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def get_statuses(pr, session): base_url = pr['_links']['statuses']['href'] statuses = [] for i in count(): new_statuses = fetch_page(base_url, i, session) if ((not new_statuses) or ('context' not in new_statuses[0])): break statuses.extend(new_statuses) by_context = {} for s in statuses: by_context.setdefault(s['context'], []).append(s) return map(final_status, by_context.values())
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get all of the statuses for a pull request .
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@click.command(u'remove-from-installed-apps') @click.argument(u'app') @pass_context def remove_from_installed_apps(context, app): from frappe.installer import remove_from_installed_apps for site in context.sites: try: frappe.init(site=site) frappe.connect() remove_from_installed_apps(app) finally: frappe.destroy()
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remove app from sites installed-apps list .
train
false
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def prepare_token_request(grant_type, body=u'', **kwargs): params = [(u'grant_type', grant_type)] if (u'scope' in kwargs): kwargs[u'scope'] = list_to_scope(kwargs[u'scope']) for k in kwargs: if kwargs[k]: params.append((unicode_type(k), kwargs[k])) return add_params_to_qs(body, params)
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prepare the access token request .
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def getfslineno(obj): import _pytest._code try: code = _pytest._code.Code(obj) except TypeError: try: fn = (py.std.inspect.getsourcefile(obj) or py.std.inspect.getfile(obj)) except TypeError: return ('', (-1)) fspath = ((fn and py.path.local(fn)) or None) lineno = (-1) if fspath: try: (_, lineno) = findsource(obj) except IOError: pass else: fspath = code.path lineno = code.firstlineno assert isinstance(lineno, int) return (fspath, lineno)
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return source location for the given object .
train
false
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def get_anonymous_cart_from_token(token, cart_queryset=Cart.objects.all()): return cart_queryset.open().filter(token=token, user=None).first()
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returns open anonymous cart with given token or none if not found .
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def connect_cloudtrail(aws_access_key_id=None, aws_secret_access_key=None, **kwargs): from boto.cloudtrail.layer1 import CloudTrailConnection return CloudTrailConnection(aws_access_key_id=aws_access_key_id, aws_secret_access_key=aws_secret_access_key, **kwargs)
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connect to aws cloudtrail :type aws_access_key_id: string .
train
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def register_module(mod): for f in dir(mod.lib): f = getattr(mod.lib, f) if isinstance(f, BuiltinFunctionType): _ool_func_types[f] = mod.ffi.typeof(f) addr = mod.ffi.addressof(mod.lib, f.__name__) _ool_func_ptr[f] = int(mod.ffi.cast('uintptr_t', addr)) _ffi_instances.add(mod.ffi)
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add typing for all functions in an out-of-line cffi module to the typemap .
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def etc_services(attrs=None, where=None): return _osquery_cmd(table='etc_services', attrs=attrs, where=where)
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return etc_services information from osquery cli example: .
train
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def periphery(G, e=None): if (e is None): e = eccentricity(G) diameter = max(e.values()) p = [v for v in e if (e[v] == diameter)] return p
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return the periphery of the graph g .
train
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def performance_log(request): event = {'ip': _get_request_header(request, 'REMOTE_ADDR'), 'referer': _get_request_header(request, 'HTTP_REFERER'), 'accept_language': _get_request_header(request, 'HTTP_ACCEPT_LANGUAGE'), 'event_source': 'browser', 'event': _get_request_value(request, 'event'), 'agent': _get_request_header(request, 'HTTP_USER_AGENT'), 'page': _get_request_value(request, 'page'), 'id': _get_request_value(request, 'id'), 'expgroup': _get_request_value(request, 'expgroup'), 'value': _get_request_value(request, 'value'), 'time': datetime.datetime.utcnow(), 'host': _get_request_header(request, 'SERVER_NAME')} log.info(json.dumps(event, cls=DateTimeJSONEncoder)) return HttpResponse(status=204)
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log when post call to "performance" url is made by a user .
train
false
35,268
def add_error_class(klass, code): if (not isinstance(code, python.str_types)): code = code.decode('utf-8') if (not isinstance(klass, python.class_types)): raise TypeError('klass must be a class type') mro = inspect.getmro(klass) if (not (Exception in mro)): raise TypeError('Error classes must subclass the __builtin__.Exception class') if (code in ERROR_CLASS_MAP): raise ValueError(('Code %s is already registered' % (code,))) ERROR_CLASS_MAP[code] = klass
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maps an exception class to a string code .
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true
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def is_increasing(f, interval=S.Reals, symbol=None): f = sympify(f) free_sym = f.free_symbols if (symbol is None): if (len(free_sym) > 1): raise NotImplementedError('is_increasing has not yet been implemented for all multivariate expressions') if (len(free_sym) == 0): return True symbol = free_sym.pop() df = f.diff(symbol) df_nonneg_interval = solveset((df >= 0), symbol, domain=S.Reals) return interval.is_subset(df_nonneg_interval)
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returns if a function is increasing or not .
