sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
4f6df6dcca00bb5c7e49bf2ea5ab6fb56744273eb486fea75a4c1cc5d44dccf3 | Python | 2,486 | 77 | from typing import Dict
from keras.models import load_model
from keras.backend import clear_session
import numpy as np
from common import XAIScenarios, SEED
from utils import load_json_file, append_date, dump_as_pickle, load_pickle
from xai.methods_keras import get_keras_attributions
import gc
from glob import glob
... |
b7c9d8362b535f430bc844645ba2d53e982c57db9cfab89a5bda6ce5d86d3db8 | Python | 2,486 | 93 | #!/usr/bin/env python
"""
Collect raw read count metrics. Writes stats to stdout.
Metrics:
counts_qN : Nth percentile
counts_num_intervals : number of records
counts_intervals_size : sum of interval sizes
"""
import gzip
import argparse
import sys
import numpy as np
import svtest.utils.TestUtils ... |
f91bb6da13d603d4e7f7ba59baf15bc935fa77c8980fea3334da723b05589462 | Python | 2,486 | 67 | from txgnn import TxData, TxGNN, TxEval
import argparse
parser = argparse.ArgumentParser('')
parser.add_argument('--device', type=int, default=0)
parser.add_argument('--split', type=str, choices = ['random', 'complex_disease', 'complex_disease_cv', 'disease_eval', 'cell_proliferation', 'mental_health', 'cardiovascular... |
3340f312e454d2a77b41ca7619016d4db053fabd2031513485694dbf3173cf27 | Python | 2,488 | 78 | # -*- coding: utf-8 -*-
# (C) Copyright 2020, 2021, 2022, 2023, 2024 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.
#... |
377b44d6cb7f4bec606edbdad017e022507836fce496f86af95de4d808fe72d7 | Python | 2,488 | 55 | ####################################################################################################
# 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... |
8a515adb16f9821695d2a154e873d8fb8c85104a9f8d5488a5aebd81d812e18f | Python | 2,488 | 93 | """
test lif_curr_exp_no_delay
"""
import os
import matplotlib.pyplot as plt
# get results and plot
import numpy as np
from spinnaker2 import hardware, snn
def test_lif_curr_exp_no_delay(do_plot=False):
params = {
"threshold": 1000.0, # high value so neurons don't spike
"alpha_decay": 0.9,
... |
06774c0ce0882e60b01e5115ac4c3d7c3d2db850907ea9f49c766b3450edadb8 | Python | 2,489 | 69 | """
This module defines project-level constants.
"""
import os
import numpy as np
from tensorflow.keras.losses import MeanSquaredError
from tensorflow.keras.optimizers.legacy import Adam
from tensorflow.keras.metrics import RootMeanSquaredError
from . import regressor_tools as rt
from . import experiments_tools as et
... |
e37404a28d02bb245e8cc8af997ab8b38227f205f94d1231fac2ea7cadf8ce3d | Python | 2,490 | 84 | """
This script provides the functionality to generate metadata.npz files necessary
for load_balancing the DataLoader.
1. Copy from: https://github.com/Open-Catalyst-Project/ocp/blob/09f0d3bdf4c9154c2f11105eb5d61e1cc0d8c638/scripts/make_lmdb_sizes.py
2. Used for generating sizes of data for S2EF ta... |
484a7644d92868787e7733471fd7f4b90fe6fa52eb64dc915e3eccf9dbb976a7 | Python | 2,491 | 69 | import torch
import logging
from torch.utils.data import TensorDataset
from sklearn.model_selection import train_test_split
from agent.data.entities.config import FC_CLASS_VALUES
from agent.classifiers.utils.class_mgmt import get_number_of_classes
from agent.classifiers.data.transformer_text_triple_fc_dataset_mgmt i... |
a7a889078baa680505d2140d5ea04b3cd0246870228f2037d7c196dcf1da7d05 | Python | 2,491 | 81 | import numpy as np
import os
import json
from ..io import SAVED_DIR, load_network_all
from types import SimpleNamespace
from copy import deepcopy
def analyze_weights(run_name, directory=SAVED_DIR, auto_save=True):
print("starting weights analysis")
try:
# Loading the Network
print("1")
... |
a81388f8295bfdd4481d599f69d2ea857e796b1918caf524ebb262ef15665f5d | Python | 2,491 | 49 | # -*- coding: utf-8 -*-
"""
Spyder Editor
This is a temporary script file.
"""
#------------------------------------------------------------------------------
# Analysis Parameters (modify if required)
min_per = 18 #min period (in h) to be analysed
max_per = 30 #max period (in h) to be analysed
pixels_per_... |
c43f2076621df64760ed9ff04322fcdd82d6175ab8741764e9b4b880e0ac7e7a | Python | 2,491 | 69 | #
# Copyright (c) 2021, NVIDIA CORPORATION.
#
# 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 ... |
17501e6b1c56867bbdb4052106e438fc007077f0e8dc89c0921738d895b7fb85 | Python | 2,492 | 77 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
import argparse
import gzip
import pysam
def load_introns_for_contig(intron_file, contig):
introns = []
is_gzipped = intron_file.endswith('.gz')
opener = gzip.open if is_gzipped else open
with opener(intron_file, 'rt') as f:
for line in f:
... |
4885d438cfcc39d2edb32c5462f3f1351040ce40293bbf66d1c1c713866d7ced | Python | 2,492 | 80 | # built-in dependencies
from typing import List, Union, Any, cast
# 3rd party dependencies
import numpy as np
from numpy.typing import NDArray
# project dependencies
from deepface.commons import weight_utils
from deepface.models.FacialRecognition import FacialRecognition
from deepface.commons.logger import Logger
lo... |
a34b205456e1df53bc7448871c9df76bcf8a20424e6fea8d8c74ac0a2a4b1572 | Python | 2,492 | 86 | # -*- coding: utf-8 -*-
# (C) Copyright 2026 IBM. All Rights Reserved.
#
# Licensed under the MIT license. See LICENSE file in the project root for details.
"""Global drift compensation for inference."""
