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Erotemic/utool | utool/_internal/win32_send_keys.py | KeyAction.key_description | def key_description(self):
"Return a description of the key"
vk, scan, flags = self._get_key_info()
desc = ''
if vk:
if vk in CODE_NAMES:
desc = CODE_NAMES[vk]
else:
desc = "VK %d"% vk
else:
desc = "%s"% self.key
return desc | python | def key_description(self):
"Return a description of the key"
vk, scan, flags = self._get_key_info()
desc = ''
if vk:
if vk in CODE_NAMES:
desc = CODE_NAMES[vk]
else:
desc = "VK %d"% vk
else:
desc = "%s"% self.key
return desc | [
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Erotemic/utool | utool/_internal/win32_send_keys.py | VirtualKeyAction._get_key_info | def _get_key_info(self):
"Virtual keys have extended flag set"
# copied more or less verbatim from
# http://www.pinvoke.net/default.aspx/user32.sendinput
if (
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flags = KEYEVENTF_EXTENDEDKEY;
else:
flags = 0
# This works for %{F4} - ALT + F4
#return self.key, 0, 0
# this works for Tic Tac Toe i.e. +{RIGHT} SHIFT + RIGHT
return self.key, MapVirtualKey(self.key, 0), flags | python | def _get_key_info(self):
"Virtual keys have extended flag set"
# copied more or less verbatim from
# http://www.pinvoke.net/default.aspx/user32.sendinput
if (
(self.key >= 33 and self.key <= 46) or
(self.key >= 91 and self.key <= 93) ):
flags = KEYEVENTF_EXTENDEDKEY;
else:
flags = 0
# This works for %{F4} - ALT + F4
#return self.key, 0, 0
# this works for Tic Tac Toe i.e. +{RIGHT} SHIFT + RIGHT
return self.key, MapVirtualKey(self.key, 0), flags | [
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Erotemic/utool | utool/_internal/win32_send_keys.py | EscapedKeyAction._get_key_info | def _get_key_info(self):
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vkey_scan = LoByte(VkKeyScan(self.key))
return (vkey_scan, MapVirtualKey(vkey_scan, 0), 0) | python | def _get_key_info(self):
"""EscapedKeyAction doesn't send it as Unicode and the vk and
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vkey_scan = LoByte(VkKeyScan(self.key))
return (vkey_scan, MapVirtualKey(vkey_scan, 0), 0) | [
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ThreatResponse/aws_ir_plugins | aws_ir_plugins/revokests_key.py | Plugin.setup | def setup(self):
"""Method runs the plugin attaching policies to the user in question"""
self.template = self._generate_inline_policy()
if self.dry_run is not True:
self.client = self._get_client()
username = self._get_username_for_key()
policy_document = self._generate_inline_policy()
self._attach_inline_policy(username, policy_document)
pass | python | def setup(self):
"""Method runs the plugin attaching policies to the user in question"""
self.template = self._generate_inline_policy()
if self.dry_run is not True:
self.client = self._get_client()
username = self._get_username_for_key()
policy_document = self._generate_inline_policy()
self._attach_inline_policy(username, policy_document)
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ThreatResponse/aws_ir_plugins | aws_ir_plugins/revokests_key.py | Plugin._get_policies | def _get_policies(self):
"""Returns all the policy names for a given user"""
username = self._get_username_for_key()
policies = self.client.list_user_policies(
UserName=username
)
return policies | python | def _get_policies(self):
"""Returns all the policy names for a given user"""
username = self._get_username_for_key()
policies = self.client.list_user_policies(
UserName=username
)
return policies | [
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ThreatResponse/aws_ir_plugins | aws_ir_plugins/revokests_key.py | Plugin._get_username_for_key | def _get_username_for_key(self):
"""Find the user for a given access key"""
response = self.client.get_access_key_last_used(
AccessKeyId=self.compromised_resource['access_key_id']
)
username = response['UserName']
return username | python | def _get_username_for_key(self):
"""Find the user for a given access key"""
response = self.client.get_access_key_last_used(
AccessKeyId=self.compromised_resource['access_key_id']
)
username = response['UserName']
return username | [
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ThreatResponse/aws_ir_plugins | aws_ir_plugins/revokests_key.py | Plugin._generate_inline_policy | def _generate_inline_policy(self):
"""Renders a policy from a jinja template"""
template_name = self._locate_file('deny-sts-before-time.json.j2')
template_file = open(template_name)
template_contents = template_file.read()
template_file.close()
jinja_template = Template(template_contents)
policy_document = jinja_template.render(
before_date=self._get_date()
)
return policy_document | python | def _generate_inline_policy(self):
"""Renders a policy from a jinja template"""
template_name = self._locate_file('deny-sts-before-time.json.j2')
template_file = open(template_name)
template_contents = template_file.read()
template_file.close()
jinja_template = Template(template_contents)
policy_document = jinja_template.render(
before_date=self._get_date()
)
return policy_document | [
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ThreatResponse/aws_ir_plugins | aws_ir_plugins/revokests_key.py | Plugin._attach_inline_policy | def _attach_inline_policy(self, username, policy_document):
"""Attaches the policy to the user"""
response = self.client.put_user_policy(
UserName=username,
PolicyName="threatresponse-temporal-key-revocation",
PolicyDocument=policy_document
)
logger.info(
'An inline policy has been attached for'
' {u} revoking sts tokens.'.format(u=username)
)
return response | python | def _attach_inline_policy(self, username, policy_document):
"""Attaches the policy to the user"""
response = self.client.put_user_policy(
UserName=username,
PolicyName="threatresponse-temporal-key-revocation",
PolicyDocument=policy_document
)
logger.info(
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)
return response | [
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ThreatResponse/aws_ir_plugins | aws_ir_plugins/revokests_key.py | Plugin._locate_file | def _locate_file(self, pattern, root=os.path.dirname('revokests_key.py')):
"""Locate all files matching supplied filename pattern in and below
supplied root directory.
"""
for path, dirs, files in os.walk(os.path.abspath(root)):
for filename in fnmatch.filter(files, pattern):
return os.path.join(path, filename) | python | def _locate_file(self, pattern, root=os.path.dirname('revokests_key.py')):
"""Locate all files matching supplied filename pattern in and below
supplied root directory.
"""
for path, dirs, files in os.walk(os.path.abspath(root)):
for filename in fnmatch.filter(files, pattern):
return os.path.join(path, filename) | [
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glormph/msstitch | src/app/readers/tsv.py | generate_tsv_pep_protein_quants | def generate_tsv_pep_protein_quants(fns):
"""Unlike generate_tsv_lines_multifile, this generates tsv lines
from multiple files that may have different headers. Yields
fn, header as well as quant data for each protein quant"""
for fn in fns:
header = get_tsv_header(fn)
for pquant in generate_split_tsv_lines(fn, header):
yield os.path.basename(fn), header, pquant | python | def generate_tsv_pep_protein_quants(fns):
"""Unlike generate_tsv_lines_multifile, this generates tsv lines
from multiple files that may have different headers. Yields
fn, header as well as quant data for each protein quant"""
for fn in fns:
header = get_tsv_header(fn)
for pquant in generate_split_tsv_lines(fn, header):
yield os.path.basename(fn), header, pquant | [
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glormph/msstitch | src/app/readers/tsv.py | mzmlfn_kronikfeature_generator | def mzmlfn_kronikfeature_generator(mzmlfns, kronikfns):
"""Generates tuples of spectra filename and corresponding output
features from kronik"""
for mzmlfn, kronikfn in zip(mzmlfns, kronikfns):
for quant_el in generate_kronik_feats(kronikfn):
yield os.path.basename(mzmlfn), quant_el | python | def mzmlfn_kronikfeature_generator(mzmlfns, kronikfns):
"""Generates tuples of spectra filename and corresponding output
features from kronik"""
for mzmlfn, kronikfn in zip(mzmlfns, kronikfns):
for quant_el in generate_kronik_feats(kronikfn):
yield os.path.basename(mzmlfn), quant_el | [
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glormph/msstitch | src/app/readers/tsv.py | generate_split_tsv_lines | def generate_split_tsv_lines(fn, header):
"""Returns dicts with header-keys and psm statistic values"""
for line in generate_tsv_psms_line(fn):
yield {x: y for (x, y) in zip(header, line.strip().split('\t'))} | python | def generate_split_tsv_lines(fn, header):
"""Returns dicts with header-keys and psm statistic values"""
for line in generate_tsv_psms_line(fn):
yield {x: y for (x, y) in zip(header, line.strip().split('\t'))} | [
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glormph/msstitch | src/app/readers/tsv.py | get_proteins_from_psm | def get_proteins_from_psm(line):
"""From a line, return list of proteins reported by Mzid2TSV. When unrolled
lines are given, this returns the single protein from the line."""
proteins = line[mzidtsvdata.HEADER_PROTEIN].split(';')
outproteins = []
for protein in proteins:
prepost_protein = re.sub('\(pre=.*post=.*\)', '', protein).strip()
outproteins.append(prepost_protein)
return outproteins | python | def get_proteins_from_psm(line):
"""From a line, return list of proteins reported by Mzid2TSV. When unrolled
lines are given, this returns the single protein from the line."""
proteins = line[mzidtsvdata.HEADER_PROTEIN].split(';')
outproteins = []
for protein in proteins:
prepost_protein = re.sub('\(pre=.*post=.*\)', '', protein).strip()
outproteins.append(prepost_protein)
return outproteins | [
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Erotemic/utool | utool/util_arg.py | aug_sysargv | def aug_sysargv(cmdstr):
""" DEBUG FUNC modify argv to look like you ran a command """
import shlex
argv = shlex.split(cmdstr)
sys.argv.extend(argv) | python | def aug_sysargv(cmdstr):
""" DEBUG FUNC modify argv to look like you ran a command """
import shlex
argv = shlex.split(cmdstr)
sys.argv.extend(argv) | [
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] | 3b27e1f4e6e6fb23cd8744af7b7195b57d99e03a | https://github.com/Erotemic/utool/blob/3b27e1f4e6e6fb23cd8744af7b7195b57d99e03a/utool/util_arg.py#L40-L44 | train |
Erotemic/utool | utool/util_arg.py | get_module_verbosity_flags | def get_module_verbosity_flags(*labels):
""" checks for standard flags for enableing module specific verbosity """
verbose_prefix_list = ['--verbose-', '--verb', '--verb-']
veryverbose_prefix_list = ['--veryverbose-', '--veryverb', '--veryverb-']
verbose_flags = tuple(
[prefix + lbl for prefix, lbl in
itertools.product(verbose_prefix_list, labels)])
veryverbose_flags = tuple(
[prefix + lbl for prefix, lbl in
itertools.product(veryverbose_prefix_list, labels)])
veryverbose_module = get_argflag(veryverbose_flags) or VERYVERBOSE
verbose_module = (get_argflag(verbose_flags) or veryverbose_module or VERBOSE)
if veryverbose_module:
verbose_module = 2
return verbose_module, veryverbose_module | python | def get_module_verbosity_flags(*labels):
""" checks for standard flags for enableing module specific verbosity """
verbose_prefix_list = ['--verbose-', '--verb', '--verb-']
veryverbose_prefix_list = ['--veryverbose-', '--veryverb', '--veryverb-']
verbose_flags = tuple(
[prefix + lbl for prefix, lbl in
itertools.product(verbose_prefix_list, labels)])
veryverbose_flags = tuple(
[prefix + lbl for prefix, lbl in
itertools.product(veryverbose_prefix_list, labels)])
veryverbose_module = get_argflag(veryverbose_flags) or VERYVERBOSE
verbose_module = (get_argflag(verbose_flags) or veryverbose_module or VERBOSE)
if veryverbose_module:
verbose_module = 2
return verbose_module, veryverbose_module | [
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Erotemic/utool | utool/util_arg.py | get_argflag | def get_argflag(argstr_, default=False, help_='', return_specified=None,
need_prefix=True, return_was_specified=False, argv=None,
debug=None,
**kwargs):
"""
Checks if the commandline has a flag or a corresponding noflag
Args:
argstr_ (str, list, or tuple): the flag to look for
default (bool): dont use this (default = False)
help_ (str): a help string (default = '')
return_specified (bool): returns if flag was specified or not (default = False)
Returns:
tuple: (parsed_val, was_specified)
TODO:
depricate return_was_specified
CommandLine:
python -m utool.util_arg --exec-get_argflag --noface --exec-mode
python -m utool.util_arg --exec-get_argflag --foo --exec-mode
python -m utool.util_arg --exec-get_argflag --no-foo --exec-mode
python -m utool.util_arg --exec-get_argflag --foo=True --exec-mode
python -m utool.util_arg --exec-get_argflag --foo=False --exec-mode
Example:
>>> # DISABLE_DOCTEST
>>> from utool.util_arg import * # NOQA
>>> argstr_ = '--foo'
>>> default = False
>>> help_ = ''
>>> return_specified = True
>>> (parsed_val, was_specified) = get_argflag(argstr_, default, help_, return_specified)
>>> result = ('(parsed_val, was_specified) = %s' % (str((parsed_val, was_specified)),))
>>> print(result)
"""
if argv is None:
argv = sys.argv
assert isinstance(default, bool), 'default must be boolean'
argstr_list = meta_util_iter.ensure_iterable(argstr_)
#if VERYVERBOSE:
# print('[util_arg] checking argstr_list=%r' % (argstr_list,))
# arg registration
_register_arg(argstr_list, bool, default, help_)
parsed_val = default
was_specified = False
if debug is None:
debug = DEBUG
# Check environment variables for default as well as argv
import os
#"""
#set UTOOL_NOCNN=True
#export UTOOL_NOCNN True
#"""
#argv_orig = argv[:]
# HACK: make this not happen very time you loop
for key, val in os.environ.items():
key = key.upper()
sentinal = 'UTOOL_'
if key.startswith(sentinal):
flag = '--' + key[len(sentinal):].lower().replace('_', '-')
if val.upper() in ['TRUE', 'ON']:
pass
elif val.upper() in ['FALSE', 'OFF']:
continue
else:
continue
#flag += '=False'
new_argv = [flag]
argv = argv[:] + new_argv
if debug:
print('ENV SPECIFIED COMMAND LINE')
print('argv.extend(new_argv=%r)' % (new_argv,))
for argstr in argstr_list:
#if VERYVERBOSE:
# print('[util_arg] * checking argstr=%r' % (argstr,))
if not (argstr.find('--') == 0 or (argstr.find('-') == 0 and len(argstr) == 2)):
raise AssertionError('Invalid argstr: %r' % (argstr,))
if not need_prefix:
noprefix = argstr.replace('--', '')
if noprefix in argv:
parsed_val = True
was_specified = True
break
#if argstr.find('--no') == 0:
#argstr = argstr.replace('--no', '--')
noarg = argstr.replace('--', '--no')
if argstr in argv:
parsed_val = True
was_specified = True
#if VERYVERBOSE:
# print('[util_arg] * ...WAS_SPECIFIED. AND PARSED')
break
elif noarg in argv:
parsed_val = False
was_specified = True
#if VERYVERBOSE:
# print('[util_arg] * ...WAS_SPECIFIED. AND NOT PARSED')
break
elif argstr + '=True' in argv:
parsed_val = True
was_specified = True
break
elif argstr + '=False' in argv:
parsed_val = False
was_specified = True
break
if return_specified is None:
return_specified = return_was_specified
if return_specified:
return parsed_val, was_specified
else:
return parsed_val | python | def get_argflag(argstr_, default=False, help_='', return_specified=None,
need_prefix=True, return_was_specified=False, argv=None,
debug=None,
**kwargs):
"""
Checks if the commandline has a flag or a corresponding noflag
Args:
argstr_ (str, list, or tuple): the flag to look for
default (bool): dont use this (default = False)
help_ (str): a help string (default = '')
return_specified (bool): returns if flag was specified or not (default = False)
Returns:
tuple: (parsed_val, was_specified)
TODO:
depricate return_was_specified
CommandLine:
python -m utool.util_arg --exec-get_argflag --noface --exec-mode
python -m utool.util_arg --exec-get_argflag --foo --exec-mode
python -m utool.util_arg --exec-get_argflag --no-foo --exec-mode
python -m utool.util_arg --exec-get_argflag --foo=True --exec-mode
python -m utool.util_arg --exec-get_argflag --foo=False --exec-mode
Example:
>>> # DISABLE_DOCTEST
>>> from utool.util_arg import * # NOQA
>>> argstr_ = '--foo'
>>> default = False
>>> help_ = ''
>>> return_specified = True
>>> (parsed_val, was_specified) = get_argflag(argstr_, default, help_, return_specified)
>>> result = ('(parsed_val, was_specified) = %s' % (str((parsed_val, was_specified)),))
>>> print(result)
"""
if argv is None:
argv = sys.argv
assert isinstance(default, bool), 'default must be boolean'
argstr_list = meta_util_iter.ensure_iterable(argstr_)
#if VERYVERBOSE:
# print('[util_arg] checking argstr_list=%r' % (argstr_list,))
# arg registration
_register_arg(argstr_list, bool, default, help_)
parsed_val = default
was_specified = False
if debug is None:
debug = DEBUG
# Check environment variables for default as well as argv
import os
#"""
#set UTOOL_NOCNN=True
#export UTOOL_NOCNN True
#"""
#argv_orig = argv[:]
# HACK: make this not happen very time you loop
for key, val in os.environ.items():
key = key.upper()
sentinal = 'UTOOL_'
if key.startswith(sentinal):
flag = '--' + key[len(sentinal):].lower().replace('_', '-')
if val.upper() in ['TRUE', 'ON']:
pass
elif val.upper() in ['FALSE', 'OFF']:
continue
else:
continue
#flag += '=False'
new_argv = [flag]
argv = argv[:] + new_argv
if debug:
print('ENV SPECIFIED COMMAND LINE')
print('argv.extend(new_argv=%r)' % (new_argv,))
for argstr in argstr_list:
#if VERYVERBOSE:
# print('[util_arg] * checking argstr=%r' % (argstr,))
if not (argstr.find('--') == 0 or (argstr.find('-') == 0 and len(argstr) == 2)):
raise AssertionError('Invalid argstr: %r' % (argstr,))
if not need_prefix:
noprefix = argstr.replace('--', '')
if noprefix in argv:
parsed_val = True
was_specified = True
break
#if argstr.find('--no') == 0:
#argstr = argstr.replace('--no', '--')
noarg = argstr.replace('--', '--no')
if argstr in argv:
parsed_val = True
was_specified = True
#if VERYVERBOSE:
# print('[util_arg] * ...WAS_SPECIFIED. AND PARSED')
break
elif noarg in argv:
parsed_val = False
was_specified = True
#if VERYVERBOSE:
# print('[util_arg] * ...WAS_SPECIFIED. AND NOT PARSED')
break
elif argstr + '=True' in argv:
parsed_val = True
was_specified = True
break
elif argstr + '=False' in argv:
parsed_val = False
was_specified = True
break
if return_specified is None:
return_specified = return_was_specified
if return_specified:
return parsed_val, was_specified
else:
return parsed_val | [
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Args:
argstr_ (str, list, or tuple): the flag to look for
default (bool): dont use this (default = False)
help_ (str): a help string (default = '')
return_specified (bool): returns if flag was specified or not (default = False)
Returns:
tuple: (parsed_val, was_specified)
TODO:
depricate return_was_specified
CommandLine:
python -m utool.util_arg --exec-get_argflag --noface --exec-mode
python -m utool.util_arg --exec-get_argflag --foo --exec-mode
python -m utool.util_arg --exec-get_argflag --no-foo --exec-mode
python -m utool.util_arg --exec-get_argflag --foo=True --exec-mode
python -m utool.util_arg --exec-get_argflag --foo=False --exec-mode
Example:
>>> # DISABLE_DOCTEST
>>> from utool.util_arg import * # NOQA
>>> argstr_ = '--foo'
>>> default = False
>>> help_ = ''
>>> return_specified = True
>>> (parsed_val, was_specified) = get_argflag(argstr_, default, help_, return_specified)
>>> result = ('(parsed_val, was_specified) = %s' % (str((parsed_val, was_specified)),))
>>> print(result) | [
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] | 3b27e1f4e6e6fb23cd8744af7b7195b57d99e03a | https://github.com/Erotemic/utool/blob/3b27e1f4e6e6fb23cd8744af7b7195b57d99e03a/utool/util_arg.py#L135-L253 | train |
Erotemic/utool | utool/util_arg.py | get_arg_dict | def get_arg_dict(argv=None, prefix_list=['--'], type_hints={}):
r"""
Yet another way for parsing args
CommandLine:
python -m utool.util_arg --exec-get_arg_dict
python -m utool.util_arg --test-get_arg_dict
Example:
>>> # ENABLE_DOCTEST
>>> from utool.util_arg import * # NOQA
>>> import utool as ut
>>> import shlex
>>> argv = shlex.split('--test-show_name --name=IBEIS_PZ_0303 --db testdb3 --save "~/latex/crall-candidacy-2015/figures/IBEIS_PZ_0303.jpg" --dpath figures --caption="Shadowed" --figsize=11,3 --no-figtitle -t foo bar baz biz --notitle')
>>> arg_dict = ut.get_arg_dict(argv, prefix_list=['--', '-'], type_hints={'t': list})
>>> result = ut.repr2(arg_dict, nl=1)
>>> # verify results
>>> print(result)
{
'caption': 'Shadowed',
'db': 'testdb3',
'dpath': 'figures',
'figsize': '11,3',
'name': 'IBEIS_PZ_0303',
'no-figtitle': True,
'notitle': True,
'save': '~/latex/crall-candidacy-2015/figures/IBEIS_PZ_0303.jpg',
't': ['foo', 'bar', 'baz', 'biz'],
'test-show_name': True,
}
"""
if argv is None:
argv = sys.argv
arg_dict = {}
def startswith_prefix(arg):
return any([arg.startswith(prefix) for prefix in prefix_list])
def argx_has_value(argv, argx):
# Check if has a value
if argv[argx].find('=') > -1:
return True
if argx + 1 < len(argv) and not startswith_prefix(argv[argx + 1]):
return True
return False
def get_arg_value(argv, argx, argname):
if argv[argx].find('=') > -1:
return '='.join(argv[argx].split('=')[1:])
else:
type_ = type_hints.get(argname, None)
if type_ is None:
return argv[argx + 1]
else:
return parse_arglist_hack(argx, argv=argv)
for argx in range(len(argv)):
arg = argv[argx]
for prefix in prefix_list:
if arg.startswith(prefix):
argname = arg[len(prefix):]
if argx_has_value(argv, argx):
if arg.find('=') > -1:
argname = arg[len(prefix):arg.find('=')]
argvalue = get_arg_value(argv, argx, argname)
arg_dict[argname] = argvalue
else:
arg_dict[argname] = True
break
return arg_dict | python | def get_arg_dict(argv=None, prefix_list=['--'], type_hints={}):
