sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
eebf48519fe8fe76d844558f63fdbe55f0bbf8d8abd8599c710e540e5f686828 | Python | 20,034 | 490 | import os
import sys
import base64
import struct
from collections import defaultdict
import argparse
import h5py
import xmltodict
import numpy as np
import pandas as pd
from tensorflow.keras.models import load_model
from ml4h.TensorMap import TensorMap, Interpretation
from ml4h.defines import ECG_REST_AMP_LEADS
from m... |
6868ba1a13a0bb3c7b3d7c09993ae97b6d2461afb249a2213ccaec3d5227923f | Python | 20,037 | 545 | """
Copyright (c) Meta Platforms, Inc. and affiliates.
This source code is licensed under the MIT license found in the
LICENSE file in the root directory of this source tree.
"""
from __future__ import annotations
import copy
import logging
from abc import ABCMeta, abstractmethod
from collections import defaultdict
... |
f271c8e8266788921ac4a480bf35c10d50cdb8a526db4b6413afea68287c22ad | Python | 20,060 | 567 | # Copyright 2023 The HuggingFace Team. 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 applicabl... |
83bb6f0795ddd6147c9a1507bcc3059cbfff6aa4b75300094c562cffec3d1929 | Python | 20,078 | 623 | """
Step-by-step processing functions for memory-efficient single-cell analysis.
This allows users to run each step individually and save results between steps.
"""
import os
import anndata
import numpy as np
import scanpy as sc
from .._settings import add_reference, settings
from ..pp import (
mde,
neighbor... |
f300c0ab27797671f4858c042116e6640e63a0e3812e87c1ae06d52c7786c363 | Python | 20,081 | 450 | import argparse
import pickle
from collections import namedtuple
from typing import List
import numpy as np
import torch
import tqdm
import visionloader as vl
from torch import autocast
from whitenoise import RandomNoiseFrameGenerator
import lib.data_utils.data_util as du
import lib.data_utils.dynamic_data_util as dd... |
ce435cb66dab7d60323ab604c5d768738e6dd54af120959e434ed48f94b578bc | Python | 20,086 | 474 | """ToolRuntime — tool dispatch hub and runtime facade.
Extracted from ``smart_agent.py`` to keep tool handling in one place.
Concrete handler implementations live in dedicated handler modules:
- ``tool_runtime_exec`` — execute_code / run_snippet / bash / agent / inspect / search / finish
- ``tool_runtime_io`` ... |
6196348ab272f2765c6d6db378b14df208c34165c705490de495b9fa26874132 | Python | 20,097 | 507 | import pandas as pd
import numpy as np
# non-motor
def UPDRS1(dataframe, seq_data, feature_map, visit):
target_vars = ['updrs1', 'hallucination', 'Apathy', 'Pain', 'Fatigue']
updrs1_idxs = [feature_map[ft] for ft in ['NP1COG', 'NP1HALL', 'NP1DPRS', 'NP1ANXS', 'NP1APAT', 'NP1DDS', 'NP1SLPN', 'NP1SLPD', 'NP1PAIN... |
b746b038fa3ae39572dc98726390b342e571d2944f344d649d3c732565da450b | Python | 20,115 | 419 | import torch
import torch.nn as nn
from torch.optim import Optimizer, AdamW
from torch.optim.lr_scheduler import LambdaLR
import numpy as np
from tqdm import tqdm
import os
import platform
from sklearn.model_selection import KFold
from splam_utils import *
from splam_dataset_Chromsome import *
from SPLAM import *
impor... |
35b3f334f6547fd9183dd28e4ddfc239e773a471880c978a7bd79d8904b510fe | Python | 20,129 | 604 | """Test utilities for Ray.
This module contains test utility classes that are distributed with the Ray package
and can be used by external libraries and tests. These utilities must remain in
_common/ (not in tests/) to be accessible in the Ray package distribution.
"""
import asyncio
import inspect
import logging
imp... |
325a4d6b2d836212dfb14347d33c3f6e9311aaffc2f3ad9111fa1db2843b7ebb | Python | 20,134 | 588 | # Copyright 2023 Google LLC
# 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
# https://www.apache.org/licenses/LICENSE-2.0
# Unless required by applicable law or agreed to in writing, sof... |
19e490ce4b49ca73918639940c64d17be76d5b117c6b178ecb4a8417649240bb | Python | 20,147 | 546 | import torch
import torch.nn as nn
from typing import List, Union, Sequence, Tuple, Dict
from monai.networks.blocks import ResidualUnit, MaxAvgPool, UpSample, Convolution
from monai.utils.enums import UpsampleMode
from src.networks.vqvae.vqvae import VQVAEBase
from src.layers.vector_quantization import VectorQuantiz... |
11a4d93a46e8522eb002e1a1c81a059e5944c6d75167fce93c9bbf0ad794f2d7 | Python | 20,167 | 493 | from typing import List, Optional, Union
import matplotlib.pyplot as plt
import numpy as np
import pandas as pd
import scanpy
import torch
from anndata import AnnData
from pyro import clear_param_store
from pyro.infer import Trace_ELBO, TraceEnum_ELBO
from pyro.nn import PyroModule
from scvi import REGISTRY_KEYS
from ... |
691c3d04c568d7ff679ad19f97f58ac9a942c73e587913c625bd33330e5b98d5 | Python | 20,171 | 383 | """PCA -> fixed+adaptive Gabor -> sign hashing -> sparse block histograms."""
