sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
88378665f0b1b2ff1b0b52880669b1746c7d9632fc4958863abc99877415b721 | Python | 3,773 | 128 | """
Extract static/dynamic featuresfor single residue classification
"""
import argparse
import os
from collections import OrderedDict
import nearl.data
import numpy as np
import nearl
from nearl.io.traj import MisatoTraj
nearl.update_config(
verbose=False,
debug=False,
# verbose = True,
# debug =... |
e86cd6475aac4cc4b387190251cf1eeb6f335132b7a71a8b12455886b7c58d26 | Python | 3,775 | 106 | # -*- coding: utf-8 -*-
# tests/test_xarray.py
################################################################################
# EncoderMap: A python library for dimensionality reduction.
#
# Copyright 2019-2024 University of Konstanz and the Authors
#
# Authors:
# Kevin Sawade, Tobias Lemke
#
# Encodermap is free sof... |
0da5b1b768b56851aef211299254f2d1acf1cb12dfcb673783c6ad2ff8af60cd | Python | 3,778 | 123 | import itertools
import ase.io as aio
import numpy as np
import torch
from ase import Atoms
from fire import Fire
from mace import data, tools
from mace.tools import torch_geometric
from energy_model.diffusion_tools import (
HeunSampler,
SamplerNoiseParameters,
)
from simgen.utils import get_system_torch_devi... |
6e02b876b9c22ceb901198cadfcdb3ff1c1b4208994d03b84a71f44fa5c2d262 | Python | 3,778 | 113 | import socket
import time
import numpy as np
import pandas as pd
import panel as pn
import pytest
from playwright.sync_api import expect
from guppy.frontend.frontend_utils import scanPortsAndFind
from guppy.frontend.parameterized_plotter import ParameterizedPlotter
from guppy.frontend.visualization_dashboard import V... |
6edfd9e065e8c792ef38660aa4e7d5dfb2ad68808cdbdebb8a0cddb5d4fb21f2 | Python | 3,780 | 123 | import pickle
from types import SimpleNamespace
import numpy as np
import pandas as pd
from scipy.interpolate import interp1d
from masscube.alignment import gap_filling
from masscube.mzpkl import convert_MSData_to_mzpkl, read_mzpkl_to_MSData
from masscube.raw_data_utils import MSData, Scan, save_mcraw
def _make_msd... |
1e0e8df3017445271da4de1e4e63a9abca55765d227daf4fca0b8ec39afaf627 | Python | 3,781 | 102 | #!/usr/bin/env python
import sys, os
from argparse import ArgumentParser, FileType
def get_data(small = False):
data_root = "http://www.ccb.jhu.edu/software/hisat2/downloads/evaluation"
# Download the reference human genome, SNPs, and gene annotations
if not os.path.exists("data"):
os.mkdir("... |
c082543294c6160ae8db27002069deaec0e66e0bcc90404be1a2d631945ba2b4 | Python | 3,783 | 80 | # coding=utf-8
# Copyright 2022 IDEA-CCNL and The HuggingFace Inc. team. 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.... |
23fb332a8d44182f51ed492153ac58c8f39e4fcae725ef8d4db7a9886a6a956d | Python | 3,784 | 87 | from modules.atlas_read_cluster import atlas_read_cluster
from modules.time_func import get_current_datetime_for_filename
from modules.time_func import easy_time
from modules.load_lesions_and_behaviors import load_lesions_and_behaviors
from modules.filter_voxels_by_patient_count import filter_voxels_by_patient_coun... |
67a305bd58ba1232b886f5e7381654e97f73d311435fe7b72586ae81d510bb07 | Python | 3,785 | 127 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
# tests/run_doctests.py
################################################################################
# EncoderMap: A python library for dimensionality reduction.
#
# Copyright 2019-2024 University of Konstanz and the Authors
#
# Authors:
# Kevin Sawade
#
# Encodermap is... |
8b9b3303db4fe3a0f00328dc6f62551dfb4daa32c66a24ca943c694fd724b2f7 | Python | 3,785 | 121 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
from common import db_connection
import sys
import os
first_migration = '2011-07-10T19:23:39'
if len(sys.argv) != 1:
print >> sys.stderr, "Usage: " + sys.argv[0]
sys.exit(1)
everything_ok = True
c = db_connection.cursor()
c.execute("select tablename from pg_t... |
8e12c1ddfa705c7b84502b6a2260ae515b459837d1bd2c5e7aadc08392abb007 | Python | 3,786 | 94 | from CybORG.Shared import Observation
from CybORG.Simulator.Actions.Action import RemoteAction
from CybORG.Simulator.Actions.ConcreteActions.StopProcess import StopProcess
from CybORG.Simulator.State import State
from ipaddress import IPv4Address
class Withdraw(RemoteAction):
""" A red action that removes all the ... |
335a477dcc6488722957d8716ae069e1585fc65957903d21e7e59fe77ef462cb | Python | 3,788 | 95 | # pytest unit tests for spinalcordtoolbox.resampling
# TODO: add test for 2d image
import logging
import pytest
import numpy as np
import nibabel as nib
from spinalcordtoolbox import resampling
@pytest.fixture(scope="session")
def fake_3dimage_nib():
"""
:return: an almost empty 3-d nibabel Image
"""
... |
630a9a91b26fafdf94e80dab5d7810b9bd22b007f1c34760f025ddd2bf7e54a2 | Python | 3,791 | 86 | # -*- coding: utf-8 -*-
from django.db import migrations, models
forward = """
-- Remove constraints if they exist (in case they have been added manually
ALTER TABLE ONLY class_instance_class_instance
DROP CONSTRAINT IF EXISTS class_instance_class_instance_project_id_fkey;
ALTER TABLE ONLY class_i... |
519e514abfb1964cba406b44ffda740f81be1754f61181cca8933e96b7b4de4b | Python | 3,793 | 80 | #############################################
# See GASTON code: https://github.com/raphael-group/GASTON/blob/main/src/gaston/isodepth_scaling.py
#############################################
import numpy as np
from sklearn.metrics import pairwise_distances
import matplotlib.pyplot as plt
# Linearly scale isodepth r... |
63716ff66d43fc99216da87a78fa686e56b14af722bd23eebeb17cd22fcd12e4 | Python | 3,794 | 103 | """Layer 1: static schema audit for RoomScopedEvent subclasses.
