sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
78f83ddb5c69b11e62549c24978966254ef7d44a883b7bb5e6817f9000ffaaaf | Python | 6,602 | 143 | """Ratified V2 relocation gates (C01 item 6; architecture memo 3.3).
Executed moves (each with its published closure and a shim keeping every
historical spelling + pickle-visible identity):
- ``_trace_state`` -> ``_vocab/trace_state`` (closure: 1 module, enum only)
- ``visualization/node_spec`` VOCABULARY -> ``_vocab... |
69649d1301587d2a1e6b353d6722f8e321b99fa4d49fb570a2ed5c8c6ee024b7 | Python | 6,603 | 200 | """Smoke tests for fastlog RAM, disk, and recovery storage paths."""
from __future__ import annotations
import time
from pathlib import Path
import pytest
import torch
from torch import nn
import torchlens as tl
from torchlens.fastlog import CaptureSpec
from torchlens.fastlog.exceptions import PredicateError, Recor... |
6ebe1c887007b5a349c2a1373ab668e098dc9034d2312e0c1fe8de8e66accdee | Python | 6,603 | 183 | """
test_canonical_pipeline.py — Smoke tests for the deposit.
Three tests, each fast (< 1 minute total):
1. test_build_trained_model_reproduces_paper_numbers
Runs build_trained_model.py against the bundled feature JSONs and
asserts the four paper headline numbers are within tolerance.
2. test_rank_norm... |
efed86a89b69b7aed6bb0405f1b7a48b2bf5bcbee277ef60bf291eb9d1b4302d | Python | 6,603 | 221 | import matplotlib.pyplot as plt
from itertools import combinations
import torch
import pandas as pd
import numpy as np
from utils_ensemble import (
list_of_result_to_dico,
acc_of_ensemble,
acc_of_ensemble_with_cross_val,
)
import matplotlib.patches as mpatches
import argparse
import scipy
import copy
import... |
18ba7bd323d616b03c4b8afb1e8103a01debce330175ce058090839d50b8f256 | Python | 6,605 | 199 | import os
import argparse
from tlib import ttorch
from . import config
def load_trainer(log_dir=config.log_path, deactivate_logger=False, model_init_kwargs=None, datamodule_init_kwargs=None):
trainer = ttorch.train.load_trainer(
log_dir=log_dir,
device=config.device,
deactivate_logge... |
909b88caa01e7a71d11620f7dac8db005e6fde315a520b08c0d0aa8ac045834b | Python | 6,605 | 261 | """
Test configuration and fixtures for ethoscope device tests.
This module provides common pytest fixtures and configuration for all tests
in the ethoscope device package.
"""
import os
import shutil
import tempfile
from pathlib import Path
from unittest.mock import Mock, patch
import numpy as np
import pytest
# T... |
09410bf371dbc15b13328249bda93484baa92fc79b15b1185bfd7ff511a2a2f7 | Python | 6,607 | 203 | # Author: Christian Brodbeck <christianbrodbeck@nyu.edu>
"Internet communication utilities"
from distutils.version import LooseVersion
from email.mime.multipart import MIMEMultipart
from email.mime.text import MIMEText
import keyring
from keyring.errors import KeyringError
import smtplib
import socket
import sys
import... |
4f1bac6dc5861b0f65e0adb42a34ecbaf100b63969eeb4eb48139b99e1fa9b1f | Python | 6,607 | 147 | """
Quadratic Integrate-and-Fire (QIF) Spiking Neuron Model
=======================================================
The `QIF <https://en.wikipedia.org/wiki/Quadratic_integrate_and_fire>`_ neuron model is a spiking point neuron model
that simplifies the dynamics of a neuron to the evolution of a single, dimensionless s... |
665ea278c73d2077877d22baf7792c4a1ba4fe489e538b29dc40693c355ded9e | Python | 6,607 | 242 | import locale
locale.setlocale( locale.LC_ALL, 'en_US.UTF-8' )
import cv2
import io
import math
import os
import re
import pdfplumber
import tempfile
from wand.image import Image
from wand.color import Color
from PyPDF2 import PdfFileReader, PdfFileWriter
def convert_page_to_img(pdf_fpath, img_fpath, pageno=0):
... |
b525823c7068bc013da5f4d6e895572e7ebc5d6df25daed935128b909c182ac7 | Python | 6,607 | 147 | """
Quadratic Integrate-and-Fire (QIF) Spiking Neuron Model
=======================================================
The `QIF <https://en.wikipedia.org/wiki/Quadratic_integrate_and_fire>`_ neuron model is a spiking point neuron model
that simplifies the dynamics of a neuron to the evolution of a single, dimensionless s... |
f7ca4d24f2d9b8fa417a8216c394b79b72b89f22411d0fd61ce5fb238f8accb7 | Python | 6,607 | 215 | '''
The setup of the dataframe including the splits into training, testing,
and validation dataframes.
Credit to Dr. Pau Riba & Dr. Anjan Dutta for the original MPNN code.
'''
import numpy as np
import pandas as pd
from rdkit import Chem
from collections import Counter
########### DATAFRAME PREPARATION ###########
'... |
603002cb9b3dc2f04ea2c2dabbd5ca3b03ea572cde1e40200faa5e86a9394d7a | Python | 6,608 | 141 | import sys
import os
import argparse
sys.path.append("../src")
import data_prep
import numpy as np
import matplotlib.pyplot as plt
import pandas as pd
import seaborn as sns
from matplotlib import rcParams
# Define plot aestherics.
plt.style.use('seaborn-deep')
rcParams['figure.dpi'] = 200
rcParams['savefig.dpi'] = 30... |
94b214bec33ae0034e303a2d009f690649962c133ef39411999f2ce271fa9b32 | Python | 6,609 | 190 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
import argparse
import subprocess
import sys
from collections import defaultdict
from common import Dict
def parse_args():
parser = argparse.ArgumentParser(
description="Generate ST phrase entries from regional phrase keys."
