sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
42836710f9e0ac605b946c959bbf6d8dae36bd1dfe1da2f8911f90cd42b63139 | Python | 54,543 | 1,143 | import inspect
import re
from typing import Callable, List, Optional, Union
import numpy as np
import PIL
import torch
from packaging import version
from transformers import CLIPImageProcessor, CLIPTokenizer
import diffusers
from diffusers import OnnxRuntimeModel, OnnxStableDiffusionPipeline, SchedulerMixin
from diff... |
1d85831d689c0b836db64d7acb20846160871b88e999f01bbb08c46674b1f87b | Python | 54,613 | 1,232 | # coding: utf-8
import os
import sys
from typing import Dict, List, Tuple
import pytest
from ray.actor import ActorHandle
from ray.dag import ClassMethodNode, InputNode, MultiOutputNode
from ray.dag.compiled_dag_node import CompiledTask
from ray.dag.dag_node_operation import (
_add_edge,
_build_dag_node_opera... |
5532d9c4ae9b5141b3258dfd1596c389d65f63a2b9e40ac2c1c6bede52472d25 | Python | 54,648 | 1,173 | #!/usr/bin/env python
import argparse
import gzip
import logging
import sys
from collections import Counter
from statistics import median
from typing import List, Text, Dict, Optional, Set
from pysam import VariantFile
from intervaltree import IntervalTree
# Parameters
MIN_SIZE = 1000
MIN_DIFF = 0.4
MIN_SIZE_IDEL =... |
91f7f4ea788dfe34c7e4eef69e2c68a9f6810fc1aa849c5e2afc485bb1fb4de9 | Python | 54,723 | 1,331 | # -------------------------------------------------------------------------------------------------------------------------------------
# Following code curated for Bio-Diffusion (https://github.com/BioinfoMachineLearning/bio-diffusion):
# --------------------------------------------------------------------------------... |
fd78fe42cfa745af4b6fc6975e301cc503af9f247a9a2c0c2ee2b48f8db72271 | Python | 54,845 | 1,140 | import os
from pathlib import Path
from collections import OrderedDict
from random import sample
from typing import Optional, List, Iterable
import fire
import humanize
import numpy as np
from rich.console import Console
from rich.table import Table
from rich.progress import Progress
import tables as tb
from textdista... |
6dfc3b522bca744a9865b7292b1f094f44ddad76a6c3cc4cccc1b6cf9c550cef | Python | 54,976 | 1,721 | import pytest
import sys
import fastremap
import cc3d
import numpy as np
INT_TYPES = [
np.int8, np.int16, np.int32, np.int64,
np.uint8, np.uint16, np.uint32, np.uint64,
]
TEST_TYPES = INT_TYPES + [ np.float16, np.float32, np.float64 ]
OUT_TYPES = [ np.uint16, np.uint32, np.uint64 ]
def gt_c2f(gt):
f_gt = np.... |
35987462f58c212dbcff65b885b5e0fb2ca82eb09a1517ac7261ab9035bb7a65 | Python | 55,064 | 1,121 | # Inspired by: https://github.com/haofanwang/ControlNet-for-Diffusers/
import inspect
from typing import Any, Callable, Dict, List, Optional, Union
import numpy as np
import PIL.Image
import torch
import torch.nn.functional as F
from transformers import CLIPImageProcessor, CLIPTextModel, CLIPTokenizer
from diffusers... |
d73ae1e24f1c7111dd24e1f178b118ff76ed4b9706a34a782706578f10268c2d | Python | 55,075 | 1,276 | import os
import argparse
from sklearn.model_selection import train_test_split
from check_params import *
from read_input import *
from process_input import *
from plot_images import *
from data_generation import DataGenerator
import gpustat
import itertools
import PIL.Image as Image
from matplotlib import pyplot as pl... |
a8e7a443f9087df99bd0670a28ed3010ebd837cc05c7eb54e0d7da5cd497d553 | Python | 55,167 | 1,192 | import pandas
import numpy
import warnings
from typing \
import Optional, Callable, Any, Union, Mapping, List, Tuple, Iterator, Collection, Text, Dict, TypeVar, Iterable
from types import MappingProxyType
from tqdm.auto import tqdm
with warnings.catch_warnings():
# pympler has some deprecated matrix stuff, I do... |
05edccf7010398a1feecfc77f650ef401b44c2c7e92169ad70d958c9e66f02d5 | Python | 55,327 | 1,467 | """
Feishu webhook channel for OmicVerse Jarvis (feature-parity focused).
Capabilities:
- URL verification handshake
- Websocket long-connection event subscription
- Deterministic session routing by chat/thread
- Streaming draft updates (edit message)
- Send images/files from analysis artifacts
- Receive .h5ad file me... |
9c5b08fe5b1644859741a8cf0810ca067a96d1bad415198c99c6c2a0decab7ed | Python | 55,456 | 1,412 | # -*- coding: utf-8 -*-
# (C) Copyright 2026 IBM. All Rights Reserved.
#
# Licensed under the MIT license. See LICENSE file in the project root for details.
# pylint: disable=too-many-lines, disable=possibly-used-before-assignment
# mypy: disable-error-code=attr-defined
"""Base tile with added periphery and common u... |
6276d2e71879d3fa05a559ce630a2a6f9716a6ef93461ad54884df0b4d1f77b2 | Python | 55,519 | 1,562 | import contextlib
import enum
import itertools
import logging
import math
from collections import abc
from typing import (
TYPE_CHECKING,
Any,
ClassVar,
Final,
Literal as L, # noqa: N817
SupportsIndex,
TypeAlias,
TypeVar,
cast,
overload,
)
import numpy as np
import numpy.typing... |
d2254f1428c0d4c953a309fbc5517ce29bace796fdbf5af2f92e85ad3820ca15 | Python | 55,559 | 907 | # -*- coding: utf-8 -*-
"""
Module containing vision specific analysis.