import logging
from pathlib import Path
import numpy as np
from scipy import sparse
import torch
from torch import nn
from torch.nn import functional as F
from .config import PalmConfig
from .gabor import fixed_gabor_bank, search_orientations... |
0698d59106476202f6f63ba616c32073b6daea8aa530425baa2f4d6a6fc27f81 | Python | 20,182 | 436 | from sklearn.preprocessing import MinMaxScaler
from torch.utils.data import DataLoader, Dataset, random_split
import pandas as pd
import numpy as np
import os
import torch
import pickle
def _get_ModNN_input(start_time, timestep_minutes, occupancy=None, hvac=None,
temp_amb=None, solar=None, te... |
581504c7525e9d447a7998a5a60fc3cfaa1d2e190564af8fd8cd2ef0a207d048 | Python | 20,199 | 593 | # -*- coding: utf-8 -*-
from vtkplotlib._get_vtk import vtk
import numpy as np
from pathlib import Path
from vtkplotlib.plots.BasePlot import ConstructedPlot
from vtkplotlib.plots.Lines import Lines
try:
from stl.mesh import Mesh as NumpyMesh
NUMPY_STL_AVAILABLE = True
except ImportError:
NumpyMesh = Non... |
ed07fac3dda3c5846f808c37cedb338114dce1a09e908b0973e1195c47653508 | Python | 20,199 | 568 | import copy
import json
import warnings
from importlib.metadata import version as package_version
from pathlib import Path
from typing import Any, Optional, Union
from data_profiling.utils.backend import is_pyspark_installed
if not is_pyspark_installed():
from typing import TypeVar
sDataFrame = TypeVar("sDat... |
37cdfeeadbb3aa526ede6f6a885b58adf052593f81ef1c2aeffaadd269a9eddc | Python | 20,200 | 505 | r"""Let the ``AnnData``-shaped plots in ``ov.pl`` accept a plain table.
Most plotting functions in ``ov.pl`` only ever touch five things on an
``AnnData``: ``.obs``, ``.var_names``, the expression matrix (``.X`` /
``.layers`` / ``.raw``), ``.obsm``, and ``.uns`` for stored colours. Requiring
the whole container for th... |
35ee4101016ca5bb99472e307df33cdfc34f1e8f80d5c2fc6d38dc18b959a762 | Python | 20,201 | 511 | """10x Xenium In Situ reader for OmicVerse spatial I/O."""
from __future__ import annotations
import json
import warnings
from pathlib import Path
from typing import Any, Optional, Union
import numpy as np
import pandas as pd
from anndata import AnnData
from ..._registry import register_function
from ..single impor... |
6771f9a6f36926eb1876237074ca6974be9b77a62a659479509c64d7ff39ca43 | Python | 20,206 | 480 | import argparse, os, sys
from os import listdir
from os.path import isfile, join
from ipywidgets import widgets
import pickle
import math
import collections
import time
import numpy as np
import pandas as pd
import scanpy as sc
import warnings
from .._registry import register_function
warnings.filterwarnings('ignore'... |
9c7a6b44a7806e4c62e90c5f071c6d6ee53c2ca5b2ac00e7337fc6d0ce3c3e7d | Python | 20,207 | 437 | import scanpy as sc
import numpy as np
import matplotlib.pyplot as plt
from collections.abc import Collection
from sklearn.feature_selection import mutual_info_classif
import pandas as pd
from scipy.sparse import hstack, issparse
def moe_correct_ridge(Z_orig, Z_cos, Z_corr, R, W, K, Phi_Rk, Phi_moe, lamb):
Z_corr ... |
b175cfe2ca6ad1679487dc7f9d88c0e3f385c6f90b676018653f7566defb2581 | Python | 20,218 | 524 | import logging
import re
from collections import defaultdict
from typing import AsyncIterable, Awaitable, Callable, Dict, List, Optional, Tuple
from ray import ActorID, NodeID, WorkerID
from ray._common.pydantic_compat import BaseModel
from ray.core.generated.gcs_pb2 import ActorTableData
from ray.dashboard.modules.jo... |
34ad0fd7f169168c7cc3aa6e98e7fcad8fe6a0a9284a403b99d0133c88456ced | Python | 20,226 | 496 | from collections import Counter
from dataclasses import dataclass, field
from typing import Any, Dict, Optional
import numpy as np
from .conv import Conv1d, Conv2d
from .flatten import Flatten
from .node import NIRNode
from .pooling import AvgPool2d, SumPool2d
from .typing import Edges, Nodes, Types
from .utils impor... |
044b8c0e289a4663f33db761d10bfb74db49563c9234e70eea70ba04ba458a96 | Python | 20,228 | 448 | from typing import Any, Dict, List, Optional
import numpy as np
import pandas as pd
from anndata import AnnData
try:
from typing import Literal
except ImportError:
from typing_extensions import Literal
from .color import assign_color
from .distance import spatial_distance
from .logging import logger_manager ... |
2f0e20ad83c44a335833b4bc0a295a6e0beecd4d2174cf62d5035772ed2cd0e0 | Python | 20,263 | 504 | import asyncio
import errno
import ipaddress
import logging
import os
import pathlib
import posixpath
import sys
import time
from math import floor
from typing import List
import multidict
from packaging.version import Version
import ray
import ray.dashboard.optional_utils as dashboard_optional_utils
import ray.dashb... |
b54c73e4e79fa6c6831167f82f8067f2d5cb7fdb07b04d1e0ecc1b726d7f9c9f | Python | 20,265 | 520 | #
# CEBRA: Consistent EmBeddings of high-dimensional Recordings using Auxiliary variables
# © Mackenzie W. Mathis & Steffen Schneider (v0.4.0+)
# Source code:
# https://github.com/AdaptiveMotorControlLab/CEBRA
#
# Please see LICENSE.md for the full license document:
# https://github.com/AdaptiveMotorControlLab/CEBRA/bl... |
d58723a93088fd7bd5cd42c677399731c658066531de8f0b567434fda8788eed | Python | 20,279 | 503 | """
Core functional building blocks, composed in a Dask graph for distributed computation.
