clean up imports #476

looper/cli_pydantic.py

@@ -17,7 +17,6 @@
 # with types.
 from __future__ import annotations
 
-import os
 import sys
 
 import logmuse
@@ -29,7 +28,6 @@
 
 from divvy import select_divvy_config
 
-from .const import PipelineLevel
 from . import __version__
 
 from .command_models.arguments import ArgumentEnum

looper/const.py

@@ -2,7 +2,6 @@
 
 import os
 from enum import Enum
-from peppy.const import SAMPLE_MODS_KEY
 
 __author__ = "Databio lab"
 __email__ = "[email protected]"

looper/divvy.py

@@ -1,18 +1,13 @@
 """ Computing configuration representation """
 
 import logging
-import logmuse
 import os
-import sys
 import shutil
-import yaml
 
 
 from shutil import copytree
 from yacman import FutureYAMLConfigManager as YAMLConfigManager
 from yacman import write_lock, FILEPATH_KEY, load_yaml, select_config
-from yaml import SafeLoader
-from ubiquerg import is_writable, VersionInHelpParser
 
 
 from .const import (
@@ -24,7 +19,6 @@
 )
 from .utils import write_submit_script
 
-# from . import __version__
 
 _LOGGER = logging.getLogger(__name__)
 

looper/looper.py

@@ -33,14 +33,12 @@
 from rich.console import Console
 from rich.table import Table
 from ubiquerg.cli_tools import query_yes_no
-from ubiquerg.collection import uniqify
 
 
 from .conductor import SubmissionConductor
 
 from .exceptions import *
 from .const import *
-from .pipeline_interface import PipelineInterface
 from .project import Project
 from .utils import (
     desired_samples_range_skipped,

looper/pipeline_interface.py

@@ -17,7 +17,7 @@
     InvalidResourceSpecificationException,
     PipelineInterfaceConfigError,
 )
-from .utils import jinja_render_template_strictly, render_nested_var_templates
+from .utils import render_nested_var_templates
 
 __author__ = "Michal Stolarczyk"
 __email__ = "[email protected]"

looper/project.py

@@ -10,18 +10,14 @@
 except ImportError:
     # cached_property was introduced in python 3.8
     cached_property = property
-from logging import getLogger
 
 from .divvy import ComputingConfiguration
 from eido import PathAttrNotFoundError, read_schema
 from jsonschema import ValidationError
 from pandas.core.common import flatten
-from peppy import CONFIG_KEY, OUTDIR_KEY
-from peppy import Project as peppyProject
 from peppy.utils import make_abs_via_cfg
-from pipestat import PipestatError, PipestatManager
-from ubiquerg import expandpath, is_command_callable, deep_update
-from yacman import YAMLConfigManager
+from pipestat import PipestatManager
+
 from .conductor import write_pipestat_config
 
 from .exceptions import *

looper/utils.py

@@ -1,12 +1,11 @@
 """ Helpers without an obvious logical home. """
 
 import argparse
-from collections import defaultdict, namedtuple
+from collections import defaultdict
 import glob
 import itertools
 from logging import getLogger
 import os
-import sys
 from typing import *
 import re
 
@@ -21,7 +20,7 @@
 
 from .const import *
 from .command_models.commands import SUPPORTED_COMMANDS
-from .exceptions import MisconfigurationException, RegistryPathException
+from .exceptions import MisconfigurationException
 
 _LOGGER = getLogger(__name__)