)
parser.add_argument("-... |
5e2f4262cbbc68949559fc24efc20dc9d050a94645e34b57a27fb8ad9701030e | Python | 6,610 | 210 | r"""
Test behavioral simulation of rover/sitter larvae with DEB energetics.
This script verifies that:
1. Rover/sitter models load correctly (k_X variants)
2. Behavioral simulation runs (feeding, gut, energetics integrated)
3. Feeding → gut → stepped DEB integration pipeline works
4. RvsS_on preset experiment executes... |
4a7b848172693f6fac7ad06fc16a158ae8728b3abef6c377029e98db0d2c4618 | Python | 6,611 | 135 | # !/usr/bin/env python
## created by Yun Hao @MooreLab 2021
## This script contains functions used to process sorted DTox hiearchy files and compute model statistics
## Module
import numpy as np
import pandas as pd
## This function computes the input and output size of each node module in DTox model, i.e. the numb... |
2a9757bcc0d3586027e9a892f168792e8f4a426625eb1e0e6823a4fda95fd3b6 | Python | 6,612 | 161 | """04. Testing PoseNet from image sequences with pre-trained Monodepth2 Pose models
===========================================================================
This is a quick demo of using the GluonCV Monodepth2 model for KITTI on real-world images.
Please follow the `installation guide <../../index.html#installation... |
acf14e8b1dd26ccb61517ad8afe22870f3823a9d884bdf5819d851715ba927e3 | Python | 6,612 | 127 | from ovseg.model.SegmentationModel import SegmentationModel
from ovseg.preprocessing.SegmentationPreprocessingV2 import SegmentationPreprocessingV2
from ovseg.data.SegmentationDataV2 import SegmentationDataV2
from ovseg.utils.io import save_nii_from_data_tpl, save_npy_from_data_tpl, load_pkl, read_nii, save_dcmrt_from_... |
0b6e6e2483b5dbcf006569b39aa2448fd9c6420cc8bec8f8ec1017209d9f3c0f | Python | 6,613 | 219 | import numpy as np
import scipy
import scipy.spatial
import string
import os,re
import random
import util
import gzip
to1letter = {
"ALA":'A', "ARG":'R', "ASN":'N', "ASP":'D', "CYS":'C',
"GLN":'Q', "GLU":'E', "GLY":'G', "HIS":'H', "ILE":'I',
"LEU":'L', "LYS":'K', "MET":'M', "PHE":'F', "PRO":'P',
"SER":... |
6a29636a15d165f0895c7eafbf79be0308942d8bc2f199dc783404392f614443 | Python | 6,613 | 159 | """Frozen legacy-artifact gate: pre-refactor .tlspec files must always load.
The two committed artifacts under ``goldens/`` were produced at the
pre-columnar baseline (tree ``db2bc7a5``) and are NEVER regenerated: they ARE
the old format. Every wave of the columnar re-plumbing must load them through
the (eventually on... |
edeffd6406f875878d93c0d8b7736264f0395b4596f9f89d44eadf0bb7e27610 | Python | 6,613 | 209 | import abc
import os
import typing
import warnings
import weakref
import rpy2.rinterface
import rpy2.rinterface_lib.callbacks
from rpy2.robjects import conversion
rpy2.rinterface.initr()
def _add_warn_reticulate_hook():
msg = """
WARNING: Using old versions of R package "reticulate"
within rpy2 leads to... |
b640e3749a82f28cdaee855407d8218d745936cb852df0b8c19cb663a22facb7 | Python | 6,615 | 123 | # pylint: disable=line-too-long,too-many-lines,missing-docstring
"""HMDB51 action classification dataset.
http://serre-lab.clps.brown.edu/resource/hmdb-a-large-human-motion-database/.
Code adapted from https://github.com/open-mmlab/mmaction and
https://github.com/bryanyzhu/two-stream-pytorch"""
import os
from ..video_c... |
3dada637c37050715a2d77da4d5c9bdd7c15ff3d31d8714084d5c599ec069a81 | Python | 6,616 | 189 | import os
import json
import random
import itertools
import numpy as np
import torch
from collections import defaultdict
from src.data.tokenize import tokenize_pet_txt, tokenize_pet_mlm_txt
from src.utils.util import device
class BoolQReader(object):
'''
BoolQReader reads BoolQ dataset
'''
def __init... |
7f8ac572564f3a290f662c02e02cdf4543260c1abd65f2ef983197fdab58ae44 | Python | 6,616 | 164 | """The module describes the ``core`` job metrics plugin."""
import datetime
import json
import logging
import zoneinfo
from typing import (
Any,
)
from galaxy.util import asbool
from . import (
InstrumentPlugin,
ProvidesJobMetricsContext,
)
from ..formatting import (
FormattedMetric,
JobMetricForm... |
686ccaceeb1ff65c28764628573bca563c963836f5961cd0c2bb79d307ff5de6 | Python | 6,617 | 133 | from matplotlib import pyplot as plt
import numpy as np
import h5py
import os
import time
from tqdm import tqdm
_FACTORS_IN_ORDER = ['floor_hue', 'wall_hue', 'object_hue', 'scale', 'shape', 'orientation']
_NUM_VALUES_PER_FACTOR = {'floor_hue': 10, 'wall_hue': 10, 'object_hue': 10, 'scale': 8, 'shape': 4, 'orientation'... |
0d7088f6b8ace1d5772be4431c52c9094dc02bdf0a2fb74f57305d315bd8e96a | Python | 6,618 | 182 | from typing import Callable
import torch
import torch.nn.functional as F
from torch import Tensor
from lightly.loss.msn_loss import MSNLoss
class PMSNLoss(MSNLoss):
"""Implementation of the loss function from PMSN [0] using a power law target
distribution.