r"""
Yet another way for parsing args
CommandLine:
python -m utool.util_arg --exec-get_arg_dict
python -m utool.util_arg --test-get_arg_dict
Example:
>>> # ENABLE_DOCTEST
>>> from utool.util_arg import * # NOQA
>>> import utool as ut
>>> import shlex
>>> argv = shlex.split('--test-show_name --name=IBEIS_PZ_0303 --db testdb3 --save "~/latex/crall-candidacy-2015/figures/IBEIS_PZ_0303.jpg" --dpath figures --caption="Shadowed" --figsize=11,3 --no-figtitle -t foo bar baz biz --notitle')
>>> arg_dict = ut.get_arg_dict(argv, prefix_list=['--', '-'], type_hints={'t': list})
>>> result = ut.repr2(arg_dict, nl=1)
>>> # verify results
>>> print(result)
{
'caption': 'Shadowed',
'db': 'testdb3',
'dpath': 'figures',
'figsize': '11,3',
'name': 'IBEIS_PZ_0303',
'no-figtitle': True,
'notitle': True,
'save': '~/latex/crall-candidacy-2015/figures/IBEIS_PZ_0303.jpg',
't': ['foo', 'bar', 'baz', 'biz'],
'test-show_name': True,
}
"""
if argv is None:
argv = sys.argv
arg_dict = {}
def startswith_prefix(arg):
return any([arg.startswith(prefix) for prefix in prefix_list])
def argx_has_value(argv, argx):
# Check if has a value
if argv[argx].find('=') > -1:
return True
if argx + 1 < len(argv) and not startswith_prefix(argv[argx + 1]):
return True
return False
def get_arg_value(argv, argx, argname):
if argv[argx].find('=') > -1:
return '='.join(argv[argx].split('=')[1:])
else:
type_ = type_hints.get(argname, None)
if type_ is None:
return argv[argx + 1]
else:
return parse_arglist_hack(argx, argv=argv)
for argx in range(len(argv)):
arg = argv[argx]
for prefix in prefix_list:
if arg.startswith(prefix):
argname = arg[len(prefix):]
if argx_has_value(argv, argx):
if arg.find('=') > -1:
argname = arg[len(prefix):arg.find('=')]
argvalue = get_arg_value(argv, argx, argname)
arg_dict[argname] = argvalue
else:
arg_dict[argname] = True
break
return arg_dict | [
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Yet another way for parsing args
CommandLine:
python -m utool.util_arg --exec-get_arg_dict
python -m utool.util_arg --test-get_arg_dict
Example:
>>> # ENABLE_DOCTEST
>>> from utool.util_arg import * # NOQA
>>> import utool as ut
>>> import shlex
>>> argv = shlex.split('--test-show_name --name=IBEIS_PZ_0303 --db testdb3 --save "~/latex/crall-candidacy-2015/figures/IBEIS_PZ_0303.jpg" --dpath figures --caption="Shadowed" --figsize=11,3 --no-figtitle -t foo bar baz biz --notitle')
>>> arg_dict = ut.get_arg_dict(argv, prefix_list=['--', '-'], type_hints={'t': list})
>>> result = ut.repr2(arg_dict, nl=1)
>>> # verify results
>>> print(result)
{
'caption': 'Shadowed',
'db': 'testdb3',
'dpath': 'figures',
'figsize': '11,3',
'name': 'IBEIS_PZ_0303',
'no-figtitle': True,
'notitle': True,
'save': '~/latex/crall-candidacy-2015/figures/IBEIS_PZ_0303.jpg',
't': ['foo', 'bar', 'baz', 'biz'],
'test-show_name': True,
} | [
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] | 3b27e1f4e6e6fb23cd8744af7b7195b57d99e03a | https://github.com/Erotemic/utool/blob/3b27e1f4e6e6fb23cd8744af7b7195b57d99e03a/utool/util_arg.py#L602-L671 | train |
Erotemic/utool | utool/util_arg.py | argv_flag_dec | def argv_flag_dec(*argin, **kwargs):
"""
Decorators which control program flow based on sys.argv
the decorated function does not execute without its corresponding
flag
Kwargs:
default, quiet, indent, default
ReturnKwargs:
alias_flags
"""
kwargs = kwargs.copy()
kwargs['default'] = kwargs.get('default', False)
from utool import util_decor
@util_decor.ignores_exc_tb(outer_wrapper=False)
def wrap_argv_flag_dec(func):
return __argv_flag_dec(func, **kwargs)
assert len(argin) < 2, 'specify 0 or 1 args'
if len(argin) == 1 and util_type.is_funclike(argin[0]):
func = argin[0]
return wrap_argv_flag_dec(func)
else:
return wrap_argv_flag_dec | python | def argv_flag_dec(*argin, **kwargs):
"""
Decorators which control program flow based on sys.argv
the decorated function does not execute without its corresponding
flag
Kwargs:
default, quiet, indent, default
ReturnKwargs:
alias_flags
"""
kwargs = kwargs.copy()
kwargs['default'] = kwargs.get('default', False)
from utool import util_decor
@util_decor.ignores_exc_tb(outer_wrapper=False)
def wrap_argv_flag_dec(func):
return __argv_flag_dec(func, **kwargs)
assert len(argin) < 2, 'specify 0 or 1 args'
if len(argin) == 1 and util_type.is_funclike(argin[0]):
func = argin[0]
return wrap_argv_flag_dec(func)
else:
return wrap_argv_flag_dec | [
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Kwargs:
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ReturnKwargs:
alias_flags | [
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Erotemic/utool | utool/util_arg.py | __argv_flag_dec | def __argv_flag_dec(func, default=False, quiet=QUIET, indent=False):
"""
Logic for controlling if a function gets called based on command line
"""
from utool import util_decor
flagname = meta_util_six.get_funcname(func)
if flagname.find('no') == 0:
flagname = flagname[2:]
flags = (
'--' + flagname.replace('_', '-'),
'--' + flagname,
)
@util_decor.ignores_exc_tb(outer_wrapper=False)
def GaurdWrapper(*args, **kwargs):
from utool import util_print
# FIXME: the --print-all is a hack
default_ = kwargs.pop('default', default)
alias_flags = kwargs.pop('alias_flags', [])
is_flagged = (get_argflag(flags, default_) or
get_argflag('--print-all') or
any([get_argflag(_) for _ in alias_flags]))
if flagname in kwargs:
is_flagged = kwargs.pop(flagname)
if is_flagged:
func_label = flags[0].replace('--', '').replace('print-', '')
# print('')
print('\n+ --- ' + func_label + ' ___')
use_indent = indent is not False
if indent is True:
indent_ = '[%s]' % func_label
else:
indent_ = indent
with util_print.Indenter(indent_, enabled=use_indent):
ret = func(*args, **kwargs)
print('L ___ ' + func_label + '___\n')
return ret
else:
PRINT_DISABLED_FLAGDEC = not get_argflag(
'--noinform', help_='does not print disabled flag decorators')
if not quiet and PRINT_DISABLED_FLAGDEC:
#print('\n~~~ %s ~~~' % flag)
print('~~~ %s ~~~' % flags[0])
meta_util_six.set_funcname(GaurdWrapper, meta_util_six.get_funcname(func))
return GaurdWrapper | python | def __argv_flag_dec(func, default=False, quiet=QUIET, indent=False):
"""
Logic for controlling if a function gets called based on command line
"""
from utool import util_decor
flagname = meta_util_six.get_funcname(func)
if flagname.find('no') == 0:
flagname = flagname[2:]
flags = (
'--' + flagname.replace('_', '-'),
'--' + flagname,
)
@util_decor.ignores_exc_tb(outer_wrapper=False)
def GaurdWrapper(*args, **kwargs):
from utool import util_print
# FIXME: the --print-all is a hack
default_ = kwargs.pop('default', default)
alias_flags = kwargs.pop('alias_flags', [])
is_flagged = (get_argflag(flags, default_) or
get_argflag('--print-all') or
any([get_argflag(_) for _ in alias_flags]))
if flagname in kwargs:
is_flagged = kwargs.pop(flagname)
if is_flagged:
func_label = flags[0].replace('--', '').replace('print-', '')
# print('')
print('\n+ --- ' + func_label + ' ___')
use_indent = indent is not False
if indent is True:
indent_ = '[%s]' % func_label
else:
indent_ = indent
with util_print.Indenter(indent_, enabled=use_indent):
ret = func(*args, **kwargs)
print('L ___ ' + func_label + '___\n')
return ret
else:
PRINT_DISABLED_FLAGDEC = not get_argflag(
'--noinform', help_='does not print disabled flag decorators')
if not quiet and PRINT_DISABLED_FLAGDEC:
#print('\n~~~ %s ~~~' % flag)
print('~~~ %s ~~~' % flags[0])
meta_util_six.set_funcname(GaurdWrapper, meta_util_six.get_funcname(func))
return GaurdWrapper | [
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Erotemic/utool | utool/util_arg.py | get_argv_tail | def get_argv_tail(scriptname, prefer_main=None, argv=None):
r"""
gets the rest of the arguments after a script has been invoked hack.
accounts for python -m scripts.
Args:
scriptname (str):
CommandLine:
python -m utool.util_arg --test-get_argv_tail
Example:
>>> # ENABLE_DOCTEST
>>> from utool.util_arg import * # NOQA
>>> import utool as ut
>>> from os.path import relpath, dirname
>>> scriptname = 'utool.util_arg'
>>> prefer_main = False
>>> argv=['python', '-m', 'utool.util_arg', '--test-get_argv_tail']
>>> tail = get_argv_tail(scriptname, prefer_main, argv)
>>> # hack
>>> tail[0] = ut.ensure_unixslash(relpath(tail[0], dirname(dirname(ut.__file__))))
>>> result = ut.repr2(tail)
>>> print(result)
['utool/util_arg.py', '--test-get_argv_tail']
Example:
>>> # ENABLE_DOCTEST
>>> from utool.util_arg import * # NOQA
>>> import utool as ut
>>> from os.path import relpath, dirname
>>> scriptname = 'utprof.py'
>>> prefer_main = True
>>> argv=['utprof.py', '-m', 'utool', '--tf', 'get_argv_tail']
>>> tail = get_argv_tail(scriptname, prefer_main, argv)
>>> # hack
>>> tail[0] = ut.ensure_unixslash(relpath(tail[0], dirname(dirname(ut.__file__))))
>>> result = ut.repr2(tail)
>>> print(result)
['utool/__main__.py', '--tf', 'get_argv_tail']
"""
if argv is None:
argv = sys.argv
import utool as ut
modname = ut.get_argval('-m', help_='specify module name to profile', argv=argv)
if modname is not None:
# hack to account for -m scripts
modpath = ut.get_modpath(modname, prefer_main=prefer_main)
argvx = argv.index(modname) + 1
argv_tail = [modpath] + argv[argvx:]
else:
try:
argvx = argv.index(scriptname)
except ValueError:
for argvx, arg in enumerate(argv):
# HACK
if scriptname in arg:
break
argv_tail = argv[(argvx + 1):]
return argv_tail | python | def get_argv_tail(scriptname, prefer_main=None, argv=None):
r"""
gets the rest of the arguments after a script has been invoked hack.
accounts for python -m scripts.
Args:
scriptname (str):
CommandLine:
python -m utool.util_arg --test-get_argv_tail
Example:
>>> # ENABLE_DOCTEST
>>> from utool.util_arg import * # NOQA
>>> import utool as ut
>>> from os.path import relpath, dirname
>>> scriptname = 'utool.util_arg'
>>> prefer_main = False
>>> argv=['python', '-m', 'utool.util_arg', '--test-get_argv_tail']
>>> tail = get_argv_tail(scriptname, prefer_main, argv)
>>> # hack
>>> tail[0] = ut.ensure_unixslash(relpath(tail[0], dirname(dirname(ut.__file__))))
>>> result = ut.repr2(tail)
>>> print(result)
['utool/util_arg.py', '--test-get_argv_tail']
Example:
>>> # ENABLE_DOCTEST
>>> from utool.util_arg import * # NOQA
>>> import utool as ut
>>> from os.path import relpath, dirname
>>> scriptname = 'utprof.py'
>>> prefer_main = True
>>> argv=['utprof.py', '-m', 'utool', '--tf', 'get_argv_tail']
>>> tail = get_argv_tail(scriptname, prefer_main, argv)
>>> # hack
>>> tail[0] = ut.ensure_unixslash(relpath(tail[0], dirname(dirname(ut.__file__))))
>>> result = ut.repr2(tail)
>>> print(result)
['utool/__main__.py', '--tf', 'get_argv_tail']
"""
if argv is None:
argv = sys.argv
import utool as ut
modname = ut.get_argval('-m', help_='specify module name to profile', argv=argv)
if modname is not None:
# hack to account for -m scripts
modpath = ut.get_modpath(modname, prefer_main=prefer_main)
argvx = argv.index(modname) + 1
argv_tail = [modpath] + argv[argvx:]
else:
try:
argvx = argv.index(scriptname)
except ValueError:
for argvx, arg in enumerate(argv):
# HACK
if scriptname in arg:
break
argv_tail = argv[(argvx + 1):]
return argv_tail | [
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gets the rest of the arguments after a script has been invoked hack.
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Args:
scriptname (str):
CommandLine:
python -m utool.util_arg --test-get_argv_tail
Example:
>>> # ENABLE_DOCTEST
>>> from utool.util_arg import * # NOQA
>>> import utool as ut
>>> from os.path import relpath, dirname
>>> scriptname = 'utool.util_arg'
>>> prefer_main = False
>>> argv=['python', '-m', 'utool.util_arg', '--test-get_argv_tail']
>>> tail = get_argv_tail(scriptname, prefer_main, argv)
>>> # hack
>>> tail[0] = ut.ensure_unixslash(relpath(tail[0], dirname(dirname(ut.__file__))))
>>> result = ut.repr2(tail)
>>> print(result)
['utool/util_arg.py', '--test-get_argv_tail']
Example:
>>> # ENABLE_DOCTEST
>>> from utool.util_arg import * # NOQA
>>> import utool as ut
>>> from os.path import relpath, dirname
>>> scriptname = 'utprof.py'
>>> prefer_main = True
>>> argv=['utprof.py', '-m', 'utool', '--tf', 'get_argv_tail']
>>> tail = get_argv_tail(scriptname, prefer_main, argv)
>>> # hack
>>> tail[0] = ut.ensure_unixslash(relpath(tail[0], dirname(dirname(ut.__file__))))
>>> result = ut.repr2(tail)
>>> print(result)
['utool/__main__.py', '--tf', 'get_argv_tail'] | [
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Erotemic/utool | utool/util_arg.py | get_cmdline_varargs | def get_cmdline_varargs(argv=None):
"""
Returns positional args specified directly after the scriptname
and before any args starting with '-' on the commandline.
"""
if argv is None:
argv = sys.argv
scriptname = argv[0]
if scriptname == '':
# python invoked by iteself
pos_start = 0
pos_end = 0
else:
pos_start = pos_end = 1
for idx in range(pos_start, len(argv)):
if argv[idx].startswith('-'):
pos_end = idx
break
else:
pos_end = len(argv)
cmdline_varargs = argv[pos_start:pos_end]
return cmdline_varargs | python | def get_cmdline_varargs(argv=None):
"""
Returns positional args specified directly after the scriptname
and before any args starting with '-' on the commandline.
"""
if argv is None:
argv = sys.argv
scriptname = argv[0]
if scriptname == '':
# python invoked by iteself
pos_start = 0
pos_end = 0
else:
pos_start = pos_end = 1
for idx in range(pos_start, len(argv)):
if argv[idx].startswith('-'):
pos_end = idx
break
else:
pos_end = len(argv)
cmdline_varargs = argv[pos_start:pos_end]
return cmdline_varargs | [
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Erotemic/utool | utool/util_arg.py | argval | def argval(key, default=None, type=None, smartcast=True, return_exists=False,
argv=None):
"""
alias for get_argval
Example:
>>> # ENABLE_DOCTEST
>>> import utool as ut
>>> import sys
>>> argv = ['--aids=[1,2,3]']
>>> value = ut.argval('--aids', default=[1, 2], argv=argv)
>>> assert isinstance(value, list)
>>> value2 = ut.argval('--aids', smartcast=False, argv=argv)
>>> assert isinstance(value2, str)
>>> value2 = ut.argval('--aids', smartcast=True, argv=argv)
>>> assert isinstance(value2, list)
"""
defaultable_types = (tuple, list, int, float)
if type is None and isinstance(default, defaultable_types):
type = builtins.type(default)
return get_argval(key, type_=type, default=default,
return_was_specified=return_exists, smartcast=smartcast,
argv=argv) | python | def argval(key, default=None, type=None, smartcast=True, return_exists=False,
argv=None):
"""
alias for get_argval
Example:
>>> # ENABLE_DOCTEST
>>> import utool as ut
>>> import sys
>>> argv = ['--aids=[1,2,3]']
>>> value = ut.argval('--aids', default=[1, 2], argv=argv)
>>> assert isinstance(value, list)
>>> value2 = ut.argval('--aids', smartcast=False, argv=argv)
>>> assert isinstance(value2, str)
>>> value2 = ut.argval('--aids', smartcast=True, argv=argv)
>>> assert isinstance(value2, list)
"""
defaultable_types = (tuple, list, int, float)
if type is None and isinstance(default, defaultable_types):
type = builtins.type(default)
return get_argval(key, type_=type, default=default,
return_was_specified=return_exists, smartcast=smartcast,
argv=argv) | [
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>>> import sys
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>>> value = ut.argval('--aids', default=[1, 2], argv=argv)
>>> assert isinstance(value, list)
>>> value2 = ut.argval('--aids', smartcast=False, argv=argv)
>>> assert isinstance(value2, str)
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YuriyGuts/pygoose | pygoose/kg/eda.py | plot_real_feature | def plot_real_feature(df, feature_name, bins=50, figsize=(15, 15)):
"""
Plot the distribution of a real-valued feature conditioned by the target.
Examples:
`plot_real_feature(X, 'emb_mean_euclidean')`
Args:
df: Pandas dataframe containing the target column (named 'target').
feature_name: The name of the feature to plot.
bins: The number of histogram bins for the distribution plot.
figsize: The size of the plotted figure.
"""
ix_negative_target = df[df.target == 0].index
ix_positive_target = df[df.target == 1].index
plt.figure(figsize=figsize)
ax_overall_dist = plt.subplot2grid((3, 2), (0, 0), colspan=2)
ax_target_conditional_dist = plt.subplot2grid((3, 2), (1, 0), colspan=2)
ax_botplot = plt.subplot2grid((3, 2), (2, 0))
ax_violin_plot = plt.subplot2grid((3, 2), (2, 1))
ax_overall_dist.set_title('Distribution of {}'.format(feature_name), fontsize=16)
sns.distplot(
df[feature_name],
bins=50,
ax=ax_overall_dist
)
sns.distplot(
df.loc[ix_positive_target][feature_name],
bins=bins,
ax=ax_target_conditional_dist,
label='Positive Target'
)
sns.distplot(
df.loc[ix_negative_target][feature_name],
bins=bins,
ax=ax_target_conditional_dist,
label='Negative Target'
)
ax_target_conditional_dist.legend(loc='upper right', prop={'size': 14})
sns.boxplot(
y=feature_name,
x='target',
data=df,
ax=ax_botplot
)
sns.violinplot(
y=feature_name,
x='target',
data=df,
ax=ax_violin_plot
)
plt.show() | python | def plot_real_feature(df, feature_name, bins=50, figsize=(15, 15)):
"""
Plot the distribution of a real-valued feature conditioned by the target.
Examples:
`plot_real_feature(X, 'emb_mean_euclidean')`
Args:
df: Pandas dataframe containing the target column (named 'target').
feature_name: The name of the feature to plot.
bins: The number of histogram bins for the distribution plot.
figsize: The size of the plotted figure.
"""
ix_negative_target = df[df.target == 0].index
ix_positive_target = df[df.target == 1].index
plt.figure(figsize=figsize)
ax_overall_dist = plt.subplot2grid((3, 2), (0, 0), colspan=2)
ax_target_conditional_dist = plt.subplot2grid((3, 2), (1, 0), colspan=2)
ax_botplot = plt.subplot2grid((3, 2), (2, 0))
ax_violin_plot = plt.subplot2grid((3, 2), (2, 1))
ax_overall_dist.set_title('Distribution of {}'.format(feature_name), fontsize=16)
sns.distplot(
df[feature_name],
bins=50,
ax=ax_overall_dist
)
sns.distplot(
df.loc[ix_positive_target][feature_name],
bins=bins,
ax=ax_target_conditional_dist,
label='Positive Target'
)
sns.distplot(
df.loc[ix_negative_target][feature_name],
bins=bins,
ax=ax_target_conditional_dist,
label='Negative Target'
)
ax_target_conditional_dist.legend(loc='upper right', prop={'size': 14})
sns.boxplot(
y=feature_name,
x='target',
data=df,
ax=ax_botplot
)
sns.violinplot(
y=feature_name,
x='target',
data=df,
ax=ax_violin_plot
)
plt.show() | [
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Args:
df: Pandas dataframe containing the target column (named 'target').
feature_name: The name of the feature to plot.
bins: The number of histogram bins for the distribution plot.
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YuriyGuts/pygoose | pygoose/kg/eda.py | plot_pair | def plot_pair(df, feature_name_1, feature_name_2, kind='scatter', alpha=0.01, **kwargs):
"""
Plot a scatterplot of two features against one another,
and calculate Pearson correlation coefficient.
Examples:
`plot_pair(X, 'emb_mean_euclidean', 'emb_mean_cosine')`
Args:
df:
feature_name_1: The name of the first feature.
feature_name_2: The name of the second feature.
kind: One of the values { 'scatter' | 'reg' | 'resid' | 'kde' | 'hex' }.
alpha: Alpha channel value.
**kwargs: Additional argument to 'sns.jointplot'.
"""
plt.figure()
sns.jointplot(
feature_name_1,
feature_name_2,
df,
alpha=alpha,
kind=kind,
**kwargs
)
plt.show() | python | def plot_pair(df, feature_name_1, feature_name_2, kind='scatter', alpha=0.01, **kwargs):
"""
Plot a scatterplot of two features against one another,
and calculate Pearson correlation coefficient.
Examples:
`plot_pair(X, 'emb_mean_euclidean', 'emb_mean_cosine')`
Args:
df:
feature_name_1: The name of the first feature.
feature_name_2: The name of the second feature.
kind: One of the values { 'scatter' | 'reg' | 'resid' | 'kde' | 'hex' }.
alpha: Alpha channel value.
**kwargs: Additional argument to 'sns.jointplot'.
"""
plt.figure()
sns.jointplot(
feature_name_1,
feature_name_2,
df,
alpha=alpha,
kind=kind,
**kwargs
)
plt.show() | [
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feature_name_2: The name of the second feature.
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YuriyGuts/pygoose | pygoose/kg/eda.py | plot_feature_correlation_heatmap | def plot_feature_correlation_heatmap(df, features, font_size=9, figsize=(15, 15), save_filename=None):
"""
Plot a correlation heatmap between every feature pair.
Args:
df: Pandas dataframe containing the target column (named 'target').
features: The list of features to include in the correlation plot.
font_size: Font size for heatmap cells and axis labels.
figsize: The size of the plot.
save_filename: (Optional) The path of the file to save a high-res version of the plot to.
"""
features = features[:]
features += ['target']
mcorr = df[features].corr()
mask = np.zeros_like(mcorr, dtype=np.bool)
mask[np.triu_indices_from(mask)] = True
cmap = sns.diverging_palette(220, 10, as_cmap=True)
fig = plt.figure(figsize=figsize)
heatmap = sns.heatmap(
mcorr,
mask=mask,
cmap=cmap,
square=True,
annot=True,
fmt='0.2f',
annot_kws={'size': font_size},
)
heatmap.tick_params(axis='both', which='major', labelsize=font_size)
heatmap.tick_params(axis='both', which='minor', labelsize=font_size)
heatmap.set_xticklabels(features, rotation=90)
heatmap.set_yticklabels(reversed(features))
plt.show()
if save_filename is not None:
fig.savefig(save_filename, dpi=300) | python | def plot_feature_correlation_heatmap(df, features, font_size=9, figsize=(15, 15), save_filename=None):
"""
Plot a correlation heatmap between every feature pair.
Args:
df: Pandas dataframe containing the target column (named 'target').
features: The list of features to include in the correlation plot.
font_size: Font size for heatmap cells and axis labels.
figsize: The size of the plot.
save_filename: (Optional) The path of the file to save a high-res version of the plot to.
