content stringlengths 42 6.51k |
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def make_url(path, api=False):
"""Make a bigg api request url."""
if api:
return 'http://bigg.ucsd.edu/api/v2/%s' % path.lstrip('/')
else:
return 'http://bigg.ucsd.edu/%s' % path.lstrip('/') |
def make_fai_cmd(in_fa):
"""return cmd string to make fai"""
return 'samtools faidx %s' % in_fa |
def get_section_link(header):
"""
Add a section link
Args:
:header: (str) section header
Returns:
:rst: (str) RST documentation
"""
rst = ""
rst += f".. _sec_mframwork_{header.lower().replace(' ', '_')}:"
rst += "\n\n"
return rst |
def dSquaredLoss(a, y):
"""
:param a: vector of activations output from the network
:param y: the corresponding correct label
:return: the vector of partial derivatives of the squared loss with respect to the output activations
"""
# assuming that we measure the L(a, y) by sum(1/2*square(y_i - a... |
def extract_file_paths(argv):
"""Extract file paths from the command-line.
File path arguments follow a `--` end-of-options delimiter, if any.
"""
try: # extract file paths, separated by `--`
i = argv.index("--")
input_files = argv[i + 1:]
argv = argv[:i]
except ValueError:... |
def SIMD_vectorization_latency_pruning(config):
"""Perform latency-based pruning at the SIMD vectorization stage.
We have already reordered the SIMD candidate loops in descending order.
Therefore, if the last design evaluated is slower than the opt design found
so far, there is no chance for the rest o... |
def parse_input(text):
"""Parse a list of destinations and weights
Returns a list of tuples (source, dest, weight).
Edges in this graph are undirected.
The input contains multiple rows appearing like so:
A to B = W
Where A and B are strings and W is the weight to travel
between them i... |
def _nb_subst_metric(seq1, seq2, subst_dict, as_similarity=False):
"""Computes sequence similarity based on the substitution matrix.
Requires that sequences are pre-aligned and equal length.
Operates on strings and a dict substitution matrix"""
assert len(seq1) == len(seq2)
def _sim_func(s1, s2, su... |
def sfc_lw_cld(lwup_sfc, lwup_sfc_clr, lwdn_sfc, lwdn_sfc_clr):
"""Cloudy-sky surface net longwave radiative flux into atmosphere."""
return lwup_sfc - lwup_sfc_clr - lwdn_sfc + lwdn_sfc_clr |
def class_to_dict(inst, ignore_list=[], attr_prefix=''):
""" Writes state of class instance as a dict
Includes both attributes and properties (i.e. those methods labeled with @property)
Note: because this capture properties, it should be viewed as a snapshot of instance state
:param inst: insta... |
def sample_to_plane(sample_orientation: str):
"""Return a Cartesian circle plane type for a given sample orienation type"""
sample_to_plane = {'S1': 'YZ', 'S2': 'XZ', 'S3': 'XY',
'S1R': 'ZY', 'S2R': 'ZX', 'S3R': 'YX',
'S4': 'YX to YZ', 'S5': 'XY to XZ', 'S6': 'XZ ... |
def find_keys_with_duplicate_values(ini_dict, value_to_key_function):
"""Finding duplicate values from dictionary using flip.
Parameters
----------
ini_dict: dict
A dict.
value_to_key_function : function
A function that transforms the value into a hashable type.
For example ... |
def calculate_federal_income_tax(taxable_income):
"""Returns the federal income tax"""
fed_tax = 0
if taxable_income <= 9700:
fed_tax = taxable_income*0.1
elif taxable_income > 9700 and taxable_income <= 39475:
fed_tax = 9700*0.1 + (taxable_income-9700)*.12
elif taxable_income > 39475 and taxable_income... |
def convertTime(time):
"""
Converts any entered time to seconds
"""
pos = ["s","m","h","d","mth","y"]
time_dict = {"s":1,"m":60,"h":3600,"d":3600*24,"mth":3600*24*30,"y":3600*24*30*365}
unit = time[-1]
if unit not in pos:
return -1
try:
val = int(time[:-1])
ex... |
def closest(arr, value):
"""
:return: The index of the member of `arr` which is closest to `value`
"""
if value == None:
return -1
for i,ele in enumerate(arr):
value = float(str(value).replace(',', '.'))
if ele > value:
return i - 1
return len(arr)-1 |
def extract_properties(data:dict) -> tuple:
"""
Extract properties from dictionary to generate a list of contours, a list
of continents and an int for priority score.
