sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
9635bc139048437f374578ef7424e8349c1d5a4ee4375499c62958fca5b9987c | Python | 11,418 | 278 | # 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 typing import Optional, Tuple
import torch
from torch import Tensor
from torch.nn.functional import (
linear, softmax, dropout, pad,
... |
6d08dde879db4bf6699e4dd893f273c432a459c7eca5c736402b49a9539347ed | Python | 11,424 | 285 | from __future__ import annotations
import logging
import os
import warnings
from collections.abc import Callable
from datetime import datetime
from shutil import rmtree
from typing import TYPE_CHECKING
import pyro
import torch
from lightning.pytorch.callbacks import Callback, ModelCheckpoint
from lightning.pytorch.ca... |
ce277356d4ee81c3ff73454584ca82d50ac2bfbaac95ddd647724edd503b59fc | Python | 11,425 | 234 | from TrainingAlgos import *
from GenerativeModel import *
from data_funcs import *
import collections
class VIMCO(TrainingAlgo):
"""
Unsupervised training using the VIMCO algorithm to reduce variance in the gradient estimations.
"""
def __init__(self,
init_params, # dictionary of gene... |
e6a4f52457220c9b73fb01ae504f66feb29a122425ae29aaddff26232a412a76 | Python | 11,425 | 391 | import functools
import json
import logging
import os
from pathlib import Path
import random
import subprocess
from typing import Dict, List, Optional, Tuple, Union
import numpy as np
import torch
import pandas as pd
from anndata import AnnData
import scib
from matplotlib import pyplot as plt
from matplotlib import ax... |
1cb2e6266a4028bd69551d8969990aa181d3e65665337397834e2fde92a4caa7 | Python | 11,432 | 629 | import logging
import anndata
import numpy as np
import pandas as pd
import scanpy as sc
from anndata import AnnData
from ...utils import spatial_neighbors
log = logging.getLogger(__name__)
def toy_dataset(
n_panels: int = 3,
n_domains: int = 4,
n_slides_per_panel: int = 1,
xmax: int = 500,
n_v... |
21adece197914a37445a4eecaf9c7e278ff6429716c5d6340cd225ce057e62b9 | Python | 11,432 | 391 | #!/usr/bin/env python
"""
Setuptools bootstrapping installer.
Run this script to install or upgrade setuptools.
"""
import os
import shutil
import sys
import tempfile
import zipfile
import optparse
import subprocess
import platform
import textwrap
import contextlib
import warnings
from distutils import log
try:
... |
a58d40d4989b51ac0ddffd7ce513732df499cf367eb73c13d4841966eaa8e4b3 | Python | 11,440 | 329 | import os
from pathlib import Path
import numpy as np
import pandas as pd
from typing import Dict, Tuple, List
from numpy.typing import NDArray
from cachecache import Cacher, distributed_cacher
__cachedir__ = "~/.bombcell"
global_bc_cacher = Cacher(__cachedir__)
def path_handler(path: str) -> None:
path = Path(... |
d6df512bb6fa2e1aaf811f266d310180b7f1c831256695c5c2c99ab5192929d0 | Python | 11,444 | 371 | """Utility functions for plotting."""
# Author: Oualid Benkarim <oualid.benkarim@mcgill.ca>
# License: BSD 3 clause
from itertools import product as iter_prod
import collections
from collections import namedtuple
import numpy as np
class PTuple(collections.abc.Sequence):
def __init__(self, *args):
sel... |
22c9f5a990f80fa2603c148ca7c3da8d753e812b4f86596ae8f867cac1ab55df | Python | 11,448 | 318 | # 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 copy
import math
import re
import torch
from fairseq.data import data_utils
from fairseq.data.language_pair_dataset import LanguagePa... |
9ca50c2a7ccded890ec2a84f4c3b65992ae9c9cab92d3aec43d01e08be28d5d2 | Python | 11,451 | 291 | """Select stimuli from the COCO overlap dataset."""
import copy
import io
import os
import click
import networkx as nx
import numpy as np
import pandas as pd
from datasets import Dataset, load_from_disk
from loguru import logger
from PIL import Image
from psmpy import PsmPy
from scipy.stats import ttest_ind
from com... |
2bd3d479162696188a9e62533bac439d2ac075182be4954b2c4a4659cff1a1aa | Python | 11,452 | 299 | # -------------------------------------------------------------------------------------------------------------------------------------
# Following code curated for GCPNet-EMA (https://github.com/BioinfoMachineLearning/GCPNet-EMA):
# --------------------------------------------------------------------------------------... |
488e4166c2005e7f2dfed06395b2587c65610da5586f5e1922419f77527880a5 | Python | 11,455 | 296 | import os
import json
import numpy as np
import copy
import torch
import random
from tqdm import tqdm
from utils import UnionFindSet, get_bfs_sub_graph, get_dfs_sub_graph
from torch_geometric.data import Data, Dataset, InMemoryDataset, DataLoader
class GNN_DATA:
def __init__(self, ppi_path, exclude_protein_path=... |
1eb0f9b7f1a6991d8960b98647594a35ebba3c6e509a12359c8fbeafe09f7615 | Python | 11,464 | 358 | import torch
import torch.nn.functional as F
import torch.nn as nn
from torch.optim import Adam
from torch.optim.lr_scheduler import LinearLR
import lightning.pytorch as pl
from lightning.pytorch.loggers.wandb import WandbLogger
from lightning.pytorch.callbacks.lr_monitor import LearningRateMonitor
from lightning.pyt... |
3dc2efaa654c256fd5c0110c991869b131e4ec44edeb9bff4eb6dd4dbf1b0060 | Python | 11,465 | 317 | #!/usr/bin/env python3 -u
# 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.
"""
Translate raw text with a trained model. Batches data on-the-fly.
