sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
102c7d3c62a48764979e60a403f90333c142ecf539b9772caf94d9394d368610 | Python | 2,180 | 56 | import numpy as np
import pytest
import gym
from gym.vector.sync_vector_env import SyncVectorEnv
from tests.vector.utils import make_env
ENV_ID = "CartPole-v1"
NUM_ENVS = 3
ENV_STEPS = 50
SEED = 42
@pytest.mark.parametrize("asynchronous", [True, False])
def test_vector_env_info(asynchronous):
env = gym.vector.m... |
4d170ce5ed6d6fd1ad8eab5243ce6d81cae5b6817b944e967f177ea14f8b1275 | Python | 2,180 | 69 | from keras.src import backend
from keras.src.api_export import keras_export
from keras.src.layers.merging.base_merge import Merge
@keras_export("keras.layers.Minimum")
class Minimum(Merge):
"""Computes elementwise minimum on a list of inputs.
It takes as input a list of tensors, all of the same shape,
an... |
6ed08910a3884245f68f5f5bafec7be7ad7999ea5e73a30f29e0e0e94d216a46 | Python | 2,180 | 53 | """
tool_audit_battery — Backward-compat shim.
Historical diagnostic_*.py scripts in this testsuite import `_fit_lda`,
`load_cohort`, and `_data_path` from a sibling `paper_disorder_angle/`
testsuite via:
TA_DIR = os.path.join(..., "paper_disorder_angle", "analyses")
sys.path.insert(0, TA_DIR)
from tool_a... |
8f933238d6c90926f993eb47d78d5ce14b646b80cee478e72b3e40ef66a362db | Python | 2,180 | 79 | '''=========================================================================
'
' Copyright NumFOCUS
'
' 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.o... |
d70ffe1ebd4f88603c72e57f42ec6707ce261652c43c20591905e918dd863ddb | Python | 2,180 | 78 | import json
import logging
import os
import pwd
import re
from autouri import AutoURI
from .dict_tool import merge_dict
logger = logging.getLogger(__name__)
RE_ILLEGAL_STR_LABEL_CHRS = r'[\:\?\*]'
SUB_ILLEGAL_STR_LABEL_CHRS = '_'
class CaperLabels:
KEY_CAPER_STR_LABEL = 'caper-str-label'
KEY_CAPER_USER =... |
420db0e6d48f6858a560a67bab534aad4a13a2ed714a17c9d79dc166c91f965e | Python | 2,182 | 69 | from keras.src import backend
from keras.src.api_export import keras_export
from keras.src.layers.merging.base_merge import Merge
@keras_export("keras.layers.Maximum")
class Maximum(Merge):
"""Computes element-wise maximum on a list of inputs.
It takes as input a list of tensors, all of the same shape,
a... |
7710d9ba8e6f225288ba63e5df7961cbef9857cb1a3c08458f83334d023d9c76 | Python | 2,182 | 65 | # Purpose of this script is to write the functions that help facilitate
# subsetting of the data depending on the users input
import numpy
def printOut(text, fileName="stdout.txt", close=True, file=None):
"""Prints to the specified file name. Used for debugging.
If close is Fale, returns open file.
"""
... |
c83a314625d966d838da6e6f55f156b9f93c500959c4fe04538f41fcb3a53f20 | Python | 2,182 | 69 | import pandas as pd
import numpy as np
from sklearn.metrics import log_loss, roc_auc_score, auc, precision_recall_curve, precision_score
from tqdm import tqdm
tqdm.pandas()
from drug_interactions.utils.calc_metrics import calc_average_precision_k, calc_mrr
def load_df(path, dataset_type=None):
if dataset_type is ... |
f1589e13d76f7ae271de915e2ecd6e19a12e3a5483cfca2419d7f15d1de9e47e | Python | 2,182 | 85 | import networkx as nx
from pyvis.network import Network
from matplotlib import pyplot as plt
def visualize_scene_graph(relations, save_path, use_pyvis=True):
objs = set()
for rel in relations:
objs.add(rel[0])
objs.add(rel[1])
G = nx.DiGraph()
for obj in objs:
G.add_node(obj)
... |
8f06c3d9ad66fce550c7364963fbcd7ecc17d458256ef3741008f8bd8a44dea3 | Python | 2,183 | 56 | ######################################################
# This file prepares the DGSplicer data set for use #
# in CMKN experiments. The script assumes that #
# positive and negative sequences are provided in #
# different files. #
# ... |
3adb0e37a27cbfd459bb56c84dff92786bd392b905ef5d42deedd1787ea16c00 | Python | 2,184 | 58 | ''' Example to generate a population of cells from input files'''
import json
import os
import tns
from tns import extract_input
def get_log_data(mtype, number_of_cells, params, output_path):
'''Creates log and returns it.