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def classlock(f): def inner(self, *args, **kwargs): curframe = inspect.currentframe() calframe = inspect.getouterframes(curframe, 2) if calframe[1][1].endswith('database.py'): return f(self, *args, **kwargs) with self._lock: return f(self, *args, **kwargs) return inner
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classlock decorator .
train
false
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def _loadDescriptionFile(descriptionPyPath): global g_descriptionImportCount if (not os.path.isfile(descriptionPyPath)): raise RuntimeError((('Experiment description file %s does not exist or ' + 'is not a file') % (descriptionPyPath,))) mod = imp.load_source(('pf_description%d' % g_descriptionImportCount), descriptionPyPath) g_descriptionImportCount += 1 if (not hasattr(mod, 'descriptionInterface')): raise RuntimeError(('Experiment description file %s does not define %s' % (descriptionPyPath, 'descriptionInterface'))) if (not isinstance(mod.descriptionInterface, expdescriptionapi.DescriptionIface)): raise RuntimeError((('Experiment description file %s defines %s but it ' + 'is not DescriptionIface-based') % (descriptionPyPath, name))) return mod
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loads a description file and returns it as a module .
train
true
35,273
def _set_properties_for_image(context, image_ref, properties, purge_props=False, session=None): orig_properties = {} for prop_ref in image_ref.properties: orig_properties[prop_ref.name] = prop_ref for (name, value) in properties.iteritems(): prop_values = {'image_id': image_ref.id, 'name': name, 'value': value} if (name in orig_properties): prop_ref = orig_properties[name] _image_property_update(context, prop_ref, prop_values, session=session) else: image_property_create(context, prop_values, session=session) if purge_props: for key in orig_properties.keys(): if (key not in properties): prop_ref = orig_properties[key] image_property_delete(context, prop_ref, session=session)
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create or update a set of image_properties for a given image .
train
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def hubCapacity(): from multiprocessing import Pool import itertools print 'Hub capacity test' p = Pool(2) results = p.map(worker, itertools.product([1, 2, 3, 4, 5, 6, 7, 8], xrange(1, 2000, 200))) f = open('results-numPerfect.11.22.10.txt', 'w') for (i, r) in enumerate(results): print >>f, ('{%d,%d,%d,%d,%d,%d,%d,%d,%d},' % r) f.close()
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study hub capacity .
train
false
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def _parse_response(header_data, ignore_bad_cookies=False, ignore_bad_attributes=True): cookie_dicts = [] for line in Definitions.EOL.split(header_data.strip()): if (not line): break cookie_dict = parse_one_response(line, ignore_bad_cookies=ignore_bad_cookies, ignore_bad_attributes=ignore_bad_attributes) if (not cookie_dict): continue cookie_dicts.append(cookie_dict) if (not cookie_dicts): if (not ignore_bad_cookies): raise InvalidCookieError(data=header_data) _report_invalid_cookie(header_data) return cookie_dicts
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turn one or more lines of set-cookie: header data into a list of dicts mapping attribute names to attribute values .
train
true
35,277
@with_setup(step_runner_environ) def test_steps_are_aware_of_its_definitions(): f = Feature.from_string(FEATURE1) feature_result = f.run() scenario_result = feature_result.scenario_results[0] for step in scenario_result.steps_passed: assert step.has_definition step1 = scenario_result.steps_passed[0] assert_equals(step1.defined_at.line, 124) assert_equals(step1.defined_at.file, core.fs.relpath(__file__.rstrip('c')))
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steps are aware of its definitions line numbers and file names .
train
false
35,278
def get_volume_type(ctxt, id, expected_fields=None): if (id is None): msg = _('id cannot be None') raise exception.InvalidVolumeType(reason=msg) if (ctxt is None): ctxt = context.get_admin_context() return db.volume_type_get(ctxt, id, expected_fields=expected_fields)
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retrieves single volume type by id .
train
false
35,279
@requires_segment_info def frame_lister(pl, segment_info, full_stack=False, maxframes=3): if full_stack: initial_stack_length = 0 frames = segment_info[u'pdb'].stack else: initial_stack_length = segment_info[u'initial_stack_length'] frames = segment_info[u'pdb'].stack[initial_stack_length:] if (len(frames) > maxframes): frames = frames[(- maxframes):] return (({u'curframe': frame[0], u'initial_stack_length': initial_stack_length}, {}) for frame in frames)
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list all frames in segment_info format .
train
false
35,280
def exhaust_iterator(iterator): data = b('') try: chunk = b(next(iterator)) except StopIteration: chunk = b('') while (len(chunk) > 0): data += chunk try: chunk = b(next(iterator)) except StopIteration: chunk = b('') return data
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exhaust an iterator and return all data returned by it .
train
false
35,282
def at_server_stop(): pass
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this is called just before the server is shut down .
train
false
35,284
def pvariance(data, mu=None): if (iter(data) is data): data = list(data) n = len(data) if (n < 1): raise StatisticsError('pvariance requires at least one data point') (T, ss) = _ss(data, mu) return _convert((ss / n), T)
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return the population variance of data .
