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theonion/djes | djes/models.py | Indexable.to_dict | def to_dict(self):
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out = {}
fields = self.__class__.search_objects.mapping.properties.properties
for key in fields:
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theonion/djes | djes/models.py | Indexable.index | def index(self, refresh=False):
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theonion/djes | djes/models.py | Indexable.delete_index | def delete_index(self, refresh=False, ignore=None):
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theonion/djes | djes/models.py | Indexable.get_doc_types | def get_doc_types(cls, exclude_base=False):
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pvizeli/tellcore-net | tellcorenet.py | TellCoreClient.start | def start(self):
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ssato/python-anytemplate | anytemplate/engines/jinja2.py | _load_file_itr | def _load_file_itr(files, encoding):
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ssato/python-anytemplate | anytemplate/engines/jinja2.py | FileSystemExLoader.get_source | def get_source(self, environment, template):
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ssato/python-anytemplate | anytemplate/engines/jinja2.py | Engine._render | def _render(self, template, context, is_file, at_paths=None,
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ssato/python-anytemplate | anytemplate/engines/jinja2.py | Engine.renders_impl | def renders_impl(self, template_content, context, **opts):
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PMBio/limix-backup | limix/deprecated/archive/qtl_old.py | estimateKronCovariances | def estimateKronCovariances(phenos,K1r=None,K1c=None,K2r=None,K2c=None,covs=None,Acovs=None,covar_type='lowrank_diag',rank=1):
"""
estimates the background covariance model before testing
Args:
phenos: [N x P] SP.array of P phenotypes for N individuals
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PMBio/limix-backup | limix/deprecated/archive/qtl_old.py | updateKronCovs | def updateKronCovs(covs,Acovs,N,P):
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PMBio/limix-backup | limix/deprecated/archive/qtl_old.py | simple_interaction_kronecker_deprecated | def simple_interaction_kronecker_deprecated(snps,phenos,covs=None,Acovs=None,Asnps1=None,Asnps0=None,K1r=None,K1c=None,K2r=None,K2c=None,covar_type='lowrank_diag',rank=1,searchDelta=False):
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PMBio/limix-backup | limix/deprecated/archive/qtl_old.py | simple_interaction_kronecker | def simple_interaction_kronecker(snps,phenos,covs=None,Acovs=None,Asnps1=None,Asnps0=None,K1r=None,K1c=None,K2r=None,K2c=None,covar_type='lowrank_diag',rank=1,NumIntervalsDelta0=100,NumIntervalsDeltaAlt=0,searchDelta=False):
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PMBio/limix-backup | limix/deprecated/archive/qtl_old.py | kronecker_lmm | def kronecker_lmm(snps,phenos,covs=None,Acovs=None,Asnps=None,K1r=None,K1c=None,K2r=None,K2c=None,covar_type='lowrank_diag',rank=1,NumIntervalsDelta0=100,NumIntervalsDeltaAlt=0,searchDelta=False):
"""
simple wrapper for kroneckerLMM code
Args:
snps: [N x S] SP.array of S SNPs for N individuals (t... | python | def kronecker_lmm(snps,phenos,covs=None,Acovs=None,Asnps=None,K1r=None,K1c=None,K2r=None,K2c=None,covar_type='lowrank_diag',rank=1,NumIntervalsDelta0=100,NumIntervalsDeltaAlt=0,searchDelta=False):
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PMBio/limix-backup | limix/deprecated/archive/qtl_old.py | simple_lmm | def simple_lmm(snps,pheno,K=None,covs=None, test='lrt',NumIntervalsDelta0=100,NumIntervalsDeltaAlt=0,searchDelta=False):
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PMBio/limix-backup | limix/deprecated/archive/qtl_old.py | interact_GxG | def interact_GxG(pheno,snps1,snps2=None,K=None,covs=None):
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pheno: [N x 1] SP.array of 1 phenotype for N individuals
snps1: [N x S1] SP.array of S1 SNPs for N individuals
snps2: [N x S2] SP.array of S2 SNPs for N individuals
... | python | def interact_GxG(pheno,snps1,snps2=None,K=None,covs=None):
"""
Epistasis test between two sets of SNPs
Args:
pheno: [N x 1] SP.array of 1 phenotype for N individuals
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PMBio/limix-backup | limix/deprecated/archive/qtl_old.py | interact_GxE_1dof | def interact_GxE_1dof(snps,pheno,env,K=None,covs=None, test='lrt'):
"""
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Args:
snps: [N x S] SP.array of S SNPs for N individuals
pheno: [N x 1] SP.array of 1 phenotype ... | python | def interact_GxE_1dof(snps,pheno,env,K=None,covs=None, test='lrt'):
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PMBio/limix-backup | limix/deprecated/archive/qtl_old.py | phenSpecificEffects | def phenSpecificEffects(snps,pheno1,pheno2,K=None,covs=None,test='lrt'):
"""
Univariate fixed effects interaction test for phenotype specific SNP effects
