Merge pull request #550 from jmchilton/import_order_fixes

Fix import order throughout project.

dev-requirements.txt

@@ -18,6 +18,7 @@ readme
 # Used for code checking.
 pyflakes
 flake8
+flake8-import-order
 
 # For release
 wheel

planemo/cli.py

@@ -6,14 +6,15 @@
 
 import click
 
-from .io import error
+from planemo import __version__
+from planemo.exit_codes import ExitCodeException
+from planemo.galaxy import profiles
+
 from .config import (
-    read_global_config,
     OptionSource,
+    read_global_config,
 )
-from planemo.galaxy import profiles
-from planemo.exit_codes import ExitCodeException
-from planemo import __version__
+from .io import error
 
 PYTHON_2_7_COMMANDS = ["run", "cwl_script"]
 IS_PYTHON_2_7 = sys.version_info[0] == 2 and sys.version_info[1] >= 7

planemo/commands/cmd_brew.py

@@ -1,16 +1,15 @@
 """Module describing the planemo ``brew`` command."""
 import click
 
-from planemo.cli import command_function
-from planemo import options
-
-from galaxy.tools.loader_directory import load_tool_elements_from_path
-
-from galaxy.tools.deps.requirements import parse_requirements_from_xml
 from galaxy.tools.deps import brew_exts
 from galaxy.tools.deps import brew_util
+from galaxy.tools.deps.requirements import parse_requirements_from_xml
+from galaxy.tools.loader_directory import load_tool_elements_from_path
 from galaxy.util import bunch
 
+from planemo import options
+from planemo.cli import command_function
+
 
 @click.command('brew')
 @options.optional_tools_arg()

planemo/commands/cmd_brew_env.py

@@ -1,18 +1,19 @@
 """Module describing the planemo ``brew_env`` command."""
 from __future__ import print_function
-import click
 import os
 
-from planemo.cli import command_function
-from planemo import options
-from planemo.io import ps1_for_path
+import click
 
-from galaxy.tools.loader import load_tool
-from galaxy.tools.deps.requirements import parse_requirements_from_xml
 from galaxy.tools.deps import brew_exts
 from galaxy.tools.deps import brew_util
+from galaxy.tools.deps.requirements import parse_requirements_from_xml
+from galaxy.tools.loader import load_tool
 from galaxy.util import bunch
 
+from planemo import options
+from planemo.cli import command_function
+from planemo.io import ps1_for_path
+
 
 @click.command('brew_env')
 @options.optional_tools_arg()

planemo/commands/cmd_brew_init.py

@@ -1,9 +1,9 @@
 """Module describing the planemo ``brew_init`` command."""
-import click
-
 import urllib
 from tempfile import mkstemp
 
+import click
+
 from planemo.cli import command_function
 from planemo.io import shell
 

planemo/commands/cmd_conda_env.py

@@ -1,16 +1,15 @@
 """Module describing the planemo ``conda_env`` command."""
 from __future__ import print_function
-import click
 
-from planemo.cli import command_function
-from planemo import options
+import click
 
-from planemo.io import ps1_for_path
-from planemo.io import error
+from galaxy.tools.deps import conda_util
 
+from planemo import options
+from planemo.cli import command_function
 from planemo.conda import build_conda_context, collect_conda_targets
-
-from galaxy.tools.deps import conda_util
+from planemo.io import error
+from planemo.io import ps1_for_path
 
 
 SOURCE_COMMAND = """

planemo/commands/cmd_conda_init.py

@@ -1,12 +1,12 @@
 """Module describing the planemo ``conda_init`` command."""
 import click
 
-from planemo.cli import command_function
+from galaxy.tools.deps import conda_util
+
 from planemo import options
+from planemo.cli import command_function
 from planemo.conda import build_conda_context
 
-from galaxy.tools.deps import conda_util
-
 
 @click.command('conda_init')
 @options.conda_target_options()

planemo/commands/cmd_conda_install.py

@@ -1,13 +1,12 @@
 """Module describing the planemo ``conda_install`` command."""
 import click
 
-from planemo.cli import command_function
-from planemo.io import coalesce_return_codes
-from planemo import options
+from galaxy.tools.deps import conda_util
 
+from planemo import options
+from planemo.cli import command_function
 from planemo.conda import build_conda_context, collect_conda_targets
-
-from galaxy.tools.deps import conda_util
+from planemo.io import coalesce_return_codes
 
 
 @click.command('conda_install')

planemo/commands/cmd_config_init.py

@@ -4,10 +4,10 @@
 
 import click
 
-from planemo.cli import command_function
-from planemo import options
 from planemo import config
-from planemo.io import warn, info
+from planemo import options
+from planemo.cli import command_function
+from planemo.io import info, warn
 
 CONFIG_TEMPLATE = """## Planemo Global Configuration File.
 ## Everything in this file is completely optional - these values can all be

planemo/commands/cmd_create_gist.py

@@ -1,9 +1,9 @@
 """Module describing the planemo ``create_gist`` command."""
 import click
 
+from planemo import github_util
 from planemo.cli import command_function
 from planemo.io import info
-from planemo import github_util
 
 target_path = click.Path(
     file_okay=True,

planemo/commands/cmd_cwl_script.py

@@ -3,8 +3,8 @@
 
 import click
 
-from planemo.cli import command_function
 from planemo import options
+from planemo.cli import command_function
 from planemo.cwl import to_script
 
 

planemo/commands/cmd_database_create.py

@@ -3,8 +3,8 @@
 
 import click
 
-from planemo.cli import command_function
 from planemo import options
+from planemo.cli import command_function
 from planemo.database import create_database_source
 
