sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
47f4abf56e2e75b129d20b1a3c0eb7e711e3d0328493237ad95cee1767c653bb | Python | 4,745 | 163 | # --- 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 Number(_BaseTraceHierarchyType):
_parent_path_str = "indicator"
_path_str... |
b419c265fcc514fd9864b9ab8f0579653d41da5c5dced567e4ea0bac42b014a3 | Python | 4,745 | 82 | import torch
#import opt_einsum as oe
class Neigh_List(torch.nn.Module):
def __init__(self,cutoff:float,nlinked:int):
# nliked used for the periodic boundary condition in cell linked list
super(Neigh_List,self).__init__()
self.cutoff=cutoff
self.cell_list=self.cutoff/nlinked
... |
eac8c8c12a77f993159525b2edb8268ef92ea3a1add0b825d82e3d4f2e5c8ff1 | Python | 4,745 | 99 | """Regression guards for the torch-2.13 arg-spec capture-gap fix (R18CG).
Two related findings surfaced while reconciling ``tests/test_arg_spec_coverage.py`` against
torch 2.13:
* ``torch.align_as`` (the named-tensor ``Tensor.align_as`` method) was REMOVED in torch 2.13. It
is therefore version-varying: still decor... |
f0a01cd0b697d5826ffca47c6c0ac6843a86ec28c7c9743736bc9eb7f6fc1d00 | Python | 4,745 | 140 | #!/usr/bin/env python
"""
Utilities to convert sleepsign output files.
"""
import numpy as np
from somnotate._utils import convert_state_vector_to_state_intervals
from data_io import (
ArgumentParser,
load_dataframe,
check_dataframe,
export_hypnogram,
)
SLEEPSIGN_KEY = dict([
('w' , 'awake... |
5b324c6632184b34818cd835d335800e49b95dce3f867ab4fe22b69fe5962df6 | Python | 4,746 | 126 | import unittest
from unittest.mock import patch
from carbontracker.components.apple_silicon.powermetrics import (
AppleSiliconCPU,
AppleSiliconGPU,
PowerMetricsUnified,
)
class TestAppleSiliconCPU(unittest.TestCase):
def setUp(self):
self.cpu_handler = AppleSiliconCPU(pids=[], devices_by_pid=F... |
b7fcce72f56a64348838627ed8256ac232eac32416be5e04fa0456b93c3df73d | Python | 4,746 | 135 | """Backend trace-option honesty checks."""
from __future__ import annotations
from typing import Any
import pytest
from torchlens.backends import BackendSpec, BackendUnsupportedError, registered_backend_specs
from torchlens.backends._options import (
JAX_PREVIEW_TRACE_OPTION_POLICY,
MLX_PREVIEW_TRACE_OPTION... |
d321d2f1b9804a53759eb6e944d9f53deb7fa2ba70b99307235519e399fa1d9a | Python | 4,747 | 130 | """ArgSpec lookup table coverage test and usage report generation.
This test runs LAST (via pytest_collection_modifyitems in conftest.py) so it
can inspect the accumulated _function_call_counts from all other tests.
"""
import csv
import os
from os.path import join as opj
import pytest
from torchlens import _state
... |
aaf62439bd1440300122a61f55cecc049f7b1d60825457eb0b4c83b64eb3decd | Python | 4,748 | 142 | import tensorflow as tf
from tensorflow import keras
from tensorflow.keras import layers
import numpy as np
class Capsule_Mul(layers.Layer):
def __init__(self, num_classes):
super(Capsule_Mul, self).__init__()
self.num_classes = num_classes
def build(self, input_shape):
# -*... |
307a1a011c2cbd539263a636bb22bb838111dc2233e269d4542afae6c14dc988 | Python | 4,750 | 125 | #!/usr/bin/python
###########################################################
# eQTL file has to follow the following structure and tabixable
# chr pos A1 A2 tested-allele statistics P FDR/corrected P
#
# A1/A2 are in arbitrary order
# If alleles are provided but tested allele is not specified,
# teste-allele column ... |
77af5179fa915f87bd46574f9cb3e02c5b4bb06e592610d9eda839ed8c1c9e1d | Python | 4,750 | 110 | import sys
# setting path
sys.path.append('../TM2_segmentation')
import os
import SimpleITK as sitk
import numpy as np
import functools
from skimage.transform import resize
import nibabel as nib
import numpy as np
import pandas as pd
from scripts.preprocess_utils import load_nii,find_file_in_path
# helper function... |
3cb29893a60d8ff2f7c7110fb30784941b89ef4bfd1ea87156a93548a696f665 | Python | 4,751 | 145 | import os
from importlib import import_module
import matplotlib
matplotlib.use('Agg')
import matplotlib.pyplot as plt
import numpy as np
import torch
import torch.nn as nn
import torch.nn.functional as F
class Loss(nn.modules.loss._Loss):
def __init__(self, args, ckp):
super(Loss, self).__init__()
... |
9e7117c3dc5aebba9662a043c0c41c4d04a700906dcbe212b6894701bcb5b9de | Python | 4,751 | 80 | # Generated by Django 3.2.6 on 2022-05-18 16:06
import biomedisa_app.models
from django.conf import settings
from django.db import migrations, models
import django.db.models.deletion
class Migration(migrations.Migration):
dependencies = [
migrations.swappable_dependency(settings.AUTH_USER_MODEL),
... |
b836dbf368d42f7769a761ab4c46bca32f791e9fd17f83050cf74c79414ee993 | Python | 4,755 | 111 | """Блок B: валидация движка чужим предсказанием (Requejo & Camacho, 1312.3450).