"""
features = features[:]
features += ['target']
mcorr = df[features].corr()
mask = np.zeros_like(mcorr, dtype=np.bool)
mask[np.triu_indices_from(mask)] = True
cmap = sns.diverging_palette(220, 10, as_cmap=True)
fig = plt.figure(figsize=figsize)
heatmap = sns.heatmap(
mcorr,
mask=mask,
cmap=cmap,
square=True,
annot=True,
fmt='0.2f',
annot_kws={'size': font_size},
)
heatmap.tick_params(axis='both', which='major', labelsize=font_size)
heatmap.tick_params(axis='both', which='minor', labelsize=font_size)
heatmap.set_xticklabels(features, rotation=90)
heatmap.set_yticklabels(reversed(features))
plt.show()
if save_filename is not None:
fig.savefig(save_filename, dpi=300) | [
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YuriyGuts/pygoose | pygoose/kg/eda.py | scatterplot_matrix | def scatterplot_matrix(df, features, downsample_frac=None, figsize=(15, 15)):
"""
Plot a scatterplot matrix for a list of features, colored by target value.
Example: `scatterplot_matrix(X, X.columns.tolist(), downsample_frac=0.01)`
Args:
df: Pandas dataframe containing the target column (named 'target').
features: The list of features to include in the correlation plot.
downsample_frac: Dataframe downsampling rate (0.1 to include 10% of the dataset).
figsize: The size of the plot.
"""
if downsample_frac:
df = df.sample(frac=downsample_frac)
plt.figure(figsize=figsize)
sns.pairplot(df[features], hue='target')
plt.show() | python | def scatterplot_matrix(df, features, downsample_frac=None, figsize=(15, 15)):
"""
Plot a scatterplot matrix for a list of features, colored by target value.
Example: `scatterplot_matrix(X, X.columns.tolist(), downsample_frac=0.01)`
Args:
df: Pandas dataframe containing the target column (named 'target').
features: The list of features to include in the correlation plot.
downsample_frac: Dataframe downsampling rate (0.1 to include 10% of the dataset).
figsize: The size of the plot.
"""
if downsample_frac:
df = df.sample(frac=downsample_frac)
plt.figure(figsize=figsize)
sns.pairplot(df[features], hue='target')
plt.show() | [
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LEMS/pylems | lems/parser/LEMS.py | LEMSFileParser.process_nested_tags | def process_nested_tags(self, node, tag = ''):
"""
Process child tags.
@param node: Current node being parsed.
@type node: xml.etree.Element
@raise ParseError: Raised when an unexpected nested tag is found.
"""
##print("---------Processing: %s, %s"%(node.tag,tag))
if tag == '':
t = node.ltag
else:
t = tag.lower()
for child in node.children:
self.xml_node_stack = [child] + self.xml_node_stack
ctagl = child.ltag
if ctagl in self.tag_parse_table and ctagl in self.valid_children[t]:
#print("Processing known type: %s"%ctagl)
self.tag_parse_table[ctagl](child)
else:
#print("Processing unknown type: %s"%ctagl)
self.parse_component_by_typename(child, child.tag)
self.xml_node_stack = self.xml_node_stack[1:] | python | def process_nested_tags(self, node, tag = ''):
"""
Process child tags.
@param node: Current node being parsed.
@type node: xml.etree.Element
@raise ParseError: Raised when an unexpected nested tag is found.
"""
##print("---------Processing: %s, %s"%(node.tag,tag))
if tag == '':
t = node.ltag
else:
t = tag.lower()
for child in node.children:
self.xml_node_stack = [child] + self.xml_node_stack
ctagl = child.ltag
if ctagl in self.tag_parse_table and ctagl in self.valid_children[t]:
#print("Processing known type: %s"%ctagl)
self.tag_parse_table[ctagl](child)
else:
#print("Processing unknown type: %s"%ctagl)
self.parse_component_by_typename(child, child.tag)
self.xml_node_stack = self.xml_node_stack[1:] | [
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LEMS/pylems | lems/parser/LEMS.py | LEMSFileParser.parse | def parse(self, xmltext):
"""
Parse a string containing LEMS XML text.
@param xmltext: String containing LEMS XML formatted text.
@type xmltext: str
"""
xml = LEMSXMLNode(xe.XML(xmltext))
if xml.ltag != 'lems' and xml.ltag != 'neuroml':
raise ParseError('<Lems> expected as root element (or even <neuroml>), found: {0}'.format(xml.ltag))
'''
if xml.ltag == 'lems':
if 'description' in xml.lattrib:
self.description = xml.lattrib['description']
'''
self.process_nested_tags(xml) | python | def parse(self, xmltext):
"""
Parse a string containing LEMS XML text.
@param xmltext: String containing LEMS XML formatted text.
@type xmltext: str
"""
xml = LEMSXMLNode(xe.XML(xmltext))
if xml.ltag != 'lems' and xml.ltag != 'neuroml':
raise ParseError('<Lems> expected as root element (or even <neuroml>), found: {0}'.format(xml.ltag))
'''
if xml.ltag == 'lems':
if 'description' in xml.lattrib:
self.description = xml.lattrib['description']
'''
self.process_nested_tags(xml) | [
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LEMS/pylems | lems/parser/LEMS.py | LEMSFileParser.raise_error | def raise_error(self, message, *params, **key_params):
"""
Raise a parse error.
"""
s = 'Parser error in '
self.xml_node_stack.reverse()
if len(self.xml_node_stack) > 1:
node = self.xml_node_stack[0]
s += '<{0}'.format(node.tag)
if 'name' in node.lattrib:
s += ' name=\"{0}\"'.format(node.lattrib['name'])
if 'id' in node.lattrib:
s += ' id=\"{0}\"'.format(node.lattrib['id'])
s += '>'
for node in self.xml_node_stack[1:]:
s += '.<{0}'.format(node.tag)
if 'name' in node.lattrib:
s += ' name=\"{0}\"'.format(node.lattrib['name'])
if 'id' in node.lattrib:
s += ' id=\"{0}\"'.format(node.lattrib['id'])
s += '>'
s += ':\n ' + message
raise ParseError(s, *params, **key_params)
self.xml_node_stack.reverse() | python | def raise_error(self, message, *params, **key_params):
"""
Raise a parse error.
"""
s = 'Parser error in '
self.xml_node_stack.reverse()
if len(self.xml_node_stack) > 1:
node = self.xml_node_stack[0]
s += '<{0}'.format(node.tag)
if 'name' in node.lattrib:
s += ' name=\"{0}\"'.format(node.lattrib['name'])
if 'id' in node.lattrib:
s += ' id=\"{0}\"'.format(node.lattrib['id'])
s += '>'
for node in self.xml_node_stack[1:]:
s += '.<{0}'.format(node.tag)
if 'name' in node.lattrib:
s += ' name=\"{0}\"'.format(node.lattrib['name'])
if 'id' in node.lattrib:
s += ' id=\"{0}\"'.format(node.lattrib['id'])
s += '>'
s += ':\n ' + message
raise ParseError(s, *params, **key_params)
self.xml_node_stack.reverse() | [
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LEMS/pylems | lems/parser/LEMS.py | LEMSFileParser.parse_component_by_typename | def parse_component_by_typename(self, node, type_):
"""
Parses components defined directly by component name.
@param node: Node containing the <Component> element
@type node: xml.etree.Element
@param type_: Type of this component.
@type type_: string
@raise ParseError: Raised when the component does not have an id.
"""
#print('Parsing component {0} by typename {1}'.format(node, type_))
if 'id' in node.lattrib:
id_ = node.lattrib['id']
else:
#self.raise_error('Component must have an id')
id_ = node.tag #make_id()
if 'type' in node.lattrib:
type_ = node.lattrib['type']
else:
type_ = node.tag
component = Component(id_, type_)
if self.current_component:
component.set_parent_id(self.current_component.id)
self.current_component.add_child(component)
else:
self.model.add_component(component)
for key in node.attrib:
if key.lower() not in ['id', 'type']:
component.set_parameter(key, node.attrib[key])
old_component = self.current_component
self.current_component = component
self.process_nested_tags(node, 'component')
self.current_component = old_component | python | def parse_component_by_typename(self, node, type_):
"""
Parses components defined directly by component name.
@param node: Node containing the <Component> element
@type node: xml.etree.Element
@param type_: Type of this component.
@type type_: string
@raise ParseError: Raised when the component does not have an id.
"""
#print('Parsing component {0} by typename {1}'.format(node, type_))
if 'id' in node.lattrib:
id_ = node.lattrib['id']
else:
#self.raise_error('Component must have an id')
id_ = node.tag #make_id()
if 'type' in node.lattrib:
type_ = node.lattrib['type']
else:
type_ = node.tag
component = Component(id_, type_)
if self.current_component:
component.set_parent_id(self.current_component.id)
self.current_component.add_child(component)
else:
self.model.add_component(component)
for key in node.attrib:
if key.lower() not in ['id', 'type']:
component.set_parameter(key, node.attrib[key])
old_component = self.current_component
self.current_component = component
self.process_nested_tags(node, 'component')
self.current_component = old_component | [
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glormph/msstitch | src/app/readers/xml.py | generate_tags_multiple_files | def generate_tags_multiple_files(input_files, tag, ignore_tags, ns=None):
"""
Calls xmltag generator for multiple files.
"""
return itertools.chain.from_iterable([generate_xmltags(
fn, tag, ignore_tags, ns) for fn in input_files]) | python | def generate_tags_multiple_files(input_files, tag, ignore_tags, ns=None):
"""
Calls xmltag generator for multiple files.
"""
return itertools.chain.from_iterable([generate_xmltags(
fn, tag, ignore_tags, ns) for fn in input_files]) | [
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glormph/msstitch | src/app/readers/xml.py | generate_tags_multiple_files_strings | def generate_tags_multiple_files_strings(input_files, ns, tag, ignore_tags):
"""
Creates stringified xml output of elements with certain tag.
"""
for el in generate_tags_multiple_files(input_files, tag, ignore_tags, ns):
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"""
Creates stringified xml output of elements with certain tag.
"""
for el in generate_tags_multiple_files(input_files, tag, ignore_tags, ns):
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glormph/msstitch | src/app/readers/xml.py | generate_xmltags | def generate_xmltags(fn, returntag, ignore_tags, ns=None):
"""
Base generator for percolator xml psm, peptide, protein output,
as well as for mzML, mzIdentML.
ignore_tags are the ones that are cleared when met by parser.
"""
xmlns = create_namespace(ns)
ns_ignore = ['{0}{1}'.format(xmlns, x) for x in ignore_tags]
for ac, el in etree.iterparse(fn):
if el.tag == '{0}{1}'.format(xmlns, returntag):
yield el
elif el.tag in ns_ignore:
formatting.clear_el(el) | python | def generate_xmltags(fn, returntag, ignore_tags, ns=None):
"""
Base generator for percolator xml psm, peptide, protein output,
as well as for mzML, mzIdentML.
ignore_tags are the ones that are cleared when met by parser.
"""
xmlns = create_namespace(ns)
ns_ignore = ['{0}{1}'.format(xmlns, x) for x in ignore_tags]
for ac, el in etree.iterparse(fn):
if el.tag == '{0}{1}'.format(xmlns, returntag):
yield el
elif el.tag in ns_ignore:
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LEMS/pylems | lems/model/model.py | Model.add_component_type | def add_component_type(self, component_type):
"""
Adds a component type to the model.
@param component_type: Component type to be added.
@type component_type: lems.model.fundamental.ComponentType
"""
name = component_type.name
# To handle colons in names in LEMS
if ':' in name:
name = name.replace(':', '_')
component_type.name = name
self.component_types[name] = component_type | python | def add_component_type(self, component_type):
"""
Adds a component type to the model.
@param component_type: Component type to be added.
@type component_type: lems.model.fundamental.ComponentType
"""
name = component_type.name
# To handle colons in names in LEMS
if ':' in name:
name = name.replace(':', '_')
component_type.name = name
self.component_types[name] = component_type | [
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LEMS/pylems | lems/model/model.py | Model.add | def add(self, child):
"""
Adds a typed child object to the model.
@param child: Child object to be added.
"""
if isinstance(child, Include):
self.add_include(child)
elif isinstance(child, Dimension):
self.add_dimension(child)
elif isinstance(child, Unit):
self.add_unit(child)
elif isinstance(child, ComponentType):
self.add_component_type(child)
elif isinstance(child, Component):
self.add_component(child)
elif isinstance(child, FatComponent):
self.add_fat_component(child)
elif isinstance(child, Constant):
self.add_constant(child)
else:
raise ModelError('Unsupported child element') | python | def add(self, child):
"""
Adds a typed child object to the model.
@param child: Child object to be added.
"""
if isinstance(child, Include):
self.add_include(child)
elif isinstance(child, Dimension):
self.add_dimension(child)
elif isinstance(child, Unit):
self.add_unit(child)
elif isinstance(child, ComponentType):
self.add_component_type(child)
elif isinstance(child, Component):
self.add_component(child)
elif isinstance(child, FatComponent):
self.add_fat_component(child)
elif isinstance(child, Constant):
self.add_constant(child)
else:
raise ModelError('Unsupported child element') | [
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LEMS/pylems | lems/model/model.py | Model.include_file | def include_file(self, path, include_dirs = []):
"""
Includes a file into the current model.
@param path: Path to the file to be included.
@type path: str
@param include_dirs: Optional alternate include search path.
@type include_dirs: list(str)
"""
if self.include_includes:
if self.debug: print("------------------ Including a file: %s"%path)
inc_dirs = include_dirs if include_dirs else self.include_dirs
parser = LEMSFileParser(self, inc_dirs, self.include_includes)
if os.access(path, os.F_OK):
if not path in self.included_files:
parser.parse(open(path).read())
self.included_files.append(path)
return
else:
if self.debug: print("Already included: %s"%path)
return
else:
for inc_dir in inc_dirs:
new_path = (inc_dir + '/' + path)
if os.access(new_path, os.F_OK):
if not new_path in self.included_files:
parser.parse(open(new_path).read())
self.included_files.append(new_path)
return
else:
if self.debug: print("Already included: %s"%path)
return
msg = 'Unable to open ' + path
if self.fail_on_missing_includes:
raise Exception(msg)
elif self.debug:
print(msg) | python | def include_file(self, path, include_dirs = []):
"""
Includes a file into the current model.
@param path: Path to the file to be included.
@type path: str
@param include_dirs: Optional alternate include search path.
@type include_dirs: list(str)
"""
if self.include_includes:
if self.debug: print("------------------ Including a file: %s"%path)
inc_dirs = include_dirs if include_dirs else self.include_dirs
parser = LEMSFileParser(self, inc_dirs, self.include_includes)
if os.access(path, os.F_OK):
if not path in self.included_files:
parser.parse(open(path).read())
self.included_files.append(path)
return
else:
if self.debug: print("Already included: %s"%path)
return
else:
for inc_dir in inc_dirs:
new_path = (inc_dir + '/' + path)
if os.access(new_path, os.F_OK):
if not new_path in self.included_files:
parser.parse(open(new_path).read())
self.included_files.append(new_path)
return
else:
if self.debug: print("Already included: %s"%path)
return
msg = 'Unable to open ' + path
if self.fail_on_missing_includes:
raise Exception(msg)
elif self.debug:
print(msg) | [
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LEMS/pylems | lems/model/model.py | Model.import_from_file | def import_from_file(self, filepath):
"""
Import a model from a file.
@param filepath: File to be imported.
@type filepath: str
"""
inc_dirs = self.include_directories[:]
inc_dirs.append(dirname(filepath))
parser = LEMSFileParser(self, inc_dirs, self.include_includes)
with open(filepath) as f:
parser.parse(f.read()) | python | def import_from_file(self, filepath):
"""
Import a model from a file.
@param filepath: File to be imported.
@type filepath: str
"""
inc_dirs = self.include_directories[:]
inc_dirs.append(dirname(filepath))
parser = LEMSFileParser(self, inc_dirs, self.include_includes)
with open(filepath) as f:
parser.parse(f.read()) | [
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LEMS/pylems | lems/model/model.py | Model.export_to_dom | def export_to_dom(self):
"""
Exports this model to a DOM.
"""
namespaces = 'xmlns="http://www.neuroml.org/lems/%s" ' + \
'xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" ' + \
'xsi:schemaLocation="http://www.neuroml.org/lems/%s %s"'
namespaces = namespaces%(self.target_lems_version,self.target_lems_version,self.schema_location)
xmlstr = '<Lems %s>'%namespaces
for include in self.includes:
xmlstr += include.toxml()
for target in self.targets:
xmlstr += '<Target component="{0}"/>'.format(target)
for dimension in self.dimensions:
xmlstr += dimension.toxml()
for unit in self.units:
xmlstr += unit.toxml()
for constant in self.constants:
xmlstr += constant.toxml()
for component_type in self.component_types:
xmlstr += component_type.toxml()
for component in self.components:
xmlstr += component.toxml()
xmlstr += '</Lems>'
xmldom = minidom.parseString(xmlstr)
return xmldom | python | def export_to_dom(self):
"""
Exports this model to a DOM.
"""
namespaces = 'xmlns="http://www.neuroml.org/lems/%s" ' + \
'xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" ' + \
'xsi:schemaLocation="http://www.neuroml.org/lems/%s %s"'
namespaces = namespaces%(self.target_lems_version,self.target_lems_version,self.schema_location)
xmlstr = '<Lems %s>'%namespaces
for include in self.includes:
xmlstr += include.toxml()
for target in self.targets:
xmlstr += '<Target component="{0}"/>'.format(target)
for dimension in self.dimensions:
xmlstr += dimension.toxml()
for unit in self.units:
xmlstr += unit.toxml()
for constant in self.constants:
xmlstr += constant.toxml()
for component_type in self.component_types:
xmlstr += component_type.toxml()
for component in self.components:
xmlstr += component.toxml()
xmlstr += '</Lems>'
xmldom = minidom.parseString(xmlstr)
return xmldom | [
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LEMS/pylems | lems/model/model.py | Model.export_to_file | def export_to_file(self, filepath, level_prefix = ' '):
"""
Exports this model to a file.
@param filepath: File to be exported to.
@type filepath: str
"""
xmldom = self.export_to_dom()
xmlstr = xmldom.toprettyxml(level_prefix, '\n',)
f = open(filepath, 'w')
f.write(xmlstr)
f.close() | python | def export_to_file(self, filepath, level_prefix = ' '):
"""
Exports this model to a file.
@param filepath: File to be exported to.
@type filepath: str
"""
xmldom = self.export_to_dom()
xmlstr = xmldom.toprettyxml(level_prefix, '\n',)
f = open(filepath, 'w')
f.write(xmlstr)
f.close() | [
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LEMS/pylems | lems/model/model.py | Model.resolve | def resolve(self):
"""
Resolves references in this model.
"""
model = self.copy()
for ct in model.component_types:
model.resolve_component_type(ct)
for c in model.components:
if c.id not in model.fat_components:
model.add(model.fatten_component(c))
for c in ct.constants:
c2 = c.copy()
c2.numeric_value = model.get_numeric_value(c2.value, c2.dimension)
model.add(c2)
return model | python | def resolve(self):
"""
Resolves references in this model.
"""
model = self.copy()
for ct in model.component_types:
model.resolve_component_type(ct)
for c in model.components:
if c.id not in model.fat_components:
model.add(model.fatten_component(c))
for c in ct.constants:
c2 = c.copy()
c2.numeric_value = model.get_numeric_value(c2.value, c2.dimension)
model.add(c2)
return model | [
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LEMS/pylems | lems/model/model.py | Model.resolve_component_type | def resolve_component_type(self, component_type):
"""
Resolves references in the specified component type.
@param component_type: Component type to be resolved.
@type component_type: lems.model.component.ComponentType
"""
# Resolve component type from base types if present.
if component_type.extends:
try:
base_ct = self.component_types[component_type.extends]
except:
raise ModelError("Component type '{0}' trying to extend unknown component type '{1}'",
component_type.name, component_type.extends)
self.resolve_component_type(base_ct)
self.merge_component_types(component_type, base_ct)
component_type.types = set.union(component_type.types, base_ct.types)
component_type.extends = None | python | def resolve_component_type(self, component_type):
"""
Resolves references in the specified component type.
@param component_type: Component type to be resolved.
@type component_type: lems.model.component.ComponentType
"""
# Resolve component type from base types if present.
if component_type.extends:
try:
base_ct = self.component_types[component_type.extends]
except:
raise ModelError("Component type '{0}' trying to extend unknown component type '{1}'",
component_type.name, component_type.extends)
self.resolve_component_type(base_ct)
self.merge_component_types(component_type, base_ct)
component_type.types = set.union(component_type.types, base_ct.types)
component_type.extends = None | [
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LEMS/pylems | lems/model/model.py | Model.merge_component_types | def merge_component_types(self, ct, base_ct):
"""
Merge various maps in the given component type from a base
component type.
@param ct: Component type to be resolved.
@type ct: lems.model.component.ComponentType
@param base_ct: Component type to be resolved.
@type base_ct: lems.model.component.ComponentType
"""
#merge_maps(ct.parameters, base_ct.parameters)
for parameter in base_ct.parameters:
if parameter.name in ct.parameters:
p = ct.parameters[parameter.name]
basep = base_ct.parameters[parameter.name]
if p.fixed:
p.value = p.fixed_value
p.dimension = basep.dimension
else:
ct.parameters[parameter.name] = base_ct.parameters[parameter.name]
merge_maps(ct.properties, base_ct.properties)
merge_maps(ct.derived_parameters, base_ct.derived_parameters)
merge_maps(ct.index_parameters, base_ct.index_parameters)
merge_maps(ct.constants, base_ct.constants)
merge_maps(ct.exposures, base_ct.exposures)
merge_maps(ct.requirements, base_ct.requirements)
merge_maps(ct.component_requirements, base_ct.component_requirements)
merge_maps(ct.instance_requirements, base_ct.instance_requirements)
merge_maps(ct.children, base_ct.children)
merge_maps(ct.texts, base_ct.texts)
merge_maps(ct.links, base_ct.links)
merge_maps(ct.paths, base_ct.paths)
merge_maps(ct.event_ports, base_ct.event_ports)
merge_maps(ct.component_references, base_ct.component_references)
merge_maps(ct.attachments, base_ct.attachments)
merge_maps(ct.dynamics.state_variables, base_ct.dynamics.state_variables)
merge_maps(ct.dynamics.derived_variables, base_ct.dynamics.derived_variables)
merge_maps(ct.dynamics.conditional_derived_variables, base_ct.dynamics.conditional_derived_variables)
merge_maps(ct.dynamics.time_derivatives, base_ct.dynamics.time_derivatives)
#merge_lists(ct.dynamics.event_handlers, base_ct.dynamics.event_handlers)
merge_maps(ct.dynamics.kinetic_schemes, base_ct.dynamics.kinetic_schemes)
merge_lists(ct.structure.event_connections, base_ct.structure.event_connections)
merge_lists(ct.structure.child_instances, base_ct.structure.child_instances)
merge_lists(ct.structure.multi_instantiates, base_ct.structure.multi_instantiates)
merge_maps(ct.simulation.runs, base_ct.simulation.runs)
merge_maps(ct.simulation.records, base_ct.simulation.records)
merge_maps(ct.simulation.event_records, base_ct.simulation.event_records)
merge_maps(ct.simulation.data_displays, base_ct.simulation.data_displays)
merge_maps(ct.simulation.data_writers, base_ct.simulation.data_writers)
merge_maps(ct.simulation.event_writers, base_ct.simulation.event_writers) | python | def merge_component_types(self, ct, base_ct):
"""
Merge various maps in the given component type from a base
component type.
@param ct: Component type to be resolved.
@type ct: lems.model.component.ComponentType
@param base_ct: Component type to be resolved.
