sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
75d72a409759ed1ec8827dee13faefe468116c1ff48fddc1a3768d5a9d615820 | Python | 707 | 25 | from typing import TYPE_CHECKING, Any
from langchain_classic._api import create_importer
if TYPE_CHECKING:
from langchain_community.chat_message_histories import CassandraChatMessageHistory
# Create a way to dynamically look up deprecated imports.
# Used to consolidate logic for raising deprecation warnings and
... |
e4ecbcb1597e7c349fcd1e9213269860d4793af03a2505d953bf03cb846d0936 | Python | 707 | 25 | from typing import TYPE_CHECKING, Any
from langchain_classic._api import create_importer
if TYPE_CHECKING:
from langchain_community.document_loaders import AzureBlobStorageContainerLoader
# Create a way to dynamically look up deprecated imports.
# Used to consolidate logic for raising deprecation warnings and
# ... |
ed08cf24968a5dbf3ad46f7742af9c5237fefbc708bf9dc14a755bce9bb0b706 | Python | 707 | 19 | from langchain_core.prompts.prompt import PromptTemplate
_template = """Given the following conversation and a follow up question, rephrase the follow up question to be a standalone question.
Chat History:
{chat_history}
Follow Up Input: {question}
Standalone question:""" # noqa: E501
CONDENSE_QUESTION_PROMPT = Prom... |
f671ece8f4a129ff44a1712ae9e1a1945b7394820bb2d73d3045a543ba278c61 | Python | 707 | 25 | from typing import TYPE_CHECKING, Any
from langchain_classic._api import create_importer
if TYPE_CHECKING:
from langchain_community.chat_message_histories import FirestoreChatMessageHistory
# Create a way to dynamically look up deprecated imports.
# Used to consolidate logic for raising deprecation warnings and
... |
4b160e7cfaceb3d4a4308e29893fa73eca33d58c1640cd6f7177fb2764c67e32 | Python | 708 | 19 | import numpy as np
from pycromanager import JavaBackendAcquisition, multi_d_acquisition_events
with JavaBackendAcquisition("/Users/henrypinkard/tmp", "l_axis") as acq:
# create one event for the image at each z-slice
events = []
for time in range(5):
for index, z_um in enumerate(np.arange(start=0,... |
3bada76fd842d28485b8c310722c734586089ad205670be18503e824fe116c62 | Python | 710 | 23 | import math
import torch
def get_betas(n_timestep, schedule):
if schedule == 'linear':
return linear_beta_schedule(n_timestep)
elif schedule == 'cosine':
return cosine_beta_schedule(n_timestep)
else:
print('Invalid schedule: {}'.format(schedule))
exit(0)
def linear_beta_schedule(n_timestep, start=0.0001, ... |
5134dde056cb0b826d21d41f3af85fd2f8533bea01d7e5f8100e5dc1cda71c53 | Python | 710 | 31 | from langchain_classic.schema.runnable.utils import __all__
EXPECTED_ALL = [
"AddableDict",
"ConfigurableField",
"ConfigurableFieldMultiOption",
"ConfigurableFieldSingleOption",
"ConfigurableFieldSpec",
"GetLambdaSource",
"IsFunctionArgDict",
"IsLocalDict",
"SupportsAdd",
"aadd"... |
997f12a5f6c51f125d137179fb11bf2759b95ed353ad515071a5cb3a4f7e5a49 | Python | 710 | 25 | from typing import TYPE_CHECKING, Any
from langchain_classic._api import create_importer
if TYPE_CHECKING:
from langchain_community.chat_models.meta import convert_messages_to_prompt_llama
# Create a way to dynamically look up deprecated imports.
# Used to consolidate logic for raising deprecation warnings and
#... |
baef44f0ceab054f1faa6d086f716f5a00790f945f511ad94e0733f2218082b9 | Python | 710 | 24 | import numpy as np
from pycromanager import multi_d_acquisition_events, JavaBackendAcquisition
# Version 1:
def img_process_fn(image, metadata):
image[250:350, 100:300] = np.random.randint(0, 4999)
# raise Exception()
return image, metadata
with JavaBackendAcquisition(
directory=r"C:\Users\henry\Deskt... |
2ac57f5e901e35d4e76230276f2c44ecf53ee3b7b95a40d34dc46fb0669e40ea | Python | 711 | 37 | from bindsnet.encoding.encodings import bernoulli, poisson, rank_order, repeat, single
from bindsnet.encoding.loaders import (
bernoulli_loader,
poisson_loader,
rank_order_loader,
)
from .encoders import (
BernoulliEncoder,
Encoder,
NullEncoder,
PoissonEncoder,
RankOrderEncoder,
Rep... |
90268eab410505b4e60ddb4cec51eb542c98618ecf05e0ae47d2fff94984c45e | Python | 711 | 24 | # third party modules
import torch
# pnabind modules
from pnabind.nn import processBatch
def classWeights(data, nc, device='cpu', use_mask=True):
if isinstance(data, torch.Tensor):
# a tensor of class labels
weight = data.shape[0]/(nc*torch.eye(nc)[data].sum(axis=0))
else:
# a dataload... |
ded6be5f9cc33c93eb44493a3059becb63d116bfb744cdae09a3d162dfbcfd5a | Python | 711 | 28 | from sys import argv, exit
import pandas as pd
"""
Add TPM values from lines with same 'Gene_Name'
"""
# all_genes_human_protein_atlas_rna_expression_tpm.tsv.tmp
input_file = argv[1]
df = pd.read_csv(input_file, sep='\t')
print(df.head())
target_col = 'ProteinAtlas_RNA_expression_TMP'
dupl_genes = ['ARL14EPL', '... |
321d0333f6502fb82ad7dc511d35cfd277cadb57eccfd06c316b74222a098ff4 | Python | 712 | 20 | from .darknet import Darknet
from .detectors_resnet import DetectoRS_ResNet
from .detectors_resnext import DetectoRS_ResNeXt
from .hourglass import HourglassNet
from .hrnet import HRNet
from .regnet import RegNet
from .res2net import Res2Net
from .resnest import ResNeSt
from .resnet import ResNet, ResNetV1d
from .resne... |
5aaa9d318f1a1a1bbfdb32911b15b7b67c4aad3130433a511ff19ac0e3e11ce5 | Python | 713 | 20 | """Generate the upstream xxd-compatible embedded help arrays without xxd."""