from typing import Tuple, TYPE_CHECKING
from torch.autograd import no_grad
from torch import abs as torch_abs
fr... |
b984b0e93940e34fa034be4f2e8a5c36f28e6279a265bdc84045b1711dc625d0 | Python | 2,493 | 81 | """Script to run a jupyter notebook for an ensemble."""
import argparse
import logging
import sys
from importlib import resources
from typing import List
from flyvis.utils.compute_cloud_utils import launch_single
logging.basicConfig(
format="[%(asctime)s] [%(filename)s:%(lineno)d] %(message)s", level=logging.INF... |
bb6c52b8c41535ced3208bc432bde76a2ef12df03bc5a4e174cda97d42bd02b2 | Python | 2,493 | 79 | """Allow ``python -m omicverse.mcp`` to start the MCP server."""
import sys
def _requested_transport(argv: list[str]) -> str | None:
"""Return the requested transport, or ``None`` when argparse should handle exit-only flags."""
args = list(argv[1:])
for index, token in enumerate(args):
if token i... |
f3a43de98331f55c9eb19d22417449ae667108b3642e6bf7be5885fe3e51ccb0 | Python | 2,493 | 64 | ####################################################################################################
# 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... |
965fcbee7b9049f19724eeddf489499e594540b5ebef7bab8935249c588f8e7d | Python | 2,494 | 98 | import pandas as pd
from neuron_morphology.morphology import Morphology
from cloudfiles import CloudFiles
import io
import os
import csv
SWC_COLUMNS = (
"id",
"type",
"x",
"y",
"z",
"radius",
"parent",
)
COLUMN_CASTS = {"id": int, "parent": int, "type": int}
def read_swc(path, columns=SW... |
b16aae810deeae9bbe00f5e6242ca683e631b103b08096a42548071330099d3a | Python | 2,494 | 90 | from functools import partial
from typing import Annotated, Callable, Iterable, Literal, Any
import numpy as np
from numpy.typing import NDArray
from sklearn import model_selection
from sklearn.base import BaseEstimator
from siapy.core.types import ArrayLike1dType, ArrayLike2dType
from siapy.optimizers.evaluators imp... |
d8a13f6e57c6b8aefea518538375995c95769faaf5ab411a46aa53a8e32b4d56 | Python | 2,494 | 65 | # -*- coding: utf-8 -*-
# @Time :2024/6/6 20:23
# @Author :MENGLong Li
# @File :main.py
# @Software:PyCharm
import numpy as np
from lib.ReadTxtDataFromOdbFile import ReadTxtDataFromOdbFile
from lib.MachineLearning import MachineLearningSet
"-------------------------------------------------- Step 1 -----------... |
e6471025d8b892e4bc4008c64619d4266c35ce72d9352c13657c0a351134f255 | Python | 2,494 | 77 |
import numpy
class ContextHandler:
"""
Handles different contextual information.
Available modes are:
- `mean`: The average of the image
- `quantile`: The quantiles of the image
- `image`: The entire image
"""
def __init__(self, ctx_info):
"""
Initializes the class wit... |
9fb218061ef15f775b5c15cb56778a7e7fff147da8a15c25d509bdd750568c81 | Python | 2,495 | 57 | import numpy as np
import h5py
import argparse
import pickle
from typing import Dict
import lib.dataset_config_parser.dataset_config_parser as dcp
from lib.data_utils import sta_metadata
from lib.data_utils.matched_cells_struct import OrderedMatchedCellsStruct
if __name__ == '__main__':
parser = argparse.Argu... |
3dd3523d146a7c757dddc3d2854698a4b575f2123b532ab26dab0533fb68c128 | Python | 2,496 | 95 | import numpy as np
class gene(object):
def __init__(self, geneID, geneType, binID = -1):
"""
geneType: 'MR' master regulator or 'T' target
bindID is optional
"""
self.ID = geneID
self.Type = geneType
self.binID = binID
self.Conc = []
self.... |
14350c2940ed9c3a95bead764100e930fbce9976f7996739e2db469c5a5bae42 | Python | 2,497 | 73 | __author__ = 'jfaskowitz'
'''
josh faskowitz
Indiana University
Computational Cognitive Neurosciene Lab
Copyright (c) 2018 Josh Faskowitz
See LICENSE file for license
'''
import numpy as np
import nibabel as nib
from sys import argv
import json
def main():
i_file = str(argv[1])
o_file = str(argv[2])
la... |
3e32613ba3a790b6c9222af58f8dc169f75ed5b20758416f496a7f0572e0af8b | Python | 2,497 | 64 | #!/usr/bin/env python
import argparse
import os
import sys
import json
import dxpy
import requests
from dxencode import dxencode as dxencode
ASSAY_TYPE = 'RNA-seq'
ASSAY_TERM_ID = "OBI:0001271"
PROJECT_NAME = 'long-rna-seq-pipeline'
def get_args():
'''Parse the input arguments.'''
ap = argparse.ArgumentPars... |
297604aab5a16da4ae627232ee840245fdd81ec789ef54d92812273c720e8cb2 | Python | 2,498 | 90 | """
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.