Аналитическое предсказание: при изобилии ресурса популяция однородно
предательская, при падении ресурса ниже порога выживают безусловные
кооператоры — у агентов БЕЗ памяти и БЕЗ узнавания (recognition=False).
Ищем РЕЗКИЙ переход доли коопе... |
d1437f84e8bd8870f6c3456b2dc9e5c689f48900e8be92419d2e5f187a51f88b | Python | 4,755 | 150 | #!/usr/bin/env python3
'''Read a line formated like a spearmint results.dat line,
construct the corresponding model, run the model with cross validation,
and print the results; dies with error if parameters are invalid'''
import sys,os
def get_script_path():
return os.path.dirname(os.path.realpath(sys.argv[0]))
... |
4bb2318ada21a2921e9bf8869135bdcf6a2997a6efd43749a880a25a1af6605b | Python | 4,756 | 144 | #!/usr/bin/env python
__author__ = "Bjoern Gruening"
__version__ = "0.1"
__date__ = "2012"
__license__ = "GLP3+"
import argparse
import os
import sys
from multiprocessing import Pool
import cheminfolib
import GenericMoleculeDB
import pybel
from GenericMoleculeDB import build_database, create_indices
from sqlalchemy.... |
6292f8cdb5c8469102785827c52590084fb1241884ba7dba752cf78dacc7a315 | Python | 4,756 | 116 | """Revoked ids received from another worker, on mingle or through ``hello``.
They are stamped with the receiving worker's own clock, whatever stamps
they come with (#4300): a set filled with stamps ahead of the local clock
would otherwise purge every id revoked from then on the moment it is
added, and the task would r... |
c3edc421052db8d24b4b66005d6b4c8513f62c14d5709bd73e0fc5650869fd63 | Python | 4,756 | 123 | """The SG-regression manifest gate (compo memo stratum 3; F36 waves A-D).
"No SG number without a node": all fifty DIGEST-AUDIT section-1 silent gaps
are enumerated in ``data/sg_manifest.tsv``. Regression-node rows must name a
test node that EXISTS on disk (file, or file::test verified against source);
ledgered-open r... |
f87567c2b15bbbd0d6568c116cc2e04e5b115a72e45491f75f48b40a1c941a73 | Python | 4,756 | 104 | #The related files involved in tutorials are available at: http://www.cellgo.world
from CellGO import Modeling
import pandas as pd
import numpy as np
import scanpy as sc
#####Step1 Importing the single-cell expression matrix and the cell identity list
GeneExpMatrix=sc.read('Example_ExpressionMatrix.csv.gz')
CellType=l... |
b24281be8085f1edce2d6a05ad1499054b8612082793e8b002a14897dc550ccf | Python | 4,758 | 152 | # 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
#
# Unless required by app... |
65289869cfb5e500d7593b50f11819e6598c7032897d1199f2e4a9a9c16f3aa5 | Python | 4,759 | 128 | import os
from pathlib import Path
from pydantic import Field, field_validator
from pydantic_settings import (
BaseSettings,
PydanticBaseSettingsSource,
TomlConfigSettingsSource,
)
from neurogym.config.base import CONFIG_DIR, LOCAL_DIR, PKG_DIR, ROOT_DIR, ConfigBase
from neurogym.config.components.agent i... |
92f492eec1a9d54b2bf15cce44db19529d734a0643fb7c30ba37105334c37e97 | Python | 4,759 | 144 | """Premature stop codon, frameshift"""
import logging
import os.path
from math import floor
import re
from Bio import SeqIO
from .GeneCutter import submit_GC, process_GC
# pylint: disable=C0103
# Invalid constant name
logger = logging.getLogger('pipe.psc')
def psc(configs, seqs):
"""Premature stop codon"""
... |
d6e271bebf6ca2a67ed590b45071d697211ca40e8f95f5fe2c5ef5eb50a10660 | Python | 4,759 | 100 | #==============================================================================#
# Author: Dominik Müller #
# Copyright: 2024 IT-Infrastructure for Translational Medical Research, #
# University of Augsburg ... |
ed54487d4a28d0ee3870bf87d1abdda4a260d79fabf1da5303b9f32c49e79d3a | Python | 4,760 | 156 | import numpy as np
import cv2
from xml.dom.minidom import parse
import re
from math import pow, sqrt, floor
from PIL import Image
import torchvision
from torchvision.models.detection.faster_rcnn import FastRCNNPredictor
from typing import List, Tuple, Dict, Optional
from torch import nn, Tensor
from torchvision.transfo... |
f4fb975cb9cf948e6ebd6a5c4aa3aff1201866805863f76c0827514d77f55dc9 | Python | 4,760 | 148 | from __future__ import annotations
import collections
import time
from typing import TYPE_CHECKING
from typing import Final
import numpy as np
from loguru import logger
from numpy.typing import NDArray
if TYPE_CHECKING:
import osam
def _elapsed_ms(*, t_start: float) -> float:
return (time.perf_counter() - ... |
f8aaa6dec9b485c1bbd75c5eaae7649c969866d892fc19cd19ffc1aee98d4abf | Python | 4,760 | 135 | """IO functions for SeqScope technology.
