sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
fafb272d77a4c5f153b2489e4be692f8197db94d21364b5a03a94165ac51e91d | Python | 14,847 | 319 | import tensorflow as tf
#import tensorflow as tf
tf.compat.v1.disable_v2_behavior()
import tensorflow.compat.v1 as tf
import numpy as np
from tqdm import tqdm
from colorama import Fore
import random
import os
import matplotlib.pyplot as plt
os.environ["CUDA_VISIBLE_DEVICES"]="0"
#Custom implementation of a hybrid de... |
0bea8cc9dd5ffc56d0c8f1eb8f406943e0ae20afaeb9e1627d46829e0055e913 | Python | 14,868 | 342 | """regression test - the ported craniometrics has to give the same numbers as
the old algorithm on the same mesh.
baseline came from running the unmodified old CranioMetrics math against
tests/fixtures/test_mesh.ply, see
tests/fixtures/test_mesh_craniometrics_baseline.json for the details.
tolerances aren't zero beca... |
ede0346d65c239c07312d5361d515003458a274391825a3751deccdf78484c5b | Python | 14,871 | 378 |
from sklearn.tree import BaseDecisionTree
from sklearn.ensemble import RandomForestRegressor, ExtraTreesRegressor
from sklearn.metrics import roc_auc_score
from numpy import *
import time
from operator import itemgetter
from multiprocessing import Pool
def COMPUTE_GRN_AUROC(VIM, grn_true):
import numpy as np
... |
8d9f9cd83e37c9bdd9c2bcffbf2af0d2dd92b43084efc8ba38f90cced0b650a1 | Python | 14,877 | 341 | import torch.nn.functional as F
import torch
import torch.nn as nn
from utils import grid
# ----------------------------------------------------------------------------------------------------------------------
# Baseline FNO: code from https://github.com/neural-operator/fourier_neural_operator
# ---------------------... |
0efbb70f9e21fde4e7e186700200cde25b8ed95511678322faa4c32cdf269aec | Python | 14,878 | 415 | import unittest
import subprocess
import glob
import datetime
import os
import torch
from shutil import copyfile
from rfdiffusion.inference import utils as iu
from rfdiffusion.util import calc_rmsd
import sys, json
script_dir = os.path.dirname(os.path.abspath(__file__))
class TestSubmissionCommands(unittest.TestCase... |
fed3b12f8e9712440fe0fc0938a993a83769985dbbcb07408f347688c93602bb | Python | 14,893 | 416 | import json
import uuid
from contextvars import copy_context
from typing import Any, cast
import pytest
from langchain_core.callbacks.manager import (
AsyncCallbackManager,
CallbackManager,
atrace_as_chain_group,
trace_as_chain_group,
)
from langchain_core.callbacks.stdout import StdOutCallbackHandler... |
640c0182cf329eb7257bcd0ac8a7a07eba5d0d18f6924318f3fda2bd7c032992 | Python | 14,900 | 380 | from collections import OrderedDict
import csv
from logging import Logger
from random import Random
from typing import List, Optional, Set, Tuple, Union
import os
from rdkit import Chem
import numpy as np
from tqdm import tqdm
from .data import MoleculeDatapoint, MoleculeDataset
from HMSA.args import PredictArgs, Train... |
3d4fb24fb7cd6a46355ce647f2281dfad6e3dd45fb8051b1a8fd786753c2dc1b | Python | 14,908 | 343 | # -- coding: utf-8 --
# @Time : 2023/3/12 21:34
# @Author : Biao Zhang
# @Email : littlebiao@outlook.com
# @File : analysis_utils.py
# @Description: This file is used to ...
import pickle
import numpy as np
import scanpy as sc, anndata as ad
import scipy.sparse as sp
import pandas as pd
import sys
import matplotlib.p... |
722dca01eb6ab0713fff9158e71faa7bedfdd9b127893d427812f428da91f397 | Python | 14,912 | 375 | """ Class for generating datasets with different properties.
:Version:
2.0.0
:Date:
04.07.2018
:Author:
Jan Melchior
:Contact:
JanMelchior@gmx.de
:License:
Copyright (C) 2018 Jan Melchior
This program is free software: you can redistribute it a... |
d39ffd43bba4095424a695dbb68efdfa6cbe228e533b3c2edda1fba60f0c4013 | Python | 14,926 | 345 | import argparse
import logging
import os
import random
import shutil
import sys
import time
import numpy as np
import torch
import torch.backends.cudnn as cudnn
import torch.nn as nn
import torch.nn.functional as F
import torch.optim as optim
from tensorboardX import SummaryWriter
from torch.nn import BCEWithLogitsLos... |
8b86615b8652881439a3a5b76461201c5571016c79c6725e3db1e022bcb198ae | Python | 14,934 | 443 | # dataloader for RGAN
# Created: 6/16/2021
# Status: ok
import copy
import glob
import json
import os
import random
import sys
# from typing import Literal
import nibabel as nib
import numpy as np
import pandas as pd
import torch
from torch.utils.data import Dataset
from utils import read_csv_cox_ext as read_csv_ext... |
ffba4ee0dcfe027cd5d2bc8b0891a6c50161f0f56c9ede1fefdbccf9b7658733 | Python | 14,937 | 329 | """
Adapted from:
https://github.com/karpathy/nanoGPT/blob/eba36e84649f3c6d840a93092cb779a260544d08/model.py
"""
import math
from dataclasses import dataclass
import torch
from torch import Tensor
import torch.nn as nn
from torch.nn import functional as F
from mat2seq import CIFTokenizer
@dataclass
class GPTConfig:... |
5a0000d179c76e9d83e24e25702e0737655806e8067440a1a6e3afcaf0bb8ecb | Python | 14,958 | 366 | import albumentations as A
from albumentations.pytorch import ToTensorV2
from joblib import Parallel, delayed
from torch.utils.data import DataLoader
from modulable_CNN3D import CNN3D
import os
import torch
from torch import nn
import numpy as np
from skimage.io import imread, imsave
from src.napari_svetlana.CustomDa... |
abe6b532f1f181f518809f8be8ec43b3485492f33b9d800ff016def7ca686ea3 | Python | 14,962 | 438 | """
Evaluate a flow-matching checkpoint on a data split (default: test).
