sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
c16b2dee725d96fa8ef684b36190fe57bd3cbf83ac1c68cbde3664c055a97ed8 | Python | 10,241 | 278 | #!/usr/bin/env python3
"""Calculates the Frechet Inception Distance (FID) to evalulate GANs
The FID metric calculates the distance between two distributions of images.
Typically, we have summary statistics (mean & covariance matrix) of one
of these distributions, while the 2nd distribution is given by a GAN.
When run... |
7aadbce39cfce90fe05ccd64875728c522f3081b661056e3dfbaaf13755fe5cd | Python | 10,244 | 245 | ''' Models to create diameters of synthesized cells '''
import numpy as np
from tns.morphio_utils import STR_TO_TYPES, TYPE_TO_STR
from tns.morphio_utils import section_filter, root_section_filter
def sample(data):
"""Returns a value according to the input data"""
return np.random.choice(data)
def section_l... |
56ac8c2fcc955f311eba2a28667069f74ba882d112ee841c21918fc818689f1b | Python | 10,245 | 229 | # 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"); you may not u... |
c4422d0ba40d209a085925c7e99b7cd8da6185e6bee660378c81937ddfc30013 | Python | 10,249 | 256 | import logging
import shlex
from pathlib import Path
import pytest
from pyrosm import OSM, enable_logging, get_data
from pyrosm import _log
from pyrosm.utils import progress
@pytest.fixture
def pyrosm_logger():
"""The ``pyrosm`` logger, with its handlers, level and propagation, and the progress setting
of e... |
921dd74df42377b9c07045c8e3e0de856b97d77226551c6182c8e3f0c6b6a0be | Python | 10,252 | 228 | #!/usr/bin/env python3
# Tractor script to extract out ancestry segments from each reference population from admixed samples.
# The original ExtractTracts.py has been modified to work with FLARE output wherein ancestry calls
# are saved within the VCF file itself, and no MSP file is generated.
# Several changes were m... |
42f19706732ceead2632af0369df36dbf3afd747511a4bd2e17c26ab12d37ed9 | Python | 10,254 | 296 | from abc import ABC, abstractmethod
import math
import geopandas as gpd
from shapely.geometry import MultiPolygon, Polygon, Point
from shapely.ops import cascaded_union
from ..utils import constants, utils
import numpy as np
import h3.api.numpy_int as h3
import warnings
class TessellationTilers:
def __init__(sel... |
fc327ea847eda210e4cae88a7a9c4b701f9fbfb6a57739bf45344ff13c15bf8b | Python | 10,254 | 310 | import numpy as np
import torch
import torch.nn as nn
import torch.nn.functional as F
from opt_einsum import contract as einsum
import copy
import dgl
from util import base_indices, RTs_by_torsion, xyzs_in_base_frame, rigid_from_3_points
def init_lecun_normal(module, scale=1.0):
def truncated_normal(uniform, mu=0.... |
0232829430f1d5b033426cb37bb517214b700256a9be59ad1f6300ea47a90b5e | Python | 10,255 | 354 | from tempfile import NamedTemporaryFile
from permacache import permacache, stable_hash
import numpy as np
import matplotlib as mpl
import matplotlib.pyplot as plt
from PIL import Image
from modular_splicing.motif_names import get_motif_names
from modular_splicing.utils.construct import construct
from modular_splicin... |
93ad150e6bc3d5b9bc9edaf0b1c4e183560368d4cb3a4e13b27ed432ad77fb91 | Python | 10,256 | 314 | """Aproximate joint diagonalization algorithms."""
import numpy as np
from .utils import check_weights
def _check_init_diag(init, n):
if init.shape != (n, n):
raise ValueError(
'Initial diagonalizer shape must be %d x % d (Got %s).'
% (n, n, init.shape,))
return init
def rjd... |
114a1dcae637190992f755b35e7e1f3ad0d998c38acea5a28ec7d81155a0c77f | Python | 10,257 | 250 | #!/usr/bin/env python3
"""
File: correlate_align_metrics_with_genes.py
Created: 2021/11/09
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 ... |
6ec20fc9e0a7d091d83861d065e09be45c28c8cc54b79afabda70334b2572059 | Python | 10,257 | 274 | """Regression tests for the capture-cache path (r19c hardening).
Covers a previously-uncovered gap: nothing combined ``cache=True`` with an
activation/grad transform (F2) or exercised a capability-option cache
collision (F3), and a pre-forward setup failure leaked capture-global state
(SOL-A5-002). The ``trace()`` doc... |
676e8bf2ce3a75d10aca8e1c8ec8ffe1e9813b1fae6293edaeb6754869b3ba6d | Python | 10,258 | 262 | """Event dispatcher sends events."""
import os
import threading
import time
from collections import defaultdict, deque
from kombu import Producer
from celery.app import app_or_default
from celery.utils.nodenames import anon_nodename
from celery.utils.time import utcoffset
from .event import Event, get_exchange, gro... |
43521e6c58413f6545a91109ef47f17b5938e7835a4d3565295c867bca2bdb0c | Python | 10,260 | 277 | """B1-18: the H2 hot-AST release is a TOTAL postprocess epilogue.
