sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
fed61f7cd59871fb39c22c72744ffebe7557cdc9eacc2b48398769e06601822b | Python | 945 | 33 | from typing import TYPE_CHECKING, Any
from langchain_classic._api import create_importer
if TYPE_CHECKING:
from langchain_community.callbacks.streamlit.mutable_expander import (
ChildRecord,
ChildType,
MutableExpander,
)
# Create a way to dynamically look up deprecated imports.
# Used... |
094c7bc535c7251d00e5cd9cf1f06cde746f9e497b99f51a9b7b3a656ed9b9c3 | Python | 946 | 36 | """Test suite for the util module."""
import os
from nose.tools import with_setup
from ..utils import path
def f_setup():
"""Creates test file in `./data/` dir."""
open("../data/test.txt", "w")
def f_teardown():
"""Removes test file from `./data/` dir."""
files = os.listdir("../data/")
if "test... |
114342e246d824a903ab325dfd0cb7638bea70b0a5aeb089e6ac1e5aca204be8 | Python | 946 | 32 | ''' Module initializer includes all sub-modules.
:Version:
1.0
:Date:
06.06.2016
:Author:
Jan Melchior
:Contact:
JanMelchior@gmx.de
:License:
Copyright (C) 2016 Jan Melchior
This program is free software: you can redistribute it and/or m... |
1eb9d7da062e6cdba04da7c83d3f1cf10bb0204b541de19732e08c7b01efaebd | Python | 946 | 32 | ''' Module initializer includes all sub-modules.
:Version:
1.0
:Date:
08.02.2016
:Author:
Jan Melchior
:Contact:
JanMelchior@gmx.de
:License:
Copyright (C) 2016 Jan Melchior
This program is free software: you can redistribute it and/or m... |
784eb2348138e9b39a990100cc0527710b6e58f4231b93b8d8aaedd2ab553ba4 | Python | 946 | 23 | import glob
import os
import subprocess
import pandas as pd
from tqdm import tqdm
list_biscov = glob.glob('./data/**/*bismark.cov*', recursive=True) +\
glob.glob('./data/**/*bismark.sort.cov*', recursive=True)
list_xbpwin = glob.glob('./data/**/*bpwin.bed*', recursive=True)
for winbp in tqdm(['100','500','1000']):
... |
8c2db49ee23fc2534d4cbe672ca2b3d286c0aa6a0b9ae547e018a1520c600f64 | Python | 946 | 25 | # Copyright 2022 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 writi... |
1f8bb1bc3a74bb8eadf3692488ce17dfdc92c25ad2f00900d5187d056b8354d3 | Python | 947 | 29 | from typing import TYPE_CHECKING, Any
from langchain_classic._api import create_importer
if TYPE_CHECKING:
from langchain_community.retrievers.web_research import (
QuestionListOutputParser,
SearchQueries,
WebResearchRetriever,
)
# Create a way to dynamically look up deprecated import... |
45ce180a01650b151e02f78d17a1e5905065ccd71798e58295309a487f02717f | Python | 947 | 47 | '''
Created on Oct 17, 2011
@author: yjin
'''
def base_m(m_ref1,m_ref2):
target = []
for i in range(len(m_ref1)):
target.append((m_ref1[i]+m_ref2[i])/2)
return target
def raw_count_mean(m_ref1,m_ref2,norm_ref) :
target_ref = []
for i in range(len(m_ref1)):
target_ref.append(raw_... |
e1e1e8c0b1dd7eede87fab87dc764161d0ebcbee18d6652ec67bbb28802f3a56 | Python | 947 | 39 | import sys
sys.path.append("/yourpath/comformer")
from comformer.train_props import train_prop_model
props = [
"formation_energy_peratom",
"optb88vdw_bandgap",
"bulk_modulus_kv",
"shear_modulus_gv",
"mbj_bandgap",
"slme",
"magmom_oszicar",
"spillage",
"kpoint_length_unit",
"encu... |
c3e87ce51a8be4995468a56a409e4dfe956ea2321732dfc4be8326f9a9ab5285 | Python | 948 | 25 | # third party modules
import numpy
def visualizeMesh(mesh, data=None, color_map='seismic', shift_axis='x', **kwargs):
if data is None:
return mesh.show(**kwargs)
try:
import trimesh
except ModuleNotFoundError:
raise ModuleNotFoundError("The dependency 'Trimesh' is required for this ... |
00f5088c7df22dbe6950a3b247e1b96f1ff9b9324209b28da982b1b1abedd1df | Python | 949 | 33 | from typing import TYPE_CHECKING, Any
from langchain_classic._api import create_importer
if TYPE_CHECKING:
from langchain_community.callbacks.aim_callback import (
AimCallbackHandler,
BaseMetadataCallbackHandler,
import_aim,
)
# Create a way to dynamically look up deprecated imports.
... |
067b19fcf45167d2feb079b2ef35354056ab98952e7e3a34a6f489a5a898ac76 | Python | 950 | 35 | import pandas as pd
pd.set_option('display.max_columns', None)
pd.set_option('display.max_rows', 80)
import re
from IPython.core.interactiveshell import InteractiveShell
InteractiveShell.ast_node_interactivity = "all"
# more inclusive
all_df = pd.read_csv('ALL_SOURCES_ALL_FREQUENCIES_genes_to_phenotype.txt', sep='\t... |
1f2086ff098b4ebc21318c908ef0a16dd8763e86b1de5b3481deee686ee4c052 | Python | 950 | 28 | ### Revert ordering and save likelihoods
import sys
sys.path.append('/project/src/python/')
from pathlib import Path
import mlflow.pytorch
import torch
import numpy as np
run_dir="get_likelihood_ADHD200_8"
transformer_uri="/project/mlruns/0/281c9ece0d8f44d6b05f4ce1836fda35/artifacts/final_model"
output_dir = Path("... |
e841e25535ee8e9171bb7c4e69045ba743aebe22584e3cb10dfea50d4f73fdd5 | Python | 950 | 35 | def plot_roi_step(roi_path, template_path, title=None, cut_coords=(0, -34, -9), cmap='autumn', threshold=0.0, draw_cross=False, save_path=None):
'''
Plot an ROI mask over a template brain and optionally save the figure.