"""
import ast
import fileinput
import logging... |
e857bc4d6d551915a375116208f7f74b286e7fc88d0d54f54b2746b2fb02e1ca | Python | 11,467 | 304 | import logging
import typing
import torch
import torch.nn as nn
import torch.nn.functional as F
from .modeling_utils import ProteinConfig
from .modeling_utils import ProteinModel
from .modeling_utils import ValuePredictionHead
from .modeling_utils import SequenceClassificationHead
from .modeling_utils import SequenceT... |
817a5e7d0cc287eaea313f0cd993f7884ac7d88733cad43c95fa7f9efdc3e6f6 | Python | 11,468 | 408 | import math
from typing import List, Optional
import haiku as hk
import jax
from einops import rearrange
from jax import numpy as jnp
from nucleotide_transformer.borzoi.layers import get_positional_embed_borzoi
def get_positional_features_exponential(
positions: jnp.ndarray, features: int, seq_len: int, min_hal... |
c95dfd7610d7eba229090bd605caa3929f33dd0379eb0048b9ff2eb467a1e1a1 | Python | 11,474 | 268 | """Phase 8 — bond percolation universality test (C and Si).
Repeats phase 5 (C-AIREBO) and phase 6 (Si-Tersoff) with **bond**
percolation instead of site percolation, on the same 3 lattices:
honeycomb bond p_c = 1 − 2 sin(π/18) ≈ 0.6527036
square bond p_c = 0.5 exact (Kesten 1980)
tria... |
e157fdb5d36300a8e222c2f3936d4e06b0b8df6261418dd1f0814c56ca5cf946 | Python | 11,474 | 321 | # analysis script for the results from the BEM simulation with realistic sensor noise
#%% Imports
import numpy as np
import matplotlib.pyplot as plt
import mne
import functions
font = { 'size' : 20}
plt.rc('font', **font)
#%% Plot parameters
legendfontsize = 15
linewidth = 2.5
#%% The parameters used in the simu... |
3ed193d5d5d9782b359b7bec41e7569c9b49b576b374d22c9217ca2696829f86 | Python | 11,480 | 297 | import itertools
from pgmpy.factors.discrete import DiscreteFactor
from pgmpy.models import DiscreteBayesianNetwork, DynamicBayesianNetwork
from pgmpy.utils import compat_fns
class ApproxInference:
"""
Initializes the Approximate Inference class.
Parameters
----------
model: Instance of pgmpy.mo... |
aa8f67e0104ce4e55f3b42a13211fc3745465420ec8c2d5add308ddd7fa8b342 | Python | 11,485 | 378 | def set_defaults_explain(args):
if args.project == "stad_pglcn":
# set seed
args.seed = 666666
# dataset & method
args.dataset = args.project.split("_")[0]
args.method = args.project.split("_")[1]
# io utils
args.ckptdir = "log/" + args.dataset + "_explain... |
569907c5af8b5460787d62c55b44d86315e715fec847e41335eb554c973f887e | Python | 11,491 | 322 | import math
from functools import partial
import haiku as hk
import jax
import jax.numpy as jnp
import optax
from .device_utils import DEVICE_AXIS, rng_iterator_on_devices, split_rng_key_on_devices
from .types import ModelDimensions, MolecularConfiguration, RandomKey, ScfParams
from .wf.base import init_wf_params
fro... |
bba7318bddf7b9207a98c42ca5f0a0e86f010e1bde85422e29d4376def7af889 | Python | 11,491 | 224 |
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import numpy as np
from batchgenerators.transforms.abstract_transforms import AbstractTransform
from batchgenerators.augmentations.utils import create_zero_centered_coordinate_mesh
from batchgenerators.augmen... |
413267ffb764e70d6a91af15d1d05980e04616d6bf12425abab72f0618d9e6e9 | Python | 11,494 | 216 | # -*- coding: utf-8 -*-
import pandas as pd
import numpy as np
from datetime import datetime
import pickle
import os
import multiprocessing
from tqdm import tqdm
from sklearn.svm import SVC
from sklearn.linear_model import SGDClassifier
from sklearn.model_selection import cross_val_predict, KFold
from skmultilearn.pro... |
94e6bdc088cfc89048d4b8b124f98cecb5960c31c769e84f8ec2f496522e0fa7 | Python | 11,498 | 308 | """The compile A/B is only worth reading if its two arms really are two arms.
Wall-clock timing is the easiest measurement to get confidently wrong: nothing
crashes when a second variable drifts between the arms, when every epoch's
timing is flattened onto the last one, when the arm that died is quietly
dropped and th... |
5b57c9cfe69d0793770755d129d0f215e3df2399aee1f87a620284f3dd70026b | Python | 11,500 | 196 | # -*- coding: utf-8 -*-
# Form implementation generated from reading ui file 'MainWindow.ui'
#
# Created by: PyQt5 UI code generator 5.10.1
#
# WARNING! All changes made in this file will be lost!
from PyQt5 import QtCore, QtGui, QtWidgets
class Ui_MapsVisualizer(object):
def setupUi(self, MapsVisualizer):
... |
e150d243a31dd2979d7fa43f939f7c90caf76e567865d5253e11e106c4a62907 | Python | 11,503 | 313 | import os
