Fix flake8 setup (#1288)

mr-c · web-flow · commit 4fd230884287 · 2020-05-20T16:59:22.000+02:00
diff --git a/cwltool/builder.py b/cwltool/builder.py
@@ -1,7 +1,7 @@
 import copy
 import logging
-import os
 import math
+import os
 from typing import (
     IO,
     Any,
@@ -18,14 +18,13 @@
 
 from rdflib import Graph, URIRef
 from rdflib.namespace import OWL, RDFS
-from typing_extensions import TYPE_CHECKING, Type  # pylint: disable=unused-import
-
 from ruamel.yaml.comments import CommentedMap
 from schema_salad import validate
 from schema_salad.avro.schema import Schema, make_avsc_object
 from schema_salad.schema import Names, convert_to_dict
 from schema_salad.sourceline import SourceLine
 from schema_salad.utils import json_dumps
+from typing_extensions import TYPE_CHECKING, Type  # pylint: disable=unused-import
 
 from . import expression
 from .errors import WorkflowException
diff --git a/cwltool/command_line_tool.py b/cwltool/command_line_tool.py
@@ -29,13 +29,12 @@
 )
 
 import shellescape
-from typing_extensions import TYPE_CHECKING, Type
-
 from schema_salad import validate
 from schema_salad.avro.schema import Schema
 from schema_salad.ref_resolver import file_uri, uri_file_path
 from schema_salad.sourceline import SourceLine
 from schema_salad.utils import json_dumps
+from typing_extensions import TYPE_CHECKING, Type
 
 from .builder import Builder, content_limit_respected_read_bytes, substitute
 from .context import LoadingContext, RuntimeContext, getdefault
@@ -633,8 +632,8 @@ def update_status_output_callback(
                             t["entry"]["writable"] = t.get("writable")
                         ls[i] = t["entry"]
             j.generatefiles["listing"] = ls
-            for l in ls:
-                self.updatePathmap(builder.outdir, builder.pathmapper, l)
+            for entry in ls:
+                self.updatePathmap(builder.outdir, builder.pathmapper, entry)
             visit_class(
                 [builder.files, builder.bindings], ("File", "Directory"), _check_adjust
             )
diff --git a/cwltool/context.py b/cwltool/context.py
@@ -3,12 +3,11 @@
 import threading
 from typing import Any, Callable, Dict, Iterable, List, MutableMapping, Optional
 
-from typing_extensions import TYPE_CHECKING
-
 # move to a regular typing import when Python 3.3-3.6 is no longer supported
 from ruamel.yaml.comments import CommentedMap
 from schema_salad import schema
 from schema_salad.ref_resolver import Loader
+from typing_extensions import TYPE_CHECKING
 
 from .builder import Builder, HasReqsHints
 from .mutation import MutationManager
diff --git a/cwltool/cwlrdf.py b/cwltool/cwlrdf.py
@@ -2,7 +2,6 @@
 from typing import IO, Any, Dict, MutableMapping, cast
 
 from rdflib import Graph
-
 from schema_salad.jsonld_context import makerdf
 from schema_salad.ref_resolver import ContextType
 
diff --git a/cwltool/docker.py b/cwltool/docker.py
@@ -1,15 +1,15 @@
 """Enables Docker software containers via the {dx-,u,}docker runtimes."""
 
-import datetime
 import csv
+import datetime
 import os
 import re
 import shutil
 import sys
 import tempfile
 import threading
 from distutils import spawn
-from io import open, StringIO  # pylint: disable=redefined-builtin
+from io import StringIO, open  # pylint: disable=redefined-builtin
 from typing import Dict, List, MutableMapping, Optional, Set, Tuple
 
 import requests
diff --git a/cwltool/executors.py b/cwltool/executors.py
@@ -12,17 +12,16 @@
     Dict,
     Iterable,
     List,
+    MutableMapping,
     Optional,
     Set,
     Tuple,
     Union,
-    MutableMapping,
 )
 
 import psutil
-
-from schema_salad.validate import ValidationException
 from schema_salad.sourceline import SourceLine
+from schema_salad.validate import ValidationException
 
 from .command_line_tool import CallbackJob
 from .context import RuntimeContext, getdefault
diff --git a/cwltool/flatten.py b/cwltool/flatten.py
@@ -3,23 +3,23 @@
 # http://rightfootin.blogspot.com/2006/09/more-on-python-flatten.html
 