``ast_branches`` keeps a process-wide, 256-file-bounded ``_file_cache`` split
into a cold tier (spans, projected calls, retained source) and a hot tier
(``_HeavyAst``: parsed module AST, parent map, scope nodes) for whole source
files -- including torch... |
fb7695191ab70395c567882a3fe44a3ceeab9fba83268618da6d168a3119c03a | Python | 10,260 | 273 | """Preflight fetcher for the real-model artifact cache (testing MEMO 4.3, A2).
No pytest body reaches the network, ever. This script runs BEFORE pytest:
it fetches exactly the registry blobs for the requested venue/rows into an
isolated cache, verifies size and SHA-256 for every file (including every
cache-restored fi... |
6aa38b0bb7890d801336fbeef28f44cdbbc4d7d60b6f81155036368c93469676 | Python | 10,261 | 307 | import numpy as np
import torch
from chemical import INIT_CRDS
PARAMS = {
"DMIN" : 2.0,
"DMAX" : 20.0,
"DBINS" : 36,
"ABINS" : 36,
}
# ============================================================
def get_pair_dist(a, b):
"""calculate pair distances between two sets of points
Par... |
50f930b1944994db83d52a2450c237f1696bb3af53d4d4c07193f97861ec6426 | Python | 10,262 | 103 | """4. Computing FLOPS, latency and fps of a model
=======================================================
It is important to have an idea of how to measure a video model's speed, so that you can choose the model that suits best for your use case.
In this tutorial, we provide two simple scripts to help you compute (1) ... |
34cbdeb3dfef9a2ed13d55e94f700ce3c53bf513c2dbe2f7030a1635607d9ebc | Python | 10,264 | 301 | # --- 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 Dimension(_BaseTraceHierarchyType):
_parent_path_str = "parcats"
_path_st... |
ed53d997401193cab27e598b29783ab374a30fdc878af6cadc7123fd973c0ae1 | Python | 10,264 | 244 | """MNASNet model definition, adapted from https://pytorch.org/docs/stable/torchvision/models.html,
to take single channel instead of 3-channel images.
"""
import warnings
import torch
import torch.nn as nn
_BN_MOMENTUM = 1 - 0.9997
class _InvertedResidual(nn.Module):
def __init__(self, in_ch, out_ch, kernel_... |
fd30a658126e768ad44afb8a8c95ec583371e9f438f0bbf9c3b466c935a48cd6 | Python | 10,265 | 198 | import os
import argparse
import mxnet as mx
class MonodepthOptions:
def __init__(self):
self.parser = argparse.ArgumentParser(description="Monodepthv2 options")
# PATHS
self.parser.add_argument("--data_path",
type=str,
hel... |
9b74570191ffcf9b4db0e6a2f9e774aad350abbb16aa9873f234e0f4133ace9a | Python | 10,266 | 269 | import argparse
from .tools import folder
import os
if int(os.environ.get("NOTEBOOK_MODE", 0)) == 1:
from tqdm import tqdm_notebook as tqdm
else:
from tqdm import tqdm as tqdm
import shutil
import time
import numpy as np
import torch as ch
import torch.utils.data
from torch.utils.data import DataLoader
from ... |
d73c37a0daa69f3b455dfba6a4d9e88711ca8a622e894e59e0f9b19f006eda1e | Python | 10,266 | 290 | #!/usr/bin/env python3
"""
File: visualise_cmv_violinplot.py
Created: 2020/11/24
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 tre... |
9fbe3432c474706df812ebc658ccdd565d2e200dd4218c75ffde4552c4e4b4dd | Python | 10,272 | 306 | from __future__ import absolute_import
import json
import logging
from pip._vendor import six
from pip._vendor.six.moves import zip_longest
from pip._internal.cli import cmdoptions
from pip._internal.cli.base_command import Command
from pip._internal.exceptions import CommandError
from pip._internal.index import Pac... |
2d65da9f1c1b98c21fbe499125e39265d6b85d1fc9f49871ce1856ea0c9e552b | Python | 10,275 | 285 | from pyrosm.graph_export import _create_igraph, _create_nxgraph, _create_pdgraph, generate_directed_edges
from pyrosm.graph_connectivity import get_connected_edges
from pyrosm.utils import validate_edge_gdf, validate_node_gdf
from pyrosm.config import Conf
def get_directed_edges(nodes,
edges,
... |
5d7d2564a3c43be24b7de06b592e1be68853facfd347a4cb5f8e7894e6e7ade0 | Python | 10,278 | 256 | """One-backward reads on real checkpoints (F04 gate rows RG06/RG11-flavored).
