Merge pull request #407 from manu-chroma/master

sorting python imports using isort

Author: mr-c

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")