sorting python imports using isort

Makefile

@@ -26,7 +26,7 @@ MODULE=cwltool
 # `SHELL=bash` doesn't work for some, so don't use BASH-isms like
 # `[[` conditional expressions.
 PYSOURCES=$(wildcard ${MODULE}/**.py tests/*.py) setup.py
-DEVPKGS=pep8 diff_cover autopep8 pylint coverage pep257 flake8 pytest
+DEVPKGS=pep8 diff_cover autopep8 pylint coverage pep257 flake8 pytest isort
 DEBDEVPKGS=pep8 python-autopep8 pylint python-coverage pep257 sloccount python-flake8
 VERSION=1.0.$(shell date +%Y%m%d%H%M%S --date=`git log --first-parent \
 	--max-count=1 --format=format:%cI`)
@@ -65,6 +65,11 @@ clean: FORCE
 	rm -Rf .coverage
 	rm -f diff-cover.html
 
+# Linting and code style related targets
+## sorting imports using isort: https://github.com/timothycrosley/isort
+sort_imports:
+	isort ${MODULE}/*.py tests/*.py setup.py
+
 ## pep8        : check Python code style
 pep8: $(PYSOURCES)
 	pep8 --exclude=_version.py  --show-source --show-pep8 $^ || true

cwltool/builder.py

@@ -1,17 +1,19 @@
 import copy
+from typing import Any, Callable, Text, Type, Union
+
+from six import iteritems, string_types
 
 import avro
 import schema_salad.validate as validate
 from schema_salad.sourceline import SourceLine
-from typing import Any, Callable, Text, Type, Union
-from six import string_types, iteritems
 
 from . import expression
 from .errors import WorkflowException
-from .pathmapper import PathMapper, normalizeFilesDirs, get_listing, visit_class
+from .mutation import MutationManager
+from .pathmapper import (PathMapper, get_listing, normalizeFilesDirs,
+                         visit_class)
 from .stdfsaccess import StdFsAccess
 from .utils import aslist
-from .mutation import MutationManager
 
 CONTENT_LIMIT = 64 * 1024
 

cwltool/cwlrdf.py

@@ -1,7 +1,9 @@
+from typing import IO, Any, Dict, Text
+
 from rdflib import Graph
+
 from schema_salad.jsonld_context import makerdf
 from schema_salad.ref_resolver import ContextType
-from typing import Any, Dict, IO, Text
 from six.moves import urllib
 
 from .process import Process

cwltool/docker.py

@@ -4,9 +4,9 @@
 import subprocess
 import sys
 import tempfile
+from typing import Text
 
 import requests
-from typing import Text
 
 from .errors import WorkflowException
 

cwltool/docker_uid.py

@@ -1,6 +1,6 @@
 from __future__ import print_function
-import subprocess
 
+import subprocess
 from typing import Text
 
 

cwltool/draft2tool.py

@@ -6,32 +6,33 @@
 import re
 import shutil
 import tempfile
-from six.moves import urllib
-from six import string_types, u
 from functools import partial
+from typing import Any, Callable, Dict, Generator, Optional, Text, Union, cast
+
+from six import string_types, u
 
 import schema_salad.validate as validate
 import shellescape
 from schema_salad.ref_resolver import file_uri, uri_file_path
 from schema_salad.sourceline import SourceLine, indent
-from typing import Any, Callable, cast, Generator, Optional, Text, Union, Dict
+from six.moves import urllib
 
-from .builder import CONTENT_LIMIT, substitute, Builder
-from .pathmapper import adjustFileObjs, adjustDirObjs, visit_class
+from .builder import CONTENT_LIMIT, Builder, substitute
 from .errors import WorkflowException
-from .job import JobBase, CommandLineJob, DockerCommandLineJob
-from .pathmapper import PathMapper, get_listing, trim_listing
-from .process import (Process, shortname, uniquename, normalizeFilesDirs,
-                      compute_checksums, _logger_validation_warnings,
-                      UnsupportedRequirement)
+from .flatten import flatten
+from .job import CommandLineJob, DockerCommandLineJob, JobBase
+from .pathmapper import (PathMapper, adjustDirObjs, adjustFileObjs,
+                         get_listing, trim_listing, visit_class)
+from .process import (Process, UnsupportedRequirement,
+                      _logger_validation_warnings, compute_checksums,
+                      normalizeFilesDirs, shortname, uniquename)
 from .stdfsaccess import StdFsAccess
 from .utils import aslist
 
 ACCEPTLIST_EN_STRICT_RE = re.compile(r"^[a-zA-Z0-9._+-]+$")
 ACCEPTLIST_EN_RELAXED_RE = re.compile(r".*")  # Accept anything
 ACCEPTLIST_RE = ACCEPTLIST_EN_STRICT_RE
 
-from .flatten import flatten
 
 _logger = logging.getLogger("cwltool")
 

cwltool/expression.py

@@ -2,8 +2,8 @@
 import json
 import logging
 import re
+from typing import Any, AnyStr, Dict, List, Text, Union
 