Real ``openai-community/gpt2`` (the literature's model, RG06's artifact) and
torchvision PRETRAINED ResNet-18 (RG11's artifact): the substrate census,
target-kind-keyed reachability, split-slot discipline on the fused QKV, the
mid-stack line... |
d41f7f265acc040e27e5a403b82a57e9beea3849e16a6f34170196cc0357ea66 | Python | 10,278 | 311 | """L5 M4 pins: checked suppression of redundant constructor-arg rows (DEFAULT-ON).
Covers the design-memo sec-5 contract: the closed candidate table (both
directions per row — suppresses on PROVEN equality, survives on mismatch,
including a deliberately-lying func_config), the never-candidate set, the
input-side singl... |
52d20a8c5babfd930e70cc3920fbc4d34a8b94d50a67e455f7f3a683ede84362 | Python | 10,281 | 273 | """Variational inference implementation of a negative binomial mixture model
using Pyro.
"""
from typing import Dict, Optional, Tuple, Union
import numpy as np
import pyro
import pyro.distributions as dist
import torch
import torch.nn.functional as F
from pyro import poutine
from pyro.infer import SVI, TraceEnum_ELBO
... |
bb8691ac486518dca045dbaa1f48fe0f3f3fdfc58985428203fbad88b1ef8d77 | Python | 10,281 | 228 |
__author__ = 'Aaron Gudmundson'
__email__ = 'agudmund@uci.edu'
__date__ = '2020/12/05'
__version__ = '10.0.0'
__status__ = 'beta'
from scipy.optimize import curve_fit, minimize # Optimization
import matplotlib.patches as mpatches ... |
e29e10addb9f7a078557bf3b12157bf1f0e80193811990dc0a17041df6bd7219 | Python | 10,283 | 271 | import os
import pytest
import numpy as np
from mirp import extract_images
from mirp.settings.import_config_parameters import import_configuration_settings
from mirp._masks.base_mask import BaseMask
# Find path to the test directory. This is because we need to read datafiles stored in subdirectories.
CURRENT_DIR = os... |
7adfb4a2e68d2d3c6c84e0ee78b44eb3c9ab7d65d73ce7e6b7e43b3c56ed59ad | Python | 10,284 | 321 | import os
import numpy as np
import torch
import torch.distributed
from torch.distributed import tensor as torch_distributed_tensor
from keras.src.backend.torch.ops import core as torch_core
from keras.src.backend.torch.ops.core import _parse_device_input
from keras.src.backend.torch.ops.core import convert_to_tensor... |
24d59d5c9f66781021def7b3a331c6e619c50f00e1b6f26925db6653ad6f1a1c | Python | 10,285 | 262 | """Functions for building the input features for the HelixFold model."""
import json
import pickle
import os
from typing import Any, Mapping, MutableMapping, Optional, Sequence, Union
from absl import logging
from helixfold.common import residue_constants
from helixfold.data import msa_identifiers
from helixfold.data i... |
94800d26870ac04f179cd62900ca291f30a9cc2be4d5d642cee819796997f756 | Python | 10,288 | 303 | #!/usr/bin/env python3
"""Diagnostic N — Tier 3.2: nonlinear classifiers.
Tests whether the 0.751 LOCO ceiling reflects a classifier-shape limit
or a data-scale limit. All on HC-anchored per-cohort normalization.
Classifiers:
- LDA baseline (our current best)
- QDA (class-specific covariance)
- Logistic Regress... |
7200a1c3b61f0e53ddbb5956a70698b987b489bd83dd459e0ac2687d5d6b6add | Python | 10,289 | 214 | from __future__ import division
from __future__ import print_function
import argparse
import logging
logging.basicConfig(level=logging.INFO)
import time
import sys
import numpy as np
import mxnet as mx
from tqdm import tqdm
from mxnet import nd
from mxnet import gluon
import gluoncv as gcv
gcv.utils.check_version('0.6... |
2ab7d8936d7c2c9fa5a0a2737dc5803e706747596ddb44ed61eebb3e683bfcff | Python | 10,290 | 233 | import argparse
import logging
import os
import sys
from jbrowse2 import JbrowseConnector as jbC
logging.basicConfig(level=logging.DEBUG)
log = logging.getLogger("jbrowse")
if __name__ == "__main__":
parser = argparse.ArgumentParser(description="", epilog="")
parser.add_argument("--sessName", help="Session ... |
ee30a6957e0b0f24873bd2efc10a45b0e3cccacf4cbd2f63e12434f0a04f1dd5 | Python | 10,290 | 238 | """Written by @Jinerhal, adapted by @Xiaojieqiu.
