sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
bbd9cbeb2e973113eb55d83a37f4175556a0a15c0438969e53da8afcb19ab3de | Python | 3,096 | 77 | from .base import BSVTKObjectWrapper
from .data_object import BSTable, BSPolyData, BSUnstructuredGrid
from .algorithm import (BSDataSetMapper, BSPolyDataMapper,
BSLabeledContourMapper, BSLabeledDataMapper,
BSLabelPlacementMapper, BSPolyDataMapper2D,
... |
7e866de7cea1caeb579d176a627aca2b53ee8a493872ebcfaef3bde8789c1dbd | Python | 3,097 | 92 | import os
from typing import Tuple
# disable numpy multithreading
os.environ["OMP_NUM_THREADS"] = "1"
os.environ["MKL_NUM_THREADS"] = "1"
os.environ["NUMEXPR_NUM_THREADS"] = "1"
os.environ["OPENBLAS_NUM_THREADS"] = "1"
os.environ["VECLIB_MAXIMUM_THREADS"] = "1"
import numpy as np
import pandas as pd
from scipy import... |
90eba18c307d09f211d0d0c2db4254479e0ce31880488f6df1478a1ba27e8151 | Python | 3,097 | 77 | """Create a pydot Edge for a GO Term."""
__copyright__ = "Copyright (C) 2019-2020, DV Klopfenstein, H Tang, All rights reserved."
__author__ = "DV Klopfenstein"
import itertools
import pydot
from goatools.gosubdag.utils import extract_kwargs
#pylint: disable=too-few-public-methods
class GoEdgeOpts:
"""Processes... |
23c826643454346210e900ecd2c6f6a168ef38668e14f080d8ba2098e101c161 | Python | 3,098 | 100 | """Tests asserting that ``AESTETIK`` honours the scikit-learn estimator
contract: clone round-trip, get/set_params symmetry, fit_predict ==
labels_, and the modality-only cluster attributes added in 0.3.
"""
from __future__ import annotations
import logging
import numpy as np
import pytest
from sklearn.base import cl... |
44bdc36aed52585f64b3b58cb5c971fce5dba36a899b5d6f0589c0c300518ecd | Python | 3,100 | 86 | import numpy as np
from phantoms.phantom import phantom
import func.geometry_func as gf
import func.BphP_func as bf
class plane_cyclinder_tumour(phantom):
def create_volume(self, cfg : dict, mu_a_background=0.7, r_tumour=0.001):
mu_s_background = 2500 # [m^-1]
mu_s_tumour = 1700 #... |
e62ec2cab5af1028e1f774ea29a947be5a648e7c54fb06bf5b44a6447973c9bc | Python | 3,100 | 89 | """Property-based tests for `Vocabulary`'s payload round trip.
`test_vocabulary.py` pins this at one hand-built vocabulary. The property — any
constructible vocabulary survives `to_payload`/`from_payload` unchanged, class
order and membership included — is generated here instead. Marked `slow`.
"""
import pytest
from... |
0d166293513ccbc7e02fc2d1e5a5dbddf4499c1706eb98166ccf429619b2d3c5 | Python | 3,102 | 85 | ###########################################################################
# Created by: CASIA IVA
# Email: jliu@nlpr.ia.ac.cn
# Copyright (c) 2018
###########################################################################
# source : https://github.com/junfu1115/DANet/blob/master/encoding/nn/attention.py
import num... |
91d4f15e41fe1a1896e1e4368e810990e8191b78c57845cc8f9c60c82d27b587 | Python | 3,107 | 88 | # Copyright (C) 2025 ETH Zurich, Moritz Thürlemann, and other AMP contributors
import json
import os
import numpy as np
from helper_functions import write_config_yaml
import yaml
from pathlib import Path
def load_yaml(path:str):
parameters = yaml.safe_load(Path(path).read_text())
return parameters
... |
c865c90c6e07d2435142eea593179d2048ae715a0e2d6b3cfa1f686fba171222 | Python | 3,109 | 99 | from __future__ import annotations
import logging
from typing import TYPE_CHECKING
from poetry.publishing.uploader import Uploader
from poetry.utils.authenticator import Authenticator
if TYPE_CHECKING:
from pathlib import Path
from cleo.io.io import IO
from poetry.poetry import Poetry
logger = loggi... |
dba58794dc52ef4ce1119aac3f14c87191750b8501423be66538582f6f86dd12 | Python | 3,109 | 95 | # Copyright (c) Facebook, Inc. and its affiliates.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
import unittest
from collections import OrderedDict
import numpy as np
import torch
from fairseq.data import LanguagePairDataset, TokenBlockD... |
9cea3bab0cd7cd4add5409963e3e6f19cb3fff525021bf33df47eeaa15d56722 | Python | 3,110 | 112 | """
Copyright (c) Facebook, Inc. and its affiliates.
Copyright (c) Microsoft Corporation.
Licensed under the MIT License.
Adapted from https://github.com/FAIR-Chem/fairchem/blob/main/src/fairchem/core/models/gemnet/layers/base_layers.py.
"""
import math
from collections.abc import Callable
from typing import Optional
... |
1df6a5ba9ef5366c34f0c44f159d5aef126942773fbacd3a82256ae71f7358c7 | Python | 3,113 | 88 | from unittest import mock
import pandas as pd
import pytest
import vak
FAKE_SOURCE_FILES_DF = pd.DataFrame.from_records(
[
{'audio_path': 'bird0-2023.10.12.cbin',
'spect_path': 'bird0-2023.10.12.cbin.spect.npz',
'annot_path': 'bird0-2023.10.12.cbin.not.mat'}
]
)
@pytest.mark.param... |
e9631c28e682ae74257491461cf20b7777da4b2a5f77d72f8c439be02ca5f22f | Python | 3,113 | 81 | """End-to-end smoke + reproducibility for all pipeline families.