"""
import mozaik
import numpy
import scipy
import quantities as qt
from .analysis import Analysis
from mozaik.tools.mozaik_parametrized import colapse, colapse_to_dictionary, MozaikParametrized
from mozaik.analysis.data_structures import PerNeuron... |
7261e60096fc1474d1da838f891306a5cc2e4f92e41374d2b422a36ec1bd7221 | Python | 55,604 | 1,235 | r"""Tuning a construct rather than just building one.
Five gaps that are individually small and collectively the difference between a
design that works and one that works *at the level you wanted*.
* :func:`tai` — the tRNA adaptation index. ``cai`` measures how closely a gene's
codons match the *codon usage* of hig... |
b8166a31551f655bc9f8f8ec3588860bd6c514edcf481449f8896083b74ecee0 | Python | 55,607 | 1,313 | """
Module to write a Ray Dataset into an iceberg table, by using the Ray Datasink API.
"""
import logging
from dataclasses import dataclass, field
from typing import (
TYPE_CHECKING,
Any,
Callable,
Dict,
Iterable,
List,
Optional,
Tuple,
Union,
)
import ray
from ray._common.retry im... |
0df298c92f45fbcbe5f0ae460687fdd038563cef798de7ffcafd4404f417224c | Python | 55,872 | 1,211 | import numpy as np
import scipy.sparse as _sp
import scanpy as sc
import warnings
from ..pp import preprocess
from .._settings import add_reference
from .._registry import register_function
def _select_significant_svg_names(qvals, *, n_svgs, qval_threshold):
"""Return at most ``n_svgs`` finite q-values below the ... |
5cddc32a43803fd64d9d90a9fcbf82f01a3b2a5eb227b5837f29e7a5771f8ee6 | Python | 56,018 | 1,325 | import io
import subprocess
import sys
import tempfile
import unittest
from pathlib import Path
from typing import Optional
from unittest.mock import patch
import pytest
import runfiles
from click.testing import CliRunner
from networkx import topological_sort
from ci.raydepsets.cli import (
DEFAULT_UV_FLAGS,
... |
ba1be7cfebf6ef225c5f8bbeb74633d14005904593467da14ef47eda9f3f9148 | Python | 56,039 | 1,516 | r"""
See :mod:`mozaik.visualization` for more general documentation.
"""
import mozaik.visualization.helper_functions as phf
import pylab
import numpy
import math
import mozaik
import mozaik.tools.units
import quantities as pq
from matplotlib.colors import *
from matplotlib.ticker import MultipleLocator, AutoMinorLocat... |
07b2058b9a573b09d0d824427aa90a3c5195c161e3bc82518dd59f8b5e5f4dd8 | Python | 56,235 | 1,414 | import numpy as np
import pandas as pd
import scanpy as sc
import anndata as ad
from joblib import Parallel, delayed
from scipy.sparse import coo_matrix, csr_matrix
from scipy.stats import mode
from collections import Counter
import matplotlib.pyplot as plt
import seaborn as sns
from typing import Dict, List, Tuple, O... |
726afb7504004ff37becb867227fe322cfb5134c9f10fc20f0797a50725216c2 | Python | 56,375 | 997 | import numpy as np; np.set_printoptions(precision=2)
import torch; torch.set_printoptions(precision=2)
import torch.nn as nn
import time
import sys
import itertools
import random; random.seed(0)
import datetime
import copy
import scipy
import matplotlib.pyplot as plt
# This is added by VScode
class BioRNN_working(to... |
67cd749e4cf6a16e242e8f7993228e1958b7fd70328809a7161e95fe5f8d1c0c | Python | 56,376 | 1,601 | """
Function Registry System for OmicVerse
This module provides a decorator-based function registration system that allows
users to discover functions using natural language queries, aliases, and semantic search.
"""
from typing import Dict, List, Optional, Callable, Any, Union, Tuple
from functools import wraps
from... |
0af92d4a6bc707d7c5ac39492435eba9cfaf18e2ab6836c3a059eb85d88eb970 | Python | 56,490 | 1,076 | """Unified cell-cell communication entry point: ``ov.single.run_ccc(method=...)``.
Every backend is reduced to one *long table* with the columns in
:data:`LONG_COLUMNS` (one row per sender, receiver and ligand-receptor pair).
The long table is what the consensus, the method comparison and the
``ov.pl.ccc_*`` communica... |
89a7df499acf807f745d11df33e7379e84cfa55c21dfd552957b8c0e576b6314 | Python | 56,527 | 1,295 | # built-in dependencies
import os
from typing import Any, Dict, IO, List, Tuple, Union, Optional, cast, TYPE_CHECKING
import uuid
import time
import math
import tempfile
from concurrent.futures import ThreadPoolExecutor
# 3rd party dependencies
import numpy as np
from numpy.typing import NDArray
# project dependencie... |
e48f8594d09411adcc1d3443996c375b802f534e0855daa6264cae55690f605c | Python | 56,574 | 1,663 | # Copyright (C) 2019-2022 Intel Corporation
# Copyright (C) CVAT.ai Corporation
#
# SPDX-License-Identifier: MIT
from __future__ import annotations
import io
import itertools
import os
import shutil
import stat
import tempfile
import zipfile
from abc import ABC, abstractmethod
from bisect import bisect
from collectio... |
42e2ff9e4792e2157daacc744b158fe46257181c7aa3e36e16ed2db772187c3f | Python | 56,716 | 1,062 | # -*- coding: utf-8 -*-
"""
Module containing lfp specific analysis.