"""
import os
from typing import Optional
import numpy as np
import pandas as pd
import scipy.io
from anndata import AnnData
from scipy.sparse import coo_matrix
try:
from typing import Literal
except ImportError:
from typing_extensions import Literal
from ..configurat... |
545f1dbfe612b0f8b41766d5cbb13e9cae229b1ea0e18ccf33e45fd629fdb2a0 | Python | 4,761 | 187 | """Load the classics corpus manifest and build its vendored models.
The corpus is a coverage-chosen sample of hand-built, trace-verified "classics"
(historical and unusual architectures written directly in PyTorch). Each model
file under ``models/`` is vendored byte-identical to its source and pinned by
sha256 in ``ma... |
ab7c34434600eaff2867310ccd97ebacc56dc5c4d4f184e5e3a0b4078b67e109 | Python | 4,761 | 155 | """
All classes supporting objects, agents and environment of the agent-based-modeling
simulations, as well as the modules comprising the layered behavioral architecture
modeling the nervous system, body and metabolism.
"""
from __future__ import annotations
from typing import Any
__displayname__ = "Modeling"
# Pro... |
e19d2e2004ff01adef73690542a4bde3e137a0295ea4c045e5f5b6a4b40c2049 | Python | 4,761 | 88 | #==============================================================================#
# Author: Dominik Müller #
# Copyright: 2024 IT-Infrastructure for Translational Medical Research, #
# University of Augsburg ... |
e55eb8d90b7f71fc410be27ec072b273707e6746af8d5493e0b938299aa1ee61 | Python | 4,761 | 135 | """Smoke tests for the RPC result backend.
Regression coverage for https://github.com/celery/celery/issues/4830:
polling the RPC backend for a completed task used to requeue the final
result message instead of acking it, so final results recirculated on
the reply queue on every state poll. These tests run against a re... |
df897830f137d4a0bc08e955d881e834eb4574a27f06c6fb360052ec5aa452a0 | Python | 4,762 | 128 | """Example template for contributing new tasks.""" # noqa: INP001
import numpy as np
from neurogym import spaces
from neurogym.core import TrialEnv
class YourTask(TrialEnv):
def __init__(self, dt=100, rewards=None, timing=None, sigma=1) -> None:
super().__init__(dt=dt)
# Possible decisions at t... |
b393619e6948a2918092b27456359d173b1225728646ef97b2fe5e2323d46eba | Python | 4,763 | 136 | from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
from __future__ import unicode_literals
import numpy as np
import tensorflow as tf
import pandas as pd
import argparse
import os
import sys
import pwd
import pdb
import csv
import re
import math
import time
de... |
36ffb9d473e34735a13aa7c451b8d492b87547fc0442cab7e57068bb91f7d074 | Python | 4,764 | 157 | #!/usr/bin/env python
# encoding: utf-8
from __future__ import (absolute_import, division,
print_function, unicode_literals)
import os, sys, re
import logging
import argparse
import collections
logging.basicConfig(stream=sys.stderr, level=logging.INFO)
logger = logging.getLogger(__file__)
de... |
cc150b60344b762cfcf5ab1dd110e0cbf876eae75b8dec3f1bcd13fd926bfe26 | Python | 4,764 | 149 | import pytest
from pyrosm import get_data
@pytest.fixture
def helsinki_pbf():
pbf_path = get_data("helsinki_pbf")
return pbf_path
@pytest.fixture
def helsinki_region_pbf():
pbf_path = get_data("helsinki_region_pbf")
return pbf_path
REQUIRED_COLUMNS = [
"name",
"admin_level",
"boundary"... |
86459a422f3653e49c64c0ad3f6f611d5bb0d0eb7d66c2d8f604bf6b0ffccdec | Python | 4,765 | 138 | from ._RL_agent import *
from numba import njit
@njit
def latent_state_rewasym_session_value(choices, second_steps, outcomes, n_trials, transition_type, params):
# Unpack parameters.
p_r, weight_inf = params[:2]
rew_good = 0.4
rew_bad = 0.1
non_rew = 0.5
V_s = np.zeros((n_trials, 2)) # Second step TD v... |
58d1606beb93f6563e5112b9108cdeffda42657efe9918b7a6c2d3006a479d74 | Python | 4,766 | 88 | #==============================================================================#
# Author: Dominik Müller #
# Copyright: 2022 IT-Infrastructure for Translational Medical Research, #
# University of Augsburg ... |
adf824d542a1fc3f736d68ad7dbf62a5634cb0c633fcebd95d5d6a29737e18b8 | Python | 4,766 | 88 | #==============================================================================#
# Author: Dominik Müller #
# Copyright: 2022 IT-Infrastructure for Translational Medical Research, #
# University of Augsburg ... |
6261b34fcf691d190ba5a714953df37dc279d0fc1b18d7e20332ac9283e17fb6 | Python | 4,768 | 152 | import click
from dataclasses import dataclass
import logging
import multiprocessing
import os
from pathlib import Path
import re
from regression_data import EXPECTED_OUTPUT
import shutil
from subprocess import PIPE, Popen, TimeoutExpired
import sys
import time
logging.basicConfig()
logging.getLogger().setLevel(loggin... |
68141c643c9a05e1d974d3ac86f723dde114311531289d6be1d90ab0cae34f00 | Python | 4,769 | 162 | #!/usr/bin/env python
"""
Modified version of code examples from the chemfp project.
http://code.google.com/p/chem-fingerprints/
Thanks to Andrew Dalke of Andrew Dalke Scientific!
