code stringlengths 114 1.05M | path stringlengths 3 312 | quality_prob float64 0.5 0.99 | learning_prob float64 0.2 1 | filename stringlengths 3 168 | kind stringclasses 1
value |
|---|---|---|---|---|---|
r"""rna_rosetta_run.py - prepare & run ROSETTA simulations
Based on C. Y. Cheng, F. C. Chou, and R. Das, Modeling complex RNA tertiary folds with Rosetta, 1st ed., vol. 553. Elsevier Inc., 2015.
http: // www.sciencedirect.com / science / article / pii / S0076687914000524
The script makes(1) a folder for you job, with... | /rna_tools-3.13.7-py3-none-any.whl/rna_tools-3.13.7.data/scripts/rna_rosetta_run.py | 0.547222 | 0.426979 | rna_rosetta_run.py | pypi |
r"""rna_plot_density.py - generate a density plot
Don't open Excel, Jupyter. Simple plot a density of one column and save it to a file.
Example::
# file
fn rmsd_all
0 19_Bujnicki_Human_4_rpr_n0-000001.pdb-000001_A... 14.73
1 19_Bujnicki_Human_4... | /rna_tools-3.13.7-py3-none-any.whl/rna_tools-3.13.7.data/scripts/rna_plot_boxplotlike.py | 0.681621 | 0.332907 | rna_plot_boxplotlike.py | pypi |
import logging
import argparse
from Bio.SeqRecord import SeqRecord
from Bio import SeqIO
from Bio.PDB import PDBParser
from Bio.PDB import PDBIO
from Bio.PDB.Atom import PDBConstructionWarning
import warnings
warnings.simplefilter('ignore', PDBConstructionWarning)
# logger
logger = logging.getLogger()
handler = loggin... | /rna_tools-3.13.7-py3-none-any.whl/rna_tools-3.13.7.data/scripts/renum_pdb_to_aln.py | 0.62223 | 0.210401 | renum_pdb_to_aln.py | pypi |
# RNAfbinv 2.0
RNAfbinv is a fragment based RNA design tool. It uses a simulated annealing process to optimize a 2D RNA structure.<br/>
The similarity is based on fragment based design. A tree alignment is done based on nodes (structural motifs).<br/>
Nodes are comparable if they are both bounded motifs (stems) or unb... | /rnafbinv-2.0.3.tar.gz/rnafbinv-2.0.3/README.md | 0.409811 | 0.842928 | README.md | pypi |
<p align="center">
<h1 align="center">
RNAIndel
</h1>
<p align="center">
<a href="https://github.com/stjude/RNAIndel" target="_blank">
<img alt="Status"
src="https://img.shields.io/badge/status-active-success.svg" />
</a>
<a href="https://github.com/stjude/RNAIndel/issues" target="_b... | /rnaindel-3.0.9.tar.gz/rnaindel-3.0.9/README.md | 0.431944 | 0.93611 | README.md | pypi |
import json
import logging
from pathlib import Path
from typing import Union, List
import jsonschema
import randname.error
from . import set_logging_level
set_logging_level("error")
class Database:
schema_info_json = {
"type": "object",
"title": "info.json schema",
"description": "Sche... | /rname-0.3.7.tar.gz/rname-0.3.7/randname/database.py | 0.568296 | 0.236946 | database.py | pypi |
<p align="center"><a href="https://rnasamba.lge.ibi.unicamp.br/"><img src="https://raw.githubusercontent.com/apcamargo/RNAsamba/master/logo.png" width="350rem"></a></p>
- [Overview](#overview)
- [Documentation](#documentation)
- [Installation](#installation)
- [Download the pre-trained models](#download-the-pre-traine... | /rnasamba-0.2.3.tar.gz/rnasamba-0.2.3/README.md | 0.724968 | 0.974988 | README.md | pypi |
import os
import shutil
import textwrap
from multiprocessing import cpu_count
from subprocess import call
import pandas as pd
from rnaseq_lib.docker import fix_directory_ownership
from rnaseq_lib.tissues import get_tumor_samples, get_gtex_samples, get_normal_samples, map_genes
from rnaseq_lib.utils import mkdir_p
d... | /rnaseq-lib-1.0a21.tar.gz/rnaseq-lib-1.0a21/src/rnaseq_lib/R/__init__.py | 0.485112 | 0.300483 | __init__.py | pypi |
from collections import defaultdict
import gzip
import pandas as pd
import re
GTF_HEADER = ['seqname', 'source', 'feature', 'start', 'end', 'score',
'strand', 'frame']
R_SEMICOLON = re.compile(r'\s*;\s*')
R_COMMA = re.compile(r'\s*,\s*')
R_KEYVALUE = re.compile(r'(\s+|\s*=\s*)')
def dataframe_f... | /rnaseq-lib-1.0a21.tar.gz/rnaseq-lib-1.0a21/src/rnaseq_lib/gtf/__init__.py | 0.57821 | 0.303919 | __init__.py | pypi |
import os
import pickle
import pandas as pd
from rnaseq_lib.utils import flatten
__location__ = os.path.realpath(os.path.join(os.getcwd(), os.path.dirname(__file__)))
def return_samples():
"""
Returns sample dictionary which maps TCGA and GTEx samples to a tissue.
Synapse ID: syn10296681
:return: ... | /rnaseq-lib-1.0a21.tar.gz/rnaseq-lib-1.0a21/src/rnaseq_lib/tissues/__init__.py | 0.692122 | 0.32469 | __init__.py | pypi |
import argparse
import os
import requests
def usage():
description = '''
Problem:
I choose project BRCA on GDC(https://gdc-portal.nci.nih.gov/projects/t)
and forward to WXS(1,050 cases, 2,175 bam files). Download manifest file from the summary tab.