Fails fast at collect time if any subclass forgets to declare both
``room_id: UUID`` and ``room_address: str``.
LIMITATION: discovery uses ``RoomScopedEvent.__subclasses__()``, which
only enumerates classes that have been imported. The audit imports
``zn... |
6a6ae8dbc6605aca12c4ce31dc51641c186293a0871dd6ebc750ab84022f9b5b | Python | 3,794 | 111 | import numpy as np
import random
# from IPython.display import display, HTML
def fetchSize(genome):
'''Input a genome.fa file, get the chromsome bounderies.'''
genomeSize = {}
sequence = ''
with open(genome, 'r') as refFh:
for line in refFh:
line = line.strip()
if '... |
6e9c62a56919587c4b213b78914239b8c98e5e945e6b7ce00333979ab0a17cca | Python | 3,795 | 102 | import os
import torch
import pandas as pd
from PIL import Image
import numpy as np
import torchvision.transforms as transforms
from models import model_attributes
from torch.utils.data import Dataset, Subset
from data.confounder_dataset import ConfounderDataset
class CUBDataset(ConfounderDataset):
"""
... |
8d6b41d520e315fc5262bae7e7b9c451a8cfdf4b087e13224e4b1951c03e347f | Python | 3,795 | 97 | #-*- coding: utf-8 -*-
#setting##############################################
n_jobs=16 #並列処理の数
t_n_jobs=16
PARAMETER_DIR='/Volumes/Siena/CP/parameter'
#n_jobs=40 #並列処理の数
#t_n_jobs='cuda'
#PARAMETER_DIR='/home/takeiyuuichi/Dropbox (MEG)/CP/parameter'
set_environment='main'
SET_EVENTID=[2,3]
event_id = dict(control=2... |
db5023f1452a35f0be42bdaebe040184f576cdb1289a74d9662d26a3fcdb59e3 | Python | 3,797 | 124 | from __future__ import annotations
import json
from typing import Annotated
import typer
from zndraw.schemas import (
SelectionGroupResponse,
SelectionGroupsListResponse,
StatusResponse,
)
from .connection import (
PasswordOpt,
RoomOpt,
TokenOpt,
UrlOpt,
UserOpt,
cli_error_handle... |
35464d7a54c8f4db1bdf0146b3f2887e132c1c82784a1db33062393c253e6509 | Python | 3,798 | 119 | import pytest
from cutadapt.kmer_heuristic import (
kmer_chunks,
minimize_kmer_search_list,
create_back_overlap_searchsets,
create_positions_and_kmers,
)
@pytest.mark.parametrize(
["sequence", "chunks", "expected"],
[
("ABC", 3, {"A", "B", "C"}),
("ABCD", 3, {"AB", "C", "D"}),... |
c87b978e9054be71f6a2773d72e0a78eede8237743707fc9522b7f5564696450 | Python | 3,798 | 104 | import numpy as np
import torch
from SurrGradSpikeLIF import SurrGradSpikeLIF
from SurrGradSpikeIZ import SurrGradSpikeIZ
class surrParams:
def __init__(self):
self.version = 1.2
self.simTag = "Test"
self.debug = False
# the other option for dataset is the "SHD"
self.data_s... |
cf7138b761d3ab0afe3e28104c7b1e53fc24371f6c7a190c253d7539fb30da8d | Python | 3,798 | 114 | from dfa_lib_python.extractor import Extractor
from dfa_lib_python.extractor_cartridge import ExtractorCartridge
from dfa_lib_python.extractor_extension import ExtractorExtension
def test_get_cartridge_pass():
tag = "ext1"
cartridge = ExtractorCartridge.EXTRACTION
extension = ExtractorExtension.FITS
e... |
6c632be65b5b97eb2adcd43877a8450d37b9665da887780ebb4965a185276b77 | Python | 3,801 | 133 | import re
import sys
import time
import multiprocessing
import logging
import locale
logger = logging.getLogger(__name__)
try:
"µ".encode(locale.getpreferredencoding())
MICRO = "µ"
except UnicodeEncodeError:
MICRO = "u"
def available_cpu_count():
"""
Return the number of available virtual or phy... |
aff884bb16e2e3a2add2c188e7603420add6f5d8f9d16d796e5ad5d07a9e3b0d | Python | 3,802 | 101 | from __future__ import annotations
import base64
import logging
from medperf.entities.interface import Entity
from medperf.entities.schemas import EncryptedKeySchema
from medperf import config
from medperf.exceptions import (
MedperfException,
DecryptionError,
PrivateContainerAccessError,
)
from medperf.com... |
b8350635e25b8b1a249291d6dfd98cbc52776373dc64d528171e988a5e33a531 | Python | 3,802 | 115 | """MLCube handler file"""
import typer
import os
from collaborator import start_collaborator
from aggregator import start_aggregator
from plan import generate_plan
from utils import (
get_train_val_paths,
get_server_connection,
setup_job,
get_collaborators_public_keys,
get_openssh_format_private_k... |
c80d761b6a5174e037c8e3bb906f2f4fd8e889baee70195d185eec0fb0d93155 | Python | 3,802 | 84 | from contextlib import contextmanager
from json import JSONDecodeError
from urllib.error import HTTPError
import pytest
from src.categories import ANATOMICAL_ENTITY, CELLULAR_COMPONENT, GROSS_ANATOMICAL_STRUCTURE, PHENOTYPIC_FEATURE
from src.createcompendia import anatomy, diseasephenotype
from src.datahandlers impor... |
5b99a100de17bb324c7c366b330bff8c8b62833c809d55dc14a3dfe795457e1d | Python | 3,803 | 101 | import shutil
from pathlib import Path
import pytest
from guppy.testing import compare_output_folders
from guppy.testing.api import (
group_analysis,
label_groups,
locate_run_folder,
step1,
step2,
step3,
step4,
)
from guppy_test_data import TESTING_DATA, event_ts_offset_for
SESSION_SUBDIR... |
97f86164033c94ea7fd10166ce6f0e784194da9d183dc633a26b5395ed9eb715 | Python | 3,803 | 94 | import torch
from torch.utils.data import Dataset, DataLoader
from torchvision import datasets
import numpy as np
import matplotlib.pyplot as plt
import pathlib
import os
class Digit(Dataset):
'''
Sequence of images
'''
def __init__(self, digit_mode, n_samples, topdown, noise=0):
self.n_sampl... |
e7ddf15930c5004197589f6175b1273158dea66abd714dd95bff16e4bc5ae216 | Python | 3,803 | 122 | """Unit tests for InternalProviderExecutor."""
