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Code Issues Releases Wiki Activity

Proper check for dependencies; Fallback if appropriate

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This commit is contained in:
Alexander Minges 2015-08-24 10:45:49 +02:00
parent 28bf76029b
commit d9179b4221
1 changed files with 47 additions and 19 deletions
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66
analyze-cli.py
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@ -4,13 +4,35 @@
import argparse import argparse
import logging import logging
import csv import csv
import matplotlib.pyplot as plt
import numpy as np
from pathlib import Path from pathlib import Path
from colorlog import ColoredFormatter
import libkinetics # check for third party modules. Matplotlib and NumPy are essential
try:
import matplotlib.pyplot as plt
except ImportError:
print('----- Matplotlib must be installed! -----')
try:
import numpy as np
except ImportError:
print('----- NumPy must be installed! -----')
# colorlog is optional; inform user of non-colored output if not found
try:
from colorlog import ColoredFormatter
COLORED_LOG = True
except ImportError:
COLORED_LOG = False
print('----- Module colorlog not found. Console output will not be '
'colored! -----')
pass
# check for libkinetics; if not found, there is something wrong with the
# installation if pyKinetics
try:
import libkinetics
except ImportError:
print('---- Cannot find libkinetics! Check your installation! -----')
class ExperimentHelper(): class ExperimentHelper():
@ -150,17 +172,23 @@ def initialize_logger():
'fh' which logs to a log file and 'ch' which logs to standard output. 'fh' which logs to a log file and 'ch' which logs to standard output.
:return logger: returns a logger instance :return logger: returns a logger instance
""" """
fmt = '%(log_color)s%(levelname)-8s%(reset)s %(message)s' if COLORED_LOG:
formatter = ColoredFormatter(fmt, fmt = '%(log_color)s%(levelname)-8s%(reset)s %(message)s'
datefmt=None, formatter = ColoredFormatter(fmt,
reset=True, datefmt=None,
log_colors={'DEBUG': 'cyan', reset=True,
'INFO': 'green', log_colors={'DEBUG': 'cyan',
'WARNING': 'yellow', 'INFO': 'green',
'ERROR': 'red', 'WARNING': 'yellow',
'CRITICAL': 'red,bg_white'}, 'ERROR': 'red',
secondary_log_colors={}, 'CRITICAL': 'red,bg_white'},
style='%') secondary_log_colors={},
style='%')
else:
fmt = '%(levelname)-8s%(message)s'
formatter = logging.Formatter(fmt,
datefmt=None,
style='%')
logging.captureWarnings(True) logging.captureWarnings(True)
logger = logging.getLogger('pyKinetics-cli') logger = logging.getLogger('pyKinetics-cli')
@ -190,8 +218,8 @@ def main():
args = parse_arguments() args = parse_arguments()
# initialize logger # initialize logger
logger = initialize_logger() logger = initialize_logger()
# grab fitting window from provided arguments
xlim = (args.start, args.end) fitting_window = (args.start, args.end)
if args.hill: if args.hill:
do_hill = args.hill do_hill = args.hill
@ -225,7 +253,7 @@ def main():
msg = '{} including Hill kinetics'.format(msg) msg = '{} including Hill kinetics'.format(msg)
logger.info('{}'.format(msg)) logger.info('{}'.format(msg))
exp = libkinetics.Experiment(data_files, exp = libkinetics.Experiment(data_files,
xlim, fitting_window,
do_hill=do_hill, do_hill=do_hill,
logger=logger, logger=logger,
fit_to_replicates=fit_to_replicates) fit_to_replicates=fit_to_replicates)