sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
423f82724e3636338b408fbc7e5ed5604986ce7be1826d867775a82bbd95c152 | Python | 9,931 | 217 | import sys
from Reptile.meta import MetaLearner
from AttentiveFP.AttentiveLayers import Fingerprint
import torch
from torch.autograd import Variable
import numpy as np
from torch.utils.data import DataLoader
from utils.data_split import kinaseNshot
import pickle
import os
# os.environ["CUDA_VISIBLE_DEVICES"] = '1'
from... |
be5e38eca78d5893f0d435eea27795fda3bb8c75c7bc0f3d491f9a992c900a81 | Python | 9,934 | 252 | #!/usr/bin/env python3
"""
Dx BD — Bootstrap CIs on §3.2 4×4 normalization cells
======================================================
Reviewer ask: bootstrap CIs on each cell of the §3.2 normalization-vs-mode
table. Four normalization × mode combinations:
rank-norm × deployment, rank-norm × strict
z-score × depl... |
cbf43e5073e1fb434923984dbd9aa8bd093ad1d72df835fdf8b7f5259a768d2a | Python | 9,935 | 252 | import numpy as np
import pandas as pd
import os
from .conf_ranker import ConfRanker
from rdkit import Chem
from rdkit.Chem.rdchem import Mol, EditableMol
from typing import Sequence, Tuple, Union
from bioconfpred.conf_ensemble import ConfEnsembleLibrary
from bioconfpred.data.utils import SimilaritySearch
from bioconf... |
890ca9b35602bf7855ba2e47be98b9ec8d354dad51c8f9b79a66a8336ce577e5 | Python | 9,940 | 297 | #!/usr/bin/env python3
"""
Script to validate file sources configuration by attempting to create instances
of each configured file source.
This script loads the currently configured file_sources_config_file YAML file
and tries to instantiate each of the specified file sources in order to validate
the configuration mod... |
0b7bb7436e19fa9d8bc045f6d747a712ac5b2d2d951f2ace8c263ef529c50bcd | Python | 9,942 | 254 | # adapted from https://github.com/facebookresearch/detectron2/blob/master/detectron2/structures/keypoints.py
from typing import Any, List, Tuple, Union
import numpy as np
import torch
class Keypoints:
"""
Stores keypoint **annotation** data. GT Instances have a `gt_keypoints` property
containing the x,y l... |
178cb5aedc8eb59b0ff65d3409287ed50c691fe8d11ec2d13346cb7294385022 | Python | 9,944 | 249 | """Observe items 11-13: timeline v2 artifact, deterministic SVG, liveness view.
Conservation and honesty pins: closed categories with named-absent facts,
output pseudo-rows excluded, tied parameters counted once, the saved band
never stacked (gross beside decomposition), module rollup conservation, a
byte-exact SVG go... |
b1290f315ecf8b87b094d56832002553be3fa4270891f743301625e73187610f | Python | 9,945 | 241 | #!/usr/bin/env python3
"""
Dx AD — investigate which pipeline component creates the 0.70 noise floor.
HC-vs-HC scramble configurations:
baseline_rank_white_quad : rank-norm + whitening + Quad_LDA (Dx AA canonical) — 0.70
zscore_white_quad : z-score + whitening + Quad_LDA
rank_no_white_quad : rank-no... |
9e36544e21a07767ac1781016deaee7ef928624d20d13b2c9b314cf90265ef00 | Python | 9,946 | 254 | """Projective per-unit membership-transpose and geometric-adjoint goldens."""
from __future__ import annotations
from collections.abc import Callable, Iterator
from fractions import Fraction
import pytest
import torch
from support.rf_isolation import preserved_rf_registry
from torch import nn
import torchlens as tl... |
ca9b5a3fd154553e65baabf756961f4e76a0092aae1e0ee1f7dfaa8af25d19dc | Python | 9,948 | 276 | """Capture-door intervention glue for ``tl.trace(intervene=...)``.
Split out of ``user_funcs.py`` (C03 fix cycle): the backward sticky-spec
builder for backward-only selectors and the capture-door fire-evidence
envelope (ledger memo 3.1) are intervention machinery, not trace-entry
resolution; ``user_funcs`` imports th... |
d1a3bfcc4567301065580a0997878527f507db5b2e65d41112387f24f3425e7d | Python | 9,948 | 230 | """Regression tests for SEC-H1: INST/OBJ opcode allocation-belt bypass.
The ``SafeBundleUnpickler`` allocation belt (r49 storage, r63 tensor/ndarray) refuses
constructing an attacker-sized ALLOCATION type (a torch storage, a ``torch.Tensor``
subclass or legacy ``torch.<dtype>Tensor``, or a ``numpy.ndarray`` subclass) ... |
a0a2204e767f2557a00a14443daf3ad8e8d73198debc39711c4820d690784b1d | Python | 9,949 | 241 | """Round-31 security regression: structural stdlib/builtin deny under trust.
