sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
65bb6102051d8e84a8b1c63d4d6e8540663576c1681aa9ea0080806869562e61 | Python | 1,789 | 60 | """Tests for `multimodal_ad.models.gradcam`."""
from __future__ import annotations
from typing import TYPE_CHECKING
import numpy as np
import pytest
pytest.importorskip("tensorflow")
keras = pytest.importorskip("keras")
from multimodal_ad.models.architecture import Cnn3DConfig, build_3d_cnn # noqa: E402
from mult... |
af0243c0deb4dbc698db8ad8baa9b963dd3d0aeac59d29ef34640dec79e9923d | Python | 1,792 | 63 | """NotebookManager protocol."""
from __future__ import annotations
from dataclasses import dataclass
from typing import Protocol
class NotebookManagerError(RuntimeError):
"""Raised by any manager when a session lifecycle op fails."""
@dataclass
class SessionDescriptor:
"""What a Manager returns after spaw... |
c1f456bdd921417118c70347586d79d94f958446ac8840e12edbe66abd1c25ec | Python | 1,793 | 44 | import os
# path to this repo
BASE_DIR = os.path.dirname(__file__)
# path to save download checkpoints
CHECKPOINT_DIR = os.path.join(BASE_DIR, "checkpoints")
# URLs to download checkpoints of different models
SVORT_URL_DICT = {
"v1": "https://zenodo.org/record/7486938/files/checkpoint.pt?download=1",
"v2": "... |
c6a20b0060242b82e26251c9890a0c1ea0f294c19954e65f973c0bbe40d77a28 | Python | 1,793 | 42 | #!/usr/bin/env python3
from pathlib import Path
import gzip, itertools, csv, sys
import pheweb
from pheweb.file_utils import VariantFileReader, read_maybe_gzip
sites_filepath = Path(sys.argv[1])
vep_filepath = Path(sys.argv[2])
out_filepath = Path(sys.argv[3])
def sites_reader():
with VariantFileReader(sites_f... |
0b3b330a5aab76fff0717d32959422e92d75b81c49c12a0ba113df573328468b | Python | 1,794 | 55 | import os
import shutil
class models_genesis_config:
DATA_DIR = "/mnt/dataset/shared/zongwei/LUNA16/Self_Learning_Cubes"
nb_epoch = 1000
patience = 20
lr = 1e-1
train_fold=[0,1,2,3,4]
valid_fold=[5,6]
test_fold=[7,8,9]
hu_max = 1000.0
hu_min = -1000.0
def __init__(self,
... |
12243d78f340cfa7a10ec112a79ca7ecdfa1cfc312683a9332b69b271b76f6cd | Python | 1,794 | 51 | # -*- coding: utf-8 -*-
class Kmers(object):
"""
Class is primarily used to determine the error probabilities based on k-mers.
"""
@staticmethod
def _default_error_function(kmer_amount):
"""
Default/Fallback function to calculate error probabilities based on k-mers.
:param... |
f464711e79d8de7c6303a4b016775e53802a52caf74711ac4cd7fa46e60165dc | Python | 1,795 | 65 | """
Stub file for a guaranteed safe import of duecredit constructs: if duecredit
is not available.
To use it, place it into your project codebase to be imported, e.g. copy as
cp stub.py /path/tomodule/module/due.py
Note that it might be better to avoid naming it duecredit.py to avoid shadowing
installed duecredit.... |
e02d669c89ad232db875be9b7dc15320f986aba261894f9a11ef4943baaffd26 | Python | 1,798 | 57 | # Copyright 2018-2023 Xanadu Quantum Technologies Inc.
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
# http://www.apache.org/licenses/LICENSE-2.0
# Unless required by applicable law or... |
66c014d1f6f2c121b7f6e5cf5091b88ea9b7540fa8c46a655b1743376d1269c1 | Python | 1,799 | 62 | """
Unopinionated display configuration.
"""
from __future__ import annotations
import locale
import sys
import pandas._config.config as cf
# -----------------------------------------------------------------------------
# Global formatting options
_initial_defencoding: str | None = None
def detect_console_encodin... |
4d0bf3096b0d46db6cb67ef3cac759d53f8f98d44122215d7171ca76e56b3eab | Python | 1,800 | 65 | """Screenshots for quick guide R-lme4"""
import pathlib
import sys
from PyQt6 import QtCore
from PyQt6.QtWidgets import QApplication
from shapeout2.gui.main import ShapeOut2
from shapeout2.gui import compute
test_data = pathlib.Path(__file__).parent / ".." / ".." / "tests" / "data"
app = QApplication(sys.argv)
QtC... |
d312bf19ce47669980b5b7e39b67eab65a12dbf9610e26b1753ce1a4c1903df6 | Python | 1,801 | 34 | import enum
import pytest
from pgen import models, esm_msa_sampler, utils
from pgen import pgen_msa_revised
from io import StringIO
from pgen.esm_msa_sampler import ESM_MSA_ALLOWED_AMINO_ACIDS
import tempfile
def test_pgen_msa_revised_legacy_1(shared_datadir):
with tempfile.TemporaryDirectory() as output_dir:
... |
ec45a69d8906dd792d2ca95f35017f774af7a6d4645301a0939c6f763f60cb15 | Python | 1,801 | 65 | """
Stub file for a guaranteed safe import of duecredit constructs: if duecredit
is not available.
