sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
9c64eed6f6075817001ed50ea0c680e99c070e851aeca99777702fe22f1dc271 | Python | 885 | 32 | from typing import TYPE_CHECKING, Any
from langchain_classic._api import create_importer
if TYPE_CHECKING:
from langchain_community.example_selectors.ngram_overlap import (
NGramOverlapExampleSelector,
ngram_overlap_score,
)
# Create a way to dynamically look up deprecated imports.
# Used to ... |
fd3f687ce37b068a0f263fdb2a5bd3b802f2552a664fa604a63ff3b90beb61fb | Python | 885 | 32 | # Copyright (c) Microsoft Corporation.
# Licensed under the MIT license.
import os
from pdearena import utils
from pdearena.data.datamodule import PDEDataModule
from pdearena.lr_scheduler import LinearWarmupCosineAnnealingLR # noqa: F401
from pdearena.models.pdemodel import PDEModel
logger = utils.get_logger(__name_... |
8cdcab1249ecc96cfd2bdaf540a6283075ff9baf012f7c6c9f1c10e998c8c6a9 | Python | 887 | 31 | import setuptools
setuptools.setup(
name="pyebm",
version="2.0.3",
author="Vikram Venkatraghavan",
author_email="v.venkatraghavan@erasmusmc.nl",
description="Toolbox for event-based modeling",
long_description="Contains codes for EBM and DEBM with several options for mixture modeling",
long... |
b50ece2acdddfb8273cf98703bd405b84e47d68147e6858cd1cf6f24f33ebd35 | Python | 887 | 28 | from typing import TYPE_CHECKING, Any
from langchain_classic._api import create_importer
if TYPE_CHECKING:
from langchain_community.document_loaders import AssemblyAIAudioTranscriptLoader
from langchain_community.document_loaders.assemblyai import TranscriptFormat
# Create a way to dynamically look up deprec... |
5fdf18357ddcd97ce3b68c42eadc09e1060d7eab51ed55be30f830ca041d4e1f | Python | 889 | 30 | from typing import TYPE_CHECKING, Any
from langchain_classic._api import create_importer
if TYPE_CHECKING:
from langchain_community.embeddings import (
SelfHostedHuggingFaceEmbeddings,
SelfHostedHuggingFaceInstructEmbeddings,
)
# Create a way to dynamically look up deprecated imports.
# Used ... |
bd5fd1af11aa4ad290f24eea1730f172b0c671eec7b0c018dbc27c05d6be8a94 | Python | 890 | 20 | from typing import Any
def __getattr__(name: str) -> Any:
"""Get attr name."""
if name == "create_python_agent":
msg = (
"This agent has been moved to langchain_experimental. "
"This agent relies on python REPL tool under the hood, so to use it "
"safely please sand... |
2a2d4fbbf05dec64eabdd1f83e6172b4f37fd74875eee48b449168c9e9ca6112 | Python | 891 | 36 | from matformer.train_props import train_prop_model
props = [
"formation_energy_peratom",
"optb88vdw_bandgap",
"bulk_modulus_kv",
"shear_modulus_gv",
"mbj_bandgap",
"slme",
"magmom_oszicar",
"spillage",
"kpoint_length_unit",
"encut",
"optb88vdw_total_energy",
"epsx",
... |
cf8473e9d51113ff0063634b32f5423dc2a123fcf877f3a03f0774a254a4a1f7 | Python | 892 | 32 | from typing import TYPE_CHECKING, Any
from langchain_classic._api.module_import import create_importer
if TYPE_CHECKING:
from langchain_community.chat_loaders.facebook_messenger import (
FolderFacebookMessengerChatLoader,
SingleFileFacebookMessengerChatLoader,
)
module_lookup = {
"SingleF... |
dac0117511e33debadc6491657bc93b8f920c00447ba0aafd9287ae3fb89a49d | Python | 892 | 20 | from typing import Any
def __getattr__(name: str) -> Any:
"""Get attr name."""
if name == "create_xorbits_agent":
msg = (
"This agent has been moved to langchain_experimental. "
"This agent relies on python REPL tool under the hood, so to use it "
"safely please san... |
1d5b4bedf179836b945f8cfd75fe915915a340cb62f25835f3be43368d813ecd | Python | 893 | 32 | from typing import TYPE_CHECKING, Any
from langchain_classic._api import create_importer
if TYPE_CHECKING:
