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def standard_date_format(input_date): """ Try to convert input date into standard format """ # in case input date is in datetime or pandas timestamp format if type(input_date) != str: input_date = "{0}-{1:02}-{2:02}".format( input_date.year, input_date.month, input_date.day ) # in case input date is in format YYYY/MM/DD or YYYY MM DD input_date = input_date.replace("/", "-") input_date = input_date.replace(" ", "-") # in case input date is in format YYYYMMDD or DDMMYYYY if len(input_date) == 8 and "-" not in input_date: if input_date.startswith(("20", "19")): input_date = input_date[:4] + "-" + input_date[4:6] + "-" + input_date[6:] else: input_date = input_date[4:] + "-" + input_date[2:4] + "-" + input_date[:2] return input_date
def merge(old, new, update): """ Merge `new` data into `old` data. :param list(dict) old: old data :param list(dict) new: new data :return: the new data merged into the old data :rtype: list(dict) """ old_dict = {entry["ID"]: entry for entry in old} new_dict = {entry["ID"]: entry for entry in new} final_dict = {} for entry in old_dict: old_entry = old_dict.get(entry, {}) new_entry = new_dict.pop(entry, {}) # Inject new values into the old entry. # Existing values will not be overriden unless they are empty. merged_entries = old_entry for key, value in new_entry.items(): old_entry_value = old_entry.get(key) if isinstance(old_entry_value, str): old_entry_value = old_entry_value.strip() if update: merged_entries[key] = value else: if not old_entry_value: merged_entries[key] = value final_dict[entry] = merged_entries final_dict.update(new_dict) return list(final_dict.values())
def _fetch_ret_config(ret): """ Fetches 'ret_config' if available. @see :func:`get_returner_options` """ if not ret: return None if "ret_config" not in ret: return "" return str(ret["ret_config"])
def BoringCallers(mangled, use_re_wildcards): """Return a list of 'boring' function names (optinally mangled) with */? wildcards (optionally .*/.). Boring = we drop off the bottom of stack traces below such functions. """ need_mangling = [ # Don't show our testing framework: ("testing::Test::Run", "_ZN7testing4Test3RunEv"), ("testing::TestInfo::Run", "_ZN7testing8TestInfo3RunEv"), ("testing::internal::Handle*ExceptionsInMethodIfSupported*", "_ZN7testing8internal3?Handle*ExceptionsInMethodIfSupported*"), # Depend on scheduling: ("MessageLoop::Run", "_ZN11MessageLoop3RunEv"), ("MessageLoop::RunTask", "_ZN11MessageLoop7RunTask*"), ("RunnableMethod*", "_ZN14RunnableMethod*"), ("DispatchToMethod*", "_Z*16DispatchToMethod*"), ("base::internal::Invoker*::DoInvoke*", "_ZN4base8internal8Invoker*DoInvoke*"), # Invoker{1,2,3} ("base::internal::RunnableAdapter*::Run*", "_ZN4base8internal15RunnableAdapter*Run*"), ] ret = [] for pair in need_mangling: ret.append(pair[1 if mangled else 0]) ret += [ # Also don't show the internals of libc/pthread. "start_thread", "main", "BaseThreadInitThunk", ] if use_re_wildcards: for i in range(0, len(ret)): ret[i] = ret[i].replace('*', '.*').replace('?', '.') return ret
def sort(data, delimiter=","): """ Sorts an array of CSV data rows stored as strings and returns it as a list. Args: data (list): input list of string rows or row values as a list to sort. delimiter (str): delimiter of the CSV format to use for value splitting. Returns: list of sorted rows in string format. """ data_sorted = [] for row in data: # Convert our string row into a list of strings if it's not already one. values = row.split(delimiter) if type(row) is str else row # Store our identifier. id = values[0] # Sort our row and add the identifier back to the start. row_sorted = sorted(values[1:]) row_sorted.insert(0, id) # Insert our sorted data back into list. data_sorted.append(row_sorted) return data_sorted
def _extract(content: str, name: str): """Extracts information from document content. :param content: document text content :type content: str :param name: item to extract name :type name: str :return: parsed number """ try: splitted_content = content.split(name) content_behind = splitted_content[1] trimmed_number = content_behind.split('|')[1] parsed = float(trimmed_number.replace(',', '.')) except IndexError: parsed = None return parsed
def validateUser(username, password, authProfile="", timeout=60000): """Tests credentials (username and password) against an authentication profile. Returns a boolean based upon whether or not the authentication profile accepts the credentials. If the authentication profile name is omitted, then the current project's default authentication profile is used. Args: username (str): The username to validate. password (str): The password for the user. authProfile (str): The name of the authentication profile to run against. Optional. Leaving this out will use the project's default profile. timeout (int): Timeout for client-to-gateway communication. Optional. (default: 60,000ms) Returns: bool: False(0) if the user failed to authenticate, True(1) if the username/password was a valid combination. """ print(username, password, authProfile, timeout) return True