 
-def flatten(l, ltypes=(list, tuple)):
+def flatten(thing, ltypes=(list, tuple)):
     # type: (Any, Any) -> List[Any]
-    if l is None:
+    if thing is None:
         return []
-    if not isinstance(l, ltypes):
-        return [l]
+    if not isinstance(thing, ltypes):
+        return [thing]
 
-    ltype = type(l)
-    l = list(l)
+    ltype = type(thing)
+    thing_list = list(thing)
     i = 0
-    while i < len(l):
-        while isinstance(l[i], ltypes):
-            if not l[i]:
-                l.pop(i)
+    while i < len(thing_list):
+        while isinstance(thing_list[i], ltypes):
+            if not thing_list[i]:
+                thing_list.pop(i)
                 i -= 1
                 break
             else:
-                l[i : i + 1] = l[i]
+                thing_list[i : i + 1] = thing_list[i]
         i += 1
-    return cast(Callable[[Any], List[Any]], ltype)(l)
+    return cast(Callable[[Any], List[Any]], ltype)(thing_list)
diff --git a/cwltool/job.py b/cwltool/job.py
@@ -34,10 +34,9 @@
 import psutil
 import shellescape
 from prov.model import PROV
-from typing_extensions import TYPE_CHECKING
-
 from schema_salad.sourceline import SourceLine
 from schema_salad.utils import json_dump, json_dumps
+from typing_extensions import TYPE_CHECKING
 
 from .builder import Builder, HasReqsHints
 from .context import RuntimeContext, getdefault
diff --git a/cwltool/load_tool.py b/cwltool/load_tool.py
@@ -20,7 +20,6 @@
 )
 
 import requests.sessions
-
 from ruamel.yaml.comments import CommentedMap, CommentedSeq
 from schema_salad import schema
 from schema_salad.ref_resolver import ContextType, Fetcher, Loader, SubLoader, file_uri
diff --git a/cwltool/main.py b/cwltool/main.py
@@ -32,7 +32,6 @@
 
 import coloredlogs
 import pkg_resources  # part of setuptools
-
 from ruamel import yaml
 from ruamel.yaml.comments import CommentedMap, CommentedSeq
 from schema_salad import validate
diff --git a/cwltool/pack.py b/cwltool/pack.py
@@ -19,9 +19,9 @@
 from schema_salad.ref_resolver import Loader, SubLoader
 from schema_salad.sourceline import cmap
 
-from .process import shortname, uniquename
 from .context import LoadingContext
 from .load_tool import fetch_document, resolve_and_validate_document
+from .process import shortname, uniquename
 
 
 def flatten_deps(d, files):  # type: (Any, Set[str]) -> None
diff --git a/cwltool/pathmapper.py b/cwltool/pathmapper.py
@@ -23,7 +23,6 @@
 import requests
 from cachecontrol import CacheControl
 from cachecontrol.caches import FileCache
-
 from schema_salad import validate
 from schema_salad.ref_resolver import uri_file_path
 from schema_salad.sourceline import SourceLine
@@ -135,9 +134,9 @@ def dedup(listing: List[Any]) -> List[Any]:
     def mark(d: Dict[str, str]) -> None:
         marksub.add(d["location"])
 