The "denied even under trust_custom_callables" contract for attacker-controllable
``.tlspec`` bundles was historically enforced by a hand-maintained DENYLIST of
dangerous stdlib/builtin modules (``_DENIED_MODULES`` /
``_DENIED_FOREIGN_MODULES... |
c32b2b27813c12fdccce2461c4aa74879cd5c387a29b02fc6eb6f8cd36f7e5f3 | Python | 9,949 | 197 | # -*- coding: utf-8 -*-
"""
Created on Mon Sep 26 15:33:40 2022
This distributer contains a special case condition, if user waits more than
1.5 seconds after successfully doing a double or triple blink, the algorithm
won't wait for the next event but sends the double blink event. Since 1.5
seconds is enough... |
28b1dd5cd7772cf4889fd092855b91d721a18ab36bd783da25ade748ea328eb2 | Python | 9,950 | 309 | """
Methods for detecting and combining files
"""
from __future__ import annotations
import os
import subprocess
import numpy as np
__all__: list[str] = [
"files_in_dir",
"combine_images",
"combine_videos",
"combine_pdfs",
]
def select_filenames(filenames: list[str], suf: str = "", pref: str = "")... |
b9c1da0a5e6f63eb6e4b701d79e6fbb110ddb6254abce659220b4a20da4a944a | Python | 9,954 | 246 | import os
import pandas as pd
import logging
from utils.json_loader import load_json_into_pandas_dataframe
class SequenceIdentityCleanUp:
"""
This class take a list of path of folder dataset and allow us to generate the same dataset folder without inter contamination.
A contamination is when some sequence... |
87777fb7f000a0f736f91251a515785ca77fca070fe151c75ff00b2b08cf67bb | Python | 9,955 | 232 | import math
from typing import Optional, Union
import matplotlib.pyplot as plt
import numpy as np
import pandas as pd
import seaborn as sns
from anndata import AnnData
try:
from typing import Literal
except ImportError:
from typing_extensions import Literal
from .utils import save_return_show_fig_utils
def... |
e48922b29afbfe7e66fbb7fc464f4ea9f999f83bff10f314f2af47ab1ea1b756 | Python | 9,956 | 227 | # 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... |
23122b550be4030db56f839da054917c2d044e1131cb56b3130afc30559688fa | Python | 9,957 | 236 | """Pose utils"""
import time
import logging
import datetime
import numpy as np
import torch
from .. import comm
from ..utils import AverageMeter
from ..model_utils import save_model
from ..optimizer import maybe_add_gradient_clipping
from ..eval_utils.coco_eval import COCOEvaluator
logger = logging.getLogger(__name_... |
fed5ea43324937438b8ef27127df5f95ff4cc7f4c6afbcb24f73bfd6c27baf5f | Python | 9,959 | 244 | """Fixwave-2 FW2-POLISH pins for R19-3/4/5/7: module-cluster honesty.
The dashed cluster style is a semantic claim ("no input ancestor"). The b6
probes found it lying in two ways: the input-connectivity propagation broke
after the outermost module (a tautological loop guard), and clusters whose
ops were condensed away... |
1b78b1dc796e6e75874832cf62ece80575150ec36ee2caaf0243d07c083fa126 | Python | 9,960 | 267 | # SPDX-License-Identifier: LGPL-2.1-or-later
#!/usr/bin/env python
from __future__ import print_function, division, absolute_import
import unittest
import numpy as np
from pyEcoHAB import dominance_in_2_cages as dom
from pyEcoHAB import SetupConfig, data_path
class TestGetStates(unittest.TestCase):
@classmethod
... |
fe71376dec4981be03aa0f4e09dc6ca15e267e40ab8b1bb80a65ab88b8f63661 | Python | 9,960 | 261 | """Smoke tests for ``--concurrency=auto`` (cgroup-aware concurrency).
These tests run real workers in Docker containers with real CFS quotas
(``cpu_quota``/``cpu_period`` on the container), so the cgroup files read by
``celery.utils.sysinfo.cpu_budget()`` are written by the kernel —
nothing is mocked. They complement ... |
5cba4f02c4fa4eaeda1603df6dbc5444028f3ba93bb2991544468ab76e5346cc | Python | 9,961 | 287 | """Streaming, truncating, non-recursive version of :func:`repr`.
Differences from regular :func:`repr`:
- Sets are represented the Python 3 way: ``{1, 2}`` vs ``set([1, 2])``.
- Unicode strings does not have the ``u'`` prefix, even on Python 2.
- Empty set formatted as ``set()`` (Python 3), not ``set([])`` (Python 2)... |
078b8a9b4c3659a1e1c3046b28991519e8cbf7c288d1d0d20274ce6fe1502842 | Python | 9,963 | 265 | """Episode honesty refusals (lane F40a): pre-execution intervene refusal,
declared-step cost ceiling, partial_log on settlement refusals, and the
discoverability seam (capture_kind / episode step access)."""
from __future__ import annotations
import pytest
import torch
import torch.nn as nn
import torchlens as tl
fr... |
91ee9a7f8896ceb6687371ed88f2a709926f0fa1a55fc751c01c291428356b17 | Python | 9,963 | 278 | """Base Command class, and related routines"""
from __future__ import absolute_import
import logging
import logging.config
import optparse
import os
import sys
from pip._internal.cli import cmdoptions
from pip._internal.cli.parser import (
ConfigOptionParser, UpdatingDefaultsHelpFormatter,
)
from pip._internal.cl... |
3bc90dbfcb5b2d4f8768c39e852b1497e280f96d6d313c36a180dd3f930aa822 | Python | 9,964 | 223 | """
variability.py — Rolling-window temporal variability of acoustic features.
