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calmjs/calmjs | src/calmjs/cli.py | PackageManagerDriver.pkg_manager_install | def pkg_manager_install(
self, package_names=None,
production=None, development=None,
args=(), env={}, **kw):
"""
This will install all dependencies into the current working
directory for the specific Python package from the selected
JavaScript package... | python | def pkg_manager_install(
self, package_names=None,
production=None, development=None,
args=(), env={}, **kw):
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calmjs/calmjs | src/calmjs/cli.py | PackageManagerDriver.run | def run(self, args=(), env={}):
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Returns decoded output of stdout and stderr; decoding determine
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"""
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calmjs/calmjs | src/calmjs/base.py | _get_exec_binary | def _get_exec_binary(binary, kw):
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calmjs/calmjs | src/calmjs/base.py | BaseRegistry._init_entry_points | def _init_entry_points(self, entry_points):
"""
Default initialization loop.
"""
logger.debug(
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try:
... | python | def _init_entry_points(self, entry_points):
"""
Default initialization loop.
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calmjs/calmjs | src/calmjs/base.py | BasePkgRefRegistry.store_records_for_package | def store_records_for_package(self, entry_point, records):
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calmjs/calmjs | src/calmjs/base.py | BaseModuleRegistry.register_entry_point | def register_entry_point(self, entry_point):
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calmjs/calmjs | src/calmjs/base.py | BaseModuleRegistry._register_entry_point_module | def _register_entry_point_module(self, entry_point, module):
"""
Private method that registers an entry_point with a provided
module.
"""
records_map = self._map_entry_point_module(entry_point, module)
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calmjs/calmjs | src/calmjs/base.py | BaseModuleRegistry.get_record | def get_record(self, name):
"""
Get a record by name
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result = {}
result.update(self.records.get(name, {}))
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"""
Get a record by name
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calmjs/calmjs | src/calmjs/base.py | BaseModuleRegistry.get_records_for_package | def get_records_for_package(self, package_name):
"""
Get all records identified by package.
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names = self.package_module_map.get(package_name, [])
result = {}
for name in names:
result.update(self.get_record(name))
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calmjs/calmjs | src/calmjs/base.py | BaseChildModuleRegistry.resolve_parent_registry_name | def resolve_parent_registry_name(self, registry_name, suffix):
"""
Subclasses should override to specify the default suffix, as the
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calmjs/calmjs | src/calmjs/base.py | BaseDriver.which | def which(self):
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Figure out which binary this will execute.
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calmjs/calmjs | src/calmjs/base.py | BaseDriver._set_env_path_with_node_modules | def _set_env_path_with_node_modules(self):
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calmjs/calmjs | src/calmjs/base.py | BaseDriver._exec | def _exec(self, binary, stdin='', args=(), env={}):
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calmjs/calmjs | src/calmjs/base.py | BaseDriver.dump | def dump(self, blob, stream):
"""
Call json.dump with the attributes of this instance as
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"""
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Call json.dump with the attributes of this instance as
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Call json.dumps with the attributes of this instance as
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calmjs/calmjs | src/calmjs/base.py | BaseDriver.join_cwd | def join_cwd(self, path=None):
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Join the path with the current working directory. If it is
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calmjs/calmjs | src/calmjs/base.py | BaseLoaderPluginHandler.modname_source_to_target | def modname_source_to_target(
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... | python | def modname_source_to_target(
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weso/CWR-DataApi | cwr/parser/encoder/cwrjson.py | _unicode_handler | def _unicode_handler(obj):
"""
Transforms an unicode string into a UTF-8 equivalent.
:param obj: object to transform into it's UTF-8 equivalent
:return: the UTF-8 equivalent of the string
"""
try:
result = obj.isoformat()
except AttributeError:
raise TypeError("Unserializabl... | python | def _unicode_handler(obj):
"""
Transforms an unicode string into a UTF-8 equivalent.
:param obj: object to transform into it's UTF-8 equivalent
:return: the UTF-8 equivalent of the string
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try:
result = obj.isoformat()
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weso/CWR-DataApi | cwr/parser/encoder/cwrjson.py | JSONEncoder.encode | def encode(self, entity):
"""
Encodes the data, creating a JSON structure from an instance from the
domain model.
:param entity: the instance to encode
:return: a JSON structure created from the received data
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encoded = self._dict_encoder.encode(entity)
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Encodes the data, creating a JSON structure from an instance from the
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:param entity: the instance to encode
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encoded = self._dict_encoder.encode(entity)
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weso/CWR-DataApi | cwr/grammar/field/special.py | ipi_base_number | def ipi_base_number(name=None):
"""
IPI Base Number field.
An IPI Base Number code written on a field follows the Pattern
C-NNNNNNNNN-M. This being:
- C: header, a character.
- N: numeric value.
- M: control digit.
So, for example, an IPI Base Number code field can contain I-000000229-... | python | def ipi_base_number(name=None):
"""
IPI Base Number field.
An IPI Base Number code written on a field follows the Pattern
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- C: header, a character.
- N: numeric value.
- M: control digit.
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weso/CWR-DataApi | cwr/grammar/field/special.py | ipi_name_number | def ipi_name_number(name=None):
"""
IPI Name Number field.
An IPI Name Number is composed of eleven digits.
So, for example, an IPI Name Number code field can contain 00014107338.
:param name: name for the field
:return: a parser for the IPI Name Number field
"""
if name is None:
... | python | def ipi_name_number(name=None):
"""
IPI Name Number field.
An IPI Name Number is composed of eleven digits.
