sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
7ac48a99a74959f41397bf4739f436a2b364e207311ca1fe9d01551e50252aee | Python | 750 | 29 | from typing import TYPE_CHECKING, Any
from langchain_classic._api import create_importer
if TYPE_CHECKING:
from langchain_community.document_loaders.parsers.language.code_segmenter import (
CodeSegmenter,
)
# Create a way to dynamically look up deprecated imports.
# Used to consolidate logic for rais... |
c8f89745b87da2688c6032062224d933c6ea08dac3e4d3a3ef4f7f44cd4680aa | Python | 750 | 27 | from typing import TYPE_CHECKING, Any
from langchain_classic._api import create_importer
if TYPE_CHECKING:
from langchain_community.llms import PromptLayerOpenAI, PromptLayerOpenAIChat
# Create a way to dynamically look up deprecated imports.
# Used to consolidate logic for raising deprecation warnings and
# han... |
51e01bf21205403c3051ebdf8a8d7f314c051c1b3d5476faaf2c59d05514d6a3 | Python | 751 | 27 | import numpy as np
from .base_cam import BaseCAM
class GradCAM(BaseCAM):
def __init__(self, model, target_layers, use_cuda=False,
reshape_transform=None):
super(
GradCAM,
self).__init__(
model,
target_layers,
use_cuda,
... |
b288c6c871267be3da3cdb38a96405d14a31406b44464f8c86fd19b5665e53db | Python | 751 | 27 | from typing import TYPE_CHECKING, Any
from langchain_classic._api import create_importer
if TYPE_CHECKING:
from langchain_community.query_constructors.timescalevector import (
TimescaleVectorTranslator,
)
# Create a way to dynamically look up deprecated imports.
# Used to consolidate logic for raisin... |
f084024d655abf4b517cb5feda1202b1587091800873b93c8d9fcc57b56a8958 | Python | 751 | 27 | from typing import TYPE_CHECKING, Any
from langchain_classic._api import create_importer
if TYPE_CHECKING:
from langchain_community.query_constructors.tencentvectordb import (
TencentVectorDBTranslator,
)
# Create a way to dynamically look up deprecated imports.
# Used to consolidate logic for raisin... |
0a24e484328644949716426da49fa0d903713189cd46f2d149f8962089701248 | Python | 752 | 27 | import os
import pickle
def listdir_extension(folder_path, extension, return_full_path=True):
if os.path.exists(folder_path) and os.path.isdir(folder_path):
listdir = os.listdir(folder_path)
else:
return None
to_pop = []
for i_l, file in enumerate(listdir):
if file[-len(extensi... |
d5fdac6db75c1eba2b00a330d3d41af98eb814a7f9f80051f000961510a400b4 | Python | 753 | 21 | import math
import numpy as np
def shape_matching(im, size):
sz=im.shape
if sz[0] >size[0]:
xstart=int(math.ceil(sz[0]/2)- int(size[0]/2-1))
im=im[xstart-1:xstart+size[0]-1,:]
else:
npad1=int(math.floor(float(size[0])/2-float(sz[0])/2))
npad2=int(math.ceil(float(size[0])/2-f... |
e2ffbe67a3efa5299233819909c20e68038dd544db168c1aff09f1f7ec3b51be | Python | 753 | 26 | from joblib import Parallel, delayed
import mne
import pandas as pd
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 ... |
0429e3c175429f6bdaef69ae791eeffa6b6396bca771b80f8f7fcc6f1dbb3ca5 | Python | 754 | 25 | """
Specifying the parameters for the matplotlib figures produced by visualize_gradients.py
"""
UR_CORNER_PARAMS = {'axis':'both', 'which':'both', 'left':'off', 'right':'off', 'bottom':'off', 'top': 'off', 'labelbottom':'off','labelleft':'off', 'labeltop':'off'}
BOTTOM_EDGE_PARAMS = UR_CORNER_PARAMS.copy()
BOTTOM_EDG... |
1ec32d4434bc58df46f430948da5cb8d0d5f3f2c87510e8a23eb5312e0960079 | Python | 754 | 18 | # 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 ... |
340b6094c1c39aa4854fabe5c54554301c24d4fc64e1adbf47e41cc874c826d7 | Python | 754 | 29 | from typing import TYPE_CHECKING, Any
from langchain_classic._api import create_importer
if TYPE_CHECKING:
from langchain_community.agent_toolkits.file_management.toolkit import (
FileManagementToolkit,
)
