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def fetch_ref_codon(ref_pos, curr_gene, curr_seq): """ Fetch codon within gene for given site """ # position of site in gene within_gene_pos = ref_pos - curr_gene['start'] if curr_gene['strand'] == '+' else curr_gene['end'] - ref_pos # position of site in codon within_codon_pos = within_gene_pos % 3 # gene sequence (oriented start to stop) ref_codon = curr_seq[within_gene_pos-within_codon_pos:within_gene_pos-within_codon_pos+3] return ref_codon, within_codon_pos
bigcode/self-oss-instruct-sc2-concepts
import numbers def _scale(scale): """ Given a numeric input, return a 2-tuple with the number repeated. Given a 2-tuple input, return the input >>> _scale(2) (2, 2) >>> _scale((1, 2,)) (1, 2) >>> _scale('nonsense') Traceback (most recent call last): ... TypeError: argument should be a number or a tuple >>> _scale((1,2,3)) Traceback (most recent call last): ... ValueError: scale should be a 2-tuple """ if isinstance(scale, tuple): if len(scale) != 2: raise ValueError('scale should be a 2-tuple') return scale elif isinstance(scale, numbers.Real): return (scale, scale) else: raise TypeError('argument should be a number or a tuple')
bigcode/self-oss-instruct-sc2-concepts
def checkValid(s, row, col): """ Returns True if a given cell is valid in a Sudoku puzzle, and False if not. A cell is valid if the number in that cell is not present in any of the cells in the same row, or the same column, or the same block. """ block_row = row // 3 block_col = col // 3 # Row and Column # Ignore blank spots for m in range(9): if s[row][m] != 0 and m != col and s[row][m] == s[row][col]: return False if s[m][col] != 0 and m != row and s[m][col] == s[row][col]: return False # Block for m in range(3): for n in range(3): newRow = m + block_row*3 newCol = n + block_col*3 if s[newRow][newCol] != 0 and newRow != row and newCol != col\ and s[newRow][newCol ] == s[row][col]: return False return True
bigcode/self-oss-instruct-sc2-concepts
from typing import Any def _len(x: Any) -> int: """Return len of x if it is iterable, else 0.""" return max(1, len(x)) if isinstance(x, list) else 0
bigcode/self-oss-instruct-sc2-concepts
def timedelta_to_seconds(td): """ Converts a timedelta to total seconds, including support for microseconds. Return value is (potentially truncated) integer. (This is built-in in Python >= 2.7, but we are still supporting Python 2.6 here.) :param td: The timedelta object :type td: :class:`datetime.timedelta` :return: The number of total seconds in the timedelta object. :rtype: int """ if not td: return None return (td.microseconds + (td.seconds + td.days * 24 * 3600) * 10**6) / 10**6
bigcode/self-oss-instruct-sc2-concepts
def luhn_checksum(num: str) -> str: """Calculate a checksum for num using the Luhn algorithm. :param num: The number to calculate a checksum for as a string. :return: Checksum for number. """ check = 0 for i, s in enumerate(reversed(num)): sx = int(s) sx = sx * 2 if i % 2 == 0 else sx sx = sx - 9 if sx > 9 else sx check += sx return str(check * 9 % 10)
bigcode/self-oss-instruct-sc2-concepts
def test_chess_cell(x, y): """ Source https://pythontutor.ru/lessons/ifelse/problems/chess_board/ Condition Two checkerboard squares are set. If they are painted the same color, print the word YES, and if in different colors - then NO. The program receives four numbers from 1 to 8 each, specifying the column number and   line number first for the first cell, then for the second cell. """ if x % 2 != 0 and y % 2 != 0: # False if cell white, True if cell black return True if x % 2 != 0 and y % 2 == 0: return False if x % 2 == 0 and y % 2 != 0: return False else: return True
bigcode/self-oss-instruct-sc2-concepts
import re def parse_description(dsc): """ Parse the given string into a hash. The string format is `key: value`, where key gets converted to upper case and value extends until a new line. A special last field `Abstract:` extends until the end of string. """ meta, abstract = re.split('abstract:\s*\n*', dsc, flags=re.I) ret = {'ABSTRACT': abstract} for line in meta.splitlines(): if ':' in line: key, value = re.split('\s*:\s*', line, 1) key = key.upper() ret[key] = value return ret
bigcode/self-oss-instruct-sc2-concepts
def decode(packet): """ https://raw.githubusercontent.com/telldus/telldus/master/telldus-core/service/ProtocolOregon.cpp >>> decode(dict(data=0x201F242450443BDD, model=6701))["data"]["temp"] 24.2 >>> decode(dict(data=0x201F242450443BDD, model=6701))["data"]["humidity"] 45.0 """ if packet["model"] != 6701: raise NotImplementedError( "The Oregon model %i is not implemented." % packet["model"] ) data = packet["data"] value = int(data) value >>= 8 checksum1 = value & 0xFF value >>= 8 checksum = ((value >> 4) & 0xF) + (value & 0xF) hum1 = value & 0xF value >>= 8 checksum += ((value >> 4) & 0xF) + (value & 0xF) neg = value & (1 << 3) hum2 = (value >> 4) & 0xF value >>= 8 checksum += ((value >> 4) & 0xF) + (value & 0xF) temp2 = value & 0xF temp1 = (value >> 4) & 0xF value >>= 8 checksum += ((value >> 4) & 0xF) + (value & 0xF) temp3 = (value >> 4) & 0xF value >>= 8 checksum += ((value >> 4) & 0xF) + (value & 0xF) address = value & 0xFF value >>= 8 checksum += ((value >> 4) & 0xF) + (value & 0xF) checksum += 0x1 + 0xA + 0x2 + 0xD - 0xA if checksum != checksum1: raise ValueError( "The checksum in the Oregon packet does not match " "the caluclated one!" ) temperature = ((temp1 * 100) + (temp2 * 10) + temp3) / 10.0 if neg: temperature = -temperature humidity = (hum1 * 10.0) + hum2 return dict( packet, sensorId=address, data=dict(temp=temperature, humidity=humidity), )
bigcode/self-oss-instruct-sc2-concepts
import codecs def is_ascii_encoding(encoding): """Checks if a given encoding is ASCII.""" try: return codecs.lookup(encoding).name == "ascii" except LookupError: return False
bigcode/self-oss-instruct-sc2-concepts
