Commit 057a240d authored by Amir MOHAMMADI's avatar Amir MOHAMMADI

Merge branch 'pre_commit_cleanup' into 'master'

Pre commit cleanup

See merge request !126
parents 8ea89087 4c771e17
Pipeline #41802 passed with stages
in 39 minutes and 6 seconds
[flake8]
max-line-length = 80
max-line-length = 88
select = B,C,E,F,W,T4,B9,B950
ignore = E501, W503, E203
[settings]
multi_line_output=3
include_trailing_comma=true
force_grid_wrap=0
use_parentheses=true
ensure_newline_before_comments=true
line_length=88
force_single_line=true
# See https://pre-commit.com for more information
# See https://pre-commit.com/hooks.html for more hooks
repos:
- repo: https://github.com/ambv/black
rev: stable
- repo: https://github.com/timothycrosley/isort
rev: 5.0.4
hooks:
- id: black
exclude: beat/core/test/prefix/algorithms/errors/syntax_error/1.py|beat/core/test/prefix/databases/invalid/1.py
- id: isort
files: .*.py
- repo: https://github.com/psf/black
rev: 19.10b0
hooks:
- id: black
exclude: beat/core/test/prefix/algorithms/errors/syntax_error/1.py|beat/core/test/prefix/databases/invalid/1.py
- repo: https://github.com/pre-commit/pre-commit-hooks
rev: v2.0.0
rev: v3.1.0
hooks:
- id: check-ast
exclude: beat/core/test/prefix/algorithms/errors/syntax_error/1.py|beat/core/test/prefix/databases/invalid/1.py
- id: check-case-conflict
- id: trailing-whitespace
- id: end-of-file-fixer
- id: debug-statements
exclude: beat/core/test/prefix/algorithms/errors/syntax_error/1.py|beat/core/test/prefix/databases/invalid/1.py
- id: check-added-large-files
- id: check-docstring-first
- id: flake8
- id: check-yaml
exclude: conda/meta.yaml
- repo: https://github.com/PyCQA/flake8
rev: 3.8.3
hooks:
- id: flake8
- repo: https://github.com/PyCQA/bandit
rev: 'master' # Update me!
rev: 1.6.2
hooks:
- id: bandit
exclude: beat/core/test/prefix/algorithms/errors/syntax_error/1.py|beat/core/test/prefix/databases/invalid/1.py
......
......@@ -33,8 +33,8 @@
# #
###################################################################################
# see https://docs.python.org/3/library/pkgutil.html
from pkgutil import extend_path
__path__ = extend_path(__path__, __name__)
......@@ -45,22 +45,21 @@ Forward importing from :py:mod:`beat.backend.python.algorithm`
:py:class:`beat.backend.python.algorithm.Storage`
:py:class:`beat.backend.python.algorithm.Runner`
"""
import os
import six
import numpy
import pkg_resources
import simplejson as json
import six
from beat.backend.python.algorithm import Algorithm as BackendAlgorithm
from beat.backend.python.algorithm import Runner # noqa
from beat.backend.python.algorithm import Storage
from . import dataformat
from . import library
from . import schema
from . import prototypes
from beat.backend.python.algorithm import Storage
from beat.backend.python.algorithm import Runner # noqa
from beat.backend.python.algorithm import Algorithm as BackendAlgorithm
from . import schema
def load_algorithm_prototype(prefix):
......
......@@ -49,15 +49,14 @@ Options:
-V, --version Show version
-v, --verbose Increases the output verbosity level
"""
import os
import sys
from docopt import docopt
from ..bcpapi.broker import BeatComputationBroker
from ..version import __version__
from ..utils import setup_logging
from ..version import __version__
def run(port=5555, verbose=1, callbacks=None):
......
......@@ -61,28 +61,25 @@ Options:
--cache-mount-point=<cache_mount_point> NFS mount point to use for cache setup
"""
import os
import sys
import signal
import sys
import tempfile
import simplejson as json
from socket import gethostname
import simplejson as json
import zmq
from socket import gethostname
from docopt import docopt
from ..bcpapi import BCP
from ..bcpapi.worker import BeatComputationWorker
from ..bcpapi.processor import BeatComputationProcessor
from ..bcpapi.execution import ExecutionProcess
from ..bcpapi.processor import BeatComputationProcessor
from ..bcpapi.worker import BeatComputationWorker
from ..dock import Host
from ..utils import find_free_port
from ..utils import setup_logging
from ..version import __version__
logger = None
......