# Create a way to dynamically look up deprecated imports.
# Used to consolidate logic for raisin... |
81d6b0a134d11d32613e9419b7238c9632eb05ab74872ba6045ad886badbd7b4 | Python | 754 | 30 | import unittest
import pandas
import cgatpipelines.tasks.counts as Counts
class TestCountsClass(unittest.TestCase):
def setUp(self):
self.counts = Counts.Counts(pandas.DataFrame(
{'sample1': [0, 1, 2],
'sample2': [2, 4, 3]}))
def test_removeSamples_removes_low_counts(self):... |
fdfc0876c0476ac52d9fd2d907a0fdaa3aecd2dff0c0bb82052647d29d227de9 | Python | 754 | 25 | # 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 = gzip.open(sys.arg... |
14c08d40d88218405a87ac59f5bd1eee4f103201bb3b162b1e262752fc0e4926 | Python | 755 | 23 | import argparse
import pandas as pd
if __name__ == '__main__':
parser = argparse.ArgumentParser()
parser.add_argument('lv_file', help='File containing LVs to be filtered by variance')
parser.add_argument('out_file', help='File to store the filtered LVs to ')
parser.add_argument('--n_to_keep', help='Th... |
3a074991bda7d53e17c7bdd63c6f09aa90f4d6aaff8cb99414b597cefa6ad686 | Python | 755 | 25 | import numpy as np
from neurovisfit.common.splits import get_train_val_split
def test_get_train_val_split():
n = 1000
train_frac = 0.8
seed = 123
train_idx, val_idx = get_train_val_split(n, train_frac, seed)
assert isinstance(train_idx, np.ndarray)
assert isinstance(val_idx, np.ndarray)
... |
a315eab9345c9ae08a0ed7460eb91eb4bd096eecd69b7d8f6333526953c89039 | Python | 755 | 26 | import numpy as np
import random
def random_no_repeat(numbers, count):
number_list = list(numbers)
random.shuffle(number_list)
return np.array(number_list[:count])
def brunel(r , J , g, epsilon):
def f(size):
sol = np.zeros(size)
if size[0]!=size[1] :
print('Not right')
... |
d1812c5eac3556b8b79e658b1864a4d85e90a8a6fcc65d445c7b5c7760566444 | Python | 755 | 19 | """Test formatting functionality."""
from langchain_core.language_models.base import _get_token_ids_default_method
class TestTokenCountingWithGPT2Tokenizer:
def test_tokenization(self) -> None:
# Check that the tokenization is consistent with the GPT-2 tokenizer
assert _get_token_ids_default_meth... |
ed4f8f51be284c2a6adbc1b918286dcb8cad2c76cd377b4903f1fc89253cee42 | Python | 755 | 29 | from typing import TYPE_CHECKING, Any
from langchain_classic._api import create_importer
if TYPE_CHECKING:
from langchain_community.document_loaders.parsers.language.language_parser import (
LanguageParser,
)
# Create a way to dynamically look up deprecated imports.
# Used to consolidate logic for ra... |
38e12ef8e04e8f26b399352dd00b89156ae60cc60e3f024a9b226b7d1cd5b8fd | Python | 756 | 25 | import torch
import torch.nn as nn
import torch.nn.functional as F
from . import resnet
class WideBottleneck(resnet.Bottleneck):
expansion = 2
def generate_model(model_depth, k=2, **kwargs):
assert model_depth in [50, 101, 152, 200]
inplanes = [x * k for x in resnet.get_inplanes()]
if model_depth ... |
586a622d71a684373eb2e010c1fd07bc3c68cf5c6660ca1cea31653a19f4c2de | Python | 756 | 23 | from langchain_core.agents import AgentAction
def format_log_to_str(
intermediate_steps: list[tuple[AgentAction, str]],
observation_prefix: str = "Observation: ",
llm_prefix: str = "Thought: ",
) -> str:
"""Construct the scratchpad that lets the agent continue its thought process.
Args:
i... |
fc540b7296edd728fbac28c2a236b6f85a9c5b3b28dcf79010ef227c09ea98d2 | Python | 756 | 27 | from typing import TYPE_CHECKING, Any
from langchain_classic._api import create_importer
if TYPE_CHECKING:
from langchain_community.tools.ainetwork.base import AINBaseTool, OperationType
# Create a way to dynamically look up deprecated imports.
# Used to consolidate logic for raising deprecation warnings and
# h... |
dee576864fb168c0d61d9a048d6e4b9ec6cb56d7b26997ec36e86fa38907e2d4 | Python | 757 | 24 | from typing import TYPE_CHECKING, Any
from langchain_classic._api import create_importer
if TYPE_CHECKING:
from langchain_community.agent_toolkits.json.prompt import JSON_PREFIX, JSON_SUFFIX
# Create a way to dynamically look up deprecated imports.
# Used to consolidate logic for raising deprecation warnings and... |
15b25383a8a93056de91957078f7729986113b86377bc49d8494c5782f8d990f | Python | 758 | 23 | from skspatial.objects import Line, Points, Vector
from scipy.sparse import csr_matrix
from scipy.sparse.linalg import svds
# faster and leaner Line.best_fit
def best_line_fit(points, tol=None, **kwargs) -> Line:
points_spatial = Points(points)
if points_spatial.are_concurrent(tol=tol):
raise ValueErr... |
0b8e1924c5e2dd47527b7ed7009f44f125cb1c2f62e6bd48a2fea74cbfffafef | Python | 759 | 27 | from typing import TYPE_CHECKING, Any
from langchain_classic._api import create_importer
if TYPE_CHECKING:
from langchain_community.callbacks.tracers.wandb import WandbRunArgs, WandbTracer
# Create a way to dynamically look up deprecated imports.
# Used to consolidate logic for raising deprecation warnings and
#... |
9aa9c6bd62de185bafe4009851ba77ed9b4f7ed447d7b3a3b6768fcd4f340d50 | Python | 759 | 27 | from typing import TYPE_CHECKING, Any
from langchain_classic._api import create_importer
if TYPE_CHECKING:
from langchain_community.storage import UpstashRedisByteStore, UpstashRedisStore
# Create a way to dynamically look up deprecated imports.
# Used to consolidate logic for raising deprecation warnings and
# ... |
d344883db67cf8d8b686f59deb65fcb257ac1c7a7f0fd00e827c8bd377c5b2cf | Python | 759 | 28 | from typing import TYPE_CHECKING, Any
from langchain_classic._api import create_importer
if TYPE_CHECKING:
from langchain_community.tools import SleepTool
from langchain_community.tools.sleep.tool import SleepInput
# Create a way to dynamically look up deprecated imports.
# Used to consolidate logic for rais... |
fffbe87b5555d5505041fba77c834967523d85cce45b01912194a9c9767c2d9a | Python | 759 | 28 | from typing import TYPE_CHECKING, Any
from langchain_classic._api import create_importer
if TYPE_CHECKING:
from langchain_community.tools import ShellTool
from langchain_community.tools.shell.tool import ShellInput
# Create a way to dynamically look up deprecated imports.
# Used to consolidate logic for rais... |
10f26f858c74b584b5765bf93016d68f971d85541caa76e9925f173dd320ff9e | Python | 760 | 29 | from typing import TYPE_CHECKING, Any
from langchain_classic._api import create_importer
if TYPE_CHECKING:
from langchain_community.document_loaders.parsers.language.javascript import (
JavaScriptSegmenter,
)
# Create a way to dynamically look up deprecated imports.
# Used to consolidate logic for ra... |
845b7f13b74f98ca0073a604e443b8b8f946ebc6ca4565b30251fff384e08547 | Python | 760 | 31 | import time
import zmq
from math import ceil
IP_ADDR = "tcp://127.0.0.1:5557"
NB_NRN = 512
NB_REGS_SPK = 16
NB_TAB_PER_FRAME = 512
NB_BYTES_PER_REGS = 4
BYTE_SIZE_FRAME = (NB_REGS_SPK+1)*NB_BYTES_PER_REGS
def producer():
context = zmq.Context()
zmq_sock... |
b4a8b95be0bdd0b4ee9e8a03c5fbd4b9246f60d91bd05b59f4bf5e1c1c1d9187 | Python | 761 | 28 | 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 way to dynamically look up deprecated imports.
# Used to consolidate logic for rai... |
e91d5324bf64a966b1f23c6816a8727d245b872ca781d87b606303913a51e0ad | Python | 761 | 29 | """Bing Search API toolkit."""
from typing import TYPE_CHECKING, Any
from langchain_classic._api import create_importer
if TYPE_CHECKING:
from langchain_community.tools import BingSearchResults, BingSearchRun
# Create a way to dynamically look up deprecated imports.
# Used to consolidate logic for raising depre... |
1787026c122101f3334a75d1d588a9b3fbdaf6f210335d56b6b57450b38a1d98 | Python | 762 | 27 | #python scripts/coverage.py
cand = open('core-wln-global/model-300-3-direct/test_withReagents.cbond')
gold = open('data/test.txt.proc')
ks = [6, 8, 10, 12, 14, 16, 18, 20]
topks = [0 for k in ks]
tot = 0
for line in cand:
tot += 1
cand_bonds = []
for v in line.split():
x,y,t = v.split('-')
... |
e849193081ef242f4b09d278be622b41c94346c0e0b670041d0bf43bbbf8a1ab | Python | 762 | 27 | from typing import TYPE_CHECKING, Any
from langchain_classic._api import create_importer
if TYPE_CHECKING:
from langchain_community.document_loaders import CSVLoader, UnstructuredCSVLoader
# Create a way to dynamically look up deprecated imports.
# Used to consolidate logic for raising deprecation warnings and
#... |
1280e094fcceabe8dc018a12c8a7ee928828c175931c33330be79b8c7ccf1169 | Python | 763 | 24 | from typing import Any
from langchain_classic.base_memory import BaseMemory
class ReadOnlySharedMemory(BaseMemory):
"""Memory wrapper that is read-only and cannot be changed."""
memory: BaseMemory
@property
def memory_variables(self) -> list[str]:
"""Return memory variables."""
retu... |
391f1ae0bccc4eb82f2f49d3dd9be2d40aa122bd640fc6af8a527f924b93f9fa | Python | 763 | 22 | # Obtain the affinity corresponding to each protein
import os
import pandas as pd
# Program root directory
path = os.path.abspath(os.path.dirname(os.getcwd()))
# index directory
index_path = path + r'\pre-data\PDBbind_index\index\INDEX_general_PL_data.2020'
# Affinity storage directory
affinity_data_path = path... |
e5218b5b03c3a522d133a241a59a4401145fd3329a14036a7b06fa6e4f707d8e | Python | 764 | 37 | import numpy as np
from os import path
from sys import argv
from voxcell import VoxelData
argc = len(argv)
def loadext(filename):
_, ext = path.splitext(filename)
if ext == ".img":
return np.fromfile(filename, dtype=np.float32)
elif ext == ".nrrd":
return VoxelData.load_nrrd(filename).raw
... |
f7a4344bc15ac7ce28da54889dd3693a45bb4774f010b5e13697b95c2731bb9a | Python | 764 | 29 | from typing import TYPE_CHECKING, Any
from langchain_classic._api import create_importer
if TYPE_CHECKING:
from langchain_community.embeddings.cloudflare_workersai import (
CloudflareWorkersAIEmbeddings,
)
# Create a way to dynamically look up deprecated imports.
# Used to consolidate logic for raisi... |
12d7ccba326be968b35b4fe7b6080f96bdadbc0ec0d9ec5fc7e2f0a56d3b8716 | Python | 765 | 27 | from typing import TYPE_CHECKING, Any
from langchain_classic._api import create_importer
if TYPE_CHECKING:
from langchain_community.chat_models.bedrock import BedrockChat, ChatPromptAdapter