import h5py
import numpy as np
import surfa as sf
import tensorflow as tf
import voxelmorph as vxm
# set model dir
import synthmorph_models
models_home = synthmorph_models.models_dir
# Settings.
weights = {
'joint': ('synthmorph.affine.2.h5', 'synthmorph.deform.3.h5',),
'deform': ('synthmorph.deform... |
0c121c6896dd5fa9eedd1e9301a071a039ea18571f4a8c3f3b96c8aeb2102ac0 | Python | 11,508 | 277 | import joblib
import numpy as np
from pathlib import Path
from sklearn.random_projection import SparseRandomProjection
from sklearn.metrics.pairwise import cosine_similarity, cosine_distances
import pandas as pd
import warnings
from sklearn.decomposition import PCA
from numpy.testing import assert_allclose
### This sc... |
d53efd0430b73a8af5b771a180724d8909df1c905c7d512b25aee76fa50d155c | Python | 11,508 | 333 | # Copyright 2015 Google Inc. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or a... |
4ed132872b888dbb6a2ceaaf92f61761aaf1b7d9f112e49f373d3fb506473a86 | Python | 11,510 | 315 | # 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 copy
import logging
from fairseq.models import (
FairseqEncoderModel,
FairseqLanguageModel,
register_model,
register_m... |
ab6e7ac3e9dd11b44d52bce28c49bab97c0e15068219875da1ebb15d8aefd1eb | Python | 11,511 | 310 | import torch
import torch.nn as nn
import torch.nn.functional as F
import numpy as np
from pathlib import Path
from typing import Dict, Tuple, Callable
from einops import rearrange
from torch.utils.data import DataLoader
import pytorch_lightning as L
from datasets import load_dataset, load_from_disk, DatasetDict
from k... |
507f95682fd74d37f32a2d627ca76ca835994e22a0823764d08d33fe72e153cf | Python | 11,523 | 297 | #!/usr/bin/env python3
"""
Fix Benchmark Figure - Adjust radar plot and spacing
"""
import numpy as np
import pandas as pd
import networkx as nx
import matplotlib.pyplot as plt
import matplotlib.patches as mpatches
from matplotlib.gridspec import GridSpec
from sklearn.metrics import silhouette_score, roc_auc_score, av... |
6442c32584c2cfce338955b3b9295a3c6dbbdcba623bcbe7261ff5da55b1562b | Python | 11,526 | 282 | """
Sophisticated label update with territory expansion, morphological cleanup,
attribution-aware filtering, and hole filling.
When ``attributions`` is None (default), the attribution filtering step is
skipped and the function behaves as a prediction-only updater -- backward
compatible with the previous simple v... |
6aeb311e2893f0fa6f95678a6c4df341ffa56b887a2263aa2a96c6831623f8a1 | Python | 11,530 | 281 | #
# 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 sys
import numpy as np
sys.path.append("..")
from simulator import CrossSimParameters
def ... |
0a2e420febd88fb4978a7f06e2b7559bf1cc55c8f8b7cd3a8c4dcd57aa7d47c1 | Python | 11,538 | 282 | # Copyright (c) Microsoft Corporation.
# Licensed under the MIT License.
from typing import Callable
import torch
import torch.nn as nn
from mattergen.common.data.chemgraph import ChemGraph
from mattergen.common.data.types import PropertySourceId
from mattergen.common.utils.globals import MAX_ATOMIC_NUM, SELECTED_AT... |
733986c3339aa9d54c074ca5a9043765fe35dadb78fb22548565169a4bc1d9ba | Python | 11,543 | 273 | from mot.lib.cl_function import SimpleCLFunctionParameter
from .parameter_functions.numdiff_info import SimpleNumDiffInfo
from .parameter_functions.priors import UniformWithinBoundsPrior
from .parameter_functions.transformations import IdentityTransform
import numpy as np
__author__ = 'Robbert Harms'
__date__ = "2016-... |
e5cb60e77e3ceb9ae5a58d8a1f63c000abd1048aa66c250cd5424840ecabb14b | Python | 11,543 | 325 | from abc import abstractmethod
from typing import List, Tuple, Union
import torch
from torch import nn, autocast
from dynamic_network_architectures.architectures.primus import Primus
from nnunetv2.training.nnUNetTrainer.nnUNetTrainer import nnUNetTrainer
from nnunetv2.training.nnUNetTrainer.variants.lr_schedule.nnUNetT... |
0d91531891e82cac5f6a1c4ed64c1fa353ab1d3deab42ba5bcafd0cea7d04e64 | Python | 11,549 | 324 | import pandas as pd
import pdb
# sys.path.append("../../corecode/")
from build import *
import matplotlib.pyplot as plt
import seaborn as sns
import numpy as np
from scipy.stats import gaussian_kde
import matplotlib.colors as colors
import matplotlib.pyplot as plt
plt.switch_backend('agg')
from pathlib imp... |
7cde3d56b88f8288b096a9a8e2d170fd3639f519a05ec4378babf5e868f66de2 | Python | 11,550 | 371 | # _ _
# | | | |
# ___ __ _ __ _ ___| |_ ___ ___ | |___
# / __/ _` |/ _` / __| __/ _ \ / _ \| / __|
# | (_| (_| | (_| \__ \ || (_) | (_) | \__ \
# \___\__,_|\__,_|___/\__\___/ \___/|_|___/
'''
A Convergent Amino Acid Substitution identif... |
e96d5258f4f1d427e5035502e80bfe31224cc833e858988af775210bd05f5933 | Python | 11,560 | 319 | """
This module contains generic base model functionalities, added as a Mixin to the
NicheCompass model.
