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inveniosoftware/invenio-db | invenio_db/shared.py | do_sqlite_connect | def do_sqlite_connect(dbapi_connection, connection_record):
"""Ensure SQLite checks foreign key constraints.
For further details see "Foreign key support" sections on
https://docs.sqlalchemy.org/en/latest/dialects/sqlite.html#foreign-key-support
"""
# Enable foreign key constraint checking
curs... | python | def do_sqlite_connect(dbapi_connection, connection_record):
"""Ensure SQLite checks foreign key constraints.
For further details see "Foreign key support" sections on
https://docs.sqlalchemy.org/en/latest/dialects/sqlite.html#foreign-key-support
"""
# Enable foreign key constraint checking
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inveniosoftware/invenio-db | invenio_db/shared.py | SQLAlchemy.apply_driver_hacks | def apply_driver_hacks(self, app, info, options):
"""Call before engine creation."""
# Don't forget to apply hacks defined on parent object.
super(SQLAlchemy, self).apply_driver_hacks(app, info, options)
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connect_args = options.setdefault('conn... | python | def apply_driver_hacks(self, app, info, options):
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# Don't forget to apply hacks defined on parent object.
super(SQLAlchemy, self).apply_driver_hacks(app, info, options)
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inveniosoftware/invenio-db | invenio_db/cli.py | create | def create(verbose):
"""Create tables."""
click.secho('Creating all tables!', fg='yellow', bold=True)
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table.create(bind=_db... | python | def create(verbose):
"""Create tables."""
click.secho('Creating all tables!', fg='yellow', bold=True)
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inveniosoftware/invenio-db | invenio_db/cli.py | drop | def drop(verbose):
"""Drop tables."""
click.secho('Dropping all tables!', fg='red', bold=True)
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for table in bar:
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click.echo(' Dropping table {0}'.format(table))
table.drop(bind=_d... | python | def drop(verbose):
"""Drop tables."""
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inveniosoftware/invenio-db | invenio_db/cli.py | init | def init():
"""Create database."""
click.secho('Creating database {0}'.format(_db.engine.url),
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if not database_exists(str(_db.engine.url)):
create_database(str(_db.engine.url)) | python | def init():
"""Create database."""
click.secho('Creating database {0}'.format(_db.engine.url),
fg='green')
if not database_exists(str(_db.engine.url)):
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inveniosoftware/invenio-db | invenio_db/cli.py | destroy | def destroy():
"""Drop database."""
click.secho('Destroying database {0}'.format(_db.engine.url),
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if _db.engine.name == 'sqlite':
try:
drop_database(_db.engine.url)
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click.secho('Sqlite database has no... | python | def destroy():
"""Drop database."""
click.secho('Destroying database {0}'.format(_db.engine.url),
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quantmind/dynts | dynts/stats/rolling.py | rollingOperation.rolling | def rolling(self, op):
"""Fast rolling operation with O(log n) updates where n is the
window size
"""
missing = self.missing
ismissing = self.ismissing
window = self.window
it = iter(self.iterable)
queue = deque(islice(it, window))
ol = self.skip... | python | def rolling(self, op):
"""Fast rolling operation with O(log n) updates where n is the
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missing = self.missing
ismissing = self.ismissing
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doakey3/DashTable | dashtable/dashutils/get_span_column_count.py | get_span_column_count | def get_span_column_count(span):
"""
Find the length of a colspan.
Parameters
----------
span : list of lists of int
The [row, column] pairs that make up the span
Returns
-------
columns : int
The number of columns included in the span
Example
-------
Consi... | python | def get_span_column_count(span):
"""
Find the length of a colspan.
Parameters
----------
span : list of lists of int
The [row, column] pairs that make up the span
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-------
columns : int
The number of columns included in the span
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eaton-lab/toytree | toytree/TreeStyle.py | TreeStyle.to_dict | def to_dict(self):
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ndict[key[1:]] = val
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doakey3/DashTable | dashtable/dashutils/get_span_char_width.py | get_span_char_width | def get_span_char_width(span, column_widths):
"""
Sum the widths of the columns that make up the span, plus the extra.
Parameters
----------
span : list of lists of int
list of [row, column] pairs that make up the span
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"""
Sum the widths of the columns that make up the span, plus the extra.
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inveniosoftware/invenio-db | invenio_db/utils.py | rebuild_encrypted_properties | def rebuild_encrypted_properties(old_key, model, properties):
"""Rebuild a model's EncryptedType properties when the SECRET_KEY is changed.
:param old_key: old SECRET_KEY.
:param model: the affected db model.
:param properties: list of properties to rebuild.
"""
inspector = reflection.Inspector... | python | def rebuild_encrypted_properties(old_key, model, properties):
"""Rebuild a model's EncryptedType properties when the SECRET_KEY is changed.
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:param model: the affected db model.