Args:
data (dict): Dictionary with svg extracted data
Returns:
tuple: Tuple of (contour:list, continents:list, prio... |
def hosts_to_endpoints(hosts, port=2181):
"""
return a list of (host, port) tuples from a given host[:port],... str
"""
endpoints = []
for host in hosts.split(","):
endpoints.append(tuple(host.rsplit(":", 1)) if ":" in host else (host, port))
return endpoints |
def always_str_list(list_or_str):
"""Makes sure list_or_str is always a tuple or list
Parameters
----------
list_or_str: str or str iterable (tuple, list, ...)
Parameter to set as iterable if single str.
Returns
-------
Iterable
Iterable equivalent to list_or_str."""
if... |
def get_message_payload(channel_id, msg):
"""Gets the message payload to be sent in the post message api"""
return {
"ts": "",
"channel": channel_id,
"username": "Market Bot",
"attachments": [
msg
]
} |
def filter_tasks_for_slaves(slaves, tasks):
""" Given a list of slaves and a list of tasks, return a filtered
list of tasks, where those returned belong to slaves in the list of
slaves
:param slaves: the list of slaves which the tasks provided should be
running on.
:param tasks: the tasks to fi... |
def fib(x):
"""
Returns the xth term of the Fibonacci sequence
"""
a, b = 1, 1
for i in range(1, x):
a, b = b, a + b
x += 1
return(a) |
def solve_timestep_differencer(z_future,z_downstream,z_past,dt,dx,U,K,A,m,n):
"""Solves the transient equations
E = K A^m S^n
dz/dt = U - E
dz/dt = U - K A^m S^n
(z^j+1-z^j)/dt = U - K A^m ((z_i^j+1-z_i-1^j+1)/dx)^n
We move all terms to one side:
0 = U - K A^m ((z_i^j... |
def cors(support="*", response=None, **kwargs):
"""Adds the the Access-Control-Allow-Origin header to this endpoint, with the specified support"""
response and response.set_header("Access-Control-Allow-Origin", support)
return support |
def _align(value, alignment):
"""Find the smallest multiple of `alignment` that is at least as large as `value`."""
return ((value - 1) // alignment + 1) * alignment |
def get_parents_from_list_of_attributes(fields):
"""Returns a list of parent ids from a list of column 9 entries."""
for field in fields:
if "Parent" in field:
return field.split("=")[1].split(",") |
def coh_transform(coh, max_coh):
"""Convert coherence from 0-100 to -1-1"""
return (coh-50)/(max_coh-50) |
def precision(actual, predicted, k=10):
"""
"""
m = len(actual)
if m == 0:
return -1
actual = set(actual)
hit = 0.
for i in range(k):
p = predicted[i]
if p in actual:
hit += 1
return hit / k |
def __get_col_name(col):
"""
Internal helper function to get the actual name of a pandas DataFrame column from a
column name that may consists of an arbitrary sequence of tuples. The function
will return the last value of the innermost tuple.
"""
curr_val = col
while isinstance(curr_val, tup... |
def percent_avoid_rounding_to_zero(numerator, denominator, default_decimals=1, max_decimals=2):
"""Calculates percentage to `default_decimals` number of decimal places. If
the percentage would round to 0, calculates with more decimal places until
either it doesn't round to 0, or until `max_decimals`. ... |
def getErrorMsg(error=None, detail=None):
"""
print LogMapper Agent Menu
"""
msg = "ERROR"
if error:
msg = msg + ": " + str(error)
if detail:
msg = msg + " Detail: " + str(detail)
return msg |
def findAlphabeticallyLastWord(text):
"""
Given a string |text|, return the word in |text| that comes last
alphabetically (that is, the word that would appear last in a dictionary).
A word is defined by a maximal sequence of characters without whitespaces.
You might find max() and list comprehension... |
def format_cell(x):
"""Formats the content of a cell so it is displayed nicely."""
r = hex(x)[2:]
if len(r) == 1:
r = '0' + r
return r.upper() |
def get_frames_per_sample(fps, sample_time):
"""
Converts a specified sample_time from seconds to # of samples.