In fact the manifest only contai... | /rnaseq-lib-1.0a21.tar.gz/rnaseq-lib-1.0a21/src/rnaseq_lib/utils/gdc.py | 0.428712 | 0.295192 | gdc.py | pypi |
import os
from subprocess import call
import logging
logging.basicConfig(level=logging.INFO)
def filter_aligned_reads(bam_path, output_name=None, paired=True):
"""
Filters bams for aligned reads
:param str bam_path: Path to bam file
:param str output_name: Defaults to input bam with '.filtered' inse... | /rnaseq-lib-1.0a21.tar.gz/rnaseq-lib-1.0a21/src/rnaseq_lib/utils/bam.py | 0.47098 | 0.29954 | bam.py | pypi |
import holoviews as hv
import pandas as pd
from rnaseq_lib.dim_red import run_tsne, run_tete
from rnaseq_lib.utils import flatten
def plot_boxplot(df,
plot_info,
feature,
norm_func=None,
title=None,
value_label='counts', group_label... | /rnaseq-lib-1.0a21.tar.gz/rnaseq-lib-1.0a21/src/rnaseq_lib/plotting/__init__.py | 0.823612 | 0.585634 | __init__.py | pypi |
import urllib2
import requests
import xmltodict
from bs4 import BeautifulSoup
def get_drug_target_from_wiki(drug):
"""
Scrape wikipedia for the target of a drug
:param str drug: Drug to lookup
:return: Drug target
:rtype: str
"""
# Look for wiki page
url = 'https://en.wikipedia.org/w... | /rnaseq-lib-1.0a21.tar.gz/rnaseq-lib-1.0a21/src/rnaseq_lib/web/__init__.py | 0.487063 | 0.230909 | __init__.py | pypi |
from typing import List, Tuple
import pandas as pd
from pandas import DataFrame
# These functions are for data stored in this Synapse ID:
# Expression: pd.read_hdf(data_path, key='exp')
# Metadata: pd.read_hdf(data_path, key='met')
def add_metadata_to_exp(exp: DataFrame, met: DataFrame) -> DataFrame:
"""Adds met... | /rnaseq-lib3-1.0a1.tar.gz/rnaseq-lib3-1.0a1/src/rnaseq_lib3/exp/__init__.py | 0.872863 | 0.691555 | __init__.py | pypi |
from collections import defaultdict
from typing import List, Set
import pandas as pd
from rnaseq_lib3.math import log2fc
# TCGA Mapping
subtype_abbrev = {
'LAML': 'Acute Myeloid Leukemia',
'ACC': 'Adrenocortical carcinoma',
'BLCA': 'Bladder Urothelial Carcinoma',
'LGG': 'Brain Lower Grade Glioma',
... | /rnaseq-lib3-1.0a1.tar.gz/rnaseq-lib3-1.0a1/src/rnaseq_lib3/tcga/__init__.py | 0.84869 | 0.5047 | __init__.py | pypi |
from genericdiff.generic_diff import *
import math
class sin(GenericDiff):
def __init__(self, obj):
def _sin_generic(obj):
self.val = math.sin(obj.val)
self.der = math.cos(obj.val)*obj.der
try:
_sin_generic(obj)
except AttributeError:
obj ... | /rnavelocity-genericdiff-0.1.0.tar.gz/rnavelocity-genericdiff-0.1.0/genericdiff/elemental_functions.py | 0.403567 | 0.244566 | elemental_functions.py | pypi |
import math
import matplotlib.pyplot as plt
from .Generaldistribution import Distribution
class Gaussian(Distribution):
""" Gaussian distribution class for calculating and
visualizing a Gaussian distribution.
Attributes:
mean (float) representing the mean value of the distribution
stdev (float) representing ... | /rnc_mlnd_distributions-0.1.tar.gz/rnc_mlnd_distributions-0.1/rnc_mlnd_distributions/Gaussiandistribution.py | 0.688364 | 0.853058 | Gaussiandistribution.py | pypi |
from __future__ import print_function
import hashlib
import hmac
import sys
from Crypto import Random
from Crypto.Cipher import AES
from Crypto.Protocol import KDF
__all__ = ('RNCryptor', 'decrypt', 'encrypt')
__version__ = '3.3.0'
PY2 = sys.version_info[0] == 2
PY3 = sys.version_info[0] == 3
if PY2:
def to_by... | /rncryptor-3.3.0.tar.gz/rncryptor-3.3.0/rncryptor.py | 0.650689 | 0.265678 | rncryptor.py | pypi |
import math
import matplotlib.pyplot as plt
from .Generaldistribution import Distribution
class Gaussian(Distribution):
""" Gaussian distribution class for calculating and
visualizing a Gaussian distribution.
Attributes:
mean (float) representing the mean value of the distribution
stdev (float) representing ... | /rnd_probability-0.1.tar.gz/rnd_probability-0.1/rnd_probability/Gaussiandistribution.py | 0.688364 | 0.853058 | Gaussiandistribution.py | pypi |
[](https://codecov.io/gh/davips/rndqts)
# rndqts
Random stock market quotes
<img src="https://raw.githubusercontent.com/davips/rndqts/main/chart.png">
[Latest version](https:/... | /rndqts-0.2105.28.tar.gz/rndqts-0.2105.28/README.md | 0.444324 | 0.684178 | README.md | pypi |
from collections import OrderedDict
from functools import reduce, partial
def make_form(rng, root_name='ArchiveTransfer'):
"""Takes an rng, returns a html form.
Should be reworked.
"""
results = rng.to_form()
inside = results[root_name]
def make_input(value):
""" depending on what i... | /rng_to_html_form-1.0.2-py3-none-any.whl/rng_to_form/form_maker.py | 0.704058 | 0.207696 | form_maker.py | pypi |
from __future__ import unicode_literals, print_function
import sys
from os import path
import os
import glob
import itertools
import operator
import shutil
import pkg_resources
from invoke import ctask as task
import six
from six.moves import shlex_quote, reduce
import wheel.pep425tags
ROOT = path.relpath(path.dirn... | /rnginline-0.0.2.tar.gz/rnginline-0.0.2/tasks.py | 0.496094 | 0.253188 | tasks.py | pypi |
# rnmd - markdown execution runtime
RNMD is a mardown execution runtime which can be used to run code contained inside of a markdown file.
The vision behind it is to have your documentation and code together in one place and not maintain
2 versions of the same code (1 in .md and 1 script file).
