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from bs4 import BeautifulSoup import requests def get_soup(url: str) -> BeautifulSoup: """Get an instance of BeautifulSoup for a specific url""" response = requests.get(url) if response.status_code != requests.codes.ok: print(f"url request error: response.status_code is {response.status_code}") raise requests.ConnectionError html = response.text soup: BeautifulSoup = BeautifulSoup(html, "html.parser") return soup
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def quaternion_upper_hemispher(q): """ The quaternion q and โˆ’q represent the same rotation be- cause a rotation of ฮธ in the direction v is equivalent to a rotation of 2ฯ€ โˆ’ ฮธ in the direction โˆ’v. One way to force uniqueness of rotations is to require staying in the โ€œupper halfโ€ of S 3 . For example, require that a โ‰ฅ 0, as long as the boundary case of a = 0 is handled properly because of antipodal points at the equator of S 3 . If a = 0, then require that b โ‰ฅ 0. However, if a = b = 0, then require that c โ‰ฅ 0 because points such as (0,0,โˆ’1,0) and (0,0,1,0) are the same rotation. Finally, if a = b = c = 0, then only d = 1 is allowed. :param q: :return: """ a, b, c, d = q if a < 0: q = -q if a == 0: if b < 0: q = -q if b == 0: if c < 0: q = -q if c == 0: print(q) q[3] = 1 return q
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def get_leaf_artists(root_artist, matchfunc): """Return all the leaf artists. which Args: root_artist: Artist. matchfunc: callable: artist -> bool. Return: All the decendant Artists matched with `matchfunc`. Note ---- As you might notice, this class is similar to `Artist.findobj`. However, only leaf artists are gathered. * https://matplotlib.org/_modules/matplotlib/artist.html#Artist.findobj """ def _inner(artist, is_target): if matchfunc(artist): is_target = True children = artist.get_children() if children: result = sum([_inner(elem, is_target) for elem in children], []) else: if is_target: result = [artist] else: result = [] return result result = _inner(root_artist, False) return result
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def intersect(hrect, r2, centroid): """ checks if the hyperrectangle hrect intersects with the hypersphere defined by centroid and r2 """ maxval = hrect[1, :] minval = hrect[0, :] p = centroid.copy() idx = p < minval p[idx] = minval[idx] idx = p > maxval p[idx] = maxval[idx] return ((p - centroid) ** 2).sum() < r2
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import re def remove_trailing_commas(json_like): """ Removes trailing commas from `json_like` and returns the result. Examples -------- >>> remove_trailing_commas('{"foo":"bar","baz":["blah",],}') '{"foo":"bar","baz":["blah"]}' """ trailing_object_commas_re = re.compile( r'(,)\s*}(?=([^"\\]*(\\.|"([^"\\]*\\.)*[^"\\]*"))*[^"]*$)') trailing_array_commas_re = re.compile( r'(,)\s*\](?=([^"\\]*(\\.|"([^"\\]*\\.)*[^"\\]*"))*[^"]*$)') # Fix objects {} first objects_fixed = trailing_object_commas_re.sub("}", json_like) # Now fix arrays/lists [] and return the result return trailing_array_commas_re.sub("]", objects_fixed)
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def is_method_of(method, obj): """Return True if *method* is a method of *obj*. *method* should be a method on a class instance; *obj* should be an instance of a class. """ # Check for both 'im_self' (Python < 3.0) and '__self__' (Python >= 3.0). cls = obj.__class__ mainObj = getattr(method, "im_self", getattr(method, "__self__", None)) return isinstance(mainObj, cls)
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import os def make_fig_save_dirs(save_dir_root, pdf=False): """Create directories for saving figures in svg and png formats Args: save_dir_root (string): root directory for saving figures Returns: dir_svg (string): valid directory dir_png (string): valid directory """ dir_png = os.path.join(save_dir_root, 'png') dir_svg = os.path.join(save_dir_root, 'svg') if not os.path.exists(dir_png): os.makedirs(dir_png) if not os.path.exists(dir_svg): os.makedirs(dir_svg) return dir_svg, dir_png
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import os def get_workflow_config_path(repo): """Returns the full path for the git workflow config file.""" return os.path.join(repo.git_dir, 'config_workflow')
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def callback(func): """ A decorator to add a keyword arg 'callback' to execute a method on the return value of a function Used to add callbacks to the API calls :param func: The function to decorate :return: The wrapped function """ def wrap(*args, **kwargs): callback_ = kwargs.pop('callback', None) result = func(*args, **kwargs) if callback_: callback_(result) return result return wrap
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def remove_dups_stringlist(str): """Remove duplicates from list as string""" arr = str.split(',') arr = list(dict.fromkeys(arr)) return ','.join(arr)
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import torch def dice_loss_norm(input, target): """ input is a torch variable of size BatchxnclassesxHxW representing log probabilities for each class target is a 1-hot representation of the groundtruth, should have same size as the input """ assert input.size() == target.size(), "Input sizes must be equal." assert input.dim() == 4, "Input must be a 4D Tensor." # uniques = np.unique(target.numpy()) # assert set(list(uniques)) <= set([0, 1]), "target must only contain zeros and ones" probs = input num = probs * target # b,c,h,w--p*g num = torch.sum(num, dim=3) num = torch.sum(num, dim=2) # num = torch.sum(num, dim=0)# b,c den1 = probs * probs # --p^2 den1 = torch.sum(den1, dim=3) den1 = torch.sum(den1, dim=2) # b,c,1,1 den1 = torch.sum(den1, dim=0) den2 = target * target # --g^2 den2 = torch.sum(den2, dim=3) den2 = torch.sum(den2, dim=2) # b,c,1,1 den2 = torch.sum(den2, dim=0) dice = 2 * ((num+0.0000001) / (den1 + den2+0.0000001)) # dice_eso = dice[1:] # we ignore bg dice val, and take the fg dice_eso = dice dice_total = -1 * torch.sum(dice_eso) / dice_eso.size(0) # divide by batch_sz return dice_total
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import os def files_in_current_dir(dir_name): """list all files in a dir. Args: dir_name (str): path to a dir Returns: list: files in a dir. """ return [os.path.abspath(os.path.join(dir_name, x)) for x in os.listdir(dir_name) if os.path.isfile(os.path.abspath(os.path.join(dir_name, x)))]
