sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
d7a8ebc7adc9228c324523c7f5e648580937a21d25ea6439bee5e5d122aee549 | Python | 6,663 | 192 | #!/usr/bin/env python3
#
# Copyright 2015 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... |
af947fe4fac12071fc6c82acc81d7eacb36485f96a7f813e742ea2e7b0df5084 | Python | 6,664 | 170 | import numpy as np
import pytest
import pandas._config.config as cf
import pandas as pd
import pandas._testing as tm
class TestIndexRendering:
def test_repr_is_valid_construction_code(self):
# for the case of Index, where the repr is traditional rather than
# stylized
idx = pd.Index(["a"... |
a8fd52890e8f1ac41e267bff1894550e2ec7e0aebf5177ac12bf2caf51b780fc | Python | 6,665 | 184 | import pandas as pd
from sklearn.base import BaseEstimator, TransformerMixin
from sklearn.compose import ColumnTransformer, make_column_selector
from src import prep
from src.nodim import transform_nodim, estimate_params
class DiMap(BaseEstimator, TransformerMixin):
"""Distribution Mapping Transformer."""
def... |
ee48370204003d31ed61975084cf43e94ba416ebe6fc75be864a2a65cad53180 | Python | 6,665 | 200 | """Platform backup + restore — superuser-only.
Two endpoints:
GET /admin/backup
Stream a tarball containing:
* ``database.json`` — all rows from every table (UUIDs preserved)
* ``artifacts/<run_id>/...`` — raw artifact files
POST /admin/restore (multipart upload of a tarball)
... |
cc54907bc96d427e7211aa9089c2a4fb5fbd9f1a00830e8f82f5c548cf01a1e4 | Python | 6,666 | 142 | import torch
from tnn.layers import View, Permute, tLinearLayer, LinearLayer
from tnn.networks import tHamiltonianResNet
from tnn.loss import tCrossEntropyLoss
from tnn.regularization import SmoothTimeRegularization, TikhonovRegularization, BlockRegularization
from tnn.training.batch_train import train
from tnn.utils i... |
a571e522cf399429c6fe8058ee276244ac73550c948d0b720f071f1407e7c45b | Python | 6,668 | 175 | import warnings
warnings.filterwarnings('ignore')
import os
os.environ['TF_CPP_MIN_LOG_LEVEL'] = '3'
from tqdm import tqdm
import matplotlib.pyplot as plt
import numpy as np
from utils import *
from config import models_genesis_config
from torch import nn
import torch
from nnunet.training.learning_rate.poly_lr import ... |
75102f0b4f44a396fe8fa43bbbaf88add09b3892334a4975552e9d7118e11a1d | Python | 6,673 | 185 | #!/usr/bin/python
import numpy as np
import warnings
internal_os = 2
pcs_directions = ["dSag", "dCor", "dTra"]
# p. 418 - pcs to dcs
pcs_transformations = {
"HFS": [[1, 0, 0], [0, -1, 0], [0, 0, -1]],
"HFP": [[-1, 0, 0], [0, 1, 0], [0, 0, -1]],
"FFS": [[-1, 0, 0], [0, -1, 0], [0, 0, 1]],
}
# scalar first... |
6f5422103e772874dccd02be57409596f4476252d2ac7b502801ae2cbbf0521d | Python | 6,677 | 218 | import numpy as np
import sys
import gvar as gv
import vegas
try:
import corner
except ImportError:
corner = None
try:
import lsqfit
except ImportError:
lsqfit = None
if sys.argv[1:]:
SHOW_PLOTS = eval(sys.argv[1]) # display picture of grid ?