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:param name: name for the field
:return: a parser for the IPI Name Number field
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weso/CWR-DataApi | cwr/grammar/field/special.py | iswc | def iswc(name=None):
"""
ISWC field.
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- T: header, it is always T.
- N: numeric value.
- C: control digit.
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:param name: name for the field
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"""
ISWC field.
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- T: header, it is always T.
- N: numeric value.
- C: control digit.
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weso/CWR-DataApi | cwr/grammar/field/special.py | percentage | def percentage(columns, maximum=100, name=None):
"""
Creates the grammar for a Numeric (N) field storing a percentage and
accepting only the specified number of characters.
It is possible to set the maximum allowed value. By default this is 100
(for 100%), and if modified it is expected to be reduc... | python | def percentage(columns, maximum=100, name=None):
"""
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weso/CWR-DataApi | cwr/grammar/field/special.py | _assert_is_percentage | def _assert_is_percentage(value, maximum=100):
"""
Makes sure the received value is a percentage. Otherwise an exception is
thrown.
:param value: the value to check
"""
if value < 0 or value > maximum:
message = 'The value on a percentage field should be between 0 and %s' \
... | python | def _assert_is_percentage(value, maximum=100):
"""
Makes sure the received value is a percentage. Otherwise an exception is
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"""
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weso/CWR-DataApi | cwr/grammar/field/special.py | ean_13 | def ean_13(name=None):
"""
Creates the grammar for an EAN 13 code.
These are the codes on thirteen digits barcodes.
:param name: name for the field
:return: grammar for an EAN 13 field
"""
if name is None:
name = 'EAN 13 Field'
field = basic.numeric(13)
field = field.set... | python | def ean_13(name=None):
"""
Creates the grammar for an EAN 13 code.
These are the codes on thirteen digits barcodes.
:param name: name for the field
:return: grammar for an EAN 13 field
"""
if name is None:
name = 'EAN 13 Field'
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weso/CWR-DataApi | cwr/grammar/field/special.py | isrc | def isrc(name=None):
"""
Creates the grammar for an ISRC code.
ISRC stands for International Standard Recording Code, which is the
standard ISO 3901. This stores information identifying a particular
recording.
:param name: name for the field
:return: grammar for an ISRC field
"""
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"""
Creates the grammar for an ISRC code.
ISRC stands for International Standard Recording Code, which is the
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recording.
:param name: name for the field
:return: grammar for an ISRC field
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weso/CWR-DataApi | cwr/grammar/field/special.py | _isrc_long | def _isrc_long(name=None):
"""
Creates the grammar for a short ISRC code.
ISRC stands for International Standard Recording Code, which is the
standard ISO 3901. This stores information identifying a particular
recording.
This variant contain no separator for the parts, and follows the pattern:... | python | def _isrc_long(name=None):
"""
Creates the grammar for a short ISRC code.
ISRC stands for International Standard Recording Code, which is the
standard ISO 3901. This stores information identifying a particular
recording.
This variant contain no separator for the parts, and follows the pattern:... | [
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weso/CWR-DataApi | cwr/grammar/field/special.py | visan | def visan(name=None):
"""
Creates the grammar for a V-ISAN code.
This is a variation on the ISAN (International Standard Audiovisual Number)
:param name: name for the field
:return: grammar for an ISRC field
"""
if name is None:
name = 'V-ISAN Field'
field = pp.Regex('[0-9]{2... | python | def visan(name=None):
"""
Creates the grammar for a V-ISAN code.
This is a variation on the ISAN (International Standard Audiovisual Number)
:param name: name for the field
:return: grammar for an ISRC field
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weso/CWR-DataApi | cwr/grammar/field/special.py | audio_visual_key | def audio_visual_key(name=None):
"""
Creates the grammar for an Audio Visual Key code.
This is a variation on the ISAN (International Standard Audiovisual Number)
:param name: name for the field
:return: grammar for an ISRC field
"""
if name is None:
name = 'AVI Field'
societ... | python | def audio_visual_key(name=None):
"""
Creates the grammar for an Audio Visual Key code.
This is a variation on the ISAN (International Standard Audiovisual Number)
:param name: name for the field
:return: grammar for an ISRC field
"""
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name = 'AVI Field'
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weso/CWR-DataApi | cwr/grammar/field/special.py | date_time | def date_time(name=None):
"""
Creates the grammar for a date and time field, which is a combination of
the Date (D) and Time or Duration field (T).
This field requires first a Date, and then a Time, without any space in
between.
:param name: name for the field
:return: grammar for a Date a... | python | def date_time(name=None):
"""
Creates the grammar for a date and time field, which is a combination of
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This field requires first a Date, and then a Time, without any space in
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:param name: name for the field
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weso/CWR-DataApi | cwr/grammar/field/special.py | lookup_int | def lookup_int(values, name=None):
"""
Lookup field which transforms the result into an integer.
:param values: values allowed
:param name: name for the field
:return: grammar for the lookup field
"""
field = basic.lookup(values, name)
field.addParseAction(lambda l: int(l[0]))
ret... | python | def lookup_int(values, name=None):
"""
Lookup field which transforms the result into an integer.
:param values: values allowed
:param name: name for the field
:return: grammar for the lookup field
"""
field = basic.lookup(values, name)
field.addParseAction(lambda l: int(l[0]))
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calmjs/calmjs | src/calmjs/interrogate.py | extract_function_argument | def extract_function_argument(text, f_name, f_argn, f_argt=asttypes.String):
"""
Extract a specific argument from a specific function name.