'''
from nilearn import plotting, image
import matplotlib.pyplot as plt
im... |
b48d399339fe8a2f6238507421550eded17bb619db993876c7ebc7a2f8b12776 | Python | 951 | 31 | import os
import random
import shutil
def obtain_files_list():
for root, dirs, files in os.walk(test_set_path):
return files
def move_step_files(move_list):
for file_name in move_list:
move_file = test_set_path + "\\" + file_name
new_path = val_set_path + "\\" + file_name
shu... |
0c403ce5440950ddaf143c0fada0e17001277395dc85e9cdd2c08b7a8a5ea929 | Python | 952 | 28 | #!/usr/bin/env python
import os
import tempfile
class IntersectedBED:
@staticmethod
def intersectRegions(snps, regions, bed, wb = False):
if os.system("bedtools intersect -a \"{snps}\" -b \"{regions}\" -wa {wb} | sort | uniq > {bed}".format(
snps = snps, regions = regions, bed = bed, wb =... |
28d98d28b267372ea3417b41b900d9e8f3fe65dbc7b79d0e96b3037173343cf2 | Python | 952 | 29 | """Signature inspection that does not evaluate annotations."""
import inspect
import sys
from collections.abc import Callable, Mapping
from typing import Any
if sys.version_info >= (3, 14):
from annotationlib import Format
def _signature_parameters(obj: Callable[..., Any]) -> Mapping[str, inspect.Parameter]:
... |
0b634fa5f46725e9b54b055b28fabec185b7b045c23f77eb7ca9e473df4b3c7a | Python | 953 | 29 | from mimic3models import common_utils
import numpy as np
import os
def load_data(reader, discretizer, normalizer, small_part=False, return_names=False):
N = reader.get_number_of_examples()
if small_part:
N = 1000
ret = common_utils.read_chunk(reader, N)
data = ret["X"]
ts = ret["t"]
la... |
d540578e6839eba8f1363da502aeef28f1eeb245964ef0c19ca504134c384805 | Python | 956 | 28 | from tensorflow.keras import layers
from tensorflow.keras.models import Sequential
class ReadoutLayer(layers.Layer):
def __init__(
self,
hidden_size,
num_readout_fc_layers,
name='readout_layer',
num_targets=12,
activation=None,
kernel_initializer='glorot_uni... |
8590e94c3cc1f92843eed2240685f47d7af60ae8e622b021a7339101486e2819 | Python | 957 | 36 | #### Combine data
import session_info
import polars as pl
import pandas as pd
def load_data(tissue, dx):
new_dx = dx.replace("SZD", "SZ")
fn = f"../../_m/{tissue.lower()}/{dx}/zsummary_table.tsv"
return pl.from_pandas(pd.read_csv(fn, sep='\t')\
.reset_index()\
... |
da6f9a144fc2252f801f3a1ca2469d40eec0b5dde3254c3f458281eb5c4661ee | Python | 959 | 22 | import numpy as np
from sys import argv
argc = len(argv)
fit_r0_file = argv[1]
fit_r1_file = argv[2]
fit_err_file = argv[3]
fxlen = int(argv[4])
fit_r0 = np.fromfile(fit_r0_file, dtype=np.float32).reshape((fxlen, fxlen))
fit_r1 = np.fromfile(fit_r1_file, dtype=np.float32).reshape((fxlen, fxlen))
fit_err = np.fromfile... |
3ea3d853ec9f40f648250e2c2daa076bb7b4fe5c1ecc6e5fd775a15930e42a0f | Python | 960 | 33 | class BoundingBox:
def __init__(self, classID, confidence, x1, x2, y1, y2, image_width, image_height):
self.classID = classID
self.confidence = confidence
self.x1 = x1
self.x2 = x2
self.y1 = y1
self.y2 = y2
self.u1 = x1 / image_width
self.u2 = x2 / ima... |
7b6f3cb51e3eb889201b7a7cae9860a9114db7b83cac183b0e0bc46c6c92981e | Python | 961 | 33 | from typing import TYPE_CHECKING, Any
from langchain_classic._api import create_importer
if TYPE_CHECKING:
from langchain_community.vectorstores import TencentVectorDB
from langchain_community.vectorstores.tencentvectordb import (
ConnectionParams,
IndexParams,
)
# Create a way to dynamic... |
8d1fe55585411dcbc21885124a10ca64a563501518bd0c5193043f99c00f7805 | Python | 961 | 27 | import pandas as pd
import matplotlib.pyplot as plt
df = pd.DataFrame({
"Ratio of training set" : [.0, .2, .4, .6, .8, 1],
"Avg_pwn_one_inter" : [0.532047788, 0.612610353, 0.634283209, 0.663306835, 0.707324699, 0.734117295],
# "Avg_pwn_no_inter" : [0.0, 0.0, 0.0, 0.0, 0.0, 0.0]
})
plt.plot(df["Ratio of tr... |
b3b7068fee1e9ecbddd58a458ea40bcaa30dc099add09adde58544607af1601b | Python | 961 | 23 | from train_prop import train_prop_model
import yaml
import argparse
# Set up argument parser
if __name__ == '__main__':
parser = argparse.ArgumentParser(description='Training configuration of PotNet')