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def make_usage(template, command_map, alias_map): """Generate the usage doc based on configured commands and aliases""" def format_command_info(command_name): func = command_map[command_name] # Some commands (but not all) have aliases aliases = [k for k in alias_map.keys() if alias_map[k] == command_name] aliases = " ".join(sorted(aliases)) if aliases else "" aliases = f"\n Aliases: {aliases}" return f" {command_name:8s} {func.__doc__}{aliases}\n" command_info_parts = map( format_command_info, (name for name in sorted(command_map.keys())) ) return template.format(COMMANDS="\n".join(command_info_parts))
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import threading def setInterval(interval): """ Decorator generator. Calls the decorated methods every `interval` seconds. Args: interval (int): Period Returns: (function) Decorated Function. """ def decorator(function): """ Helper method. """ def wrapper(*args, **kwargs): """ Manages the thread. """ stopped = threading.Event() def loop(): # executed in another thread while not stopped.wait(interval): # until stopped function(*args, **kwargs) t = threading.Thread(target=loop) t.daemon = True # stop if the program exits t.start() return stopped return wrapper return decorator
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def save_group(batch_dir, group): """ make group directory and save group info. """ group_name = group["group_name"] group_dir = batch_dir / group_name group_dir.mkdir() # save group information info_file = group_dir / "group_info.txt" with open(info_file, "w") as info_f: info_f.write(f"group_name: {group_name}\n") info_f.write(f"group_info: {group['group_info']}\n") return group_dir
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def log2(instructions): """Integer only algorithm to calculate the number of bits needed to store a number""" bits = 1 power = 2 while power < instructions: bits += 1 power *= 2 return bits
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def codepipeline_approval(message): """Uses Slack's Block Kit.""" console_link = message['consoleLink'] approval = message['approval'] pipeline_name = approval['pipelineName'] action_name = approval['actionName'] approval_review_link = approval['approvalReviewLink'] expires = approval['expires'] return ( { 'type': 'section', 'text': { 'type': 'plain_text', 'text': f'Pipeline "{pipeline_name}" is waiting for approval.', }, 'accessory': { 'type': 'button', 'text': { 'type': 'plain_text', 'text': 'Open in :aws: Console', 'emoji': True, }, 'url': console_link, }, }, { 'type': 'section', 'fields': [ { 'type': 'mrkdwn', 'text': f'*Action name*:\n{action_name}', }, { 'type': 'mrkdwn', 'text': f'*Expires:* {expires}', }, ], }, { 'type': 'actions', 'elements': [ { 'type': 'button', 'text': { 'type': 'plain_text', 'emoji': False, 'text': 'Review approve', }, 'style': 'primary', 'url': approval_review_link, }, ], }, )
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def fetch_intron(start, cigar): """ To retrieve the 'N' cigar :param start: :param cigar: :return: """ intronbound = [] for c, l in cigar: if c == 3: intronbound.append((start + 1, start + l)) start += l elif c == 1: continue elif c == 2: start += l elif c == 4: # start += l # u'3.15 ่ฟ™้‡Œๅฅฝๅƒๆœ‰้—ฎ้ข˜๏ผŒๅพ—ๆ”น??' continue elif c == 0: start += l else: continue return intronbound
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def _formatted_hour_min(seconds): """Turns |seconds| seconds into %H:%m format. We don't use to_datetime() or to_timedelta(), because we want to show hours larger than 23, e.g.: 24h:00m. """ time_string = '' hours = int(seconds / 60 / 60) minutes = int(seconds / 60) % 60 if hours: time_string += '%dh' % hours if minutes: if hours: time_string += ':' time_string += '%dm' % minutes return time_string
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from typing import Counter def number_of_pairs(gloves): """ Given an array describing the color of each glove, return the number of pairs you can constitute, assuming that only gloves of the same color can form pairs. Examples: input = ["red", "green", "red", "blue", "blue"] result = 2 (1 red pair + 1 blue pair) """ count = 0 gloves = Counter(gloves) for x in gloves.values(): count += x // 2 return count
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def Rmax_Q11(Vmax): """ Estimation of the radius of maximum wind according to the formula proposed by Quiring et al. (2011); Vmax and Rmax are in nautical miles. Expression herein converted in km""" Vm= Vmax * 0.5399568 Rmax = ((49.67 - 0.24 * Vm)) * 1.852 return Rmax
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def get_option_value(elem): """ Get the value attribute, or if it doesn't exist the text content. <option value="foo">bar</option> => "foo" <option>bar</option> => "bar" :param elem: a soup element """ value = elem.get("value") if value is None: value = elem.text.strip() if value is None or value == "": msg = u"Error parsing value from {}.".format(elem) raise ValueError(msg) return value
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def scatter_scale(target, max_size=50.0): """Return a scaled list of sizes.""" result = target.apply(lambda x:max_size*(1-x)) return result
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def clearDiskCache(): """ clearDiskCache() -> None Clear the disk cache of all files. """ return None
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def EI(sections, normal=None): # {{{ """Calculate the bending stiffnes of a cross-section. The cross-section is composed out of rectangular nonoverlapping sections that can have different Young's moduli. Each section is represented by a 4-tuple (width, height, offset, E). The offset is the distance from the top of the section to the top of the highest section. This should always be a positive value. E is the Young's modulus of the material of this section. Arguments: sections: Iterable of section properties. normal: The Young's modulus to which the total cross-section will be normalized. (Not used anymore, retained for compatibility.) Returns: Tuple of EI, top and bottom. Top and bottom are with respect to the neutral line. Examples: >>> E = 210000 >>> B = 100 >>> H = 20 >>> sections = ((B, H, 0, E),) >>> EI(sections) (14000000000.0, 10.0, -10.0) >>> B = 100 >>> h = 18 >>> t = 1 >>> H = h + 2 * t >>> E = 210000 >>> sections = ((B, t, 0, E), (B, t, h+t, E)) >>> EI(sections) (3794000000.0, 10.0, -10.0) >>> E1, E2 = 200000, 71000 >>> t1, t2 = 1.5, 2.5 >>> H = 31 >>> B = 100 >>> sections = ((B, t1, 0, E1), (B, t2, H-t2, E2)) >>> EI(sections) (9393560891.143106, 11.530104712041885, -19.469895287958117) """ normal = sections[0][-1] normalized = tuple((w * E / normal, h, offs) for w, h, offs, E in sections) A = sum(w * h for w, h, _ in normalized) S = sum(w * h * (offs + h / 2) for w, h, offs in normalized) yn = S / A # Find any geometry that straddles yn. to_split = tuple(g for g in sections if g[2] < yn and g[1] + g[2] > yn) geom = tuple(g for g in sections if g not in to_split) # split that geometry. # The new tuple has the format (width, height, top, bottom) new_geom = [] for w, h, offs, E in to_split: h1 = yn - offs h2 = h - h1 new_geom.append((w, h1, h1, 0, E)) new_geom.append((w, h2, 0, -h2, E)) # Convert the remaining geometry to reference yn. for w, h, offs, E in geom: new_geom.append((w, h, yn - offs, yn - offs - h, E)) EI = sum(E * w * (top ** 3 - bot ** 3) / 3 for w, h, top, bot, E in new_geom) top = max(g[-3] for g in new_geom) bot = min(g[-2] for g in new_geom) return EI, top, bot
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def filter_labels_by_class(obj_labels, classes): """Filters object labels by classes. Args: obj_labels: List of object labels classes: List of classes to keep, e.g. ['Car', 'Pedestrian', 'Cyclist'] Returns: obj_labels: List of filtered labels class_mask: Mask of labels to keep """ class_mask = [(obj.type in classes) for obj in obj_labels] return obj_labels[class_mask], class_mask
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def _update_entries(data_arr, first_one, second_one): """ Replaces 2 entries in the array, and returns the modified array. This only operates on arrays returned by the likes of _augment_array(). """ temp1 = data_arr[first_one] temp2 = data_arr[second_one] intended_index = temp2[0] - 1 difference = abs(intended_index - first_one) if difference == 0: data_arr[first_one] = temp2[0] else: data_arr[first_one] = (temp2[0],) + (difference,) intended_index = temp1[0] - 1 difference = abs(intended_index - second_one) if difference == 0: data_arr[second_one] = temp1[0] else: data_arr[second_one] = (temp1[0],) + (difference,) return data_arr
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def probably_reconstruction(file) -> bool: """Decide if a path may be a reconstruction file.""" return file.endswith("json") and "reconstruction" in file
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import re def error_086_ext_link_two_brackets(text): """Fix some cases and return (new_text, replacements_count) tuple.""" # case: [[http://youtube.com/|YouTube]] def _process_link(match_obj): """Deals with founded wiki-link.""" link = match_obj.group(1) name = match_obj.group(2) if "wikipedia.org" in link.lower(): link = re.sub(" ", "_", link) else: link = re.sub(" ", "%20", link) return "[" + link + " " + name + "]" exp1 = r"\[\[(https?://[^|\[\]\n]+)\|([^|\[\]\n]+)\]\]" (text, count1) = re.subn(exp1, _process_link, text, flags=re.I) # case: [[http://youtube.com YouTube]] exp2 = r"\[(\[https?://[^\[\]\n]+\])\]" (text, count2) = re.subn(exp2, "\\1", text, flags=re.I) return (text, count1 + count2)
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import re def get_ip(ip_str): """ input format: SH-IDC1-10-5-30-[137,152] or SH-IDC1-10-5-30-[137-142,152] or SH-IDC1-10-5-30-[152, 137-142] output format 10.5.30.137 """ # return ".".join(ip_str.replace("[", "").split(',')[0].split("-")[2:]) return ".".join(re.findall(r'\d+', ip_str)[1:5])
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from typing import Counter def check_author_count(counter: Counter) -> bool: """ Takes a set of documents and counts the number of authors. If less than 2, returns False otherwise True. :param counter: a Counter object for author counts. :return: a boolean indicating whether or not the document set can be analyzed (True for yes, no for False). """ if len(counter) == 1: return False return True
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def default_destinations(iata_code_original_destination): """Get three default destinations different from original destination of query.""" # Paris, London, Rome, New York defaults = ['CDG', 'LHR', 'FCO', 'JFK'] if iata_code_original_destination in defaults: defaults.remove(iata_code_original_destination) else: defaults.remove('JFK') return defaults
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def _ToCamelCase(name): """Converts hyphen-case name to CamelCase.""" parts = name.split('-') return ''.join(x.title() for x in parts)
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def tree_intersection(tree_one,tree_two): """[given two binarytrees as parameters returns the itersection of the trees values] Args: tree_one ([binarytree]): [description] tree_two ([binarytree]): [description] Returns: [list]: [intersection of trees] """ intersection = [] for item in tree_two.breadth_first(): if item in tree_one.breadth_first(): intersection.append(item) return intersection
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def name_records_summary(self): """ Count records for every name record. Args: mod_name (str): Return: None """ counts = {} for mod, records in self.records.items(): for rec in records: if rec['id'] not in counts: counts[rec['id']] = {'name': self.name_records[rec['id']], 'counts': {}} if mod not in counts[rec['id']]['counts']: counts[rec['id']]['counts'][mod] = 1 else: counts[rec['id']]['counts'][mod] += 1 return counts
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import hashlib def same_files(fname, fname2): """ Two files are the same if they have the same hash. :param fname String: The first filename. :param fname2 String: The second filename. """ try: hash1 = hashlib.sha512() with open(fname, 'rb') as fin: hash1.update(fin.read()) hash2 = hashlib.sha512() with open(fname2, 'rb') as fin: hash2.update(fin.read()) return hash1.hexdigest() == hash2.hexdigest() except IOError: return False
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import os import glob import itertools import re def get_machine_id_list_for_test(target_dir, dir_name="test", ext="wav"): """ target_dir : str base directory path of "dev_data" or "eval_data" test_dir_name : str (default="test") directory containing test data ext : str (default="wav) file extension of audio files return : machine_id_list : list [ str ] list of machine IDs extracted from the names of test files """ # create test files dir_path = os.path.abspath("{dir}/{dir_name}/*.{ext}".format(dir=target_dir, dir_name=dir_name, ext=ext)) file_paths = sorted(glob.glob(dir_path)) # extract id machine_id_list = sorted(list(set(itertools.chain.from_iterable( [re.findall('id_[0-9][0-9]', ext_id) for ext_id in file_paths])))) return machine_id_list