Arguments:
text
The source text.
f_name
The name of the function
f_argn
The argument position
f_argt
The argument type... | python | def extract_function_argument(text, f_name, f_argn, f_argt=asttypes.String):
"""
Extract a specific argument from a specific function name.
Arguments:
text
The source text.
f_name
The name of the function
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calmjs/calmjs | src/calmjs/interrogate.py | yield_amd_require_string_arguments | def yield_amd_require_string_arguments(
node, pos,
reserved_module=reserved_module, wrapped=define_wrapped):
"""
This yields only strings within the lists provided in the argument
list at the specified position from a function call.
Originally, this was implemented for yield a list of m... | python | def yield_amd_require_string_arguments(
node, pos,
reserved_module=reserved_module, wrapped=define_wrapped):
"""
This yields only strings within the lists provided in the argument
list at the specified position from a function call.
Originally, this was implemented for yield a list of m... | [
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calmjs/calmjs | src/calmjs/interrogate.py | yield_string_argument | def yield_string_argument(node, pos):
"""
Yield just a string argument from position of the function call.
"""
if not isinstance(node.args.items[pos], asttypes.String):
return
yield to_str(node.args.items[pos]) | python | def yield_string_argument(node, pos):
"""
Yield just a string argument from position of the function call.
"""
if not isinstance(node.args.items[pos], asttypes.String):
return
yield to_str(node.args.items[pos]) | [
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calmjs/calmjs | src/calmjs/interrogate.py | yield_module_imports | def yield_module_imports(root, checks=string_imports()):
"""
Gather all require and define calls from unbundled JavaScript source
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"""
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Gather all require and define calls from unbundled JavaScript source
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"""
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calmjs/calmjs | src/calmjs/interrogate.py | yield_module_imports_nodes | def yield_module_imports_nodes(root, checks=import_nodes()):
"""
Yield all nodes that provide an import
"""
if not isinstance(root, asttypes.Node):
raise TypeError('provided root must be a node')
for child in yield_function(root, deep_filter):
for f, condition in checks:
... | python | def yield_module_imports_nodes(root, checks=import_nodes()):
"""
Yield all nodes that provide an import
"""
if not isinstance(root, asttypes.Node):
raise TypeError('provided root must be a node')
for child in yield_function(root, deep_filter):
for f, condition in checks:
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pandeylab/pythomics | pythomics/parsers/fasta.py | FastaIterator.open_fasta_index | def open_fasta_index(self):
"""
custom type for file made w/ buildFastaIndex, fai for ones made with samtools
"""
index = self.fasta_index
try:
handle = open(index, 'rb')
except (IOError, TypeError):
sys.stderr.write('index not found, creating it\n... | python | def open_fasta_index(self):
"""
custom type for file made w/ buildFastaIndex, fai for ones made with samtools
"""
index = self.fasta_index
try:
handle = open(index, 'rb')
except (IOError, TypeError):
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pandeylab/pythomics | pythomics/parsers/fasta.py | FastaIterator.get_sequence | def get_sequence(self, chrom, start, end, strand='+', indexing=(-1, 0)):
"""
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"""
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calmjs/calmjs | src/calmjs/module.py | resolve_child_module_registries_lineage | def resolve_child_module_registries_lineage(registry):
"""
For a given child module registry, attempt to resolve the lineage.
Return an iterator, yielding from parent down to the input registry,
inclusive of the input registry.
"""
children = [registry]
while isinstance(registry, BaseChild... | python | def resolve_child_module_registries_lineage(registry):
"""
For a given child module registry, attempt to resolve the lineage.
Return an iterator, yielding from parent down to the input registry,
inclusive of the input registry.
"""
children = [registry]
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pandeylab/pythomics | pythomics/proteomics/structures.py | PeptideObject.addModification | def addModification(self, aa,position, modMass, modType):
"""
!!!!MODIFICATION POSITION IS 0 BASED!!!!!!
Modifications are stored internally as a tuple with this format:
(amino acid modified, index in peptide of amino acid, modification type, modification mass)
ie (M, 7, Oxidatio... | python | def addModification(self, aa,position, modMass, modType):
"""
!!!!MODIFICATION POSITION IS 0 BASED!!!!!!
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calmjs/calmjs | src/calmjs/indexer.py | resource_filename_mod_dist | def resource_filename_mod_dist(module_name, dist):
"""
Given a module name and a distribution, attempt to resolve the
actual path to the module.
"""
try:
return pkg_resources.resource_filename(
dist.as_requirement(), join(*module_name.split('.')))
except pkg_resources.Distri... | python | def resource_filename_mod_dist(module_name, dist):
"""
Given a module name and a distribution, attempt to resolve the
actual path to the module.
"""
try:
return pkg_resources.resource_filename(
dist.as_requirement(), join(*module_name.split('.')))
except pkg_resources.Distri... | [
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calmjs/calmjs | src/calmjs/indexer.py | resource_filename_mod_entry_point | def resource_filename_mod_entry_point(module_name, entry_point):
"""
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calmjs/calmjs | src/calmjs/indexer.py | modgen | def modgen(
module, entry_point,
modpath='pkg_resources', globber='root', fext=JS_EXT,
registry=_utils):
"""
JavaScript styled module location listing generator.
Arguments:
module
The Python module to start fetching from.
entry_point
This is the original en... | python | def modgen(
module, entry_point,
modpath='pkg_resources', globber='root', fext=JS_EXT,
registry=_utils):
"""
JavaScript styled module location listing generator.
Arguments:
module
The Python module to start fetching from.
entry_point
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calmjs/calmjs | src/calmjs/indexer.py | register | def register(util_type, registry=_utils):
"""
Crude, local registration decorator for a crude local registry of
all utilities local to this module.