"""
import numpy as np
import pandas as pd
import logging
import scipy
from sklearn.ensemble import GradientBoostingRegressor, RandomForestRegressor, ExtraTreesRegressor
from dask import delayed
from dask.dataframe import from_... |
4e74903ba9952b7c9d621fbeef95a31b393feb1f06609a11fad6c20678e8a44e | Python | 20,307 | 458 | ####################################################################################################
# Copyright (c) 2016 - 2024, EPFL / Blue Brain Project
# Author(s): Marwan Abdellah <marwan.abdellah@epfl.ch>
#
# This file is part of NeuroMorphoVis <https://github.com/BlueBrain/NeuroMorphoVis>
#
# This program is fre... |
6112da7cf78443f3bcb6f520e1b153721871a35fd6532a66e73cc8cae0008677 | Python | 20,327 | 532 | import torch
import torch.nn as nn
import torch.nn.functional as F
import numpy as np
eps = 1e-8
def tmscore_torch(coords1, true_coords, dcut=15.0):
N, L, _ = coords1.shape
coords2 = torch.tile(true_coords[None, :, :], (N, 1, 1))
center1 = torch.mean(coords1, dim=1, keepdim=True)
center... |
4804b190e42a01e23e1e902777e3f09f523239bc6ac943bd646125711d770664 | Python | 20,328 | 642 | # This file is part of the INTREPPPID programme.
# Copyright (c) 2023 Joseph Szymborski.
#
# This programme is free software: you can redistribute it and/or modify
# it under the terms of the GNU Affero General Public License as
# published by the Free Software Foundation, version 3.
#
# This programme is distributed i... |
8616ad9808abc8d84bd6a7e4cab80d38e90cc701d18122e96cd1fc9b5ad9e134 | Python | 20,329 | 511 | #!/usr/bin/env python3.7
"""Defines Waveform class.
The copyrights of this software are owned by Duke University. Please
refer to the LICENSE and README.md files for licensing instructions. The
source code can be found on the following GitHub repository:
https://github.com/wmglab-duke/ascent
"""
import csv
import ma... |
e138cf0da021c4944baca8aeb05bd493c367a769ff0d629b85dd78cf8eddc659 | Python | 20,332 | 395 | """
This scripts implements a hacky solution to measure a some metrics on the STR expansion loci.
These metrics could be ideally extracted from the STR expansion caller, ExpansionHunter;
but the tool is not currently maintained. Hence, this script leverages parsing SVG images
that render a locus to measure the metrics.... |
cba6478b74108522f484f12bd571fe564fa0edbfa88785f992d26dc15752d519 | Python | 20,352 | 415 | # --- START OF FILE paper_checker_mode.py ---
import streamlit as st
import ast
import os
from google import genai
from google.genai import types
from token_counter import count_tokens_decorator
from logger_setup import logger
from rag_system import RAGSystem, PackageConfig
# NOTE: For production, set your GEMINI_API_... |
2108bd3cb78f42d625c82765fd94a85e96922625c6d3a24f0e7908f12fb6cfe3 | Python | 20,353 | 473 | import numpy as np
import pandas as pd
from utils import get_survey_items_order
# *********************************
# helper functions
# *********************************
def get_drop_columns(df, columns=None, use_default=True):
"""
defines columns to drop when converting from _clean to _event
files each ev... |
0bd225c5bf2481d90b704c5043528d2011adea12b360255ff72739ac49bcd48c | Python | 20,370 | 525 | # Copyright 2023 The HuggingFace Team. 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 applicabl... |
e622cf4cfb965295fa74be558f254290cd1b84113371114f970e1e92f434f96d | Python | 20,372 | 429 |
import numpy
import os
import time
import yaml
import platform
import copy
import datetime
import matplotlib
import h5py
import random
import multiprocessing
from copy import deepcopy
from matplotlib import pyplot
from shutil import copyfile
from collections import defaultdict
from functools import partial
from pyst... |
8d06752daa3e0e8568ddd5fd4d18b1f32f058440ef6f468f0cdb5549c24f8a99 | Python | 20,377 | 684 | r"""
Genomics operations
Copy from scglue: https://github.com/gao-lab/GLUE/
"""
import collections
import os
import re
from ast import literal_eval
from functools import reduce
from itertools import chain, product
from operator import add
from typing import Any, Callable, List, Mapping, Optional, Union
import network... |
f41207f4b575db586f6dc5d175615c4fc4b73cfbfc9d0e5ce3a268c91027695c | Python | 20,383 | 479 | # -------------------------------------------------------------------------------------------------------------------------------------
# Following code curated for Bio-Diffusion (https://github.com/BioinfoMachineLearning/bio-diffusion):
# --------------------------------------------------------------------------------... |
fbdc6a5faab4960c70ca802e81f471fe61f2ba138fcb1856eae4af5e4a0c619a | Python | 20,393 | 641 | #!/usr/bin/env python
"""
Copyright (C) 2017 Allen Institute for Brain Science
This program is free software: you can redistribute it and/or modify it
under the terms of the GNU General Public License Version 3
as published by the Free Software Foundation on 29 June 2007.