If output_path saves the data in json
'''
from tns.version import VERSION as... |
53114272cf6ee538993758982e990d7a0ea5126a97bc9499033b1688d2991186 | Python | 2,184 | 68 | import pickle
import torch
import torch.nn as nn
import torch.nn.functional as F
import torch.nn.init as init
# from utils.modules.lightWeightNet import WeightNet
from . import lapar_weightnet as LW
def make_model(args, parent=False):
return LAPAR_A(args)
class ComponentDecConv(nn.Module):
def __init__(self... |
7eb672572f5884acd86264ad4e93c47796832df87490a59e867a174acf1e6f75 | Python | 2,184 | 68 | import pickle
import torch
import torch.nn as nn
import torch.nn.functional as F
import torch.nn.init as init
# from utils.modules.lightWeightNet import WeightNet
from . import lapar_weightnet as LW
def make_model(args, parent=False):
return LAPAR_B(args)
class ComponentDecConv(nn.Module):
def __init__(self... |
b4b38761d84ef85b3381553e34537a848233babca273f1a4a70af162f3d04c44 | Python | 2,184 | 57 | import torch
import torchvision.transforms as transforms
from torch.utils.data import DataLoader
import utils.data_transforms as data_transforms
from utils.datasets import DiffusionDataset
def batch_mean_and_sd(loader):
cnt = 0
fst_moment = torch.empty(3)
snd_moment = torch.empty(3)
for images, _ in... |
be85dc31ae56d14172de601c8204044fa349c303b2ab95d080a4dc99b602f975 | Python | 2,184 | 68 | import pickle
import torch
import torch.nn as nn
import torch.nn.functional as F
import torch.nn.init as init
# from utils.modules.lightWeightNet import WeightNet
from . import lapar_weightnet as LW
def make_model(args, parent=False):
return LAPAR_C(args)
class ComponentDecConv(nn.Module):
def __init__(self... |
2ac624bfb4fb8cce3e44c2a21598e86d2b244d122b7d0d292ca257fc89f06988 | Python | 2,185 | 58 | # Copyright (c) 2024 PaddlePaddle Authors. All Rights Reserved.
#
# 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 app... |
9f05afac36acf72f9a7e7c4d46b929a26db783d332ba197f004619999a4f6d35 | Python | 2,185 | 82 | """Morris-Lecar neuron, 1981.
Morris and Lecar's barnacle muscle-fiber model integrates voltage and potassium
activation with voltage-dependent calcium, potassium, and leak conductances.
"""
from __future__ import annotations
import torch
from torch import Tensor, nn
class MorrisLecarNeuron(nn.Module):
"""Eule... |
ab08344c5118dbd87a2ccb8301876e6b308446af1febc7b5b23bdfe4aae29431 | Python | 2,185 | 88 | #!/usr/bin/env python3
"""
Command-line client for the Ethoscope light daemon.
Talks to ``ethoscope_light.service`` over its Unix control socket.
Useful for diagnostics, manual override during maintenance, and scripts.
Examples:
ethoscope-light on
ethoscope-light off
ethoscope-light release
ethoscope-... |
b8afcab41e07af86ecae56748589892b66dce8321936f50d5a98086058f15005 | Python | 2,185 | 73 | import os
import subprocess
import bbi
from modular_splicing.dataset.datafile_object import SpliceAIDatafile
import modular_splicing
from modular_splicing.dataset.additional_data import DatafileReferencingAdditionalData
PHYLO_P_DATA_WEB = "rsync://hgdownload.cse.ucsc.edu/goldenPath/hg19/phyloP100way/hg19.100way.ph... |
e21a241f7fe8ee437c148b620df74b42eee54856740692147f35a29d5e5e4398 | Python | 2,185 | 71 | """The lightly.models.modules package provides reusable modules.
This package contains reusable modules such as the NNmemoryBankModule which
can be combined with any lightly model.
"""
# Copyright (c) 2021. Lightly AG and its affiliates.
# All Rights Reserved
from lightly.models.modules.heads import (
BarlowTwi... |
21109732bf7cb31a14e5c55c31caee4f76d42d7115441e931db4071010a726b5 | Python | 2,186 | 79 | #!/usr/bin/env python3
"""
"""
import pytest
from caper.cromwell import Cromwell
def pytest_addoption(parser):
parser.addoption(
'--ci-prefix', default='default_ci_prefix', help='Prefix for CI test.'
)
parser.addoption(
'--gcs-root',
default='gs://encode-test-caper',
help=... |
a67895fdf22c5f398c68c544b6f14a858abdf583dbca1d90f2cbefdf2b598d2b | Python | 2,186 | 83 | """
Records describing a replay source and its prepared frames.
"""
from __future__ import annotations
from dataclasses import dataclass, field
from typing import Any, Literal
import pandas as pd
from larvaworld.portal.datasets.models import (
WorkspaceDatasetRecord,
WorkspaceReplayDatasetRecord,
)
Replay... |
abedb471ddcb246322b2a4f12745faf8df999cd19f5af939e70d1fff4dfc8348 | Python | 2,186 | 65 | import os
import numpy as np
from mirp._images.rtdose_image import RTDoseImage
from mirp._masks.base_mask import BaseMask
from mirp.extract_features_and_images import extract_features_and_images, extract_images
CURRENT_DIR = os.path.dirname(os.path.abspath(__file__))
def test_basic_rtdose_feature_extraction():
... |
0d3c08aaaaf575e45daa45bdf35857d8c86142f2077599177fa8ed83e3f1cccb | Python | 2,187 | 64 | '''Tests for dataform'''
import os
import tempfile
import unittest
import numpy as np
from bdpy.dataform.sparse import load_array, save_array
class TestSparse(unittest.TestCase):
def test_load_save_dense_array(self):
payloads = [
[(10,), 'test_array_dense_ndim1.mat'], # ndim = 1
... |
4e6cae19e5dfb9e133cadf71922ea0899045593119c580de97cb34d6ad0c5026 | Python | 2,187 | 77 | """Update postgresql trigger to use clock_timestamp function
NOTE: This migration will not be applied on SQLIte.