parser.add_argument('--config', type=str, help='Path to YAML configuration file')
parser.add_argument('--... |
24d41740e12d406e2479b6682c3c65f91df9468b38662222c9e836836aff09b8 | Python | 964 | 29 | clmns = ["290", "293", "296", "299", "302", "305", "308", "311", "314", "317", "320", "323", "326", "329", "332", "335"]
threads = len(clmns)
import pandas as pd
import sys,os
file_name = 'Cell'
idf = sys.argv[1] + '_' + sys.argv[2] + '_' + sys.argv[3]
at_least = 0
values = []
names = []
for i in range(th... |
878b8ac21fd7246c62cd263fd690707d5e13fa6163148a1fdfdf2e8993fbf7fb | Python | 964 | 34 | import os
import cv2
from glob import glob
from tqdm import tqdm
from joblib import Parallel,delayed
from engine import utils
from constants import NIH_DIR,CXRAY_SZ
def resize_nih_images():
def resize_save(src):
name = src.split('/')[-1].replace('.png','.jpg')
dst = '%snih_images_320/%s'%(NI... |
8b870b6b10392bb04ef1397b96a53df527af8842ac09a5cc855f3fc814afae32 | Python | 964 | 29 | clmns = ["290", "293", "296", "299", "302", "305", "308", "311", "314", "317", "320", "323", "326", "329", "332", "335"]
threads = len(clmns)
import pandas as pd
import sys,os
file_name = 'Cell'
idf = sys.argv[1] + '_' + sys.argv[2] + '_' + sys.argv[3]
at_least = 0
values = []
names = []
for i in range(th... |
8ed255ede9a0deb5ed9366a14095187b4ba396e16ff672cecaea858b03fca816 | Python | 964 | 29 | clmns = ["290", "293", "296", "299", "302", "305", "308", "311", "314", "317", "320", "323", "326", "329", "332", "335"]
threads = len(clmns)
import pandas as pd
import sys,os
file_name = 'Cell'
idf = sys.argv[1] + '_' + sys.argv[2] + '_' + sys.argv[3]
at_least = 0
values = []
names = []
for i in range(th... |
a8711e719e47752eba9959aaf178bcb0fbe661f9d6e6df657cc44cbe53059ec0 | Python | 964 | 33 | from typing import TYPE_CHECKING, Any
from langchain_classic._api import create_importer
if TYPE_CHECKING:
from langchain_community.vectorstores import Redis
from langchain_community.vectorstores.redis.base import (
RedisVectorStoreRetriever,
check_index_exists,
)
# Create a way to dynami... |
ee440d3c3d09769fb2cf62c164d93cc465f2d92753b3f21258eab6dcd936f362 | Python | 964 | 35 | import torch
import torch.nn as nn
from torch.autograd import Function
class ReverseLayerF(Function):
@staticmethod
def forward(ctx, x, alpha):
ctx.alpha = alpha
return x.view_as(x)
@staticmethod
def backward(ctx, grad_output):
output = grad_output.neg() * ctx.alpha
re... |
340ba75104c62ba329a3e0ac5e891a264093c17a88e71e61c4d0bd0d8a410757 | Python | 965 | 33 | from typing import TYPE_CHECKING, Any
from langchain_classic._api import create_importer
if TYPE_CHECKING:
from langchain_community.tools import BearlyInterpreterTool
from langchain_community.tools.bearly.tool import (
BearlyInterpreterToolArguments,
FileInfo,
)
# Create a way to dynamica... |
ca5552c57bcebd71e0a15cc3270f02056e10fdd8de32b8355691cd0bfd71f847 | Python | 966 | 33 | from typing import TYPE_CHECKING, Any
from langchain_classic._api import create_importer
if TYPE_CHECKING:
from langchain_community.vectorstores.utils import (
DistanceStrategy,
filter_complex_metadata,
maximal_marginal_relevance,
)
# Create a way to dynamically look up deprecated imp... |
61e935130f8830b117daa554d003a99ff99bf9d8d8475cf387afb6f1cf2f0f58 | Python | 967 | 30 | import pytest
from langchain_core.utils.iter import batch_iterate
@pytest.mark.parametrize(
("input_size", "input_iterable", "expected_output"),
[
(2, [1, 2, 3, 4, 5], [[1, 2], [3, 4], [5]]),
(3, [10, 20, 30, 40, 50], [[10, 20, 30], [40, 50]]),
(1, [100, 200, 300], [[100], [200], [300... |
2f2a94d05a674bc4a0816223c4b2f50eb0ea8a2ef281aedcce53a04aba087b3a | Python | 968 | 38 | from logging import Logger
from pathlib import Path
from typing import List
from ..data import AnnotationTable, WorldlineTable, Annotation
def insert_annotation(
dataset: Path,
annotations: AnnotationTable,
worldlines: WorldlineTable,
window_state,
arg: str,
logger: Logger
) -> List[dict]:
... |
95a5ed2e7b45babf78df37f61a2313da7cb7daf016e12e1cac34ef74ef01f777 | Python | 968 | 34 | """Top-level package for MRdataset."""