Args:
snps: [N x S] SP.array of S SNPs for N individuals (test SNPs)
pheno1: [N x 1] SP.array of 1 phenotype for N individuals
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"""
Univariate fixed effects interaction test for phenotype specific SNP effects
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PMBio/limix-backup | limix/deprecated/archive/qtl_old.py | simple_interaction | def simple_interaction(snps,pheno,Inter,Inter0=None,covs = None,K=None,test='lrt'):
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I-variate fixed effects interaction test for phenotype specific SNP effects
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snps: [N x S] SP.array of S SNPs for N individuals (test SNPs)
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PMBio/limix-backup | limix/deprecated/archive/qtl_old.py | forward_lmm_kronecker | def forward_lmm_kronecker(snps,phenos,Asnps=None,Acond=None,K1r=None,K1c=None,K2r=None,K2c=None,covs=None,Acovs=None,threshold = 5e-8, maxiter = 2,qvalues=False, update_covariances = False,**kw_args):
"""
Kronecker fixed effects test with forward selection
Args:
snps: [N x S] SP.array of S SNPs f... | python | def forward_lmm_kronecker(snps,phenos,Asnps=None,Acond=None,K1r=None,K1c=None,K2r=None,K2c=None,covs=None,Acovs=None,threshold = 5e-8, maxiter = 2,qvalues=False, update_covariances = False,**kw_args):
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PMBio/limix-backup | limix/deprecated/archive/qtl_old.py | forward_lmm | def forward_lmm(snps,pheno,K=None,covs=None,qvalues=False,threshold = 5e-8, maxiter = 2,test='lrt',**kw_args):
"""
univariate fixed effects test with forward selection
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StyXman/ayrton | ayrton/parser/pyparser/parser.py | Parser.prepare | def prepare(self, start=-1):
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StyXman/ayrton | ayrton/parser/pyparser/parser.py | Parser.classify | def classify(self, token_type, value, lineno, column, line):
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tchx84/grestful | grestful/object.py | Object._call | def _call(self, method, url, params, uploads):
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tchx84/grestful | grestful/object.py | Object._updated_cb | def _updated_cb(self, downtotal, downdone, uptotal, updone):
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praekelt/django-moderator | moderator/management/commands/classifycomments.py | Command.handle | def handle(self, *args, **options):
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Collect all comments that hasn't already been
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Order randomly so we don't rehash previously unsure classifieds
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"""
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xmikos/reparser | reparser.py | Segment.update_text | def update_text(self, token, match):
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xmikos/reparser | reparser.py | Parser.get_params | def get_params(self, token_stack):
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xmikos/reparser | reparser.py | Parser.remove_token | def remove_token(self, token_stack, token):
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xmikos/reparser | reparser.py | Parser.parse | def parse(self, text):
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"""
:return: Whether the engine can process given template file or not.
"""
if anytemplate.compat.IS_PYTHON_3:
cls._priority = 99
return False # Always as it's not ported to python 3.
return super(Engine, cls).suppo... | python | def supports(cls, template_file=None):
"""
:return: Whether the engine can process given template file or not.
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Render template.
:param context: A dict or dict-like object to instantiate given
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inveniosoftware-contrib/invenio-classifier | invenio_classifier/regexs.py | compute_arxiv_re | def compute_arxiv_re(report_pattern, report_number):
"""Compute arXiv report-number."""
if report_number is None:
report_number = r"\g<name>"
report_re = re.compile(r"(?<!<cds\.REPORTNUMBER>)(?<!\w)" +
"(?P<name>" + report_pattern + ")" +
old_arx... | python | def compute_arxiv_re(report_pattern, report_number):
"""Compute arXiv report-number."""
if report_number is None:
report_number = r"\g<name>"
report_re = re.compile(r"(?<!<cds\.REPORTNUMBER>)(?<!\w)" +
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inveniosoftware-contrib/invenio-classifier | invenio_classifier/regexs.py | _create_regex_pattern_add_optional_spaces_to_word_characters | def _create_regex_pattern_add_optional_spaces_to_word_characters(word):
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inveniosoftware-contrib/invenio-classifier | invenio_classifier/regexs.py | get_reference_section_title_patterns | def get_reference_section_title_patterns():
"""Return a list of compiled regex patterns used to search for the title.