These exercise the full per-subject driver (feature extraction, domain adaptation
via da4bci, scoring, combiners and output writing) on synthetic sessions.
"""
import glob
import os
import pandas as pd
import pytest
pytest.importorskip("da4bci") # th... |
8a21a749e1f13ec45334494d06ce1275e3557882531c999868352c902e8b1fea | Python | 3,114 | 97 | # @license
# Copyright 2020 Google 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 to in... |
f51eb5b7dfb8cdab8d2cc3919bb1db82ab511858a37094b4fd60660550b7c259 | Python | 3,115 | 102 | #
# Copyright 2017-2023 Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with
# Sandia Corporation, the U.S. Government retains certain rights in this software.
#
# See LICENSE for full license details
#
import numpy as np
from scipy.optimize import minimize
import time
import os
# Use th... |
3c8ffca3ecac5fa4c0d209cbbb4738823b5ba2ce6a9cb1f0435bfc05352dc50f | Python | 3,116 | 93 | from __future__ import annotations
import dataclasses
import shutil
import sysconfig
from pathlib import Path
from typing import TYPE_CHECKING
import findpython
from findpython.providers.path import PathProvider
from poetry.config.config import Config
from poetry.utils._compat import WINDOWS
if TYPE_CHECKING:
... |
c60087966c1c535f911d2c6c1a29dccfa3db7a09abd29c887e51288c9027b61e | Python | 3,116 | 89 | # Copyright (c) Facebook, Inc. and its affiliates.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
import argparse
from collections import defaultdict
from itertools import chain
from pathlib import Path
import numpy as np
import torchaudi... |
9762de686c2cee58434ec6114cd1793ff4eb12ede983ac47a0dd633a88fa185e | Python | 3,117 | 90 | # /usr/bin/env python
'''
Written by Kong Xiaolu and CBIG under MIT license:
https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
'''
import numpy as np
import torch
import os
import scipy.io as sio
import CBIG_pMFM_basic_functions as fc
def CBIG_mfm_validation_desikan_main(gpu_index=0):
'''
This func... |
e8206671e506de9fb76eb577854acbf083c5b1d8d27f902d66c7e9c7e938407a | Python | 3,117 | 102 | #
# Copyright 2017-2023 Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with
# Sandia Corporation, the U.S. Government retains certain rights in this software.
#
# See LICENSE for full license details
#
import numpy as np
from scipy.optimize import minimize
import time
import os
# Use th... |
459e30aacca54bcff09e458bd74a858428883c2982adde662dcd6ca688beb2ed | Python | 3,120 | 82 | import logging
import string
import pandas
from .. import Constants
from .. import PredictionModel
from ..gwas import Utilities as GWASUtilities
EA, NEA = Constants.EFFECT_ALLELE, Constants.NON_EFFECT_ALLELE
EA_BASE, NEA_BASE = EA + "_BASE", NEA + "_BASE"
def align_data_to_alleles(data, base, left_on, right_on):
... |
6522530257e133ffbde9d434cdc3e1f0b91c8ed84dc227d26f6c89e12f6708ad | Python | 3,120 | 93 | # Copyright (c) Facebook, Inc. and its affiliates.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
import logging
import os
import sys
import fairseq
import soundfile as sf
import torch
import torch.nn.functional as F
from feature_utils im... |
38d3344a69baadd6d2ceba9e163e9ce11580b7376b3540c211e158cb3951bba7 | Python | 3,121 | 83 |
from cyvcf2 import VCF
import logging
import pandas
import numpy
from metax.misc import Genomics
def vcf_file_geno_lines(path, mode="genotyped", variant_mapping=None, whitelist=None, skip_palindromic=False, liftover_conversion=None):
logging.log(9, "Processing vcf %s", path)
vcf_reader = VCF(path)
is_di... |
b7d35d6908f0028683b8941f49da23689f6f0e8a35440195e75c61a50266091a | Python | 3,121 | 84 | import torch
from tqdm import tqdm
from torch.nn.functional import normalize
from transformers import BertConfig, BertModel, BertTokenizer
class TextEncoder(torch.nn.Module):
def __init__(self,
config_path: str,
out_dim: int,
load_pretrained: bool = True,
... |
2ed4dd989d67069da73b89851e56cd84d44361573384fbc49fbb2f5d63a8c2ed | Python | 3,123 | 100 | import math
import omegaconf
import pandas as pd
import pytorch_lightning as pl
import torch
import wandb
from torch_geometric.utils import to_dense_batch
from utils.data.dataholder import DataHolder
def to_batch(data: DataHolder, device=None) -> DataHolder:
"""
Convert data to dense representation.
I.e... |
425e0f0744fc9185061bcc1c0e5a2f4108eb823f14b51b5049b9b91d74e75233 | Python | 3,123 | 94 | # Copyright (c) Facebook, Inc. and its affiliates.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
import logging
from dataclasses import dataclass, field
from typing import Optional
import torch
from omegaconf import II
from .dummy_datase... |
5854bd2a2c8b9dfa80fea6275bae480dc5033d517dd5f974440326ad8d5acf30 | Python | 3,123 | 87 | #!/usr/bin/env python3
import os
import sys
import pickle
import argparse
import numpy as np
import pandas as pd
from tqdm import tqdm
from sklearn.metrics import roc_auc_score, f1_score, average_precision_score
import torch
import torch.nn.functional as F
from torch.utils.data import DataLoader
sys.path.append("../sc... |
340aa2a948fe59cfbbe7c8a439548c79a00728776979f3c685236ac4de5f3327 | Python | 3,124 | 83 | """GUI tests for the Relabel dialog (window_utils.open_relabel_window).