else:
SHOW_PLOTS = True
# options (default i... |
7d0751d388bea224a9337c9e1909f1abb2ac551802e6f476fa6da95852dc3547 | Python | 6,678 | 170 | # 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... |
df169fcd31898646bcd06e24cc2a03b8d379fdca7237a48ef72245680a7082bf | Python | 6,683 | 157 | # 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... |
2586cb0ef289355cc649eacbf7acf05ae4f42db0a5383796f7be18562a4c4254 | Python | 6,684 | 180 | import torch
import numpy
import argparse
import bionetwork
import plotting
import pandas
inputAmplitude = 3
projectionAmplitude = 1.2
batchSize = 5
noiseLevel = 1e-3
MoAFactor = 1e-1
spectralFactor = 1e-3
maxIter = 8000
L2 = 1e-6
#weightAidFactor = 1e-8
#Get data number
parser = argparse.ArgumentParser(prog='Signa... |
38e643d1391bad5c29a95177048bb188854a0ad45fdfbd8e2ba34bad1f7476e4 | Python | 6,686 | 156 | # 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... |
eb28dee3b5ce26251ac19f532c410547f42af7e9de6371807ba6697dd64d7941 | Python | 6,686 | 160 | import numpy as np
import os, sys
import nibabel as nib
from neuroxai.utils.process import norm_image
from tensorflow.keras import Input, Model
from tensorflow.keras.layers import concatenate, Conv2D, Conv3D, UpSampling3D, Activation, BatchNormalization
from tensorflow.keras.layers import SpatialDropout3D, MaxPooling3... |
08eaa9cb798b875c6c52453305cdca339a7dd9c1bdb6d72b95ec7e849e98914a | Python | 6,687 | 189 | from __future__ import print_function, division
import torch
import torch.nn as nn
class ConvLayer(nn.Module):
"""
Convolutional operation on graphs
"""
def __init__(self, atom_fea_len, nbr_fea_len):
"""
Initialize ConvLayer.
Parameters
----------
atom_fea_l... |
a363db1eedd040f93c16b60381fea58833fc8b3c2f3493db2e33d7486217e257 | Python | 6,689 | 158 |
# 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 condi... |
9f18d0d3c8c5e4305a6fc922ad77307643a2bced55a758abe84b4cf4261664cb | Python | 6,692 | 193 | import numpy as np
import pytest
import pandas as pd
import pandas._testing as tm
def test_reindex(idx):
result, indexer = idx.reindex(list(idx[:4]))
assert isinstance(result, pd.MultiIndex)
assert result.names == ["first", "second"]
assert [level.name for level in result.levels] == ["first", "second... |
b7f26749f7e45b2738889be1be692b8d0219c8515aaf36cd8e43e901dd0d9312 | Python | 6,694 | 199 | # Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
# http://www.apache.org/licenses/LICENSE-2.0
# Unless required by applicable law or agreed to in writing, software
# distributed under the ... |
6f43c6476e3bd6e844e191c482b6ce48fdf2abdabb16032d2cf4668e28c8959d | Python | 6,695 | 146 | """Build IntrinClock370 and PhenoAge partitions from original author assets.
Run from the repository root:
uv run --with rdata --with remotezip python clocks/build_author_extensions.py \
--intrin-source /tmp/intrinclock-original --prc-source /tmp/pyaging-prc-original
Without a source directory the pinned ... |
0e55bd3fcc100f31efe1fe4beed91d5b25eaf6ee6168c21a8bb4b1cd45bf4620 | Python | 6,698 | 263 | #scatterplots.py
from initialization.config import *
from initialization.initialization import *
import seaborn as sns
import matplotlib.pyplot as plt
import plotly
import plotly.graph_objects as go
from plotly.subplots import make_subplots
import plotly.express as px
def seaborn_jointplot(df, pair, savepath=PLOT_OU... |
b039a54479c5a7e9cba146d3be020c3641c5050a3c1774439afb6f8401dd13ee | Python | 6,698 | 246 | import matplotlib.pyplot as plt
import numpy as np
import pandas as pd
import matplotlib.ticker as ticker
import matplotlib.transforms as transforms
import numpy as np
from pathlib import Path
from statistics import mean, stdev
from fpdf import FPDF
import math
import sys
sys.path.append('../')
from plotting_function... |
1144f20fa03fbda092abc801a5472766c5e3aaf4959068ab4520e9ee38db1ebf | Python | 6,705 | 202 | # 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... |
1e616734a7436e113c9b9c0be597d18afa0bd15759e8ec63a88696546bad9d5d | Python | 6,708 | 209 | # 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... |
968bcaf645ea354253267e0678b382eb01151926e237e58f2b44e72e00665b3b | Python | 6,709 | 224 | """History class for undo stack."""
from dataclasses import dataclass, replace
# ------------------------------------------------------------------------------
# Imports
# ------------------------------------------------------------------------------
# ---------------------------------------------------------------... |
a323648e4da2d2dfe3e0a6b3421a603ebfccdd9114fc2c6f82beeca331c1620e | Python | 6,710 | 179 | """
Worker script: runs inside a single Lightning AI job.