from langchain_community.llms import AzureOpenAI, OpenAI, OpenAIChat
from langchain_community.llms.openai import BaseOpenAI
# Create a way to dynamically look up deprecated imports.
# Used to consolidat... |
7700b571ecee8c4cda61138907f85b36722f96866ad6784b2608d1dcb0ad74dc | Python | 894 | 31 | """
imagingplus: integrated tool-suite of essential processing and analysis of imaging+ experiments
"""
import warnings
warnings.filterwarnings("ignore")
from ._version import __version__
from .utils.io import import_obj
from imagingplus.main.core import SingleImage
from imagingplus.utils import utils
from imaging... |
f92efa2cbff9b424f4959a5f70a222fe2e154cb760bcfa5a2843a49786a2b301 | Python | 895 | 33 | import argparse
from pipeline import Pipeline
from inverse_fold_models.proteinmpnn import ProteinMPNN
from fold_models.esmfold import ESMFold
def main(args):
# inverse fold model
inverse_fold_model = ProteinMPNN()
# fold model
fold_model = ESMFold()
# pipeline
pipeline = Pipeline(inverse_fold_model, fold_mod... |
46256e25fa286c016a52102dda3198cb32f34163574ddd2ec1ffd9d2484f8cfd | Python | 896 | 33 | #!/usr/bin/env python
"""Setup script for the theta package
"""
from setuptools import setup, find_packages, Extension
from Cython.Build import cythonize
from Cython.Distutils import build_ext
import numpy
extensions = [
Extension('series',
sources=['series.pyx',
'bessel.c'],
... |
6f3617879cdfeef59633a3c5b84da7838e2c66d6b2e5fb3266bc696749090f5c | Python | 896 | 19 | import torch
from torchvision import datasets, transforms
def data_generator(root, batch_size):
train_set = datasets.MNIST(root=root, train=True, download=True,
transform=transforms.Compose([
transforms.ToTensor(),
... |
b2db01bac2497a4313e088932ad4e96de2be2908c5fb5905c9ff2351c131320a | Python | 896 | 29 | import argparse
def main():
parser = argparse.ArgumentParser()
parser.add_argument('infile', help='the transformed values of latent variables')
parser.add_argument('outfile', help='the reformated values of latent variables')
args = parser.parse_args()
outfh = open(args.outfile, 'w')
### the he... |
5b4563e3a3d6db33da12f7fabc8d82b6de5f782c9d13d42ff2b4d02f8f0f1bc4 | Python | 897 | 35 | import torch
import torch.nn
import torch.utils.data
def compute_forces(energy, positions, training=True):
grad_outputs = [torch.ones_like(energy)]
gradient = torch.autograd.grad(
outputs=[energy],
inputs=[positions],
grad_outputs=grad_outputs,
retain_graph=training,
... |
809b84e957398aa547eb9df3698ac3a5e852f7078ad309cbb912d19b14b8818d | Python | 897 | 33 | from typing import TYPE_CHECKING, Any
from langchain_classic._api import create_importer
if TYPE_CHECKING:
from langchain_community.utilities.redis import (
TokenEscaper,
check_redis_module_exist,
get_client,
)
# Create a way to dynamically look up deprecated imports.
# Used to consol... |
0523350a64dd12e9b43e1d4055e61f8662cb01de1cfe0a20d6da2b266bea68f6 | Python | 898 | 35 | from logging import Logger
from pathlib import Path
from typing import List
from ..data import AnnotationTable, WorldlineTable
from ...methods.overwrite_checkpoint import overwrite_checkpoint
from ._utilities import default_args
@default_args("None, None")
def overwrite_zeir_checkpoint(
dataset: Path,
annot... |
6f475b777608c4a6440be721a3cabb07e21a6c113dfc37f6999580bd39b03df3 | Python | 898 | 20 | from typing import Any
def __getattr__(name: str) -> Any:
"""Get attr name."""
if name == "create_spark_dataframe_agent":
msg = (
"This agent has been moved to langchain_experimental. "
"This agent relies on python REPL tool under the hood, so to use it "
"safely pl... |
96b32f528a15fccfba4c979745f64a153b65baafc11f363e31f6bffb8441a3a5 | Python | 898 | 30 | from typing import TYPE_CHECKING, Any
from langchain_classic._api import create_importer
if TYPE_CHECKING:
from langchain_community.vectorstores import MyScale, MyScaleSettings
from langchain_community.vectorstores.myscale import MyScaleWithoutJSON
# Create a way to dynamically look up deprecated imports.
# ... |
b6c39e619e76bd441d8281698f94d1f8731da2f44f1306185d337a4e637025af | Python | 898 | 30 | from typing import TYPE_CHECKING, Any
from langchain_classic._api import create_importer
if TYPE_CHECKING:
from langchain_community.embeddings import (
AlephAlphaAsymmetricSemanticEmbedding,
AlephAlphaSymmetricSemanticEmbedding,
)
# Create a way to dynamically look up deprecated imports.
# Us... |
1cdadfc195682931eca4be529d0551ec7c2cb6d97d8a23e9f110e0eaf673de43 | Python | 899 | 30 | from ChipseqReport import *
# for trackers_derived_sets and trackers_master
if not os.path.exists("conf.py"):
raise IOError("could not find conf.py")
exec(compile(open("conf.py").read(), "conf.py", 'exec'))
class CountsTranscripts (TrackerSQL):
mPattern = "transcripts"
mAsTables = True
def getSlice... |
24053805a2ac2c1189be93219ed1311ee92c55974f3790af5942b9bc72edafb3 | Python | 899 | 32 | import torch
import numpy as np
import argparse
parser = argparse.ArgumentParser(description='')
parser.add_argument('--save_dir', type=str, help='')
args = parser.parse_args()
write_path = f'<path to the generated sequences folder>/log.txt'
path = f"../sample_output/vina_output/{args.save_dir}/qvina2_scores.pt"
... |
2f13dbcb5614e65b8ecb8c4e0e320389655bece9db01c3f8b9aca8ab428da557 | Python | 899 | 23 | # Python function that creates tall transformation matrices that project a heartbeat onto the phase domain.
# In order for the model to work, the length of the heartbeats in the phase domain is always greater than the length of the heartbeats in the time domain
# Inputs
# N - the length of the heartbeat in time dom... |
4c4fae692c027e7f009459ac611abf61ccef78af83741711458a6d76211d905e | Python | 899 | 30 | import pandas as pd
import mne
from config_chbp_eeg import bids_root, deriv_root
subjects_list = list(bids_root.glob('*'))
subjects_df = pd.read_csv(bids_root / "participants.tsv", sep='\t')
subjects = [sub for sub in subjects_df.participant_id if
(deriv_root / sub / 'eeg').exists()]
eeg_template_monta... |
c0a69e0684c9404c7fdde5ba35b58ff35dbb8824678f65de8849aee292b84709 | Python | 899 | 27 | import logging
import os
import sys
import os.path as osp
import time
def setup_logger(name, save_dir, if_train):
logger = logging.getLogger(name)
logger.setLevel(logging.DEBUG)
ch = logging.StreamHandler(stream=sys.stdout)
ch.setLevel(logging.DEBUG)
formatter = logging.Formatter("%(asctime)s %(nam... |
69c9eaa8090507216367855214801d7fc2587bc8fe2060c3907401e85afc0278 | Python | 900 | 20 | from typing import Any
def __getattr__(name: str) -> Any:
"""Get attr name."""