-    for l in listing:
-        if l["class"] == "Directory":
-            for e in l.get("listing", []):
+    for entry in listing:
+        if entry["class"] == "Directory":
+            for e in entry.get("listing", []):
                 adjustFileObjs(e, mark)
                 adjustDirObjs(e, mark)
 
diff --git a/cwltool/process.py b/cwltool/process.py
@@ -35,12 +35,11 @@
 
 from pkg_resources import resource_stream
 from rdflib import Graph
-from typing_extensions import TYPE_CHECKING
-
 from ruamel.yaml.comments import CommentedMap, CommentedSeq
 from schema_salad import schema, validate
 from schema_salad.ref_resolver import Loader, file_uri, uri_file_path
 from schema_salad.sourceline import SourceLine, strip_dup_lineno
+from typing_extensions import TYPE_CHECKING
 
 from . import expression
 from .builder import Builder, HasReqsHints
@@ -260,7 +259,7 @@ def stage_files(
 
     targets = {}  # type: Dict[str, MapperEnt]
     for key, entry in pathmapper.items():
-        if not "File" in entry.type:
+        if "File" not in entry.type:
             continue
         if entry.target not in targets:
             targets[entry.target] = entry
diff --git a/cwltool/provenance.py b/cwltool/provenance.py
@@ -34,11 +34,10 @@
 from pathlib2 import Path, PurePath, PurePosixPath
 from prov.identifier import Identifier, Namespace
 from prov.model import PROV, ProvDocument, ProvEntity
-from typing_extensions import TYPE_CHECKING
-
 from ruamel import yaml
 from schema_salad.sourceline import SourceLine
 from schema_salad.utils import json_dumps
+from typing_extensions import TYPE_CHECKING
 
 from .context import RuntimeContext
 from .errors import WorkflowException
@@ -1679,7 +1678,7 @@ def _relativise_files(self, structure):
                         prefix = checksum[0:2]
                         relative_path = PurePosixPath("data") / prefix / checksum
 
-                if not relative_path is not None and "location" in structure:
+                if not (relative_path is not None and "location" in structure):
                     # Register in RO; but why was this not picked
                     # up by used_artefacts?
                     _logger.info("[provenance] Adding to RO %s", structure["location"])
diff --git a/cwltool/resolver.py b/cwltool/resolver.py
@@ -6,7 +6,6 @@
 from typing import Any, Optional
 
 from pathlib2 import Path
-
 from schema_salad.ref_resolver import Loader
 
 from .loghandler import _logger
diff --git a/cwltool/sandboxjs.py b/cwltool/sandboxjs.py
@@ -13,7 +13,6 @@
 from typing import Any, Dict, List, Optional, Tuple, Union, cast
 
 from pkg_resources import resource_stream
-
 from schema_salad.utils import json_dumps
 
 from .loghandler import _logger
diff --git a/cwltool/stdfsaccess.py b/cwltool/stdfsaccess.py
@@ -35,7 +35,9 @@ def _abs(self, p):  # type: (str) -> str
         return abspath(p, self.basedir)
 
     def glob(self, pattern):  # type: (str) -> List[str]
-        return [file_uri(str(self._abs(l))) for l in glob.glob(self._abs(pattern))]
+        return [
+            file_uri(str(self._abs(line))) for line in glob.glob(self._abs(pattern))
+        ]
 
     def open(self, fn, mode):  # type: (str, str) -> IO[Any]
         return open(self._abs(fn), mode)
@@ -54,7 +56,8 @@ def isdir(self, fn):  # type: (str) -> bool
 
     def listdir(self, fn):  # type: (str) -> List[str]
         return [
-            abspath(urllib.parse.quote(str(l)), fn) for l in os.listdir(self._abs(fn))
+            abspath(urllib.parse.quote(str(entry)), fn)
+            for entry in os.listdir(self._abs(fn))
         ]
 
     def join(self, path, *paths):  # type: (str, *str) -> str
diff --git a/cwltool/utils.py b/cwltool/utils.py
@@ -54,11 +54,11 @@ def versionstring():
     return "%s %s" % (sys.argv[0], "unknown version")
 