"""
import inspect
import os
from copy import deepcopy
import warnings
from typing import Optional
import numpy as np
# import pickle
import scipy.sparse as sp
import torch
from anndata import AnnData
from .util... |
fae72596953189da0d80a650359463b203bd01105fe97c99c43d2fe39d6e987c | Python | 11,560 | 306 | #!/usr/bin/env python
import argparse
import itertools
import logging
import pathlib
from d3text import (
checkpoint,
data,
encodings_store,
factory,
linking_corpora,
runtime,
token_labels,
tracking,
)
from d3text.cli.args import non_negative_limit
from d3text.datasets.brenda import BR... |
4272a6cd5e63cd015fcabade62be1dbee2fbb09554aa87d2fe13d9c7361dcd7c | Python | 11,563 | 199 | import multiprocessing
import os
from time import sleep
from typing import List, Type, Union
import numpy as np
from batchgenerators.utilities.file_and_folder_operations import load_json, join, save_json, isfile, maybe_mkdir_p
from tqdm import tqdm
from nnunetv2.imageio.base_reader_writer import BaseReaderWriter
from... |
207d680581d174f13e1cce02b18cf7001394292d7ec30562fdddaa799bbb95fb | Python | 11,565 | 347 | import argparse
from datetime import datetime
from pathlib import Path
import h5py
import nibabel.freesurfer.mghformat as mgh
import numpy as np
import scipy.io
from scipy.optimize import linear_sum_assignment
from sklearn.mixture import GaussianMixture
from spacestream.core.paths import DATA_PATH, RESULTS_PATH
from ... |
23719537f613d180833d1ddd558d85406af8649dc048fe25095e9ac51bcf411a | Python | 11,570 | 291 | #!/usr/bin/env python3
import argparse
import shutil
import os
import sys
import numpy as np
import pandas as pd
from tqdm import tqdm
from sklearn.metrics import roc_auc_score, f1_score
import torch
from torch import Tensor
import torch.nn as nn
import torch.nn.functional as F
from torch.utils.data import DataLoader,... |
a4875c06784aa5a91ba6346314a39fcbcb1df6cb01e50b88252990cc300090f1 | Python | 11,578 | 220 | #!/usr/bin/env python3
"""run_pseudobulk_reanalysis.py — donor-level pseudobulk MS-vs-HC for Tier 1 candidates.
Addresses verdict critical issue #1: cell-level Wilcoxon FDR magnitudes (10⁻¹⁵⁶)
inflated by pseudo-replication. This script:
1. Aggregates per-cell log-normalised expression to DONOR-level means
per... |
0bcf895422605eb2782cb7c645bb798f5d35d5751e9698021be76850d4612aa5 | Python | 11,585 | 330 | # %%
import os
import pickle
import torch
import numpy as np
from config import CONFIG
from model_config import MODEL_CONFIG
import torchvision.transforms as T
from torch.utils.data import Dataset
TARGET_SF = 256
# make sz_table
sz_table = CONFIG.sz_times.copy()
sz_table.index = sz_table.index.map(CONFIG.hup_to_ri... |
4093fd8dddc3cfd6fe33655e6e2c99c06f29cadb1104c92f74b110ed9dc70fc9 | Python | 11,585 | 269 | import torch
import torch.nn as nn
class Predictor(nn.Module):
r"""
Implements a predictor module. Predictors generate predictions via the given `pmodule` from input representations.
A Predictor contains three main attributes:
* :attr:`pmodule` is a callable module inherited from `torch.nn.Module` wit... |
0b1b6f4e6e54b4233ce2d0127ffa110bd4aa5f2c6f907e03e85e9eeeb2bca07d | Python | 11,587 | 378 | import torch
import torch.nn.functional as F
from math import pi as PI
# import geomstats.backend as gs
# from geomstats.geometry.hypersphere import Hypersphere, HypersphereMetric
# from geomstats.geometry.product_manifold import ProductManifold, ProductRiemannianMetric
class BaseManifold:
def __init__(self):
... |
10bd5c9b4a0d829b3494dde403008978fc4ba2c0c400faa7c541c41a1870b972 | Python | 11,591 | 282 | __author__ = 'heroico'
import weakref
from Tkinter import *
from ttk import *
from Utilities import TS
RHW = 70
LHW = 20
class MainScreenView(Frame):
def __init__(self, root, controller):
Frame.__init__(self, root)
self.pack(fill=BOTH, expand=1)
self.controller = weakref.ref(controller)
... |
a1d90a7bb53190a2f6876668f071a69bde534a8160aea4c29330d84c44088b11 | Python | 11,593 | 319 | from __future__ import annotations
import itertools
import json
import logging
from importlib import metadata
from pathlib import Path
from typing import TYPE_CHECKING
from packaging.utils import canonicalize_name
from poetry.core.packages.package import Package
from poetry.core.packages.utils.utils import is_python... |
ef9e4c6f888cbc29a3ad12967365f7b79065e40d901eabeeb1ada449463e50a9 | Python | 11,598 | 212 |
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import os
from os.path import join
from importlib.resources import files, as_file
from tqdm import tqdm
from tractseg.libs import img_utils
def reorient_to_std_space(input_file, bvals, bvecs, brain_mask, ou... |
1ad9e5c413aa71548c3f13e7ad83f2b58adc97d05ed5f64b3ae70251ec1eede1 | Python | 11,600 | 243 | import torch
import os
import toml
import warnings
def imports_str(is_3d=False, p_imports=None, same_hp=False, gscale=False, indent=""):
if gscale:
imports = indent + "from predify.modules import PCoderN" + os.linesep
else:
imports = indent + "from predify.modules import PCoder" + os.linesep
... |
0200ee9bd96b5da3789f0efe3b17530a4300cbb6b253c478ac3cec8a997a2b82 | Python | 11,601 | 246 | #!/usr/bin/env python3
"""
═══════════════════════════════════════════════════════════════════════════════
EIF2S1 R3 REVISION — PIPELINE 1: TCF25 + ASC-1 COMPLEX EXTENSION
═══════════════════════════════════════════════════════════════════════════════
Author: Drake H. Harbert (D.H.H.) | ORCID: 0009-0007-7740-3616
Affi... |
f1db06d7d89026bd88711d2e8304d83c2d1d790e7312a72255ad08492a299179 | Python | 11,603 | 308 | #
# 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 .wrapper_core import WrapperCore
from simulator.parameters.core_parameters... |
09510d8f8e9c8e96aa4724f6e3fd2ebf7929d67bf3f9dc9f4ce96bae7a877289 | Python | 11,613 | 293 | """Plot a GODagSmall."""