Parameters
----------
fps: float
Video sampling rate
sample_time: float
Duration (in seconds) to sample
Returns
-------
int
The # of samples that ... |
def tplink_build_url(host, path):
""" A helper function to build URL's for the device """
return f"http://{host}/{path}" |
def generate_key(message: str, key: str) -> str:
"""
>>> generate_key("THE GERMAN ATTACK","SECRET")
'SECRETSECRETSECRE'
"""
x = len(message)
i = 0
while True:
if x == i:
i = 0
if len(key) == len(message):
break
key += key[i]
... |
def isZeroRow(m, row):
""" (int, [m]) => boolean
check if row with length m consists of only zeros
"""
for i in range(m):
if row[i] != 0:
return False
return True |
def isSubset(normalset1, normalset2):
# print(len(normalset2))
"""I need to make sure that """
# if(len(normalset1) > len(normalset2)):
# return False;
for i in normalset1:
if i not in normalset2:
return False;
return True |
def __process_line(line, spaces, padding, left_justify):
"""
Core method to indent each line.
"""
while (" " * 3) in line:
line = line.replace((" " * 3), (" " * 2))
temp = line.strip()
if left_justify and len(temp) == 1:
newline = temp + "\r\n"
else:
list_line = ... |
def GetErrorsForTemplate(api_query):
"""Prepares and returns the template values for API Query error responses.
Args:
api_query: The API Query for which to prepare the errors template values.
Returns:
A dict containing a list of template values to use for each API Query
error responses.
"""
error... |
def triangleNum(n):
"""Returns the nth triangle number."""
return int(n * (n + 1) / 2) |
def get_port_numbers(ports):
"""
Get all port number from response and make comma-separated string
:param ports: Port portion from response.
:return: Comma-separated port numbers.
"""
return ', '.join([str(port['number']) for port in ports]) |
def str2fmap(line):
"""converts a string of the type 'f1=v1 f2=v2' into a feature map {f1: v1, f2: v2}"""
return {k: float(v) for k, v in (pair.split('=') for pair in line.split())} |
def yoToZA( yo_i ) :
"""Returns ZA designator, or special code, from yo id. That is, ::
yo_i = 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16
is converted to
0, 1, 1001, 1002, 1003, 2003, 2004, 0, -8, -9, -10, 1, 1001, 1002, 1003, 2003, 2004
with ... |
def close(conn):
"""This closes the database connection.
"""
try:
conn.close()
except:
pass
return True |
def find_colours(shapes):
""" Takes a list of shapes with cells (y, x, colour) and finds their common and uncommon colours.
Note that uncommon colours are a nested list, where each nested list corresponds to uncommon colours
of a particular shape - different shapes could have different uncommon colours.
... |
def vecvecsum(vec1, vec2):
"""Elementwise sum res[i] = vec1[i] + vec2[i]"""
return [v1 + v2 for v1, v2 in zip(vec1, vec2)] |
def hexstring_to_wydelist(s):
"""Takes hexadecimal string representation and breaks it up into a list of wydes.
This could be factored into hextsinrg_to_intlist function but it is useful standalone
for exploring and debugging."""
n = 4
return list([s[i:i+n] for i in range(0, len(s), n)]) |
def get_groups(lines):
""" Seperates lines in groups of declarations.
:param lines: lines that were read from a file
"""
groups = []
group = []
for line in lines:
# if empty line: add current group to groups
if line == '\n':
groups.append(group)
group = [... |
def url_to_chat_id(slack_url):
"""Convert a copy-n-pasted slack chat URL to the chat_id
Go from: https://xyz.slack.com/archives/.../p1614771038052300
To: 1614771038.052300
"""
# Recover the last element in URL and convert to chat_id. handle trailing /
try:
chat_id = [part for part in ... |
def BoundingBox_collision(BB1, BB2):
""" return true if two N-D bounding boxes collide, False otherwise"""
for B1, B2 in zip(BB1,BB2):
if (B1[1] < B2[0]) or (B2[1] < B1[0]):
return False
return True |
def solution1(A): # O(N)
"""
You are given a list A (eg. [1, 2, 3, 7, 1, 5]).
Write a function to calculate the pivot of the array such that the
left hand side = right hand side.