from pathlib import Path
import re
import sys
def generate(source, destination):
source, destination = Path(source), Path(destination)
data = source.read_bytes()
symbol = re.sub(r'[^A-Za-z0-9_]', '_', source.name)
rows = [', ... |
ed8602f46c235f516f8cf12b1ab2c9798aab58fe89b46406d42fdece08503b40 | Python | 713 | 21 | import contextlib
import joblib
# From https://stackoverflow.com/a/61689175
@contextlib.contextmanager
def tqdm_joblib(tqdm_object):
"""Context manager to patch joblib to report into tqdm progress bar given as argument"""
def tqdm_print_progress(self):
if self.n_completed_tasks > tqdm_object.n:
... |
fcb70991b09df15c9448a0421dc12d0b73e9f00c7997a7d56ee9b4a7d62a37b8 | Python | 715 | 27 | """
Generate a movie from atom-by-atom proposal PMF and placement PDB files.
Run with `run movie.py` in PyMOL
"""
iteration = 6
from pymol import cmd, movie
#cmd.mclear()
#cmd.mset('1')
cmd.set('sphere_scale', 0.02)
cmd.rewind()
cmd.delete('all')
cmd.load('geometry-%d-forward-proposal.pdb' % iteration)
cmd.hide('all'... |
00575a29aab9e8edc152fd51a8bd19d62feda639a5d13eb370427edda8a3427a | Python | 716 | 19 | import numpy as np
def getAtomKDTree(atoms, engine='scipy'):
# check if we're passed a list of atom objects or a higher level entity
if not isinstance(atoms, list):
atoms = [atom for atom in atoms.get_atoms()]
# check which KDTree we want to construct. These have non-equilvalent methods
if... |
12f6d8cb406f01f941d70e00a38f8d6931d2e1cdba22076a4cce2389ab5744b6 | Python | 716 | 25 | import numpy as np
import scipy.sparse as sp
import torch
def normalize(mx):
"""Row-normalize sparse matrix"""
rowsum = np.array(mx.sum(1))
r_inv = np.power(rowsum, -1).flatten()
r_inv[np.isinf(r_inv)] = 0.
r_mat_inv = sp.diags(r_inv)
mx = r_mat_inv.dot(mx)
return mx
def sparse_mx_to_tor... |
70fd7f2f4dd2340a4773260838cfe0d66a2f11766bd1ad208551356fe59e8d1c | Python | 716 | 24 |
from pipeline_functions import *
def main():
# Create synthetic dataset with 2 longitudinal views
data, y = synthetic_data(eps=0.75, eta=0.75, plots=True)
# Perform variable selection using method = 'LMM', 'DGB', 'JPTA' or 'nothing'
data = variable_selection(data, y, method='LMM', top_fea... |
933dc548c155357c339aa0e9645eec78ea49c2e0fcfd84f2d37f620bf30ae82a | Python | 716 | 22 | import torch
from .rk_common import _ButcherTableau, RKAdaptiveStepsizeODESolver
_BOGACKI_SHAMPINE_TABLEAU = _ButcherTableau(
alpha=torch.tensor([1/2, 3/4, 1.], dtype=torch.float64),
beta=[
torch.tensor([1/2], dtype=torch.float64),
torch.tensor([0., 3/4], dtype=torch.float64),
torch.t... |
bd6a12ebb263c3916cd2580e42418c5d5b9def79f1812aa3e2efdb0f26c1b2ca | Python | 716 | 25 | import numpy as np
import copy
class inputClass:
parameters = {}
def __init__(self, neuronInstance, I_value, noise=None):
self.neurons = neuronInstance
self.noise = noise
self.I_value = I_value
self.current_I_input = I_value
self.neurons.input.append(self)
def subc... |
182dda74fea011ddee23080571c363993024a90c56dd9eb7af2a81df45bf887b | Python | 717 | 27 | from typing import TYPE_CHECKING, Any
from langchain_classic._api import create_importer
if TYPE_CHECKING:
from langchain_community.llms import VertexAI, VertexAIModelGarden
# Create a way to dynamically look up deprecated imports.
# Used to consolidate logic for raising deprecation warnings and
# handling optio... |
4bbe8254044f448416130f6afec70037d4d52dd5ea627af4eb1775a825dcf6a2 | Python | 717 | 26 | import os
import importlib
from typing import List
def open_txt_file(file_path: str) -> List[str]:
ret = []
with open(file_path, "r") as f:
ret = f.readlines()
ret = [s.strip("\n") for s in ret]
return ret
def list_subdir(path: str):
return sorted([folder for folder in os.listdir(path) i... |
e26ddc9448786636f8acc52468e67ca7142d285ad8f6633d94ba430a49a09113 | Python | 717 | 27 | """
openforcefields.py
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 importlib.resources import files
def get_forcefield_dirs_paths() -> list[str]:
"""
Return the paths to the directories ... |
24e2334a9b032056c11b3ab58f08db7a7ac081498a30b3a443bd411654447c33 | Python | 718 | 27 | from typing import TYPE_CHECKING, Any
from langchain_classic._api import create_importer
if TYPE_CHECKING:
from langchain_community.document_compressors.flashrank_rerank import (
FlashrankRerank,
)
