sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
144ce94455f2cfafb26b593f352593d5322689e76c567bcdf3c3032a2f11f1ee | Python | 7,928 | 266 | # Copyright 2018-2021 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... |
9ff225d4b49267cc94623e2afd93385d623b9a0de132a08914c96a7fbcc73136 | Python | 7,935 | 185 | # SPDX-FileCopyrightText: Copyright (c) 2021 NVIDIA CORPORATION & AFFILIATES. All rights reserved.
# SPDX-License-Identifier: BSD-3-Clause
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
#
# 1. Redistributions of sourc... |
6b81df1b209df830dd99a5170de9cd6cda3ff7b4e685ad02eeb62d598ffd568e | Python | 7,938 | 238 | """
Created on Jan 3, 2023.
utils.py
@author: Soroosh Tayebi Arasteh <soroosh.arasteh@rwth-aachen.de>
https://github.com/tayebiarasteh/
"""
import numpy as np
import pdb
import pandas as pd
from tqdm import tqdm
import os
import matplotlib.pyplot as plt
import warnings
warnings.filterwarnings('ignore')
warnings.simp... |
f390ed3c8ec8ebb1b159969b446d10573d3fbe4de5dd07b401a24722067c1859 | Python | 7,938 | 201 | import torch
import numpy
import bionetwork
import plotting
import pandas
import saveSimulations
import matplotlib.pyplot as plt
import copy
#Load network
networkList, nodeNames, modeOfAction = bionetwork.loadNetwork('data/KEGGnet-Model.tsv')
annotation = pandas.read_csv('data/KEGGnet-Annotation.tsv', sep='\t')
unipro... |
87346119def4a39849fbc3599cc339be35a51c79725c9efdf2657a486f2f7eb9 | Python | 7,943 | 201 | #
# Equivariant Batch Normalization Layer
#
from keras import backend as K
from keras.engine import InputSpec
from keras.layers import BatchNormalization
import tensorflow as tf
class LBatchNorm(BatchNormalization):
def __init__(self, axis: int=-2,momentum: float=0.99, epsilon: float=1e-3, center: bool=False,
... |
ebd12553aaffb092e4d35ae1d2ec0852fe8a7f14d3f69ff0f4f336f500a75deb | Python | 7,944 | 210 | from PIL import Image
import cv2
import glob
import pandas as pd
import os
import numpy as np
import collections
import pickle
import os
import openslide
import numpy as np
from tqdm import tqdm
from math import ceil
import shutil
import argparse
def tile_saving(path, window_size, save_folder_png, ):
source_slid... |
3caada41c12ebe7b053d5d5def111a74e0851c0630a7a7a5a6859f0166344433 | Python | 7,946 | 244 | # -*- coding: utf-8 -*-
#
# microplastic-detection documentation build configuration file, created by
# sphinx-quickstart.
#
# This file is execfile()d with the current directory set to its containing dir.
#
# Note that not all possible configuration values are present in this
# autogenerated file.
#
# All configuratio... |
9e731414e1ec2d661d7092e01a88558ca8661e47e81640e492399d78571dd256 | Python | 7,951 | 261 | # Copyright 2018-2024 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... |
b4722d10c8e923e4b9a94c27540f9ad91ca2d02e20dc9eb9dd42c5e68cc905d7 | Python | 7,952 | 191 | # -*- coding: utf-8 -*-
"""
Created on Sun Dec 20 17:02:31 2020
@author: Wladek
"""
import numpy as np
import matplotlib.pyplot as py
import matplotlib as mpl
from matplotlib.colors import LogNorm
from figure_properties import *
import matplotlib.patches as mpatches
from scipy.signal import welch, argrelmin, butter,... |
d209fbd8ae07e37508a2d75e333f82f57cbfc2f5497c87478659b3fcab88d588 | Python | 7,952 | 242 | # 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... |
2c053aa2d2611e8bb5ba097c879001fbdc36aaf43ea078a1fa20b29e25cddfaf | Python | 7,956 | 202 | # Copyright 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 agre... |
0b4ae46af1f21b63d966b80451eadae06f9c9638876090237eb3239a2b81144f | Python | 7,958 | 333 | # Copyright 2018-2021 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... |
3e084e07daeae36ca242734dbef5bcf99bc9c4a9e9f86e7f522161d680beda7c | Python | 7,958 | 250 | """
@author: mkowalska
"""
import os
from os.path import expanduser
import numpy as np
from numpy.linalg import LinAlgError
import matplotlib.pyplot as plt
from figure_properties import *
import matplotlib.gridspec as gridspec
import matplotlib.cm as cm
import datetime
import time
from kcsd import KCSD2D, ValidateKCSD... |
828c7f4943d938314384f28b3a7c213cf355cb595d387f1d28717210b591e17d | Python | 7,965 | 260 | # -*- coding: utf-8 -*-
"""
Created on Sun May 1 17:33:44 2022
@author: jeanbaptiste
"""
import os
import json
import pycromanager_tessie as pmt
from pycromanager_tessie.acquisitions import experiment
# Start platform:
platform = pmt.microscope.platform.Platform(load_synchronizer=True)
# Set LED ring
platform.neop... |
990eda72dd7ffe66cdfefa684df35d895687c7d72b180ae480ad12e786bef719 | Python | 7,967 | 237 | """
Tests parsers ability to read and parse non-local files
and hence require a network connection to be read.
