Reorganize common and wf manager

beeflow/client/bee_client.py

@@ -22,9 +22,9 @@
 import yaml
 
 from beeflow.common import config_driver
-from beeflow.common.cli import NaturalOrderGroup
+from beeflow.common.util.cli import NaturalOrderGroup
 from beeflow.common.connection import Connection
-from beeflow.common import paths
+from beeflow.common.util import paths
 from beeflow.common.parser import CwlParser
 from beeflow.common.wf_data import generate_workflow_id
 from beeflow.client import core

beeflow/client/core.py

@@ -24,7 +24,7 @@
 from beeflow.client import bee_client
 from beeflow.common.config_driver import BeeConfig as bc
 from beeflow.common import cli_connection
-from beeflow.common import paths
+from beeflow.common.util import paths
 from beeflow.wf_manager.resources import wf_utils
 
 from beeflow.common.deps import container_manager

beeflow/common/build/container_drivers.py

@@ -8,7 +8,7 @@
 import subprocess
 import tempfile
 from beeflow.common.config_driver import BeeConfig as bc
-from beeflow.common import log as bee_logging
+from beeflow.common.util import log as bee_logging
 from beeflow.common.build.utils import ContainerBuildError
 from beeflow.common.build.build_driver import BuildDriver
 from beeflow.common.crt.charliecloud_driver import CharliecloudDriver as crt_driver

beeflow/common/build_interfaces.py

@@ -13,7 +13,7 @@
 from subprocess import CalledProcessError
 from beeflow.common.build.container_drivers import CharliecloudBuildDriver
 from beeflow.common.config_driver import BeeConfig as bc
-from beeflow.common import log as bee_logging
+from beeflow.common.util import log as bee_logging
 from beeflow.common.build.utils import arg2task, ContainerBuildError
 
 

beeflow/common/config_driver.py

@@ -11,9 +11,9 @@
 import typer
 
 from beeflow.common.config_validator import ConfigValidator
-from beeflow.common.cli import NaturalOrderGroup
-from beeflow.common import validation
-from beeflow.common.tab_completion import filepath_completion
+from beeflow.common.util.cli import NaturalOrderGroup
+from beeflow.common.util import validation
+from beeflow.common.util.tab_completion import filepath_completion
 
 
 # System specific path set up

beeflow/common/config_validator.py

@@ -1,6 +1,6 @@
 """Config validation code."""
 
-from beeflow.common import log as bee_logging
+from beeflow.common.util import log as bee_logging
 
 log = bee_logging.setup(__name__)
 

beeflow/common/crt/charliecloud_driver.py

@@ -10,7 +10,7 @@
 from beeflow.common.config_driver import BeeConfig as bc
 from beeflow.common.build.utils import task2arg
 from beeflow.common.container_path import convert_path
-from beeflow.common import log as bee_logging
+from beeflow.common.util import log as bee_logging
 
 
 log = bee_logging.setup(__name__)

beeflow/common/db/tm_db.py

@@ -4,7 +4,7 @@
 import jsonpickle
 
 from beeflow.common.db import bdb
-from beeflow.common import log as bee_logging
+from beeflow.common.util import log as bee_logging
 from beeflow.common.wf_data import TaskStateUpdate
 
 log = bee_logging.setup(__name__)

beeflow/common/deps/container_manager.py

@@ -7,7 +7,7 @@
 import subprocess
 
 from beeflow.common.config_driver import BeeConfig as bc
-from beeflow.common import paths
+from beeflow.common.util import paths
 from celery import shared_task #noqa pylama can't find celery
 
 

beeflow/common/deps/neo4j_manager.py

@@ -9,11 +9,11 @@
 from beeflow.wf_manager.resources import wf_utils
 from beeflow.common.db import wfm_db
 
-from beeflow.common import paths
+from beeflow.common.util import paths
 from beeflow.common.deps import container_manager
 
 from beeflow.common.config_driver import BeeConfig as bc
-from beeflow.common import log as bee_logging
+from beeflow.common.util import log as bee_logging
 
 # Define directories within module scope
 bee_workdir = paths.workdir()

beeflow/common/deps/redis_manager.py

@@ -2,7 +2,7 @@
 import os
 import subprocess
 
-from beeflow.common import paths
+from beeflow.common.util import paths
 
 
 def start(log):

beeflow/common/gdb/gdb_driver.py

@@ -1,7 +1,7 @@
 """Abstract base class for the handling of workflow DAGs."""
 