This script provides the functionality to generate metadata.npz files necessary
for load_balancing the DataLoader.
"""
from __future__ import... |
53fd2a6c356c85e485797ebf4f63b38d15c86cff2836976119d6eb646a51e1fb | Python | 2,498 | 48 | import numpy as np
from numba import njit
@njit
def forward(input_size, indices, timestamps, weights, thresholds, leak_tau=None, max_time=1, dropout_in=None, dropout_out=None):
# Init membrane potentials
mem_pots = np.zeros(weights.shape[0], dtype=np.float32)
# Record input and output spike timestamps
... |
f6c67822305ab80c71923e4dee064af54dca2266f6bc16ba5208b05e5bceb59a | Python | 2,498 | 58 | ####################################################################################################
# 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... |
f7cd88301be5fa375f7415643efa85e76c9ca08a3010b1dc02481b44822df2ce | Python | 2,498 | 58 | import os
import nibabel as nib
import pandas as pd
import numpy as np
from scipy.stats import ttest_ind, mannwhitneyu
# Load participant data
participants_df = pd.read_csv("participants.tsv", sep="\t")
# Function to calculate lesion volume (in cc)
def calculate_lesion_volume(nifti_path):
img = nib.load(nifti_pat... |
a26f772e9bbc9b08826831cfb4534858c75f2b3e0087d2a478e1e47b3f3d02df | Python | 2,499 | 80 | """
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 gzip
import json
import os
from glob import glob
from typing import TYPE_CHECKING, TypeVar
if T... |
e638c71242082f77721085560c61fc3b5a8dd726ed30604986e5ab771be61452 | Python | 2,500 | 63 | from __future__ import absolute_import, print_function
# checks
try:
import tensorflow
del tensorflow
except ModuleNotFoundError as e:
from six import raise_from
raise_from(RuntimeError('Please install TensorFlow: https://www.tensorflow.org/install/'), e)
import tensorflow, sys
from ..utils.tf import... |
140baf3cb49808b0f32757761a7b53c105e9c6000111aa0bae3e4b7503adc690 | Python | 2,502 | 71 | from dataclasses import dataclass
from enum import Enum
from typing import List, Optional, Union
import numpy as np
import PIL
from PIL import Image
from ...utils import BaseOutput, is_torch_available, is_transformers_available
@dataclass
class SafetyConfig(object):
WEAK = {
"sld_warmup_steps": 15,
... |
280eeff997742439e30ad95b88e71a3dffa10ee2a94ff85413199d775c134ea1 | Python | 2,503 | 62 | import nibabel as nib
import numpy as np
import pyvista as pv
from lib.qc_surface import compute_topology
from lib.surface import write_points_faces_to_gifti
from lib.surface_repair import fill_holes, repair_mesh
from lib.utils import setup_logger
log_file = snakemake.log[0] if snakemake.log else None
logger = setup_l... |
296522a08f41a520e752c0bb21a1cda2821d434813e715b4de5212af9b870efb | Python | 2,504 | 54 | import logging
from datetime import datetime
from transformers import FunnelForSequenceClassification
from agent.classifiers.transformer_classifier import transformer_classifier
from agent.classifiers.transformer_classifier_text_trainer import train_loop, eval_loop
from agent.classifiers.data.transformer_text_cw_data... |
77ece7506e0da16c3d0ad15314a2c8fcf19910cf7d7a878d0bac2f6fad8d73d6 | Python | 2,504 | 68 | import os
import numpy as np
import pandas as pd
import pyranges as pr
def annotate(df, genes):
gr = pr.PyRanges(df)
return gr.nearest(genes)
def fdr(p, n=None):
"""Give a numpy array, convert P values to FDRs"""
if not n:
n = len(p)
p = np.array(p)
# do not allow nan values
asser... |
a43214a4b58f06625dd817b759974c826eb6e7cdcec76685e6418e62329acace | Python | 2,504 | 78 | # built-in dependencies
from typing import List, Any
# 3rd party dependencies
from numpy.typing import NDArray
from retinaface import RetinaFace as rf
# project dependencies
from deepface.models.Detector import Detector, FacialAreaRegion
# pylint: disable=too-few-public-methods
class RetinaFaceClient(Detector):
... |
cbc1e00f5333626aa577c1281882bcb127ad84cc682f380eaf0f8cc64012d452 | Python | 2,506 | 79 | # type: ignore
# pylint: disable-all
# -*- coding: utf-8 -*-
# (C) Copyright 2026 IBM. All Rights Reserved.
#
# Licensed under the MIT license. See LICENSE file in the project root for details.
"""aihwkit example 31: Using half precision training.