Revision ID: a91ea1d97111
Revises: f070559879f1
Create Date: 2025-06-09 12:21:53.427419
"""
from alembic import op
from galaxy.model.migrations.util import _is_sqlite
# revision identifiers, used by Al... |
9e7307ced0c49854bda26bf2b69d177ce8448420a6fa5add812a6df9366d2cfa | Python | 2,187 | 72 | # This example requires the following dependencies to be installed:
# pip install lightly
# Note: The model and training settings do not follow the reference settings
# from the paper. The settings are chosen such that the example can easily be
# run on a small dataset with a single GPU.
import torch
import torchvisi... |
2514cee0131bd7ab5b22dc54e75fe4baab84baddf6eeca064fa6d854ba72ad57 | Python | 2,188 | 61 | # LICENSE
#
# _This file is Copyright 2018 by the Image Processing and Analysis Group (BioImage Suite Team). Dept. of Radiology & Biomedical Imaging, Yale School of Medicine._
#
# BioImage Suite Web is licensed under the Apache License, Version 2.0 (the "License");
#
# - you may not use this software except in compl... |
4d57c7b9cd2aa9de06b00790ec229d18aa7aaa9e35106ed6a64cb694534c9b97 | Python | 2,188 | 65 | """Regression tests for the agent-index clamping of the annotated track plots.
`track_annotated_data` defaults to plotting agents 3, 4, 5 and 6, which raised an
IndexError on any dataset holding fewer than seven of them - including every
short tutorial run and the `track` graphgroup built on top of it.
"""
import pyt... |
85e0920936825ab442c963cdac9a965a539881863edb21701728e54f32f113ee | Python | 2,189 | 67 | import os
import pytest
from mirp._images.ct_image import CTImage
from mirp._masks.base_mask import BaseMask
from mirp.extract_features_and_images import extract_features_and_images, extract_images
CURRENT_DIR = os.path.dirname(os.path.abspath(__file__))
@pytest.mark.ci
def test_basic_ct_feature_extraction():
... |
8702de98ee9601ca01dc0eef9cde1f032efa5e7c79e7a4216640a39a0666749f | Python | 2,189 | 73 | import warnings
import unittest
import logging
from pmsurv.models.exponential_model import ExponentialModel
import tests.syntheticdata
warnings.simplefilter("ignore")
logger = logging.getLogger(__name__)
class TestSamplers(unittest.TestCase):
def get_data():
lam_ctrl = 1
lam_trt = 2.5
k ... |
0108da62c04bbfe4de259a0b4d8fe9a2b4b62ca3d404aeb9806370ebe85308e4 | Python | 2,190 | 57 | # LICENSE
#
# _This file is Copyright 2018 by the Image Processing and Analysis Group (BioImage Suite Team). Dept. of Radiology & Biomedical Imaging, Yale School of Medicine._
#
# BioImage Suite Web is licensed under the Apache License, Version 2.0 (the "License");
#
# - you may not use this software except in compl... |
6150d9ab6ab85a36249155b4a7607b44ff3141487556044865441977c9a47ea2 | Python | 2,190 | 60 |
# generate a pipeline file for creating multiple sequences based on iterations,
# when multiple solutions to TSP exist.
# different solvestrs represent different preprocessing of the percent matches matrix.
# based on the same loop structure in workflow.bash order-iter
import argparse
## argparse
parser = argpar... |
bc5f962c23fb661255dc83ccf7e4073d9d9686423a1402c46c44a8e1a098bf5e | Python | 2,190 | 75 | import numpy as np
from gym import utils
from gym.envs.mujoco import MuJocoPyEnv
from gym.spaces import Box
class ReacherEnv(MuJocoPyEnv, utils.EzPickle):
metadata = {
"render_modes": [
"human",
"rgb_array",
"depth_array",
],
"render_fps": 50,
}
... |
cee7a1acbe7b121a5830343b66855b26778066da743f95cc3a4748675efe8dd0 | Python | 2,190 | 76 | import dataclasses
import getpass
import requests
from codecarbon.core.api_client import ApiClient
from codecarbon.external.logger import logger
from codecarbon.output_methods.base_output import BaseOutput
from codecarbon.output_methods.emissions_data import EmissionsData
class HTTPOutput(BaseOutput):
"""
S... |
239884967cb2125f89c8aec3fa4477691d963bccc35b028b842db62821b493ee | Python | 2,191 | 54 | #!/usr/bin/env python
"""Custom data types for simplifying data communication."""
import itertools
import statistics
from collections import namedtuple
from typing import List, Union
import numpy as np
try:
from mpi4py import MPI
except ImportError:
MPI = None
StatBundle = namedtuple("StatBundle", ["numb_co... |
376871e1d49906e4e85682dd5420079566e5a1f65779305002f9ba9a45f4ca29 | Python | 2,191 | 79 | from torch_geometric.data import Data
class Multi_Data(Data):
"""
A class for loading multiple datapoints from a pytorch geometric dataset
...
