sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
d50e2218b285202e3721342558cd31eaab7b849534abd44cbccb97c2630d2b9f | Python | 833 | 28 | from typing import TYPE_CHECKING, Any
from langchain_classic._api import create_importer
if TYPE_CHECKING:
from langchain_community.tools import GetElementsTool
from langchain_community.tools.playwright.get_elements import GetElementsToolInput
# Create a way to dynamically look up deprecated imports.
# Used ... |
d5b5232917fee18b7d82892999f72d33297b6e704b68afe0f3555452dc535625 | Python | 833 | 28 | from scipy.io import loadmat
import torch
import numpy as np
def data_generator(dataset):
if dataset == "JSB":
print('loading JSB data...')
data = loadmat('./mdata/JSB_Chorales.mat')
elif dataset == "Muse":
print('loading Muse data...')
data = loadmat('./mdata/MuseData.mat')
... |
567eca1d8b41a419842a57b6781f0b15e67da2ba361b943567ac2f0f02bca89d | Python | 834 | 31 | import sys
def all2lower(ifn):
idx = ifn.rfind(".")
ofn = ifn[:idx] + ".lower.txt"
with open(ifn, "r") as fr, open(ofn, "w") as fw:
for i, line in enumerate(fr):
nline = " ".join([w.lower() for w in line.split(" ")])
fw.write(nline)
def all2upper(ifn):
idx = ifn.rfin... |
cb5b090d926d5687256b78809bfdf12e52997b4be0a4d4ba70fd96c48893cb62 | Python | 835 | 33 | import torch
from bindsnet.datasets.collate import time_aware_collate
class DataLoader(torch.utils.data.DataLoader):
def __init__(
self,
dataset,
batch_size=1,
shuffle=False,
sampler=None,
batch_sampler=None,
num_workers=0,
collate_fn=time_aware_col... |
480810429dc3db8f4434128e602be68cd11b554bcbe17c12da454fd4566b7c39 | Python | 836 | 19 | # These are all the procedures that appear in the annotator.
from .delete_annotations import delete_annotations
from .insert_local_max import insert_local_max
from .insert_annotation import insert_annotation
from .worldline_utilities import randomly_color_worldlines, renumber_worldlines
from .navigation import jump_to... |
dcef991263b0d3ef33bdfd5a278e3a20e1802f1404b3e3df05be1e99e172655a | Python | 836 | 29 | import rdkit.Chem as Chem
import numpy as np
from collections import defaultdict
'''
This script looks at how many bond changes actually occur in forward reactions (in this dataset)
'''
def process_file(fpath):
counter = defaultdict(int)
with open(fpath, 'r') as fid_in, open(fpath + '.proc', 'w') as fid_out:... |
ce7c0a77c9c035fcefe4eb76247d7845c111ca5caa4e7c60dc68e9cab7d6caf6 | Python | 837 | 24 | import os
import shutil
import pathlib
def move_files(source_directory, target_directory):
files_list = os.listdir(source_directory)
for filename in files_list:
shutil.move(os.path.join(source_directory, filename), target_directory)
return
if '__main__' == __name__:
working_directory = ... |
968c534cc3ce344033d881a1830b457df807ecca6c130973d7894df70831ec1e | Python | 838 | 24 | import os
from django.db import models
from django.conf import settings
def get_upload_path(instance, filename):
return '/'.join(filter(None, ('clustering/files', filename)))
class Cluster(models.Model):
DATA_TYPES = [
('pca', 'PCA'),
]
ALGORITHM_TYPES = [
('gmm', 'Gaussian Mi... |
39fe0da6821ada24a7df64cead328f9112fdbaba013ff6e17fc5fd1b4440c842 | Python | 840 | 28 | from typing import TYPE_CHECKING, Any
from langchain_classic._api import create_importer
if TYPE_CHECKING:
from langchain_community.document_loaders import GitHubIssuesLoader
from langchain_community.document_loaders.github import BaseGitHubLoader
# Create a way to dynamically look up deprecated imports.
# U... |
f5248ae40cf7de6af6cdb2099d9323512206bb5ca5fcb97d6091dfaa4282b8f1 | Python | 840 | 33 | from .statistics import \
kolmogorov_smirnov_analysis, \
mean_difference_analysis, \
feature_correlation
from .relative_entropy import \
relative_entropy_analysis
from .statespecific import \
ssi_feature_analysis, \
ssi_ensemble_analysis, \
cossi_featens_analysis
from .visualization impor... |
2e52d2ac17293930eff04f559a177dc8beb6c39c377992f23ef573e97b5c6bd6 | Python | 841 | 30 | from typing import TYPE_CHECKING, Any
from langchain_classic._api import create_importer
if TYPE_CHECKING:
from langchain_community.vectorstores import (
AlibabaCloudOpenSearch,
AlibabaCloudOpenSearchSettings,
)
# Create a way to dynamically look up deprecated imports.
# Used to consolidate l... |
5b31efcf9cef2d2a558cf43d019fef314e853fa495ab8485b7b6652f4ebd2ba9 | Python | 841 | 30 | from typing import TYPE_CHECKING, Any
from langchain_classic._api import create_importer
if TYPE_CHECKING:
from langchain_community.agent_toolkits.openapi.spec import (
ReducedOpenAPISpec,
reduce_openapi_spec,
)
# Create a way to dynamically look up deprecated imports.
# Used to consolidate l... |
908b67e389564bfda2e68bf994a0ae42497c56d1730f9d6064a63c201b06a45f | Python | 841 | 30 | from typing import TYPE_CHECKING, Any
from langchain_classic._api import create_importer
if TYPE_CHECKING:
from langchain_community.tools.amadeus.flight_search import (
AmadeusFlightSearch,
FlightSearchSchema,
)