Why this exists
----------------
Phase E analysis against the lab's real, curated starling corpus (5355
labeled bouts, 54 birds -- see project_vocal_recorder memory) found that
several features' variability ACROSS a bout (std) was a stronge... |
1eb037e98ec8634f313231aa68c11bf49e24ab6d90f8cab1f17ba23bb2c552a0 | Python | 9,965 | 249 | """Test of data set functionalities"""
import pathlib
import shutil
import tempfile
import nanite.model as nmodel
import numpy as np
import pytest
from PyQt5 import QtCore, QtWidgets
import pyjibe.head
from helpers import MockModelModule, make_directory_with_data
data_path = pathlib.Path(__file__).parent / "data"
... |
39272f0058102606ef5ae6fac2b82b1f98285768b1066f6101357d57d6c8bc12 | Python | 9,968 | 235 | """Cancellation-aware reconstruction tolerance model (A03; mikit F4/F5).
The reconstruction gate used to borrow the REPLAY tolerance table, whose
absolute term sits at denormal scale by design; a reconstruction is an
independent summation, so at cancellation sites (large addends, small output)
the replay-shaped gate r... |
d1d9c7616118e120b699b38d5c6bc84e07d09faf7b70cc70685ade0bd0a500de | Python | 9,970 | 251 | '''
Copyright 2021 Twente Medical Systems international B.V., Oldenzaal The Netherlands
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 requir... |
dffc42bad798fd53cd0dc8be7636da7298c583a117b0984fd8e2fcf9332e18b4 | Python | 9,978 | 318 | """Tests for TorchLens debug analysis utilities."""
from __future__ import annotations
from inspect import signature
from typing import Any
import torch
from torch import nn
import torchlens as tl
class TinyMlp(nn.Module):
"""Small MLP used by debug analysis tests."""
def __init__(self) -> None:
... |
190af62fe6192caabb2c685d33b918b41bb1d60a37da9f0185647dbdca58ccdb | Python | 9,979 | 299 | # Copyright 2025 Google.
#
# 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, soft... |
751eda68e4cbe6750bfacfb75225203b4fd0547b123ee3e26737dfd7c25345c5 | Python | 9,979 | 339 | from abc import ABC, abstractmethod
import attr
import numpy as np
import torch
ONLY_TRAIN_MAP = {"acceptor": 1, "donor": 2}
class EvaluationCriterion(ABC):
@abstractmethod
def loss_criterion(self):
"""
Returns the loss criterion to use.
E.g., an instance of `torch.nn.CrossEntropyLos... |
85b51c22213f337e20c55fe9894c300a29d2994f2f379365a466a3dd337f00f1 | Python | 9,979 | 207 | import numpy as np
import torch
from .base_model import BaseModel
from . import networks
from .nce import PatchNCELoss
import util.util as util
class CUTModel(BaseModel):
""" This class implements CUT and FastCUT model
The code borrows heavily from the PyTorch implementation of CycleGAN
https://github.com... |
2efb77bea06ed3856ecb510806437f02e5869d42515e052a1f39f7730613a671 | Python | 9,982 | 366 | import random
import logging
import traceback
import datetime, time
import os
import re
from uuid import uuid4
def pi_version():
"""
Detect the version of the Raspberry Pi.
https://www.raspberrypi.org/documentation/hardware/raspberrypi/revision-codes/README.md
We used to use cat /proc/cpuinfo but ... |
bd97a6375c66fbb5b81419d86611196a447547241ddd31aa17bc6f1af0847408 | Python | 9,983 | 279 | # 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... |
c803ee9c1bfae386e013264730a146420ef364015f0f5212410fbb64b7337bfa | Python | 9,985 | 279 | # 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... |
15861bdbad46d35d2289c8c323d3f4ade9e562e7aee15ecf7c5c2cc535d2f396 | Python | 9,990 | 256 | from __future__ import annotations
from typing import cast
import torch
from torch import Tensor
from torch.nn import Module
from torch.nn import functional as F
from lightly.models.modules.center import Center
class IBOTPatchLoss(Module):
"""Implementation of the iBOT patch loss [0] as used in DINOv2 [1].
... |
180ea18465ec6740c61b96d00943faecd809e0ebe0e88ef1dfe1ea6ccfff9247 | Python | 9,991 | 261 | # Copyright 2021 DeepMind Technologies Limited
#
# 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 agr... |
76e5470ba9a5c4e74156d5754cd1132f72dd93490616986b771b50c66ed93b27 | Python | 9,991 | 316 | """
Contract tests for the DEB model's integration surface.
These pin the boundary between ``lib/model/deb`` and the rest of larvaworld -- the
stored-config keys, the recorded dict, the reporter codenames, the attributes the
gut reads back, and the sim-loop stepping protocol. They are deliberately about the
*interface... |
7bc9cc91c6d1bbbe75136e2578a618600744f13d2d5301181465c6df84527e75 | Python | 9,993 | 293 | """Evaluation code for BDD100K lane marking.