This program is distributed WITHOUT WARRANTY OF... |
443e2a9245c39407db2ed3c8f68996c5f85d9ef52e95a5316ded99463496863f | Python | 20,395 | 506 | ####################################################################################################
# Copyright (c) 2016 - 2024, EPFL / Blue Brain Project
# Author(s): Marwan Abdellah <marwan.abdellah@epfl.ch>
#
# This file is part of NeuroMorphoVis <https://github.com/BlueBrain/NeuroMorphoVis>
#
# This program is fre... |
229a8448430c852e151404ce96988a734bb9883ca37c0e367fe3ed302e5823d6 | Python | 20,404 | 439 | import argparse
import pickle
from typing import Dict, List
import numpy as np
import torch
import tqdm
import visionloader as vl
from whitenoise import RandomNoiseFrameGenerator
import lib.data_utils.data_util as du
import lib.data_utils.dynamic_data_util as ddu
import lib.dataset_config_parser.dataset_config_parser... |
e45cc3a2cf92330e0bd2c1b027ce4130c505a631e957e5545ba3c1a88457480e | Python | 20,417 | 433 | from __future__ import annotations
import logging
from concurrent.futures import Future, ThreadPoolExecutor, as_completed
from dataclasses import dataclass
from typing import TYPE_CHECKING, AbstractSet, Iterable, Iterator, NamedTuple, Tuple
import pyarrow as pa
import pyarrow.dataset as pds
import pyarrow.fs as pafs
... |
c137faa04a18ec22f6479a9b2d7b648aecef029159c5942637a8ee64c68b9e27 | Python | 20,453 | 375 | class Reservoir:
def __init__(self,Utotal,hyperparameters):
'''
Initialize the reservoir, input the training set, initialize some parameters, and input hyperparameters
'''
# Input layer
u=Utotal[0]
self.NumBifurPara=np.shape(Utotal)[0]
sel... |
106f3fedc760168e62bc397f983828a73b798d87aa62fbf0134b7057c60f5f3b | Python | 20,456 | 612 | import torch
import torch.nn as nn
import torch.optim as optim
from torchvision import datasets, transforms
from torch.utils.data import Dataset, DataLoader
from copy import deepcopy
import numpy as np
import matplotlib.pyplot as plt
import argparse
import pdb
import os
import sys
import scipy.io
import mat73
import ma... |
c0ef7dfa599ab4d6b81105b554cf52f9b6c8244134e3fdedeae833d35f2a7635 | Python | 20,461 | 591 | import os
import pytest
import numpy as np
import tensorflow as tf
from itertools import cycle
from collections import defaultdict
from typing import List, Optional, Dict, Tuple, Iterator
from ml4h.TensorMap import TensorMap
from ml4h.models.model_factory import make_multimodal_multitask_model
from ml4h.models.train i... |
019febb73054791e1c05e1849959953168d3998cb1d4e4020e5476fabbd584a5 | Python | 20,474 | 516 | # utility function for loading files etc
import numpy as np
import pandas as pd
import os
import matplotlib.pyplot as plt
def load_tsv(path):
"""
Loads a tsv, as a numpy array with the headers removed.
"""
df = pd.read_csv(path, sep='\t', skiprows = 0)
return df.values
def get_session_number(unit... |
8b0b4c0459c142fa0b6c4a28d5f21c8ccca520011d920e0c9f178fe88190056c | Python | 20,483 | 492 | """
Copyright (c) Meta Platforms, Inc. and affiliates.
This source code is licensed under the MIT license found in the
LICENSE file in the root directory of this source tree.
Post-Relaxation Structure Filtering, Deduplication, and Ranking Module
This module provides comprehensive functionality for processing ML-rela... |
a9aea8af1a6cecd883f480d73437fa95066576479937af55e50e1ef21e9ee3db | Python | 20,493 | 663 | """A collection of utilities used by snap polygons to manipulate shapely
objects.
"""
from typing import (
Optional, Dict, Union, Sequence, Callable, Iterable, Iterator
)
import collections
import math
from functools import partial
import sys
import itertools as it
import shapely.ops
from shapely.geometry.base imp... |
b570755ac12905ba49659440a7030e135311411ecb1d13edf115806fc4c2e3b4 | Python | 20,496 | 495 | from typing import List, Optional, Callable, Dict, Tuple, Union
import numpy as np
import torch
import tqdm
from lib.data_utils.dynamic_data_util import _JitterReconstructionBrownianMovieBlock
from lib.data_utils import dynamic_data_util as ddu
from lib.data_utils.matched_cells_struct import OrderedMatchedCellsStruct... |
dfd1a1385ee16973e058be62b0f542cd52ccc639bff215cbe3acbc1f60a17984 | Python | 20,500 | 568 | """
Classes for creating patient objects compatible with TWSTRS.
"""
import logging
import networkx as nx
import numpy as np
import pandas as pd
import scipy as sc
import simdkalman
from scipy import signal, ndimage
from .structural_features import compute_distances
from .utils import pre_high_pass_filter, pre_low_pas... |
cb60df99594167f06fa33bd5f41db2f5669a362ae44934022482c32da2077523 | Python | 20,506 | 508 | import os
import math
import numpy as np
import scipy.sparse
from enum import Enum
import struct
import spinnaker2
APP_BASE_PATH = os.path.abspath(os.path.join(
os.path.dirname(os.path.realpath(__file__)),
"../../../s2-sim2lab-app/chip/app-pe/s2app"))
APP_BASE_PATH_FPGA = os.path.join(
os.path.dirname(os.... |
916b2a81c5c3f165da72a28ad62ec76d974c9817d7c6fddb696c0517a03e82cc | Python | 20,507 | 450 | """Build-time fetch and Sphinx wiring for external Anyscale example templates.