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def line_animation(line, idx, limit=10, step=1): """ Animate long string """ line = line+' | ' line_start = 0 line_end = len(line) short_line_start = line_start+idx short_line_end = limit+idx short_line = line[short_line_start:short_line_end] add_line_end = abs(len(short_line)-limit) if short_line_end > line_end: short_line = short_line + line[0:add_line_end] idx += step if idx > (line_end + limit) - 1: idx = 0 return idx, short_line
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def format_date(value): """Return value as string.""" return_value = None if value: return_value = str(value) return return_value
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def bbox2points(bbox): """ From bounding box yolo format to corner points cv2 rectangle """ x, y, w, h = bbox xmin = int(round(x - (w / 2))) xmax = int(round(x + (w / 2))) ymin = int(round(y - (h / 2))) ymax = int(round(y + (h / 2))) return xmin, ymin, xmax, ymax
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def level_to_rgb(level, background): """ Converts internal consept of level to a gray color for text in RGB :param level: range from 1 to 15 :return: tuple referring to (R, G, B) """ #Level goes from 1 to 15, starting from level1:(30,30,30), and getting darker with 1 point if level not in range(1, 16): return None gray_code = background[0]+15-level+1 print(f"{level}::{gray_code}") return (gray_code, gray_code, gray_code)
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import os def extension(path: str) -> str: """ finds extension """ base_name = os.path.basename(path) name = os.path.splitext(base_name) extension = name[1] return extension
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def get_message_relay(celery_app): """ Function that return a celery task list. """ return celery_app.tasks['eduid_msg.tasks.send_message']
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import json def get_boxnote_text(filepath): """Convert a boxnote to plain text. Parameters: filepath (str): the path to the boxfile Returns: the text of the boxfile as a string """ f = open(filepath, encoding="utf8") text = json.loads(f.read())["atext"]["text"] f.close() return text
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def func_args_realizer(args): """ Using an ast.FunctionDef node, create a items list node that will give us the passed in args by name. def whee(bob, frank=1): pass whee(1, 3) => [('bob', 1), ('frank', 3)] whee(1) => [('bob', 1), ('frank', 1)] """ items = map("('{0}', {0})".format, args) items_list = "[ {0} ]".format(', '.join(items)) return items_list
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def categorical_log_prob(self, logits): """ torch RelaxedOneHotCategorical log_prob is weird (uses that of TransformedDistribution) need to use log_prob from base_dist instead """ return self.base_dist.log_prob(logits)
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from typing import Dict def filter_val_not_none(d: Dict) -> Dict: """ Return a new dictionary composed of all key-value pairs (k, v) in d where v is not None. :param d: original dictionary :return: d, without key-value pairs where value is None >>> filter_val_not_none({"a": 5, "b": 10, "c": None}) == {"a": 5, "b": 10} True """ return {k: v for k, v in d.items() if v is not None}
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def get_card_ids(db) -> list: """ Gets a list of all card IDs in the datase. :return: List of card IDs. """ return db['cards'].distinct('_id')
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import time def datetime_to_integer(datetime): """Convert datetime object to integer value. 'datetime' is the datetime object""" return time.mktime(datetime.timetuple())
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import operator def sort_load_list_by_time(load_list): """Given the standard load list return a list orderd by time The list contains a tuple of the load_id and the actual load_set """ return sorted(load_list, key=operator.itemgetter(1))
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def crop_to_ratio(im, desired_ratio=4 / 3): """ Crop (either) the rows or columns of an image to match (as best as possible) the desired ratio. Arguments: im (np.array): Image to be processed. desired_ratio (float): The desired ratio of the output image expressed as width/height so 3:2 (= 3/2) or 16:9 ( = 16/9). Returns: An image (np.array) with the desired ratio. """ height = im.shape[0] width = im.shape[1] if width / height < desired_ratio: # Crop rows desired_height = int(round(width / desired_ratio)) to_crop = height - desired_height top_crop = to_crop // 2 bottom_crop = to_crop - top_crop cropped_image = im[top_crop:height - bottom_crop, :] else: # Crop columns desired_width = int(round(height * desired_ratio)) to_crop = width - desired_width left_crop = to_crop // 2 right_crop = to_crop - left_crop cropped_image = im[:, left_crop:width - right_crop] return cropped_image
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def grompp_npt(job): """Run GROMACS grompp for the npt step.""" npt_mdp_path = "npt.mdp" msg = f"gmx grompp -f {npt_mdp_path} -o npt.tpr -c em.gro -p init.top --maxwarn 1" return msg
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def uri_leaf(uri): """ Get the "leaf" - fragment id or last segment - of a URI. Useful e.g. for getting a term from a "namespace like" URI. >>> uri_leaf("http://purl.org/dc/terms/title") == 'title' True >>> uri_leaf("http://www.w3.org/2004/02/skos/core#Concept") == 'Concept' True >>> uri_leaf("http://www.w3.org/2004/02/skos/core#") # returns None """ for char in ('#', '/', ':'): if uri.endswith(char): break if char in uri: sep = char leaf = uri.rsplit(char)[-1] else: sep = '' leaf = uri if sep and leaf: return leaf
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import yaml def load_yaml_config(filename): """Load a YAML configuration file.""" with open(filename, "rt", encoding='utf-8') as file: config_dict = yaml.safe_load(file) return config_dict
