Fix to restore linting of tests directory.

Fix up regressions missed while linting was off and add import order linting for the whole module.

tests/shed_app.py

@@ -1,11 +1,11 @@
 """ Test app to emulate planemo-relevant portions of the
 the ToolShed API... for now :).
 """
-import os
 import json
+import os
 import tarfile
-from uuid import uuid4
 
+from uuid import uuid4
 from xml.etree import ElementTree
 
 from flask import (

tests/shed_app_test_utils.py

@@ -1,17 +1,19 @@
-from collections import namedtuple
 import contextlib
 import shutil
-from tempfile import mkdtemp
 import threading
-from requests import post
 
+from collections import namedtuple
+from tempfile import mkdtemp
+
+from requests import post
 from werkzeug.serving import run_simple
 
+from planemo import network_util
+
 from .shed_app import (
     app,
     InMemoryShedDataModel,
 )
-from planemo import network_util
 
 DEFAULT_OP_TIMEOUT = 2
 

tests/test_cmd_serve.py

@@ -1,20 +1,20 @@
 import functools
 import os
-import time
 import threading
+import time
 import uuid
 
-from planemo.galaxy import api
 from planemo import network_util
+from planemo.galaxy import api
 from planemo.io import kill_pid_file
 
 from .test_utils import (
     CliTestCase,
+    PROJECT_TEMPLATES_DIR,
     skip_if_environ,
     skip_unless_environ,
-    TEST_REPOS_DIR,
-    PROJECT_TEMPLATES_DIR,
     TEST_DATA_DIR,
+    TEST_REPOS_DIR,
 )
 
 TEST_HISTORY_NAME = "Cool History 42"
@@ -106,7 +106,6 @@ def _launch_thread_and_wait(self, func, args=[]):
         assert network_util.wait_net_service("127.0.0.1", port)
 
     def _run(self, serve_args=[]):
-        cat_path = os.path.join(TEST_REPOS_DIR, "single_tool", "cat.xml")
         test_cmd = [
             "serve",
             "--install_galaxy",

tests/test_cmd_shed_serve.py

@@ -1,14 +1,15 @@
 import functools
 import os
-import time
 import threading
+import time
+
+from planemo import network_util
 
 from .test_utils import (
     CliTestCase,
     skip_if_environ,
     TEST_REPOS_DIR,
 )
-from planemo import network_util
 
 
 class ShedServeTestCase(CliTestCase):

tests/test_cmd_test.py

@@ -6,9 +6,9 @@
     assert_exists,
     CliTestCase,
     PROJECT_TEMPLATES_DIR,
-    skip_unless_python_2_7,
     skip_if_environ,
     skip_unless_environ,
+    skip_unless_python_2_7,
     TEST_DATA_DIR,
 )
 

tests/test_command_io.py

@@ -1,7 +1,8 @@
 """Test cases for the CommandIO abstraction in tool_builder."""
 
 from planemo.tool_builder import CommandIO
-from test_utils import assert_equal
+
+from .test_utils import assert_equal
 
 
 def test_simplest_command():

tests/test_dependency_script.py

@@ -1,11 +1,11 @@
-import os
 import glob
+import os
 import tempfile
 
 from .test_utils import (
     CliTestCase,
-    TEST_REPOS_DIR,
     skip_if_environ,
+    TEST_REPOS_DIR,
 )
 
 

tests/test_engines.py

@@ -1,12 +1,12 @@
 """Unit tests for engines and runnables."""
+
 import os
 
 from planemo.engine import engine_context
 from planemo.runnable import for_path
 from planemo.runnable import get_outputs
 
-
-from .test_utils import CWL_DRAFT3_DIR, TEST_DATA_DIR, test_context
+from .test_utils import CWL_DRAFT3_DIR, test_context, TEST_DATA_DIR
 
 A_CWL_TOOL = os.path.join(CWL_DRAFT3_DIR, "cat3-tool.cwl")
 A_CWL_WORKFLOW = os.path.join(CWL_DRAFT3_DIR, "count-lines1-wf.cwl")

tests/test_galaxy_config.py

@@ -2,10 +2,10 @@
 import contextlib
 import os
 
-from .test_utils import TempDirectoryContext, test_context
-
 from planemo.galaxy.config import galaxy_config
 
+from .test_utils import TempDirectoryContext, test_context
+
 
 def test_defaults():
     """Test by default Galaxy files are stored in temp ``config_directory``."""

tests/test_galaxy_serve.py

@@ -5,17 +5,18 @@
 """
 import os
 
+from planemo import network_util
+from planemo import shed
+from planemo.galaxy import galaxy_serve, shed_serve
+from planemo.runnable import for_path
+
 from .test_utils import (
     CliTestCase,
+    PROJECT_TEMPLATES_DIR,
     skip_if_environ,
-    TEST_REPOS_DIR,
     TEST_DATA_DIR,
-    PROJECT_TEMPLATES_DIR,
+    TEST_REPOS_DIR,
 )
-from planemo.runnable import for_path
-from planemo.galaxy import galaxy_serve, shed_serve
-from planemo import network_util
-from planemo import shed
 
 
 class GalaxyServeTestCase(CliTestCase):

tests/test_galaxy_test.py

@@ -3,16 +3,15 @@
 import os
 import shutil
 
-from .test_utils import (
-    test_context,
-    TempDirectoryTestCase,
-    TEST_DATA_DIR,
-)
-
 from planemo.galaxy.test import structures
 from planemo.galaxy.test.actions import passed
 from planemo.galaxy.test.actions import run_in_config
 