@type base_ct: lems.model.component.ComponentType
"""
#merge_maps(ct.parameters, base_ct.parameters)
for parameter in base_ct.parameters:
if parameter.name in ct.parameters:
p = ct.parameters[parameter.name]
basep = base_ct.parameters[parameter.name]
if p.fixed:
p.value = p.fixed_value
p.dimension = basep.dimension
else:
ct.parameters[parameter.name] = base_ct.parameters[parameter.name]
merge_maps(ct.properties, base_ct.properties)
merge_maps(ct.derived_parameters, base_ct.derived_parameters)
merge_maps(ct.index_parameters, base_ct.index_parameters)
merge_maps(ct.constants, base_ct.constants)
merge_maps(ct.exposures, base_ct.exposures)
merge_maps(ct.requirements, base_ct.requirements)
merge_maps(ct.component_requirements, base_ct.component_requirements)
merge_maps(ct.instance_requirements, base_ct.instance_requirements)
merge_maps(ct.children, base_ct.children)
merge_maps(ct.texts, base_ct.texts)
merge_maps(ct.links, base_ct.links)
merge_maps(ct.paths, base_ct.paths)
merge_maps(ct.event_ports, base_ct.event_ports)
merge_maps(ct.component_references, base_ct.component_references)
merge_maps(ct.attachments, base_ct.attachments)
merge_maps(ct.dynamics.state_variables, base_ct.dynamics.state_variables)
merge_maps(ct.dynamics.derived_variables, base_ct.dynamics.derived_variables)
merge_maps(ct.dynamics.conditional_derived_variables, base_ct.dynamics.conditional_derived_variables)
merge_maps(ct.dynamics.time_derivatives, base_ct.dynamics.time_derivatives)
#merge_lists(ct.dynamics.event_handlers, base_ct.dynamics.event_handlers)
merge_maps(ct.dynamics.kinetic_schemes, base_ct.dynamics.kinetic_schemes)
merge_lists(ct.structure.event_connections, base_ct.structure.event_connections)
merge_lists(ct.structure.child_instances, base_ct.structure.child_instances)
merge_lists(ct.structure.multi_instantiates, base_ct.structure.multi_instantiates)
merge_maps(ct.simulation.runs, base_ct.simulation.runs)
merge_maps(ct.simulation.records, base_ct.simulation.records)
merge_maps(ct.simulation.event_records, base_ct.simulation.event_records)
merge_maps(ct.simulation.data_displays, base_ct.simulation.data_displays)
merge_maps(ct.simulation.data_writers, base_ct.simulation.data_writers)
merge_maps(ct.simulation.event_writers, base_ct.simulation.event_writers) | [
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LEMS/pylems | lems/model/model.py | Model.resolve_simulation | def resolve_simulation(self, fc, ct):
"""
Resolve simulation specifications.
"""
for run in ct.simulation.runs:
try:
run2 = Run(fc.component_references[run.component].referenced_component,
run.variable,
fc.parameters[run.increment].numeric_value,
fc.parameters[run.total].numeric_value)
except:
raise ModelError("Unable to resolve simulation run parameters in component '{0}'",
fc.id)
fc.simulation.add(run2)
for record in ct.simulation.records:
try:
record2 = Record(fc.paths[record.quantity].value,
fc.parameters[record.scale].numeric_value if record.scale else 1,
fc.texts[record.color].value if record.color else '#000000')
except:
raise ModelError("Unable to resolve simulation record parameters in component '{0}'",
fc.id)
fc.simulation.add(record2)
for event_record in ct.simulation.event_records:
try:
event_record2 = EventRecord(fc.paths[event_record.quantity].value,
fc.texts[event_record.eventPort].value)
except:
raise ModelError("Unable to resolve simulation event_record parameters in component '{0}'",
fc.id)
fc.simulation.add(event_record2)
for dd in ct.simulation.data_displays:
try:
dd2 = DataDisplay(fc.texts[dd.title].value,
'')
if 'timeScale' in fc.parameters:
dd2.timeScale = fc.parameters['timeScale'].numeric_value
except:
raise ModelError("Unable to resolve simulation display parameters in component '{0}'",
fc.id)
fc.simulation.add(dd2)
for dw in ct.simulation.data_writers:
try:
path = '.'
if fc.texts[dw.path] and fc.texts[dw.path].value:
path = fc.texts[dw.path].value
dw2 = DataWriter(path,
fc.texts[dw.file_name].value)
except:
raise ModelError("Unable to resolve simulation writer parameters in component '{0}'",
fc.id)
fc.simulation.add(dw2)
for ew in ct.simulation.event_writers:
try:
path = '.'
if fc.texts[ew.path] and fc.texts[ew.path].value:
path = fc.texts[ew.path].value
ew2 = EventWriter(path,
fc.texts[ew.file_name].value,
fc.texts[ew.format].value)
except:
raise ModelError("Unable to resolve simulation writer parameters in component '{0}'",
fc.id)
fc.simulation.add(ew2) | python | def resolve_simulation(self, fc, ct):
"""
Resolve simulation specifications.
"""
for run in ct.simulation.runs:
try:
run2 = Run(fc.component_references[run.component].referenced_component,
run.variable,
fc.parameters[run.increment].numeric_value,
fc.parameters[run.total].numeric_value)
except:
raise ModelError("Unable to resolve simulation run parameters in component '{0}'",
fc.id)
fc.simulation.add(run2)
for record in ct.simulation.records:
try:
record2 = Record(fc.paths[record.quantity].value,
fc.parameters[record.scale].numeric_value if record.scale else 1,
fc.texts[record.color].value if record.color else '#000000')
except:
raise ModelError("Unable to resolve simulation record parameters in component '{0}'",
fc.id)
fc.simulation.add(record2)
for event_record in ct.simulation.event_records:
try:
event_record2 = EventRecord(fc.paths[event_record.quantity].value,
fc.texts[event_record.eventPort].value)
except:
raise ModelError("Unable to resolve simulation event_record parameters in component '{0}'",
fc.id)
fc.simulation.add(event_record2)
for dd in ct.simulation.data_displays:
try:
dd2 = DataDisplay(fc.texts[dd.title].value,
'')
if 'timeScale' in fc.parameters:
dd2.timeScale = fc.parameters['timeScale'].numeric_value
except:
raise ModelError("Unable to resolve simulation display parameters in component '{0}'",
fc.id)
fc.simulation.add(dd2)
for dw in ct.simulation.data_writers:
try:
path = '.'
if fc.texts[dw.path] and fc.texts[dw.path].value:
path = fc.texts[dw.path].value
dw2 = DataWriter(path,
fc.texts[dw.file_name].value)
except:
raise ModelError("Unable to resolve simulation writer parameters in component '{0}'",
fc.id)
fc.simulation.add(dw2)
for ew in ct.simulation.event_writers:
try:
path = '.'
if fc.texts[ew.path] and fc.texts[ew.path].value:
path = fc.texts[ew.path].value
ew2 = EventWriter(path,
fc.texts[ew.file_name].value,
fc.texts[ew.format].value)
except:
raise ModelError("Unable to resolve simulation writer parameters in component '{0}'",
fc.id)
fc.simulation.add(ew2) | [
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LEMS/pylems | lems/model/model.py | Model.get_numeric_value | def get_numeric_value(self, value_str, dimension = None):
"""
Get the numeric value for a parameter value specification.
@param value_str: Value string
@type value_str: str
@param dimension: Dimension of the value
@type dimension: str
"""
n = None
i = len(value_str)
while n is None:
try:
part = value_str[0:i]
nn = float(part)
n = nn
s = value_str[i:]
except ValueError:
i = i-1
number = n
sym = s
numeric_value = None
if sym == '':
numeric_value = number
else:
if sym in self.units:
unit = self.units[sym]
if dimension:
if dimension != unit.dimension and dimension != '*':
raise SimBuildError("Unit symbol '{0}' cannot "
"be used for dimension '{1}'",
sym, dimension)
else:
dimension = unit.dimension
numeric_value = (number * (10 ** unit.power) * unit.scale) + unit.offset
else:
raise SimBuildError("Unknown unit symbol '{0}'. Known: {1}",
sym, self.units)
#print("Have converted %s to value: %s, dimension %s"%(value_str, numeric_value, dimension))
return numeric_value | python | def get_numeric_value(self, value_str, dimension = None):
"""
Get the numeric value for a parameter value specification.
@param value_str: Value string
@type value_str: str
@param dimension: Dimension of the value
@type dimension: str
"""
n = None
i = len(value_str)
while n is None:
try:
part = value_str[0:i]
nn = float(part)
n = nn
s = value_str[i:]
except ValueError:
i = i-1
number = n
sym = s
numeric_value = None
if sym == '':
numeric_value = number
else:
if sym in self.units:
unit = self.units[sym]
if dimension:
if dimension != unit.dimension and dimension != '*':
raise SimBuildError("Unit symbol '{0}' cannot "
"be used for dimension '{1}'",
sym, dimension)
else:
dimension = unit.dimension
numeric_value = (number * (10 ** unit.power) * unit.scale) + unit.offset
else:
raise SimBuildError("Unknown unit symbol '{0}'. Known: {1}",
sym, self.units)
#print("Have converted %s to value: %s, dimension %s"%(value_str, numeric_value, dimension))
return numeric_value | [
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glormph/msstitch | src/app/drivers/startup.py | start_msstitch | def start_msstitch(exec_drivers, sysargs):
"""Passed all drivers of executable, checks which command is passed to
the executable and then gets the options for a driver, parses them from
command line and runs the driver"""
parser = populate_parser(exec_drivers)
args = parser.parse_args(sysargs[1:])
args.func(**vars(args)) | python | def start_msstitch(exec_drivers, sysargs):
"""Passed all drivers of executable, checks which command is passed to
the executable and then gets the options for a driver, parses them from
command line and runs the driver"""
parser = populate_parser(exec_drivers)
args = parser.parse_args(sysargs[1:])
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TriOptima/tri.struct | lib/tri/struct/__init__.py | merged | def merged(*dicts, **kwargs):
"""
Merge dictionaries. Later keys overwrite.
.. code-block:: python
merged(dict(a=1), dict(b=2), c=3, d=1)
"""
if not dicts:
return Struct()
result = dict()
for d in dicts:
result.update(d)
result.update(kwargs)
struct_type = type(dicts[0])
return struct_type(**result) | python | def merged(*dicts, **kwargs):
"""
Merge dictionaries. Later keys overwrite.
.. code-block:: python
merged(dict(a=1), dict(b=2), c=3, d=1)
"""
if not dicts:
return Struct()
result = dict()
for d in dicts:
result.update(d)
result.update(kwargs)
struct_type = type(dicts[0])
return struct_type(**result) | [
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LEMS/pylems | lems/sim/build.py | order_derived_parameters | def order_derived_parameters(component):
"""
Finds ordering of derived_parameters.
@param component: Component containing derived parameters.
@type component: lems.model.component.Component
@return: Returns ordered list of derived parameters.
@rtype: list(string)
@raise SimBuildError: Raised when a proper ordering of derived
parameters could not be found.
"""
if len(component.derived_parameters) == 0:
return []
ordering = []
dps = []
for dp in component.derived_parameters:
dps.append(dp.name)
maxcount = 5
count = maxcount
while count > 0 and dps != []:
count = count - 1
for dp1 in dps:
#exp_tree = regime.derived_variables[dv1].expression_tree
value = component.derived_parameters[dp1].value
found = False
for dp2 in dps:
if dp1 != dp2 and dp2 in value:
found = True
if not found:
ordering.append(dp1)
del dps[dps.index(dp1)]
count = maxcount
break
if count == 0:
raise SimBuildError(("Unable to find ordering for derived "
"parameter in component '{0}'").format(component))
#return ordering + dvsnoexp
return ordering | python | def order_derived_parameters(component):
"""
Finds ordering of derived_parameters.
@param component: Component containing derived parameters.
@type component: lems.model.component.Component
@return: Returns ordered list of derived parameters.
@rtype: list(string)
@raise SimBuildError: Raised when a proper ordering of derived
parameters could not be found.
"""
if len(component.derived_parameters) == 0:
return []
ordering = []
dps = []
for dp in component.derived_parameters:
dps.append(dp.name)
maxcount = 5
count = maxcount
while count > 0 and dps != []:
count = count - 1
for dp1 in dps:
#exp_tree = regime.derived_variables[dv1].expression_tree
value = component.derived_parameters[dp1].value
found = False
for dp2 in dps:
if dp1 != dp2 and dp2 in value:
found = True
if not found:
ordering.append(dp1)
del dps[dps.index(dp1)]
count = maxcount
break
if count == 0:
raise SimBuildError(("Unable to find ordering for derived "
"parameter in component '{0}'").format(component))
#return ordering + dvsnoexp
return ordering | [
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LEMS/pylems | lems/sim/build.py | order_derived_variables | def order_derived_variables(regime):
"""
Finds ordering of derived_variables.
@param regime: Dynamics Regime containing derived variables.
@type regime: lems.model.dynamics.regime
@return: Returns ordered list of derived variables.
@rtype: list(string)
@raise SimBuildError: Raised when a proper ordering of derived
variables could not be found.
"""
ordering = []
dvs = []
dvsnoexp = []
maxcount = 5
for dv in regime.derived_variables:
if dv.expression_tree == None:
dvsnoexp.append(dv.name)
else:
dvs.append(dv.name)
for dv in regime.conditional_derived_variables:
if len(dv.cases) == 0:
dvsnoexp.append(dv.name)
else:
dvs.append(dv.name)
count = maxcount
while count > 0 and dvs != []:
count = count - 1
for dv1 in dvs:
if dv1 in regime.derived_variables:
dv = regime.derived_variables[dv1]
else:
dv = regime.conditional_derived_variables[dv1]
found = False
if isinstance(dv, DerivedVariable):
exp_tree = dv.expression_tree
for dv2 in dvs:
if dv1 != dv2 and is_var_in_exp_tree(dv2, exp_tree):
found = True
else:
for case in dv.cases:
for dv2 in dvs:
if dv1 != dv2 and (is_var_in_exp_tree(dv2, case.condition_expression_tree) or
is_var_in_exp_tree(dv2, case.value_expression_tree)):
found = True
if not found:
ordering.append(dv1)
del dvs[dvs.index(dv1)]
count = maxcount
break
if count == 0:
raise SimBuildError(("Unable to find ordering for derived "
"variables in regime '{0}'").format(regime.name))
#return ordering + dvsnoexp
return dvsnoexp + ordering | python | def order_derived_variables(regime):
"""
Finds ordering of derived_variables.
@param regime: Dynamics Regime containing derived variables.
@type regime: lems.model.dynamics.regime
@return: Returns ordered list of derived variables.
@rtype: list(string)
@raise SimBuildError: Raised when a proper ordering of derived
variables could not be found.
"""
ordering = []
dvs = []
dvsnoexp = []
maxcount = 5
for dv in regime.derived_variables:
if dv.expression_tree == None:
dvsnoexp.append(dv.name)
else:
dvs.append(dv.name)
for dv in regime.conditional_derived_variables:
if len(dv.cases) == 0:
dvsnoexp.append(dv.name)
else:
dvs.append(dv.name)
count = maxcount
while count > 0 and dvs != []:
count = count - 1
for dv1 in dvs:
if dv1 in regime.derived_variables:
dv = regime.derived_variables[dv1]
else:
dv = regime.conditional_derived_variables[dv1]
found = False
if isinstance(dv, DerivedVariable):
exp_tree = dv.expression_tree
for dv2 in dvs:
if dv1 != dv2 and is_var_in_exp_tree(dv2, exp_tree):
found = True
else:
for case in dv.cases:
for dv2 in dvs:
if dv1 != dv2 and (is_var_in_exp_tree(dv2, case.condition_expression_tree) or
is_var_in_exp_tree(dv2, case.value_expression_tree)):
found = True
if not found:
ordering.append(dv1)
del dvs[dvs.index(dv1)]
count = maxcount
break
if count == 0:
raise SimBuildError(("Unable to find ordering for derived "
"variables in regime '{0}'").format(regime.name))
#return ordering + dvsnoexp
return dvsnoexp + ordering | [
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LEMS/pylems | lems/sim/build.py | SimulationBuilder.build | def build(self):
"""
Build the simulation components from the model.
@return: A runnable simulation object
@rtype: lems.sim.sim.Simulation
"""
self.sim = Simulation()
for component_id in self.model.targets:
if component_id not in self.model.components:
raise SimBuildError("Unable to find target component '{0}'",
component_id)
component = self.model.fat_components[component_id]
runnable = self.build_runnable(component)
self.sim.add_runnable(runnable)
return self.sim | python | def build(self):
"""
Build the simulation components from the model.
@return: A runnable simulation object
@rtype: lems.sim.sim.Simulation
"""
self.sim = Simulation()
for component_id in self.model.targets:
if component_id not in self.model.components:
raise SimBuildError("Unable to find target component '{0}'",
component_id)
component = self.model.fat_components[component_id]
runnable = self.build_runnable(component)
self.sim.add_runnable(runnable)
return self.sim | [
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LEMS/pylems | lems/sim/build.py | SimulationBuilder.build_event_connections | def build_event_connections(self, component, runnable, structure):
"""
Adds event connections to a runnable component based on the structure
specifications in the component model.
@param component: Component model containing structure specifications.
@type component: lems.model.component.FatComponent
@param runnable: Runnable component to which structure is to be added.
@type runnable: lems.sim.runnable.Runnable
@param structure: The structure object to be used to add
structure code in the runnable component.
@type structure: lems.model.structure.Structure
"""
if self.debug: print("\n++++++++ Calling build_event_connections of %s with runnable %s, parent %s"%(component.id, runnable.id, runnable.parent))
# Process event connections
for ec in structure.event_connections:
if self.debug: print(ec.toxml())
source = runnable.parent.resolve_path(ec.from_)
target = runnable.parent.resolve_path(ec.to)
if ec.receiver:
receiver_template = self.build_runnable(ec.receiver,
target)
#receiver = copy.deepcopy(receiver_template)
receiver = receiver_template.copy()
receiver.id = "{0}__{1}__".format(component.id,
receiver_template.id)
if ec.receiver_container:
target.add_attachment(receiver, ec.receiver_container)
target.add_child(receiver_template.id, receiver)
target = receiver
else:
source = runnable.resolve_path(ec.from_)
target = runnable.resolve_path(ec.to)
source_port = ec.source_port
target_port = ec.target_port
if not source_port:
if len(source.event_out_ports) == 1:
source_port = source.event_out_ports[0]
else:
raise SimBuildError(("No source event port "
"uniquely identifiable"
" in '{0}'").format(source.id))
if not target_port:
if len(target.event_in_ports) == 1:
target_port = target.event_in_ports[0]
else:
raise SimBuildError(("No destination event port "
"uniquely identifiable "
"in '{0}'").format(target))
if self.debug: print("register_event_out_callback\n Source: %s, %s (port: %s) \n -> %s, %s (port: %s)"%(source, id(source), source_port, target, id(target), target_port))
source.register_event_out_callback(\
source_port, lambda: target.inc_event_in(target_port)) | python | def build_event_connections(self, component, runnable, structure):
"""
Adds event connections to a runnable component based on the structure
specifications in the component model.
@param component: Component model containing structure specifications.
@type component: lems.model.component.FatComponent
@param runnable: Runnable component to which structure is to be added.
@type runnable: lems.sim.runnable.Runnable
@param structure: The structure object to be used to add
structure code in the runnable component.
@type structure: lems.model.structure.Structure
"""
if self.debug: print("\n++++++++ Calling build_event_connections of %s with runnable %s, parent %s"%(component.id, runnable.id, runnable.parent))
# Process event connections
for ec in structure.event_connections:
if self.debug: print(ec.toxml())
source = runnable.parent.resolve_path(ec.from_)
target = runnable.parent.resolve_path(ec.to)
if ec.receiver:
receiver_template = self.build_runnable(ec.receiver,
target)
#receiver = copy.deepcopy(receiver_template)
receiver = receiver_template.copy()
receiver.id = "{0}__{1}__".format(component.id,
receiver_template.id)
if ec.receiver_container:
target.add_attachment(receiver, ec.receiver_container)
target.add_child(receiver_template.id, receiver)
target = receiver
else:
source = runnable.resolve_path(ec.from_)
target = runnable.resolve_path(ec.to)
source_port = ec.source_port
target_port = ec.target_port
if not source_port:
if len(source.event_out_ports) == 1:
source_port = source.event_out_ports[0]
else:
raise SimBuildError(("No source event port "
"uniquely identifiable"
" in '{0}'").format(source.id))
if not target_port:
if len(target.event_in_ports) == 1:
target_port = target.event_in_ports[0]
else:
raise SimBuildError(("No destination event port "
"uniquely identifiable "
"in '{0}'").format(target))
if self.debug: print("register_event_out_callback\n Source: %s, %s (port: %s) \n -> %s, %s (port: %s)"%(source, id(source), source_port, target, id(target), target_port))
source.register_event_out_callback(\
source_port, lambda: target.inc_event_in(target_port)) | [
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] | 4eeb719d2f23650fe16c38626663b69b5c83818b | https://github.com/LEMS/pylems/blob/4eeb719d2f23650fe16c38626663b69b5c83818b/lems/sim/build.py#L231-L289 | train |
LEMS/pylems | lems/sim/build.py | SimulationBuilder.build_structure | def build_structure(self, component, runnable, structure):
"""
Adds structure to a runnable component based on the structure
specifications in the component model.
@param component: Component model containing structure specifications.
@type component: lems.model.component.FatComponent
@param runnable: Runnable component to which structure is to be added.
@type runnable: lems.sim.runnable.Runnable
@param structure: The structure object to be used to add
structure code in the runnable component.
@type structure: lems.model.structure.Structure
"""
if self.debug: print("\n++++++++ Calling build_structure of %s with runnable %s, parent %s"%(component.id, runnable.id, runnable.parent))
# Process single-child instantiations
for ch in structure.child_instances:
child_runnable = self.build_runnable(ch.referenced_component, runnable)
runnable.add_child(child_runnable.id, child_runnable)
runnable.add_child_typeref(ch.component, child_runnable)
# Process multi-child instatiantions
for mi in structure.multi_instantiates:
template = self.build_runnable(mi.component,
runnable)
for i in range(mi.number):
#instance = copy.deepcopy(template)
instance = template.copy()
instance.id = "{0}__{1}__{2}".format(component.id,
template.id,
i)
runnable.array.append(instance)
# Process foreach statements
for fe in structure.for_eachs:
self.build_foreach(component, runnable, fe)
self.build_event_connections(component, runnable, structure) | python | def build_structure(self, component, runnable, structure):
"""
Adds structure to a runnable component based on the structure
specifications in the component model.
@param component: Component model containing structure specifications.
@type component: lems.model.component.FatComponent
@param runnable: Runnable component to which structure is to be added.
@type runnable: lems.sim.runnable.Runnable
@param structure: The structure object to be used to add
structure code in the runnable component.
@type structure: lems.model.structure.Structure
"""
if self.debug: print("\n++++++++ Calling build_structure of %s with runnable %s, parent %s"%(component.id, runnable.id, runnable.parent))
# Process single-child instantiations
for ch in structure.child_instances:
child_runnable = self.build_runnable(ch.referenced_component, runnable)
runnable.add_child(child_runnable.id, child_runnable)
runnable.add_child_typeref(ch.component, child_runnable)
# Process multi-child instatiantions
for mi in structure.multi_instantiates:
template = self.build_runnable(mi.component,
runnable)
for i in range(mi.number):
#instance = copy.deepcopy(template)
instance = template.copy()
instance.id = "{0}__{1}__{2}".format(component.id,
template.id,
i)
runnable.array.append(instance)
# Process foreach statements
for fe in structure.for_eachs:
self.build_foreach(component, runnable, fe)
self.build_event_connections(component, runnable, structure) | [
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LEMS/pylems | lems/sim/build.py | SimulationBuilder.build_foreach | def build_foreach(self, component, runnable, foreach, name_mappings = {}):
"""
Iterate over ForEach constructs and process nested elements.
@param component: Component model containing structure specifications.
@type component: lems.model.component.FatComponent
@param runnable: Runnable component to which structure is to be added.
@type runnable: lems.sim.runnable.Runnable
@param foreach: The ForEach structure object to be used to add
structure code in the runnable component.