Especially useful ... | /rnmd-1.1.0.tar.gz/rnmd-1.1.0/README.md | 0.478773 | 0.813387 | README.md | pypi |
## Training continuous time Recurrent Neural Networks (RNNs) on various behavioral tasks
This project aims to establish a pipeline for seamlessly defining the behavioral task and training RNNs on it using
backpropagation (BPTT) on *PyTorch*.
It also implements a useful class for the post-training task-performance ana... | /rnn_coach-0.1.tar.gz/rnn_coach-0.1/README.md | 0.954879 | 0.933975 | README.md | pypi |
import sys
sys.path.insert(0, "../")
from copy import deepcopy
import torch
import numpy as np
from numpy import linalg
# Connectivity defining methods
def sparse(tensor, sparsity, mean=0, std=1, generator=None):
r"""Fills the 2D input `Tensor` as a sparse matrix, where the
non-zero elements will be drawn fr... | /rnn_coach-0.1.tar.gz/rnn_coach-0.1/src/RNN_torch.py | 0.826817 | 0.78287 | RNN_torch.py | pypi |
from copy import deepcopy
import numpy as np
import torch
def L2_ortho(rnn, X=None, y=None):
# regularization of the input and ouput matrices
b = torch.cat((rnn.input_layer.weight, rnn.output_layer.weight.t()), dim=1)
b = b / torch.norm(b, dim=0)
return torch.norm(b.t() @ b - torch.diag(torch.diag(b.... | /rnn_coach-0.1.tar.gz/rnn_coach-0.1/src/Trainer.py | 0.893071 | 0.512144 | Trainer.py | pypi |
import sys
from copy import deepcopy
import numpy as np
import scipy.optimize
from matplotlib import pyplot as plt
from scipy.optimize import fsolve, minimize
from tqdm.auto import tqdm
sys.path.insert(0, '../')
from src.utils import get_colormaps, in_the_list, sort_eigs, make_orientation_consistent
import warnings
... | /rnn_coach-0.1.tar.gz/rnn_coach-0.1/src/DynamicSystemAnalyzer.py | 0.609524 | 0.577436 | DynamicSystemAnalyzer.py | pypi |
from copy import deepcopy
import numpy as np
from matplotlib import pyplot as plt
class PerformanceAnalyzer():
'''
Generic class for analysis of the RNN performance on the given task
'''
def __init__(self, rnn_numpy, task=None):
self.RNN = rnn_numpy
self.Task = task
def get_vali... | /rnn_coach-0.1.tar.gz/rnn_coach-0.1/src/PerformanceAnalyzer.py | 0.809991 | 0.423995 | PerformanceAnalyzer.py | pypi |
import json
import os
import sys
sys.path.insert(0, '../')
sys.path.insert(0, '../../')
from src.DynamicSystemAnalyzer import DynamicSystemAnalyzer
from src.PerformanceAnalyzer import PerformanceAnalyzer
from src.RNN_numpy import RNN_numpy
from src.utils import get_project_root, numpify, orthonormalize
from src.Traine... | /rnn_coach-0.1.tar.gz/rnn_coach-0.1/src/training_RNNs/training_MemoryAntiAngle.py | 0.526586 | 0.2296 | training_MemoryAntiAngle.py | pypi |
import os
import sys
sys.path.insert(0, '../')
sys.path.insert(0, '../../')
import json
from src.DataSaver import DataSaver
from src.DynamicSystemAnalyzer import DynamicSystemAnalyzer
from src.PerformanceAnalyzer import PerformanceAnalyzer
from src.RNN_numpy import RNN_numpy
from src.utils import get_project_root, num... | /rnn_coach-0.1.tar.gz/rnn_coach-0.1/src/training_RNNs/training_NBitFlipFlop.py | 0.487551 | 0.219662 | training_NBitFlipFlop.py | pypi |
import os
import sys
sys.path.insert(0, '../')
sys.path.insert(0, '../../')
import json
from src.DataSaver import DataSaver
from src.DynamicSystemAnalyzer import DynamicSystemAnalyzer
from src.PerformanceAnalyzer import PerformanceAnalyzer
from src.RNN_numpy import RNN_numpy
from src.utils import get_project_root, num... | /rnn_coach-0.1.tar.gz/rnn_coach-0.1/src/training_RNNs/training_DMTS.py | 0.490724 | 0.212743 | training_DMTS.py | pypi |
import datajoint as dj
dj.config['database.host'] = 'localhost'
dj.config['database.user'] = 'ptolmachev'
dj.config['database.password'] = 'pawa'
# dj.config['database.host'] = 'datajoint-tengel.pni.princeton.edu'
# dj.config['database.user'] = 'pt1290'
# dj.config['database.password'] = 'a9Ab?spCKz$Zh@24h'
dj.config[... | /rnn_coach-0.1.tar.gz/rnn_coach-0.1/src/datajoint/datajoint_config.py | 0.510496 | 0.211885 | datajoint_config.py | pypi |
import math
import time
import RNS
from RNS.Cryptography import Fernet
class Callbacks:
def __init__(self):
self.link_established = None
self.packet = None
self.proof_requested = None
class Destination:
"""
A class used to describe endpoints in a Reticulum Network. Destination
... | /rns-0.5.7-py3-none-any.whl/RNS/Destination.py | 0.673192 | 0.277905 | Destination.py | pypi |
from __future__ import annotations
import collections
import enum
import threading
import time
from types import TracebackType
from typing import Type, Callable, TypeVar, Generic, NewType
import abc
import contextlib
import struct
import RNS
from abc import ABC, abstractmethod
TPacket = TypeVar("TPacket")
class Syste... | /rns-0.5.7-py3-none-any.whl/RNS/Channel.py | 0.891982 | 0.180089 | Channel.py | pypi |
from __future__ import annotations
import bz2
import sys
import time
import threading
from threading import RLock
import struct
from RNS.Channel import Channel, MessageBase, SystemMessageTypes
import RNS
from io import RawIOBase, BufferedRWPair, BufferedReader, BufferedWriter
from typing import Callable
from contextlib... | /rns-0.5.7-py3-none-any.whl/RNS/Buffer.py | 0.769514 | 0.195844 | Buffer.py | pypi |
import math
import os
import RNS
import time
import atexit
import hashlib
from .vendor import umsgpack as umsgpack
from RNS.Cryptography import X25519PrivateKey, X25519PublicKey, Ed25519PrivateKey, Ed25519PublicKey
from RNS.Cryptography import Fernet
class Identity:
"""
This class is used to manage identit... | /rns-0.5.7-py3-none-any.whl/RNS/Identity.py | 0.514644 | 0.20832 | Identity.py | pypi |
import warnings as _warnings
import hashlib as _hashlib
trans_5C = bytes((x ^ 0x5C) for x in range(256))
trans_36 = bytes((x ^ 0x36) for x in range(256))