Uses ``ChgFlowMatchingModule.predict_coeffs`` (Euler CFM integration by default) then
``orbital_inference`` for nMAPE — same probe chunking as ``scdp/scripts/test.py``.
Euler time grids: ``--integrate_schedule uniform|endpoint_refine|power`` (se... |
17304e08f26045d4a8b14ab522eec35875cb323e457205f20d2e305e88acca60 | Python | 14,992 | 321 | import torch
from CEL.networks.models.meta_model import ModelClass
from torch.autograd import Function
from itertools import chain
from copy import deepcopy
from tqdm import tqdm
from torch.func import stack_module_state
from torch.func import functional_call
from einops import rearrange, reduce, repeat, pack, unpack
i... |
7dddb90575b68f209128a7a7aa44a2b0d5646fe85057bca203ade63523330998 | Python | 15,001 | 431 | """Model utilities for torch implementation."""
import copy
import time
import math
import torch
from ._torch_linalg_utils import (
one_hot_encoding, matern_type_kernel, matrix_inv_cholesky,
matrix_block_indexing, matrix_trace_of_product,
matrix_blockdiag_rotation, matrix_block_trace,
)
def get_hyperpar... |
60f6418377faee7a2c33ae478215407dae2960de7cbee89af4bcff643b20eb7c | Python | 15,010 | 409 | """
##############################################################################
#
# Cluster the set of alternatively spliced exons
#
# AUTHOR: Maciej_Bak
# AFFILIATION: University_of_Basel
# AFFILIATION: Swiss_Institute_of_Bioinformatics
# CONTACT: wsciekly.maciek@gmail.com
# CREATED: 26-03-2020
# LICE... |
fe13df8ffb2f7b40ec3aa2910718375895984a946006df86a60ac11f53f13cda | Python | 15,019 | 407 | """Retriever that generates and executes structured queries over its own data source."""
import logging
from collections.abc import Sequence
from typing import Any
from langchain_core.callbacks.manager import (
AsyncCallbackManagerForRetrieverRun,
CallbackManagerForRetrieverRun,
)
from langchain_core.document... |
105f5a254c2b1af875b52c2416d5df98590c1392a6f5b627d9e23b5eaaca7375 | Python | 15,028 | 338 | from torch import nn
import torch
import math
class GCL(nn.Module):
def __init__(self, input_nf, output_nf, hidden_nf, normalization_factor, aggregation_method,
edges_in_d=0, nodes_att_dim=0, act_fn=nn.SiLU(), attention=False):
super(GCL, self).__init__()
input_edge = input_nf * 2... |
2b014e58599b8de43d35b0d660ca9476722dfb086b81aac18a8f6c5fce9ced87 | Python | 15,056 | 432 |
'''
morphological helper functions for app.py
import to app.py and use
morph_with_none, sec_coordinates, stem2plot, sec2stem = morph_lib_creator.create()
to create needed libraries of default morphology.
'''
import numpy as np
import pickle
import json
def map_sec2stem(morphology):
'''create sec->stem dict... |
a33f0ae51326864b1b72e58aec807ef74e81252767da4adf996e934dbf192f94 | Python | 15,084 | 449 | # -*- coding: utf-8 -*-
"""
This file defines a set of functions useful for working with pandas
dataframes full of tabular data
"""
import numpy as np
import pandas as pd
import logging
from itertools import groupby
from sklearn import preprocessing
import torch
from torch.utils.data import TensorDataset
logger = log... |
46db79dbf56973a821dfdcb864d7715d549b4387a46699f01c152122c0ce3c45 | Python | 15,085 | 332 | import torch
from torch import nn
from nnsegnext.network_architecture.neural_network import SegmentationNetwork
import numpy as np
from copy import deepcopy
from timm.models.layers import DropPath
class ConvDropoutNormNonlin(nn.Module):
def __init__(self,input_features,output_features,conv_kwargs,dropout_op_kwargs... |
9fdf29e5ce140a8ebbc28fb57b78ff6e571ded7090f16a624ec7fcc9eec488e6 | Python | 15,094 | 459 | """Neural networks for all experiments."""
import snntorch
from snntorch import surrogate
import torch
class RLIF(torch.nn.Module):
"""Simple spiking neural network in snntorch."""
