from .pathmapper import MapperEnt, PathMapper

cwltool/docker_id.py

@@ -1,7 +1,7 @@
 """Helper functions for docker."""
 
 import subprocess
-from typing import List, Optional, Tuple, cast
+from typing import List, Optional, Tuple
 
 
 def docker_vm_id():  # type: () -> Tuple[Optional[int], Optional[int]]

cwltool/job.py

@@ -43,7 +43,6 @@
 from .builder import Builder, HasReqsHints
 from .context import RuntimeContext, getdefault
 from .errors import UnsupportedRequirement, WorkflowException
-from .expression import JSON
 from .loghandler import _logger
 from .pathmapper import MapperEnt, PathMapper
 from .process import stage_files
@@ -426,7 +425,7 @@ def _execute(
         except WorkflowException as err:
             _logger.error("[job %s] Job error:\n%s", self.name, str(err))
             processStatus = "permanentFail"
-        except Exception as e:
+        except Exception:
             _logger.exception("Exception while running job")
             processStatus = "permanentFail"
         if (
@@ -604,22 +603,19 @@ def create_runtime(
         self, env: MutableMapping[str, str], runtime_context: RuntimeContext,
     ) -> Tuple[List[str], Optional[str]]:
         """Return the list of commands to run the selected container engine."""
-        pass
 
     @staticmethod
     @abstractmethod
     def append_volume(
         runtime: List[str], source: str, target: str, writable: bool = False
     ) -> None:
         """Add binding arguments to the runtime list."""
-        pass
 
     @abstractmethod
     def add_file_or_directory_volume(
         self, runtime: List[str], volume: MapperEnt, host_outdir_tgt: Optional[str]
     ) -> None:
         """Append volume a file/dir mapping to the runtime option list."""
-        pass
 
     @abstractmethod
     def add_writable_file_volume(
@@ -630,7 +626,6 @@ def add_writable_file_volume(
         tmpdir_prefix: str,
     ) -> None:
         """Append a writable file mapping to the runtime option list."""
-        pass
 
     @abstractmethod
     def add_writable_directory_volume(
@@ -641,7 +636,6 @@ def add_writable_directory_volume(
         tmpdir_prefix: str,
     ) -> None:
         """Append a writable directory mapping to the runtime option list."""
-        pass
 
     def create_file_and_add_volume(
         self,

cwltool/load_tool.py

@@ -19,7 +19,6 @@
     cast,
 )
 
-import requests.sessions
 from ruamel.yaml.comments import CommentedMap, CommentedSeq
 from schema_salad.exceptions import ValidationException
 from schema_salad.ref_resolver import (

cwltool/main.py

@@ -2,7 +2,6 @@
 """Entry point for cwltool."""
 
 import argparse
-import copy
 import functools
 import io
 import logging
@@ -12,7 +11,7 @@
 import time
 import urllib
 from codecs import StreamWriter, getwriter
-from collections.abc import Iterable, MutableMapping, MutableSequence, Sequence
+from collections.abc import Iterable, MutableMapping, MutableSequence
 from typing import (
     IO,
     Any,
@@ -385,7 +384,7 @@ def init_job_order(
                     MutableMapping[str, Any],
                     loader.resolve_ref(cmd_line["job_order"])[0],
                 )
-            except Exception as err:
+            except Exception:
                 _logger.exception(
                     "Failed to resolv job_order: %s", cmd_line["job_order"]
                 )
@@ -781,7 +780,7 @@ def check_working_directories(
             if not os.path.exists(os.path.dirname(getattr(runtimeContext, dirprefix))):
                 try:
                     os.makedirs(os.path.dirname(getattr(runtimeContext, dirprefix)))
-                except Exception as e:
+                except Exception:
                     _logger.exception("Failed to create directory.")
                     return 1
     return None

cwltool/pathmapper.py

@@ -4,8 +4,6 @@
 import stat
 import urllib
 import uuid
-from functools import partial
-from tempfile import NamedTemporaryFile
 from typing import (
     Any,
     Callable,
@@ -22,15 +20,12 @@
     cast,
 )
 
-import requests
-from cachecontrol import CacheControl
-from cachecontrol.caches import FileCache
 from schema_salad.exceptions import ValidationException
 from schema_salad.ref_resolver import uri_file_path
 from schema_salad.sourceline import SourceLine
 
 from .loghandler import _logger
-from .stdfsaccess import StdFsAccess, abspath
+from .stdfsaccess import abspath
 from .utils import (
     CWLObjectType,
     Directory,

cwltool/process.py

@@ -1,6 +1,5 @@
 import abc
 import copy
-import errno
 import functools
 import hashlib
 import json
@@ -664,7 +663,7 @@ def __init__(
                 try:
                     with open(loadingContext.js_hint_options_file) as options_file:
                         validate_js_options = json.load(options_file)
-                except (OSError, ValueError) as err:
+                except (OSError, ValueError):
                     _logger.error(
                         "Failed to read options file %s",
                         loadingContext.js_hint_options_file,
@@ -916,7 +915,9 @@ def inc(d):  # type: (List[int]) -> None
             builder.resources = self.evalResources(builder, runtime_context)
         return builder
 