if name == "create_pandas_dataframe_agent":
msg = (
"This agent has been moved to langchain_experimental. "
"This agent relies on python REPL tool under the hood, so to use it "
"safely p... |
d39c914dada96e7210065d67b4802e621877464cc825dc8a68e891249a4caed5 | Python | 900 | 29 | import os
# Build paths inside the project like this: os.path.join(BASE_DIR, ...)
BASE_DIR = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
def get_weights_path(weights_key):
path = os.path.join(BASE_DIR, 'weights', weights_key + '.pt')
return path
def save_weights(reconstructor, weights_key, ... |
83503f2cb7358cba9e94a3dfb951c519809144f1881216834753ceb49b4aa07e | Python | 901 | 24 | import os
import sys
from indoor3d_util import DATA_PATH, collect_point_label
BASE_DIR = os.path.dirname(os.path.abspath(__file__))
ROOT_DIR = os.path.dirname(BASE_DIR)
sys.path.append(BASE_DIR)
anno_paths = [line.rstrip() for line in open(os.path.join(BASE_DIR, 'meta/anno_paths.txt'))]
anno_paths = [os.path.join(DAT... |
5982ecd125f37e2e27500d946826846791783fc896da8257723c06029f02cdd3 | Python | 903 | 30 | from typing import TYPE_CHECKING, Any
from langchain_classic._api import create_importer
if TYPE_CHECKING:
from langchain_community.embeddings import InfinityEmbeddings
from langchain_community.embeddings.infinity import (
TinyAsyncOpenAIInfinityEmbeddingClient,
)
# Create a way to dynamically lo... |
5dace3d33dd1463b040078bfa809f6061340f2abd26eb6ecd67b9f60bf75dcf1 | Python | 903 | 32 |
from abc import ABC, abstractmethod
from collections import OrderedDict
import numpy as np
from typing import Union, Mapping, Callable
class ABCFeatures(ABC):
"""
"""
def __init__(
self,
compute_basic_stats: Callable[[Union[list, np.ndarray]],
... |
1edb506f30d07a1b44d00f9715b210ffa604dc6a44e4c783a955e9243f706ada | Python | 904 | 29 | from typing import TYPE_CHECKING, Any
from langchain_classic._api import create_importer
if TYPE_CHECKING:
from langchain_community.agent_toolkits.sql.prompt import (
SQL_FUNCTIONS_SUFFIX,
SQL_PREFIX,
SQL_SUFFIX,
)
# Create a way to dynamically look up deprecated imports.
# Used to co... |
4dad188a2be560cecb1093e5e473cc15a8cb488c35975dedbbd76948efe9a10c | Python | 905 | 31 | import torch
def test_image_cache_len(mock_image_cache) -> None:
assert len(mock_image_cache) == 3
def test_image_cache_contains(mock_image_cache) -> None:
assert 1 in mock_image_cache
assert 2 in mock_image_cache
assert 3 in mock_image_cache
assert 4 not in mock_image_cache
def test_image_cac... |
763ad31e20e98f7bdddf1e5f00f042d25fbec7b3f667ff193e7b6762df0bd833 | Python | 905 | 32 | from typing import TYPE_CHECKING, Any
from langchain_classic._api import create_importer
if TYPE_CHECKING:
from langchain_community.tools.dataforseo_api_search.tool import (
DataForSeoAPISearchResults,
DataForSeoAPISearchRun,
)
# Create a way to dynamically look up deprecated imports.
# Used ... |
88f7fdb9f1166e9453ff09a168a3ac01e5988e497956f6b204c655466612662d | Python | 905 | 34 | import pickle
from config import conf
from runner import Runner
import torch
runner = Runner(conf)
known_binding_site = True
node_temp = 0.5
dist_temp = 0.3
angle_temp = 0.4
torsion_temp = 1.0
min_atoms = 10
max_atoms = 45
focus_th = 0.5
contact_th = 0.5
num_gen = 100 # number generate for each reference rec-lig p... |
d45234b7571d2c74684f0e607d60639e3ec6f3e92d7cb6d4c022032e617880c1 | Python | 905 | 34 | from pathlib import Path
import pytest
# Getting the absolute path of the current file's directory
ABS_PATH = Path(__file__).resolve().parent
# Getting the absolute path of the project's root directory
PROJECT_DIR = ABS_PATH.parent.parent
# Loading the .env file if it exists
def _load_env() -> None:
dotenv_pat... |
5276b65c1efad2db4a362d4dc0bd6aa923011ac14471489c43cdf8e17834d4fa | Python | 906 | 29 | """Calculate depth based on the boarders of each barrel column"""
import pandas as pd
from tqdm import tqdm
barrels_positions = pd.read_feather("../data/annotated_barrels.feather")
barrels_names = barrels_positions.barrel.unique()
barrels_layers = barrels_positions.layer.unique()
depth_df = []
for barrel in tqdm(bar... |
935836d8b16080a3a5a66a10e2f3fdba20a9188df5f744d4fbcac3593be4a1e6 | Python | 906 | 31 | from setuptools import setup, find_packages
__version__ = "0.0.1"
setup(
name="fetalxbrainxmultiomics",
version=__version__,
packages=find_packages(),
install_requires=[
'loompy',
'numpy',
'scikit-learn',
'seaborn',
'numba==0.51.0',
'deeplift',
'twobitreader',
'captum',
... |
ea4662302df54bc91425e6994e9e591f2062b2bdda2c1814e3dfcdd91d4a9046 | Python | 906 | 33 | import sys
import os
import subprocess
import tempfile
#Only execute inside IDE with rayx as root
def checkForTerminal():
cwd = os.getcwd()
TerminalApp_Path = 'build/bin/TerminalApp'
path_to_terminal = 'build/bin/'
test = os.path.join(cwd,TerminalApp_Path)
return os.path.exists(test),test,path_t... |