-from typing import Any, AnyStr, Union, Text, Dict, List
 from six import u
 
 from . import sandboxjs

cwltool/factory.py

@@ -1,11 +1,8 @@
 import os
-
-from typing import Any, Text, Union, Tuple
 from typing import Callable as tCallable
+from typing import Any, Text, Tuple, Union
 
-from . import load_tool
-from . import main
-from . import workflow
+from . import load_tool, main, workflow
 from .process import Process
 
 

cwltool/flatten.py

@@ -1,6 +1,5 @@
 from typing import Any, Callable, List, cast
 
-
 # http://rightfootin.blogspot.com/2006/09/more-on-python-flatten.html
 
 

cwltool/job.py

@@ -8,18 +8,18 @@
 import subprocess
 import sys
 import tempfile
+from typing import (IO, Any, Callable, Iterable, List, MutableMapping, Text,
+                    Tuple, Union, cast)
 
 import shellescape
-from typing import (Any, Callable, Union, Iterable, MutableMapping,
-                    IO, Text, Tuple, cast, List)
 
 from . import docker
 from .builder import Builder
 from .docker_uid import docker_vm_uid
 from .errors import WorkflowException
 from .pathmapper import PathMapper
-from .process import (get_feature, empty_subtree, stageFiles,
-                      UnsupportedRequirement)
+from .process import (UnsupportedRequirement, empty_subtree, get_feature,
+                      stageFiles)
 
 _logger = logging.getLogger("cwltool")
 

cwltool/load_tool.py

@@ -5,20 +5,20 @@
 import os
 import re
 import uuid
+from typing import Any, Callable, Dict, Text, Tuple, Union, cast
 
 import requests.sessions
+from six import itervalues, string_types
+
 import schema_salad.schema as schema
 from avro.schema import Names
-from ruamel.yaml.comments import CommentedSeq, CommentedMap
-from schema_salad.ref_resolver import Loader, Fetcher, file_uri
+from ruamel.yaml.comments import CommentedMap, CommentedSeq
+from schema_salad.ref_resolver import Fetcher, Loader, file_uri
 from schema_salad.sourceline import cmap
 from schema_salad.validate import ValidationException
-from typing import Any, Callable, cast, Dict, Text, Tuple, Union
 from six.moves import urllib
-from six import itervalues, string_types
 
-from . import process
-from . import update
+from . import process, update
 from .errors import WorkflowException
 from .process import Process, shortname
 

cwltool/main.py

@@ -8,29 +8,31 @@
 import os
 import sys
 import tempfile
+from typing import (IO, Any, AnyStr, Callable, Dict, Sequence, Text, Tuple,
+                    Union, cast)
 
 import pkg_resources  # part of setuptools
 import requests
+
 import ruamel.yaml as yaml
 import schema_salad.validate as validate
-from schema_salad.ref_resolver import Loader, Fetcher, file_uri, uri_file_path
+from schema_salad.ref_resolver import Fetcher, Loader, file_uri, uri_file_path
 from schema_salad.sourceline import strip_dup_lineno
-from typing import (Union, Any, AnyStr, cast, Callable, Dict, Sequence, Text,
-                    Tuple, IO)
-
-from . import draft2tool
-from . import workflow
-from .pathmapper import adjustDirObjs, get_listing, adjustFileObjs, trim_listing, visit_class
-from .cwlrdf import printrdf, printdot
-from .errors import WorkflowException, UnsupportedRequirement
-from .load_tool import fetch_document, validate_document, make_tool
+
+from . import draft2tool, workflow
+from .cwlrdf import printdot, printrdf
+from .errors import UnsupportedRequirement, WorkflowException
+from .load_tool import fetch_document, make_tool, validate_document
+from .mutation import MutationManager
 from .pack import pack
-from .process import (shortname, Process, relocateOutputs, cleanIntermediate,
-                      scandeps, normalizeFilesDirs, use_custom_schema, use_standard_schema)
-from .resolver import tool_resolver, ga4gh_tool_registries
+from .pathmapper import (adjustDirObjs, adjustFileObjs, get_listing,
+                         trim_listing, visit_class)
+from .process import (Process, cleanIntermediate, normalizeFilesDirs,
+                      relocateOutputs, scandeps, shortname, use_custom_schema,
+                      use_standard_schema)
+from .resolver import ga4gh_tool_registries, tool_resolver
 from .stdfsaccess import StdFsAccess
-from .mutation import MutationManager
-from .update import UPDATES, ALLUPDATES
+from .update import ALLUPDATES, UPDATES
 