"""
import random
from typing import Any, List, Optional, Tuple, Union
import cv2
import numpy as np
from anndata import AnnData
from skimage import morphology
from ..configuration import SKM
from ..logging import logger_manager as lm
@SKM.check_adata_is_type(SKM.AD... |
9d152b94777aaa4f63015dd24628d7acd51298fcba4f22069ac5fd06ca27a1b4 | Python | 10,293 | 267 | """Dead-model persistent-buffer universe for NON-TENSOR-STATE models (r77 F2).
Round-76 (free-roam) found the r75 F2 gc-independent-save closure one model class short:
``snapshot_capture_state`` deliberately returns ``None`` when ANY ``state_dict()`` value is
non-tensor (``get_extra_state()``, packed/quantized entries... |
cdc093a5daf24c323e9138cd982262b209fb1f7fefec60ad3590814e8eeba15e | Python | 10,294 | 328 | """Optimization for rotations on Grassmann manifold"""
import warnings
import numpy as np
from ..geometry.base import invsqrtm, logm, sqrtm
from ..geometry.distance import distance
from ..utils._check import check_weights
def _project(X, U):
"""Projection.
Project U on the tangent space of orthogonal matr... |
4793a4e9614c467bcacd5606f904ff293be487ded6e6868797aa975f1e412777 | Python | 10,296 | 279 | import os
import nitorch as ni
from nitorch.mesh import mbf
import glob
import torch
import json
import os
root = '.'
stain = 'calb'
odir = root + f'/warp2surf/{stain}'
os.makedirs(odir, exist_ok=True)
mri = root + '/mri/mri.mgz'
mri_samseg_600 = root + '/mri/samseg/mri.600.mgz'
lsfm_stain = root + f'/lsfm/init_oct/{... |
3047ec7be2aaf16793460c89f25da92767b3da15e15ca40a549a05a97c4c1b41 | Python | 10,297 | 297 | """Differential property tests: native R=2 Ragged vs awkward oracle.
Each property test draws a random nested R=2 structure and checks that the
native implementation agrees with an awkward-array oracle built from the same
raw buffers. Empty groups (outer_counts == 0) and empty inner segments
(inner_lens == 0) are exe... |
e488c7b9db61a8dd533fa2c33ff789072fbe90a86a5202c48d4f04e1287ea7e0 | Python | 10,299 | 293 | from contextlib import nullcontext as does_not_raise
import numpy as np
import pytest
import pynapple as nap
from .helper_tests import MockArray
class TestTsArray:
@pytest.mark.filterwarnings("ignore")
@pytest.mark.parametrize(
"time, expectation",
[
(MockArray(np.array([1, 2, ... |
f8d887b6bf7b731700674e17c84352cb7f06d51c0064c1ceb9bface6459bbf28 | Python | 10,299 | 267 | #!/usr/bin/env python3
# Copyright (c) Facebook, Inc. and its affiliates. All Rights Reserved.
"""Multi-view test a video classification model."""
import os
import pickle
import numpy as np
import slowfast.utils.checkpoint as cu
import slowfast.utils.distributed as du
import slowfast.utils.logging as logging
import ... |
9d63bc4602b4cb39b63de4701a00dd64fa3d2c102382c27375a2e828817a701a | Python | 10,300 | 272 | from . import InvertibleModule
import warnings
from copy import deepcopy
import numpy as np
import torch
import torch.nn as nn
import torch.nn.functional as f
class InvAutoActTwoSided(InvertibleModule):
'''A nonlinear invertible activation analogous to Leaky ReLU, with
learned slopes.
The slopes are le... |
b518dcc47989dbf2c4341a9c4a99a218e1692f38094962e2c7ff215c149d45a7 | Python | 10,300 | 271 | """This module defines the job metrics collection framework for Galaxy jobs.
The framework consists of two parts - the :class:`JobMetrics` class and
individual :class:`JobInstrumenter` plugins.
A :class:`JobMetrics` object reads any number of plugins from a configuration
source such as an XML file, a YAML file, or a ... |
bac4cd506bd246a59195eb65cbbb09d3d9b25d60c497e613339bd3a14e3b752c | Python | 10,302 | 297 | """Tests for TorchLens private ``._tl`` metadata helpers."""
from __future__ import annotations
import copy
import pickle
from dataclasses import replace
from typing import Any
import pytest
import torch
from torch import nn
from torchlens.backends.torch._tl import (
DecorationTag,
ModuleMeta,
ParamMeta... |
9b46e95c27d8f1975a25616c7f6b71759b0cb650dfd20c82f42110251547f53f | Python | 10,304 | 278 | #!/usr/bin/env python3
"""
File: Correlate_correlations_with_smartseq.py
Created: 2021/05/25
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 thi... |
5466aef66fb73dd7312229457e8654f2fcd1e5fb116331b260fff29b3f600e06 | Python | 10,306 | 202 | import random
import os
from re import I
from agents.model_1d import *
from envs.int_discrim import IntervalDiscrimination
import numpy as np
import torch
import matplotlib.pyplot as plt
from datetime import datetime
import argparse
from tqdm import tqdm
import re
import sys
sys.path.insert(1,'/home/mila/l/lindongy/dee... |
9cc1d9255433942b683565da9496eda44eaa0d062be6652c0a1cc9a9697dfb21 | Python | 10,306 | 339 | # --- 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 Font(_BaseTraceHierarchyType):
_parent_path_str = "carpet"
_path_str = "c... |
070d599b68239bccf1730978f439fb8233fd0b956fae786c54b7f8d8290e53e6 | Python | 10,308 | 239 | """Lane W051-HONESTY: live ``run()`` output-contract honesty (AUD-HONESTY H1/H2/H3).