@type foreach: lems.model.structure.ForEach
"""
if self.debug: print("\n++++++++ Calling build_foreach of %s with runnable %s, parent %s, name_mappings: %s"%(component.id, runnable.id, runnable.parent, name_mappings))
target_array = runnable.resolve_path(foreach.instances)
for target_runnable in target_array:
if self.debug: print("Applying contents of for_each to %s, as %s"%(target_runnable.id, foreach.as_))
name_mappings[foreach.as_] = target_runnable
# Process foreach statements
for fe2 in foreach.for_eachs:
#print fe2.toxml()
target_array2 = runnable.resolve_path(fe2.instances)
for target_runnable2 in target_array2:
name_mappings[fe2.as_] = target_runnable2
self.build_foreach(component, runnable, fe2, name_mappings)
# Process event connections
for ec in foreach.event_connections:
source = name_mappings[ec.from_]
target = name_mappings[ec.to]
source_port = ec.source_port
target_port = ec.target_port
if not source_port:
if len(source.event_out_ports) == 1:
source_port = source.event_out_ports[0]
else:
raise SimBuildError(("No source event port "
"uniquely identifiable"
" in '{0}'").format(source.id))
if not target_port:
if len(target.event_in_ports) == 1:
target_port = target.event_in_ports[0]
else:
raise SimBuildError(("No destination event port "
"uniquely identifiable "
"in '{0}'").format(target))
if self.debug: print("register_event_out_callback\n Source: %s, %s (port: %s) \n -> %s, %s (port: %s)"%(source, id(source), source_port, target, id(target), target_port))
source.register_event_out_callback(\
source_port, lambda: target.inc_event_in(target_port)) | python | def build_foreach(self, component, runnable, foreach, name_mappings = {}):
"""
Iterate over ForEach constructs and process nested elements.
@param component: Component model containing structure specifications.
@type component: lems.model.component.FatComponent
@param runnable: Runnable component to which structure is to be added.
@type runnable: lems.sim.runnable.Runnable
@param foreach: The ForEach structure object to be used to add
structure code in the runnable component.
@type foreach: lems.model.structure.ForEach
"""
if self.debug: print("\n++++++++ Calling build_foreach of %s with runnable %s, parent %s, name_mappings: %s"%(component.id, runnable.id, runnable.parent, name_mappings))
target_array = runnable.resolve_path(foreach.instances)
for target_runnable in target_array:
if self.debug: print("Applying contents of for_each to %s, as %s"%(target_runnable.id, foreach.as_))
name_mappings[foreach.as_] = target_runnable
# Process foreach statements
for fe2 in foreach.for_eachs:
#print fe2.toxml()
target_array2 = runnable.resolve_path(fe2.instances)
for target_runnable2 in target_array2:
name_mappings[fe2.as_] = target_runnable2
self.build_foreach(component, runnable, fe2, name_mappings)
# Process event connections
for ec in foreach.event_connections:
source = name_mappings[ec.from_]
target = name_mappings[ec.to]
source_port = ec.source_port
target_port = ec.target_port
if not source_port:
if len(source.event_out_ports) == 1:
source_port = source.event_out_ports[0]
else:
raise SimBuildError(("No source event port "
"uniquely identifiable"
" in '{0}'").format(source.id))
if not target_port:
if len(target.event_in_ports) == 1:
target_port = target.event_in_ports[0]
else:
raise SimBuildError(("No destination event port "
"uniquely identifiable "
"in '{0}'").format(target))
if self.debug: print("register_event_out_callback\n Source: %s, %s (port: %s) \n -> %s, %s (port: %s)"%(source, id(source), source_port, target, id(target), target_port))
source.register_event_out_callback(\
source_port, lambda: target.inc_event_in(target_port)) | [
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@param runnable: Runnable component to which structure is to be added.
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LEMS/pylems | lems/sim/build.py | SimulationBuilder.process_simulation_specs | def process_simulation_specs(self, component, runnable, simulation):
"""
Process simulation-related aspects to a runnable component based on the
dynamics specifications in the component model.
@param component: Component model containing dynamics specifications.
@type component: lems.model.component.FatComponent
@param runnable: Runnable component to which dynamics is to be added.
@type runnable: lems.sim.runnable.Runnable
@param simulation: The simulation-related aspects to be implemented
in the runnable component.
@type simulation: lems.model.simulation.Simulation
@raise SimBuildError: Raised when a time derivative expression refers
to an undefined variable
@raise SimBuildError: Raised when there are invalid time
specifications for the <Run> statement.
@raise SimBuildError: Raised when the component reference for <Run>
cannot be resolved.
"""
# Process runs
for run in simulation.runs:
cid = run.component.id + '_' + component.id
target = self.build_runnable(run.component, runnable, cid)
self.sim.add_runnable(target)
self.current_record_target = target
target.configure_time(run.increment,
run.total) | python | def process_simulation_specs(self, component, runnable, simulation):
"""
Process simulation-related aspects to a runnable component based on the
dynamics specifications in the component model.
@param component: Component model containing dynamics specifications.
@type component: lems.model.component.FatComponent
@param runnable: Runnable component to which dynamics is to be added.
@type runnable: lems.sim.runnable.Runnable
@param simulation: The simulation-related aspects to be implemented
in the runnable component.
@type simulation: lems.model.simulation.Simulation
@raise SimBuildError: Raised when a time derivative expression refers
to an undefined variable
@raise SimBuildError: Raised when there are invalid time
specifications for the <Run> statement.
@raise SimBuildError: Raised when the component reference for <Run>
cannot be resolved.
"""
# Process runs
for run in simulation.runs:
cid = run.component.id + '_' + component.id
target = self.build_runnable(run.component, runnable, cid)
self.sim.add_runnable(target)
self.current_record_target = target
target.configure_time(run.increment,
run.total) | [
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LEMS/pylems | lems/sim/build.py | SimulationBuilder.build_expression_from_tree | def build_expression_from_tree(self, runnable, regime, tree_node):
"""
Recursively builds a Python expression from a parsed expression tree.
@param runnable: Runnable object to which this expression would be added.
@type runnable: lems.sim.runnable.Runnable
@param regime: Dynamics regime being built.
@type regime: lems.model.dynamics.Regime
@param tree_node: Root node for the tree from which the expression
is to be built.
@type tree_node: lems.parser.expr.ExprNode
@return: Generated Python expression.
@rtype: string
"""
component_type = self.model.component_types[runnable.component.type]
dynamics = component_type.dynamics
if tree_node.type == ExprNode.VALUE:
if tree_node.value[0].isalpha():
if tree_node.value == 't':
return 'self.time_completed'
elif tree_node.value in component_type.requirements:
var_prefix = 'self'
v = tree_node.value
r = runnable
while (v not in r.instance_variables and
v not in r.derived_variables):
var_prefix = '{0}.{1}'.format(var_prefix, 'parent')
r = r.parent
if r == None:
raise SimBuildError("Unable to resolve required "
"variable '{0}'".format(v))
return '{0}.{1}'.format(var_prefix, v)
elif (tree_node.value in dynamics.derived_variables or (regime is not None and tree_node.value in regime.derived_variables)):
return 'self.{0}'.format(tree_node.value)
else:
return 'self.{0}_shadow'.format(tree_node.value)
else:
return tree_node.value
elif tree_node.type == ExprNode.FUNC1:
pattern = '({0}({1}))'
func = self.convert_func(tree_node.func)
if 'random.uniform' in func:
pattern = '({0}(0,{1}))'
return pattern.format(\
func,
self.build_expression_from_tree(runnable,
regime,
tree_node.param))
else:
return '({0}) {1} ({2})'.format(\
self.build_expression_from_tree(runnable,
regime,
tree_node.left),
self.convert_op(tree_node.op),
self.build_expression_from_tree(runnable,
regime,
tree_node.right)) | python | def build_expression_from_tree(self, runnable, regime, tree_node):
"""
Recursively builds a Python expression from a parsed expression tree.
@param runnable: Runnable object to which this expression would be added.
@type runnable: lems.sim.runnable.Runnable
@param regime: Dynamics regime being built.
@type regime: lems.model.dynamics.Regime
@param tree_node: Root node for the tree from which the expression
is to be built.
@type tree_node: lems.parser.expr.ExprNode
@return: Generated Python expression.
@rtype: string
"""
component_type = self.model.component_types[runnable.component.type]
dynamics = component_type.dynamics
if tree_node.type == ExprNode.VALUE:
if tree_node.value[0].isalpha():
if tree_node.value == 't':
return 'self.time_completed'
elif tree_node.value in component_type.requirements:
var_prefix = 'self'
v = tree_node.value
r = runnable
while (v not in r.instance_variables and
v not in r.derived_variables):
var_prefix = '{0}.{1}'.format(var_prefix, 'parent')
r = r.parent
if r == None:
raise SimBuildError("Unable to resolve required "
"variable '{0}'".format(v))
return '{0}.{1}'.format(var_prefix, v)
elif (tree_node.value in dynamics.derived_variables or (regime is not None and tree_node.value in regime.derived_variables)):
return 'self.{0}'.format(tree_node.value)
else:
return 'self.{0}_shadow'.format(tree_node.value)
else:
return tree_node.value
elif tree_node.type == ExprNode.FUNC1:
pattern = '({0}({1}))'
func = self.convert_func(tree_node.func)
if 'random.uniform' in func:
pattern = '({0}(0,{1}))'
return pattern.format(\
func,
self.build_expression_from_tree(runnable,
regime,
tree_node.param))
else:
return '({0}) {1} ({2})'.format(\
self.build_expression_from_tree(runnable,
regime,
tree_node.left),
self.convert_op(tree_node.op),
self.build_expression_from_tree(runnable,
regime,
tree_node.right)) | [
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@type regime: lems.model.dynamics.Regime
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@type tree_node: lems.parser.expr.ExprNode
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LEMS/pylems | lems/sim/build.py | SimulationBuilder.build_event_handler | def build_event_handler(self, runnable, regime, event_handler):
"""
Build event handler code.
@param event_handler: Event handler object
@type event_handler: lems.model.dynamics.EventHandler
@return: Generated event handler code.
@rtype: list(string)
"""
if isinstance(event_handler, OnCondition):
return self.build_on_condition(runnable, regime, event_handler)
elif isinstance(event_handler, OnEvent):
return self.build_on_event(runnable, regime, event_handler)
elif isinstance(event_handler, OnStart):
return self.build_on_start(runnable, regime, event_handler)
elif isinstance(event_handler, OnEntry):
return self.build_on_entry(runnable, regime, event_handler)
else:
return [] | python | def build_event_handler(self, runnable, regime, event_handler):
"""
Build event handler code.
@param event_handler: Event handler object
@type event_handler: lems.model.dynamics.EventHandler
@return: Generated event handler code.
@rtype: list(string)
"""
if isinstance(event_handler, OnCondition):
return self.build_on_condition(runnable, regime, event_handler)
elif isinstance(event_handler, OnEvent):
return self.build_on_event(runnable, regime, event_handler)
elif isinstance(event_handler, OnStart):
return self.build_on_start(runnable, regime, event_handler)
elif isinstance(event_handler, OnEntry):
return self.build_on_entry(runnable, regime, event_handler)
else:
return [] | [
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@type event_handler: lems.model.dynamics.EventHandler
@return: Generated event handler code.
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LEMS/pylems | lems/sim/build.py | SimulationBuilder.build_on_condition | def build_on_condition(self, runnable, regime, on_condition):
"""
Build OnCondition event handler code.
@param on_condition: OnCondition event handler object
@type on_condition: lems.model.dynamics.OnCondition
@return: Generated OnCondition code
@rtype: list(string)
"""
on_condition_code = []
on_condition_code += ['if {0}:'.format(\
self.build_expression_from_tree(runnable,
regime,
on_condition.expression_tree))]
for action in on_condition.actions:
code = self.build_action(runnable, regime, action)
for line in code:
on_condition_code += [' ' + line]
return on_condition_code | python | def build_on_condition(self, runnable, regime, on_condition):
"""
Build OnCondition event handler code.
@param on_condition: OnCondition event handler object
@type on_condition: lems.model.dynamics.OnCondition
@return: Generated OnCondition code
@rtype: list(string)
"""
on_condition_code = []
on_condition_code += ['if {0}:'.format(\
self.build_expression_from_tree(runnable,
regime,
on_condition.expression_tree))]
for action in on_condition.actions:
code = self.build_action(runnable, regime, action)
for line in code:
on_condition_code += [' ' + line]
return on_condition_code | [
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@type on_condition: lems.model.dynamics.OnCondition
@return: Generated OnCondition code
@rtype: list(string) | [
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] | 4eeb719d2f23650fe16c38626663b69b5c83818b | https://github.com/LEMS/pylems/blob/4eeb719d2f23650fe16c38626663b69b5c83818b/lems/sim/build.py#L791-L814 | train |
LEMS/pylems | lems/sim/build.py | SimulationBuilder.build_on_event | def build_on_event(self, runnable, regime, on_event):
"""
Build OnEvent event handler code.
@param on_event: OnEvent event handler object
@type on_event: lems.model.dynamics.OnEvent
@return: Generated OnEvent code
@rtype: list(string)
"""
on_event_code = []
if self.debug: on_event_code += ['print("Maybe handling something for %s ("+str(id(self))+")")'%(runnable.id),
'print("EICs ("+str(id(self))+"): "+str(self.event_in_counters))']
on_event_code += ['count = self.event_in_counters[\'{0}\']'.\
format(on_event.port),
'while count > 0:',
' print(" Handling event")' if self.debug else '',
' count -= 1']
for action in on_event.actions:
code = self.build_action(runnable, regime, action)
for line in code:
on_event_code += [' ' + line]
on_event_code += ['self.event_in_counters[\'{0}\'] = 0'.\
format(on_event.port),]
return on_event_code | python | def build_on_event(self, runnable, regime, on_event):
"""
Build OnEvent event handler code.
@param on_event: OnEvent event handler object
@type on_event: lems.model.dynamics.OnEvent
@return: Generated OnEvent code
@rtype: list(string)
"""
on_event_code = []
if self.debug: on_event_code += ['print("Maybe handling something for %s ("+str(id(self))+")")'%(runnable.id),
'print("EICs ("+str(id(self))+"): "+str(self.event_in_counters))']
on_event_code += ['count = self.event_in_counters[\'{0}\']'.\
format(on_event.port),
'while count > 0:',
' print(" Handling event")' if self.debug else '',
' count -= 1']
for action in on_event.actions:
code = self.build_action(runnable, regime, action)
for line in code:
on_event_code += [' ' + line]
on_event_code += ['self.event_in_counters[\'{0}\'] = 0'.\
format(on_event.port),]
return on_event_code | [
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@param on_event: OnEvent event handler object
@type on_event: lems.model.dynamics.OnEvent
@return: Generated OnEvent code
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LEMS/pylems | lems/sim/build.py | SimulationBuilder.build_on_start | def build_on_start(self, runnable, regime, on_start):
"""
Build OnStart start handler code.
@param on_start: OnStart start handler object
@type on_start: lems.model.dynamics.OnStart
@return: Generated OnStart code
@rtype: list(string)
"""
on_start_code = []
for action in on_start.actions:
code = self.build_action(runnable, regime, action)
for line in code:
on_start_code += [line]
return on_start_code | python | def build_on_start(self, runnable, regime, on_start):
"""
Build OnStart start handler code.
@param on_start: OnStart start handler object
@type on_start: lems.model.dynamics.OnStart
@return: Generated OnStart code
@rtype: list(string)
"""
on_start_code = []
for action in on_start.actions:
code = self.build_action(runnable, regime, action)
for line in code:
on_start_code += [line]
return on_start_code | [
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LEMS/pylems | lems/sim/build.py | SimulationBuilder.build_on_entry | def build_on_entry(self, runnable, regime, on_entry):
"""
Build OnEntry start handler code.
@param on_entry: OnEntry start handler object
@type on_entry: lems.model.dynamics.OnEntry
@return: Generated OnEntry code
@rtype: list(string)
"""
on_entry_code = []
on_entry_code += ['if self.current_regime != self.last_regime:']
on_entry_code += [' self.last_regime = self.current_regime']
for action in on_entry.actions:
code = self.build_action(runnable, regime, action)
for line in code:
on_entry_code += [' ' + line]
return on_entry_code | python | def build_on_entry(self, runnable, regime, on_entry):
"""
Build OnEntry start handler code.
@param on_entry: OnEntry start handler object
@type on_entry: lems.model.dynamics.OnEntry
@return: Generated OnEntry code
@rtype: list(string)
"""
on_entry_code = []
on_entry_code += ['if self.current_regime != self.last_regime:']
on_entry_code += [' self.last_regime = self.current_regime']
for action in on_entry.actions:
code = self.build_action(runnable, regime, action)
for line in code:
on_entry_code += [' ' + line]
return on_entry_code | [
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@param on_entry: OnEntry start handler object
@type on_entry: lems.model.dynamics.OnEntry
@return: Generated OnEntry code
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LEMS/pylems | lems/sim/build.py | SimulationBuilder.build_action | def build_action(self, runnable, regime, action):
"""
Build event handler action code.
@param action: Event handler action object
@type action: lems.model.dynamics.Action
@return: Generated action code
@rtype: string
"""
if isinstance(action, StateAssignment):
return self.build_state_assignment(runnable, regime, action)
if isinstance(action, EventOut):
return self.build_event_out(action)
if isinstance(action, Transition):
return self.build_transition(action)
else:
return ['pass'] | python | def build_action(self, runnable, regime, action):
"""
Build event handler action code.
@param action: Event handler action object
@type action: lems.model.dynamics.Action
@return: Generated action code
@rtype: string
"""
if isinstance(action, StateAssignment):
return self.build_state_assignment(runnable, regime, action)
if isinstance(action, EventOut):
return self.build_event_out(action)
if isinstance(action, Transition):
return self.build_transition(action)
else:
return ['pass'] | [
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@param action: Event handler action object
@type action: lems.model.dynamics.Action
@return: Generated action code
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LEMS/pylems | lems/sim/build.py | SimulationBuilder.build_state_assignment | def build_state_assignment(self, runnable, regime, state_assignment):
"""
Build state assignment code.
@param state_assignment: State assignment object
@type state_assignment: lems.model.dynamics.StateAssignment
@return: Generated state assignment code
@rtype: string
"""
return ['self.{0} = {1}'.format(\
state_assignment.variable,
self.build_expression_from_tree(runnable,
regime,
state_assignment.expression_tree))] | python | def build_state_assignment(self, runnable, regime, state_assignment):
"""
Build state assignment code.
@param state_assignment: State assignment object
@type state_assignment: lems.model.dynamics.StateAssignment
@return: Generated state assignment code
@rtype: string
"""
return ['self.{0} = {1}'.format(\
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LEMS/pylems | lems/sim/build.py | SimulationBuilder.build_event_out | def build_event_out(self, event_out):
"""
Build event out code.
@param event_out: event out object
@type event_out: lems.model.dynamics.EventOut
@return: Generated event out code
@rtype: string
"""
event_out_code = ['if "{0}" in self.event_out_callbacks:'.format(event_out.port),
' for c in self.event_out_callbacks[\'{0}\']:'.format(event_out.port),
' c()']
return event_out_code | python | def build_event_out(self, event_out):
"""
Build event out code.
@param event_out: event out object
@type event_out: lems.model.dynamics.EventOut
@return: Generated event out code
@rtype: string
"""
event_out_code = ['if "{0}" in self.event_out_callbacks:'.format(event_out.port),
' for c in self.event_out_callbacks[\'{0}\']:'.format(event_out.port),
' c()']
return event_out_code | [
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@param event_out: event out object
@type event_out: lems.model.dynamics.EventOut
@return: Generated event out code
@rtype: string | [
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LEMS/pylems | lems/sim/build.py | SimulationBuilder.build_reduce_code | def build_reduce_code(self, result, select, reduce):
"""
Builds a reduce operation on the selected target range.
"""
select = select.replace('/', '.')
select = select.replace(' ', '')
if reduce == 'add':
reduce_op = '+'
acc_start = 0
else:
reduce_op = '*'
acc_start = 1
#bits = select.split('[*]')
bits = re.split('\[.*\]', select)
seps = re.findall('\[.*\]', select)
code = ['self.{0} = {1}'.format(result, acc_start)]
code += ['self.{0}_shadow = {1}'.format(result, acc_start)]
code += ['try:']
if len(bits) == 1:
target = select
code += [' self.{0} = self.{1}'.format(result, target)]
code += [' self.{0}_shadow = self.{1}'.format(result, target)]
elif len(bits) == 2:
sep = seps[0][1:-1]
if sep == '*':
array = bits[0]
ref = bits[1]
code += [' acc = {0}'.format(acc_start)]
code += [' for o in self.{0}:'.format(array)]
code += [' acc = acc {0} o{1}'.format(reduce_op, ref)]
code += [' self.{0} = acc'.format(result)]
code += [' self.{0}_shadow = acc'.format(result)]
else:
bits2 = sep.split('=')
if len(bits2) > 1:
array = bits[0]
ref = bits[1]
code += [' acc = {0}'.format(acc_start)]
code += [' for o in self.{0}:'.format(array)]
code += [' if o.{0} == {1}:'.format(bits2[0], bits2[1])]
code += [' acc = acc {0} o{1}'.format(reduce_op, ref)]
code += [' self.{0} = acc'.format(result)]
code += [' self.{0}_shadow = acc'.format(result)]
else:
raise SimbuildError("Invalid reduce target - '{0}'".format(select))
else:
raise SimbuildError("Invalid reduce target - '{0}'".format(select))
code += ['except:']
code += [' pass']
return code | python | def build_reduce_code(self, result, select, reduce):
"""
Builds a reduce operation on the selected target range.
"""
select = select.replace('/', '.')
select = select.replace(' ', '')
if reduce == 'add':
reduce_op = '+'
acc_start = 0
else:
reduce_op = '*'
acc_start = 1
#bits = select.split('[*]')
bits = re.split('\[.*\]', select)
seps = re.findall('\[.*\]', select)
code = ['self.{0} = {1}'.format(result, acc_start)]
code += ['self.{0}_shadow = {1}'.format(result, acc_start)]
code += ['try:']
if len(bits) == 1:
target = select
code += [' self.{0} = self.{1}'.format(result, target)]
code += [' self.{0}_shadow = self.{1}'.format(result, target)]
elif len(bits) == 2:
sep = seps[0][1:-1]
if sep == '*':
array = bits[0]
ref = bits[1]
code += [' acc = {0}'.format(acc_start)]
code += [' for o in self.{0}:'.format(array)]
code += [' acc = acc {0} o{1}'.format(reduce_op, ref)]
code += [' self.{0} = acc'.format(result)]
code += [' self.{0}_shadow = acc'.format(result)]
else:
bits2 = sep.split('=')
if len(bits2) > 1:
array = bits[0]
ref = bits[1]
code += [' acc = {0}'.format(acc_start)]
code += [' for o in self.{0}:'.format(array)]
code += [' if o.{0} == {1}:'.format(bits2[0], bits2[1])]
code += [' acc = acc {0} o{1}'.format(reduce_op, ref)]
code += [' self.{0} = acc'.format(result)]
code += [' self.{0}_shadow = acc'.format(result)]
else:
raise SimbuildError("Invalid reduce target - '{0}'".format(select))
else:
raise SimbuildError("Invalid reduce target - '{0}'".format(select))
code += ['except:']
code += [' pass']
return code | [
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LEMS/pylems | lems/sim/build.py | SimulationBuilder.add_recording_behavior | def add_recording_behavior(self, component, runnable):
"""
Adds recording-related dynamics to a runnable component based on
the dynamics specifications in the component model.
@param component: Component model containing dynamics specifications.
@type component: lems.model.component.FatComponent runnable: Runnable component to which dynamics is to be added.
@type runnable: lems.sim.runnable.Runnable
@raise SimBuildError: Raised when a target for recording could not be
found.
"""
simulation = component.simulation
for rec in simulation.records:
rec.id = runnable.id
self.current_record_target.add_variable_recorder(self.current_data_output, rec) | python | def add_recording_behavior(self, component, runnable):
"""
Adds recording-related dynamics to a runnable component based on
the dynamics specifications in the component model.
@param component: Component model containing dynamics specifications.