def __init__(self, timesteps, hidden, num_output):
super().__init__()
self.timesteps = timesteps
self.hi... |
12d1cf5d2724c5710e8e6001406fb5af81dd00a21980fcab0639cf82f1db01ca | Python | 15,107 | 307 | """in-memory session store - one uploaded mesh + whatever state it's in, per
session. actual pipeline work runs on a background thread pool so the
request doesn't just hang there for minutes.
kept this deliberately simple, no redis/celery/database. this is a
single-process tool (either the desktop app or a small inter... |
982e668737599df3a4cf88d6127d19c745be2a0920c9a9e6f4bb4abe6c2b7923 | Python | 15,120 | 438 | # Copyright 2021 AlQuraishi Laboratory
# Copyright 2021 DeepMind Technologies Limited
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# U... |
df1b3c3ea0e6fdc15ade2ea64fa55f80b8ba03014779e9a5ba92d0ffeaaa8f36 | Python | 15,158 | 344 | """tests for metopic.py.
there's no clinical baseline for any of this (see metopic.py's module
docstring) - these check the math against synthetic contours with known
shapes instead: a plain fitted parabola (should recover its own
coefficients and read ~zero deviation everywhere), a bump added at a known
position (sho... |
d8d64046e2e758ab6e43ef4d6f9e48078993f47bff83b8d25638d10b1cc4baa3 | Python | 15,182 | 349 | import argparse
import logging
import os
import random
import shutil
import sys
import time
import numpy as np
import torch
import torch.backends.cudnn as cudnn
import torch.nn as nn
import torch.nn.functional as F
import torch.optim as optim
from tensorboardX import SummaryWriter
from torch.nn import BCEWithLogitsLos... |
94e84b082667876ab2f604328b02d92a6758f9e99f7faa0b7d4139a905e1a680 | Python | 15,186 | 342 | # coding: utf-8
""" MIT License """
'''
Project: Parenchymal Attention Network
Authors: Axel Masquelin
Description:
'''
# Libraries
# ---------------------------------------------------------------------------- #
from argparse import Namespace
from sklearn.model_selection import train_test_split
from torchi... |
3a2f87802b5b4368c761713cf6734920416c36f571da2e644ca7107c0b7b8bab | Python | 15,195 | 344 | # Copyright 2020 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 of the License at
#
# http://w... |
ccc9d3d12911d1c65560f8b4b6ab12c98e24770b6017b717056278c56c712283 | Python | 15,209 | 492 | # Copyright (c) <2021> <University of Paderborn>
# Signal and System Theory Group, Univ. of Paderborn, https://sst-group.org/
# https://github.com/SSTGroup/independent_vector_analysis
#
# Permission is hereby granted, free of charge, to any person
# obtaining a copy of this software and associated d... |
62bb5160d183790ab14fb262c73482dc7d30e4e48d792e5a854d0e793270935f | Python | 15,211 | 630 | import json
from collections.abc import AsyncIterator, Iterator
from typing import Any
import pytest
from pydantic import BaseModel, Field
from langchain_core.exceptions import OutputParserException
from langchain_core.output_parsers.json import (
SimpleJsonOutputParser,
)
from langchain_core.utils.function_calli... |
49d35a0ef81d9591432ba89d3713c982ebc7f588dbbca856a9fd0cabe7369446 | Python | 15,213 | 352 | # coding=utf-8
from pyexpat import features
import matplotlib.pyplot as plt
import seaborn as sns
import pandas as pd
import torch
import torch.nn as nn
import torch.nn.functional as F
from alg.modelopera import get_fea
from network import common_network
from alg.pl_algs.base import Algorithm
import numpy as np
import... |
414ee253336747239113b6b0d47b883c3b7f2d486e7d1b866b574b617e07805a | Python | 15,216 | 343 | import torch
import torch.nn as nn
import torch.nn.functional as F
from models.FNO import MLP2d, MLP3d
from utils import grid
################################################################
# 2d radial fourier layers
################################################################
class radialSpectralConv2d(nn.Module... |
d107d8af1adb009c012b78dc6a3b699e450a6cbbff258b4889fa547a1ddbbfc1 | Python | 15,217 | 387 | # Copyright (c) <2021> <University of Paderborn>
# Signal and System Theory Group, Univ. of Paderborn, https://sst-group.org/
# https://github.com/SSTGroup/independent_vector_analysis
#
# Permission is hereby granted, free of charge, to any person
# obtaining a copy of this software and associated d... |
fc80f21bef47eea5b888d1020fe89835010c2e20cdc29a5d0980d4d3810f4920 | Python | 15,221 | 402 | import numpy as np
import networkx as nx
from tqdm import tqdm
from copy import deepcopy
from scipy.sparse.linalg import eigsh
from scipy.sparse import coo_matrix, csr_matrix, identity
from scipy import sparse
from numpy.random import randn
import os
import random
import torch
from torch_scatter import scatter_sum, sca... |
ae6a2ed54bd42a5aacb96b86fce9c86bc101dfceaa590f226f27bfcae403eec8 | Python | 15,235 | 431 | ####################################################################################
#
# STEPS - STochastic Engine for Pathway Simulation
# Copyright (C) 2007-2026 Okinawa Institute of Science and Technology, Japan.
# Copyright (C) 2003-2006 University of Antwerp, Belgium.
#
# See the file AUTHORS for detai... |
2cbbecfacef18cd57b1ab11fddc61259f313aab896404efea4a79b65dcc70518 | Python | 15,236 | 433 | """File search middleware for Anthropic text editor and memory tools.