Tests verify the dialog opens correctly with scope radio buttons,
model combobox, overwrite checkbox, and action button.
"""
import pytest
from PyQt6.QtWidgets import (
QDialog, QRadioButton, QComboBox, QPushButton,
QCheckBox, QProgressBar... |
4c5724a5939e32bfdce35dee333bf87fb81e142c0ced03a9339db7c4d9ef7e78 | Python | 3,124 | 102 | import os
import random
class _Faker:
clothes = ["衬衫", "毛衣", "领带", "裤子", "风衣", "高跟鞋", "袜子"]
drinks = ["可乐", "雪碧", "橙汁", "绿茶", "奶茶", "百威", "青岛"]
phones = ["小米", "三星", "华为", "苹果", "魅族", "VIVO", "OPPO"]
fruits = ["草莓", "芒果", "葡萄", "雪梨", "西瓜", "柠檬", "车厘子"]
animal = ["河马", "蟒蛇", "老虎", "大象", "兔... |
bae04f21128f68eb551c6349094324c31d465cf4960df98fecaba3f822f5c70f | Python | 3,126 | 105 | import os
import sys
from shutil import rmtree
from setuptools import Command, find_packages, setup
# RELEASE STEPS
# $ python setup.py upload
__title__ = "pyecharts"
__description__ = "Python options, make charting easier"
__url__ = "https://github.com/pyecharts/pyecharts"
__author_email__ = "chenjiandongx@qq.com"... |
857d42f518cd0a3643a838b83848de53bb71dcf2c6ee81a2458e7758460f2b0a | Python | 3,127 | 92 | from ... import options as opts
from ... import types
from ...charts.basic_charts.geo import GeoChartBase
from ...commons.utils import OrderedSet
from ...exceptions import NonexistentCoordinatesException
from ...globals import ChartType
BAIDU_MAP_API = "https://api.map.baidu.com/api?v=2.0&ak={}"
BAIDU_MAP_GETSCRIPT = ... |
85cb2989de2ff7d93d7ff8012043fddd7bb932069c5c1bbc89aeecd054fd5cfe | Python | 3,127 | 91 | import numpy as np
import pytest
from pgmpy.ci_tests import WilksLambda
from pgmpy.tests.test_ci_tests import _multivariate_fixtures
pillai_data = _multivariate_fixtures.pillai_data
skip_gh_actions = _multivariate_fixtures.skip_gh_actions
@skip_gh_actions
def test_wilks_no_cond(pillai_data):
expected_stats = [0... |
d5cc2c62ee4dffee500f85ae96c4c63e53894dfbd27e0d449a70e2772097c830 | Python | 3,127 | 82 | """parses [SPECT_PARAMS] section of config"""
import attr
from attr import converters, validators
from attr.validators import instance_of
def freq_cutoffs_validator(instance, attribute, value):
if len(value) != 2:
raise ValueError(
f"freq_cutoffs should be a list of two elements, but instead ... |
fddc20afc86d9542f9511793b3aaf6229f8a4861417dc744c9e6f8e73814a826 | Python | 3,128 | 88 | import unittest
from unittest.mock import patch
from pyecharts.charts import WordCloud
from pyecharts.exceptions import WordCloudMaskImageException
words = [
("Sam S Club", 10000),
("Macys", 6181),
("Amy Schumer", 4386),
("Jurassic World", 4055),
("Charter Communications", 2467),
("Chick Fil A... |
595d7535a370968cdb96f7073257061d12ab14f730019bba723ebf9a0798a237 | Python | 3,129 | 96 | import pandas as pd
import matplotlib
matplotlib.use("TkAgg")
target_len = 20
dat = pd.read_csv("./data/DTCR_blosum/results.txt")
all_true_tcr = []
min_n = 30
max_n = 0
for i in range(len(dat)):
epi = dat["MT_pep"][i]
mhc = dat["HLA_sequence"][i]
tcr = dat["CDR3"][i]
label = dat["Label"]... |
8fe826aa3d966de1692cad37b5892a883280a55cff14dc5334a22a1cffab2e6f | Python | 3,129 | 95 | # Copyright (c) Facebook, Inc. and its affiliates.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
import logging
import os
import sys
import fairseq
import soundfile as sf
import torch
import torch.nn.functional as F
from feature_utils im... |
6c5219eb87ec3f75b41c2c36f96fe56dc857e1633275c0d28ea35abc901772e1 | Python | 3,130 | 83 | import numpy as np
import pandas as pd
from st_risk.models.base import BaseSpatialModelOutput
from st_risk.risk.features import (
ambiguity_score,
build_feature_table,
confidence_proxy_score,
local_residual_score,
stability_score,
uncertainty_score,
)
def test_local_residual_score_is_zero_for... |
5f0560827de21f22e5123dedd1181b27f3c2656b591dcf9ab651e2665249b916 | Python | 3,132 | 86 | import numpy as np
import torch
from PIL import Image
import tqdm
import cv2
from sklearn.cluster import KMeans, kmeans_plusplus
import time
from msi_visual.utils import normalize
from msi_visual.saliency_opt import SaliencyOptimization
class SaliencyClusteringOptimization(SaliencyOptimization):
def _... |
73b5b6ec11a8333c8b81bb76bab2e49e2d5f9d4b79d2766fcb3252f57d81574f | Python | 3,132 | 91 | import argparse
from collections import namedtuple
import os
DATADIR = "/path/to/train_data"
DEDUP_FROM_DIR = "/path/to/eval/data"
OUTPUT_DIR = "/path/to/output/data"
def main(args):
languages = set()
for language_directory in os.listdir(DATADIR):
if "_" in language_directory:
src, tgt = ... |
68100cd6802355415e43a1ea446f65a00d709aee445e52e954a144cba220c345 | Python | 3,133 | 98 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