ef3e2771d68c7c22468bc6182a6aec0e48ce3485c19a0a3e1c523dc949dac825 | Python | 907 | 40 | import math
import torch
def sinusoidal_encoding(v, N, D):
# v: [*]
# [D]
k = torch.arange(1, D+1).to(v.device)
# [*, D]
sin_div_term = N ** (2 * k / D)
sin_div_term = sin_div_term.view(*((1, ) * len(v.shape) + (len(sin_div_term), )))
sin_enc = torch.sin(v.unsqueeze(-1) * math.pi / sin_div_term)
# [*, D]
... |
dae79b3d629ec70cabace950b66528bd44b640408420eb4f803298261cfd65d1 | Python | 908 | 30 | from typing import TYPE_CHECKING, Any
from langchain_classic._api import create_importer
if TYPE_CHECKING:
from langchain_community.embeddings import SagemakerEndpointEmbeddings
from langchain_community.embeddings.sagemaker_endpoint import (
EmbeddingsContentHandler,
)
# Create a way to dynamical... |
f9d06790fa193bf4552b7a95456ea5aafcd9a7781b58c0f63a09a24f45187a52 | Python | 908 | 30 | import torch
import torch.nn as nn
def get_activation(activation):
if activation == "CReLU":
return complexReLU()
if activation == "modReLU":
return modReLU()
if activation == "zReLU":
return zReLU()
raise ValueError(f"Activation {activation} not recognized")
class modReLU(nn.M... |
072aa82c676f5bda539a43b2569d7847ecc517622cdb786bf75b7ac95b973740 | Python | 909 | 25 | import os
from langchain_core.prompts import ChatPromptTemplate
from langchain_classic import hub
def test_hub_pull_public_prompt() -> None:
prompt = hub.pull("efriis/my-first-prompt")
assert isinstance(prompt, ChatPromptTemplate)
assert prompt.metadata is not None
assert prompt.metadata["lc_hub_own... |
1f31f199b0e627710dc6c9d2c8aa81ceeafebf7df2ccc9f87682d4d9a6778da9 | Python | 909 | 17 | # Python function that computes the optimal Tau (i.e. number of samples of the beats in the phase space)
# For every beat in time domain the region between the starting point and the corresponding R-peak is consdiered, and the maximum is selected; same for the region between the R-peak and the ending point; the sum is ... |
31156f230482945afcd8a418373e1522729deb3eb348163191aec99efa6b59f8 | Python | 911 | 33 | import os
import tempfile
import pytest
import chroma
import chroma.utility.api as api
from chroma.models.graph_backbone import GraphBackbone
from chroma.utility.model import load_model
KEY_PATH = os.path.dirname(os.path.dirname(chroma.__file__))
KEY_PATH = os.path.join(KEY_PATH, "config.json")
@pytest.mark.skipif... |
d22885b7fc1038478193d4bf15cf86f30770ae98b93431e444066a37c6f71a5b | Python | 911 | 30 | """Script to check if python modules can be imported."""
import random
import string
import sys
import traceback
from importlib.machinery import SourceFileLoader
from importlib.util import module_from_spec, spec_from_loader
if __name__ == "__main__":
files = sys.argv[1:]
has_failure = False
for file in fi... |
32cf547236ab1147581aef695270ed94771038b3b0a7e9e1b22ad512a673a454 | Python | 913 | 33 | """
Combine parquet files into one. This uses with to reduce memory
by only needing to load one files at a time.
"""
import argparse
import session_info
import pandas as pd
from pathlib import Path
def combine_files(output, label):
data_dir = Path(output+"/")
with open("%s.sex_interaction.txt" % label, "a+") a... |
35eb8072ee4caa7a5e3d84438149ddb54b960f049b2460f353e2e9e8e5eb41f2 | Python | 913 | 25 | import sys
sys.path.append('../source')
from matplotlib import pyplot as plt # for visualisation of imagedata
import networkx as nx
import tinaui
plt.ion()
# if only networks will be used load_imagedata can be set False
t2 = tinaui.load_status(folder='../test/sampledata/ocn', load_imagedata=True)
plt.imshow(t2.imgdic... |
ef9ba8e6118133026f9a7145d74ce01e537d495c4d5ba82ee18df18b78c1c787 | Python | 913 | 32 | from typing import TYPE_CHECKING, Any
from langchain_classic._api import create_importer
if TYPE_CHECKING:
from langchain_community.tools import O365CreateDraftMessage
from langchain_community.tools.office365.create_draft_message import (
CreateDraftMessageSchema,
)
# Create a way to dynamically ... |
f34b82bdea3a697b174be843994755269a386ce48244ad4ec6deb60709b5df95 | Python | 913 | 33 | from typing import TYPE_CHECKING, Any
from langchain_classic._api import create_importer
if TYPE_CHECKING:
from langchain_community.document_loaders import (
GoogleApiClient,
GoogleApiYoutubeLoader,
YoutubeLoader,
)
# Create a way to dynamically look up deprecated imports.
# Used to c... |
7c3728d26ad5182a45b0cd17322f2b57cd5e268e864ef7180edc28584f13e433 | Python | 914 | 35 | """DEPRECATED: Kept for backwards compatibility."""
from typing import TYPE_CHECKING, Any
from langchain_classic._api import create_importer
if TYPE_CHECKING:
from langchain_community.utilities import (
Requests,
RequestsWrapper,
TextRequestsWrapper,
)
# Create a way to dynamically l... |
a2cbee16c38b65b5435a564d09f2ae02fa8c2a98eb0d424fcce887f604b45cd1 | Python | 914 | 30 | """Amadeus tools."""