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inveniosoftware/invenio-db | invenio_db/utils.py | create_alembic_version_table | def create_alembic_version_table():
"""Create alembic_version table."""
alembic = current_app.extensions['invenio-db'].alembic
if not alembic.migration_context._has_version_table():
alembic.migration_context._ensure_version_table()
for head in alembic.script_directory.revision_map._real_head... | python | def create_alembic_version_table():
"""Create alembic_version table."""
alembic = current_app.extensions['invenio-db'].alembic
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alembic.migration_context._ensure_version_table()
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inveniosoftware/invenio-db | invenio_db/utils.py | drop_alembic_version_table | def drop_alembic_version_table():
"""Drop alembic_version table."""
if _db.engine.dialect.has_table(_db.engine, 'alembic_version'):
alembic_version = _db.Table('alembic_version', _db.metadata,
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alembic_version.drop(bind=_db.engine) | python | def drop_alembic_version_table():
"""Drop alembic_version table."""
if _db.engine.dialect.has_table(_db.engine, 'alembic_version'):
alembic_version = _db.Table('alembic_version', _db.metadata,
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inveniosoftware/invenio-db | invenio_db/utils.py | versioning_model_classname | def versioning_model_classname(manager, model):
"""Get the name of the versioned model class."""
if manager.options.get('use_module_name', True):
return '%s%sVersion' % (
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inveniosoftware/invenio-db | invenio_db/utils.py | versioning_models_registered | def versioning_models_registered(manager, base):
"""Return True if all versioning models have been registered."""
declared_models = base._decl_class_registry.keys()
return all(versioning_model_classname(manager, c) in declared_models
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declared_models = base._decl_class_registry.keys()
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quantmind/dynts | dynts/stats/variates.py | vector_to_symmetric | def vector_to_symmetric(v):
'''Convert an iterable into a symmetric matrix.'''
np = len(v)
N = (int(sqrt(1 + 8*np)) - 1)//2
if N*(N+1)//2 != np:
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sym = ndarray((N,N))
iterable = iter(v)
for r in range(N):
f... | python | def vector_to_symmetric(v):
'''Convert an iterable into a symmetric matrix.'''
np = len(v)
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if N*(N+1)//2 != np:
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quantmind/dynts | dynts/stats/variates.py | Variates.cov | def cov(self, ddof=None, bias=0):
'''The covariance matrix from the aggregate sample. It accepts an
optional parameter for the degree of freedoms.
:parameter ddof: If not ``None`` normalization is by (N - ddof), where N is
the number of observations; this overrides the value im... | python | def cov(self, ddof=None, bias=0):
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quantmind/dynts | dynts/stats/variates.py | Variates.corr | def corr(self):
'''The correlation matrix'''
cov = self.cov()
N = cov.shape[0]
corr = ndarray((N,N))
for r in range(N):
for c in range(r):
corr[r,c] = corr[c,r] = cov[r,c]/sqrt(cov[r,r]*cov[c,c])
corr[r,r] = 1.
return corr | python | def corr(self):
'''The correlation matrix'''
cov = self.cov()
N = cov.shape[0]
corr = ndarray((N,N))
for r in range(N):
for c in range(r):
corr[r,c] = corr[c,r] = cov[r,c]/sqrt(cov[r,r]*cov[c,c])
corr[r,r] = 1.
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quantmind/dynts | dynts/stats/functions.py | calmar | def calmar(sharpe, T = 1.0):
'''
Calculate the Calmar ratio for a Weiner process
@param sharpe: Annualized Sharpe ratio
@param T: Time interval in years
'''
x = 0.5*T*sharpe*sharpe
return x/qp(x) | python | def calmar(sharpe, T = 1.0):
'''
Calculate the Calmar ratio for a Weiner process
@param sharpe: Annualized Sharpe ratio
@param T: Time interval in years
'''
x = 0.5*T*sharpe*sharpe
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quantmind/dynts | dynts/stats/functions.py | calmarnorm | def calmarnorm(sharpe, T, tau = 1.0):
'''
Multiplicator for normalizing calmar ratio to period tau
'''
return calmar(sharpe,tau)/calmar(sharpe,T) | python | def calmarnorm(sharpe, T, tau = 1.0):
'''
Multiplicator for normalizing calmar ratio to period tau
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return calmar(sharpe,tau)/calmar(sharpe,T) | [
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inveniosoftware/invenio-db | invenio_db/alembic/35c1075e6360_force_naming_convention.py | upgrade | def upgrade():
"""Upgrade database."""
op.execute('COMMIT') # See https://bitbucket.org/zzzeek/alembic/issue/123
ctx = op.get_context()
metadata = ctx.opts['target_metadata']
metadata.naming_convention = NAMING_CONVENTION
metadata.bind = ctx.connection.engine
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"""Upgrade database."""
op.execute('COMMIT') # See https://bitbucket.org/zzzeek/alembic/issue/123
ctx = op.get_context()
metadata = ctx.opts['target_metadata']
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doakey3/DashTable | dashtable/data2simplerst/data2simplerst.py | data2simplerst | def data2simplerst(table, spans=[[[0, 0]]], use_headers=True, headers_row=0):
"""
Convert table data to a simple rst table
Parameters
----------
table : list of lists of str
A table of strings.
spans : list of lists of lists of int
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Convert table data to a simple rst table
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table : list of lists of str
A table of strings.