__author__ = """Pradeep Raamana"""
__email__ = 'raamana@gmail.com'
# __version__ = '0.1.0'
import logging
import sys
from MRdataset.config import configure_logger
logger = logging.getLogger(__name__)
logger = configure_logger(logger, output_dir=None, mode='w')
from MRdataset.... |
99038d41b7c97851a363ccd549cea6be95aaf670d01f1121688e8772acb6b6c5 | Python | 968 | 25 | # this is a class to contain all parameters for a run
# it also contains parameters generated at runtime
class RunParameters:
# empirical hyperparameter 0.001; 1000; 10000; 512*4
LEARNING_RATE = LR = 1 * 10 ** -3
BATCH_SIZE = 1000
MAX_EPOCHS = 10000
FINGERPRINT_VECTOR_SIZE = FP_SIZE = 512 * 6 # ... |
33d84783ca2cb929b51f89b4b5eeb4f873fdd798a3ba280d2344d27f6c598046 | Python | 969 | 25 | """Test conversation chain and memory."""
from langchain_core.documents import Document
from langchain_core.language_models import FakeListLLM
from langchain_core.prompts.prompt import PromptTemplate
from langchain_classic.chains import create_retrieval_chain
from tests.unit_tests.retrievers.parrot_retriever import F... |
58076cd6cf675dfce6330021a729b690d63b30bee12ebdb3cb9a36c53a3fce81 | Python | 969 | 38 | """
This script consolidates qc reports from individual samples into one report
Usage: python3 consolidate_qc_report.py --qc_dir qc_logs --output_name Sinai_batch1_qc_info_bic.csv
"""
import argparse
import os
import pandas as pd
def main():
parser = argparse.ArgumentParser()
parser.add_argument(
'-... |
8d5e2ee81c27342b07bc2b2ae7a2268d3d3393b84a693165b04e8d1dc0275761 | Python | 969 | 23 | from EPI_MRI.EPIMRIDistortionCorrection import *
from optimization.GaussNewton import *
from optimization.LinearSolvers 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... |
385e43c28dc13672acd45b3301e7313c2c6200c259be3bbfa2e5d72130f9aea4 | Python | 970 | 32 | from LSTM import preprocess, train
from utils import *
from DirStrategy import get_pre_len
setting = {
'train_size': 0.8,
'epochs': 100,
'input_size': 60,
'batch_size': 16,
'pre_len': 1,
'fileName': "",
'model_name': 'cnn-lstm',
'checkpoint_ro... |
17ea710dfe62e43f5a57da0251dc35a3028785918cebd8fe2b253d20bf76ecfe | Python | 971 | 40 | #!/usr/bin/python
# see https://github.com/fabridamicelli/kuramoto
from SMdRQA.RQA2 import RQA2, RQA2_simulators, RQA2_tests, RQA2_ml
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 p... |
53b33549c6a3195099051d3fedc30809c95c416db172fbccd6a275e7345dda28 | Python | 971 | 29 | from typing import TYPE_CHECKING, Any
from langchain_classic._api import create_importer
if TYPE_CHECKING:
from langchain_community.chains.openapi.requests_chain import (
REQUEST_TEMPLATE,
APIRequesterChain,
APIRequesterOutputParser,
)
# Create a way to dynamically look up deprecated ... |
61532e5dc1dcc058c858fff39a527b03d86a88251662f0b82f50b42bdad1c012 | Python | 971 | 37 | import hydra
from hydra.core.config_store import ConfigStore
from config import Scenario
from model import Net
from make_data import make_data
from train import Trainer
from analyzer import Analyzer
from utils import plot
import numpy as np
import torch
import time
import os
cs = ConfigStore.instance()
... |
9c6900ff96e50461a9888a7a1344287d220b6784650964720d9207f21757dca2 | Python | 971 | 33 | """Package version information."""
from typing import Optional
def _get_version() -> Optional[str]:
"""
Retrieve the package version.
Using setuptools-scm dynamically sets the package version depending on the
latest git release and commits since that point. This function returns the
current versi... |
aba298e1158413c7da9b00fb7be94263137a76a58a8401f0bc6ab964d6458968 | Python | 971 | 35 | # -*- coding: utf-8 -*-
"""
Created on Thu Aug 31 13:35:22 2023
@author: biener
"""
import os
import numpy as np
import mAECell_Utils as utils
import re
File_Names = utils.fOpen(Title = 'Load Data File')
# directory/folder path
dir_path = os.path.dirname(File_Names)
Data_fName = os.path.basename(F... |
eb08ef0087508d1ae7d4c158734a650f77b587fd61089c344b291a5974e8d8fe | Python | 971 | 38 | from synister.catmaid_interface import Catmaid
import numpy as np
from get_neurotransmitter import catmaid_transform
import configargparse
import csv
p = configargparse.ArgParser()
p.add("-s", required=True,
help="FAFB skid")
p.add("-o", required=True,
help="out file")
p.add("-n", action='store_true',
... |
5ea329c78582c40389266866e040e56e7cedcb2b4e5749452974a0ae26d7dd9f | Python | 972 | 33 | from typing import TYPE_CHECKING, Any
from langchain_classic._api import create_importer
if TYPE_CHECKING:
from langchain_community.document_loaders import NotebookLoader
from langchain_community.document_loaders.notebook import (
concatenate_cells,
remove_newlines,
)
# Create a way to dy... |
757209dcf72d9ec31f7b8b7bedb03fbba0aa1222794385e2e8a78be50502e1e0 | Python | 972 | 34 | """Package version information."""
from typing import Optional
def _get_version() -> Optional[str]:
"""
Retrieve the package version.