# Create a way to dynamically look up deprecated imports.
# Used to consolidate logic for raising deprecation warnings and
... |
617e96b96a05ae25935c1be1615c85aa02cf8869a835c37240039f8ced639402 | Python | 765 | 27 | from typing import TYPE_CHECKING, Any
from langchain_classic._api import create_importer
if TYPE_CHECKING:
from langchain_community.vectorstores import ElasticKnnSearch, ElasticVectorSearch
# Create a way to dynamically look up deprecated imports.
# Used to consolidate logic for raising deprecation warnings and
... |
11dde732e82aea331c0337baa7cf432f15ae95cc3b40e6485e62c45ba7cef773 | Python | 766 | 20 | # 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 ... |
316f95314b5b5c7ffd37c8e41ccddf0437523d3c389a2d21a6cbf3ca3862f27d | Python | 766 | 19 | # 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 ... |
34c474eb32fbea08c2b8dfd5e17636d73cc1fdb6ab6deb69eca9d9fdeec04334 | Python | 766 | 28 | from typing import TYPE_CHECKING, Any
from langchain_classic._api import create_importer
if TYPE_CHECKING:
from langchain_community.llms import GradientLLM
from langchain_community.llms.gradient_ai import TrainResult
# Create a way to dynamically look up deprecated imports.
# Used to consolidate logic for ra... |
786c6995f9b58e578710422c658c05619d61fd26844078559f0b65f06a0970ca | Python | 766 | 21 | # TODO: deprecate
agent_instructions = """You are a helpful assistant. Help the user answer any questions.
You have access to the following tools:
{tools}
In order to use a tool, you can use <tool></tool> and <tool_input></tool_input> tags. \
You will then get back a response in the form <observation></observation>
... |
a0a8e15c11082495d70a45c931de9125904ffff41de9d9ec9192bef92cac5da6 | Python | 766 | 29 | from typing import TYPE_CHECKING, Any
from langchain_classic._api import create_importer
if TYPE_CHECKING:
from langchain_community.document_loaders.baiducloud_bos_directory import (
BaiduBOSDirectoryLoader,
)
# Create a way to dynamically look up deprecated imports.
# Used to consolidate logic for r... |
42660b79f178058bcf156c05842e830ab553d05690aef9e7f681ade7dc709ebb | Python | 768 | 27 | from typing import TYPE_CHECKING, Any
from langchain_classic._api import create_importer
if TYPE_CHECKING:
from langchain_community.tools.nuclia.tool import NUASchema, NucliaUnderstandingAPI
# Create a way to dynamically look up deprecated imports.
# Used to consolidate logic for raising deprecation warnings and... |
805a97e519a60c0368e495767d28dccc8b19654b5960625a4af58fffaa5ab356 | Python | 768 | 33 | """
Utils
=====
Utility functions meant to be used in the different openmm modules or tests.
This module provides a common API point for different utility functions that serve as convenience
or help users in different miscellaneous tasks.
"""
from .utils import (
_RESERVED_WORDS_PATTERNS,
deserialize,
fin... |
3bc78faa7ba39bfa3beaa3b8992d7845ec8d347b229ed533480bd65c4e1674ee | Python | 769 | 14 | data_collection = "E_coli_PRECISE2" # Data set to train on.
tied = True # Specifies if the autoencoder is tied.
layer_sizes = [2000, 1000, 50] # Sizes of hidden layers up to and including the bottleneck. If untied, decoder layers must be given explicitly.
layer_actis = ['sigmoid' for i in range(2*len(layer_... |
059a2e6f80a3aa55b0bfa389bc23a48c34a9a1cfcc0206bfd125a951d630979b | Python | 770 | 28 | from typing import TYPE_CHECKING, Any
from langchain_classic._api import create_importer
if TYPE_CHECKING:
from langchain_community.tools import AINRuleOps
from langchain_community.tools.ainetwork.rule import RuleSchema
# Create a way to dynamically look up deprecated imports.
# Used to consolidate logic for... |
a59a6e5615ce8972588f057475171ddb9fc176896d80920bb5e5c300b1710653 | Python | 770 | 19 | # 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 ... |
a5d736a877c120fa28592595002ea35b7ebfe0b3a8cd5760fb92dd9b2bd5f8f8 | Python | 771 | 28 | from typing import TYPE_CHECKING, Any
from langchain_classic._api import create_importer
if TYPE_CHECKING:
from langchain_community.tools import ArxivQueryRun
from langchain_community.tools.arxiv.tool import ArxivInput
# Create a way to dynamically look up deprecated imports.
# Used to consolidate logic for ... |
6b677856a054bfffc307d17289c338bcc1ef3a8d50a9ecd309a1661463fcaae6 | Python | 772 | 29 | """Playwright browser toolkit."""
from typing import TYPE_CHECKING, Any
from langchain_classic._api import create_importer
if TYPE_CHECKING:
from langchain_community.agent_toolkits.playwright.toolkit import (
PlayWrightBrowserToolkit,
)
# Create a way to dynamically look up deprecated imports.
# Use... |
fdfe5c6ec3d1714764056b77a1fa74d2ab7551d2376fed0888b76a5a1f66738f | Python | 772 | 26 | import pytest
from qupkake.featurizer import Featurizer
@pytest.fixture
def example_featurizer():
smiles = "CCO"
return Featurizer(smiles=smiles, name="example_molecule", xtb=True)
def test_featurizer(example_featurizer):
# Call the featurizer to get the PyTorch Geometric Data object
data = example... |
20ce774b22b61023dab88f2574de610378abe5e17d9807a3a64e9a9fc60fec0c | Python | 773 | 29 | """Zapier Tool."""