# Create a way to dynamically look up deprecated imports.
# Used to consolidate l... |
e1365bebd8cac6494187a99da1a365017cea6b6f8f176ce146b859720fdd1490 | Python | 841 | 30 | from typing import TYPE_CHECKING, Any
from langchain_classic._api import create_importer
if TYPE_CHECKING:
from langchain_community.tools.multion.close_session import (
CloseSessionSchema,
MultionCloseSession,
)
# Create a way to dynamically look up deprecated imports.
# Used to consolidate l... |
e5bd931c22b5d0b0cf38757f363b0bb32ee466bb1489cfc600a85942dcb7c82e | Python | 841 | 28 | from typing import TYPE_CHECKING, Any
from langchain_classic._api import create_importer
if TYPE_CHECKING:
from langchain_community.retrievers import TavilySearchAPIRetriever
from langchain_community.retrievers.tavily_search_api import SearchDepth
# Create a way to dynamically look up deprecated imports.
# U... |
1d5d67a00e68e9fac6152b1188e56ae840cf61218f6a79d2f3b757edb5817e8c | Python | 842 | 46 | import pandas as pd
import numpy as np
import random
data = pd.read_csv('data.csv')
signal = data['num'].values
seq = np.array(signal)
c = (len(seq)//(96))
# print(c)
seq = seq[:(len(seq)//(96)) * (96)]
seq = seq.reshape((-1,(96)))
e = 0
t = 0
for i in range(seq.shape[1]):
col = seq[:,i]
#... |
4bde12e61fa33ee2813d7cf55abbcf8dd255c60ab3290a952a92b4d3499becb0 | Python | 842 | 34 | import time
from dliplib.reconstructors import learnedpd_dip_reconstructor, diptv_reconstructor
from dliplib.utils.helper import load_standard_dataset, set_use_latex
set_use_latex()
# load data
dataset = load_standard_dataset('ellipses')
test_data = dataset.get_data_pairs('test', 100)
obs, gt = test_data[0]
data_s... |
f3e64e1f63085a97cc8873821665f67190a84f7fbf44dacc079dd339c46d9b8d | Python | 842 | 30 | """Utility functions for parsing an OpenAPI spec. Kept for backwards compat."""
from typing import TYPE_CHECKING, Any
from langchain_classic._api import create_importer
if TYPE_CHECKING:
from langchain_community.tools import OpenAPISpec
from langchain_community.utilities.openapi import HTTPVerb
# Create a w... |
513d86e3e3653561e359ed8a7875d7342ffcabad5e474fbf7a971dd44c54a876 | Python | 843 | 28 | import numpy as np
from voxcell import VoxelData
from scipy.ndimage import generate_binary_structure, label
import sys
input_nrrd = sys.argv[1]
output_xyz = sys.argv[2]
vd = VoxelData.load_nrrd(input_nrrd)
ntot = np.sum(vd.raw)
# get connected components
ball = generate_binary_structure(3, 3)
cc = label(vd.raw, ball... |
152275014c663a2f107c26f557404b36105c11ca9037f15e7d5af2fa2cefe159 | Python | 844 | 26 | #!/usr/bin/env python
"""
Generate ffxml files for ligands in a multi-mole mol2.
"""
mol2_filename = 'Imatinib-epik-charged.mol2'
ffxml_filename = 'Imatinib-epik-charged.ffxml'
# Read mol2 file containing protonation states and extract canonical isomeric SMILES from this.
print("Reading molecules")
from openeye impo... |
1561c60bdfe6a9acb5265b3e625ff8f15e64dde784be9012f9bf7f7a5d2b731c | Python | 844 | 31 | from typing import Any
from langchain_core.documents import Document
from langchain_core.retrievers import BaseRetriever
from typing_extensions import override
class SequentialRetriever(BaseRetriever):
"""Test util that returns a sequence of documents."""
sequential_responses: list[list[Document]]
respo... |
559d5109b0a32430b07464c34403f7fa44a4b8cfe53ee3e499e7e82afee07245 | Python | 844 | 11 | """Per-page layout scan of a PDF: body words, float captions, and the share of the page height covered by images/tables.
Usage: python src/page_scan.py paper/main_2col.pdf [first last]"""
import fitz, re, sys
sys.stdout.reconfigure(encoding="utf-8")
d = fitz.open(sys.argv[1])
a, b = (int(sys.argv[2]), int(sys.argv... |
5fc1e16ea79d22527ae2c24491234b4f1094d5b8ea9cfbc993fd1d7e297dd532 | Python | 844 | 28 | from typing import TYPE_CHECKING, Any
from langchain_classic._api import create_importer
if TYPE_CHECKING:
from langchain_community.tools import ListDirectoryTool
from langchain_community.tools.file_management.list_dir import DirectoryListingInput
# Create a way to dynamically look up deprecated imports.
# U... |
a2316a2643a925880320ec74376ec0f57d723aed936c3b3535cb04d46b69c32d | Python | 845 | 28 | from langchain_classic.memory import chat_message_histories
EXPECTED_ALL = [
"AstraDBChatMessageHistory",
"ChatMessageHistory",
"CassandraChatMessageHistory",
"CosmosDBChatMessageHistory",
"DynamoDBChatMessageHistory",
"ElasticsearchChatMessageHistory",
"FileChatMessageHistory",
"Firest... |
a92324d90e1919f0985f518281891837ed33dc2edb9251d383da55baa6d0c0a5 | Python | 845 | 36 | import numpy as np
import os
import sys
dtype = np.dtype(np.uint32)
fpath = "/home/ubuntu/data/rx_chan_11.txt"
nb_samples = int(os.path.getsize(fpath)/dtype.itemsize)
data = np.fromfile(fpath, dtype=dtype, count=nb_samples)
if len(sys.argv) > 1:
if sys.argv[1] == "all":
for i in r... |
383c55de2b82cecede6fc822e0f0d19ec0b6fa8f070000a735111ed1d7d51d86 | Python | 846 | 11 | PREFIX = """You are an agent designed to answer questions about sets of documents.