import json
import time
from pathlib import Path
import httpx
import pytest
from httpx import MockTransport, Response
from zndraw import ZnDraw
from zndraw.providers.executor import InternalProviderExecutor
from zndraw.providers.filesystem import FilesystemRead
@pytes... |
ac1467eb219187c8f9e8a9a9f4c6f2fd40eaed20bfa25221a5d695d3cd7eb64d | Python | 3,805 | 108 | from typing import Dict
from hypothesis import given, note, settings, strategies
import xgboost as xgb
from xgboost import testing as tm
pytestmark = tm.timeout(20)
parameter_strategy = strategies.fixed_dictionaries({
'booster': strategies.just('gblinear'),
'eta': strategies.floats(0.01, 0.25),
'tolera... |
597f50a990902868c6e48cc087b9e459680f93b43c3780148a9d4d6cacf70909 | Python | 3,806 | 122 | from __future__ import annotations
import pathlib
from typing import Annotated
import typer
from zndraw.schemas import (
CollectionResponse,
FigureCreateResponse,
FigureData,
FigureResponse,
StatusResponse,
)
from .connection import (
PasswordOpt,
RoomOpt,
TokenOpt,
UrlOpt,
U... |
9d62fbe4930731da0436b47d475edd22d75766a7f3d8b3090c693797f8f47078 | Python | 3,806 | 135 | """Tests for CLI geometries commands."""
from __future__ import annotations
import json
from typing import TYPE_CHECKING
from zndraw.cli_agent import app
from zndraw.schemas import GeometryResponse, StatusResponse
from .conftest import invoke_cli
if TYPE_CHECKING:
from typer.testing import CliRunner
def test... |
73423562558e2cdbf1450a0202d7badc614ba7f97d65ed039e2d97d87af841dc | Python | 3,807 | 92 | from mpi4py import MPI
import numpy as np
from grid_cell.persistent_homology import Is_Torus
from grid_cell.manifold_fitter import GP_Fitter, Avg_Fitter
import matplotlib.pyplot as plt
import tensorflow as tf
import os
from sklearn import datasets
from global_setting import *
comm = MPI.COMM_WORLD
size = comm.Get_size... |
13602b8d87b5afa0ee162da0010328f6b13652de30f7d4532504e593b3155389 | Python | 3,808 | 125 | # Copyright (c) Facebook, Inc. and its affiliates. All Rights Reserved.
# pyre-strict
import itertools
import unittest
from typing import Iterable
import torch
from fvcore.nn.squeeze_excitation import (
ChannelSpatialSqueezeExcitation,
SpatialSqueezeExcitation,
SqueezeExcitation,
)
class TestSqueezeExci... |
dbba024498246b3e821929df48a323aa340505847012b56f69a6cff4e0d9fd87 | Python | 3,811 | 102 | from transformers.models.llama import LlamaForCausalLM, LlamaTokenizer, LlamaConfig
from fengshen.models.megatron import mpu
from fengshen.models.llama.modeling_llama import LlamaForCausalLM as FengshenLlama
from fengshen.models.llama.configuration_llama import LlamaConfig as FengshenConfig
import argparse
import torch... |
7ff769e6a96027c0a220b3e2018ef1349db624b4a7a57f9dfc8b59885df644b9 | Python | 3,812 | 84 | import numpy as np
import scipy.io as scio
import datetime
from configobj import ConfigObj
def init_params():
'''
Initialize network training parameters.
tc: training_configurations
always define x as the prior dimension (matrix rows, along the height),
y as the following inner (last) dimension
... |
9754f24d37e5e9f797bada76ad3169d225a847f40404e8fadeacd4de2b558fc5 | Python | 3,812 | 109 | # select a group of metabolic features for correcting m/z and retention time error
# the selected features should be:
# 1. present in all (most) biological samples
# 2. confirmed by unique m/z, good peak shape, and MS/MS spectra
# input: a list of files
from __future__ import annotations
from typing import TYPE_CHECK... |
f913b910af55445c8d459ae783cdf16c1ea4f74cbbb16630d963b4693ebc875e | Python | 3,812 | 146 | """Server management utilities for ZnDraw CLI.