This module provides Glob and Grep search tools that operate on files stored
in state or filesystem.
"""
from __future__ import annotations
import fnmatch
import json
import operator
import os
import re
import subprocess
from contextlib import sup... |
1735e2ecb3be098af204c074aecb897d865172b57adf4710ddd0fd77d0550ec7 | Python | 15,243 | 316 | '''
Count chronic stats of a mouse
8/30/2022
'''
import os
import json
import re
import datetime
import traceback
from collections import OrderedDict
# import typing
import shutil
import numpy as np
import matplotlib.pyplot as plt
import matplotlib
import pandas as pd
# font = {# 'family' : 'monospace',
# # 'w... |
dbab0467c78e8adb6d4321cb0f69424bba2b3dd5a7531206da91205de678f9eb | Python | 15,261 | 400 | """Chain that makes API calls and summarizes the responses to answer a question."""
from __future__ import annotations
from collections.abc import Sequence
from typing import Any
from urllib.parse import urlparse
from langchain_core._api import deprecated
from langchain_core.callbacks import (
AsyncCallbackManag... |
0dc4075ff9c30752db9ec9797c313ad1c79d33a799a334d4ce73fd96ceeed9a6 | Python | 15,265 | 390 | # Copyright 2024 DeepMind Technologies Limited
#
# AlphaFold 3 source code is 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... |
3c90ca5c158a8c3e8d8f9a9ee6a84c6a0286c17900b55b897c14dd76ad47803d | Python | 15,267 | 456 | """Data loaders for the de novo sequencing task."""
import functools
import logging
import math
import os
import pathlib
from typing import Optional, Sequence
import lightning.pytorch as pl
import numpy as np
import pyarrow as pa
import spectrum_utils.spectrum as sus
import torch.utils.data._utils.collate
from depthc... |
05e4c85bacc078313b355a13fb51cbe2c264ee81f3fda2a0c5e53328f8befc4b | Python | 15,279 | 453 | # Copyright Generate Biomedicines, 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 ... |
852347a530ee29e11b5e1d5dfef4f981e4bc2bfacea0099c855be5f6dc0802c0 | Python | 15,280 | 329 | import re
import hashlib
import pathlib
import itertools
import subprocess
import collections
import unicodedata
from pybtex import errors, database
import attr
from csvw import dsv
from csvw.metadata import ForeignKey, Datatype
from cldfbench import Dataset as BaseDataset
from cldfbench import CLDFSpec
from cldfcatal... |
bcd5bf68468cbe7798882c3663f4f6713355a5fa3ac9860fb22d241b510e5d14 | Python | 15,281 | 416 | #!/usr/bin/env python
import pysam
import argparse, sys
import math, time, re
from collections import Counter
from argparse import RawTextHelpFormatter
__author__ = "Colby Chiang (cc2qe@virginia.edu)"
__version__ = "$Revision: 0.0.1 $"
__date__ = "$Date: 2015-04-22 09:31 $"
# --------------------------------------
#... |
955325d3c2c7105130e0e47b20458ee3ea9656af9a2de838cff64f3c03430435 | Python | 15,290 | 360 | import tensorflow as tf
from tensorflow.keras import backend as K
import numpy as np
from utils.utils import read_mrc,prctile_norm
from scipy.interpolate import interp1d
import numpy.fft as F
from scipy import asarray as ar, exp
from scipy.optimize import leastsq, minimize, curve_fit
import math
def create_psf_loss(ps... |
df9da316d32c998fa0bd1b531b00c64fb816e37b672206996baecc02daa78e37 | Python | 15,290 | 436 | ####################################################################################
#
# STEPS - STochastic Engine for Pathway Simulation
# Copyright (C) 2007-2026 Okinawa Institute of Science and Technology, Japan.
# Copyright (C) 2003-2006 University of Antwerp, Belgium.
#
# See the file AUTHORS for detai... |
83cf6b9bc1d92184a9b389528f2e82b375d3689abff8bf7f4c109f8c8bc5502c | Python | 15,294 | 477 | """Module to generate networkx graphs."""
"""Implementation based on the template of Matformer."""
from multiprocessing.context import ForkContext
from re import X
import numpy as np
import pandas as pd
from jarvis.core.specie import chem_data, get_node_attributes
# from jarvis.core.atoms import Atoms
from collections... |
11b60961d1d08db75238f0beeb8e6e68eda475b09f8e5c40396a79d03a5be3de | Python | 15,306 | 436 | ####################################################################################
#
# STEPS - STochastic Engine for Pathway Simulation
# Copyright (C) 2007-2023 Okinawa Institute of Science and Technology, Japan.
# Copyright (C) 2003-2006 University of Antwerp, Belgium.
#
# See the file AUTHORS for d... |
d01507060c76f90969e457ba757cef891c84bbc0ec503e974da6e78be0b13062 | Python | 15,319 | 397 | ####################################################################################
#
# STEPS - STochastic Engine for Pathway Simulation
# Copyright (C) 2007-2026 Okinawa Institute of Science and Technology, Japan.
# Copyright (C) 2003-2006 University of Antwerp, Belgium.
#
# See the file AUTHORS for detai... |
e766a81446bd232fa3b8d82e881de7c16b3be27cb7d00019ae3839742b3625f6 | Python | 15,319 | 447 | """Training and testing functionality for the de novo peptide sequencing
model."""