"""
import mozaik
import numpy
import scipy
import quantities as qt
from .analysis import Analysis
from mozaik.tools.mozaik_parametrized import colapse, colapse_to_dictionary, MozaikParametrized
from mozaik.analysis.data_structures import AnalogSignal... |
ac0426cf2983a569280603edc9163978aa26167cb7a8a1513b77d32433ffa529 | Python | 57,201 | 1,150 | import inspect
import re
from typing import Callable, List, Optional, Union
import numpy as np
import PIL
import torch
from packaging import version
from transformers import CLIPImageProcessor, CLIPTextModel, CLIPTokenizer
import diffusers
from diffusers import SchedulerMixin, StableDiffusionPipeline
from diffusers.m... |
d4a3177c75e0e82d15fe246df693b4422b20dbd951ce1f9e781f6e95ed0004f8 | Python | 57,685 | 1,355 | # coding=utf-8
# Copyright 2023 The HuggingFace Inc. team.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable... |
105d2901cebf4bfadbe93ce1703a81f2c71f162c325975608daa243a8dcda3e9 | Python | 57,728 | 1,495 | # Copyright (C) CVAT.ai Corporation
#
# SPDX-License-Identifier: MIT
import textwrap
from collections.abc import Iterable, Iterator, Mapping
from enum import Enum
from typing import Any
from django.conf import settings as django_settings
from django.db import models as django_models
from django.db import transaction
... |
81e2100140817341b056ff75db8eb60e58a7156ea8803ae45bdb523293a56947 | Python | 57,751 | 1,353 | from typing import Callable, List, Iterator, Tuple, Union
from abc import ABCMeta, abstractmethod
import numpy as np
import torch
import torch.nn as nn
import torch.nn.functional as F
from movie_upsampling import batch_compute_interval_overlaps, TimeUpsampleTransposeFlat, JitterFrame
from convex_optim_base.optim_base... |
4a3b23b90397a7a5161b28e7e6daee07814c4f016690760552b148a2c542eda8 | Python | 57,874 | 1,142 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
# pylint: disable=broad-except
# pylint: disable=invalid-name
# pylint: disable=line-too-long
# pylint: disable=multiple-statements
# pylint: disable=too-many-lines
#-------------------------------------------------------------------------------
'''
This file contains th... |
86bc2ef0484cbce9b59c66f2b2eb09bb05bb5634d81691d7c467c1da6eab7a28 | Python | 58,114 | 1,208 | import torch
import numpy as np
import time
def dist2bins(mat):
"""
This function is for label
bins definition: left open, right close. Because cutoff 8 definition: d<=8
two kinds of bin length: 0.5,1.0
bins:3.0],(3.0,3.5],(3.5,4.0],...,(21.5,22],(22,23],(23,24],...,(29,30],(30,
Nbi... |
2bf3349236f40cef0f4bffd027d9f502dfa2e010344dfaa9dcaf685710832eba | Python | 58,258 | 1,481 | '''
test_device_azurekinect.py
Tests for the Device class for Azure Kinect device.
Copyright (C) Microsoft Corporation. All rights reserved.
'''
import unittest
import copy
from time import sleep
import numpy as np
import k4a
import test_config
def k4a_device_set_and_get_color_control(
device:k4a.Device,
... |
91394e1a59bbbf4f09482f92d6247cd14c06ca69b6b9b1ae4686e6b55831a235 | Python | 58,325 | 1,683 | """
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.
Tests: radius-graph construction — fcc/molecular/water-box structure
helpers, partition utilities, multi-radius PBC graph builders
... |
6676ee91d7862190e180b3bddea0b63804ec8b265f5aea41bc6a5c94a1c29f55 | Python | 58,441 | 1,599 | import base64
import json
import sys
import uuid
from typing import Optional
from unittest.mock import MagicMock
import pytest
from google.protobuf.timestamp_pb2 import Timestamp
import ray.dashboard.consts as dashboard_consts
from ray._common.network_utils import find_free_port
from ray._common.test_utils import wai... |
5f3e97070c87165f45fcd4cccc2f7520bf448c332ecf641dd7ee4d5113c2465f | Python | 58,610 | 1,210 | import copy
import itertools as it
import logging
import math
import os
import random
import sys
from statistics import median
import numpy as np
import pandas as pd
import torch
import torch.utils.data
import torch_geometric.transforms as T
from rdkit import Chem
from torch.distributions.uniform import... |
aee6d4338f3dd41b2f277661a38176f58dfbec58856f997da433bdf892d105c7 | Python | 58,774 | 1,718 | import sys
import math as python_lib_Math
import math as Math
import inspect as python_lib_Inspect
import sys as python_lib_Sys
import builtins as python_lib_Builtins
import functools as python_lib_Functools
import re as python_lib_Re
import traceback as python_lib_Traceback
from io import StringIO as python_lib_io_St... |
9d94e10e7183e8dfd3cfd6367ff3ab3d1fb1bb90b2bf4ab6c77e0e0d195b6fd6 | Python | 58,808 | 1,492 | """
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.