def removeDuplicatesFromListOfDicts(list_of_dicts, key): """ remove duplicates from a list of dicts based on key, returns the list in the format it arrived. only checks key. Does not check anything else. """ ulist = [] newlist = [] dupecount = 0 for line in list_of_dicts: if line[key] in ulist: # don't write this enty, dupecount +=1 else: # add to ulist and write to file; if line[key]: # if column is empty don't add it to the list, but write to file ulist.append(line[key]) newlist.append(line) #print ">> Duplicates Found:", dupecount return newlist
def get_vgci_warnings(tc): """ extract warnings from the parsed test case stderr """ warnings = [] if tc['stderr']: for line in tc['stderr'].split('\n'): # For each line if "WARNING" in line and "vgci" in line: # If it is a CI warning, keep it warnings.append(line.rstrip()) return warnings
def generate_caption(data): """ return raw: raw picture in jpeg formate caption: generated image caption in string formate attention: attention picture in jpeg formate """ # results = classify(data) # return jsonify({'res': classify(data)}) return data,'helloworld',data
def dot_vectors(u, v): """Compute the dot product of two vectors. Parameters ---------- u : tuple, list, Vector XYZ components of the first vector. v : tuple, list, Vector XYZ components of the second vector. Returns ------- dot : float The dot product of the two vectors. Examples -------- >>> dot_vectors([1.0, 0, 0], [2.0, 0, 0]) 2.0 """ return sum(a * b for a, b in zip(u, v))
def frontiers_from_time_to_frame_idx(seq, hop_length_seconds): """ Converts a sequence of frontiers in time to their values in frame indexes. Parameters ---------- seq : list of float/times The list of times to convert. hop_length_seconds : float hop_length (time between two consecutive frames), in seconds. Returns ------- list of integers The sequence, as a list, in frame indexes. """ return [int(round(frontier/hop_length_seconds)) for frontier in seq]
def log_stability(x): """ """ if x==0: return 10e-9 elif x==1: return 1.0-10e-9 else: return x
def validate_list(option, value): """Validates that 'value' is a list.""" if not isinstance(value, list): raise TypeError("%s must be a list" % (option,)) return value
def nvidiaDevice(devices): """ Checks if any Nvidia device exist """ nvDevices = [] for device in devices: if device.startswith('nv'): nvDevices.append('/dev/{}'.format(device)) return nvDevices
def is_matrix(A): """Tells whether an input is actually a matrix or not. Args ---- A (compulsory) A matrix. Returns ------- bool True if the input is a matrix, False otherwise. """ for row in A: if len(row) != len(A[0]): return False for element in row: if type(element) not in [int, float, complex]: return False return True
def _start_time_from_groupdict(groupdict): """Convert the argument hour/minute/seconds minute into a millisecond value. """ if groupdict['hours'] is None: groupdict['hours'] = 0 return (int(groupdict['hours']) * 3600 + int(groupdict['minutes']) * 60 + int(groupdict['seconds'])) * 1000
def is_subset(remote_dic, local_dic): """remote_dic is or not subset of local_dic""" return set(remote_dic).issubset(set(local_dic))
def equiangular_dimension_unpack(nodes, ratio): """Calculate the two underlying dimensions from the total number of nodes Args: nodes (int): combined dimensions ratio (float): ratio between the two dimensions Returns: int, int: separated dimensions """ dim1 = int((nodes / ratio) ** 0.5) dim2 = int((nodes * ratio) ** 0.5) if dim1 * dim2 != nodes: # Try to correct dim1 or dim2 if ratio is wrong if nodes % dim1 == 0: dim2 = nodes // dim1 if nodes % dim2 == 0: dim1 = nodes // dim2 assert dim1 * dim2 == nodes, f'Unable to unpack nodes: {nodes}, ratio: {ratio}' return dim1, dim2
def insert(serverName, itemId, value, date, quality): """Insert values on the OPC-HDA server if the given item ID does not exist. Args: serverName (str): The name of the defined OPC-HDA server. itemId (str): The item ID to perform the operation on. value (object): The value to insert. date (object): The date to insert. quality (int): The quality to insert. Returns: int: The items quality form the operation. """ print(serverName, itemId, value, date, quality) return 192
def _expand_total_pairs(total_pairs): """Expands total_pairs so that it has one key per direction. e.g., 'breitbart-foxnews' and 'foxnews-breitbart' exist as keys. If expansion is skipped, then total_pairs only has one key per pair of (unordered) elements. e.g., 'breitbart-foxnews' exists as a key but 'foxnews-breitbart' does not. The total per element-pair is the same value for both directions. e.g., 'breitbart-foxnews' and 'foxnews-breitbart' are assigned the same total count. """ total_pairs_expanded = {} for k, v in total_pairs.items(): total_pairs_expanded[(k[0], k[1])] = v total_pairs_expanded[(k[1], k[0])] = v total_pairs_expanded = dict(sorted(total_pairs_expanded.items())) return total_pairs_expanded
def list_dropdownScatter(dic_df): """ """ l_choice = [] for key_cont, value_cont in dic_df['var_Y'].items(): for key_cat, value_cat in dic_df['var_X'].items(): l_choice.append(value_cont['name'] + '-' + value_cat['name']) l_choice = ['-'] + l_choice return l_choice
def len_column(table): """ Add length column containing the length of the original entry in the seq column. Insert a number column with numbered entries for each row. """ for pos, i in enumerate(table): i.insert(0, pos) i.append(len(i[1])) return table
def calculate_change(total: float) -> float: """Determine how much change is needed.""" return round(1 - (total - int(total)), 2)