# Create a way to dynamically look up deprecated imports.
# Used to consolidate logic for raising depre... |
4de8bfc113b0779097467ec3b9282221e3f2bc293015083db212d9f5bca2ee7f | Python | 718 | 17 | import pandas as pd
from tqdm import tqdm
df_encode_meta = pd.read_csv('../data/ENCODE/metadata.tsv', sep='\t')
df_encode_meta = df_encode_meta[df_encode_meta['Output type'] == 'methylation state at CpG']
for pos,row in tqdm(df_encode_meta.iterrows(), total=df_encode_meta.shape[0]):
f_enc = '../data/ENCODE/{}.bed... |
5d386d5e795af89ff0d48ec74168dfd0d638266eabdea3a3a7bb5b53870e3a02 | Python | 718 | 15 | from setuptools import setup
from predmoter.core.constants import PREDMOTER_VERSION
setup(
name="predmoter",
version=PREDMOTER_VERSION,
author="Felicitas Kindel",
url="https://github.com/weberlab-hhu/Predmoter",
description="Deep Learning model predicting ATAC- and ChIP-seq data",
packages=["predmote... |
c10b09df53e9027b2c7df9e0eced9c81650b4c344a529c7a7aabcf639d76872a | Python | 718 | 22 | import pandas as pd
import re
import sys
input_file = 'InBio_Map_core_2016_09_12/core.psimitab'
df = pd.read_csv(input_file, sep='\t', header=None) #, nrows=4000)
# drop rows where only one gene is provided - no interaction can be captured
df.dropna(subset=[4], inplace=True)
df.dropna(subset=[5], inplace=True)
cols... |
c87ede8acb18bbe715c0c799153f3a9f1886bec1d646b93e47df39e46ded2b54 | Python | 718 | 25 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Tue Dec 20 23:37:56 2022
@author: biener
"""
import numpy as np
import mAECell_Utils as utils
#%%
selEpoch = -1
nInterm = 3
strFName = utils.fOpen(Title = 'Load DED Maps with coordinates')
ED = np.loadtxt(strFName)
strFName = utils.fOpen(Title = 'Lo... |
99b441519272b96c8ec84125d1bf4f180f668c7006cde30db26c8fc72c6b19ee | Python | 719 | 27 | from typing import TYPE_CHECKING, Any
from langchain_classic._api import create_importer
if TYPE_CHECKING:
from langchain_community.document_loaders.parsers.language.cobol import (
CobolSegmenter,
)
# Create a way to dynamically look up deprecated imports.
# Used to consolidate logic for raising depr... |
887fd703a4a88c46d4bc08ca15ecced2d0ae0f20a1a5b02a59a872766c492364 | Python | 720 | 36 | # Configuration file for the Sphinx documentation builder.
# -- Project information
project = "SEDR"
copyright = "2023, Hang Xu"
author = "Hang Xu"
release = '1.0'
version = '1.0.0'
# -- General configuration
extensions = [
'sphinx.ext.duration',
'sphinx.ext.doctest',
'sphinx.ext.autodoc',
'sphinx.... |
b0da229a7a6676097532290c8bf4cc08f5d6b55b6cdfcc528299ac8f8fbfa467 | Python | 720 | 23 | import inspect
from typing import cast
def is_caller_internal(depth: int = 2) -> bool:
"""Return whether the caller at `depth` of this function is internal."""
try:
frame = inspect.currentframe()
except AttributeError:
return False
if frame is None:
return False
try:
... |
ff6e1a7ecafa278e588f2fc7228a54a9ddae927fcd63320823160011c7fd75b6 | Python | 720 | 27 | from typing import TYPE_CHECKING, Any
from langchain_classic._api import create_importer
if TYPE_CHECKING:
from langchain_community.utilities import Requests, RequestsWrapper
# Create a way to dynamically look up deprecated imports.
# Used to consolidate logic for raising deprecation warnings and
# handling opti... |
338a9692331b1da4165063ad1ceba79b4e88b38f9708614328d130db98fd5d39 | Python | 722 | 25 | from typing import TYPE_CHECKING, Any
from langchain_classic._api import create_importer
if TYPE_CHECKING:
from langchain_community.query_constructors.mongodb_atlas import (
MongoDBAtlasTranslator,
)
# Create a way to dynamically look up deprecated imports.
# Used to consolidate logic for raising dep... |
50c82ce59faa255667fb13e4ae9bf253acbf51539538f70e080c29909c1510ab | Python | 722 | 25 | from typing import TYPE_CHECKING, Any
from langchain_classic._api import create_importer
if TYPE_CHECKING:
from langchain_community.chains.graph_qa.ontotext_graphdb import (
OntotextGraphDBQAChain,
)
# Create a way to dynamically look up deprecated imports.
# Used to consolidate logic for raising dep... |
56af8f90708d61a95978bea6a74474bec88733ae69762d422ba742d64547a189 | Python | 722 | 25 | """
Tests for nwb compatibility and interfacing functions.