def _find_idx_without_numerical_difference(df, column1, column2, delta, idx=None, equal_nan=False): """ Returns indices which have bigger numerical difference than delta. INPUT: **df** (DataFrame) **column1** (str) - name of first column within df to compare. The values of df[column1] must be numericals. **column2** (str) - name of second column within df to compare. The values of df[column2] must be numericals. **delta** (numerical) - value which defines whether indices are returned or not OPTIONAL: **idx** (iterable, None) - list of indices which should be considered only **equal_nan** (bool, False) - if True, indices are included where at least value in df[column1] or df[column2] is NaN OUTPUT: **index** (pandas.Index) - index within idx where df[column1] and df[column2] deviates by at least delta or, if equal_na is True, one value is NaN """ idx = idx if idx is not None else df.index idx_isnull = df.index[df[[column1, column2]].isnull().any(axis=1)] idx_without_null = idx.difference(idx_isnull) idx_no_delta = idx_without_null[( df.loc[idx_without_null, column1] - df.loc[idx_without_null, column2]).abs().values <= delta] if equal_nan: return idx.difference(idx_no_delta) else: return idx_without_null.difference(idx_no_delta)
bigcode/self-oss-instruct-sc2-concepts
def getDomainOnly(url): """Return the domain out from a url url = the url """ # print ("getDomainOnly : ", url) tmp = url.split('.')[-2] + '.' + url.split('.')[-1] tmp = tmp.split('/')[0] return tmp
bigcode/self-oss-instruct-sc2-concepts
import time def sb_session_login(sb_session, sb_username, sb_password=None): """ login in to sb session using the input credentials. Checks to see if you are already logged in. If no password is given, the password will be requested through the command prompt. .. note:: iPython shells will echo your password. Use a Python command shell to not have your password echoed. :param sb_session: sciencebase session object :type sb_session: sciencebasepy.SbSession :param sb_username: sciencebase username, typically your full USGS email :type sb_username: string :param sb_password: AD password :type sb_password: string :returns: logged in sciencebasepy.SbSession """ if not sb_session.is_logged_in(): if sb_password is None: sb_session.loginc(sb_username) else: sb_session.login(sb_username, sb_password) time.sleep(5) return sb_session
bigcode/self-oss-instruct-sc2-concepts
def subroutine_type(name): """Returns type of subroutine, 'setup' or 'teardown' if it has either of those names, or module setup or teardown, otherwise None.""" lowername = name.lower() if lowername == 'setup': subtype = 'global setup' elif lowername == 'teardown': subtype = 'global teardown' elif lowername.startswith('test_'): subtype = 'test' elif 'setup_' in lowername or '_setup' in lowername: subtype = 'setup' elif 'teardown_' in lowername or '_teardown' in lowername: subtype = 'teardown' else: subtype = None return subtype
bigcode/self-oss-instruct-sc2-concepts
def permutation(s): """ @s: list of elements, eg: [1,2,3] return: list of permutations, eg: [[1,2,3], [1,3,2], [2,1,3], [2,3,1], [3,1,2], [3,2,1]] """ ret = [] length = len(s) if length == 0: return ret if length == 1: return [s] curr = s[0] for prev in permutation(s[1:]): for i in range(length): ret.append(prev[:i] + [curr] + prev[i:]) return ret
bigcode/self-oss-instruct-sc2-concepts
import torch def rot90(input_, k=1, axes=(0, 1)): """Wrapper of `torch.rot90` Parameters ---------- input_ : DTensor Input dense tensor. k : int, optional Number of rotation times, by default 1 axes : tuple, optional The axes in which the input is rotated, by default (0, 1) """ return torch.rot90(input_._data, k, dims=axes)
bigcode/self-oss-instruct-sc2-concepts
import torch def get_optimizer(model, learning_rate, optimizer_state_dict=None, verbose=False): """ Returns an ADAM optimizer attached to the given model (and stored on the same device). If optimizer_state_dict is not None, it will fill in the optimizer state. However, learning_rate will override and saved optimizer state (to allow you to adjust during training.) """ if verbose: print("Building optimizer... ", end='') optimizer = torch.optim.Adam(model.parameters(), learning_rate) if optimizer_state_dict: optimizer.load_state_dict(optimizer_state_dict) # allow for change in learning rate: for param_group in optimizer.param_groups: param_group['lr'] = learning_rate if verbose: print("Done.") return optimizer
bigcode/self-oss-instruct-sc2-concepts
def inc(x): """ Returns a number one greater than num. """ return x + 1
bigcode/self-oss-instruct-sc2-concepts
import requests def get_latest_release_from_pypi(*, package: str) -> str: """Get the latest release of a package on pypi""" response = requests.get(f"https://pypi.org/pypi/{package}/json").json() return response["info"]["version"]
bigcode/self-oss-instruct-sc2-concepts
def filter_to_sentry(event, hint): """filter_to_sentry is used for filtering what to return or manipulating the exception before sending it off to Sentry (sentry.io) The 'extra' keyword is part of the LogRecord object's dictionary and is where the flag for sending to Sentry is set. Example use case: current_app.logger.error( err_formatted, exc_info=ex, extra={'to_sentry': True}) """ # By default, we send to sentry to_sentry = event['extra'].get('to_sentry', True) if to_sentry: return event return None
bigcode/self-oss-instruct-sc2-concepts
def _capture_callback(x): """Validate the passed options for capturing output.""" if x in [None, "None", "none"]: x = None elif x in ["fd", "no", "sys", "tee-sys"]: pass else: raise ValueError("'capture' can only be one of ['fd', 'no', 'sys', 'tee-sys'].") return x
bigcode/self-oss-instruct-sc2-concepts
def get_new_sol_file(test_nr): """ Get name of new solution file """ return "test/{0}-new.sol".format(test_nr)
bigcode/self-oss-instruct-sc2-concepts
import re def unwrap_wrapped_text(text): """ Unwraps multi-line strings, but keeps paragraphs separated by two or more newlines separated by newlines. """ result = [] _re_indentation = re.compile(r'^[ \t]*|[ \t]*$', re.MULTILINE) for paragraph in re.split(r'\n{2,}', text): paragraph = _re_indentation.sub('', paragraph) result.append(re.sub(r'\n', ' ', paragraph)) return '\n'.join(result)