def _get_location_end(element: str) -> str: """Translates element suffix to end of location code""" if "_Sat" in element: return "1" if "_Dist" in element: return "D" if "_SQ" in element: return "Q" if "_SV" in element: return "V" return "0"
def is_args(x): """ Is x a traditional iterable? """ return type(x) in (tuple, list, set)
def calculate_temperature_rise_power_loss_surface( power_operating: float, area: float, ) -> float: """Calculate the temperature rise based on the power loss and surface area. :param power_operating: the power loss in W. :param area: the radiating surface area of the case in sq. inches. :return: _temperature_rise; the calculated temperature rise in C. :rtype: float :raise: ZeroDivisionError if passed an area=0.0. """ return 125.0 * power_operating / area
def some_function(var_one, var_two, var_three): """This is a function that do things""" if var_one > var_two: if var_two*var_three > var_one: return "blab" #this happens else: return "blob" else: return "fish"
def get_name(name: str, incl_ext: bool=False) -> str: """ Get the name of a directory of file, specified in path Path can either be relative or absolute :param name: the name of a directory or a file, specified in path :param incl_ext: flag to include the extension if it is a file :return: the name of the directory or the file, excluding path """ import os ext_delim = "." # Filter the directory delimiter and get the last element # It is assumed here that if it is a directory, it will not end with "/" name = os.path.split(name)[-1] if ext_delim in name: # Then it is a file with an extension if incl_ext: return name else: return name.split(ext_delim)[0] else: # Then it is a directory return name
def takemod(nvols): """ Determine if the input is odd or even values and return a of 0 and 1 depending on the truth value Parameters ---------- nvols : int Returns ------- decisions : int """ mod = int(int(nvols) % 2) if mod == 1: return 0 else: return 1
def names2dnsrepr(x): """ Take as input a list of DNS names or a single DNS name and encode it in DNS format (with possible compression) If a string that is already a DNS name in DNS format is passed, it is returned unmodified. Result is a string. !!! At the moment, compression is not implemented !!! """ if type(x) is str: if x and x[-1] == '\x00': # stupid heuristic return x x = [x] res = [] for n in x: termin = "\x00" if n.count('.') == 0: # single-component gets one more termin += '\x00' n = "".join(map(lambda y: chr(len(y))+y, n.split("."))) + termin res.append(n) return "".join(res)
def _policy_dict_at_state(callable_policy, state): """Turns a policy function into a dictionary at a specific state. Args: callable_policy: A function from `state` -> lis of (action, prob), state: the specific state to extract the policy from. Returns: A dictionary of action -> prob at this state. """ infostate_policy_list = callable_policy(state) infostate_policy = {} for ap in infostate_policy_list: infostate_policy[ap[0]] = ap[1] return infostate_policy
def _get_reason(cluster_or_step): """Get state change reason message.""" # StateChangeReason is {} before the first state change return cluster_or_step['Status']['StateChangeReason'].get('Message', '')
def oracle_add_escape(_value, _escape_character): """Add the oracle escape ke_delimiteryword if nessesary.""" if _escape_character not in ('', None): return _value + ' ESCAPE \'' + _escape_character + '\'' else: return _value
def colorCycle(color,polyNumber): """ Adjusts contents of self.color as needed for plotting methods.""" if len(color) < polyNumber: for i in range(polyNumber - len(color)): color.append(color[i]) else: for i in range(len(color) - polyNumber): del color[-(i+1)] return color
def _float_or_none(x, digits=3): """ Helper function to format a variable that can be a float or None""" if x is None: return str(x) fmtstr = "{0:.{digits}g}".format(x, digits=digits) return fmtstr.format(x)
def replace_value(template, pattern, value, count=1): """Set the given pattern to the desired value in the template, after making sure that the pattern is found exactly once.""" assert isinstance(template, str) assert template.count(pattern) == count return template.replace(pattern, value)
def kkt_get_nthreads(d): """Return sorted list of #threads used in the data. Return also the corresponding exespace tuples.""" s = set() for es in d.keys(): s.add((es[1]*es[2], es)) s = list(s) s.sort() return [i[0] for i in s], [i[1] for i in s]
def split(alist, split): """ split a list into 'split' items """ newlist = [] accum = [] for i, element in enumerate(alist): accum.append(element) if (len(accum) == split) or (i == len(alist)-1): newlist.append(accum) accum = [] return newlist
def solve_for_scale(a_scale, a_n_bits, b_scale, b_n_bits, y_n_bits): """ Finds the scale factor for the following case: y = a * b We know the scale factor and the number of bits of a, as well as b. We also know the number of bits for y. This function computes the resulting scale factor for y Parameters: - a_scale: float - a_n_bits: int - b_scale: float - b_n_bits: int - y_n_bits: int Returns: float, resulting scale factor for y, can be used for dequantization """ a_range = (1 << (a_n_bits - 1)) b_range = (1 << (b_n_bits - 1)) y_range = (1 << (y_n_bits - 1)) return (y_range * a_scale * b_scale) / (a_range * b_range)