You have access to tools for interacting with the documents, and the inputs to the tools are questions.
Sometimes, you will be asked to provide sources for your questions, in which case you should use the appropriate tool to do so.
If th... |
e1565360bea1bcb38c78c9e7bdade2e5748f917b07ec17f953b0aaa8ba6e06dd | Python | 846 | 28 | from typing import TYPE_CHECKING, Any
from langchain_classic._api import create_importer
if TYPE_CHECKING:
from langchain_community.document_loaders import DataFrameLoader
from langchain_community.document_loaders.dataframe import BaseDataFrameLoader
# Create a way to dynamically look up deprecated imports.
... |
e8caabe2ed9a8c0b8d200af651d9b631192b05c885cefed4660e75ab89ea325f | Python | 846 | 34 | import glob
import os
import torch
from torch.utils.ffi import create_extension
this_file = os.path.dirname(__file__)
sources = ['src/batchnormp.c']
headers = ['src/batchnormp.h']
defines = []
with_cuda = False
abs_path = os.path.dirname(os.path.realpath(__file__))
extra_objects = [os.path.join(abs_path, 'dense/batc... |
0acad52295e823e7503ce51ea68e71fecdc4db6553e1ec20ee6021c44a63f37c | Python | 847 | 30 | from typing import TYPE_CHECKING, Any
from langchain_classic._api import create_importer
if TYPE_CHECKING:
from langchain_community.utilities.anthropic import (
get_num_tokens_anthropic,
get_token_ids_anthropic,
)
# Create a way to dynamically look up deprecated imports.
# Used to consolidate... |
499fa3ead3b10f0afbcb4fc845d77c22dd2f68e95e576404d61cc9c0c4256bed | Python | 848 | 32 | """Tavily Search API toolkit."""
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,
TavilySearchResults,
)
# Create a way to dynamically look up deprecated imports... |
56eb597e86b8bbfc005cffc1c9df3537bdfb59c2d41d5ee9cd5e994ea641d245 | Python | 848 | 23 | import importlib
import pandas as pd
dfs = list()
for dataset in ['chbp', 'lemon', 'tuab', 'camcan']:
config_map = {'chbp': "config_chbp_eeg",
'lemon': "config_lemon_eeg",
'tuab': "config_tuab",
'camcan': "config_camcan_meg"}
if dataset not in config_map:
... |
7a9ddfaf1a7dd10e7297b6e6dfe9fd584b6aacf775918ef3eaf381b85c8ec119 | Python | 848 | 25 | from voxcell import VoxelData, RegionMap, OrientationField
import numpy as np
# load region annotations
annot = VoxelData.load_nrrd('brain_regions.nrrd')
rmap = RegionMap.load_json('hierarchy.json')
# find voxels in region S1HL
ids = list(rmap.find('S1HL', 'acronym', with_descendants=True))
mask = np.isin(annot.raw, ... |
a74e858b525ecad67aa43d8de7332e7129f201b42aabf6c44b55fbcb79a9465a | Python | 848 | 31 | # -*- coding: utf-8 -*-
"""
Created on Thu May 5 19:58:48 2022
@author: ywjin0707
"""
import tensorflow as tf
def pearson_cor(targets, logits):
mx = tf.reduce_mean(logits)
my = tf.reduce_mean(targets)
xm, ym = logits - mx, targets - my
r_num = tf.reduce_sum(input_tensor=tf.multiply(xm, ym))
r_d... |
0a562be40f8597bba72cb5a1d952af4756b2f6a8e4afa1a56b5fd0c9bc6de1da | Python | 849 | 28 | from typing import TYPE_CHECKING, Any
from langchain_classic._api import create_importer
if TYPE_CHECKING:
from langchain_community.tools import SlackScheduleMessage
from langchain_community.tools.slack.schedule_message import ScheduleMessageSchema
# Create a way to dynamically look up deprecated imports.
# ... |
1023141a22c526bd5b7c2096d9646fdc111e22baf6b7cbe6f45b479663fc7e92 | Python | 849 | 26 | """Tests for the string run evaluator."""
from unittest.mock import MagicMock
from langchain_classic.evaluation import criteria
from langchain_classic.smith.evaluation.string_run_evaluator import (
ChainStringRunMapper,
StringRunEvaluatorChain,
)
from tests.unit_tests.llms import fake_llm
def test_evaluate_... |
7ef8b976999f7970e37a4cf6b8ee99d5d6ba230f542828e1bed49b392ee49e29 | Python | 850 | 27 | from setuptools import setup, find_packages
try:
with open("README.md", "r", encoding="utf-8") as fp:
long_description = "\n" + fp.read()
except FileNotFoundError:
long_description = "TensorFlow implementation of DONE (Direct ONE-shot learning with Hebbian weight imprinting)"
setup(
name="tfdone",
... |
8d1841eeac0bf2a4480a518575d2552397601e45d43bdf73b0f10fc5e1719ad9 | Python | 850 | 30 | from typing import TYPE_CHECKING, Any
from langchain_classic._api import create_importer
if TYPE_CHECKING:
from langchain_community.tools.multion.update_session import (
MultionUpdateSession,
UpdateSessionSchema,
)