To use it, place it into your project codebase to be imported, e.g. copy as
cp stub.py /path/tomodule/module/due.py
Note that it might be better to avoid naming it duecredit.py to avoid shadowing
installed duecredit.... |
775b1ae794a03400720ccc91df9bf12226bf34a5bcafcf0e3ae62c04adb2319d | Python | 1,803 | 63 | """Test simple key-based indexing of files"""
import os
import pickle
import shutil
import pytest
from pheweb import weetabix
FIXTURE = os.path.join(os.path.dirname(__file__), 'input_files/correlations/rg-pipeline-output.txt')
# TODO: Add unit tests for the various indexing options (eg column number etc)
@pytes... |
e436c3a22896c6e711cc2a5a9af253f4388cefb11a8605427e69e1958653625d | Python | 1,804 | 51 | from Curves.curves import *
from Common.kernelFunctions import *
from Curves.curveMultiPhase import *
from Common import loggingUtils
def compute():
outputDir='/Users/younes/Development/Results/curves_Stitched_0'
if __name__ == "__main__":
loggingUtils.setup_default_logging(outputDir, fileName='info')... |
a90bb0ac214c851e9c3f345ca3fb97f7653fdb5af79602849f27a1859f0fdea6 | Python | 1,806 | 55 | # MOFTransformer version 2.0.0
import torch
from torchmetrics import Metric
class Accuracy(Metric):
def __init__(self, dist_sync_on_step=False):
super().__init__(dist_sync_on_step=dist_sync_on_step)
self.add_state("correct", default=torch.tensor(0.0), dist_reduce_fx="sum")
self.ad... |
0fc8de52d17c54a44c1458426dbeb806b69db6f0cd7f2b5ce55d43b4162c2f3e | Python | 1,809 | 42 | '''
This script creates generated-by-pheweb/best-of-pheno/<pheno> which contains the strongest 100k associations for the phenotype.
'''
from ..file_utils import VariantFileReader, VariantFileWriter, get_pheno_filepath
from ..utils import chrom_order
from .load_utils import MaxPriorityQueue, parallelize_per_pheno, get_... |
4b4c93be9cb0869fbb01dd9750d151dbe0d1892caa82b8a727748a4d329e20e6 | Python | 1,809 | 36 | #!/usr/bin/env python3
#Convert the RepeatMasker output to a zero-based UCSC track
#script provided by Gabby Hartley
import sys
with open(sys.argv[1],'r') as rpmsk:
with open(sys.argv[2],'w') as bed:
for line in rpmsk:
line = line.replace("/","\t")
spl=line.split()
zer... |
d458129dad36d8ed9affac50b0a1f69418434ecec27ab12d1b92f2226330495c | Python | 1,809 | 70 | __all__ = ["normalize_by_max", "dot_product"]
from typing import Literal
import numpy as np
def normalize_by_max(x: np.ndarray) -> np.ndarray:
x_max = np.nanmax(np.abs(x))
if x_max == 0.0:
return x
else:
return np.divide(x, x_max)
def dot_product(x: np.ndarray, y: np.ndarray):
# avo... |
30f250782a08b6798303de81c153c21816a535b341b6f74005c539875f20e591 | Python | 1,810 | 57 | from setuptools import setup, Extension, find_packages
from codecs import open
from os import path
import warnings
package_name = 'qbiome'
example_dir = 'examples/'
example_data_dir = example_dir + 'example_data/'
version = {}
with open("version.py") as fp:
exec(fp.read(), version)
here = path.abspath(path.dirna... |
57f1a26b05f5cda7a1a6f3e1d252e9702ca5370bde7c1a317704bcb34b1a7d03 | Python | 1,810 | 48 | # Gudied BackPropagartion
from ..utils.process import get_last_layer
import numpy as np
import tensorflow as tf
from skimage.transform import resize # for N-dimensional images
@tf.custom_gradient
def guided_relu(x):
def grad(dy):
return tf.cast(dy>0,"float32") * tf.cast(x>0, "float32") * dy
return tf.... |
92c94188cbede6423109600bbea6a5c1239ab56ab35073c6d3171c9a89f3dc86 | Python | 1,811 | 64 | """
Copyright (c) Facebook, Inc. and its affiliates.
This source code is licensed under the MIT license found in the
LICENSE file in the root directory of this source tree.
"""
import torch
import torch.nn as nn
import torch.nn.functional as F
class SSIMLoss(nn.Module):
"""
SSIM loss module.
"""
de... |
ff48c9c0f19daa4f1b09c4a5fcba22163e13c06c08b602386f9b0b3c068c64a4 | Python | 1,811 | 43 | import io
import requests
import pandas as pd
from typing import NamedTuple
from ._preference import path_exists
class Data(NamedTuple):
data: pd.DataFrame
meta: pd.DataFrame
class SuematsuData:
def __init__(
self,
data_path: str = "https://drive.google.com/file/d/1-CyJhEb3kkkcM... |
23dffd510c9446ccc285a859a44e616d64d0296bf9faa1f350f1ad8ddd65e8ef | Python | 1,813 | 35 | from Environment import *
from Data_preprocessing.utils import intensity_normalization, segmentation_quick_view, dot_2d_slice_by_slice_wrapper
from Data_preprocessing.edge_dection import remove_edge
from Parameter import *
def spot_seg(train_image_path, save_seg_path, channel, scaling_param, wrapper_param):
data_p... |
3b6ad1335eba53e0097239dbcb57a1553711d16494423ed7c2223a39ca2d4f67 | Python | 1,814 | 59 | import argparse
import os
import shutil
import pandas as pd
def get_args():
"""
Get arguments from command line with argparse.