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doakey3/DashTable | dashtable/html2data/restructify/add_links.py | add_links | def add_links(converted_text, html):
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link_exceptions = [
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footnotes = {}
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backrefs = {}
lin... | python | def add_links(converted_text, html):
"""
Add the links to the bottom of the text
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quantmind/dynts | dynts/data/__init__.py | TimeSerieLoader.load | def load(self, providers, symbols, start, end, logger, backend, **kwargs):
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:keyword providers: Dictionary of registered data providers.
:keyword symbols: list of symbols to load.
:keyword start: start date.
:keyword end: end date.
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quantmind/dynts | dynts/data/__init__.py | TimeSerieLoader.dates | def dates(self, start, end):
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:keyword end: end date.
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quantmind/dynts | dynts/data/__init__.py | TimeSerieLoader.parse_symbol | def parse_symbol(self, symbol, providers):
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:keyword symbol: string associated with market data to load.
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quantmind/dynts | dynts/data/__init__.py | TimeSerieLoader.symbol_for_ticker | def symbol_for_ticker(self, ticker, field, provider, providers):
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provider = provider or settings.default_provider
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'''Return an instance of *symboldata* containing
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quantmind/dynts | dynts/data/__init__.py | TimeSerieLoader.preprocess | def preprocess(self, ticker, start, end, logger, backend, **kwargs):
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It must return an instance of :attr:`TimeSerieLoader.preprocessdata`.
By default it returns::
self.preprocessdata(in... | python | def preprocess(self, ticker, start, end, logger, backend, **kwargs):
'''Preprocess **hook**. This is first loading hook and it is
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quantmind/dynts | dynts/data/__init__.py | DataProviders.register | def register(self, provider):
'''Register a new data provider. *provider* must be an instance of
DataProvider. If provider name is already available, it will be replaced.'''
if isinstance(provider,type):
provider = provider()
self[provider.code] = provider | python | def register(self, provider):
'''Register a new data provider. *provider* must be an instance of
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provider = provider()
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quantmind/dynts | dynts/data/__init__.py | DataProviders.unregister | def unregister(self, provider):
'''Unregister an existing data provider.
*provider* must be an instance of DataProvider.
If provider name is already available, it will be replaced.
'''
if isinstance(provider, type):
provider = provider()
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*provider* must be an instance of DataProvider.
If provider name is already available, it will be replaced.
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quantmind/dynts | dynts/dsl/__init__.py | parse | def parse(timeseries_expression, method=None, functions=None, debug=False):
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If succesful, it returns an instance of :class:`dynts.dsl.Expr` which
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quantmind/dynts | dynts/dsl/__init__.py | evaluate | def evaluate(expression, start=None, end=None, loader=None, logger=None,
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doakey3/DashTable | dashtable/grid2data/grid2data.py | grid2data | def grid2data(text):
"""
Convert Grid table to data (the kind used by Dashtable)
Parameters
----------
text : str
The text must be a valid rst table
Returns
-------
table : list of lists of str
spans : list of lists of lists of int
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"""
Convert Grid table to data (the kind used by Dashtable)
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The text must be a valid rst table
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eaton-lab/toytree | toytree/Multitree.py | MultiTree.get_consensus_tree | def get_consensus_tree(self, cutoff=0.0, best_tree=None):
"""
Returns an extended majority rule consensus tree as a Toytree object.
Node labels include 'support' values showing the occurrence of clades
in the consensus tree across trees in the input treelist.
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Returns an extended majority rule consensus tree as a Toytree object.
Node labels include 'support' values showing the occurrence of clades
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eaton-lab/toytree | toytree/Multitree.py | MultiTree.draw_tree_grid | def draw_tree_grid(self,
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Draw a slice of x*y trees into a x,y grid non-overlapping.
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x (int):
N... | python | def draw_tree_grid(self,
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ncols=None,
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**kwargs):
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Draw a slice of x*y trees into a x,y grid non-overlapping.
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eaton-lab/toytree | toytree/Multitree.py | MultiTree.draw_cloud_tree | def draw_cloud_tree(self,
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Draw a series of trees overlapping each other in coordinate space.
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Draw a series of trees overlapping each other in coordinate space.