The review-5.1 audit found that every tuple/dict/HF-container model settled
``unverifiable`` + poisoned on a DEFAULT-capture live ``run()`` with a remedy-less
``output_structure_mismatch`` (H2; closed for good by W051-CAPT2, which reg... |
9c131452107026e2edc6eb6147022c4118dc7973f832e0724ee9c1e7ee20048b | Python | 10,309 | 276 | #!/usr/bin/env python
import argparse
import json
from cp_common_functions import (get_json_value,
get_pipeline_lines,
get_total_number_of_modules,
INDENTATION, update_module_count,
... |
ccc5d8e1c974e673528921100112b51d7b6194bb93019d138e7d32af8e37af20 | Python | 10,310 | 301 | import os
from os import PathLike
from typing import Dict, List, Type, Union, Literal, Optional
import seqdata as sd
import xarray as xr
from ..models import SequenceModule
from pytorch_lightning import LightningModule, Trainer, seed_everything
from pytorch_lightning.callbacks import ModelCheckpoint
from pytorch_light... |
7428cd0ac7280947685ec81c3795d250d1d1e227b18bc746f2e2b718d40e5062 | Python | 10,311 | 234 | """r7 R80 (fable b10 MED x2): freeze the sprint-token test-naming namespace.
Two naming diseases grew unchecked through six rounds:
1. **rN-token filenames**: 141 test files carry a bare sprint-round
token (``test_r55_*``, ``*_r10r60``), and 32 distinct tokens appear in MORE
THAN ONE file under DIFFERENT number... |
b518048171d33f80a08db7aa779f337186e47f0822b1db4a96ad3aec4ca61662 | Python | 10,312 | 340 | # --- 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 Font(_BaseLayoutHierarchyType):
_parent_path_str = "layout.title"
_path... |
75b8cfb79a6504bd8f37231d7d473352ceaf43e9c65be07a2725feb772a8c73e | Python | 10,313 | 317 | from pathlib import Path
from typing import Any, Dict, List, Literal, Optional, Union, cast
import joblib
import numpy as np
import polars as pl
import pyBigWig
import zarr
from more_itertools import split_when
from numcodecs import (
Blosc,
Delta,
VLenArray,
VLenUTF8,
blosc, # type: ignore
)
from... |
2322e1364675f6fae54005df5a79a99f8d9153bda87b5cd3870b4e8280322f5f | Python | 10,315 | 340 | # --- 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 Textfont(_BaseTraceHierarchyType):
_parent_path_str = "heatmap"
_path_str... |
92e407bfbcc9333ae4901456b9948d77831f7105cea4f0539f793a4d95eeb75f | Python | 10,315 | 234 | from . import InvertibleModule
from typing import Union
import numpy as np
import torch
import torch.nn as nn
from torch.nn.functional import conv2d, conv_transpose2d
from torch.cuda.amp import autocast
class ActNorm(InvertibleModule):
'''A technique to achieve a stable initlization.
First introduced in Kin... |
b17b00a2a10b978dde5f4b0470dbfba130c10d2d443630af1c84091881d84b8c | Python | 10,320 | 340 | # --- 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 Textfont(_BaseTraceHierarchyType):
_parent_path_str = "sankey"
_path_str ... |
1be480bf6b13adc2bf8f2261a882a04ccc1d6694d579625e41d286e8e239eabf | Python | 10,321 | 256 | #!/usr/bin/python3
# -*- coding: utf-8 -*-
"""Workflow for gridsearching parameters for training a graphical model on neuronal
spiketrain data.
"""
import time
import sys
import os
import logging
import crf_util
from workflow import Workflow
class GridsearchTrial(Workflow):
"""Class to gridsearch parameters ... |
5307e5c41a0593ca72edd7cf828836539d823075e6874af1652de9ed5d304929 | Python | 10,322 | 222 | # 均匀采样效果较差
import json
import numpy as np
import os, sys
from collections import Counter
from sklearn import preprocessing
from sklearn.metrics import f1_score
from sklearn.metrics import confusion_matrix
import torch
import torch.nn as nn
import torch.nn.utils.rnn as rnn_utils
import torch.nn.functional as F
from torc... |
1e45eafdd80820270ad3f0566611edfabed6d1aa7428a90edec85579acc93ccb | Python | 10,323 | 302 | """
Process an input dataset into a format suitable for machine learning.