"""
from imagingplus.utils.nwb import newImagingNWB, readImagingNWB
def test_WriteImagingNWB(new_imaging_nwb_fixture):
subject = new_imaging_nwb_fixture[0]
expobj = new_imaging_nwb_fixture[1]
trialobj = new_imaging_nwb_fixture[2]
expobj.experi... |
58fdcd2f4a5ee6f8efb7e29cb75c24f720b6615bcfb12ea124df3de1adba9daa | Python | 723 | 34 | from langchain_core.utils import __all__
EXPECTED_ALL = [
"StrictFormatter",
"check_package_version",
"convert_to_secret_str",
"formatter",
"get_bolded_text",
"abatch_iterate",
"batch_iterate",
"get_color_mapping",
"get_colored_text",
"get_pydantic_field_names",
"guard_impor... |
596fd0b18759d2278e8b92673c720281b34b3daca2de077f9cc67ba861841702 | Python | 723 | 20 | import torch
import torch.nn as nn
#from torch.nn import functional as F
from VariationalNC.Variational_layers import VariationalLinear, VariationalConv2d, VariationalConv3d
from VariationalNC.Variational_utils import variational_estimator
@variational_estimator
class VariationalLN(nn.Module):
def __init... |
f25adf6106e0f928fdcdd515bfa14673e2ed52392533245a63be0aa025ca58e2 | Python | 723 | 27 | from typing import TYPE_CHECKING, Any
from langchain_classic._api import create_importer
if TYPE_CHECKING:
from langchain_community.tools import SearchAPIResults, SearchAPIRun
# Create a way to dynamically look up deprecated imports.
# Used to consolidate logic for raising deprecation warnings and
# handling opt... |
f53e22b6808ce58d8f64bbc7e42afdc59ca6ac9eadd123150bee14fe613e24ea | Python | 723 | 27 | from typing import TYPE_CHECKING, Any
from langchain_classic._api import create_importer
if TYPE_CHECKING:
from langchain_community.docstore.base import AddableMixin, Docstore
# Create a way to dynamically look up deprecated imports.
# Used to consolidate logic for raising deprecation warnings and
# handling opt... |
2ffea84363847e760d939f0283efffde038e959bd646e9c33fe82bf026527b12 | Python | 724 | 27 | """Google Trends API Toolkit."""
from typing import TYPE_CHECKING, Any
from langchain_classic._api import create_importer
if TYPE_CHECKING:
from langchain_community.tools.google_trends.tool import GoogleTrendsQueryRun
# Create a way to dynamically look up deprecated imports.
# Used to consolidate logic for rais... |
46d1deb3a872efd84e213d3e74da9e5942d37d562e63f7b4cc375bc70fd32bd2 | Python | 724 | 27 | from typing import TYPE_CHECKING, Any
from langchain_classic._api import create_importer
if TYPE_CHECKING:
from langchain_community.document_loaders.parsers.language.python import (
PythonSegmenter,
)
# Create a way to dynamically look up deprecated imports.
# Used to consolidate logic for raising de... |
51e84d4829c8b8d04498461159b8e78116f124d3ceb23b0bc10bfe31fb37dcf6 | Python | 724 | 27 | from typing import TYPE_CHECKING, Any
from langchain_classic._api import create_importer
if TYPE_CHECKING:
from langchain_community.callbacks.sagemaker_callback import (
SageMakerCallbackHandler,
)
# Create a way to dynamically look up deprecated imports.
# Used to consolidate logic for raising depre... |
acc2a00d2586fa73830c0132ddc9764b909f732bd102620d796c38f04d359f6a | Python | 724 | 27 | from typing import TYPE_CHECKING, Any
from langchain_classic._api import create_importer
if TYPE_CHECKING:
from langchain_community.callbacks.llmonitor_callback import (
LLMonitorCallbackHandler,
)
# Create a way to dynamically look up deprecated imports.
# Used to consolidate logic for raising depre... |
bd6b74e03ed7c4e5ad4bd40d108e4e90e55f0f6a0430cea8baebfe30dab7df5c | Python | 724 | 20 | """
Plot an example subject session for each task.
"""
import subject_sessions
example_ada_pos_data_file = "data/ada-pos_subject-60290c574980dd7f8e378b84_run-63a9838a208f5a27774db1a4_2022-12-26.csv"
example_ada_pos_isess = 0
example_ada_prob_data_file = "data/ada-prob_subject-582ee44408b46b00010dbb07_run-63c01ead873... |
f3271a01b3ad7aa9160faffe8078221244124d5d7f8d2528c8a2ef29475d9412 | Python | 724 | 27 | from typing import TYPE_CHECKING, Any
from langchain_classic._api import create_importer
if TYPE_CHECKING:
from langchain_community.chat_models.baidu_qianfan_endpoint import (
QianfanChatEndpoint,
)
# Create a way to dynamically look up deprecated imports.
# Used to consolidate logic for raising depr... |
001549f11d47aa0698ed76198949ce3c020b71e0e15a61c428405c738aab4943 | Python | 725 | 34 | from logging import Logger
from pathlib import Path
from typing import List
from ..data import (AnnotationTable, WorldlineTable,
Worldline, get_nearby_max)
from ._utilities import default_args
def create_track(
dataset: Path,
annotations: AnnotationTable,
worldlines: Worldlin... |
12befe28620d1efce70d004cff515b6096c258334c163a040416a09b28e622f1 | Python | 725 | 30 | """Optional RGI integration for the ColabFold diffusion notebooks."""