Attributes
----------
h : list, tensor, array
the features of each node in the graph
edge_index : list, tensor, array
defines the ... |
bcceb3440d5f254bacedf89eae0edefb3fd3d15b53ea385f6658981f2e7e0185 | Python | 2,191 | 61 | """
CREaTor
Copyright (C) 2023 Microsoft Research
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
This program is distributed... |
c9b2cafc1cb995d621d9dca04664238a0871d35a8c66e2861ca5975daae734bd | Python | 2,191 | 60 | import os
import h5py
import numpy as np
import scanpy as sc
from dca.api import dca
from scbig.utils import read_data, setup_seed, louvain, calculate_metric
for dataset in ['10X_PBMC','mouse_bladder_cell','mouse_ES_cell','human_kidney_counts','Adam','Human_pancreatic_islets','Macosko_mouse_retina']:
print('----... |
52b6903d5d62b3639ec609166cd08c36342588bd7988fe41ac72f3cfc496ce4f | Python | 2,192 | 56 | import torch
import torch.nn as nn
import torch.nn.functional as F
from torch import Tensor
from models.mn.utils import collapse_dim
class MultiHeadAttentionPooling(nn.Module):
"""Multi-Head Attention as used in PSLA paper (https://arxiv.org/pdf/2102.01243.pdf)
"""
def __init__(self, in_dim, out_dim, att... |
732523bc05a5fc7d6ee75054bf5c276adaeca32dfbccb1930fb82fddf251242d | Python | 2,192 | 80 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Wed Nov 24 16:04:35 2021
@author: fcheng
"""
import os
import cv2
import numpy as np
from eval.image_process import img_process, normalise_img
def MakeRegressor(image_name, path_to_regressor, regressor, img_size, normalization=1, redness=None ,
... |
cbf149aef1f206700e2f8c5a426fa9fb5d986ca319d4dab30c2eed8fc5f04f05 | Python | 2,192 | 57 | from typing import Union
import gymnasium as gym
from angorapy.common.postprocessors import StateNormalizer, RewardNormalizer, BasePostProcessor
from angorapy.tasks.wrappers import TaskWrapper, PostProcessingWrapper
from angorapy.utilities.core import env_extract_dims
def make_task(env_name,
reward_co... |
b664cf21ab37d3e69cc0baabb56e5958d8c7d2db8e46ba001c19a582db7d774d | Python | 2,194 | 89 | import os
import fire
from .grab_sequence import grab_sequence
from .create_datafile import create_datafile
from .create_dataset import create_dataset
def full_pipeline(
*,
ref_genome,
splice_table,
sequence_out,
data_segments,
data_dir,
CL_max=10_000,
SL=5000,
):
grab_sequence(
... |
7a71cb15f6c18537c84bbb954d0f3782d7631943bddcd074cca6b4729a5469b0 | Python | 2,195 | 82 | """
Portal apps for inspecting and building models and environments.
"""
from __future__ import annotations
from .model_inspector_app import _ModelInspectorController, model_inspector_app
from .model_inspector_data import (
BASELINE_MODULES,
DEFAULT_LIVE_PREVIEW_REPORTER_KEYS,
LIVE_PREVIEW_REPORTER_KEYS,
... |
07424e4efbb73ed084da1a04ee8ba434966b03010e354facab285fac0af591ff | Python | 2,196 | 78 | """ Math utils """
from math import sqrt
import numpy as np
from scipy.spatial import cKDTree
# The smallest representable positive number such that 1.0 + eps != 1.0
# around 1e-7 for float32
EPS = np.finfo(np.float32).eps
def norm(vector):
"""Returns the norm of the numpy array"""
return sqrt(vector.dot(vec... |
4bde031b241fbabcc94713502096d9e6438ffdf269c8f5f1fec414b7da0a341a | Python | 2,196 | 89 | import hvplot.pandas
import numpy as np
import pandas as pd
import panel as pn
from panel.template import DarkTheme
import larvaworld.lib.model as model
M = model.NeuralOscillator
module_attrs = ["input", "activation", "output"]
title = "Neural lateral oscillator"
sidebar_width, sidebar_height = 400, 500
widget_kws =... |
a045e63ae8cde0c4142fafe3ddf946d9825530bc9f15a91dc32f35054f91be2a | Python | 2,196 | 87 | '''
load the RBNS data
'''
import csv
import re
import h5py
import urllib3
import urllib
import gzip
from io import StringIO
import requests
import numpy as np
import time
from utils_rbns import create_datapoints
rbns_data = 'metadata_rbns.csv'
encode_dir = 'encode/'
data_dir = 'data/'
protein_idx_map_txt = 'protein... |
09eb0d3cfbe554ce47fa2eaa78e8733c94008d71d3edd8ae972e4cfb88886989 | Python | 2,197 | 79 | """
Rendering and visualization on a pygame display
"""
from __future__ import annotations
from typing import Any
from importlib import import_module
__all__: list[str] = [
"drawing",
"rendering",
"side_panel",
# Commonly used symbols expected at package level (legacy surface)
"ScreenOps",
"... |
6f6e81324ae24cedc4e620f471c5f9df77aa9d7c4ae61f4c03d864593eb79462 | Python | 2,197 | 65 | """Smoke tests for chord_unlock routing to quorum queues.
Reproduces Celery Discussion #9742: when chord_unlock is routed to a
quorum queue via topic exchange, it may not be consumed even if declared
and bound.
"""
from __future__ import annotations
import pytest
from pytest_celery import RESULT_TIMEOUT, CeleryTestS... |
9649da632e405898e2a8a7e181685012894df1ee020dee6294d0e90b995e9f0c | Python | 2,197 | 68 | # -*- coding: utf-8 -*-
# tests for toy_graphs.py
"""
@author: Quentin Lutz <qlutz@enst.fr>
@author: Nathan de Lara <nathan.delara@polytechnique.org>
@author: Thomas Bonald <tbonald@enst.fr>
"""
import unittest
from sknetwork.data.toy_graphs import *
class TestToys(unittest.TestCase):
def test_undirected(self):... |
7611586f15a5b372440919724c46a6a6ba7fd8a7c5e83b62034ddf566fdb6fa6 | Python | 2,198 | 76 | from .bulletin import Bulletin
from bs4 import BeautifulSoup
class Goa(Bulletin):
def __init__(self, basedir):
statename = 'GA'
super().__init__(basedir, statename)
def get_urls(self, url: str):
try:
html = self.get_url_html(url)
except:
prin... |
1960cb4f69537077c1a5738900e90a647e14083d213721c7348b85e2f9086c04 | Python | 2,200 | 59 | import spikeinterface.full as si
import numpy as np
from pathlib import Path
import shutil
import subprocess
from probeinterface import ProbeGroup
from probeinterface import write_prb, read_prb
from scipy.io import savemat
from sorting.readSGLX import readMeta
def unlock_files(directory):
# Find the process IDs us... |
08b5115bb68d3f78d71a249fa1d22a77864081eedee8ad79b0046c2f148bb34d | Python | 2,201 | 54 | import glob
import h5py
import numpy as np
import os
import pandas as pd
from sklearn import preprocessing
import sys
"""
hi. this is going to read these in, you basically just need
subjects: path to subjects!