:return: (list) of compiled regex patterns.
"""
patterns = []
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u'r\u00C9f\... | python | def get_reference_section_title_patterns():
"""Return a list of compiled regex patterns used to search for the title.
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patterns = []
titles = [u'references',
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inveniosoftware-contrib/invenio-classifier | invenio_classifier/regexs.py | get_reference_line_numeration_marker_patterns | def get_reference_line_numeration_marker_patterns(prefix=u''):
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Marker of a reference line in a full-text document.
:param prefix: (string) the possible prefix to a reference line
:return: (list) of compiled regex patterns.
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inveniosoftware-contrib/invenio-classifier | invenio_classifier/regexs.py | get_post_reference_section_title_patterns | def get_post_reference_section_title_patterns():
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:return: (list) of compiled regex patterns.
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"""Return a list of compiled regex patterns for post title section.
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:return: (list) of compiled regex patterns.
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millar/provstore-api | provstore/bundle_manager.py | BundleManager.refresh | def refresh(self):
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Reload list of bundles from the store
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heuer/cablemap | cablemap.tm/cablemap/tm/handler.py | create_ctm_miohandler | def create_ctm_miohandler(fileobj, title=None, comment=None, register_prefixes=True, register_templates=True, detect_prefixes=False):
"""\
"""
handler = CTMHandler(fileobj)
handler.title = title
handler.comment = comment
handler.detect_prefixes = detect_prefixes
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heuer/cablemap | cablemap.tm/cablemap/tm/handler.py | create_xtm_miohandler | def create_xtm_miohandler(fileobj, title=None, comment=None):
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handler.comment = comment
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handler.comment = comment
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heuer/cablemap | cablemap.tm/cablemap/tm/handler.py | create_ctm_handler | def create_ctm_handler(fileobj, title=u'Cablegate Topic Map', comment=u'Generated by Cablemap - https://github.com/heuer/cablemap', detect_prefixes=False):
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heuer/cablemap | cablemap.tm/cablemap/tm/handler.py | create_xtm_handler | def create_xtm_handler(fileobj, title=u'Cablegate Topic Map', comment=u'Generated by Cablemap - https://github.com/heuer/cablemap'):
"""\
Returns a `ICableHandler` instance which writes XML Topic Maps syntax (XTM) 2.1.
`fileobj`
A file-like object.
"""
return MIOCableHandler(create_xtm_mioh... | python | def create_xtm_handler(fileobj, title=u'Cablegate Topic Map', comment=u'Generated by Cablemap - https://github.com/heuer/cablemap'):
"""\
Returns a `ICableHandler` instance which writes XML Topic Maps syntax (XTM) 2.1.
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A file-like object.
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heuer/cablemap | cablemap.tm/cablemap/tm/handler.py | BaseMIOCableHandler._occ | def _occ(self, value, typ, datatype=None):
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`value`
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The occurrence type
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heuer/cablemap | cablemap.tm/cablemap/tm/handler.py | BaseMIOCableHandler._assoc | def _assoc(self, typ, role1, player1, role2=None, player2=None, reifier=None):
"""\
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h.startAssociation(typ)
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if reifier:
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"""\
"""
h = self._handler
h.startAssociation(typ)
h.role(role1, player1)
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heuer/cablemap | cablemap.tm/cablemap/tm/handler.py | MIOCableHandler._handle_recipient | def _handle_recipient(self, typ, recipient):
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heuer/cablemap | cablemap.tm/cablemap/tm/handler.py | MIOCableHandler._handle_reference_cable | def _handle_reference_cable(self, reference, handler, reifier):
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heuer/cablemap | cablemap.tm/cablemap/tm/handler.py | MIOCableHandler._sent_by | def _sent_by(self, origin, cable):
"""\
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Topic identity (commonly a subject identifier) of the originator of the cable
`cable`
Topic identity (commonly a subject identifier) of the cable.
"""
self._assoc(psis.SENT_BY_TYPE,
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"""\
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Topic identity (commonly a subject identifier) of the originator of the cable
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Topic identity (commonly a subject identifier) of the cable.
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ael-code/pyFsdb | fsdb/hashtools.py | calc_digest | def calc_digest(origin, algorithm="sha1", block_size=None):
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origin -- a readable object for which calculate digest
algorithn -- the algorithm to use. See ``hashlib.algorithms_available`` for supported algorithms.