#
# fairseq documentation build configuration file, created by
# sphinx-quickstart on Fri Aug 17 21:45:30 2018.
#
# This file is execfile()d with the current directory set to its
# containing dir.
#
# Note that not all possible configuration values are present in this
# au... |
c800fc0d961e0d5200a8dc4471a4b680f2e64e7a353e69b6d878f2009002746e | Python | 3,133 | 80 | import requests
try:
from tqdm import tqdm
except ImportError:
tqdm = lambda x, total, unit: x # If tqdm doesn't exist, replace it with a function that does nothing
print('**** Could not import tqdm. Please install tqdm for download progressbars! (pip install tqdm) ****')
# Python2 compatibility
try:
... |
34848019e4fe3131f4f6bbf696541009224df35a06940eb6ddd9ed83f10293bc | Python | 3,134 | 89 | # Copyright (c) Microsoft Corporation.
# Licensed under the MIT License.
from typing import Optional, Tuple
import torch
import mattergen.diffusion.sampling.predictors_correctors as pc
from mattergen.diffusion.corruption import sde_lib
from mattergen.diffusion.corruption.corruption import Corruption
from mattergen.d... |
44cc4380bbf04e689a0015c428128b356799c3755255cd99ce094b702f6666ea | Python | 3,135 | 88 | #!/usr/bin/env python
# Author_and_contribution: Jieran Sun & Mark Robinson; implmented method
# Author_and_contribution: Peiying Cai; created template
# Author_and_contribution: ENTER YOUR NAME AND CONTRIBUTION HERE
import argparse
# TODO adjust description
parser = argparse.ArgumentParser(description="Calculate co... |
baa8b9801d797ef69ab7261bc199c43e21e2bbdbbafb5ea9420efaf8977ec885 | Python | 3,136 | 67 | # coding=utf-8
# Copyright 2018 The Google AI Language Team Authors and The HuggingFace Inc. team.
# Copyright (c) 2018, 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 cop... |
ae1e8f0f4192f2cd19525f88fc3d1bd7c8ee282b2706bdc80b7c42d67b1b14ab | Python | 3,137 | 68 | # coding=utf-8
# Copyright 2018 The Google AI Language Team Authors and The HuggingFace Inc. team.
# Copyright (c) 2018, 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 cop... |
9c2d54cca7d974f596ef15985662eed62cd6e7089e668ddf5925709ee437f8d4 | Python | 3,139 | 69 | # Copyright 2021 HIP Applied Computer Vision Lab, Division of Medical Image Computing, German Cancer Research Center
# (DKFZ), Heidelberg, Germany
#
# 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... |
1dba629ffc2f10de9cc6832a5feae5f636caefeb31ffa032dd395bece4a69e4a | Python | 3,140 | 100 | """Supplemental pipeline schematics — PhysMAP and NEMO hyperparameter tuning flows.
Simplified version of figure_2_panel_a_pipeline.py (no architectural ablation
rung — PhysMAP and NEMO are fixed architectures, only hyperparameters vary).
Outputs:
figures/20_figure_2_pipeline/pipeline_schematic_physmap.{svg,png}
... |
d97c22466bae8c5ca6f7753f7a94f53e89a96dad1dd45c9c6fd40b3ca7272acf | Python | 3,141 | 89 | # /usr/bin/env python
'''
Written by Kong Xiaolu and CBIG under MIT license:
https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
'''
import numpy as np
import torch
import CBIG_pMFM_basic_functions as fc
import os
def CBIG_mfm_validation_desikan_main(gpu_index=0):
'''
This function is to validate the... |
9e0ad91bedefe1249d373c05af37c1adecc7a7a4cf888d4f512b60c1cd5684bb | Python | 3,142 | 69 | def resnet18_layers():
return (['conv1'] +
# note that while relu is used multiple times, by default the last one will overwrite all previous ones
[f"layer{block + 1}[{unit}].relu"
for block, block_units in enumerate([2, 2, 2, 2]) for unit in range(block_units)] +
['... |
d3ab83d547d52fe71dade1c60b6b64e7139c0dcf214d5dd6fe1862d385770c1f | Python | 3,144 | 103 | import cellxgene_census
import pandas as pd
import numpy as np
from data_config import VERSION
from typing import List
import os
import argparse
parser = argparse.ArgumentParser(
description='Download a given partition cell of the query in h5ad')
parser.add_argument("--query-name",
type=str,
... |
4f64d53a82948c7996d8b88b4766514429fa845d32761fa935194b886e998f9b | Python | 3,145 | 95 | """
Copyright (c) Facebook, Inc. and its affiliates.
This source code is licensed under the MIT license found in the
LICENSE file in the root directory of this source tree.