Retained utilities: process checking, server readiness polling, and shutdown.
Server registry and token storage moved to zndraw.state_file.
"""
from __future__ import annotations
import logging
import os
import time
import httpx
log = logging.getLogger(__name__)
DEFA... |
567831a14bf8585f100bef52533c4c7da2a9c7ec8433df262b919a6ae6a3ea66 | Python | 3,813 | 126 | """Tests for local admin token authentication.
Tests cover:
- Local token grants admin access to the shutdown endpoint
- Wrong local token is rejected
- Normal JWT auth still works when no local token is configured
"""
from unittest.mock import patch
import pytest
import pytest_asyncio
from helpers import create_tes... |
1445bdc4a08dca7e28918393e41d37d37018bdfff5c1a066a52b6fc811061051 | Python | 3,816 | 122 | """Quality control for data set."""
import argparse
import os
from typing import Tuple
import matplotlib.pyplot as plt
import numpy as np
import pandas as pd
from brainbuilder.utils import utils
from joblib import Parallel, delayed
def get_min_max(fn: str) -> str:
"""Get min and max values from image file.
... |
4d7de81663ac7efdf56a0934426d63d2379e3bf970a97acef9fd2069db285d6b | Python | 3,816 | 107 | import os
import gensim
from Utils.dataloader_GRAZPEDWRI import *
from Utils.models import *
from Utils.TrainModel import *
from Utils.config import *
# OPTIONAL: Load the "autoreload" extension so that code can change
#%load_ext autoreload
# OPTIONAL: always reload modules so that as you change code in src, it gets ... |
5c3f61860ade714d3dbf4af550a0d0ea0ca80728b72c9129422a89dbd9553cf2 | Python | 3,817 | 115 | import io
import logging
import os
import pytest
import nearl
@pytest.fixture
def isolated_logger(tmp_path, monkeypatch):
stdout_buf = io.StringIO()
stderr_buf = io.StringIO()
monkeypatch.setattr(nearl._stdout_handler, "stream", stdout_buf)
monkeypatch.setattr(nearl._stderr_handler, "stream", stderr... |
f6313c991ae34129361df2b67ce20aab2f52e3f9741c17f4fc7fd31049135032 | Python | 3,817 | 66 | # preprocess and fitting GKR model
import numpy as np
import os
import hickle as hkl
from grid_cell.grid_cell_processor import Grid_Cell_Processor, Data_Transformer
from sklearn.decomposition import PCA
from grid_cell.gkr import GKR_Fitter
import argparse
from global_setting import *
parser = argparse.ArgumentParser(d... |
0a8fe4fa9eec374aeb90fa64eeabf786f77bcf5bf533c505ac4e0bc193693f72 | Python | 3,819 | 128 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Fri Mar 10 14:22:45 2023
@author: george
"""
#%matplotlib qt
import numpy as np
import pandas as pd
import skimage.io as skio
from tqdm import tqdm
import os, glob
from matplotlib import pyplot as plt
import pyqtgraph as pg
tiffFile = '/Users/george/Data... |
25aa4517db725eb425c917149545937964fb0e9fdd4727ac2ccaadbc0c7d1978 | Python | 3,819 | 83 | import sys
class Ts2vcf:
"""
tree sequence from msprime simulation will be converted to vcf file and will be printed in stdout. given a msprime
function coming from demography.py and set of parameters defined by a tsv file with first column names of the
parameters and the second columns are the parame... |
a0105c2e2eb6996c6fc93fa07c6280393e77f3ca5b211148f3b84314a92933fa | Python | 3,820 | 119 | # Configuration file for the Sphinx documentation builder.
#
# This file only contains a selection of the most common options. For a full
# list see the documentation:
# https://www.sphinx-doc.org/en/master/usage/configuration.html
# -- Path setup --------------------------------------------------------------
# If ex... |
e3cc32573d83bbf268a4f7558ce56469b577b05d663ec8c924f8526d879bf93e | Python | 3,824 | 91 | # MLCube Entrypoint
#
# This script shows how you can bridge your app with an MLCube interface.
# MLCubes expect the entrypoint to behave like a CLI, where tasks are
# commands, and input/output parameters and command-line arguments.
# You can provide that interface to MLCube in any way you prefer.
# Here, we show a wa... |
5c48c7aca8d0de7fef88ca5734940586cc8f420164683f4de64ade1fb53f8d38 | Python | 3,828 | 106 | import time
import numpy as np
from nearl import all_actions, commands
np.random.seed(0)
# For dummp data generation
atom_nr = 100
frame_nr = 30
# For the settings of the grid
dims = np.array([32, 32, 32], dtype=np.int32)
spacing = 0.5
cutoff = 0.5
sigma = 1.0
def test_frame_voxelize():
"""
Voxelize a se... |
c7ea538347d79352b7ed53fd6503c3f53ac5690ab50e2342fc2decd49970fc67 | Python | 3,830 | 112 | # Copyright (c) OpenMMLab. All rights reserved.
from argparse import ArgumentParser
import cv2
from mmengine.model.utils import revert_sync_batchnorm
from mmseg.apis import inference_model, init_model
from mmseg.apis.inference import show_result_pyplot
def main():
parser = ArgumentParser()
parser.add_argume... |
e818e4ca18d986460db7bae146ad7c7bf3341f82643c90ce0fe5db3a1a6431a0 | Python | 3,830 | 114 | import torch
import torch.nn as nn
import torch.nn.functional as F
from rde.modules.encoders.single import PerResidueEncoder
from rde.modules.encoders.pair import ResiduePairEncoder
from rde.modules.encoders.attn import GAEncoder
from rde.utils.protein.constants import BBHeavyAtom
from .rde import CircularSplineRotame... |
1a98e10e61ab88db9fb7ef644c4e3be5f812799c2926ad2c43b8ae24fbc213c4 | Python | 3,833 | 136 | from asciitree import LeftAligned
from ..client import inject_client
from .general import fetch_meta
@inject_client
def fetch_all_rois(*, client=None):
"""
List all ROIs in the dataset.