"""
from io import BytesIO
import logging
import re
import numpy as np
import pytest
import pandas as pd
import pandas._testing as tm
from pandas.io.feather_format import read_feather
from pandas.io.parser... |
4e19612dbc8651dabe7bdcb4dd569b4873d425d8cc3373c09faae86f59354146 | Python | 7,970 | 208 | """Estimate the empircal error rate.
"""
from collections import defaultdict
import csv
import re
from atropos import AtroposError
from atropos.commands.base import (
BaseCommandRunner, Pipeline, SingleEndPipelineMixin, PairedEndPipelineMixin)
from atropos.io import open_output
from atropos.util import qual2prob, r... |
9eddcc24ef454f1bef3c700c06ed50e5e2900803338d8ae5cf96512d9ce85df2 | Python | 7,974 | 216 | # Copyright (c) 2018-2023, NVIDIA Corporation
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
#
# 1. Redistributions of source code must retain the above copyright notice, this
# list of condit... |
1a49fb8ed68ec579f1c4524887d44897faf6ab9de41224e94863c81b483473a0 | Python | 7,975 | 208 | """Session 32 — drain add_metric / remove_metric onto a per-Experiment registry.
After session 31, the only secondary verbs still on `self._legacy` were
``add_metric`` / ``remove_metric`` / ``get_config`` / ``set_config`` /
``plot_model`` / ``evaluate_model``. Session 32 drains the first two by
promoting the metric re... |
a9131a9ffccbcc59e3c2c58311da5b41990db0aad709ddfecbbc5627d069723c | Python | 7,975 | 226 | #
# Python module protein.py for holographic machine learning
#
# This module contains all structures relating to protein conventions including...
# - dictionaries for translating amino acids to indices and vice-versa
# - dictionaries for translating elements to indices and vice-versa
# - dictionaries for amino acid... |
296d144b02b21db2b96895f877a3ca0b879d6a3ddc46f39d57b5011a16dc538b | Python | 7,978 | 151 | """Transient steady state signal models."""
from collections.abc import Sequence
import torch
from mrpro.operators.SignalModel import SignalModel
from mrpro.utils.reshape import unsqueeze_right
class TransientSteadyStateWithPreparation(SignalModel[torch.Tensor, torch.Tensor, torch.Tensor]):
r"""Signal model fo... |
338deaed9acdf59d79bb7af1fd1b1004afcd70deadf7401478c3587cb067537e | Python | 7,980 | 173 | #!/usr/bin/env python
__author__ = 'etseng@pacb.com'
"""
Similar to chain_samples.py, but specifically for chaining fusions.
Difference with regular chaining:
1. A fusion consists of several transcript records, denoted by PB.X.1, PB.X.2, ... where PB.X is one fusion
(must always consider possibility of a fusion c... |
4b455dcddeee85a7b55ad8419b85916bdfe3d8335ea8f023d494a93da74f8e57 | Python | 7,981 | 231 | __all__ = ["InputGlycanEncoding", "GlycoPeptideTreeLSTM"]
from typing import Optional
import dgl
import torch
from torch import nn
from ....util.collections.dict import chain_get_typed, chain_item_typed
from ...pep.common.model import InputPeptideCharge, InputPeptideEncoding
from ...util.treelstm import TreeLSTM
from... |
2371cf1c5156a0ccb15206aee2074702740f99e6fcdf79c95aa7cdce8fca52d9 | Python | 7,987 | 159 | """Runtime regressions using small local models and unchanged clock formulas."""
import math
import pytest
import torch
from scipy.stats import rankdata
from pyaging.models import Pasta, PastaMouse, PCGrimAge, PhenoAge, Reg, epiTOC1, stemTOC
from pyaging.models._base_models import pyagingModel
from pyaging.predict._... |
0ef9b836a6a0afc353c8470f3613d38038076b4370820e99dcb2d97129c152c8 | Python | 7,991 | 221 | #!/usr/bin/env python
# coding: utf-8
"""
for subset in `seq 0 9`
do
python -W ignore infinite_generator_3D.py \
--fold $subset \
--scale 32 \
--data /mnt/dataset/shared/zongwei/LUNA16 \
--save generated_cubes
done
"""
# In[1]:
import warnings
warnings.filterwarnings('ignore')
import os
import keras
print("Keras = ... |
8b3ae9288577feecbe80208bcb435c9bfa3e69c96bbbb65900fd2aca9051134a | Python | 7,992 | 193 | """Convert a SLEAP ``.pkg.slp`` package into a Lightning Pose project directory.
Only single-view, single-animal SLEAP projects are supported.