......@@ -37,20 +37,16 @@
Inspired by the Majordomo Protocol Broker
"""
import logging
import time
import signal
import time
from binascii import hexlify
import zmq
# local
from . import BCP
from .zhelpers import dump
logger = logging.getLogger(__name__)
......
......@@ -40,17 +40,16 @@ management
Execution utilities
"""
import logging
import multiprocessing
import signal
import zmq
import simplejson as json
import zmq
from ..dock import Host
from ..execution.local import LocalExecutor
from ..execution.docker import DockerExecutor
from ..execution.local import LocalExecutor
from . import BCP
......
......@@ -34,8 +34,8 @@
"""BEAT Computation worker"""
import logging
import zmq
from .zhelpers import dump
......
......@@ -34,14 +34,12 @@
"""BEAT Computation worker"""
import logging
import time
import zmq
# BEAT Computation protocol constants:
from . import BCP
from .zhelpers import dump
logger = logging.getLogger(__name__)
......@@ -58,8 +56,8 @@ class BeatComputationWorker(object):
service = service.encode("utf-8")
self.heartbeat_at = (
0
) # When to send HEARTBEAT (relative to time.time(), so in seconds)
0 # When to send HEARTBEAT (relative to time.time(), so in seconds)
)
self.liveness = 0 # How many attempts left
self.heartbeat = 2500 # Heartbeat delay, msecs
self.reconnect = 2500 # Reconnect delay, msecs
......
......@@ -38,9 +38,9 @@ Helper module for common zmq task
Based on Majordomo protocol zhelpers.
"""
import binascii
import logging
import zmq
logger = logging.getLogger(__name__)
......
......@@ -53,16 +53,15 @@ Forward importing from :py:mod:`beat.backend.python.data`:
:py:func:`beat.backend.python.data.load_data_index_db`
:py:func:`beat.backend.python.data.foundSplitRanges`
"""
from beat.backend.python.data import mixDataIndices # noqa
from beat.backend.python.data import getAllFilenames # noqa
from beat.backend.python.data import DataSource # noqa
from beat.backend.python.data import CachedDataSink # noqa
from beat.backend.python.data import CachedDataSource # noqa
from beat.backend.python.data import DatabaseOutputDataSource # noqa
from beat.backend.python.data import RemoteDataSource # noqa
from beat.backend.python.data import DataSink # noqa
from beat.backend.python.data import CachedDataSink # noqa
from beat.backend.python.data import DataSource # noqa
from beat.backend.python.data import RemoteDataSource # noqa
from beat.backend.python.data import StdoutDataSink # noqa
from beat.backend.python.data import foundSplitRanges # noqa
from beat.backend.python.data import getAllFilenames # noqa
from beat.backend.python.data import load_data_index # noqa
from beat.backend.python.data import load_data_index_db # noqa
from beat.backend.python.data import foundSplitRanges # noqa
from beat.backend.python.data import mixDataIndices # noqa
......@@ -44,8 +44,6 @@ Forward importing from :py:mod:`beat.backend.python.data_loaders`
:py:class:`beat.backend.python.data_loaders.DataLoader`
:py:class:`beat.backend.python.data_loaders.DataView`
"""
from beat.backend.python.data_loaders import DataLoaderList # noqa
from beat.backend.python.data_loaders import DataLoader # noqa
from beat.backend.python.data_loaders import DataLoaderList # noqa
from beat.backend.python.data_loaders import DataView # noqa
......@@ -44,22 +44,19 @@ Validation of databases
Forward importing from :py:mod:`beat.backend.python.database`:
:py:class:`beat.backend.python.database.Storage`
"""
import os
import six
from . import schema
from beat.backend.python.database import Database as BackendDatabase
from beat.backend.python.database import Storage
from beat.backend.python.protocoltemplate import Storage as PTStorage
from . import prototypes
from . import schema
from .dataformat import DataFormat
from .protocoltemplate import ProtocolTemplate
from . import prototypes
from beat.backend.python.database import Storage
from beat.backend.python.database import Database as BackendDatabase
from beat.backend.python.protocoltemplate import Storage as PTStorage
def get_first_procotol_template(prefix):
pt_root_folder = os.path.join(prefix, PTStorage.asset_folder)
......