"""
from __future__ import print_function
from __future__ import division
from __future__ import unicode_literals
import os
import gzip
import pandas as pd
import numpy as np
import csv
import numbers
import tempfile
from rdkit.Chem import rdmolf... |
349f58e8a0e5f0458d87caa3593da0efce6d02e055a22466f51f39bc468f13c7 | Python | 10,325 | 340 | # --- 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 Textfont(_BaseTraceHierarchyType):
_parent_path_str = "histogram"
_path_s... |
1de07f92f0f924b244f16fa0ba38ad70da9655c9f0b7844aff79eef3e046bbc7 | Python | 10,329 | 288 | #!/usr/bin/env python3
"""
File: compare_gene_expression_per_pic.py
Created: 2022/05/03
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 sou... |
559ace1362fcea2f7abd5cdba49f038b2c9e84c0bbb8635bacb10506d59d7f81 | Python | 10,332 | 254 | import os
import numpy as np
import pandas as pd
from abc import ABC, abstractmethod
from rdkit.Chem import Mol
from typing import List, Sequence, Dict, Tuple
from torch.utils.data import Subset
from tqdm import tqdm
from bioconfpred.data.split import DataSplit
from bioconfpred.conf_ensemble import ConfEnsembleLibrary... |
e484d71d34bf11716a2e5b1419289a359f306fc327a9e501f80802aa8da27244 | Python | 10,333 | 229 | import os
import torch
from collections import OrderedDict
from abc import ABC, abstractmethod
from . import networks
class BaseModel(ABC):
"""This class is an abstract base class (ABC) for models.
To create a subclass, you need to implement the following five functions:
-- <__init__>: ... |
217ade9fbad2aed838150bfb05948e5ff83ebe9b0c354d31857dc938ba5f0293 | Python | 10,334 | 270 | import sys
import os
import glob
import numpy as np
import nibabel as nib
from sklearn.linear_model import LinearRegression
import warnings
warnings.simplefilter('ignore')
subject = sys.argv[1]
funcDir = sys.argv[2]
labelDir = sys.argv[3]
parcDir = sys.argv[4]
# check if surface directory exist; exit if false
if os.... |
3d754789f9543a5e41e94b8cd3c1117629ca54f0345e70ef07995d92aeab470c | Python | 10,334 | 306 | from argparse import ArgumentParser
from copy import deepcopy
from typing import Any, Union
import torch
from pytorch_lightning import LightningModule, Trainer, seed_everything
from torch.nn import functional as F
from torch.optim import Adam
from pl_bolts.callbacks.byol_updates import BYOLMAWeightUpdate
from pl_bolt... |
6060c459156d564e7c6900bdfdecad383f7a88b03365c2862821532d7b2a26b8 | Python | 10,335 | 327 | import math
import jax
import jax.numpy as jnp
from keras.src.backend.common import standardize_dtype
from keras.src.backend.jax.ops.core import convert_to_tensor
from keras.src.utils.module_utils import scipy
def segment_sum(data, segment_ids, num_segments=None, sorted=False):
if num_segments is None:
... |
e588ad8a05e3d66f323026f316d6fba842a890adf73beafd0fcd29749e471f44 | Python | 10,335 | 340 | # --- 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 Textfont(_BaseTraceHierarchyType):
_parent_path_str = "histogram2d"
_path... |
651bef8cdbd1e242afa9d678d348c50e90617e8da1db96f00b69f7903685f569 | Python | 10,336 | 340 | # --- 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 Tickfont(_BaseTraceHierarchyType):
_parent_path_str = "parcats"
_path_str... |
053fe5ed677121312bcb62b653beafccc4c95898cb0d05eb594463bb422d630f | Python | 10,337 | 340 | # --- 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 Font(_BaseLayoutHierarchyType):
_parent_path_str = "layout.slider"
_pat... |
9b54572d2bf2d997ffe3e9c808ff471c75cc783988f25002ff7a5e02e3a4573a | Python | 10,338 | 292 | """Round-3 security regression: torch-namespace RCE / arbitrary-file-write.
A crafted ``.tlspec`` bundle op keyed ``("torch", "load")`` or ``("torch",
"save")`` historically resolved ``torch.load`` / ``torch.save`` through the
untrusted callable resolvers (filtered only by ``callable(...)``), giving RCE
(unpickle) or ... |
a9c3e9a9bf6ad473ac62957cec13e8b304e68d9cf1a846a3231fbcf5c5cf0ed0 | Python | 10,338 | 277 | """Surface punch-list pins: List-C removals and the zero-evidence demotions.