Downloads a dataset's zip archive from HuggingFace, extracts it to local (ephemeral)
studio disk, trains one Lightning Pose model via `litpose train`, and deletes model
weights. Results land in --output_dir (a path on teamspace storage).
Can also be called dir... |
c563b7fa925d54eabcecf6d8cd82344484fb93e1dbe64156ab3837ded5ccc3b4 | Python | 6,711 | 190 | # 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... |
0ba84d6925b8a5ab1b1aa7c92f1c7b420739814d748b59f3176614c5acd7839e | Python | 6,716 | 147 | import pytest
import pandas as pd
import pandas._testing as tm
class TestCombine:
def test_combine_scalar(self):
# GH#21248
ser = pd.Series([i * 10 for i in range(5)])
result = ser.combine(3, lambda x, y: x + y)
expected = pd.Series([i * 10 + 3 for i in range(5)])
tm.asser... |
46c678b9bb56b471b9c55273d23c0476db9ba650125b757001834e89c1c71e80 | Python | 6,718 | 218 | """
Tests for the following offsets:
- BMonthBegin
- BMonthEnd
"""
from __future__ import annotations
from datetime import datetime
import pytest
import pandas as pd
from pandas.tests.tseries.offsets.common import (
assert_is_on_offset,
assert_offset_equal,
)
from pandas.tseries.offsets import (
BMonth... |
a82355b4a834b84e6d894e4adf9ffb44db73b9c04d78f1b1e724e583e037216f | Python | 6,719 | 195 | import sys
import warnings
from io import StringIO
import numpy as np
import pandas as pd
from pybedtools import BedTool
from . import _blo_algorithms as algorithms
from . import _blo_utilities as utilities
# Suppress certain warnings
warnings.simplefilter("ignore", category=FutureWarning)
warnings.simplefilter("ign... |
4a1710e24c272a6fcd34e99c592a013534491259cefcd1724bc22174d33f1bc1 | Python | 6,724 | 177 | """Session 31 — drain the secondary verbs: pull / models / get_metrics.
After session 30 finished the internal-state drain, only setup() and a
handful of advisory verbs remained on self._legacy. Session 31 drains
the three that have a clean native equivalent:
- ``pull()`` reads from ``self._fit_state["last_metrics"... |
cd3c342c0c498fb256fd2f38416cb14b27bcee31cbb6802b09ef00845c957d30 | Python | 6,724 | 232 | from __future__ import annotations
from typing import TYPE_CHECKING
import numpy as np
from pandas.core.dtypes.missing import (
isna,
na_value_for_dtype,
)
if TYPE_CHECKING:
from pandas._typing import (
ArrayLike,
Scalar,
npt,
)
def quantile_compat(
values: ArrayLike, q... |
4dc3078241cbddc240e8978ae8c5bbfff9ab2f4b80624cd6b596c9341b2542c4 | Python | 6,726 | 192 | ######################
### Import Library ###
######################
# my library
from statistics import harmonic_mean
from molgraph.dataset import *
from molgraph.benchmark import *
from molgraph.gineconv import * # used modified version from torch_geometric
# standard
import numpy as np
import copy as copy
# rdkit
... |
fdbf55c3c62059bf4f37f10342a5d0fc22574df31b079633668c337e03508757 | Python | 6,728 | 202 | # The following implementation is based on the techniques described in:
# "Object Landmark Discovery Through Unsupervised Adaptation" by Enrique Sanchez and Georgios Tzimiropoulos
# You can find the article here: http://papers.nips.cc/paper/9505-object-landmark-discovery-through-unsupervised-adaptation.pdf
#
# For ... |
1d8da6de016b30a68a5eb0fa202fdf6cef10ead92e556640b0e3fd4f57fe139b | Python | 6,729 | 209 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Fri Feb 10 16:41:48 2023
@author: jlugagne
"""
import os
import copy
import time
import sys
import json
import uuid
import numpy as np
import tensorflow as tf
import matplotlib.pyplot as plt
# Make sure the proper package is used:
sys.path.insert(0,'./..... |
bd894b5c2354b758401caf4caadfb7d09dd9d2bda84ff82a05d070426043b388 | Python | 6,731 | 196 | #! /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... |
c0ad939f75ad6a1c123d4f9b2624709caa1ce6caf7c294baeb601fe929b36683 | Python | 6,732 | 269 | from textwrap import dedent
import pytest
import pandas as pd
pytest.importorskip("jinja2")
from pandas.io.formats.style import Styler
@pytest.fixture
def df():
return pd.DataFrame(
{"A": [0, 1], "B": [-0.61, -1.22], "C": pd.Series(["ab", "cd"], dtype=object)}
)
@pytest.fixture
def styler(df):
... |
7e0c7b6768eb6e61b6b45a9532307333c4c8cf2cf385aaf02689319ca2592100 | Python | 6,733 | 187 | """Add `array-support` directive."""