......@@ -44,17 +44,17 @@ Validation and parsing for dataformats
Forward importing from :py:mod:`beat.backend.python.dataformat`:
:py:class:`beat.backend.python.dataformat.Storage`
"""
import copy
import six
from . import schema
from beat.backend.python.dataformat import DataFormat as BackendDataFormat
from beat.backend.python.dataformat import Storage # noqa
from . import prototypes
from . import schema
from . import utils
from beat.backend.python.dataformat import Storage # noqa
from beat.backend.python.dataformat import DataFormat as BackendDataFormat
class DataFormat(BackendDataFormat):
"""Data formats define the chunks of data that circulate between blocks.
......
......@@ -41,18 +41,16 @@ dock
Docker helper classes
"""
import ast
import logging
import os
import simplejson as json
import socket
import subprocess as sp # nosec
import tempfile
import time
import docker
import subprocess as sp # nosec
import logging
import docker
import simplejson as json
from packaging import version
from beat.core import stats
......
......@@ -41,10 +41,8 @@ environment
Helper functions related to environment management
"""
import re
import logging
import re
logger = logging.getLogger(__name__)
......
......@@ -41,21 +41,19 @@ base
Execution utilities
"""
import os
import glob
import collections
import glob
import logging
import simplejson as json
import os
from .. import schema
from .. import database
from .. import algorithm
from .. import stats
import simplejson as json
from beat.backend.python.helpers import convert_experiment_configuration_to_container
from .. import algorithm
from .. import database
from .. import schema
from .. import stats
logger = logging.getLogger(__name__)
......
......@@ -41,24 +41,21 @@ docker
Execution utilities
"""
import logging
import os
import shutil
import logging
from collections import namedtuple
import requests
import simplejson as json
from collections import namedtuple
from beat.backend.python.execution import MessageHandler
from beat.backend.python.data import getAllFilenames
from beat.backend.python.execution import MessageHandler
from .. import stats
from .. import utils
from .remote import RemoteExecutor
logger = logging.getLogger(__name__)
......
......@@ -41,20 +41,19 @@ local
Execution utilities
"""
import logging
import os
import shutil
import sys
import tempfile
import shutil
import zmq
import time
import logging
import zmq
from beat.backend.python.execution import AlgorithmExecutor
from beat.backend.python.execution import MessageHandler
from beat.backend.python.execution import LoopExecutor
from beat.backend.python.execution import LoopMessageHandler
from beat.backend.python.execution import MessageHandler
from .base import BaseExecutor
......
......@@ -41,12 +41,11 @@ remote
Execution utilities
"""
from .base import BaseExecutor
from beat.backend.python.helpers import create_inputs_from_configuration
from beat.backend.python.helpers import create_outputs_from_configuration
from .base import BaseExecutor
class RemoteExecutor(BaseExecutor):
"""Base class for Executors that communicate with a message handler
......
......@@ -40,22 +40,19 @@ subprocess
Execution utilities
"""
import logging
import os
import shutil
import logging
import sys
import subprocess as sp # nosec
import sys
import tempfile
from beat.backend.python.execution import MessageHandler
from .. import stats
from .. import utils
from .remote import RemoteExecutor
logger = logging.getLogger(__name__)
......
......@@ -41,19 +41,18 @@ experiment
Validation for experiments
"""
import os
import collections
import itertools
import os
import simplejson as json
from . import utils
from . import algorithm
from . import schema
from . import database
from . import toolchain
from . import hash
from . import schema
from . import toolchain
from . import utils
EVALUATOR_PREFIX = "evaluator_"
PROCESSOR_PREFIX = "processor_"
......@@ -84,9 +83,13 @@ class Storage(utils.Storage):
if len(s) == 4:
name = os.path.join(s[0], name)
self.username, self.toolchain_username, self.toolchain, self.version, self.name = name.split(
os.sep
)
(
self.username,
self.toolchain_username,
self.toolchain,
self.version,
self.name,
) = name.split(os.sep)
self.label = name
self.toolchain = os.path.join(
......