from typing import TYPE_CHECKING, Any
from langchain_classic._api import create_importer
if TYPE_CHECKING:
from langchain_community.tools import ZapierNLAListActions, ZapierNLARunAction
# Create a way to dynamically look up deprecated imports.
# Used to consolidate logic for raising deprecati... |
1d39d06d309de4c92b6cff37f8b7dcc12138b6b77953ba4fe4330286f492d103 | Python | 774 | 28 | from pathlib import Path
from libs.eval.expresult import ExpResult
from libs.visualizer.metrics import GenVisualizer, Visualizer
class Eval:
def __init__(self, dir_output: Path) -> None:
self.dir_output = dir_output / "metrics"
if not self.dir_output.exists():
self.dir_output.mkdir()... |
6ca84769e111dc53571068bad3cd5943b0da11f3b4dda1e43b1b012d3b1a300b | Python | 774 | 20 | # Python function that computes the
# input, output and delta SNR
# Inputs:
# the (input) signal x
# the noise (i.e. the noise contained in x) n
# the (output, i.e. the filtered signal) s
# Ouputs:
# input_SNR_db - the SNR computed for the (input) signal x and the noise n
# output_SNR_db - t... |
a2978a0e7180314b107d017c300bbd8c3c76b154ed6d08bf236459e236058cf5 | Python | 774 | 30 | import pytest
import torch
from neurovisfit.models.core import TaskDrivenCore
@pytest.fixture(scope="module")
def sample_input():
return torch.randn(1, 3, 224, 224) # Example input tensor
@pytest.fixture(scope="module")
def task_core_layer3_resnet50():
return TaskDrivenCore(
input_channels=3,
... |
d127dc764552497993157ce7532799abf6f56a3a702060ee7860007f0c8ca546 | Python | 774 | 31 | """Embeddings."""
from typing import TYPE_CHECKING
from langchain_core._import_utils import import_attr
if TYPE_CHECKING:
from langchain_core.embeddings.embeddings import Embeddings
from langchain_core.embeddings.fake import (
DeterministicFakeEmbedding,
FakeEmbeddings,
)
__all__ = ("Det... |
037b292d779934f69e69381202fe56e7b68121690970a64a40bd0e7bbcfbc685 | Python | 775 | 28 | from typing import TYPE_CHECKING, Any
from langchain_classic._api import create_importer
if TYPE_CHECKING:
from langchain_community.tools import AINOwnerOps
from langchain_community.tools.ainetwork.owner import RuleSchema
# Create a way to dynamically look up deprecated imports.
# Used to consolidate logic f... |
050567bf5d8bea38cb921ddee363918bcccd0694f5314a567c3f4f1532df2b5e | Python | 775 | 23 | import setuptools
with open("README.md", "r") as fh:
long_description = fh.read()
setuptools.setup(
name="pnabind",
version="1.0",
author="Jared Sagendorf",
author_email="sagendor@usc.edu",
description="A package for predicting protein binding sites and binding function using geometric deep le... |
4b6c9022cc6eeb02d63998f9c0d11a8cca592eefbd7c83a9fc5e758eb0ea678f | Python | 775 | 29 | """Google Search API Toolkit."""
from typing import TYPE_CHECKING, Any
from langchain_classic._api import create_importer
if TYPE_CHECKING:
from langchain_community.tools import GoogleSearchResults, GoogleSearchRun
# Create a way to dynamically look up deprecated imports.
# Used to consolidate logic for raising... |
d31454a432255d3dc5f57b36327fe46f6a7454c7495c8b85556f879ee9944981 | Python | 775 | 25 | """Different methods for rendering Tools to be passed to LLMs.
Depending on the LLM you are using and the prompting strategy you are using,
you may want Tools to be rendered in a different way.
This module contains various ways to render tools.
"""
# For backwards compatibility
from langchain_core.tools import (
... |
e05aa9e4f4f7487ae21a68065959acc1664fe12a8d163e681baa51046f023340 | Python | 775 | 28 | """Helper functions for managing the LangChain API.
This module is only relevant for LangChain developers, not for users.
!!! warning
This module and its submodules are for internal use only. Do not use them in your
own code. We may change the API at any time with no warning.