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import uuid def build_request_body(method, params): """Build a JSON-RPC request body based on the parameters given.""" data = { "jsonrpc": "2.0", "method": method, "params": params, "id": str(uuid.uuid4()) } return data
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def part1(input_data): """ >>> part1(["939","7,13,x,x,59,x,31,19"]) 295 """ timestamp = int(input_data[0]) bus_ids = input_data[1].split(',') # Ignore bus_ids with 'x' bus_ids = map(int, filter(lambda bus_id: bus_id != 'x', bus_ids)) # (id, time_to_wait) # last_busstop = timestamp % id # time_to_wait = id - last_busstop bus_ids = [(bus_id, bus_id - (timestamp % bus_id)) for bus_id in bus_ids] bus_ids.sort(key=lambda x: x[1]) next_bus_id, next_bus_time_to_wait = bus_ids[0] return next_bus_id * next_bus_time_to_wait
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import uuid def read_bootid(): """ Mocks read_bootid as this is a Linux-specific operation. """ return uuid.uuid4().hex
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def list_group(flatten_list, offset_list): """list_flatten็š„้€†ๆ“ไฝœ""" pos_lists = [] for offset in offset_list: pos_lists.append(flatten_list[offset[0] : offset[1]]) return pos_lists
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import numpy def normalized(vector): """ Get unit vector for a given one. :param vector: Numpy vector as coordinates in Cartesian space, or an array of such. :returns: Numpy array of the same shape and structure where all vectors are normalized. That is, each coordinate component is divided by its vector's length. """ length = numpy.sum(vector * vector, axis=-1) length = numpy.sqrt(length.reshape(length.shape + (1, ))) return vector / length
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def sample_conditional_random(generator, m, n, **kwargs): """ Sample `m * n` points from condition space completely randomly. """ return generator.condition_distribution.sample(m * n).eval()
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import torch def fetch_optimizer(lr, wdecay, epsilon, num_steps, params): """ Create the optimizer and learning rate scheduler """ optimizer = torch.optim.AdamW(params, lr=lr, weight_decay=wdecay, eps=epsilon) scheduler = torch.optim.lr_scheduler.OneCycleLR(optimizer, lr, num_steps+100, pct_start=0.05, cycle_momentum=False, anneal_strategy='linear') return optimizer, scheduler
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def load_bmrbm(table_fname, resname_col, atom_col, shift_col): """Load a BMRBM table and return a dictionary.""" bmrb_dic = {} with open(table_fname, "r") as bmrb_file: for line in bmrb_file.readlines(): # Split so that the whitespaces don't matter c_shift = line.split() if not c_shift: # line is empty continue # bmrb_columns starts with index 1 so here we need to -1 all positions bmrb_resnum = int(c_shift[resname_col - 1]) bmrb_atom = c_shift[atom_col - 1] bmrb_shift = float(c_shift[shift_col - 1]) if bmrb_resnum not in bmrb_dic: bmrb_dic[bmrb_resnum] = {} bmrb_dic[bmrb_resnum][bmrb_atom] = bmrb_shift return bmrb_dic
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def yp_raw_competitors(data_path): """ The file contains the list of business objects. File Type: JSON """ return f'{data_path}/yp_competitors.json'
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import re def to_num(string): """Convert string to number (or None) if possible""" if type(string) != str: return string if string == "None": return None if re.match("\d+\.\d*$", string): return float(string) elif re.match("\d+$", string): return int(string) else: return string
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def button_action (date, action, value) : """ Create a button for time-tracking actions """ ''"approve", ''"deny", ''"edit again" if not date : return '' return \ '''<input type="button" value="%s" onClick=" if(submit_once()) { document.forms.edit_daily_record ['@action'].value = 'daily_record_%s'; document.forms.edit_daily_record ['date'].value = '%s' document.edit_daily_record.submit (); } "> ''' % (value, action, date)
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def get_tidy_invocation(f, clang_tidy_binary, checks, build_path, quiet, config): """Gets a command line for clang-tidy.""" start = [clang_tidy_binary] # Show warnings in all in-project headers by default. start.append('-header-filter=src/') if checks: start.append('-checks=' + checks) start.append('-p=' + build_path) if quiet: start.append('-quiet') if config: start.append('-config=' + config) start.append(f) return start
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def get_control_colors(): """ Returns control colors available in DCC :return: list(tuple(float, float, float)) """ return list()
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import torch def _pre_conv(input, weight, bias=None, stride=1, padding=0, dilation=1, groups=1): """ This is a block of local computation done at the beginning of the convolution. It basically does the matrix unrolling to be able to do the convolution as a simple matrix multiplication. Because all the computation are local, we add the @allow_command and run it directly on each share of the additive sharing tensor, when running mpc computations """ assert len(input.shape) == 4 assert len(weight.shape) == 4 # Change to tuple if not one stride = torch.nn.modules.utils._pair(stride) padding = torch.nn.modules.utils._pair(padding) dilation = torch.nn.modules.utils._pair(dilation) # Extract a few useful values batch_size, nb_channels_in, nb_rows_in, nb_cols_in = input.shape nb_channels_out, nb_channels_kernel, nb_rows_kernel, nb_cols_kernel = weight.shape if bias is not None: assert len(bias) == nb_channels_out # Check if inputs are coherent assert nb_channels_in == nb_channels_kernel * groups assert nb_channels_in % groups == 0 assert nb_channels_out % groups == 0 # Compute output shape nb_rows_out = int( ((nb_rows_in + 2 * padding[0] - dilation[0] * (nb_rows_kernel - 1) - 1) / stride[0]) + 1 ) nb_cols_out = int( ((nb_cols_in + 2 * padding[1] - dilation[1] * (nb_cols_kernel - 1) - 1) / stride[1]) + 1 ) # Apply padding to the input if padding != (0, 0): padding_mode = "constant" input = torch.nn.functional.pad( input, (padding[1], padding[1], padding[0], padding[0]), padding_mode ) # Update shape after padding nb_rows_in += 2 * padding[0] nb_cols_in += 2 * padding[1] # We want to get relative positions of values in the input tensor that are used # by one filter convolution. # It basically is the position of the values used for the top left