Everything here exists because the docs build pulls example templates from
``templates.ci.ray.io`` at build time (via sphinx-collections) and then renders
the fetched ``_collections/`` content. It is kept out of ``conf.py`` so that
changes ... |
a369492592c904c40ed340a08dea7bbb665ed7ddbeaeeb553a3ff48fc7933796 | Python | 20,525 | 352 | import cloudpickle
import queue
import os
import projectmetis.python.utils.proto_messages_factory as proto_factory
from pebble import ProcessPool
from projectmetis.python.logging.metis_logger import MetisLogger
from projectmetis.python.models.model_dataset import ModelDataset, ModelDatasetClassification, ModelDatase... |
5dc1342117d02aa367545c1e750812d1526458bafb8a6b77fbf44a81762aff4c | Python | 20,531 | 694 |
# coding: utf-8
# # Table of Contents
#
# 1. [Import & Set Up](#import_everything)
# 2. [Load in data](#load_files)
# 3. [Center of Mass](#c_o_m)
# 1. [distance apart](#distance_apart)
# 2. [error by overlap](#error_by_overlap)
# 4. [Face Associate Task](#face_task)
# # Import Stuff
# <a id='import_everythi... |
dd7231d5e6ec2465bbf5e9991ded58566384cc635e3d6a85820aafe032cc1de7 | Python | 20,537 | 427 | import os
import time
from subprocess import call
import numpy as np
import pandas as pd
import seaborn as sns
from scipy import stats
import seaborn as sns
import matplotlib.pyplot as plt
import scipy as sc
from matplotlib.colors import ListedColormap
import scipy.sparse as sparse
import importlib
import copy
import ... |
87866843ca23701fbac3c7ccd16723b48679dcd86fbbbc2060cce90d84feb5c0 | Python | 20,544 | 708 | import torch
import numpy as np
import torch.nn as nn
import shutil, os
from m2snn.spikes import *
from m2snn.surrogate import spike_fn
from PIL import Image
import matplotlib.pyplot as plt
from copy import deepcopy
class SNN(nn.Sequential):
def __init__(self, *modules):
super(SNN, self).__init__(*module... |
3136938cce31bd64359f332302852ec24169713c95dab30eb1fae769e483574f | Python | 20,546 | 432 | import networkx as nx
import numpy as np
import pandas as pd
import scipy, random
import scanpy as sc
from tqdm import tqdm
import matplotlib.pyplot as plt
from sklearn.metrics import pairwise_distances_chunked, pairwise_distances
from .visualize import link_plot
def coords2adjacentmat(coords,output_mode = 'adjacent',... |
1e08a356ec7f411cf9ba641c1685cced06cb05aa4837b6604bce2e8312b62ad8 | Python | 20,553 | 668 | import numpy as np
import pandas as pd
from sklearn.linear_model import Lasso
from sklearn.preprocessing import PolynomialFeatures
from sklearn.linear_model import LinearRegression
from sklearn.pipeline import Pipeline
from sklearn.preprocessing import StandardScaler
import scipy.stats as stat
import math
import os
im... |
94e50526690ba45e3076ff048b1550642461fcd5b1b88250349dfa2529b543ff | Python | 20,568 | 606 | import tqdm
import numpy as np
import matplotlib.pyplot as plt
from matplotlib.animation import FuncAnimation, writers
from matplotlib.collections import LineCollection
from sklearn.neighbors import NearestNeighbors
from scipy.stats import norm as normal
from .._registry import register_function
class Streamlines(obj... |
5756e713591d963b00939563ece122c82dbe3d95755e84ce8357c77bf6e57c24 | Python | 20,569 | 592 | ####################################################################################################
# Copyright (c) 2016 - 2024, EPFL / Blue Brain Project
# Author(s): Marwan Abdellah <marwan.abdellah@epfl.ch>
#
# This file is part of NeuroMorphoVis <https://github.com/BlueBrain/NeuroMorphoVis>
#
# This program is fre... |
ebf3cc6707577e4696801eddaaee7089aa37db71c748c352d66353d61f3b4081 | Python | 20,575 | 625 | """Evolution example: STO surface with NNFF"""
import copy
import pathlib
from typing import Callable, NamedTuple, Tuple
import numpy as np
import numpy.typing as npt
import torch
from mace import data
from mace.calculators import MACECalculator
from mace.tools import torch_geometric, torch_tools, utils
from surface_... |
05fe559c2cc7aa0260a643cc79c345f4ba6679643ea62f10f690f811e47e6a87 | Python | 20,578 | 410 | """
Cache final choice decoding models for all recording sites.
Original analysis ran parallelized on David lab compute cluster.
Reproduced here running all analyses in series. Could take a little while.
"""
# STEP 1: Import modules and set up queue job
import os
rdir = os.path.dirname(os.path.dirname(__file__))
imp... |
7426cb938703bf11dddf871d030eca03c75b380874dda4c7bc7b272e642284b7 | Python | 20,582 | 541 | """
LLMFormatter - Format validation results for LLM consumption.