"""
from __future__ import annotations
import io
import json
import logging
import math
import time
from collections import OrderedDict, defau... |
902aaa7301f34ba42f64806e38873a3e6abb91b8af6f198e0f2711b620ae4c6d | Python | 58,829 | 1,633 | # Copyright (C) 2022 Intel Corporation
# Copyright (C) CVAT.ai Corporation
#
# SPDX-License-Identifier: MIT
from __future__ import annotations
from collections.abc import Sequence
from enum import StrEnum
from typing import TYPE_CHECKING, Any, cast
from django.conf import settings
from django.shortcuts import get_ob... |
29c2c0fee031a762ae3096fdbda4d5bdeec52c5510bbb998903ddd0ac7317917 | Python | 58,874 | 1,552 | """Pickler class to extend the standard pickle.Pickler functionality
The main objective is to make it natural to perform distributed computing on
clusters (such as PySpark, Dask, Ray...) with interactively defined code
(functions, classes, ...) written in notebooks or console.
In particular this pickler adds the foll... |
0fc13774e8254acbbd0804d89627e7763bd2859917dfb24f2e1ed7c7a3970e65 | Python | 59,027 | 1,261 | import torch
import numpy as np
import os, time
import scipy
import pandas as pd
import Loss
def dist2bins(mat):
"""
This function is for label
bins definition: left open, right close. Because cutoff 8 definition: d<=8
two kinds of bin length: 0.5,1.0
bins:3.0],(3.0,3.5],(3.5,4.0],...... |
e9168c549284cdf23f1d2f136bbf8f0b671d14eaf9388a398f13651cea57fad1 | Python | 59,183 | 1,402 | import time
import sys
import argparse
from itertools import cycle
import threading
import os
import numpy as np
from collections import deque
from bisect import insort, bisect_left
from itertools import islice
import matplotlib.pyplot as plt
class Evt(object):
def __init__(self,id,direction,starti,endi,ampi,X,Y... |
4f7489abe0f69fc1486e10e7239dfe1c4c7c4d091c6939b96c003e8b475474ea | Python | 59,184 | 1,402 | import time
import sys
import argparse
from itertools import cycle
import threading
import os
import numpy as np
from collections import deque
from bisect import insort, bisect_left
from itertools import islice
import matplotlib.pyplot as plt
class Evt(object):
def __init__(self,id,direction,starti,endi,ampi,X,Y... |
1f3e8b5c12595ee1482d020afdbaf3ce16a6c19a4b7800b9eb04d5131fb41727 | Python | 59,378 | 1,563 | # __init__.py
#
# Copyright 2018 Chichau Miau <zmiao@ebi.ac.uk>
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 of the License, or
# (at your option) any later version.
... |
6d648dacb8fee7938f74dc19118e3e0a8f11ae8e9f8b39291f66ff8f189a5d66 | Python | 59,514 | 2,104 | BROWNIAN_CELL_MATCHES = {
('2018-08-07-5', 'data011'):
'''#ON parasol
12:data009,307;data010,808
1046:data009,637;data010,632
359:data009,119;data010,814
364:data009,884;data010,947
33:data009,335;data010,838
1052:data009,943;data010,927
369:data009,1138;data010,651
370:data009,856;data010,1099
373:data009,... |
3dec761218f9474b1ae57603965d59128be040f720431ecf96a132bdafc07fa3 | Python | 59,725 | 1,254 | # Copyright 2023 Pix2Pix Zero Authors and 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
#
# Unl... |
ddedf675d05c756660d4d3124cb68abcee1908d4148b0f01c4f604710420d004 | Python | 59,726 | 1,712 | import asyncio
import json
import os
import secrets
import signal
import sys
import tempfile
import time
import urllib.request
from unittest.mock import patch
from uuid import uuid4
import pytest
# RayConfig reads the auth mode once at import, so set the mode before importing
# ray. A per-process random token, inheri... |
b6d67e60c7ad62116366825d7251cee76cfe503e596e1ef7b9cbd9b12b75e56b | Python | 59,805 | 1,415 | import time
import sys
import argparse
from itertools import cycle
import threading
import os
import numpy as np
from collections import deque
from bisect import insort, bisect_left
from itertools import islice
import matplotlib.pyplot as plt
class Evt(object):
def __init__(self,id,direction,starti,endi,ampi,X,Y... |
7638d9302e7c2d0962a522077b035854259d61cd8527e99b6099a0481f99e39e | Python | 59,806 | 1,415 | import time
import sys
import argparse
from itertools import cycle
import threading
import os
import numpy as np
from collections import deque
from bisect import insort, bisect_left
from itertools import islice
import matplotlib.pyplot as plt
class Evt(object):
def __init__(self,id,direction,starti,endi,ampi,X,Y... |
02f456cf3d2b957574e94a2268c3978f353d1d74a2491680b6d1a8597844b46c | Python | 59,950 | 1,614 | #
# 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... |
775f6c6be795112802179ea2e7faf76e677573a264019dd426b4a37b7960d4a0 | Python | 60,125 | 1,591 | from typing import Tuple, Optional, Union, List
try:
from typing import Literal
except ImportError:
from typing_extensions import Literal
import logging
from tqdm import tqdm
import numpy as np
import pandas as pd
import scipy.sparse as sp
from pandas.api.types import is_numeric_dtype, is_categorical_dtype
fro... |
a80f4d91f2724d3f850685cf796ed94a1c247f8a95bef620ff2de35889548615 | Python | 60,179 | 1,667 | import json
import os
import pathlib
import sys
import threading
import time
from dataclasses import asdict
from http.server import BaseHTTPRequestHandler, HTTPServer
from pathlib import Path
from unittest.mock import Mock, patch
import pytest
import requests
from jsonschema import validate
import ray
import ray._com... |
a061c37c7dddb882962c972814aae94e1c0f0a564e5cfb9021591d333fbcf01b | Python | 60,328 | 1,514 | """
QQ Bot channel for OmicVerse Jarvis.
