How to use the gillespy2.core.log.handlers function in gillespy2

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github StochSS / stochss / stochss / handlers / util / run_workflow.py View on Github external
def setup_logger(log_path):
    '''
    Changer the GillesPy2 logger to record only error level logs and higher
    to the console and to log warning level logs and higher to a log file in
    the workflow directory.

    Attributes
    ----------
    workflow_path : str
        Path to the workflow directory
    '''
    formatter = log.handlers[0].formatter # gillespy2 log formatter
    fh_is_needed = True
    for handler in log.handlers:
        if type(handler) is logging.StreamHandler:
            handler.stream = sys.stderr # Reset the stream to stderr
            handler.setLevel(logging.ERROR) # Only log error and critical logs to console 
        elif type(handler) is logging.FileHandler:
            fh_is_needed = False # File Handler was already added to the log
    # Add the file handler if it not in the log already
    if fh_is_needed:
        fh = logging.FileHandler(log_path) # initialize file handler
        fh.setLevel(logging.WARNING) # log warning, error, and critical logs to file
        fh.setFormatter(formatter) # add gillespy2 log formatter
        log.addHandler(fh) # add file handler to log
github StochSS / stochss / stochss / handlers / util / run_model.py View on Github external
#!/usr/bin/env python3

import os
import sys
import json
import argparse
import logging
import pickle
import plotly

from io import StringIO
from gillespy2.core import log
log_stream = StringIO()
for handler in log.handlers:
    if type(handler) is logging.StreamHandler:
        handler.stream = log_stream


from gillespy2 import Species, Parameter, Reaction, RateRule, Model, AssignmentRule, FunctionDefinition

import numpy
import gillespy2.core.gillespySolver
from gillespy2.core.events import EventAssignment, EventTrigger, Event
from gillespy2.core.gillespyError import ModelError, SolverError, DirectoryError, BuildError, ExecutionError
from gillespy2.solvers.numpy.basic_tau_leaping_solver import BasicTauLeapingSolver
from gillespy2.solvers.numpy.basic_tau_hybrid_solver import BasicTauHybridSolver
from gillespy2.solvers.cpp.variable_ssa_c_solver import VariableSSACSolver

import warnings
warnings.simplefilter("ignore")