This module provides the LLMFormatter class which formats validation results
into natural language and LLM-friendly formats with prompt templates.
"""
from typing import Dict, List, Optional, Any, Literal
from dataclasses import dataclass
from enum imp... |
7604b6b5bfebe0aaf37a708d25e6f4b7072cb66730b8822a798fc418d1b2c8ea | Python | 20,594 | 416 | from attention import pHLA_attns_draw_save
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
from tqdm import tqdm, trange
from copy import deepcopy
import matplotlib as mpl
import seaborn as sns
import difflib
from collections import OrderedDict
def pHLA_attns_keyaatype_keyaacontrib(data, attns, ... |
1c8e2e96f83e697a9bf697c09d73b6f1135168572d00c046e00d36f0794ae0bc | Python | 20,609 | 509 | # -*- coding: utf-8 -*-
"""Base model class"""
import matplotlib
import matplotlib.pyplot as plt
import numpy as np
import pandas as pd
from scipy.optimize import linear_sum_assignment
from ...plt.plot_heatmap import clustermap
# base model class - defining shared methods but not the model itself
class BaseModel:
... |
1233464321577d37348566e672d4e590e3c185bddf6379a0c345cd416ab4fd65 | Python | 20,613 | 568 | # Copyright (c) 2017-present, Facebook, Inc.
#
# 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... |
f5d8881770e286d6434c8030af93a2ba86c9567bfbfc48583df6eda633422691 | Python | 20,617 | 332 | """Windows/Linux command-line runner."""
import argparse
import csv
import json
import logging
from pathlib import Path
import sys
import time
from dataclasses import replace
import numpy as np
from PIL import Image
from scipy import sparse
import torch
from .config import PalmConfig
from .data import Record, balance, ... |
b22c786d23e2b4435524c9e97d0e2418e7dceb91c4bcba6ef9a244720afefa73 | Python | 20,633 | 558 | from abc import ABC, abstractmethod
from dataclasses import dataclass
from typing import Any, Iterable, Optional
import pandas as pd
from pydantic import BaseModel, ConfigDict
from siapy.core.exceptions import InvalidInputError
from siapy.entities import Signatures
from .helpers import generate_classification_target... |
4d9c5fa09d28009a7ce1a822be0bd1c00d1a3c38008609a3421f7021ca03b5c5 | Python | 20,638 | 520 | import os, easydict, time
import numpy as np
from tqdm import tqdm
import matplotlib.pyplot as plt
# moviepy is only needed for the region-video helpers, and its import path changed between
# 1.x ('moviepy.editor') and 2.x ('moviepy'). Import it defensively so that simply importing
# motionmapperpy never fails just be... |
8b3cc621e13e8801cfe9ac9415644f1626ed520cf9d0b868c060110b9e8169d8 | Python | 20,649 | 391 | """
The files "data_preparation.py" and "thresholding.py" need to be executed before this script!
This script will create a mask for the image, in which both markers (ch2 and ch3, i.e. CHCHD2 and TOM20) are present.
This will be used as the intersection mask for further analyzations.
The mean intensity per cell line an... |
a6d94229bada68c5a333060e30cdee91c5825f1b6d5fa2964f9ab086caeef6df | Python | 20,659 | 488 | r"""Group comparisons and the brackets that report them.
``ov.pl.add_palue`` can draw a significance bracket, but the caller has to
supply the coordinates *and* run the test. That is where hand-annotated
figures go wrong: the bracket ends up over the wrong pair, or the P value is
uncorrected, or the test does not matc... |
061b32e8eb7d0355f2bd4dfd492dc404b5dc603cccac5b8aa79659e5fe697427 | Python | 20,679 | 593 | """
Copyright (c) Meta Platforms, Inc. and affiliates.
This source code is licensed under the MIT license found in the
LICENSE file in the root directory of this source tree.
"""
from __future__ import annotations
import itertools
import json
import logging
import os
import re
import socket
import subprocess
import ... |
fe28cc7f69f1268cf569b34e7a5ca69cade0dda4ae8b812c974743b2f6ab23b5 | Python | 20,690 | 605 | import h5py
import nibabel
import numpy as np
from tensorflow.keras.utils import to_categorical
from ml4h.normalizer import ZeroMeanStd1
from ml4h.metrics import weighted_crossentropy
from ml4h.TensorMap import TensorMap, Interpretation
from ml4h.tensormap.general import get_tensor_at_first_date, normalized_first_date... |
a930cfbd232688c45f9bcc858f87da65407bc0c33634b14af319a80a4fceacee | Python | 20,698 | 549 | # Copyright (c) 2021 Qualcomm Technologies, Inc.
# All Rights Reserved.
# pylint: skip-file
# type: ignore
import copy
from collections import namedtuple
from enum import Enum
import numpy as np
import torch
from scipy.optimize import minimize_scalar
from torch import nn
from torch.nn import functional as F
from ai... |
a607d8383170d63e5d189ba507cca12eb201918d58d2db37644dee16e71cfae7 | Python | 20,714 | 547 | # coding: utf-8
"""
Test recovery behavior for the ALLOCATION_TIMEOUT scenario.