bigcode/self-oss-instruct-sc2-concepts
def test_hindcast_verify_brier_logical(hindcast_recon_1d_ym): """Test that a probabilistic score requiring a binary observations and probability initialized inputs gives the same results whether passing logical as kwarg or mapping logical before for hindcast.verify().""" he = hindcast_recon_1d_ym def logical(ds): return ds > 0.5 brier_logical_passed_as_kwarg = he.verify( metric="brier_score", comparison="m2o", logical=logical, dim="member", alignment="same_verif", ) brier_logical_mapped_before_and_member_mean = ( he.map(logical) .mean("member") .verify(metric="brier_score", comparison="e2o", dim=[], alignment="same_verif") ) brier_logical_mapped_before_no_member_mean = he.map(logical).verify( metric="brier_score", comparison="m2o", dim="member", alignment="same_verif" ) assert ( brier_logical_mapped_before_and_member_mean == brier_logical_passed_as_kwarg ).all() assert ( brier_logical_mapped_before_no_member_mean == brier_logical_passed_as_kwarg ).all()
bigcode/self-oss-instruct-sc2-concepts
import re def could_be_content_page(url: str) -> bool: """ Try to guess if the link is a content page. It's not a perfect check, but it can identify URLs that are obviously not content. """ url = url.lower().rstrip('/') if url.endswith('/signin') or url.endswith('/login') or \ url.endswith('/login-page') or url.endswith('/logout'): return False if url.endswith('/my-account') or url.endswith('/my-wishlist'): return False if re.search('/(lost|forgot)[_-]password$', url): return False if url.endswith('/search') or url.endswith('/archive'): return False if url.endswith('/privacy-policy') or url.endswith('/cookie-policy') or \ url.endswith('/terms-conditions'): return False if url.endswith('/tos') or re.search('/terms[_-]of[_-](service|use)$', url): return False # Yei, it might be a content page return True
bigcode/self-oss-instruct-sc2-concepts
def collide_rect(sprite1, sprite2): """ **pyj2d.sprite.collide_rect** Check if the rects of the two sprites intersect. Can be used as spritecollide callback function. """ return sprite1.rect.intersects(sprite2.rect)
bigcode/self-oss-instruct-sc2-concepts
def compute_image_data_statistics(data_loader): """ Return the channel wise mean and std deviation for images loaded by `data_loader` (loads WebDataset defined in `datasets.py`) """ mean = 0. std = 0. n_samples = 0. for images, bboxes, labels in data_loader: batch_samples = images.size(0) images = images.view(batch_samples, images.size(1), -1) mean += images.mean(2).sum(0) std += images.std(2).sum(0) n_samples += batch_samples mean /= n_samples std /= n_samples return mean, std
bigcode/self-oss-instruct-sc2-concepts
def int_to_roman(n): """ Convert an integer to its standard Roman Numeral representation """ V = [1000, 900, 500, 400, 100, 90, 50, 40, 10, 9, 5, 4, 1] S = ["M", "CM", "D", "CD", "C", "XC", "L", "XL", "X", "IX", "V", "IV", "I"] out = "" for val,sym in zip(V,S): while n >= val: out += sym n -= val return out
bigcode/self-oss-instruct-sc2-concepts
def _get_module_ver_hash(prov): """Get module commit hash, falling back to semantic version, and finally 'UNKNOWN'""" ver = None subacts = prov[0].get('subactions') if subacts: ver = subacts[0].get('commit') if not ver: ver = prov[0].get('service_ver', 'UNKNOWN') return ver
bigcode/self-oss-instruct-sc2-concepts
def get_nominal_conc(df, species): """ Get the nominal hector concentration for a given species Parameters ---------- df : Pandas DataFrame DataFrame containing output from a nominal hector run species : str Species to retrieve output for Return ------ species_df : Pandas DataFrame Pandas DataFrame containing hector concentration output for the given species """ species = species.upper() # Ensure string is all uppercase # ensure correct string for atmospheric co2 concentration if (species == 'CO2'): species = 'Ca' species_df = df.loc[df['variable'] == species] return species_df
bigcode/self-oss-instruct-sc2-concepts
def gpib_control_ren(library, session, mode): """Controls the state of the GPIB Remote Enable (REN) interface line, and optionally the remote/local state of the device. Corresponds to viGpibControlREN function of the VISA library. :param library: the visa library wrapped by ctypes. :param session: Unique logical identifier to a session. :param mode: Specifies the state of the REN line and optionally the device remote/local state. (Constants.GPIB_REN*) :return: return value of the library call. :rtype: :class:`pyvisa.constants.StatusCode` """ return library.viGpibControlREN(session, mode)
bigcode/self-oss-instruct-sc2-concepts
def truncate(string: str, width: int, ending: str = "...") -> str: """Truncate string to be no longer than provided width. When truncated, add add `ending` to shortened string as indication of truncation. Parameters ---------- string: str String to be truncated. width: int Maximum amount of characters before truncation. ending: str, optional Indication string of truncation. Returns ------- Truncated string. """ if not len(string) > width: return string length = width - len(ending) return string[:length] + ending
bigcode/self-oss-instruct-sc2-concepts
def split_ver_str(ver_str): """Split version string into numeric components. Return list of components as numbers additionally checking that all components are correct (i.e. can be converted to numbers). """ ver_list = [] for c in ver_str.split('.')[0:3]: if not c.isdecimal(): raise RuntimeError("Malformed version string '{}'. " "Component '{}' is not an integer." .format(ver_str, c)) ver_list.append(int(c)) return ver_list
bigcode/self-oss-instruct-sc2-concepts