from __future__ import annotations
from itertools import groupby
from typing import TYPE_CHECKING
from docutils import nodes
from sphinx.util.docutils import SphinxDirective
from sphinx.util.typing import ExtensionMetadata
from scanpy._utils import _docs
if TYPE_CHECKING:
f... |
368493bbfd2a557be9ce9d15650cde72909c7b0348443cbe90c4611dddfa7db3 | Python | 6,738 | 188 | import pytest
from umap import AlignedUMAP
from umap.aligned_umap import expand_relations
from sklearn.metrics import pairwise_distances
from sklearn.cluster import KMeans
import numpy as np
from sklearn.metrics import adjusted_rand_score
# ===============================
# Test AlignedUMAP on sliced iris
# ==========... |
8f11e64c0d74db52700fcd6930a96f8291c4dba7359a110ac701aae48d21ece9 | Python | 6,741 | 156 | """Tests for transient steady state signal model."""
from collections.abc import Sequence
import pytest
import torch
from mrpro.operators.models import TransientSteadyStateWithPreparation
from mrpro.utils import RandomGenerator
from tests import autodiff_test
from tests.operators.models.conftest import SHAPE_VARIATIO... |
9560ebf1ba7f4243d56540ee4e8f7f7eba0efaeb5f3b25fa7a5693d666b3147e | Python | 6,742 | 197 | """
This file contains a minimal set of tests for compliance with the extension
array interface test suite, and should contain no other tests.
The test suite for the full functionality of the array is located in
`pandas/tests/arrays/`.
The tests in this file are inherited from the BaseExtensionTests, and only
minimal ... |
0bc8c6634264898a6fb3543181e1becc94b06c3e28581edc8423dc5f29537e02 | Python | 6,746 | 197 | # 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... |
8df4e7a607d268d41018e611f2ff1a0644d6e8b13e5315f52b0fbe03bff416f6 | Python | 6,747 | 169 | # 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... |
89832a8ecd96ed8faab320e70e3a1293a24d0fc8754e30a26a36600d4d6c5eb5 | Python | 6,753 | 221 | import argparse
import gc
import gzip
import os
import os.path as op
import pickle
from glob import glob
import matplotlib
import matplotlib.image as mpimg
import nibabel as nib
import numpy as np
import pandas as pd
from gradec.fetcher import _fetch_metamaps
matplotlib.use("Agg")
from matplotlib import pyplot as plt... |
85a558b65ad6b9a62d0580f556cb308916a88e25854456512af5cda58f346787 | Python | 6,754 | 166 | # 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... |
e4fcefac7662efecf711d55e98bfc2291a2beb47a602c2da46dae97779c4f0b2 | Python | 6,754 | 136 | # Implementation of Non-linear Least Squares
import logging
import numpy as np
import scipy.optimize as op
from tqdm import tqdm
from joblib import Parallel, delayed
####################################################################
# Parallelized NLS
#################################################################... |
68875367d8e558c9a812c7641b2ef08c9157007f92c24fbae7ce781a74441f89 | Python | 6,755 | 139 | from Environment import *
from Parameter import *
PARAMETER_DIR = Registration['parameters_root']
def get_sitk_transform(elastix_param):
tf_type = elastix_param['Transform'][0]
image_spec = {'Size': [int(i) for i in elastix_param['Size']],
'Origin': [float(i) for i in elastix_param['Origin']]... |
678fc92caafbe4ad48d0a603022219cb7c530c874b093f8d76bfb13735455cd8 | Python | 6,756 | 226 | # -*- 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... |
f15b92c0ac1256f3ca14137b26c981b28ac99e91eb1adf07a8bef1448234aa80 | Python | 6,757 | 139 |
'''
This avoids reading any variant more than once.