from typing import TYPE_CHECKING, Any
from langchain_classic._api import create_importer
if TYPE_CHECKING:
from langchain_community.tools.amadeus.closest_airport import AmadeusClosestAirport
from langchain_community.tools.amadeus.flight_search import AmadeusFlightSearch
# Create a way t... |
b054f285885e2e8a83a0d5652bdd7f4ab6042da9c25d4505e46b53f99cc6cb5e | Python | 914 | 40 | #!/usr/bin/env python
import os
import sys
from Bio.PDB import PDBParser, PDBIO
from Bio.PDB.Model import Model
available_chain_ids = list("ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz")
parser = PDBParser(QUIET=True)
io = PDBIO()
# load the structure
structure = parser.get_structure("", sys.argv[1])
ent = os... |
d88812f613cf3f6da7e4ccb629536ccbdeaac4723ec8c7826ec147bde43dfdc7 | Python | 914 | 32 | from typing import TYPE_CHECKING, Any
from langchain_classic._api import create_importer
if TYPE_CHECKING:
from langchain_community.tools import ExtractHyperlinksTool
from langchain_community.tools.playwright.extract_hyperlinks import (
ExtractHyperlinksToolInput,
)
# Create a way to dynamically ... |
12838f83998042f332d20f67799d312fe61e6888c084d1923d42db99a7f83e64 | Python | 915 | 36 | # Copyright (c) 2021, David Williams, Reza Sameni
# All rights reserved.
# This source code is licensed under the BSD-style license found in the
# LICENSE file in the root directory of this source tree.
import numpy as np
def RLS(x,d,p,lamb,delta):
x = np.transpose(x)
d = np.transpose(d)
T = len(x)
... |
53b8e8419d58b8867081a76d5ded7316298ecee03fb93a15d09eebf5f77862b4 | Python | 915 | 28 | """**Graphs** provide a natural language interface to graph databases."""
from typing import TYPE_CHECKING, Any
from langchain_classic._api import create_importer
if TYPE_CHECKING:
from langchain_community.graphs.index_creator import GraphIndexCreator
from langchain_community.graphs.networkx_graph import Net... |
65a272feeb52d78dd311714cbcd0e8a3d2aa09ca24adc9fca2da5f7a5989876c | Python | 915 | 44 | from langchain_classic.schema import __all__
EXPECTED_ALL = [
"BaseCache",
"BaseMemory",
"BaseStore",
"AgentFinish",
"AgentAction",
"Document",
"BaseChatMessageHistory",
"BaseDocumentTransformer",
"BaseMessage",
"ChatMessage",
"FunctionMessage",
"HumanMessage",
"AIMe... |
a3ac82321642431e259c09cf8ede9723fdf5880d19fc7f2fe5fb71474f352ba2 | Python | 915 | 32 | import argparse
def main():
parser = argparse.ArgumentParser()
parser.add_argument('--old_listfile', type=str, required=True)
parser.add_argument('--new_listfile', type=str, required=True)
parser.add_argument('--sort', dest='sort', action='store_true')
parser.set_defaults(sort=False)
args = pa... |
a1b395b9a1e736f30f9d2a6ed583758c7ac114cbe854c820b8d5cd4233b7784a | Python | 916 | 24 | from typing import Optional
from typing import Tuple
import numpy as np
from numpy.typing import NDArray
def get_train_val_split(n: int, train_frac: float, seed: Optional[int] = None) -> Tuple[NDArray, NDArray]:
"""
Splits the total number of images into train and test set.
This ensures that in every ses... |
ee05fd97780c96aa8e1b8dcb557c1115bed47a16d5c1e40921002d10c20c2718 | Python | 917 | 29 | from typing import TYPE_CHECKING, Any
from langchain_classic._api import create_importer
if TYPE_CHECKING:
from langchain_community.agent_toolkits.openapi.prompt import (
DESCRIPTION,
OPENAPI_PREFIX,
OPENAPI_SUFFIX,
)
# Create a way to dynamically look up deprecated imports.
# Used to... |
32ccf1476764fa180bd403e8a9055483e72dee5b3e57f1b44ae8979989ba1684 | Python | 921 | 28 | from langchain_core.prompts.prompt import PromptTemplate
from langchain_classic.memory.prompt import (
ENTITY_EXTRACTION_PROMPT,
ENTITY_MEMORY_CONVERSATION_TEMPLATE,
ENTITY_SUMMARIZATION_PROMPT,
KNOWLEDGE_TRIPLE_EXTRACTION_PROMPT,
SUMMARY_PROMPT,
)
DEFAULT_TEMPLATE = """The following is a friendly... |
6b8d2ecca8f4639a5c64216aa0ba85f88b7cb8cf7b98d611bd3e259489f6f682 | Python | 921 | 33 | from typing import TYPE_CHECKING, Any
from langchain_classic._api import create_importer
if TYPE_CHECKING:
from langchain_community.tools.tavily_search.tool import (
TavilyAnswer,
TavilyInput,
TavilySearchResults,
)
# Create a way to dynamically look up deprecated imports.
# Used to c... |
5b2eaa2e148803ad3643c7a56079043162d4f68de9f1f300fe6f63d153f1d266 | Python | 922 | 36 | """Run the two guarded MCP servers the graph factory talks to.
`graph_factory.py` points `SERVERS` at fixed ports; this starts a server on
each. Both verify tokens against the shared keypair (`MCP_DEMO_KEYFILE`), the
same one `langgraph dev` mints with, so a token minted in the factory process
validates here.