"""
import argparse
import os
import subprocess
import sys
import tempfile
import chemfp
from chemfp import search
def unix_... |
16d2669bcc9ce8f71de163aee9a052e5eb34728461ae12727168ee7fa88e8ff8 | Python | 4,770 | 88 | #==============================================================================#
# Author: Dominik Müller #
# Copyright: 2022 IT-Infrastructure for Translational Medical Research, #
# University of Augsburg ... |
23df75150e74815621a99b36f63b9accadbb92c5c232ff749eec23e9193bb4ea | Python | 4,770 | 144 | #!/usr/bin/env python3
from GNNSubNet import GNNSubNet as gnn
import ensemble_gnn as egnn
import copy
import random
import time
from sklearn.metrics import balanced_accuracy_score
from sklearn.metrics import accuracy_score
from sklearn.metrics import matthews_corrcoef
RANDOM_SEED: int = 23215600
# location of the ... |
048bf58d887cd80adc848b43ab02c5939276be227b4bdfbd2ea0f3c5f348b1de | Python | 4,771 | 88 | #==============================================================================#
# Author: Dominik Müller #
# Copyright: 2022 IT-Infrastructure for Translational Medical Research, #
# University of Augsburg ... |
d6347f25f19638a32b3e91cb72da1096ce1fd13d619463c1560cc38a4ba8f45c | Python | 4,771 | 150 | # 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 with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by app... |
a6ecc8e0aafebee31784b6c8672da6431e37ab7e4988a9d2f5e36ab890d9bb93 | Python | 4,773 | 148 | # copyright (c) 2021 PaddlePaddle Authors. All Rights Reserve.
#
# 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 applica... |
b1eed0f461d8869e21abd8bfe12b58f7f13d772384bba52a1c0ce3cb8079513d | Python | 4,773 | 135 | """Offline coverage of the Geofabrik / BBBike data-source accessors (#272).
These walk the static source tables shipped with the package (no network I/O)
and assert every region/city resolves to a real ``*.osm.pbf`` URL, exercising the
per-region ``__getattr__`` / ``__call__`` accessors on every source class.
"""
imp... |
2f66fab93f025e624f29596c0a6b76c062453812dc3204cf91f695f40797699b | Python | 4,774 | 168 | import abc
import pathlib
from typing import Optional, Sequence, Union
from dm_control import mjcf
class _Entity(abc.ABC):
def __init__(self,
root: mjcf.RootElement,
name: str,
position: Optional[Sequence[float]] = (0, 0, 0),
rotation: Optional... |
dd833f6a3efed5dbb9644ca96eed891caf71d68647a3a3f1b54b5859507663c3 | Python | 4,774 | 134 | """F02 backend refusal matrix (edits memo D36; row A6, structural half).
The stochastic/population family executes on torch only. Construction, repr,
equality, and pickle identity work backend-free; EXECUTION on a preview
backend refuses at that backend's helper-resolution preflight, because the
adapters resolve built... |
de553b5d5ddf79275e6b92a35ac8d356514194986c78ef40681977e24ea9c77c | Python | 4,774 | 131 | """Define common base objects."""
from copy import deepcopy
from specparam.utils.checks import check_array_dim
from specparam.modes.modes import Modes
from specparam.reports.strings import gen_issue_str
###################################################################################################
##############... |
2e27b1c94d2e99707a5cb3445d9c6da419876f73ff909cd783a50b427fefe435 | Python | 4,776 | 111 | # SPDX-License-Identifier: LGPL-2.1-or-later
#!/usr/bin/env python
#-*- coding: utf-8 -*-
import os
import numpy as np
from collections import OrderedDict
from .utils import general as utils
from .write_to_file import write_registrations_stats
from .plotting_functions import single_timeline_heat_map
def get_single_a... |
374db6209d70269407ef05a8d2538a02cb718a67c1072401bedbc8c7975762c5 | Python | 4,776 | 165 | """Runtime handle accessors for live Torch objects."""
from __future__ import annotations
import gc
import weakref
from pathlib import Path
from typing import Any
import torch
from torch import nn
import torchlens as tl
class _HandleModel(nn.Module):
"""Small module with params, buffers, submodules, and autog... |
455e24f208ab31d5915c9c25a2e43b4a859a1cd539d57052164937c084e98b07 | Python | 4,776 | 117 | """Utilities shared by the built-in datasets."""
import io
import pickle
import zipfile
import numpy as np
# A dataset npz member is rejected as a decompression bomb when its declared
# size is above this floor and far larger than the bytes stored on disk. Genuine
# dataset members store real data and should not app... |
b0dd159ad1d0c661157eeeee12559d52dfc30a891c496886b2ae63ee03194396 | Python | 4,776 | 117 | """The per-symbol realism registry + PR closure gate (memo D5/E1; F36).
Every live public symbol needs realism-graded test evidence and a docs
reference, or a dated owner-carrying gap row -- checklists rot, so the
registry is closure-checked against ``torchlens.__all__`` in BOTH
directions on every run. Realism ratche... |
03a210792b629ad369f3ac73fbe4d6c1b6e7198bb37a9656dfb5c1a058d18bd5 | Python | 4,777 | 117 | import pathlib
import sys
import unittest
import numpy as np
from asmc.asmc import *
data_dir = pathlib.Path(__file__).resolve().parent.parent / 'ASMC_data'
if not data_dir.exists():
print(f'ERROR. {data_dir} does not exist. Did you clone ASMC recursively with submodules?')
sys.exit()
class TestASMCRegress... |
18b2c27f186296dc5d34577395d66b7a21467dc11bf9203444bea71bf6f98d4c | Python | 4,779 | 130 | """Tests for user-managed annotation dictionaries on TorchLens logs."""