"""
def marker(f):
mark = util_type + '_'
if not f.__name__.startswith(mark):
raise TypeError(
'not registe... | python | def register(util_type, registry=_utils):
"""
Crude, local registration decorator for a crude local registry of
all utilities local to this module.
"""
def marker(f):
mark = util_type + '_'
if not f.__name__.startswith(mark):
raise TypeError(
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calmjs/calmjs | src/calmjs/indexer.py | modpath_all | def modpath_all(module, entry_point):
"""
Provides the raw __path__. Incompatible with PEP 302-based import
hooks and incompatible with zip_safe packages.
Deprecated. Will be removed by calmjs-4.0.
"""
module_paths = getattr(module, '__path__', [])
if not module_paths:
logger.war... | python | def modpath_all(module, entry_point):
"""
Provides the raw __path__. Incompatible with PEP 302-based import
hooks and incompatible with zip_safe packages.
Deprecated. Will be removed by calmjs-4.0.
"""
module_paths = getattr(module, '__path__', [])
if not module_paths:
logger.war... | [
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calmjs/calmjs | src/calmjs/indexer.py | modpath_last | def modpath_last(module, entry_point):
"""
Provides the raw __path__. Incompatible with PEP 302-based import
hooks and incompatible with zip_safe packages.
Deprecated. Will be removed by calmjs-4.0.
"""
module_paths = modpath_all(module, entry_point)
if len(module_paths) > 1:
log... | python | def modpath_last(module, entry_point):
"""
Provides the raw __path__. Incompatible with PEP 302-based import
hooks and incompatible with zip_safe packages.
Deprecated. Will be removed by calmjs-4.0.
"""
module_paths = modpath_all(module, entry_point)
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log... | [
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calmjs/calmjs | src/calmjs/indexer.py | modpath_pkg_resources | def modpath_pkg_resources(module, entry_point):
"""
Goes through pkg_resources for compliance with various PEPs.
This one accepts a module as argument.
"""
result = []
try:
path = resource_filename_mod_entry_point(module.__name__, entry_point)
except ImportError:
logger.war... | python | def modpath_pkg_resources(module, entry_point):
"""
Goes through pkg_resources for compliance with various PEPs.
This one accepts a module as argument.
"""
result = []
try:
path = resource_filename_mod_entry_point(module.__name__, entry_point)
except ImportError:
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calmjs/calmjs | src/calmjs/indexer.py | mapper | def mapper(module, entry_point,
modpath='pkg_resources', globber='root', modname='es6',
fext=JS_EXT, registry=_utils):
"""
General mapper
Loads components from the micro registry.
"""
modname_f = modname if callable(modname) else _utils['modname'][modname]
return {
... | python | def mapper(module, entry_point,
modpath='pkg_resources', globber='root', modname='es6',
fext=JS_EXT, registry=_utils):
"""
General mapper
Loads components from the micro registry.
"""
modname_f = modname if callable(modname) else _utils['modname'][modname]
return {
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calmjs/calmjs | src/calmjs/indexer.py | mapper_python | def mapper_python(module, entry_point, globber='root', fext=JS_EXT):
"""
Default mapper using python style globber
Finds the latest path declared for the module at hand and extract
a list of importable JS modules using the es6 module import format.
"""
return mapper(
module, entry_poin... | python | def mapper_python(module, entry_point, globber='root', fext=JS_EXT):
"""
Default mapper using python style globber
Finds the latest path declared for the module at hand and extract
a list of importable JS modules using the es6 module import format.
"""
return mapper(
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weso/CWR-DataApi | cwr/other.py | _ThreePartsCode._printable_id_code | def _printable_id_code(self):
"""
Returns the code in a printable form, filling with zeros if needed.
:return: the ID code in a printable form
"""
code = str(self.id_code)
while len(code) < self._code_size:
code = '0' + code
return code | python | def _printable_id_code(self):
"""
Returns the code in a printable form, filling with zeros if needed.
:return: the ID code in a printable form
"""
code = str(self.id_code)
while len(code) < self._code_size:
code = '0' + code
return code | [
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weso/CWR-DataApi | cwr/other.py | ISWCCode._printable_id_code | def _printable_id_code(self):
"""
Returns the code in a printable form, separating it into groups of
three characters using a point between them.
:return: the ID code in a printable form
"""
code = super(ISWCCode, self)._printable_id_code()
code1 = code[:3]
... | python | def _printable_id_code(self):
"""
Returns the code in a printable form, separating it into groups of
three characters using a point between them.
:return: the ID code in a printable form
"""
code = super(ISWCCode, self)._printable_id_code()
code1 = code[:3]
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calmjs/calmjs | src/calmjs/vlqsm.py | SourceWriter.write | def write(self, s):
"""
Standard write, for standard sources part of the original file.
"""
lines = s.splitlines(True)
for line in lines:
self.current_mapping.append(
(self.generated_col, self.index, self.row, self.col_last))
self.stream.w... | python | def write(self, s):
"""
Standard write, for standard sources part of the original file.
"""
lines = s.splitlines(True)
for line in lines:
self.current_mapping.append(
(self.generated_col, self.index, self.row, self.col_last))
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calmjs/calmjs | src/calmjs/vlqsm.py | SourceWriter.discard | def discard(self, s):
"""
Discard from original file.
"""
lines = s.splitlines(True)
for line in lines:
if line[-1] not in '\r\n':
if not self.warn:
logger.warning(
'partial line discard UNSUPPORTED; source ... | python | def discard(self, s):
"""
Discard from original file.