# The size of the digests returned by HMAC depends on the underlying
# hashing module used. Use digest_size from the instance of HMAC instead.
digest_size = None
... | /rns-0.5.7-py3-none-any.whl/RNS/Cryptography/HMAC.py | 0.833663 | 0.412471 | HMAC.py | pypi |
# WARNING! Only the X25519PrivateKey.exchange() method attempts to hide execution time.
# In the context of Reticulum, this is sufficient, but it may not be in other systems. If
# this code is to be used to provide cryptographic security in an environment where the
# start and end times of the execution can be guessed... | /rns-0.5.7-py3-none-any.whl/RNS/Cryptography/X25519.py | 0.718693 | 0.555134 | X25519.py | pypi |
import os
import time
from RNS.Cryptography import HMAC
from RNS.Cryptography import PKCS7
from RNS.Cryptography.AES import AES_128_CBC
class Fernet():
"""
This class provides a slightly modified implementation of the Fernet spec
found at: https://github.com/fernet/spec/blob/master/Spec.md
According... | /rns-0.5.7-py3-none-any.whl/RNS/Cryptography/Fernet.py | 0.668339 | 0.334481 | Fernet.py | pypi |
from cryptography.hazmat.primitives import serialization
from cryptography.hazmat.primitives.asymmetric.ed25519 import Ed25519PrivateKey, Ed25519PublicKey
from cryptography.hazmat.primitives.asymmetric.x25519 import X25519PrivateKey, X25519PublicKey
# These proxy classes exist to create a uniform API accross
# cryptog... | /rns-0.5.7-py3-none-any.whl/RNS/Cryptography/Proxies.py | 0.849847 | 0.272287 | Proxies.py | pypi |
from base64 import b64decode, b64encode, b32encode
from hashlib import sha256
import struct
import re
I2P_B64_CHARS = "-~"
def i2p_b64encode(x):
"""Encode I2P destination"""
return b64encode(x, altchars=I2P_B64_CHARS.encode()).decode()
def i2p_b64decode(x):
"""Decode I2P destination"""
return b64de... | /rns-0.5.7-py3-none-any.whl/RNS/vendor/i2plib/sam.py | 0.686685 | 0.258063 | sam.py | pypi |
import asyncio
from . import sam
from . import exceptions
from . import utils
from .log import logger
def parse_reply(data):
if not data:
raise ConnectionAbortedError("Empty response: SAM API went offline")
try:
msg = sam.Message(data.decode().strip())
logger.debug("SAM reply: "+str(m... | /rns-0.5.7-py3-none-any.whl/RNS/vendor/i2plib/aiosam.py | 0.68616 | 0.200382 | aiosam.py | pypi |
Reticulum Network Stack β <img align="right" src="https://static.pepy.tech/personalized-badge/rns?period=total&units=international_system&left_color=grey&right_color=blue&left_text=Installs"/>
==========
<p align="center"><img width="200" src="https://raw.githubusercontent.com/markqvist/Reticulum/master/docs/source/gr... | /rnspure-0.5.7.tar.gz/rnspure-0.5.7/README.md | 0.520253 | 0.90813 | README.md | pypi |
import math
import time
import RNS
from RNS.Cryptography import Fernet
class Callbacks:
def __init__(self):
self.link_established = None
self.packet = None
self.proof_requested = None
class Destination:
"""
A class used to describe endpoints in a Reticulum Network. Destination
... | /rnspure-0.5.7.tar.gz/rnspure-0.5.7/RNS/Destination.py | 0.673192 | 0.277905 | Destination.py | pypi |
from __future__ import annotations
import collections
import enum
import threading
import time
from types import TracebackType
from typing import Type, Callable, TypeVar, Generic, NewType
import abc
import contextlib
import struct
import RNS
from abc import ABC, abstractmethod
TPacket = TypeVar("TPacket")
class Syste... | /rnspure-0.5.7.tar.gz/rnspure-0.5.7/RNS/Channel.py | 0.891982 | 0.180089 | Channel.py | pypi |
from __future__ import annotations
import bz2
import sys
import time
import threading
from threading import RLock
import struct
from RNS.Channel import Channel, MessageBase, SystemMessageTypes
import RNS
from io import RawIOBase, BufferedRWPair, BufferedReader, BufferedWriter
from typing import Callable
from contextlib... | /rnspure-0.5.7.tar.gz/rnspure-0.5.7/RNS/Buffer.py | 0.769514 | 0.195844 | Buffer.py | pypi |
import math
import os
import RNS
import time
import atexit
import hashlib
from .vendor import umsgpack as umsgpack
from RNS.Cryptography import X25519PrivateKey, X25519PublicKey, Ed25519PrivateKey, Ed25519PublicKey
from RNS.Cryptography import Fernet
class Identity:
"""
This class is used to manage identit... | /rnspure-0.5.7.tar.gz/rnspure-0.5.7/RNS/Identity.py | 0.514644 | 0.20832 | Identity.py | pypi |
import warnings as _warnings
import hashlib as _hashlib
trans_5C = bytes((x ^ 0x5C) for x in range(256))
trans_36 = bytes((x ^ 0x36) for x in range(256))
# The size of the digests returned by HMAC depends on the underlying
# hashing module used. Use digest_size from the instance of HMAC instead.
digest_size = None
... | /rnspure-0.5.7.tar.gz/rnspure-0.5.7/RNS/Cryptography/HMAC.py | 0.833663 | 0.412471 | HMAC.py | pypi |