train
true
35,286
def makeFactory(configdict): pubkeyfile = os.path.join(_GAME_DIR, 'server', 'ssh-public.key') privkeyfile = os.path.join(_GAME_DIR, 'server', 'ssh-private.key') def chainProtocolFactory(username=None): return insults.ServerProtocol(configdict['protocolFactory'], *configdict.get('protocolConfigdict', (username,)), **configdict.get('protocolKwArgs', {})) rlm = PassAvatarIdTerminalRealm() rlm.transportFactory = TerminalSessionTransport_getPeer rlm.chainedProtocolFactory = chainProtocolFactory factory = ConchFactory(Portal(rlm)) factory.sessionhandler = configdict['sessions'] try: (publicKey, privateKey) = getKeyPair(pubkeyfile, privkeyfile) factory.publicKeys = {'ssh-rsa': publicKey} factory.privateKeys = {'ssh-rsa': privateKey} except Exception as err: print('getKeyPair error: {err}\n WARNING: Evennia could not auto-generate SSH keypair. Using conch default keys instead.\nIf this error persists, create {pub} and {priv} yourself using third-party tools.'.format(err=err, pub=pubkeyfile, priv=privkeyfile)) factory.services = factory.services.copy() factory.services['ssh-userauth'] = ExtraInfoAuthServer factory.portal.registerChecker(PlayerDBPasswordChecker(factory)) return factory
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creates the ssh server factory .
train
false
35,288
def _convertToNewStyle(newClass, oldInstance): if (oldInstance.__class__.__name__ == 'ExperimentHandler'): newHandler = psychopy.data.ExperimentHandler() else: newHandler = newClass([], 0) for thisAttrib in dir(oldInstance): if ('instancemethod' in str(type(getattr(oldInstance, thisAttrib)))): continue elif (thisAttrib == '__weakref__'): continue else: value = getattr(oldInstance, thisAttrib) setattr(newHandler, thisAttrib, value) return newHandler
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converts un-pickled old-style compatibility classes to new-style ones by initializing a new-style class and copying the old compatibility instances attributes .
train
false
35,291
def template_info(template_name): if (template_name in _template_info_cache): t_data = _template_info_cache[template_name] return (t_data['template_path'], t_data['template_type']) template_path = find_template(template_name) if (not template_path): raise TemplateNotFound(('Template %s cannot be found' % template_name)) t_type = template_type(template_path) if (not config.get('debug', False)): t_data = {'template_path': template_path, 'template_type': t_type} _template_info_cache[template_name] = t_data return (template_path, t_type)
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returns the path and type for a template .
train
false
35,292
def text_param(registry, xml_parent, data): base_param(registry, xml_parent, data, True, 'hudson.model.TextParameterDefinition')
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yaml: text a text parameter .
train
false
35,293
@manager.command def createall(): db.create_all()
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creates database tables .
train
false
35,294
def get_LEA_seq_consensus_seqs(fwd_read_f, rev_read_f, map_f, output_dir, barcode_type, barcode_len, barcode_correction_fn, max_barcode_errors, min_consensus, max_cluster_ratio, min_difference_in_bcs, fwd_length, rev_length, min_reads_per_random_bc, min_difference_clusters, barcode_column, reverse_primer_column): (bc_to_sid, bc_to_fwd_primers, bc_to_rev_primers) = process_mapping_file(map_f, barcode_len, barcode_type, barcode_column, reverse_primer_column) (random_bc_lookup, random_bc_reads, random_bcs, barcode_errors_exceed_max_count, barcode_not_in_map_count, primer_mismatch_count, seq_too_short_count, input_seqs_count, total_seqs_kept) = read_fwd_rev_read(fwd_read_f, rev_read_f, bc_to_sid, barcode_len, barcode_correction_fn, bc_to_fwd_primers, bc_to_rev_primers, max_barcode_errors, fwd_length, rev_length) consensus_seq_lookup = get_consensus_seqs_lookup(random_bc_lookup, random_bc_reads, random_bcs, min_difference_in_bcs, min_reads_per_random_bc, output_dir, min_difference_clusters, max_cluster_ratio, min_consensus) log_out = format_lea_seq_log(input_seqs_count, barcode_errors_exceed_max_count, barcode_not_in_map_count, primer_mismatch_count, seq_too_short_count, total_seqs_kept) return (consensus_seq_lookup, log_out)
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reads mapping file .
train
false
35,296
def StringToCMakeTargetName(a): return a.translate(string.maketrans(' /():."', '_______'))
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converts the given string a to a valid cmake target name .
train
false
35,298
def _number_format(val, dec): return ((dec and ((('%.' + str(dec)) + 'f') % val)) or int(round(val)))
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return float with dec decimals; if dec is 0 .
train
false
35,300
def retention_policy_add(database, name, duration, replication, default=False, user=None, password=None, host=None, port=None): client = _client(user=user, password=password, host=host, port=port) client.create_retention_policy(name, duration, replication, database, default) return True
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add a retention policy .
train
true
35,301
def grab_certbot_log(): sudo('if [ -f /var/log/letsencrypt/letsencrypt.log ]; then cat /var/log/letsencrypt/letsencrypt.log; else echo "[novarlog]"; fi') sudo('if [ -f ./certbot.log ]; then cat ./certbot.log; else echo "[nolocallog]"; fi')
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grabs letsencrypt .
train
false
35,302
def strip_ansi(source): return re.sub('\\033\\[(\\d|;)+?m', '', source)
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strip ansi sequences from text .