from __future__ import annotations
from pathlib import Path
import numpy as np
import torch
from torch import nn
import torchlens as tl
from torchlens.constants import (
LAYER_LOG_FIELD_ORDER,
LAYER_PASS_LOG_FIELD_ORDER,
MODEL_LOG_F... |
3c881866dac21906fe64fbf992787da793b143680ff6786e3000678cd2c94f27 | Python | 4,779 | 152 | from functools import lru_cache
import numpy as np
import torch
import torch.nn as nn
import tqdm.auto as tqdm
from permacache import permacache
from modular_splicing.dataset.data_rewriter import DataRewriter
from modular_splicing.evaluation.evaluation_criterion import EvaluationCriterion
from modular_splicing.models... |
89e9a43a51ca50df4ccf1656c84dbdf8d0bc02c1dca21d2f10da5c57a6411d32 | Python | 4,780 | 120 | """This script is for preprocessing something-something-v2 dataset.
The code is largely borrowed from https://github.com/MIT-HAN-LAB/temporal-shift-module
and https://github.com/metalbubble/TRN-pytorch/blob/master/process_dataset.py
"""
import os
import sys
import threading
import argparse
import json
def parse_args(... |
5cda1f88e25ab9475490d46b1d67aa0f6e20c53c01322531ab0c96f991c26b4b | Python | 4,782 | 145 | """Random dot motion task."""
import numpy as np
from neurogym.core import TrialEnv
from neurogym.utils import spaces
class ProbabilisticReasoning(TrialEnv):
"""Probabilistic reasoning.
The agent is shown a sequence of stimuli. Each stimulus is associated
with a certain log-likelihood of the correct re... |
27674e6d0aa59540e2383bdb5012262c5532cab7d419413c614f3f56c051d73e | Python | 4,784 | 112 | #!/usr/bin/env python3
import os
import sys
import pandas as pd
import random
from random import shuffle
import argparse
# the following line is to deal with the case that self-defined module
# in the submission directory are not found when submitted through sbatch, as in
# https://stackoverflow.com/questions/46718... |
78cb1a270ee18a100d9d88332fcb39249a963ae73fe55cb587dcf798af9e6823 | Python | 4,784 | 138 | import torch as ch
import numpy as np
from torch import nn
from robustness.audio_functions import audio_transforms
from torch._jit_internal import _copy_to_script_wrapper
import numpy as np
from .layers.padding import pad_valid_time, pad_same
class FakeReLU(ch.autograd.Function):
@staticmethod
def forward(ctx,... |
9f746b68d9df2c64f67f4ac8d70b476826c29c2f8458950a3c4ac83182002b9b | Python | 4,784 | 155 | import pytest
import nway.nway_matching as nway
import os
from jinja2 import Template
import json
import numpy as np
import copy
import contextlib
import PIL.Image
from pathlib import Path
TEST_FILE_DIR = os.path.join(
os.path.dirname(os.path.abspath(__file__)),
'test_files')
@pytest.fixture(scope='... |
e0bef5cb8dae81baee161ce8303822cf93d4cee41ff0120326652d96eab8e864 | Python | 4,784 | 131 | #!/usr/bin/env python3
# coding: utf-8
"""
Created in January 2021
@author: Thomas Bonald <bonald@enst.fr>
"""
from abc import ABC
from typing import Union
import numpy as np
from scipy import sparse
from sknetwork.embedding.base import BaseEmbedding
from sknetwork.linalg import Regularizer, Normalizer, normalize
fro... |
23d2521bbb31baa42916759f57b51a75f7b01aa4746c62aa297c34680d33c853 | Python | 4,785 | 83 | #### Modified from TAURUS Lee et al., Nat Methods 2019 (https://github.com/dixonlab/Taurus-MH)
import sys
fn=sys.argv[1]
dfh=open(fn,'r')
rfh=open('./'+fn.split('/')[-1]+'_2_contacts.txt','w')
stat_rfh=open('./'+fn.split('/')[-1]+'_2_contacts.stats.txt','w')
dfh.readline()
def foo(x, y):
return 0 if y == 0 else x... |
3efc320a697e0b594580dfa2117ef5923a75fb539dfeab4f2abc3c1665c092bb | Python | 4,786 | 133 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
00_bootstrap.py — 精简导入（不安装 torch）
为什么需要这个
------------------------------------------------------------------
proteoclock 的 __init__.py 会无条件导入深度时钟（ipfP3GPT, Galkin 2025），
而深度时钟依赖 torch（约 250 MB）。但：
· 深度时钟的权重已被 UK Biobank 要求下架，公开环境里【永远无法运行】；
· 本方案只用简单时钟（OrganAge / P... |
9261f696e66108974bb8ac98d951daca10e5c9f971ce54e120c7a60fba9fd828 | Python | 4,786 | 146 |
import numpy as np
#import scipy.stats
import random
import sys
def zscore(mat, return_unzvals=False):
"""Z-scores the rows of [mat] by subtracting off the mean and dividing
by the standard deviation.
If [return_unzvals] is True, a matrix will be returned that can be used
to return the z-scored values... |
96a7736b1e8b36ae6a3372cb4dcdebf55e5bf128f2bb878c07c55b948f1a1682 | Python | 4,787 | 134 | import torch
import torch.nn.functional as F
from torchmetrics.functional import pairwise_cosine_similarity
import numpy as np
from metrics.losses import cosine_push_loss, uniform_loss, kl_divergence_to_standard_gaussian, \
sliced_wasserstein_distance_to_uniform_hypercube, sliced_wasserstein_distance_to_standard_g... |
35797c5f64497056c27c7cf539126c7dc998626c8f4aa361d669efd0a3599773 | Python | 4,788 | 138 | """Generate the fish completion script for vsearch.