MCP... |
d383edbc79ef6d9d33eb9381e32052eb899988360d53d829e3f7873536c49edf | Python | 922 | 28 | #!/usr/bin/env python3
import os
import sys
def run(command, condition, message):
if condition: return 0
print(message, file = sys.stderr)
return os.system(command)
def main():
return sum([
run(
f"twoBitToFa /usr/local/genome/hg38.2bit {sys.argv[1]}/hg38.fa",
os.path.e... |
00da1005a8a4e38d3601d71abd8722f1e75d55c89afd30f6212d9abb182a55af | Python | 923 | 23 | # third party modules
import torch
def processBatch(device, batch, xtras=None):
batch_data = {}
if isinstance(batch, list):
batch_data['train_mask'] = torch.cat([data.train_mask for data in batch]).to(device)
batch_data['test_mask'] = torch.cat([data.test_mask for data in batch]).to(device)
... |
dfbac8915cb0bee50ee7bd21e971e0aff20102ca5896ed49feea015a56f44ca8 | Python | 923 | 32 | #!/usr/bin/env python
import os
import tempfile
import requests
import bz2
from ..constants.constants import HAPMAP3_SNPS_URL
class HapMap3SNPs:
@classmethod
def fromBroad(cls, withoutHeader = False):
return cls(bz2.decompress(requests.get(HAPMAP3_SNPS_URL).content).decode(), withoutHeader = without... |
bcf2f225cdf154e3e258bf87529be9c533387001bda7dbb0e787dcec772d736b | Python | 924 | 29 | import logging
import platform
import socket
# print('__file__={0:<35} | __name__={1:<20} | __package__={2:<20}'.format(__file__,__name__,str(__package__)))
# Defaults
GIT_REPO_NAME="STEP"
LOGGING_LEVEL = logging.INFO
EXTERNAL_LOGGING_LEVEL = logging.ERROR
home_base_dir = "~/git/" + GIT_REPO_NAME
BASE_DATA_DIR = ho... |
9040a6de1b6e556d559304e6da6ec82e839aabe97073645720e989671bc269b8 | Python | 925 | 32 | from pycromanager import JavaBackendAcquisition, multi_d_acquisition_events, start_headless, ZMQRemoteMMCoreJ
import threading
def snap_image():
while True:
core = ZMQRemoteMMCoreJ()
try:
core.snap_image()
image = core.get_tagged_image()
except Exception as e:
... |
215c8d1102b42dc4adbdff494f21dfad8147ec021f040eb237abb6231ae60fb8 | Python | 926 | 28 | import setuptools
with open("README.md", "r") as fh:
long_description = fh.read()
setuptools.setup(
install_requires=[
"numpy>=1.18.5,<=1.19.5",
"mpmath>=1.1.0",
"pandas>=0.24.2,<=1.1.5",
"patsy==0.5.1"
],
name="combat",
version="0.3.2",
author="Abdelkader Behde... |
d312208e4c53a14b4885d93a2c896c8ddb3a8124af5ed195515f510233ec603b | Python | 926 | 25 | import random
from animalai.envs.environment import AnimalAIEnvironment
from animalai.envs.arena_config import ArenaConfig
from gym_unity.envs import UnityToGymWrapper
def load_env(config_file, args, training = True):
return AnimalAIEnvironment(
file_name = 'env/AnimalAI',
base_port = 5005 + rando... |
dafa7aeb43ac068a63c76b72d8f20bb6b74f12194a2c1134442c94c149946c98 | Python | 926 | 27 | # -- coding: utf-8 --
# @Time : 2023/3/6 19:55
# @Author : Biao Zhang
# @Email : littlebiao@outlook.com
# @File : get_human_acronym_color.py
# @Description: This file is used to ...
import pandas as pd
if __name__ == '__main__':
human_structure_df = pd.read_csv('./human_query.csv')
name_list = human_structure... |
e698273b576c10149e32aeac16f39063f995d3e1aa96f2fc561e86b643a081e3 | Python | 926 | 32 | from typing import TYPE_CHECKING, Any
from langchain_classic._api import create_importer
if TYPE_CHECKING:
from langchain_community.utils.math import (
cosine_similarity,
cosine_similarity_top_k,
)
# Create a way to dynamically look up deprecated imports.
# Used to consolidate logic for raisi... |
3c9f3664b2c2df1b8655852ebb72c66c29ad823ddd10b9426139ac401317eecd | Python | 927 | 22 | from openbabel.pybel import readfile,Outputfile
import os
def MolFormatConversion(input_file,output_file,input_format="mol2",output_format="smi"):
molecules = readfile(input_format,input_file)
output_file_writer = Outputfile(output_format,output_file, overwrite=True)
for i,molecule in enumerate(molec... |
d10d379179d4cc8eefef9d4d6055fb2d500525a7974ba80f97090f4342a90b5e | Python | 927 | 28 | from models.lstm import LSTMParams, get_model
from utils.io import load_data_as_tensorflow_datasets
import tensorflow as tf
TRAIN_SAMPLES = 64
for i in range(4):
model = get_model()
model_params = LSTMParams(f"DUMMY_{i}")
train_spectra = tf.random.normal((TRAIN_SAMPLES, 41, 1))
train_oxy = tf.random.n... |
e4aba52170ea78648c4f60466438e1a34f186761f1f27a2679d6a73b4ba3123b | Python | 930 | 32 | """
Usage:
python3 scripts/validate_jsons.py input_json/test3/set3_rnaseq.json
input_json/test4/test_batchac_rnaseq.json
"""
import argparse
import json
def main():
parser = argparse.ArgumentParser(description="script to compare and validate json files")
parser.add_argument("infile1", type=str, he... |
685e4ac7526babb61779ce6c97cefbe857e7c26aea1acbcd1365c90707f89d35 | Python | 932 | 30 | import numpy as np
import pandas as pd
import pytest
from imagingplus import TwoPhotonImaging
import imagingplus as pli
from imagingplus.processing import anndata
from conftest import anndata_trial_data, existing_trialobj_alloptical_fixture
def test_AnnotatedData(existing_trialobj_alloptical_fixture):
aotrial =... |
7c788052034f8a4c631818c392ba28d12d1229fc42e285aebcfc47e6376f6580 | Python | 932 | 35 | from langchain_classic.callbacks.manager import __all__
EXPECTED_ALL = [
"BaseRunManager",
"RunManager",
"ParentRunManager",
"AsyncRunManager",
"AsyncParentRunManager",
"CallbackManagerForLLMRun",
"AsyncCallbackManagerForLLMRun",
"CallbackManagerForChainRun",
"AsyncCallbackManagerFo... |
18414027976e2918ff0d8202776de9c8b5a1d0f59c0fb6ddb426c844a5edf308 | Python | 933 | 29 | from typing import TYPE_CHECKING, Any
from langchain_classic._api import create_importer
if TYPE_CHECKING:
from langchain_community.chains.graph_qa.falkordb import (
INTERMEDIATE_STEPS_KEY,
FalkorDBQAChain,
extract_cypher,
)