train
false
35,305
def update_version_number(file_obj, new_version_number): updated = u'{0}.updated_version_number'.format(file_obj.file_path) with zipfile.ZipFile(file_obj.file_path, 'r') as source: file_list = source.infolist() with zipfile.ZipFile(updated, 'w', zipfile.ZIP_DEFLATED) as dest: for file_ in file_list: content = source.read(file_.filename) if (file_.filename == 'install.rdf'): content = _update_version_in_install_rdf(content, new_version_number) if (file_.filename in ['package.json', 'manifest.json']): content = _update_version_in_json_manifest(content, new_version_number) dest.writestr(file_, content) shutil.move(updated, file_obj.file_path)
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update the manifest to have the new version number .
train
false
35,306
def stripped_path_components(path, strip_prefixes): normalized_path = os.path.abspath(path) sorted_strip_prefixes = sorted(strip_prefixes, key=len, reverse=True) for bp in sorted_strip_prefixes: normalized_bp = os.path.abspath(bp) if (normalized_bp == '/'): continue if normalized_path.startswith(normalized_bp): prefix = normalized_path[:len(normalized_bp)] result = [] for p in normalized_path[len(normalized_bp):].split('/'): if p: prefix += '/' prefix += p result.append((p, prefix)) return result return path_components(path)
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strip any prefix in strip_prefixes from path and return a list of path components where each component is .
train
false
35,308
def get_global_size(*args, **kargs): raise _stub_error
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opencl get_global_size() .
train
false
35,309
def _exit(code=0): try: code = int(code) except ValueError: pass raise SystemExit, code
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internal function .
train
false
35,310
def win_get_unicode_stream(stream, excepted_fileno, output_handle, encoding): old_fileno = getattr(stream, 'fileno', (lambda : None))() if (old_fileno == excepted_fileno): from ctypes import windll, WINFUNCTYPE from ctypes.wintypes import DWORD, HANDLE GetStdHandle = WINFUNCTYPE(HANDLE, DWORD)(('GetStdHandle', windll.kernel32)) real_output_handle = GetStdHandle(DWORD(output_handle)) if win_handle_is_a_console(real_output_handle): return WinUnicodeConsoleOutput(real_output_handle, old_fileno, stream.name, encoding) return WinUnicodeOutput(stream, old_fileno, encoding)
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returns a unicode-compatible stream .
train
false
35,311
@hook.command def munge(text): return formatting.munge(text)
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replaces characters in a string with visually similar characters to avoid pinging users in irc .
train
false
35,314
def enable_dhcp(): current = network() if (current['Network Settings']['DHCP_ENABLE']['VALUE'] == 'Y'): return True _xml = '<RIBCL VERSION="2.0">\n <LOGIN USER_LOGIN="adminname" PASSWORD="password">\n <RIB_INFO MODE="write">\n <MOD_NETWORK_SETTINGS>\n <DHCP_ENABLE value="Yes"/>\n </MOD_NETWORK_SETTINGS>\n </RIB_INFO>\n </LOGIN>\n </RIBCL>' return __execute_cmd('Enable_DHCP', _xml)
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enable dhcp cli example: .
train
false
35,316
def assert_event_matches(expected, actual, tolerate=None): differences = get_event_differences(expected, actual, tolerate=tolerate) if (len(differences) > 0): debug_info = ['', 'Expected:', block_indent(expected), 'Actual:', block_indent(actual), 'Tolerating:', block_indent(EventMatchTolerates.default_if_not_defined(tolerate))] differences = [('* ' + d) for d in differences] message_lines = (differences + debug_info) raise AssertionError(('Unexpected differences found in structs:\n\n' + '\n'.join(message_lines)))
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compare two event dictionaries .
train
false
35,317
def replace_file_special_chars(filename_path): return filename_path.replace(':', '_')
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this is a *very* incomplete function which i added to fix a bug: URL and after realizing that it was very hard to perform a replace that worked for all platforms and when the thing to sanitize was a path+filename and not only a filename .
train
false
35,318
def award_badge(config, count, user): slug = config.get(count) if (not slug): return badge_class = BadgeClass.get_badge_class(slug=slug, issuing_component='openedx__course', create=False) if (not badge_class): return if (not badge_class.get_for_user(user)): badge_class.award(user)
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given one of the configurations for enrollments or completions .
train
false
35,320
def _community(G, u, community): node_u = G.node[u] try: return node_u[community] except KeyError: raise nx.NetworkXAlgorithmError('No community information')
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get the community of the given node .
train
false
35,321
def left_trim_lines(lines): lines_striped = list(zip(lines[1:], list(map(str.lstrip, lines[1:])))) lines_striped = list(filter(itemgetter(1), lines_striped)) indent = min(([(len(line) - len(striped)) for (line, striped) in lines_striped] + [sys.maxsize])) if (indent < sys.maxsize): return [line[indent:] for line in lines] else: return list(lines)
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remove all unnecessary leading space from lines .