 
-def aslist(l):  # type: (Any) -> MutableSequence[Any]
+def aslist(thing):  # type: (Any) -> MutableSequence[Any]
     """Wrap any non-MutableSequence/list in a list."""
-    if isinstance(l, MutableSequence):
-        return l
-    return [l]
+    if isinstance(thing, MutableSequence):
+        return thing
+    return [thing]
 
 
 def copytree_with_merge(src, dst):  # type: (str, str) -> None
diff --git a/cwltool/validate_js.py b/cwltool/validate_js.py
@@ -16,7 +16,6 @@
 )
 
 from pkg_resources import resource_stream
-
 from ruamel.yaml.comments import CommentedMap
 from schema_salad import avro
 from schema_salad.sourceline import SourceLine
diff --git a/setup.cfg b/setup.cfg
@@ -1,10 +1,19 @@
 [flake8]
 ignore = E124,E128,E129,E201,E202,E225,E226,E231,E265,E271,E302,E303,F401,E402,E501,W503,E731,F811,F821,F841
 exclude = cwltool/schemas
+max-line-length = 88
+extend-ignore = E203, W503
 
 [aliases]
 test=pytest
 
 [tool:pytest]
 addopts=--ignore cwltool/schemas --basetemp ./tmp
 testpaths = tests
+
+[tool:isort]
+multi_line_output = 3
+include_trailing_comma = True
+force_grid_wrap = 0
+use_parentheses = True
+line_length = 88
diff --git a/tests/test_default_path.py b/tests/test_default_path.py
@@ -1,6 +1,7 @@
-from cwltool.load_tool import fetch_document, resolve_and_validate_document
 from schema_salad.ref_resolver import Loader
 
+from cwltool.load_tool import fetch_document, resolve_and_validate_document
+
 from .util import get_data
 
 
diff --git a/tests/test_examples.py b/tests/test_examples.py
@@ -6,14 +6,14 @@
 from io import BytesIO, StringIO
 
 import pytest
+import schema_salad.validate
 
 import cwltool.checker
 import cwltool.expression as expr
 import cwltool.factory
 import cwltool.pathmapper
 import cwltool.process
 import cwltool.workflow
-import schema_salad.validate
 from cwltool.context import RuntimeContext
 from cwltool.errors import WorkflowException
 from cwltool.main import main
diff --git a/tests/test_fetch.py b/tests/test_fetch.py
@@ -2,10 +2,10 @@
 import urllib
 
 import pytest
-
 import schema_salad.main
 import schema_salad.ref_resolver
 import schema_salad.schema
+
 from cwltool.context import LoadingContext
 from cwltool.load_tool import load_tool
 from cwltool.main import main
diff --git a/tests/test_load_tool.py b/tests/test_load_tool.py
@@ -1,15 +1,12 @@
-import pytest
 import pkg_resources
+import pytest
 
 from cwltool.context import LoadingContext, RuntimeContext
 from cwltool.errors import WorkflowException
 from cwltool.load_tool import load_tool
+from cwltool.process import use_custom_schema, use_standard_schema
 from cwltool.resolver import Path, resolve_local
 from cwltool.update import INTERNAL_VERSION
-from cwltool.process import (
-    use_custom_schema,
-    use_standard_schema,
-)
 
 from .test_fetch import norm
 from .util import (
diff --git a/tests/test_pack.py b/tests/test_pack.py
diff --git a/tests/test_singularity.py b/tests/test_singularity.py
diff --git a/tests/test_subgraph.py b/tests/test_subgraph.py
diff --git a/tests/test_toolargparse.py b/tests/test_toolargparse.py
diff --git a/tests/test_validate_js.py b/tests/test_validate_js.py
diff --git a/tox.ini b/tox.ini

Original file line number	Diff line number	Diff line change
`@@ -20,7 +20,6 @@`
`20`	`20`	`)`
`21`	`21`
`22`	`22`	`import requests.sessions`
`23`		`-`
`24`	`23`	`from ruamel.yaml.comments import CommentedMap, CommentedSeq`
`25`	`24`	`from schema_salad import schema`
`26`	`25`	`from schema_salad.ref_resolver import ContextType, Fetcher, Loader, SubLoader, file_uri`