Using setuptools-scm dynamically sets the package version depending on the
latest git release and commits since that point. This function returns the
current vers... |
c80eda0e87d6393d3fae2ae01334ce23c3907335fa74ca4e3b7f2c37df0c6742 | Python | 972 | 33 | from typing import TYPE_CHECKING, Any
from langchain_classic._api import create_importer
if TYPE_CHECKING:
from langchain_community.document_loaders import LakeFSLoader
from langchain_community.document_loaders.lakefs import (
LakeFSClient,
UnstructuredLakeFSLoader,
)
# Create a way to dy... |
db08cf0ce6333b8d8d4fa80931fc9d02da9153906e08ab53310cf288b456b34f | Python | 972 | 42 | import logging.config
import os
import torch
import random
import numpy as np
DEFAULT_RANDOM_SEED = 42
log_config_path = os.path.join(os.path.dirname(os.path.abspath(__file__)),
'logging.conf')
if not os.path.isfile(log_config_path):
raise IOError
log_output_path = "logfile.log"
... |
3d77d4465f74226397afb80f7dbac8824ce26a12b4fad20b655b7a9c7ee3058e | Python | 973 | 28 | from tensorflow.keras import layers
from tensorflow.keras.models import Sequential
class ResidualLayer(layers.Layer):
def __init__(
self,
tensor_size,
name='residual_layer',
activation=None,
use_bias=True,
kernel_initializer='glorot_uniform',
bias_initialize... |
94fbfb11207449c200eb19e87c8c05f934f4c44779d2dba9bc53d979f66a47e3 | Python | 973 | 33 | """
Transplant of pregenerated barrel annotations into the annotation_10.nrrd file. This script overwrittes parts of the SSp-bfd (primary somatosensory barrel cortex) with new barel column in the mouse annotations in place, following the indices in hierarchy.json.
Input files:
- annotation_barrels.nrrd
- annotatio... |
538f3f6e18cad7f3a54b3956bdf0b18b343266edca1284397b47c2a7ea625192 | Python | 974 | 29 | from typing import TYPE_CHECKING, Any
from langchain_classic._api import create_importer
if TYPE_CHECKING:
from langchain_community.chains.openapi.response_chain import (
RESPONSE_TEMPLATE,
APIResponderChain,
APIResponderOutputParser,
)
# Create a way to dynamically look up deprecated... |
0e464fa7d704566b27cfd48cd71b6e79f1ff7c6405bc0d96b69446ea278f3c1b | Python | 975 | 39 | """Document loaders."""
from typing import TYPE_CHECKING
from langchain_core._import_utils import import_attr
if TYPE_CHECKING:
from langchain_core.document_loaders.base import BaseBlobParser, BaseLoader
from langchain_core.document_loaders.blob_loaders import Blob, BlobLoader, PathLike
from langchain_co... |
2716d71feec76b02ebae2d45264a438ff6c80856b0f55f83a4083d5e30923267 | Python | 975 | 30 | # #! /bin/env python
# #
# # Michael Gibson 27 April 2015
# # modified by jz103 Dec 20 2021
# import numpy as np
# import scipy.signal as signal
# def notch_filter(input, fSample, fNotch, Bandwidth):
# """Implements a notch filter (e.g., for 50 or 60 Hz) on vector 'input'.
# fSample = sample rate of data (i... |
f98be17d3e26b6a3a6bad5abe78822f6f849671777f6518756d22531b9c76bc9 | Python | 975 | 28 | import warnings
from unittest.mock import MagicMock, patch
class TestHubPullDeprecation:
"""Tests that `hub.pull` is deprecated in favor of the LangSmith SDK."""
def test_pull_emits_deprecation(self) -> None:
from langchain_core._api import LangChainDeprecationWarning
from langchain_classic.... |
99d93a946a6fca07acf8c9ac8f02c22a868d12628f69d12495dfe655c58ad6f6 | Python | 976 | 30 | import numpy as np
from napari_svetlana import napari_get_reader
# tmp_path is a pytest fixture
def test_reader(tmp_path):
"""An example of how you might test your plugin."""
# write some fake data using your supported file format
my_test_file = str(tmp_path / "myfile.npy")
original_data = np.random.... |
c91b7e38d318dd5f2cb2cd0134978e76a6bbeeef925a8a023726a3619e4bd362 | Python | 976 | 44 | import click
import pandas
from pathlib import Path
@click.command()
@click.argument(
"amber_frcmod_path",
type = click.Path(),
)
def main(amber_frcmod_path):
ion_nb_params = list()
nonbonded = False
with open(Path(amber_frcmod_path), "r") as amber_frcmod_file:
for line in amber_frcmod_f... |
021cbbd485d6f2f8a882ac48b2bc675e49aab921df2eeb013adbc75d5613046a | Python | 977 | 33 | import pandas as pd
from sklearn.impute import SimpleImputer, KNNImputer
def impute(df, imputation):
"""
Apply imputation method to a DataFrame with missing values.
Parameters:
df (pd.DataFrame): Input data.
imputation (str): Method to use: 'none', 'zeros', 'median', or 'knn'.
... |
2d9135b11a56e640c56e0029ae64a8973b7800de15d23ca2594345b547c1838d | Python | 980 | 29 | clmns = ["1160", "1163", "1166", "1169", "1172", "1175", "1178", "1181", "1184", "1187", "1190", "1193", "1196", "1199", "1202", "1205"]
threads = len(clmns)
import pandas as pd
import sys,os
file_name = 'Cell'
idf = sys.argv[1] + '_' + sys.argv[2] + '_' + sys.argv[3]
at_least = 0
values = []
names = []
f... |
2f6ec1e75f2becaf8531ce8a9a152a5bb626614fbacb81f5710171cfdde6ce8a | Python | 980 | 29 | clmns = ["1160", "1163", "1166", "1169", "1172", "1175", "1178", "1181", "1184", "1187", "1190", "1193", "1196", "1199", "1202", "1205"]
threads = len(clmns)
import pandas as pd
import sys,os
file_name = 'Cell'
idf = sys.argv[1] + '_' + sys.argv[2] + '_' + sys.argv[3]
at_least = 0
values = []
names = []
f... |
549ff5b7843720737608a2a99b8bcd75c461a724634d583b9ee91c2ff6736f4d | Python | 980 | 29 | clmns = ["1160", "1163", "1166", "1169", "1172", "1175", "1178", "1181", "1184", "1187", "1190", "1193", "1196", "1199", "1202", "1205"]
threads = len(clmns)
import pandas as pd
import sys,os
file_name = 'Cell'
idf = sys.argv[1] + '_' + sys.argv[2] + '_' + sys.argv[3]
at_least = 0
values = []
names = []
f... |
f7f7940947d1e04b355e54a408ea2cc4bf23c000f3b9940bb2bcf52d60f8befc | Python | 982 | 31 | """Test formatting functionality."""