import torch def get_first_idx(numel_per_tensor): """Returns the first indices of each tensor in the :ref:`packed tensor <packed>`. See :ref:`first_idx definition <packed_first_idx>` for more information. Args: numel_per_tensor (torch.LongTensor): The number of elements (vertices, faces, points...) in each unbatched tensor, as a 1D tensor. Returns: (torch.LongTensor): first indices for each unbatched tensor in the packed tensor, and the last index + 1, as 1D tensor. Example: >>> numel_per_tensor = torch.LongTensor([2, 3, 5]) >>> get_first_idx(numel_per_tensor) tensor([ 0, 2, 5, 10]) """ output = torch.zeros((numel_per_tensor.shape[0] + 1,), dtype=torch.long, device=numel_per_tensor.device) torch.cumsum(numel_per_tensor, dim=0, out=output[1:]) return output
bigcode/self-oss-instruct-sc2-concepts
def shipping_charge(method, basket, postcode): """ Template tag for calculating the shipping charge for a given shipping method and basket, and injecting it into the template context. """ return method.calculate(basket, postcode)
bigcode/self-oss-instruct-sc2-concepts
import re def _re_compile(regex): """Compile a string to regex, I and UNICODE.""" return re.compile(regex, re.I | re.UNICODE)
bigcode/self-oss-instruct-sc2-concepts
from io import StringIO def df_to_csv_string(df): """Converts pandas DataFrame to a CSV string.""" out = StringIO() df.to_csv(out, encoding='utf-8') return out.getvalue()
bigcode/self-oss-instruct-sc2-concepts
def left_shift(number, n): """ Left shift on 10 base number. Parameters ---------- number : integer the number to be shift n : integer the number of digit to shift Returns ------- shifted number : integer the number left shifted by n digit Examples -------- >>> left_shift(152, 1) 15 >>> left_shift(14589, 3) 14 """ return number // 10 ** n
bigcode/self-oss-instruct-sc2-concepts
import math def calculate_distance(location1, location2): """ Calculates the distance between two pairs of lat, long coordinates using the Haversine formula Inputs: location1 - [lat, lon] array with first location location2 - [lat, lon] array with second location Outputs: distance - in kilometers """ lat1 = math.radians(abs(location1[0])) lon1 = math.radians(abs(location1[1])) lat2 = math.radians(abs(location2[0])) lon2 = math.radians(abs(location2[1])) # haversine formula dlon = lon2 - lon1 dlat = lat2 - lat1 a = math.sin(dlat/2)**2 + math.cos(lat1) * math.cos(lat2) * math.sin(dlon/2)**2 c = 2 * math.asin(math.sqrt(a)) # Radius of earth in kilometers r = 6371.0 return c * r
bigcode/self-oss-instruct-sc2-concepts
import re def rmsp(s): """Replace multiple spaces with one. """ return re.sub(r"\ +", ' ', s.strip())
bigcode/self-oss-instruct-sc2-concepts
def ir(some_value): """ Rounds and casts to int Useful for pixel values that cannot be floats Parameters ---------- some_value : float numeric value Returns -------- Rounded integer Raises ------ ValueError for non scalar types """ return int(round(some_value))
bigcode/self-oss-instruct-sc2-concepts
def decibels_to_amplitude_ratio(decibels): """The ratio between two amplitudes given a decibel change""" return 2 ** (decibels/10)
bigcode/self-oss-instruct-sc2-concepts
import requests def get_stock_data(symbol, token): """Send a request to the API with the symbol and token. Return the stock data we want: Symbol, Company Name, Current Price""" url = f"https://cloud.iexapis.com/stable/stock/{symbol}/quote?token={token}" response = requests.get(url) if response.status_code != 200: print(response.text) return None all_stock_data = response.json() name = all_stock_data["companyName"] symbol = all_stock_data["symbol"] current_price = all_stock_data["latestPrice"] stock_data = {"name": name, "symbol": symbol, "current_price": current_price} return stock_data
bigcode/self-oss-instruct-sc2-concepts
def handle_exhibition_desc(company: str, desc: str) -> str: """ Handles exhibition description special formatting needs. Returns the updated description. :param company: company name :param desc: company description """ if company.lower() == "mathworks": desc = desc.replace(" o ", "\n- ") if company.lower() == "simulation and data lab neuroscience": desc = desc.replace("\n•", "\n- ") return desc
bigcode/self-oss-instruct-sc2-concepts
import click def soft_nprocs(soft, nprocs): """Reduce the number of ranks to the largest acceptable soft value""" # If no soft specification given, use -n value if not soft: return nprocs # Filter to values between 1 and nprocs try: return max([x for x in soft if 0 < x <= nprocs]) except ValueError: # pylint: disable=raise-missing-from raise click.UsageError("No soft values found between 1 and %d" % nprocs)
bigcode/self-oss-instruct-sc2-concepts
def _IsOverlapping(alert_entity, start, end): """Whether |alert_entity| overlaps with |start| and |end| revision range.""" return (alert_entity.start_revision <= end and alert_entity.end_revision >= start)
bigcode/self-oss-instruct-sc2-concepts
import torch def GTA_prop_to_hot(img, n_classes: int, width: int, height: int): """ This function turns the output of the network (given in probability format) into the most likely onehot encoded output. Args: img (tensor): The tensor with probabilities. n_classes (int): Amount of classes in the onehot encoded format. width (int): Size width of the given tensor. height (int): Size height of the given tensor. Returns: Tensor: In onehot encoded format. """ mat = torch.argmax(img, dim=1) map = torch.zeros((n_classes, height, width), dtype=torch.uint8) for r in range(height): for c in range(width): map[mat[0][r][c]][r][c] = 1 return map
bigcode/self-oss-instruct-sc2-concepts
import math def polar2cart(r, x0, y0, theta): """Changes polar coordinates to cartesian coordinate system. :param r: Radius :param x0: x coordinate of the origin :param y0: y coordinate of the origin :param theta: Angle :return: Cartesian coordinates :rtype: tuple (int, int) """ x = int(x0 + r * math.cos(theta)) y = int(y0 + r * math.sin(theta)) return x, y
bigcode/self-oss-instruct-sc2-concepts