import glob
import logging
import os
import tempfile
import uuid
import warnings
from pathlib import Path
from typing import Iterable, List, Optional, Union
import lightning.pytorch as pl
import numpy as np
import torch
from depthcharge... |
7d8d03fefeca1ab4160bd5655bb9f677a7044541a653315425c7691b40224208 | Python | 15,321 | 414 | # Copyright (c) MONAI Consortium
# 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 writing, so... |
3dd69549734e519b5a15baf83d0624e141fa6f87d99134566b5a5c0e2010f54b | Python | 15,336 | 378 | # Copyright (c) 2021, NVIDIA CORPORATION & AFFILIATES. All rights reserved.
#
# NVIDIA CORPORATION and its licensors retain all intellectual property
# and proprietary rights in and to this software, related documentation
# and any modifications thereto. Any use, reproduction, disclosure or
# distribution of this sof... |
75ad6473e49145774dc83d3d372da0a54cde1bc5586d99b901b92675a326a160 | Python | 15,338 | 322 | import torch
from CEL.networks.models.meta_model import ModelClass
from torch.autograd import Function
from itertools import chain
from copy import deepcopy
from tqdm import tqdm
from torch.func import stack_module_state
from torch.func import functional_call
from einops import rearrange, reduce, repeat, pack, unpack
i... |
5cac4269f702cafac55fdb0b89c7afa1f93eb82a652216da153b514dceedf796 | Python | 15,348 | 353 | """Dataloaders for genomics datasets, including pretraining and downstream tasks.
- Adapted from:
https://github.com/huggingface/transformers/blob/master/examples/pytorch/language-modeling/run_clm.py
- Adapted from:
https://github.com/HazyResearch/flash-attention/blob/main/training/src/datamodu... |
72feec8061d353611d8c478375cee175fd7a2034e182d9f4d049e458295b027b | Python | 15,350 | 318 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
POCIF-BAT R2 — H-R2-2, H-R2-3 et H-R2-4.
H-R2-2 L'écart d'ordre est structuré et prédictible sur permutation non vue.
H-R2-3 Le modèle généralise à une précédence absente de l'entraînement.
H-R2-4 La contrainte de complète positivité améliore la prédiction.
Protoc... |
42669e55daee58c822ed04319014a1fae8369b3a63aaee387ad1acf6cf809bf5 | Python | 15,355 | 432 | """Chain that just formats a prompt and calls an LLM."""
from __future__ import annotations
import warnings
from collections.abc import Sequence
from typing import Any, cast
from langchain_core._api import deprecated
from langchain_core.callbacks import (
AsyncCallbackManager,
AsyncCallbackManagerForChainRun... |
62a6a43ebdca336e5115cf143cc44ec7a8924a483ef7c1896e916dbd33a0c925 | Python | 15,393 | 304 | ###########################################
# IMPORTS
###########################################
from openmmtools.states import SamplerState, ThermodynamicState, CompoundThermodynamicState
from simtk import unit, openmm
from perses.dispersed.utils import compute_potential_components
from openmmtools.constants import k... |
7431b43a30f7fd9f1eb1d15fc82c4850d8d18940ad502e0cea3e6081be05301a | Python | 15,393 | 304 | ###########################################
# IMPORTS
###########################################
from openmmtools.states import SamplerState, ThermodynamicState, CompoundThermodynamicState
from simtk import unit, openmm
from perses.tests.utils import compute_potential_components
from openmmtools.constants import kB
fr... |
736c19f01723b07c394fd824e887bbfd7383852725a88f7620d2fb1c28d98654 | Python | 15,395 | 567 | import torch
from EPI_MRI.utils import m_plus
from abc import ABC, abstractmethod
class LinearOperator(ABC):
"""
Abstract class to define operations of LinearOperator subclasses. A LinearOperator object must define methods for
multiplication and transpose multiplication.
"""
@abstractmethod
d... |
a97d2f5b1a322e35944c21f7a7c724a8547eaacfc5af94c0fca475f881b6c5b3 | Python | 15,395 | 456 | ########################################################################
# Well-mixed chemical reactions.
# AIMS: to verify STEPS well-mixed stochastic solver 'Wmrssa' computes
# reaction rates correctly when many different chemical species and
# reactions are present in the model.
# This model combines all well... |
33a6d4971f06778d07f199725908add42f7b2af8b3fc43746333468a5c5acbd9 | Python | 15,401 | 265 | # Copyright 2020 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 of the License at
#
# http://w... |
11cddddc20866a121c8510c887202604f2d0df4bd43742f3dac27bee8087a1d7 | Python | 15,402 | 456 | ########################################################################