"""
parser = argparse.ArgumentParser(
prog='Copy-Final-MAGs.py',
description="""Copy MAGs passing filters to final directory.""")
parser.add_argument("-i", ... |
d7f91419969f9a15b1934ca73db61e022d4860b6ff354c94765ab7c3bbe2df88 | Python | 1,814 | 49 | import torch
import torch.nn.functional as F
import torch.autograd as autograd
# Typing
from torch import Tensor
from typing import List, Optional, Tuple
# Adopted from https://github.com/ermongroup/sliced_score_matching
def sliced_score_estimation(score_net, data):
x = data.view(-1, *data.shape[1:])
x.requi... |
520a2fdec895e1808a0d10978ecffb1f04e3836cb149d30a4c1c91a951d03f01 | Python | 1,815 | 53 | import pytest
from scripts.check_test_imports import main
@pytest.mark.parametrize(
"src, expected_out, expected_ret",
[
(
"from pandas import Series\n",
"t.py:1:0 use 'pd.Series' rather than importing 'Series' "
"from the pandas namespace\n",
1,
... |
ff96e308d3621b5e0484a4ab66c8ccb0c286cd1833a19f76e4389bef3180506f | Python | 1,815 | 55 | """RayVecEnv call sites batch shipped asymmetric observations without Ray in CI."""
import sys
import types
import numpy as np
import pytest
from rl_games.common import env_configurations
from rl_games.common.vecenv import RayVecEnv
class _Remote:
def __init__(self, fn):
self._fn = fn
def remote(se... |
282dc54ab8cf1691703b7f54ac4493cdab019aa5821e781e6288b66aa160c25e | Python | 1,816 | 61 | # Copyright 2018-2025 Xanadu Quantum Technologies Inc.
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
# http://www.apache.org/licenses/LICENSE-2.0
# Unless required by applicable law or... |
646af6e776c6998a05f2679cec4e514534ffec0aff8954cca48b1c4520d554e5 | Python | 1,817 | 70 | import tensorflow as tf
import subprocess
import sys
import numpy as np
from halo import Halo
from const import SIZE
from dataset import load_all_datasets
BATCH_SIZE = 1
def load_iterators(train_dataset, val_dataset):
batch_size = BATCH_SIZE
train_dataset = train_dataset.shuffle(batch_size)
val_dataset... |
e9881190eae7fe9ce0ca39ab3b89b7430cfb2470963ead491e7332fee95f3551 | Python | 1,817 | 69 | import torch
import torch.nn.functional as F
from torch import Tensor
from torch.nn import (
Sequential,
Linear,
ReLU,
GRU,
Embedding,
BatchNorm1d,
Dropout,
LayerNorm,
)
from torch_geometric.nn import (
Set2Set,
global_mean_pool,
global_add_pool,
global_m... |
0a1b9a10d8cb4b0dab9f424409dbb1ebfa4bfdbd31c1fc288bb6d29db0507e0f | Python | 1,818 | 53 | from torchvision.transforms import *
from PIL import Image
import random
import math
import numpy as np
import torch
class RandomErasing(object):
'''
Class that performs Random Erasing in Random Erasing Data Augmentation by Zhong et al.
--------------------------------------------------------------------... |
cce0461d5b4e8395e4132fd9b0ebe5c14bdc051776a412a0ca689c337ed0450a | Python | 1,818 | 59 | import pytest
from scripts.validate_exception_location import (
ERROR_MESSAGE,
validate_exception_and_warning_placement,
)
PATH = "t.py"
# ERRORS_IN_TESTING_RST is the set returned when parsing testing.rst for all the
# exceptions and warnings.
CUSTOM_EXCEPTION_NOT_IN_TESTING_RST = "MyException"
CUSTOM_EXCEP... |
9a9e49b96ea39598a9d6daff67abc304797e6315ea1ddc4885b81f3bd965cb90 | Python | 1,819 | 60 | """Tests for scripts/inference-timing/plot_results.py.
Exercises the pure data-shaping helpers plus a full main() run against
synthetic CSVs, so a change to the CSV schema written by
benchmark_single_config.py that plot_results.py doesn't know about gets
caught without needing real benchmark data or a GPU.
"""
import ... |
a5ec6001284a5642ccf44331a01e6ea1eb58a300c94aacdada9f97af950e11c5 | Python | 1,819 | 43 | from . import kernelFunctions as kfun
## Parameter class for matching
# timeStep: time discretization
# KparDiff: object kernel: if not specified, use typeKernel with width sigmaKernel
# KparDist: kernel in current/measure space: if not specified, use gauss kernel with width sigmaDist
# sigmaError... |
d1886460de0a854daac4c4526ceb8aec1886b799ea3d88d6df27422df8d3858a | Python | 1,821 | 69 | import pytest
from pandas.util._validators import (
validate_bool_kwarg,
validate_kwargs,
)
@pytest.fixture
def _fname():
return "func"
def test_bad_kwarg(_fname):
good_arg = "f"
bad_arg = good_arg + "o"
compat_args = {good_arg: "foo", bad_arg + "o": "bar"}
kwargs = {good_arg: "foo", b... |
4f2ffa9e491fb6af0e935aac51d698b3896d63e1870bcd785e1a6a4f764ac397 | Python | 1,822 | 51 | import os
import pysam
def filter_survivor_by_supp(vcf_path, min_supp=10):
print(vcf_path)
out_vcf_path = vcf_path.replace(".vcf", ".s{}.vcf".format(min_supp))
vcf_file = pysam.VariantFile(vcf_path)
with open(out_vcf_path, "w") as out_vcf_file:
out_vcf_file.write(str(vcf_file.header))
... |
cd2b5f5a9b3dfc4f2dcae8c5c7238b5a67629dc8016448363b32ededb58c89fd | Python | 1,822 | 57 | from os.path import join
from dredda.download import download_if_not_exist
def get_remote_files_manifest(remote_prefix, local_prefix, fp_list):
remote_prefix = remote_prefix.rstrip("/")
local_prefix = local_prefix.rstrip("/")
fp_list = [fp.rstrip("/") for fp in fp_list]
remote_files_manifest = []
f... |
049fd1d38c4616d4ab804a5099497a6123150f4d368b07aaf1d795191e53a432 | Python | 1,824 | 42 |
from ..file_utils import VariantFileReader, get_filepath, get_tmp_path
import sqlite3
from pathlib import Path
from typing import List,Iterator,Tuple,Optional
def run(argv:List[str]) -> None:
if '-h' in argv or '--help' in argv:
print('Make sqlite3 db for converting between chr-pos-ref-alt and rsid')
... |
f26ae3bdddad43c2d4b81bcc7c98b47e61b6c571f9bcfb11260b81d09a5016d8 | Python | 1,825 | 45 | #MIT License
#
#Copyright (c) 2019 Inigo Prada Luengo
#
#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 Software without restriction, including without limitation the rights
#to use, copy, modify, merge,... |
a3a2de071e4ebf89f8a51b21a37cc8769b72a1be05f7e2671e048ca4b382ecfc | Python | 1,826 | 50 | # -*- coding: utf-8 -*-
import json
import regex as re
UNDESIRED_SEQUENCES_JSON = "../config/error_detection/undesired_sequences.json"
class UndesiredSequences(object):
def __init__(self, seq_file=UNDESIRED_SEQUENCES_JSON):
"""
Class is used for checking existing undesired subsequences.