The 2026-08 completeness audit (E1 + E1-r2, adopted by RULINGS Batch-8 as the
funded punch list) classified the advertised public surface into REMOVE rows
(dead renames, duplicate exports -- deleted outright) and DEMOTE rows
(zero-external-ev... |
3c6daea7d90f1aa544b0aec60d45e6ab85fcd26a3d3eb68f00a81f335ce5e55b | Python | 10,340 | 340 | # --- 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 Tickfont(_BaseTraceHierarchyType):
_parent_path_str = "carpet.aaxis"
_pat... |
7bf55d821acc8f6958850f544688b99e7f1cc44adcf3125fb036cb02b226fe6e | Python | 10,340 | 340 | # --- 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 Tickfont(_BaseTraceHierarchyType):
_parent_path_str = "carpet.baxis"
_pat... |
9267671e1b54af65e9d0c62b2ff44c23a172d03853a7f0903942fd5178d0533e | Python | 10,341 | 340 | # --- 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 Font(_BaseLayoutHierarchyType):
_parent_path_str = "layout.legend"
_pat... |
ab17b53f1f07f53859717f34b50b4348850822c0efc4f8fb25f3ec342923d317 | Python | 10,341 | 380 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Wed Feb 24 17:48:18 2021
This scripts contains little helper functions to do with data paths, binning labels, sorting data and circular
statistics methods.
@author: emilia
"""
import numpy as np
import os.path
from pathlib import Path
import torch
import pi... |
34bf1028b8217803b2586fa871a713bda7a3cc73dc162ab2d4dddcbf1e1c055a | Python | 10,342 | 340 | # --- 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 Font(_BaseTraceHierarchyType):
_parent_path_str = "indicator.delta"
_path... |
4a5039550e143b8d01d8d2d6541f0a7f77bc093078160de824bcff07f893a67f | Python | 10,342 | 340 | # --- 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 Font(_BaseTraceHierarchyType):
_parent_path_str = "indicator.title"
_path... |
787415fb6134cbd3efd6499f36c0b92d41b64164c26acc6855172ef6cb62a354 | Python | 10,343 | 340 | # --- 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 Tickfont(_BaseLayoutHierarchyType):
_parent_path_str = "layout.xaxis"
_... |
975d00bf6d568211a4da74362da0c1b8c00f2751431735df7e36b13a6ea11ef5 | Python | 10,343 | 340 | # --- 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 Tickfont(_BaseLayoutHierarchyType):
_parent_path_str = "layout.yaxis"
_... |
36f81f1ceaae2c6dd49b7d5d00a3b51bfd3333359fd2e6afcdbd186fbbb1a765 | Python | 10,344 | 268 | # Copyright (c) 2025, Tri Dao.
import os
from typing import Tuple
from functools import lru_cache
import torch
from torch._subclasses.fake_tensor import FakeTensor
try:
from triton.tools.disasm import extract
except ImportError:
extract = None
import cutlass
import cutlass.cute as cute
from cutlass.cutlass_... |
aa5871f69098277b0b0b4b630bf9298089ac1ae85b8192894cead0d3a09f754a | Python | 10,345 | 340 | # --- 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 Labelfont(_BaseTraceHierarchyType):
_parent_path_str = "parcats"
_path_st... |
1dd10533c8d67fdcea95a6607fa038e67f75596f59d4796f558d60c3fd6b993c | Python | 10,346 | 340 | # --- 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 Font(_BaseTraceHierarchyType):
_parent_path_str = "carpet.baxis.title"
_p... |
5d8ad057bc32e8fca8aff04149d1477671932f5ef7936a047154f6d300df4584 | Python | 10,346 | 196 | import os
import voxcell
import json
import numpy
# from .parcellation_levels import AibsLevel
from . import parcellation_levels
class ParcellationProject(object):
_path_config = "input/configuration/config.json"
def __init__(self, root, resume=False):
"""
root: Path to project root. A confi... |
809af771d0cadae285e922b6e5527bc94f940c880ec6574cfd1b8eacbe23a987 | Python | 10,346 | 340 | # --- 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 Font(_BaseTraceHierarchyType):
_parent_path_str = "carpet.aaxis.title"
_p... |
757c5c0c9bd675a763dcd57ad509311caea3dee5879d5971a943a69cfa411684 | Python | 10,347 | 340 | # --- 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 Font(_BaseLayoutHierarchyType):
_parent_path_str = "layout.annotation"
... |
2ef096fe6ab33ea8ee2dd23781ab034fe0c2d88036542b7d15012429bc300cc5 | Python | 10,349 | 340 | # --- 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 Font(_BaseLayoutHierarchyType):
_parent_path_str = "layout.xaxis.title"
... |
832e5eea23eef007ecb2b3d74ad162b66298b5b8b81ffdc9b67bee047b590697 | Python | 10,349 | 340 | # --- 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 Font(_BaseTraceHierarchyType):
_parent_path_str = "indicator.number"
_pat... |
fb2432161918b91773d498e663d40a9035362b1c45600c1c9c45846efaff734f | Python | 10,349 | 340 | # --- 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 Font(_BaseLayoutHierarchyType):
_parent_path_str = "layout.yaxis.title"
... |
eaa6f87abc05e8f5053a6dc0ee6f3e448b488d405df4c74b8444da645b633267 | Python | 10,350 | 255 | from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
from __future__ import unicode_literals
import pandas as pd
import os
import time
import pdb
import csv
import re
from dcCustom.trans import undo_transforms
import dcCustom
from collections import OrderedDict
... |
6649412269901597bbfa64ac67851183c71abebb6370a7cf76aa8d6a0b33b898 | Python | 10,351 | 250 | """
Fitting Power Spectrum Models Across 3D Arrays
==============================================
Fitting power spectrum models across 3D arrays of power spectra.