__copyright__ = "Copyright (C) 2016-2018, DV Klopfenstein, H Tang, All rights reserved."
__author__ = "DV Klopfenstein"
import sys
import os
import collections as cx
from collections import OrderedDict
from goatools.godag_obosm import OboToGoDagSmall
def plot_gos(fout_png, goids, obo_dag, *a... |
57a7fe6647eb5dd60a66816177d174373b7a90b5724c0499dd98b5787a3c9460 | Python | 11,619 | 284 | import unittest
import os
import subprocess
import tempfile
import medaka.common
import medaka.tandem.tandem
import medaka.medaka
import pysam
import gzip
def decompress_gz_file(input_path, output_path):
"""
Decompress a gzipped file to a specified output file using the gzip command.
Args:
input_p... |
af339ec4896fb3efb75f0e9b8bc5336307537e6bac667356444d653990e08528 | Python | 11,622 | 428 | # _ _
# | | | |
# ___ __ _ __ _ ___| |_ ___ ___ | |___
# / __/ _` |/ _` / __| __/ _ \ / _ \| / __|
# | (_| (_| | (_| \__ \ || (_) | (_) | \__ \
# \___\__,_|\__,_|___/\__\___/ \___/|_|___/
'''
A Convergent Amino Acid Substitution identif... |
1b37543fb33292a40456bb70f9862f73f2e5fc7d23b361b0b12cfb9f4fa4b599 | Python | 11,629 | 370 | #!/usr/bin/env python3
"""
Simulate tree sequences and parameters for posterior analysis.
This script simulates data using msprime directly (without popgen-npe simulator classes)
and outputs:
1. A tree sequence file (.trees)
2. A parameters file (.yaml) compatible with plot-variable-popsize-posterior.py
Available mod... |
8b9ccbbe8548e55b7d2f1ede87f99a92f952a0aa7775292e0a608b1133d797ae | Python | 11,633 | 319 | #!/usr/bin/env python
# @license
# Copyright 2018 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 applicab... |
51e8602a58e7c52c27a8f8cbe59e53d3d361f23ab68c58c904d1be3cee7318c6 | Python | 11,643 | 303 | """
Usage:
python /path/to/genome_gibson_assembly.py
Requirements:
- Input CSV with a column 'sequence' containing genome sequences to be split into Gibson assembly fragments
- Path to save an updated CSV with Gibson assembly data
"""
from Bio.Seq import Seq
from Bio.SeqUtils import MeltingTemp as mt
from typing imp... |
8f0301125bfd6bd0d0b2e0bfcbc8ec2b2b5d98d7f5389fbed130357c575b9f5e | Python | 11,644 | 291 | import unittest
import numpy as np
import pandas as pd
from pgmpy.estimators import K2, ExpertKnowledge, HillClimbSearch
from pgmpy.models import DiscreteBayesianNetwork
class TestHillClimbEstimatorDiscrete(unittest.TestCase):
def setUp(self):
self.rand_data = pd.DataFrame(
np.random.randint... |
9ad246a98ce3078e6392bdcb58d154c1ba7d8ec9e5b948b1281de13a3558b6c2 | Python | 11,645 | 281 | import os
import shutil
from PIL import Image
import numpy as np
import matplotlib.pyplot as plt
from matplotlib.widgets import Button
import matplotlib.gridspec as gridspec
from ..utils.decorators import error_handler
@error_handler(cluster=False)
def process_images_and_masks(DIR: str, N_classes: int, debug: bool=Fal... |
054372f27b6aea4750c71958573c4d377c181aba3667cbf6b317284b53dd700f | Python | 11,650 | 314 | # Copyright (c) 2025, Shenghao Cao & Ye Yuan. Shanghai Jiao Tong University, Shanghai 200240, China
# The classes and functions are modified from scGPT (https://github.com/bowang-lab/scGPT), copyright (c) 2022 suber
import sys
import os
os.environ['PYTORCH_CUDA_ALLOC_CONF'] = 'expandable_segments:True'
from typing imp... |
2e9b6d892f237bc137d2db74f2ca25caa4f1887e09d02ebb6cc0ef75ee1f99dc | Python | 11,650 | 228 | """tests for vak.config.eval module"""
import pytest
import vak.config
class TestEval:
@pytest.mark.parametrize(
'config_dict',
[
{
'checkpoint_path': '~/Documents/repos/coding/birdsong/TweetyNet/results/BFSongRepository/gy6or6/results_200620_165308/Tw... |
cae8fcb3de5f80dc083ee307a608cd3410460f0cf9fc9f877faf15dcc87e9e47 | Python | 11,652 | 361 | """
Utility functions for distillation training
"""
import inspect
import math
from pathlib import Path
from typing import Dict, Callable, Optional, Tuple, List
import torch
import torch.nn as nn
from nnunetv2.utilities.plans_handling.plans_handler import PlansManager
from nnunetv2.utilities.get_network_from_plans im... |
4f4581b8fad7d8fe6d94b6d15c86ccd0ded85c9a05a87c77204c99b03c4a21f4 | Python | 11,654 | 365 | """A dataset class used to train Parametric UMAP models."""