- [0]: Prior Matching for Siamese Networks, 20... |
4ab9da8c022d63754fe0af14ef4a0ce9873e0ac3a3f31b696dedefe7c07da9e3 | Python | 6,618 | 147 | import os, sys, csv, re
import numpy as np
from scipy import stats
from scipy.signal import welch
import matplotlib; matplotlib.use("Agg")
import matplotlib.pyplot as plt
ROOT = os.path.dirname(os.path.abspath(__file__))
sys.path.insert(0, ROOT); sys.path.insert(0, os.path.join(ROOT, "src"))
from data_loader_01 import... |
aaf7a73696e0a287aa791916cc7839730ee0dd17c9613f4e472a96504029edfc | Python | 6,618 | 186 | """Canonical-container pooling tests for ``recurrent_ops`` and Layer ``equivalent_ops``.
``recurrent_ops`` shares ONE canonical list per recurrence group (mirroring the
``equivalent_ops`` canonical-set pooling), with a copy-on-read barrier in
``Op.__getattribute__`` so no holder can alias-corrupt the group. ``Layer``
... |
4b9b2851c0cb00271b60200f015fe3f5bfb4d8d73eced399d1f8d4efacbffa0a | Python | 6,619 | 285 | import re
from googletrans import Translator
from sentence_splitter import SentenceSplitter
def clean_text(text):
clean_text = []
text = text.strip()
lines = text.splitlines()
for line in lines:
line = line.strip()
if line:
line = re.sub('\s+', ' ', line)
clean_t... |
5a27859f9c19e20737d00bb8a53025bc77bf46e93df413fe98adbbf43399b6fc | Python | 6,621 | 170 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
from __future__ import absolute_import, division, print_function
import argparse
import numpy as np
import shlex
import subprocess
import sys
import wave
import json
from deepspeech import Model, version
from timeit import default_timer as timer
try:
from shhlex impo... |
0cef6858e010be5ae233f622972ce04d90efb0a8cc2a57eab1a80afc12e87fe2 | Python | 6,622 | 259 | import pytest
import flask
from flask.globals import app_ctx
from flask.testing import FlaskClient
def test_basic_url_generation(app):
app.config["SERVER_NAME"] = "localhost"
app.config["PREFERRED_URL_SCHEME"] = "https"
@app.route("/")
def index():
pass
with app.app_context():
r... |
771eabdabca6c7451a494894e754d4458037fe5007c1be1c4719e613e3ac7a83 | Python | 6,622 | 225 | #!/usr/bin/python
#-*-coding:utf-8-*-
# Copyright (c) 2022 PaddlePaddle Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance wi... |
76689426accb50b22cba4b8cf6f317feec4f1056992b1d7351cecfb9ff74bf81 | Python | 6,624 | 168 | #!/usr/bin/env python
import argparse
import os
from Bio import SeqIO
from Bio.Restriction import Restriction_Dictionary, RestrictionBatch
import csv
import sqlite3
import sys
import pandas as pd
def digest_genome(
genome_fp,
restriction_enzyme,
output_dir,
linear=False):
base_fp ... |
0afd96b6aaa6f879581e4cf1e3e2eb97cc490e350b8a3d9927d5ecd9e051b230 | Python | 6,625 | 182 | #Keras modules
from tensorflow.keras.layers import Conv2D, MaxPool2D, Dense, UpSampling2D
from tensorflow.keras import Sequential
from tensorflow.keras import Input
from tensorflow.keras import Model
import tensorflow as tf
import numpy as np
#File I/O
import os, glob
import glob
import tempfile, os
from tqdm import t... |
44000a5539afd48c8c9ab9606c8d5c49f349b8319aa759ea93ea39bb1ff53d25 | Python | 6,626 | 180 | """Fork serialization round-trips (pickle, tl.save/tl.load, deepcopy).
``Trace.fork()`` builds COW shells over the parent's sealed stores; detached
fallback records (modules fork detached by design) must decode BOTH internal
M14 cell encodings (``PooledCell`` pooling and compacted singleton labels)
while copying, beca... |
44fcc35633c16028dead38a06b59753d38f13bb5129284457a2f067833995692 | Python | 6,630 | 218 |
import time
import logging
import numpy as np
import pylsl
import ipdb
from libmushu.amplifier import Amplifier
logger = logging.getLogger(__name__)
logger.info('Logger started.')
class LSLAmp(Amplifier):
"""Pseudo Amplifier for lab streaming layer (lsl).
This amplifier connects to an arbitrary EEG dev... |
2dbfad1a04e89c095958915c159599c45488af552ca05a9bb937eeab60027b77 | Python | 6,631 | 198 | """Tests that `gym.register` works as expected."""
import re
from typing import Optional
import pytest
import gym
@pytest.fixture(scope="function")
def register_testing_envs():
"""Registers testing environments."""