def translate(x: str, d: dict) -> str: """ Convert english digits to persian digits. :param x: string to translate :param d: dict for using on translate :return: translated string """ if not isinstance(x, str): raise TypeError("x is not string") if not isinstance(d, dict): raise TypeError("d is not dict") trans = str.maketrans(d) return x.translate(trans)
def absoadd(n, m): """(num, num) -> num Gives the absolute value of the difference of two numbers. >>> absoadd(5, 6) 11 """ first = abs(n - m) return (first)
def pairwiseCombinations(initialList): """ Creates the minimum set of combinations that will make available every possible pair available. """ r = [len(x) for x in initialList] m = min(r) M = max(r) n = len(initialList) R = set() for i in range(m): t = [initialList[x][i] for x in range(n)] R.add(tuple(t)) for i in range(m,M): t = [initialList[x][min(r[x]-1,i)] for x in range(n)] R.add(tuple(t)) for i in range(m): for j in range(n): for k in range(i+1,r[j]): prejth = [initialList[x][i] for x in range(j)] jth = initialList[j][k] postjth = [initialList[x][i] for x in range(j+1, n)] t = prejth + [jth] + postjth R.add(tuple(t)) for i in range(m,M): for j in range(n): if r[i] < i: continue for k in range(i+1,r[j]): prejth = [initialList[x][min(r[x]-1,i)] for x in range(j)] jth = initialList[j][k] postjth = [initialList[x][min(r[x]-1,i)] for x in range(j+1, n)] t = prejth + [jth] + postjth R.add(tuple(t)) return R
def parse_executable_str(exec_str): """ Split the string describing the executable into a path part and an options part. """ first_space = exec_str.find(" ") if first_space == -1: first_space = len(exec_str) return exec_str[:first_space], exec_str[first_space:]
def fetch_json_by_path(json_object, path): """Recursively fetch a string value from a JSON object given an xpath.""" first_id = path.find("#") second_id = path.find("#", first_id + 1) first_key = path.find("/") second_key = path.find("/", first_key + 1) indices = [x for x in [first_id, second_id, first_key, second_key] if x > 0] indices.sort() indices.append(len(path) + 1) if isinstance(json_object, str): return str(json_object) elif path[0] == "#" and isinstance(json_object, list): child_id = path[1:indices[0]] path_remainder = path[indices[0]:] for sub_object in json_object: try: if sub_object["id"] == child_id: return fetch_json_by_path(sub_object, path_remainder) except KeyError: pass elif path[0] == "/" and isinstance(json_object, dict): child_key = path[1:indices[0]] path_remainder = path[indices[0]:] try: sub_object = json_object[child_key] return fetch_json_by_path(sub_object, path_remainder) except KeyError: pass return None
def jim_orders(orders): """Hackerrank Problem: https://www.hackerrank.com/challenges/jim-and-the-orders/problem Jim's Burgers has a line of hungry customers. Orders vary in the time it takes to prepare them. Determine the order the customers receive their orders. Start by numbering each of the customers from 1 to n, front of the line to the back. You will then be given an order number and a preparation time for each customer. The time of delivery is calculated as the sum of the order number and the preparation time. If two orders are delivered at the same time, assume they are delivered in ascending customer number order. Solve: We store the orders in a dictionary with the key being the total prep time for each customer. The value is then a list containing the customer number, so if we have multiple customers with the same prep time, we just append to the list. We then iterate through the dictionary in increasing prep time order and extend those customers to a final list containing the order in which customers will receive their burgers Args: orders (list): list of tuples containing the order number and prep time for customer[i] Returns: list: list containing the order in which customers will receive their burgers """ times = {} for i, order in enumerate(orders): time = sum(order) if time in times: times[time].append(i+1) else: times[time] = [i+1] customers = [] for i in sorted(times): customers.extend(times[i]) return customers
def get_clean_tree_str(tree_str): """Remove all blanks and return a very clean tree string. >>> get_clean_tree_str('((a ,((b, c), (d, e))), (f, g));'') '((a,((b,c),(d,e))),(f,g));' """ return tree_str.replace(' ', '').replace('\n', '').replace('\t', '')
def module_level_function(param1, param2=None, *args, **kwargs): """This is an example of a module level function. Function parameters should be documented in the ``Args`` section. The name of each parameter is required. The type and description of each parameter is optional, but should be included if not obvious. If \*args or \*\*kwargs are accepted, they should be listed as ``*args`` and ``**kwargs``. The format for a parameter is:: name (type): description The description may span multiple lines. Following lines should be indented. The "(type)" is optional. Multiple paragraphs are supported in parameter descriptions. Args: param1 (int): The first parameter. param2 (:obj:`str`, optional): The second parameter. Defaults to None. Second line of description should be indented. *args: Variable length argument list. **kwargs: Arbitrary keyword arguments. Returns: bool: True if successful, False otherwise. The return type is optional and may be specified at the beginning of the ``Returns`` section followed by a colon. The ``Returns`` section may span multiple lines and paragraphs. Following lines should be indented to match the first line. The ``Returns`` section supports any reStructuredText formatting, including literal blocks:: { 'param1': param1, 'param2': param2 } Raises: AttributeError: The ``Raises`` section is a list of all exceptions that are relevant to the interface. ValueError: If `param2` is equal to `param1`. """ if param1 == param2: raise ValueError('param1 may not be equal to param2') return True