SUPPORTED_MODELS = frozenset(
{
"alphafold3",
"openbind0",
"openfold3",
"boltz2",
"protenix2",
"protenix1",
"rosettafold3",
"chai1",
"opendde",
"helixfold3",
... |
78c4d00ee8bc0b276757d0c7c76c00a9920a8fad49a211f4c905c89138628e37 | Python | 725 | 25 | from typing import TYPE_CHECKING, Any
from langchain_classic._api import create_importer
if TYPE_CHECKING:
from langchain_community.query_constructors.elasticsearch import (
ElasticsearchTranslator,
)
# Create a way to dynamically look up deprecated imports.
# Used to consolidate logic for raising de... |
f2c715ce6fd7d49bca2d26050eb8295e6d5f220859618985a3c84389164aaea5 | Python | 725 | 27 | from typing import TYPE_CHECKING, Any
from langchain_classic._api import create_importer
if TYPE_CHECKING:
from langchain_community.document_loaders.baiducloud_bos_file import (
BaiduBOSFileLoader,
)
# Create a way to dynamically look up deprecated imports.
# Used to consolidate logic for raising dep... |
3b6f6df6ef4ffe5f24136078b21d4e888056a2b4428401516cf2eaf9b19655d9 | Python | 726 | 20 | from langchain_core.embeddings import DeterministicFakeEmbedding
def test_deterministic_fake_embeddings() -> None:
"""Test that DeterministicFakeEmbedding is deterministic.
Test that the deterministic fake embeddings return the same
embedding vector for the same text.
"""
fake = DeterministicFake... |
b119407bab1e2f0b8ebcd6e81899a7d3d293a2c616c849bc8c2eb0c93d229af7 | Python | 726 | 27 | from typing import TYPE_CHECKING, Any
from langchain_classic._api import create_importer
if TYPE_CHECKING:
from langchain_community.agent_toolkits.powerbi.chat_base import (
create_pbi_chat_agent,
)
# Create a way to dynamically look up deprecated imports.
# Used to consolidate logic for raising depr... |
b85961324d6ec6c648b8f447dd8d29582f50e02b1b38f3a4adb10b4ed4be5e0c | Python | 726 | 15 | import re, os
ROOT = os.path.join(os.path.dirname(__file__), "..")
s = open(os.path.join(ROOT, "paper", "main.tex"), encoding="utf-8").read()
a = re.search(r"\\begin\{abstract\}(.*?)\\end\{abstract\}", s, re.S).group(1)
a = a.replace("\\%", "PCT")
a = re.sub(r"%[^\n]*", "", a)
a = a.replace("PCT", "%").replace("\\,", "... |
c08b989de086ceb9378ef3d972a4387e5d3e9d2cd7aebbb85ea469fc669ff715 | Python | 726 | 27 | from langchain_classic import prompts
EXPECTED_ALL = [
"AIMessagePromptTemplate",
"BaseChatPromptTemplate",
"BasePromptTemplate",
"ChatMessagePromptTemplate",
"ChatPromptTemplate",
"FewShotPromptTemplate",
"FewShotPromptWithTemplates",
"HumanMessagePromptTemplate",
"LengthBasedExamp... |
c9e0014c557d483c340751da6f2c59bae96de8509718ab1f2b38e5b27431138e | Python | 727 | 26 | from typing import TYPE_CHECKING, Any
from langchain_classic._api import create_importer
if TYPE_CHECKING:
from langchain_community.document_loaders.pyspark_dataframe import (
PySparkDataFrameLoader,
)
# Create a way to dynamically look up deprecated imports.
# Used to consolidate logic for raising ... |
024db7e9403cd9a45648eb698e6fc0cb51a776bf62bee1055495300151ba58b5 | Python | 728 | 23 | #!/usr/bin/env python
# Imports
import unittest
import os.path
import sys
import subprocess
###############################################################################
path_to_script = os.path.join(os.path.dirname(os.path.realpath(__file__)),'..','bin','enrichm')
path_to_data = os.path.join(os.path.dirname(os.pat... |
0b8fe640ca6268ce7adaf7da0bbdf3a1f7901a0621a8d5f34aaacf23fd2cb14e | Python | 728 | 25 | from langchain_core.messages import (
AIMessage,
AIMessageChunk,
HumanMessage,
HumanMessageChunk,
SystemMessage,
SystemMessageChunk,
ToolMessage,
ToolMessageChunk,
)
from langchain_core.prompt_values import ChatPromptValueConcrete
def test_chat_prompt_value_concrete() -> None:
mess... |
75efc34e1e1ed6e1b34b396fb25d93a040ca8b1d9b0f8bdb66182614b6c5b0fe | Python | 728 | 23 | import tensorflow as tf
from tensorflow.keras.layers import Activation, ReLU
from typing import List
from .layer import LRPLayer
class ReLULRP(LRPLayer):
def __init__(self, layer, *args, name: str = 'relu_lrp', **kwargs):
assert isinstance(layer, ReLU) or \
(isinstance(layer, Activation) ... |
b441d5dc9e61de1332c5efef202f3ffa78f21332715417ed11149dd62300f113 | Python | 728 | 24 | # third-party modules
import numpy as np
def generateUniformSpherePoints(n, r=1):
"""Implemented from note by Markus Deserno: https://www.cmu.edu/biolphys/deserno/pdf/sphere_equi.pdf"""
alpha = 4.0*np.pi*r*r/n
d = np.sqrt(alpha)
m_nu = int(np.round(np.pi/d))
d_nu = np.pi/m_nu
d_phi = alpha... |
55c110a2507e388350ef75736dd2d73bdd2e10a6d29fbf848cab3015de1311c8 | Python | 729 | 27 | 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 deprecation warnings and
# handling o... |
d78919c121406d64b880d8e65998f3af690f5758adea487a9cc14ad6e6632f61 | Python | 729 | 21 | from setuptools import setup
# with open("README.rst", "r", encoding="utf-8") as f:
# __long_description__ = f.read()
if __name__ == "__main__":
setup(
name = "SEDR",
version = "1.0.0",
description = "Unsupervised spatially embedded deep representation of spatial transcriptomics.",
... |
1908eb8cff28bfb890f14399c53e6ef8c1668bb41fa1962ed9622468a8e378b5 | Python | 730 | 18 | """
This simple example uses pycromanager to vary exposure times with three repetitions
and can be run with Micro-manager's virtual DemoCamera / DCam device. The resulting
dataset is saved to 'democam_X/Full Resolution/democam_MagellanStack.tif` within the
current folder; consecutively numbered `X` separate individual ... |
34e8fba99b5f352ce1719f2eed907ee976fdcc4008517fd995869d122c2addb8 | Python | 730 | 27 | """Google Scholar API Toolkit."""