convolution. pattern_ind = [] for ch in range(nb_channels_in): for r in range(nb_rows_kernel): for c in range(nb_cols_kernel): pixel = r * nb_cols_in * dilation[0] + c * dilation[1] pattern_ind.append(pixel + ch * nb_rows_in * nb_cols_in) # The image tensor is reshaped for the matrix multiplication: # on each row of the new tensor will be the input values used for each filter convolution # We will get a matrix [[in values to compute out value 0], # [in values to compute out value 1], # ... # [in values to compute out value nb_rows_out*nb_cols_out]] im_flat = input.reshape(batch_size, -1) im_reshaped = [] for cur_row_out in range(nb_rows_out): for cur_col_out in range(nb_cols_out): # For each new output value, we just need to shift the receptive field offset = cur_row_out * stride[0] * nb_cols_in + cur_col_out * stride[1] tmp = [ind + offset for ind in pattern_ind] im_reshaped.append(im_flat[:, tmp]) im_reshaped = torch.stack(im_reshaped).permute(1, 0, 2) # The convolution kernels are also reshaped for the matrix multiplication # We will get a matrix [[weights for out channel 0], # [weights for out channel 1], # ... # [weights for out channel nb_channels_out]].TRANSPOSE() weight_reshaped = weight.reshape(nb_channels_out // groups, -1).t() return ( im_reshaped, weight_reshaped, torch.tensor(batch_size), torch.tensor(nb_channels_out), torch.tensor(nb_rows_out), torch.tensor(nb_cols_out), )
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def dataset_pre_0_3(client): """Return paths of dataset metadata for pre 0.3.4.""" project_is_pre_0_3 = int(client.project.version) < 2 if project_is_pre_0_3: return (client.path / 'data').rglob(client.METADATA) return []
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import copy def sanitize_slicing(slice_across, slice_relative_position): """ Return standardized format for `slice_across` and `slice_relative_position`: - either `slice_across` and `slice_relative_position` are both `None` (no slicing) - or `slice_across` and `slice_relative_position` are both lists, with the same number of elements Parameters ---------- slice_relative_position : float, or list of float, or None slice_across : str, or list of str, or None Direction(s) across which the data should be sliced """ # Skip None and empty lists if slice_across is None or slice_across == []: return None, None # Convert to lists if not isinstance(slice_across, list): slice_across = [slice_across] if slice_relative_position is None: slice_relative_position = [0]*len(slice_across) if not isinstance(slice_relative_position, list): slice_relative_position = [slice_relative_position] # Check that the length are matching if len(slice_across) != len(slice_relative_position): raise ValueError( 'The argument `slice_relative_position` is erroneous: \nIt should have' 'the same number of elements as `slice_across`.') # Return a copy. This is because the rest of the `openPMD-viewer` code # sometimes modifies the objects returned by `sanitize_slicing`. # Using a copy avoids directly modifying objects that the user may pass # to this function (and live outside of openPMD-viewer, e.g. directly in # a user's notebook) return copy.copy(slice_across), copy.copy(slice_relative_position)
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def is_dependency_valid(dep: dict, dep_dict: dict) -> bool: """ :param dep: a dependency that may or may not be valid or up-to-date :param dep_dict: a dictionary mapping dependency identifiers to their up-to-date dependency counterparts :return: a boolean indicating whether the dependency is out-of-date or not """ if not dep or 'org' not in dep or 'name' not in dep or '{}-{}'.format(dep['org'], dep['name']) not in dep_dict: return False return True
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def equations(abs1, abs2, abs3, solvent): """Contains absorption constans (coef) and formulas.""" separator = "___________________________________________" coef = [[10.05, 0.97, 16.36, 2.43, 7.62, 15.39, 1.43, 35.87, 205], [9.93, 0.75, 16.23, 2.42, 7.51,15.48, 1.3, 33.12, 213], [10.36, 1.28, 17.49, 2.72, 7.64, 16.21, 1.38, 40.05, 211], [13.36, 5.19, 27.43, 8.12, 5.24, 22.24, 2.13, 97.64, 209], [11.24, 2.04, 20.13, 4.19, 7.05, 18.09, 1.90, 63.14, 214], [12.25, 2.79, 21.50, 5.10, 7.15, 18.71, 1.82, 85.02, 198], [16.72, 9.16, 34.09, 15.28, 1.44, 24.93, 1.63, 104.96, 221], [16.82, 9.28, 36.92, 16.54, 0.28, 27.64, 1.91, 95.15, 225]] chl_a = coef[solvent][0] * abs3 - coef[solvent][1] * abs2 chl_b = coef[solvent][2] * abs2 - coef[solvent][3] * abs3 chl_ab = coef[solvent][4] * abs3 + coef[solvent][5] * abs2 car = (1000 * abs1 - coef[solvent][6] * chl_a - coef[solvent][7] * chl_b)/coef[solvent][8] results = [chl_a, chl_b, chl_ab, car] return results
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def get_traitset_map(pop): """ Utility method which returns a map of culture ID's (hashes) and the trait set corresponding to a random individual of that culture (actually, the first one we encounter). """ traitsets = {} graph = pop.agentgraph for nodename in graph.nodes(): traits = graph.node[nodename]['traits'] culture = pop.get_traits_packed(traits) if culture not in traitsets: traitsets[culture] = traits return traitsets
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def prefix(txt, pref): """ Place a prefix in front of the text. """ return str(pref) + str(txt)
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def _fix_basebox_url(url): """ Kinda fix a basebox URL """ if not url.startswith('http'): url = 'http://%s' % url if not url.endswith('/meta'): url += '/meta' return url
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def isinstance_all(iterable, class_or_tuple): """ Check if all items of an iterable are instance of a class ou tuple of classes >>> isinstance_all(['Hello', 'World'], str) True >>> isinstance_all([1, 'Hello'], (str, int)) True >>> isinstance_all([True, 'Hello', 5], int) False """ return all( isinstance(obj, class_or_tuple) for obj in iterable )
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import os def root_dir(): """ find the root directory for web static files Returns: root path for static files """ return os.path.join( os.path.join( os.path.dirname(os.path.dirname(__file__)), "web" ), "static" )
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import imp import sys def main_is_frozen(): """Return ``True`` if we're running from a frozen program.""" return ( # new py2exe hasattr(sys, "frozen") or # tools/freeze imp.is_frozen("__main__"))