from __future__ import annotations
import pathlib
import warnings
import numpy as np
import numpy.typing as npt
import pandas as pd
import scipy.sparse._coo
import torchvision.transforms
from pynndescent import NNDescent
from sklearn.utils import check_rand... |
4d00d4371eddedec12eeeea09aec8830ff58689c33a4a2d5875ca5d8249bd950 | Python | 11,657 | 341 | #!/usr/bin/env python
# Author_and_contribution: Niklas Mueller-Boetticher; created template
# Author_and_contribution: Florian Heyl (heylf); created code
import argparse
import os
import json
###### Template arguments ##################################################
parser = argparse.ArgumentParser(description="c... |
e5eef0e7b38fd57c0636a010aef17b1e314e54a963dd31de418c70179e3df208 | Python | 11,657 | 383 | # Copyright 2016 Google Inc. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or a... |
13abf770279059bce3c83fb7c4f27606f8e355672c73163cd995d65c6fe40422 | Python | 11,667 | 267 | # (C) Copyright 2015 Frankfurt Institute for Advanced Studies
# (C) Copyright 2016 Max-Planck Institute for Brain Research
#
# Author: Philipp Huelsdunk <huelsdunk@fias.uni-frankfurt.de>
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following con... |
655929240716ff2ba910178a6b7e54e06a3210eb26515893fd95de1f8f1fa06c | Python | 11,672 | 256 | """Controller for telemetry cluster compute orchestration."""
from __future__ import annotations
import logging
import re
logger = logging.getLogger(__name__)
from src.processing.cluster_detection import (
find_longest_cluster_times,
group_clusters_by_time_period,
select_peak_clusters,
)
from src.process... |
a07c7dd05a82bd77b70e778bdd56dbd63ec531704e93a56181c41b97f7d06ec1 | Python | 11,673 | 288 | from pathlib import Path
from typing import Dict, Set, Tuple
import pandas as pd
from BLEval.evaluator import Evaluator
from BLEval.data import EvaluationData
def _load_signed_ground_truth(
gt_path: Path,
) -> Tuple[Set[Tuple[str, str]], Set[Tuple[str, str]]]:
"""
Load a ground truth network and split e... |
1773472c654d29a8b69fa9c89aa1eb44909310d1a9f1eb1abdb6e8c2734f6c64 | Python | 11,674 | 268 | import matplotlib.pyplot as plt
import glob, os
from pathlib import Path
import pathlib
import numpy as np
from matplotlib.lines import Line2D
import matplotlib.patches as mpatches
# from scipy.interpolate import make_interp_spline, BSpline
import matplotlib.lines as mlines
import pandas as pd
import scipy as sp
import... |
7583f426d49885c4b702964f35fc11500f7bcc595b968922c1760078f18c86c5 | Python | 11,678 | 347 | import argparse
import os
import random
from concurrent.futures import ProcessPoolExecutor
from copy import deepcopy
import h5py
import numpy as np
import torch
import torch.nn as nn
import torch.optim as optim
from sklearn.model_selection import KFold
from torch.utils.data import DataLoader, Dataset
from torchdiffeq ... |
9d8272815206c1c0e14f6bb1664cb4f2af4cb99aadaf68b06ddcf08b77805be5 | Python | 11,684 | 308 | """Numerical-vs-analytic gradient tests for :mod:`oce.forces`.
These tests fix the *interface* and the success criterion before the
actual derivatives are implemented. In v0.1.0 the analytic gradient
routines return zero (mock); the cross-checks against central
differences are therefore expected to fail and are decor... |
0cc3df962e89c65c4a400f901842994a29835d98a8cc2c17ab0c0a0c5a66bbdf | Python | 11,687 | 321 | import boto3
import ujson as json
from tqdm import tqdm
from concurrent.futures import ThreadPoolExecutor
from tempfile import NamedTemporaryFile, TemporaryDirectory
from pybloof import StringBloomFilter
from collections import defaultdict
import random
import os
import re
from boto3.s3.transfer import TransferConfig
i... |
b151204bffb62b0c4b6a94c7a54172e34306a3efeca65f5862ae78fa6729abfd | Python | 11,689 | 294 | # utils/syllable_utils.py
import numpy as np
import os
from matplotlib.patches import Rectangle
def add_new_segment(event, app_state):
"""Add a new segment based on user input from a mouse event."""