"""
from langchain_classic._a... |
039ffefe833e3956677d239f811cbc0804aa747618062e4c6ef45a5e8b6a08a5 | Python | 777 | 28 | import sys
try:
from .energy_space_explorer import EnergyExplorer
except (ModuleNotFoundError, NameError):
print('EnergyExplorer Module is not available. Check Rosetta installation.', sys.stderr)
from .reaction_network import ReactionNetwork
from .vectorized_rxn_net import VectorizedRxnNet
from .vectorized_rxn_... |
26a0d3b025b0ec2778ee6fd1aea987a016eb5912b99fa7bcf0fef48f4793f4a1 | Python | 777 | 23 | import importlib.util
import os.path as op
def loadModule(module_path, model_name=None, model_args=[], model_kwargs={}, return_model=True):
# specify the module that needs to be
# imported relative to the path of the
# module
name = op.basename(module_path).strip('.py')
spec = importlib.util.spe... |
a2b39c552d9441b06cc2000ddd7bf686f1cd7a845dc9f1df24454fd1542e4a7f | Python | 777 | 25 | from langchain_core.documents import Document
from langchain_classic.retrievers.document_compressors.listwise_rerank import (
LLMListwiseRerank,
)
def test_list_rerank() -> None:
from langchain_openai import ChatOpenAI
documents = [
Document("Sally is my friend from school"),
Document("S... |
34cdbf538e5e1468730cc6adf7b2086b424b19cf9052f35bf07c136b9877dab9 | Python | 778 | 28 | from typing import TYPE_CHECKING, Any
from langchain_classic._api import create_importer
if TYPE_CHECKING:
from langchain_community.tools import AINValueOps
from langchain_community.tools.ainetwork.value import ValueSchema
# Create a way to dynamically look up deprecated imports.
# Used to consolidate logic ... |
8bd6cf9ad0766901e2eaee8412816d36a88eb45081e1af78fa64c4b2ef7e8028 | Python | 779 | 32 | # -*- coding: utf-8 -*-
# @title Main
# @file main.py
# @author Romain Beaubois
# @date 20 Feb 2023
# @copyright
# SPDX-FileCopyrightText: © 2023 Romain Beaubois <refbeaubois@yahoo.com>
# SPDX-License-Identifier: GPL-3.0-or-later
#
# @brief
#
# @details
# > **20 Feb 2023** : file creat... |
9594be634d2e76de79a285476891c198bbacdb11fac1c47152a27c83f1daae41 | Python | 779 | 17 | #TO BE UPDATED
from NeuronModel.NeuronClass import neuronClass
import numpy as np
class stein(neuronClass):
parameters = {'save': True, 'spike':False,'tau':10.,'R':10.,'E_l':-65., 'a_e':0.1, 'a_i':0.1}
def __init__(self,**kwargs):
neuronClass.__init__(self,**kwargs)
neuronClass.subclass(self,s... |
b3f3af0828ea5af95ebe1d53ef882f026bd02df3ab13d8b8eb93dbc71307c339 | Python | 779 | 27 | import pytest
def pytest_addoption(parser):
parser.addoption(
"--runslow", action="store_true", default=False, help="run slow tests"
)
def pytest_configure(config):
config.addinivalue_line("markers", "slow: mark test as slow to run")
config.addinivalue_line("markers", "gpu_ci: mark test as u... |
18eed4d87d6090005b5cb0a67f0ed168c27717a5c3603905e8c76a0022f3a964 | Python | 780 | 28 | from typing import TYPE_CHECKING, Any
from langchain_classic._api import create_importer
if TYPE_CHECKING:
from langchain_community.llms import JavelinAIGateway
from langchain_community.llms.javelin_ai_gateway import Params
# Create a way to dynamically look up deprecated imports.
# Used to consolidate logic... |
7043ab964d4d3e62f8f6941139a2c2b3fb40260acccaeae6355160004652c52a | Python | 780 | 24 | # 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
import scipy.linalg as sp
def TikhonovRegularization(x,DiffOrderOrFilterCoefs,lamb):
if n... |
cfa058df55ed553021fa9682e5dd2e58955968696302842574794db1a4aa09ff | Python | 780 | 25 | from prettyplot import *
import h5py
import os
### TABLE8 ###
savepath = '../data/simulation_outputs/factor_fixing'
file_name = "factor_fixing.h5"
path = os.path.join(savepath, file_name)
hf = h5py.File(path, 'r')
# Open results
output_samples = hf['output_samples'][()]
first_order_indices = hf['S1'][()]
total_order... |
d51d68b870d245880982acde89bd0ae48bad0c7a4b7f226a1d174c1606535669 | Python | 780 | 29 | from typing import TYPE_CHECKING, Any
from langchain_classic._api import create_importer
if TYPE_CHECKING:
from langchain_community.agent_toolkits.azure_cognitive_services import (
AzureCognitiveServicesToolkit,
)
# Create a way to dynamically look up deprecated imports.
# Used to consolidate logic f... |
72461b49fc10e13f09ecd0cee55f95bfd720849df8b98ada0f3c332935d15683 | Python | 781 | 24 | # 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
import scipy.linalg as sp
def tikhonov_regularization(x,DiffOrderOrFilterCoefs,lamb):
if ... |
8654eb1e080af4b0870e70204dc6cf4cfaeeb2f3f243f36c11be6483d2e08481 | Python | 781 | 38 | from langchain_core.runnables.base import (
Other,
Runnable,
RunnableBinding,
RunnableBindingBase,
RunnableEach,
RunnableEachBase,
RunnableGenerator,
RunnableLambda,
RunnableLike,
RunnableParallel,
RunnableSequence,
RunnableSerializable,
coerce_to_runnable,
)
from lan... |
2c65992e0c9787861964bc9e55a53e8e1a188882dfbee596f050bd0961116aed | Python | 782 | 24 | from typing import Dict
import pytorch_lightning as pl
import torch
from utilities import instantiate_from_config
class DiffusionDenoise(pl.LightningModule):
def __init__(self, model_config: Dict, lr: float = 1e-5) -> None:
super().__init__()
self.lr = lr
self.model = instantiate_from_conf... |
eccc0345578263800a81bc4bb245a998df833c349f8142923d8f159ef7141dca | Python | 782 | 28 | import unittest
import filecmp
import tempfile
import os
import sys
sys.path = [os.path.join(os.path.dirname(
os.path.realpath(__file__)), '..', )]+sys.path
from enrichm.writer import Writer
class Tests(unittest.TestCase):
def test_write(self):
output_file = tempfile.mktemp()
output_lines = ... |
1972221deffc5274e4df9467a333747991593ab9ea5513852760c9e7aa488407 | Python | 783 | 32 | # -*- coding: utf-8 -*-
# @title Main
# @file main.py
# @author Romain Beaubois
# @date 20 Feb 2023
# @copyright
# SPDX-FileCopyrightText: © 2023 Romain Beaubois <refbeaubois@yahoo.com>
# SPDX-License-Identifier: GPL-3.0-or-later
#
# @brief
#
# @details
# > **20 Feb 2023** : file creat... |
82744b3a792ba7b93db129c70188c96341aad066f51861f7a3756d2ee08c380f | Python | 783 | 28 | from typing import TYPE_CHECKING, Any
from langchain_classic._api import create_importer
if TYPE_CHECKING:
from langchain_community.tools import ClickTool
from langchain_community.tools.playwright.click import ClickToolInput
# Create a way to dynamically look up deprecated imports.
# Used to consolidate logi... |
e43bf8cbf16cb42f55033ed92667ce6152929004f8b763f7a94f2f72820e1d2d | Python | 783 | 32 | """Top-level package for mrQA."""
__author__ = """Harsh Sinha"""
__email__ = 'harsh.sinha@pitt.edu'
# __version__ = '0.1.0'
import logging
import sys
from mrQA.config import configure_logger
logger = logging.getLogger(__name__)
logger = configure_logger(logger, output_dir=None, mode='w')
from mrQA.monitor import m... |
e4afe8e328f05942cae1a349ffe8a93ece60f9aeaa19d9412ce537e963f84c22 | Python | 783 | 23 | import numpy as np
import matplotlib
import matplotlib.pyplot as plt
from mpl_toolkits.axes_grid1 import ImageGrid
from scipy.ndimage import zoom
ori = '/data/datasets/ADNI_NoBack/ADNI_002_S_0295_MR_MPR__GradWarp__B1_Correction__N3__Scaled_2_Br_20081001114556321_S13408_I118671.npy'
MRI = '../ADNIP_NoBack/ADNI_002_S_02... |
01f113cc8c57ddc50fb3c8501467c0d326d2405ac1cfb8db19826af74ed7d9aa | Python | 784 | 24 | from setuptools import setup, find_packages
setup(
name='e3nn_Unet',
version='0.1.0',
description='Segmentation network with O3 and SO3 equivariant convolutions',
url='https://github.com/SCAN-NRAD/e3nn_Unet',
classifiers=[
'Development Status :: 3 - Alpha',
'Intended Audience :: Sci... |
15dddd5d1543fc69fb6de1b5849fb73e14b35a958e09da977c3ea49cb016a507 | Python | 785 | 28 | from typing import TYPE_CHECKING, Any
from langchain_classic._api import create_importer
if TYPE_CHECKING:
from langchain_community.vectorstores import Qdrant
from langchain_community.vectorstores.qdrant import QdrantException
# Create a way to dynamically look up deprecated imports.
# Used to consolidate lo... |
69bab0d75753ca18c4df963f393b19afff6bfb81bf8e0b89c328c28a8d7a9582 | Python | 785 | 28 | from typing import TYPE_CHECKING, Any
from langchain_classic._api import create_importer
if TYPE_CHECKING:
from langchain_community.llms.fake import FakeStreamingListLLM
from langchain_core.language_models import FakeListLLM
# Create a way to dynamically look up deprecated imports.
# Used to consolidate logi... |
1daffa047f21fc96334120d4101e6bfa136209308008899ef70439c45ff952f8 | Python | 786 | 37 | # 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 SynchPhaseTimes2(peaks):
I = np.where(peaks)
I = I[0]
D = I[1:] - I[0:-1]
... |
9f60809d7d622a88cba548d1ea5bc23aee334ed1d129b2062774c407911f138b | Python | 788 | 25 | import os
import pathlib
import config_chbp_eeg as cfg
import pandas as pd
"""Fixing the participants.tsv in the derivatives folder
The current release of the CHBP has a faulty participants.tsv
that doesn't include age. This script carries over the info
from the demographics directory shipped by the CHBP and writes a... |
a4368a101a36bcd989d3cbc2ea390e50eb38b416f7b47137be24b2b4b87b0ed5 | Python | 789 | 27 | import os
import random
def obtain_files_list():
for root, dirs, files in os.walk(training_set_path):
return files
def remove_step_files(remove_list):
for file_name in remove_list:
del_file = training_set_path + "\\" + file_name
os.remove(del_file)
print("已经删除：", del_file)
... |
aa68b52f82e9a061d36575f17b25e01a721bf692f9b5c8bda04223a169ef0073 | Python | 789 | 12 | """
Perform optimization to find optimal field map for distortion correction.
Files:
- `ADMM`: A class implementing the Alternating Direction Method of Multipliers optimization algorithm.
- `EPIOptimize`: A base class for different optimization algorithms in EPI-MRI distortion correction.