def binary_search(query, array): """ Determine whether the query is in an sorted array. Return the index of the query if it is present in the array. If the query is not in the array, return -1 >>> binary_search(4, [1, 2, 3, 4, 5, 6, 7, 8, 9]) 3 >>> binary_search(8, [1, 2, 3, 4, 5, 6, 7, 8, 9]) 7 >>> binary_search(10, [1, 2, 3, 4, 5, 6, 7, 8, 9]) -1 """ lo, hi = 0, len(array) - 1 while lo <= hi: mid = (lo + hi) // 2 if query < array[mid]: hi = mid - 1 elif query > array[mid]: lo = mid + 1 else: return mid return -1
bigcode/self-oss-instruct-sc2-concepts
import torch def calculate_output_dim(net, input_shape): """Calculates the resulting output shape for a given input shape and network. Args: net (torch.nn.Module): The network which you want to calculate the output dimension for. input_shape (int | tuple[int]): The shape of the input being fed into the :obj:`net`. Batch dimension should not be included. Returns: The shape of the output of a network given an input shape. Batch dimension is not included. """ if isinstance(input_shape, int): input_shape = (input_shape,) placeholder = torch.zeros((0,) + tuple(input_shape)) output = net(placeholder) return output.size()[1:]
bigcode/self-oss-instruct-sc2-concepts
def markdown_escape_filter(text): """Escape special characters in Markdown.""" return text.replace("\\", "\\\\").replace("`", "\\`").replace( "*", "\\*").replace("_", "\\_").replace("{", "\\{").replace( "}", "\\}").replace("[", "\\[").replace("]", "\\]").replace( "(", "\\(").replace(")", "\\)").replace("#", "\\#").replace( "+", "\\+").replace("-", "\\-").replace(".", "\\.").replace( "!", "\\!").replace("|", "\\|")
bigcode/self-oss-instruct-sc2-concepts
def thousands_separator(value): """ 千位分隔符 例如传入 1000000000,返回 1,000,000,000 :param value: 需要转换的数字 :return: 格式化后的字符串 """ return '{:,}'.format(value)
bigcode/self-oss-instruct-sc2-concepts
from typing import List import math def equal_split(s: str, width: int) -> List[str]: """ Split the string, each split has length `width` except the last one. """ num = int(math.ceil(len(s) / width)) # python3 return [s[i * width: (i + 1) * width] for i in range(num)]
bigcode/self-oss-instruct-sc2-concepts
def prob1(l): """Accept a list 'l' of numbers as input and return a list with the minimum, maximum, and average of the original list. """ ans = [] ans.append(min(l)) ans.append(max(l)) ans.append(float(sum(l))/len(l)) return ans
bigcode/self-oss-instruct-sc2-concepts
def get_ns_name(uri): """ Get the namespace (the namespace is placed before the first '#' character or the last '/' character) """ hash_index = uri.find('#') index = hash_index if hash_index != -1 else uri.rfind('/') namespace = uri[0: index + 1] return namespace
bigcode/self-oss-instruct-sc2-concepts
import struct def pack_date(date): """ Packs a date (assumed to be UTC) as a struct with of 16-bit, unsigned `year` (big endian), 1 byte `month`, and 1 byte `day`. """ return struct.pack("!HBB", date.year, date.month, date.day)
bigcode/self-oss-instruct-sc2-concepts
from typing import Set def allocate_mid(mids: Set[str]) -> str: """ Allocate a MID which has not been used yet. """ i = 0 while True: mid = str(i) if mid not in mids: mids.add(mid) return mid i += 1
bigcode/self-oss-instruct-sc2-concepts
def _xor(a,b): """Return true iff exactly one of and b are true. Used to check some conditions.""" return bool(a) ^ bool(b)
bigcode/self-oss-instruct-sc2-concepts
from typing import Any from typing import get_args from typing import get_origin from typing import Literal def is_str_literal(hint: Any) -> bool: """Check if a type hint is Literal[str].""" args = get_args(hint) origin = get_origin(hint) if origin is not Literal: return False if not len(args) == 1: return False return isinstance(args[0], str)
bigcode/self-oss-instruct-sc2-concepts
def get_pitch_at_time(genotype, time): """given genotype and durk time point, returns pitch being played at that durk point and whether or not pitch ends perfectly on time Args: genotype ((int, int)[]): genotype of chromosome, which is list of (pitch, dur) time (int): time point in durks Returns: (int, bool): (pitch, end_on_time) where pitch is [1,21] and end_on_time represents whether or not the pitch ends perfectly at the time point time. """ pitch = -9999 dur_running_total = 0 end_on_time = False for i, (ed, dur) in enumerate(genotype): dur_running_total += dur if dur_running_total > time: pitch = ed break elif dur_running_total == time: pitch = ed end_on_time = True break return (pitch, end_on_time)
bigcode/self-oss-instruct-sc2-concepts
def _get_source_files(commands): """Return a list of all source files in the compilation.""" return list(commands.keys())
bigcode/self-oss-instruct-sc2-concepts
def dnode(period): """ Orbit nodal precession on each rev. Orbits below GEO move (drift) Westerly while orbits above GEO move Easterly. Orbits at GEO are stationary, 0 deg drift. Use siderial day rotation for better accuracy. Arg: period [sec] Return: node precession (dn) [deg] """ return 360 - 360/(23*3600+56*60+4)*period
bigcode/self-oss-instruct-sc2-concepts
def process_search_term(lookup): """ Removes any whitespace from the search string, and replaces them with the appropriate character to pass as a URL :param lookup: :return: lookup """ lookup = lookup.replace(" ", "+") return lookup
bigcode/self-oss-instruct-sc2-concepts
import torch def check_gpu(gpu): """ Fuction takes one argument as boolean and provides support for gpu or cpu selection and print out the current device being used. Command Line Arguments: 1. GPU as True value that enables GPU support and use cuda for calculation, and False to enable CPU. Function returns device and print out the device being used, either for trianing or inference. """ # If gpu is True gpu is enabled and print out "\nGPU is availabe...". if the gpu didn't exist device switchs to cpu and print out "\nDevice didn't find GPU, using CPU instead" if gpu: device = torch.device("cuda" if torch.cuda.is_available() else "cpu") if torch.cuda.is_available(): print("\nGPU is availabe...") else: print("\nDevice didn't find GPU, using CPU instead") else: print("\nCPU is availabe...") return torch.device("cpu") return device
bigcode/self-oss-instruct-sc2-concepts