# Create a way to dynamically look up deprecated imports.
# ... |
bc583ca5aa4fc74d6147627bfcb5ae81765c14c1fb19d181dd002f9f7e5717d7 | Python | 933 | 23 | from networks.unet_3D import unet_3D
from networks.vnet import VNet
from networks.VoxResNet import VoxResNet
from networks.attention_unet import Attention_UNet
from networks.nnunet import initialize_network
def net_factory_3d(net_type="unet_3D", in_chns=1, class_num=2):
if net_type == "unet_3D":
net = une... |
cc96f57bfb0014ccf6ec7a85e6fa2d89a5f52ea1bb6f62b2390a8489882dbd64 | Python | 933 | 45 | import torch
import torch.nn as nn
import torch.nn.functional as F
from bindsnet.conversion import ann_to_snn
class FullyConnectedNetwork(nn.Module):
# language=rst
"""
Simply fully-connected network implemented in PyTorch.
"""
def __init__(self):
super(FullyConnectedNetwork, self).__ini... |
67d37bd87e1d563db433d70f2b6d53ef2f4ab2d12b4e77e813619868a1cd0927 | Python | 934 | 27 | from torch import nn
class Shifter(nn.Module):
"""
Abstract base class for a shifter. It's strongly adviced that the regularizer and initialize methods are implemented by the inheriting class.
"""
def __repr__(self):
s = super().__repr__()
s += " [{} regularizers: ".format(self.__clas... |
7a870ad85ee859889806ba12750225282788d88988d3508168aaf1cd20323c65 | Python | 934 | 30 | import numpy as np
def shape_data(data):
timestamps = []
activeneurons = []
neuron = data[:,1]
neuron_list = np.unique(data[:,1])
for k in range(len(neuron_list)):
index = np.where(neuron == neuron_list [k])[0]
if len(index) >= 2 : # C... |
1151d2a396d571e0bdb9b3c8ae072552649cf112202ce4baa7830487cc97b89b | Python | 935 | 35 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Mon Dec 19 17:15:11 2022
@author: biener
"""
import torch
import sys
import numpy as np
from NN_Rslt_Anal import NN_Rslt_Anal as Ana
Ana_O = Ana()
for ii in range(1,len(sys.argv)):
curVar = sys.argv[ii]
if '.inp' in curVar:
TS_fName = cur... |
22b015b711c5c39e53965bd3edc1bd27e6408120aeb54cc293ab391e6f51f4d9 | Python | 935 | 31 | """Contains tests for the Conv2D-layer LRP implementations"""
import numpy as np
from tensorflow.keras.initializers import Constant
from tensorflow.keras import Model
from tensorflow.keras.layers import BatchNormalization, Input
from explainability.layers import BatchNormalizationLRP
def test_batchnormalization_lr... |
2a08d9e5aab72d00566f8d0c53a2f0fdac8b801f4c6a9fdbfadf13ac506338e6 | Python | 936 | 34 | """DataForSeo API Toolkit."""
from typing import TYPE_CHECKING, Any
from langchain_classic._api import create_importer
if TYPE_CHECKING:
from langchain_community.tools.dataforseo_api_search.tool import (
DataForSeoAPISearchResults,
DataForSeoAPISearchRun,
)
# Create a way to dynamically look... |
41a79392903ae3a27790838f43c5ce0ca965f6a9a8bd2c7ff52519adc64e930c | Python | 936 | 24 | # write output file
def dump(output_file_name, time, number_of_atoms, dimensions, configurations):
output_file = open(output_file_name, 'a')
output_file.write("ITEM: TIMESTEP\n")
output_file.write(str(time) + "\n")
output_file.write("ITEM: NUMBER OF ATOMS\n")
output_file.write(str(number_of_atoms... |
fb5c4805ddc817bf9109c7933644564cb43754a471994a5c71ed9fd642688b31 | Python | 936 | 39 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Mon Apr 24 00:48:43 2023
@author: weihan
"""
from torch import nn
class DeepNeuralNetworks(nn.Module):
def __init__(self, col, D):
super().__init__()
self.encoder = nn.Sequential(
nn.Linear(col, 2048),
nn.Tanh()... |
05ed0b479846ef23d2c810ce3de8bbe4fc38f6740c9004e63665bb3dd7da79b6 | Python | 937 | 32 | from typing import TYPE_CHECKING, Any
from langchain_classic._api import create_importer
if TYPE_CHECKING:
from langchain_community.document_transformers import OpenAIMetadataTagger
from langchain_community.document_transformers.openai_functions import (
create_metadata_tagger,
)
# Create a way t... |
60a549e9ef859b32763622a8ae477c70dabb7c687bc9e874053217450722cf3c | Python | 937 | 27 | import matplotlib
from Articles.Sequential_Learning_Striatum.Figures.cfg_color import colors, cm
matplotlib.rcParams['font.size'] = 8
matplotlib.rcParams['text.usetex'] = False
matplotlib.rcParams['svg.fonttype'] = 'none'
matplotlib.rcParams['lines.linewidth'] = 0.5
matplotlib.rcParams['axes.linewidth'] = 1.