"""
import sympy as sym
import torch
from torch_geometric.nn.models.schnet import GaussianSmearing
from .basis_utils import real_sph_harm
from .... |
bfc770aa1522206016dddffb5589f36bf152ec41e4f95a5d2622d003fd2b53dc | Python | 3,146 | 77 | # Copyright (C) 2025 ETH Zurich, Moritz Thürlemann, and other AMP contributors
import os
import torch
from utilities.Scatter import scatter_sum as scatter
from datastructures.Graphs import Graph
from utilities.Utilities import build_Rx2
def compute_com(coords, masses):
masses = masses.reshape((coords.shape[0], ... |
c55327e3ba8faa5764c3a57c34eeebb66b7d5a256f0006b2c2840238c2c13f20 | Python | 3,146 | 72 | import torch
from tangle_tracer.modules import NFTDetector
from pathlib import Path
from ultralytics import YOLO
import zarr
class YOLOModule(NFTDetector):
def __init__(self, *args, load_path='yolov8m.pt', devices = (1), **kwargs):
super().__init__(*args, **kwargs)
try:
self.devices = s... |
6ea26320edb2da305e6ceeaf226f08640089e7e13e3fc2a86a4e1a54e7a95688 | Python | 3,147 | 56 | import numpy as np
from nnunetv2.training.dataloading.base_data_loader import nnUNetDataLoaderBase
from nnunetv2.training.dataloading.nnunet_dataset import nnUNetDataset
class nnUNetDataLoader3D(nnUNetDataLoaderBase):
def generate_train_batch(self):
selected_keys = self.get_indices()
# preallocate... |
479ff099f7462121508f23c41946d22d0fb370e73df48efc12f5728d5a4c1fca | Python | 3,148 | 81 | """Diagnostic: where does the relaxation energy go in the OCE basis?
Decompose Π¹F, Π²F, Π³F values and totals before/after xtb relaxation,
using the SAME free-atom ε_μ in both cases (the table is composition-only).
"""
from __future__ import annotations
import json
import sys
from pathlib import Path
ROOT = Path(__... |
91035e3a04b12541973137b7c7b479a69ecfaeb0c20ecd6680476abac02d143d | Python | 3,149 | 109 | # _ _
# | | | |
# ___ __ _ __ _ ___| |_ ___ ___ | |___
# / __/ _` |/ _` / __| __/ _ \ / _ \| / __|
# | (_| (_| | (_| \__ \ || (_) | (_) | \__ \
# \___\__,_|\__,_|___/\__\___/ \___/|_|___/
'''
A Convergent Amino Acid Substitution identif... |
45d8c7d81643c7e84d0b8e941bd39cfaf6c58c4d80c8707e91c0a61f18ab3c14 | Python | 3,150 | 114 | """Consensus and variant calling of Nanopore sequencing data."""
import functools
import os
import subprocess
import sys
from packaging.version import Version
__version__ = "2.2.2"
try:
import pyabpoa as abpoa
except ImportError:
sys.stderr.write(
"Cannot import pyabpoa, some features may not be avai... |
87bc8264dc3158817aadca389058c831895685ecf26089e79829b443b3deb74d | Python | 3,150 | 100 | """
Patch Embedding for 3D Medical Images
Converts 3D image patches (voxels) into embedding vectors using a linear projection.
"""
from functools import partial
import torch.nn as nn
from einops import rearrange
from torch import _assert
from torch.nn.modules.utils import _pair
try:
from flash_attn.ops.fused_de... |
f2e78b260b1f8009e15f213fa37f4493918e63ebdbf594fad1f4d2d1ddcac56c | Python | 3,150 | 77 | import glob
import os
import numpy as np
from mdt.utils import restore_volumes
from mdt.lib.nifti import write_nifti, load_nifti
__author__ = 'Robbert Harms'
__date__ = "2017-02-28"
__maintainer__ = "Robbert Harms"
__email__ = "robbert@xkls.nl"
def volume_map_npy_to_nifti(npy_fname, nifti_header, nifti_fname=None):
... |
234bb3672a19f4ced8aa8bb53e27b26e4e657a50ca4748c22fe595eed6a413f7 | Python | 3,153 | 106 | """functions for making spectrogram
filters adapted from SciPy cookbook
https://scipy-cookbook.readthedocs.io/items/ButterworthBandpass.html
spectrogram adapted from code by Kyle Kastner and Tim Sainburg
https://github.com/timsainb/python_spectrograms_and_inversion
"""
import numpy as np
from matplotlib.mlab import s... |
649c47a43aa91b3c741c1282e229fee6971d8ade09b584ac5806076630fec1cb | Python | 3,153 | 63 | # encoding: utf-8
"""
@author: Jiayang Chen
@contact: yjcmydkzgj@gmail.com
"""
from .custom import Custom
def build_dataset(dataset_names, set_name, root_paths, transforms):
"""
:param dataset_name: the name of dataset
:param root_path: data is usually located under the root path
:param set_name: "tr... |
0309c39ae6ce182dcc8c107cd73f1c09bf0e3b652d649312594a3a69b46e22eb | Python | 3,154 | 92 | import os
import matplotlib.pyplot as plt
from skimage import io
from skimage.segmentation import mark_boundaries
import numpy as np
def plot_image_mask_segmentation(file_path):
"""
Given a file path, this function checks whether the file is in the 'images' or 'masks' directory.