from typing import TYPE_CHECKING, Any
from langchain_classic._api import create_importer
if TYPE_CHECKING:
from langchain_community.tools.google_scholar.tool import GoogleScholarQueryRun
# Create a way to dynamically look up deprecated imports.
# Used to consolidate logic for r... |
4adbf18446ffd7c963e91e8ac361de0fd19bef836d1ac2603f87b156b21b2794 | Python | 730 | 28 | import torch
import torch.nn.functional as F
from torch.autograd import Variable
import numpy as np
def _iou(pred, target, size_average = True):
b = pred.shape[0]
IoU = 0.0
for i in range(0,b):
#compute the IoU of the foreground
Iand1 = torch.sum(target[i,:,:,:]*pred[i,:,:,:])
Ior1... |
c2ea52d710cc1e163b4f1deaa06aff1f3f6f84afcb28c709676b81729005f946 | Python | 730 | 27 | """Google Finance API Toolkit."""
from typing import TYPE_CHECKING, Any
from langchain_classic._api import create_importer
if TYPE_CHECKING:
from langchain_community.tools.google_finance.tool import GoogleFinanceQueryRun
# Create a way to dynamically look up deprecated imports.
# Used to consolidate logic for r... |
43cb4424551ba1804cfd10e90caccfe12dff38baeedaa9d4c358072d5e9fc8c1 | Python | 732 | 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 ... |
81c292e318a85b96540697f064c522116f61814d2581a249a2f3ae7901cc2888 | Python | 732 | 26 | import numpy as np
import torch
from neurovisfit.common.random import set_random_seed
def test_set_random_seed():
seed = 123
deterministic = True
set_random_seed(seed, deterministic)
# Check NumPy random seed
assert np.random.get_state()[1][0] == seed
# Check PyTorch random seed
assert... |
2d9485a4ef6cedee5a5c1f165ac82ab791b66ddb9b48871790366eaeeee4ef51 | Python | 733 | 19 | from langchain_core.prompts.prompt import PromptTemplate
_template = """Given the following conversation and a follow up question, rephrase the follow up question to be a standalone question, in its original language.
Chat History:
{chat_history}
Follow Up Input: {question}
Standalone question:""" # noqa: E501
CONDE... |
7ac598e0641409d496b91a422b64141f75d09f2871dfe67849c5f2fdc05ef468 | Python | 733 | 33 |
import pandas as pd
from PoET import POET
# =============================================================================
# Perform tracking of videos
# =============================================================================
# instantiate POET object with path to video folder
folder = './data/'
poet = POET(fo... |
85beee2c567d2de74501f3bcf18605f9fe9f6066ef94c967bf91a2914ef4b70b | Python | 733 | 27 | from typing import TYPE_CHECKING, Any
from langchain_classic._api import create_importer
if TYPE_CHECKING:
from langchain_community.chat_message_histories import (
UpstashRedisChatMessageHistory,
)
# Create a way to dynamically look up deprecated imports.
# Used to consolidate logic for raising depre... |
509329c3e49c4ac3c8631fc5eccf70992c3aed79f14c34e60b85bad51c4d2d62 | Python | 734 | 23 | import pnabind.utils
import pnabind.structure
import pnabind.mesh
import pnabind.nn
from .map_structure_features_to_mesh import mapStructureFeaturesToMesh
from .assign_vertex_labels_to_mesh import assignMeshLabelsFromStructure, AtomToClassMapper, assignMeshLabelsFromList, maskClassBoundary
from .vertex_labels_to_resid... |
82c97fae24c5dbaa5a53ed311b072d50f7e870f93db67cc8d6bfe7c7d3cf48fe | Python | 734 | 18 | # Copyright (c) MONAI Consortium
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
# http://www.apache.org/licenses/LICENSE-2.0
# Unless required by applicable law or agreed to in writing, so... |
aa4822674ee5feb610f4acfd8b174a760a803242dd47934b4b755d5c740fe93a | Python | 734 | 29 | from langchain_core.prompts import __all__
EXPECTED_ALL = [
"AIMessagePromptTemplate",
"BaseChatPromptTemplate",
"BasePromptTemplate",
"ChatMessagePromptTemplate",
"ChatPromptTemplate",
"DictPromptTemplate",
"FewShotPromptTemplate",
"FewShotPromptWithTemplates",
"FewShotChatMessageP... |
c19c05d5ce00ceeac4f40da75cda0ebfc00751450e8c06a62ae5f25e99c40df9 | Python | 734 | 27 | from typing import TYPE_CHECKING, Any
from langchain_classic._api import create_importer
if TYPE_CHECKING:
from langchain_community.callbacks.promptlayer_callback import (
PromptLayerCallbackHandler,
)