# set ti... |
53c05e3e7b050351a7f5ba1d915b6df4af714f4491c9683b8e5782dcd9ab5253 | Python | 938 | 35 | from qtpy.QtWidgets import QDialog, QDialogButtonBox, QVBoxLayout, QLabel, QPushButton
from qtpy.QtCore import Qt
class DemoDialog(QDialog):
def __init__(self, parent=None):
super().__init__(parent)
self.case = 0
self.setWindowTitle("Choose the image type")
b1 = QPushButton("2D")
... |
7309dd4f2ac1167c118502168b985c548141e024ffec63ad2579744f1b177578 | Python | 938 | 30 | import torch
from torch import Tensor
def get_angle(v1: Tensor, v2: Tensor) -> Tensor:
return torch.atan2(
torch.cross(v1, v2, dim=1).norm(p=2, dim=1), (v1 * v2).sum(dim=1))
def edge_pair_features(
edge_index: Tensor,
pos: Tensor,
normal: Tensor,
faces: Optional[Tensor] = N... |
4eb75ac1358eb8ac8cacb96554df59b898ceaefbb4d8fd09743fbc5cbe7e469d | Python | 939 | 27 | import parmed
import tempfile
import os
import shutil
# Get the paths to the gaff.dat and leaprc files:
leaprc_path = os.path.join(os.getenv("CONDA_PREFIX"), 'dat', 'leap', 'cmd', 'leaprc.gaff')
gaffdat_path = os.path.join(os.getenv("CONDA_PREFIX"), 'dat', 'leap', 'parm', 'gaff.dat')
# Make a temporary directory (oth... |
fa7ae26bacd4d290b8df11d3b50cecd4b52d58fecea80a83273b6398dace3b06 | Python | 939 | 25 | import pandas as pd
import os
from tqdm import tqdm
df_artemis = pd.read_csv(os.path.join('./data/artemis_index', 'artemis_dataset_release_v0.csv'))
for split in ['train','val','test']:
print('Processing', split, 'set...')
df = pd.read_json(os.path.join('./data/artemis_index', split + '_index.json'))
df_0... |
54071f8939a0aea8f48f0346fef052842f8039c0e4b17baf68ae3dd3ba4ffa5d | Python | 941 | 30 | #!/usr/bin/env python
from .get_atom_kdtree import getAtomKDTree
def pruneStructure(structure, target_chains, threshold=30.0, size_limit=45000):
target_atoms = []
prune_chains = []
total_size = 0
for chain in structure.get_chains():
for residue in chain:
total_size += len(residue)
... |
a8b11a9738e58c563e14190685753df36bfcbfd51fd2da4310263e8f8f84185d | Python | 941 | 26 | from django import forms
from django.forms import ModelForm
from .models import Analysis
class PsthAnalysisForm(ModelForm):
trial_type = forms.CharField(
max_length=15,
widget=forms.Select(choices=Analysis.TRIAL_TYPES),
required=True,
)
unit_type = forms.CharField(
max_len... |
6fd8e13b75bdc8b382612b1f39d0fe8b75ddf2dd9edd4cb2f0e4a2dced4aa9cc | Python | 943 | 32 | from typing import TYPE_CHECKING, Any
from langchain_classic._api import create_importer
if TYPE_CHECKING:
from langchain_community.tools import AIPluginTool
from langchain_community.tools.plugin import AIPlugin, AIPluginToolSchema, ApiConfig
# Create a way to dynamically look up deprecated imports.
# Used t... |
bfb2e2e1a84f7bec4df599a12ca560ee0cff3d006b7c0a756eee462924cfeb86 | Python | 943 | 26 | from langchain_core.agents import AgentAction
from langchain_core.messages import AIMessage, BaseMessage, HumanMessage
def format_log_to_messages(
intermediate_steps: list[tuple[AgentAction, str]],
template_tool_response: str = "{observation}",
) -> list[BaseMessage]:
"""Construct the scratchpad that lets... |
5abe627902e4aeac2fd0fcb96d4fa6dbfb11d8f593ebe1966a65dd4588f352db | Python | 945 | 33 | import os
import sys
import re
import types
import itertools
import matplotlib.pyplot as plt
import numpy
import numpy.ma
import Stats
import Histogram
from cpgReport import *
from cgatReport.Tracker import *
from cgatReport.odict import OrderedDict as odict
############################################################... |
8f55eca649244b02f824b5d9001c52babd0b9c0475cab9fd137038ba7e791209 | Python | 945 | 30 | """Test Base Schema of documents."""
from collections.abc import Iterator
from langchain_core.document_loaders import BaseBlobParser, Blob
from langchain_core.documents import Document
from typing_extensions import override
def test_base_blob_parser() -> None:
"""Verify that the eager method is hooked up to the... |
fdf1ee9ffdfdaa6a466e55741c898c947d7cca3efe706950bcfcd7f85c1d6661 | Python | 945 | 30 | from LSTM import preprocess, train, predict, evaluate
import os
from utils import *
setting = {
'train_size': 0.8,
'epochs': 100,
'input_size': 60,
'batch_size': 32,
'pre_len': 1,
'fileName': "o1_i1800s_w10_s1_fmean",
'model_name': 'lstm',
'ch... |
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