"""
lines = s.splitlines(True)
for line in lines:
if line[-1] not in '\r\n':
if not self.warn:
logger.warning(
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calmjs/calmjs | src/calmjs/vlqsm.py | SourceWriter.write_padding | def write_padding(self, s):
"""
Write string that are not part of the original file.
"""
lines = s.splitlines(True)
for line in lines:
self.stream.write(line)
if line[-1] in '\r\n':
self._newline()
else:
# this ... | python | def write_padding(self, s):
"""
Write string that are not part of the original file.
"""
lines = s.splitlines(True)
for line in lines:
self.stream.write(line)
if line[-1] in '\r\n':
self._newline()
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Suor/django-easymoney | easymoney.py | format_currency | def format_currency(number, currency, format, locale=babel.numbers.LC_NUMERIC,
force_frac=None, format_type='standard'):
"""Same as ``babel.numbers.format_currency``, but has ``force_frac``
argument instead of ``currency_digits``.
If the ``force_frac`` argument is given, the argument is... | python | def format_currency(number, currency, format, locale=babel.numbers.LC_NUMERIC,
force_frac=None, format_type='standard'):
"""Same as ``babel.numbers.format_currency``, but has ``force_frac``
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cihai/cihai | examples/variants.py | run | def run(unihan_options={}):
"""Wrapped so we can test in tests/test_examples.py"""
print("This example prints variant character data.")
c = Cihai()
if not c.unihan.is_bootstrapped: # download and install Unihan to db
c.unihan.bootstrap(unihan_options)
c.unihan.add_plugin(
'cihai.d... | python | def run(unihan_options={}):
"""Wrapped so we can test in tests/test_examples.py"""
print("This example prints variant character data.")
c = Cihai()
if not c.unihan.is_bootstrapped: # download and install Unihan to db
c.unihan.bootstrap(unihan_options)
c.unihan.add_plugin(
'cihai.d... | [
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cihai/cihai | cihai/db.py | Database.reflect_db | def reflect_db(self):
"""
No-op to reflect db info.
This is available as a method so the database can be reflected
outside initialization (such bootstrapping unihan during CLI usage).
"""
self.metadata.reflect(views=True, extend_existing=True)
self.base = automap... | python | def reflect_db(self):
"""
No-op to reflect db info.
This is available as a method so the database can be reflected
outside initialization (such bootstrapping unihan during CLI usage).
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favalex/python-asciimathml | asciimathml.py | parse | def parse(s, element=Element, atomicstring=lambda s: s):
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favalex/python-asciimathml | asciimathml.py | trace_parser | def trace_parser(p):
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Decorator for tracing the parser.
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baccuslab/shannon | shannon/bottleneck.py | remove_symbol_from_dist | def remove_symbol_from_dist(dist, index):
'''
prob is a ndarray representing a probability distribution.
index is a number between 0 and and the number of symbols ( len(prob)-1 )
return the probability distribution if the element at 'index' was no longer available
'''
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'''
prob is a ndarray representing a probability distribution.
index is a number between 0 and and the number of symbols ( len(prob)-1 )
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N = (x==index).sum()
#x[x==index]=9
x[x==index] = dist.sample(N) | python | def change_response(x, prob, index):
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change every response in x that matches 'index' by randomly sampling from prob
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baccuslab/shannon | shannon/bottleneck.py | toy_example | def toy_example():
"""
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x=1 -> y=1 + e
x=2 -> y=2 + 2*e
...
x=n -> y=n + n*e
where by n*e I am saying that the noise grows
"""
#pdb.set_trace()
N=4
... | python | def toy_example():
"""
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x=0 -> y=0
x=1 -> y=1 + e
x=2 -> y=2 + 2*e
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baccuslab/shannon | shannon/bottleneck.py | differentiate_mi | def differentiate_mi(x, y):
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for each symbol in x, change x such that there are no more of such symbols
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'''
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cihai/cihai | cihai/log.py | default_log_template | def default_log_template(self, record):
"""Return the prefix for the log message. Template for Formatter.
:param: record: :py:class:`logging.LogRecord` object. this is passed in
from inside the :py:meth:`logging.Formatter.format` record.
"""
reset = Style.RESET_ALL
levelname = [
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"""Return the prefix for the log message. Template for Formatter.
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cihai/cihai | cihai/utils.py | merge_dict | def merge_dict(base, additional):
"""
Combine two dictionary-like objects.
Notes
-----
Code from https://github.com/pypa/warehouse
Copyright 2013 Donald Stufft
Licensed under the Apache License, Version 2.0 (the "License");
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"""
Combine two dictionary-like objects.
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cihai/cihai | cihai/config.py | expand_config | def expand_config(d, dirs):
"""
Expand configuration XDG variables, environmental variables, and tildes.
Parameters
----------
d : dict
config information
dirs : appdirs.AppDirs
XDG application mapping
Notes
-----
*Environmentable variables* are expanded via :py:fun... | python | def expand_config(d, dirs):
"""
Expand configuration XDG variables, environmental variables, and tildes.