 from abc import ABC, abstractmethod
-from beeflow.common import log as bee_logging
+from beeflow.common.util import log as bee_logging
 
 log = bee_logging.setup(__name__)
 

beeflow/common/gdb/neo4j_cypher.py

@@ -1,7 +1,7 @@
 """Neo4j/Cypher transaction functions used by the Neo4jDriver class."""
 
 from re import fullmatch
-from beeflow.common import log as bee_logging
+from beeflow.common.util import log as bee_logging
 
 log = bee_logging.setup(__name__)
 

beeflow/common/gdb/neo4j_driver.py

@@ -12,7 +12,7 @@
 from beeflow.common.gdb import neo4j_cypher as tx
 from beeflow.common.wf_data import (Workflow, Task, Requirement, Hint,
                                     InputParameter, OutputParameter, StepInput, StepOutput)
-from beeflow.common import log as bee_logging
+from beeflow.common.util import log as bee_logging
 
 log = bee_logging.setup(__name__)
 

beeflow/common/wf_interface.py

@@ -4,7 +4,7 @@
 """
 
 import re
-from beeflow.common import log as bee_logging
+from beeflow.common.util import log as bee_logging
 from beeflow.common.gdb.neo4j_driver import Neo4jDriver
 
 log = bee_logging.setup(__name__)

beeflow/common/worker/flux_worker.py

@@ -2,7 +2,7 @@
 
 import io
 import os
-from beeflow.common import log as bee_logging
+from beeflow.common.util import log as bee_logging
 from beeflow.common.worker.worker import Worker
 
 log = bee_logging.setup(__name__)

beeflow/common/worker/slurm_worker.py

@@ -11,9 +11,9 @@
 import requests_unixsocket
 import requests
 
-from beeflow.common import log as bee_logging
+from beeflow.common.util import log as bee_logging
 from beeflow.common.worker.worker import (Worker, WorkerError)
-from beeflow.common import validation
+from beeflow.common.util import validation
 from beeflow.common.worker.utils import get_state_sacct
 from beeflow.common.worker.utils import parse_key_val
 

beeflow/common/worker/utils.py

@@ -2,7 +2,7 @@
 
 import subprocess
 from beeflow.common.worker.worker import WorkerError
-from beeflow.common import log as bee_logging
+from beeflow.common.util import log as bee_logging
 
 
 log = bee_logging.setup(__name__)

beeflow/common/worker/worker.py

@@ -2,7 +2,7 @@
 
 from abc import ABC, abstractmethod
 import os
-from beeflow.common import log as bee_logging
+from beeflow.common.util import log as bee_logging
 from beeflow.common.crt_interface import ContainerRuntimeInterface
 
 

beeflow/remote/remote.py

@@ -6,7 +6,7 @@
 import uvicorn
 
 from beeflow.common import cli_connection
-from beeflow.common import paths
+from beeflow.common.util import paths
 from beeflow.client import bee_client
 from beeflow.common.config_driver import BeeConfig as bc
 

beeflow/scheduler/scheduler.py

@@ -12,7 +12,7 @@
 from beeflow.scheduler import resource_allocation
 from beeflow.common.config_driver import BeeConfig as bc
 from beeflow.common.db import sched_db
-from beeflow.common import log as bee_logging
+from beeflow.common.util import log as bee_logging
 
 from beeflow.common.db.bdb import connect_db
 

beeflow/task_manager/background.py

@@ -6,7 +6,7 @@
 import traceback
 import jsonpickle
 from beeflow.task_manager import utils
-from beeflow.common import log as bee_logging
+from beeflow.common.util import log as bee_logging
 from beeflow.common.build.utils import ContainerBuildError
 from beeflow.common.build_interfaces import build_main
 from beeflow.common.worker import WorkerError

beeflow/task_manager/task_actions.py

@@ -2,7 +2,7 @@
 import traceback
 from flask import jsonify, make_response
 from flask_restful import Resource
-from beeflow.common import log as bee_logging
+from beeflow.common.util import log as bee_logging
 from beeflow.task_manager import utils
 
 log = bee_logging.setup(__name__)

beeflow/task_manager/task_submit.py

@@ -2,7 +2,7 @@
 from flask import jsonify, make_response
 from flask_restful import Resource, reqparse
 import jsonpickle
-from beeflow.common import log as bee_logging
+from beeflow.common.util import log as bee_logging
 from beeflow.task_manager import utils
 
 log = bee_logging.setup(__name__)

beeflow/task_manager/utils.py

@@ -6,7 +6,7 @@
 from beeflow.common.db import tm_db
 from beeflow.common.db import bdb
 from beeflow.common import worker
-from beeflow.common import paths
+from beeflow.common.util import paths
 from beeflow.common.connection import Connection
 from beeflow.common.worker_interface import WorkerInterface