... |
66b6a35ecc55fcd931c8a44c679c89fb9d796f9d539e90c0f1652a70bf5fb694 | Python | 1,827 | 35 | import numpy as np
from PIL import Image
from .corruptions import *
corruption_tuple = (gaussian_noise, shot_noise, impulse_noise, defocus_blur,
glass_blur, motion_blur, zoom_blur, snow, frost, fog,
brightness, contrast, elastic_transform, pixelate, jpeg_compression,
... |
9d9e6672dc2f37ea18203f9d8e2583835753f185451c469006fa7eb37f0e28b2 | Python | 1,827 | 59 | import os
import requests
import hashlib
from pathlib import Path
from tqdm import tqdm
def download_if_not_exist(fp, url, md5sum=None):
"""
Download file from the given URL to the given fp if it doesn't exist.
:param url: The URL of the file to download.
:param fp: The local fp to save the file as.
... |
c85ba320541f9d65154122a3f43613383447371bde43c9ea97a57913ccb8533e | Python | 1,827 | 75 | import os
import h5py
import nibabel as nib
import numpy as np
DIR = os.path.dirname(os.path.realpath(__file__))
# %% b-values and vectors
f = h5py.File(DIR + '/1shell_30dir_diff_encoding.h5', 'r')
bvals = f['bvals'][:]
bvecs = f['bvecs'][:]
# bvals = bvals.reshape(-1, 1)
# B = epi.get_B(bvals, bvecs)
print(bvals.... |
252a7452da1733c4ec33a4026db5cbc6f043b6d6fb415ac5dac753ebacda5039 | Python | 1,828 | 50 | from base.surfaces import Surface
from base.kernelFunctions import Kernel
#from surfaceMatching import SurfaceMatchingParam
from base.surfaceTemplate import SurfaceTemplate, SurfaceTemplateParam
from base import loggingUtils
def main():
# [x,y,z] = np.mgrid[0:200, 0:200, 0:200]/100.
# y = y-1
# z = z-1
... |
865f1ecbefad7c25db16ba7065a9a7066cd4b1450719cc5b1214598324d2651a | Python | 1,829 | 53 | import numpy as np
import matplotlib.pyplot as plt
from mpl_toolkits.mplot3d import Axes3D
from matplotlib import cm
import csv
from read_grd import read_grd
x, y, Z = read_grd('../data/Bolund.grd')
with open('../data/Measurements/Dir_270.dat', 'rb') as csvfile:
reader = csv.reader(csvfile, delimiter=' ', skipini... |
9747ebf4949abcb5bbf55a3edc359dc3dd371b680bb32946dbed0b5dfe35b3b6 | Python | 1,829 | 58 | # !/usr/bin/env python
# -*- coding: utf-8 -*-
import time
from onmt.utils.logging import init_logger
from onmt.utils.misc import split_corpus
from onmt.translate.translator import build_translator
import onmt.opts as opts
from onmt.utils.parse import ArgumentParser
from collections import defaultdict
def translate(o... |
9803dcd3b23500e69eddd0f516f8c90850d763174482674c8b357c55339970dd | Python | 1,829 | 66 | """Functions for tensor shaping, unit conversion, typing, etc."""
from mrpro.utils import slice_profiles
from mrpro.utils import typing
from mrpro.utils import unit_conversion
from mrpro.utils.fill_range import fill_range_
from mrpro.utils.smap import smap
from mrpro.utils.reduce_repeat import reduce_repeat
from mrpro... |
9eb6b96e66c820b31dd8a85c3354907e2cdeac356436bc25b893a5344c05bd91 | Python | 1,830 | 55 | import numpy as np
from PyQt6 import QtCore, QtGui, QtWidgets
import pyqtgraph as pg
from .simple_plot_widget import SimpleViewBox
class SimpleImageView(pg.ImageView):
"""Custom class for data visualization in Shape-Out"""
def __init__(self, *args, **kwargs):
super(SimpleImageView, self).__init__(vi... |
aabda795f96d8e07acb6991673b20f02ff9c8d7458b21ca66ab7093088929e6f | Python | 1,830 | 46 | from typing import Tuple
from functools import cached_property
import torch
from torch import Tensor
from torch.nn import Module
class PoissonGaussianNoiseModel(Module):
"""Poisson-Gaussian noise model for CM2 sensor: https://ieeexplore.ieee.org/document/4623175"""
def __init__(self, config: dict):
s... |
bed5ac19a80c125d3e57170ea0bc55429b311da8722ffbbe757eb760e8e97b20 | Python | 1,830 | 45 | import os
from unittest import TestCase, mock
import dynast.preprocessing.bam as bam
import dynast.preprocessing.coverage as coverage
from .. import mixins
class TestCoverage(mixins.TestMixin, TestCase):
def test_read_coverage(self):
coverage.read_coverage(self.control_coverage_path)
def test_calc... |
59f4675b55388cfdf1bd2fff65789dd704301487bc966b721370f94c8a166d39 | Python | 1,831 | 68 | # JN 2015-05-11
"""
small function to copy start of ncs file to folders
"""
from __future__ import print_function, division, absolute_import
import os
from argparse import ArgumentParser
from combinato.basics.nlxio import NCS_RECSIZE, NLX_OFFSET
def start_to_folder(ncsfname, destination=None):
"""
read the... |
b47c479251d8eff96764e263b11e1aa5219cd513a6224ef9793dcc7e9bd92b54 | Python | 1,831 | 45 | from botocore.client import Config
import ibm_boto3
# import types
import os
import sys
sys.path.append(os.path.dirname(os.path.dirname(os.path.abspath(__file__))))
sys.path.append(os.path.abspath(os.path.join(os.path.dirname(__file__), "..", "..")))