************************************
Byte structure for lane marking:
+---+---+---+---+---+---+---+---+
| - | - | d | s | b | c | c | c |
+---+---+---+---+---+---+---+---+
d: direction
s: style
b: background
c: category
More details: bdd100k.label.label.py
***************... |
1fe84a743c737520271fcd2099f563db0c4b3efad44facc6ef604e6d0663271f | Python | 9,996 | 211 | import numpy as np
import pandas as pd
import time
import pickle
import os
from PCAfold import preprocess
from PCAfold import analysis
from PCAfold import __version__ as PCAfold_version
print('numpy==' + np.__version__)
print('pandas==' + pd.__version__)
print('PCAfold==' + PCAfold_version)
# Select one dataset:
data... |
655fdeaec6bc01c68e0db9acdb99a6bcde15549e5eb7a55e6ada633b977aead9 | Python | 9,997 | 205 | import pandas as pd
import numpy as np
import sklearn
from sklearn.decomposition import PCA
import scipy.linalg as linalg
import scipy.stats as stats
from sklearn.linear_model import Ridge, LinearRegression
from sklearn.model_selection import cross_val_score
from sklearn.metrics import make_scorer, r2_score
import pyal... |
6ed27fdbb0525890b348c7841c2fe6c0c6df17d75a5b8948e33a3ed646d90c80 | Python | 9,997 | 285 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Mon Nov 2 23:07:28 2020
@author: emilia
"""
import numpy as np
from sklearn.metrics.pairwise import euclidean_distances
from scipy.spatial import ConvexHull
from scipy.linalg import orthogonal_procrustes
def make_vec(point):
"""
Turn a point into... |
0a6bddc8f9e6870f280b7dede703d7bb4184050e921b2022a3d3d93c54f0b99a | Python | 10,001 | 251 | # TODO: Add examples, tables and best practice links to command
# TODO: Examples of truevalue, falsevalue
# TODO: Test param extra_file
# Things dropped from schema_template.md (still documented inside schema).
# - request_parameter_translation
import sys
from io import StringIO
from lxml import etree
from yaml impo... |
94300bc8d14fb5153cdb5d0ae8a1c0e0657120a26cb6a04cd11c3848677d7cea | Python | 10,002 | 248 | """Order-isolation infrastructure guards (R76, reopened 2026-08-15).
The suite's order-isolation story leans on ``pytest-randomly``: randomized
default ordering surfaces order-coupling, and every ``-p no:randomly`` in the
drivers/regen paths deliberately opts back into deterministic order. All of
that is REAL only whi... |
2e342aab161ddc212af0ea75745e81518375c15c57062a4aa2ffc7975901627d | Python | 10,003 | 294 | # --- THIS FILE IS AUTO-GENERATED ---
# Modifications will be overwitten the next time code generation run.
from plotly.basedatatypes import BaseLayoutHierarchyType as _BaseLayoutHierarchyType
import copy as _copy
class Hoverlabel(_BaseLayoutHierarchyType):
_parent_path_str = "layout"
_path... |
44b9dd5eb6e950203ebbc6c4ef8f2c66e4acc9fc9d0aa8b40a2bbadac08cf02f | Python | 10,003 | 313 |
from database import (
fix_ids,
ImageModel,
CategoryModel,
AnnotationModel,
DatasetModel,
TaskModel,
ExportModel
)
# import pycocotools.mask as mask
import numpy as np
import time
import json
import os
from celery import shared_task
from ..socket import create_socket
from mongoengine impo... |
97fb2b598843b365e5e0088cae29be15406d2e28a256cd5933db3662ac5fb66e | Python | 10,003 | 235 | import torch.nn as nn
import torch
try:
from torchvision.models.utils import load_state_dict_from_url
except:
from torch.hub import load_state_dict_from_url
from .custom_modules import FakeReLUM, SequentialWithArgs, FakeReLU
__all__ = [
'VGG', 'vgg11', 'vgg11_bn', 'vgg13', 'vgg13_bn', 'vgg16', 'vgg16_bn',
... |
b13b2d3836579e95c1b653ee751f1e31ed75cd9137eb2ad2d55ce54effd25273 | Python | 10,003 | 371 | import seaborn as sns
import matplotlib.pyplot as plt
from controller_validation.data.preprocessing import crop_values
import numpy as np
import ptitprince
from scipy.stats import ks_2samp
from statannotations.stats.StatTest import StatTest
from statannotations.Annotator import Annotator
import scipy
def ridgeplot(da... |
f41044acc0a2edc6fe28d7f470a36caf53d1b0acbcb3e64dd869743ca9f354f0 | Python | 10,003 | 271 | """Wrap-state-independent ground truth (R75-1, b9-fable round-2 probe).
Once torch is wrapped, the phase-0 ground-truth forward, the per-op replay,
and backward validation's stock-autograd pass all observed through the SAME
installed wrapper closures, so a TorchLens-induced numeric distortion (a
planted 0.1% ``tanh`` ... |
4ed96e6af603b5614628828cb97ebf9cb307194d7b57a62925aa68ea5e01003d | Python | 10,004 | 309 | import argparse
from collections import OrderedDict
from typing import List, Tuple
import numpy as np
import torch
from pytorch_lightning import LightningModule, Trainer, seed_everything
from pytorch_lightning.callbacks import ModelCheckpoint
from torch import Tensor, optim
from torch.nn.functional import log_softmax,... |
8c83368ee3acc7e53914f6c5d7abadacb98c8137b30b46c0a63f75c57cee7705 | Python | 10,007 | 151 | cat_names = ['SEX', 'TEACHINGSTATUS', 'BEDSIZE', 'VERIFICATIONLEVEL',
'CC_ADHD', 'CC_ALCOHOLISM', 'CC_ANGINAPECTORIS'
, 'CC_ANTICOAGULANT', 'CC_BLEEDING', 'CC_CHEMO', 'CC_CIRRHOSIS', 'CC_COPD', 'CC_CVA', 'CC_DEMENTIA'
, 'CC_DIABETES', 'CC_CHF', 'CC_HYPERTENSION', 'CC_MI', 'CC_PA... |
ea014084246e68996d752f21c6a429fff0dc2364885a1caef211c7618571feb5 | Python | 10,009 | 247 | """Helpers for the dense relational PatchKernelAlignmentLoss.