The sum of unpadded lengths of all 20k genes is 1400Mbases.
The sum of the padded lengths is 5400Mbases.
The total number of bases in the padded genes (without double-counting overlaps) is 2100Mbases (40%) (in 16k intervals)
'''
from ..utils import get_padded_gen... |
9cd993800ca152da3cd53a5d2f7e79e4fdf0c0fecc67bd0c40b0b7434f1f39ba | Python | 6,760 | 168 | """Tests for data I/O functionality."""
import copy
import numpy as np
import pandas as pd
import pytest
from pcntoolkit.dataio.norm_data import NormData
class TestDataIO:
"""Test data I/O functionality."""
@pytest.fixture(autouse=True)
def setup(self, synthetic_data):
"""Setup test environmen... |
06dde9b092907f930283fbd147d0c00c173d1e3f1a8899e5ceae767b63945d8e | Python | 6,762 | 198 | """Experiment CRUD (nested under a project)."""
from __future__ import annotations
from typing import Annotated
from fastapi import APIRouter, Depends, HTTPException, status
from pycaret.core.tasks import TaskType
from sqlalchemy import func, select
from sqlalchemy.orm import Session
from pycaret_server.api.schemas... |
6907808ccba80d15c29ba9e075ce9f1a5c3dfb0f4e7a271767d3f3469d724cdf | Python | 6,763 | 227 | #!/usr/bin/env python
from __future__ import print_function
import windseer.data as nn_data
import windseer.nn as nn
import windseer.utils as utils
import argparse
import numpy as np
import os
import torch
parser = argparse.ArgumentParser(
description='Script to plot a prediction of the network'
)
parser.ad... |
ec4c7f1feeec8acf74288b7479de5186e2827a09bc6cd876f0629d96fee7b2af | Python | 6,767 | 213 | """
Code for identifying Pfam domains and mapping Pfam
alignments and ECs into target sequence mode.
Authors:
Thomas A. Hopf
.. todo::
1. Write code to create list of family sizes
2. Implement alignments against Pfam-HMM so precomputed results can be reused in focus mode
"""
import gzip
import pandas as p... |
2297c36eefdc6577d6b24ef5732c2133df7ec74eae1d28265f605a919a6688e4 | Python | 6,770 | 138 | from Environment_ui import *
PARAMETER_DIR = 'pages/Registration/parameters'
def get_sitk_transform(elastix_param):
tf_type = elastix_param['Transform'][0]
image_spec = {'Size': [int(i) for i in elastix_param['Size']],
'Origin': [float(i) for i in elastix_param['Origin']],
'... |
949194e155dab4fa931b0210246817394a8fa60d1a1073f76a8a110ffbd7acae | Python | 6,771 | 184 | # 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... |
56c0c67fed0f9815d63eaa6cef233be5761b49e0901ffe1f97ab62cfbb399cac | Python | 6,779 | 219 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