# WARNING! Only the X25519PrivateKey.exchange() method attempts to hide execution time.
# In the context of Reticulum, this is sufficient, but it may not be in other systems. If
# this code is to be used to provide cryptographic security in an environment where the
# start and end times of the execution can be guessed... | /rnspure-0.5.7.tar.gz/rnspure-0.5.7/RNS/Cryptography/X25519.py | 0.718693 | 0.555134 | X25519.py | pypi |
import os
import time
from RNS.Cryptography import HMAC
from RNS.Cryptography import PKCS7
from RNS.Cryptography.AES import AES_128_CBC
class Fernet():
"""
This class provides a slightly modified implementation of the Fernet spec
found at: https://github.com/fernet/spec/blob/master/Spec.md
According... | /rnspure-0.5.7.tar.gz/rnspure-0.5.7/RNS/Cryptography/Fernet.py | 0.668339 | 0.334481 | Fernet.py | pypi |
from cryptography.hazmat.primitives import serialization
from cryptography.hazmat.primitives.asymmetric.ed25519 import Ed25519PrivateKey, Ed25519PublicKey
from cryptography.hazmat.primitives.asymmetric.x25519 import X25519PrivateKey, X25519PublicKey
# These proxy classes exist to create a uniform API accross
# cryptog... | /rnspure-0.5.7.tar.gz/rnspure-0.5.7/RNS/Cryptography/Proxies.py | 0.849847 | 0.272287 | Proxies.py | pypi |
from base64 import b64decode, b64encode, b32encode
from hashlib import sha256
import struct
import re
I2P_B64_CHARS = "-~"
def i2p_b64encode(x):
"""Encode I2P destination"""
return b64encode(x, altchars=I2P_B64_CHARS.encode()).decode()
def i2p_b64decode(x):
"""Decode I2P destination"""
return b64de... | /rnspure-0.5.7.tar.gz/rnspure-0.5.7/RNS/vendor/i2plib/sam.py | 0.686685 | 0.258063 | sam.py | pypi |
import asyncio
from . import sam
from . import exceptions
from . import utils
from .log import logger
def parse_reply(data):
if not data:
raise ConnectionAbortedError("Empty response: SAM API went offline")
try:
msg = sam.Message(data.decode().strip())
logger.debug("SAM reply: "+str(m... | /rnspure-0.5.7.tar.gz/rnspure-0.5.7/RNS/vendor/i2plib/aiosam.py | 0.68616 | 0.200382 | aiosam.py | pypi |
# RNT - Reddit Network Toolkit
A simple tool for generating and extracting network objects from Reddit data sets.
## Author
**Jacob Rohde**
Email: [jarohde1\@gmail.com](mailto:jarohde1@gmail.com) \| Twitter: [\@jacobrohde](https://twitter.com/JacobRohde) \| GitHub: [\@jarohde](https://github.com/jarohde)
## Featur... | /rnt-0.1.6.tar.gz/rnt-0.1.6/README.md | 0.788583 | 0.809276 | README.md | pypi |
from pyquery import PyQuery as pq
from urllib.parse import urljoin
base_url = 'https://www.rnz.co.nz/'
categories = [
('news/national', 'New Zealand'),
('news/world', 'World'),
('news/political', 'Politics'),
('international/pacific-news', 'Pacific News'),
('news/te-manu-korihi', 'Te Ao Māori'),
... | /rnz_news-1.0.1.tar.gz/rnz_news-1.0.1/rnz_news/__init__.py | 0.754915 | 0.155015 | __init__.py | pypi |
import zipfile
import logging
from pathlib import Path
import numpy as np
import torch
from torch.utils.data import DataLoader, IterableDataset
from collections import OrderedDict
from urllib.request import urlretrieve
from tqdm import tqdm
from .diacritics_dataset import DiacriticsDataset
from .diacritics_model imp... | /ro-diacritics-0.9.3.tar.gz/ro-diacritics-0.9.3/ro_diacritics/diacritics_inference.py | 0.61659 | 0.235064 | diacritics_inference.py | pypi |
import torch
import torch.nn as nn
class Diacritics(nn.Module):
"""
The pytorch model :class:Diacritics for diacritics restoration
:param nr_classes: for Romanian language we defined 3 classes
0 - No diacritics,
1 - One of the following transform... | /ro-diacritics-0.9.3.tar.gz/ro-diacritics-0.9.3/ro_diacritics/diacritics_model.py | 0.929656 | 0.499207 | diacritics_model.py | pypi |
from pathlib import Path
import numpy as np
import torch
import torch.nn.functional as F
import torch.optim as optim
from sklearn.metrics import f1_score, accuracy_score, classification_report
from torch.utils.data import DataLoader
from tqdm import tqdm
def train(
model,
loss_func,
train_dataloader: Dat... | /ro-diacritics-0.9.3.tar.gz/ro-diacritics-0.9.3/ro_diacritics/diacritcs_train.py | 0.791781 | 0.368292 | diacritcs_train.py | pypi |
import pickle as pkl
from collections import Counter
from pathlib import Path
import numpy as np
import torch
from nltk.tokenize import TreebankWordTokenizer, PunktSentenceTokenizer
from nltk.tokenize import sent_tokenize, word_tokenize
from torch.utils.data import IterableDataset
from torchtext.vocab import FastText
... | /ro-diacritics-0.9.3.tar.gz/ro-diacritics-0.9.3/ro_diacritics/diacritics_dataset.py | 0.762424 | 0.183795 | diacritics_dataset.py | pypi |
__author__ = "Graham Klyne (GK@ACM.ORG)"
__copyright__ = "Copyright 2011-2013, Graham Klyne, University of Oxford"
__license__ = "MIT (http://opensource.org/licenses/MIT)"
import unittest
import logging
junitxml_present = False
try:
import junitxml
junitxml_present = True
except ImportError:
p... | /ro-manager-0.2.20.tar.gz/ro-manager-0.2.20/MiscUtils/TestUtils.py | 0.442637 | 0.386706 | TestUtils.py | pypi |
__author__ = "Graham Klyne (GK@ACM.ORG)"
__copyright__ = "Copyright 2011-2013, Graham Klyne, University of Oxford"
__license__ = "MIT (http://opensource.org/licenses/MIT)"
from operator import concat, and_, or_
def concatMap(f,vs):
"""
Map function over list and concatenate results.