# Create a way to dynamically look up deprecated imports.
# Used to consolidat... |
b2414448413465664afbe5e8c1504cf52e66bd0f1d0c64d680a522aefc15623e | Python | 850 | 30 | from typing import TYPE_CHECKING, Any
from langchain_classic._api import create_importer
if TYPE_CHECKING:
from langchain_community.tools.multion.create_session import (
CreateSessionSchema,
MultionCreateSession,
)
# Create a way to dynamically look up deprecated imports.
# Used to consolidat... |
c17d6ff343a3014597a801acffbc4f1e1cdffa63cf7ee8f95843ec2bad3bc8e5 | Python | 851 | 23 | """tffp URL Configuration
The `urlpatterns` list routes URLs to views. For more information please see:
https://docs.djangoproject.com/en/1.11/topics/http/urls/
Examples:
Function views
1. Add an import: from my_app import views
2. Add a URL to urlpatterns: url(r'^$', views.home, name='home')
Class-based... |
f0c65c4b1d72213a14876e7c095da7fee7bc14adbdc0145d316fb0e9c5813494 | Python | 851 | 27 | from pathlib import Path
from langchain_core._api import path
HERE = Path(__file__).parent
ROOT = HERE.parent.parent.parent
def test_as_import_path() -> None:
"""Test that the path is converted to a LangChain import path."""
# Verify that default paths are correct
# if editable install, check director... |
6e18e2aacb20779be4f73f9b7e66be17c5655865ea9afe36be68a387e612fbb2 | Python | 852 | 24 | from NeuronModel.NeuronClass import neuronClass
import numpy as np
import matplotlib.pyplot as plt
hsv = plt.get_cmap('hsv')
def colors(n):
return hsv(np.linspace(0., 1.0, len(n)+1))
class poissonPop(neuronClass):
parameters = {'save': True, 'spike': True, 'b': 1., 'N': 1}
def __init__(self, **kwargs):
... |
ebba4217b7eecacd817a873dc7e25ea92f7b8fa3b934226d5f422ef951ce3ccb | Python | 852 | 22 | from setuptools import setup, find_packages
with open("README.md", "r") as fh:
long_description = fh.read()
with open("requirements.txt", "r") as f:
requirements = f.read().splitlines()
requirements = [l for l in requirements if not l.startswith('#')]
setup(
name="DN_network_analysis",
version="0... |
f7548db8847a78a9fa09cc67cb160fd562b0bc5cb5fac15d429536b144c2d5b1 | Python | 853 | 30 | from typing import TYPE_CHECKING, Any
from langchain_classic._api import create_importer
if TYPE_CHECKING:
from langchain_community.chat_models.volcengine_maas import (
VolcEngineMaasChat,
convert_dict_to_message,
)
# Create a way to dynamically look up deprecated imports.
# Used to consolida... |
17800fdae7982abadabda435bf54657b04c883f48f95fc1dbfbc396c1c9a2230 | Python | 854 | 28 | from typing import TYPE_CHECKING, Any
from langchain_classic._api import create_importer
if TYPE_CHECKING:
from langchain_community.document_loaders import FacebookChatLoader
from langchain_community.document_loaders.facebook_chat import concatenate_rows
# Create a way to dynamically look up deprecated impor... |
c51eab3206240e7257a7a3f210d06b63314bee540b81cc02fca7e2ffe72795b7 | Python | 854 | 28 | from typing import TYPE_CHECKING, Any
from langchain_classic._api import create_importer
if TYPE_CHECKING:
from langchain_community.document_loaders import WhatsAppChatLoader
from langchain_community.document_loaders.whatsapp_chat import concatenate_rows
# Create a way to dynamically look up deprecated impor... |
7f90602768859092b3f8cc5278c7a343bebc8cb028ca6d1114b60d77407a7bb0 | Python | 855 | 28 | from typing import TYPE_CHECKING, Any
from langchain_classic._api import create_importer
if TYPE_CHECKING:
from langchain_community.tools import SteamshipImageGenerationTool
from langchain_community.tools.steamship_image_generation.tool import ModelName
# Create a way to dynamically look up deprecated import... |
b66de7ce869a686e3a90babc0a371788c540adc01fd8a764b9fcd4f5579616ca | Python | 856 | 28 | from setuptools import setup, find_packages
classifiers = [
'Development Status :: 5 - Production/Stable',
'Operating System :: Microsoft :: Windows :: Windows 10',
'Operating System :: POSIX :: Linux',
'License :: OSI Approved :: MIT License',
'Programming Language :: Python :: 3'
]
setup(
name='Spati... |
bcfc1a717655bc799e2b99be998248fd1a2e3dccd51ddf6df52079962dd1c0e2 | Python | 856 | 28 | from setuptools import setup, find_packages
classifiers = [
'Development Status :: 5 - Production/Stable',
'Operating System :: Microsoft :: Windows :: Windows 10',
'Operating System :: POSIX :: Linux',
'License :: OSI Approved :: MIT License',
'Programming Language :: Python :: 3'
]
setup(
name='Spati... |
fba3460eaee9c267512d1a953f3c81487605cebb574651bc9a07003821e613fa | Python | 856 | 30 | from typing import TYPE_CHECKING, Any
from langchain_classic._api import create_importer
if TYPE_CHECKING:
from langchain_community.document_loaders.parsers.grobid import (
GrobidParser,
ServerUnavailableException,
)
# Create a way to dynamically look up deprecated imports.
# Used to consolid... |
98c997fa229e75d220d1f9b11e92bedfcfa99352a374253dbfc8f7d38c2b9851 | Python | 857 | 33 | from typing import TYPE_CHECKING, Any
from langchain_classic._api import create_importer
if TYPE_CHECKING:
from langchain_community.tools import (
InfoPowerBITool,
ListPowerBITool,
QueryPowerBITool,
)