def determine_issues(project): """ Get the list of issues of a project. :rtype: list """ issues = project["Issue"] if not isinstance(issues, list): return [issues] return issues
def token_to_dirname(token: str) -> str: """Cleans up a given token from quotes, strip from spaces, etc. The returned string is a valid directory name on the current platform. Args: token(str): 'dirty' folder name obained from the user through CLI Returns: valid directory name """ foldername = token foldername = foldername.replace('"', '') foldername = foldername.strip(' ') return foldername
def is_pangram(sentence): """Determines if a sentence is a pangram.""" from string import ascii_lowercase sentence = sentence.lower() for letter in ascii_lowercase: if letter not in sentence: return False return True
def _sort_pages(pages): """Sort given pages by date""" return sorted(pages, key=lambda p: p['date'], reverse=True)
def fileconcat(f): """Return concatination of all numbers in file f""" return int("".join(l.strip() for l in f))
def str_format(l): """ Take a list l and returns a string of those elements converted to strings. """ if len(l) < 1: return "" new_string = "" for e in l: new_string += str(e) return new_string
def create_serialization_name(cls, serialization_name=None): """ Helper function for creating a serialization name """ _serialization_name = serialization_name if serialization_name: if callable(serialization_name): _serialization_name = serialization_name(cls) return _serialization_name
def format_sqlite_value(in_value): """ will add quotes around it if its a string or convert the string to NULL if it is a python None value :param in_value: an object that is to be returned with or without quotes. NULL if None """ if type(in_value) in (int, float, bool): return str(in_value) elif in_value is None: return "NULL" else: # escape strings with single-quotes in_value = in_value.replace("'", "''") return "'{}'".format(in_value)
def lowercase(string: str): """Safely recast a string to lowercase""" try: return string.lower() except AttributeError: return string
def parent(name: str, *, level: int = 1) -> str: """Get parent name with level.""" return name.rsplit('.', maxsplit=level)[0]
def _analyse_gdal_output(output): """ Analyse the output from gpt to find if it executes successfully. Parameters ---------- output : str Ouptut from gpt. Returns ------- flag : boolean False if "Error" is found and True if not. """ # return false if "Error" is found. if 'error' in output.lower(): return False # return true if "100%" is found. elif '100 - done' in output.lower(): return True # otherwise return false. else: return False
def validateTransferBody(data): """Validates incoming json body Arguments: data {[dict]} -- [json body] Returns: [bool] -- [if validation passes] [dict] -- [if validation fails] """ keys = [*data] allowedKeys = ["routingNumber", "accountNumber", "amount"] if len(keys) != 3: return {"error": "three keys are required in transfer body"} for key in keys: if key not in allowedKeys: return { "error": "only the following keys are allowed in transfer body:" + ",".join(allowedKeys) } return True
def no_of_misplaced_tiles(node): """Function to get the number of misplaced tiles for a particular configuration Parameters ---------- node : [list] [list to check for the heuristics] Return ------ [int] [returns the heuristic distance for a particular node] """ h_score = 0 goal_state = [0, 1, 2, 3, 4, 5, 6, 7, 8] for idx, i in enumerate(goal_state): if goal_state[idx] != node[idx]: h_score += 1 return h_score
def usn_in_range(usn, range): """Check if the usn is in one of the range provided. To do so, the value is checked to be between the lower bound and higher bound of a range :param usn: A integer value corresponding to the usn that we want to update :param range: A list of integer representing ranges, lower bounds are in the even indices, higher in odd indices :return: True if the usn is in one of the range, False otherwise """ idx = 0 cont = True ok = False while cont: if idx == len(range): cont = False continue if usn < int(range[idx]): if idx %2 == 1: ok = True cont = False if usn == int(range[idx]): cont = False ok = True idx = idx + 1 return ok
def reduceDimensions(matrix): """ Decrease any list/matrix dimensions by one. Parameters ---------- matrix: Multidimensional Array Returns ------- list: The matrix after reducing it's dimensions. """ # Doesn't accept vectors/(1-dimensional matrices) # If matrix is a vector return it without changes if (type(matrix[0]) is not list): return matrix new_matrix = [] for item in matrix: new_matrix += item return new_matrix