It then finds the correspon... |
0371a3102e14e014fb210668b881d0be2355af55c3ef0f0f92b7c00863b6d91d | Python | 3,154 | 85 | # Copyright (c) Facebook, Inc. and its affiliates.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
from collections.abc import Collection
from dataclasses import dataclass, field
from typing import List
from omegaconf import II
from fairse... |
507732e8050b6b72ce0a3e7a8ad9ce102b303c6b3498aac9b9e84cf6eb546727 | Python | 3,155 | 81 | # Copyright (c) Facebook, Inc. and its affiliates.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
import os
import omegaconf
from omegaconf import OmegaConf
def load_config(args=None, config_file=None, overwrite_fairseq=False):
"""TODO... |
c98eab8fe895b28225642322835615d2848662a015347f82c787170b419bf7c2 | Python | 3,155 | 96 | # Copyright (c) Facebook, Inc. and its affiliates.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
import torch.nn as nn
from fairseq.modules import TransformerSentenceEncoder
from fairseq.modules.sparse_transformer_sentence_encoder_layer im... |
debbdb206348f26c4c44ae30803766b0a0d43255dc85b3bfbd7c6e3c3490d14c | Python | 3,155 | 87 | from ... import options as opts
from ... import types
from ...charts.chart import Chart
from ...globals import ChartType
class Parallel(Chart):
"""
<<< Parallel >>>
Parallel coordinate systems are commonly used to visualize graphs of
high dimensional data.
"""
def __init__(
... |
3c2912c2e2b645f815e0a3d8309a38790d432c333e83132443f1a7283c822239 | Python | 3,157 | 89 | import logging
import community
import leidenalg
import networkx as nx
import igraph as ig
import numpy as np
from sklearn.neighbors import NearestNeighbors
from scipy.sparse.csgraph import connected_components
import loompy
class UnpolishedLouvain:
def __init__(self, resolution: float = 1.0, min_cells: int = 10, gr... |
695c0667f6a723ebad9236ae3c282c3cf1c1496892c93ccd35ef28d2269c0261 | Python | 3,157 | 112 | import os
import anndata
import pytest
import scvi
from .utils import unsupervised_training_one_epoch
@pytest.mark.internet
def test_pbmc_dataset(save_path: str):
dataset = scvi.data.pbmc_dataset(
save_path=save_path,
remove_extracted_data=True,
)
unsupervised_training_one_epoch(dataset... |
7f9a1ff6c03415c577a425187ddf74c45d85d793b4f79b8950fc8070640ae6ae | Python | 3,157 | 60 | import torch
from nnunetv2.training.nnUNetTrainer.nnUNetTrainer import nnUNetTrainer
class nnUNetTrainer_250epochs_NoMirroring(nnUNetTrainer):
def __init__(self, plans: dict, configuration: str, fold: int, dataset_json: dict, unpack_dataset: bool = True,
device: torch.device = torch.device('cuda... |
f680e1e4115150f60cf0677ad7ba2ef17f53dbdeb3760df7bb2156897b8faf2b | Python | 3,157 | 88 | """Given user GO ids and parent terms, group user GO ids under one parent term.
Given a group of GO ids with one or more higher-level grouping terms, group
each user GO id under the most descriptive parent GO term.
Each GO id may have more than one parent. One of the parent(s) is chosen
to best represent... |
77cab40bc567d3d084ccf01af2624b27ba97eeb88d7c7e62faf9938d63632ecc | Python | 3,158 | 95 | # Configuration file for the Sphinx documentation builder.
#
# This file only contains a selection of the most common options. For a full
# list see the documentation:
# http://www.sphinx-doc.org/en/master/config
# -- Path setup --------------------------------------------------------------
# If extensions (or module... |
3170a89b1b92f4bb6cb2306f15c2c56aef282e2fdbfa7ad20ee7da20273a4282 | Python | 3,159 | 83 | import re
from datetime import time
import pandas as pd
# Centralized Conversion Factors and Labels
# Each value = how many minutes equal 1 of that unit.
# e.g. 1 second = 1/60 minute, 1 hour = 60 minutes.
CONVERSION_FACTORS: dict[str, float] = {
"minutes": 1,
"seconds": 1 / 60,
"hours": 60,
}
TIME_LABEL... |
3f9de4d2914d3601b5e67714c22d3681f7521b5a44f41ff962e4cfad6387d0a1 | Python | 3,159 | 95 | # Copyright (c) Microsoft Corporation.
# Licensed under the MIT License.
from functools import partial
from typing import Callable, Iterable, Sequence
import torch
from torch.utils.data import DataLoader, Dataset
from mattergen.common.data.chemgraph import ChemGraph
from mattergen.common.data.collate import collate
... |
154f906dfc90e2dbfb260d9400aa29441eb5683398e51549947a91db15fb6f81 | Python | 3,161 | 87 | import torch
import math
import torch.nn as nn
import torch.nn.functional as F
class Flatten(nn.Module):
def forward(self, x):
return x.view(x.size(0), -1)
class ChannelGate(nn.Module):
def __init__(self, gate_channel, reduction_ratio=16, num_layers=1):
super(ChannelGate, self).__init__()
... |
4713d6b3619ef6265f7c5e92433fcc7c49dc496fa46b0f22e100918e72bce899 | Python | 3,162 | 85 | import numpy as np
from mdt import CompositeModelTemplate
__author__ = 'Robbert Harms'
__date__ = '2017-07-19'
__maintainer__ = 'Robbert Harms'
__email__ = 'robbert@xkls.nl'
__licence__ = 'LGPL v3'
class ActiveAx(CompositeModelTemplate):
"""The ActiveAx model for use in in-vivo measurements.