"""
meta = fetch_meta(client=client)
return _all_rois_from_meta(meta)
def _all_rois_from_meta(meta):
rois... |
81e1946d43cfde5a9a6213def5e5eda349268ea2b9478ef32e1e378569d0e040 | Python | 3,833 | 100 | import logging
from pathlib import Path
import numpy as np
from .standard_io import (
read_freq_and_amp_from_hdf5,
write_freq_and_amp_to_csv,
write_freq_and_amp_to_hdf5,
)
from ..utils.utils import output_label_under
logger = logging.getLogger(__name__)
def average_transients_for_group(
*, member_r... |
8681e69db1b855f6c828f9848d2091aeb7206defd67f1dfcae82c8fcfc1a5be3 | Python | 3,835 | 108 | from __future__ import annotations
from typing import TYPE_CHECKING, Literal
import pytest
from pymatgen.core import Lattice, Structure
from chgnet.graph import CrystalGraph
from chgnet.graph.converter import CrystalGraphConverter
if TYPE_CHECKING:
from collections.abc import Generator
lattice = Lattice.cubic(... |
ef14584d6ea13a121b79aa2f73808d0e769916c0677cd700ef1676b0e711863d | Python | 3,835 | 95 | # %%
from PIL import Image
from os.path import join
import os, glob, re
import pathlib
# def gifify(sub, img_dir, save_dir, file_pattern, save_fname):
# image_files = glob.glob(join(img_dir, f"{file_pattern}"))# f"*sbref*.png"))
# images = []
# for filename in sorted(image_files):
# img = Image.ope... |
a4b82183539d8893f2914382c2122a2080290db7f5acf7bf0817171997d576c9 | Python | 3,836 | 105 | from torch.utils.data import Dataset, DataLoader
from torchvision.transforms import Normalize, Compose, RandomResizedCrop, InterpolationMode, ToTensor, Resize, \
CenterCrop
from transformers import BertTokenizer
import pytorch_lightning as pl
from PIL import Image
import os
class flickr30k_CNA(Dataset):
def _... |
b12aac0fb633af665440839ec3c38fd46de213160ad566dc7c71a089b4639b7b | Python | 3,837 | 90 | """Unit tests for src/datahandlers/obo.py that don't require network access."""
import json
import pytest
from src.datahandlers import obo
from tests.conftest import assert_synonyms_file_valid
class _FakeUberGraph:
"""Stand-in for src.ubergraph.UberGraph returning a fixed synonym set."""
def __init__(self... |
ed4fdb3ef68249298b1fd17e3b9640d37983070b1c8d055362130733e4d01242 | Python | 3,841 | 126 | from fastapi import Request, Form, APIRouter, Depends
from fastapi.responses import HTMLResponse, JSONResponse
from medperf.web_ui.common import (
initialize_state_task,
reset_state_task,
templates,
)
from medperf.account_management import read_user_account
from email_validator import validate_email, Email... |
e3ec365f2ab00c6e813d5596a81b12e5cceb8e54998af7b9176d0b08c428bca3 | Python | 3,844 | 124 | import numpy as np
from pyscf import gto, dft
from pyscf.geomopt.geometric_solver import optimize
from pyscf.hessian import thermo
# from pyscf import dftd3
from molSimplify.Classes.mol3D import mol3D
from pymatgen.core import Molecule
from pymatgen.analysis.molecule_matcher import BruteForceOrderMatcher
from pymatge... |
6ed8e567275afbdcdf986e28d35ead6c5117ed0d042a2c10c25ca1c4f1680c0d | Python | 3,847 | 99 | import json
import numpy as np
import pickle as pkl
import random
from collections import defaultdict
from tqdm import tqdm
from concurrent.futures import ThreadPoolExecutor
def load_data(filename):
with open(filename, 'rb') as f:
return pkl.load(f)
def two_hop_mapping(mapping_dict, umls_cuis, triple_set,... |
c2f3dab95e8169711118a0333f3bd8e975381a316d8efd1ff9a96c68f93c0bc9 | Python | 3,847 | 90 | #!/usr/bin/env python
# -*- coding: utf-8
# TODO
#
# For usage, type: python average_images.py -h
# Example:
# python average_images.py -path-data ~/duke/temp/sebeda/rootlet_reg/results_spine-generic_sub-amu01_rootlets_2024-10-18/data_processed/ -path-file reg_discs -path-out ~/duke/temp/sebeda/rootlet_reg/results_spin... |
93248e1b9771ff09ec988631b30463138058c1b618e9ac18bb13e4abf7622425 | Python | 3,850 | 108 | import os
import torch
import random
import numpy as np
import cv2
from typing import List, Tuple
from torch import nn, Tensor
import torch.distributed as dist
def get_params_groups(model):
regularized = []
not_regularized = []
for name, param in model.named_parameters():
if not param.requires_gra... |
0674046985e940a104fb08b1fc05f08e50257d667a88fc2e22c096dfbab207bd | Python | 3,851 | 96 | #!/usr/bin/env python
# -*- coding: utf-8
# fslstats thresh_zstat1_med.nii.gz -V | cut -d " " -f1 >> voxels_med.txt
# fslstats thresh_zstat1_high.nii.gz -M >> zscore_high.txt
# fslstats thresh_zstat1_med.nii.gz -H 15 3.1 9 >> hitogram_med_15_3.1-9.txt
import os
import argparse
import nibabel as nib
import numpy as np... |
2da2287d4c779bab999ef67f6d5aa306bd17d8e9eb0996b60cbb7b4dda2e28b3 | Python | 3,851 | 107 | """Smoothing the raw channels before they are fit and normalized."""
