diff --git a/planemo/commands/cmd_conda_lint.py b/planemo/commands/cmd_conda_lint.py index 984c0bd7c..566e7c486 100644 --- a/planemo/commands/cmd_conda_lint.py +++ b/planemo/commands/cmd_conda_lint.py @@ -1,8 +1,8 @@ """Module describing the planemo ``conda_lint`` command.""" import click -from planemo import options from planemo import conda_lint +from planemo import options from planemo.cli import command_function diff --git a/planemo/commands/cmd_travis_init.py b/planemo/commands/cmd_travis_init.py index 193fe197d..c60ee011f 100644 --- a/planemo/commands/cmd_travis_init.py +++ b/planemo/commands/cmd_travis_init.py @@ -5,8 +5,8 @@ from galaxy.tools.deps.commands import shell -from planemo import options from planemo import RAW_CONTENT_URL +from planemo import options from planemo.cli import command_function from planemo.io import info, warn diff --git a/planemo/engine/factory.py b/planemo/engine/factory.py index 8e9cf8d8d..989288a2b 100644 --- a/planemo/engine/factory.py +++ b/planemo/engine/factory.py @@ -20,7 +20,7 @@ def build_engine(ctx, **kwds): engine_type_str = kwds.get("engine", "galaxy") if engine_type_str == "galaxy": engine_type = GalaxyEngine - elif engine_type_str == "dockerize_galaxy": + elif engine_type_str == "docker_galaxy": engine_type = DockerizedGalaxyEngine elif engine_type_str == "cwltool": engine_type = CwlToolEngine diff --git a/planemo/galaxy/test/structures.py b/planemo/galaxy/test/structures.py index aa7240eb5..dccb19fc9 100644 --- a/planemo/galaxy/test/structures.py +++ b/planemo/galaxy/test/structures.py @@ -1,6 +1,6 @@ """Utilities for reasoning about Galaxy test results.""" -from __future__ import print_function from __future__ import absolute_import +from __future__ import print_function import os import xml.etree.ElementTree as ET diff --git a/planemo/glob.py b/planemo/glob.py index e03e3a5b8..63adb9f0c 100644 --- a/planemo/glob.py +++ b/planemo/glob.py @@ -1,5 +1,5 @@ -from __future__ import print_function from __future__ import absolute_import +from __future__ import print_function NO_GLOB_2 = "glob2 library unavailabile, please install with pip install glob2." diff --git a/planemo/shed2tap/base.py b/planemo/shed2tap/base.py index f4de640e8..3e13ea9bd 100644 --- a/planemo/shed2tap/base.py +++ b/planemo/shed2tap/base.py @@ -9,8 +9,8 @@ from ftplib import all_errors as FTPErrors # tuple of exceptions from xml.etree import ElementTree -from six import string_types from six import iteritems +from six import string_types from six.moves import map as imap from six.moves.urllib.error import URLError from six.moves.urllib.request import urlretrieve