"""
###################################################################################################
# Running Across 3D
# -----------------
#
# Most of... |
df9c5c60947e2ec656a8b1f41f6645622251ac789addc31b0f60ff03adcf3a63 | Python | 10,352 | 340 | # --- 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 Tickfont(_BaseTraceHierarchyType):
_parent_path_str = "parcoords"
_path_s... |
7a5a7a892b6685789ec47e7728ad4506362b0e7b82defb11a22de003813c878a | Python | 10,353 | 240 | __doc__ = """
Compute log likelihood values for crossvaldiation.
In order to run this file, you will need to first run the "analysis*.py" scripts. This will
generate backup files in the folder sim_backup.
This code was adapted from Fründ, Wichmann, Macke (2014): Quantifying the effect of inter-trial dependence on per... |
add8e188e6912042585a8470e85f971101e7ec601ae712dec58d90e3aa6ac16f | Python | 10,353 | 262 | #!/usr/bin/env python
"""Tests for `stlearn` package."""
import os
import unittest
import numpy as np
from numba.typed import List
import stlearn as st
import scanpy as sc
from tests.utils import read_test_data
import stlearn.tools.microenv.cci.het_helpers as het_hs
import stlearn.tools.microenv.cci.het as het
g... |
ca94043844019a8316be902167169e515e9553713f596a9c63f96ecbd2549fd5 | Python | 10,353 | 340 | # --- 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 Font(_BaseLayoutHierarchyType):
_parent_path_str = "layout.shape.label"
... |
193700b8682f650ddf9f7df7e801b87e9d498ec0a1ba7b79761c4755c632f50f | Python | 10,354 | 361 | import h5py
import numpy as np
import torch
from torch.utils.data import DataLoader
import torch.nn as nn
import os
# from motifs import read_motifs, motifs_for
from utils import clip_datapoint, modify_sl, print_topl_statistics
class ResidualUnit(nn.Module):
"""
Residual unit proposed in "Identity mappings... |
49b2c35aaf8976a26332b2ccd4d5a8038c3922c7cda15abec9d4a77638c34ec7 | Python | 10,355 | 340 | # --- 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 Labelfont(_BaseTraceHierarchyType):
_parent_path_str = "parcoords"
_path_... |
5c6b763ddead2928554b6980b53dc79e0525c223bf0f0168b12a108a0231232d | Python | 10,355 | 294 | """Datamodules for RL models that rely on experiences generated during training Based on implementations found
here: https://github.com/Shmuma/ptan/blob/master/ptan/experience.py."""
from abc import ABC
from collections import deque, namedtuple
from typing import Callable, Iterator, List, Tuple
import torch
from torch... |
1b298cf4c82d49dfdbbabaa9d4410c4063b444905d0dafc4c658892f18c1b575 | Python | 10,357 | 340 | # --- 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 Font(_BaseTraceHierarchyType):
_parent_path_str = "cone.colorbar.title"
_... |
716eb6139238d464a871ee483272fbfb967aaf608f9ed90a264fde5d742a00cf | Python | 10,358 | 334 | from ..utils import constants, gislib
import pandas as pd
import geopandas as gpd
import shapely
import os
import errno
import requests
import numpy as np
distance = gislib.getDistance
def diff_seconds(t_0, t_1):
return (t_1 - t_0).total_seconds()
def is_multi_user(data):
if constants.UID in data.columns:
... |
5fdf61cfdd014ed35cb2db530bbd5960b438da1d67ecb892615c8aa11e744091 | Python | 10,359 | 223 | # 均匀采样效果较差
import json
import numpy as np
import os, sys
import random
from collections import Counter
from sklearn import preprocessing
from sklearn.metrics import f1_score
from sklearn.metrics import confusion_matrix
import torch
import torch.nn as nn
import torch.nn.utils.rnn as rnn_utils
import torch.nn.functional ... |
2427549143081ca9ae8f87d0763d5b18a7aa7e265b9dee5ca92ae9ac6688a175 | Python | 10,360 | 221 | 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... |
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