"""
from __future__ import annotations
import io
import json
import logging
from pathlib import Path
from typing import cast
import h5py
import numpy as np
import pandas as ... |
3e2e5544cadf9217da58bcb803595037e5faad068580d24e7375aae43bf06177 | Python | 7,993 | 231 | # Copyright 2018-2026 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... |
a2bbb7623b4265fa6d807e4f84ac248aa2fba9c9b95edf32ccfb5f7102ad3c2c | Python | 7,993 | 238 | __all__ = ["GlycoPeptideMS2TreeLSTM"]
from typing import Optional
import dgl
import torch
from torch import nn
from dgl.nn.pytorch.glob import GlobalAttentionPooling
from dgl.ops import copy_u_sum # type: ignore
from ....util.collections.dict import chain_get_typed, chain_item_typed
from ...util.attention import Att... |
dfe8a8791938cfd4de9c995fcc273f5f5712bb6bef24f00d932eb453c469eac1 | Python | 7,993 | 190 | # Copyright 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 agre... |
58da7c319e1bfbd86588340fe5c16024585f82e9923c0c19a2e1b10de72b1ded | Python | 7,998 | 269 | import numpy as np
import matplotlib.pyplot as plt
import matplotlib as mpl
# increase the figure size
plt.rcParams["figure.figsize"] = [12, 10]
# remove the top and right spines from plot in the global plt setting
plt.rcParams["axes.spines.top"] = False
plt.rcParams["axes.spines.right"] = False
# change the linewidt... |
a800828da9cc2b58c99cb13e74d186e4b71bb281836c4bdefa4305c82638cc7c | Python | 7,998 | 244 | import torch
import math
import torch.nn as nn
from torch.utils.data import Dataset
from torch.distributions import normal
from scipy.stats import beta
import numpy as np
class SamplesDataset(Dataset):
def __init__(self, x):
self.x = x
def __len__(self):
return len(self.x)
def __g... |
f6cc4772c5df5bedfcaad1b14d7b1e4cfe1e1f1f6690d23e78267bdd4138e426 | Python | 7,998 | 249 | #! /usr/bin/env python
# -*- coding: utf-8
#
# Copyright (c) 2023 Kenneth Atz, Clemens Isert & Gisbert Schneider (ETH Zurich)
from rdkit import Chem, RDLogger
from rdkit.rdBase import DisableLog
for level in RDLogger._levels:
DisableLog(level)
import argparse
import configparser
import os
import random
import h5... |
b718bc0334527dada6253cc974a920d8e5c87defe19f1c26fcad8477096a9f11 | Python | 7,999 | 231 | #!/usr/bin/env python
# coding: utf-8
### Author: federica.magnabosco@mrc-cbu.cam.ac.uk
### Fit decoding model LDvsSD individual ROIs and save accuracy
# Import some relevant packages.
import numpy as np
import pandas as pd
import pickle
import seaborn as sns
import matplotlib.pyplot as plt
from scipy.stats import se... |
c6e7a2035e39f45350f5ee2dffb10386e99f89d7c467c86f498cb1027aa3eb7e | Python | 7,999 | 212 | from itertools import permutations
import numpy as np
import pytest
from pandas._libs.interval import IntervalTree
import pandas._testing as tm
@pytest.fixture(params=[1, 2, 10])
def leaf_size(request):
"""
Fixture to specify IntervalTree leaf_size parameter; to be used with the
tree fixture.
"""
... |
7cadb926b35053c3b7982c95d5ab71b2e1039878e352442f3c0550f5d05857f7 | Python | 8,003 | 244 | # Copyright 2026 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 agre... |
d89bf9aed2a10185ed395cadefd2f8594f97d7d82a06b420b5101d2b0650835a | Python | 8,003 | 219 | # Module: containers.models.base_model
# Author: Antoni Baum (Yard1) <antoni.baum@protonmail.com>
# License: MIT
from __future__ import annotations
from typing import Any, Dict, List, Optional
from pycaret.containers.base_container import BaseContainer
from pycaret.internal.distributions import CategoricalDistributi... |
17b5f336bf14f0f345e92c1236a076f49af2979c55f22a34e1d29dad3fa8d969 | Python | 8,004 | 203 | #!/usr/bin/env python
# coding: utf-8
import sys
import numpy as np
import pandas as pd
import pickle
from sklearn.pipeline import make_pipeline
from sklearn.preprocessing import StandardScaler
from sklearn.feature_selection import SelectKBest, f_classif
from sklearn.linear_model import LogisticRegression
from skl... |
51f3c88576734d4d3f7324dd15d1325cfabfaf27ebdeaa9cd7303aaddc8f25c9 | Python | 8,004 | 245 | """Workspace member CRUD — multi-user collaboration.