import pytest
from langchain_core.utils import formatter
def test_valid_formatting() -> None:
"""Test formatting works as expected."""
template = "This is a {foo} test."
output = formatter.format(template, foo="good")
expected_output = "This is a good test."
a... |
08074288571246c18f2714720e6150e7de7dba39409aac3dc030e9997a08e5b0 | Python | 983 | 33 | ''' Module initializer includes all sub-modules.
:Version:
1.0
:Date:
08.02.2016
:Author:
Jan Melchior
:Contact:
JanMelchior@gmx.de
:License:
Copyright (C) 2016
This program is free software: you can redistribute it and/or modify
... |
6e0de5ee9e98f8891be85a828069033dbbc30399222f4e6ae33be0a9f876279a | Python | 984 | 22 | from EPI_MRI.EPIMRIDistortionCorrection import *
from optimization.ADMM 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.n... |
c581652ecbcf22d3aa24f648ba475f6ceafeb52ea1d273442217b07169233d3b | Python | 984 | 32 | import numpy as np
from torch.utils.data import Dataset
from genie.utils.data_io import load_coord
class SCOPeDataset(Dataset):
# Assumption: all domains have at least n_res residues
def __init__(self, filepaths, max_n_res, min_n_res):
super(SCOPeDataset, self).__init__()
self.filepaths = filepaths
self.max... |
dcc3f18ed290c28200ccd73ae4c4588a4f41b533cd8f42a075aa13305bc79785 | Python | 984 | 32 | """
This script generated input json files for a set of files for computing md5sums
Usage : python make_json.py comma_separated_list_of_files path_to_run_folder
"""
import sys
import os
import simplejson
def main():
filelist = sys.argv[1].split(",")
output_path = sys.argv[2]
os.chdir(output_path)
for... |
24e694fab9381d5085e5188b017fb641405e70eb6e448efbb0a3e142112850da | Python | 985 | 25 | import numpy as np
import omicscope as omics
np.seterr(divide='ignore', invalid='ignore')
class TestOmicScope(object):
def test_user_input_stat(self):
progenesis = omics.OmicScope(Table='tests/data/proteins/progenesis.xls',
Method='Progenesis',
... |
e1f63ecacd49c7999cca70eeeb674c401f76f2b48aeffbf88058be530c96d744 | Python | 985 | 33 | ''' Module initializer includes all sub-modules.
:Version:
1.0
:Date:
08.02.2016
:Author:
Jan Melchior
:Contact:
JanMelchior@gmx.de
:License:
Copyright (C) 2016
This program is free software: you can redistribute it and/or modify
... |
4cc523a384f3bc106f259e3cf181a28712dc992a592a2dee9d71595f96c29ba8 | Python | 986 | 34 | from torch import nn
class SqueezeExcitationBlock(nn.Module):
def __init__(self, in_ch, reduction=16):
"""
A squeeze and excitation block as proposed by https://arxiv.org/abs/1709.01507
Args:
in_ch (int): number of input channels
reduction (int): reduction factor to... |
604170351b8ea5b3fb52994c0efddebf2681caa91e64a6b0ce968a629cc880df | Python | 987 | 33 | from typing import TYPE_CHECKING, Any
from langchain_classic._api import create_importer
if TYPE_CHECKING:
from langchain_community.retrievers import AmazonKnowledgeBasesRetriever
from langchain_community.retrievers.bedrock import (
RetrievalConfig,
VectorSearchConfig,
)
# Create a way to... |
ab01dbac521c7a4e013269d95b84a0699a24e60890191b62c202a2f72fed5eae | Python | 988 | 40 | from langchain_classic.agents import agent_toolkits
EXPECTED_ALL = [
"AINetworkToolkit",
"AmadeusToolkit",
"AzureCognitiveServicesToolkit",
"FileManagementToolkit",
"GmailToolkit",
"JiraToolkit",
"JsonToolkit",
"MultionToolkit",
"NasaToolkit",
"NLAToolkit",
"O365Toolkit",
... |
c36103c1ae509623a7585eb231c9b883f18dbe2334f1afad93e89aae70bb164c | Python | 988 | 31 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
from MEnet import utils, _version
import os
import argparse
def tile(args):
f_input = args.input
tile_bp = args.bp
print(f_input, tile_bp)
if os.path.exists('{n}.tile{t}bp.csv'.format(n=f_input.split('.bis')[0].split('_bis')[0], t=tile_bp)):
prin... |
6858fdc0e68dd4a3383765709ccdca15b739cfaea00efb90201b86b8f87b95ce | Python | 990 | 26 | import sys
import os
import os.path
###############################################To convert neoloop CNV segment to circos format CNV## new format CNV outputs are located in the same folder with old##########
inputdir=sys.argv[1]
##########################'/home/uni08/txie/analysis/Pan/08trans/cnv'
def g... |
94da36b979af449cde3aec307ea66eb732d1cfb490dff8672aa1d302f63807d0 | Python | 991 | 33 | # coding: utf-8
""" MIT License """
'''
Project: Parenchymal Attention Network
Authors: Axel Masquelin
Description: Utility functions to plot metrics
'''
# Libraries
# ---------------------------------------------------------------------------- #
from sklearn.metrics import roc_curve, auc, confusion_matrix
... |
04a15b8b11708108277e2b59d313e78921a8dde4590c855fdcbbe81c043524e3 | Python | 992 | 38 | """Slack tools."""