from app import create_app
from utils import compare_dataset_bucket_d... |
c33f4305301aabb5d1c8fcb6a5d498bf2e04a72daaf1d3d421ff943cabac68bb | Python | 1,831 | 57 | """Test some private functions."""
from pathlib import Path
from fmriprep_denoise.features import derivatives
import pandas as pd
import numpy as np
import pytest
fake_timeseries_template = (
"task-test_space-MNI152NLin6Asym_" "atlas-test_nroi-100_desc-test_timeseries.tsv"
)
def _make_fake_timeseries_collection... |
092f0fe5af99ff3a0b08f3e5a7bdb486ff002362bb8b02a90ba99b3f69c3a37e | Python | 1,833 | 54 | import pandas as pd
import pandas._testing as tm
class TestToFrame:
def test_to_frame_respects_name_none(self):
# GH#44212 if we explicitly pass name=None, then that should be respected,
# not changed to 0
# GH-45448 this is first deprecated & enforced in 2.0
ser = pd.Series(range... |
86b448a5e755e03b795e2490476ede6783245426a5f9dc77af7bf9a8e11a9796 | Python | 1,835 | 55 | from rl_games.common.algo_observer import AlgoObserver
from isaacgymenvs.utils.utils import retry
from isaacgymenvs.utils.reformat import omegaconf_to_dict
class WandbAlgoObserver(AlgoObserver):
"""Need this to propagate the correct experiment name after initialization."""
def __init__(self, cfg):
s... |
28c914441cf6feb1e41ea0ba8d8a8356bb2a7a8a8752a9af6faf19813e487dbe | Python | 1,836 | 58 | ''''
This extends the cloudsqlitedict module to support tuples of strings as keys.
Currently, this comes at the cost, that '@' in keys is not allowed anymore.
The class SqliteDict in this module does not inherit from cloudsqlitedict.SqliteDict,
however it contains an instance of it. In case, some API is missing, simpl... |
f6762b927d5671c4c018c71332e98325941a4e9f0c248ae5483913dccb40b2a5 | Python | 1,836 | 69 | import pickle
import tree
import re
import sys
def readStrFromTree(f):
strDic = {}
for line in file(f):
t = tree.Tree()
t.read(line)
s = re.sub(" +", " ",t.leaf())
strDic[s]=line
return strDic
dev = "genmodel/chccg.dev.linetrees"
train = "genmodel/chccg.train.linetrees"
#... |
294b198e98528c509edbf2ef83eabdb4e2715ddd18ff9ce0b2a5b909bb117469 | Python | 1,837 | 52 | from torch.optim.lr_scheduler import _LRScheduler
class ConstantLR (_LRScheduler):
def __init__(self, optimizer, last_epoch=-1):
super (ConstantLR, self).__init__ (optimizer, last_epoch)
def get_lr(self):
return [base_lr for base_lr in self.base_lrs]
class PolynomialLR (_LRSchedu... |
3bf83a2ee7704982bb53848b64a1fe8a7e7313b91fd826770854eff430ec7c3b | Python | 1,838 | 50 | #-----------------------------------------------------------------------------
# Combine Features
#-----------------------------------------------------------------------------
import pandas as pd
import os
def read_file(Vina58,SASA,dE,Water,Ion):
combine = "pdb"
f_V58 = pd.read_csv(Vina58,dtype={"pdb":str})
... |
bbc2241716864306930a02ef64e8cbe78bb9988654aa21826086eb1b4e7be2cf | Python | 1,838 | 48 | import os
# import cloudpickle
import compatibility
'''Module implements a database concept, using two interfaces:
(1) the dump function
(2) the loader class
To save an object, the dump method is called, e.g.
> import myDumper
> myDumper.dump(obj, savedir)
This saves the object using a method specified in the res... |
e109f7b4287cc5634b5069ae73ffba03c04700ee76ced35fb6ae41affa427d54 | Python | 1,838 | 55 | #!/usr/bin/env python
# Filename: clean_up_annotations.py
# Author: Alessandro Gerada
# Date: 2023-03-17
# Copyright: Alessandro Gerada 2023
# Email: alessandro.gerada@liverpool.ac.uk
"""Script that cleans up duplicate images in annotation folders. Use clean_up_annotations.py -h for help."""
import argparse
impo... |
aef064e2b8781bfe0b428acbe2a3913ee952afec080c6679d08b57e91fb9429c | Python | 1,839 | 57 | import numpy as np
from pandas import (
DataFrame,
Index,
date_range,
read_stata,
)
from ..pandas_vb_common import BaseIO
class Stata(BaseIO):
params = ["tc", "td", "tm", "tw", "th", "tq", "ty"]
param_names = ["convert_dates"]
def setup(self, convert_dates):
self.fname = "__test... |
4e3a09656ce09247a95241c78e416d91869b70d82aae58529109e874fb595e05 | Python | 1,842 | 60 | """Index for splitting data."""
import torch
def split_idx(idx: torch.Tensor, blocksize: int, overlap: int = 0, cyclic: bool = False) -> torch.Tensor:
"""Split a tensor of indices into different blocks.