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eaton-lab/toytree | toytree/Multitree.py | ConsensusTree.hash_trees | def hash_trees(self):
"hash ladderized tree topologies"
observed = {}
for idx, tree in enumerate(self.treelist):
nwk = tree.write(tree_format=9)
hashed = md5(nwk.encode("utf-8")).hexdigest()
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observed[hashed] = ... | python | def hash_trees(self):
"hash ladderized tree topologies"
observed = {}
for idx, tree in enumerate(self.treelist):
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eaton-lab/toytree | toytree/Multitree.py | ConsensusTree.find_clades | def find_clades(self):
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namedict = {i: j for i, j in enumerate(self.names)}
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eaton-lab/toytree | toytree/Multitree.py | ConsensusTree.filter_clades | def filter_clades(self):
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eaton-lab/toytree | toytree/Multitree.py | ConsensusTree.build_trees | def build_trees(self):
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Lilykos/pyphonetics | pyphonetics/phonetics/phonetic_algorithm.py | PhoneticAlgorithm.sounds_like | def sounds_like(self, word1, word2):
"""Compare the phonetic representations of 2 words, and return a boolean value."""
return self.phonetics(word1) == self.phonetics(word2) | python | def sounds_like(self, word1, word2):
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Lilykos/pyphonetics | pyphonetics/phonetics/phonetic_algorithm.py | PhoneticAlgorithm.distance | def distance(self, word1, word2, metric='levenshtein'):
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if metric in self.distances:
distance_func = self.distances[metric]
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doakey3/DashTable | dashtable/data2rst/get_output_row_heights.py | get_output_row_heights | def get_output_row_heights(table, spans):
"""
Get the heights of the rows of the output table.
Parameters
----------
table : list of lists of str
spans : list of lists of int
Returns
-------
heights : list of int
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"""
heigh... | python | def get_output_row_heights(table, spans):
"""
Get the heights of the rows of the output table.
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----------
table : list of lists of str
spans : list of lists of int
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-------
heights : list of int
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quantmind/dynts | dynts/lib/fallback/operators.py | smedian | def smedian(olist,nobs):
'''Generalised media for odd and even number of samples'''
if nobs:
rem = nobs % 2
midpoint = nobs // 2
me = olist[midpoint]
if not rem:
me = 0.5 * (me + olist[midpoint-1])
return me
else:
return NaN | python | def smedian(olist,nobs):
'''Generalised media for odd and even number of samples'''
if nobs:
rem = nobs % 2
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me = olist[midpoint]
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quantmind/dynts | dynts/lib/fallback/operators.py | roll_mean | def roll_mean(input, window):
'''Apply a rolling mean function to an array.
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'''Apply a rolling mean function to an array.
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quantmind/dynts | dynts/lib/fallback/operators.py | roll_sd | def roll_sd(input, window, scale = 1.0, ddof = 0):
'''Apply a rolling standard deviation function
to an array. This is a simple rolling aggregation of squared
sums.'''
nobs, i, j, sx, sxx = 0,0,0,0.,0.
N = len(input)
sqrt = np.sqrt
if window > N:
raise ValueError('Out of bound')
... | python | def roll_sd(input, window, scale = 1.0, ddof = 0):
'''Apply a rolling standard deviation function
to an array. This is a simple rolling aggregation of squared
sums.'''
nobs, i, j, sx, sxx = 0,0,0,0.,0.
N = len(input)
sqrt = np.sqrt
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doakey3/DashTable | dashtable/dashutils/check_span.py | check_span | def check_span(span, table):
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"""
Ensure the span is valid.
A span is a list of [row, column] pairs. These coordinates
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doakey3/DashTable | dashtable/data2rst/merge_all_cells.py | merge_all_cells | def merge_all_cells(cells):
"""
Loop through list of cells and piece them together one by one
Parameters
----------
cells : list of dashtable.data2rst.Cell
Returns
-------
grid_table : str
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"""
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count = 0... | python | def merge_all_cells(cells):
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Loop through list of cells and piece them together one by one
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grid_table : str
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eaton-lab/toytree | toytree/utils.py | bpp2newick | def bpp2newick(bppnewick):
"converts bpp newick format to normal newick"
regex1 = re.compile(r" #[-+]?[0-9]*\.?[0-9]*[:]")
regex2 = re.compile(r" #[-+]?[0-9]*\.?[0-9]*[;]")
regex3 = re.compile(r": ")
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new = regex2.sub(";", new)
new = regex3.sub(":", new)
r... | python | def bpp2newick(bppnewick):
"converts bpp newick format to normal newick"
regex1 = re.compile(r" #[-+]?[0-9]*\.?[0-9]*[:]")
regex2 = re.compile(r" #[-+]?[0-9]*\.?[0-9]*[;]")
regex3 = re.compile(r": ")
new = regex1.sub(":", bppnewick)
new = regex2.sub(";", new)
new = regex3.sub(":", new)
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eaton-lab/toytree | toytree/utils.py | return_small_clade | def return_small_clade(treenode):
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node = treenode
while 1:
if node.children:
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node = sorted([c1, c2], key=lambda x: len(x.get_leaves()))[0]
else:
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eaton-lab/toytree | toytree/utils.py | fuzzy_match_tipnames | def fuzzy_match_tipnames(ttree, names, wildcard, regex, mrca=True, mono=True):
"""
Used in multiple internal functions (e.g., .root()) and .drop_tips())
to select an internal mrca node, or multiple tipnames, using fuzzy matching
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name: verb... | python | def fuzzy_match_tipnames(ttree, names, wildcard, regex, mrca=True, mono=True):
"""
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eaton-lab/toytree | toytree/utils.py | TreeMod.node_scale_root_height | def node_scale_root_height(self, treeheight=1):
"""
Returns a toytree copy with all nodes scaled so that the root
height equals the value entered for treeheight.
