From 7b2c229ad505f2ee2216f78296a2ed974ad23679 Mon Sep 17 00:00:00 2001 From: Donald Campbell <125581724+donaldcampbelljr@users.noreply.github.com> Date: Fri, 21 Jun 2024 15:51:54 -0400 Subject: [PATCH] clean up imports #476 --- looper/cli_pydantic.py | 2 -- looper/const.py | 1 - looper/divvy.py | 6 ------ looper/looper.py | 2 -- looper/pipeline_interface.py | 2 +- looper/project.py | 8 ++------ looper/utils.py | 5 ++--- 7 files changed, 5 insertions(+), 21 deletions(-) diff --git a/looper/cli_pydantic.py b/looper/cli_pydantic.py index 31fd7577e..9e5aca16a 100644 --- a/looper/cli_pydantic.py +++ b/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 diff --git a/looper/const.py b/looper/const.py index 017aceb45..e38cee180 100644 --- a/looper/const.py +++ b/looper/const.py @@ -2,7 +2,6 @@ import os from enum import Enum -from peppy.const import SAMPLE_MODS_KEY __author__ = "Databio lab" __email__ = "nathan@code.databio.org" diff --git a/looper/divvy.py b/looper/divvy.py index bd880f948..38dd8fe21 100644 --- a/looper/divvy.py +++ b/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__) diff --git a/looper/looper.py b/looper/looper.py index 1eea6edd6..18f0d9ed8 100755 --- a/looper/looper.py +++ b/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, diff --git a/looper/pipeline_interface.py b/looper/pipeline_interface.py index 1064f20f3..f796354a4 100644 --- a/looper/pipeline_interface.py +++ b/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__ = "michal@virginia.edu" diff --git a/looper/project.py b/looper/project.py index 6487513c4..6daecac1b 100644 --- a/looper/project.py +++ b/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 * diff --git a/looper/utils.py b/looper/utils.py index 6e052f96e..26776db7a 100644 --- a/looper/utils.py +++ b/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__)