Verifies that when an instance reaches ALLOCATION_TIMEOUT, the autoscaler can:
1. Terminate the timed-out old instance.
2. Launch a replacement instance.
3. Avoid a QUEUED->REQUESTED->QUEUED loop.
Test design principles:
- Pure Python, mo... |
33a729953cc231e4c2647d078b43d1f2084671174a5e5612bc3f0a27169b5b49 | Python | 20,722 | 417 | import argparse
import collections
import json
import logging
import os
import pathlib
import re
import numpy as np
import pandas as pd
from combine_json_to_tsv import get_sample_id_column_index
logging.basicConfig(level=logging.INFO, format="%(asctime)s %(levelname)s: %(message)s")
ALREADY_WARNED_ABOUT = set() # u... |
5453660057d716d0226ff991369d04ae66e8c0c20483090a621f0779a4ba90f7 | Python | 20,735 | 497 | # --------------------------------------------------------
# Swin Transformer
# Copyright (c) 2021 Microsoft
# Licensed under The MIT License [see LICENSE for details]
# Written by Ze Liu
# --------------------------------------------------------
import torch
import torch.nn as nn
import torch.nn.functional a... |
c4f3bd1eca8fc28c193434d8c515a24919d8b43ff10ee3a3364b149ee1d999d8 | Python | 20,738 | 464 | import xml.etree.ElementTree as ET
import json
import csv
import copy
import logging
from difflib import SequenceMatcher
from agent.data.entities.config import ROOT_LOGGER_ID
from agent.data.sql.sql_mgmt import select_fields_where, update_text_field, update_non_text_field
from agent.data.entities.config import METAMA... |
7df58a8935926a4824d1cf841b03f344fcd2d4ad02b5a49f3a2f599037e79f43 | Python | 20,761 | 471 | ####################################################################################################
# Copyright (c) 2016 - 2024, EPFL / Blue Brain Project
# Author(s): Marwan Abdellah <marwan.abdellah@epfl.ch>
#
# This file is part of NeuroMorphoVis <https://github.com/BlueBrain/NeuroMorphoVis>
#
# This program is fre... |
221ecb283c85479c257b2eb3c847ffe0d08c36d05cae692fa947972269f78974 | Python | 20,762 | 467 | # Copyright 2023 The HuggingFace Team. 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 applicabl... |
0388d8865ae28833bbed10a3fccf7cf9cfdc59dbe7aa9442253ecc1d97a8a4de | Python | 20,763 | 517 | # Copyright 2025 Google LLC
#
# 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
#
# https://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, ... |
a6992e413a3fdc58425e0e222bff1a0a821c98eb5329c40e6b651806ed4fd5a0 | Python | 20,775 | 517 | import math
import sys
import pandas as pd
import numpy as np
from scipy.stats import fisher_exact
import matplotlib.pyplot as plt
import pickle
import seaborn as sns
import networkx as nx
from matplotlib import cm
from matplotlib.colors import ListedColormap
from matplotlib.lines import Line2D
# bcolors
HEADER = "\... |
c2e99a81383980137ff38f8a45c8eee283118313547e829d08beac64ba71a91d | Python | 20,795 | 561 | import tempfile
import os
from os.path import *
import shutil
from glob import glob
import fnmatch
import re
import json
from StringIO import StringIO
import tempfile
import mock
import unittest
from nose.plugins.attrib import attr
from .. import ion_sync
FILE = mock.Mock()
seqrec = '@read\nATGC\n+\n!!!!\n'
class B... |
6e3116f64ec52547d6fea500ccc2616e8f62389b2cfdb5ee1ed390a3de75a9c8 | Python | 20,811 | 692 | # Copyright 2021 AlQuraishi Laboratory
# 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
#
# U... |
4ad716bc62ad2f0c6f2a4accd49e974ab20193f849771ea355f0178038b99b47 | Python | 20,812 | 425 | import os
rdir = os.path.dirname(__file__)
import sys
sys.path.append(rdir)
from nems.tools import recording
from settings import RESULTS_DIR
import preprocessing as preproc
import tin_helpers as thelp
import numpy as np
import pandas as pd
import pickle
import logging
log = logging.getLogger(__name__)
db = pd.rea... |
fb0eff0659a6c3c6bd2af78acca0c087f763e9bf39c5ce2377520c175ef2f044 | Python | 20,814 | 522 | """
DDRTree: Discriminative Dimensionality Reduction via Learning a Tree.
Pure Python/NumPy/SciPy implementation of the DDRTree algorithm,
faithfully ported from the R/C++ DDRTree package.
"""
import numpy as np
from scipy import sparse as _sparse
from scipy.sparse import csr_matrix
from scipy.sparse.linalg import ei... |
f53a71ec6128fb4adb5800ec765da6eb01da0f84cf7c59697b09d0eedf22ba61 | Python | 20,815 | 494 | """Defines Model class.
The copyrights of this software are owned by Duke University. Please
refer to the LICENSE and README.md files for licensing instructions. The
source code can be found on the following GitHub repository:
https://github.com/wmglab-duke/ascent
"""
import os
from copy import deepcopy
import numpy ... |
c5b7215e1099226ce31814e74bd0a82e442539d0bf1a0c95dd01ba726085a86d | Python | 20,831 | 482 | import numpy as np
import networkx as nx
import os.path
import matplotlib.pyplot as plt
from scipy import signal
import time
import math
import gc
gc.collect()
import warnings
from filterpy.kalman import KalmanFilter
warnings.filterwarnings('ignore')
import os
os.system('cls' if os.name == 'nt' else 'clear... |
6e0d984d5617c734f84286e012012101e12c7c1fe06d0c997472f3aa1432e2dc | Python | 20,843 | 523 | import copy
import json
import logging
import os
import subprocess
import tempfile
import time
from typing import Dict, Optional
import yaml
import ray
import ray._private.services
from ray._private import ray_constants
from ray._private.authentication.authentication_token_setup import (
AUTH_MODE_ENV_VAR,
en... |
fb1898e20fda3a5991c2e3a94af331f6d63b436b775278c396577573fe9a93aa | Python | 20,888 | 456 | from dataclasses import dataclass, field
import os
import json
import mlflow
from torch import nn
from torch import tensor
from torch.nn import CrossEntropyLoss, MSELoss
from torch.nn.parallel import DataParallel
from torch.utils.data.sampler import RandomSampler, Sampler
from torch.utils.data.dataset import Dataset, I... |
fc1ad1d247808355d9c7fd5bfcd7fb18c988bc5ea615bb2f4a133f0323f06bfb | Python | 20,899 | 646 | import copy
import numpy as np
import pandas as pd
from scipy.sparse import csr_matrix, save_npz
from tqdm import tqdm
from . import build_graph
class SEACellsCPUDense:
"""Fast kernel archetypal analysis.