@type component: lems.model.component.FatComponent runnable: Runnable component to which dynamics is to be added.
@type runnable: lems.sim.runnable.Runnable
@raise SimBuildError: Raised when a target for recording could not be
found.
"""
simulation = component.simulation
for rec in simulation.records:
rec.id = runnable.id
self.current_record_target.add_variable_recorder(self.current_data_output, rec) | [
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Erotemic/utool | utool/util_inspect.py | check_static_member_vars | def check_static_member_vars(class_, fpath=None, only_init=True):
"""
class_ can either be live object or a classname
# fpath = ut.truepath('~/code/ibeis/ibeis/viz/viz_graph2.py')
# classname = 'AnnotGraphWidget'
"""
#import ast
#import astor
import utool as ut
if isinstance(class_, six.string_types):
classname = class_
if fpath is None:
raise Exception('must specify fpath')
else:
# We were given a live object
if not isinstance(class_, type):
# We were given the class instance not the class
class_instance = class_
class_ = class_instance.__class__
classname = class_.__name__
if fpath is None:
module = ut.get_module_from_class(class_)
fpath = ut.get_modpath(module)
sourcecode = ut.readfrom(fpath)
import redbaron
# Pares a FULL syntax tree that keeps blockcomments
baron = redbaron.RedBaron(sourcecode)
for node in baron:
if node.type == 'class' and node.name == classname:
classnode = node
break
def find_parent_method(node):
par = node.parent_find('def')
if par is not None and par.parent is not None:
if par.parent.type == 'class':
return par
else:
return find_parent_method(par)
# TODO: Find inherited attrs
#classnode.inherit_from
# inhertied_attrs = ['parent']
# inhertied_attrs = []
class_methods = []
for node in classnode:
if node.type == 'def':
if only_init:
if node.name == '__init__':
class_methods.append(node)
else:
class_methods.append(node)
class_vars = []
self_vars = []
for method_node in class_methods:
self_var = method_node.arguments[0].dumps()
self_vars.append(self_var)
for assign in method_node.find_all('assignment'):
# method_node = find_parent_method(assign)
if assign.target.dumps().startswith(self_var + '.'):
class_vars.append(assign.target.value[1].dumps())
static_attrs = ut.unique(class_vars)
return static_attrs
# class_members = ut.unique(class_vars + class_methods + inhertied_attrs)
if False:
self_var = self_vars[0]
# Find everything that is used
complex_cases = []
simple_cases = []
all_self_ref = classnode.find_all(
'name_', value=re.compile('.*' + self_var + '\\.*'))
for x in all_self_ref:
if x.parent.type == 'def_argument':
continue
if x.parent.type == 'atomtrailers':
atom = x.parent
if ut.depth(atom.fst()) <= 3:
simple_cases.append(atom)
else:
complex_cases.append(atom)
#print(ut.depth(atom.value.data))
#print(atom.value)
#print(atom.dumps())
#if len(atom.dumps()) > 200:
# break
accessed_attrs = []
for x in simple_cases:
if x.value[0].dumps() == self_var:
attr = x.value[1].dumps()
accessed_attrs.append(attr)
accessed_attrs = ut.unique(accessed_attrs)
ut.setdiff(accessed_attrs, class_vars) | python | def check_static_member_vars(class_, fpath=None, only_init=True):
"""
class_ can either be live object or a classname
# fpath = ut.truepath('~/code/ibeis/ibeis/viz/viz_graph2.py')
# classname = 'AnnotGraphWidget'
"""
#import ast
#import astor
import utool as ut
if isinstance(class_, six.string_types):
classname = class_
if fpath is None:
raise Exception('must specify fpath')
else:
# We were given a live object
if not isinstance(class_, type):
# We were given the class instance not the class
class_instance = class_
class_ = class_instance.__class__
classname = class_.__name__
if fpath is None:
module = ut.get_module_from_class(class_)
fpath = ut.get_modpath(module)
sourcecode = ut.readfrom(fpath)
import redbaron
# Pares a FULL syntax tree that keeps blockcomments
baron = redbaron.RedBaron(sourcecode)
for node in baron:
if node.type == 'class' and node.name == classname:
classnode = node
break
def find_parent_method(node):
par = node.parent_find('def')
if par is not None and par.parent is not None:
if par.parent.type == 'class':
return par
else:
return find_parent_method(par)
# TODO: Find inherited attrs
#classnode.inherit_from
# inhertied_attrs = ['parent']
# inhertied_attrs = []
class_methods = []
for node in classnode:
if node.type == 'def':
if only_init:
if node.name == '__init__':
class_methods.append(node)
else:
class_methods.append(node)
class_vars = []
self_vars = []
for method_node in class_methods:
self_var = method_node.arguments[0].dumps()
self_vars.append(self_var)
for assign in method_node.find_all('assignment'):
# method_node = find_parent_method(assign)
if assign.target.dumps().startswith(self_var + '.'):
class_vars.append(assign.target.value[1].dumps())
static_attrs = ut.unique(class_vars)
return static_attrs
# class_members = ut.unique(class_vars + class_methods + inhertied_attrs)
if False:
self_var = self_vars[0]
# Find everything that is used
complex_cases = []
simple_cases = []
all_self_ref = classnode.find_all(
'name_', value=re.compile('.*' + self_var + '\\.*'))
for x in all_self_ref:
if x.parent.type == 'def_argument':
continue
if x.parent.type == 'atomtrailers':
atom = x.parent
if ut.depth(atom.fst()) <= 3:
simple_cases.append(atom)
else:
complex_cases.append(atom)
#print(ut.depth(atom.value.data))
#print(atom.value)
#print(atom.dumps())
#if len(atom.dumps()) > 200:
# break
accessed_attrs = []
for x in simple_cases:
if x.value[0].dumps() == self_var:
attr = x.value[1].dumps()
accessed_attrs.append(attr)
accessed_attrs = ut.unique(accessed_attrs)
ut.setdiff(accessed_attrs, class_vars) | [
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# fpath = ut.truepath('~/code/ibeis/ibeis/viz/viz_graph2.py')
# classname = 'AnnotGraphWidget' | [
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Erotemic/utool | utool/util_inspect.py | get_funcnames_from_modpath | def get_funcnames_from_modpath(modpath, include_methods=True):
"""
Get all functions defined in module
"""
import utool as ut
if True:
import jedi
source = ut.read_from(modpath)
#script = jedi.Script(source=source, source_path=modpath, line=source.count('\n') + 1)
definition_list = jedi.names(source)
funcname_list = [definition.name for definition in definition_list if definition.type == 'function']
if include_methods:
classdef_list = [definition for definition in definition_list if definition.type == 'class']
defined_methods = ut.flatten([definition.defined_names() for definition in classdef_list])
funcname_list += [method.name for method in defined_methods
if method.type == 'function' and not method.name.startswith('_')]
else:
import redbaron
# Pares a FULL syntax tree that keeps blockcomments
sourcecode = ut.read_from(modpath)
baron = redbaron.RedBaron(sourcecode)
funcname_list = [node.name for node in baron.find_all('def', recursive=include_methods)
if not node.name.startswith('_')]
return funcname_list | python | def get_funcnames_from_modpath(modpath, include_methods=True):
"""
Get all functions defined in module
"""
import utool as ut
if True:
import jedi
source = ut.read_from(modpath)
#script = jedi.Script(source=source, source_path=modpath, line=source.count('\n') + 1)
definition_list = jedi.names(source)
funcname_list = [definition.name for definition in definition_list if definition.type == 'function']
if include_methods:
classdef_list = [definition for definition in definition_list if definition.type == 'class']
defined_methods = ut.flatten([definition.defined_names() for definition in classdef_list])
funcname_list += [method.name for method in defined_methods
if method.type == 'function' and not method.name.startswith('_')]
else:
import redbaron
# Pares a FULL syntax tree that keeps blockcomments
sourcecode = ut.read_from(modpath)
baron = redbaron.RedBaron(sourcecode)
funcname_list = [node.name for node in baron.find_all('def', recursive=include_methods)
if not node.name.startswith('_')]
return funcname_list | [
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Erotemic/utool | utool/util_inspect.py | help_members | def help_members(obj, use_other=False):
r"""
Inspects members of a class
Args:
obj (class or module):
CommandLine:
python -m utool.util_inspect help_members
Example:
>>> # ENABLE_DOCTEST
>>> from utool.util_inspect import * # NOQA
>>> import utool as ut
>>> obj = ut.DynStruct
>>> result = help_members(obj)
>>> print(result)
"""
import utool as ut
attrnames = dir(obj)
attr_list = [getattr(obj, attrname) for attrname in attrnames]
attr_types = ut.lmap(ut.type_str, map(type, attr_list))
unique_types, groupxs = ut.group_indices(attr_types)
type_to_items = ut.dzip(unique_types, ut.apply_grouping(attr_list, groupxs))
type_to_itemname = ut.dzip(unique_types, ut.apply_grouping(attrnames, groupxs))
#if memtypes is None:
# memtypes = list(type_to_items.keys())
memtypes = ['instancemethod'] # , 'method-wrapper']
func_mems = ut.dict_subset(type_to_items, memtypes, [])
func_list = ut.flatten(func_mems.values())
defsig_list = []
num_unbound_args_list = []
num_args_list = []
for func in func_list:
#args = ut.get_func_argspec(func).args
argspec = ut.get_func_argspec(func)
args = argspec.args
unbound_args = get_unbound_args(argspec)
defsig = ut.func_defsig(func)
defsig_list.append(defsig)
num_unbound_args_list.append(len(unbound_args))
num_args_list.append(len(args))
group = ut.hierarchical_group_items(defsig_list, [num_unbound_args_list, num_args_list])
print(repr(obj))
print(ut.repr3(group, strvals=True))
if use_other:
other_mems = ut.delete_keys(type_to_items.copy(), memtypes)
other_mems_attrnames = ut.dict_subset(type_to_itemname, other_mems.keys())
named_other_attrs = ut.dict_union_combine(other_mems_attrnames, other_mems, lambda x, y: list(zip(x, y)))
print(ut.repr4(named_other_attrs, nl=2, strvals=True)) | python | def help_members(obj, use_other=False):
r"""
Inspects members of a class
Args:
obj (class or module):
CommandLine:
python -m utool.util_inspect help_members
Example:
>>> # ENABLE_DOCTEST
>>> from utool.util_inspect import * # NOQA
>>> import utool as ut
>>> obj = ut.DynStruct
>>> result = help_members(obj)
>>> print(result)
"""
import utool as ut
attrnames = dir(obj)
attr_list = [getattr(obj, attrname) for attrname in attrnames]
attr_types = ut.lmap(ut.type_str, map(type, attr_list))
unique_types, groupxs = ut.group_indices(attr_types)
type_to_items = ut.dzip(unique_types, ut.apply_grouping(attr_list, groupxs))
type_to_itemname = ut.dzip(unique_types, ut.apply_grouping(attrnames, groupxs))
#if memtypes is None:
# memtypes = list(type_to_items.keys())
memtypes = ['instancemethod'] # , 'method-wrapper']
func_mems = ut.dict_subset(type_to_items, memtypes, [])
func_list = ut.flatten(func_mems.values())
defsig_list = []
num_unbound_args_list = []
num_args_list = []
for func in func_list:
#args = ut.get_func_argspec(func).args
argspec = ut.get_func_argspec(func)
args = argspec.args
unbound_args = get_unbound_args(argspec)
defsig = ut.func_defsig(func)
defsig_list.append(defsig)
num_unbound_args_list.append(len(unbound_args))
num_args_list.append(len(args))
group = ut.hierarchical_group_items(defsig_list, [num_unbound_args_list, num_args_list])
print(repr(obj))
print(ut.repr3(group, strvals=True))
if use_other:
other_mems = ut.delete_keys(type_to_items.copy(), memtypes)
other_mems_attrnames = ut.dict_subset(type_to_itemname, other_mems.keys())
named_other_attrs = ut.dict_union_combine(other_mems_attrnames, other_mems, lambda x, y: list(zip(x, y)))
print(ut.repr4(named_other_attrs, nl=2, strvals=True)) | [
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Inspects members of a class
Args:
obj (class or module):
CommandLine:
python -m utool.util_inspect help_members
Example:
>>> # ENABLE_DOCTEST
>>> from utool.util_inspect import * # NOQA
>>> import utool as ut
>>> obj = ut.DynStruct
>>> result = help_members(obj)
>>> print(result) | [
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Erotemic/utool | utool/util_inspect.py | is_defined_by_module | def is_defined_by_module(item, module, parent=None):
"""
Check if item is directly defined by a module.
This check may be prone to errors.
"""
flag = False
if isinstance(item, types.ModuleType):
if not hasattr(item, '__file__'):
try:
# hack for cv2 and xfeatures2d
import utool as ut
name = ut.get_modname_from_modpath(module.__file__)
flag = name in str(item)
except:
flag = False
else:
item_modpath = os.path.realpath(dirname(item.__file__))
mod_fpath = module.__file__.replace('.pyc', '.py')
if not mod_fpath.endswith('__init__.py'):
flag = False
else:
modpath = os.path.realpath(dirname(mod_fpath))
modpath = modpath.replace('.pyc', '.py')
flag = item_modpath.startswith(modpath)
elif hasattr(item, '_utinfo'):
# Capture case where there is a utool wrapper
orig_func = item._utinfo['orig_func']
flag = is_defined_by_module(orig_func, module, parent)
else:
if isinstance(item, staticmethod):
# static methods are a wrapper around a function
item = item.__func__
try:
func_globals = meta_util_six.get_funcglobals(item)
func_module_name = func_globals['__name__']
if func_module_name == 'line_profiler':
valid_names = dir(module)
if parent is not None:
valid_names += dir(parent)
if item.func_name in valid_names:
# hack to prevent small names
#if len(item.func_name) > 8:
if len(item.func_name) > 6:
flag = True
elif func_module_name == module.__name__:
flag = True
except AttributeError:
if hasattr(item, '__module__'):
flag = item.__module__ == module.__name__
return flag | python | def is_defined_by_module(item, module, parent=None):
"""
Check if item is directly defined by a module.
This check may be prone to errors.
"""
flag = False
if isinstance(item, types.ModuleType):
if not hasattr(item, '__file__'):
try:
# hack for cv2 and xfeatures2d
import utool as ut
name = ut.get_modname_from_modpath(module.__file__)
flag = name in str(item)
except:
flag = False
else:
item_modpath = os.path.realpath(dirname(item.__file__))
mod_fpath = module.__file__.replace('.pyc', '.py')
if not mod_fpath.endswith('__init__.py'):
flag = False
else:
modpath = os.path.realpath(dirname(mod_fpath))
modpath = modpath.replace('.pyc', '.py')
flag = item_modpath.startswith(modpath)
elif hasattr(item, '_utinfo'):
# Capture case where there is a utool wrapper
orig_func = item._utinfo['orig_func']
flag = is_defined_by_module(orig_func, module, parent)
else:
if isinstance(item, staticmethod):
# static methods are a wrapper around a function
item = item.__func__
try:
func_globals = meta_util_six.get_funcglobals(item)
func_module_name = func_globals['__name__']
if func_module_name == 'line_profiler':
valid_names = dir(module)
if parent is not None:
valid_names += dir(parent)
if item.func_name in valid_names:
# hack to prevent small names
#if len(item.func_name) > 8:
if len(item.func_name) > 6:
flag = True
elif func_module_name == module.__name__:
flag = True
except AttributeError:
if hasattr(item, '__module__'):
flag = item.__module__ == module.__name__
return flag | [
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Erotemic/utool | utool/util_inspect.py | is_bateries_included | def is_bateries_included(item):
"""
Returns if a value is a python builtin function
Args:
item (object):
Returns:
bool: flag
References:
http://stackoverflow.com/questions/23149218/check-if-a-python-function-is-builtin
CommandLine:
python -m utool._internal.meta_util_six is_builtin
Example:
>>> # DISABLE_DOCTEST
>>> from utool._internal.meta_util_six import * # NOQA
>>> item = zip
>>> flag = is_bateries_included(item)
>>> result = ('flag = %s' % (str(flag),))
>>> print(result)
"""
flag = False
if hasattr(item, '__call__') and hasattr(item, '__module__'):
if item.__module__ is not None:
module = sys.modules[item.__module__]
if module == builtins:
flag = True
elif hasattr(module, '__file__'):
flag = LIB_PATH == dirname(module.__file__)
return flag | python | def is_bateries_included(item):
"""
Returns if a value is a python builtin function
Args:
item (object):
Returns:
bool: flag
References:
http://stackoverflow.com/questions/23149218/check-if-a-python-function-is-builtin
CommandLine:
python -m utool._internal.meta_util_six is_builtin
Example:
>>> # DISABLE_DOCTEST
>>> from utool._internal.meta_util_six import * # NOQA
>>> item = zip
>>> flag = is_bateries_included(item)
>>> result = ('flag = %s' % (str(flag),))
>>> print(result)
"""
flag = False
if hasattr(item, '__call__') and hasattr(item, '__module__'):
if item.__module__ is not None:
module = sys.modules[item.__module__]
if module == builtins:
flag = True
elif hasattr(module, '__file__'):
flag = LIB_PATH == dirname(module.__file__)
return flag | [
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Returns:
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CommandLine:
python -m utool._internal.meta_util_six is_builtin
Example:
>>> # DISABLE_DOCTEST
>>> from utool._internal.meta_util_six import * # NOQA
>>> item = zip
>>> flag = is_bateries_included(item)
>>> result = ('flag = %s' % (str(flag),))
>>> print(result) | [
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Erotemic/utool | utool/util_inspect.py | dummy_func | def dummy_func(arg1, arg2, arg3=None, arg4=[1, 2, 3], arg5={}, **kwargs):
"""
test func for kwargs parseing
"""
foo = kwargs.get('foo', None)
bar = kwargs.pop('bar', 4)
foo2 = kwargs['foo2']
foobar = str(foo) + str(bar) + str(foo2)
return foobar | python | def dummy_func(arg1, arg2, arg3=None, arg4=[1, 2, 3], arg5={}, **kwargs):
"""
test func for kwargs parseing
"""
foo = kwargs.get('foo', None)
bar = kwargs.pop('bar', 4)
foo2 = kwargs['foo2']
foobar = str(foo) + str(bar) + str(foo2)
return foobar | [
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Erotemic/utool | utool/util_inspect.py | get_docstr | def get_docstr(func_or_class):
""" Get the docstring from a live object """
import utool as ut
try:
docstr_ = func_or_class.func_doc
except AttributeError:
docstr_ = func_or_class.__doc__
if docstr_ is None:
docstr_ = ''
docstr = ut.unindent(docstr_)
return docstr | python | def get_docstr(func_or_class):
""" Get the docstring from a live object """
import utool as ut
try:
docstr_ = func_or_class.func_doc
except AttributeError:
docstr_ = func_or_class.__doc__
if docstr_ is None:
docstr_ = ''
docstr = ut.unindent(docstr_)
return docstr | [
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Erotemic/utool | utool/util_inspect.py | find_funcs_called_with_kwargs | def find_funcs_called_with_kwargs(sourcecode, target_kwargs_name='kwargs'):
r"""
Finds functions that are called with the keyword `kwargs` variable
CommandLine:
python3 -m utool.util_inspect find_funcs_called_with_kwargs
Example:
>>> # ENABLE_DOCTEST
>>> import utool as ut
>>> sourcecode = ut.codeblock(
'''
x, y = list(zip(*ut.ichunks(data, 2)))
somecall(arg1, arg2, arg3=4, **kwargs)
import sys
sys.badcall(**kwargs)
def foo():
bar(**kwargs)
ut.holymoly(**kwargs)
baz()
def biz(**kwargs):
foo2(**kwargs)
''')
>>> child_funcnamess = ut.find_funcs_called_with_kwargs(sourcecode)
>>> print('child_funcnamess = %r' % (child_funcnamess,))
>>> assert 'foo2' not in child_funcnamess, 'foo2 should not be found'
>>> assert 'bar' in child_funcnamess, 'bar should be found'
"""
import ast
sourcecode = 'from __future__ import print_function\n' + sourcecode
pt = ast.parse(sourcecode)
child_funcnamess = []
debug = False or VERYVERB_INSPECT
if debug:
print('\nInput:')
print('target_kwargs_name = %r' % (target_kwargs_name,))
print('\nSource:')
print(sourcecode)
import astor
print('\nParse:')
print(astor.dump(pt))
class KwargParseVisitor(ast.NodeVisitor):
"""
TODO: understand ut.update_existing and dict update
ie, know when kwargs is passed to these functions and
then look assume the object that was updated is a dictionary
and check wherever that is passed to kwargs as well.
"""
def visit_FunctionDef(self, node):
if debug:
print('\nVISIT FunctionDef node = %r' % (node,))
print('node.args.kwarg = %r' % (node.args.kwarg,))
if six.PY2:
kwarg_name = node.args.kwarg
else:
if node.args.kwarg is None:
kwarg_name = None
else:
kwarg_name = node.args.kwarg.arg
#import utool as ut
#ut.embed()
if kwarg_name != target_kwargs_name:
# target kwargs is still in scope
ast.NodeVisitor.generic_visit(self, node)
def visit_Call(self, node):
if debug:
print('\nVISIT Call node = %r' % (node,))
#print(ut.repr4(node.__dict__,))
if isinstance(node.func, ast.Attribute):
try:
funcname = node.func.value.id + '.' + node.func.attr
except AttributeError:
funcname = None
elif isinstance(node.func, ast.Name):
funcname = node.func.id
else:
raise NotImplementedError(
'do not know how to parse: node.func = %r' % (node.func,))
if six.PY2:
kwargs = node.kwargs
kwargs_name = None if kwargs is None else kwargs.id
if funcname is not None and kwargs_name == target_kwargs_name:
child_funcnamess.append(funcname)
if debug:
print('funcname = %r' % (funcname,))
print('kwargs_name = %r' % (kwargs_name,))
else:
if node.keywords:
for kwargs in node.keywords:
if kwargs.arg is None:
if hasattr(kwargs.value, 'id'):
kwargs_name = kwargs.value.id
if funcname is not None and kwargs_name == target_kwargs_name:
child_funcnamess.append(funcname)
if debug:
print('funcname = %r' % (funcname,))
print('kwargs_name = %r' % (kwargs_name,))
ast.NodeVisitor.generic_visit(self, node)
try:
KwargParseVisitor().visit(pt)
except Exception:
raise
pass
#import utool as ut
#if ut.SUPER_STRICT:
# raise
return child_funcnamess | python | def find_funcs_called_with_kwargs(sourcecode, target_kwargs_name='kwargs'):
r"""
Finds functions that are called with the keyword `kwargs` variable
CommandLine:
python3 -m utool.util_inspect find_funcs_called_with_kwargs
Example:
>>> # ENABLE_DOCTEST
>>> import utool as ut
>>> sourcecode = ut.codeblock(
'''
x, y = list(zip(*ut.ichunks(data, 2)))
somecall(arg1, arg2, arg3=4, **kwargs)
import sys
sys.badcall(**kwargs)
def foo():
bar(**kwargs)
ut.holymoly(**kwargs)
baz()
def biz(**kwargs):
foo2(**kwargs)
''')
>>> child_funcnamess = ut.find_funcs_called_with_kwargs(sourcecode)
>>> print('child_funcnamess = %r' % (child_funcnamess,))
>>> assert 'foo2' not in child_funcnamess, 'foo2 should not be found'
>>> assert 'bar' in child_funcnamess, 'bar should be found'
"""
import ast
sourcecode = 'from __future__ import print_function\n' + sourcecode
pt = ast.parse(sourcecode)
child_funcnamess = []
debug = False or VERYVERB_INSPECT
if debug:
print('\nInput:')
print('target_kwargs_name = %r' % (target_kwargs_name,))
print('\nSource:')
print(sourcecode)
import astor
print('\nParse:')
print(astor.dump(pt))
class KwargParseVisitor(ast.NodeVisitor):
"""
TODO: understand ut.update_existing and dict update
ie, know when kwargs is passed to these functions and
then look assume the object that was updated is a dictionary
and check wherever that is passed to kwargs as well.