data_path: path to the actual features
phenotypes: path to a csv with the to-be-predicted and the noise
"""
... |
d7ab879f3985f4e2e1c2b6a2a544f9d3a520529cef7083066c52ab749560525a | Python | 2,201 | 57 | # LICENSE
#
# _This file is Copyright 2018 by the Image Processing and Analysis Group (BioImage Suite Team). Dept. of Radiology & Biomedical Imaging, Yale School of Medicine._
#
# BioImage Suite Web is licensed under the Apache License, Version 2.0 (the "License");
#
# - you may not use this software except in compl... |
3b92cc7dc531c61da85adeb612cf257a4a86366f5e0f533bd5a569d983826139 | Python | 2,202 | 65 | import os.path as osp
import torch
import torch.nn.functional as F
import torch_geometric.transforms as T
from torch_geometric.datasets import Planetoid
from torch_geometric.logging import init_wandb, log
from torch_geometric.nn import GCNConv
device = torch.device('cuda' if torch.cuda.is_available() else 'cpu')
cl... |
6836c7e03d97bb26868ed4634cb4213730a501c2d974908a4873bcc5b6529850 | Python | 2,202 | 62 | from pip._vendor.packaging.utils import canonicalize_name
class FormatControl(object):
"""A helper class for controlling formats from which packages are installed.
If a field is falsy, it isn't set. If it is {':all:'}, it should match all
packages except those listed in the other field. Only one field can... |
7852ac7d12574eb8c952cd49f09c39edfb83cc260983eaa1d6a567958284b755 | Python | 2,202 | 75 | import attr
import more_itertools
from permacache import permacache, stable_hash
import tqdm.auto as tqdm
import numpy as np
from .utils import second_half_of_spliceai_cached
@attr.s
class FullTable:
values = attr.ib()
indices = attr.ib()
@indices.validator
def check(self, _attribute, _value):
... |
abd017add69914e46f0fcfc017ad51c3d07d79fd87d15f969036ddd82bcc7da2 | Python | 2,203 | 61 | # Copyright (c) 2025, Jay Shah, Ganesh Bikshandi, Ying Zhang, Vijay Thakkar, Pradeep Ramani, Tri Dao.
# SM120 (Blackwell GeForce / DGX Spark) forward pass.
#
# SM120 uses the same SM80-era MMA instructions (mma.sync.aligned.m16n8k16) but has
# a smaller shared memory capacity (99 KB vs 163 KB on SM80). This module subc... |
490118531111ad123e2a6487e070e7ae8243f74c63c9cf3cf71b2ff1fe49312d | Python | 2,204 | 54 | '''Script for running and analysing simulation experiments comprised of multiple simulation runs.'''
# © Thomas Akam, 2023, released under the GPLv3 licence.
import os
from concurrent.futures import ProcessPoolExecutor
import analysis as an
import model as md
# Run simulation and save data to disk.
def run_experime... |
91edf9822d8ce1fa68cf50ba482b617360a229ea6dd2c21fddb9836248502a8e | Python | 2,204 | 80 | from logging.config import fileConfig
from alembic import context
from sqlalchemy import engine_from_config, pool
from carbonserver.config import settings
# this is the Alembic Config object, which provides
# access to the values within the .ini file in use.
config = context.config
# this will overwrite the ini-fil... |
d706b9b83446579eb93d36a74319034c9feb67db75d1cca2db27affbbe713585 | Python | 2,204 | 93 | from __future__ import annotations
from typing import Any
import hvplot.pandas
import numpy as np
import pandas as pd
import panel as pn
from panel.template import DarkTheme
import larvaworld.lib.model as model
__all__: list[str] = [
"lateral_oscillator_app",
]
M = model.NeuralOscillator
module_attrs = ["input"... |
0c095d57089e99fb759fc8641ba55fc1eaa2cfe710571e4a450ed316eda42471 | Python | 2,206 | 77 | # --- THIS FILE IS AUTO-GENERATED ---
# Modifications will be overwitten the next time code generation run.
from plotly.basedatatypes import BaseTraceHierarchyType as _BaseTraceHierarchyType
import copy as _copy
class Marker(_BaseTraceHierarchyType):
_parent_path_str = "choropleth.selected"
... |
9ad5bdb0e917847abf2ba44042f4b0076b52b5eabac3be35dfe91a70a7407391 | Python | 2,206 | 48 | import os
import numpy as np
import cv2
import argparse
parser = argparse.ArgumentParser('create image pairs')
parser.add_argument('--fold_A', dest='fold_A', help='input directory for image A', type=str, default='../dataset/50kshoes_edges')
parser.add_argument('--fold_B', dest='fold_B', help='input directory for image... |
e80c815c69e63dc1295719cc2ae4117dc76ee09df74a5b020a07898d1f437351 | Python | 2,206 | 79 | import numpy as np
from neuron import h, gui
from neuron.units import ms
# The tests "thread variables". Thread variables are how global variables in
# THREADSAFE code are implemented if they're not read-only. The idea is that
# each thread has it's own copy of the global, with zero synchronization.
#
# The test work... |
3514f6be9c272309943faaa2215d8fb46602e2e69d3e7b37a7c5cf1ba3ab2ea2 | Python | 2,207 | 72 | import easygui
import threading
from telnetlib import Telnet
class DoCamera(threading.Thread):
''' to kind-of automatize the camera action...