# Well-mixed chemical reactions.
# AIMS: to verify STEPS well-mixed stochastic solver 'Wmdirect' computes
# reaction rates correctly when many different chemical species and
# reactions are present in the model.
# This model combines all we... |
3778dc772b1c324572684176fc72c10c0783feca04b82711bf950e3d729bfdbf | Python | 15,412 | 379 | import sys;sys.path.append('../src/')
import pylab
import spiketools
import defaultSimulate as default
from copy import deepcopy
from bisect import bisect_right
from matplotlib.ticker import MaxNLocator
import pandas as pd
import pickle
from joblib import Parallel, delayed
import numpy as np
# Local modules (not instal... |
54ae9fdfa40ae8e0fbb7b0d7647b87ce642a3c654c996173f45f51770f18f140 | Python | 15,412 | 456 | ########################################################################
# Well-mixed chemical reactions.
# AIMS: to verify STEPS well-mixed stochastic solver 'Wmrssa' computes
# reaction rates correctly when many different chemical species and
# reactions are present in the model.
# This model combines all well... |
ca9461add1abc5fb57f3b2b01066756e8bd5035afb08b1a1d1d41c6f66bdeac8 | Python | 15,417 | 402 | import logging
import platform
import tempfile
import time
from pathlib import Path
import numpy as np
import pytest
from matplotlib import pyplot as plt
from astrocast.clustering import HdbScan, Linkage, Distance
from astrocast.helper import DummyGenerator
class TestHdbscan:
def test_plain(self):
dg =... |
e3abe155040b224a82dfdafcff07cc2386d0d2700600cff40f171aacd1ba8cba | Python | 15,419 | 456 | ########################################################################
# Well-mixed chemical reactions.
# AIMS: to verify STEPS well-mixed stochastic solver 'Wmdirect' computes
# reaction rates correctly when many different chemical species and
# reactions are present in the model.
# This model combines all we... |
87eabb638165db0fdca6955f28ace0eb85a9e509bab0a7de59bf8223b5d49a5c | Python | 15,434 | 389 | # Copyright 2023 DeepMind Technologies Limited. 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
#
# https://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by... |
7a37b989b25e4d36f0b92dde0294812db96f66fea96c0ad4307f45efa057ba45 | Python | 15,437 | 316 | import torch
from CEL.networks.models.meta_model import ModelClass
from torch.autograd import Function
from itertools import chain
from copy import deepcopy
from tqdm import tqdm
from torch.func import stack_module_state
from torch.func import functional_call
from einops import rearrange, reduce, repeat, pack, unpack
i... |
c60658ccdc6be6728005cc5178b5448d5c994c3c9e9068243c96189e27cfd97d | Python | 15,437 | 421 | """Tool retry middleware for agents."""
from __future__ import annotations
import asyncio
import time
import warnings
from typing import TYPE_CHECKING, Any
from langchain_core.messages import ToolMessage
from langgraph.errors import GraphBubbleUp
from langchain.agents.middleware._retry import (
OnFailure,
R... |
31a5ef341c4128a2d45c35482626a7e977e01ae75f6db43eac2d672d02ef44db | Python | 15,438 | 404 | import torch
import torch.nn as nn
import torch.nn.functional as F
import math
from opt_einsum import contract as einsum
from rfdiffusion.util_module import init_lecun_normal
class FeedForwardLayer(nn.Module):
def __init__(self, d_model, r_ff, p_drop=0.1):
super(FeedForwardLayer, self).__init__()
s... |
c8d8e52499a5490d487fc2f310f49df22c18e3f70efe91f5c2b54a541a57b1ea | Python | 15,438 | 434 | ####################################################################################
#
# STEPS - STochastic Engine for Pathway Simulation
# Copyright (C) 2007-2023 Okinawa Institute of Science and Technology, Japan.
# Copyright (C) 2003-2006 University of Antwerp, Belgium.
#
# See the file AUTHORS for d... |
fd7390ffc6ca8272526820e865d7458f62638d33e6fd5c9ccc33c6f710b504a0 | Python | 15,438 | 459 | ########################################################################
# Spatial chemical reactions.
# AIMS: to verify STEPS spatial deterministic solver 'TetODE' computes
# reaction rates correctly when many different chemical species and
# reactions are present in the model.
# This model combines all validat... |
02976491071c613ff8f8e8dc0327bac895cdc40b3094cc50491a797aba357520 | Python | 15,442 | 438 | """unit tests for src/craniumpy_core/cohort.py - pure function tests, no
FastAPI needed, same style as test_reporting.py testing the underlying
math/IO directly. api/routers/cohort.py's own request/response plumbing is
covered separately in test_api.py."""
from __future__ import annotations
import io
from pathlib imp... |
2796b86d1be786a859eec407572460d98ca647e594fb8cbe866cc3b386f27273 | Python | 15,450 | 466 | import logging
import os
import mxnet as mx
import numpy as np
import scipy.stats
import pickle
from ..utils import *
class IdentityOp(mx.operator.CustomOp):
def __init__(self, logging_prefix="identity", input_debug=False, grad_debug=False):
super(IdentityOp, self).__init__()
self.logging_prefix=lo... |
69e76d8e4548791efe098ed3a511fbb4b06bad5bcef5ca560c72d62915094895 | Python | 15,454 | 484 | """Base classes for scoring the output of a model on a scale of 1-10."""