def calc_bpe_bulk_electrolyte_resistance(characteristic_length, sigma): """ The area specific charge transfer resistance through the bulk electrolyte units: Ohm*m2 Notes: Adjari, 2006 - "(area specific) bulk electrolyte resistance" Squires, 2010 - does not explicitly define this but uses the same equation Inputs: char_length: (m) length of BPE sigma (S/m) conductivity of electrolyte/buffer Output: Resistance: Ohm*m^2 """ R_0 = characteristic_length / sigma return R_0
def resize(matrix, row, col=0): """resize the matrix to requried size""" current_size = len(matrix) new_size = (row if row > col else col) + 1 if new_size > current_size: new_matrix = [[None for x in range(new_size)] for y in range(new_size)] for i in range(len(matrix)): for j in range(len(matrix[i])): new_matrix[i][j] = matrix[i][j] return new_matrix return matrix
def population_nucleotide_diversity(H, p, D): """ # ======================================================================== POPULATION NUCLEOTIDE DIVERSITY PURPOSE ------- Calculates the population nucleotide diversity. INPUT ----- [INT] [H] The number of haplotypes. [FLOAT] [p] A list of (relative) frequencies. [2D ARRAY] [D] A distance matrix of haplotypes pair-wise genetic distances (fraction of nt differences). RETURN ------ [FLOAT] The population nucleotide diversity. # ======================================================================== """ diversity = 0 for i in range(0, H): for j in range(0, H): diversity += p[i] * D[i][j] * p[j] return diversity
def mml_namelist(namelist): """padding to be same length""" N = max([len(s) for s in namelist]) return ["'%s'" % s.ljust(N, ' ') for s in namelist]
def gf_rshift(f, n, K): """Efficiently divide `f` by `x**n`. """ if not n: return f, [] else: return f[:-n], f[-n:]
def countBins(sortedData, binBoundaries): """ This method counts the number of data items in the sorted_data Returns an array with the number. ret[0] is the number of data points <= binBoundaries[0], ret[len(binBoundaries)] is the number of points > binBoundaries[len(binBoundaries)-1] @ In, sortedData, list or np.array,the data to be analyzed @ In, binBoundaries, list or np.array, the bin boundaries @ Out, ret, list, the list containing the number of bins """ binIndex = 0 sortedIndex = 0 ret = [0]*(len(binBoundaries)+1) while sortedIndex < len(sortedData): while not binIndex >= len(binBoundaries) and \ sortedData[sortedIndex] > binBoundaries[binIndex]: binIndex += 1 ret[binIndex] += 1 sortedIndex += 1 return ret
def convertRange(value, oldRange, newRange, rounded=True): """Compute the value within the new provided range""" # Value is tested against new range, and divided against old range value = ((value - oldRange[0]) * (newRange[1] - newRange[0]) ) / (oldRange[1] - oldRange[0]) + newRange[0] # Result is a valid integer, return is casted as valid integer if (not rounded): # send back a valid integer return round(value * 10) / 10 return round(value)
def slice_to_interval(slice_): """ Convert slice object to (start, stop, direction). """ start = slice_.start or 0 # Handles case where slice_.start is None. step = slice_.step or 1 # Handles case where slice_.step is None. if step == 1: if start < 0: raise ValueError( "Tree sequence slices with start < 0 must have step=-1. " f"Use for example [{slice_.start}:{slice_.stop}:-1]" "(This is a limitation of slicing on Tree sequences " "that does not apply to Python sequences in general.)" ) if (slice_.stop is not None) and (slice_.stop < start): raise ValueError( "Tree sequence slices with step=1 must have stop >= start. " "(This is a limitation of slicing on Tree sequences " "that does not apply to Python sequences in general.)" ) start_ = start stop_ = slice_.stop direction = 1 elif step == -1: if start >= 0: raise ValueError( "Tree sequence slices with start >= 0 must have step=1. " "(This is a limitation of slicing on Tree sequences " "that does not apply to Python sequences in general.)" ) if slice_.stop is not None: if slice_.stop > start: raise ValueError( "Tree sequence slices with step=-1 must have stop <= start." ) stop_ = 1 - slice_.stop else: stop_ = slice_.stop start_ = 1 - start direction = -1 else: raise ValueError( "Only step of 1 or -1 is supported in a Tree sequence slice. " f"Step {slice_.step} is disallowed." ) assert start_ >= 0 assert (stop_ is None) or (stop_ >= start_) return start_, stop_, direction
def TDict(val): """Checks if the given value is a dictionary. """ return isinstance(val, dict)
def linearProbe(hk, size, i): """Default linear probe using c= 101.""" return (hk+101) % size
def task2(a): """ Function that calculates square value of argument Input: one integer Output: one integer """ return a**2 #return iloczyn
def _geo_sum(r: int, n: int): """Calculate the geometric sum for ratio, r, and number of terms, n.""" return (1 - r ** n) / (1 - r)
def get_orders_list(orders_dict): """Returns orders list from orders dict""" return orders_dict.get('orders')
def face_sort(faces_in): """ sorts each face so that lowest index is first but retaining face order then sorts all the faces used to compare equality of two face lists """ faces_out = [] for face in faces_in: argmin = face.index(min(face)) face_out = [] for v_ind, v1 in enumerate(face): face_out.insert(0, face[argmin - v_ind - 1]) faces_out.append(tuple(face_out)) return sorted(faces_out)