'''
def __init__(self, ip='20.100.0.201', port=6802):
super(DoCamera, self).__init__()
self._state='RECORDING'
self.current_counter = 1
... |
7ded729c16ed42cccecd19c3ff77ef52df11dc0161caf8b0f0ef8c5dac70fbfa | Python | 2,207 | 83 | import numpy as np
import matplotlib.pyplot as plt
from library.Tempotron import Tempotron
import time
def demo():
# # Input patterns (X) and labels (Y)
M = 700
N = 500
T = 500
num_iter = 2000
lr = 0.005
nsp = 3
assert N % 2 == 0
assert M % 2 == 0
minus_gpid1 = np.random.perm... |
f7a9c9bc5d10dc38024f46e7c6bd2781dfdec4c335c006d7353d78b63d8b8c39 | Python | 2,207 | 90 | import numpy as np
from neuron import h, gui
from neuron.units import ms
# A test that demonstrates the behaviour of `net_move` and
# `flag`.
#
# The `flag == 0` means that an external event was received. Therefore, we send
# 2 external events at times `1.001` and `2.001`. External events increment the
# counter `y`;... |
7257dc6e1bced4eb02cfebcc707961fe1ca3a21fd9adb8bcf7d6bc4ed5913617 | Python | 2,208 | 71 | from flask import send_file
from flask_restplus import Namespace, Resource, reqparse
from flask_login import login_required, current_user
import datetime
from ..util import query_util
from database import (
ExportModel,
DatasetModel,
fix_ids
)
api = Namespace('export', description='Export related operat... |
392ad6134813d0070f2382ca9942fe0657e0e44af19e34b7778acf36703adff6 | Python | 2,209 | 57 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on March 2019
@author: Thomas Bonald <bonald@enst.fr>
@author: Quentin Lutz <qlutz@enst.fr>
"""
import unittest
from sknetwork.data import karate_club
from sknetwork.hierarchy import Paris, cut_straight, cut_balanced, aggregate_dendrogram
# noinspection PyM... |
e8db8096899e03291c3661de2c47bb2c2ff22176a7154a590cea952f1f45cae7 | Python | 2,209 | 75 | from __future__ import annotations
import pytest
from pytest_celery import CeleryBackendCluster, CeleryTestWorker, CeleryWorkerCluster
from celery.canvas import Signature, chain
from celery.result import AsyncResult
from t.integration.tasks import StampOnReplace, identity
from t.smoke.tests.stamping.tasks import wait... |
38192c4db4194790e313429562e0e3601d536c757e124426f1e401c95c6a4ee4 | Python | 2,210 | 92 | """
Abstract base class for cli job plugins.
"""
from abc import (
ABCMeta,
abstractmethod,
)
from enum import Enum
from typing import TypeAlias
try:
from galaxy.model import Job
job_states: TypeAlias = Job.states
except ImportError:
# Not in Galaxy, map Galaxy job states to Pulsar ones.
clas... |
9bae754dcb989d770cacb076d2e345fb896b5ca56d0be0e74a2ba16035c2a98b | Python | 2,210 | 55 | from .version import __version__
from . import models
from . import datasets
from .models.utils import pretrained_settings
from .models.utils import model_names
# to support pretrainedmodels.__dict__['nasnetalarge']
# but depreciated
from .models.fbresnet import fbresnet152
from .models.cafferesnet import cafferesne... |
f63a37ec0b417a2c86b08fce5326b1773793c9168fcec4b6e486f945934f3270 | Python | 2,210 | 67 | """
A tool to backup incrementally one source to one destination directory.
It copies files to the destination if and only if they are larger than in the destination
"""
from optparse import OptionParser
import os
import shutil
import glob
import time
def copy_one_file(src, dst):
src_size = os.stat(src).st_siz... |
672dd564ab6ce2ff25b442337b1cd4e2a9b1022c7d8ef274d172804aa9be1617 | Python | 2,211 | 59 | import os
import pandas as pd
from sklearn.preprocessing import MinMaxScaler
import numpy as np
def file_name(file_dir):
for root, dirs, files in os.walk(file_dir):
# print(root) # 当前目录路径
# print(dirs) # 当前路径下所有子目录
return files # 当
def casefile_clean():
file_list = file_name('/home... |
1e713c0fbd9d30de669dc608b728b560fe02466b528ac8986b8402980b1856ee | Python | 2,212 | 70 | #!/usr/bin/env python
"""
Input: Molecular input file.
Output: Physico-chemical properties are computed and stored as metadata in the sdf output file.