......@@ -43,16 +43,14 @@ Various functions for hashing platform contributions and others
Also forward importing from :py:mod:`beat.backend.python.hash`
"""
import collections
import simplejson as json
from beat.backend.python.hash import * # noqa
from beat.backend.python.hash import _compact
from beat.backend.python.hash import _sha256 # noqa
from beat.backend.python.hash import _stringify
from beat.backend.python.hash import _compact
# ----------------------------------------------------------
......
......@@ -45,8 +45,6 @@ Forward imported from :py:mod:`beat.backend.python.inputs`:
:py:class:`beat.backend.python.inputs.Input`
:py:class:`beat.backend.python.inputs.InputGroup`
"""
from beat.backend.python.inputs import InputList # noqa
from beat.backend.python.inputs import Input # noqa
from beat.backend.python.inputs import InputGroup # noqa
from beat.backend.python.inputs import InputList # noqa
......@@ -44,14 +44,13 @@ Validation for libraries
Forward imported from :py:mod:`beat.backend.python.library`:
:py:class:`beat.backend.python.library.Storage`
"""
import six
from . import schema
from . import prototypes
from beat.backend.python.library import Storage
from beat.backend.python.library import Library as BackendLibrary
from beat.backend.python.library import Storage
from . import prototypes
from . import schema
class Library(BackendLibrary):
......
......@@ -44,8 +44,6 @@ Forward imported from :py:mod:`beat.backend.python.outputs`:
:py:class:`beat.backend.python.outputs.Output`
:py:class:`beat.backend.python.outputs.OutputList`
"""
from beat.backend.python.outputs import SynchronizationListener # noqa
from beat.backend.python.outputs import Output # noqa
from beat.backend.python.outputs import OutputList # noqa
from beat.backend.python.outputs import SynchronizationListener # noqa
......@@ -41,18 +41,17 @@ plotter
Validation for plotters
"""
import os
import six
import sys
from . import dataformat
import six
from . import algorithm
from . import schema
from . import dataformat
from . import loader
from . import prototypes
from . import schema
from . import utils
from . import loader
# ----------------------------------------------------------
......
......@@ -41,13 +41,12 @@ plotterparameter
Validation for plotterparameters
"""
import simplejson as json
from . import schema
from . import plotter
from . import prototypes
from . import schema
from . import utils
from . import plotter
class Storage(utils.Storage):
......
......@@ -44,16 +44,15 @@ Validation of protocoltemplate
Forward importing from :py:mod:`beat.backend.python.protocoltemplate`:
:py:class:`beat.backend.python.protocoltemplate.Storage`
"""
import six
from . import schema
from . import prototypes
from beat.backend.python.protocoltemplate import Storage
from beat.backend.python.protocoltemplate import (
ProtocolTemplate as BackendProtocolTemplate,
)
from beat.backend.python.protocoltemplate import Storage
from . import prototypes
from . import schema
class ProtocolTemplate(BackendProtocolTemplate):
......
import numpy
from collections import namedtuple
import numpy
from beat.backend.python.database import View
......
......@@ -34,14 +34,12 @@
###################################################################################
"""Schema validation for BEAT JSON I/O"""
import os
import pkg_resources
import six
import simplejson as json
import jsonschema
import pkg_resources
import simplejson as json
import six
from beat.backend.python.utils import error_on_duplicate_key_hook
......@@ -98,7 +96,7 @@ def load_schema(schema_name, version=1):
try:
schema = json.loads(data)
except json.errors.JSONDecodeError:
print("Invalid json:\n {data}".format(data))
print("Invalid json:\n {}".format(data))
raise
basedir = os.path.realpath(os.path.dirname(fname))
......
import time
import numpy as np
import pkg_resources
import zmq
from ..agent import MessageHandler
from ..dataformat import DataFormat
from ..data import DataSource
from ..inputs import RemoteInput
from ..dataformat impo