# Create a way to dynamically look up deprecated imports.
# Used to consolidate logi... |
cec517401de4a8b9da9549097b7114b80c0e81ee1d0b1cbb5e0dadf36cc482b1 | Python | 857 | 21 | from django.db import models
class Analysis(models.Model):
TRIAL_TYPES = [
#('individual', 'Individual'),
('sequence', 'Sequence'),
]
UNIT_TYPES = [
#('1', 'Multi Units'),
('2', 'Single Units'),
]
trial_type = models.CharField(max_length=15, choices=TRIAL_TYP... |
ff65120e2264b7c6fc0d1c89bc46a81b18f62c4b1076935800adf47cd92da767 | Python | 857 | 22 | from EPI_MRI.EPIMRIDistortionCorrection import *
from optimization.LBFGS import *
import torch
device = 'cuda:0' if torch.cuda.is_available() else 'cpu'
# load the image and domain information
# change this function call to be the filepath for your data
data = DataObject('../data/156334_v.nii.gz', '../data/156334_-v.... |
459c255890354868e84c0d984b855618ff08439da6e20d77396552421df4b7e9 | Python | 858 | 35 | from enum import Enum
import pytest
from langchain_core.exceptions import OutputParserException
from langchain_classic.output_parsers.enum import EnumOutputParser
class Colors(Enum):
RED = "red"
GREEN = "green"
BLUE = "blue"
def test_enum_output_parser_parse() -> None:
parser = EnumOutputParser(en... |
6912b8a99fb4373964d67d6303e6d9e3fe18692f693724d2828df333fc9153ed | Python | 859 | 30 | from typing import TYPE_CHECKING, Any
from langchain_classic._api import create_importer
if TYPE_CHECKING:
from langchain_community.chat_models.anthropic import (
ChatAnthropic,
convert_messages_to_prompt_anthropic,
)
# Create a way to dynamically look up deprecated imports.
# Used to consoli... |
8ae6d7be99636638c69979fe73d7b32b7ea3c7e51b17171c5eda183afbb5c24f | Python | 859 | 29 | """Test the initialize module."""
from langchain_core.tools import tool
from langchain_classic.agents.agent_types import AgentType
from langchain_classic.agents.initialize import initialize_agent
from tests.unit_tests.llms.fake_llm import FakeLLM
@tool
def my_tool(query: str) -> str: # noqa: ARG001
"""A fake t... |
8cc8f081cb22bee163b7001d012682683dd9578978bcb206dc3759eeab291178 | Python | 859 | 30 | from typing import TYPE_CHECKING, Any
from langchain_classic._api import create_importer
if TYPE_CHECKING:
from langchain_community.chat_loaders.langsmith import (
LangSmithDatasetChatLoader,
LangSmithRunChatLoader,
)
# Create a way to dynamically look up deprecated imports.
# Used to consoli... |
8edf69b8245ad93657a1a7317b4b4331d6c4d66c396d2cebb88a76ddab8ef684 | Python | 859 | 21 | import logging
logger = logging.getLogger(__name__)
def corr(y1, y2, dim=-1, eps=1e-8, **kwargs):
"""
Compute the correlation between two PyTorch tensors along the specified dimension(s).
Args:
y1: first PyTorch tensor
y2: second PyTorch tensor
dim: dimension(s) alo... |
9f3b8d6282ff59bdc7d42a5f742b3344beb43d10f0a4658a05f5f1ef20935e35 | Python | 859 | 30 | 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,
ClosestAirportSchema,
)
# Create a way to dynamically look up deprecated imports.
# Used to consoli... |
ddc6a789a17a2b1eba31b85fdd1c6facb3d48d40c9cd456af4b6ca92bde107bb | Python | 859 | 31 | """
openforcefields.py
A general small molecule forcefield descended from AMBER99 and parm@Frosst in the SMIRNOFF format.
This module only contains the function that will be the entry point that
will be used by the openforcefield toolkit to find the installed forcefield
files.
"""
from typing import List
from pkg_re... |
38acf3d5f247c9abbbf71afe77541b9f190bc046a21cb678c27d6cd3527d340a | Python | 860 | 28 | from typing import TYPE_CHECKING, Any
from langchain_classic._api import create_importer
if TYPE_CHECKING:
from langchain_community.document_loaders import BlockchainDocumentLoader
from langchain_community.document_loaders.blockchain import BlockchainType
# Create a way to dynamically look up deprecated impo... |
622cb131f0a8f342374382afeb23c9f8117c02c8035bed9a5e46a3d35082218b | Python | 860 | 25 | from engine import sup_classifier
from engine.arg_handler import get_combined_args
from engine import utils
import torch
torch.autograd.set_detect_anomaly(False)
torch.autograd.profiler.profile(False)
torch.autograd.profiler.emit_nvtx(False)
if __name__=='__main__':
# Gets CLI args and overwrites preset params
... |
bb731f7bb2c7fb7ec137d37eece5baaee40c59c8f5b9f2bd96433865afe8a8d2 | Python | 860 | 24 | # Python function that returns the mid points relative to the R-peaks. (using this convention that a heartbeat is starting at the middle point between two R peaks and ends up at the middle point between the next two R peaks.)