Parameters
----------
idx
1D indices to be split into different blocks.
blocksize
... |
a268363de303dcfc6b3b9d931e060d2edad70d7da6ad51e23326398c8fd24ce9 | Python | 1,842 | 53 | #!/usr/bin/env python
__author__ = 'etseng@pacb.com'
"""
Helper script for calculating expected accuracy from FASTQ sequences.
ex:
i0_LQ_sample32f89e|c32/f1p0/929 isoform=c32;full_length_coverage=1;non_full_length_coverage=0;isoform_length=929;expected_accuracy=1.0
"""
import os, sys
from Bio import SeqIO
def phred... |
1979394c24b032f6671881f18eddef83874ccc7fee1c59c97a5298cc4fbc6465 | Python | 1,843 | 62 | from sys import path as sys_path
sys_path.append('..')
sys_path.append('../base')
import os
import matplotlib
if 'DISPLAY' in os.environ:
matplotlib.use('qt5Agg')
else:
matplotlib.use("Agg")
import matplotlib.pyplot as plt
import numpy as np
from scipy.linalg import expm
from base import pointSets
from base imp... |
22f50dbae5425bafd74e8c1e56df069439a1318a26bbc80e64d7b6e624c9bd9b | Python | 1,843 | 57 | import math
from numpy import random
import math
class viewContainer():
# container 应该包含所有刺激所需的要素
def __init__(self, config) -> None:
# w 代表window,所有的刺激都要在win上显示
self.w = None
# displayFrame是呈现最终结果的刺激帧
self.displayFrame = None
# frameSet是ImageStim的集合,是刺激帧
... |
faf6e46f9ac78dea651be969ff09785627e946ac440412969bd8dd882a525f1b | Python | 1,844 | 57 | # -------------------------------------------------------------------------------------------------------------------------------------
# Following code curated for GCPNet (https://github.com/BioinfoMachineLearning/GCPNet):
# ----------------------------------------------------------------------------------------------... |
4589b62be5a08ae69d39cfca07fe9285732187b2d75c01322a06720a9adf0ba4 | Python | 1,845 | 57 | """Integrity check for the bundled AAL2 atlas asset (no TensorFlow needed).
Guards the repository-root `atlas.nii.gz` + `AAL2_Atlas_Labels.csv` pair
that `multimodal_ad.models.regions` depends on: wrong shape/voxel size or a
label mismatch would silently break region ranking without failing loudly
elsewhere.
"""
from... |
1c066e2809ba8095c108ab43eb550a930307602d5c8fa9b9ed5787afa4e00adc | Python | 1,846 | 44 | from csv import DictReader, DictWriter
import gzip
import os, sys
def main(bc_info_csv, input_csv, output_csv):
bc_info = {} # BC --> cell type
reader = DictReader(open(bc_info_csv), delimiter=',')
if 'BCrev' not in reader.fieldnames or 'Celltype' not in reader.fieldnames:
print(f"ERROR: Expected ... |
440e053e42acfc3d55627289eb48da5b4ae2089881e2906e1038352b37b4c3aa | Python | 1,846 | 75 | from textwrap import dedent
import pytest
from pandas.util._decorators import deprecate
import pandas._testing as tm
def new_func():
"""
This is the summary. The deprecate directive goes next.
This is the extended summary. The deprecate directive goes before this.
"""
return "new_func called"
... |
c3c60bbab38d7b004645f3e74f0b93eeda57028b9211566e759d5b6ca3a5c628 | Python | 1,848 | 51 | import importlib.resources
from PyQt6 import uic, QtGui, QtWidgets
from ... import meta_tool
class LME4Dataset(QtWidgets.QDialog):
def __init__(self, parent, slot, *args, **kwargs):
super(LME4Dataset, self).__init__(parent, *args, **kwargs)
ref = importlib.resources.files(
"shapeout2... |
096ba81c1aaa3dd17d02a21843bfddb40f3b6b540e62541b69134a8bf58c1480 | Python | 1,849 | 59 | import numpy as np
import pytest
import pandas as pd
import pandas._testing as tm
def test_astype(using_infer_string):
# with missing values
arr = pd.array([True, False, None], dtype="boolean")
with pytest.raises(ValueError, match="cannot convert NA to integer"):
arr.astype("int64")
with py... |
6b7e44febe608782d1c9cfb66cdda5ec973dfe6dc273c34487c11a17c7af2305 | Python | 1,849 | 53 | #! /usr/bin/env python
##############################################################################
## DendroPy Phylogenetic Computing Library.
##
## Copyright 2010-2015 Jeet Sukumaran and Mark T. Holder.
## All rights reserved.
##
## See "LICENSE.rst" for terms and conditions of usage.
##
## If you use this wo... |
1c3fbe3a58aa28363add3ea4e79048938ab70193c3aca4c40249cc29ea1bffa7 | Python | 1,850 | 65 | # neural network for Hb
import tensorflow as tf
import numpy as np
from keras.models import Sequential
from keras.layers import Dense
import matplotlib.pyplot as plt
# load the dataset
X = np.loadtxt('hb_all_for_mlp.csv', delimiter=',')
y = np.loadtxt('raphe_all_for_mlp.csv', delimiter=',')
# Plot original... |
8c9b23d3425a61c62bf1fdf6e8a63fd62259e06da1d06f4de3d7c13c741a5105 | Python | 1,852 | 63 | """Random B0 map generation."""
import torch
from scipy.special import sph_harm_y
from mrpro.data.SpatialDimension import SpatialDimension
from mrpro.utils.RandomGenerator import RandomGenerator
def random_b0map(
shape: SpatialDimension[int],
fov: SpatialDimension[float],
l_max: int = 3,
sigma_ppm: ... |
30709072cdec4b2afb2d938d99a34048e4ba95faadcb8c5acc7e26f398d0fdbd | Python | 1,854 | 50 | """
Supported Arguments for model variant:
* For GPT-Neo and OPT family, everything before the slash shown in the get_llm_vec.py
file (i.e., EleutherAI/ and facebook/) is not needed in any step after get_llm_vec.py
GPT-2 family:
"gpt2", "gpt2-medium", "gpt2-large", "gpt2-xl"
GPT-Neo family:
"gpt-neo-125M", "gpt-ne... |
c907fcc73d788bda806c73e00577c115c09ecc0a28026b66c6fc9c5eb772da0e | Python | 1,854 | 104 | """
Arithmetic operations for PandasObjects
This is not a public API.