#
# mol2vec documentation build configuration file, created by
# sphinx-quickstart on Mon Oct 30 21:41:26 2017.
#
# 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
# au... |
c25a72b38a3e7381da428645c8ad5aa8eb0632d9e5d0ccbfe7d6f4ba8360a607 | Python | 6,780 | 204 | from __future__ import absolute_import
from __future__ import print_function
import numpy as np
import time
import sys
import os
import six
import marshal
import types as python_types
import logging
def get_from_module(identifier, module_params, module_name,
instantiate=False, kwargs=None):
if... |
315856774e51a5672b464bcfba9eeca55e262e7b468df2f673996b47c69e88ee | Python | 6,783 | 225 |
import torch
import matplotlib.pyplot as plt
from tnn.utils import seed_everything
from examples.tensor_trajectories.utils import setup_circle_3D, setup_circle_3D_grid, split_data, DummyData
seed_everything(42)
# plot data to check classes
x, y = setup_circle_3D(n=2000)
# fig = plt.figure()
# ax = fig.add_subplot(pr... |
dd0dff60b7eb3dd6b0970b1d43a0b190c62af124b35ca848ee76f91d4a65cd8c | Python | 6,785 | 179 | import numpy as np
import pytest
from pandas.errors import Pandas4Warning
import pandas as pd
import pandas._testing as tm
from pandas.io.sas.sas_xport import XportReader
from pandas.io.sas.sasreader import read_sas
# CSV versions of test xpt files were obtained using the R foreign library
# Numbers in a SAS xport... |
b8399857a783a3f537efc96652fbbb5a766da51da5bd191fb06e18269c40eb03 | Python | 6,787 | 171 | """Common utility functions for rolling operations"""
from __future__ import annotations
from collections import defaultdict
from typing import cast
import numpy as np
from pandas.core.dtypes.generic import (
ABCDataFrame,
ABCSeries,
)
from pandas.core.indexes.api import MultiIndex
def flex_binary_moment... |
6372b56efed4d73c3c20b82104991ca8550516f76bd6cc87a17c008a6e45520c | Python | 6,789 | 170 | #!/usr/bin/env python2
# -*- coding: utf-8 -*-
"""
Sort multiecho DICOM for all subjects. This use the multiecho BEM from
https://github.com/mcvinding/mri_stuff/tree/master/multiecho_bem
"""
# Import
import os.path as op
import sys
import subprocess
sys.path.append('/home/mikkel/mri_scripts/multiecho_bem') # Path to... |
43a548cf94020273bbf7537120717bb1bad85eeb3adb38e97ef3495a64627f59 | Python | 6,791 | 160 | # Imports
from sklearn.metrics import confusion_matrix
from sklearn.preprocessing import StandardScaler
from sklearn.model_selection import train_test_split
from sklearn.linear_model import LogisticRegression
from sklearn.metrics import accuracy_score
from sklearn.decomposition import PCA
from sklearn.svm import... |
8ca359452ac86f69d207736072e843e9c27db02a9027fd6cea7a2524006093fc | Python | 6,792 | 148 | """Command-line interface for the detect command.
"""
from atropos.io import STDOUT, STDERR
from atropos.commands.cli import (
BaseCommandParser, positive, readable_url, writeable_file,
readwriteable_file, probability)
class CommandParser(BaseCommandParser):
name = 'detect'
usage = """
atropos detect -... |
e6be9c1103e9c5274c85922dddb0c90927492befbf7524bb7138e0e95666aab4 | Python | 6,792 | 185 | import sys
import os
import numpy as np
import torch
import torch.utils.data as du
from torch.autograd import Variable
import torch.nn as nn
import torch.nn.functional as F
import util
from util import *
class drugcell_nn(nn.Module):
def __init__(self, term_size_map, term_direct_gene_map, dG, ngene, ndrug, root, nu... |
f897b9e58556b455d36313a2ba273f97f534f074b6e25d34385f01f1ea72cfe1 | Python | 6,793 | 172 | from functools import lru_cache
from langcodes import Language, best_match
# Text in scripts written without spaces has to be handled specially in our
# tokenization regex (see TOKEN_RE in tokens.py). Also, when one of these is
# the script of the language we're analyzing, then we need to either have
# a specific tok... |
a64141a2da5133e20d74900ca0c3f5839527f0fb8da951539aad6fb29392bf59 | Python | 6,799 | 154 | import os
import pandas as pd
import numpy as np
import argparse
import pickle
import tensorflow as tf
import scipy.sparse as sp
from util import splitData, preprocess
from tensorflow.keras.models import load_model
def get_index(y, diff_mins, diff_maxs, cat, alpha=10, diff=None):
if diff is None:
upper = y... |
e0f7f1bb3fdc5e7bd81adf874948f05bf617acb8decc531d464ff9ab54f52a27 | Python | 6,805 | 227 | """
Core eval alignment algorithms.