These utilities back :class:`~lightly.loss.PatchKernelAlignmentLoss`. The loss
compares the pairwise similarity (kernel) structure of student and teacher dense
features of shape ``(B, N, D)``. The helpers here cover:
- validating dense-feature inputs,
- op... |
c4f6d5967cface67ec0b0d143d03dd89f147139d6b15671dc376393c33edfc58 | Python | 10,011 | 257 | # Ultralytics 🚀 AGPL-3.0 License - https://ultralytics.com/license
from __future__ import annotations
import contextlib
import glob
import importlib.util
import os
import shutil
import struct
import sys
import tempfile
from contextlib import contextmanager
from datetime import datetime
from pathlib import Path
cla... |
c62462b0cf6a653d904194457716e5841df2901b85d298e18138f569d638fd54 | Python | 10,011 | 226 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Fri Jan 29 18:04:08 2021
This is the configuration file for Experiment 4, cue validity 1.0.
To run the experiment, pass the path to the folder which is to contain the data from all Experiments on lines 197-198.
@author: emilia
"""
import numpy as np
import ... |
0000c3607eafe3b69d1e920765df66d9ab0f06d349a6758c192dc37954fb1fb6 | Python | 10,016 | 282 | '''
load the RBNS data
'''
import csv
import re
import h5py
import urllib
import gzip
from io import StringIO
import requests
import numpy as np
import time
import os
from utils_rbns import create_datapoints
from constants import get_args
from map_protein_name import (
get_map_protein,
get_rbns_name_psam_idx_... |
e19c05aa425a3c88b673ace2a290e8ee1a395623800433c4513adafb8a5e9c54 | Python | 10,016 | 254 | """Round-39 security regression: close the arbitrary-callable-INVOKE class in the
``is_pure_forward_callable`` denylist (finding secE-r38-1).
The central runnable-``.tlspec`` purity gate ``is_pure_forward_callable`` denies
side-effecting torch/tensor callables resolved from an UNTRUSTED bundle. r26 denied
the elementw... |
fc96f1370e22229e460915fa8ef0e4951cbe63335791dd475c087d0635be3b4c | Python | 10,016 | 225 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Fri Jan 29 18:04:08 2021
This is the configuration file for Experiment 4, cue validity 0.75.
To run the experiment, pass the path to the folder which is to contain the data from all Experiments on lines 196-197.
@author: emilia
"""
import numpy as np
import... |
734b6d873626629b171f2b7f9015d9386a50a31cfe4db702eab9269974f3e072 | Python | 10,018 | 280 | #!/usr/bin/env python3
"""
File: plot_ieqtl_barplot.py
Created: 2022/05/05
Last Changed:
Author: M.Vochteloo
Copyright (C) 2020 University Medical Center Groningen.
A copy of the BSD 3-Clause "New" or "Revised" License can be found in the
LICENSE file in the root directory of this source tree.
"""... |
d2a895b6cc4c8a0cdc4b4916a45130dafbe3cb1334b47dbc05d8fa7fd77c3765 | Python | 10,018 | 249 | from typing import List, Union
from rdkit import Chem
from rdkit.Chem import SDWriter
from rdkit.Chem.rdchem import Mol
from rdkit.Chem.rdFMCS import FindMCS
from rdkit.Chem.AllChem import AssignBondOrdersFromTemplate
from bioconfpred.data.preprocessing import MolStandardizer
from bioconfpred.data.pose_reader import Po... |
3f08b5d78e47423b37421bd4f49b50bb0633e06329103fac27cee1f1d2ab80f2 | Python | 10,019 | 350 | from typing import Optional
import pytest
import torch
import torch.nn.functional as F
from flash_attn.cute import flash_attn_varlen_func
@pytest.mark.parametrize("B", [1, 7, 20])
@pytest.mark.parametrize("H", [1, 4, 6])
@pytest.mark.parametrize("D", [64, 128, 256])
@pytest.mark.parametrize("min_seq_len", [1, 32, 128... |
b37b0b268af9a20f2e2eeef6ab08935d0baad84c415ec0861b60c2a7c0310978 | Python | 10,020 | 309 | import numpy as np
import logging
from cuteSV.cuteSV_genotype import cal_GL, threshold_ref_count, count_coverage
import pickle
'''
*******************************************
TO DO LIST
*******************************************
1. Adjust format in BND format;
2. Make TRA calls more sensitivity;
3. Collect DP ... |
439bf812e28c3d49c9988d0310728a0a0447bf42f0c7f79db800bd3e8ac5ef2e | Python | 10,022 | 237 | """MS COCO Detection Evaluate Metrics."""
from __future__ import absolute_import
import sys
try:
from StringIO import StringIO
except ImportError:
from io import StringIO
import os
from os import path as osp
import warnings
import numpy as np
import mxnet as mx
try:
from mxnet.metric import EvalMetric
exce... |
2d33b4159ccab36674301c6471c6831be75012c99b68b2e12a9fb4811e077500 | Python | 10,023 | 312 | """AMQP 0.9.1 REPL."""
import pprint
import click
from amqp import Connection, Message
from click_repl import register_repl
__all__ = ('amqp',)
from celery.bin.base import handle_preload_options
def dump_message(message):
if message is None:
return 'No messages in queue. basic.publish something.'