Writes to stdout. Invoked from completion/Makefile.am:
cd scripts && python3 gen_fish.py > ../completions/vsearch.fish
"""
from __future__ import annotations
import sys
import spec as spec_mod
HEADER = """\
# vsearch completion for fish
# Auto-generated from... |
3d72c28eec2291dd5d7128e41da2bc1622e8cf64dea789f146174057a8d61eae | Python | 4,788 | 109 | from cProfile import label
import pylustrator
pylustrator.start()
import os
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
from scipy.optimize import curve_fit
initializers = ["const", "binned"]
datasets = ["mnist", "mnist_with_brightness_offset", "fashion_mnist", "fashion_mnist_with_bright... |
e10a698eeb0680267ab7f47ee346f3aee9d0a65d0711c61639441ddf7e12c682 | Python | 4,788 | 136 | """
Unit tests for core/tracking_unit.py.
Tests TrackingUnit class including initialization, tracker/stimulator binding,
position retrieval, and the track pipeline.
"""
import unittest
from unittest.mock import MagicMock, Mock, patch
import numpy as np
from ethoscope.core.data_point import DataPoint
from ethoscope.... |
300c5b538a49e3c9498d77dcaa0a7d95360f68bb29514640effd04b463e134fb | Python | 4,790 | 135 | # Configuration file for the Sphinx documentation builder.
# This file only contains a selection of the most common options. For a full
# list see the documentation:
# https://www.sphinx-doc.org/page/usage/configuration.html
# -- Path setup --------------------------------------------------------------
import shutil
... |
b8479126cca84bde75a3ad4c9adfe82f39bc6dfdb976cca12dc40fc1aa3faf95 | Python | 4,790 | 144 | # -*- coding: utf-8 -*-
import logging
import os
import subprocess
from galaxy.datatypes.data import get_file_peek, Text
from galaxy.datatypes.metadata import MetadataElement
def count_special_lines(word, filename, invert=False):
"""
searching for special 'words' using the grep tool
grep is... |
4a4c0504ff1bdad2d8fa6057b4bba5c7ed3f6b153f6755c211f2b69089ba454e | Python | 4,791 | 156 | import sys
import collections
from collections import Counter
def Merge(dict1, dict2):
res = dict()
for k,v in dict1.items():
if k in dict2:
v = dict2[k] + v
res[k] = v
else:
v = v
res[k] = v
return res
def reverse_base(base):
if base == 'A':
rev_base = 'T'
elif base == 'T':
rev_base = '... |
9ed2a3e3bff732686a50a82e6495d35b702dfc2f5092be2dd105211292b2e081 | Python | 4,791 | 109 | """
@Time: 4/8/2023 下午1:48
@Author: Heng Cai
@FileName: run_screening.py
@Copyright: 2020-2023 CarbonSilicon.ai
@Description:
"""
import argparse
import os
import numpy as np
import pandas as pd
import torch
from rdkit import Chem
import multiprocessing as mp
from tqdm import tqdm
from RTMScore.utils... |
20b3b735c7c643c12e328f44dc688b3a07609c11a8f1e937a7fc5befafe91751 | Python | 4,792 | 142 | """Scoped, NON-attaching payload reads for analytics over lazy artifacts.
The interactive ``op.out`` read on a lazily loaded trace MATERIALIZES the
blob and ATTACHES it to the op (user semantics: read once, keep it). An
analytics/agent layer that walks every site through that door turns one
bounded question into a who... |
3be41a58a063dd01a8c9f4ed6f72ad880fde38fdd207350e8af23f84e2090939 | Python | 4,797 | 143 | """Tier-(ii) edits COMPOSE and never silently revert (AUD-CODE 2.9b / 4.10).
Before the fix EDGE-kind tier-(ii) entries were excluded from the cone
re-splice, so any later recompute of the child (a second edge edit on
another arg, an upstream act edit, a param edit reaching the child)
silently reverted the substitutio... |
c8e7e32d10f3202b227f0a511970eb84e804d1e8366e64383be05658cea8ad53 | Python | 4,797 | 146 | # Copyright (c) Facebook, Inc. and its affiliates.