"""
# make tree height = 1 * treeheight
ctree = self._ttree.copy()
_height = ctree.treenode.height
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"""
Returns a toytree copy with all nodes scaled so that the root
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"""
# make tree height = 1 * treeheight
ctree = self._ttree.copy()
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eaton-lab/toytree | toytree/utils.py | TreeMod.node_slider | def node_slider(self, seed=None):
"""
Returns a toytree copy with node heights modified while retaining
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eaton-lab/toytree | toytree/utils.py | TreeMod.node_multiplier | def node_multiplier(self, multiplier=0.5, seed=None):
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Returns a toytree copy with all nodes multiplied by a constant
sampled uniformly between (multiplier, 1/multiplier).
"""
random.seed(seed)
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"""
Returns a toytree copy with all nodes multiplied by a constant
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eaton-lab/toytree | toytree/utils.py | TreeMod.make_ultrametric | def make_ultrametric(self, strategy=1):
"""
Returns a tree with branch lengths transformed so that the tree is
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of the fartest tip from the root; (2) non-parametric rate-smoothing:
minimize ancestor-descend... | python | def make_ultrametric(self, strategy=1):
"""
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eaton-lab/toytree | toytree/utils.py | RandomTree.coaltree | def coaltree(ntips, ne=None, seed=None):
"""
Returns a coalescent tree with ntips samples and waiting times
between coalescent events drawn from the kingman coalescent:
(4N)/(k*(k-1)), where N is population size and k is sample size.
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... | python | def coaltree(ntips, ne=None, seed=None):
"""
Returns a coalescent tree with ntips samples and waiting times
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eaton-lab/toytree | toytree/utils.py | RandomTree.unittree | def unittree(ntips, treeheight=1.0, seed=None):
"""
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spaced between the root and time 0.
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ntips (int):
... | python | def unittree(ntips, treeheight=1.0, seed=None):
"""
Returns a random tree topology w/ N tips and a root height set to
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spaced between the root and time 0.
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ntips (int):
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eaton-lab/toytree | toytree/utils.py | RandomTree.imbtree | def imbtree(ntips, treeheight=1.0):
"""
Return an imbalanced (comb-like) tree topology.
"""
rtree = toytree.tree()
rtree.treenode.add_child(name="0")
rtree.treenode.add_child(name="1")
for i in range(2, ntips):
# empty node
cherry = toytre... | python | def imbtree(ntips, treeheight=1.0):
"""
Return an imbalanced (comb-like) tree topology.
"""
rtree = toytree.tree()
rtree.treenode.add_child(name="0")
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eaton-lab/toytree | toytree/utils.py | RandomTree.baltree | def baltree(ntips, treeheight=1.0):
"""
Returns a balanced tree topology.
"""
# require even number of tips
if ntips % 2:
raise ToytreeError("balanced trees must have even number of tips.")
# make first cherry
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rtree.tree... | python | def baltree(ntips, treeheight=1.0):
"""
Returns a balanced tree topology.
"""
# require even number of tips
if ntips % 2:
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html_string : str
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eaton-lab/toytree | toytree/Toytree.py | ToyTree.newick | def newick(self, tree_format=0):
"Returns newick represenation of the tree in its current state."
# checks one of root's children for features and extra feats.
if self.treenode.children:
features = {"name", "dist", "support", "height", "idx"}
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eaton-lab/toytree | toytree/Toytree.py | ToyTree.get_edge_values | def get_edge_values(self, feature='idx'):
"""
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elist.append(
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eaton-lab/toytree | toytree/Toytree.py | ToyTree.get_mrca_idx_from_tip_labels | def get_mrca_idx_from_tip_labels(self, names=None, wildcard=None, regex=None):
"""
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eaton-lab/toytree | toytree/Toytree.py | ToyTree.get_node_values | def get_node_values(
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feature=None,
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Returns node values from tree object in node plot order. To modify
values you must modify the .treenode object directly by setting new
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... | python | def get_node_values(
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show_root=False,
show_tips=False,
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eaton-lab/toytree | toytree/Toytree.py | ToyTree.get_node_dict | def get_node_dict(self, return_internal=False, return_nodes=False):
"""
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eaton-lab/toytree | toytree/Toytree.py | ToyTree.get_tip_coordinates | def get_tip_coordinates(self, axis=None):
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"""
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eaton-lab/toytree | toytree/Toytree.py | ToyTree.get_tip_labels | def get_tip_labels(self, idx=None):
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eaton-lab/toytree | toytree/Toytree.py | ToyTree.is_bifurcating | def is_bifurcating(self, include_root=True):
"""
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argument.