"""
ret... | /ro-manager-0.2.20.tar.gz/ro-manager-0.2.20/MiscUtils/Functions.py | 0.594316 | 0.481393 | Functions.py | pypi |
__author__ = "Graham Klyne (GK@ACM.ORG)"
__copyright__ = "Copyright 2011-2013, University of Oxford"
__license__ = "MIT (http://opensource.org/licenses/MIT)"
import re # Used for link header parsing
import httplib
import urlparse
import rdflib
import logging
# Logger for this module
log = logging.getLog... | /ro-manager-0.2.20.tar.gz/ro-manager-0.2.20/MiscUtils/HttpSession.py | 0.534612 | 0.251889 | HttpSession.py | pypi |
__author__ = "Graham Klyne (GK@ACM.ORG)"
__copyright__ = "Copyright 2011-2013, University of Oxford"
__license__ = "MIT (http://opensource.org/licenses/MIT)"
from django.http import HttpResponse
from django.views import generic
class ContentNegotiationView(generic.View):
"""
Generic view class with... | /ro-manager-0.2.20.tar.gz/ro-manager-0.2.20/roverlay/rovweb/rovserver/ContentNegotiationView.py | 0.533884 | 0.218993 | ContentNegotiationView.py | pypi |
from ro_py.utilities.url import url
endpoint = url("groups")
class RolePermissions:
"""
Represents role permissions.
"""
view_wall = None
post_to_wall = None
delete_from_wall = None
view_status = None
post_to_status = None
change_rank = None
invite_members = None
remove_mem... | /ro-py-1.2.0.5.tar.gz/ro-py-1.2.0.5/ro_py/roles.py | 0.84346 | 0.26445 | roles.py | pypi |
from lxml import html
from io import StringIO
class EndpointDocsPathRequestTypeProperties:
def __init__(self, data):
self.internal = data["internal"]
self.metric_ids = data["metricIds"]
class EndpointDocsPathRequestTypeResponse:
def __init__(self, data):
self.description = None
... | /ro-py-1.2.0.5.tar.gz/ro-py-1.2.0.5/ro_py/robloxdocs.py | 0.431944 | 0.268053 | robloxdocs.py | pypi |
import enum
from ro_py.utilities.url import url
endpoint = url("accountsettings")
class PrivacyLevel(enum.Enum):
"""
Represents a privacy level as you might see at https://www.roblox.com/my/account#!/privacy.
"""
no_one = "NoOne"
friends = "Friends"
everyone = "AllUsers"
class PrivacySettin... | /ro-py-1.2.0.5.tar.gz/ro-py-1.2.0.5/ro_py/accountsettings.py | 0.577495 | 0.164215 | accountsettings.py | pypi |
from urllib.parse import quote
from math import floor
import re
from ro_py.utilities.url import url
endpoint = url("gamepersistence")
class DataStore:
"""
Represents the in-game datastore system for storing data for games (https://gamepersistence.roblox.com).
This is only available for authenticated clie... | /ro-py-1.2.0.5.tar.gz/ro-py-1.2.0.5/ro_py/gamepersistence.py | 0.811228 | 0.299502 | gamepersistence.py | pypi |
from datetime import datetime
from ro_py.gender import RobloxGender
from ro_py.utilities.url import url
endpoint = url("accountinformation")
class AccountInformationMetadata:
"""
Represents account information metadata.
"""
def __init__(self, metadata_raw):
self.is_allowed_notifications_endpo... | /ro-py-1.2.0.5.tar.gz/ro-py-1.2.0.5/ro_py/accountinformation.py | 0.929871 | 0.198646 | accountinformation.py | pypi |
from ro_py.robloxbadges import RobloxBadge
from ro_py.utilities.pages import Pages
from ro_py.assets import UserAsset
from ro_py.badges import Badge
import iso8601
from ro_py.utilities.url import url
endpoint = url("users")
def limited_handler(requests, data, args):
assets = []
for asset in data:
ass... | /ro-py-1.2.0.5.tar.gz/ro-py-1.2.0.5/ro_py/bases/baseuser.py | 0.649579 | 0.204104 | baseuser.py | pypi |
class ApiError(Exception):
"""Called in requests when an API request fails with an error code that doesn't have an independent error."""
pass
class BadRequest(ApiError):
"""400 HTTP error"""
pass
class Unauthorized(ApiError):
"""401 HTTP error"""
pass
class Forbidden(ApiError):
"""403 ... | /ro-py-1.2.0.5.tar.gz/ro-py-1.2.0.5/ro_py/utilities/errors.py | 0.817137 | 0.226473 | errors.py | pypi |
from ro_py.utilities.errors import InvalidPageError
import enum
class SortOrder(enum.Enum):
"""
Order in which page data should load in.
"""
Ascending = "Asc"
Descending = "Desc"
class Page:
"""
Represents a single page from a Pages object.
"""
def __init__(self,... | /ro-py-1.2.0.5.tar.gz/ro-py-1.2.0.5/ro_py/utilities/pages.py | 0.840881 | 0.190969 | pages.py | pypi |
from datetime import datetime
from LatLon import LatLon, Latitude, Longitude
class Agent():
"""
Agents are located at ther *point*, which is a lat-lon coordinate pair.
They move through their route, which is a series of points that
connect their current location to their destination.
