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Merge pull request #775 from apdavison/spring-clean

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50.67

/pyNN/utility/script_tools.py

"""
A collection of functions to help writing simualtion scripts.

:copyright: Copyright 2006-2023 by the PyNN team, see AUTHORS.
:license: CeCILL, see LICENSE for details.
"""

from datetime import datetime
import os
import sys
from importlib import import_module
import logging

# If there is a settings.py file on the path, defaults will be
# taken from there.
try:
    from settings import SMTPHOST, EMAIL
except ImportError:
    SMTPHOST = None
    EMAIL = None


def get_script_args(n_args, usage=''):
    """
    Get command line arguments.

    This works by finding the name of the main script and assuming any
    arguments after this in sys.argv are arguments to the script.
    It would be nicer to use optparse, but this doesn't seem to work too well
    with nrniv or mpirun.
    """
    calling_frame = sys._getframe(1)
    if '__file__' in calling_frame.f_locals:
        script = calling_frame.f_locals['__file__']
        try:
            script_index = sys.argv.index(script)
        except ValueError:
            try:
                script_index = sys.argv.index(os.path.abspath(script))
            except ValueError:
                script_index = 0
    else:
        script_index = 0
    args = sys.argv[script_index + 1:script_index + 1 + n_args]
    if len(args) != n_args:
        usage = usage or "Script requires %d arguments, you supplied %d" % (n_args, len(args))
        raise Exception(usage)
    return args


def get_simulator(*arguments):
    """
    Import and return a PyNN simulator backend module based on command-line
    arguments.

    The simulator name should be the first positional argument. If your script
    needs additional arguments, you can specify them as (name, help_text) tuples.
    If you need more complex argument handling, you should use argparse
    directly.

    Returns (simulator, command-line arguments)
    """
    import argparse
    parser = argparse.ArgumentParser()
    parser.add_argument("simulator",
                        help="neuron, nest, brian or another backend simulator")
    for argument in arguments:
        arg_name, help_text = argument[:2]
        extra_args = {}
        if len(argument) > 2:
            extra_args = argument[2]
        parser.add_argument(arg_name, help=help_text, **extra_args)
    args = parser.parse_args()
    sim = import_module("pyNN.%s" % args.simulator)
    return sim, args


def init_logging(logfile, debug=False, num_processes=1, rank=0, level=None):
    """
    Simple configuration of logging.
    """
    # allow logfile == None
    # which implies output to stderr
    # num_processes and rank should be obtained using mpi4py, rather than having them as arguments
    if logfile:
        if num_processes > 1:
            logfile += '.%d' % rank
        logfile = os.path.abspath(logfile)

    # prefix log messages with mpi rank
    mpi_prefix = ""
    if num_processes > 1:
        mpi_prefix = 'Rank %d of %d: ' % (rank, num_processes)

    if debug:
        log_level = logging.DEBUG
    else:
        log_level = logging.INFO

    # allow user to override exact log_level
    if level:
        log_level = level

    logging.basicConfig(
        level=log_level,
        format=mpi_prefix + '%(asctime)s %(levelname)-8s [%(name)s] %(message)s (%(pathname)s[%(lineno)d]:%(funcName)s)',  # noqa: E501
        filename=logfile,
        filemode='w')
    return logging.getLogger("PyNN")


def normalized_filename(root, basename, extension, simulator,
                        num_processes=None, use_iso8601=False):
    """
    Generate a file path containing a timestamp and information about the
    simulator used and the number of MPI processes.

    The date is used as a sub-directory name, the date & time are included in the
    filename.
    If use_iso8601 is True, follow https://en.wikipedia.org/wiki/ISO_8601
    """
    timestamp = datetime.now()
    if use_iso8601:
        date = timestamp.strftime("%Y-%m-%d")
        date_time = timestamp.strftime("%Y-%m-%dT%H:%M:%S")
    else:
        date = timestamp.strftime("%Y%m%d")
        date_time = timestamp.strftime("%Y%m%d-%H%M%S")

    if num_processes:
        np = "_np%d" % num_processes
    else:
        np = ""
    return os.path.join(root,
                        date,
                        "%s_%s%s_%s.%s" % (basename,
                                           simulator,
                                           np,
                                           date_time,
                                           extension))


def notify(
    msg="Simulation finished.",
    subject="Simulation finished.",
    smtphost=SMTPHOST,
    address=EMAIL,
):
    """Send an e-mail stating that the simulation has finished."""
    if not (smtphost and address):
        print(
            "SMTP host and/or e-mail address not specified.\n"
            "Unable to send notification message."
        )
    else:
        import smtplib

        msg = ("From: %s\r\nTo: %s\r\nSubject: %s\r\n\r\n") % (
            address,
            address,
            subject,
        ) + msg
        msg += "\nTimestamp: %s" % datetime.now().strftime("%H:%M:%S, %F")
        server = smtplib.SMTP(smtphost)
        server.sendmail(address, address, msg)
        server.quit()