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import sys def create_nonce(context, ag): """ Creates a nonce to this actor for passing to the second actor; the second actor will use the nonce to message back to the first actor. :param context: :return: """ try: rsp = ag.actors.addNone() except Exception as e: print("Got exception {} trying to create nonce.".format(e)) sys.exit() return rsp
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import random def make_data(n,m): """make_data: prepare matrix of m times n random processing times""" p = {} for i in range(1,m+1): for j in range(1,n+1): p[i,j] = random.randint(1,10) return p
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def to_gigabytes(number): """Convert a number from KiB to GiB This is used mainly for the gauge, everything else uses the dynamic `unit` function. """ return number / 1024 ** 2
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import torch def differential(f, A, E): """ Computes the differential of f at A when acting on E: (df)_A(E) """ n = A.size(0) M = torch.zeros(2*n, 2*n, dtype=A.dtype, device=A.device, requires_grad=False) M[:n, :n] = A M[n:, n:] = A M[:n, n:] = E return f(M)[:n, n:]
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def get_distance(vectors): """[Calculate the euclidian distance between two vectors, represented as columns in a DataFrame.] Args: vectors ([DataFrame]): [DataFrame containing the two columns representing the vectors.] Returns: [Float]: [Euclidian distance of the vectors.] """ # get distance between vectors by essentially creating a vector which points from one # to the other (difference of input vectors) and than calculating the length of the # new vector through (summ_components**2)**(1/2) diff_summ = 0 for i in range(len(vectors.index)): diff_summ = diff_summ + (vectors.iloc[i, 0] - vectors.iloc[i, 1]) ** 2 distance = (diff_summ) ** (1 / 2) return distance
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import tarfile import pathlib def _strip_paths(tarinfo: tarfile.TarInfo) -> tarfile.TarInfo: """Ensure source filesystem absolute paths are not reflected in tar file.""" original_path = pathlib.Path(tarinfo.name) tarinfo.name = f"{original_path.name}" return tarinfo
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def sequentially_executed(nb): """Return True if notebook appears freshly executed from top-to-bottom.""" exec_counts = [ cell["execution_count"] for cell in nb.get("cells", []) if ( cell["source"] and cell.get("execution_count", None) is not None ) ] sequential_counts = list(range(1, 1 + len(exec_counts))) # Returns True if there are no executed code cells, which is fine? return exec_counts == sequential_counts
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def my_func_3(x, y): """ ะ’ะพะทะฒั€ะฐั‰ะฐะตั‚ ะฒะพะทะฒะตะดะตะฝะธะต ั‡ะธัะปะฐ x ะฒ ัั‚ะตะฟะตะฝัŒ y. ะ˜ะผะตะฝะพะฒะฐะฝะฝั‹ะต ะฟะฐั€ะฐะผะตั‚ั€ั‹: x -- ั‡ะธัะปะพ y -- ัั‚ะตะฟะตะฝัŒ (number, number) -> number >>> my_func_3(2, 2) 4 """ if y < 0: r = 1.0 for _ in range(abs(y)): r *= x r = 1 / r return r elif y > 0: r = 1 for _ in range(abs(y)): r *= x return r return 1
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def flavors_ram(nova): """Get a dict of flavor IDs to the RAM limits. :param nova: A Nova client. :return: A dict of flavor IDs to the RAM limits. """ return dict((str(fl.id), fl.ram) for fl in nova.flavors.list())
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import re def re_cap(*regexes): """ Capture first of the supplied regex :param regexes: list or regex strings :return: captured string | None """ def go(string): for reg in regexes: matches = re.search(reg, string) if matches: return matches.group(1) return None return go
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def score2act(score): """ Convert the Z-score predicted by PADDLE to a fold-activation value. Only useful as a rough reference for activation in S. cerevisiae, as the fold-activation will vary between different experimental conditions. """ return 1.5031611623938073**score
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import os import shutil def make_saliency_dir(date_time: str) -> str: """Make directories for saving saliency map result.""" save_dir = f"./data/saliency_map/{date_time}" if os.path.exists(save_dir): shutil.rmtree(save_dir) os.makedirs(save_dir) os.makedirs(f"./data/saliency_map/{date_time}/input_image") os.makedirs(f"./data/saliency_map/{date_time}/state") os.makedirs(f"./data/saliency_map/{date_time}/saliency") os.makedirs(f"./data/saliency_map/{date_time}/overlay") saliency_map_dir = f"./data/saliency_map/{date_time}/" return saliency_map_dir
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import os import time def intro(): """intro screen, self explanatory""" os.system('clear') print("\n\n Welcome to the grand game of 'Mushroom Picking'!\n\n") time.sleep(1) print("""'Tales border on the thin line between reality and myth' - Mc' Dingus\n\n You wake up in your wooden shed, the first thing your senses pick up is a message:\n "Johny my boy, I'd like some mushrooms for my soup, could you get me some from The Dark Forest? Thanks. Oh actually bring me... 23 of the small ones and that funny one~"\n In that instant you know what date it is, it's your grandmas death aniversary~! You take your basket, put on your special camo outfit and go mushroom picking.\n\nHint: Don't starve. """) time.sleep(2) print("Mdlkxzmcp, Rafaล‚ Sebestjanski and Pawel Potaczek present:::\n\n") time.sleep(1) print (""" โ–„โ–€โ–€โ–ˆโ–„โ–„ โ–„โ–€โ–€โ–ˆโ–„ โ–„โ–€โ–€โ–„โ–€โ–€โ–€โ–„ โ–„โ–€โ–€โ–„ โ–ˆ โ–„โ–€โ–€โ–€โ–ˆโ–„ โ–„โ–€โ–€โ–€โ–€โ–„ โ–„โ–€โ–€โ–„โ–€โ–€โ–€โ–„ โ–„โ–€โ–€โ–ˆโ–„โ–„โ–„โ–„ โ–„โ–€โ–€โ–€โ–€โ–„ โ–„โ–€โ–€โ–€โ–ˆโ–€โ–€โ–„ โ–ˆ โ–„โ–€ โ–ˆ โ– โ–„โ–€ โ–€โ–„ โ–ˆ โ–ˆ โ–ˆ โ–ˆ โ–ˆ โ–„โ–€ โ–ˆ โ–„โ–€ โ–€โ–„ โ–ˆ โ–ˆ โ–ˆ โ–ˆ โ–ˆ โ– โ–„โ–€ โ– โ–ˆ โ–ˆ โ– โ–ˆ โ–ˆ โ– โ– โ–ˆ โ–ˆ โ–ˆโ–„โ–„โ–„โ–ˆ โ– โ–ˆโ–€โ–€โ–ˆโ–€ โ– โ–ˆโ–€โ–„ โ– โ–ˆโ–„โ–„โ–„โ–„ โ–ˆ โ–ˆ โ– โ–ˆโ–€โ–€โ–ˆโ–€ โ–ˆโ–„โ–„โ–„โ–„โ–„ โ–€โ–„ โ– โ–ˆ โ–ˆ โ–ˆ โ–„โ–€ โ–ˆ โ–„โ–€ โ–ˆ โ–ˆ โ–ˆ โ–ˆ โ– โ–€โ–„ โ–„โ–€ โ–„โ–€ โ–ˆ โ–ˆ โ–Œ โ–€โ–„ โ–ˆ โ–ˆ โ–„โ–€โ–„โ–„โ–„โ–„โ–€ โ–ˆ โ–„โ–€ โ–ˆ โ–ˆ โ–„โ–€ โ–ˆ โ–ˆ โ–€โ–€โ–€โ–€ โ–ˆ โ–ˆ โ–„โ–€โ–„โ–„โ–„โ–„ โ–ˆโ–€โ–€โ–€ โ–„โ–€ โ–ˆ โ– โ– โ– โ– โ– โ–ˆ โ– โ–ˆ โ– โ– โ–ˆ โ– โ– โ–ˆ โ– โ– โ– โ– โ– """) time.sleep(3) print("\nCONTROL:\nA - move left\nS - move down\nD - move right\nW - move up\n") print("OBJECTS:\n@ - player\n# - tree\nA - mountain\n~ - water\n= - bridge\nqp - mushroosm\n% - shoes\n& - meat") print("u - basket\nS - extra life") while True: ready = input("\nAre you ready for the greatest adventure of your life? ").lower() if ready in ("yes", "y", "ye"): return False elif ready in ("quit", "q"): quit() else: time.sleep(1) continue
