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train | BitReader.get_bits | Get an integer containing the next [count] bits from the source. | mrcrowbar/utils.py | def get_bits( self, count ):
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Number of bits to push to the target.
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train | BitWriter.get_buffer | Return a byte string containing the target as currently written. | mrcrowbar/utils.py | def get_buffer( self ):
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train | syllabify | Syllabify the given word, whether simplex or complex. | finnsyll/prev/v07.py | def syllabify(word, compound=None):
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train | ModelCompiler.convert_case | Converts name from CamelCase to snake_case | algen/compilers.py | def convert_case(name):
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s1 = re.sub('(.)([A-Z][a-z]+)', r'\1_\2', name)
return re.sub('([a-z0-9])([A-Z])', r'\1_\2', s1).lower() | def convert_case(name):
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train | ModelCompiler.table_name | Pluralises the class_name using utterly simple algo and returns as table_name | algen/compilers.py | def table_name(self):
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train | ModelCompiler.types | All the unique types found in user supplied model | algen/compilers.py | def types(self):
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train | ModelCompiler.basic_types | Returns non-postgres types referenced in user supplied model | algen/compilers.py | def basic_types(self):
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train | ModelCompiler.primary_keys | Returns the primary keys referenced in user supplied model | algen/compilers.py | def primary_keys(self):
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res = []
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train | ModelCompiler.compiled_named_imports | Returns compiled named imports required for the model | algen/compilers.py | def compiled_named_imports(self):
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res = []
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train | ModelCompiler.compiled_orm_imports | Returns compiled named imports required for the model | algen/compilers.py | def compiled_orm_imports(self):
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module = 'sqlalchemy.orm'
labels = []
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labels.append("relationship")
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labels.append("relationship")
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train | ModelCompiler.compiled_columns | Returns compiled column definitions | algen/compilers.py | def compiled_columns(self):
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train | ModelCompiler.compiled_foreign_keys | Returns compiled foreign key definitions | algen/compilers.py | def compiled_foreign_keys(self):
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train | ModelCompiler.compiled_relationships | Returns compiled relationship definitions | algen/compilers.py | def compiled_relationships(self):
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train | ModelCompiler.columns | Return names of all the addressable columns (including foreign keys) referenced in user supplied model | algen/compilers.py | def columns(self):
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train | SixteenS.fasta | Convert the subsampled reads to FASTA format using reformat.sh | sixteenS/sixteens_full.py | def fasta(self):
"""
Convert the subsampled reads to FASTA format using reformat.sh
"""
logging.info('Converting FASTQ files to FASTA format')
# Create the threads for the analysis
for _ in range(self.cpus):
threads = Thread(target=self.fastathreads, args=())
... | def fasta(self):
"""
Convert the subsampled reads to FASTA format using reformat.sh
"""
logging.info('Converting FASTQ files to FASTA format')
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train | SixteenS.makeblastdb | Makes blast database files from targets as necessary | sixteenS/sixteens_full.py | def makeblastdb(self):
"""
Makes blast database files from targets as necessary
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# Iterate through the samples to set the bait file.
for sample in self.runmetadata.samples:
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Makes blast database files from targets as necessary
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train | SixteenS.blast | Run BLAST analyses of the subsampled FASTQ reads against the NCBI 16S reference database | sixteenS/sixteens_full.py | def blast(self):
"""
Run BLAST analyses of the subsampled FASTQ reads against the NCBI 16S reference database
"""
logging.info('BLASTing FASTA files against {} database'.format(self.analysistype))
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Run BLAST analyses of the subsampled FASTQ reads against the NCBI 16S reference database
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train | SixteenS.blastparse | Parse the blast results, and store necessary data in dictionaries in sample object | sixteenS/sixteens_full.py | def blastparse(self):
"""
Parse the blast results, and store necessary data in dictionaries in sample object
"""
logging.info('Parsing BLAST results')
# Load the NCBI 16S reference database as a dictionary
for sample in self.runmetadata.samples:
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Parse the blast results, and store necessary data in dictionaries in sample object