Routes under ``/api/v1/workspaces/{workspace_id}/members``:
GET /members list members with role
POST /members invite an existing user (by email) with a role
PATCH /members/{user_id} change a member's role
DELETE /members/{use... |
a8ef5a38e551a9273b6aed1bbabb58f09063771743dd24ae87650346c8758b87 | Python | 8,004 | 182 |
import numpy as np
import matplotlib.pyplot as plt
from scipy.interpolate import griddata
from matplotlib import gridspec
import matplotlib.cm as cm
import config
def show_csd(csd_at, csd, show_ele=None, show_kcsd=False, show_mask=None):
if config.dim == 1:
fig = plt.figure(figsize=(6, 6))
ax = p... |
4fb657130d16ec5a1d67f5388862dcdfa38a5cff8191e8d2140f0d5e0dc80f5b | Python | 8,007 | 346 | from __future__ import annotations
__docformat__ = "restructuredtext"
# Let users know if they're missing any of our hard dependencies
# except tzdata (see https://github.com/pandas-dev/pandas/issues/63264)
_hard_dependencies = ("numpy", "dateutil")
for _dependency in _hard_dependencies:
try:
__import__(... |
3f4d1e1ac11dfa9b5418b2a52e8387aad07fc500bac40ccb493d2956d20812f2 | Python | 8,010 | 229 | import numpy as np
import pytest
import pandas as pd
import pandas._testing as tm
class TestDataFrameIsIn:
def test_isin(self):
# GH#4211
df = pd.DataFrame(
{
"vals": [1, 2, 3, 4],
"ids": ["a", "b", "f", "n"],
"ids2": ["a", "n", "c", "n"... |
7c1c7f38ef7d5747ce44bb5cea5ce92206c4acf7de73c1dfd8d1053bd998f312 | Python | 8,010 | 223 | #!/usr/bin/env python
from __future__ import print_function
try:
import numpy as np
except ImportError:
print("'numpy' is not installed. Use the command below to install it:")
print(" sudo apt-get install python-numpy")
try:
from osgeo import gdal
except ImportError:
print("'pygdal' is not ins... |
2b4db0bf9202d861590499426e257ed94ff11186c83c3cfc0ea4ba2a5fb904c7 | Python | 8,011 | 270 | """ predict and write pseudoenergies for a set of proteins """
from argparse import ArgumentParser
from functools import partial
import logging
import os
from typing import List
import h5py
import numpy as np
import pandas as pd
from protein_holography.coordinates.get_neighborhoods import (
get_padded_neighborhoo... |
7a63c6e95bb6babfb9f98ccd0b4f5574cdbe3058ecbed3ccdd1c181ec30c8b03 | Python | 8,011 | 233 | #!/usr/bin/env python
import os, sys
import argparse
from argparse import RawTextHelpFormatter
###################################################
### 0. script description and parsing arguments ###
###################################################
synopsis1 = "\
convert a BLAST tabular output into a table of one... |
3f2e5bf8da63319033a0a99537363a2c85bb1aae1f6ffc945bdf1d02164c159d | Python | 8,015 | 210 | '''
cell parser and synapse mapper
for single cell simulations
with NeuroNet subcellular synapse distributions
'''
import tables #so florida servers have no problem with neuron
from .writer import write_cell_simulation
from .writer import write_landmark_file
from .writer import write_cell_synapse_locations
from .writ... |
0b5eab2c9fd161d2bde555ea77aabfe66dffd38e199c87d59659dc1cb8597081 | Python | 8,016 | 172 | #!/usr/bin/env python
# Filename: main.py
# Author: Alessandro Gerada
# Date: 2023-01-27
# Copyright: Alessandro Gerada 2023
# Email: alessandro.gerada@liverpool.ac.uk
"""Script to predict MICs from agar dilution images. Use main.py -h for help."""
import pathlib
from aigarmic.process_plate_image import split_by... |
9dfb65a494c39e8a6fb19e3070269f8daf3aabbc802056bb258e5c011d8a9712 | Python | 8,021 | 267 | """
Templates for invalid operations.
"""
from __future__ import annotations
import datetime
import operator
from typing import (
TYPE_CHECKING,
Any,
NoReturn,
)
import numpy as np
from pandas._libs import lib
from pandas._libs.missing import NAType
from pandas._libs.tslibs import (
BaseOffset,
... |
a914cffbe646a081820f8d5465908a484a7e5b9e963847a8cbafd532586c36bc | Python | 8,022 | 272 | # -*- coding: utf-8 -*-
"""
Created on Thu Dec 9 14:18:03 2021
@author: jeanbaptiste
"""
# Not necessary once these are added to the python path permanently:
import sys
# Append paths to delta-dev and deep cell control before import:
sys.path.append('C:/DeepLearning/DeLTA_dev')
sys.path.append('C:/Users/System 6/Doc... |
2b02b6182ba2e0bb9382b83fd0a23df3b456f5dd7e3184b1379e8472a3855c1c | Python | 8,026 | 215 | # Copyright 2018-2021 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... |
8dd048e9cd1b561b9cd97d18fc7610015f8f2edd56dd0af3819201cfd4f29257 | Python | 8,026 | 189 | import math
import torch
import torch.nn as nn
import numpy as np
from .syncbn import SyncBatchNorm
from torch.nn.functional import upsample
from torch.nn import Module, Sequential, Conv2d, ReLU,AdaptiveMaxPool2d, AdaptiveAvgPool2d, \
NLLLoss, BCELoss, CrossEntropyLoss, AvgPool2d, MaxPool2d, Parameter, Linea... |
4777e7ca51861b81fd170238a2393fb8d7f62199540fa9fe686603ed62301eb5 | Python | 8,027 | 225 | import statsmodels.api as sm
lowess = sm.nonparametric.lowess
import warnings
import pylab as plt
import pandas as pd
def saveFIG(filename='tmp.pdf',
axis=False,
transparent=True):
"""save fig for publication
Args:
filename (str, optional): filename to save figure. (Default value... |
db3e40d2eafc8a60e225d38e2b00df2418d32fee2adacee730af94cd937573c7 | Python | 8,031 | 172 | #!/usr/bin/env python3
"""Build the tAge gene/ortholog mapping asset from the reference package's tables.