"""
ctn1 = -1 + (2 * len(self))
ctn2 = -2 + (2 * len(self))
... | python | def is_bifurcating(self, include_root=True):
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eaton-lab/toytree | toytree/Toytree.py | ToyTree.ladderize | def ladderize(self, direction=0):
"""
Ladderize tree (order descendants) so that top child has fewer
descendants than the bottom child in a left to right tree plot.
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"""
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"""
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eaton-lab/toytree | toytree/Toytree.py | ToyTree.collapse_nodes | def collapse_nodes(self, min_dist=1e-6, min_support=0):
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newtre = tre.collapse_nodes(min_dist=0.001)
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eaton-lab/toytree | toytree/Toytree.py | ToyTree.drop_tips | def drop_tips(self, names=None, wildcard=None, regex=None):
"""
Returns a copy of the tree with the selected tips removed. The entered
value can be a name or list of names. To prune on an internal node to
create a subtree see the .prune() function instead.
Parameters:
ti... | python | def drop_tips(self, names=None, wildcard=None, regex=None):
"""
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eaton-lab/toytree | toytree/Toytree.py | ToyTree.rotate_node | def rotate_node(
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names=None,
wildcard=None,
regex=None,
idx=None,
# modify_tree=False,
):
"""
Returns a ToyTree with the selected node rotated for plotting.
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wildcard=None,
regex=None,
idx=None,
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eaton-lab/toytree | toytree/Toytree.py | ToyTree.resolve_polytomy | def resolve_polytomy(
self,
dist=1.0,
support=100,
recursive=True):
"""
Returns a copy of the tree with all polytomies randomly resolved.
Does not transform tree in-place.
"""
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... | python | def resolve_polytomy(
self,
dist=1.0,
support=100,
recursive=True):
"""
Returns a copy of the tree with all polytomies randomly resolved.
Does not transform tree in-place.
"""
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eaton-lab/toytree | toytree/Toytree.py | ToyTree.unroot | def unroot(self):
"""
Returns a copy of the tree unrooted. Does not transform tree in-place.
"""
nself = self.copy()
nself.treenode.unroot()
nself.treenode.ladderize()
nself._coords.update()
return nself | python | def unroot(self):
"""
Returns a copy of the tree unrooted. Does not transform tree in-place.
"""
nself = self.copy()
nself.treenode.unroot()
nself.treenode.ladderize()
nself._coords.update()
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eaton-lab/toytree | toytree/Toytree.py | ToyTree.root | def root(self, names=None, wildcard=None, regex=None):
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(Re-)root a tree by creating selecting a existing split in the tree,
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"""
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eaton-lab/toytree | toytree/Toytree.py | ToyTree.draw | def draw(
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height=None,
width=None,
axes=None,
orient=None,
tip_labels=None,
tip_labels_colors=None,
tip_labels_style=None,
tip_labels_align=None,
node_labels=None,
node_labels_style=None,
... | python | def draw(
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tree_style=None,
height=None,
width=None,
axes=None,
orient=None,
tip_labels=None,
tip_labels_colors=None,
tip_labels_style=None,
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node_labels_style=None,
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doakey3/DashTable | dashtable/data2rst/cell/get_merge_direction.py | get_merge_direction | def get_merge_direction(cell1, cell2):
"""
Determine the side of cell1 that can be merged with cell2.
This is based on the location of the two cells in the table as well
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For example these cells can merge::
cell1 cell2 merge "RIGHT"
... | python | def get_merge_direction(cell1, cell2):
"""
Determine the side of cell1 that can be merged with cell2.
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eaton-lab/toytree | toytree/TreeParser.py | parse_nhx | def parse_nhx(NHX_string):
"""
NHX format: [&&NHX:prop1=value1:prop2=value2]
MB format: ((a[&Z=1,Y=2], b[&Z=1,Y=2]):1.0[&L=1,W=0], ...
"""
# store features
ndict = {}
# parse NHX or MB features
if "[&&NHX:" in NHX_string:
NHX_string = NHX_string.replace("[&&NHX:", "")
... | python | def parse_nhx(NHX_string):
"""
NHX format: [&&NHX:prop1=value1:prop2=value2]
MB format: ((a[&Z=1,Y=2], b[&Z=1,Y=2]):1.0[&L=1,W=0], ...
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# store features
ndict = {}
# parse NHX or MB features
if "[&&NHX:" in NHX_string:
NHX_string = NHX_string.replace("[&&NHX:", "")
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eaton-lab/toytree | toytree/TreeParser.py | TreeParser.get_data_from_intree | def get_data_from_intree(self):
"""
Load *data* from a file or string and return as a list of strings.
