remove wildcard imports

looper/__init__.py

@@ -26,7 +26,6 @@
     write_sample_yaml_prj,
     write_custom_template,
 )
-from .const import *
 from .pipeline_interface import PipelineInterface
 from .project import Project
 

looper/cli_pydantic.py

@@ -17,6 +17,7 @@
 # with types.
 from __future__ import annotations
 
+import os
 import sys
 
 import logmuse
@@ -35,11 +36,32 @@
     TopLevelParser,
     add_short_arguments,
 )
-from .const import *
+from .const import (
+    CLI_KEY,
+    CLI_PROJ_ATTRS,
+    EXAMPLE_COMPUTE_SPEC_FMT,
+    PipelineLevel,
+    PROJECT_PL_ARG,
+    SAMPLE_EXCLUSION_OPTNAME,
+    SAMPLE_INCLUSION_OPTNAME,
+    SAMPLE_PL_ARG,
+)
 from .divvy import DEFAULT_COMPUTE_RESOURCES_NAME, select_divvy_config
-from .exceptions import *
-from .looper import *
-from .parser_types import *
+from .exceptions import (
+    MisconfigurationException,
+    PipestatConfigurationException,
+    SampleFailedException,
+)
+from .looper import (
+    Checker,
+    Cleaner,
+    Collator,
+    Destroyer,
+    Linker,
+    Reporter,
+    Runner,
+    Tabulator,
+)
 from .project import Project, ProjectContext
 from .utils import (
     dotfile_path,

looper/conductor.py

@@ -12,7 +12,7 @@
 from math import ceil
 from json import loads
 from subprocess import check_output
-from typing import *
+from typing import Optional
 
 from eido import read_schema, get_input_files_size
 from eido.const import INPUT_FILE_SIZE_KEY, MISSING_KEY
@@ -25,15 +25,31 @@
 from yaml import dump
 from yacman import FutureYAMLConfigManager as YAMLConfigManager
 
-from .const import *
+from .const import (
+    EXTRA_PROJECT_CMD_TEMPLATE,
+    EXTRA_SAMPLE_CMD_TEMPLATE,
+    JOB_NAME_KEY,
+    NOT_SUB_MSG,
+    OUTDIR_KEY,
+    OUTPUT_SCHEMA_KEY,
+    PipelineLevel,
+    PRE_SUBMIT_CMD_KEY,
+    PRE_SUBMIT_HOOK_KEY,
+    PRE_SUBMIT_PY_FUN_KEY,
+    PROJECT_PL_KEY,
+    RESULTS_SUBDIR_KEY,
+    SAMPLE_CWL_YAML_PATH_KEY,
+    SAMPLE_PL_KEY,
+    SUBMISSION_SUBDIR_KEY,
+    VAR_TEMPL_KEY,
+)
 from .exceptions import JobSubmissionException
 from .processed_project import populate_sample_paths
 from .utils import (
     fetch_sample_flags,
     jinja_render_template_strictly,
     expand_nested_var_templates,
 )
-from .const import PipelineLevel
 
 
 _LOGGER = logging.getLogger(__name__)

looper/looper.py

@@ -27,7 +27,6 @@
 from eido import validate_config, validate_sample
 from eido.exceptions import EidoValidationError
 from jsonschema import ValidationError
-from peppy.const import *
 from peppy.exceptions import RemoteYAMLError
 from rich.color import Color
 from rich.console import Console
@@ -37,8 +36,19 @@
 
 from .conductor import SubmissionConductor
 
-from .exceptions import *
-from .const import *
+from .exceptions import (
+    JobSubmissionException,
+    LooperReportError,
+    MisconfigurationException,
+    SampleFailedException,
+)
+from .const import (
+    DEBUG_COMMANDS,
+    DEBUG_EIDO_VALIDATION,
+    DEBUG_JOBS,
+    NOT_SUB_MSG,
+    SUBMISSION_FAILURE_MESSAGE,
+)
 from .project import Project
 from .utils import (
     desired_samples_range_skipped,

looper/pipeline_interface.py

@@ -12,7 +12,19 @@
 from ubiquerg import expandpath, is_url
 from yacman import load_yaml, YAMLConfigManager
 