Run once; the output ships to Hugging Face alongside the tAge weights:
uv run python clocks/build_tage_gene_mapping.py "$SCRATCH/tAge" clocks/weights/tage_gene_mapping.csv.gz
Output contract: a four-column f... |
5d5260a76426d0b457ee4e96be7a4a7a7d48f2b25d1272673b10341faec70a12 | Python | 8,035 | 257 | # -*- coding: utf-8 -*-
"""
Created on Sun May 1 17:33:44 2022
@author: jeanbaptiste
"""
import os
import json
import numpy as np
import pycromanager_tessie as pmt
from pycromanager_tessie.acquisitions import experiment
# Start platform:
platform = pmt.microscope.platform.Platform(load_synchronizer=True)
# Set L... |
9c1ef96fbe4bbeb1eae982ebe2148e32dcd705c510237272513f4d2b0876deb8 | Python | 8,035 | 251 | # Copyright 2018-2022 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... |
c0e93711d296be1665c02c15c27655308f4966baf11fa9f90c407c16b17fdc82 | Python | 8,044 | 244 | """
viterbi.py
Created June 1, 2021
...
"""
from collections import defaultdict
from functools import partial
from dataclasses import dataclass
from ecgdigitize import signal
from math import isnan, sqrt, asin, pi
from typing import Dict, Iterable, Iterator, List, Optional, Tuple, Union
import numpy as np
import mat... |
a339b9871ff8db9aee55f2f7677ba0dd6151ffd6841b8fb02f4313fa38199870 | Python | 8,046 | 210 | ''' This program will check neuronMetadata for a NeuronBridge release for
sample issues, optionally retagging documents. Documents will be tagged
with the word "unreleased" as well as the ALPS release.
'''
__version__ = '0.0.3'
import argparse
from operator import attrgetter
import sys
from time import strftim... |
6159993b0beb6eb213b1f5c8fb880f0595d2537b04d7c84ddbc1cc0a0abe3635 | Python | 8,049 | 216 | # -*- coding: utf-8 -*-
"""
Created on Mon Mar 13 19:12:54 2023
Figure 2. striatal neurons are phase locked to gait cycle
@author: lonya
"""
#%% Load Data
from tkinter import messagebox
import tkinter as tk
import tkinter.filedialog as fd
import os
import numpy as np
import matplotlib.pyplot as plt
fro... |
cffc5b7ef8c96d68c3d05aa215258ee374e75b4eb91b49247bd3b3ff08479924 | Python | 8,056 | 179 | """
Tests for CategoricalIndex.__repr__ and related methods.
"""
import pandas._config.config as cf
import pandas as pd
class TestCategoricalIndexReprStringCategories:
def test_string_categorical_index_repr(self):
# short
idx = pd.CategoricalIndex(["a", "bb", "ccc"])
expected = (
... |
9f2442fa759e0b765a36fd7f00067319221d2084c29c330683c08e7a8a36e464 | Python | 8,057 | 238 | from copy import deepcopy
import tensorflow as tf
from tensorflow.keras import Model
from .actor import Actor
from .critic import MultiCritic
class ActorCritic(Model):
"""
Actor-Critic
===========
Attributes:
actor_units (list): list of the numbers of units in each Actor's layer
cri... |
858adc3ff8d4eb7dbcd388b82b1f12bd2f0f4b558cb4e1d8b9c4246404ddfdec | Python | 8,059 | 179 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Sun Mar 27 14:12:48 2022
@author: wirrbel
"""
import pandas as pd
import numpy as np
import os
region_overview_file = '/home/wirrbel/2023-08-07_delivr_run_results/2023-08-15_delivr_run_results/re-calculated tables/region_overview.xlsx'
#alternatively, coll... |
9c3ee5b8a2d4624e681577330c9720612e0897d245c1a187e6683d408da48854 | Python | 8,060 | 220 | # -------------------------------------------------------------------------------------------------------------------------------------
# Following code curated for GCPNet (https://github.com/BioinfoMachineLearning/GCPNet):
# ----------------------------------------------------------------------------------------------... |
6a347dce5997b262647b421d93fc2820ee1067be31014c6dba3002898915159c | Python | 8,061 | 136 | import argparse
import os
from util import util
import torch
import models
import data
class BaseOptions():
"""This class defines options used during both training and test time.
It also implements several helper functions such as parsing, printing, and saving the options.
It also gathers additional opti... |
6c7022f03273b31103531a9f330303b95c360c89db42eb040c41949c86e09fe5 | Python | 8,062 | 173 | """Public API and CLI regressions for long fragments (#807)."""
import math
from types import SimpleNamespace
import pytest
from MACS3.Signal.FixWidthTrack import FWTrack
from MACS3.Signal.PairedEndTrack import PETrackI
from MACS3.Signal.PeakDetect import PeakDetect
def inputs(tmp_path, fmt, length):
paths = [... |
21556e9be45f630c3b1411c1752c1144ba0a1d9818ff1054d8243e75001d11aa | Python | 8,063 | 227 | # Copyright 2024 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 agre... |
f8a8b072694e59c2188b6dfa9fd386186ab6982c4c443758fffc9c3cc2ebc91e | Python | 8,063 | 201 | """
Note: for naming purposes, most tests are title with as e.g. "test_nlargest_foo"
but are implicitly also testing nsmallest_foo.