import torch
import torch.nn as nn
class Mlp(nn.Module):
def __init__(
self,
in_features,
hidden_features=None,
out_features=None,
act_layer=nn.GELU,
drop_rate=0.0,
):
super().__init__()
self.dr... |
cca86a983327ad7e4e4d2350e31070fa6379993195bbac2388d156f9a8d66042 | Python | 4,797 | 142 | """Build Environment used for isolation during sdist building
"""
import logging
import os
import sys
from distutils.sysconfig import get_python_lib
from sysconfig import get_paths
from pip._vendor.pkg_resources import Requirement, VersionConflict, WorkingSet
from pip._internal.utils.misc import call_subprocess
from... |
0ced9087f0f227adef8b6704ef1856a7cc25c374720e371fb8fd1c9b8933a8e5 | Python | 4,798 | 121 | import SimpleITK as sitk
import numpy as np
from skimage.transform import resize
def resize_image(image, old_spacing, new_spacing, order=3):
new_shape = (int(np.round(old_spacing[0]/new_spacing[0]*float(image.shape[0]))),
int(np.round(old_spacing[1]/new_spacing[1]*float(image.shape[1]))),
... |
95f41295cb9ad25add639b0c8a92d9bc61663f0f1487bb4ed634d0bec5063bfe | Python | 4,798 | 164 | import os
from .cromwell import Cromwell
from .cromwell_backend import (
BACKEND_ALIAS_LOCAL,
BACKEND_AWS,
BACKEND_GCP,
BACKEND_LOCAL,
BACKEND_LSF,
BACKEND_PBS,
BACKEND_SGE,
BACKEND_SLURM,
)
CONF_CONTENTS_TMP_DIR = """
# Local directory for localized files and Cromwell's intermediate f... |
0e5e2f14cd849a262d29eb0f0b5dfd79decb89dfa6ab330a99e471f24608709b | Python | 4,799 | 150 | """Generate a .csv file with the points to validate the transform"""
from time import strftime,localtime
from os.path import join, dirname, abspath
import SimpleITK as sitk
import pathlib
import glob
import sys
import os
TRANSFORM_FILES = []
def main(argv):
if len(sys.argv)<2:
print('python generateValida... |
eaf18e3aa4563d7ec6219ad4348976211cc95be37bdbe3d3b4175b3e780c52f9 | Python | 4,799 | 136 | # SOURCE: vendored from autonlab/auton-survival @ master
#
# Files combined below (imports/paths adjusted only, architecture untouched):
# auton_survival/models/dsm/dsm_torch.py (create_representation helper only)
# auton_survival/models/dcm/dcm_torch.py -> DeepCoxMixturesTorch
#
# The queued candidate repo (chirag... |
280d5a84c5fda7e4c7bf2852b156f725d74381824b350f948094a30558ac2935 | Python | 4,800 | 150 | # coding=utf-8
# Copyright 2026 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... |
9f82efb5a7bc13de5a45c5cfbeb074ae5272a98d9170b427d7fdbe02622f0bc9 | Python | 4,800 | 121 | # General imports
import os
import glob
import sys
import torch
import numpy as np
import pandas as pd
import seaborn as sns
import matplotlib.pyplot as plt
import pytorch_lightning
from tqdm.auto import tqdm
# EUGENe imports and settings
import eugene as eu
from eugene import models, evaluate, settings
from eugene.mo... |
baad14e3d2442ee207612fe686fd1ebd82fd9e88b6e5fe711b48a42224020eb7 | Python | 4,803 | 144 | import torch.nn as nn
from modular_splicing.models.modules.spliceai import SpliceAIModule
from modular_splicing.models.modules.sparsity_enforcer.sparsity_enforcer import (
sparsity_enforcer_types,
)
from modular_splicing.models.motif_models.types import motif_model_types
from modular_splicing.models.modules.lssi_in... |
9ff4c08018a8e914c615886dfb4223e2cf5997284be02498b475951ccbb931ac | Python | 4,804 | 142 | import sys
from scipy.fft import skip_backend
sys.path.insert(1, '/u/home/r/ryo10244/Xiao_lab/dsRNA_pred/script/utils')
import re
import pysam
import argparse as ap
import pandas as pd
import numpy as np
from utils import *
import random
#import multiprocessing as mp
#from functools import partial
def... |
fb036a73713767f6b26529ca1f7e7cb667995eb5f5aed3f38fa6177a0416671b | Python | 4,804 | 139 | # Copyright (c) 2024 PaddleHelix Authors. All Rights Reserved.
#
# Licensed under Creative Commons Attribution-NonCommercial-ShareAlike 4.0
# International License (the "License"); you may not use this file except
# in compliance with the License. You may obtain a copy of the License at
#
# http://creativecommo... |
48b663b89cbe06356de5d78f1b1507d08736672bf5e02e56b1d971f01fc735ad | Python | 4,805 | 175 | from ast import (
parse,
walk,
)
AST_NODE_TYPE_ALLOWLIST = [
"Expr",
"Load",
"Str",
"Num",
"BoolOp",
"Compare",
"And",
"Eq",
"NotEq",
"Or",
"GtE",
"LtE",
"Lt",
"Gt",
"BinOp",
"Add",
"Div",
"Sub",
"Mult",
"Mod",
"Pow",
"LShi... |
a130c9087e841d58c98d29e695d93aca96cb78949cee3d1f086a93f72464e758 | Python | 4,805 | 156 | from __future__ import annotations
import dataclasses
from typing import TYPE_CHECKING
import numpy as np
from loguru import logger
from numpy.typing import NDArray
from .._shape import Shape
from ._geometry import round_bbox_to_int
from ._osam_session import get_osam_session
from ._shape_builders import Detection
f... |
c4bf5d895ce4bf46c5fbd66c2480a83ebcb348b4b885a1b8dc1daaf94ee3a198 | Python | 4,805 | 142 | from typing import Union
import torch
import torch.distributed as dist
from torch import Tensor
from lightly.utils.dist import gather
class TiCoLoss(torch.nn.Module):
"""Implementation of the Tico Loss from Tico[0] paper.