... |
71b2d35edca5afe92adcfbd24c228c18be89f5397bd4e374c4109892ab2e7bb0 | Python | 10,024 | 218 | #%% Packages
import os
import torch
import copy
import utils
import warnings
import numpy as np
import tgan_utils
import datetime
import matplotlib.pyplot as plt
import torch.optim as optim
from TGGAN.TGAN import Discriminator, Generator
import draw_utils
warnings.filterwarnings('ignore')
os.environ["CUDA_VISIBLE_DEVI... |
3d53fe2e88ddbaf9fc93e851ff47201a3cd0d431f642bd1f85bc7e53dd626535 | Python | 10,025 | 312 | #############################################
# This file contains scripts to perform the #
# Random Forest experiments. #
# #
# Author: Jonas Ditz #
#############################################
import argparse
import os
import pickle
fro... |
4c32bfe61ef09d46b60c37c3d087f29a7fc2d08a54e33196b9d03de8a245cd98 | Python | 10,025 | 322 | # coding=utf-8
# Copyright 2024 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... |
1186bc8fde2e9179b4a04deb2cc57500dc5584b2044c6cc1fcc3f0c86c2e00f1 | Python | 10,027 | 225 | from importlib import resources
import pickle
import json
import dill
import pandas as pd
import numpy as np
import warnings
# Class for OrganAge
class CreateOrganAgeObject:
# init method or constructor
def __init__(self,
path_version_scale_factors_v4='v4_to_v4.1_scale_dict.json',
... |
691f22594e0937bf3ea35c600bbe6ca09c0484b48978797d71bab87faae77a93 | Python | 10,027 | 299 | import pkg_resources
import logging
from PyQt6 import QtWidgets, QtCore, uic
from matplotlib.patches import Circle as MPLCircle
import matplotlib
import numpy as np
from bmlab.session import Session
from bmlab.controllers import ExtractionController
from bmicro.BGThread import BGThread
from bmicro.gui.mpl import Mp... |
50ce2a6f0d8c06edc64c98e99f3fef141806a5c8db2ddd0af33abfbd96f19060 | Python | 10,028 | 277 | #!/usr/bin/env python3
"""
File: correlate_with_residual_effect.py
Created: 2022/04/28
Last Changed:
Author: M.Vochteloo
Copyright (C) 2020 University Medical Center Groningen.
A copy of the BSD 3-Clause "New" or "Revised" License can be found in the
LICENSE file in the root directory of this sour... |
f704254923f1f1d0fe4d88da4742954e29fab0469198e5854edbe976d41ad437 | Python | 10,028 | 272 | # coding: utf-8
# Licensed to the Apache Software Foundation (ASF) under one
# or more contributor license agreements. See the NOTICE file
# distributed with this work for additional information
# regarding copyright ownership. The ASF licenses this file
# to you under the Apache License, Version 2.0 (the
# "License... |
de09856d0a8abf6a24721984f4521945c5e28bbe8509b47b9d72f20902af4a03 | Python | 10,029 | 254 | from keras.src import backend
from keras.src import constraints
from keras.src import initializers
from keras.src import ops
from keras.src import regularizers
from keras.src.api_export import keras_export
from keras.src.layers.input_spec import InputSpec
from keras.src.layers.layer import Layer
@keras_export("keras.... |
b2d81e90df7ceeca546dd97d908c87335f5518e04889a9caf8b12776831c5403 | Python | 10,030 | 283 | """Entity-property tests for receptive-field views."""
from __future__ import annotations
from collections.abc import Iterator
from pathlib import Path
import pytest
import torch
from support.rf_isolation import preserved_rf_registry
from torch import nn
import torchlens as tl
from torchlens._io import FieldPolicy
... |
cfc37e05bce92b7e625a73a1a3c2082ebc10c6c0827f2a4dc41a73bef172602a | Python | 10,030 | 296 | import ast
import itertools
import random
import re
import time
import warnings
from copy import deepcopy
import casadi as cas
import numpy as np
import pandas as pd
from casadi import SX, integrator, vertcat
from rdkit import Chem, RDLogger, rdBase
from rdkit.Chem import AllChem, Descriptors
from tqdm import tqdm
fr... |
ac0a733ed8c4048238582611e8d841b7c7e53f57037a8e30559c75e1eff7b316 | Python | 10,032 | 226 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Fri Jan 29 18:04:08 2021
This is the configuration file for Experiment 4, cue validity 0.5.
To run the experiment, pass the path to the folder which is to contain the data from all Experiments on lines 196-197.