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train | SixteenS.reporter | Creates a report of the results | sixteenS/sixteens_full.py | def reporter(self):
"""
Creates a report of the results
"""
# Create the path in which the reports are stored
make_path(self.reportpath)
logging.info('Creating {} report'.format(self.analysistype))
# Initialise the header and data strings
header = 'Strain,... | def reporter(self):
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Creates a report of the results
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train | Observable.add_listener | 添加观察者函数。
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:params fn: 要注册的触发函数函数
.. note::
允许一个函数多次注册，多次注册意味着一次 :func:`fire_event` 多次调用。 | qg/core/observer.py | def add_listener(self, evt_name, fn):
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:params evt_name: 事件名称
:params fn: 要注册的触发函数函数
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self._listeners.setdefault(evt_name, [])
listeners = self.__get_listeners(evt_name)
lis... | def add_listener(self, evt_name, fn):
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train | Observable.remove_listener | 删除观察者函数。
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train | Observable.has_listener | 指定listener是否存在
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:params fn: 要注册的触发函数函数
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:params evt_name: 事件名称
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:params kwargs: 给事件接受者的参数 | qg/core/observer.py | def fire_event(self, evt_name, *args, **kwargs):
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:params kwargs: 给事件接受者的参数
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train | create_server_ec2 | Creates EC2 Instance | bookshelf/api_v2/ec2.py | def create_server_ec2(connection,
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disk_size,
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key_pair,
instance_type,
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security_groups=None,
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train | destroy_ebs_volume | destroys an ebs volume | bookshelf/api_v2/ec2.py | def destroy_ebs_volume(connection, region, volume_id, log=False):
""" destroys an ebs volume """
if ebs_volume_exists(connection, region, volume_id):
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log_yellow('destroying EBS volume ...')
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log_yellow('destroying EBS volume ...')
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train | destroy_ec2 | terminates the instance | bookshelf/api_v2/ec2.py | def destroy_ec2(connection, region, instance_id, log=False):
""" terminates the instance """
data = get_ec2_info(connection=connection,
instance_id=instance_id,
region=region)
instance = connection.terminate_instances(instance_ids=[data['id']])[0]
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region=region)
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train | down_ec2 | shutdown of an existing EC2 instance | bookshelf/api_v2/ec2.py | def down_ec2(connection, instance_id, region, log=False):
""" shutdown of an existing EC2 instance """
# get the instance_id from the state file, and stop the instance
instance = connection.stop_instances(instance_ids=instance_id)[0]
while instance.state != "stopped":
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""" shutdown of an existing EC2 instance """
# get the instance_id from the state file, and stop the instance
instance = connection.stop_instances(instance_ids=instance_id)[0]
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train | ebs_volume_exists | finds out if a ebs volume exists | bookshelf/api_v2/ec2.py | def ebs_volume_exists(connection, region, volume_id):
""" finds out if a ebs volume exists """
for vol in connection.get_all_volumes():
if vol.id == volume_id:
return True
return False | def ebs_volume_exists(connection, region, volume_id):
""" finds out if a ebs volume exists """
for vol in connection.get_all_volumes():
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return True
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train | get_ec2_info | queries EC2 for details about a particular instance_id | bookshelf/api_v2/ec2.py | def get_ec2_info(connection,
instance_id,
region,
username=None):
""" queries EC2 for details about a particular instance_id
"""
instance = connection.get_only_instances(
filters={'instance_id': instance_id}
)[0]
data = instance.__dict_... | def get_ec2_info(connection,
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region,
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filters={'instance_id': instance_id}
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train | up_ec2 | boots an existing ec2_instance | bookshelf/api_v2/ec2.py | def up_ec2(connection,
region,
instance_id,
wait_for_ssh_available=True,
log=False,
timeout=600):
""" boots an existing ec2_instance """
# boot the ec2 instance
instance = connection.start_instances(instance_ids=instance_id)[0]
instance.update()
... | def up_ec2(connection,
region,
instance_id,
wait_for_ssh_available=True,
log=False,
timeout=600):
""" boots an existing ec2_instance """
# boot the ec2 instance
instance = connection.start_instances(instance_ids=instance_id)[0]
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train | apply_T4 | An agglutination diphthong that ends in /u, y/ usually contains a
syllable boundary when -C# or -CCV follow, e.g., [lau.ka.us],
[va.ka.ut.taa]. | finnsyll/prev/v03.py | def apply_T4(word):
'''An agglutination diphthong that ends in /u, y/ usually contains a
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# i % 2 != 0 prevents this rule from applying to first, third, etc.