-    def evalResources(self, builder: Builder, runtimeContext: RuntimeContext) -> Dict[str, int]:
+    def evalResources(
+        self, builder: Builder, runtimeContext: RuntimeContext
+    ) -> Dict[str, int]:
         resourceReq, _ = self.get_requirement("ResourceRequirement")
         if resourceReq is None:
             resourceReq = {}
@@ -940,9 +941,19 @@ def evalResources(self, builder: Builder, runtimeContext: RuntimeContext) -> Dic
         for a in ("cores", "ram", "tmpdir", "outdir"):
             mn = mx = None  # type: Optional[int]
             if resourceReq.get(a + "Min"):
-                mn = cast(int, eval_resource(builder, cast(Union[str, int], resourceReq[a + "Min"])))
+                mn = cast(
+                    int,
+                    eval_resource(
+                        builder, cast(Union[str, int], resourceReq[a + "Min"])
+                    ),
+                )
             if resourceReq.get(a + "Max"):
-                mx = cast(int, eval_resource(builder, cast(Union[str, int], resourceReq[a + "Max"])))
+                mx = cast(
+                    int,
+                    eval_resource(
+                        builder, cast(Union[str, int], resourceReq[a + "Max"])
+                    ),
+                )
             if mn is None:
                 mn = mx
             elif mx is None:

cwltool/provenance.py

@@ -15,7 +15,6 @@
 from io import BytesIO, FileIO, TextIOWrapper, open
 from pathlib import Path, PurePath, PurePosixPath
 from socket import getfqdn
-from types import ModuleType
 from typing import (
     IO,
     Any,
@@ -33,7 +32,6 @@
     cast,
 )
 
-from ruamel import yaml
 from schema_salad.sourceline import SourceLine
 from schema_salad.utils import json_dumps
 from typing_extensions import TYPE_CHECKING
@@ -42,7 +40,6 @@
 from prov.identifier import Identifier, Namespace
 from prov.model import PROV, ProvDocument, ProvEntity
 
-from .context import RuntimeContext
 from .errors import WorkflowException
 from .loghandler import _logger
 from .process import Process, shortname

cwltool/resolver.py

@@ -1,10 +1,9 @@
 """Resolves references to CWL documents from local or remote places."""
 
 import os
-import sys
 import urllib
 from pathlib import Path
-from typing import Any, Optional
+from typing import Optional
 
 from schema_salad.ref_resolver import Loader
 

cwltool/singularity.py

@@ -22,7 +22,6 @@
 from .builder import Builder
 from .context import RuntimeContext
 from .errors import UnsupportedRequirement, WorkflowException
-from .expression import JSON
 from .job import ContainerCommandLineJob
 from .loghandler import _logger
 from .pathmapper import MapperEnt, PathMapper

cwltool/subgraph.py

@@ -1,11 +1,9 @@
-import copy
 import urllib
 from collections import namedtuple
 from typing import Any, Dict, MutableMapping, MutableSequence, Optional, Set, Tuple
 
 from ruamel.yaml.comments import CommentedMap
 
-from .process import shortname
 from .utils import aslist
 from .workflow import Workflow
 

cwltool/update.py

@@ -1,5 +1,4 @@
 import copy
-import re
 from functools import partial
 from typing import (
     Any,

cwltool/utils.py

@@ -14,7 +14,6 @@
 import uuid
 from functools import partial
 from itertools import zip_longest
-from pathlib import Path
 from tempfile import NamedTemporaryFile
 from types import ModuleType
 from typing import (

cwltool/workflow.py

@@ -5,7 +5,6 @@
 import random
 import tempfile
 import threading
-from collections import namedtuple
 from typing import (
     Any,
     Callable,
@@ -34,10 +33,8 @@
 from . import command_line_tool, context, expression, procgenerator
 from .builder import content_limit_respected_read
 from .checker import can_assign_src_to_sink, static_checker
-from .command_line_tool import CallbackJob, ExpressionJob, ExpressionTool
 from .context import LoadingContext, RuntimeContext, getdefault
 from .errors import WorkflowException
-from .job import JobBase
 from .load_tool import load_tool
 from .loghandler import _logger
 from .process import Process, get_overrides, shortname, uniquename

tests/test_default_path.py

@@ -1,5 +1,3 @@
-from schema_salad.ref_resolver import Loader
-
 from cwltool.load_tool import fetch_document, resolve_and_validate_document
 
 from .util import get_data

tests/test_docker.py

@@ -2,10 +2,9 @@
 
 import py.path
 
-from cwltool.docker import DockerCommandLineJob
 from cwltool.main import main
 
-from .util import get_data, get_main_output, needs_docker, needs_singularity
+from .util import get_data, get_main_output, needs_docker
 
 
 @needs_docker  # type: ignore

tests/test_docker_paths_with_colons.py

@@ -1,9 +1,6 @@
 from typing import Any
 
 from cwltool.docker import DockerCommandLineJob
-from cwltool.main import main
-
-from .util import needs_docker
 
 
 def test_docker_append_volume_read_only(mocker: Any) -> None:

tests/test_docker_warning.py

@@ -1,12 +1,12 @@
-from typing import Any, List, cast
+from typing import Any, cast
 
 import pytest  # type: ignore
 from ruamel.yaml.comments import CommentedMap
 from schema_salad.sourceline import cmap
 
-from cwltool import command_line_tool, loghandler
+from cwltool import command_line_tool
 from cwltool.context import LoadingContext, RuntimeContext
-from cwltool.utils import CWLObjectType, onWindows, windows_default_container_id
+from cwltool.utils import onWindows, windows_default_container_id
 
 
 @pytest.mark.skip(not onWindows(), reason="MS Windows only")  # type: ignore