"""
import numpy as np
import pytest
import pandas as pd
import pandas._testing as tm
def assert_check_nselect_boundary(vals, dtype, method):
# helper function for 'test_boundary_{... |
aa2a5a85348be4336535a51bca4ce4f3ba7811cf6bfaade712dd8f5e86231304 | Python | 8,064 | 192 | from utils import print_from_history
import os
import pandas as pd
import datetime
from evaluators.evaluator_globals import ARGS_COL_MAP, COLS_IN_ORDER
class Evaluator(object):
METRICS = ['acc', 'bal_acc', 'auc', 'prec', 'rec', 'f1', 'loss'] # Performance metrics to evaluate
def __init__(self,
... |
46c8a14079428271d1afd1ce0c5554195c1a72a623b2170b1c116889007ac647 | Python | 8,067 | 344 | from datetime import (
date,
time,
timedelta,
)
import pickle
import numpy as np
import pytest
from pandas._libs.missing import NA
from pandas.core.dtypes.common import is_scalar
import pandas as pd
import pandas._testing as tm
from pandas.core import roperator
def test_singleton():
assert NA is N... |
b0e7a802c7d3c05cc6d10b5d98f0b84b5d3b813ab6141c47f32b7b660176310c | Python | 8,068 | 249 | # -*- coding: utf-8 -*-
#
# vegas documentation build configuration file, created by
# sphinx-quickstart on Sat Dec 7 11:14:42 2013.
#
# This file is execfile()d with the current directory set to its containing dir.
#
# Note that not all possible configuration values are present in this
# autogenerated file.
#
# All c... |
8a285ce278e9e6a9f0e6a85cd8381eab0fbe397b8798559569540ed3a1f741b1 | Python | 8,074 | 221 | """Session 41 — phase 5c: drain ``TimeSeriesExperiment.predict_model``.
Phase 5b (s40) drained ``create_model``. This session drains the second
TS verb. ``exp.predict_model(forecaster)`` no longer touches
``self._legacy.predict_model`` — predictions go directly through
``get_predictions_with_intervals`` and metrics ar... |
3ef9e26ecac648917e425d83180fff78a4a83f964e5a65aa305b06ff5aa47b4d | Python | 8,076 | 300 | import warnings
import numpy as np
from pandas import (
NA,
Categorical,
DataFrame,
Index,
Series,
StringDtype,
)
from pandas.arrays import StringArray
class Dtypes:
params = ["str", "string[python]", "string[pyarrow]"]
param_names = ["dtype"]
def setup(self, dtype):
try... |
00104e7a8affb163fd416e7e8f084c3e7ad34da8982ef5d90539ee09d0549881 | Python | 8,077 | 188 | import math
import torch
import numpy as np
def make_beta_schedule(schedule="linear", num_timesteps=1000, start=1e-5, end=1e-2):
if schedule == "linear":
betas = torch.linspace(start, end, num_timesteps)
elif schedule == "const":
betas = end * torch.ones(num_timesteps)
elif schedule == "qua... |
cfe77a0767e1308946e455e30ff1dbec2f4d7c1df4b3160d941a705ab564c975 | Python | 8,079 | 180 | """solver_mod.py"""
import warnings
warnings.filterwarnings("ignore")
import os
import numpy as np
import random
from tqdm import tqdm
import matplotlib.pyplot as plt
#from IPython.display import Image
import sys
from scipy.io import savemat
import pickle
from generate_mod import sample_clutter
import io_mod, genera... |
59e4a4de7f13862b90e6f427f1688bbeb246884e18f03e511d479fee77dddfb6 | Python | 8,086 | 231 | """Transforms relate to hamming distance sampling."""
import random
import numpy as np
from onmt.constants import DefaultTokens
from onmt.transforms import register_transform
from .transform import Transform, ObservableStats
class HammingDistanceSampling(object):
"""Functions related to (negative) Hamming Distanc... |
1db3d429310d77df4f69df79261566cbe97b0cf8c962325acd0cde421b3e2934 | Python | 8,089 | 176 | """Checks on the frozen LinAge2 constants the parity tests are anchored to.
``clocks/notebooks/linage2.ipynb`` re-derives these constants from the published
archive every time it runs, so this snapshot is not a build input. It is the
independent reference: these tests confirm the snapshot alone reproduces the
paper's ... |
d377233343b72f5cb3993b4a3e8d521bd2931f6c2cc3850769a34f2762c1aa6c | Python | 8,089 | 181 | import pandas as pd
import numpy
def contains(haystack, needles):
result = numpy.full(len(haystack), False, dtype=bool)
for curNeedle in needles:
result = numpy.logical_or(result, [curNeedle in x for x in haystack])
return result
def mergeContent(df):
A = df.iloc[0,:]
B = df.iloc[1,:]
r... |
a3911b9233f99d129a18ddaa2d66c7b8cd18a734e105d66279cdbe808b95202a | Python | 8,092 | 222 | # %% [markdown]