train
false
35,322
@require_POST @login_required def create_order(request): course_id = request.POST['course_id'] course_id = CourseKey.from_string(course_id) donation_for_course = request.session.get('donation_for_course', {}) contribution = request.POST.get('contribution', donation_for_course.get(unicode(course_id), 0)) try: amount = decimal.Decimal(contribution).quantize(decimal.Decimal('.01'), rounding=decimal.ROUND_DOWN) except decimal.InvalidOperation: return HttpResponseBadRequest(_('Selected price is not valid number.')) current_mode = None sku = request.POST.get('sku', None) if sku: try: current_mode = CourseMode.objects.get(sku=sku) except CourseMode.DoesNotExist: log.exception(u'Failed to find CourseMode with SKU [%s].', sku) if (not current_mode): paid_modes = CourseMode.paid_modes_for_course(course_id) if paid_modes: if (len(paid_modes) > 1): log.warn(u"Multiple paid course modes found for course '%s' for create order request", course_id) current_mode = paid_modes[0] if (not current_mode): log.warn(u"Create order requested for course '%s' without a paid mode.", course_id) return HttpResponseBadRequest(_("This course doesn't support paid certificates")) if CourseMode.is_professional_mode(current_mode): amount = current_mode.min_price if (amount < current_mode.min_price): return HttpResponseBadRequest(_('No selected price or selected price is below minimum.')) if current_mode.sku: payment_data = checkout_with_ecommerce_service(request.user, course_id, current_mode, request.POST.get('processor')) else: payment_data = checkout_with_shoppingcart(request, request.user, course_id, current_mode, amount) if ('processor' not in request.POST): payment_data = payment_data['payment_form_data'] return HttpResponse(json.dumps(payment_data), content_type='application/json')
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helper method for creating an order for testing .
train
false
35,323
def topic_parent_document_link(obj): if (not obj.parent_topic): return '' url = reverse('admin:wiki_document_change', args=[obj.parent_topic.id]) return ('<a href="%s">Topic&nbsp;Parent&nbsp;(#%s)</a>' % (url, obj.parent_topic.id))
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html link to the parent document for admin change list .
train
false
35,324
def get_series(model, extra_field=None, source=None, **filters): extra = (() if (extra_field is None) else (extra_field,)) qs = model.search().order_by('-date').filter(**filters).values_dict('date', 'count', *extra) if source: qs = qs.source(source) for val in qs[:365]: date_ = parse(val['date'][0]).date() rv = dict(count=val['count'][0], date=date_, end=date_) if source: rv['data'] = extract(val[source]) elif extra_field: rv['data'] = extract(val[extra_field]) (yield rv)
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get series .
train
false
35,325
def s2n_intel(string): x = 0 y = 0 for c in string: x = (x | (ord_(c) << y)) y += (+ 8) return x
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extract multi-byte integer in intel format .
train
true
35,326
def yenc_name_fixer(p): try: return p.decode('utf-8') except: return p.decode('cp1252', errors='replace').replace('?', '!')
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return unicode name of 8bit ascii string .
train
false
35,327
def _report_new_cert(config, cert_path, fullchain_path): expiry = crypto_util.notAfter(cert_path).date() reporter_util = zope.component.getUtility(interfaces.IReporter) if fullchain_path: and_chain = 'and chain have' path = fullchain_path else: and_chain = 'has ' path = cert_path verbswitch = (' with the "certonly" option' if (config.verb == 'run') else '') msg = 'Congratulations! Your certificate {0} been saved at {1}. Your cert will expire on {2}. To obtain a new or tweaked version of this certificate in the future, simply run {3} again{4}. To non-interactively renew *all* of your certificates, run "{3} renew"'.format(and_chain, path, expiry, cli.cli_command, verbswitch) reporter_util.add_message(msg, reporter_util.MEDIUM_PRIORITY)
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reports the creation of a new certificate to the user .
train
false
35,328
def is_valid_ipv6_prefix(ipv6_prefix): if (not isinstance(ipv6_prefix, str)): return False tokens = ipv6_prefix.split('/') if (len(tokens) != 2): return False return (is_valid_ipv6(tokens[0]) and is_valid_ip_prefix(tokens[1], 128))
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returns true if given ipv6_prefix is a valid ipv6 prefix .
train
true
35,330
def test_escape_if_necessary_escapes_nothing_if_has_more_than_1_char(): assert_equals(strings.escape_if_necessary('NOT ESCAPED'), 'NOT ESCAPED')
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escape if necessary does nothing if the string has more than 1 char .
train
false
35,331
@image_comparison(baseline_images=[u'tight_layout3']) def test_tight_layout3(): fig = plt.figure() ax1 = plt.subplot(221) ax2 = plt.subplot(223) ax3 = plt.subplot(122) example_plot(ax1) example_plot(ax2) example_plot(ax3) plt.tight_layout()
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test tight_layout for mutiple subplots .
train
false
35,332
def update_entity_in_table(key, validated_entity, datastore): datastore.batch_put_entity(APP_ENTITY_TABLE, [key], APP_ENTITY_SCHEMA, validated_entity)
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updates the app_entity_table with the valid entity .
train
false
35,334
def _calc_shared_phylotypes_multiple(otu_table, idxs): if (len(idxs) < 2): raise ValueError('calc_shared_phylotypes_multiple needs at least two sampleIDs to comapre') shared_phylos = ones(len(otu_table.ids(axis='observation'))) for id_ in idxs: shared_phylos = logical_and(shared_phylos, otu_table.data(id_, 'sample')) return shared_phylos.sum()
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calculate shared otus between several samples indexed by values in idxes .
train
false
35,335
def getNewRepository(): return ExportRepository()
[ "def", "getNewRepository", "(", ")", ":", "return", "ExportRepository", "(", ")" ]
get new repository .