Capabilities:
- C2C private chat messages
- Group AT messages (group chat where @bot is mentioned)
- Guild (channel) AT messages
- Long-connection WebSocket event subscription (no public URL needed)
- Streaming status updates during analysis
- Send images from analysis artifact... |
6fa79b9f1763686df7e5b3dc81da8fd73865d1b60186a28efeed40d9955d573e | Python | 60,496 | 1,886 | # Copyright (C) 2018-2022 Intel Corporation
# Copyright (C) CVAT.ai Corporation
#
# SPDX-License-Identifier: MIT
from __future__ import annotations
import datetime
import re
import shutil
import uuid
from abc import ABCMeta, abstractmethod
from collections.abc import Collection, Iterable, Sequence
from enum import En... |
bd18fe1f2f5808025c14d9a9614a548a845088516835f5c350fbac027f5ee533 | Python | 60,574 | 1,429 |
import numpy
import copy
import random
import json
import os
import datetime
import h5py
import glob
import uuid
from functools import partial
from scipy import optimize, interpolate
from matplotlib import pyplot
from collections import defaultdict
from skimage import filters, transform
from abberior import microsco... |
ae53c3f0d83765e2380f9b9e183b6737c9391e3cee29edc03819bc67874ef27e | Python | 60,595 | 1,108 | import sys
from typing import List, Tuple, Dict, Optional, Union
from dataclasses import dataclass
import numpy as np
from rawmovie import RawMovieReader2
from lib.dataset_config_parser.dataset_config_parser import LookupKey
from lib.dataset_specific_ttl_corrections.ttl_interval_constants import NS_BROWNIAN_N_FRAMES_... |
0fe1b22b28f394aef0ef11bb9fbfa84b87aecb8cb8f0b892fe163b65eb8027a6 | Python | 60,885 | 1,551 | # Copyright (C) 2021-2022 Intel Corporation
# Copyright (C) CVAT.ai Corporation
#
# SPDX-License-Identifier: MIT
import io
import itertools
import mimetypes
import os
import re
import shutil
import stat
from abc import ABCMeta, abstractmethod
from collections import deque
from collections.abc import Collection, Iterab... |
9568f8dbcf8e38a4538299f506ddb8a085df2c6c115b5eafad0ede04a9c31fc8 | Python | 60,975 | 1,636 | import itertools
import json
import os
import re
import sys
import threading
import time
from typing import Any, Callable, Dict, List, Optional
import pandas as pd
import requests
from anndata import AnnData
import scanpy as sc
from ..datasets import download_data
from .._registry import register_function
from ..repo... |
08725e73d5d2303133e2f9bf09968fb63dc9a81a914d0c8abc230653598129e8 | Python | 60,981 | 1,576 | # internal python imports
import os
import csv
import functools
import torch
from torchvision.utils import make_grid
from tensorboardX import SummaryWriter
import sys
from itertools import permutations, combinations
# third party imports
import numpy as np
import scipy
from skimage import measure
import glob
from date... |
5e215b552b8d6ef23beee733b2b72681a84ad77b8f31a53e139552565980a3d8 | Python | 61,214 | 1,481 | """OpenAI-compatible and Responses API provider helpers for OmicVerseLLMBackend.
Internal module — import from ``omicverse.utils.agent_backend`` instead.
"""
from __future__ import annotations
import base64
import json
import logging
import os
import platform
import re
import ssl
import warnings
from typing import An... |
353de05dd80242df34e68267de39ae3f6f8a23de480170fad238b2960a759d9a | Python | 61,241 | 1,549 | r"""Plotting helpers for in-silico gene-perturbation results.
Targets the dictionary returned by :meth:`omicverse.llm.SCLLMManager.perturb_genes`
(see also :meth:`omicverse.llm.geneformer_model.GeneformerModel.perturb_genes`),
which has the schema:
{
"cosine_similarities": DataFrame (cell × gene),
... |
845db10f272851cd9b96fd1eedf32cd3d7ae106a4439d40a3bb5fc9ad0cee11d | Python | 61,335 | 1,709 | # built-in dependencies
from typing import Any, List, Union
# 3rd party dependencies
from numpy.typing import NDArray
# project dependencies
from deepface.commons import package_utils, weight_utils
from deepface.models.FacialRecognition import FacialRecognition
from deepface.commons.logger import Logger
logger = Log... |
21c33ce90af50f8d5dd6c99c55a4940d68fb5b39fcddc1b4683124533c267de9 | Python | 61,396 | 1,089 | import torch
import numpy as np
from sklearn.metrics import roc_auc_score
import torch.nn.functional as F
from sklearn.manifold import TSNE
import matplotlib.pyplot as plt
from scipy import stats
from scipy.special import softmax
from lifelines import KaplanMeierFitter, CoxPHFitter, AalenJohansenFitter
from lifelines.s... |
add9340ff20b75a8e3a2fd8a2e04574a2c7affe753c8a00e374cf27c32da7ef4 | Python | 61,496 | 1,449 | '''
CINNAMON-GUI
Convolutional Neural Network And Multimodal Learning with Graphic User Interface for Digital Pathology
Lunan Foldomics, Copyright(c) 2024
'''
import subprocess
import os
import sys
import io
import re
import shutil
import pandas as pd
import numpy as np
import json
import tensorflow as tf
from PIL imp... |
eeac400127bea666d45ca4b57728e19ce33ae0ae75676e27239bf01ca8ed1bf0 | Python | 61,796 | 1,267 | #!/usr/bin/env python
from __future__ import print_function
import argparse
import glob
import gzip
import math
import pickle
import sys
import time
import matplotlib.pyplot as plt
import numpy as np
import os
# file names
FP_NAME = "fp.vcf.gz"
FN_NAME = "fn.vcf.gz"
TP_NAME = "tp.vcf.gz"
# vcf tags
MPI_TAG = "MPI"
... |
86c5573e1b599cea4777fb4e263103ba51d4a8f31ca44e1438ee51e78358908c | Python | 61,899 | 1,479 | """TurnController — agentic orchestration loop + follow-up gate.