from moove.utils.plot_utils import update_ax2_ax3
from moove.utils import save_notmat
displ... |
28c44db28b6098bbf653db6c5e9799424ebd0820a8266efb2be733ee41089263 | Python | 11,691 | 205 | ##主要功能：对esd处理过的图像序列进行后处理，计算一个（后续开发多个）ROI内的像素平均值；
## 对相同条件实验条件不同实验对象的数据叠加平均
##20211009，增加对多个roi处理的功能
##20240122 修改了处理顺序（先组间平均再时间窗平均）改变后的代码逻辑，只限于电刺激
from PyQt5.QtWidgets import *
import os
from PyQt5.QtGui import *
from PyQt5.QtCore import *
import sys
import cv2 as cv
import numpy as np
class Dat... |
7ba05cc2d7a966d5102ad66fe1efd61dff0a3bd52dcb9a9e1cb073f14157d816 | Python | 11,696 | 296 | # Copyright 2021 DeepMind Technologies Limited
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agr... |
360757eaeff6ba1e1c831c93fcd9ae246e3d035f9b2360c7e024a8e5a0f644d7 | Python | 11,699 | 261 | """Controller for telemetry peak/cluster label settings popup."""
from __future__ import annotations
from PySide6.QtWidgets import (
QColorDialog,
QComboBox,
QDialog,
QFrame,
QGridLayout,
QLabel,
QPushButton,
QWidget,
)
from src.gui.framework.tk_compat_controls import LineEditControl,... |
a52d4420aafb61ef760d38e50261dbb08173351e77332ceb9e1d626e576d9b9d | Python | 11,703 | 272 | """Reads an NCBI Gene tsv file."""
from __future__ import print_function
import sys
import re
from collections import namedtuple
from collections import OrderedDict
__copyright__ = "Copyright (C) 2016-present, DV Klopfenstein, H Tang, All rights reserved."
__author__ = "DV Klopfenstein"
#pylint: disable=line-too-l... |
6267dff936a08299900b0120e2373ff75a4bc1458471ecdfae51d4e94671b74b | Python | 11,704 | 283 | from datetime import datetime
import argparse
import getpass
import glob
import itertools
import ntpath
import numpy as np
import os
import os.path
import pandas as pd
import random
import scipy
import scipy.io as sio
import scipy.linalg
import shutil
import six
import socket
import subprocess
import sys
import sys, tr... |
ff2dd93ce11ca21f9b309c8df1b2fa75b289f581c4a9f18a73f502ff4b37c2a3 | Python | 11,711 | 398 | from scipy.spatial import KDTree
import numpy as np
import matplotlib.pyplot as plt
from matplotlib.lines import Line2D
from matplotlib.patches import Patch
from collections import Counter
import jax
import jax.numpy as jnp
from graph_tool.all import Graph
from graph_tool.topology import max_cardinality_matching
from... |
481b94a96edd0354b0d84d7769de26adbb495a090ef2a9883efb85fa58ab7285 | Python | 11,715 | 228 | import csv
import json
import unittest
from pathlib import Path
from tempfile import TemporaryDirectory
from types import SimpleNamespace
from unittest.mock import patch
from GMXMMPBSA.exceptions import PrmtopError
from GMXMMPBSA.parm_setup import MMPBSA_System, Residue
from GMXMMPBSA.radii import (_log_advisories, _r... |
5bfa092ce3a87f9474216ee8e2a0964d46b1ea8a7ecd87c4efc6e22d16ecfe7c | Python | 11,715 | 325 | import mdtraj as md
import numpy as np
import os
import sys
import re
from pathlib import Path
HERE = Path(__file__).resolve()
EXAMPLES_DIR = HERE.parent.parent
SOURCE_DIR = EXAMPLES_DIR.parent
file_path = SOURCE_DIR / "data/1e8l.mr"
def find_missing_atoms(traj, noe_restraints):
"""
Given an mdtraj.Trajectory... |
8a82153ba8d8d5d8e01855e1d8a1f772ed8145e9f347a78085ca3f4495e61dcb | Python | 11,718 | 370 | # 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.
"""
Utilities for working with the local dataset cache.
This file is adapted from `AllenNLP <https://github.com/allenai/allennlp>`_.
and `hugg... |
885c6e97f2dc6943bff9b79e612d099505b314d7a6550a1896f4d85781adf948 | Python | 11,720 | 271 | # Copyright 2021 DeepMind Technologies Limited
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agr... |
8b3b85cf7b6f98047b7770336878e9d3a468af3523c47811ca835fe253bd13e0 | Python | 11,722 | 398 | from scipy.spatial import KDTree
import numpy as np
import matplotlib.pyplot as plt
from matplotlib.lines import Line2D
from matplotlib.patches import Patch
from collections import Counter
import jax
import jax.numpy as jnp
from graph_tool.all import Graph
from graph_tool.topology import max_cardinality_matching
from... |
91b1da3ecbfaaa937095758a89f33bb63d628eae6acb2f71722bc6507e5b0143 | Python | 11,724 | 257 | import shutil
import time
from tqdm import tqdm
from dataloadR.augmentations import *
from evalR import voc_eval
from utils.utils_basic import *
from utils.visualize import *
from utils.heatmap import Show_Heatmap
import config.cfg_lodet as cfg
current_milli_time = lambda: int(round(time.time() * 1000))
... |
f03638077b8c3a3a19cd0a067e6a98f5168961b463732e4669ee8530e9d8d013 | Python | 11,740 | 206 | # -*- coding: utf-8 -*-
# Form implementation generated from reading ui file 'UI/MainWindow.ui'
#
# Created by: PyQt5 UI code generator 5.15.9
#
# WARNING: Any manual changes made to this file will be lost when pyuic5 is
# run again. Do not edit this file unless you know what you are doing.
from PyQt5 import QtCore... |
bfd6f17c8833ec0c4e21cf22d2d2cb46ade0c1f96194bf4aac089bc918b2753f | Python | 11,743 | 334 | """
This module contains the decoder used by the Garfield model.