namespace = "MyAwesomeNamespace"
versioned_name = "MyAwesomeVersionedEnv"
unversioned... |
23508f04cdb0e777818d77b2e3d2145d1c906f12518b2da31fbff81a9478a7b0 | Python | 6,632 | 121 | """
Contains tests for the public model metamers repository
"""
import unittest
import numpy as np
import torch as ch
import faulthandler
from pathlib import Path
import os
faulthandler.enable()
import imp
import importlib
import sys
import robustness
# For testing metamer generation.
from analysis_scripts import * ... |
eefdf56fc603da1f18b512b3705301bd955160c97568fcbe11514c2aefdb8185 | Python | 6,632 | 202 | """
Video Classification with Channel-Separated Convolutional Networks
ICCV 2019, https://arxiv.org/abs/1904.02811
Large-scale weakly-supervised pre-training for video action recognition
CVPR 2019, https://arxiv.org/abs/1905.00561
"""
# pylint: disable=missing-function-docstring, missing-class-docstring
import torch
im... |
15576ad64191fad11bff75c8d8501f726b444a419cc333eab8915530be95cc17 | Python | 6,633 | 160 | import argparse
import random
import re
import sys
import time
from datetime import datetime
import boto3
from botocore.compat import total_seconds
parser = argparse.ArgumentParser(formatter_class=argparse.ArgumentDefaultsHelpFormatter)
parser.add_argument('--profile', help='profile name of aws account.', type=str,... |
6ae0a9ab8a9c46093345e839a0f91ffafa45e75b919efeef30c096f77e762bc4 | Python | 6,633 | 172 | """One-backward reads: deferred-EAP plumbing (F04 items 7+9, D16).
The GradInputUseMap is fail-closed session-time plumbing: ``exact`` only for
provably-unambiguous correspondences, candidates listed but never picked
from, and the no-positional-zipping census pinned. EAP remains honestly
blocked after this build. The ... |
9e88377f1f71572eaea75a6f539f23c4a7c1569934eb5e21f333040dd4a54e29 | Python | 6,633 | 170 | # https://github.com/jianhuupenn/SpaGCN
import os
import torch
import pandas as pd
import scanpy as sc
import numpy as np
from sklearn import metrics
import multiprocessing as mp
from sklearn.metrics.cluster import adjusted_rand_score
from sklearn.metrics.cluster import (
v_measure_score, homogeneity_score, comple... |
a92f01dc4aff3ca9ccdf9fc6270ae156daaac9b00cb2f059f0dce970967a4bf8 | Python | 6,633 | 194 | """RG10/RG14-shaped extraction workflows + the v1 acknowledgment (F18 gate).
RG10 shape: extract natural-shaped images to memory AND disk, reload, and
export — direct/batch/disk activations, ids, order, counts, and hashes
agree (ResNet-18, real torchvision class, random init, zero network).
RG14 shape: multimodal proc... |
75220f3008eb3b8d54a05358953e780ad988f350c563925d66970030e9c38d4b | Python | 6,634 | 163 | """F02 ``tl.compose``: the explicit value algebra (edits memo D20-D22; row A5).
Left-to-right order against hand oracles, syntactic flattening as audit-visible
identity, non-commutativity, the construction refusal roster, one FireRecord
with ordered leaf identities, AND-combined flags, pickle round trip through the
bu... |
8542358b8cfe12c62b9413dc1ca3139ce1e5cfdfc117362c6e954bc1c89af3aa | Python | 6,634 | 107 | import os
import logging
from svim.SVIM_clustering import partition_and_cluster
def cluster_sv_signatures(sv_signatures, options):
"""Takes a list of SVSignatures and splits them up by type. The SVSignatures of each type are clustered and returned as a tuple of
(deletion_signature_clusters, insertion_signatu... |
b98fb7a029b8568fd3f5bbed9852a8d80735a1c53f303a1455b4c01d391847ed | Python | 6,634 | 123 | """Поиск жизнеспособного предка.
Синтетической проверки «стоя на еде — ешь» оказалось недостаточно: геном
может проходить её и при этом не уметь искать еду, и тогда популяция клонов
гибнет целиком. Поэтому предок обязан доказать жизнеспособность в настоящей
мини-симуляции — вырастить популяцию, а не просто выглядеть р... |
46330f0285d73db2cfe81668338c0dbd7717d6d1357ef7b8e9c45dc41a921792 | Python | 6,636 | 190 | """
The contextual property.
"""
import pickle
from collections import Counter
from multiprocessing import Pool
import tqdm
from rdkit import Chem
from grover.data.task_labels import atom_to_vocab
from grover.data.task_labels import bond_to_vocab
class TorchVocab(object):
"""
Defines the vocabulary for atom... |
5b701213900097fbca9744fc856ca1072defff2493a9fda495c02e072c973d01 | Python | 6,636 | 183 | import unittest
from unittest import mock
import responses
from codecarbon.core import electricitymaps_api
from codecarbon.core.emissions import Emissions
from codecarbon.core.units import Energy
from codecarbon.external.geography import GeoMetadata
from codecarbon.input import DataSource
class TestElectricityMapsC... |
aa55fa3b06e26f1a170a970d4e0e2728aac7d84b0c14ba02a7621da3cbe603ac | Python | 6,637 | 195 | """Fixwave-2 FW2-POLISH pins for R19-2: rank-layout cluster geometry honesty.
The b6 probe found two coupled defects in the rank path:
- pass-qualified region keys ("cell:2") were collapsed to their pass-free
address for the ``compound_bboxes`` mapping, so EVERY pass cluster received
the same last-write-wins bbox... |
9b6ac51ec3fbd435b2b84f079b7531bd91b6cfe253526751680b7c43a3f19f99 | Python | 6,638 | 176 | """R62: gate + disclose the harvested module instance-attribute channel.
``model_prep`` harvests every public, non-callable module instance attribute into
``Module.custom_attributes`` and portable saves persisted the whole channel
verbatim with no opt-out and no disclosure — tokens, private paths, usernames,
and large... |
da90bbceffd61c64f871762d3aa5a2fb7750e3db3086b29d3ac6ce1bf8d4b17d | Python | 6,638 | 148 | """this script is used to prepare COCO dataset for tracking,
which is 2017 COCO
Code adapted from https://github.com/STVIR/pysot"""
import argparse
import zipfile
import os
from concurrent import futures
import time
import json
import numpy as np
from gluoncv.utils import download, makedirs
from gluoncv.data.mscoco.uti... |
fdd8521efbff9c59b0e8a18e7d9238c0ede8bdb68f70c00f3c01a84649f9853c | Python | 6,639 | 174 | """F29: discoverability -- taught spellings resolve, refusals teach (memo 3.10).