"""
from __future__ import annotations
from functools import (
partial,
wraps,
)
from typing import TYPE_CHECKING
import warnings
import numpy as np
from pandas._config.config import _global_config as config
from pandas.errors import PerformanceWarning
from pandas.util._... |
7b39cdf254e8107496e258eb51c8b7a8da9b487ffbae0d1c8f8abe9d93094985 | Python | 6,811 | 175 |
import torch
from torch import Tensor
import torch.nn.functional as F
from torch.nn import Sequential, Linear, BatchNorm1d
import torch_geometric
from torch_geometric.nn import (
Set2Set,
global_mean_pool,
global_add_pool,
global_max_pool,
CGConv,
)
from torch_scatter import scatter_mean, scatter_a... |
08944d8f364a0ba790f0d6fceed928b77d625ff2e3171b10fac8e8f6ec1ba4c6 | Python | 6,812 | 207 | # 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... |
ea55830499b87e19affc836ef283ecaf30991c4d8cb65dd21e52da1bc17ee7c9 | Python | 6,812 | 172 | import os
import pysam
def extrack_somatic(vcf_path, output_folder, tool):
min_supports = [2, 3, 5, 8, 10, 15, 20]
# min_supports = [1, 2, 3, 5, 8, 10]
# min_supports = [15, 20]
# min_supports = [1]
for min_support in min_supports:
output_path = os.path.join(output_folder, vcf_path.spli... |
12ed20a67f2918e85665cc438192e3ed1f303602cee47f962912a4508b082060 | Python | 6,813 | 184 | from typing import Any, Dict, List, Optional, Tuple, Union
import numpy as np
import pandas as pd
from sktime.forecasting.base import ForecastingHorizon
PyCaretForecastingHorizonTypes = Union[List[int], int, np.ndarray, ForecastingHorizon]
def _check_and_clean_coverage(coverage: Union[float, List[float]]) -> List[f... |
9c27e27c995143c09bf891d0857cfff739dc433f87c02022e35c4b21425eaf64 | Python | 6,817 | 227 | import numpy as np
import scipy.sparse
import pandas as pd
from pandas import (
MultiIndex,
Series,
date_range,
)
from pandas.arrays import SparseArray
def make_array(size, dense_proportion, fill_value, dtype):
dense_size = int(size * dense_proportion)
arr = np.full(size, fill_value, dtype)
i... |
0d34be73a2aca799c75dddf465ceaf77141f5077fb159b06f6ff35e484e1ac0b | Python | 6,820 | 187 | from game_functions import Game, Game_Bayes
from game_functions import percentile_discrete
import numpy as np
import matplotlib.pyplot as plt
from matplotlib import cm, use
from helper_set_pi import set_pi
import sys
def plot_gamefit_and_distribution(xd,yd,xf,yf,pi,eps,whichdistrib):
fig, ax = plt.subplots(1,1,figsi... |
ceb2484786bbcaaaf7741840c5d10a213d6e5cb25c675bed9da0f84205a0a927 | Python | 6,821 | 169 | # 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... |
1e426129627593e06b837fa8b1c12e4060d5c1c15a612757cc91a85916a88497 | Python | 6,825 | 193 | #!/usr/bin/env python
import pegasus as pg
import demuxEM
import numpy as np
import scanpy as sc
import argparse
import pandas as pd
import pegasusio as io
parser = argparse.ArgumentParser(description="Parser for DemuxEM - Demultiplexing")
parser.add_argument(
"--rna_matrix_dir",
help="cellranger output folder... |
91a76e4c5b93d2d61170aa972abff55b9417589c76875991817f2a30d7c6b888 | Python | 6,825 | 196 | import torch
from torch import optim, autograd
import darts.functional as F
class Hyperparameters:
alpha_lr = 3e-4
alpha_wd = 1e-3
class Architecture:
def __init__(self, model, args, hyperparams=Hyperparameters(), device='cpu'):
self.momentum = args.momentum # momentum for optimizer of theta... |
a1ca73cd93e87c0c71e645c49a8f5b3f5ae28df8babad03acf98ed59822830ee | Python | 6,831 | 190 | import numpy as np
from scipy import optimize
def fit_circle(x, y):
'''
Fit a circle through a set of points with least squares optimization.