Parameters
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config information
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XDG application mapping
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cihai/cihai | cihai/data/unihan/bootstrap.py | bootstrap_unihan | def bootstrap_unihan(metadata, options={}):
"""Download, extract and import unihan to database."""
options = merge_dict(UNIHAN_ETL_DEFAULT_OPTIONS.copy(), options)
p = unihan.Packager(options)
p.download()
data = p.export()
table = create_unihan_table(UNIHAN_FIELDS, metadata)
metadata.creat... | python | def bootstrap_unihan(metadata, options={}):
"""Download, extract and import unihan to database."""
options = merge_dict(UNIHAN_ETL_DEFAULT_OPTIONS.copy(), options)
p = unihan.Packager(options)
p.download()
data = p.export()
table = create_unihan_table(UNIHAN_FIELDS, metadata)
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cihai/cihai | cihai/data/unihan/bootstrap.py | is_bootstrapped | def is_bootstrapped(metadata):
"""Return True if cihai is correctly bootstrapped."""
fields = UNIHAN_FIELDS + DEFAULT_COLUMNS
if TABLE_NAME in metadata.tables.keys():
table = metadata.tables[TABLE_NAME]
if set(fields) == set(c.name for c in table.columns):
return True
el... | python | def is_bootstrapped(metadata):
"""Return True if cihai is correctly bootstrapped."""
fields = UNIHAN_FIELDS + DEFAULT_COLUMNS
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table = metadata.tables[TABLE_NAME]
if set(fields) == set(c.name for c in table.columns):
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cihai/cihai | cihai/data/unihan/bootstrap.py | create_unihan_table | def create_unihan_table(columns, metadata):
"""Create table and return :class:`sqlalchemy.Table`.
Parameters
----------
columns : list
columns for table, e.g. ``['kDefinition', 'kCantonese']``
metadata : :class:`sqlalchemy.schema.MetaData`
Instance of sqlalchemy metadata
Retur... | python | def create_unihan_table(columns, metadata):
"""Create table and return :class:`sqlalchemy.Table`.
Parameters
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columns for table, e.g. ``['kDefinition', 'kCantonese']``
metadata : :class:`sqlalchemy.schema.MetaData`
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namuyan/nem-ed25519 | nem_ed25519/key.py | get_address | def get_address(pk, main_net=True, prefix=None):
""" compute the nem-py address from the public one """
if isinstance(pk, str):
pk = unhexlify(pk.encode())
assert len(pk) == 32, 'PK is 32bytes {}'.format(len(pk))
k = keccak_256(pk).digest()
ripe = RIPEMD160.new(k).digest()
if prefix is N... | python | def get_address(pk, main_net=True, prefix=None):
""" compute the nem-py address from the public one """
if isinstance(pk, str):
pk = unhexlify(pk.encode())
assert len(pk) == 32, 'PK is 32bytes {}'.format(len(pk))
k = keccak_256(pk).digest()
ripe = RIPEMD160.new(k).digest()
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cihai/cihai | cihai/data/unihan/dataset.py | Unihan.lookup_char | def lookup_char(self, char):
"""Return character information from datasets.
Parameters
----------
char : str
character / string to lookup
Returns
-------
:class:`sqlalchemy.orm.query.Query` :
list of matches
"""
Unihan = s... | python | def lookup_char(self, char):
"""Return character information from datasets.
Parameters
----------
char : str
character / string to lookup
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:class:`sqlalchemy.orm.query.Query` :
list of matches
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cihai/cihai | cihai/data/unihan/dataset.py | Unihan.reverse_char | def reverse_char(self, hints):
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strings to lookup
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:class:`sqlalchemy.orm.query.Query` :
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cihai/cihai | cihai/data/unihan/dataset.py | Unihan.with_fields | def with_fields(self, *fields):
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-------
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"""Returns list of characters with information for certain fields.
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fields for which information should be available
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baccuslab/shannon | shannon/continuous.py | entropy | def entropy(data=None, prob=None, method='nearest-neighbors', bins=None, errorVal=1e-5, units='bits'):
'''
given a probability distribution (prob) or an interable of symbols (data) compute and
return its continuous entropy.
inputs:
------
data: samples by dimensions ndarray
p... | python | def entropy(data=None, prob=None, method='nearest-neighbors', bins=None, errorVal=1e-5, units='bits'):
'''
given a probability distribution (prob) or an interable of symbols (data) compute and
return its continuous entropy.
inputs:
------
data: samples by dimensions ndarray
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baccuslab/shannon | shannon/continuous.py | mi | def mi(x, y, bins_x=None, bins_y=None, bins_xy=None, method='nearest-neighbors', units='bits'):
'''
compute and return the mutual information between x and y
inputs:
-------
x, y: numpy arrays of shape samples x dimension
method: 'nearest-neighbors', 'gaussian', or 'bin'
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'''
compute and return the mutual information between x and y
inputs:
-------
x, y: numpy arrays of shape samples x dimension
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baccuslab/shannon | shannon/continuous.py | cond_entropy | def cond_entropy(x, y, bins_y=None, bins_xy=None, method='nearest-neighbors', units='bits'):
'''
compute the conditional entropy H(X|Y).
method: 'nearest-neighbors', 'gaussian', or 'bin'
if 'bin' need to provide bins_y, and bins_xy
units: 'bits' or 'nats'
'''
HXY = entr... | python | def cond_entropy(x, y, bins_y=None, bins_xy=None, method='nearest-neighbors', units='bits'):
'''
compute the conditional entropy H(X|Y).