The taught-spelling lint: every code span the surface teaches (guide
snippets, api_map rows, breadcrumbs, error remedies) resolves in a fresh
subprocess. Plus the facade repairs (tl.utils/tl.agent cold-resolve, the
did-you-mean step-5 mes... |
9baf740c1e36d69101aca5a19ad7cb909b2b6abde6736388bf709f374ac7b58b | Python | 6,642 | 180 | import logging
import time
import warnings
from typing import Union
import minknow_api.manager
from grpc import RpcError
from minknow_api.keystore_pb2 import PERSIST_ACROSS_RESTARTS
from minknow_api.keystore_service import WatchResponse
from typing_extensions import Literal
import bream4.pb.bream.hardware_check_resul... |
9ffa8ef773c2e745b8f364154e574a13f750741b00b61dcbc640a2d6fca68f8b | Python | 6,643 | 169 | """Filter functions.
"""
from typing import Optional, Sequence
import numpy as np
from anndata import AnnData
def filter_cells(
adata: AnnData,
filter_bool: Optional[np.ndarray] = None,
keep_filtered: bool = False,
min_expr_genes: int = 50,
max_expr_genes: float = np.inf,
min_area: float = 0,... |
e6ae0f285195809b97b6e9ccb922112c1a8ee9eeae3794df839026820afac3c4 | Python | 6,643 | 166 | from __future__ import print_function, division, absolute_import
"""A setuptools based setup module.
See:
https://packaging.python.org/en/latest/distributing.html
https://github.com/pypa/sampleproject
"""
# Always prefer setuptools over distutils
from setuptools import setup, find_packages
# To use a consistent encod... |
7e25296297f4d549d68d56ba3bbd23f24718c6520a7aa776c0bb53b3c4398a17 | Python | 6,644 | 188 | #coding=utf-8
import sys
import os
import argparse
try:
from lxml import etree
except ImportError:
raise ImportError('lxml library is required')
try:
from cStringIO import StringIO
except ImportError:
try:
from io import StringIO
except:
from StringIO import StringIO
try:
from sy... |
976d1fd967844358ba3330df031bb72d5311de36c96ae65459bbf8e77ebed48c | Python | 6,644 | 199 | # ---
# jupyter:
# jupytext:
# formats: ipynb,py:light
# text_representation:
# extension: .py
# format_name: light
# format_version: '1.5'
# jupytext_version: 1.14.5
# kernelspec:
# display_name: Python 3 (ipykernel)
# language: python
# name: python3
# ---
# # Convolut... |
37ff8461910be2dee94de356e89500a3a8f517f2eeef156785696c658a2ad307 | Python | 6,646 | 188 | # coding=utf-8
# Copyright 2022 The Google Research Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicab... |
10234b705652048e0dd3930414e831a10173506b37457f5c38d0c097e645af37 | Python | 6,647 | 195 | # --- THIS FILE IS AUTO-GENERATED ---
# Modifications will be overwitten the next time code generation run.
from plotly.basedatatypes import BaseTraceHierarchyType as _BaseTraceHierarchyType
import copy as _copy
class Tiling(_BaseTraceHierarchyType):
_parent_path_str = "treemap"
_path_str =... |
75f2d3f21aa1f4e0fdd9ce537e8df383ca944d215273ab23ce7beca12fd27188 | Python | 6,648 | 168 | import unittest
from spitfire import Library, Dimension
import numpy as np
from os import remove
from shutil import rmtree
from os.path import isfile
import pickle
machine_epsilon = np.finfo(float).eps
class SaveAndLoad(unittest.TestCase):
def test_save_and_load_1d(self):
file_name = 'l1test.pkl'
... |
90c890e10a4fcc56aca1ff534efc06b64081e64c4ec4689a48f389b46a3aa82b | Python | 6,648 | 127 | # -*- coding: utf-8 -*-
# Resource object code
#
# Created by: The Resource Compiler for PyQt5 (Qt v5.6.2)
#
# WARNING! All changes made in this file will be lost!
from PyQt5 import QtCore
qt_resource_data = b"\
\x00\x00\x05\x73\
\x89\
\x50\x4e\x47\x0d\x0a\x1a\x0a\x00\x00\x00\x0d\x49\x48\x44\x52\x00\
\x00\x00\x51\x0... |
ed2c177c7627f1a2364e98da22de5cb82c81c8cc0b340b7a424f415a6f85bdba | Python | 6,648 | 176 | """Functions concerning the creation of cross-validation folds.