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StyXman/ayrton | ayrton/execute.py | Command.prepare_fds | def prepare_fds (self):
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logger.debug ('_in: %r', i)
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StyXman/ayrton | ayrton/parser/pyparser/metaparser.py | nfa_to_dfa | def nfa_to_dfa(start, end):
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"""Convert an NFA to a DFA(s)
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limodou/par | par/md.py | MarkdownHtmlVisitor.visit_wiki_link | def visit_wiki_link(self, node):
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[[(wiki:)name(#anchor)(|alter name)]]
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PMBio/limix-backup | limix/stats/geno_summary.py | calc_AF | def calc_AF(M,major=0,minor=2):
"""calculate minor allelel frequency, by default assuming that minor==2"""
if minor==2:
Nhet = (M==0).sum(axis=0)
Nmajor = 2*(M==0).sum(axis=0)
Nminor = 2*(M==2).sum(axis=0)
af = Nminor/sp.double(2*M.shape[0])
else:
Nmajor = (M==0).s... | python | def calc_AF(M,major=0,minor=2):
"""calculate minor allelel frequency, by default assuming that minor==2"""
if minor==2:
Nhet = (M==0).sum(axis=0)
Nmajor = 2*(M==0).sum(axis=0)
Nminor = 2*(M==2).sum(axis=0)
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PMBio/limix-backup | limix/stats/geno_summary.py | calc_LD | def calc_LD(M,pos,i_start=[0],max_dist=1000000):
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M: genotype matrix
pos: position vector
i_start: index to start from for LD calculation
dist: distance
"""
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M: genotype matrix
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dist: distance
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StyXman/ayrton | ayrton/expansion.py | ToExpand.expand_one | def expand_one (self):
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left_cb, right_cb= data
prefix= self.text[:left_cb]
# the body includes the {}'s
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postfix= self.text[righ... | python | def expand_one (self):
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wilzbach/smarkov | smarkov/utils.py | get_suffixes | def get_suffixes(arr):
""" Returns all possible suffixes of an array (lazy evaluated)
Args:
arr: input array
Returns:
Array of all possible suffixes (as tuples)
"""
arr = tuple(arr)
return [arr]
return (arr[i:] for i in range(len(arr))) | python | def get_suffixes(arr):
""" Returns all possible suffixes of an array (lazy evaluated)
Args:
arr: input array
Returns:
Array of all possible suffixes (as tuples)
"""
arr = tuple(arr)
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wilzbach/smarkov | smarkov/utils.py | weighted_choice | def weighted_choice(item_probabilities):
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Args:
item_probabilities: list of (item, probability)-tuples
Returns:
random item according to the given weights
"""
probability_sum = sum(x[1] for x in item_probabilities)
assert pr... | python | def weighted_choice(item_probabilities):
""" Randomly choses an item according to defined weights
Args:
item_probabilities: list of (item, probability)-tuples
Returns:
random item according to the given weights
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probability_sum = sum(x[1] for x in item_probabilities)
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benjamin-hodgson/build | src/build/__init__.py | evaluate_callables | def evaluate_callables(data):
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whtsky/parguments | parguments/cli.py | prompt | def prompt(name, default=None):
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Grab user input from command line.
:param name: prompt text
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Grab user input from command line.
:param name: prompt text
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KelSolaar/Foundations | foundations/guerilla.py | attribute_warfare | def attribute_warfare(object):
"""
Alterates object attributes using guerilla / monkey patching.
:param object: Object to alterate.
:type object: object
:return: Object.
:rtype: object
"""
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"""
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KelSolaar/Foundations | foundations/guerilla.py | base_warfare | def base_warfare(name, bases, attributes):
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pennlabs/penncoursereview-sdk-python | penncoursereview/api.py | Resource._update | def _update(self, data):
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rjw57/starman | starman/stats.py | MultivariateNormal.rvs | def rvs(self, size=1):
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Args:
size (int or tuple): Shape of return value. Each element is drawn
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"""
return np.random.multivariate_normal(self.mean, self.cov, size) | python | def rvs(self, size=1):
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carta/franz | franz/kafka/producer.py | Producer._send_message_to_topic | def _send_message_to_topic(self, topic, message):
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carta/franz | franz/kafka/producer.py | Producer.check_for_message_exception | def check_for_message_exception(cls, message_result):
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message_result : FutureRecordMetadata
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heuer/cablemap | examples/converttocsv.py | generate_csv | def generate_csv(in_dir, out):
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KelSolaar/Foundations | foundations/rotating_backup.py | RotatingBackup.source | def source(self, value):
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KelSolaar/Foundations | foundations/rotating_backup.py | RotatingBackup.destination | def destination(self, value):
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KelSolaar/Foundations | foundations/rotating_backup.py | RotatingBackup.count | def count(self, value):
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KelSolaar/Foundations | foundations/rotating_backup.py | RotatingBackup.backup | def backup(self):
"""
Does the rotating backup.