This model has ... |
e4c9e72ecf0ee842b059c0b30e22c17e7f61de823de2fc8f4ac8dacf85993488 | Python | 3,164 | 68 | #!/usr/bin/env python3
# MIT License
#
# Copyright 2025 Broad Institute
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to u... |
00574bbaef4129aae7153f5216dacde601c2b042896ae62278f1883d4814c2e2 | Python | 3,166 | 77 | import argparse
import pandas as pd
from utils import HBR
from pathlib import Path
def prep_dlst(dir, dir_exl=None,
hst=20480, wst=40960, size=256,
hnm=16, wnm=16, to_csv=False):
gn_lst, rel_pad =[], size // 2
mouse = dir.name.split('_')[-1]
# Here, we assume no boundar... |
fc9d493eaa319fc810931abfa68a91f145b4f3fe529b7fd5779135c28d5b5659 | Python | 3,166 | 102 | # Copyright (c) Facebook, Inc. and its affiliates.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
import argparse
import random
import numpy as np
from fairseq import options
from examples.noisychannel import rerank, rerank_options
def ... |
e37bb844478f87dee833721221d88c70b9e5f938534d413cdd602305f3bba3d7 | Python | 3,167 | 92 | import numpy as np
import pandas as pd
from scipy import stats
from sklearn.linear_model import LinearRegression
from pgmpy.utils import preprocess_data
from ._base import BaseCITest, _CITestResult, _ResidualMixin
class GCM(_ResidualMixin, BaseCITest):
r"""
Generalized Covariance Measure (GCM) [1] test for ... |
98189d595f285727dd9daae3e6259c7c8cf3714f35c10bd2b4453d7bbb1aadc5 | Python | 3,169 | 95 | # Configuration file for the Sphinx documentation builder.
#
# This file only contains a selection of the most common options. For a full
# list see the documentation:
# https://www.sphinx-doc.org/en/master/usage/configuration.html
# -- Path setup --------------------------------------------------------------
# If ex... |
9e72de89deb5e8884e3a84c918f74a8dbb34973c26e686dac9115baef6e0a1a0 | Python | 3,170 | 71 | #
# Copyright 2017-2023 Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with
# Sandia Corporation, the U.S. Government retains certain rights in this software.
#
# See LICENSE for full license details
#
import numpy as np
from simulator.parameters.core_parameters import CoreStyle, BitSlicedCoreStyle
... |
e680f00ec4b98ae6ccd93dc740e33f4b7aa75bfa2967088931d6eb9659da3f55 | Python | 3,170 | 94 | # /usr/bin/env python
'''
Written by Kong Xiaolu and CBIG under MIT license:
https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
'''
import os
import numpy as np
import torch
import CBIG_pMFM_basic_functions as fc
import warnings
def CBIG_mfm_validation_desikan_main(gpu_index=0):
'''
This function is... |
17bc81d50bdc77102b1a29bb3e462d6df83e840ee5f207ed731924199012f12c | Python | 3,171 | 119 | # -*- coding: utf-8 -*-
"""
Created on Fri Apr 3 14:23:24 2026
@author: Satoru Muro
"""
import io
import requests
import numpy as np
from PIL import Image
from PyQt6.QtGui import QPainterPath
class RemoteSAM2Interface:
def __init__(self, base_url: str = ""):
self.base_url = base_url.rstrip("/")
... |
145324762742992e0bb70d3f256f1e5f01dee92b69642a921c009a3f77a6f388 | Python | 3,172 | 79 | from model.builders.prostate_models import build_pnet2
task = 'classification_binary'
selected_genes = 'tcga_prostate_expressed_genes_and_cancer_genes.csv'
data_base = {'id': 'ALL', 'type': 'prostate_paper',
'params': {
'data_type': ['mut_important', 'cnv_del', 'cnv_amp'],
... |
bb2134098b8aabe90d68161bbf9c99b4c1a2ead1a334a4c9fbb1f2f667658e78 | Python | 3,172 | 79 | from model.builders.prostate_models import build_pnet2
task = 'classification_binary'
selected_genes = 'tcga_prostate_expressed_genes_and_cancer_genes.csv'
data_base = {'id': 'ALL', 'type': 'prostate_paper',
'params': {
'data_type': ['mut_important', 'cnv_del', 'cnv_amp'],
... |
d182ac99ecfab3d84a8a43c0fcfa38740c4029a425f2c165e647a24619f02023 | Python | 3,172 | 79 | import re
import pandas as pd
from collections import defaultdict
# log_path = r"D:\FangX24\code\LO-Det-main\04log\fs\04_DIOR_maml_K10_2.txt"04_mobv3_log_fea_s1_noweight_withBN_0.675.
log_path = r"D:\FangX24\code\LO-Det-main\04log\fs\D_04_mobv3_test.txt"
# 用于存储每个 epoch 的所有 batch loss（取平均）
epoch_data = defaultdi... |
117fb3225714ebd2d279d206320b883362da2363cccda9bdde4d3b652109fb36 | Python | 3,173 | 70 | from pathlib import Path
import os
import sys
import argparse
import random
import numpy as np
from tqdm import tqdm
from sklearn.model_selection import train_test_split
from build_translation_manifests import get_utt_id
def train_val_test_split(tsv_lines, km_lines, valid_percent, test_percent, seed=42):
utt_ids ... |
d52e4e5bb8bb0d6db3f1d39f05660827a0e04ab272cc5570f953c8d791217673 | Python | 3,173 | 79 | from model.builders.prostate_models import build_pnet2
task = 'classification_binary'
selected_genes = 'tcga_prostate_expressed_genes_and_cancer_genes.csv'
data_base = {'id': 'ALL', 'type': 'prostate_paper',
'params': {
'data_type': ['mut_important', 'cnv_del', 'cnv_amp'],
... |
03e3883a9dfebdde048dc5cbc2e8fe43076944c415c68281aa46b93928368f43 | Python | 3,174 | 81 | #!/usr/bin/env python3
import argparse
import csv
import os
from collections import defaultdict
def parse_args():
parser = argparse.ArgumentParser(description="Summarize stats from multiple stats files into one summary file.")