"""
from __future__ import annotations
from pandas.core.ops.array_ops import (
arithmetic_op,
comp_method_OBJECT_ARRAY,
comparison_op,
fill_binop,
get_array_op,
logical_op,
maybe_prepare_scalar_for_op,
)
from pandas.cor... |
dbadc2ccf73faaff7b58aa87c7a78fa2300d62cafa696d4dda3f4fd869d8a46a | Python | 1,854 | 53 | import numpy as np
import pandas as pd
import pandas._testing as tm
class TestInferObjects:
def test_copy(self, index_or_series):
# GH#50096
# case where we don't need to do inference because it is already non-object
obj = index_or_series(np.array([1, 2, 3], dtype="int64"))
resul... |
04c5804af7c78447720511929f54af70d880686d83ed5c1e44f4803a522ff2d2 | Python | 1,855 | 58 | import sys
import re
rword = re.compile('^[^ ]*')
#rlpar = re.compile('-LRB-')
rlpar = re.compile('[(]')
#rrpar = re.compile('-RRB-')
rrpar = re.compile('[)]')
renclitic = re.compile("([a-zA-Z]\'s)|([a-zA-Z]\'d)|([a-zA-Z]n\'t)|([a-zA-Z]\'ll)|([a-zA-Z]\'m)|([a-zA-Z]'re)|([a-zA-Z]'ve)")
rproclitic = re.compile("([yY]'[k... |
117e3fe49df03633f203e8068f785daba9e9666d642a442f2e8520fe02b8799f | Python | 1,855 | 60 | from __future__ import annotations
from typing import TYPE_CHECKING
import pandas as pd
if TYPE_CHECKING:
from pandas._typing import AxisInt
def _check_mixed_float(df, dtype=None):
# float16 are most likely to be upcasted to float32
dtypes = {"A": "float32", "B": "float32", "C": "float16", "D": "float6... |
44045ba810209a4d3a68d0711991178d7a3bc2d6fdcb60168b2cb2d479e4a2a0 | Python | 1,856 | 58 | #%%
from src.trainer import Trainer
from src.workflow import WorkflowBuilder, WorkFlowSpecs, WorkflowResults
import numpy as np
import pandas as pd
from sklearn.model_selection import KFold
from sklearn import set_config
from src.test_config import pipe_config, model_config
import yaml
import tempfile
import pytest
se... |
7645337d35ca35617a8ac26413a80c7bbfa9c5d3119646c0303e11225564535e | Python | 1,856 | 64 | #!/usr/bin/env python
__version__ = '1.0'
import os, sys
import gzip
import numpy as np
from Bio import SeqIO
def type_fa_or_fq(file):
file = file.upper()
if file.endswith('.FA') or file.endswith('.FASTA') or file.endswith('CLIPS'): return 'fasta'
else: return 'fastq'
def get_seq_stats(file, binwidth):
... |
a1e301d5b81555ae2b958209873fbdfa612abac1ecf933c8df9265ad1457f148 | Python | 1,856 | 50 | import sys
import os
sys.path.append(os.path.dirname(os.path.dirname(os.path.abspath(__file__))))
sys.path.append(os.path.abspath(os.path.join(os.path.dirname(__file__), "..", "..")))
from app.models import Condition
def get_adni_dx(visit_dx):
condition = None
if not isinstance(visit_dx, str):
return N... |
172cd3bdbe5e4952566a5612b8ced8fd5bf77f08b896fefe72be02f223ff3f77 | Python | 1,857 | 62 | import os, sys, re, argparse
sys.path.append(os.path.join(os.path.dirname(__file__), '..', '..', 'resource-gcg', 'scripts'))
import model, tree
argparser = argparse.ArgumentParser('''
Takes a linetrees file and headedness model and produces most probable dependency graphs.
''')
argparser.add_argument('model', nargs=1,... |
223cb2c0241bb19a8c2895be35e2fa09f0413f99a7ea08ea15365febc58013b9 | Python | 1,857 | 70 | #! /usr/bin/env python
# -*- coding: utf-8
#
# Copyright (c) 2023 Kenneth Atz, Clemens Isert & Gisbert Schneider (ETH Zurich)
import argparse
import numpy as np
import pandas as pd
from rdkit import Chem
from tqdm import tqdm
from dragonfly_gen.ranking.qsar.cats2d import CATS2D
cats2d = CATS2D()
def get_cats_sim(s... |
dfb2da3bab944dd9c7eca5b7ad316bc4ebda535eae0619864cd68510361ebe84 | Python | 1,859 | 57 | import numpy as np
import pytest
import pandas as pd
import pandas._testing as tm
from pandas.arrays import BooleanArray
from pandas.tests.arrays.masked_shared import ComparisonOps
@pytest.fixture
def data():
"""Fixture returning boolean array with valid and missing data"""
return pd.array(
[True, Fa... |
e2c8f1d086d63743a1127b8ad4e8af4bee6e7331cc8c42951152f721ef281a01 | Python | 1,860 | 60 | #!/usr/bin/env python3
#
# Copyright 2014 Google Inc. 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 requir... |
5d261dc39fb7b1d13e4be705ce69eb710806fd407d3a03bc329d4aa395c4b1be | Python | 1,862 | 59 | # -------------------------------------------------------------------------------------------------------------------------------------
# Following code curated for GCPNet (https://github.com/BioinfoMachineLearning/GCPNet):
# ----------------------------------------------------------------------------------------------... |
0bbf242611fafdfe43f6609fef6e49753bc6ae2a83a856a5db05b3063cc41317 | Python | 1,864 | 56 | # -*- coding: utf-8 -*-
"""
Created on Sat Sep 10 09:10:23 2022
@author: Anonymous
Example code to quickly load data from tfrecords into data.Dataset.