train
false
35,336
def commit(): connection._commit() set_clean()
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to commit the changes loaded in the candidate configuration .
train
false
35,337
def dot_shape(x, y): if isinstance(x, LinearTransform): return dot_shape_from_shape(x, tuple(y.shape)) elif isinstance(y, LinearTransform): return dot_shape_from_shape(tuple(x.shape), y) else: raise TypeError('One of x or y should be a LinearTransform')
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return the linear transformation of y by x or x by y when one or both of x and y is a lineartransform instance parameters x : writeme y : writeme returns writeme .
train
false
35,338
def get_regions(service_name, region_cls=None, connection_cls=None): endpoints = load_regions() if (service_name not in endpoints): raise BotoClientError(("Service '%s' not found in endpoints." % service_name)) if (region_cls is None): region_cls = RegionInfo region_objs = [] for (region_name, endpoint) in endpoints.get(service_name, {}).items(): region_objs.append(region_cls(name=region_name, endpoint=endpoint, connection_cls=connection_cls)) return region_objs
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given a service name .
train
false
35,340
def filter_mapping_file_from_mapping_f(mapping_f, sample_ids_to_keep, negate=False): (mapping_data, header, comments) = parse_mapping_file(mapping_f) filtered_mapping_data = [] sample_ids_to_keep = {}.fromkeys(sample_ids_to_keep) for mapping_datum in mapping_data: hit = (mapping_datum[0] in sample_ids_to_keep) if (hit and (not negate)): filtered_mapping_data.append(mapping_datum) elif ((not hit) and negate): filtered_mapping_data.append(mapping_datum) else: pass return format_mapping_file(header, filtered_mapping_data)
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filter rows from a metadata mapping file .
train
false
35,341
def format_timedelta(datetime_or_timedelta, granularity='second', threshold=0.85): return get_i18n().format_timedelta(datetime_or_timedelta, granularity, threshold)
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wrapper around babels format_timedelta to make it user language aware .
train
false
35,344
@pytest.mark.usefixtures('break_getuser') @pytest.mark.skipif(sys.platform.startswith('win'), reason='no os.getuid on windows') def test_tmpdir_fallback_uid_not_found(testdir): testdir.makepyfile('\n import pytest\n def test_some(tmpdir):\n assert tmpdir.isdir()\n ') reprec = testdir.inline_run() reprec.assertoutcome(passed=1)
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test that tmpdir works even if the current processs user id does not correspond to a valid user .
train
false
35,347
def check_env_cache(opts, env_cache): if (not os.path.isfile(env_cache)): return None try: with salt.utils.fopen(env_cache, 'rb') as fp_: log.trace('Returning env cache data from {0}'.format(env_cache)) serial = salt.payload.Serial(opts) return serial.load(fp_) except (IOError, OSError): pass return None
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returns cached env names .
train
true
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def test_side_effect_completion(): _GlobalNameSpace.SideEffectContainer.foo = 1 side_effect = get_completion('SideEffectContainer', _GlobalNameSpace.__dict__) assert isinstance(side_effect._definition.base, mixed.MixedObject) foo = get_completion('SideEffectContainer.foo', _GlobalNameSpace.__dict__) assert (foo.name == 'foo')
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in the repl its possible to cause side effects that are not documented in python code .
train
false
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def remote_get(cwd, remote='origin', user=None, password=None, redact_auth=True, ignore_retcode=False): cwd = _expand_path(cwd, user) all_remotes = remotes(cwd, user=user, password=password, redact_auth=redact_auth, ignore_retcode=ignore_retcode) if (remote not in all_remotes): raise CommandExecutionError("Remote '{0}' not present in git checkout located at {1}".format(remote, cwd)) return all_remotes[remote]
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get the fetch and push url for a specific remote cwd the path to the git checkout remote : origin name of the remote to query user user under which to run the git command .
train
true
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def send_registration_completion_email(email, request, realm_creation=False): prereg_user = create_preregistration_user(email, request, realm_creation) context = {'support_email': settings.ZULIP_ADMINISTRATOR, 'verbose_support_offers': settings.VERBOSE_SUPPORT_OFFERS} return Confirmation.objects.send_confirmation(prereg_user, email, additional_context=context, host=request.get_host())
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send an email with a confirmation link to the provided e-mail so the user can complete their registration .
train
false
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def maybe_signature(d, app=None, clone=False): if (d is not None): if isinstance(d, abstract.CallableSignature): if clone: d = d.clone() elif isinstance(d, dict): d = signature(d) if (app is not None): d._app = app return d
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ensure obj is a signature .
train
false
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def justTransportResponse(transport): return Response(('HTTP', 1, 1), 200, 'OK', _boringHeaders, transport)
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helper function for creating a response which uses the given transport .
train
false
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def mobilityTest(): info('* Simple mobility test\n') net = Mininet(topo=LinearTopo(3), switch=MobilitySwitch) info('* Starting network:\n') net.start() printConnections(net.switches) info('* Testing network\n') net.pingAll() info('* Identifying switch interface for h1\n') (h1, old) = net.get('h1', 's1') for s in (2, 3, 1): new = net[('s%d' % s)] port = randint(10, 20) info('* Moving', h1, 'from', old, 'to', new, 'port', port, '\n') (hintf, sintf) = moveHost(h1, old, new, newPort=port) info('*', hintf, 'is now connected to', sintf, '\n') info('* Clearing out old flows\n') for sw in net.switches: sw.dpctl('del-flows') info('* New network:\n') printConnections(net.switches) info('* Testing connectivity:\n') net.pingAll() old = new net.stop()
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a simple test of mobility .