"""
def ... | /road_agent-1.0.1.tar.gz/road_agent-1.0.1/road_agent/__init__.py | 0.939464 | 0.532729 | __init__.py | pypi |
import uuid
from typing import (
Any,
Iterable,
Mapping
)
class GenericObjects():
def __init__(self, *args, **kwargs):
'''
:kwarg data:
:kwarg child_class:
'''
self._uuid = kwargs.get('uuid', None)
self.child_class = kwargs.get('child_class', GenericOb... | /road_collisions_base-0.0.22.tar.gz/road_collisions_base-0.0.22/src/road_collisions_base/models/generic.py | 0.746786 | 0.175044 | generic.py | pypi |
class Casualties():
def __init__(self, *args, **kwargs):
self._data = kwargs.get('data', [])
def __getitem__(self, i):
return self._data[i]
def __iter__(self):
return (i for i in self._data)
def __len__(self):
return len(self._data)
def append(self, data):
... | /road_collisions_france-0.0.3-py3-none-any.whl/road_collisions_france/models/casualty.py | 0.538255 | 0.154376 | casualty.py | pypi |
class Vehicles():
def __init__(self, *args, **kwargs):
self._data = kwargs.get('data', [])
def __getitem__(self, i):
return self._data[i]
def __iter__(self):
return (i for i in self._data)
def __len__(self):
return len(self._data)
def append(self, data):
... | /road_collisions_france-0.0.3-py3-none-any.whl/road_collisions_france/models/vehicle.py | 0.5769 | 0.229956 | vehicle.py | pypi |
class Casualties():
def __init__(self, *args, **kwargs):
self._data = kwargs.get('data', [])
def __getitem__(self, i):
return self._data[i]
def __iter__(self):
return (i for i in self._data)
def __len__(self):
return len(self._data)
def append(self, data):
... | /road_collisions_uk-0.0.3-py3-none-any.whl/road_collisions_uk/models/casualty.py | 0.572364 | 0.180107 | casualty.py | pypi |
class Casualties():
def __init__(self, *args, **kwargs):
self._data = kwargs.get('data', [])
def __getitem__(self, i):
return self._data[i]
def __iter__(self):
return (i for i in self._data)
def __len__(self):
return len(self._data)
def append(self, data):
... | /road_collisions_us-0.0.1.tar.gz/road_collisions_us-0.0.1/src/road_collisions_us/models/casualty.py | 0.572364 | 0.180107 | casualty.py | pypi |
import uuid
from typing import (
Any,
Iterable,
Mapping
)
class GenericObjects():
def __init__(self, *args, **kwargs):
'''
:kwarg data:
:kwarg child_class:
'''
self._uuid = kwargs.get('uuid', None)
self.child_class = kwargs.get('child_class', GenericOb... | /road_collisions-0.0.6-py3-none-any.whl/road_collisions/models/generic.py | 0.746786 | 0.175044 | generic.py | pypi |
import ast
import calendar
import configparser
import logging
import shutil
import time
from datetime import datetime
from functools import partial
from pathlib import Path
from dateutil.relativedelta import relativedelta
from road_data_scraper import TMP_LOG_PATH
from road_data_scraper.report.report import run_repor... | /road_data_scraper-0.0.20-py3-none-any.whl/road_data_scraper/main.py | 0.783119 | 0.318631 | main.py | pypi |
import glob
import logging
import warnings
from pathlib import Path
import pandas as pd
with warnings.catch_warnings():
warnings.simplefilter(action="ignore", category=FutureWarning)
import papermill as pm
from nbconvert.exporters import HTMLExporter
from nbconvert.preprocessors import TagRemovePreprocessor
... | /road_data_scraper-0.0.20-py3-none-any.whl/road_data_scraper/report/report.py | 0.703753 | 0.550305 | report.py | pypi |
```
# This cell is tagged parameters
title = "Road Data Dumps"
data = None
import warnings
warnings.filterwarnings("ignore")
from IPython.display import Markdown as md
from IPython.display import HTML
import pandas as pd
import panel as pn
import plotly.express as px
def create_counts_table(df):
df = df["status... | /road_data_scraper-0.0.20-py3-none-any.whl/road_data_scraper/report/road_data_report_template.ipynb | 0.472927 | 0.357876 | road_data_report_template.ipynb | pypi |
import ast
import datetime
import glob
import logging
import os
from pathlib import Path
from google.cloud import storage
LOGGER = logging.getLogger(__name__)
def file_handler(config: dict, api_run: bool, start_date: str, end_date: str) -> tuple:
"""
Creates directories to store scraped data and returns new... | /road_data_scraper-0.0.20-py3-none-any.whl/road_data_scraper/steps/file_handler.py | 0.690559 | 0.270706 | file_handler.py | pypi |
import csv
import logging
import multiprocessing
import threading
import time
from concurrent.futures import ThreadPoolExecutor
from dataclasses import dataclass
from itertools import repeat
from pathlib import Path
from typing import Callable
import pandas as pd
import requests
THREAD_POOL = multiprocessing.cpu_coun... | /road_data_scraper-0.0.20-py3-none-any.whl/road_data_scraper/steps/download.py | 0.87168 | 0.356699 | download.py | pypi |
import datetime
from functools import partial
import pandas as pd
import requests
BASE_URL = "https://webtris.highwaysengland.co.uk/api/v1/"
def create_sensor_metadata_tuples(
sensor_tables: dict[str, pd.DataFrame],
start_date: str,
end_date: str,
sensor_name: str = None,
) -> list[tuple[str, int, s... | /road_data_scraper-0.0.20-py3-none-any.whl/road_data_scraper/steps/metadata.py | 0.835886 | 0.388444 | metadata.py | pypi |
from .base_dataset import BaseDataset
from .file_operation import download_file, unzip_file, random_filename
import os
from xml.dom import minidom
from cv2 import cv2
class KaggleRoadSign(BaseDataset):
website_prefix = "https://github.com/elem3ntary/roadsign_db/raw/master/"
download_folder_name = "KaggleRoadSi... | /road-signs-db-convertion-michael-0.0.5.tar.gz/road-signs-db-convertion-michael-0.0.5/src/database_convertion/stefan.py | 0.406862 | 0.172817 | stefan.py | pypi |
import os
from abc import ABC, abstractmethod
from .AnalysisADT import SignPointArray
class BaseDataset(ABC):
"""
This module a database dosnloader & processor inherits.