def is_magnet(magnet: str): """Check if provided string is a magnet. >>> is_magnet('13600b294191fc92924bb3ce4b969c1e7e2bab8f4c93c3fc6d0a51733df3c060') True >>> is_magnet('123') False >>> is_magnet(b'123') False >>> is_magnet('x3600b294191fc92924bb3ce4b969c1e7e2bab8f4c93c3fc6d0a51733df3c060') False """ if not isinstance(magnet, str): return False if len(magnet) != 64: return False try: bytes.fromhex(magnet) except ValueError: return False return True
def hamming_distance(dna1, dna2): """ Finds the Hamming Distance between two strings of DNA. :param dna1: a string of DNA :param dna2: a string of DNA :return: the computed Hamming Distance """ distance = 0 for i in range(len(dna1)): if dna1[i] != dna2[i]: distance += 1 return distance
def is_named_tuple(obj): """ Check if the object is a named tuple. Parameters ---------- obj : The object to check. Returns ------- is_named_tuple : bool Whether `obj` is a named tuple. Examples -------- >>> Point = namedtuple("Point", ["x", "y"]) >>> p = Point(1, 2) >>> >>> is_named_tuple(p) True >>> is_named_tuple((1, 2)) False """ return isinstance(obj, tuple) and hasattr(obj, '_fields')
def coeff(t, secret): """ Randomly generate a list of coefficients for a polynomial with degree of `t` - 1, whose constant is `secret`. For example with a 3rd degree coefficient like this: 3x^3 + 4x^2 + 18x + 554 554 is the secret, and the polynomial degree + 1 is how many points are needed to recover this secret. (in this case it's 4 points). """ coeff = [i for i in range(t - 1)] coeff.append(secret) return coeff
def _partition(sequence, size, count): """ Partition sequence into C{count} subsequences of length C{size}, and a remainder. Return C{(partitions, remainder)}, where C{partitions} is a sequence of C{count} subsequences of cardinality C{size}, and C{apply(append, partitions) + remainder == sequence}. """ partitions = [] for index in range(0, size * count, size): partitions.append(sequence[index:index + size]) return (partitions, sequence[size * count:])
def rsa_crt_dmq1(private_exponent: int, q: int) -> int: """ Compute the CRT private_exponent % (q - 1) value from the RSA private_exponent (d) and q. """ return private_exponent % (q - 1)
def set_positional_arguments(positional_parameters, positional_arguments, command_line_options): """ Validate and set positional command line arguments. """ if len(positional_parameters) < len(positional_arguments): return (True, 'Too many parameters') if len(positional_parameters) > len(positional_arguments): return (True, 'Not enough required parameters') for i, parm in enumerate(positional_parameters): command_line_options[parm] = positional_arguments[i] return None
def _rmcmd(s, cmd, left='', right=''): """ Remove the LaTeX command ``cmd`` from the string ``s``. This function is used by ``detex``. INPUT: - ``s`` - (string) string from which to remove the command - ``cmd`` - (string) command to be removed. This should be a command which takes a single argument, like 'emph' or 'url'; the command is removed, but its argument is not. - ``left``, ``right`` - (string, optional, default '') add these strings at the left and right ends of the command. See the examples. EXAMPLES:: sage: from sage.misc.sagedoc import _rmcmd sage: _rmcmd('Check out \\url{http://www.sagemath.org}.', 'url') 'Check out http://www.sagemath.org.' sage: _rmcmd('Text in \\emph{italics} looks like this.', 'emph', '*', '*') 'Text in *italics* looks like this.' sage: _rmcmd('This is a \\very{silly} example.', 'very', right='!?') 'This is a silly!? example.' """ c = '\\%s{' % cmd while True: i = s.find(c) if i == -1: return s nesting = 1 j = i+len(c)+1 while j < len(s) and nesting > 0: if s[j] == '{': nesting += 1 elif s[j] == '}': nesting -= 1 j += 1 j -= 1 # j is position of closing '}' if j < len(s): s = s[:i] + left + s[i+len(c):j] + right + s[j+1:] else: return s
def ensure_input(input, encoding="utf-8"): """Ensure the type of input and the path of outfile.""" if isinstance(input, (list, tuple)): outfile = input[1] input = "\n".join(input).encode(encoding) else: outfile = input.split("\n")[1] input = input.encode(encoding) return input, outfile
def remove_indices_from_dict(obj): """ Removes indices from a obj dict. """ if not isinstance(obj, dict): raise ValueError(u"Expecting a dict, found: {}".format(type(obj))) result = {} for key, val in obj.items(): bracket_index = key.find('[') key = key[:bracket_index] if bracket_index > -1 else key val = remove_indices_from_dict(val) if isinstance(val, dict) else val if isinstance(val, list): _val = [] for row in val: if isinstance(row, dict): row = remove_indices_from_dict(row) _val.append(row) val = _val if key in result: result[key].extend(val) else: result[key] = val return result
def expo_ma(data, period): """ input a list of data points and return EMA with period points averaged :param data: the list of data points :type data: list :param period: averaged over past period data points :param period: int :return a list of EMA with period points averaged """ if period > len(data): # print("Error in expo_ma function: the length of data points is too short!") return [] ret = [None] * (len(data)-period+1) # initialize the first element in the EMA series to the SMA of first period data points ret[0] = sum(data[:period])/period # set smoothing factor to be 2/(period+1) factor = float(2/(period+1)) # calculate the rest of series by the formula: factor * P(t) + (1-factor) * EXP(t-1) for i in range(1, len(data)-period+1): ret[i] = factor*data[period+i-1] + (1-factor)*ret[i-1] return list(ret)