train
false
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def saveProfileDifferenceFromDefault(filename): global settingsList profileParser = ConfigParser.ConfigParser() profileParser.add_section('profile') for set in settingsList: if (set.isPreference() or set.isMachineSetting() or set.isAlteration()): continue if (set.getDefault() == set.getValue()): continue profileParser.set('profile', set.getName(), set.getValue().encode('utf-8')) try: profileParser.write(open(filename, 'w')) except: print ('Failed to write profile file: %s' % filename)
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save the current profile to an ini file .
train
false
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def annotate(**kwargs): if (not kwargs): raise ValueError('annotations must be provided as keyword arguments') def dec(f): if hasattr(f, '__annotations__'): for (k, v) in kwargs.items(): f.__annotations__[k] = v else: f.__annotations__ = kwargs return f return dec
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python 3 compatible function annotation for python 2 .
train
false
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def smartos_build(): with settings(hide('running', 'stdout')): return run('uname -v')
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get the build of smartos .
train
false
35,361
def _filter_values(vals, vlist=None, must=False): if (not vlist): return vals if isinstance(vlist, basestring): vlist = [vlist] res = [] for val in vlist: if (val in vals): res.append(val) if must: if res: return res else: raise MissingValue('Required attribute value missing') else: return res
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removes values from *vals* that does not appear in vlist .
train
false
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def remove_document_permissions(apps, schema_editor): ContentType = apps.get_model(u'contenttypes.ContentType') Permission = apps.get_model(u'auth.Permission') document_content_type = ContentType.objects.get(model=u'document', app_label=u'wagtaildocs') Permission.objects.filter(content_type=document_content_type, codename__in=(u'add_document', u'change_document', u'delete_document')).delete()
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reverse the above additions of permissions .
train
false
35,363
def install_pandas(): chdir(SRC_DIR) apt_command('build-dep pandas') run_command('pip install pandas')
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docstring for install_pandas .
train
false
35,364
def SimplifyNode(node): if (not node.getType()): return SimplifyNode(node.children[0]) elif ((node.getType() == QueryParser.CONJUNCTION) and (node.getChildCount() == 1)): return SimplifyNode(node.children[0]) elif ((node.getType() == QueryParser.DISJUNCTION) and (node.getChildCount() == 1)): return SimplifyNode(node.children[0]) elif (((node.getType() == QueryParser.EQ) or (node.getType() == QueryParser.HAS)) and (node.getChildCount() == 1)): return SimplifyNode(node.children[0]) for (i, child) in enumerate(node.children): node.setChild(i, SimplifyNode(child)) return node
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simplifies the node removing singleton conjunctions and others .
train
false
35,366
def _redirect_with_params(url_name, *args, **kwargs): url = urlresolvers.reverse(url_name, args=args) params = parse.urlencode(kwargs, True) return '{0}?{1}'.format(url, params)
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helper method to create a redirect response with url params .
train
true
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def _get_function_from_pyopengl(funcname): func = None try: func = getattr(_GL, funcname) except AttributeError: try: func = getattr(_FBO, funcname) except AttributeError: func = None if (not bool(func)): if funcname.endswith('f'): try: func = getattr(_GL, funcname[:(-1)]) except AttributeError: pass if (func is None): func = _make_unavailable_func(funcname) logger.warning(('warning: %s not available' % funcname)) return func
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try getting the given function from pyopengl .
train
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@register.simple_tag(takes_context=True) def escape_format_html(context): return format_html('Hello {0}!', context['name'])
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a tag that uses format_html .
train
false
35,371
def measure_partial(qubit, bits, format='sympy', normalize=True): m = qubit_to_matrix(qubit, format) if isinstance(bits, (int, Integer)): bits = (int(bits),) if (format == 'sympy'): if normalize: m = m.normalized() possible_outcomes = _get_possible_outcomes(m, bits) output = [] for outcome in possible_outcomes: prob_of_outcome = 0 prob_of_outcome += (outcome.H * outcome)[0] if (prob_of_outcome != 0): if normalize: next_matrix = matrix_to_qubit(outcome.normalized()) else: next_matrix = matrix_to_qubit(outcome) output.append((next_matrix, prob_of_outcome)) return output else: raise NotImplementedError("This function can't handle non-sympy matrix formats yet")
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perform a partial ensemble measure on the specifed qubits .
train
false
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def blend_channels_multiply(bottom_chan, top_chan): return (bottom_chan[:, :] * top_chan[:, :])
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return combination of bottom and top channels .
train
false
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def restore_caches(old): global FS_CACHE, MR_CACHE (FS_CACHE, MR_CACHE) = old
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restores caches from the result of a previous clear_caches call .
train
false
35,375
def delete_quota(tenant_id, profile=None): conn = _auth(profile) return conn.delete_quota(tenant_id)
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delete the specified tenants quota value cli example: .