:return: Method success.
:rtype: bool
"""
LOGGER.debug("> Storing '{0}' file backup.".format(self.__source))
foundations.common.path_exists(self.__destination) or foundations.io.set_directory(self.__destination)
... | python | def backup(self):
"""
Does the rotating backup.
:return: Method success.
:rtype: bool
"""
LOGGER.debug("> Storing '{0}' file backup.".format(self.__source))
foundations.common.path_exists(self.__destination) or foundations.io.set_directory(self.__destination)
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KelSolaar/Foundations | foundations/common.py | ordered_uniqify | def ordered_uniqify(sequence):
"""
Uniqifies the given hashable sequence while preserving its order.
:param sequence: Sequence.
:type sequence: object
:return: Uniqified sequence.
:rtype: list
"""
items = set()
return [key for key in sequence if key not in items and not items.add(k... | python | def ordered_uniqify(sequence):
"""
Uniqifies the given hashable sequence while preserving its order.
:param sequence: Sequence.
:type sequence: object
:return: Uniqified sequence.
:rtype: list
"""
items = set()
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KelSolaar/Foundations | foundations/common.py | unpack_default | def unpack_default(iterable, length=3, default=None):
"""
Unpacks given iterable maintaining given length and filling missing entries with given default.
:param iterable: iterable.
:type iterable: object
:param length: Iterable length.
:type length: int
:param default: Filling default objec... | python | def unpack_default(iterable, length=3, default=None):
"""
Unpacks given iterable maintaining given length and filling missing entries with given default.
:param iterable: iterable.
:type iterable: object
:param length: Iterable length.
:type length: int
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KelSolaar/Foundations | foundations/common.py | dependency_resolver | def dependency_resolver(dependencies):
"""
Resolves given dependencies.
:param dependencies: Dependencies to resolve.
:type dependencies: dict
:return: Resolved dependencies.
:rtype: list
"""
items = dict((key, set(dependencies[key])) for key in dependencies)
resolved_dependencies ... | python | def dependency_resolver(dependencies):
"""
Resolves given dependencies.
:param dependencies: Dependencies to resolve.
:type dependencies: dict
:return: Resolved dependencies.
:rtype: list
"""
items = dict((key, set(dependencies[key])) for key in dependencies)
resolved_dependencies ... | [
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KelSolaar/Foundations | foundations/common.py | is_internet_available | def is_internet_available(ips=CONNECTION_IPS, timeout=1.0):
"""
Returns if an internet connection is available.
:param ips: Address ips to check against.
:type ips: list
:param timeout: Timeout in seconds.
:type timeout: int
:return: Is internet available.
:rtype: bool
"""
whil... | python | def is_internet_available(ips=CONNECTION_IPS, timeout=1.0):
"""
Returns if an internet connection is available.
:param ips: Address ips to check against.
:type ips: list
:param timeout: Timeout in seconds.
:type timeout: int
:return: Is internet available.
:rtype: bool
"""
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KelSolaar/Foundations | foundations/common.py | get_host_address | def get_host_address(host=None, default_address=DEFAULT_HOST_IP):
"""
Returns the given host address.
:param host: Host to retrieve the address.
:type host: unicode
:param default_address: Default address if the host is unreachable.
:type default_address: unicode
:return: Host address.
... | python | def get_host_address(host=None, default_address=DEFAULT_HOST_IP):
"""
Returns the given host address.
:param host: Host to retrieve the address.
:type host: unicode
:param default_address: Default address if the host is unreachable.
:type default_address: unicode
:return: Host address.
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getfleety/coralillo | coralillo/core.py | Form.validate | def validate(cls, **kwargs):
''' Validates the data received as keyword arguments whose name match
this class attributes. '''
# errors can store multiple errors
# obj is an instance in case validation succeeds
# redis is needed for database validation
errors = ValidationE... | python | def validate(cls, **kwargs):
''' Validates the data received as keyword arguments whose name match
this class attributes. '''
# errors can store multiple errors
# obj is an instance in case validation succeeds
# redis is needed for database validation
errors = ValidationE... | [
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