import logging
import numpy as np
from scipy import signal as ss
logger = logging.getLogger(__name__)
def validate_chunk_lengths_for_filtering(tsNew: np.ndarray, coords: np.ndarray, filter_window: int) -> None:
"""
Ensure every artifact-r... |
d502f0c14b7017c764b16a71f2b118b3b63637cb7433b55a242666f4abc20939 | Python | 3,851 | 70 | import sys
sys.path.append('../')
from data import make_loaders,create_dataset,MaskAtom,MolGraphSet,Mol2HeteroGraph
from dgl.dataloading import GraphDataLoader
from omegaconf import DictConfig, OmegaConf
import pandas as pd
from rdkit import Chem
import torch
# def get_dataset(dataset, mask_edge=False):
# transfor... |
81442bfbb13ce79ed5be9f6d0aa39ebcdd974ceb67dc6ec4cfb76a930092a369 | Python | 3,852 | 118 | # Copyright (c) OpenMMLab. All rights reserved.
import torch.nn as nn
from mmcv.cnn import ConvModule, build_norm_layer
from mmseg.registry import MODELS
class MLAModule(nn.Module):
def __init__(self,
in_channels=[1024, 1024, 1024, 1024],
out_channels=256,
norm... |
ae26bb368f70832b40de556644b129530ead2c83aeb0bf37b7b2ff610a3d1dbf | Python | 3,853 | 85 | # SPDX-License-Identifier: Apache-2.0
from transformers import T5ForConditionalGeneration
from .models import CombinedDecoder, SimplifiedT5Encoder
import torch
def create_t5_encoder_decoder(pretrained_version='t5-base'):
""" Generates an encoder and a decoder model with a language model head from a pretrained hu... |
950c3084586c712c8bfa52f89b1e63a8254fa7072a02b40f2d4dd2a77212bb89 | Python | 3,854 | 89 | from experiment import *
from behavior_analysis.io import TrackingInterface
import pandas as pd
import numpy as np
from scipy.interpolate import interp1d
from scipy.stats import linregress
if __name__ == "__main__":
strike_clusters = [1, 2, 4]
time_window = 0.2 # time (seconds) to study pre-strike
onset... |
ff5e6d5e39560c94f2f761109729b73ef1b70d034263ae81db60444ef744fd46 | Python | 3,856 | 134 | # pylint: disable=invalid-name, too-many-arguments, too-many-positional-arguments
"""Tests for compatiblity with sklearn."""
from typing import Callable, Optional, Type
import numpy as np
import pytest
from ..core import DMatrix
from ..sklearn import XGBClassifier, XGBRFRegressor
from .utils import Device
def run_... |
9356f86f8a631ccbf8d0f10a115a592b361cf673e0d46f8f9791c1908ddde927 | Python | 3,858 | 91 | from __future__ import print_function, division
import torch
import torch.nn as nn
class ConvLayer(nn.Module):
def __init__(self, atom_fea_len, nbr_fea_len):
super(ConvLayer, self).__init__()
self.atom_fea_len = atom_fea_len
self.nbr_fea_len = nbr_fea_len
self.fc_full = nn.Linear(... |
b60eeb20de7a78bdf5c1391a32b43d9783a1056e571556e9e544aa01eb0c6f91 | Python | 3,858 | 91 | """Network tests for the UniChem download.
These verify that the UniChem HTTP mirror URLs are reachable with the User-Agent
Babel sends, that each file is a valid gzip archive, and that the reference file
header matches the constant in unichem.py.
Run with: uv run pytest --network tests/datahandlers/test_unichem.py
""... |
9c7a8ec4db3a0b3fc46fb09625faec8fd642b3f92b8e535c1cc9db57d9448b5e | Python | 3,859 | 109 | """
Functions for loading models and datasets from experiment folders.
Author: Hanna Tolle
Date: 2025-01-12
License: BSD-3-Clause
"""
import sys
sys.path.append('../')
import os
import importlib
import copy
import torch
from utils.configs import fill_missing_configs
from experiments.ingredients.data_ingredient impo... |
d3ac7898b4a7f7a1918fe2a76fe003d9d5d1a9ba0b8444b069eb2f5d953f1635 | Python | 3,862 | 94 | import json
from importlib.metadata import version
from pathlib import Path
import numpy as np
import pytest
from guppy.testing.api import default_output_root_folder, save_parameters_snapshot
@pytest.fixture(scope="function")
def default_parameters():
return {
"combine_data": False,
"isosbestic_... |
7a909454f8347ce7b9de9a6718e73e562551595b32725875cfca897c07e5c047 | Python | 3,865 | 114 | """
Demonstrate the use of h5py in SWMR mode to write to a dataset (appending)
from one process while monitoring the growing dataset from another process.
Usage:
swmr_multiprocess.py [FILENAME [DATASETNAME]]
FILENAME: name of file to monitor. Default: swmrmp.h5
D... |
c667e1179bc788d7f71b92827185c3e042c5bde08cd249f32a5c9d424a5a723c | Python | 3,866 | 80 | # Copyright 2020 Division of Medical Image Computing, German Cancer Research Center (DKFZ), Heidelberg, Germany
#
# 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://w... |
c022bde96e7e6d1ff2c33d78ae553887ae0e5a8e95d712f566ede49fbcf61161 | Python | 3,867 | 117 | # Copyright (c) OpenMMLab. All rights reserved.
import torch
import torch.nn as nn
from mmcv.cnn import ConvModule
from mmseg.registry import MODELS
from ..utils import resize
from .decode_head import BaseDecodeHead
class PPM(nn.ModuleList):
"""Pooling Pyramid Module used in PSPNet.