from __future__ import annotations
import logging
import re
from typing import Any
from langchain_core.callbacks import Callbacks
from langchain_core.language_models import BaseLanguageModel
from langchain_core.output_parsers import BaseOutputP... |
b3db6c0270728ad70692c50220a5c333cf855e238c01cce224c31b2228f530a4 | Python | 15,455 | 459 | ########################################################################
# Spatial chemical reactions.
# AIMS: to verify STEPS spatial deterministic solver 'TetODE' computes
# reaction rates correctly when many different chemical species and
# reactions are present in the model.
# This model combines all validat... |
692dcf343cddbe893c6386a7e0ecab62a3830289dd724a68413beac97d662d7f | Python | 15,458 | 410 | """
Helper functions for use with our topic heatmap visualization Jupyter notebook
Authors: Lexie Li, George H. Chen
"""
import matplotlib
import numpy as np
import os
import pickle
import re
import matplotlib.pyplot as plt
from matplotlib import colors
import seaborn as sb
import warnings
matplotlib.rcParams['pdf.fon... |
1e40b5953ddbb91b9fdea629ddc6aee18e5d6dbc57b243000e7c998755b68a46 | Python | 15,463 | 371 | from __future__ import division
import multiprocessing as mp
import itertools as it
import numpy as np
import scipy
from scipy.special import factorial, comb as nchoosek
import logging
LOG = logging.getLogger(__name__)
IMAG_CONST = scipy.sqrt(-1)
PI_CONST = np.pi
NAN_CONST = np.NaN
def nested_loop(stack, args):
... |
8d8109eb96eb485e69fed732853ac1d4f9c2de03c457878e2d8eaa5898f68f08 | Python | 15,467 | 481 | import csv
from pathlib import Path
import matplotlib.pyplot as plt
import numpy as np
import time
from typing import Any, Dict, Union, Tuple
import pickle as pk
import os
import torch.distributed as dist
import torch
from jarvis.core.atoms import Atoms
from jarvis.db.jsonutils import dumpjson, loadjson
from torch ... |
683bc1c9922b6104e4b9b6fa4760b1bbdde36740eea8ded132a43913b6ba0db3 | Python | 15,471 | 490 | '''
PipelineTransfacMatch.py
========================
- Classes and functions used in pipeline_trasfacmatch.py
=========================================================
'''
################
# import modules
################
import re
import os
import sqlite3
import collections
from cgatcore import pipeline as P
impor... |
a64506ed9b6ede9f9a1b4b2047cc9d3ebc9b8372849b1725a23099ee50dd3165 | Python | 15,493 | 464 | import os
import sys
import re
import types
import itertools
import matplotlib.pyplot as plt
import numpy
import numpy.ma
from ChipseqReport import *
import Annotations
from cgatReport.Tracker import *
##########################################################################
#########################################... |
83dccdddba2736947f987b10caa5505d4d3ef990d9964ee16080678005acae00 | Python | 15,495 | 382 | """ This module contains functions to run the compliance checks in parallel"""
import argparse
import sys
import time
from pathlib import Path
from typing import Iterable, Union
from MRdataset import load_mr_dataset, MRDS_EXT, DatasetEmptyException
from mrQA import check_compliance
from mrQA import logger
from mrQA.c... |
ed7e1df1b7d62617daacfdbc7b816b6719ecf81556be70d1de89365395ae46e6 | Python | 15,505 | 427 | import keras
from keras.models import Sequential, Model, load_model
from keras.layers import Dense, Dropout, Activation, Flatten, Input, Lambda
from keras.layers import Conv2D, MaxPooling2D, Conv1D, MaxPooling1D, LSTM, ConvLSTM2D
from keras.layers import GRU, BatchNormalization, LocallyConnected2D, Permute
from keras.l... |
0e07b36e6a8a216f1111de48c899d7464311400263ee02e0b65c26b9596595d1 | Python | 15,506 | 434 | ####################################################################################
#
# STEPS - STochastic Engine for Pathway Simulation
# Copyright (C) 2007-2023 Okinawa Institute of Science and Technology, Japan.
# Copyright (C) 2003-2006 University of Antwerp, Belgium.
#
# See the file AUTHORS for d... |
fbfb23fcdb4eb7692158426db055cd502bbd2584a4b146adbcc4de84ba0de261 | Python | 15,524 | 446 | # Copyright 2021 AlQuraishi Laboratory
# Copyright 2021 DeepMind Technologies Limited
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# U... |
2e37ab7af3a2a4977e87612d8ed59a59f6d89e15f3723371ced170ccdc4de491 | Python | 15,530 | 468 | """
Codes borrowed from Open Catalyst Project (OCP) https://github.com/Open-Catalyst-Project/ocp and https://github.com/yuanqidu/M2Hub/ (MIT license)
---
This code borrows heavily from the DimeNet implementation as part of
pytorch-geometric: https://github.com/rusty1s/pytorch_geometric. License:
---
Copyright (c) 2... |
dca1e724b2ef40a5a045bd4cf2902e128e1006c5e77e130a664d77f44d4e1abe | Python | 15,533 | 357 | """Planning and task management middleware for agents."""