Authors
-------
Marijn van Vliet <marijn.vanvliet@aalto.fi>
Yuan-Fang Zhao <distancejay@gmail.com>
"""
import numpy as np
from mne.utils import logger
from sklearn.model_selection import StratifiedKFold
from sklearn.preprocessing import OneHotEncoder
d... |
d0324bd06e4d286b7b2107e6085590b46d0d1b238694daf4244cc5400c933517 | Python | 6,650 | 223 | #!/usr/bin/env python
# Data manager for reference data for the SortMeRNA Galaxy tools
import argparse
import json
import os
import shutil
import subprocess
import tarfile
import requests
# Utility functions for interacting with Galaxy JSON
def read_input_json(jsonfile):
"""Read the JSON supplied from the data ... |
1f99f39166bbbfede293fc8be6d72bca88b75e83330944ef1985a5a24b921f14 | Python | 6,651 | 168 | import pathlib
import pkg_resources
import signal
import sys
import traceback
from PyQt6 import uic, QtCore, QtWidgets
import pyqtgraph as pg
from .widgets import ShowWaitCursor
from ..session import ImposeDataFileNotFoundError, ImposeSession
from .._version import version as __version__
pg.setConfigOption("backgro... |
a1f1bc5eced10fd84aa9f2136dad434f0956343e1ab12d55918153cba151d18c | Python | 6,651 | 239 | import numpy as np
import matplotlib.pyplot as plt
import random as rnd
import Code_General_utility_spikes_pickling as util
from copy import deepcopy as dcp
import scipy.ndimage as scp
from numpy import exp as exp
import matplotlib as mpl
import warnings
import logging
logging.getLogger('matplotlib.font_manager').disa... |
1df8d70b5bb9bc8621d751af5545b82e467a0cdc4c0779ebfb9f83e8cfe02b98 | Python | 6,652 | 193 | import unittest
import torch
from modular_splicing.models.modules.influence_value.tanh_attention.tanh_convolved_attn import (
compute_unnormalized_attn_within_window,
)
def compute_attn_directly(q, k, v, *, ocpe=None, zero_value, activation, window):
"""
See compute_unnormalized_attn_within_window for do... |
53e3c8633a38c4c72e2cd7769cae15c91c23413d30d13e286bfa6d77fded6b72 | Python | 6,652 | 176 | # !/usr/bin/env python3
# Copyright (c) 2020 PaddlePaddle Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
... |
a51828edc2f7a575be9cb65e7f464992c96e8e7ca358e029a8d7508073af869b | Python | 6,652 | 146 | from typing import Optional, Union
import numpy as np
import pandas as pd
import pyvista as pv
import vtk
from anndata import AnnData
from numpy import ndarray
from ...logging import logger_manager as lm
try:
from typing import Literal
except ImportError:
from typing_extensions import Literal
def vtk_inter... |
7db18f10f6e0b7816d60368dbc0c411add0439bbc77548a7ce1b20cef97a1bc4 | Python | 6,653 | 157 | # SOURCE: vendored from Singingkettle/ChangShuoRadioRecognition @ main
# https://raw.githubusercontent.com/Singingkettle/ChangShuoRadioRecognition/main/csrr/models/backbones/cldnn.py
#
# CLDNN for Automatic Modulation Classification (AMC): a CNN+LSTM+DNN backbone that
# classifies raw I/Q radio frames -- stacked Conv2d... |
8ef5d674d747d1488ffb7bd99e068494f1bde997fe3c6d4d89243d5678eb9425 | Python | 6,654 | 190 | import math
import random
from PIL import Image
import blobfile as bf
from mpi4py import MPI
import numpy as np
from torch.utils.data import DataLoader, Dataset
import glob
import os
def load_encoded_feature(feature_dir, target_layer):
files = glob.glob(os.path.join(feature_dir, f'{target_layer}*.npy'))
num... |
5eee063602be8ce17b8e719d552ff5d44114c95d497e3426484dcc8812e87dbd | Python | 6,655 | 172 | # Run test with:
# torchrun --no_python --nproc_per_node=8 pytest -q -s tests/models/test_gpt_generation_parallel.py -k "parallel"
import os
import re
import pytest
import torch
from einops import rearrange
from flash_attn.models.gpt import GPTLMHeadModel, remap_state_dict_hf_gpt2
from flash_attn.utils.distributed imp... |
22f2cfffd2601a709afc6285d1baf7490e11fc15f7ad93a35a0567409109dc37 | Python | 6,658 | 197 | # General functions for multi-coil radial sampling MRI
# Apr-12-2021==Zhao He==Original code
# May-11-2021==Zhao He==Add MCNUFFT function
# May-16-2021==Zhao He==Add crop function for 3-dimension data
# May-17-2021==Zhao He==Revise MCNUFFT function
# Jun-20-2021==Zhao He==Add comments
import os
os.environ['KMP... |
d582225406a25362b1170a1f6cba70e91a6d430a7891bcd73adadf5b189bfa0c | Python | 6,658 | 176 | import numpy as np
import tensorflow as tf
import sys
import os
from keras import layers, backend
sys.path.append("../utils")
from func_model import extraData, apply_rev_comp, train, evaluate
os.environ['TF_CPP_MIN_LOG_LEVEL'] = '2'
# tf.config.threading.set_intra_op_parallelism_threads(5)
tf.config.threading.set_inte... |
fbeff85641e14501b5e83177c8a4df61c62db1b29c5aef9a12871930a24f6b92 | Python | 6,658 | 170 | """The README first-screen subprocess golden gate (F17 B16; memo D15/D16).
The block a newcomer actually copies (the FIRST ```python fence in
README.md) runs in a fresh subprocess with every warning recorded, twice:
- ZERO warnings (deprecations included) -- the gate that guards the first
screen forever;
- the two ... |
af6e134a80a6154ee21a5ae520a50dea359ba870b6d6d919db6bf1d187e17a02 | Python | 6,659 | 163 | # Written by Seonwoo Min, Seoul National University (mswzeus@gmail.com)
# Some parts of the code were referenced from or inspired by below
# - Dong-Hyun Lee's code (https://github.com/dhlee347/pytorchic-bert)
# PLUS functions
""" Optimizer functions for PLUS-TFM pre-training """
import math
import torch
from torch.op... |
43c9c01aa107c779077dfe3250c27d74d360f7cfbc769b6409f73d996773fc06 | Python | 6,660 | 191 | # -----------------------------------------------------------------------------