"""
def visit_FunctionDef(self, node):
if debug:
print('\nVISIT FunctionDef node = %r' % (node,))
print('node.args.kwarg = %r' % (node.args.kwarg,))
if six.PY2:
kwarg_name = node.args.kwarg
else:
if node.args.kwarg is None:
kwarg_name = None
else:
kwarg_name = node.args.kwarg.arg
#import utool as ut
#ut.embed()
if kwarg_name != target_kwargs_name:
# target kwargs is still in scope
ast.NodeVisitor.generic_visit(self, node)
def visit_Call(self, node):
if debug:
print('\nVISIT Call node = %r' % (node,))
#print(ut.repr4(node.__dict__,))
if isinstance(node.func, ast.Attribute):
try:
funcname = node.func.value.id + '.' + node.func.attr
except AttributeError:
funcname = None
elif isinstance(node.func, ast.Name):
funcname = node.func.id
else:
raise NotImplementedError(
'do not know how to parse: node.func = %r' % (node.func,))
if six.PY2:
kwargs = node.kwargs
kwargs_name = None if kwargs is None else kwargs.id
if funcname is not None and kwargs_name == target_kwargs_name:
child_funcnamess.append(funcname)
if debug:
print('funcname = %r' % (funcname,))
print('kwargs_name = %r' % (kwargs_name,))
else:
if node.keywords:
for kwargs in node.keywords:
if kwargs.arg is None:
if hasattr(kwargs.value, 'id'):
kwargs_name = kwargs.value.id
if funcname is not None and kwargs_name == target_kwargs_name:
child_funcnamess.append(funcname)
if debug:
print('funcname = %r' % (funcname,))
print('kwargs_name = %r' % (kwargs_name,))
ast.NodeVisitor.generic_visit(self, node)
try:
KwargParseVisitor().visit(pt)
except Exception:
raise
pass
#import utool as ut
#if ut.SUPER_STRICT:
# raise
return child_funcnamess | [
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Finds functions that are called with the keyword `kwargs` variable
CommandLine:
python3 -m utool.util_inspect find_funcs_called_with_kwargs
Example:
>>> # ENABLE_DOCTEST
>>> import utool as ut
>>> sourcecode = ut.codeblock(
'''
x, y = list(zip(*ut.ichunks(data, 2)))
somecall(arg1, arg2, arg3=4, **kwargs)
import sys
sys.badcall(**kwargs)
def foo():
bar(**kwargs)
ut.holymoly(**kwargs)
baz()
def biz(**kwargs):
foo2(**kwargs)
''')
>>> child_funcnamess = ut.find_funcs_called_with_kwargs(sourcecode)
>>> print('child_funcnamess = %r' % (child_funcnamess,))
>>> assert 'foo2' not in child_funcnamess, 'foo2 should not be found'
>>> assert 'bar' in child_funcnamess, 'bar should be found' | [
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Erotemic/utool | utool/util_inspect.py | get_func_argspec | def get_func_argspec(func):
"""
wrapper around inspect.getargspec but takes into account utool decorators
"""
if hasattr(func, '_utinfo'):
argspec = func._utinfo['orig_argspec']
return argspec
if isinstance(func, property):
func = func.fget
try:
argspec = inspect.getargspec(func)
except Exception:
argspec = inspect.getfullargspec(func)
return argspec | python | def get_func_argspec(func):
"""
wrapper around inspect.getargspec but takes into account utool decorators
"""
if hasattr(func, '_utinfo'):
argspec = func._utinfo['orig_argspec']
return argspec
if isinstance(func, property):
func = func.fget
try:
argspec = inspect.getargspec(func)
except Exception:
argspec = inspect.getfullargspec(func)
return argspec | [
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Erotemic/utool | utool/util_inspect.py | parse_func_kwarg_keys | def parse_func_kwarg_keys(func, with_vals=False):
""" hacky inference of kwargs keys
SeeAlso:
argparse_funckw
recursive_parse_kwargs
parse_kwarg_keys
parse_func_kwarg_keys
get_func_kwargs
"""
sourcecode = get_func_sourcecode(func, strip_docstr=True,
strip_comments=True)
kwkeys = parse_kwarg_keys(sourcecode, with_vals=with_vals)
#ut.get_func_kwargs TODO
return kwkeys | python | def parse_func_kwarg_keys(func, with_vals=False):
""" hacky inference of kwargs keys
SeeAlso:
argparse_funckw
recursive_parse_kwargs
parse_kwarg_keys
parse_func_kwarg_keys
get_func_kwargs
"""
sourcecode = get_func_sourcecode(func, strip_docstr=True,
strip_comments=True)
kwkeys = parse_kwarg_keys(sourcecode, with_vals=with_vals)
#ut.get_func_kwargs TODO
return kwkeys | [
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recursive_parse_kwargs
parse_kwarg_keys
parse_func_kwarg_keys
get_func_kwargs | [
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Erotemic/utool | utool/util_inspect.py | get_func_kwargs | def get_func_kwargs(func, recursive=True):
"""
func = ibeis.run_experiment
SeeAlso:
argparse_funckw
recursive_parse_kwargs
parse_kwarg_keys
parse_func_kwarg_keys
get_func_kwargs
"""
import utool as ut
argspec = ut.get_func_argspec(func)
if argspec.defaults is None:
header_kw = {}
else:
header_kw = dict(zip(argspec.args[::-1], argspec.defaults[::-1]))
if argspec.keywords is not None:
header_kw.update(dict(ut.recursive_parse_kwargs(func)))
return header_kw | python | def get_func_kwargs(func, recursive=True):
"""
func = ibeis.run_experiment
SeeAlso:
argparse_funckw
recursive_parse_kwargs
parse_kwarg_keys
parse_func_kwarg_keys
get_func_kwargs
"""
import utool as ut
argspec = ut.get_func_argspec(func)
if argspec.defaults is None:
header_kw = {}
else:
header_kw = dict(zip(argspec.args[::-1], argspec.defaults[::-1]))
if argspec.keywords is not None:
header_kw.update(dict(ut.recursive_parse_kwargs(func)))
return header_kw | [
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parse_kwarg_keys
parse_func_kwarg_keys
get_func_kwargs | [
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Erotemic/utool | utool/util_inspect.py | argparse_funckw | def argparse_funckw(func, defaults={}, **kwargs):
"""
allows kwargs to be specified on the commandline from testfuncs
Args:
func (function):
Kwargs:
lbl, verbose, only_specified, force_keys, type_hint, alias_dict
Returns:
dict: funckw
CommandLine:
python -m utool.util_inspect argparse_funckw
SeeAlso:
exec_funckw
recursive_parse_kwargs
parse_kwarg_keys
Example:
>>> # ENABLE_DOCTEST
>>> from utool.util_inspect import * # NOQA
>>> import utool as ut
>>> func = get_instance_attrnames
>>> funckw = argparse_funckw(func)
>>> result = ('funckw = %s' % (ut.repr3(funckw),))
>>> print(result)
funckw = {
'default': True,
'with_methods': True,
'with_properties': True,
}
"""
import utool as ut
funckw_ = ut.get_funckw(func, recursive=True)
funckw_.update(defaults)
funckw = ut.argparse_dict(funckw_, **kwargs)
return funckw | python | def argparse_funckw(func, defaults={}, **kwargs):
"""
allows kwargs to be specified on the commandline from testfuncs
Args:
func (function):
Kwargs:
lbl, verbose, only_specified, force_keys, type_hint, alias_dict
Returns:
dict: funckw
CommandLine:
python -m utool.util_inspect argparse_funckw
SeeAlso:
exec_funckw
recursive_parse_kwargs
parse_kwarg_keys
Example:
>>> # ENABLE_DOCTEST
>>> from utool.util_inspect import * # NOQA
>>> import utool as ut
>>> func = get_instance_attrnames
>>> funckw = argparse_funckw(func)
>>> result = ('funckw = %s' % (ut.repr3(funckw),))
>>> print(result)
funckw = {
'default': True,
'with_methods': True,
'with_properties': True,
}
"""
import utool as ut
funckw_ = ut.get_funckw(func, recursive=True)
funckw_.update(defaults)
funckw = ut.argparse_dict(funckw_, **kwargs)
return funckw | [
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Args:
func (function):
Kwargs:
lbl, verbose, only_specified, force_keys, type_hint, alias_dict
Returns:
dict: funckw
CommandLine:
python -m utool.util_inspect argparse_funckw
SeeAlso:
exec_funckw
recursive_parse_kwargs
parse_kwarg_keys
Example:
>>> # ENABLE_DOCTEST
>>> from utool.util_inspect import * # NOQA
>>> import utool as ut
>>> func = get_instance_attrnames
>>> funckw = argparse_funckw(func)
>>> result = ('funckw = %s' % (ut.repr3(funckw),))
>>> print(result)
funckw = {
'default': True,
'with_methods': True,
'with_properties': True,
} | [
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Erotemic/utool | utool/Preferences.py | _qt_set_leaf_data | def _qt_set_leaf_data(self, qvar):
""" Sets backend data using QVariants """
if VERBOSE_PREF:
print('')
print('+--- [pref.qt_set_leaf_data]')
print('[pref.qt_set_leaf_data] qvar = %r' % qvar)
print('[pref.qt_set_leaf_data] _intern.name=%r' % self._intern.name)
print('[pref.qt_set_leaf_data] _intern.type_=%r' % self._intern.get_type())
print('[pref.qt_set_leaf_data] type(_intern.value)=%r' % type(self._intern.value))
print('[pref.qt_set_leaf_data] _intern.value=%r' % self._intern.value)
#print('[pref.qt_set_leaf_data] qvar.toString()=%s' % six.text_type(qvar.toString()))
if self._tree.parent is None:
raise Exception('[Pref.qtleaf] Cannot set root preference')
if self.qt_is_editable():
new_val = '[Pref.qtleaf] BadThingsHappenedInPref'
if self._intern.value == PrefNode:
raise Exception('[Pref.qtleaf] Qt can only change leafs')
elif self._intern.value is None:
# None could be a number of types
def cast_order(var, order=[bool, int, float, six.text_type]):
for type_ in order:
try:
ret = type_(var)
return ret
except Exception:
continue
new_val = cast_order(six.text_type(qvar))
self._intern.get_type()
if isinstance(self._intern.value, bool):
#new_val = bool(qvar.toBool())
print('qvar = %r' % (qvar,))
new_val = util_type.smart_cast(qvar, bool)
#new_val = bool(eval(qvar, {}, {}))
print('new_val = %r' % (new_val,))
elif isinstance(self._intern.value, int):
#new_val = int(qvar.toInt()[0])
new_val = int(qvar)
# elif isinstance(self._intern.value, float):
elif self._intern.get_type() in util_type.VALID_FLOAT_TYPES:
#new_val = float(qvar.toDouble()[0])
new_val = float(qvar)
elif isinstance(self._intern.value, six.string_types):
#new_val = six.text_type(qvar.toString())
new_val = six.text_type(qvar)
elif isinstance(self._intern.value, PrefChoice):
#new_val = qvar.toString()
new_val = six.text_type(qvar)
if new_val.upper() == 'NONE':
new_val = None
else:
try:
#new_val = six.text_type(qvar.toString())
type_ = self._intern.get_type()
if type_ is not None:
new_val = type_(six.text_type(qvar))
else:
new_val = six.text_type(qvar)
except Exception:
raise NotImplementedError(
('[Pref.qtleaf] Unknown internal type. '
'type(_intern.value) = %r, '
'_intern.get_type() = %r, ')
% type(self._intern.value), self._intern.get_type())
# Check for a set of None
if isinstance(new_val, six.string_types):
if new_val.lower() == 'none':
new_val = None
elif new_val.lower() == 'true':
new_val = True
elif new_val.lower() == 'false':
new_val = False
# save to disk after modifying data
if VERBOSE_PREF:
print('---')
print('[pref.qt_set_leaf_data] new_val=%r' % new_val)
print('[pref.qt_set_leaf_data] type(new_val)=%r' % type(new_val))
print('L____ [pref.qt_set_leaf_data]')
# TODO Add ability to set a callback function when certain
# preferences are changed.
return self._tree.parent.pref_update(self._intern.name, new_val)
return 'PrefNotEditable' | python | def _qt_set_leaf_data(self, qvar):
""" Sets backend data using QVariants """
if VERBOSE_PREF:
print('')
print('+--- [pref.qt_set_leaf_data]')
print('[pref.qt_set_leaf_data] qvar = %r' % qvar)
print('[pref.qt_set_leaf_data] _intern.name=%r' % self._intern.name)
print('[pref.qt_set_leaf_data] _intern.type_=%r' % self._intern.get_type())
print('[pref.qt_set_leaf_data] type(_intern.value)=%r' % type(self._intern.value))
print('[pref.qt_set_leaf_data] _intern.value=%r' % self._intern.value)
#print('[pref.qt_set_leaf_data] qvar.toString()=%s' % six.text_type(qvar.toString()))
if self._tree.parent is None:
raise Exception('[Pref.qtleaf] Cannot set root preference')
if self.qt_is_editable():
new_val = '[Pref.qtleaf] BadThingsHappenedInPref'
if self._intern.value == PrefNode:
raise Exception('[Pref.qtleaf] Qt can only change leafs')
elif self._intern.value is None:
# None could be a number of types
def cast_order(var, order=[bool, int, float, six.text_type]):
for type_ in order:
try:
ret = type_(var)
return ret
except Exception:
continue
new_val = cast_order(six.text_type(qvar))
self._intern.get_type()
if isinstance(self._intern.value, bool):
#new_val = bool(qvar.toBool())
print('qvar = %r' % (qvar,))
new_val = util_type.smart_cast(qvar, bool)
#new_val = bool(eval(qvar, {}, {}))
print('new_val = %r' % (new_val,))
elif isinstance(self._intern.value, int):
#new_val = int(qvar.toInt()[0])
new_val = int(qvar)
# elif isinstance(self._intern.value, float):
elif self._intern.get_type() in util_type.VALID_FLOAT_TYPES:
#new_val = float(qvar.toDouble()[0])
new_val = float(qvar)
elif isinstance(self._intern.value, six.string_types):
#new_val = six.text_type(qvar.toString())
new_val = six.text_type(qvar)
elif isinstance(self._intern.value, PrefChoice):
#new_val = qvar.toString()
new_val = six.text_type(qvar)
if new_val.upper() == 'NONE':
new_val = None
else:
try:
#new_val = six.text_type(qvar.toString())
type_ = self._intern.get_type()
if type_ is not None:
new_val = type_(six.text_type(qvar))
else:
new_val = six.text_type(qvar)
except Exception:
raise NotImplementedError(
('[Pref.qtleaf] Unknown internal type. '
'type(_intern.value) = %r, '
'_intern.get_type() = %r, ')
% type(self._intern.value), self._intern.get_type())
# Check for a set of None
if isinstance(new_val, six.string_types):
if new_val.lower() == 'none':
new_val = None
elif new_val.lower() == 'true':
new_val = True
elif new_val.lower() == 'false':
new_val = False
# save to disk after modifying data
if VERBOSE_PREF:
print('---')
print('[pref.qt_set_leaf_data] new_val=%r' % new_val)
print('[pref.qt_set_leaf_data] type(new_val)=%r' % type(new_val))
print('L____ [pref.qt_set_leaf_data]')
# TODO Add ability to set a callback function when certain
# preferences are changed.
return self._tree.parent.pref_update(self._intern.name, new_val)
return 'PrefNotEditable' | [
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Erotemic/utool | utool/Preferences.py | Pref.toggle | def toggle(self, key):
""" Toggles a boolean key """
val = self[key]
assert isinstance(val, bool), 'key[%r] = %r is not a bool' % (key, val)
self.pref_update(key, not val) | python | def toggle(self, key):
""" Toggles a boolean key """
val = self[key]
assert isinstance(val, bool), 'key[%r] = %r is not a bool' % (key, val)
self.pref_update(key, not val) | [
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Erotemic/utool | utool/Preferences.py | Pref.change_combo_val | def change_combo_val(self, new_val):
"""
Checks to see if a selection is a valid index or choice of a combo
preference
"""
choice_obj = self._intern.value
assert isinstance(self._intern.value, PrefChoice), 'must be a choice'
return choice_obj.get_tuple() | python | def change_combo_val(self, new_val):
"""
Checks to see if a selection is a valid index or choice of a combo
preference
"""
choice_obj = self._intern.value
assert isinstance(self._intern.value, PrefChoice), 'must be a choice'
return choice_obj.get_tuple() | [
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preference | [
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Erotemic/utool | utool/Preferences.py | Pref.iteritems | def iteritems(self):
"""
Wow this class is messed up. I had to overwrite items when
moving to python3, just because I haden't called it yet
"""
for (key, val) in six.iteritems(self.__dict__):
if key in self._printable_exclude:
continue
yield (key, val) | python | def iteritems(self):
"""
Wow this class is messed up. I had to overwrite items when
moving to python3, just because I haden't called it yet
"""
for (key, val) in six.iteritems(self.__dict__):
if key in self._printable_exclude:
continue
yield (key, val) | [
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Erotemic/utool | utool/Preferences.py | Pref.to_dict | def to_dict(self, split_structs_bit=False):
""" Converts prefeters to a dictionary.
Children Pref can be optionally separated """
pref_dict = {}
struct_dict = {}
for (key, val) in six.iteritems(self):
if split_structs_bit and isinstance(val, Pref):
struct_dict[key] = val
continue
pref_dict[key] = val
if split_structs_bit:
return (pref_dict, struct_dict)
return pref_dict | python | def to_dict(self, split_structs_bit=False):
""" Converts prefeters to a dictionary.
Children Pref can be optionally separated """
pref_dict = {}
struct_dict = {}
for (key, val) in six.iteritems(self):
if split_structs_bit and isinstance(val, Pref):
struct_dict[key] = val
continue
pref_dict[key] = val
if split_structs_bit:
return (pref_dict, struct_dict)
return pref_dict | [
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Erotemic/utool | utool/Preferences.py | Pref.save | def save(self):
""" Saves prefs to disk in dict format """
fpath = self.get_fpath()
if fpath in ['', None]:
if self._tree.parent is not None:
if VERBOSE_PREF:
print('[pref.save] Can my parent save me?') # ...to disk
return self._tree.parent.save()
if VERBOSE_PREF:
print('[pref.save] I cannot be saved. I have no parents.')
return False
with open(fpath, 'wb') as f:
print('[pref] Saving to ' + fpath)
pref_dict = self.to_dict()
pickle.dump(pref_dict, f, protocol=2) # Use protocol 2 to support python2 and 3
return True | python | def save(self):
""" Saves prefs to disk in dict format """
fpath = self.get_fpath()
if fpath in ['', None]:
if self._tree.parent is not None:
if VERBOSE_PREF:
print('[pref.save] Can my parent save me?') # ...to disk
return self._tree.parent.save()
if VERBOSE_PREF:
print('[pref.save] I cannot be saved. I have no parents.')
return False
with open(fpath, 'wb') as f:
print('[pref] Saving to ' + fpath)
pref_dict = self.to_dict()
pickle.dump(pref_dict, f, protocol=2) # Use protocol 2 to support python2 and 3
return True | [
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Erotemic/utool | utool/Preferences.py | Pref.load | def load(self):
""" Read pref dict stored on disk. Overwriting current values. """
if VERBOSE_PREF:
print('[pref.load()]')
#if not os.path.exists(self._intern.fpath):
# msg = '[pref] fpath=%r does not exist' % (self._intern.fpath)
# return msg
fpath = self.get_fpath()
try:
with open(fpath, 'rb') as f:
if VERBOSE_PREF:
print('load: %r' % fpath)
pref_dict = pickle.load(f)
except EOFError as ex1:
util_dbg.printex(ex1, 'did not load pref fpath=%r correctly' % fpath, iswarning=True)
#warnings.warn(msg)
raise
#return msg
except ImportError as ex2:
util_dbg.printex(ex2, 'did not load pref fpath=%r correctly' % fpath, iswarning=True)
#warnings.warn(msg)
raise
#return msg
if not util_type.is_dict(pref_dict):
raise Exception('Preference file is corrupted')
self.add_dict(pref_dict)
return True | python | def load(self):
""" Read pref dict stored on disk. Overwriting current values. """
if VERBOSE_PREF:
print('[pref.load()]')
#if not os.path.exists(self._intern.fpath):
# msg = '[pref] fpath=%r does not exist' % (self._intern.fpath)
# return msg
fpath = self.get_fpath()
try:
with open(fpath, 'rb') as f:
if VERBOSE_PREF:
print('load: %r' % fpath)
pref_dict = pickle.load(f)
except EOFError as ex1:
util_dbg.printex(ex1, 'did not load pref fpath=%r correctly' % fpath, iswarning=True)
#warnings.warn(msg)
raise
#return msg
except ImportError as ex2:
util_dbg.printex(ex2, 'did not load pref fpath=%r correctly' % fpath, iswarning=True)
#warnings.warn(msg)
raise
#return msg
if not util_type.is_dict(pref_dict):
raise Exception('Preference file is corrupted')
self.add_dict(pref_dict)
return True | [
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Erotemic/utool | utool/Preferences.py | Pref.full_name | def full_name(self):
""" returns name all the way up the tree """
if self._tree.parent is None:
return self._intern.name
return self._tree.parent.full_name() + '.' + self._intern.name | python | def full_name(self):
""" returns name all the way up the tree """
if self._tree.parent is None:
return self._intern.name
return self._tree.parent.full_name() + '.' + self._intern.name | [
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Erotemic/utool | utool/Preferences.py | Pref.pref_update | def pref_update(self, key, new_val):
""" Changes a preference value and saves it to disk """
print('Update and save pref from: %s=%r, to: %s=%r' %
(key, six.text_type(self[key]), key, six.text_type(new_val)))
self.__setattr__(key, new_val)
return self.save() | python | def pref_update(self, key, new_val):
""" Changes a preference value and saves it to disk """
print('Update and save pref from: %s=%r, to: %s=%r' %
(key, six.text_type(self[key]), key, six.text_type(new_val)))
self.__setattr__(key, new_val)
return self.save() | [
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product-definition-center/pdc-client | pdc_client/plugins/permission.py | PermissionPlugin.__get_permissions | def __get_permissions(self, res, **kwargs):
"""
This call returns current login user's permissions.
"""
response = res._(**kwargs)
return response.get('permissions', None) | python | def __get_permissions(self, res, **kwargs):
"""
This call returns current login user's permissions.