... | def apply_T4(word):
'''An agglutination diphthong that ends in /u, y/ usually contains a
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train | seqs_from_file | Extract sequences from a file
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Martin C F Thomsen
Date:
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Description:
Iterator which extract sequence data from the input file
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Name:
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Author(s):
Martin C F Thomsen
Date:
18 Jul 2013
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Martin C F Thomsen
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train | open_ | Switch for both open() and gzip.open().
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The filename argument is required; mode defaults to 'rb' for gzip and 'r'
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Determines if the file is normal or gzipped by looking at the file
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The filename argument is required; mode defaults to 'rb' for gzip and 'r'
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train | load_json | Load json from file or file name | cgecore/utility.py | def load_json(json_object):
''' Load json from file or file name '''
content = None
if isinstance(json_object, str) and os.path.exists(json_object):
with open_(json_object) as f:
try:
content = json.load(f)
except Exception as e:
debug.log("Warning: Content of '%... | def load_json(json_object):
''' Load json from file or file name '''
content = None
if isinstance(json_object, str) and os.path.exists(json_object):
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train | sort2groups | Sort an array of strings to groups by patterns | cgecore/utility.py | def sort2groups(array, gpat=['_R1','_R2']):
""" Sort an array of strings to groups by patterns """
groups = [REGroup(gp) for gp in gpat]
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train | sort_and_distribute | Sort an array of strings to groups by alphabetically continuous
distribution | cgecore/utility.py | def sort_and_distribute(array, splits=2):
""" Sort an array of strings to groups by alphabetically continuous
distribution
"""
if not isinstance(array, (list,tuple)): raise TypeError("array must be a list")
if not isinstance(splits, int): raise TypeError("splits must be an integer")
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train | mkpath | This function executes a mkdir command for filepath and with permissions
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# eg. mkpath("path/to/file", "0o775") | cgecore/utility.py | def mkpath(filepath, permissions=0o777):
""" This function executes a mkdir command for filepath and with permissions
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# eg. mkpath("path/to/file", "0o775")
"""
# Converting string of octal to integer, if string is given.
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""" This function executes a mkdir command for filepath and with permissions
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# Converting string of octal to integer, if string is given.
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train | create_zip_dir | This function creates a zipfile located in zipFilePath with the files in
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""" This function creates a zipfile located in zipFilePath with the files in
the file list
# fileList can be both a comma separated list or an array
"""
try:
if isinstance(file_list, (list, tuple)): #unfolding list of list or tuple
if len(file_... | def create_zip_dir(zipfile_path, *file_list):
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train | file_zipper | This function will zip the files created in the runroot directory and
subdirectories | cgecore/utility.py | def file_zipper(root_dir):
""" This function will zip the files created in the runroot directory and
subdirectories """
# FINDING AND ZIPPING UNZIPPED FILES
for root, dirs, files in os.walk(root_dir, topdown=False):
if root != "":
if root[-1] != '/': root += '/'
for current_file in f... | def file_zipper(root_dir):
""" This function will zip the files created in the runroot directory and
subdirectories """
# FINDING AND ZIPPING UNZIPPED FILES
for root, dirs, files in os.walk(root_dir, topdown=False):
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train | file_unzipper | This function will unzip all files in the runroot directory and
subdirectories | cgecore/utility.py | def file_unzipper(directory):
""" This function will unzip all files in the runroot directory and
subdirectories
"""
debug.log("Unzipping directory (%s)..."%directory)
#FINDING AND UNZIPPING ZIPPED FILES
for root, dirs, files in os.walk(directory, topdown=False):
if root != "":
orig_dir... | def file_unzipper(directory):
""" This function will unzip all files in the runroot directory and
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debug.log("Unzipping directory (%s)..."%directory)
#FINDING AND UNZIPPING ZIPPED FILES
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train | move_file | this function will simply move the file from the source path to the dest
path given as input | cgecore/utility.py | def move_file(src, dst):
""" this function will simply move the file from the source path to the dest
path given as input
"""
# Sanity checkpoint
src = re.sub('[^\w/\-\.\*]', '', src)
dst = re.sub('[^\w/\-\.\*]', '', dst)
if len(re.sub('[\W]', '', src)) < 5 or len(re.sub('[\W]', '', dst)) < 5:
... | def move_file(src, dst):
""" this function will simply move the file from the source path to the dest
path given as input
"""