# Copyright (c) 2013, The Deblur Development Team.
#
# Distributed under the terms of the BSD 3-clause License.
#
# The full license is in the file LICENSE, distributed with this software.
# -------------------------------------------------... |
336832a6afd3930848de4a421db1073b79fd21045fe100f757e5618edca7d539 | Python | 6,661 | 148 | # Ultralytics 🚀 AGPL-3.0 License - https://ultralytics.com/license
from __future__ import annotations
from typing import Any
import numpy as np
from ultralytics.solutions.solutions import BaseSolution, SolutionAnnotator, SolutionResults
from ultralytics.utils.plotting import colors
class RegionCounter(BaseSoluti... |
3623108ee405f7b2d9d284df8148fe73ef4c5b95fd84e11880f187c6ba307e4e | Python | 6,661 | 173 | import torch
import json
from collections import Counter
from omop_learn.data.common import ConceptTokenizer
from omop_learn.utils.date_utils import to_unixtime
class OMOPDatasetTorch(torch.utils.data.Dataset):
def __init__(
self,
omop_dataset,
tokenize_on_load=False,
max_num_visi... |
3b1989cdf9a356820c1ad0fa670d7fbc9ef636d99997b33b8a875e283d855a38 | Python | 6,664 | 230 | """
Copyright (c) 2022 EPFL-BBP, All rights reserved.
THIS SOFTWARE IS PROVIDED BY THE BLUE BRAIN PROJECT ``AS IS''
AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE BLUE BRAIN PROJE... |
9d4994d77852bb190beb4a0ea0dcc257d9777d49cfdbb38e1fa1ee321a417e39 | Python | 6,666 | 195 | from __future__ import annotations
import pytest
from larvaworld.lib import util
from larvaworld.portal.canvas_widgets.environment_mapping import (
env_params_to_canvas_state,
)
def test_env_params_to_canvas_state_maps_static_environment_layers() -> None:
env_params = util.AttrDict(
{
"a... |
03efd039fb3cd6433adcbb220496c023325cc4843f0ff52aa6be99062f0464db | Python | 6,667 | 153 | import unittest
import numpy as np
from larvaworld.lib import util
def test_rotationMatrix():
# Test 1: Check if rotation by 0 radians returns the identity matrix
result = util.rotationMatrix(0)
expected = np.array([[1, 0], [0, 1]])
np.testing.assert_array_almost_equal(result, expected)
# Test ... |
d2b2ea1be5ff506d9bcd0acd2957a934e86821adcf99b0be3febff07aec23147 | Python | 6,667 | 108 | #!/usr/bin/env python3
import os,sys,math,pickle
from lefse.lefse import *
def read_params(args):
parser = argparse.ArgumentParser(description='LEfSe 1.1.01')
parser.add_argument('input_file', metavar='INPUT_FILE', type=str, help="the input file")
parser.add_argument('output_file', metavar='OUTPUT_FILE', ... |
71193eddd8a977d6738635efc467fd77cf9fbc23d49e0c2f7e7e7e408680c92f | Python | 6,668 | 208 | """Interop helpers between seqpro _core.Ragged buffers and awkward-array layouts.
These functions are used by _ingest.py's ``layout_from_ak`` / ``to_ak`` paths to
convert between awkward's Content tree and the flat (data, offsets, shape) buffer
representation used by _core.Ragged. Awkward remains a seqpro interop/tes... |
e74f04479bf2f9167cc2ab6d74923d5017dcf119fd1e739cb9788a6a0e5ea012 | Python | 6,668 | 191 | from contextlib import contextmanager
from typing import Any, Dict, Optional, Sequence, Tuple, Union
import torch
from pytorch_lightning import Callback, LightningModule, Trainer
from pytorch_lightning.utilities import rank_zero_warn
from torch import Tensor, nn
from torch.nn import functional as F
from torch.optim im... |
1e12821cf8836314661827508c4b74f1291d7d10782aac95246a42a8ec3a3d62 | Python | 6,669 | 199 | import io
import os
import av
from torch.utils.data import Dataset as TorchDataset, WeightedRandomSampler
import torch
import numpy as np
import h5py
from datasets.helpers.audiodatasets import PreprocessDataset, get_roll_func
# specify OpenMic location in 'dataset_dir'
# 2 files have to be located there:
# - openmic_... |
525ac11ed52cce1246ef94719918baf011d77a8c71ccb85560214225bbc0438e | Python | 6,673 | 151 | #!/usr/bin/env python3
"""
Dx AN — random K-channel sweep (figshare cohort).