Copyright 2012, Bjoern Gruening and Xavier Lucas
"""
import argparse
import sys
import cheminfolib
import openbabel
from openbabel import pybel
openbabel.o... |
58f35628b4c87f53b5fcb17c42ca329212f3e94e35626448a3772dcde4eabb2c | Python | 2,212 | 74 | import os
from unittest.mock import patch
import pytest
from click.testing import CliRunner
from celery.bin.celery import celery
@pytest.fixture(autouse=True)
def clean_os_environ():
# Celery modifies os.environ when given the CLI option --broker memory://
with patch.dict(os.environ, clear=True):
yi... |
69fd1620eb157899577ef79afa7f2ffc536398a7ccfe87f8632f93a3f9c33c56 | Python | 2,212 | 65 | import tensorflow as tf
import tensorflow_graphics as tfg
def multi_point_euclidean_distance(a: tf.Tensor, b: tf.Tensor):
"""Calculate mean euclidean distance between flattened points in 3D euclidean space.
Args:
a (object): Tensor of shape (BATCH, FLATPOINTS); missing batch dimension will be ins... |
bde1b3c26d3f140b0c7deed1a7c7009e203095dbf0f58e502c791b636befd792 | Python | 2,212 | 80 | from sys import argv
from msp import MSP
msp = MSP()
msp.file = __file__
msp.seed = int(argv[1])
msp.architecture["splicepoint_model_spec"] = dict(
type="BothLSSIModels",
acceptor="model/splicepoint-model-acceptor-1",
donor="model/splicepoint-model-donor-1",
)
msp.architecture["motif_model_spec"]["motif_... |
c739cf32d6c18aa5fb97c0f24a2cc4ccd3e7d8b93aa5361ddc45347cc7d9b5b5 | Python | 2,213 | 69 | #!/usr/bin/env python
import unittest
import numpy as np
from wyrm.types import Data
from wyrm.processing import lda_train, lda_apply
class TestLDA(unittest.TestCase):
def test_correct_classlabels(self):
"""lda_train must throw an error if the class labels are not exactly [0, 1]."""
data = np... |
d8678f5efb9355ecaea78ae64a025b2be3e2a2fdc8cb5bb32d4d5b0842d894e7 | Python | 2,213 | 74 | from sys import argv
from msp import MSP
msp = MSP()
msp.file = __file__
msp.seed = int(argv[1])
msp.architecture["num_motifs"] = 82
msp.architecture["motif_model_spec"]["motif_width"] = 13
msp.architecture["motif_model_spec"]["motif_feature_extractor_spec"] = dict(
type="ResidualStack",
depth=3,
)
msp.arch... |
8b30b83aca1bdda512719f45e09002410842dafdf1f66a2f5014335c9928306f | Python | 2,214 | 63 | # -*- coding: utf-8 -*-
import os
import numpy as np
import pandas as pd
# Tanimoto
def tanimoto(v1, v2):
ab = np.dot(v1, v2)
a_norm = np.dot(v1, v1)
b_norm = np.dot(v2, v2)
result = ab/(a_norm+b_norm-ab)
return result
def calc_tanimoto(ref_df, search_df):
ref_vecs = ref_df.values
tm... |
479cf3b98d90492a34a0d0497114706369f49ab234e66c2922e5e8f036f663b7 | Python | 2,215 | 72 | import sys
import csv
import powerlaw
import simulatorutils
import utils
def GetPathlengths(simulations):
PathlengthXYZ = []
pathlengthdata = utils.CalculateDistPerCellPerTimeStamp(simulations)
for dataPoint in pathlengthdata:
ID = dataPoint['track ID']
path_ = dataPoint['DistXYZ']
... |
4cc10f802341d487004cce1156e991229c3d22e96b3f6c28fd18a6d2fef67489 | Python | 2,215 | 55 | # LICENSE
#
# _This file is Copyright 2018 by the Image Processing and Analysis Group (BioImage Suite Team). Dept. of Radiology & Biomedical Imaging, Yale School of Medicine._
#
# BioImage Suite Web is licensed under the Apache License, Version 2.0 (the "License");
#
# - you may not use this software except in compl... |
f885634681197c9887e538bab3f3a1c39e396adf2dd9736caf142a4b31fa8c26 | Python | 2,215 | 76 | """
# > Implementation of the classic paper by Zhou Wang et. al.:
# - Image quality assessment: from error visibility to structural similarity
# - https://ieeexplore.ieee.org/stamp/stamp.jsp?arnumber=1284395
# > Maintainer: https://github.com/xahidbuffon
"""
from __future__ import division
import numpy as np
im... |
4f908292f49c411a09f18f32b188fa4c3be8e0e9a9eda9f5a44a7906118097e1 | Python | 2,216 | 61 | #!/usr/bin/env python3
'''Takes a bunch of types training files. First argument is what index the receptor starts on
(ligand is assumed to be right after). Reads in the gninatypes files specified in these types
files and writes out two monolithic receptor and ligand cache files for use with recmolcache
and ligmolcac... |
7070a7b702809f211fe8c386dcd40cf1418e1cbbad90b364dfaa42bf55523ac2 | Python | 2,216 | 75 | import os
import sys
import argparse
import matplotlib
import matplotlib.image
import numpy as np
import tables
sys.path.append("../../../")
# Code adapted from Mineault et al. 2021
# This script builds the PVC1 dataset
def derive_pvc1(args):
root = f"{args.data_root}/crcns-pvc1"
movie_info ... |
fef6c8194987538e139c2ed04e7cbbfefc2317cf4078a2469ae62a1c490f2138 | Python | 2,216 | 72 | # This example requires the following dependencies to be installed:
# pip install lightly
# Note: The model and training settings do not follow the reference settings
# from the paper. The settings are chosen such that the example can easily be
# run on a small dataset with a single GPU.
import pytorch_lightning as p... |
55e482f99172072723ac98eadd6373c5144a9e2db12d35979a70290038c82b01 | Python | 2,217 | 50 | """Tests for spiketools.spatial.information"""
from spiketools.spatial.information import *
###################################################################################################
###################################################################################################
def test_compute_spatial_... |
60c3c0861c31850e647047677ed8825c1f4e4df86593d8644b41ce7e6ca284ac | Python | 2,217 | 61 | '''
train / test df for Jensen et al.'s model.