In the example, pivot (P) = 3, because 1 + 2 + 3 = 1 + 5.
Expecte... |
def newman_conway(num):
""" Returns a list of the Newman Conway numbers for the given value.
Time Complexity: O(n)
Space Complexity: O(n)
"""
if num == 0:
raise ValueError
if num == 1:
return '1'
if num == 2:
return '1 1'
sequence = [0, 1, 1]
for i ... |
def normalize_description(description):
"""
Normalizes a docstrings.
Parameters
----------
description : `str` or `None`
The docstring to clear.
Returns
-------
cleared : `str` or `None`
The cleared docstring. If `docstring` was given as `None` or is detected as... |
def bad_request(msg: str = '') -> bytes:
"""Send a 59 (bad request) response.
:param msg: Error message to display to the user.
:return: Bytes to be sent to the client.
"""
return f'59 {msg}\r\n'.encode() |
def flatten(records, fld):
""" Flatten a recordset to list of a particular field
:param records: the recordset to flatten
:param fld: the field from the records to include in list
:return: a list
"""
return [path for fields in records.values_list(fld) for path in fields] if records else [] |
def eqva(a1, a2):
"""
modified np.array_equal. considers a1 and a2
equal when there is 1 difference.
"""
a1.sort()
a2.sort()
count = 0
a1_, a2_ = a1, a2
if len(a1) > len(a2):
a1_ = a2
a2_ = a1
for s in a1:
if not s in a2:
count += 1
retur... |
def distance(strand_a, strand_b):
"""Find the number of difference between two same length strings
Parameters
----------
strand_a, strand_b : str
"""
if len(strand_a) == len(strand_b):
count = 0
# shirouto: most of the time, if you see something like this in python
# yo... |
def band_to_frequency(band):
"""
nominal band center frequency in GHz from band code
"""
if band == "L": return 1.7
elif band == "S": return 2.3
elif band == "C": return 5.0
elif band == "X": return 8.45
elif band == "Ku": return 15
elif band == "K": return 22
elif band == "Ka": return 34
e... |
def partition_on(predicate, iterable, map_fn=None):
""" Partition an iterable into two lists on the return type of the predicate. """
left, right = [], []
if map_fn is None:
for i in iterable:
if predicate(i):
left.append(i)
else:
right.appen... |
def wrap_in_list(maybe_list):
""" This function checks if maybe_list is a list (or anything derived
from list). If not, it wraps it in a list.
The motivation for this function is that some functions return either
a single object (e.g., a dictionary) or a list of those objects. The
r... |
def parse_notifier_name(name):
"""Convert the name argument to a list of names.
Examples
--------
>>> parse_notifier_name('a')
['a']
>>> parse_notifier_name(['a','b'])
['a', 'b']
>>> parse_notifier_name(None)
['anytrait']
"""
if isinstance(name, str):
return [name]
... |
def _str(_bytes):
"""
Attempt to decode bytes object back to ordinary Python string (utf-8).
Decoding cannot be guaranteed, so be careful.
@rtype: str, but will return the original data if it can't be interpreted as utf-8
"""
try:
return _bytes.decode("utf-8")
except UnicodeDecod... |
def create_response(status, meta, path=""):
"""
Create tuple representing gemini response
status: two-digit gemini status code
meta: response info depending on status
body: optional path to file to include in response body
"""
response = status, meta, path
return response |
def percentage(reviewed, voted):
"""Returns the percentage of voted contributions."""
try:
return 100.0 * voted / reviewed
except ZeroDivisionError:
return 100.0 |
def printPath(path):
"""Assuming path is a list of nodes."""
result = ''
for i in range(len(path)):
result += str(path[i])
if i != len(path) - 1:
result += ' --> '
return result |
def get_common_lists(list1, list2):
"""Compare the items in two lists
This method compares the items in two lists returning those items that
appear in both lists as well as two lists that contain those unique items
from the original lists.
For example, given {s,b,c,d,e,f} and {a,b,c,d,e,z}, the li... |
def order(sentence):
"""Return a list of strings sorted by what number is in them."""