Finds archetypes and weights given annotated data matrix.
Modifies annotated data matrix in place... |
08a4426f301b6e41182312a61096f4540b80f60cd564dc66c7ad40e88f93836d | Python | 20,906 | 572 | """
End-to-End Verifier - Phase 5
Tests the complete workflow: notebook → task extraction → LLM selection → verification.
Generates comprehensive reports on skill selection accuracy.
"""
import asyncio
from pathlib import Path
from typing import List, Dict, Optional, Tuple, Any
from dataclasses import dataclass, fiel... |
b1cc393669f59eff54ea2e8bb64e3f5b3be23ea5284d863c71710a9ab4936c33 | Python | 20,917 | 533 | import logging
import time
import math
import numpy as np
import torch
import torch.nn as nn
from pyexpat.model import XML_CQUANT_OPT
from ocpmodels.common.registry import registry
from ocpmodels.common.utils import conditional_grad
from ocpmodels.models.base import BaseModel
from ocpmodels.models.scn.sampling import ... |
54882dc922903a37800500d89c2bfe59e85508f5ab3f890522b7fadb24ca0be4 | Python | 20,933 | 554 | """Quality control for single-extracellular-vesicle (single-EV) proteomics.
These functions operate on the shared ``ov.single.ev`` AnnData schema (see
:mod:`omicverse.single.ev.io`): an EV x protein matrix with the raw values in
``layers['counts']`` and the value type recorded in ``uns['ev']``.
Single-EV QC differs f... |
d6f2245b5bc9c6aeb04d538525fa5b937308fe5f68e320e1b3254e3c484e9fa1 | Python | 20,933 | 421 | import torch,random
from tqdm import tqdm
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
import seaborn as sns
from scipy.sparse import csr_matrix
from sklearn.metrics import pairwise_distances,pairwise_distances_chunked,confusion_matrix
import scanpy as sc
from scipy.sparse import csr_matrix as... |
de712941b006d3f3fb5a3354ba3e3e6df82edcd6f967f3e7b178b4790388bad7 | Python | 20,938 | 611 | from typing import Optional, IO, Union
from pathlib import Path
import vamb.vambtools as _vambtools
from torch.utils.data.dataset import TensorDataset as _TensorDataset
from torch.utils.data import DataLoader as _DataLoader
from torch.nn.functional import softmax as _softmax
from torch.optim import Adam as _Adam
from t... |
199ce281494f1f73d9c8a479bcd814db637eca96723fd81974671df75a84b2df | Python | 20,949 | 571 | import cv2
import numpy as np
import pyqtgraph as pg
import scipy
from pyqtgraph import FileDialog
from pyqtgraph.Qt import QtGui
from pyqtgraph.parametertree import Parameter, ParameterTree
import caiman as cm
from caiman.source_extraction.cnmf.cnmf import load_CNMF
from caiman.source_extraction.cnmf.params import CN... |
14aebe1572878d3267250ffb488d77faf14f653b67c8bc7315c481904481331c | Python | 20,976 | 634 | """
Copyright (c) Meta Platforms, Inc. and affiliates.
This source code is licensed under the MIT license found in the
LICENSE file in the root directory of this source tree.
"""
from __future__ import annotations
from dataclasses import replace
from enum import Enum
from typing import TYPE_CHECKING
import torch
f... |
b97ce1a879a29da5e9c2ba4a36517edcea346286bb50f791886bbea29f11c9d9 | Python | 20,996 | 488 | import argparse
import itertools
import pickle
from collections import namedtuple
from typing import Dict, List, Tuple, Callable
import h5py
import numpy as np
import torch
import tqdm
import visionloader as vl
from whitenoise import RandomNoiseFrameGenerator
import lib.data_utils.data_util as du
import lib.data_util... |
5968df9b195997ab715995a4d72ad8be670b05cbb7e1c315a3ce884c5a0d11a0 | Python | 21,002 | 581 | import torch
from torch_geometric.data import Data
class BatchMasking(Data):
"""A plain old python object modeling a batch of graphs as one big
(disconnected) graph. With :class:`torch_geometric.data.Data` being the
base class, all its methods can also be used here.
In addition, single graphs can be r... |
131697f41214c67904c4ba64770e08b12a888742bb70ca0a6dcb94c504cb60dc | Python | 21,006 | 510 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
Created on Fri Aug 25 14:49:36 2017
"""
import cv2
try:
cv2.setNumThreads(1)
except:
print('Open CV is naturally single threaded')
try:
if __IPYTHON__:
print(1)
# this is used for debugging purposes only. allows to reload classes
... |
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