Question: how much does which-K-channels-are-kept matter? The Dx AM
result on the 4-channel Muse-like configuration (Fp1, Fp2, O1, O2)
gave AUC 0.944, and the 8-channel border-only configuration gave AUC
0.934 — counter-intuitively worse. To ... |
54aaa8c765c704855173cd4aa5c8f1eb3274c94881c903a9994a11ac9e1d8444 | Python | 6,673 | 196 | model = dict(
type='RetinaNet',
backbone=dict(
type='ResNet',
depth=50,
num_stages=4,
out_indices=(0, 1, 2, 3),
frozen_stages=0,
norm_cfg=dict(type='SyncBN', requires_grad=True),
norm_eval=False,
style='pytorch',
init_cfg=None),
neck=di... |
f09889cdb32e5d7f6cee4d7402b88f4379aaa5faea0bad77cdd21e5891b8a9f6 | Python | 6,676 | 167 | # %%
import os
import os, sys
from config import *
sys.path.append(where_am_i())
import wandb
import cv2
from skimage.metrics import structural_similarity as ssim
from models.models_system import MoDLReconstructor, UNetReconstructor
from models import alternating as altmodels
from pathlib import Path
import numpy as... |
268a3ee010ca0f90fcef07b425760c9385aebd3b67b852f31532b0c7d83e885d | Python | 6,678 | 187 | import os
import json
import random
import numpy as np
import itertools
import torch
from collections import defaultdict
from src.data.tokenize import tokenize_pet_txt, tokenize_pet_mlm_txt
from src.utils.util import device
class CBReader(object):
'''
CBReader reads BoolQ dataset
'''
def __init__(se... |
114d882043026b4cd761daaca5ad8cae6795ae3708e9f7298398fa63af9f6c68 | Python | 6,680 | 164 | import copy
import warnings
from xml.etree.ElementTree import Element
from xml.etree import ElementTree as ElemTree
from mirp.settings.generic import SettingsClass
from mirp.settings.transformation_parameters import get_image_transformation_settings
from mirp.settings.feature_parameters import get_feature_extraction_s... |
48bac771effd0592b85d0ac1f32b63fd19267eaa685897cdc15f5936daa80886 | Python | 6,680 | 174 | '''
Testing functionalities of dataloading_utilities
author: obanmarcos
'''
import os
import os, sys
sys.path.append('/home/obanmarcos/Balseiro/DeepOPT/')
import argparse
import numpy as np
import matplotlib.pyplot as plt
import pandas as pd
from utilities import dataloading_utilities as dlutils
from utilities.folde... |
60d8a069409118a95835455d40ab6fda4840292e31980b73dadb422a40f04494 | Python | 6,680 | 121 | """
constraint utils
"""
import os
import paddle
import numpy as np
import logging
from typing import Union
from helixfold.data.utils import token_completion, dist_to_bins, get_bin_masks
logger = logging.getLogger(__file__)
def get_constraint_info(feat,
all_chain_ids, chain_ids,
... |
96db9e38c78750c35154ee68f8536dd13a7d02f1edd970af1956887e18f70df2 | Python | 6,680 | 184 | # Copyright (c) 2021 PaddlePaddle Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by app... |
4c6add2b5a42b90d6e34e4951c52bba64029c3ed79de4b00fc4b7e780a81b5ad | Python | 6,683 | 204 | import csv
import numpy as np
import seaborn as sns
import matplotlib as mpl
import matplotlib.pylab as plt
OUT_CSV_hetero="CSV\heterotrimer\ALL_{}.csv"
OUT_CSV_homo="CSV\homotrimer\ALL_{}.csv"
Types=('HB','PHOB','PI','SB','STK')
D_hetero={} #Dictionary for data saving
for l in Types:
with open... |
dced07f5c11bb83f13f4aab218e97f28c7a853afeefa0cda4d7e4cd0f0ef8a9f | Python | 6,683 | 160 | """CAPI loss.
- [0]: CAPI: Cluster and Predict Latent Patches for Improved Masked Image Modeling, 2025, https://arxiv.org/abs/2502.08769
- [1]: https://github.com/facebookresearch/capi
"""
from __future__ import annotations
import torch
import torch.distributed as dist
import torch.nn.functional as F
from torch impo... |
205b560cbbe306550072f178a1c899423d9c9bfa8dbdf1be310300c2e13c397a | Python | 6,684 | 186 | import numpy as np
import pytest
from neurogym.envs.native.contextdecisionmaking import ContextDecisionMaking
@pytest.fixture
def default_env():
"""Create a default ContextDecisionMaking environment."""
return ContextDecisionMaking()
@pytest.mark.parametrize("use_expl_context", [True, False])
def test_env_... |
4aaff233cf0eaa75973ca1c232026cf6aa8cbba3918d58b5fb13f50ece91ffd3 | Python | 6,684 | 161 | """Lane W051-HONESTY: default-config HuggingFace causal LM on live ``run()`` (AUD-HONESTY H1).
The only pinned HF runnable test builds GPT-2 with ``use_cache=False`` AND captures
with ``intervention_ready=True`` -- the configuration every user actually has (KV cache
on, default capture) was never exercised by a ``run(... |
dde8769562aeed580389abfdccd5862d8547f642ff1ece5954ddba0ee678ac11 | Python | 6,684 | 135 | """Utils for Faster RCNN estimator"""
import os
from mxnet import gluon
from ....data.batchify import FasterRCNNTrainBatchify, Tuple, Append
from ....data.sampler import SplitSortedBucketSampler
from ....data.transforms.presets.rcnn import FasterRCNNDefaultValTransform
from .... import data as gdata
from ....utils.me... |
063f8054d5ef2991cadc639efec8282b250dfb4b20c10ad8a1d69deace085edc | Python | 6,686 | 176 | """repeng bridge against the real package on a tiny cached Llama.
Each test compares ``tl.bridge.repeng.control_vector`` on saved activations with
``repeng.ControlVector.train`` run directly on the same model. Skips when repeng,
transformers, or the checkpoint is unavailable.
"""
from __future__ import annotations
i... |
f7db2f7be56dd21ea6d6241808404afa0d92e4665e83e0f0ec8872e5b6791768 | Python | 6,689 | 128 | import torch
from .base_model import BaseModel
from . import networks
class Pix2PixModel(BaseModel):
""" This class implements the pix2pix model, for learning a mapping from input images to output images given paired data.
The model training requires '--dataset_mode aligned' dataset.
By default, it uses ... |
b2eedcdff9037714c8780cebf8467d8171de561a7caf0ba43b8048afce96b31d | Python | 6,690 | 170 | #%%
import os
import os, sys
from config import *
sys.path.append(where_am_i())
import wandb
import cv2
from skimage.metrics import structural_similarity as ssim
from models.models_system import MoDLReconstructor, UNetReconstructor
from models import alternating as altmodels
from pathlib import Path
import numpy as ... |
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