# example given "tw2o o1ne" returns "o1ne tw2o"
word_list = sentence.split(' ')
new_word_list = []
for i in range(1, len(word_list) + 1):
for word in word_list:
if str(i) in word:
... |
def tile(i, j, level):
"""Coordinates of tile in x, y space"""
tile_size = 256
initial_resolution = 5 / tile_size
resolution = initial_resolution / (2 ** level)
side_length = resolution * tile_size
x = i * side_length
y = j * side_length
return x, y, side_length |
def flatten_config(config):
"""Take dict with ':'-separated keys and values or tuples of values,
flattening to single key-value pairs.
Example: _flatten_config({'a:b': (1, 2), 'c': 3}) -> {'a: 1, 'b': 2, 'c': 3}."""
new_config = {}
for ks, vs in config.items():
ks = ks.split(":")
if... |
def log_simple(n, k):
"""
A function that simply finds how many k's does n have.
For example 28 = 2 * 2 * 7, so log_simple(28, 2) will return 2
and log_simple(28, 7) will return 1
"""
log_result = 0
while (n % k == 0):
log_result += 1
n /= k
return n, log_resu... |
def _is_single_iterator_type(iters):
"""Determine if there is a single or multiple type of iterator
If iters is [], this method returns True it considers the null case to be
a single iterator type.
"""
if iters:
return len(set(iters)) == 1
else:
return True |
def _validate(data, players):
"""Chat messages can be bugged - check for invalid messages."""
numbers = [p['number'] for p in players]
if 'player_number' in data and data['player_number'] not in numbers:
return False
return True |
def size_unicode(arg):
"""Calculate the size of a unicode string"""
return len(arg.encode('utf-8')) |
def release_notes_pg_minor_version(minor_version, major_version):
"""Formats the minor version number to the appropriate PostgreSQL version.
This is particularly for very old version of PostgreSQL.
"""
if str(major_version) in ['0', '1']:
return str(minor_version)[2:4]
return minor_version |
def remove_repeated_asn(path):
""" remove repeated ASN in the give path
Args:
path (list of ASN): ASN can be int for str if IXP hop
Returns:
list of ASN
"""
removed = []
for idx, hop in enumerate(path):
if idx == 0:
removed.append(hop)
elif hop != pa... |
def get_tax(base_cost: float, tax_rate: float) -> float:
"""Return the tax on base_cost."""
tax = base_cost / 100 * tax_rate
return tax |
def get_range( value ):
"""
Filter - returns a list containing range made from given value
Usage (in template):
<ul>{% for i in 3|get_range %}
<li>{{ i }}. Do something</li>
{% endfor %}</ul>
Results with the HTML:
<ul>
<li>0. Do something</li>
<li>1. Do something</li>
... |
def attrs(m, first=[], underscores=False):
"""
Given a mapping m, return a string listing its values in a
key=value format. Items with underscores are, by default, not
listed. If you want some things listed first, include them in
the list first.
"""
keys = first[:]
for k in m.keys():
... |
def detect_compression_format(filename):
"""
Attempts to detect compression format from the filename extension.
Returns None if no format could be detected.
"""
if filename.endswith('.bz2'):
return "bz2"
elif filename.endswith('.xz'):
return "xz"
elif filename.endswith('.gz')... |
def check_sign_projection_of_a_on_b(a, b):
"""
The magnitude of the projection of a on b is given by:
(a \\dot b)/|b|
However, |b| is always >= 0.
Thus, the sign is determined solely by the sign of a \\dot b.
"""
if (a[0] * b[0] + a[1] * b[1]) > 0:
return 1
else:
re... |
def patch_name_parts_limit(name_str, space_replacer=None):
""" Usage: par_name = patch_name_parts_limit(name_str, <space_replacer>)
clean up name_str such that it may be decoded with
patch_name_to_dict and serve as a valid file name
Args:
name_str: string represent... |
def update_dic_dist(dic_dist, dic_xyz, d_real, d_approx, phase):
""" For every annotation in a single image, update the final dictionary"""
# Update the dict with heights metric
if phase == 'train':
dic_dist['heights']['head'].append(float(dic_xyz['head'][0][1]))
dic_dist['heights']['should... |
def add_edge_output_graph(edge_to_add, graph):
"""
Helper function that takes an edge of the form ({"node1", "node2"},
node_weight) and adds it to the list of edges in the graph, in the form
{"node1": [("node2", node_weight)], "node2": [("node1", node_weight)]} .