import csv import re def load_peptides(input_file, peptide_column, column_separator): """ Parses the input file and extracts all peptides occuring within the file. Peptide strings are cleaned (only valid characters retained) and returned as a set. :param input_file: The file to parse :param peptide_column: The column header to extract the peptides from. :param column_separator: The separator used for the columns :return: A set of strings representing the peptides. """ with open(input_file, "r") as input_stream: csv_reader = csv.DictReader(input_stream, delimiter=column_separator) peptides = set() for row in csv_reader: if peptide_column not in row: raise Exception("Specified peptide column '" + peptide_column + "' not found in input file.") sequence = row[peptide_column] clean_sequence = re.sub("[^A-Z]", "", sequence) peptides.add(clean_sequence) return peptides
bigcode/self-oss-instruct-sc2-concepts
def input_prompt(prompt): """ Get user input """ return input(prompt)
bigcode/self-oss-instruct-sc2-concepts
from typing import List def alphabetical_binary_search(sorted_list: List, search_name: str) -> int: """Alphabetical binary search (for study purpuses) Args: sorted_list (List): A list of names (must be ordered) search_name (str): name to search Returns: int: found index or -1 """ lowest_index = 0 highest_index = len(sorted_list) - 1 intermediate_index = highest_index // 2 while lowest_index <= highest_index: name = sorted_list[intermediate_index] if search_name == name: return intermediate_index if name > search_name: highest_index = intermediate_index - 1 if name < search_name: lowest_index = intermediate_index + 1 intermediate_index = (lowest_index + highest_index) // 2 return -1
bigcode/self-oss-instruct-sc2-concepts
import torch def compute_loss(inputs, outputs, criterion, edge_criterion): """Compute loss automatically based on what the model output dict contains. 'doc_logits' -> document-label CE loss 'para_logits' -> paragraph-label CE loss 'pare_edge_weights' -> additional edge CE loss """ if 'para_logits' in outputs: loss = criterion(outputs['para_logits'], inputs['para_label']) loss *= (inputs['para_lengths'] != 0).to(torch.float) loss = loss.sum() else: loss = criterion(outputs['doc_logits'], inputs['label']).sum() if 'para_edge_weights' in outputs: edge_loss_lambda = 0.1 edge_loss = edge_criterion(outputs['para_edge_weights'], 1 - inputs['para_label']) edge_loss *= (inputs['para_lengths'] != 0).to(torch.float) loss += edge_loss_lambda * edge_loss.sum() return loss
bigcode/self-oss-instruct-sc2-concepts
import base64 def decode_base64(input_string: str) -> bytes: """Decode an unpadded standard or urlsafe base64 string to bytes.""" input_bytes = input_string.encode("ascii") input_len = len(input_bytes) padding = b"=" * (3 - ((input_len + 3) % 4)) # Passing altchars here allows decoding both standard and urlsafe base64 output_bytes = base64.b64decode(input_bytes + padding, altchars=b"-_") return output_bytes
bigcode/self-oss-instruct-sc2-concepts
def normalize_extension(extension): """ Normalize extension Converts given extension to canonical format for storage :param extension: original extension :return: normalized extension """ extension = extension.lower() exts = dict() exts['jpg'] = ['jpeg','jpe','jif','jfif','jfi''jp2','j2k','jpx','jpf','jpm'] exts['tif'] = ['tiff'] exts['tar.gz'] = ['tgz'] for canonical, variants in exts.items(): if extension in variants: extension = canonical break return extension
bigcode/self-oss-instruct-sc2-concepts
def parseTrackLog(line): """Parse trackLog line and return important fields: db, year, month, hgsid, and a list of tracks""" #### Sample line being processed #### # [Sun Mar 05 04:11:27 2017] [error] [client ###.###.###.##] trackLog 0 hg38 hgsid_### cytoBandIdeo:1,cloneEndCTD:2 #### splitLine = line.strip().split('trackLog') prefix = splitLine[0].split() month = prefix[1] year = prefix[4].replace("]","") suffix = splitLine[1].split() db = suffix[1] hgsid = suffix[2] if len(suffix) > 3: activeTracks = suffix[3] tracks = activeTracks.split(",") else: tracks = [] return db, year, month, hgsid, tracks
bigcode/self-oss-instruct-sc2-concepts
import re def getWords(text): """From a text input as a string, get the words separated by a space and return it as a list of strings""" return re.compile('\w+').findall(text)
bigcode/self-oss-instruct-sc2-concepts
def sqdist(point1, point2, rotmat): """ This routine calculates the anisotropic distance between two points given the coordinates of each point and a definition of the anisotropy. This method only consider a single anisotropy senario. Parameters ---------- point1 : tuple Coordinates of first point (x1,y1,z1) point2 : tuple Coordinates of second point (x2,y2,z2) rotmat : 3*3 ndarray matrix of rotation for this structure Returns ------- sqdist : scalar The squared distance accounting for the anisotropy and the rotation of coordinates (if any). """ dx = point1[0] - point2[0] dy = point1[1] - point2[1] dz = point1[2] - point2[2] sqdist = 0.0 for i in range(3): cont = rotmat[i, 0] * dx + \ rotmat[i, 1] * dy + \ rotmat[i, 2] * dz sqdist += cont * cont return sqdist
bigcode/self-oss-instruct-sc2-concepts
def _is_path_within_scope(scope, fullpath): """Check whether the given `fullpath` is within the given `scope`""" if scope == '/': return fullpath is not None fullpath = fullpath.lstrip('/') if fullpath else '' scope = scope.strip('/') return (fullpath + '/').startswith(scope + '/')
bigcode/self-oss-instruct-sc2-concepts
def age_interp(request): """Fixture for age_interp flag.""" return request.param
bigcode/self-oss-instruct-sc2-concepts
def avoids(word, forbidden): """ Predicate that asks whether word avoids letters in the forbidden string """ # Feels like there should be a more efficient way to do this using # set intersection, but I'll just check the word character by character for letter in forbidden: if word.find(letter)!=-1: return False return True
bigcode/self-oss-instruct-sc2-concepts