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baccuslab/shannon | shannon/discrete.py | entropy | def entropy(data=None, prob=None, tol=1e-5):
'''
given a probability distribution (prob) or an interable of symbols (data) compute and
return its entropy
inputs:
------
data: iterable of symbols
prob: iterable with probabilities
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'''
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baccuslab/shannon | shannon/discrete.py | symbols_to_prob | def symbols_to_prob(symbols):
'''
Return a dict mapping symbols to probability.
input:
-----
symbols: iterable of hashable items
works well if symbols is a zip of iterables
'''
myCounter = Counter(symbols)
N = float(len(list(symbols))) # symbols might be... | python | def symbols_to_prob(symbols):
'''
Return a dict mapping symbols to probability.
input:
-----
symbols: iterable of hashable items
works well if symbols is a zip of iterables
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baccuslab/shannon | shannon/discrete.py | combine_symbols | def combine_symbols(*args):
'''
Combine different symbols into a 'super'-symbol
args can be an iterable of iterables that support hashing
see example for 2D ndarray input
usage:
1) combine two symbols, each a number into just one symbol
x = numpy.random.randint(0,4,1000)
y... | python | def combine_symbols(*args):
'''
Combine different symbols into a 'super'-symbol
args can be an iterable of iterables that support hashing
see example for 2D ndarray input
usage:
1) combine two symbols, each a number into just one symbol
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baccuslab/shannon | shannon/discrete.py | mi | def mi(x, y):
'''
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inputs:
-------
x, y: iterables of hashable items
output:
-------
mi: float
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------
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... | python | def mi(x, y):
'''
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inputs:
-------
x, y: iterables of hashable items
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mi: float
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baccuslab/shannon | shannon/discrete.py | cond_mi | def cond_mi(x, y, z):
'''
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inputs:
-------
x, y, z: iterables with discrete symbols
output:
-------
mi: float
implementation notes:
---------------------
I(x, y | z) = H(x | z) ... | python | def cond_mi(x, y, z):
'''
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mi: float
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---------------------
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baccuslab/shannon | shannon/discrete.py | mi_chain_rule | def mi_chain_rule(X, y):
'''
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Inputs:
-------
X: iterable of iterables. You should be able to compute [mi(x, y) for x in X]
y: iterable of symbols
... | python | def mi_chain_rule(X, y):
'''
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-------
X: iterable of iterables. You should be able to compute [mi(x, y) for x in X]
y: iterable of symbols
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baccuslab/shannon | shannon/discrete.py | KL_divergence | def KL_divergence(P,Q):
'''
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P and Q should be dictionaries linking symbols to probabilities.
the keys to P and Q should be the same.
'''
assert(P.keys()==Q.keys())
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for k in P.keys():
distance += P[k] *... | python | def KL_divergence(P,Q):
'''
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P and Q should be dictionaries linking symbols to probabilities.
the keys to P and Q should be the same.
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baccuslab/shannon | shannon/discrete.py | bin | def bin(x, bins, maxX=None, minX=None):
'''
bin signal x using 'binsN' bin. If minX, maxX are None, they default to the full
range of the signal. If they are not None, everything above maxX gets assigned to
binsN-1 and everything below minX gets assigned to 0, this is effectively the same
as clippin... | python | def bin(x, bins, maxX=None, minX=None):
'''
bin signal x using 'binsN' bin. If minX, maxX are None, they default to the full
range of the signal. If they are not None, everything above maxX gets assigned to
binsN-1 and everything below minX gets assigned to 0, this is effectively the same
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cihai/cihai | doc/conf.py | linkcode_resolve | def linkcode_resolve(domain, info): # NOQA: C901
"""
Determine the URL corresponding to Python object
Notes
-----
From https://github.com/numpy/numpy/blob/v1.15.1/doc/source/conf.py, 7c49cfa
on Jul 31. License BSD-3. https://github.com/numpy/numpy/blob/v1.15.1/LICENSE.txt
"""
if domain... | python | def linkcode_resolve(domain, info): # NOQA: C901
"""
Determine the URL corresponding to Python object
Notes
-----
From https://github.com/numpy/numpy/blob/v1.15.1/doc/source/conf.py, 7c49cfa
on Jul 31. License BSD-3. https://github.com/numpy/numpy/blob/v1.15.1/LICENSE.txt
"""
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namuyan/nem-ed25519 | nem_ed25519/utils.py | inv | def inv(z):
"""$= z^{-1} \mod q$, for z != 0"""
# Adapted from curve25519_athlon.c in djb's Curve25519.
z = qdiv(z)
z2 = z * z % PRIME # 2
z9 = pow2(z2, 2) * z % PRIME # 9
z11 = z9 * z2 % PRIME # 11
z2_5_0 = (z11*z11) % PRIME * z9 % PRIME # 31 == 2^5 - 2^0
z2_10_0 = pow2(z2_5_0, 5) *... | python | def inv(z):
"""$= z^{-1} \mod q$, for z != 0"""
# Adapted from curve25519_athlon.c in djb's Curve25519.
z = qdiv(z)
z2 = z * z % PRIME # 2
z9 = pow2(z2, 2) * z % PRIME # 9
z11 = z9 * z2 % PRIME # 11
z2_5_0 = (z11*z11) % PRIME * z9 % PRIME # 31 == 2^5 - 2^0
z2_10_0 = pow2(z2_5_0, 5) *... | [
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namuyan/nem-ed25519 | nem_ed25519/utils.py | scalarmult_B | def scalarmult_B(e):
"""
Implements scalarmult(B, e) more efficiently.
"""
# scalarmult(B, l) is the identity
e %= L
P = IDENT
for i in range(253):
if e & 1:
P = edwards_add(P=P, Q=Bpow[i])
e //= 2
assert e == 0, e
return P | python | def scalarmult_B(e):
"""
Implements scalarmult(B, e) more efficiently.