'''
import pandas as pd
from reaction_numbering import *
def make_csv_friendly_labels(product_idxs):
'''
The csv file doesn't like a list of an array. So we're transforming them into strings.
'''
csv_friendly_label = ''
for i in range(len(product_idxs... |
c1be0a25ea1b987e4631cae0142c99f1e44d8c045d40a62ba2f0ba39009fbf6a | Python | 2,217 | 62 | import os
from PIL import Image
from torch.utils import data
from torchvision import transforms
class DefaultDataset(data.Dataset):
def __init__(self, root, transform=None, return_path=False, test_list=None):
if test_list is not None:
with open(test_list, "r") as f:
test_files... |
c3aed9f4b0c47f1edf1c414d72f34c8cfa3f8baf2068947733446d7c8eb5b81e | Python | 2,217 | 60 | # coding=utf-8
# Copyright 2022 The Google Research Authors.
#
# 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 applicab... |
10963fe314e2ffeab316ca99264827c0bb5ea1a91d929440733cdd30219e5ded | Python | 2,218 | 72 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""Tests for Weisfeiler-Lehman"""
import unittest
import numpy as np
from sknetwork.data import house, bow_tie, linear_graph
from sknetwork.data.test_graphs import *
from sknetwork.topology import color_weisfeiler_lehman, are_isomorphic
class TestWLKernel(unittest.Test... |
3f95df036a7d8e215411b59a500578549c51cec84d0338ae1b60b3bea92b088c | Python | 2,218 | 67 | # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
#
# Copyright 2023 The NiPreps Developers <nipreps@gmail.com>
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may... |
7c956a6fca9ac34e52d21b8ae96bf279bcdbb5b64f2574c0265b86ac018e6616 | Python | 2,218 | 78 | from pathlib import Path
from setuptools import find_packages
from setuptools import setup
this_directory = Path(__file__).parent
long_description = (this_directory / "README.md").read_text()
setup(
name='angorapy',
version='0.10.8',
description='Build Goal-driven Models of the Sensorimotor Cortex with E... |
7cab9ff13fb96d184149bc820e348930887bc4ede2f9c1d861e726c362a60741 | Python | 2,218 | 62 |
"""
Author: Derek van Tilborg -- TU/e -- 09-06-2022
Script for bayesian optimization of model hyperparameters using 5-fold cross-validation.
"""
from MoleculeACE.models import RF, SVM, GBM, KNN, MLP, GCN, MPNN, AFP, GAT, CNN
from MoleculeACE.models.optimize import BayesianOptimization
from MoleculeACE.benchmark.con... |
822b992a45fc788ff6315032df0c01bdc9a6983c523a8f24f5e033bb6400eaea | Python | 2,218 | 72 | #!/usr/bin/env python
# coding: utf-8
import sys
import re
import numpy as np
from .amira_header import AmiraHeader
from .amira_data_stream import DataStreams, write_amira
class AmiraFile(object):
"""Convenience class to handle Amira files
This class aggregates user-level classes from the :py:mod:`ahds.hea... |
815a7aafb5b890c93346aeca5c18b0a4f4d26ab2ca467bd1a700509aa8ead129 | Python | 2,219 | 69 | """IOU loss"""
import torch
from torch import nn
class IOULoss(nn.Module):
"""
Intersetion Over Union (IoU) loss which supports three
different IoU computations:
* IoU
* Linear IoU
* gIoU
"""
def __init__(self, loc_loss_type='iou'):
super(IOULoss, self).__init__()
self... |
6531800276bfec3ca8c5e6fc11f3ea5408528e16f06f29bfe233ddddabae22bf | Python | 2,220 | 70 | # -*- coding: utf-8 -*-
import os
import sys
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
fontsize = 22
plt.style.use('seaborn-colorblind')
plt.rcParams.update({'font.size': fontsize,
'font.family': 'sans-serif',
'font.sans-serif': ['Arial'],
... |
e37d67f9287a3932dc357fcf4032ad628ac7658d1a728054d318b7599e25931b | Python | 2,220 | 67 | # -*- coding: utf-8 -*-
import numpy as np
import pickle as pkl
import scipy.sparse as sp
# from scipy.sparse.linalg.eigen.arpack import eigsh
from scipy.sparse.linalg import eigsh
import sys, os
import torch
import re
import string
import torch
import torch.nn.functional as F
from sklearn import preprocessing
from skl... |
f4946912d9605a4beaa78548a584e8b2764b90843ae54ea49abbb2771b702cb3 | Python | 2,220 | 77 | """Module level utilities for managing dependencies."""
from importlib import import_module
from functools import wraps
###################################################################################################
##################################################################################################... |
fa5cf62b8fccda0f8edb9737b984fbaeedc43023de4d64d97f14a5169365643d | Python | 2,220 | 66 | #!/usr/bin/python
# -*- coding: utf-8 -*-
# Copyright: University of Zurich
# Author: Rico Sennrich
# script to allow batch-alignment of multiple files. No multiprocessing.
# syntax: python batch_align directory source_suffix target_suffix translation_suffix
#
# example: given the directory batch-test with the files 0... |
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