#Input: peaks - the R-peaks positions
# : signal_length - length of the signal
#Output: m... |
7ecd365953a838d525bfe4ec7cc4028a1eb6ad922591ec780e682e13dd0af350 | Python | 861 | 32 | import torch.nn.functional as F
import torch
from torch.utils.data import TensorDataset
from data import GenRecogClassifyData, generate_recog_data
from networks import HebbNet
from plotting import plot_train_perf
#%%
d=Nh=50
net = HebbNet([d, Nh, 2])
teacher = HebbNet([d, Nh, 1])
teacher.plastic = to... |
a40a31309acdc7542e96cd5d0bd7366b0b6937cd5905e983028f57f710717d40 | Python | 861 | 28 | """Birefringence reconstruction using the waveorder API."""
from waveorder.api import birefringence
settings = birefringence.Settings(
transfer_function=birefringence.TransferFunctionSettings(swing=0.1),
apply_inverse=birefringence.ApplyInverseSettings(
wavelength_illumination=0.532,
),
)
# Simul... |
2a27e623500aee6b9555e0b769edd6adf1c43fe99f7e34f7110d606955ea4056 | Python | 862 | 28 | # Finds how many CG sites are targeted in each species for a selected set of Infinium 2 probes
import sys
import gzip
from collections import defaultdict
def main():
if len(sys.argv) != 3:
print ("Usage: python pickInf2Probes.py <probes file> <output file>")
exit(1)
probesFile = open(sys.argv[1... |
cf56f66dbf5c5afd1476b7ceb93fd1fe3c41329117d3372cc76f56a36f9ba0ba | Python | 863 | 43 | from openff.toolkit.topology.molecule import (
Atom,
Bond,
FrozenMolecule,
HierarchyElement,
HierarchyScheme,
Molecule,
Particle,
)
from openff.toolkit.topology.topology import (
DuplicateUniqueMoleculeError,
ImproperDict,
InvalidBoxVectorsError,
InvalidPeriodicityError,
... |
feccc83706ff9b7e5dd25bc3900b037d619c2128febd68b7efa523361fcbd784 | Python | 863 | 30 | from typing import TYPE_CHECKING, Any
from langchain_classic._api import create_importer
if TYPE_CHECKING:
from langchain_community.retrievers import ZepRetriever
from langchain_community.retrievers.zep import SearchScope, SearchType
# Create a way to dynamically look up deprecated imports.
# Used to consoli... |
447856c8c1523bb436036ead2b077d13a666c4fae35f049d2c598a07db70d72e | Python | 866 | 27 | from pathlib import Path
from langchain_core.documents import Document
from langchain_core.documents.base import Blob
def test_init() -> None:
for doc in [
Document(page_content="foo"),
Document(page_content="foo", metadata={"a": 1}),
Document(page_content="foo", id=None),
Documen... |
a125f68d4cb72bf88153433ccbf51e35ae44fed9d03656c0e4109ab334910f46 | Python | 866 | 35 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
"""The setup script."""
from setuptools import setup, find_packages
with open('README.md') as readme_file:
readme = readme_file.read()
setup_requirements = ['pytest-runner']
with open('requirements.txt') as f:
requirements = list(f.readlines())
test_requiremen... |
127570ee6dd778662f2fef36f7470e1f1fd5cbfc31458a1ce74cfec49b6c96ea | Python | 867 | 43 | from langchain_core.prompts.prompt import PromptTemplate
_PROMPT_TEMPLATE = """Translate a math problem into a expression that can be executed using Python's numexpr library. Use the output of running this code to answer the question.
Question: ${{Question with math problem.}}
```text
${{single line mathematical expr... |
2408715bd3191a9e328a224a71b906a7b4050221f88e3bedd956cf24bc764a31 | Python | 867 | 26 | import re
import json
infile=open("Recon3D.json")
out=open("Recon3D_id_subsystem.txt","w")
inf=infile.read()
r3d=json.loads(inf)
#Example field input:
#{'id': '25HVITD3t', 'name': '25-hydroxyvitamin D3 transport from cytoplasm', 'metabolites': {'25hvitd3_c': -1.0, '25hvitd3_e': 1.0}, 'lower_bound': 0.0, 'upper_boun... |
33992dae122334c905731b3beedb1cf8e55bb3bf45c3d1e175e5cae477e591e9 | Python | 867 | 38 | import numpy as np
def low_pass_filter(x, tau, dt):
assert tau > dt
P = np.exp(-dt / tau)
x_filtered = np.empty_like(x)
x_filtered[0] = x[0]
for i in range(1, len(x)):
x_filtered[i] = P * x_filtered[i - 1] + (1.0 - P) * x[i]
return x_filtered
def moving_average(a, window_size):
... |
a1ef591a3173ab56e2609135df4563a1f181f61fe91b5f6cf79caeac9d6f4b0f | Python | 867 | 24 | import numpy as np
import tensorflow as tf
from tensorflow.keras import Model
from typing import List
def _is_neighbour(outputs: List[tf.Tensor], inputs: List[tf.Tensor]) -> bool:
outputs = outputs if isinstance(outputs, list) else [outputs]
outputs = [output.name for output in outputs]
inputs = inputs i... |
fd9e828f11c6b9c45342e08ed39ee766c5a09ce804e2c00155f240710926f4a2 | Python | 867 | 27 | # import sys
# if len(sys.argv) == 0:
# print("Please provide a path to a .fasta file with a sequence")
# sys.exit()
# def get_sequence(path):
# """
# Get a sequence from a FASTA file with an initial sequence for the Protein Sequence Design Algorithm
# """
# sequence = ""
# with open(path,... |
9fe186efc5013172a6ada933781cde5d8963c844c0012c7c2563a14b1ce17073 | Python | 868 | 32 | import torch
def sum_except_batch(x):
return x.view(x.size(0), -1).sum(dim=-1)
def assert_correctly_masked(variable, node_mask):
assert (variable * (1 - node_mask)).abs().sum().item() < 1e-8
def compute_loss_and_nll(args, generative_model, nodes_dist, x, h, node_mask, edge_mask, context):
bs, n_nodes,... |
9bf5cb6e872975397678fb6885094c7adeade11970d066659ac082b4cc748320 | Python | 870 | 33 | from typing import TYPE_CHECKING, Any
from langchain_classic._api import create_importer
if TYPE_CHECKING:
from langchain_community.graphs.graph_document import (
GraphDocument,
Node,
Relationship,
)