This example demonstrates how to use half precision training with aih... |
2ee59eef8e24c0e00ada2def73a1619d7bfbfb934a501af6b8bedd401a42ef8d | Python | 2,507 | 80 | """Tools for manipulating sparse matrices."""
import itertools
from typing import Any, Collection, Iterator, Sequence
import numpy as np
from scipy import sparse
def rescale(matrix, factors: Sequence[float], axis: int = 0):
diagonal = sparse.csr_array(sparse.diags(factors))
match axis:
case 0:
... |
8d3f2482b3c58ff38cc49a2b812fcc54affbda35044c0e05ce598bde8131078a | Python | 2,509 | 75 |
import numpy
import os
import json
import pickle
import bz2
import torch
import gym_sted
from .prefNet import PrefNet
def load_demonstrations(path=None, f1_score=False):
"""
Loads a set of demonstrations from the given path
:param path: A `str` of the path to the set of demonstrations
:returns : A... |
a2198fb8ee5d66524622e758d85d7aec80e8084b6759b99916a33d25d9affd82 | Python | 2,509 | 68 | # coding: utf-8
import os
import sys
import unittest
import pytest # noqa
from ray._private.test_utils import load_test_config
from ray.autoscaler.tags import TAG_RAY_NODE_KIND
from ray.autoscaler.v2.instance_manager.config import AutoscalingConfig
from ray.autoscaler.v2.instance_manager.ray_installer import RayInst... |
ea1a3ae75ee039527a160fddb56ad6efbf08a253be03b34ad2902c6aa8793232 | Python | 2,509 | 69 | import tempfile
import torch
import tqdm
from ddw.prepare_data import prepare_data
from .subtomo_dataset import SubtomoDataset
def get_avg_model_input_mean_and_std(tomo_file, subtomo_size, subtomo_extraction_strides, standardize, mw_angle, batch_size, num_workers, batches=None, verbose=False):
"""
Computes... |
12fa2efb9eb2a78de7bb11c4ef532367ccba221b9d12bd5241aba64679da3732 | Python | 2,510 | 66 | import sys
import json
import pickle
import argparse
from lop.utils.miscellaneous import *
from lop.utils.plot_online_performance import generate_online_performance_plot
def add_cfg_performance(cfg='', setting_idx=0, m=2*10*1000, num_runs=30):
with open(cfg, 'r') as f:
params = json.load(f)
list_param... |
1384bf782404897a562f1ec2e4cb49c04659cbc6167c78059b71fd0abd6a6288 | Python | 2,510 | 66 | # Copyright 2026 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, ... |
c2962b9a958249e737e30e42c83b33148b53dc54ca9474182b41e0d6843e7d0f | Python | 2,510 | 77 | # Modified from https://github.com/dbolya/tide
# This work is licensed under MIT license.
from typing import Union
class Error:
"""A base class for all error types."""
def fix(self) -> Union[tuple, None]:
"""Returns a fixed version of the AP data point for this error or None
if this error sho... |
d39743fe5ec7daa8a92349632715bd6ba581943cb72d6bdcff34f88cd972a91c | Python | 2,511 | 66 | """Helpers for recognizing and recovering from cloud credential failures.
Format-agnostic: an expired S3 session token or Azure SAS token looks the same
to any datasource or datasink that talks to object storage, so these live here
rather than next to one format's implementation.
"""
import os
from typing import Dict... |
d79ee28d2bda90be98040827899b510514919e2448e99710a8df061193af5ae7 | Python | 2,513 | 81 | import numpy as np
import gym
import exputils as eu
from .twod_object_collection import TwoDObjectCollection
class Barreto2018TwoDObjectCollection(TwoDObjectCollection):
'''
2D grid object collection task described in Barreto et al. (2018) (https://arxiv.org/pdf/1606.05312.pdf).
'''
@staticmethod
... |
b0cc21dc30d229fa8cf2644d0504608ca8c6a14a428f43a014096e5e56ab9a92 | Python | 2,514 | 78 | """
Base adapter interface for MCP tool execution.
All adapters normalize Python function calls into the standard MCP response
envelope: ``{ok, tool_name, summary, outputs, state_updates, warnings}``.
"""
from __future__ import annotations
import traceback
from abc import ABC, abstractmethod
from typing import Any, ... |
ee2bdba50f6873b7c4b8630aaa60a43fd9ebe1874971667175ef991b33463565 | Python | 2,515 | 63 | import torch
from torch.utils.data import DataLoader, TensorDataset, Dataset
import cv2
import numpy as np
import clip
import uuid
from albumentations import Compose, RandomBrightnessContrast, \
HorizontalFlip, FancyPCA, HueSaturationValue, OneOf, ToGray, \
ShiftScaleRotate, ImageCompression, PadIfNeeded, Gaus... |
623f941d3b5dfef06996189d74f3f9a8d68ca1afbcfa570bd8478fb159550392 | Python | 2,516 | 81 | _base_ = [
'../../_base_/datasets/urpc2020/urpc2020-test-A_coco_detection.py',
'../../_base_/schedules/schedule_1x.py', '../../_base_/default_runtime.py'
]
# model settings
model = dict(
type='TOOD',
data_preprocessor=dict(
type='DetDataPreprocessor',
mean=[123.675, 116.28, 103.53],
... |
d13f28af7a8b553a4c18d8dd40e68f50624836b9c4e755fdf0adf4147bbe7258 | Python | 2,516 | 81 | _base_ = [
'../../_base_/datasets/urpc2020/urpc2020-test-B_coco_detection.py',
'../../_base_/schedules/schedule_1x.py', '../../_base_/default_runtime.py'
]
# model settings
model = dict(
type='TOOD',
data_preprocessor=dict(
type='DetDataPreprocessor',
mean=[123.675, 116.28, 103.53],
... |
752573945f5d39a4ef7317d1d82a064fda9b2d3a2550fdde2cbd7a7539c1a70c | Python | 2,517 | 78 | """Provide functions for system setup"""
# general imports
import json
from openmm import unit
from openmm.app import (
CharmmPsfFile,
CharmmCrdFile,
)
def gen_box(psf: CharmmPsfFile, crd: CharmmCrdFile) -> CharmmPsfFile:
"""Function to create psf file containing information about the box used (only for ... |
0dbbda1464e19deac09407185959f5775d12bec8e02ed8877f942f3b8f4c9bb9 | Python | 2,519 | 77 | # built-in imports
from typing import List, Tuple, Optional, Any
from abc import ABC, abstractmethod
from dataclasses import dataclass
# Third party imports
from numpy.typing import NDArray
# Notice that all facial detector models must be inherited from this class
# pylint: disable=unnecessary-pass, too-few-public-... |
a130ea65f58000bd0e2be5e286c68f645494e94c783bc685442d472f4adbcb40 | Python | 2,519 | 76 | """Print the doc example test targets that a change feeds directly.