Args:
pool_scale... |
19cbb9270cd7d6194d109a108ee7060cf7a0646a33cbe5bce098acdcc0e21cc1 | Python | 3,871 | 89 | import os
def create_key(template, outtype=('nii.gz',), annotation_classes=None):
if template is None or not template:
raise ValueError('Template must be a valid format string')
return template, outtype, annotation_classes
def infotodict(seqinfo):
"""Heuristic evaluator for determining which run... |
a899faee4e3211a732f114f83b057a367b3a1ccdd1de84fceebf0525ae3ea7db | Python | 3,872 | 153 | import os
import numpy as np
import pathlib as pl
import subprocess as sp
try:
import cv2 as cv
except ImportError:
cv = None
from tifffile import imsave
def ffmpegInstalled():
"""
"""
return
def reflectVideo(video, flipAxis='hflip', suffix=' (reflected)', speed='medium', deleteOriginalVideo=Fals... |
b1322eea0ca9bb4b7940ec4ec44564716a60d220eaa7500f5ffbb09e8049389a | Python | 3,872 | 112 | from collections import Counter
import ase
import ase.io as aio
import numpy as np
from ase.calculators.mixing import LinearCombinationCalculator
from ase.calculators.morse import MorsePotential
from ase.optimize import LBFGS
from simgen.manifolds import StandardGaussianPrior
from .calculators import MopacCalculator... |
e24aa8876025ac5e7f8e78bde011f2ff66c47f3361c17854335946f280590bdb | Python | 3,873 | 108 | from rest_framework import serializers
from .models import Model
from mlcube.serializers import MlCubeSerializer
from asset.serializers import AssetSerializer
from mlcube.models import MlCube
from asset.models import Asset
from django.db import transaction
class ModelSerializer(serializers.ModelSerializer):
conta... |
eeb419625125cb78a69b2ce193d973cb614787b64d76aa7cfe0584b94726ebd2 | Python | 3,873 | 118 | import sqlite3
import collections
from datetime import datetime, timedelta
import numpy as np
import matplotlib.pyplot as plt
plt.style.use('ggplot')
def get_engine_data():
"""Main"""
conn = sqlite3.connect('tasks.db')
cursor = conn.cursor()
tasks = collections.defaultdict(list)
SQL = 'SELECT ... |
fda1d64e2228d60ea7070a3c815d01435eb09f315e5e0f98e1b4458f6e8d1167 | Python | 3,873 | 114 | import jaxlib.xla_extension
import jax.numpy as jnp
import jax
import numpy as np
import roadrunner
from jaxkineticmodel.load_sbml.sbml_model import SBMLModel
import pandas as pd
import os
from jaxkineticmodel.utils import get_logger
logger = get_logger(__name__)
import tellurium as te # noqa: E402
jax.config.updat... |
c48d814b77bc9ee03c68ccf541c6a8e815f57ed038e6e507024b1fac14618522 | Python | 3,874 | 107 | import os
import gensim
from Utils.dataloader_COVID import *
from Utils.models import *
from Utils.TrainModel import *
from Utils.config import *
# OPTIONAL: Load the "autoreload" extension so that code can change
#%load_ext autoreload
# OPTIONAL: always reload modules so that as you change code in src, it gets loade... |
ba807843ad165681e9d1483762f7010571e92fdc7380e3512c8f8832b2c97442 | Python | 3,875 | 128 | from similarity import similarity
import numpy as np
from tree import build_tree_from_list
import bisect
from mol_utils import split_molecule, join_fragments
from global_parameters import MAX_FRAGMENTS
import rdkit.Chem as Chem
import os
# Get a martix containing the similarity of different fragments
def get_dist_mat... |
8e1b67e3dd68b13e48ee17ed159a02785b3c56e1d763104bb10f315701e4b672 | Python | 3,877 | 116 | import json
from pathlib import Path
import panel as pn
import pytest
from guppy.orchestration.home import build_homepage
from guppy.orchestration.save_parameters import save_parameters
from guppy.testing.api import default_output_root_folder
# Written into the snapshot but not produced by the parameter form: the ve... |
a1c90fab53f59f6277f87e08f5b91dece0c933dd86f37a7f0f1ef56f0b9ccbf3 | Python | 3,878 | 110 | import argparse
import os
import shutil
import re
import yaml
import json
import pandas as pd
def prepare_data_input(
predictions, original_data, missing_modality_json, intermediate_folder, ssim_csv
):
modalities = {"t1c": "t1ce", "t1n": "t1", "t2f": "flair", "t2w": "t2"}
os.makedirs(intermediate_folder, ... |
0e0ad92d16b81f3bd2ca4dcd401e07ab857ec021c83ecd7be711f727c5b244b6 | Python | 3,879 | 128 | #!/usr/bin/env python
"""
MetaWIBELE: filter_prevalence module
Filtering features based on prevalence
Copyright (c) 2019 Harvard School of Public Health
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the S... |
0b7f137dc78812331ea060d6b0e10c33b87ee16acdaeca462b6f00443b752464 | Python | 3,880 | 109 | import os
import numpy as np
import pytest
import xgboost as xgb
from xgboost import testing as tm
from xgboost.core import DataSplitMode
pytestmark = pytest.mark.skipif(
tm.no_arrow()["condition"] or tm.no_pandas()["condition"],
reason=tm.no_arrow()["reason"] + " or " + tm.no_pandas()["reason"],
)
import p... |
770ec9cc64822b11498c6536c077b8cb2ca5bcb1086c4a4d644e6bd017b89607 | Python | 3,881 | 103 | from .models import BenchmarkModel
from django.http import Http404
from rest_framework.generics import GenericAPIView
from rest_framework.response import Response
from rest_framework import status
from drf_spectacular.utils import extend_schema
from .permissions import IsAdmin, IsModelOwner, IsBenchmarkOwner, IsCommit... |
4df6638567b37b17e9cb22d8c8fac0ea8a6426aac5af2b653107bb58d0b843ac | Python | 3,882 | 139 | """Progress tracking REST API endpoints.