- `GaussNewton`: A class impl... |
2cd16570b9400296943c7af07f09889201adfd516157b30711570db1a43f01a5 | Python | 790 | 28 | from typing import TYPE_CHECKING, Any
from langchain_classic._api import create_importer
if TYPE_CHECKING:
from langchain_community.utilities import SerpAPIWrapper
from langchain_community.utilities.serpapi import HiddenPrints
# Create a way to dynamically look up deprecated imports.
# Used to consolidate lo... |
a52f03ef33956a9e3231dbceadd02a3a2d8e953bdcfaa86fd2f6103400218224 | Python | 790 | 27 | from typing import TYPE_CHECKING, Any
from langchain_classic._api import create_importer
if TYPE_CHECKING:
from langchain_community.query_constructors.databricks_vector_search import (
DatabricksVectorSearchTranslator,
)
# Create a way to dynamically look up deprecated imports.
# Used to consolidate ... |
b8381c410d23474b7392e3375236e2167d4a0f2ca96fcdf3aea10151d6d6253c | Python | 790 | 23 | """Parameterizations: models of one variable given its parents, and the distributions they return.
This module is experimental: its API may change in any release without a deprecation period.
"""
from pgmpy.parameterization._base import BaseParameter
from pgmpy.parameterization.adapters import DistributionAdapter, Sk... |
741e80fa15b32bdc87151dd3119b60e32d762730b9d59452a00ae2674b6604b7 | Python | 791 | 33 | import os
import numpy as np
import glob
import mdtraj as md
def mkdir(dir_name):
if not os.path.exists(dir_name):
os.mkdir(dir_name)
def get_fns(dir_name,pattern):
return np.sort(glob.glob(os.path.join(dir_name, pattern)))
def load_traj_coords_dir(dir_name,pattern,top):
fns = get_fns(dir_name, p... |
79ac9c7615e294b9aa9ac5d960756e4813b59b2e8152c32c2b3e90efca551470 | Python | 791 | 31 | #
# Based on lsf CookieCutter.py
#
import os
import json
d = os.path.dirname(__file__)
with open(os.path.join(d, "settings.json")) as fh:
settings = json.load(fh)
class CookieCutter:
SBATCH_DEFAULTS = settings['SBATCH_DEFAULTS']
CLUSTER_NAME = settings['CLUSTER_NAME']
CLUSTER_CONFIG = settings['CLUS... |
e6a6466210a126186a110a00ba8f17eec11dfccdfcca24ec87e47ffc64c8b2d7 | Python | 791 | 27 | from typing import TYPE_CHECKING, Any
from langchain_classic._api import create_importer
if TYPE_CHECKING:
from langchain_community.agent_toolkits.spark_sql.prompt import (
SQL_PREFIX,
SQL_SUFFIX,
)
# Create a way to dynamically look up deprecated imports.
# Used to consolidate logic for rais... |
df8bf852b722b34b47c9a8f1adf96b7a893192e2a39078e05171c43f7ef8ed45 | Python | 792 | 27 | import scanpy as sc
from bayestme import data, synthetic_data
stdata = synthetic_data.generate_demo_dataset()
data.SpatialExpressionDataset()
print(stdata.gene_names)
import numpy as np
import pandas as pd
#%% de
from bayestme import deconvolution
from bayestme.common import InferenceType
best_spatial_smoothing_paramet... |
fc305ff633974b9e9cd61bb72bde1bd82d508bdd39fa6de980b9c13578e38107 | Python | 792 | 31 | """Local file management toolkit."""
from typing import TYPE_CHECKING, Any
from langchain_classic._api import create_importer
if TYPE_CHECKING:
from langchain_community.agent_toolkits.file_management.toolkit import (
FileManagementToolkit,
)
# Create a way to dynamically look up deprecated imports.
... |
3e27902c83dc2062739a67f4020cfd6d5212e0bc8958df59f6e1aa3cc57759fa | Python | 793 | 28 | from typing import TYPE_CHECKING, Any
from langchain_classic._api import create_importer
if TYPE_CHECKING:
from langchain_community.tools import AINTransfer
from langchain_community.tools.ainetwork.transfer import TransferSchema
# Create a way to dynamically look up deprecated imports.
# Used to consolidate ... |
bbf3a8713427a1669852989a76cd2c042635ab92949cc79d9934ac113b5fb63e | Python | 793 | 28 | from typing import TYPE_CHECKING, Any
from langchain_classic._api import create_importer
if TYPE_CHECKING:
from langchain_community.vectorstores import Vectara
from langchain_community.vectorstores.vectara import VectaraRetriever
# Create a way to dynamically look up deprecated imports.
# Used to consolidate... |
00f841fb6e5e0ecdc00187c3c2c2e34165c00327862ff490010f4dee3a354a0d | Python | 794 | 36 | import argparse
import pickle
def main():
parser = argparse.ArgumentParser()
parser.add_argument('--old_pkl', type=str, required=True)
parser.add_argument('--new_pkl', type=str, required=True)
args = parser.parse_args()
with open(args.old_pkl, 'rb') as f:
old = dict(pickle.load(f))
w... |
4dd026e46777b42f1e041091bb67e2d3da7962409dfa33bc23c050281b1150ac | Python | 794 | 28 | from typing import TYPE_CHECKING, Any
from langchain_classic._api import create_importer
if TYPE_CHECKING:
from langchain_community.utilities import SQLDatabase
from langchain_community.utilities.sql_database import truncate_word
# Create a way to dynamically look up deprecated imports.
# Used to consolidate... |
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