This implementation takes inspiration from the code published
by sayannag using L... |
0eb2d917e53ac1025afe7451166ec508b3e37404a8d9c22d1c197d74e53ce3ee | Python | 4,806 | 178 | """
Methods for managing angular metrics
"""
from __future__ import annotations
import math
import numpy as np
__all__: list[str] = [
"wrap_angle_to_0",
"angles_between_vectors",
"angle_dif",
"rotationMatrix",
"rotate_points_around_point",
]
def wrap_angle_to_0(angle: float, in_deg: bool = Fal... |
d063ce3b7a09b2c44f2805b6812062e0337d3852d82489a9046fc8b48559c17c | Python | 4,806 | 128 | """Hand-pinned independent facts for the ``tests/golden/`` file suite.
b9-opus R75-2: each ``tests/golden/*.json`` file is regenerated THROUGH
torchlens, so its consuming test detects CHANGE, not correctness. These pins
read the committed golden FILES as plain JSON and assert facts derived from
first principles — the ... |
2d7446197cc4b25aa1f61b00064162336b4aa4c3a41b363a0f54bdedda8786ae | Python | 4,807 | 177 | import os
import tqdm.auto as tqdm
import numpy as np
import torch.nn as nn
from permacache import permacache, drop_if_equal, stable_hash
from modular_splicing.evaluation.evaluation_criterion import DefaultEvaluationCriterion
from modular_splicing.utils.construct import construct
from modular_splicing.evaluation.ru... |
a1f3d2ac215e0473f082318396082fce3e5181ce6eba97d7d14f7ef4a4133012 | Python | 4,807 | 113 | import sys
import os
import pandas as pd
import numpy as np
from nilearn import image
from nilearn.masking import apply_mask
# input/output paths
fmri_prep = sys.argv[1]
ROIs_dir = sys.argv[2]
first_input = sys.argv[3] # contrast files location
roi_out = sys.argv[4] # fixed effect output location
# List of Subjects ... |
2d6cd749990833d0bc44f419cca93d0ab1c80f0de228467a75a6bba01b88fb03 | Python | 4,809 | 94 | import time
import logging
from svim.SVIM_intra import analyze_alignment_indel
from svim.SVIM_inter import analyze_read_segments
from svim.SVIM_COLLECT import retrieve_other_alignments
def span_position_distance(candidate, signature, position_distance_normalizer):
if candidate.type == "INS" or candidate.type == ... |
ada72905c5315e45e6d00d817d92e2502d7a144fdc972ec2323b14c8503065ac | Python | 4,809 | 140 | """
Tractor module for SMOT
"""
# pylint: disable=arguments-differ
from abc import ABC, abstractmethod
import numpy as np
import mxnet as mx
from .utils import timeit
from .general_detector import GeneralDetector
class BaseAnchorBasedTracktor(ABC):
"""
BaseAnchorBasedTracktor
"""
@abstractmethod
... |
ba6203c3926ac38bb9984348c325c1bad13daa0429a88bbf557e13aabd4caa76 | Python | 4,809 | 126 | """
Measures the model activations for a set of sounds. Uses the layers specified in the
build_network.py script.
Set up to measure activations for the set of sounds used in Norman-Haignere et al. 2015.
Please cite the assciated paper if you use these sounds.
@article{norman2015distinct,
title={Distinct cortic... |
1b6239cb872b0c3ab6ccdc55f156bb4f8d26d9221e4f5b7a3e46a3b178bcd771 | Python | 4,810 | 124 | """Vizmech wave-2 item 13: one compact legend table in a dedicated rank (D28).
The historical legend was six disconnected nodes dot packed BESIDE the model
(366 -> 1048 pt page width, 2.86x, zero collisions -- the two-oracles worked
example). Pins here:
- the role legend renders as ONE plaintext HTML-table node, plac... |
1e3d6939ee18bc196f9a29858186bf5084041e1f4d2a8fb0a4091f902258d519 | Python | 4,810 | 153 | import re
import numpy as np
from rdkit import Chem
from rdkit.Chem import rdchem
from rdkit import RDLogger
RDLogger.DisableLog('rdApp.info')
from tqdm import tqdm
def islower(self, s):
lowerReg = re.compile(r'^[a-z]+$')
return lowerReg.match(s) is not None
def isupper(self, s):
upperReg = re.compile(r'... |
22543fb0e34174754e68622381be0834b773f693166ce0f244e477f8aaa3b443 | Python | 4,811 | 139 | # This example requires the following dependencies to be installed:
# pip install "lightly[timm]"
# Note: The model and training settings do not follow the reference settings
# from the paper. The settings are chosen such that the example can easily be
# run on a small dataset with a single GPU.
import pytorch_lightni... |
43287de633fbff2a77a6f752e2d5bda4418609ff3c43178e4c220d4ba77d1c24 | Python | 4,812 | 100 | import os
import argparse
from gluoncv.torch import model_zoo
from gluoncv.torch.engine.config import get_cfg_defaults
from gluoncv.torch.utils.model_utils import download
from gluoncv.torch.utils.visualizer import ColorMode, Visualizer
from gluoncv.torch.data.registry.catalog import MetadataCatalog
from PIL import Ima... |
fce729f57442d4e89421b0d3e3e98d769028be17dc1cc27a918f642cf4939b6c | Python | 4,814 | 126 | # Copyright 2022 Deepfold Team
# 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 applicable law or agreed to in writing,... |
5448866b1549ef5b5d22d2ee67134d7cf41e4c034bc2b9d7382f43b308955233 | Python | 4,815 | 115 | """
Network Simulations
===================
`RectiPy` provides basic support for numerical simulations of network dynamics.
Neuron models of the RNN layer are governed by differential equation systems of the form
.. math::
\\dot y = F(y, \\theta, t)
With state-vector :math:`y`, parameter vector :math`\\theta`, ... |
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