train
false
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def multiclass_hinge_loss(predictions, targets, delta=1): num_cls = predictions.shape[1] if (targets.ndim == (predictions.ndim - 1)): targets = theano.tensor.extra_ops.to_one_hot(targets, num_cls) elif (targets.ndim != predictions.ndim): raise TypeError('rank mismatch between targets and predictions') corrects = predictions[targets.nonzero()] rest = theano.tensor.reshape(predictions[(1 - targets).nonzero()], ((-1), (num_cls - 1))) rest = theano.tensor.max(rest, axis=1) return theano.tensor.nnet.relu(((rest - corrects) + delta))
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computes the multi-class hinge loss between predictions and targets .
train
false
35,378
def p_multiplicative_expression_4(t): pass
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multiplicative_expression : multiplicative_expression mod cast_expression .
train
false
35,380
def behave(cmdline, cwd='.', **kwargs): assert isinstance(cmdline, six.string_types) return run(('behave ' + cmdline), cwd=cwd, **kwargs)
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run behave tests .
train
true
35,381
def funcstr(leaves, expr): (result, scope) = print_python(leaves, expr) leaf_names = [print_python([leaf], leaf)[0] for leaf in leaves] return (('lambda %s: %s' % (', '.join(leaf_names), result)), scope)
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lambda string for an expresion .
train
false
35,382
def get_running(): ret = set() out = __salt__['cmd.run'](_systemctl_cmd('--full --no-legend --no-pager'), python_shell=False, ignore_retcode=True) for line in salt.utils.itertools.split(out, '\n'): try: comps = line.strip().split() fullname = comps[0] if (len(comps) > 3): active_state = comps[3] except ValueError as exc: log.error(exc) continue else: if (active_state != 'running'): continue try: (unit_name, unit_type) = fullname.rsplit('.', 1) except ValueError: continue if (unit_type in VALID_UNIT_TYPES): ret.add((unit_name if (unit_type == 'service') else fullname)) return sorted(ret)
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return a list of all running services .
train
true
35,384
def database_files_path(test_tmpdir, prefix='GALAXY'): environ_var = ('%s_TEST_DBPATH' % prefix) if (environ_var in os.environ): db_path = os.environ[environ_var] else: tempdir = tempfile.mkdtemp(dir=test_tmpdir) db_path = os.path.join(tempdir, 'database') return db_path
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create a mock database/ directory like in galaxy_root .
train
false
35,385
def _api_set_config_default(name, output, kwargs): keywords = kwargs.get('keyword', []) if (not isinstance(keywords, list)): keywords = [keywords] for keyword in keywords: item = config.get_config('misc', keyword) if item: item.set(item.default()) config.save_config() return report(output)
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api: reset requested config variables back to defaults .
train
false
35,388
def p_specifier_qualifier_list_1(t): pass
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specifier_qualifier_list : type_specifier specifier_qualifier_list .
train
false
35,389
def tail(target, lines=None): if isinstance(target, str): with open(target) as target_file: for line in tail(target_file, lines): (yield line) return target.seek(0, 2) block_end_byte = target.tell() block_number = (-1) content = '' while (((lines is None) or (lines > 0)) and (block_end_byte > 0)): if ((block_end_byte - BLOCK_SIZE) > 0): target.seek((block_number * BLOCK_SIZE), 2) (content, completed_lines) = (target.read(BLOCK_SIZE) + content).split('\n', 1) else: target.seek(0, 0) completed_lines = (target.read(block_end_byte) + content) for line in reversed(completed_lines.splitlines()): if ((lines is None) or (lines > 0)): if (lines is not None): lines -= 1 (yield line) block_end_byte -= BLOCK_SIZE block_number -= 1
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show and then tail the event log .
train
false
35,390
def wildcard_to_re(text): return ''.join([_wildcard_to_regex.get(ch, ch) for ch in text])
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convert plain wildcard string to regex .
train
false
35,391
def projection_factory(projection, figure, rect, **kwargs): return get_projection_class(projection)(figure, rect, **kwargs)
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get a new projection instance .
train
false
35,392
def test_logxml_check_isdir(testdir): result = testdir.runpytest('--junit-xml=.') result.stderr.fnmatch_lines(['*--junitxml must be a filename*'])
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give an error if --junit-xml is a directory .
train
false
35,394
def deleteSiteInfo(self, site): try: q = SiteDB.query.filter((SiteDB.sitename == site)).first() except Exception as e: Log.debug(self, '{0}'.format(e)) Log.error(self, 'Unable to query database') if (not q): Log.error(self, '{0} does not exist in database'.format(site)) try: db_session.delete(q) db_session.commit() except Exception as e: Log.debug(self, '{0}'.format(e)) Log.error(self, 'Unable to delete site from application database.')
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delete site record in database .
train
false
35,395
def is_valid_key(key): if (PY3 and isinstance(key, bytes)): raise TypeError('needs to be str not bytes') for c in key: if ((c < ' ') or (c > '}') or (c == '=')): return False else: return bool(key)
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return true if a string is a valid vorbis comment key .
train
true
35,396
def set_asynchronous_for_sqlite(sender, connection, **kwargs): if (connection.vendor == 'sqlite'): cursor = connection.cursor() cursor.execute('PRAGMA synchronous=OFF;')
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make sqlite3 be asynchronous .
train
false