# # QMRI Challenge ISMRM 2024 - $T_1$ mapping
# In the 2024 ISMRM QMRI Challenge, the goal is to estimate $T_1$ maps from a set of inversion recovery images.
# The dataset consists of images obtained at 10 different inversion times using a turbo spin echo sequence. Each
# inversion time is saved in a se... |
e2ce2fbe0b05919d072f4d2a51e3184b184810b30b304a49b9fd457c27840b10 | Python | 8,095 | 239 | import numpy as np
import pytest
import pandas as pd
import pandas._testing as tm
def create_mock_weights(obj, com, adjust, ignore_na):
if isinstance(obj, pd.DataFrame):
if not len(obj.columns):
return pd.DataFrame(index=obj.index, columns=obj.columns)
w = pd.concat(
[
... |
7c056b7f58565efa03b9df2971a3655c738ea4b8d3c8f7dc1ba06b33655dbe23 | Python | 8,100 | 234 | # -*- coding: utf-8 -*-
# @File name: plot_day_shutter.py
# @Author: Alicia Garrido-Peña
# @Date: 2023-08-09 18:26:14
# @Contact: alicia.garrido@uam.es
# "Copyright (c) 2023 Alicia Garrido-Peña. All Rights Reserved."
# Use of this source code is govern by GPL-3.0 license that
# can be found in the LICENSE file
# C... |
0a57ad32c4946f03ec358fe596ff12d9789a190d7a461c867503c57cf67c6b74 | Python | 8,105 | 164 | '''
Created on Jul 27, 2022
@author: voodoocode
'''
import numpy as np
import finnpy.file_io.csv_data
import finnpy.file_io.nifti_data
import finnpy.visualization.volumetric_plots
import mayavi.mlab
#===============================================================================
# # Default
# # CSV_FILE = "/mnt/da... |
cec0145be29d7351b4ae3ac5995f6c0277745aee3f3c67d765dbe25a8f8de2d9 | Python | 8,107 | 210 | # Copyright (c) 2018-2023, NVIDIA Corporation
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
#
# 1. Redistributions of source code must retain the above copyright notice, this
# list of condit... |
fc6c32792d48d9075d567ed5677d7cf02f0e908be27c463ba47f5e0985338a1b | Python | 8,112 | 242 | # 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... |
3d83a136023a459ef473f56fcdd9adb4686005a7b8a435793838ad37de07423c | Python | 8,113 | 189 | # Filename: model.py
# Author: Alessandro Gerada
# Date: 2023-03-15
# Copyright: Alessandro Gerada 2023
# Email: alessandro.gerada@liverpool.ac.uk
"""Implementation of Model classes"""
from aigarmic._img_utils import convert_cv2_to_keras
import tensorflow as tf
import numpy as np
from typing import Optional
from... |
9c7b431526797b0f2503b4030508ff890d030aaf47422a1bf6e82df5d73f525c | Python | 8,117 | 245 | from functools import partial
from typing import List
import h5py
import numpy as np
from sklearn.neighbors import KDTree
from protein_holography.utils import geo
# given a set of neighbor coords, slice all info in the npProtein along neighbor inds
def get_neighborhoods(neighbor_inds: np.ndarray, structural_info: np... |
3e19d8ab94523f70eaf3892654f53a8f239db678f5de143f8414b8364097fd68 | Python | 8,118 | 242 | # Copyright 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 agre... |
1ea4ca786a3756d4fb4824930c64cf0dfa58ac6fa47687cc195dbbf945f8b72c | Python | 8,120 | 195 | import random
import math
import numpy as np
import argparse
import torch
import torch.optim as optim
import torchvision
from torch import nn
from torchvision import transforms
from dataloader.loading import *
import torch.nn.functional as F
import pandas as pd
import matplotlib.pyplot as plt
from sklearn.metrics impor... |
f5bd8b6a0cdf9f9b68d85639b66ead94704849b39d5d76c143c2baed699247d5 | Python | 8,128 | 136 | import os
import numpy as np
import pandas as pd
import statistics
path_to_brainchart = '/media/sda/Anna/brain_age/DiffMIC/dataset/csv_data/allnew_AIM_.csv'
path_to_test_1 = '/media/sda/Anna/brain_age/DiffMIC/notebooks/5models_combined_results.csv'
path_to_test_2 = '/media/sda/Anna/brain_age/DiffMIC/notebooks/brain_a... |
090e868ed289c7995c5c2bc5b8315274fd1f8c65b777a948254741936d051c03 | Python | 8,131 | 236 | # -------------------------------------------------------------------------------------------------------------------------------------
# Following code curated for GCPNet (https://github.com/BioinfoMachineLearning/GCPNet):
# ----------------------------------------------------------------------------------------------... |
74bd29e01f5d6f2998bac867bfc495d9969cc089961045be156ac3b74607878e | Python | 8,131 | 240 | # 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... |
e5b18e5f18327232bb629abb15e3238daff02c35f44f9d8c62fa6d18ec304b4d | Python | 8,131 | 227 | import re
import numpy as np
import pytest
import pandas as pd
import pandas._testing as tm
class TestIntervalIndex:
@pytest.fixture
def series_with_interval_index(self):
"""
Fixture providing a Series with an IntervalIndex.