 _logger = logging.getLogger("cwltool")
 

cwltool/mutation.py

@@ -1,6 +1,5 @@
 from collections import namedtuple
-
-from typing import Any, Callable, cast, Generator, Iterable, List, Text, Union
+from typing import Any, Callable, Generator, Iterable, List, Text, Union, cast
 
 from .errors import WorkflowException
 

cwltool/pack.py

@@ -1,7 +1,7 @@
 import copy
+from typing import Any, Callable, Dict, Text, Union, cast
 
 from schema_salad.ref_resolver import Loader
-from typing import Union, Any, cast, Callable, Dict, Text
 from six.moves import urllib
 
 from .process import shortname, uniquename

cwltool/pathmapper.py

@@ -4,14 +4,14 @@
 import stat
 import uuid
 from functools import partial
+from typing import Any, Callable, Iterable, Set, Text, Tuple, Union
 
 import schema_salad.validate as validate
 from schema_salad.ref_resolver import uri_file_path
 from schema_salad.sourceline import SourceLine
-from typing import Any, Callable, Set, Text, Tuple, Union, Iterable
 from six.moves import urllib
 
-from .stdfsaccess import abspath, StdFsAccess
+from .stdfsaccess import StdFsAccess, abspath
 
 _logger = logging.getLogger("cwltool")
 

cwltool/process.py

@@ -1,6 +1,7 @@
 import abc
 import copy
 import errno
+import functools
 import hashlib
 import json
 import logging
@@ -11,28 +12,28 @@
 import urlparse
 import uuid
 from collections import Iterable
-import functools
+from typing import (Any, AnyStr, Callable, Dict, Generator, List, Text, Tuple,
+                    Union, cast)
+
+from pkg_resources import resource_stream
+from rdflib import Graph, URIRef
+from rdflib.namespace import OWL, RDFS
 
 import avro.schema
 import schema_salad.schema
 import schema_salad.validate as validate
-from pkg_resources import resource_stream
-from rdflib import Graph
-from rdflib import URIRef
-from rdflib.namespace import RDFS, OWL
-from ruamel.yaml.comments import CommentedSeq, CommentedMap
+from ruamel.yaml.comments import CommentedMap, CommentedSeq
 from schema_salad.ref_resolver import Loader, file_uri
 from schema_salad.sourceline import SourceLine
-from typing import (Any, AnyStr, Callable, cast, Dict, List, Generator, Text,
-                    Tuple, Union)
 
 from .builder import Builder
-from .pathmapper import adjustDirObjs, get_listing
-from .errors import WorkflowException, UnsupportedRequirement
-from .pathmapper import PathMapper, normalizeFilesDirs, visit_class
+from .errors import UnsupportedRequirement, WorkflowException
+from .pathmapper import (PathMapper, adjustDirObjs, get_listing,
+                         normalizeFilesDirs, visit_class)
 from .stdfsaccess import StdFsAccess
 from .utils import aslist, get_feature
 
+
 class LogAsDebugFilter(logging.Filter):
     def __init__(self, name, parent):  # type: (str, logging.Logger) -> None
         super(LogAsDebugFilter, self).__init__(name)

cwltool/sandboxjs.py

@@ -6,9 +6,9 @@
 import subprocess
 import threading
 from io import BytesIO
+from typing import Any, Dict, List, Mapping, Text, Tuple, Union
 
 from pkg_resources import resource_stream
-from typing import Any, Dict, List, Mapping, Text, Union, Tuple
 
 
 class JavascriptException(Exception):

cwltool/stdfsaccess.py

@@ -1,9 +1,10 @@
 import glob
 import os
 import urllib
+from typing import BinaryIO, Text
 
 from schema_salad.ref_resolver import file_uri, uri_file_path
-from typing import BinaryIO, Text
+
 
 def abspath(src, basedir):  # type: (Text, Text) -> Text
     if src.startswith(u"file://"):

cwltool/update.py

@@ -3,11 +3,12 @@
 import re
 import traceback
 import urlparse
+from typing import (Any, Callable, Dict, Text,  # pylint: disable=unused-import
+                    Tuple, Union)
 
 import schema_salad.validate
-from ruamel.yaml.comments import CommentedSeq, CommentedMap
+from ruamel.yaml.comments import CommentedMap, CommentedSeq
 from schema_salad.ref_resolver import Loader
-from typing import Any, Callable, Dict, Text, Tuple, Union  # pylint: disable=unused-import
 
 from .utils import aslist
 

cwltool/workflow.py

@@ -5,14 +5,13 @@
 import random
 import tempfile
 from collections import namedtuple
-from ruamel.yaml.comments import CommentedSeq, CommentedMap
+from typing import Any, Callable, Generator, Iterable, List, Text, Union, cast
 
 import schema_salad.validate as validate
+from ruamel.yaml.comments import CommentedMap, CommentedSeq
 from schema_salad.sourceline import SourceLine, cmap
-from typing import Any, Callable, cast, Generator, Iterable, List, Text, Union
 
-from . import draft2tool
-from . import expression
+from . import draft2tool, expression
 from .errors import WorkflowException
 from .load_tool import load_tool
 from .process import Process, shortname, uniquename

tests/test_check.py

@@ -5,9 +5,11 @@
 import cwltool.pathmapper
 import cwltool.process
 import cwltool.workflow
-from .util import get_data
 from cwltool.main import main
 
+from .util import get_data
+
+
 class TestCheck(unittest.TestCase):
     def test_output_checking(self):
         self.assertEquals(main([get_data('tests/wf/badout1.cwl')]), 1)