1	"""
2	A collection of functions to help writing simualtion scripts.
3
4	:copyright: Copyright 2006-2023 by the PyNN team, see AUTHORS.
5	:license: CeCILL, see LICENSE for details.
6	"""
7
8	from datetime import datetime	4✔
9	import os	4✔
10	import sys	4✔
11	from importlib import import_module	4✔
12	import logging	4✔
13
14	# If there is a settings.py file on the path, defaults will be
15	# taken from there.
16	try:	4✔
17	from settings import SMTPHOST, EMAIL	4✔
18	except ImportError:	4✔
19	SMTPHOST = None	4✔
20	EMAIL = None	4✔
21
22
23	def get_script_args(n_args, usage=''):	4✔
24	"""
25	Get command line arguments.
26
27	This works by finding the name of the main script and assuming any
28	arguments after this in sys.argv are arguments to the script.
29	It would be nicer to use optparse, but this doesn't seem to work too well
30	with nrniv or mpirun.
31	"""
32	calling_frame = sys._getframe(1)	4✔
33	if '__file__' in calling_frame.f_locals:	4✔
NEW 34	script = calling_frame.f_locals['__file__']	×
NEW 35	try:	×
NEW 36	script_index = sys.argv.index(script)	×
NEW 37	except ValueError:	×
NEW 38	try:	×
NEW 39	script_index = sys.argv.index(os.path.abspath(script))	×
NEW 40	except ValueError:	×
NEW 41	script_index = 0	×
42	else:
43	script_index = 0	4✔
44	args = sys.argv[script_index + 1:script_index + 1 + n_args]	4✔
45	if len(args) != n_args:	4✔
NEW 46	usage = usage or "Script requires %d arguments, you supplied %d" % (n_args, len(args))	×
NEW 47	raise Exception(usage)	×
48	return args	4✔
49
50
51	def get_simulator(*arguments):	4✔
52	"""
53	Import and return a PyNN simulator backend module based on command-line
54	arguments.
55
56	The simulator name should be the first positional argument. If your script
57	needs additional arguments, you can specify them as (name, help_text) tuples.
58	If you need more complex argument handling, you should use argparse
59	directly.
60
61	Returns (simulator, command-line arguments)
62	"""
NEW 63	import argparse	×
NEW 64	parser = argparse.ArgumentParser()	×
NEW 65	parser.add_argument("simulator",	×
66	help="neuron, nest, brian or another backend simulator")
NEW 67	for argument in arguments:	×
NEW 68	arg_name, help_text = argument[:2]	×
NEW 69	extra_args = {}	×
NEW 70	if len(argument) > 2:	×
NEW 71	extra_args = argument[2]	×
NEW 72	parser.add_argument(arg_name, help=help_text, **extra_args)	×
NEW 73	args = parser.parse_args()	×
NEW 74	sim = import_module("pyNN.%s" % args.simulator)	×
NEW 75	return sim, args	×
76
77
78	def init_logging(logfile, debug=False, num_processes=1, rank=0, level=None):	4✔
79	"""
80	Simple configuration of logging.
81	"""
82	# allow logfile == None
83	# which implies output to stderr
84	# num_processes and rank should be obtained using mpi4py, rather than having them as arguments
85	if logfile:	4✔
NEW 86	if num_processes > 1:	×
NEW 87	logfile += '.%d' % rank	×
NEW 88	logfile = os.path.abspath(logfile)	×
89
90	# prefix log messages with mpi rank
91	mpi_prefix = ""	4✔
92	if num_processes > 1:	4✔
NEW 93	mpi_prefix = 'Rank %d of %d: ' % (rank, num_processes)	×
94
95	if debug:	4✔
96	log_level = logging.DEBUG	4✔
97	else:
NEW 98	log_level = logging.INFO	×
99
100	# allow user to override exact log_level
101	if level:	4✔
NEW 102	log_level = level	×
103
104	logging.basicConfig(	4✔
105	level=log_level,
106	format=mpi_prefix + '%(asctime)s %(levelname)-8s [%(name)s] %(message)s (%(pathname)s[%(lineno)d]:%(funcName)s)', # noqa: E501
107	filename=logfile,
108	filemode='w')
109	return logging.getLogger("PyNN")	4✔
110
111
112	def normalized_filename(root, basename, extension, simulator,	4✔
113	num_processes=None, use_iso8601=False):
114	"""
115	Generate a file path containing a timestamp and information about the
116	simulator used and the number of MPI processes.
117
118	The date is used as a sub-directory name, the date & time are included in the
119	filename.
120	If use_iso8601 is True, follow https://en.wikipedia.org/wiki/ISO_8601
121	"""
122	timestamp = datetime.now()	2✔
123	if use_iso8601:	2✔
NEW 124	date = timestamp.strftime("%Y-%m-%d")	×
NEW 125	date_time = timestamp.strftime("%Y-%m-%dT%H:%M:%S")	×
126	else:
127	date = timestamp.strftime("%Y%m%d")	2✔
128	date_time = timestamp.strftime("%Y%m%d-%H%M%S")	2✔
129
130	if num_processes:	2✔
NEW 131	np = "_np%d" % num_processes	×
132	else:
133	np = ""	2✔
134	return os.path.join(root,	2✔
135	date,
136	"%s_%s%s_%s.%s" % (basename,
137	simulator,
138	np,
139	date_time,
140	extension))
141
142
143	def notify(	4✔
144	msg="Simulation finished.",
145	subject="Simulation finished.",
146	smtphost=SMTPHOST,
147	address=EMAIL,
148	):
149	"""Send an e-mail stating that the simulation has finished."""
150	if not (smtphost and address):	4✔
151	print(	4✔
152	"SMTP host and/or e-mail address not specified.\n"
153	"Unable to send notification message."
154	)
155	else:
NEW 156	import smtplib	×
157
NEW 158	msg = ("From: %s\r\nTo: %s\r\nSubject: %s\r\n\r\n") % (	×
159	address,
160	address,
161	subject,
162	) + msg
NEW 163	msg += "\nTimestamp: %s" % datetime.now().strftime("%H:%M:%S, %F")	×
NEW 164	server = smtplib.SMTP(smtphost)	×
NEW 165	server.sendmail(address, address, msg)	×
NEW 166	server.quit()	×

NeuralEnsemble / PyNN / 4092881168

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