from collections.abc import Awaitable, Callable
from typing import Annotated, Any, Literal, cast
from langchain_core.messages import AIMessage, SystemMessage, ToolMessage
from langchain_core.tools import InjectedToolCallId, StructuredTool, tool
from langgraph.... |
ab2d47d04ba16db95463af4810030fde91c46b722728774ae51032cbe56212c0 | Python | 15,535 | 382 | # coding=utf-8
"""Includes TestMetrics which tests the metrics class of vulcanai."""
import pytest
import numpy as np
import torch
from vulcanai.models.metrics import Metrics
from vulcanai.models.cnn import ConvNet
from torch.utils.data import TensorDataset, DataLoader
import pandas as pd
import os
# noinspection PyP... |
818f0e885a2da20836e2dfd3b4a2c6e5879a986669dfcce550e11860ebd56250 | Python | 15,537 | 404 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Wed Aug 18 16:54:08 2021
@author: shni2598
"""
import numpy as np
import matlab.engine
import mydata
#%%
class MUA_findchangepts:
def __init__(self):
##self.stim_dura = None
self.dt = 0.1 # ms
self.mua_sampling_in... |
c45b5296b379b74ba0c2ac6439bce50d9f07441bca28148135a6614bd45c9d73 | Python | 15,540 | 345 | # Copyright Generate Biomedicines, 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 ... |
36aa4a88fdfc6c77be77561c61e30fb5fa2b28f5562d0fbe9529a59cc5cadaf1 | Python | 15,547 | 419 | import pickle
import math
import os
from .normalizer import Normalizer
from .tokenizer import Tokenizer
from .data_helper import DataHelper
class SpellCheck:
def __init__(self):
self.normalizer = Normalizer()
self.tokenizer = Tokenizer()
self.data_helper = DataHelper()
... |
72a79041c93fa030336c8021d4c133ca938506f0f2b233d47ff8e8d317ca803c | Python | 15,547 | 326 | """
Functions required for initializing the circuit.
The DSS circuit is set up along with the bus and branch objects.
The Graph model of the DSS Circuit is also instantiated here.
"""
import win32com.client
import numpy as np
import math
import networkx as nx
class DSS(): # to initialize the DSS circu... |
ded6f1bbd3628abd7fc9d8be23241e0d810e4f54cf485f3bdf2765e574d2fa75 | Python | 15,552 | 422 | # Copyright 2022 AlQuraishi Laboratory
#
# 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 i... |
a482052b38d5aa78944778448bc0d90287b948de2c3083110ff2a9e4a478d173 | Python | 15,561 | 340 | import matplotlib.pyplot as plt
import matplotlib.patches as patches
import itertools
from Simulator.SimulatorPattern import simulatorPattern
from Simulator.SimulatorPatternDual import simulatorPatternDual
from matplotlib.lines import Line2D
from Articles.Sequential_Learning_Striatum.Code.FigureSequential import *
num... |
095e5ce5b186ef11929bdfe3cfd4d7100115e9cd33fab2cae93705866892e1f7 | Python | 15,568 | 412 | # Copyright Generate Biomedicines, 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 ... |
ef548c29d72191acfddfe1a945ba7fe0856b89b5d7ca2df92519965d87b11ed3 | Python | 15,573 | 324 | """tests for clipping.py.
test_clip_plane_keeps_positive_normal_side and test_clip_sphere_keeps_inside
pin down the sign conventions - checked these against real pyvista behavior
first, getting this backwards would silently cut away the wrong half of a
head and you'd never notice from the code alone. the cranial_clip/... |
58fe58e416baae482872eb0489da64c3b5a37de83c649270a1ffb14b4486cfbd | Python | 15,581 | 404 | # code adapted from https://github.com/arneschneuing/DiffSBDD/blob/main/process_crossdock.py
from pathlib import Path
from time import time
import argparse
import shutil
import random
import matplotlib.pyplot as plt
import seaborn as sns
from tqdm import tqdm
import numpy as np
from Bio.PDB import PDBParser
from Bi... |
538681ac91d6ddc6fb28c06d57b1ff71c786f7db3bd4e4c0a0ef2b8dbd74fdf0 | Python | 15,587 | 477 | """Unique methods used within db-search mode"""
import functools
import logging
import os
import re
import string
from pathlib import Path
from typing import Dict, Iterator, Pattern, Set, Tuple
import depthcharge.constants
import depthcharge.tokenizers
import numpy as np
import pandas as pd
import pyteomics.fasta
imp... |
828766d133f2b8753aabfbada5d1e80a4f2aec821f32d98cf1a135214a7144ef | Python | 15,592 | 367 | # -*- coding: utf-8 -*-
import os
import copy
import odl
import torch
import numpy as np
from math import ceil
from tqdm import tqdm
from warnings import warn
from torch.utils.data import DataLoader
from torch.utils.tensorboard import SummaryWriter
from torch.optim.lr_scheduler import CyclicLR, OneCycleLR
from dival... |
dfc0ea1b06e610a316993dae5da01e8d75f0f4eea664499c2ea05f11a56b0f3f | Python | 15,595 | 420 | import logging
import numpy as np
import pandas as pd
import scipy.linalg as la
from helpers.data import assert_normalized
def get_phenotype_array(
phenotype_df: pd.DataFrame,
subjects_subset_list: list,
morphometricity_subject_measure: str,
) -> np.array:
"""
Returns a normalized array with val... |
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