"""
return pd.Series(np.arange(5), pd.IntervalIndex... |
457122b90005b7ed3d97f380a49377be65f6df274baec58c30d28494295b8689 | Python | 8,133 | 209 | #!/usr/bin/env python
# coding: utf-8
import sys
import numpy as np
import pandas as pd
import pickle
from sklearn.pipeline import make_pipeline
from sklearn.preprocessing import StandardScaler
from sklearn.feature_selection import SelectKBest, f_classif
from sklearn.linear_model import LogisticRegression
from skl... |
2544c4959cea6f686f7d7da15e5b517d32fd9227abf4beb04264cc459b86bac1 | Python | 8,135 | 209 | #!/usr/bin/env python
# coding: utf-8
import sys
import numpy as np
import pandas as pd
import pickle
from sklearn.pipeline import make_pipeline
from sklearn.preprocessing import StandardScaler
from sklearn.feature_selection import SelectKBest, f_classif
from sklearn.linear_model import LogisticRegression
from skl... |
3f442ee8dc2e91178b3110ea5abcc940a11e15aac27a2afa5976c5c352b2847a | Python | 8,135 | 327 | from functools import wraps
import threading
import numpy as np
from pandas import (
DataFrame,
Index,
Series,
date_range,
factorize,
read_csv,
)
from pandas.core.algorithms import take_nd
try:
from pandas import (
rolling_kurt,
rolling_max,
rolling_mean,
r... |
53a092a5da839716c7e40c6add1d7874745286c6929b1c72aea044c305062cca | Python | 8,135 | 197 | #funcsrg.py
import numpy as np
import copy
from placerg.funcs import *
def RGrealstep(pmat, cluster, corr):
"""
Perform real space RG step
Here we first calculate the correlation matrix, c_(ij)= (C_(ij))/
(sqrt(C_(ii)*C_(jj)))
Where C is the covariance matrix
A complication here is that if a c... |
ae3e3bd37c7e42d3474bfaee0f15deebed9c13adc2952349c001caf85139ea5f | Python | 8,136 | 270 | # I/O lib for molecular sequences
from os.path import isfile
from os import remove
from random import random
from copy import copy
from treeshrink import get_tmp_file
try:
import cPickle as pickle
except:
import pickle
def get_taxon_list(filename):
taxon_list = []
for line in open(filename,'r'):
... |
d63272c71b3a7f52d2df938629c7ac53b9add44cb8b0d84c65bd2ffa6a65060c | Python | 8,139 | 216 | """Tests for utility functions."""
import os
import shutil
import pytest
from pcntoolkit.normative import NormativeModel
from pcntoolkit.util.runner import Runner
from test.fixtures.blr_model_fixtures import *
from test.fixtures.norm_data_fixtures import *
from test.fixtures.test_model_fixtures import *
class Test... |
fa30834b93714fff0861c5eedd4f2565a8ced864bd9fbe92e71b34477d6e4f71 | Python | 8,139 | 229 | """High-level Git publish service.
Takes a GitRepository row + a project's data and writes the on-disk
layout described in :mod:`exporter`, then commits and pushes via the
``git`` binary over HTTPS (with the PAT injected into the URL).
We shell out instead of using GitPython / pygit2 because:
1. The set of operation... |
8841bfc7b00a8a942a4c138e19458fb62beb6070cdbd899264ba454b26a18fc8 | Python | 8,140 | 229 | # MOFTransformer version 2.0.0
# flake8: noqa
import numpy as np
# Jmol colors. See: http://jmol.sourceforge.net/jscolors/#color_U
jmol_colors = np.array(
[
(1.000, 0.000, 0.000), # None
(1.000, 1.000, 1.000), # H
(0.851, 1.000, 1.000), # He
(0.800, 0.502, 1.000), # Li
... |
cb5f36d8fd3b610d2dfc5fdccdf5cda05dae1d344416e8a2b5549dc2e9d48bdd | Python | 8,141 | 216 | import argparse
from datetime import datetime
import matplotlib.pyplot as plt
import numpy as np
import os
from scipy.interpolate import RegularGridInterpolator
import windseer.utils as utils
import windseer.plotting as plotting
if __name__ == "__main__":
parser = argparse.ArgumentParser(
description=
... |
356d78458d241025d952d2cc489d4f4c47f75085ccd205fac9f09a1f7da1770e | Python | 8,147 | 230 | """ Multi-Head Attention module """
import math
import torch
import torch.nn as nn
from onmt.utils.misc import generate_relative_positions_matrix,\
relative_matmul
# from onmt.utils.misc import aeq
class MultiHeadedAttention(nn.Module):
"""Multi-Head Attention module from "Attention i... |
258e0ebc06d3337e222564dadfcd5c04db7c8676d9745c5fb818f78c82315376 | Python | 8,152 | 233 | """Class for coil sensitivity maps (csm)."""
from __future__ import annotations
from typing import TYPE_CHECKING
import torch
from typing_extensions import Self
from mrpro.data.IData import IData
from mrpro.data.SpatialDimension import SpatialDimension
from mrpro.utils.interpolate import apply_lowres
if TYPE_CHECK... |
4ece8b7e52c9b30fb3dc946cabc9411839d33b3a23db1b69b47e7dae481fb57f | Python | 8,153 | 277 | import os
import numpy as np
import pandas as pd
from deepglyco.chem.common.elements import ElementCollection
from deepglyco.chem.pep.aminoacids import AminoAcidCollection
from deepglyco.chem.pep.mods import ModificationCollection, ModifiedSequenceParser
from deepglyco.deeplib.pep.rt.data import PeptideRTOutputConver... |
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