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def make_grpc_unary_method(channel, service_name, method_descriptor, symbol_database_instance): # type (Channel, str, MethodDescriptor, Any) -> Callable """Make grp callable on the channel. Args: channel: grpc channel service_name: name of service method_descriptor: method descriptor symbol_database_instance: symbol db instance """ input_prototype = symbol_database_instance.GetPrototype(method_descriptor.input_type) output_prototype = symbol_database_instance.GetPrototype(method_descriptor.output_type) method = channel.unary_unary( "/{}/{}".format(service_name, method_descriptor.name), request_serializer=input_prototype.SerializeToString, response_deserializer=output_prototype.FromString, ) return method
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def set_crs(gdf, crs): """ Set CRS in GeoDataFrame when current projection is not defined. Parameters ---------- gdf : geopandas.GeoDataFrame the geodataframe to set the projection Returns ------- gdf : geopandas.GeoDataFrame the geodataframe with the projection defined """ gdf = gdf.set_crs(crs) return gdf
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def dataset_type(dataset): """ Parameters ---------- dataset : dataset script object Returns ------- str : The type of dataset. Example ------- >>> for dataset in reload_scripts(): ... if dataset.name=='aquatic-animal-excretion': ... print(dataset_type(dataset)) ... tabular """ for _, table_obj in dataset.tables.items(): if hasattr(table_obj, 'dataset_type') and table_obj.dataset_type in \ ["RasterDataset", "VectorDataset"]: return "spatial" return "tabular"
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def GetDistinguishableNames(keys, delimiter, prefixes_to_remove): """Reduce keys to a concise and distinguishable form. Example: GetDistinguishableNames(['Day.NewYork.BigApple', 'Night.NewYork.BigMelon'], '.', ['Big']) results in {'Day.NewYork.BigApple': 'Day.Apple', 'Night.NewYork.BigMelon': 'Night.Melon'}. If a key has all parts commonly shared with others, then include the last shared part in the names. E.g., GetDistinguishableNames(['Day.NewYork', 'Day.NewYork.BigMelon'], '.', ['Big']) results in {'Day.NewYork.BigApple': 'NewYork', 'Night.NewYork.BigMelon': 'NewYork.Melon'}. Args: keys: The list of strings, each is delimited by parts. delimiter: The delimiter to separate parts of each string. prefixes_to_remove: The list of prefix strings to be removed from the parts. Returns: short_names: A dictionary of shortened keys. """ def RemovePrefix(part, prefixes_to_remove): for prefix in prefixes_to_remove: if part.startswith(prefix): return part[len(prefix):] return part key_part_lists = [key.split(delimiter) for key in keys] shortest_length = min(len(part_list) for part_list in key_part_lists) # common_part[i] = True if all parts at position i are the same across keys. common_part = [True] * shortest_length for part_list in key_part_lists[1:]: for i in range(shortest_length): if part_list[i] != key_part_lists[0][i]: common_part[i] = False # The prefix list to add if one of the key happens to be the concatenation of # all common parts. prefix_list = ([key_part_lists[0][shortest_length - 1]] if all(common_part) else []) short_names = {} for key, part_list in zip(keys, key_part_lists): short_names[key] = delimiter.join(prefix_list + [ RemovePrefix(part, prefixes_to_remove) for n, part in enumerate(part_list) if n >= shortest_length or not common_part[n]]) return short_names
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import binascii import re def humanhexlify(data, n=-1): """Hexlify given data with 1 space char btw hex values for easier reading for humans :param data: binary data to hexlify :param n: If n is a positive integer then shorten the output of this function to n hexlified bytes. Input like 'ab\x04ce' becomes '61 62 04 63 65' With n=3 input like data='ab\x04ce', n=3 becomes '61 62 04 ...' """ tail = b' ...' if 0 < n < len(data) else b'' if tail: data = data[:n] hx = binascii.hexlify(data) return b' '.join(re.findall(b'..', hx)) + tail
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import re def yes_workload_no_snippet_target_line(patterns, painted_lines, split_text): """Find line to use for scan process in yes workload, no code snippet use case""" faultable_line_list = [] faultable_line_number_list = [] for line_number in painted_lines: detected_parts_list_line = split_text[line_number] find_function = re.findall("def:*", detected_parts_list_line) find_class = re.findall("class:*", detected_parts_list_line) find_import = re.findall("import", detected_parts_list_line) find_comment = re.findall("#", detected_parts_list_line) if ( not find_function and not find_class and not find_import and not find_comment ): for pattern in patterns: result = re.findall(pattern, detected_parts_list_line, re.MULTILINE) if result: faultable_line_list.append(detected_parts_list_line) faultable_line_number_list.append(line_number) return faultable_line_list, faultable_line_number_list
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def make_arc_consistent(Xj, Xk, csp): """Make arc between parent (Xj) and child (Xk) consistent under the csp's constraints, by removing the possible values of Xj that cause inconsistencies.""" # csp.curr_domains[Xj] = [] for val1 in csp.domains[Xj]: keep = False # Keep or remove val1 for val2 in csp.domains[Xk]: if csp.constraints(Xj, val1, Xk, val2): # Found a consistent assignment for val1, keep it keep = True break if not keep: # Remove val1 csp.prune(Xj, val1, None) return csp.curr_domains[Xj]
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import sys def task_batch_local(): """Run batch mode locally""" return { 'basename': 'batchLocal', 'actions': ["%s -m surround_tensorboard_example --mode batch" % sys.executable] }
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import os def make_bin_path(base_path, middle=None): """Creates a path to the data binaries.""" if base_path[-1] == "/": base_path = base_path[:-1] if middle is None: base_path = os.path.join(f'{base_path}-bin') else: base_path = os.path.join(f'{base_path}-bin', middle) return base_path
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