Extracted from ``smart_agent.py``. The TurnController owns the main
turn-by-turn loop (LLM call → tool dispatch → result append → repeat)
including stall detection, cancellation, and conversation logging.
Policy helpers (FollowUpGate, ConvergenceMonito... |
af12bc52d7aff8394fedc1140e3983973cf83eff05242927abc9c911f88b5b8e | Python | 62,080 | 1,538 | #!/usr/bin/env python
'''
Find potential de novo variants in a given VCF.
de_novo_finder_3.py is a major update to the original caller. The main purpose is to
identify events that appear to be de novo in a specified VCF file that contains
sequence information from trios. Due to the nature of this variation, parents ar... |
3dadedc8a4f8926a14f83513a891bf989930fc98fe046660746b085f6ba38215 | Python | 62,193 | 1,137 | 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 ... |
a7e8b013098b321c1a2758a1651ad45b450cc9db6946dbde0fc834d576d7992a | Python | 62,613 | 1,622 | # -*- coding: utf-8 -*-
# (C) Copyright 2026 IBM. All Rights Reserved.
#
# Licensed under the MIT license. See LICENSE file in the project root for details.
# pylint: disable=too-many-lines
"""RPU configurations presets for resistive processing units."""
from dataclasses import dataclass, field
from aihwkit.simula... |
57f02efc5e37933f90350b29862655cbbc4a9af024b833dcd6783f618b590cb4 | Python | 62,837 | 873 | """Readers for mzML, mzXML, mzData, mgf, Thermo .raw, Agilent MassHunter .d and SCIEX .wiff spectra files, on the standard library and numpy"""
import base64
import heapq
import itertools
import os
import re
import struct
import zlib
import xml.etree.ElementTree as ET
import numpy as np
# Thermo .raw trailer extra fiel... |
db8bdb22029752869bd9f9033434a88dc3b424d56c10e9b0d24966ae0d46f75f | Python | 62,856 | 1,769 | import copy
import datetime
import hashlib
import json
import logging
import os
import random
import shutil
import subprocess
import sys
import tempfile
import time
from concurrent.futures import ThreadPoolExecutor
from types import ModuleType
from typing import Any, Dict, List, Optional, Tuple, Union
import click
imp... |
3bc39a4c6fb16883965921f92cb7b782caf3b012b0745dcfe7a4a29eec9e1726 | Python | 62,894 | 1,300 | import h5py
import numpy as np
import scipy
import logging
import biosppy
from typing import List, Tuple, Dict
from tensorflow.keras.utils import to_categorical
from ml4h.tensormap.ukb.demographics import age_in_years_tensor
from ml4h.normalizer import ZeroMeanStd1, Standardize, RandomStandardize
from ml4h.metrics im... |
487388e02218f34aca5aca61c98c8399f939e7542f60c4d92da789157878495c | Python | 62,933 | 1,603 | import sklearn.utils.sparsefuncs as sf
from . import q, ut, pd, sp, np, warnings, sc
from .utils import to_vo, to_vn, substr, df_to_dict, sparse_knn, prepend_var_prefix
from .samalg import SAM
from scipy.stats import rankdata
import networkx as nx
def _log_factorial(n):
return np.log(np.arange(1,n+1)).sum()
def _l... |
99ac290d093c939bc5b68b0702fb840784cad575b58edadba96b87dfbf5ed5a5 | Python | 62,957 | 1,628 | # -*- coding: utf-8 -*-