from typing import TYPE_CHECKING, Any
from langchain_classic._api import create_importer
if TYPE_CHECKING:
from langchain_community.tools import (
SlackGetChannel,
SlackGetMessage,
SlackScheduleMessage,
SlackSendMessage,
)
# Create a way to dynamically look... |
9f8ada61a57f55eeeb79e7ceb957ca8c9f140961d2da14b8d012760ac818c521 | Python | 993 | 33 | from typing import TYPE_CHECKING, Any
from langchain_classic._api import create_importer
if TYPE_CHECKING:
from langchain_community.document_loaders.parsers.audio import (
OpenAIWhisperParser,
OpenAIWhisperParserLocal,
YandexSTTParser,
)
# Create a way to dynamically look up deprecate... |
993642747c6c0b26f84441a625b9a6df999b6a76b82a340c32e89de04980ab7c | Python | 994 | 22 | import os
from django.db import models
def get_upload_path(instance, filename):
return '/'.join(filter(None, ('mapping/files', filename)))
class Map(models.Model):
PROBE_TYPES = [
('neuronexus_a1_32_poly2', 'Neuronexus_A1_32_Poly2'),
('cambridge_h7b', 'Cambridge_H7b'),
]
probe_... |
9997e7b61b0f34eccbab734c38944e45c0cdaabb0ddb069c23a64eaf7dfd7077 | Python | 994 | 33 | ''' Module initializer includes all sub-modules.
:Version:
1.0
:Date:
08.02.2016
:Author:
Jan Melchior
:Contact:
JanMelchior@gmx.de
:License:
Copyright (C) 2016 Jan Melchior
This program is free software: you can redistribute it ... |
202ffe47e7d2417ed754a1d93ed792dec1ad0be7084b2d027ae0611d90e3bfaa | Python | 995 | 41 | #! /bin/env python
#
# Michael Gibson 23 April 2015
import sys, struct, os
def read_qstring(fid):
"""Read Qt style QString.
The first 32-bit unsigned number indicates the length of the string (in bytes).
If this number equals 0xFFFFFFFF, the string is null.
Strings are stored as unicode.
""... |
303da0fe0a1122e6857403139c774ceb0ad0c8fca147d8f015623e17094b277b | Python | 996 | 27 | # Method for unpickling probabilities/logits saved in process of evaluation.
import pickle
# Example of unpickle
FILE_PATH = 'probs_resnet110_c10.p'
# Open file with pickled variables
def unpickle_probs(file, verbose = 0):
with open(file, 'rb') as f: # Python 3: open(..., 'rb')
(y_probs_val, y_val), (y... |
985da766864b6f252f929b102fcded128e7863865f1be077ca097727bc9fce69 | Python | 996 | 38 | from langchain_classic.evaluation import __all__
EXPECTED_ALL = [
"EvaluatorType",
"ExactMatchStringEvaluator",
"RegexMatchStringEvaluator",
"PairwiseStringEvalChain",
"LabeledPairwiseStringEvalChain",
"QAEvalChain",
"CotQAEvalChain",
"ContextQAEvalChain",
"StringEvaluator",
"Pa... |
e5b34c896cad6e3aa30a92c8f2bf58fb9cbc0682a2a960ba9b00584144f6b4e5 | Python | 998 | 33 | from typing import TYPE_CHECKING, Any
from langchain_classic._api import create_importer
if TYPE_CHECKING:
from langchain_community.tools import E2BDataAnalysisTool
from langchain_community.tools.e2b_data_analysis.tool import (
E2BDataAnalysisToolArguments,
UploadedFile,
)
# Create a way ... |
692fb067f242567a953f290c70394f07d31246d273630c4497e41987e642027f | Python | 999 | 28 | import setuptools
with open("README.md", "r") as fh:
long_description = fh.read()
setuptools.setup(
name = 'vmdpy',
packages=setuptools.find_packages(),
version = '0.1',
description = 'Variational Mode Decomposition (VMD) algorithm',
url='http://github.com/vrcarva/vmdpy',
... |
7b6b1a08dd452c796480231c60749ecf2fa7c9f990d569eee832ec545364b1d1 | Python | 1,000 | 22 | # Copyright 2022 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 writi... |
bce500a19cc65a9f4f847a69b2066201abd38e054b8df29396f12f6a31d217aa | Python | 1,001 | 27 | import numpy as np
from scipy.signal import filtfilt
__author__ = 'Reza Sameni'
__source__ = 'The Open-Source Electrophysiological Toolbox (OSET) - https://github.com/alphanumericslab/OSET'
__reference__ = 'Mitra, S. (2010). Digital signal processing (4th ed.) New York, NY: McGraw-Hill Professional.'
def lp_filter_ze... |
e2ed2df9bc478365cb90afb49acd816ff082e6bf9d2ae0b0a2c8e9b6c3220ce1 | Python | 1,001 | 38 | import numpy as np
import tensorflow as tf
from tensorflow.keras import Model
from tensorflow.keras.layers import Add, Dense, Input, Subtract
from explainability.utils import infer_graph_structure
def test_infer_graph_structure():
i1 = Input((5,))
d1 = Dense(5)(i1)
c1 = tf.constant(np.arange(5).reshape(... |
3e846d93380a34b4256aa8a377b7f77a27b9eff2d265fb76fefcbb61605a25d6 | Python | 1,003 | 34 | import numpy as np
import scipy.sparse as sp
####################################################
# This tool is to generate meta-path based adjacency
# matrix given original links.
####################################################
pa = np.genfromtxt("./dblp/pa.txt")
pc = np.genfromtxt("./dblp/pc.txt")
pt = np.gen... |
ea45d92b80905dd010e8b4deac259b24d56cf520af37debe1890239f5526b888 | Python | 1,004 | 33 | ''' Module initializer includes all sub-modules.