The data contents could be one newick string; a multiline NEXUS format
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eaton-lab/toytree | toytree/TreeParser.py | TreeParser.parse_nexus | def parse_nexus(self):
"get newick data from NEXUS"
if self.data[0].strip().upper() == "#NEXUS":
nex = NexusParser(self.data)
self.data = nex.newicks
self.tdict = nex.tdict | python | def parse_nexus(self):
"get newick data from NEXUS"
if self.data[0].strip().upper() == "#NEXUS":
nex = NexusParser(self.data)
self.data = nex.newicks
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eaton-lab/toytree | toytree/TreeParser.py | TreeParser.get_treenodes | def get_treenodes(self):
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extractor = Newick2TreeNode(self.data[0].strip(), fmt=self.fmt)
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"test format of intree nex/nwk, extra features"
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eaton-lab/toytree | toytree/TreeParser.py | Newick2TreeNode.newick_from_string | def newick_from_string(self):
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# split on parentheses to traverse hierarchical tree structure
for chunk in self.data.split("(")[1:]:
# add child to make this node a parent.
self.current_parent = (
self.r... | python | def newick_from_string(self):
"Reads a newick string in the New Hampshire format."
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eaton-lab/toytree | toytree/TreeParser.py | NexusParser.extract_tree_block | def extract_tree_block(self):
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lines = iter(self.data)
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except StopIteration:
break
# enter trees block
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"iterate through data file to extract trees"
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eaton-lab/toytree | versioner.py | parse_command_line | def parse_command_line():
""" Parse CLI args."""
## create the parser
parser = argparse.ArgumentParser(
formatter_class=argparse.RawDescriptionHelpFormatter,
epilog="""
* Example command-line usage:
## push test branch to conda --label=conda-test for travis CI
./versioner.py -p toyt... | python | def parse_command_line():
""" Parse CLI args."""
## create the parser
parser = argparse.ArgumentParser(
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eaton-lab/toytree | versioner.py | Version.get_git_status | def get_git_status(self):
"""
Gets git and init versions and commits since the init version
"""
## get git branch
self._get_git_branch()
## get tag in the init file
self._get_init_release_tag()
## get log commits since <tag>
try:
self... | python | def get_git_status(self):
"""
Gets git and init versions and commits since the init version
"""
## get git branch
self._get_git_branch()
## get tag in the init file
self._get_init_release_tag()
## get log commits since <tag>
try:
self... | [
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eaton-lab/toytree | versioner.py | Version.push_git_package | def push_git_package(self):
"""
if no conflicts then write new tag to
"""
## check for conflicts, then write to local files
self._pull_branch_from_origin()
## log commits to releasenotes
if self.deploy:
self._write_commits_to_release_notes()
... | python | def push_git_package(self):
"""
if no conflicts then write new tag to
"""
## check for conflicts, then write to local files
self._pull_branch_from_origin()
## log commits to releasenotes
if self.deploy:
self._write_commits_to_release_notes()
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eaton-lab/toytree | versioner.py | Version._pull_branch_from_origin | def _pull_branch_from_origin(self):
"""
Pulls from origin/master, if you have unmerged conflicts
it will raise an exception. You will need to resolve these.
"""
try:
## self.repo.git.pull()
subprocess.check_call(["git", "pull", "origin", self.branch])
... | python | def _pull_branch_from_origin(self):
"""
Pulls from origin/master, if you have unmerged conflicts
it will raise an exception. You will need to resolve these.
"""
try:
## self.repo.git.pull()
subprocess.check_call(["git", "pull", "origin", self.branch])
... | [
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eaton-lab/toytree | versioner.py | Version._get_init_release_tag | def _get_init_release_tag(self):
"""
parses init.py to get previous version
"""
self.init_version = re.search(r"^__version__ = ['\"]([^'\"]*)['\"]",
open(self.init_file, "r").read(),
re.M).group(1) | python | def _get_init_release_tag(self):
"""
parses init.py to get previous version
"""
self.init_version = re.search(r"^__version__ = ['\"]([^'\"]*)['\"]",
open(self.init_file, "r").read(),
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eaton-lab/toytree | versioner.py | Version._get_log_commits | def _get_log_commits(self):
"""
calls git log to complile a change list
"""
## check if update is necessary
cmd = "git log --pretty=oneline {}..".format(self.init_version)
cmdlist = shlex.split(cmd)
commits = subprocess.check_output(cmdlist)
## Sp... | python | def _get_log_commits(self):
"""
calls git log to complile a change list
"""
## check if update is necessary
cmd = "git log --pretty=oneline {}..".format(self.init_version)
cmdlist = shlex.split(cmd)
commits = subprocess.check_output(cmdlist)
## Sp... | [
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eaton-lab/toytree | versioner.py | Version._write_commits_to_release_notes | def _write_commits_to_release_notes(self):
"""
writes commits to the releasenotes file by appending to the end
"""
with open(self.release_file, 'a') as out:
out.write("==========\n{}\n".format(self.tag))
for commit in self.commits:
try:
... | python | def _write_commits_to_release_notes(self):
"""
writes commits to the releasenotes file by appending to the end
"""
with open(self.release_file, 'a') as out:
out.write("==========\n{}\n".format(self.tag))
for commit in self.commits:
try:
... | [
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eaton-lab/toytree | versioner.py | Version._write_new_tag_to_init | def _write_new_tag_to_init(self):
"""
Write version to __init__.py by editing in place
"""
for line in fileinput.input(self.init_file, inplace=1):
if line.strip().startswith("__version__"):
line = "__version__ = \"" + self.tag + "\""
print(line.str... | python | def _write_new_tag_to_init(self):
"""
Write version to __init__.py by editing in place
"""
for line in fileinput.input(self.init_file, inplace=1):
if line.strip().startswith("__version__"):
line = "__version__ = \"" + self.tag + "\""
print(line.str... | [
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eaton-lab/toytree | versioner.py | Version._write_branch_and_tag_to_meta_yaml | def _write_branch_and_tag_to_meta_yaml(self):
"""
Write branch and tag to meta.yaml by editing in place
"""
## set the branch to pull source from
with open(self.meta_yaml.replace("meta", "template"), 'r') as infile:
dat = infile.read()
newdat = dat.format(... | python | def _write_branch_and_tag_to_meta_yaml(self):
"""
Write branch and tag to meta.yaml by editing in place
"""
## set the branch to pull source from
with open(self.meta_yaml.replace("meta", "template"), 'r') as infile:
dat = infile.read()
newdat = dat.format(... | [
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eaton-lab/toytree | versioner.py | Version._revert_tag_in_init | def _revert_tag_in_init(self):
"""
Write version to __init__.py by editing in place
"""
for line in fileinput.input(self.init_file, inplace=1):
if line.strip().startswith("__version__"):
line = "__version__ = \"" + self.init_version + "\""
print(li... | python | def _revert_tag_in_init(self):
"""
Write version to __init__.py by editing in place
"""
for line in fileinput.input(self.init_file, inplace=1):
if line.strip().startswith("__version__"):
line = "__version__ = \"" + self.init_version + "\""
print(li... | [
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eaton-lab/toytree | versioner.py | Version._push_new_tag_to_git | def _push_new_tag_to_git(self):
"""
tags a new release and pushes to origin/master
"""
print("Pushing new version to git")
## stage the releasefile and initfileb
subprocess.call(["git", "add", self.release_file])
subprocess.call(["git", "add", self.in... | python | def _push_new_tag_to_git(self):
"""
tags a new release and pushes to origin/master
"""
print("Pushing new version to git")
## stage the releasefile and initfileb
subprocess.call(["git", "add", self.release_file])
subprocess.call(["git", "add", self.in... | [
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eaton-lab/toytree | versioner.py | Version.build_conda_packages | def build_conda_packages(self):
"""
Run the Linux build and use converter to build OSX
"""
## check if update is necessary
#if self.nversion == self.pversion:
# raise SystemExit("Exited: new version == existing version")
## tmp dir
bldir = "./tmp-bld"
... | python | def build_conda_packages(self):
"""
Run the Linux build and use converter to build OSX
"""
## check if update is necessary
#if self.nversion == self.pversion:
# raise SystemExit("Exited: new version == existing version")
## tmp dir
bldir = "./tmp-bld"
... | [
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] | train | https://github.com/eaton-lab/toytree/blob/0347ed2098acc5f707fadf52a0ecd411a6d1859c/versioner.py#L247-L285 |
doakey3/DashTable | dashtable/dashutils/get_span_row_count.py | get_span_row_count | def get_span_row_count(span):
"""
Gets the number of rows included in a span
Parameters
----------
span : list of lists of int
The [row, column] pairs that make up the span
Returns
-------
rows : int
The number of rows included in the span
Example
-------
C... | python | def get_span_row_count(span):
"""
Gets the number of rows included in a span
Parameters
----------
span : list of lists of int
The [row, column] pairs that make up the span
Returns
-------
rows : int
The number of rows included in the span
Example
-------
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The [row, column] pairs that make up the span
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-------
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The number of rows included in the span
Example
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quantmind/dynts | dynts/utils/section.py | asarray | def asarray(x, dtype=None):
'''Convert ``x`` into a ``numpy.ndarray``.'''
iterable = scalarasiter(x)
if isinstance(iterable, ndarray):
return iterable
else:
if not hasattr(iterable, '__len__'):
iterable = list(iterable)
if dtype == object_type:
a ... | python | def asarray(x, dtype=None):
'''Convert ``x`` into a ``numpy.ndarray``.'''
iterable = scalarasiter(x)
if isinstance(iterable, ndarray):
return iterable
else:
if not hasattr(iterable, '__len__'):
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if dtype == object_type:
a ... | [
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quantmind/dynts | dynts/utils/section.py | ascolumn | def ascolumn(x, dtype = None):
'''Convert ``x`` into a ``column``-type ``numpy.ndarray``.'''
x = asarray(x, dtype)
return x if len(x.shape) >= 2 else x.reshape(len(x),1) | python | def ascolumn(x, dtype = None):
'''Convert ``x`` into a ``column``-type ``numpy.ndarray``.'''
x = asarray(x, dtype)
return x if len(x.shape) >= 2 else x.reshape(len(x),1) | [
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