"""
response = res._(**kwargs)
return response.get('permissions', None) | [
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Erotemic/utool | utool/util_class.py | inject_all_external_modules | def inject_all_external_modules(self, classname=None,
allow_override='override+warn',
strict=True):
"""
dynamically injects registered module methods into a class instance
FIXME: naming convention and use this in all places where this clas is used
"""
#import utool as ut
if classname is None:
classname = self.__class__.__name__
#import utool as ut
#ut.embed()
NEW = True
if NEW:
classkey_list = [key for key in __CLASSTYPE_ATTRIBUTES__
if key[0] == classname]
else:
injected_modules = get_injected_modules(classname)
# the variable must be named CLASS_INJECT_KEY
# and only one class can be specified per module.
classkey_list = [module.CLASS_INJECT_KEY
for module in injected_modules]
for classkey in classkey_list:
inject_instance(
self, classkey=classkey,
allow_override=allow_override, strict=False)
for classkey in classkey_list:
postinject_instance(
self, classkey=classkey) | python | def inject_all_external_modules(self, classname=None,
allow_override='override+warn',
strict=True):
"""
dynamically injects registered module methods into a class instance
FIXME: naming convention and use this in all places where this clas is used
"""
#import utool as ut
if classname is None:
classname = self.__class__.__name__
#import utool as ut
#ut.embed()
NEW = True
if NEW:
classkey_list = [key for key in __CLASSTYPE_ATTRIBUTES__
if key[0] == classname]
else:
injected_modules = get_injected_modules(classname)
# the variable must be named CLASS_INJECT_KEY
# and only one class can be specified per module.
classkey_list = [module.CLASS_INJECT_KEY
for module in injected_modules]
for classkey in classkey_list:
inject_instance(
self, classkey=classkey,
allow_override=allow_override, strict=False)
for classkey in classkey_list:
postinject_instance(
self, classkey=classkey) | [
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Erotemic/utool | utool/util_class.py | decorate_class_method | def decorate_class_method(func, classkey=None, skipmain=False):
"""
Will inject all decorated function as methods of classkey
classkey is some identifying string, tuple, or object
func can also be a tuple
"""
#import utool as ut
global __CLASSTYPE_ATTRIBUTES__
assert classkey is not None, 'must specify classkey'
#if not (skipmain and ut.get_caller_modname() == '__main__'):
__CLASSTYPE_ATTRIBUTES__[classkey].append(func)
return func | python | def decorate_class_method(func, classkey=None, skipmain=False):
"""
Will inject all decorated function as methods of classkey
classkey is some identifying string, tuple, or object
func can also be a tuple
"""
#import utool as ut
global __CLASSTYPE_ATTRIBUTES__
assert classkey is not None, 'must specify classkey'
#if not (skipmain and ut.get_caller_modname() == '__main__'):
__CLASSTYPE_ATTRIBUTES__[classkey].append(func)
return func | [
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Erotemic/utool | utool/util_class.py | decorate_postinject | def decorate_postinject(func, classkey=None, skipmain=False):
"""
Will perform func with argument self after inject_instance is called on classkey
classkey is some identifying string, tuple, or object
"""
#import utool as ut
global __CLASSTYPE_POSTINJECT_FUNCS__
assert classkey is not None, 'must specify classkey'
#if not (skipmain and ut.get_caller_modname() == '__main__'):
__CLASSTYPE_POSTINJECT_FUNCS__[classkey].append(func)
return func | python | def decorate_postinject(func, classkey=None, skipmain=False):
"""
Will perform func with argument self after inject_instance is called on classkey
classkey is some identifying string, tuple, or object
"""
#import utool as ut
global __CLASSTYPE_POSTINJECT_FUNCS__
assert classkey is not None, 'must specify classkey'
#if not (skipmain and ut.get_caller_modname() == '__main__'):
__CLASSTYPE_POSTINJECT_FUNCS__[classkey].append(func)
return func | [
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Erotemic/utool | utool/util_class.py | inject_func_as_method | def inject_func_as_method(self, func, method_name=None, class_=None,
allow_override=False, allow_main=False,
verbose=True, override=None, force=False):
""" Injects a function into an object as a method
Wraps func as a bound method of self. Then injects func into self
It is preferable to use make_class_method_decorator and inject_instance
Args:
self (object): class instance
func : some function whos first arugment is a class instance
method_name (str) : default=func.__name__, if specified renames the method
class_ (type) : if func is an unbound method of this class
References:
http://stackoverflow.com/questions/1015307/python-bind-an-unbound-method
"""
if override is not None:
# TODO depcirate allow_override
allow_override = override
if method_name is None:
method_name = get_funcname(func)
if force:
allow_override = True
allow_main = True
old_method = getattr(self, method_name, None)
# Bind function to the class instance
#new_method = types.MethodType(func, self, self.__class__)
new_method = func.__get__(self, self.__class__)
#new_method = profile(func.__get__(self, self.__class__))
if old_method is not None:
old_im_func = get_method_func(old_method)
new_im_func = get_method_func(new_method)
if not allow_main and old_im_func is not None and (
get_funcglobals(old_im_func)['__name__'] != '__main__' and
get_funcglobals(new_im_func)['__name__'] == '__main__'):
if True or VERBOSE_CLASS:
print('[util_class] skipping re-inject of %r from __main__' % method_name)
return
if old_method is new_method or old_im_func is new_im_func:
#if verbose and util_arg.NOT_QUIET:
# print('WARNING: Skipping injecting the same function twice: %r' % new_method)
#print('WARNING: Injecting the same function twice: %r' % new_method)
return
elif allow_override is False:
raise AssertionError(
'Overrides are not allowed. Already have method_name=%r' %
(method_name))
elif allow_override == 'warn':
print(
'WARNING: Overrides are not allowed. Already have method_name=%r. Skipping' %
(method_name))
return
elif allow_override == 'override+warn':
#import utool as ut
#ut.embed()
print('WARNING: Overrides are allowed, but dangerous. method_name=%r.' %
(method_name))
print('old_method = %r, im_func=%s' % (old_method, str(old_im_func)))
print('new_method = %r, im_func=%s' % (new_method, str(new_im_func)))
print(get_funcglobals(old_im_func)['__name__'])
print(get_funcglobals(new_im_func)['__name__'])
# TODO: does this actually decrement the refcount enough?
del old_method
setattr(self, method_name, new_method) | python | def inject_func_as_method(self, func, method_name=None, class_=None,
allow_override=False, allow_main=False,
verbose=True, override=None, force=False):
""" Injects a function into an object as a method
Wraps func as a bound method of self. Then injects func into self
It is preferable to use make_class_method_decorator and inject_instance
Args:
self (object): class instance
func : some function whos first arugment is a class instance
method_name (str) : default=func.__name__, if specified renames the method
class_ (type) : if func is an unbound method of this class
References:
http://stackoverflow.com/questions/1015307/python-bind-an-unbound-method
"""
if override is not None:
# TODO depcirate allow_override
allow_override = override
if method_name is None:
method_name = get_funcname(func)
if force:
allow_override = True
allow_main = True
old_method = getattr(self, method_name, None)
# Bind function to the class instance
#new_method = types.MethodType(func, self, self.__class__)
new_method = func.__get__(self, self.__class__)
#new_method = profile(func.__get__(self, self.__class__))
if old_method is not None:
old_im_func = get_method_func(old_method)
new_im_func = get_method_func(new_method)
if not allow_main and old_im_func is not None and (
get_funcglobals(old_im_func)['__name__'] != '__main__' and
get_funcglobals(new_im_func)['__name__'] == '__main__'):
if True or VERBOSE_CLASS:
print('[util_class] skipping re-inject of %r from __main__' % method_name)
return
if old_method is new_method or old_im_func is new_im_func:
#if verbose and util_arg.NOT_QUIET:
# print('WARNING: Skipping injecting the same function twice: %r' % new_method)
#print('WARNING: Injecting the same function twice: %r' % new_method)
return
elif allow_override is False:
raise AssertionError(
'Overrides are not allowed. Already have method_name=%r' %
(method_name))
elif allow_override == 'warn':
print(
'WARNING: Overrides are not allowed. Already have method_name=%r. Skipping' %
(method_name))
return
elif allow_override == 'override+warn':
#import utool as ut
#ut.embed()
print('WARNING: Overrides are allowed, but dangerous. method_name=%r.' %
(method_name))
print('old_method = %r, im_func=%s' % (old_method, str(old_im_func)))
print('new_method = %r, im_func=%s' % (new_method, str(new_im_func)))
print(get_funcglobals(old_im_func)['__name__'])
print(get_funcglobals(new_im_func)['__name__'])
# TODO: does this actually decrement the refcount enough?
del old_method
setattr(self, method_name, new_method) | [
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Args:
self (object): class instance
func : some function whos first arugment is a class instance
method_name (str) : default=func.__name__, if specified renames the method
class_ (type) : if func is an unbound method of this class
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Erotemic/utool | utool/util_class.py | inject_func_as_unbound_method | def inject_func_as_unbound_method(class_, func, method_name=None):
""" This is actually quite simple """
if method_name is None:
method_name = get_funcname(func)
setattr(class_, method_name, func) | python | def inject_func_as_unbound_method(class_, func, method_name=None):
""" This is actually quite simple """
if method_name is None:
method_name = get_funcname(func)
setattr(class_, method_name, func) | [
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Erotemic/utool | utool/util_class.py | reloading_meta_metaclass_factory | def reloading_meta_metaclass_factory(BASE_TYPE=type):
""" hack for pyqt """
class ReloadingMetaclass2(BASE_TYPE):
def __init__(metaself, name, bases, dct):
super(ReloadingMetaclass2, metaself).__init__(name, bases, dct)
#print('Making rrr for %r' % (name,))
metaself.rrr = reload_class
return ReloadingMetaclass2 | python | def reloading_meta_metaclass_factory(BASE_TYPE=type):
""" hack for pyqt """
class ReloadingMetaclass2(BASE_TYPE):
def __init__(metaself, name, bases, dct):
super(ReloadingMetaclass2, metaself).__init__(name, bases, dct)
#print('Making rrr for %r' % (name,))
metaself.rrr = reload_class
return ReloadingMetaclass2 | [
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Erotemic/utool | utool/util_class.py | reload_class | def reload_class(self, verbose=True, reload_module=True):
"""
special class reloading function
This function is often injected as rrr of classes
"""
import utool as ut
verbose = verbose or VERBOSE_CLASS
classname = self.__class__.__name__
try:
modname = self.__class__.__module__
if verbose:
print('[class] reloading ' + classname + ' from ' + modname)
# --HACK--
if hasattr(self, '_on_reload'):
if verbose > 1:
print('[class] calling _on_reload for ' + classname)
self._on_reload()
elif verbose > 1:
print('[class] ' + classname + ' does not have an _on_reload function')
# Do for all inheriting classes
def find_base_clases(_class, find_base_clases=None):
class_list = []
for _baseclass in _class.__bases__:
parents = find_base_clases(_baseclass, find_base_clases)
class_list.extend(parents)
if _class is not object:
class_list.append(_class)
return class_list
head_class = self.__class__
# Determine if parents need reloading
class_list = find_base_clases(head_class, find_base_clases)
# HACK
ignore = {HashComparable2}
class_list = [_class for _class in class_list
if _class not in ignore]
for _class in class_list:
if verbose:
print('[class] reloading parent ' + _class.__name__ +
' from ' + _class.__module__)
if _class.__module__ == '__main__':
# Attempt to find the module that is the main module
# This may be very hacky and potentially break
main_module_ = sys.modules[_class.__module__]
main_modname = ut.get_modname_from_modpath(main_module_.__file__)
module_ = sys.modules[main_modname]
else:
module_ = sys.modules[_class.__module__]
if hasattr(module_, 'rrr'):
if reload_module:
module_.rrr(verbose=verbose)
else:
if reload_module:
import imp
if verbose:
print('[class] reloading ' + _class.__module__ + ' with imp')
try:
imp.reload(module_)
except (ImportError, AttributeError):
print('[class] fallback reloading ' + _class.__module__ +
' with imp')
# one last thing to try. probably used ut.import_module_from_fpath
# when importing this module
imp.load_source(module_.__name__, module_.__file__)
# Reset class attributes
_newclass = getattr(module_, _class.__name__)
reload_class_methods(self, _newclass, verbose=verbose)
# --HACK--
# TODO: handle injected definitions
if hasattr(self, '_initialize_self'):
if verbose > 1:
print('[class] calling _initialize_self for ' + classname)
self._initialize_self()
elif verbose > 1:
print('[class] ' + classname + ' does not have an _initialize_self function')
except Exception as ex:
ut.printex(ex, 'Error Reloading Class', keys=[
'modname', 'module', 'class_', 'class_list', 'self', ])
raise | python | def reload_class(self, verbose=True, reload_module=True):
"""
special class reloading function
This function is often injected as rrr of classes
"""
import utool as ut
verbose = verbose or VERBOSE_CLASS
classname = self.__class__.__name__
try:
modname = self.__class__.__module__
if verbose:
print('[class] reloading ' + classname + ' from ' + modname)
# --HACK--
if hasattr(self, '_on_reload'):
if verbose > 1:
print('[class] calling _on_reload for ' + classname)
self._on_reload()
elif verbose > 1:
print('[class] ' + classname + ' does not have an _on_reload function')
# Do for all inheriting classes
def find_base_clases(_class, find_base_clases=None):
class_list = []
for _baseclass in _class.__bases__:
parents = find_base_clases(_baseclass, find_base_clases)
class_list.extend(parents)
if _class is not object:
class_list.append(_class)
return class_list
head_class = self.__class__
# Determine if parents need reloading
class_list = find_base_clases(head_class, find_base_clases)
# HACK
ignore = {HashComparable2}
class_list = [_class for _class in class_list
if _class not in ignore]
for _class in class_list:
if verbose:
print('[class] reloading parent ' + _class.__name__ +
' from ' + _class.__module__)
if _class.__module__ == '__main__':
# Attempt to find the module that is the main module
# This may be very hacky and potentially break
main_module_ = sys.modules[_class.__module__]
main_modname = ut.get_modname_from_modpath(main_module_.__file__)
module_ = sys.modules[main_modname]
else:
module_ = sys.modules[_class.__module__]
if hasattr(module_, 'rrr'):
if reload_module:
module_.rrr(verbose=verbose)
else:
if reload_module:
import imp
if verbose:
print('[class] reloading ' + _class.__module__ + ' with imp')
try:
imp.reload(module_)
except (ImportError, AttributeError):
print('[class] fallback reloading ' + _class.__module__ +
' with imp')
# one last thing to try. probably used ut.import_module_from_fpath
# when importing this module
imp.load_source(module_.__name__, module_.__file__)
# Reset class attributes
_newclass = getattr(module_, _class.__name__)
reload_class_methods(self, _newclass, verbose=verbose)
# --HACK--
# TODO: handle injected definitions
if hasattr(self, '_initialize_self'):
if verbose > 1:
print('[class] calling _initialize_self for ' + classname)
self._initialize_self()
elif verbose > 1:
print('[class] ' + classname + ' does not have an _initialize_self function')
except Exception as ex:
ut.printex(ex, 'Error Reloading Class', keys=[
'modname', 'module', 'class_', 'class_list', 'self', ])
raise | [
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Erotemic/utool | utool/util_class.py | reload_class_methods | def reload_class_methods(self, class_, verbose=True):
"""
rebinds all class methods
Args:
self (object): class instance to reload
class_ (type): type to reload as
Example:
>>> # DISABLE_DOCTEST
>>> from utool.util_class import * # NOQA
>>> self = '?'
>>> class_ = '?'
>>> result = reload_class_methods(self, class_)
>>> print(result)
"""
if verbose:
print('[util_class] Reloading self=%r as class_=%r' % (self, class_))
self.__class__ = class_
for key in dir(class_):
# Get unbound reloaded method
func = getattr(class_, key)
if isinstance(func, types.MethodType):
# inject it into the old instance
inject_func_as_method(self, func, class_=class_,
allow_override=True,
verbose=verbose) | python | def reload_class_methods(self, class_, verbose=True):
"""
rebinds all class methods
Args:
self (object): class instance to reload
class_ (type): type to reload as
Example:
>>> # DISABLE_DOCTEST
>>> from utool.util_class import * # NOQA
>>> self = '?'
>>> class_ = '?'
>>> result = reload_class_methods(self, class_)
>>> print(result)
"""
if verbose:
print('[util_class] Reloading self=%r as class_=%r' % (self, class_))
self.__class__ = class_
for key in dir(class_):
# Get unbound reloaded method
func = getattr(class_, key)
if isinstance(func, types.MethodType):
# inject it into the old instance
inject_func_as_method(self, func, class_=class_,
allow_override=True,
verbose=verbose) | [
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Example:
>>> # DISABLE_DOCTEST
>>> from utool.util_class import * # NOQA
>>> self = '?'
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Erotemic/utool | utool/util_class.py | remove_private_obfuscation | def remove_private_obfuscation(self):
"""
removes the python obfuscation of class privates so they can be executed as
they appear in class source. Useful when playing with IPython.
"""
classname = self.__class__.__name__
attrlist = [attr for attr in dir(self) if attr.startswith('_' + classname + '__')]
for attr in attrlist:
method = getattr(self, attr)
truename = attr.replace('_' + classname + '__', '__')
setattr(self, truename, method) | python | def remove_private_obfuscation(self):
"""
removes the python obfuscation of class privates so they can be executed as
they appear in class source. Useful when playing with IPython.
"""
classname = self.__class__.__name__
attrlist = [attr for attr in dir(self) if attr.startswith('_' + classname + '__')]
for attr in attrlist:
method = getattr(self, attr)
truename = attr.replace('_' + classname + '__', '__')
setattr(self, truename, method) | [
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glormph/msstitch | src/app/actions/mslookup/proteinquant.py | create_peptidequant_lookup | def create_peptidequant_lookup(fns, pqdb, poolnames, pepseq_colnr,
ms1_qcolpattern=None, isobqcolpattern=None,
psmnrpattern=None, fdrcolpattern=None,
pepcolpattern=None):
"""Calls lower level function to create a peptide quant lookup"""
patterns = [ms1_qcolpattern, fdrcolpattern, pepcolpattern]
storefuns = [pqdb.store_precursor_quants, pqdb.store_fdr,
pqdb.store_pep]
create_pep_protein_quant_lookup(fns, pqdb, poolnames, pepseq_colnr,
patterns, storefuns,
isobqcolpattern, psmnrpattern) | python | def create_peptidequant_lookup(fns, pqdb, poolnames, pepseq_colnr,
ms1_qcolpattern=None, isobqcolpattern=None,
psmnrpattern=None, fdrcolpattern=None,
pepcolpattern=None):
"""Calls lower level function to create a peptide quant lookup"""
patterns = [ms1_qcolpattern, fdrcolpattern, pepcolpattern]
storefuns = [pqdb.store_precursor_quants, pqdb.store_fdr,
pqdb.store_pep]
create_pep_protein_quant_lookup(fns, pqdb, poolnames, pepseq_colnr,
patterns, storefuns,
isobqcolpattern, psmnrpattern) | [
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glormph/msstitch | src/app/actions/mslookup/proteinquant.py | create_proteinquant_lookup | def create_proteinquant_lookup(fns, pqdb, poolnames, protacc_colnr,
ms1_qcolpattern=None, isobqcolpattern=None,
psmnrpattern=None, probcolpattern=None,
fdrcolpattern=None, pepcolpattern=None):
"""Calls lower level function to create a protein quant lookup"""
patterns = [ms1_qcolpattern, probcolpattern, fdrcolpattern, pepcolpattern]
storefuns = [pqdb.store_precursor_quants, pqdb.store_probability,
pqdb.store_fdr, pqdb.store_pep]
create_pep_protein_quant_lookup(fns, pqdb, poolnames, protacc_colnr,
patterns, storefuns, isobqcolpattern,
psmnrpattern) | python | def create_proteinquant_lookup(fns, pqdb, poolnames, protacc_colnr,
ms1_qcolpattern=None, isobqcolpattern=None,
psmnrpattern=None, probcolpattern=None,
fdrcolpattern=None, pepcolpattern=None):
"""Calls lower level function to create a protein quant lookup"""
patterns = [ms1_qcolpattern, probcolpattern, fdrcolpattern, pepcolpattern]
storefuns = [pqdb.store_precursor_quants, pqdb.store_probability,
pqdb.store_fdr, pqdb.store_pep]
create_pep_protein_quant_lookup(fns, pqdb, poolnames, protacc_colnr,
patterns, storefuns, isobqcolpattern,
psmnrpattern) | [
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glormph/msstitch | src/app/actions/mslookup/proteinquant.py | create_pep_protein_quant_lookup | def create_pep_protein_quant_lookup(fns, pqdb, poolnames, featcolnr, patterns,
storefuns, isobqcolpattern=None,
psmnrpattern=None):
"""Does the work when creating peptide and protein quant lookups. This
loops through storing options and parses columns, passing on to the
storing functions"""
tablefn_map = create_tablefn_map(fns, pqdb, poolnames)
feat_map = pqdb.get_feature_map()
for pattern, storefun in zip(patterns, storefuns):
if pattern is None:
continue
colmap = get_colmap(fns, pattern, single_col=True)
if colmap:
store_single_col_data(fns, tablefn_map, feat_map,
storefun, featcolnr, colmap)
if isobqcolpattern is not None:
isocolmap = get_colmap(fns, isobqcolpattern, antipattern=psmnrpattern)
else:
return
if psmnrpattern is not None:
psmcolmap = get_colmap(fns, psmnrpattern)
else:
psmcolmap = False
create_isobaric_quant_lookup(fns, tablefn_map,
feat_map, pqdb,
featcolnr,
isocolmap, psmcolmap) | python | def create_pep_protein_quant_lookup(fns, pqdb, poolnames, featcolnr, patterns,
storefuns, isobqcolpattern=None,
psmnrpattern=None):
"""Does the work when creating peptide and protein quant lookups. This
loops through storing options and parses columns, passing on to the
storing functions"""
tablefn_map = create_tablefn_map(fns, pqdb, poolnames)
feat_map = pqdb.get_feature_map()
for pattern, storefun in zip(patterns, storefuns):
if pattern is None:
continue
colmap = get_colmap(fns, pattern, single_col=True)
if colmap:
store_single_col_data(fns, tablefn_map, feat_map,
storefun, featcolnr, colmap)
if isobqcolpattern is not None:
isocolmap = get_colmap(fns, isobqcolpattern, antipattern=psmnrpattern)
else:
return
if psmnrpattern is not None:
psmcolmap = get_colmap(fns, psmnrpattern)
else:
psmcolmap = False
create_isobaric_quant_lookup(fns, tablefn_map,
feat_map, pqdb,
featcolnr,
isocolmap, psmcolmap) | [
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glormph/msstitch | src/app/actions/mslookup/proteinquant.py | store_single_col_data | def store_single_col_data(fns, prottable_id_map, pacc_map, pqdbmethod,
protacc_colnr, colmap):
"""General method to store single column data from protein tables
in lookup"""
to_store = []
for fn, header, pquant in tsvreader.generate_tsv_pep_protein_quants(fns):
pacc_id = pacc_map[pquant[header[protacc_colnr]]]
pqdata = (pacc_id, prottable_id_map[fn], pquant[colmap[fn]])
to_store.append(pqdata)
if len(to_store) > 10000:
pqdbmethod(to_store)
to_store = []
pqdbmethod(to_store) | python | def store_single_col_data(fns, prottable_id_map, pacc_map, pqdbmethod,
protacc_colnr, colmap):
"""General method to store single column data from protein tables
in lookup"""
to_store = []
for fn, header, pquant in tsvreader.generate_tsv_pep_protein_quants(fns):
pacc_id = pacc_map[pquant[header[protacc_colnr]]]
pqdata = (pacc_id, prottable_id_map[fn], pquant[colmap[fn]])
to_store.append(pqdata)
if len(to_store) > 10000:
pqdbmethod(to_store)
to_store = []
pqdbmethod(to_store) | [
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glormph/msstitch | src/app/actions/mslookup/proteinquant.py | map_psmnrcol_to_quantcol | def map_psmnrcol_to_quantcol(quantcols, psmcols, tablefn_map):
"""This function yields tuples of table filename, isobaric quant column
and if necessary number-of-PSM column"""
if not psmcols:
for fn in quantcols:
for qcol in quantcols[fn]:
yield (tablefn_map[fn], qcol)
else:
for fn in quantcols:
for qcol, psmcol in zip(quantcols[fn], psmcols[fn]):
yield (tablefn_map[fn], qcol, psmcol) | python | def map_psmnrcol_to_quantcol(quantcols, psmcols, tablefn_map):
"""This function yields tuples of table filename, isobaric quant column
and if necessary number-of-PSM column"""
if not psmcols:
for fn in quantcols:
for qcol in quantcols[fn]:
yield (tablefn_map[fn], qcol)
else:
for fn in quantcols:
for qcol, psmcol in zip(quantcols[fn], psmcols[fn]):
yield (tablefn_map[fn], qcol, psmcol) | [
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] | ded7e5cbd813d7797dc9d42805778266e59ff042 | https://github.com/glormph/msstitch/blob/ded7e5cbd813d7797dc9d42805778266e59ff042/src/app/actions/mslookup/proteinquant.py#L122-L132 | train |
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