+from .test_utils import (
+    TempDirectoryTestCase,
+    test_context,
+    TEST_DATA_DIR,
+)
 
 nose_1_3_report = os.path.join(TEST_DATA_DIR, "xunit_nose_1_3.xml")
 nose_0_11_report = os.path.join(TEST_DATA_DIR, "xunit_nose_0_11.xml")

tests/test_galaxy_workflow_utils.py

@@ -1,9 +1,10 @@
 """Test utilities for dealing with Galaxy workflows."""
 import os
 
-from .test_utils import TEST_DATA_DIR
 from planemo.galaxy.workflows import describe_outputs
 
+from .test_utils import TEST_DATA_DIR
+
 
 def test_describe_outputs():
     wf_path = os.path.join(TEST_DATA_DIR, "wf1.gxwf.yml")

tests/test_git.py

@@ -1,9 +1,10 @@
 import contextlib
 import os
 
-from .test_utils import io
 from planemo import git
 
+from .test_utils import io
+
 EXPECTED_HELLO_REV = "1c36390f585f8baa953548c00fc18c58e32fcf8b"
 
 COMMITTER_DATE = "GIT_COMMITTER_DATE='2000-01-01T00:00:00+0000'"

tests/test_io.py

@@ -1,7 +1,7 @@
 """Test utilities from :module:`planemo.io`."""
 from .test_utils import (
-    io,
     assert_equal,
+    io,
 )
 
 

tests/test_lint.py

@@ -1,10 +1,10 @@
-import os
 import glob
+import os
 
 from .test_utils import (
     CliTestCase,
-    TEST_TOOLS_DIR,
     TEST_REPOS_DIR,
+    TEST_TOOLS_DIR,
 )
 
 

tests/test_profile_commands.py

@@ -1,6 +1,5 @@
 from .test_utils import (
     CliTestCase,
-    skip_unless_environ,
 )
 
 

tests/test_shed.py

@@ -2,21 +2,22 @@
 """
 
 import os
-import string
 import random
+import string
 
 import yaml
 
 from bioblend import toolshed
 
+from planemo import io
+from planemo.shed import username
+
 from .test_utils import (
-    skip_unless_environ,
     CliTestCase,
+    skip_unless_environ,
     TEST_DIR
 )
 
-from planemo.shed import username
-from planemo import io
 
 SHED_TEMPLATE = string.Template("""owner: ${owner}
 name: ${name}

tests/test_shed_create.py

@@ -1,6 +1,7 @@
+from planemo import shed
+
 from .test_utils import CliShedTestCase
 from .test_utils import skip
-from planemo import shed
 
 CS1_DESCRIPTION = "The tool Cat 1 from the cat tool suite."
 CS2_DESCRIPTION = "The tool Cat 2 from the cat tool suite."

tests/test_shed_diff.py

@@ -1,19 +1,21 @@
 """ Integration tests for shed_diff command.
 """
 
-from os.path import join
-from .test_utils import (
-    CliShedTestCase,
-    TEST_REPOS_DIR,
-)
-from planemo import io
-import tempfile
-import sys
 import os
+import sys
+import tempfile
+
+from os.path import join
 from xml.etree import ElementTree
+
+from planemo import io
 from planemo.xml.diff import diff
 
 from .test_shed_upload import update_package_1
+from .test_utils import (
+    CliShedTestCase,
+    TEST_REPOS_DIR,
+)
 
 DIFF_LINES = [
     "diff -r _workingdir_/related_file _custom_shed_/related_file",

tests/test_shed_diff_xml.py

@@ -1,8 +1,9 @@
 import os
 
-from .test_utils import TEST_DIR
 from planemo.shed import diff
 
+from .test_utils import TEST_DIR
+
 
 def test_compare():
     local = os.path.join(TEST_DIR, "repository_dependencies.xml")

tests/test_shed_expansion.py

@@ -3,10 +3,10 @@
 
 import yaml
 
-from .test_utils import TempDirectoryTestCase
-
 from planemo import shed
 
+from .test_utils import TempDirectoryTestCase
+
 
 class ShedExpansionTestCase(TempDirectoryTestCase):
 

tests/test_shed_operations.py

@@ -1,14 +1,14 @@
-""" Test some lower-level utilities in planemo.shed.
-"""
+"""Test some lower-level utilities in planemo.shed."""
+
 import os
 
+from planemo import shed
+
 from .test_utils import (
-    TEST_REPOS_DIR,
     mock_shed_context,
+    TEST_REPOS_DIR,
 )
 
-from planemo import shed
-
 
 def test_find_repository_id():
     with mock_shed_context() as shed_context:

tests/test_shed_upload.py

@@ -3,18 +3,20 @@
 Specifically, tests for shed_upload, shed_download, and shed_create.
 commands.
 """
-from os.path import exists, join
 import os
-import tarfile
 import shutil
+import tarfile
+
+from os.path import exists, join
+
+from planemo import git
+from planemo.io import shell
 
 from .test_utils import (
+    assert_exists,
     CliShedTestCase,
     TEST_REPOS_DIR,
-    assert_exists,
 )
-from planemo.io import shell
-from planemo import git
 
 
 class ShedUploadTestCase(CliShedTestCase):

tests/test_test_checker.py

@@ -2,8 +2,8 @@
 import os
 
 from planemo.runnable import (
-    for_path,
     cases,
+    for_path,
 )
 
 from .test_utils import TEST_DATA_DIR