# Create a way to dynamically look up deprecated imports.
# Used to consolidate logic... |
8707e37f8cc7324f35a92b6830bbffd41bab62f00330fc28aa6fd7446eb34a8f | Python | 871 | 30 | from typing import TYPE_CHECKING, Any
from langchain_classic._api import create_importer
if TYPE_CHECKING:
from langchain_community.chat_models.azureml_endpoint import (
AzureMLChatOnlineEndpoint,
LlamaContentFormatter,
)
# Create a way to dynamically look up deprecated imports.
# Used to con... |
b08bca8ec9f76d71f0eab82a2823c85c822fac1e7bf76e80ae9ca11fe5858131 | Python | 871 | 37 | #!/usr/bin/python
# see https://github.com/fabridamicelli/kuramoto
from kuramoto import Kuramoto, plot_phase_coherence, plot_activity
import numba
import ast
import memory_profiler
from scipy.interpolate import pchip_interpolate
from functools import partial
from p_tqdm import p_map
from scipy.stats import skew
import... |
bf33c039a30aaa8d96191ba56f75f0ace5206c69e065941dedb904ff7d0797c2 | Python | 871 | 30 | from typing import TYPE_CHECKING, Any
from langchain_classic._api import create_importer
if TYPE_CHECKING:
from langchain_community.tools import GmailSearch
from langchain_community.tools.gmail.search import Resource, SearchArgsSchema
# Create a way to dynamically look up deprecated imports.
# Used to consol... |
d01da9d1817b202dcd9b7a49741c3a2fa89f15e79070f7ebefbfb9e45fc376e7 | Python | 871 | 30 | from typing import TYPE_CHECKING, Any
from langchain_classic._api import create_importer
if TYPE_CHECKING:
from langchain_community.tools import AINAppOps
from langchain_community.tools.ainetwork.app import AppOperationType, AppSchema
# Create a way to dynamically look up deprecated imports.
# Used to consol... |
293a9ee0e2ab17ed4bc796914a84d572b0fc296b429206adc3c24fbf3345658b | Python | 872 | 27 | import os
# Subject from environment variable
SUBJECT_ID = os.environ['SUBJ']
os.environ.get("SUBJ")
# Base directories
BASE_DIR = "/scratch"
DATA_DIR = os.path.join(BASE_DIR, "data")
ROI_DIR = os.path.join(BASE_DIR, "roi_masks")
TEMPLATE_DIR = os.path.join(BASE_DIR, "template")
OUTPUT_DIR = os.path.join(BASE_DIR, "o... |
acaf0051d87af315205c67ffff788cd8eaec7ab031cce24c5e2e343b2f9b323b | Python | 873 | 28 | import numpy as np
def gaussian(mean,var):
def f(size):
return np.random.normal(mean,var,size)
return f
def gaussian_EI(r,J,sigma):
def f(size):
sol = np.zeros(size)
N = size[0]
if size[0]!=size[1] :
print('Not right')
else :
Ne = int(size[0]... |
83503ad34fd267fc5952ac8c9db43bfd8cdebee964f888e7e0c25cf9f12c64df | Python | 874 | 28 | # -*- coding: utf-8 -*-
# @title Emulate configuration
# @file SnnEmulator.py
# @author Romain Beaubois
# @date 23 Oct 2023
# @copyright
# SPDX-FileCopyrightText: © 2023 Romain Beaubois <refbeaubois@yahoo.com>
# SPDX-License-Identifier: GPL-3.0-or-later
#
# @brief
#
# @details
# > **23 Oct 2023** ... |
8a925180d53bae04c8e1a3e4ca07f4f1a14e9ed139f0d8c79ef8f76a953307bf | Python | 874 | 41 | # coding=utf-8
""" Imports network classes so they can be used directly"""
from .utils import (
round_list,
get_one_hot,
pad,
network_summary,
print_model_structure,
selu_weight_init_,
selu_bias_init_,
set_tensor_device,
master_device_setter
)
... |
9c410c419d84b4bb7aae8c9d13cfecc1eda27d4b29722857fe553a46597de3d8 | Python | 874 | 31 | import tempfile
import torch
from chroma.models.procap import ProteinCaption, load_model, save_model
def test_procap():
model = ProteinCaption(
lm_id="EleutherAI/gpt-neo-125m",
gnn_dim_edges=16,
context_size=8,
context_per_chain=1,
gnn_num_neighbors=4,
gnn_num_lay... |
3aa18aa6f496679087c1ba131428db451589eef2d88046efb08e5b018b888587 | Python | 875 | 30 | from typing import TYPE_CHECKING, Any
from langchain_classic._api import create_importer
if TYPE_CHECKING:
from langchain_community.vectorstores import AzureSearch
from langchain_community.vectorstores.azuresearch import (
AzureSearchVectorStoreRetriever,
)
# Create a way to dynamically look up d... |
f1dde68479ca30353d5e4c3f337fae7f9581b6a0387598fcd6d0fb03a660a3fa | Python | 875 | 33 | """Message responsible for deleting other messages."""
from typing import Any, Literal
from langchain_core.messages.base import BaseMessage
class RemoveMessage(BaseMessage):
"""Message responsible for deleting other messages."""