Prints one `<team> <label>` pair per line to stdout, and a report of what
runs and what doesn't to stderr. See doc_example_targets.py for the matching rules.
Pass files explicitly, or pass --base to diff HEAD against a ref. In CI,
run_doc_example_tes... |
2f5aab11c7ae2212bbe20d55395b47e2e409d9b6e2c757e32bbd3246f208f84d | Python | 2,520 | 81 | _base_ = [
'../../_base_/datasets/urpc2020/urpc2020-validation_coco_detection.py',
'../../_base_/schedules/schedule_1x.py', '../../_base_/default_runtime.py'
]
# model settings
model = dict(
type='TOOD',
data_preprocessor=dict(
type='DetDataPreprocessor',
mean=[123.675, 116.28, 103.53],... |
a2cbd11edb1dd8fb169d352832b4a296cc578f88a664766358ebf26a840fd51f | Python | 2,523 | 87 | # coding: utf-8
import os
import sys
import pytest # noqa
from ray.autoscaler.v2.instance_manager.storage import (
InMemoryStorage,
StoreStatus,
VersionedValue,
)
@pytest.mark.parametrize("storage", [InMemoryStorage()])
def test_storage(storage):
assert storage.get_version() == 0
assert storage... |
232cc06940c70b2c358c8458f02e5ad7cf55bd5758287e3c16cb98b1823e8965 | Python | 2,524 | 42 | import numpy as np, pandas as pd, json, itertools
from scipy.optimize import minimize
from scipy.special import logsumexp
from emp import counts, dm_ll, R
def prep(f,manip_col,manip_val,has_nt):
x=pd.read_excel(R+f).dropna(subset=["t_court","defbehav"]); g=(x[manip_col]==manip_val).astype(int).values
h=(~x.thre... |
f123653af57ce2fa64949728abe4a0d6de4feddb97015547fbd3c702557dacc2 | Python | 2,525 | 90 | import socket
import os
import sys
import numpy as np
import scipy as sp
import scipy.linalg as la
import scipy.io as sio
from sklearn import svm, manifold, linear_model
from sklearn.model_selection import cross_val_score as cv_score
import sklearn.kernel_approximation as kaprx
def convexify(cols, bins):
'''
... |
67630e74f6e07ee9ffdc1a469d5f94a230b3ba642e092afc542e725c47f99cc5 | Python | 2,528 | 66 | """
Shared /model command output helpers for Jarvis channels.
"""
from __future__ import annotations
from html import escape
from typing import List, Sequence
from .model_registry import iter_supported_model_catalog
_MODEL_SWITCH_EXAMPLES: Sequence[str] = (
"gpt-5.3-codex",
"claude-sonnet-4-6",
"qwen-max... |
7478699cb9e8163f6f178a15b1fd303aa3c74743bda4cfb685c417c3f1f8cdfa | Python | 2,528 | 83 | """Shared utilities for local build scripts (build_wheel.py, build_image.py)."""
from __future__ import annotations
import logging
import platform as _platform
import re
import subprocess
from pathlib import Path
class BuildError(Exception):
"""Raised when a build operation fails."""
class _ColorFormatter(logg... |
969de6389e40456fb9515eb1eda5e05474cad88645ed11e4b657c79508989399 | Python | 2,528 | 79 | #!/usr/bin/env python3
import argparse
from glob import glob
import sys
import numpy as np
import matplotlib.pyplot as plt
import pysam
import math
import pandas as pd
import haplotagging_stats
import os
import collections
import seaborn as sns
SWITCH="switch_err_rate"
HAMMING="hamming_err_rate"
HAPLOTYPE="haplotype"
... |
b152ce6547074412a69b08656a7bdfa00562fe067dec96badd948026669c6781 | Python | 2,528 | 79 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Python version: 3.10.9
pandas version: 1.5.0
numpy version: 1.23.3
"""
#%% Import Modules
import pandas as pd
import numpy as np
#%% Functions
def dice_coeff(df, thresh=None):
if thresh != None:
ses1 = df[(df["ses"]=="ses-01") & ((df["pval"] < thresh))].re... |
9863dec5e32e2906d9cde4d88fdefe7191e4198ce83193710ac3f67fa6f65199 | Python | 2,529 | 128 | from numba import jit
import pandas as pd
import numpy as np
from numba import njit
N_BIN_TARGET = 30
@jit(nopython=True)
def find_gene_p(num_umi, D):
"""
Finds gene_p such that sum of expected detects
matches our data
Performs a binary search on p in the space of log(p)
"""
low = 1e-12
... |
ade4f9403b827af383ef07e881d67ab30c09965eb29764114b99d7b5dca39a8c | Python | 2,529 | 69 | # metrics.py
from prometheus_client import Counter, Histogram, Gauge
from typing import Dict
from dataclasses import dataclass, field
import os
import psutil
import os
@dataclass
class PerformanceMetrics:
_instance: 'PerformanceMetrics' = field(default=None, init=False, repr=False)
# Prometheus Metrics
... |
57a572234f1e2b4790cc57e8faa93cc1a17608f5bd0badec8cf9a5f5f849e2c3 | Python | 2,530 | 63 | import numpy as np
import scipy.sparse as sparse
from hic3defdr.util.banded_matrix import BandedMatrix
def filter_sparse_rows_count(matrix, min_nnz=25, k=300):
"""
Wipes the sparse bins (both rows and columns) of a matrix, where "sparse"
means that the bin has less than ``min_nnz`` nonzero interactions w... |
644c1604a1c4ffbf6db6a6ecb73dce39178e9fb4e65abb3881476a9908d42ad5 | Python | 2,532 | 71 | import numpy as np
import torch
import torch.nn as nn
import torch.nn.functional as F
def init_lecun_uniform(tensor, scale=1.0):
"""Initializes the tensor with LeCunUniform."""