# (C) Copyright 2020, 2021, 2022 IBM. All Rights Reserved.
#
# This code is licensed under the Apache License, Version 2.0. You may
# obtain a copy of this license in the LICENSE.txt file in the root directory
# of this source tree or at http://www.apache.org/licenses/LICENSE-2.0.
#
# Any modif... |
bc720d8d1db2a42a7b60db71447b371967fccbff6383c3c70879988c1caf16d4 | Python | 63,042 | 1,196 | from argparse import ArgumentParser
import os
import numpy as np
import pandas as pd
import sys
from .get_cluster_helpers import Cluster_Tree, entropy_non_norm
from ..bonsai.bonsai_helpers import mp_print
from itertools import combinations
import random
from collections import defaultdict
import csv
import time
from sc... |
eb67c24b456c58d15e794aafb63257e5b13797beaf624b7e66498c7f52db4739 | Python | 63,067 | 1,582 | """Models,
author: Ting-Ting Gao"""
import numpy as np
import torch
from torch import nn
from torch.functional import F
from torch.optim import Adam
from torch_geometric.nn import MetaLayer, MessagePassing
from torch.nn import Sequential as Seq, Linear as Lin, ReLU, Softplus, Sigmoid, Softmax
from torch.autograd im... |
73ff69ad5e2119a0f5a9c7f98687009f3d320104f86ae08d460f46afd0052688 | Python | 63,131 | 1,660 | # ruff: noqa: E501
from ray.dashboard.modules.metrics.dashboards.common import (
DashboardConfig,
Panel,
PanelTemplate,
Row,
Target,
TargetTemplate,
)
# When adding a new panels for an OpRuntimeMetric, follow this format:
# Panel(
# title=title,
# description=metric.metadata.get("descr... |
90f64b1edb2e56d1b3b77fbc012a765e94e7321e3128517d8991f81cc1e4cd3c | Python | 63,391 | 1,677 | import ntpath
import os
from pathlib import Path
from typing import Optional
from urllib.request import urlretrieve
import requests
from typing import Optional
from tqdm import tqdm
import pandas as pd
import numpy as np
from anndata import AnnData, read_h5ad, read_loom
import warnings
from .._registry import registe... |
62c9579483a1b43fa7ae463aae0a8b16796300e1bded36e5f57ec4704dd72e9d | Python | 63,524 | 1,342 | # tensor_writer_ukbb.py
#
# UK Biobank-specific tensor writing, SQL querying, data munging goes here
#
# Imports
import os
import re
import csv
import glob
import time
import shutil
import logging
import datetime
import operator
import tempfile
import traceback
from functools import partial
from itertools import produ... |
0247cd3c0facbeb2c00979f17054cf4befbd7b4253f9c0106a2661605c74060f | Python | 63,650 | 1,421 | # legacy_models.py
# This file defines model factories.
# Model factories connect input TensorMaps to output TensorMaps with computational graphs.
# Imports
import os
import logging
import numpy as np
from enum import Enum, auto
from collections import defaultdict, Counter
from typing import Dict, List, Tuple, Union, ... |
b16fa650485791dbf34e5a4b5cbce147f73e2c91378e25006347afe80bc7219b | Python | 63,872 | 1,886 | from scipy.stats import binned_statistic
import sklearn.utils.sparsefuncs as sf
import typing
from numba import njit, prange
import os
from os import path
import gc
from .samalg import SAM
import time
from sklearn.preprocessing import StandardScaler
from . import q, ut, pd, sp, np, warnings, sc
from .analysis import _... |
300fe776d3027c827e225eae3e1bde6b72f4aff02ba7acc71da502317088b660 | Python | 64,058 | 1,184 | import torch
import torch.nn.functional as F
import math
class NoiseScheduleVP:
def __init__(
self,
schedule='discrete',
betas=None,
alphas_cumprod=None,
continuous_beta_0=0.1,
continuous_beta_1=20.,
):
"""Create a wrapper cla... |
e215d86a08b0ab310231766d10ff9f7d852042f94f2e3eed34cadb61ecbba969 | Python | 64,167 | 1,805 | import copy
import itertools
import logging
import math
import pickle
import os
import sys
from pathlib import Path
from pprint import pprint
from typing import Dict, List, Optional, Tuple
import click
import numpy as np
import pandas as pd
import pyranges as pr
import torch
import torch.nn as nn
import statsmodels.ap... |
47b67e722ae2b7a8e8d8a478aeda32cdff3e315c7e69a281b06265e6726b77d9 | Python | 64,239 | 1,507 | from typing import Any, Dict, List, Optional, Tuple, Union
import numpy as np
import torch
import torch.nn as nn
from ...configuration_utils import ConfigMixin, register_to_config
from ...models import ModelMixin
from ...models.attention import Attention
from ...models.attention_processor import AttentionProcessor, A... |
0e241dd2300e9508e7cd6f3ca5ce295f4bdf5f30e69169b8ea53cdac4f6aaec5 | Python | 64,568 | 1,511 | from typing import Optional
import gc
import sys
import anndata
import numpy as np
import pandas as pd
import scanpy as sc
from matplotlib import cm
import matplotlib.pyplot as plt
import plotly
from scipy import sparse
from scipy.spatial import distance_matrix
from scipy.stats import spearmanr, pearsonr
from sklearn.p... |
3e4841837e6e7794f411c52d25d4f2ba8a6a356fb0fc49a31e4ff79d797af5bd | Python | 64,673 | 1,779 | import contextlib
import importlib
import json
import logging
import multiprocessing
import os
import platform
import re
import signal
import subprocess
import sys
import threading
import time
from collections import defaultdict
from pathlib import Path
from subprocess import list2cmdline
from typing import (
TYPE_... |
e9d6c2e60c62cd1f27ece87ab1bc6de75791819884e08a1b702e1753c4a47376 | Python | 64,754 | 1,529 |
import numpy
import copy
import random
import json
import os
import datetime
import h5py
import glob
import uuid
import tifffile
from functools import partial
from scipy import optimize, interpolate
from matplotlib import pyplot
from collections import defaultdict
from skimage import filters, transform, measure
from... |
2bba8c5f4726a90e21796de74f5649d1d72992338d97ae6445d70045c6b46614 | Python | 64,868 | 1,470 | """Classes and methods for array-based spatial transcriptomics analysis."""