"""
# %% imports
from pathlib import Path
import tensorflow as tf
# %% prepare test dataset using stimuli directory
tfrecord_dir = 'C:/Users/username/tfrecord_direct... |
82b702a0a31c2aad6724591ee4eb9474f8b890fb225c3dc3dbe4e446cd66f91b | Python | 1,864 | 71 | import numpy as np
import gzip
def read_vcf(file,start_position=None,end_position=None):
if file.endswith('.gz'):
f = gzip.open(file, 'rt')
else:
f = open(file, 'rt')
con = True
head = []
while con:
line = f.readline()
if line.startswith('##'):
... |
a79f1ace20f2933277a0fd755fb910c1c8a8952c1580e1b1aaf7bd8e99d4a7a7 | Python | 1,864 | 55 | import pytest
import pandas as pd
import pandas._testing as tm
class TestMap:
def test_map(self):
rng = pd.date_range("1/1/2000", periods=10)
f = lambda x: x.strftime("%Y%m%d")
result = rng.map(f)
exp = pd.Index([f(x) for x in rng])
tm.assert_index_equal(result, exp)
... |
bc95d3721923ce2a03062163296bc8c0c2f57f0ab9550052ff3e5f4147992817 | Python | 1,864 | 52 | # 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... |
501149866fb540220b8081971e3d6ef740fae127e14e26dfe0f3f3816235283d | Python | 1,865 | 57 |
import random
import glob
from cine import Cine
import tube2
import align
from skimage.io import imsave
from numpy import int16
videonames = glob.glob("data2/*.cine")
videonames2 = glob.glob("videos_surface_bug/*.cine")
videonames.extend(videonames2)
for i, name in enumerate(videonames):
vid = Cine(name)
m... |
0d6be5a5e59c2e0a963f2c4e90bb13fc412f2868f7305b2b0a4cc927163a8098 | Python | 1,866 | 60 | import pytest
import pandas as pd
from pandas.tests.plotting.common import (
_check_plot_works,
_check_ticks_props,
_gen_two_subplots,
)
plt = pytest.importorskip("matplotlib.pyplot")
class TestCommon:
def test__check_ticks_props(self):
# GH 34768
df = pd.DataFrame({"b": [0, 1, 0], "... |
8b40eee2859dccbbec6d2c22e18fad8ffcd3d45f33f9b1c699b8557b60669cf4 | Python | 1,866 | 57 | """lightning-pose: pose estimation with supervised and semi-supervised losses."""
import importlib.metadata
from pathlib import Path
from typing import Any
from omegaconf import OmegaConf
LP_ROOT_PATH = (Path(__file__).parent.parent).absolute()
OmegaConf.register_new_resolver("LP_ROOT_PATH", lambda: LP_ROOT_PATH)
... |
5124a2237dac37ed06ea56584d826858bbf8d07bda2033d6e6c5635489d41711 | Python | 1,867 | 47 | """Serial mapping function."""
from collections.abc import Callable, Sequence
import torch
def smap(
function: Callable[[torch.Tensor], torch.Tensor],
tensor: torch.Tensor,
passed_dimensions: Sequence[int] | int = (-1,),
) -> torch.Tensor:
"""Apply a function to a tensor serially along multiple dime... |
a21e03c22d0c9234f60b88668ee6b6545a5527a3a18e8697f1bae83601f5b5e7 | Python | 1,867 | 54 | import sys
import os
def nested(A, B, max_df=1):
# Only checks nesting based on variable names and ablation configuration
# Does not check for identity of data or formula
a_vars = A.split('.')[-3].split('_')[2:-1]
b_vars = B.split('.')[-3].split('_')[2:-1]
if len(a_vars) != len(b_vars):
ret... |
e0ca3c3956118152f0601e100b64a59faae5926a93e779505b777851697b5145 | Python | 1,870 | 69 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Thu Feb 16 12:01:18 2023
@author: vman
"""
from nilearn.plotting import plot_markers, plot_roi
from nilearn import datasets
import numpy as np
import pandas as pd
import matplotlib
from matplotlib import pyplot as plt
# Define plot styling
matplotlib.rcPa... |
af0f2adf212cc35f939f0fc7a434d3574dc91e3d2d61c06b1aaa80015e5d9934 | Python | 1,872 | 69 | """
Though Index.fillna and Series.fillna has separate impl,
test here to confirm these works as the same
"""
import numpy as np
import pytest
import pandas as pd
import pandas._testing as tm
from pandas.tests.base.common import allow_na_ops
def test_fillna(index_or_series_obj):
# GH 11343
obj = index_or_se... |
c603321694ac6ad4558aa10de053966414ebee3ec1404ff5c80c2d1530ea7cab | Python | 1,872 | 49 | # Integrated Gradient
from ..utils.process import get_last_layer
import numpy as np
import tensorflow as tf
def compute_grads(model, io_imgs, class_id, LAYER_NAME=None, MODALITY="FLAIR", XAI_MODE="classification"):
modality_dict = {"FLAIR": 0, "T1": 1, "T1CE": 2, "T2": 3}
io_imgs = tf.convert_to_tensor(i... |
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