@author: emilia
"""
import numpy as np
import... |
b98cedb666d33ae174b68d755c62fd1937fb003e7a104a0b11143f33cb20ab0e | Python | 10,038 | 308 | import bottle
import updater
import logging
import traceback
import os
import socket
from optparse import OptionParser
from helpers import get_machine_id, assert_node, WrongMachineID
from helpers import get_commit_version, generate_new_device_map, updates_api_wrapper, reload_node_daemon, reload_device_daemon
app = b... |
24838a661bfb73fceedbe9bc08750db60a5a1d6dc59ca23aff6fc2163c635dcb | Python | 10,039 | 187 | import numpy as np
from gym import utils
from gym.envs.mujoco import MujocoEnv
from gym.spaces import Box
class ReacherEnv(MujocoEnv, utils.EzPickle):
"""
### Description
"Reacher" is a two-jointed robot arm. The goal is to move the robot's end effector (called *fingertip*) close to a
target that is ... |
b7f93ad0438c3f99ab1d760971e73015c7ce2be80d47068184ca0a0f711d9a92 | Python | 10,040 | 257 | from typing import Optional, Tuple, Union
import numpy as np
import pyvista as pv
from pyvista import PolyData
try:
from typing import Literal
except ImportError:
from typing_extensions import Literal
from ....logging import logger_manager as lm
from ..utilities import add_model_labels, merge_models
from .ar... |
4100662d9f1930ada4e4deedb45f4b6d6d1836046cd8b2c7caeae100f70c5b53 | Python | 10,041 | 233 | from utilities.solutionTS import Solution
from utilities.transformation import *
import copy
from scipy.special import gamma
import numpy as np
class HHO:
def __init__(self, N, function):
self.N = N
self.population = []
self.function = function
self.rabbit_location = [Non... |
5c69c8a18f9ded617adc1f9817005f739cebaef309c5cc8298ab51111bb7d38d | Python | 10,041 | 315 | """Classes & functions for managing parameters for simulating power spectra."""
from copy import deepcopy
import numpy as np
from specparam.data import SimParams
from specparam.modes.modes import check_mode_definition
from specparam.utils.checks import check_flat
from specparam.modutils.errors import InconsistentDat... |
82be1dbe53454313d71324fb5b7a7edd12ce058873d0b57b42e36ad68297810f | Python | 10,046 | 265 | import numpy as np
# from utils import Recorder, Q_nak
# from mitochondria import Mito
from mitosfns import spike_quanta, run_sim
from steady_state import get_steady_state
from gates import get_ros, get_ros_fast, get_ros_slow, ros_inf
from gates import ros_tau, ros_tau_fast, ros_tau_slow
from gates import get_ros_con... |
a68c05da53c939a9d8264ede9b86e635d5f6a116757b7e36e6cb4fa4a8d323da | Python | 10,048 | 259 | import os
import tempfile
import threading
import time
import unittest
from unittest import mock
import pandas as pd
from codecarbon.core import cpu
from codecarbon.emissions_tracker import (
EmissionsTracker,
OfflineEmissionsTracker,
track_emissions,
)
from codecarbon.external import scheduler as schedul... |
52ccc0a6ac5aee4422c61ad3de58a0c35c868d5a0218e578763f454d724f297c | Python | 10,050 | 297 | """Download packaged HOBJ datasets into a local ``data`` directory."""
from __future__ import annotations
import argparse
import shutil
import tarfile
import zipfile
from pathlib import Path
from tempfile import TemporaryDirectory
from urllib.parse import urlparse
import requests
from tqdm import tqdm
# Public OSF... |
d4f89314744e539024b032e3780c0b6d3d6027da78ef23d2f59b63b94d681107 | Python | 10,050 | 265 | # Asteroid Impact (c) Media Neuroscience Lab, Rene Weber
# Authored by Nick Winters
#
# Asteroid Impact is licensed under a
# Creative Commons Attribution-ShareAlike 4.0 International License.
#
# You should have received a copy of the license along with this
# work. If not, see <http://creativecommons.org/licenses/b... |
98b415a5748df1522c06b9685c10d214e2275644c03c9027bf3d1e64864586e7 | Python | 10,051 | 291 | """Elasticsearch result store backend."""
from datetime import datetime, timezone
from kombu.utils.encoding import bytes_to_str
from kombu.utils.url import _parse_url
from celery import states
from celery.exceptions import ImproperlyConfigured
from .base import KeyValueStoreBackend
try:
import elasticsearch
exc... |
91e988c7fa200cbfd1a0010e5489a329470dea4fd3adb7f6bfd98a542f30428c | Python | 10,054 | 286 | from __future__ import division
import sys, itertools, optparse, warnings
optParser = optparse.OptionParser(
usage = "python %prog [options] <flattened_gff_file> <alignment_file> <output_file>",
description=
"This script counts how many reads in <alignment_file> fall onto each exonic " +
"pa... |
2a44c846fd87b0fb675808d864d05e44b4cb0000664a96578a7ca6635362fd89 | Python | 10,055 | 372 | #!/usr/bin/env python
"""
Various io functions
"""
import importlib
import warnings
from pathlib import Path
from xml.dom import minidom
import numpy as np
from .. import core as nap
from .cnmfe import CNMF_E, InscopixCNMFE, Minian
from .folder import Folder
from .interface_npz import NPZFile
from .interface_nwb i... |
04eadc190d6591fe30664626a4a5d41ae4ce7465ea54ad6fde08f894f89f8c90 | Python | 10,057 | 232 | from abc import abstractmethod
from typing import Type, TypeVar
import qt, slicer, json
from SegmentEditorEffects import AbstractScriptedSegmentEditorEffect
from PyQt5.QtWidgets import QDialog
from SegmentEditorCommon.ListSelectionDialog import ListSelectionDialog
T = TypeVar('T')
class AbstractBiomedisaSegmentEditor... |