-from .const import *
+from .const import (
+    COMPUTE_KEY,
+    DYN_VARS_KEY,
+    FILE_SIZE_COLNAME,
+    ID_COLNAME,
+    INPUT_SCHEMA_KEY,
+    LOOPER_KEY,
+    PIFACE_SCHEMA_SRC,
+    PIPELINE_INTERFACE_PIPELINE_NAME_KEY,
+    RESOURCES_KEY,
+    SIZE_DEP_VARS_KEY,
+    VAR_TEMPL_KEY,
+)
 from .exceptions import (
     InvalidResourceSpecificationException,
     PipelineInterfaceConfigError,

looper/plugins.py

@@ -1,6 +1,10 @@
 import logging
 import os
-from .const import *
+from .const import (
+    SAMPLE_CWL_YAML_PATH_KEY,
+    SAMPLE_YAML_PATH_KEY,
+    SAMPLE_YAML_PRJ_PATH_KEY,
+)
 from .conductor import _get_yaml_path
 
 _LOGGER = logging.getLogger(__name__)

looper/processed_project.py

@@ -128,8 +128,8 @@
 import os
 from logging import getLogger
 
-from eido.const import *
-from eido.exceptions import *
+from eido.const import PROP_KEY
+from eido.exceptions import EidoSchemaInvalidError
 from peppy.project import Project
 from peppy.sample import Sample
 

looper/project.py

@@ -2,6 +2,7 @@
 
 import itertools
 import os
+from typing import List, NoReturn, Union
 
 from yaml import safe_load
 
@@ -15,16 +16,42 @@
 from eido import PathAttrNotFoundError, read_schema
 from jsonschema import ValidationError
 from pandas.core.common import flatten
+from peppy import Project as peppyProject
 from peppy.utils import make_abs_via_cfg
+from peppy.const import CONFIG_KEY
 from pipestat import PipestatManager
 
 from .conductor import write_pipestat_config
 
-from .exceptions import *
+from .exceptions import MisconfigurationException, PipelineInterfaceConfigError
 from .pipeline_interface import PipelineInterface
 from .processed_project import populate_project_paths, populate_sample_paths
-from .utils import *
-from .const import PipelineLevel
+from .utils import (
+    expandpath,
+    fetch_sample_flags,
+    get_sample_status,
+    getLogger,
+    is_pephub_registry_path,
+)
+from .const import (
+    CLI_PROJ_ATTRS,
+    COMPUTE_PACKAGE_KEY,
+    DRY_RUN_KEY,
+    EXTRA_KEY,
+    FILE_CHECKS_KEY,
+    INPUT_SCHEMA_KEY,
+    LOOPER_KEY,
+    OUTDIR_KEY,
+    OUTPUT_SCHEMA_KEY,
+    PIFACE_KEY_SELECTOR,
+    PIPELINE_INTERFACE_PIPELINE_NAME_KEY,
+    PIPELINE_INTERFACES_KEY,
+    PipelineLevel,
+    PIPESTAT_KEY,
+    RESULTS_SUBDIR_KEY,
+    SAMPLE_PL_ARG,
+    SUBMISSION_SUBDIR_KEY,
+)
 
 __all__ = ["Project"]
 

looper/utils.py

@@ -6,20 +6,37 @@
 import itertools
 from logging import getLogger
 import os
-from typing import *
+from typing import Iterable, List, Optional, Tuple, Union
 import re
 
 import jinja2
 import yaml
 from peppy import Project as peppyProject
-from peppy.const import *
+from peppy.const import AMENDMENTS_KEY, CONFIG_KEY, NAME_KEY, SAMPLE_MODS_KEY
 from ubiquerg import convert_value, expandpath, parse_registry_path, deep_update
 from pephubclient.constants import RegistryPath
 from pydantic import ValidationError
 from yacman import load_yaml
 from yaml.parser import ParserError
 
-from .const import *
+from .const import (
+    ALL_SUBCMD_KEY,
+    CLI_KEY,
+    FLAGS,
+    LOOPER_DOTFILE_NAME,
+    LOOPER_GENERIC_COUNT_LINES,
+    LOOPER_GENERIC_OUTPUT_SCHEMA,
+    LOOPER_GENERIC_PIPELINE,
+    LOOPER_KEY,
+    OUTDIR_KEY,
+    PEP_CONFIG_KEY,
+    PIPELINE_INTERFACES_KEY,
+    PIPESTAT_KEY,
+    POSITIONAL,
+    PROJECT_PL_ARG,
+    PipelineLevel,
+    SAMPLE_PL_ARG,
+)
 from .command_models.commands import SUPPORTED_COMMANDS
 from .exceptions import MisconfigurationException, PipelineInterfaceConfigError
 from rich.console import Console