"""
# scalarmult(B, l) is the identity
e %= L
P = IDENT
for i in range(253):
if e & 1:
P = edwards_add(P=P, Q=Bpow[i])
e //= 2
assert e == 0, e
return P | [
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namuyan/nem-ed25519 | nem_ed25519/utils.py | recover | def recover(y):
""" given a value y, recover the preimage x """
p = (y*y - 1) * inverse(D*y*y + 1)
x = powmod(p, (PRIME+3) // 8, PRIME)
if (x*x - p) % PRIME != 0:
i = powmod(2, (PRIME-1) // 4, PRIME)
x = (x*i) % PRIME
if x % 2 != 0:
x = PRIME - x
return x | python | def recover(y):
""" given a value y, recover the preimage x """
p = (y*y - 1) * inverse(D*y*y + 1)
x = powmod(p, (PRIME+3) // 8, PRIME)
if (x*x - p) % PRIME != 0:
i = powmod(2, (PRIME-1) // 4, PRIME)
x = (x*i) % PRIME
if x % 2 != 0:
x = PRIME - x
return x | [
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bmcfee/pyrubberband | pyrubberband/pyrb.py | __rubberband | def __rubberband(y, sr, **kwargs):
'''Execute rubberband
Parameters
----------
y : np.ndarray [shape=(n,) or (n, c)]
Audio time series, either single or multichannel
sr : int > 0
sampling rate of y
**kwargs
keyword arguments to rubberband
Returns
-------
y... | python | def __rubberband(y, sr, **kwargs):
'''Execute rubberband
Parameters
----------
y : np.ndarray [shape=(n,) or (n, c)]
Audio time series, either single or multichannel
sr : int > 0
sampling rate of y
**kwargs
keyword arguments to rubberband
Returns
-------
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Audio time series, either single or multichannel
sr : int > 0
sampling rate of y
**kwargs
keyword arguments to rubberband
Returns
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y_mod : np.ndarray [shape=(n,) or (n, c)]
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bmcfee/pyrubberband | pyrubberband/pyrb.py | time_stretch | def time_stretch(y, sr, rate, rbargs=None):
'''Apply a time stretch of `rate` to an audio time series.
This uses the `tempo` form for rubberband, so the
higher the rate, the faster the playback.
Parameters
----------
y : np.ndarray [shape=(n,) or (n, c)]
Audio time series, either sing... | python | def time_stretch(y, sr, rate, rbargs=None):
'''Apply a time stretch of `rate` to an audio time series.
This uses the `tempo` form for rubberband, so the
higher the rate, the faster the playback.
Parameters
----------
y : np.ndarray [shape=(n,) or (n, c)]
Audio time series, either sing... | [
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bmcfee/pyrubberband | pyrubberband/pyrb.py | timemap_stretch | def timemap_stretch(y, sr, time_map, rbargs=None):
'''Apply a timemap stretch to an audio time series.
A timemap stretch allows non-linear time-stretching by mapping source to
target sample frame numbers for fixed time points within the audio data.
This uses the `time` and `timemap` form for rubberban... | python | def timemap_stretch(y, sr, time_map, rbargs=None):
'''Apply a timemap stretch to an audio time series.
A timemap stretch allows non-linear time-stretching by mapping source to
target sample frame numbers for fixed time points within the audio data.
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bmcfee/pyrubberband | pyrubberband/pyrb.py | pitch_shift | def pitch_shift(y, sr, n_steps, rbargs=None):
'''Apply a pitch shift to an audio time series.
Parameters
----------
y : np.ndarray [shape=(n,) or (n, c)]
Audio time series, either single or multichannel
sr : int > 0
Sampling rate of `y`
n_steps : float
Shift by `n_step... | python | def pitch_shift(y, sr, n_steps, rbargs=None):
'''Apply a pitch shift to an audio time series.
Parameters
----------
y : np.ndarray [shape=(n,) or (n, c)]
Audio time series, either single or multichannel
sr : int > 0
Sampling rate of `y`
n_steps : float
Shift by `n_step... | [
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Audio time series, either single or multichannel
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n_steps : float
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cihai/cihai | cihai/conversion.py | kuten_to_gb2312 | def kuten_to_gb2312(kuten):
"""
Convert GB kuten / quwei form (94 zones * 94 points) to GB2312-1980 /
ISO-2022-CN hex (internal representation)
"""
zone, point = int(kuten[:2]), int(kuten[2:])
hi, lo = hexd(zone + 0x20), hexd(point + 0x20)
gb2312 = "%s%s" % (hi, lo)
assert isinstance(g... | python | def kuten_to_gb2312(kuten):
"""
Convert GB kuten / quwei form (94 zones * 94 points) to GB2312-1980 /
ISO-2022-CN hex (internal representation)
"""
zone, point = int(kuten[:2]), int(kuten[2:])
hi, lo = hexd(zone + 0x20), hexd(point + 0x20)
gb2312 = "%s%s" % (hi, lo)
assert isinstance(g... | [
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cihai/cihai | cihai/conversion.py | gb2312_to_euc | def gb2312_to_euc(gb2312hex):
"""
Convert GB2312-1980 hex (internal representation) to EUC-CN hex (the
"external encoding")
"""
hi, lo = int(gb2312hex[:2], 16), int(gb2312hex[2:], 16)
hi, lo = hexd(hi + 0x80), hexd(lo + 0x80)
euc = "%s%s" % (hi, lo)
assert isinstance(euc, bytes)
ret... | python | def gb2312_to_euc(gb2312hex):
"""
Convert GB2312-1980 hex (internal representation) to EUC-CN hex (the
"external encoding")
"""
hi, lo = int(gb2312hex[:2], 16), int(gb2312hex[2:], 16)
hi, lo = hexd(hi + 0x80), hexd(lo + 0x80)
euc = "%s%s" % (hi, lo)
assert isinstance(euc, bytes)
ret... | [
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