def get_vocabulary(path_to_vocab): """ Return a list of prefixes defining the vocabulary. """ vocab = [] with open(path_to_vocab) as f: for line in f: line = line.rstrip() vocab.append(line) return vocab
bigcode/self-oss-instruct-sc2-concepts
def b_delta(rewards,states,alpha): """ Implements the Resorla-Wagner (delta) learning rule. V_intial is 0. Note: Null (0 or '0') states are silently skipped. Returns two dictionaries containing value and RPE timecourses, for each state. """ # Init s_names = set(states) V_dict = {} RPE_dict = {} for s in s_names: V_dict[s] = [0.] RPE_dict[s] = [] for r,s in zip(rewards,states): ## Skip terminal states if (s == 0) | (s == '0'): continue V = V_dict[s][-1] ## the Delta rule: RPE = r - V V_new = V + alpha * RPE ## Store and shift V_new to ## V for next iter V_dict[s].append(V_new) ## Store RPE RPE_dict[s].append(RPE) return V_dict, RPE_dict
bigcode/self-oss-instruct-sc2-concepts
def get_weight_shapes(num_inputs, layer_sizes, num_outputs): """ adapted from original tf_model.get_weight_shapes() to convert from method to function """ weight_shapes = [] input_size = num_inputs for i, layer in enumerate(layer_sizes): weight_shapes.append((input_size, layer)) weight_shapes.append((layer,)) input_size = layer weight_shapes.append((input_size, num_outputs)) weight_shapes.append((num_outputs,)) return weight_shapes
bigcode/self-oss-instruct-sc2-concepts
import warnings def format_channel_id(ch): """ Function for formatting an `idelib.dataset.Channel` or `SubChannel` for display. Renders as only the channel and subchannel IDs (the other information is shown in the rest of the table). :param ch: The `idelib.dataset.Channel` or `idelib.dataset.SubChannel` to format. :return: A formatted "channel.subchannel" string. """ try: if ch.parent: return f"{ch.parent.id}.{ch.id}" else: return f"{ch.id}.*" except (AttributeError, TypeError, ValueError) as err: warnings.warn(f"format_channel_id({ch!r}) raised {type(err).__name__}: {err}") return str(ch)
bigcode/self-oss-instruct-sc2-concepts
def _IsBold(weight): """Is this weight considered bold? Per Dave C, only 700 will be considered bold. Args: weight: Font weight. Returns: True if weight is considered bold, otherwise False. """ return weight == 700
bigcode/self-oss-instruct-sc2-concepts
def add_attributes(rsrc_id, manifest): """Add additional attributes to the manifest.""" proid = rsrc_id[0:rsrc_id.find('.')] environment = 'prod' updated = { 'proid': proid, 'environment': environment } updated.update(manifest) return updated
bigcode/self-oss-instruct-sc2-concepts
def setup_walkers(cfg_emcee, params, level=0.1): """Initialize walkers for emcee. Parameters ---------- cfg_emcee: dict Configuration parameters for emcee. params: asap.Parameter object Object for model parameters. level: float, optional Returns ------- ini_positions: numpy array with (N_walker, N_param) shape Initial positions of all walkers. """ # Initialize the walkers if cfg_emcee['ini_prior']: # Use the prior distributions for initial positions of walkers. return params.sample(nsamples=cfg_emcee['burnin_n_walker']) return params.perturb(nsamples=cfg_emcee['burnin_n_walker'], level=level)
bigcode/self-oss-instruct-sc2-concepts
def pack_4_4(x: int, y: int) -> int: """Pack two 4-bit values into an 8-bit value. x and y must be in range 0..15 inclusive. Result is in range 0..255 inclusive. """ assert 0 <= x <= 15 assert 0 <= y <= 15 return (x << 4) | y
bigcode/self-oss-instruct-sc2-concepts
def _GetLibMetadata(layer): """ Return a dictionary of library-specific data found in layer.""" globalPrim = layer.GetPrimAtPath('/GLOBAL') if not globalPrim: raise Exception("Code generation requires a \"/GLOBAL\" prim with " "customData to define at least libraryName. GLOBAL prim not found.") if not globalPrim.customData: raise Exception("customData is either empty or not defined on /GLOBAL " "prim. At least \"libraryName\" entries in customData are required " "for code generation.") # Return a copy of customData to avoid accessing an invalid map proxy during # template rendering. return dict(globalPrim.customData)
bigcode/self-oss-instruct-sc2-concepts
def build_system_info(platform=None, platform_type=None, accel_type=None, cpu_cores=None, cpu_type=None, cpu_sockets=None): """Information about the system the test was executed on. Args: platform (str): Higher level platform, e.g. aws, gce, or workstation. platform_type (str): Type of platform, DGX-1, p3.8xlarge, or z420. accel_type (str, optional): Type of accelerator, e.g. K80 or P100. cpu_cores (int, optional): Number of physical cpu cores. cpu_type (str, optional): Type of cpu. cpu_sockets (int, optional): Number of sockets Returns: `dict` with system info. """ system_info = {} if platform: system_info['platform'] = platform if platform_type: system_info['platform_type'] = platform_type if accel_type: system_info['accel_type'] = accel_type if cpu_cores: system_info['cpu_cores'] = cpu_cores if cpu_type: system_info['cpu_type'] = cpu_type if cpu_type: system_info['cpu_sockets'] = cpu_sockets return system_info
bigcode/self-oss-instruct-sc2-concepts
import re def strip_spaces(string): """Remove white-space from a string Parameters ---------- string: str Returns ------- str """ pattern = re.compile(r'\s+') return re.sub(pattern, '', string)
bigcode/self-oss-instruct-sc2-concepts
def hexint_parser(arg: str) -> int: """Parse a hexadecimal starting with 0x into an integer.""" if not arg.startswith("0x"): raise Exception("Received non-hex integer where hex expected") return int(arg, 16)
bigcode/self-oss-instruct-sc2-concepts
def orbtell(orb): """Query current connection read-head position""" return orb.tell()
bigcode/self-oss-instruct-sc2-concepts