fan_in = torch.nn.init._calculate_correct_fan(tensor, "fan_in")
s = scale * np.sqrt(3.0 / fan_in)
with torch.no_grad():
... |
1b41ea5d0483e300bbe350dfbbe480a5079e96cebcc657e1d18daac813d048df | Python | 2,533 | 76 | """Exercise registration ownership with an actual on-disk Qdrant local client."""
from types import SimpleNamespace
import numpy as np
import pytest
from deepface.modules import datastore
from deepface.modules.database import qdrant
@pytest.mark.parametrize("owned", [False, True])
@pytest.mark.parametrize("fail", ... |
018706d27cd87a683578d945d1d88de0756834bf562b150a284a9c30320a0a7b | Python | 2,534 | 81 | """
Auxiliary handler methods for data summary extraction
"""
from typing import Any, Callable, Dict, List, Sequence
import networkx as nx
from visions import VisionsTypeset
def compose(functions: Sequence[Callable]) -> Callable:
"""
Compose a sequence of functions.
:param functions: se... |
16d9376d4e90fe2a6754b3802916e89e6bfee3b9191b44e7b1cc14450c1c41a5 | Python | 2,535 | 77 | # import needed libraries
import cv2
import numpy as np
import plotly.express as px
import plotly.graph_objects as go
import os
import glob
from plotly.subplots import make_subplots
def plot_part_region_spectrum(img_i, img_o, colorbar_min, colorbar_max):
img_i = np.array(img_i)
img_i = img_i / np.max(img_i)
... |
3a31bf5e47b5fd2c2b44b51b3e7519ac58fcfe310139a1020c8f257b9bff193c | Python | 2,535 | 66 | import numpy as np
import UnitMatchPy.Param_fun as pf
def get_ParameterKernels(Scores2Include, labels, Cond, param, addone = 1):
"""
Requires Score2Include, a dictionary where the keys are the metric used and the values are
nUnits * nUnits with the score for each unit.
Smoothing and add one is done to... |
5d4c6b73a52e991c743662567bbeb6c617080face7ba4222c0877b75e402eeb5 | Python | 2,535 | 71 | import marshmallow as mm
from argschema.schemas import ArgSchema, DefaultSchema
from argschema.fields import InputFile, List, Float, Int, Nested, Boolean
from neuron_morphology.transforms.affine_transformer._schemas import AffineDictSchema
def validate_input_affine(data):
has_slice_transform_dict = bool(data.get(... |
c3524b12a0b06ce4470ccee3eeab141bd39a79383b4181b05cfbd9f1716d40b0 | Python | 2,535 | 74 | # -*- coding: utf-8 -*-
# (C) Copyright 2026 IBM. All Rights Reserved.
#
# Licensed under the MIT license. See LICENSE file in the project root for details.
"""Tests for Experiment Runners."""
import os
from io import StringIO
from unittest import SkipTest, skipIf
from unittest.mock import patch
from torch import d... |
06959e77be4bef1b18bddbd0c15189a76bf79cbada0265adfca018eb73cb2e71 | Python | 2,536 | 74 | # Generated by Django 4.1.6 on 2023-02-06 04:19
from django.db import migrations, models
import django.db.models.deletion
class Migration(migrations.Migration):
dependencies = [
("infer", "0005_remove_weights_path_weights_chkpt"),
]
operations = [
migrations.CreateModel(
name... |
9ec79a46f88cd350492e7806355166b826510a7cec82af8fc3fe557ba25371ab | Python | 2,537 | 74 | # -*- coding: utf-8 -*-
# (C) Copyright 2020, 2021, 2022, 2023, 2024 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.
#... |
21ce5377d7f89c1913e5d4940cd4dc6c4f3624ca432fafde4903f85534f89f68 | Python | 2,539 | 86 | from collections.abc import MutableSequence
from typing import Any, Iterator, Iterable
class ConstantLookupList(MutableSequence):
"""A list with constant time index lookup."""
def __init__(self, values: Iterable = ()):
self._lst = list(values)
self._lookup = {}
self._generate_lookup()... |
61c617dd8d6d6f45291792a152a9d6bc6035a1645930e170756cfdeeaf498efa | Python | 2,539 | 48 | from model import (IntraEncoder, InterEncoder, ProteinInteractionNet, Trainer, Tester)
from uncertaintyAwareDeepLearn import VanillaRFFLayer
from utils import (
load_configuration,
initialize_logging,
set_random_seed,
get_computation_device,
initialize_scheduler,
train_and_validate_model
)
def ... |
efb4d6a87712a318c016f9cf8bad49344ceaeaa103f5642c70216dc5c97e02dd | Python | 2,539 | 77 | # -*- coding: utf-8 -*-
"""Simulate and export one Randomized Experanto chunk.