:Version:
1.0
:Date:
08.02.2016
:Author:
Jan Melchior
:Contact:
JanMelchior@gmx.de
:License:
Copyright (C) 2016 Jan Melchior
This program is free software: you can redistribute it and/or m... |
4b3333870981a76ac289b768093ec4a2ef1149ce3f79a9ba69b90142681bdbba | Python | 1,005 | 27 | """Logic for formatting intermediate steps into an agent scratchpad.
Intermediate steps refers to the list of (AgentAction, observation) tuples
that result from previous iterations of the agent.
Depending on the prompting strategy you are using, you may want to format these
differently before passing them into the LLM... |
adbcd32988f0965a6f3614ee9c22534e20afba1070e3fc337c602b81325b22a9 | Python | 1,005 | 33 | from typing import TYPE_CHECKING, Any
from langchain_classic._api import create_importer
if TYPE_CHECKING:
from langchain_community.callbacks.human import (
AsyncHumanApprovalCallbackHandler,
HumanApprovalCallbackHandler,
HumanRejectedException,
)
# Create a way to dynamically look up... |
0b5eb546ef0794518c30fa2ba6462d7eab67953409b254ecca94d0ae600bf5d5 | Python | 1,006 | 34 | import os
import re
import argparse
def main():
parser = argparse.ArgumentParser()
parser.add_argument('log', type=str, nargs='+')
args = parser.parse_args()
if not isinstance(args.log, list):
args.log = [args.log]
for log in args.log:
if log.find("renamed") != -1:
pr... |
dd02da3baf30abe050ba64dce30b83c9c3ae9e7c04b33cf4ac69044d35565fb3 | Python | 1,007 | 19 | import argparse
args = argparse.ArgumentParser(description='config of VGG on fMRI')
args.add_argument('--feature_map', default='all', help='feature map of dataset--all, ALFF, fALFF, ReHo, VMHC')
args.add_argument('--model', default='VGGgap', help='name of model--VGG, VGGgap')
args.add_argument('--lr', type=float, defa... |
e9c362caa5267148951eed0e8fb57582f42454345f1d9f787417525ae17dc8ec | Python | 1,007 | 32 | """
SMdRQA interactive UI.
Launch with ``smdrqa-ui`` or ``python -m SMdRQA.ui`` (requires the
``ui`` extra: ``pip install SMdRQA[ui]``).
This package deliberately avoids importing streamlit at package level so
that ``SMdRQA.ui.recorder`` and ``SMdRQA.ui.sensitivity`` stay usable
(and testable) without the UI dependen... |
3e0223e7381625f3869bdf577094235edf93f379c60b6e52f9889b7ad9c779d2 | Python | 1,009 | 38 | #### Combine data
import session_info
import polars as pl
import pandas as pd
def load_data(tissue, dx):
new_dx = dx.replace("SZD", "SZ")
fn = f"../../_m/{tissue.lower()}/{dx}/zsummary_table.tsv"
return pl.from_pandas(pd.read_csv(fn, sep='\t')\
.reset_index()\
... |
29c39aae390f427b9821f8fc2409545e6051480e967fea9e5a72986f55dd7347 | Python | 1,010 | 35 | """3D phase reconstruction using the waveorder API."""
from waveorder.api import phase
settings = phase.Settings(
transfer_function=phase.TransferFunctionSettings(
wavelength_illumination=0.532,
yx_pixel_size=0.1,
z_pixel_size=0.25,
numerical_aperture_illumination=0.9,
nume... |
ea5df7fc9da180aaf62948e9b7659f5804995b391f15e835b72d2ee405919b62 | Python | 1,010 | 26 | from neurovisfit.data import loaders
from neurovisfit.data.dataset import DataSplit
from neurovisfit.data.loaders import get_loader_split
from neurovisfit.data.params import DataLoaderParams
def test_get_loader_split(mock_image_cache, mock_toml_config):
params = DataLoaderParams(**mock_toml_config.get_dict("some_... |
67bad3789d43a9441ff1024e699125522bc1d5dd479185af4c53ca3385c019d4 | Python | 1,011 | 33 | ''' Module initializer includes all sub-modules for the autoencoder module.
:Version:
1.0
:Date:
21.01.2018
:Author:
Jan Melchior
:Contact:
JanMelchior@gmx.de
:License:
Copyright (C) 2018 Jan Melchior
This program is free software: you c... |
ceb5e7ae7a2121eb49a8f2d8a6e3ad6278472b90b66706a044f282bc4f86038b | Python | 1,011 | 37 | import numpy as np
from pycromanager import multi_d_acquisition_events, JavaBackendAcquisition
import copy
def img_process_fn(image, metadata):
image2 = np.array(image, copy=True)
image2 = np.swapaxes(image2, 0, 1)
md_2 = copy.deepcopy(metadata)
image[250:350, 100:300] = np.random.randint(0, 4999)
... |
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