parser.add_argument("stats_files", nargs="+", help="Input stats .tsv files (one or m... |
39a1bf374fa1a2f0fd9162c535b345bdb192e1cff31bf25f76fd81f4238a2355 | Python | 3,174 | 100 | # Copyright (c) Facebook, Inc. and its affiliates.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
import torch
from fairseq.models.bart import BARTModel
import argparse
XSUM_KWARGS = dict(beam=6, lenpen=1.0, max_len_b=60, min_len=10, no_re... |
9fe68ad39df9fa6556b6727f576c0b2c489ea99b06480be653a289447f9cc741 | Python | 3,176 | 66 | import torch
from torch._dynamo import OptimizedModule
from torch.nn.parallel import DistributedDataParallel as DDP
def load_pretrained_weights(network, fname, verbose=False):
"""
Transfers all weights between matching keys in state_dicts. matching is done by name and we only transfer if the
shape is also... |
1cbebeee01b698fbdd3788cb87fad1306049bdce2653b7c989b3e338cb233201 | Python | 3,177 | 97 | """Regenerate the tiny published-model alignment fixture from a local Zarr.
This utility intentionally requires an already-present multiz100way store. It never
downloads or builds an alignment dataset.
"""
from __future__ import annotations
import argparse
import hashlib
import json
from pathlib import Path
import ... |
c5f10e34d6e5b9ce3525f50cc570171b9b4bbfecb0d090683f6f29615de8e7c4 | Python | 3,178 | 105 | # Copyright (c) Facebook, Inc. and its affiliates.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
import argparse
import logging
import os
import soundfile as sf
from examples.textless_nlp.gslm.unit2speech.tts_data import (
TacotronInp... |
9d7c09794f1fa0154f36b762166eee922afaee3f714dbf710664a782351ae686 | Python | 3,179 | 85 | #!/usr/bin/env python
# PYTHON_ARGCOMPLETE_OK
"""Merge a list of volume images on the 4th dimension. Writes the result to a single image.
Please note that by default this will sort the list of volume names based on a natural key sort. This is
the most convenient option in the case of globbing files. You can disable th... |
c4cc22cb06d091a3d88c730de380e2684e8c07efef11b038594da9436f9b915d | Python | 3,180 | 76 | import polars as pl
from src.single_cell import SingleCell
from scipy.sparse import csr_array
import argparse
def main():
parser = argparse.ArgumentParser(description='Get single_cell object from long read data')
parser.add_argument('--id_to_sample', action='store', dest='id_to_sample', type=str, required=True... |
f959a14e4859a5f38b0c280bfe8c691367d4582c16f38005729884509bdbd870 | Python | 3,180 | 136 | import builtins
import pytest
from rnalysis.gui import gui_style
from rnalysis.utils import settings
def test_get_stylesheet_names(monkeypatch):
sheets = {'first': None, 'second': 'val', 'third': 3}
truth = {'First': 'first', 'Second': 'second', 'Third': 'third'}
monkeypatch.setattr(gui_style, 'STYLESHE... |
65515de46682c0949e4afb9951218372211fd7fa811e41b798b1cd5cba9e7fa1 | Python | 3,182 | 96 | #!/usr/bin/env python
# Author_and_contribution: Niklas Mueller-Boetticher; created template
# Author_and_contribution: ENTER YOUR NAME AND CONTRIBUTION HERE
import argparse
# TODO adjust description
parser = argparse.ArgumentParser(description="Load data for ...")
parser.add_argument(
"-o", "--out_dir", help="... |
93123fd26ce6501b18e33e566857a5490d7a7960a4e653997bdffbff2ed95014 | Python | 3,183 | 92 | import numpy as np
import pandas as pd
from celltype_ibl.params.config import (
ALLEN_LABELLED_PATH,
ALLEN_UNLABELLED_PATH,
CELL_EXPLORER_PATH,
SPLIT_INDEX_PATH,
INDEX_MAPPING_PATH,
)
def get_allen_labeled_dataset(padding: bool = True):
wvf, acgs, cell_types = get_cell_explorer_dataset(Allen_o... |
e5f80d3ca80fdd9e23958853058781028f5474a3a858b040b2dea61240985f50 | Python | 3,183 | 91 | import numpy as np
import pytest
from pgmpy.ci_tests import HotellingLawley
from pgmpy.tests.test_ci_tests import _multivariate_fixtures
pillai_data = _multivariate_fixtures.pillai_data
skip_gh_actions = _multivariate_fixtures.skip_gh_actions
@skip_gh_actions
def test_hotelling_no_cond(pillai_data):
expected_st... |
f96d6d988db73408e258b934a681cce621cce14cf497769c1b3e4768ec7599d0 | Python | 3,183 | 58 | #!/usr/bin/env python3
# MIT License
#
# Copyright 2024 Broad Institute
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to u... |
c65b7bc7b36d6a535f82b1f9d69b887a9062700365eec694fff37928ac1f049a | Python | 3,184 | 88 | # Copyright (c) Facebook, Inc. and its affiliates.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
import math
from fairseq import utils
from fairseq.logging import metrics
from fairseq.criterions import FairseqCriterion, register_criterion... |
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