f2338457e15697363936bbec9d9fb7121f9547e3917c4083ef19e2c499727f88 | Python | 10,058 | 299 | from importlib import resources
import logging
from PyQt6 import QtWidgets, QtCore, uic
from matplotlib.patches import Circle as MPLCircle
import matplotlib
import numpy as np
from bmlab.session import Session
from bmlab.controllers import ExtractionController
from bmicro.BGThread import BGThread
from bmicro.gui.mp... |
736ef290b23fed4020682df2136689621635a5de860e032ab369b0045a957405 | Python | 10,062 | 211 | import torch.nn as nn
import torch.nn.init as init
import torch
import math
class ACBlock(nn.Module):
def __init__(self, in_channels, out_channels, kernel_size, stride=1, padding=0, dilation=1, groups=1, padding_mode='zeros', deploy=False,
use_affine=True, reduce_gamma=False, gamma_init=None, nor... |
c6277d8796f3b6db73a9aa0ae8f06c27d9ce8d8e267fd7d482d2ca5592d44231 | Python | 10,063 | 284 | #!/usr/bin/env python
import codecs
import fnmatch
import os
import random
import subprocess
import sys
import unicodedata
import librosa
import pandas
import soundfile # <= Has an external dependency on libsndfile
from deepspeech_training.util.importers import validate_label_eng as validate_label
# Prerequisite: H... |
22a68909d85436cbe8d3c52b72516c48309b293e16e05c7bad9a1de1330a6f86 | Python | 10,064 | 302 | from typing import List, Optional, Union
try:
from typing import Literal
except ImportError:
from typing_extensions import Literal
import numpy as np
from scipy.cluster.vq import kmeans2
from sklearn.neighbors import NearestNeighbors
from ..dynamo_logger import LoggerManager
from .connectivity import k_neare... |
bd4996c4f09810a15f5536a18cd6d4a390ce2669dd6a90d4232ad97d2662b1b2 | Python | 10,064 | 197 | # -*- coding: utf-8 -*-
"""
Created on Mon Sep 26 15:33:40 2022
This distributer contains a special case condition, if user waits more than
1.5 seconds after successfully doing a double or triple blink, the algorithm
won't wait for the next event but sends the double blink event. Since 1.5
seconds is enough... |
b5495b1fcb91fee2693a3ce1e99e72d6c6956fc9545b19d8d7fea5e9b44100da | Python | 10,065 | 223 | # import numpy as np
import torch
import torch_geometric as ptgeom
from torch import nn
from torch.optim import Adam
from torch_geometric.data import Data
from tqdm import tqdm
from ExplanationEvaluation.explainers.BaseExplainer import BaseExplainer
from ExplanationEvaluation.utils.graph import index_edge
class PGEx... |
207875f2845d8e8707fb7aefacd51b6c6d622c16d7ba38f1077f54b664bf8861 | Python | 10,066 | 273 | from typing import Generator, Any
import numpy as np
import pandas as pd
import copy
from mirp._images.generic_image import GenericImage
from mirp._images.transformed_image import TransformedImage
from mirp.settings.generic import SettingsClass
from mirp._imagefilters.generic import GenericFilter
class LocalBinaryP... |
e72e5b835ea399d8436e5f456456bc63493ab67e9e9a91d794e25f32920f2d05 | Python | 10,067 | 286 | #!/usr/bin/env python
# =============================================================================
# MODULE DOCSTRING
# =============================================================================
"""
Test objects and function in tfep.nn.transformers.moebius.
"""
# =============================================... |
a8cabbd0180206a1eb7207384e1829d266e8ea6c0564abf9dee7ea77edd0ec10 | Python | 10,069 | 330 | """Phase 5 postprocess preservation tests for intervention metadata."""
from __future__ import annotations
import torch
import torchlens as tl
from torchlens.errors import MetadataInvariantError
from torchlens.fastlog import RecordContext
from torchlens.intervention.types import ParentRef, TupleIndex
from torchlens.... |
8b0de092bfea57f55a7832051230f4315988c7d98872bfd192bdd281609542b2 | Python | 10,070 | 285 | """
This file contains methods which calculate passive membrane properties from
voltage-clamp sweeps. These methods are not optimized for speed or accuracy
and are only provided for backwards compatibility. pyabf is intended to be
used just for reading ABF files, and users are encouraged to write their own
python code ... |
a71091d94d003ebce187e2a20a5066dbd86a2cc8f20eab4f25a720232c0787cb | Python | 10,072 | 285 | """
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... |
9eba8c3ed4bf1e366d373ed46df74676270a454d324f5e7e8f26057d539dc82b | Python | 10,075 | 233 | from typing import List, Optional, Tuple, Union
import numpy as np
from anndata import AnnData
from scipy.spatial.distance import cdist
try:
from typing import Literal
except ImportError:
from typing_extensions import Literal
from spateo.logging import logger_manager as lm
from spateo.tdr.interpolations impo... |
834a9963f79bdee1d2fe88b3263892cb8e384de8606b239b566fdb997fad8bed | Python | 10,079 | 338 | # coding=utf-8
# Copyright 2025 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... |
acb4b3b6d9366c71d9d080c10541032178755d39931144568cfbfa2b2867f7fc | Python | 10,080 | 252 | """L6 stage 4a: the FULL ACCEPTANCE GALLERY (design memo sec 3.4).
The flagship composition demo of the selection algebra: ablate the
INTERSECTION of two units' receptive fields vs their UNION vs a size-matched
seeded RANDOM CONTROL, using the exact METAPLAN producer-to-producer
spelling (``u.receptive_field.at(p) & u... |
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