"""
import torch
import torch.nn as nn
import torch.nn.functional as F
from torch_geometric.data import Data
from torch_geometric.nn import GCNConv, GATConv, GATv2Conv
from .utils import DSBatchNorm, compute_cosine_similarity
class GATDecoder(nn.Module... |
9f6888ea76a906cd8bed9132d1d0861338059d7deb0cfd308651abeeb968df50 | Python | 11,747 | 326 | #!/usr/bin/env python3 -u
# 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 copy
import logging
import os
from typing import Any, Dict, Iterator, List
import torch
from... |
469ddeb3e51709dc2820c237703a4ea1f3887c824ff5c004dfec19648cb4a61a | Python | 11,754 | 400 | from scipy.spatial import KDTree
import numpy as np
import matplotlib.pyplot as plt
from matplotlib.lines import Line2D
from matplotlib.patches import Patch
from collections import Counter
import jax
import jax.numpy as jnp
from graph_tool.all import Graph
from graph_tool.topology import max_cardinality_matching
from... |
c1cc122dbc5915a47cf2b148cf0be886d77547a6b24d611ae1c91d2e979a805f | Python | 11,759 | 399 | from scipy.spatial import KDTree
import numpy as np
import matplotlib.pyplot as plt
from matplotlib.lines import Line2D
from matplotlib.patches import Patch
from collections import Counter
import jax
import jax.numpy as jnp
from graph_tool.all import Graph
from graph_tool.topology import max_cardinality_matching
from... |
05d6c6dcc975c9fa8ca51fabada00c8199b48eb03a997fd5bcb73218aa43205b | Python | 11,760 | 402 | from scipy.spatial import KDTree
import numpy as np
import matplotlib.pyplot as plt
from matplotlib.lines import Line2D
from matplotlib.patches import Patch
from collections import Counter
import jax
import jax.numpy as jnp
from graph_tool.all import Graph
from graph_tool.topology import max_cardinality_matching
from... |
010f6a09a53624439309a87d6498946c4e033ffd2453cf8047f60756d5ccfa41 | Python | 11,769 | 351 | import math
from abc import ABC, abstractmethod
from pathlib import Path
from typing import Dict, Iterator, List, Tuple
import matplotlib.pyplot as plt
import pandas as pd
import seaborn as sns
def get_algo_ids(config: dict) -> List[str]:
"""
Return the list of enabled algorithm IDs from the config.
Para... |
0722b581d1467f5e49475ee480ee3dedddc573959f068b5e4594c66cdced23f8 | Python | 11,779 | 328 | # Copyright (c) 2025, Shenghao Cao & Ye Yuan. Shanghai Jiao Tong University, Shanghai 200240, China
# The classes and functions are modified from scGPT (https://github.com/bowang-lab/scGPT), copyright (c) 2022 suber
import sys
import os
os.environ['PYTORCH_CUDA_ALLOC_CONF'] = 'expandable_segments:True'
from typing imp... |
c5c46b01f9b38fb503443394751167ce79ca46b58291b3de9cba90669dcd42e7 | Python | 11,779 | 309 | import os
import csv
import copy
import json
import logging
from dataclasses import dataclass, field
from typing import Any, Optional, Dict, Sequence, Tuple, List, Union
import torch
import transformers
import sklearn
import numpy as np
from torch.utils.data import Dataset
from peft import (
LoraConfig,
get_p... |
48102f5da72ea82a0076a7e08e284d2b6204b9d5a476ecd7776a8a8fb3914fa3 | Python | 11,781 | 325 | import glob
import gzip
import os
import copy
import nibabel as nib
import numpy as np
import shutil
from mdt.lib.deferred_mappings import DeferredActionDict
__author__ = 'Robbert Harms'
__date__ = "2014-08-28"
__license__ = "LGPL v3"
__maintainer__ = "Robbert Harms"
__email__ = "robbert@xkls.nl"
def load_nifti(nif... |
abd938a1d998bd19fb73660fc86e8f01d74272d7dc60f2387810a304351a121b | Python | 11,792 | 261 | from pathlib import Path
from types import SimpleNamespace
import json
import sys
import unittest
import nibabel as nib
import numpy as np
MODULE_DIR = Path(__file__).resolve().parents[1]
if str(MODULE_DIR) not in sys.path:
sys.path.insert(0, str(MODULE_DIR))
from volume_geometry import ( # noqa: E402
Volu... |
ff6095804943b8a3fd6c1bb9520f5d2b5f46e9d0673fabcd9fe30ff40d99aa62 | Python | 11,794 | 287 | """Coordinate-mirror axis equivalence test.
Does reflecting a structure along the **Y** or **Z** axis — instead of the
**X** axis used by the production pipeline — change the results? This script
provides the *empirical* answer that complements the group-theoretic argument
in the manuscript:
* reflecting along any si... |
c4336a3b379446453a524f78ec7684f0f16c5dec0cfb4a62bf60f1529fad39ae | Python | 11,797 | 304 | # utils/file_utils.py
import evfuncs
import os
import re
import pickle
from scipy.io import wavfile as wav
from scipy.signal import spectrogram
from moove.qt_helpers import invoke_in_main_thread, show_info
from moove.utils.audio_utils import decibel
def get_directories(path):
"""Return a list of directories in t... |
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