# Sanity checkpoint
src = re.sub('[^\w/\-\.\*]', '', src)
dst = re.sub('[^\w/\-\.\*]', '', dst)
if len(re.sub('[\W]', '', src)) < 5 or len(re.sub('[\W]', '', dst)) < 5:
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train | copy_file | this function will simply copy the file from the source path to the dest
path given as input | cgecore/utility.py | def copy_file(src, dst, ignore=None):
""" this function will simply copy the file from the source path to the dest
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"""
# Sanity checkpoint
src = re.sub('[^\w/\-\.\*]', '', src)
dst = re.sub('[^\w/\-\.\*]', '', dst)
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"""
# Sanity checkpoint
src = re.sub('[^\w/\-\.\*]', '', src)
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train | copy_dir | this function will simply copy the file from the source path to the dest
path given as input | cgecore/utility.py | def copy_dir(src, dst):
""" this function will simply copy the file from the source path to the dest
path given as input
"""
try:
debug.log("copy dir from "+ src, "to "+ dst)
shutil.copytree(src, dst)
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try:
debug.log("copy dir from "+ src, "to "+ dst)
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train | Debug.graceful_exit | This function Tries to update the MSQL database before exiting. | cgecore/utility.py | def graceful_exit(self, msg):
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# Print stored errors to stderr
if self.caught_error:
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self.log(msg)
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Create the MASH report
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Create the MASH report
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train | get_function | Take a full path to a python method or class, for example
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Run the necessary methods in the correct order
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train | syllabify | Syllabify the given word, whether simplex or complex. | finnsyll/prev/v06.py | def syllabify(word):
'''Syllabify the given word, whether simplex or complex.'''
word = split(word) # detect any non-delimited compounds
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syllabify = _syllabify_compound if compound else _syllabify
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'''Syllabify the given word, whether simplex or complex.'''
word = split(word) # detect any non-delimited compounds
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train | SixteenS.runner | Run the necessary methods in the correct order | sixteenS/sixteenS.py | def runner(self):
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train | _generate_handler_wrapper | Generate a handler method for the given url method+path and operation | pymacaron_core/swagger/server.py | def _generate_handler_wrapper(api_name, api_spec, endpoint, handler_func, error_callback, global_decorator):
"""Generate a handler method for the given url method+path and operation"""
# Decorate the handler function, if Swagger spec tells us to
if endpoint.decorate_server:
endpoint_decorator = get... | def _generate_handler_wrapper(api_name, api_spec, endpoint, handler_func, error_callback, global_decorator):
"""Generate a handler method for the given url method+path and operation"""
# Decorate the handler function, if Swagger spec tells us to
if endpoint.decorate_server:
endpoint_decorator = get... | [
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train | format_escape | Returns the ANSI escape sequence to set character formatting.
foreground
Foreground colour to use. Accepted types: None, int (xterm
palette ID), tuple (RGB, RGBA), Colour
background
Background colour to use. Accepted types: None, int (xterm
palette ID), tuple (RGB, RGBA), Colou... | mrcrowbar/ansi.py | def format_escape( foreground=None, background=None, bold=False, faint=False,
italic=False, underline=False, blink=False, inverted=False ):
"""Returns the ANSI escape sequence to set character formatting.
foreground
Foreground colour to use. Accepted types: None, int (xterm
palette ID), tup... | def format_escape( foreground=None, background=None, bold=False, faint=False,
italic=False, underline=False, blink=False, inverted=False ):
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Foreground colour to use. Accepted types: None, int (xterm
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train | format_string | Returns a Unicode string formatted with an ANSI escape sequence.
string
String to format
foreground
Foreground colour to use. Accepted types: None, int (xterm
palette ID), tuple (RGB, RGBA), Colour
background
Background colour to use. Accepted types: None, int (xterm
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"""Returns a Unicode string formatted with an ANSI escape sequence.
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String to format
foreground
Foreground colour to us... | def format_string( string, foreground=None, background=None, reset=True, bold=False,
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String to format
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train | format_pixels | Return the ANSI escape sequence to render two vertically-stacked pixels as a
single monospace character.
top
Top colour to use. Accepted types: None, int (xterm
palette ID), tuple (RGB, RGBA), Colour
bottom
Bottom colour to use. Accepted types: None, int (xterm
palette ID),... | mrcrowbar/ansi.py | def format_pixels( top, bottom, reset=True, repeat=1 ):
"""Return the ANSI escape sequence to render two vertically-stacked pixels as a
single monospace character.