"""
@property
@abstractmethod
def download_folder_name(self) -> str:
"""
This property is to be set to the ... | /road-signs-db-convertion-michael-0.0.5.tar.gz/road-signs-db-convertion-michael-0.0.5/src/database_convertion/base_dataset.py | 0.689096 | 0.281937 | base_dataset.py | pypi |
import os
import sys
import ctypes
import numpy as np
from cv2 import cv2
# Contains all info about a point taken from the database.
class _SignPointStruct(ctypes.Structure):
_pack_ = 1
_fields_ = [
('image_name', ctypes.c_char * 128),
('initial_size_x', ctypes.c_int),
('initial_size_y... | /road-signs-db-convertion-michael-0.0.5.tar.gz/road-signs-db-convertion-michael-0.0.5/src/database_convertion/AnalysisADT.py | 0.507324 | 0.287056 | AnalysisADT.py | pypi |
from . import model
class Items(model.Model):
itemTypes = {
"idea": 0,
"story": 1,
"done": 2,
"attached": 3
}
columnIndexes = {
"current": 2,
"soon": 1,
"future": 0,
"team": 2,
"user": 1,
"widget": 0,
"completed": 99
... | /roadmap-py-1.0.2.tar.gz/roadmap-py-1.0.2/roadmap/resources/items.py | 0.431584 | 0.336113 | items.py | pypi |
import functools
import re
def coroutine(func):
@functools.wraps(func)
def start(*args, **kwargs):
cr = func(*args, **kwargs)
cr.next()
return cr
return start
class Router(dict):
def __init__(self, processor):
'''Creates a new :class:`roadmap.Router` and assigns a proc... | /roadmap-0.1.tar.gz/roadmap-0.1/roadmap.py | 0.688364 | 0.419172 | roadmap.py | pypi |
import json
from numpy import isnan
from schematics import Model
from schematics.types import StringType, FloatType, ListType
class CbaResult(Model):
orma_way_id = StringType(max_length=20, min_length=1)
work_class = StringType(required=True, min_length=1)
work_type = StringType(required=True, min_length... | /roads-cba-py-0.1.2.tar.gz/roads-cba-py-0.1.2/roads_cba_py/cba_result.py | 0.61173 | 0.425784 | cba_result.py | pypi |
import json
from os import stat
from typing import List, Optional
from schematics.exceptions import ConversionError
from schematics.models import Model
from schematics.types import IntType, StringType, FloatType
class InvalidSection(object):
def __init__(self, errors, original_data):
self.errors = Invali... | /roads-cba-py-0.1.2.tar.gz/roads-cba-py-0.1.2/roads_cba_py/section.py | 0.548674 | 0.33039 | section.py | pypi |
import re
from collections import defaultdict
from itertools import takewhile
from typing import List, Match, Tuple, Dict
def format_markdown(contents: Dict[str, str]) -> Dict[str, str]:
# Extract backlinks from the markdown
forward_links = {file_name: extract_links(content) for file_name, content in contents... | /roam_to_git-0.1.tar.gz/roam_to_git-0.1/roam_to_git/formatter.py | 0.467089 | 0.169303 | formatter.py | pypi |
import asyncio
import os
from pathlib import Path
import pyppeteer.connection
def patch_pyppeteer():
"""Fix https://github.com/miyakogi/pyppeteer/issues/178"""
import pyppeteer.connection
original_method = pyppeteer.connection.websockets.client.connect
def new_method(*args, **kwargs):
kwargs... | /roam_to_git-0.1.tar.gz/roam_to_git-0.1/roam_to_git/scrapping.py | 0.47926 | 0.159119 | scrapping.py | pypi |
import datetime
import json
import zipfile
from pathlib import Path
import git
from roam_to_git.formatter import format_markdown
def get_zip_path(zip_dir_path: Path) -> Path:
"""Return the path to the single zip file in a directory, and fail if there is not one single
zip file"""
zip_files = list(zip_di... | /roam_to_git-0.1.tar.gz/roam_to_git-0.1/roam_to_git/fs.py | 0.429669 | 0.372676 | fs.py | pypi |
__version__ = "0.3.1"
class _RoamMissingItem:
""" Falsey class used to flag item "missing" from traversal path """
def __bool__(self):
return False
def __len__(self):
return 0
def __iter__(self):
return self
def __next__(self):
raise StopIteration()
def __... | /roam-0.3.1-py3-none-any.whl/roam.py | 0.766643 | 0.281569 | roam.py | pypi |
import contextlib
import re
import shutil
import sys
from difflib import get_close_matches
from pathlib import Path
from types import SimpleNamespace
from typing import Dict, List, Union
from ultralytics.yolo.utils import (DEFAULT_CFG, DEFAULT_CFG_DICT, DEFAULT_CFG_PATH, LOGGER, ROOT, USER_CONFIG_DIR,
... | /roar_yolo-9.0.0-py3-none-any.whl/ultralytics/yolo/cfg/__init__.py | 0.686055 | 0.232768 | __init__.py | pypi |
import torch
from ultralytics.yolo.engine.predictor import BasePredictor
from ultralytics.yolo.engine.results import Results
from ultralytics.yolo.utils import DEFAULT_CFG, ROOT, ops
from ultralytics.yolo.utils.plotting import Annotator, colors, save_one_box
class DetectionPredictor(BasePredictor):
def get_ann... | /roar_yolo-9.0.0-py3-none-any.whl/ultralytics/yolo/v8/detect/predict.py | 0.408159 | 0.153867 | predict.py | pypi |
from itertools import repeat
from multiprocessing.pool import ThreadPool
from pathlib import Path
import cv2
import numpy as np
import torch
import torchvision
from tqdm import tqdm
from ..utils import NUM_THREADS, TQDM_BAR_FORMAT, is_dir_writeable
from .augment import Compose, Format, Instances, LetterBox, classify... | /roar_yolo-9.0.0-py3-none-any.whl/ultralytics/yolo/data/dataset.py | 0.779616 | 0.362631 | dataset.py | pypi |
import platform
import time
from pathlib import Path
import pandas as pd
from ultralytics import YOLO
from ultralytics.yolo.engine.exporter import export_formats
from ultralytics.yolo.utils import LINUX, LOGGER, ROOT, SETTINGS
from ultralytics.yolo.utils.checks import check_yolo
from ultralytics.yolo.utils.downloads ... | /roar_yolo-9.0.0-py3-none-any.whl/ultralytics/yolo/utils/benchmarks.py | 0.464659 | 0.228608 | benchmarks.py | pypi |
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