"""
for val in edge_to_add[0]:
... |
def vals_are_same(offset, *content):
"""
Determine if the values at offset of the content arrays are all the same.
:param offset: The offset into the content arrays to check.
:param content: The content arrays.
:return: True if content[0][offset] == content[1][offset] == ..., False otherwise.
""... |
def length_of_last_word(text):
"""
Given a string s consists of upper/lower-case alphabets and empty space
characters ' ', return the length of last word in the string.
NOTE: Please make sure you try to solve this problem without using library
functions. Make sure you only traverse the string once.... |
def format_offset(offset):
"""Return a right-aligned hexadecimal representation of offset.
>>> format_offset(128)
' 0080'
>>> format_offset(3735928559)
'deadbeef'
"""
return '0x%5x%03x' % (offset >> 12, offset & 0xFFF) |
def check_the_bucket(bucket):
"""checks bucket, returns true or false."""
if 'gold' in bucket:
return True
else:
return False |
def max_sum_subaarry(a):
""" Kadane's algo """
max_so_far = 0
max_ending_here = 0
n = len(a)
start = 0
end = 0
s = 0
for i in range(0, n):
max_ending_here = max_ending_here + a[i]
if max_ending_here < 0:
max_ending_here = 0
s = i + 1
if max_ending_here > max_so_far:
m... |
def list_duplicates_of(seq,item):
"""Return sequences of duplicate adjacent item in seq"""
start_at = -1
locs = []
sequences = []
start_index = -1
while True:
try:
loc = seq.index(item,start_at+1)
except ValueError:
end_index = locs[-1]
sequenc... |
def update_file_list(file_content, tag_index, formated_informations):
"""
Return the list file_content with formated_informations inserted at
tag_index position.
file_content : list containing the current file
tag_index : position, in list, of tags to insert bet... |
def parsetagvalue(term):
"""
This function obtains all attributes of a term and puts it in
a dictionary. Though it returns an empty string if function
input is not an GO term.
:param term:
A list containing all information from one term obtained
from the obofile.
:return:
"""
if ... |
def search(inp, neuron_labels):
""" Utility function to retrieve neuron labels with a filter.
# Arguments
inp (str): Keyword to use for filtering.
neuron_labels (dict): Dictionary of neuron labels, for example generated with load_normalized_hemibrain.
# Returns
list: Returns names
... |
def parse_job_line(line):
"""
>>> parse_job_line("* * * *,myquery,mycredentials\\n")
('* * * *', 'myquery', 'mycredentials', 'collect.py')
>>> parse_job_line("* * * *,myquery,mycredentials,scripts/foo.py\\n")
('* * * *', 'myquery', 'mycredentials', 'scripts/foo.py')
"""
parts = line.strip().... |
def convert_to_gbit(value):
""" convert bytes to Gbits
Args
value Value in bytes to be converted to Gbits
"""
return value/1024./1024./1024.*8 |
def minmax(data):
"""Solution to exercise R-1.3.
Takes a sequence of one or more numbers, and returns the smallest and
largest numbers, in the form of a tuple of length two. Do not use the
built-in functions min or max in implementing the solution.
"""
min_idx = 0
max_idx = 0
for idx, n... |
def diff1(arr):
"""kevin.du on CodeWars solutions."""
b = 0
c = 0
for i in arr:
a = eval(i)
if abs(a) > c:
b = i
c = abs(a)
return b |
def get_formal_writers(writers_string):
"""Return 'Lennon-McCartney' if at least one of them is present in the argument"""
first_writer = writers_string.split(',')[0]
if first_writer == 'Starkey':
return 'Starkey'
if first_writer == 'Harrison':
return 'Harrison'
if 'Lennon' in wr... |
def jaccard(setA, setB):
""""Jaccard Index"""
setA, setB = set(setA), set(setB)
return len(setA.intersection(setB)) / len(setA.union(setB)) |
def tail_avg(timeseries):
"""
This is a utility function used to calculate the average of the last three
datapoints in the series as a measure, instead of just the last datapoint.
It reduces noise, but it also reduces sensitivity and increases the delay
to detection.
"""
try:
t = (ti... |
def is_even(number:int):
"""
This function verifies if the number is even or not
Returns:
True if even false other wise
"""
return number % 2 == 0 |
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