 

planemo/commands/cmd_database_delete.py

@@ -2,8 +2,8 @@
 
 import click
 
-from planemo.cli import command_function
 from planemo import options
+from planemo.cli import command_function
 from planemo.database import create_database_source
 
 

planemo/commands/cmd_database_list.py

@@ -3,8 +3,8 @@
 
 import click
 
-from planemo.cli import command_function
 from planemo import options
+from planemo.cli import command_function
 from planemo.database import create_database_source
 
 

planemo/commands/cmd_dependency_script.py

@@ -2,14 +2,13 @@
 import os
 import sys
 
-import click
-
 from xml.etree import ElementTree as ET
 
-from planemo.io import info, error
-from planemo.cli import command_function
-from planemo import options
+import click
 
+from planemo import options
+from planemo.cli import command_function
+from planemo.io import error, info
 from planemo.shed2tap.base import BasePackage, Dependency
 
 

planemo/commands/cmd_docker_build.py

@@ -1,11 +1,13 @@
 """Module describing the planemo ``docker_build`` command."""
+
 import click
-from planemo.cli import command_function
-from planemo import options
-from planemo.io import error
 
 from galaxy.tools.deps import dockerfiles
 
+from planemo import options
+from planemo.cli import command_function
+from planemo.io import error
+
 
 @click.command('docker_build')
 @options.optional_tools_arg()

planemo/commands/cmd_docker_shell.py

@@ -11,15 +11,17 @@
 such a tag from a Dockerfile located in the tool's directory.
 """
 from __future__ import print_function
-import click
 import os
-from planemo.cli import command_function
-from planemo import options
 
-from galaxy.tools.loader import load_tool
+import click
+
 from galaxy.tools.deps import docker_util
 from galaxy.tools.deps import dockerfiles
 from galaxy.tools.deps.requirements import parse_requirements_from_xml
+from galaxy.tools.loader import load_tool
+
+from planemo import options
+from planemo.cli import command_function
 
 
 @click.command('docker_shell')

planemo/commands/cmd_lint.py

@@ -1,9 +1,8 @@
 """Module describing the planemo ``lint`` command."""
 import click
 
-from planemo.cli import command_function
 from planemo import options
-
+from planemo.cli import command_function
 from planemo.tool_lint import build_lint_args
 from planemo.tool_lint import lint_tools_on_path
 

planemo/commands/cmd_normalize.py

@@ -3,14 +3,14 @@
 
 import click
 
-from planemo.cli import command_function
-from planemo import options
-
+from galaxy.tools.linters.xml_order import TAG_ORDER
 from galaxy.tools.loader import (
     load_tool,
     raw_tool_xml_tree,
 )
-from galaxy.tools.linters.xml_order import TAG_ORDER
+
+from planemo import options
+from planemo.cli import command_function
 
 
 @click.command('normalize')

planemo/commands/cmd_profile_create.py

@@ -3,8 +3,8 @@
 
 import click
 
-from planemo.cli import command_function
 from planemo import options
+from planemo.cli import command_function
 from planemo.galaxy import profiles
 
 

planemo/commands/cmd_profile_delete.py

@@ -3,8 +3,8 @@
 
 import click
 
-from planemo.cli import command_function
 from planemo import options
+from planemo.cli import command_function
 from planemo.galaxy import profiles
 
 

planemo/commands/cmd_project_init.py

@@ -1,16 +1,16 @@
 """Module describing the planemo ``project_init`` command."""
 import os
-import tempfile
 import shutil
+import tempfile
 
 import click
 
-from planemo.cli import command_function
 from planemo import options
+from planemo.cli import command_function
 from planemo.io import (
-    warn,
+    shell,
     untar_to,
-    shell
+    warn,
 )
 
 SOURCE_HOST = "https://codeload.github.com"

planemo/commands/cmd_run.py

@@ -5,8 +5,8 @@
 
 import click
 
-from planemo.cli import command_function
 from planemo import options
+from planemo.cli import command_function
 from planemo.engine import engine_context
 from planemo.io import conditionally_captured_io, warn
 

planemo/commands/cmd_serve.py

@@ -1,10 +1,10 @@
 """Module describing the planemo ``serve`` command."""
 import click
 
+from planemo import options
 from planemo.cli import command_function
-from planemo.runnable import for_paths
 from planemo.galaxy import galaxy_serve
-from planemo import options
+from planemo.runnable import for_paths
 
 
 @click.command('serve')

planemo/commands/cmd_share_test.py

@@ -1,10 +1,10 @@
 """Module describing the planemo ``share_test`` command."""
 import click
 
-from planemo.cli import command_function
+from planemo import github_util
 from planemo import options
+from planemo.cli import command_function
 from planemo.io import info
-from planemo import github_util
 
 PLANEMO_TEST_VIEWER_URL_TEMPLATE = (
     "http://galaxyproject.github.io/planemo/tool_test_viewer.html"

planemo/commands/cmd_shed_build.py

@@ -1,12 +1,13 @@
 """Module describing the planemo ``shed_build`` command."""
+
+import shutil
 import sys
 
 import click
-import shutil
 
-from planemo.cli import command_function
 from planemo import options
 from planemo import shed
+from planemo.cli import command_function
 
 
 @click.command("shed_build")
@@ -18,7 +19,6 @@ def cli(ctx, path, **kwds):
     This will use the .shed.yml file to prepare a tarball
     (which you could upload to the Tool Shed manually).
     """
-
     def build(realized_repository):
         tarpath = shed.build_tarball(realized_repository.path)
         outpath = realized_repository.real_path + ".tar.gz"