CHUNK selects a chunk; the model's trial parameter selects its trial.
RUN_CONFIG names the launcher's run_config.json, containing input paths,
shared export settings and run provenance. Manual runs use CHUNK_DIR and BASE_PATH.
SHEET_NAMES s... |
0320d6ff6bae4756b52c3a90b770950686b8f39d8c86799dd9cfd57b154d3932 | Python | 2,540 | 72 | #!/usr/bin/python
import sys
import os
import subprocess
import argparse
####################################################################################################
# @compute_hausdorff
####################################################################################################
def compute_hausdorf... |
b27d7902cca668e9d8e74e66685de85c7ed163cb0abe2f05b6088865bcf814ce | Python | 2,540 | 76 | import unittest
from spinnaker2 import mapper
from spinnaker2.neuron_models.common import format_routing_table
from spinnaker2.coordinates import PE
class TestSynapseWordSpec(unittest.TestCase):
def test_enum(self):
s16 = mapper.SynapseWordSize.SIZE_16
self.assertEqual(s16.value, 16)
s32... |
4fdf78f360e71fb818d40583e7bdcc17b73beff298b5871f3fc3331094d10e70 | Python | 2,541 | 83 | # 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... |
88f071924f1f47766c24d4f64b763ce9b2f5496e98039ed91a590bb9f7a022ac | Python | 2,541 | 91 | _base_ = [
'../_base_/datasets/rtts_coco.py', '../_base_/schedules/schedule_1x.py',
'../_base_/default_runtime.py'
]
# model settings
model = dict(
type='FCOS',
data_preprocessor=dict(
type='DetDataPreprocessor',
mean=[102.9801, 115.9465, 122.7717],
std=[1.0, 1.0, 1.0],
... |
cdff1115fc9a2b57d6cf5a2a699d7e99541bc2b313eb93eec59be6b6c1a8b77a | Python | 2,541 | 57 | from pkg_resources import parse_version
from configparser import ConfigParser
import setuptools
assert parse_version(setuptools.__version__)>=parse_version('36.2')
# note: all settings are in settings.ini; edit there, not here
config = ConfigParser(delimiters=['='])
config.read('settings.ini')
cfg = config['DEFAULT']
... |
00cdf6d2fa038caeaf20d2c193ceb3913dc2d528e06efcbfb62ddbfa41be974b | Python | 2,543 | 75 | # -*- coding: utf-8 -*-
# (C) Copyright 2026 IBM. All Rights Reserved.
#
# Licensed under the MIT license. See LICENSE file in the project root for details.
"""Tests for Experiment Runners."""
import os
from io import StringIO
from unittest import SkipTest, skipIf
from unittest.mock import patch
from torch import d... |
c70ca867d26a937477258cf1aa7f7fa95d3360278e02b8e1c9fd91270ac55af9 | Python | 2,543 | 81 | from ogb.utils.features import (
allowable_features, atom_to_feature_vector, bond_feature_vector_to_dict,
bond_to_feature_vector, atom_feature_vector_to_dict
)
import torch
import rdkit
from rdkit import Chem
import numpy as np
def smiles2graph(smiles_string, with_amap=False):
"""
Converts SMILES stri... |
403c489ecd25c816d7fe3c1165b8d1574d1d7dda55f2c67a8e4ff0a290f2c867 | Python | 2,544 | 75 | import base64
import json
import os
import socket
import sys
import pytest
import ray
from ray._private.test_utils import (
wait_for_condition,
wait_for_dashboard_agent_available,
)
from ray.dashboard.tests.conftest import * # noqa
_RAY_EVENT_PORT = 12345
@pytest.fixture(scope="session")
def httpserver_li... |
322aa18e61c84c9e248b38211c76bc53ffaf0c9a2e21b96a6b1287d9ce13543a | Python | 2,545 | 86 | _base_ = [
'../_base_/datasets/rtts_coco.py', '../_base_/schedules/schedule_1x.py',
'../_base_/default_runtime.py'
]
# model settings
model = dict(
type='ATSS',
data_preprocessor=dict(
type='DetDataPreprocessor',
mean=[123.675, 116.28, 103.53],
std=[58.395, 57.12, 57.375],
... |
5b0042d8ea6b21e4ca8effde9788ffb71eea093b29520161d69eb84c7db6d92d | Python | 2,545 | 72 | from typing import Optional
import torch
from torch import nn
__all__ = ["MILModel", "Attention"]
class MILModel(nn.Module):
def __init__(
self,
n_feats: int,
n_out: int,
encoder: Optional[nn.Module] = None,
attention: Optional[nn.Module] = None,
head: Optional[nn... |
bac6484716f7af34f1b49ad8787a39b54520ba1981a1f0aa1e702b639a55dc80 | Python | 2,545 | 80 | from typing import List, Tuple
from ray.autoscaler._private.util import format_readonly_node_type
from ray.autoscaler.node_provider import NodeProvider
from ray.autoscaler.tags import (
NODE_KIND_HEAD,
STATUS_UP_TO_DATE,
TAG_RAY_NODE_KIND,
TAG_RAY_NODE_NAME,
TAG_RAY_NODE_STATUS,
TAG_RAY_USER_NO... |