def _job_contains_cert_data(data): """Boolean checks to ensure any received job message contains return cert data""" if data is None: return False if 'cert' in data['data']: return True else: return False
def getKoreanColors(i, n): """ Make a palette in the korean style """ n = float(i)/float(n)*3. R = (n<=1.)+ (2.-n)*(n>1.)*(n<=2.) G = n*(n<=1.)+ (n>1.)*(n<=2.)+(3.-n)*(n>2.) B = (n-1.)*(n>=1.)*(n<2.)+(n>=2.) R, G, B = [int(i*255) for i in [R,G,B]] return R,G,B
def ensure_alt_ids_are_only_in_one_nest(nest_spec, list_elements): """ Ensures that the alternative id's in `nest_spec` are only associated with a single nest. Raises a helpful ValueError if they are not. Parameters ---------- nest_spec : OrderedDict, or None, optional. Keys are strings that define the name of the nests. Values are lists of alternative ids, denoting which alternatives belong to which nests. Each alternative id must only be associated with a single nest! Default == None. list_elements : list of ints. Each element should correspond to one of the alternatives identified as belonging to a nest. Returns ------- None. """ try: assert len(set(list_elements)) == len(list_elements) except AssertionError: msg = "Each alternative id should only be in a single nest." raise ValueError(msg) return None
def csv_driver_args(distribution): """ Construct driver args for a GeoJSON distribution. """ url = distribution.get("downloadURL") or distribution.get("accessURL") if not url: raise KeyError(f"A download URL was not found for {str(distribution)}") return {"urlpath": url, "csv_kwargs": {"blocksize": None, "sample": False}}
def pxe_mac(mac): """ Create a MAC address file for pxe builds. Add O1 to the beginning, replace colons with hyphens and downcase """ return "01-" + mac.replace(":", "-").lower()
def dict_product(a, b): """Pointwise-multiply the values in two dicts with identical sets of keys. """ assert set(a.keys()) == set(b.keys()) return { k: v * b[k] for k, v in a.items() }
def ceil_shift(n, b): """Return ceil(n / 2**b) without performing any floating-point or division operations. This is done by right-shifting n by b bits and incrementing the result by 1 if any '1' bits were shifted out. """ if not isinstance(n, int) or not isinstance(b, int): raise TypeError("unsupported operand type(s): %r and %r" % (type(n).__name__, type(b).__name__)) assert n >= 0 and b >= 0 # I haven't tested or even thought about negative values mask = (1 << b) - 1 if n & mask: return (n >> b) + 1 else: return n >> b
def get_wikidata_id(wikidata_uri): """ Returns Wikidata ID (e.g. "Q92212") given Wikidata entity URI, or None. """ wikidata_base_uri = "http://www.wikidata.org/entity/" if wikidata_uri.startswith(wikidata_base_uri): wikidata_id = wikidata_uri[len(wikidata_base_uri):] else: wikidata_id = None return wikidata_id
def GetEnvCall(is_constructor, is_static, return_type): """Maps the types availabe via env->Call__Method.""" if is_constructor: return 'NewObject' env_call_map = {'boolean': 'Boolean', 'byte': 'Byte', 'char': 'Char', 'short': 'Short', 'int': 'Int', 'long': 'Long', 'float': 'Float', 'void': 'Void', 'double': 'Double', 'Object': 'Object', } call = env_call_map.get(return_type, 'Object') if is_static: call = 'Static' + call return 'Call' + call + 'Method'
def stiff_b(v1v1, v0v1, v0v0, rold): """called from stiff_a(). Decide if the iteration has degenerated because of a strongly dominant real eigenvalue. Have just computed the latest iterate. v1v1 is its dot product with itself, v0v1 is the dot product of the previous iterate with the current one, and v0v0 is the dot product of the previous iterate with itself. rold is a previous Rayleigh quotient approximating a dominant real eigenvalue. It must be computed directly the first time the subroutine is called. It is updated each call to stiff_b, hence is available for subsequent calls. If there is a strongly dominant real eigenvalue, rootre is set True, root1[:] returns the eigenvalue, rho returns the magnitude of the eigenvalue, and root2[:] is set to zero. Original source: RKSuite.f, https://www.netlib.org/ode/rksuite/ """ # real and imag parts of roots are returned in a list root1 = [0.0, 0.0] root2 = [0.0, 0.0] r = v0v1 / v0v0 rho = abs(r) det = v0v0 * v1v1 - v0v1**2 res = abs(det / v0v0) rootre = det == 0.0 or (res <= 1e-6 * v1v1 and abs(r - rold) <= 0.001 * rho) if rootre: root1[0] = r rold = r return rold, rho, root1, root2, rootre
def fun(s): """Determine if the passed in email address is valid based on the following rules: It must have the username@websitename.extension format type. The username can only contain letters, digits, dashes and underscores [a-z], [A-Z], [0-9], [_-]. The website name can only have letters and digits [a-z][A-Z][0-9] The extension can only contain letters [a-z][A-Z]. The maximum length of the extension is 3. Args: s (str): Email address to check Returns: (bool): Whether email is valid or not """ if s.count("@") == 1: if s.count(".") == 1: user, domain = s.split("@") website, extension = domain.split(".") if user.replace("-", "").replace("_", "").isalnum(): if website.isalnum(): if extension.isalnum(): if len(extension) <= 3: return True return False
def open_files(filenames): """open files and return contents.""" return list(map(lambda file: open(file, 'r').read(), filenames))