type: Literal["remove"] = "remove"
"""The type of the message (used for se... |
4761413e0d0ea11298ef2b9d9c8a4cce06e70eb9f39750b5eb986fbeb39a3238 | Python | 877 | 28 | from psychopy import parallel
import platform
PLATFORM = platform.platform()
if 'Linux' in PLATFORM:
port = parallel.ParallelPort(address='/dev/parport0') # on MEG stim PC
else: # on Win this will work, on Mac we catch error below
port = parallel.ParallelPort(address=0xDFF8) # on MEG stim PC
# NB problems ... |
650ce75c0ba2293ab368beab7c22a392213a8ecc305e38405ff3df8ed5a1dac4 | Python | 877 | 42 | #!/usr/bin/python
import sys
import os
import re
from PDBpy import *
if __name__ == "__main__":
regex = re.compile('noHet.pdb')
lstf = os.listdir('.')
for f in lstf:
if os.path.isfile(f) and regex.search(f):
basename = os.path.splitext(os.path.basename(f))[0]
pdbname = str(basename)+".pdb"
pdir = "resul... |
d4dbdcd334e459fc57d0dd88cc7db79fb72d5a90d74a27d72f0819e84e72478e | Python | 877 | 24 | from scipy import stats
import numpy as np
def compute_batch_average(df):
# Computes mean/SEM of measures across all seeds
batch_PID = {}
for i in df:
if type(df[i][0]) == list:
if type(df[i][0][0]) == dict:
pass
else:
try:
... |
b126d204e917abf64df52959d3c549901ded868aa430b685def05c18af5e4b77 | Python | 878 | 29 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
# @Time : 2023/9/28 10:39
# @Author : zhangchao
# @File : dnn.py
# @Software: PyCharm
# @Email : zhangchao5@genomics.cn
import torch.nn as nn
class DNNModel(nn.Module):
def __init__(self, input_dim, hidden_dim, output_dim, drop_rate=0.5):
super(DNNMod... |
c7825d6fb1ef71d1089a42b4b0e066a6ef5b10505880c18832572bde24b7aa81 | Python | 878 | 29 | from typing import TYPE_CHECKING, Any
from langchain_classic._api import create_importer
if TYPE_CHECKING:
from langchain_community.chains.graph_qa.kuzu import (
KuzuQAChain,
extract_cypher,
remove_prefix,
)
# Create a way to dynamically look up deprecated imports.
# Used to consolida... |
6523cd6fd64d7b17e06e68b2bc7f12b3dab61015120f654d314b1700bc04b871 | Python | 879 | 23 | import torch
from torch.utils.data import Dataset
class CustomDataset(Dataset):
def __init__(self, data_list, labels_tensor, transform=None):
self.data_list = data_list
self.labels_tensor = labels_tensor
self.transform = transform
def __getitem__(self, index):
if self.transfor... |
deca44783576ec5750d002e3a1e8f1cc518106bc424781c3cf9c5b45fd076fcc | Python | 879 | 30 | '''This files stores the constants of the project'''
# Enter your device's configuration for torch
device = 'cuda:0'
# Assign the path to the project files
import os
root_dir = os.path.dirname(os.path.abspath(__file__))
# (Optional)
# Assign the path to the pickle file that has the data
PICKLES_PATH = r"p... |
f2ebca73805f6f0ffde0ed1d071decc58a7b40ba80186225ddb556f431f03374 | Python | 879 | 25 | # Generated by Django 3.1.4 on 2021-12-06 08:47
from django.db import migrations, models
import pl2kilosort.models
class Migration(migrations.Migration):
initial = True
dependencies = [
]
operations = [
migrations.CreateModel(
name='Trial',
fields=[
... |
0000b376733c367b2e2e57487bffee6bb7acf26daf0d242c15d5a5b8286cd373 | Python | 880 | 34 | """
Parse DrugBank
"""
import pathlib
import pandas as pd
class ParseDrugBank:
"""
"""
def __init__(self, root=None , debug=False):
self.debug = debug
f_dict = {'db': 'drug_DrugBank_target.csv'}
# set root
if root is None:
raise Exception(f'Error, file path is ... |
5c0549e677b7cce659e0ed05530639e6d1b95c142e106cc27bb2224e55c6018f | Python | 881 | 28 | from typing import TYPE_CHECKING, Any
from langchain_classic._api import create_importer
if TYPE_CHECKING:
from langchain_community.vectorstores import AzureCosmosDBVectorSearch
from langchain_community.vectorstores.azure_cosmos_db import CosmosDBSimilarityType
# Create a way to dynamically look up deprecate... |
bfade2b5736ba02ec12da4ce8b8ca857748735a63ac33b6ea498036132a7a837 | Python | 882 | 32 | from setuptools import setup
from setuptools import find_packages
from glob import glob
from os.path import basename
from os.path import dirname
from os.path import join
from os.path import splitext
setup(
name='coinstac',
version='0.3.4',
description='Python utility library for coinstac',
url='https:... |
caf7c7be6aa1ecea591e5d6b3da1dab0969c71c300f6b955b07886f727073812 | Python | 884 | 27 | from langchain_core._api.deprecation import (
LangChainDeprecationWarning,
LangChainPendingDeprecationWarning,
deprecated,
suppress_langchain_deprecation_warning,
surface_langchain_deprecation_warnings,
warn_deprecated,
)
AGENT_DEPRECATION_WARNING = (
"Use `langchain.agents.create_agent` fo... |
171b1e4c5783987cc4392c4994431c95d7d33eea13cbd0ecaa3ed6651ba098ab | Python | 885 | 20 | from typing import Any
def __getattr__(name: str) -> Any:
"""Get attr name."""
if name == "create_csv_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 sandbox... |
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