a3b422f881cf0b657b45b4d1eeeff63ab5ee95cf50e9c44670d03eda79ddf525 | Python | 2,548 | 62 | ####################################################################################################
# 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... |
beaefd2662df36a5d4a31572c5e660a3d68c844d3752d1590b0d17306e4d847b | Python | 2,548 | 91 | _base_ = [
'../_base_/datasets/duo_coco_detection.py',
'../_base_/schedules/schedule_1x.py', '../_base_/default_runtime.py'
]
# model settings
model = dict(
type='FCOS',
data_preprocessor=dict(
type='DetDataPreprocessor',
mean=[102.9801, 115.9465, 122.7717],
std=[1.0, 1.0, 1.0],... |
f63b23f9f56ba8861329e524ef39a3347e4a0340005e85697a1a6ee28eab66cc | Python | 2,549 | 76 | # -*- coding: utf-8 -*-
import numpy as np
import seaborn as sns
import matplotlib.pyplot as plt
sns.set(style='white', palette='colorblind', context='poster')
n_dim = 16
n_context = 2
bank_size = 3
percept_noise = .2
n_tps_per_context = 5
T = n_tps_per_context * n_context
contexts = [np.random.normal(loc=0,scale=1,s... |
c6ff4a4251033bf066f3b0d02a56a4abbe8d677d8835db7b9e7beebc50fcb83b | Python | 2,550 | 81 | # -*- coding: utf-8 -*-
# (C) Copyright 2020, 2021, 2022, 2023, 2024 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.
#... |
df80423c3879dc4f274ac0708226b3ee6f978d76e4a072e2f72af1831682eef2 | Python | 2,550 | 92 | import os
import time
from contextlib import contextmanager
from typing import List, Optional, Tuple
import numpy as np
import ray
# Only run tests matching this filter pattern.
filter_pattern = os.environ.get("TESTS_TO_RUN", "")
skip_pattern = os.environ.get("TESTS_TO_SKIP", "")
def timeit(
name, fn, multipl... |
195aae127fb16b528016e51edf9d8a5018b581dbafe9b8b1a02797dbf1c4e450 | Python | 2,551 | 75 | # dataset settings
dataset_type = 'BasicImageDataset'
data_root = 'data/uw_enhance/'
file_client_args = dict(backend='disk')
train_pipeline = [
dict(type='LoadImageFromFile', file_client_args=file_client_args),
dict(type='LoadGTImageFromFile', file_client_args=file_client_args),
dict(
type='TransB... |
6c33b47d6676f4f5034607bc69c99774ebbf90fc142957e390c3e9c1a3f9facc | Python | 2,551 | 63 | import math
import json
import argparse
import itertools
from pathlib import Path
from tuner import KernelTuner
def forward_params_list(N):
blocksize_params = ('MAX_BLOCK_SIZE_VALUE', [64, 128, 256, 512, 1024])
thread_value_default = [2, 4, 8, 16, 32, 32, 32, 32, 32, 32]
thread_values_supported = [2, 4, ... |
00ea95d5a6dc20f3c8d4d465f9feb4dde25ef976637ac632078f43f3632fd9a4 | Python | 2,552 | 91 | _base_ = [
'../_base_/datasets/ruod_coco_detection.py',
'../_base_/schedules/schedule_1x.py', '../_base_/default_runtime.py'
]
# model settings
model = dict(
type='FCOS',
data_preprocessor=dict(
type='DetDataPreprocessor',
mean=[102.9801, 115.9465, 122.7717],
std=[1.0, 1.0, 1.0]... |
13b5b23e3db85fcd07acd8f8e0ca223a4811e2d65bdd749c2d772e0a632d8e92 | Python | 2,552 | 79 | """
_*_ coding: utf-8 _*_
"""
from sklearn import cluster
from sklearn.manifold import TSNE
import os
import numpy as np
import pandas as pd
import pickle as pkl
class Clustering:
def __init__(self, input_data, static_data):
PD_cohort = list(static_data[static_data['case_control_other_at_baseline'] == '... |
728fb7bff87a30b77c7445bdccc19d22072fb55865321d17f9eb9c83fa970916 | Python | 2,552 | 94 | from django.shortcuts import render
from django.views.decorators.cache import cache_page
from rapppid_org.settings import TEMPLATES, STATIC_URL
from glob import glob
import markdown
import os.path
import re
def index(request):
return render(request, "index.html")
@cache_page(60 * 60)
def privacy_policy(request):... |
97def89923c2725e4c3f497b8261ee965c83decd1efc2b99b5dd88fdc185983a | Python | 2,552 | 86 | _base_ = [
'../_base_/datasets/duo_coco_detection.py',
'../_base_/schedules/schedule_1x.py', '../_base_/default_runtime.py'
]
# model settings
model = dict(
type='ATSS',
data_preprocessor=dict(
type='DetDataPreprocessor',
mean=[123.675, 116.28, 103.53],
std=[58.395, 57.12, 57.37... |
4faae21361e1623dfa768ef857efac7191d00fe62265f222125664f188b9c1d5 | Python | 2,553 | 92 | # -*- coding: utf-8 -*-
# (C) Copyright 2020, 2021, 2022, 2023, 2024 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.
#... |
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