Ephemeral progress trackers stored in Redis (hash), broadcast via Socket.IO.
"""
import json
from fastapi import APIRouter, Response, status
from zndraw.broadcast import broadcast_to_room
from zndraw.dependencies import (
AccessEditDep,
RedisDep,
SioDep,
)
from z... |
9f13229547c4128438e2098c2ca207a04cfc5243aeeaf1daf9283b22b4947c34 | Python | 3,885 | 112 | import os
from typing import TYPE_CHECKING
import medperf.config as config
from medperf.entities.model import Model
from medperf.utils import remove_path
from medperf.enums import ModelType
if TYPE_CHECKING:
from medperf.commands.mlcube.submit import SubmitCube
from medperf.commands.asset.submit import Submit... |
2bb6640810465c3f044535bd99236007ae970c910f75183b4c8b64ecb77cb466 | Python | 3,886 | 120 | # Copyright (c) 2020, NVIDIA CORPORATION. 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 appli... |
395679e93796c741b60589228fdd7524e965ad0437b89d9ee4bad0e7d703fe62 | Python | 3,886 | 99 | DOCS = """
train the model on the a dataset (gabor or mnist) or show the model learns to represent the data and predict the input
Current figures: figure 2.
"""
from dataset import GaborDatasetOrientation
from model import ShallowMLP
from experiment.utils import set_seed, init_model, Logger, Trainer, Checkpointer
impo... |
30b4fbee5582b9b1fd9509d3e842e42578483d0ebfaf23982b2dac5a2c98abd0 | Python | 3,887 | 111 | #!/usr/bin/python
import logging
import os
import shutil
import sys
from isorefiner.common import get_version, run_command
logger = logging.getLogger(__name__)
def main(args):
try:
# Set variables
raw_bam_files = [os.path.abspath(_) for _ in args.bam]
raw_genome_file = os.path.ab... |
37e7575375c3fdde38fb5b0384146f7de896b09bb21a8eef319793ae4512e219 | Python | 3,890 | 82 | import pandas as pd
import matplotlib.pyplot as plt
import torch
import seaborn as sns
import scienceplots
import matplotlib.gridspec as gridspec
import matplotlib.colors as colors
import numpy as np
import nilearn
import nibabel as nib
from nilearn import plotting, datasets, surface, image
from nilearn.plotting import... |
bfc16610c13d67ca54899fb569bd2bca74506bb89331b3981f69e5c9eaf7c138 | Python | 3,890 | 124 | ##################################################################
# Selecting patient ids that have size-4 motif enriched
# Reproducibility for Figure.3F
##################################################################
import pandas as pd
import numpy as np
import re
import os
import ast
file = 'CRC_clusters_neigh... |
d581b2499e6d6bace3267665b4e2ba9124f3a930a3f5b9f7b1e1d801f88fa7d8 | Python | 3,891 | 106 | # Copyright DST Group. Licensed under the MIT license.
from datetime import datetime
from CybORG.Shared.Enums import FileType, FileVersion
from CybORG.Simulator.Entity import Entity
from CybORG.Simulator.LocalGroup import LocalGroup
from CybORG.Simulator.User import User
import enum
class File(Entity):
"""A File... |
0e4128ecde40075fab0de117d00ead131c5c974d22b66aa987ef1fb1ddea3bce | Python | 3,892 | 121 | #!/usr/bin/env python
"""
MetaWIBELE: extract_non_redundance_seq module
Extract representative sequences from the clusters based on representative IDs
Copyright (c) 2019 Harvard School of Public Health
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated docume... |
abd6b872d247b1e0f969f3428e07686a1254495c8953ab15cba02d91cb8d568d | Python | 3,892 | 117 | import pytest
from guppy.utils import progress
from guppy.utils.progress import StepProgress, _current_step, step_error_handler
@pytest.fixture
def bound_step():
"""Bind a StepProgress for the duration of one test, as ``home.py`` does per step run."""
step = StepProgress()
token = _current_step.set(step)... |
27f482a48ffd064d2f21316205d700970291a3b3c0be5e6f67742c7491095e16 | Python | 3,894 | 131 | """
Unit tests for the pipelining primitives in :mod:`nearl.pipeline`.
These tests exercise :class:`PrefetchBuffer` and :class:`AsyncWriter` in
isolation (no CUDA required) so they run on any machine.
"""
import threading
import time
import pytest
from nearl.pipeline import _ERROR, _SENTINEL, AsyncWriter, PrefetchB... |
3666e4072bc2aeaad5ce0ca40f50bbab9bc609e6315e6ea8886d0bede0aed1a4 | Python | 3,894 | 99 | import os
import pickle
import functools
os.makedirs(os.path.join('/tmp', 'luna_cfg'), exist_ok=True)
LUNA_CONFIG_PATH = os.path.join('/tmp', 'luna_cfg', 'config.pkl')
class LunaPaths:
"""
A Paths object containing config for LUNA dataset.
"""
ROOT: str = ''
"""Root directory where LUNA dataset... |
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