import random def random_bbox(config): """Generate a random tlhw with configuration. Args: config: Config should have configuration including IMG_SHAPES, VERTICAL_MARGIN, HEIGHT, HORIZONTAL_MARGIN, WIDTH. Returns: tuple: (top, left, height, width) """ img_shape = config.IMG_SHAPES img_height = img_shape[0] img_width = img_shape[1] maxt = img_height - config.VERTICAL_MARGIN - config.HEIGHT maxl = img_width - config.HORIZONTAL_MARGIN - config.WIDTH t = int(random.uniform(config.VERTICAL_MARGIN, maxt)) l = int(random.uniform(config.HORIZONTAL_MARGIN, maxl)) h = config.HEIGHT w = config.WIDTH return t, l, h, w
bigcode/self-oss-instruct-sc2-concepts
from datetime import datetime def from_epoch(seconds): """Given seconds since epoch, return a datetime object Args: seconds: Seconds since epoch Returns: datetime representation of seconds since epoch """ return datetime.utcfromtimestamp(float(seconds))
bigcode/self-oss-instruct-sc2-concepts
def _word_feats(words): """ NLTK word feature generator for the NaiveBayesClassifier """ return dict([(word, True) for word in words])
bigcode/self-oss-instruct-sc2-concepts
def build_machine(network=None, machine_type=None, preemptible=None, service_account=None, boot_disk_size_gb=None, disks=None, accelerators=None, labels=None, cpu_platform=None, nvidia_driver_version=None, enable_stackdriver_monitoring=None): """Build a VirtualMachine object for a Pipeline request. Args: network (dict): Network details for the pipeline to run in. machine_type (str): GCE Machine Type string for the pipeline. preemptible (bool): Use a preemptible VM for the job. service_account (dict): Service account configuration for the VM. boot_disk_size_gb (int): Boot disk size in GB. disks (list[dict]): List of disks to mount. accelerators (list[dict]): List of accelerators to attach to the VM. labels (dict[string, string]): Labels for the VM. cpu_platform (str): The CPU platform to request. nvidia_driver_version (str): The NVIDIA driver version to use when attaching an NVIDIA GPU accelerator. enable_stackdriver_monitoring (bool): Enable stackdriver monitoring on the VM. Returns: An object representing a VirtualMachine. """ return { 'network': network, 'machineType': machine_type, 'preemptible': preemptible, 'serviceAccount': service_account, 'bootDiskSizeGb': boot_disk_size_gb, 'disks': disks, 'accelerators': accelerators, 'labels': labels, 'cpuPlatform': cpu_platform, 'nvidiaDriverVersion': nvidia_driver_version, 'enableStackdriverMonitoring': enable_stackdriver_monitoring, }
bigcode/self-oss-instruct-sc2-concepts
def copy_event_attributes(ev1, ev2): """Copy all attributes from one roxar event to another. Args: ev1: roxar event to copy into ev2: roxar event to copy attributes from Returns: An updated version of ev1. Unaltered if the two events are not of same type. """ if ev1.type == ev2.type: for key in ev1.attribute_keys: ev1[key] = ev2[key] return ev1
bigcode/self-oss-instruct-sc2-concepts
def group_by(object_list, key_function): """ Return dictionary of objects grouped by keys returned by `key_function` for each element in `object_list`. `object_list` does not need to be sorted. >>> group_by([1, 2, 3, 4, 5], lambda x: x % 2) {0: [2, 4], 1: [1, 3, 5]} """ groups = dict() for obj in object_list: key = key_function(obj) if key not in groups: groups[key] = list() groups[key].append(obj) return groups
bigcode/self-oss-instruct-sc2-concepts
def mass_hpa_tail_boom( length_tail_boom, dynamic_pressure_at_manuever_speed, mean_tail_surface_area, ): """ Finds the mass of a tail boom structure of a human powered aircraft (HPA), following Juan Cruz's correlations in http://journals.sfu.ca/ts/index.php/ts/article/viewFile/760/718 Assumes a tubular tail boom of high modules (E > 228 GPa) graphite/epoxy :param length_tail_boom: length of the tail boom [m]. Calculated as distance from the wing 1/4 chord to the furthest tail surface. :param dynamic_pressure_at_manuever_speed: dynamic pressure at maneuvering speed [Pa] :param mean_tail_surface_area: mean of the areas of the tail surfaces (elevator, rudder) :return: mass of the tail boom [m] """ l = length_tail_boom q = dynamic_pressure_at_manuever_speed area = mean_tail_surface_area w_tb = (l * 1.14e-1 + l ** 2 * 1.96e-2) * (1 + ((q * area) / 78.5 - 1) / 2) return w_tb
bigcode/self-oss-instruct-sc2-concepts
def find_first2(l, pred1, pred2): """ Find first occurrence in list satisfying two-step predicate. :param l: list. :param pred1: predicate on the list elements. :param pred2: predicate on two list elements. :return: index of first occurrence in list satisfying pred2(l[index-1], l[index]) or pred1(l[0]) if only one elment in the list; length of the list if not found. """ length = len(l) index = length if length > 0: if length == 1: if pred1(l[0]): index = 0 else: index = 1 else: for i in range(1, length): if pred2(l[i-1], l[i]): index = i break return index
bigcode/self-oss-instruct-sc2-concepts
from datetime import datetime def meta_from_pid(product_id): """Extract metadata contained in a Landsat Product Identifier.""" meta = {} parts = product_id.split("_") meta["product_id"] = product_id meta["sensor"], meta["correction"] = parts[0], parts[1] meta["path"], meta["row"] = int(parts[2][:3]), int(parts[2][3:]) meta["acquisition_date"] = datetime.strptime(parts[3], "%Y%m%d") meta["processing_date"] = datetime.strptime(parts[4], "%Y%m%d") meta["collection"], meta["tier"] = int(parts[5]), parts[6] return meta
bigcode/self-oss-instruct-sc2-concepts
import requests def check_status(datum): """Check that both the url and image link are valid URLs and that the image link isn't just a redirect. """ if requests.get(datum["url"], verify=False).status_code != 200: return False get_ = requests.get(datum["image"], verify=False) if get_.status_code != 200: return False if get_.url != datum["image"]: return False return True
bigcode/self-oss-instruct-sc2-concepts
def recursive_find_xml_element( xmlnode, name, _nodes=None ): """ recursively finds all XML sub-elements with the name 'name', such as for nd in recursive_find_xml_element( xmlnode, 'TestList' ): pass """ if _nodes == None: _nodes = [] for nd in xmlnode: if nd.tag == name: _nodes.append( nd ) recursive_find_xml_element( nd, name, _nodes ) return _nodes
bigcode/self-oss-instruct-sc2-concepts