top
Top colour to use. Accepted types: None, int (xterm
palette ID), tuple (RGB, RGBA), Colour
bottom
Bottom colou... | def format_pixels( top, bottom, reset=True, repeat=1 ):
"""Return the ANSI escape sequence to render two vertically-stacked pixels as a
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top
Top colour to use. Accepted types: None, int (xterm
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Bottom colou... | [
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train | format_image_iter | Return the ANSI escape sequence to render a bitmap image.
data_fetch
Function that takes three arguments (x position, y position, and frame) and returns
a Colour corresponding to the pixel stored there, or Transparent if the requested
pixel is out of bounds.
x_start
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"""Return the ANSI escape sequence to render a bitmap image.
data_fetch
Function that takes three arguments (x position, y position, and frame) and returns
a Colour corresponding to... | def format_image_iter( data_fetch, x_start=0, y_start=0, width=32, height=32, frame=0, columns=1, downsample=1 ):
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data_fetch
Function that takes three arguments (x position, y position, and frame) and returns
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train | Field.update_buffer_with_value | Write a Python object into a byte array, using the field definition.
value
Input Python object to process.
buffer
Output byte array to encode value into.
parent
Parent block object where this Field is defined. Used for e.g.
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"""Write a Python object into a byte array, using the field definition.
value
Input Python object to process.
buffer
Output byte array to encode value into.
parent
Parent block object... | def update_buffer_with_value( self, value, buffer, parent=None ):
"""Write a Python object into a byte array, using the field definition.
value
Input Python object to process.
buffer
Output byte array to encode value into.
parent
Parent block object... | [
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train | Field.get_end_offset | Return the end offset of the Field's data. Useful for chainloading.
value
Input Python object to process.
parent
Parent block object where this Field is defined. Used for e.g.
evaluating Refs.
index
Index of the Python object to measure from. Us... | mrcrowbar/fields.py | def get_end_offset( self, value, parent=None, index=None ):
"""Return the end offset of the Field's data. Useful for chainloading.
value
Input Python object to process.
parent
Parent block object where this Field is defined. Used for e.g.
evaluating Refs.
... | def get_end_offset( self, value, parent=None, index=None ):
"""Return the end offset of the Field's data. Useful for chainloading.
value
Input Python object to process.
parent
Parent block object where this Field is defined. Used for e.g.
evaluating Refs.
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train | nonalpha_split | Split 'string' along any punctuation or whitespace. | finnsyll/utilities.py | def nonalpha_split(string):
'''Split 'string' along any punctuation or whitespace.'''
return re.findall(r'[%s]+|[^%s]+' % (A, A), string, flags=FLAGS) | def nonalpha_split(string):
'''Split 'string' along any punctuation or whitespace.'''
return re.findall(r'[%s]+|[^%s]+' % (A, A), string, flags=FLAGS) | [
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train | syllable_split | Split 'string' into (stressed) syllables and punctuation/whitespace. | finnsyll/utilities.py | def syllable_split(string):
'''Split 'string' into (stressed) syllables and punctuation/whitespace.'''
p = r'\'[%s]+|`[%s]+|[%s]+|[^%s\'`\.]+|[^\.]{1}' % (A, A, A, A)
return re.findall(p, string, flags=FLAGS) | def syllable_split(string):
'''Split 'string' into (stressed) syllables and punctuation/whitespace.'''
p = r'\'[%s]+|`[%s]+|[%s]+|[^%s\'`\.]+|[^\.]{1}' % (A, A, A, A)
return re.findall(p, string, flags=FLAGS) | [
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train | extract_words | Extract all alphabetic syllabified forms from 'string'. | finnsyll/utilities.py | def extract_words(string):
'''Extract all alphabetic syllabified forms from 'string'.'''
return re.findall(r'[%s]+[%s\.]*[%s]+' % (A, A, A), string, flags=FLAGS) | def extract_words(string):
'''Extract all alphabetic syllabified forms from 'string'.'''
return re.findall(r'[%s]+[%s\.]*[%s]+' % (A, A, A), string, flags=FLAGS) | [
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train | init_threads | Should define dummyThread class and dummySignal class | pyDLib/Core/threads.py | def init_threads(t=None, s=None):
"""Should define dummyThread class and dummySignal class"""
global THREAD, SIGNAL
THREAD = t or dummyThread
SIGNAL = s or dummySignal | def init_threads(t=None, s=None):
"""Should define dummyThread class and dummySignal class"""
global THREAD, SIGNAL
THREAD = t or dummyThread
SIGNAL = s or dummySignal | [
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