# Create a way to dynamically look up deprecated imports.
# Used to consolidate logic for raising d... |
4e8f30640984ad1ff054cc3324926e65036e0e5d64e49f1eeaa867aebda8903b | Python | 735 | 27 | from typing import TYPE_CHECKING, Any
from langchain_classic._api import create_importer
if TYPE_CHECKING:
from langchain_community.tools import SearxSearchResults, SearxSearchRun
# Create a way to dynamically look up deprecated imports.
# Used to consolidate logic for raising deprecation warnings and
# handling... |
0970a5b9041b4d3cdbfc5014ebc53caaa2c534afc46bb665aff69d0cbbf04594 | Python | 736 | 27 | from typing import TYPE_CHECKING, Any
from langchain_classic._api import create_importer
if TYPE_CHECKING:
from langchain_community.chat_message_histories import (
SingleStoreDBChatMessageHistory,
)
# Create a way to dynamically look up deprecated imports.
# Used to consolidate logic for raising depr... |
1493e5173593bf519421baad33f5ba5af07fb7d274135cdb51aaacda25658dee | Python | 736 | 18 | import torch
from nequip.nn import with_edge_vectors_
from nequip.data import AtomicDataDict
from allegro._compile import allegro_data_settings
def test_pair_allegro_ghost_consistency(Cu_bulk):
_, data = Cu_bulk
pair_allegro_data = allegro_data_settings(data.copy())
pair_allegro_data = with_edge_vectors_(... |
d8ff7efa26908a107649d15db9e154334629e74c231d7c0080f78dab3ad8f53e | Python | 736 | 27 | from typing import TYPE_CHECKING, Any
from langchain_classic._api import create_importer
if TYPE_CHECKING:
from langchain_community.chat_message_histories import (
ElasticsearchChatMessageHistory,
)
# Create a way to dynamically look up deprecated imports.
# Used to consolidate logic for raising depr... |
3207fb1ec2d277881d4b3e66aebc2a326dcaa9a8594c4d9a06fc71e97f9faf10 | Python | 737 | 24 | # pnabind modules
from .get_residue_id import getResidueID
def getSurfaceResidues(structure, area_key='sesa', threshold=0.0, hydrogens=False):
atoms = structure.get_atoms()
# get residue area values
residueArea = {} # dict to map rid to an area value
for atom in atoms:
if (not hydrogens) a... |
52a8cf94c6ad6539033b2fb5cd3cd815e1eeae1bbea628ac65a38b7512430167 | Python | 737 | 29 | from langchain_core.agents import AgentAction, AgentFinish
from langchain_classic.agents.output_parsers.json import JSONAgentOutputParser
def test_tool_usage() -> None:
parser = JSONAgentOutputParser()
_input = """ ```
{
"action": "search",
"action_input": "2+2"
}
```"""
output = parser.invoke(_in... |
9f6a18eb2ed1d20b64ea1a4149ad560526915310fe508244c704b0ab463066d8 | Python | 737 | 27 | 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.
# Used to consolidate logic for raising ... |
b4d9831ea75496d4f50d8d1d2b5c76831635f76e2ed93383de625eafcf2dc8c9 | Python | 738 | 27 | from typing import TYPE_CHECKING, Any
from langchain_classic._api import create_importer
if TYPE_CHECKING:
from langchain_community.tools import RedditSearchRun, RedditSearchSchema
# Create a way to dynamically look up deprecated imports.
# Used to consolidate logic for raising deprecation warnings and
# handlin... |
44e78ff16c7bb49f112860efee563f0d68a38265ace5723366cd178ba815b090 | Python | 739 | 23 | import yaml
import argparse
def load_config(config_path: str) -> dict:
""" Load configuration from YAML file. """
with open(config_path, 'r') as file:
return yaml.safe_load(file)
def parse_arguments(default_subjects: list) -> list:
""" Argument parser for parsing from command-line. """
parse... |
fc5f88086db0201abe5ada08c79ded84ff6599dd123dc4dabda92d0d3f879782 | Python | 739 | 24 | import os
import random
def obtain_files_list():
for root, dirs, files in os.walk(training_set_path):
return files
def rename_step_files(rename_list):
for i, file_name in enumerate(rename_list):
old_file = training_set_path + "\\" + file_name
new_file = training_set_path + "\\" + str... |
1ae56cb007aa7038681863bf12c75890ad963ab91ffc7d32cc98335a741246ad | Python | 741 | 22 | from langchain_core.language_models import BaseLanguageModel
from langchain_core.output_parsers import StrOutputParser
from langchain_core.prompts.few_shot import FewShotPromptTemplate
from langchain_core.prompts.prompt import PromptTemplate
TEST_GEN_TEMPLATE_SUFFIX = "Add another example."
def generate_example(
... |
3b513aa011f8093bf88840d495a3d222fc47b5048509571327726b75d030a8e2 | Python | 741 | 34 | #!/bin/env python
import web, os
from cgatReport import Cache
from cgatReport import Utils
from cgatReport import DataTree
urls = ( '/data/(.*)', 'DataTable',
'/index/(.*)', 'Index' )
# expose zip within templates
global_vars = {'zip': zip }
render = web.template.render('templates/', globals = global_var... |
61ec3708fe9252b6fd6fe1ec4381fa92d08e94818cba60cb7a81d5482e46bf64 | Python | 741 | 27 | from typing import TYPE_CHECKING, Any
from langchain_classic._api import create_importer
if TYPE_CHECKING:
from langchain_community.tools.memorize.tool import Memorize, TrainableLLM
# Create a way to dynamically look up deprecated imports.
# Used to consolidate logic for raising deprecation warnings and
# handli... |
8090f5bc714c5f9b7e38cc7f4414170e5e52f4ba4194c8f57aadfb24f37c4fd6 | Python | 741 | 27 | from typing import TYPE_CHECKING, Any
from langchain_classic._api import create_importer
if TYPE_CHECKING:
from langchain_community.tools import GoogleSerperResults, GoogleSerperRun
# Create a way to dynamically look up deprecated imports.
# Used to consolidate logic for raising deprecation warnings and
# handli... |
84405012a2234066bf076b6fbb97a70c98b8a3d423cd6c2c24639cc5b3f2acfe | Python | 741 | 27 | 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 deprecation warnings and
# handli... |
aa5d0a2466f79aefbd4eb5f767df2126b69c9090dd6a75aa8f43c1b93f7a5cde | Python | 741 | 28 | ## Run each command in parallel
import argparse
import pandas as pd
from os import system,environ
def get_cmd(task, tissue):
return pd.read_csv(f"{tissue}.assemble.cmd",
header=None).iloc[task-1,0]
def run_sge(task, tissue):
cmd = get_cmd(task, tissue)
system(cmd)
def main():
... |
bff889c743e6649009ac969e5a4bb8dd9d67e6491e26b3ce2fa4f33c66e459fe | Python | 742 | 20 | import mne
import os.path as op
from config_FaceName import MEG_data_path,group_name,Ids
for subject_id in Ids:
subject = group_name+"%02d" % subject_id
print("processing subject: %s" % subject)
fname=op.join(MEG_data_path,subject,'fname'+'_%02d'%(subject_id)+'_tsss_mc.fif')
ep... |
81422ba2a99a04d701929f68b9c6659dbeab1c0c404dd11c3ed0556997595257 | Python | 743 | 28 | from typing import TYPE_CHECKING, Any
from langchain_classic._api import create_importer
if TYPE_CHECKING:
from langchain_community.llms import AI21
from langchain_community.llms.ai21 import AI21PenaltyData
# Create a way to dynamically look up deprecated imports.
# Used to consolidate logic for raising depr... |
80a19e2b5d11af8d1cce283b704ee26fc4fa13c0b281d14464d045a5b134ab86 | Python | 744 | 27 | from typing import TYPE_CHECKING, Any
from langchain_classic._api import create_importer
if TYPE_CHECKING:
from langchain_community.vectorstores import Clickhouse, ClickhouseSettings
# Create a way to dynamically look up deprecated imports.
# Used to consolidate logic for raising deprecation warnings and
# handl... |
d45ae9fe4d0cd0851956ca382c6c9452cac7f0288ebf2660e8c7d995377e719d | Python | 744 | 27 | from typing import TYPE_CHECKING, Any
from langchain_classic._api import create_importer
if TYPE_CHECKING:
from langchain_community.llms.loading import load_llm, load_llm_from_config
# Create a way to dynamically look up deprecated imports.
# Used to consolidate logic for raising deprecation warnings and
# handl... |
5a758fb65698cc3219d31305ad08a845364579b196e74fc1b165843a85474642 | Python | 745 | 25 | import pytest
import torch
from chroma.layers.structure import backbone, symmetry
class Test_symmetry:
@pytest.mark.parametrize("group", ["C_2", "C_4", "D_2", "D_4", "T", "O", "I"])
def test_point_groups(self, group):
G = symmetry.get_point_group(group)
# test if the determinants are ones fo... |
a569e565179c767ac9005822bab7dd421890bb46424a9821c4b7468720f32767 | Python | 745 | 27 | import numpy as np
from ..brain import Brain
from ..utils import path
def test_ntf_parameters():
"""Check whether a Brain class is being initialized correctly."""
new_brain = Brain.Brain()
default_ntf_params = {
"tau_e": 0.012,
"tau_i": 0.003,
"alpha": 1.0,
"speed": 5.0,
... |
f41da006b6e893a757245ea99f584313574d7801eddd243f7c5705dcfd8b8c2a | Python | 746 | 28 | from typing import TYPE_CHECKING, Any
from langchain_classic._api import create_importer
if TYPE_CHECKING:
from langchain_community.llms import Bedrock
from langchain_community.llms.bedrock import BedrockBase
# Create a way to dynamically look up deprecated imports.
# Used to consolidate logic for raising de... |
badd4ee3f10b89db76dde164575b527c099e354c9ec0024a39bee061112cdfc5 | Python | 747 | 27 | from typing import TYPE_CHECKING, Any
from langchain_classic._api import create_importer
if TYPE_CHECKING:
from langchain_community.utilities.opaqueprompts import desanitize, sanitize
# Create a way to dynamically look up deprecated imports.
# Used to consolidate logic for raising deprecation warnings and
# hand... |
6513c77c5833f9d7d4529ec198cea9f4deff3274e957099b0c5d73b94b242c07 | Python | 748 | 31 | import torch
import torch.nn as nn
import torch.nn.functional as F
import numpy as np
class Discriminator(nn.Module):
def __init__(self, v_ft, u_ft):
super().__init__()
self.bilinear = nn.Bilinear(v_ft, u_ft, 1)
self.act = nn.Sigmoid()
for m in self.modules():
self.weig... |
c3fc7a23a567bcc64d00b318bc7a6f9f1609769eee3753f825aef2599dd5de61 | Python | 748 | 24 | import numpy as np
import torch
from torch.autograd import Variable
def data_generator(T, mem_length, b_size):
"""
Generate data for the copying memory task
:param T: The total blank time length
:param mem_length: The length of the memory to be recalled
:param b_size: The batch size
:return: ... |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.