import itertools
from typing import Iterable, Iterator, Sequence, cast
from multiprocessing import Process, Queue
from multiprocessing.shared_memory import SharedMemory
import threading
from warnings import simplefilter
import numpy as np
imp... |
b583d07b83c083ac404df06f783583a4965a52d161e210b739bf5107eeb05ab0 | Python | 64,894 | 1,681 | # 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... |
201e562cbbb990997e29e966c5d9240d7cab2aee244992d50dbedb3e3e35f271 | Python | 65,126 | 1,548 | import numpy as np
import anndata as ad
import pandas as pd
from .._registry import register_function
from .._optional import build_optional_dependency_error
@register_function(
aliases=[
'grn',
'GRN',
'infer_grn',
'GRNBoost2 prior',
'GENIE3 prior',
'TF-target netw... |
90b24899e0e47abb739b0c1720f9b75b43fd5699bf1695ad4ae2e03d5b9be2a6 | Python | 65,661 | 1,111 | import inspect
import itertools
import warnings
import multiprocessing
import os
from copy import deepcopy
from queue import Queue
from threading import Thread
from time import sleep
from typing import Tuple, Union, List, Optional
import numpy as np
import torch
from acvl_utils.cropping_and_padding.padding import pad_... |
5ca6efb210299fdd17933ab9418fff356483e1fb11e9df35f67295583356223a | Python | 65,895 | 1,494 | import tifffile as tiff
import cv2
import numpy as np
from skimage import io
import math
from sklearn.decomposition import NMF
from sklearn.cluster import KMeans
import math
import torch
import time
import datetime
import os
import scipy.io as scio
import multiprocessing as mp
import random
from DWonder.MN.ConnectedC... |
2340dbbe226f710db0fcd70ddb815029997f4fbfb5931e93537fb4023b310129 | Python | 66,178 | 1,378 | # coding=utf-8
# Copyright 2023 The HuggingFace Inc. team.
# Copyright (c) 2022, NVIDIA CORPORATION. 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.a... |
ab7187788f82cae246a40250d96abca89e269d064ecb95943ac6f6595b53fa67 | Python | 66,419 | 1,539 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Thu Jul 12 11:11:45 2018
@author: epnevmatikakis
"""
import logging
import matplotlib.pyplot as plt
import numpy as np
import scipy.sparse
from typing import List
import time
import os
import caiman
from .utilities import detrend_df_f
from .spatial import... |
24bc4c29cea85f8af23cacad868ffa9ce0535ede643cdbbac9dffbb83a8a3c22 | Python | 66,521 | 1,593 | """
Geneformer classifier.
**Input data:**
| Cell state classifier:
| Single-cell transcriptomes as Geneformer rank value encodings with cell state labels in Geneformer .dataset format (generated from single-cell RNAseq data by tokenizer.py)
| Gene classifier:
| Dictionary in format {Gene_label: list(genes)} for gen... |
60808442698c46472963e000a17e0f9933e4808bb2ca7df24bc4b30602a3a9ee | Python | 66,598 | 1,745 | import logging
import math
import os
from dataclasses import dataclass
from typing import (
TYPE_CHECKING,
Any,
Callable,
Dict,
Iterable,
Iterator,
List,
Literal,
Optional,
Tuple,
Union,
)
import numpy as np
from packaging.version import parse as parse_version
import ray
fr... |
7b207c96472e0bd384a02c302ba519d58858cd09e227a3fabda97f8f58c502f6 | Python | 66,759 | 1,715 | import itertools
import logging
from collections import defaultdict
from functools import lru_cache
from typing import TYPE_CHECKING, Any, Dict, Iterable, List, Optional, Tuple, Union
import numpy as np
import pyarrow
from packaging.version import parse as parse_version
from ray._common.utils import env_integer
from ... |
7b71f30501c7eca0e19462b07d171f7ac5e1f1c8454306501054029a67960a5c | Python | 66,807 | 1,838 | import gc
import numpy as np
from anndata import AnnData
import anndata
import scipy.sparse as sp
import time
from sklearn.preprocessing import Normalizer, StandardScaler
import pickle
import pandas as pd
from . import utilities as ut
import sklearn.manifold as man
import sklearn.utils.sparsefuncs as sf
from packaging ... |
62be3690795ad71b04e3cd7b0d8aef9d0bacdbce546d14bc5848eb06d20791b3 | Python | 66,967 | 1,872 | """Functions that will be used as steps in a decision tree."""
import logging
import numpy as np
import pandas as pd
from scipy.stats import scoreatpercentile
from tedana.docs import fill_doc
from tedana.metrics.dependence import generate_decision_table_score
from tedana.selection.selection_utils import (
change_... |
0a394db91eabcbd3ca108a49e43aee5ab0369894aaf268693d19cb2b3e770134 | Python | 66,972 | 1,839 | """
Model factory for creating and managing different scLLM models.
"""
from typing import Dict, Any, Optional, Union, List
from pathlib import Path
import numpy as np
from .._registry import register_function
from .base import SCLLMBase
class ModelFactory:
"""
Factory class for creating different single-c... |
2989d71cb52fd8fc3b4556dd9d729f3b2b213618327d728cab6de1470596b46e | Python | 67,038 | 1,468 | """
CellPLM model implementation with simplified interface.
"""
import copy
import json
import os
import time
import warnings
from pathlib import Path
from typing import Dict, Any, Optional, Union, List, Tuple
from tqdm import tqdm
import numpy as np
import pandas as pd
import torch
import torch.nn as nn
from torch.u... |
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