Parameters
----------
x : np.array
X-coordinates of the points
y : np.array
Y-coordinates of the points
Returns
-------
xc... |
e3f1e2904f055cfae19c01a7edf5017483fd6ef4cc83562b87a33fedfc11f852 | Python | 6,831 | 153 | # Imports
from sklearn.preprocessing import StandardScaler
from sklearn.decomposition import PCA
from scipy.stats import gaussian_kde
import numpy as np
import os
import matplotlib.pyplot as plt
import matplotlib.backends.backend_pdf
plt.style.use('seaborn-talk')
if __name__ == "__main__":
# Note about ... |
12e7a6da19ef1cfe15ed3da0a3bc6e4c38aee16e308c1a5a573eecae086e16f3 | Python | 6,833 | 240 | # -*- 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... |
b58e8e9c79256943fe73e6b612e2e992ccf1666166b60695c3afb5fa1afa5047 | Python | 6,833 | 198 | # 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... |
33d79e66cc4ece38559ad540447cffe609b1bd9bf3cbe78847c2c76e090d3ee7 | Python | 6,838 | 214 | import weakref
import numpy as np
import pytest
import pandas as pd
import pandas._testing as tm
from pandas.core.strings.accessor import StringMethods
# subset of the full set from pandas/conftest.py
_any_allowed_skipna_inferred_dtype = [
("string", ["a", np.nan, "c"]),
("bytes", [b"a", np.nan, b"c"]),
... |
96a6b48fb030cbedfdd16efeace885ddac59786b142e79d6cc9f5e3d7f7ad3bf | Python | 6,838 | 220 | import numpy as np
import pytest
import pandas as pd
import pandas._testing as tm
from pandas.tests.copy_view.util import get_array
# -----------------------------------------------------------------------------
# Copy/view behaviour for accessing underlying array of Series/DataFrame
@pytest.mark.parametrize(
"... |
02999e0a3fb019501c83a53381d3af27382a039f6a7714a634dc992603e8d2b0 | Python | 6,841 | 252 | # ---
# jupyter:
# jupytext:
# text_representation:
# extension: .py
# format_name: percent
# format_version: '1.3'
# jupytext_version: 1.16.0
# kernelspec:
# display_name: ol-connectome
# language: python
# name: python3
# ---
# %%
from pathlib import Path
import sys
from ... |
8bd30f20a2e6db71a6ae7905bad3b514a9cfe89b48e098e259d273bcde127499 | Python | 6,845 | 234 | import tensorflow as tf
from tensorflow.keras import Model
from tensorflow.keras.initializers import Orthogonal, TruncatedNormal
from tensorflow.keras.layers import ( # GlobalMaxPooling1D,; Lambda,
Add,
Dense,
Dropout,
GlobalAveragePooling1D,
Layer,
LayerNormalization,
MultiHeadAttention,
)... |
87d76485576aaabdff76e3687c9474424163e6ade12a00632aa62232021d3716 | Python | 6,846 | 201 | """Drift report CRUD — distribution-shift snapshots for a Deployment.
Routes under ``/api/v1/``:
POST /deployments/{deployment_id}/drift-reports record a snapshot
GET /deployments/{deployment_id}/drift-reports list snapshots
GET /drift-reports/{id} single snapshot
v1 semant... |
a7bd53767c5e3b2a53b15deba9bdc4bf74a8480389fc604622b35a41918a58c0 | Python | 6,848 | 167 | # coding: utf-8
from itertools import chain, starmap
from collections import Counter
import torch
from torchtext.data import Dataset as TorchtextDataset
from torchtext.data import Example
from torchtext.vocab import Vocab
def _join_dicts(*args):
"""
Args:
dictionaries with disjoint keys.
Return... |
89bf4452fe4e7211e6dfa488dd3e00b9c8bc703585a1e1bf742bc2476184add8 | Python | 6,849 | 189 | # 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... |
406b9f3523739b796d8bb007765e7a55952d60b50ede4c3257883d435ec3475f | Python | 6,850 | 198 | import numpy as np
import scipy as sci
import scipy.fftpack as ft
import scipy.signal as sig
from scipy.stats import norm
import matplotlib.pyplot as plt
''' Field Synthesis
Python-based demonstration of Field Synthesis
supplementary material to:
Universal Light-Sheet Generation with Field Synthesis
... |
bb0cd950f608ec886e2e8a310c071b68a9b21c56cd054a3a5ecdf391790e4896 | Python | 6,850 | 233 | """Webhook subscription CRUD.
Routes (under ``/api/v1``):
GET /workspaces/{ws_id}/webhooks
POST /workspaces/{ws_id}/webhooks
GET /webhooks/{id}
PATCH /webhooks/{id}
DELETE /webhooks/{id}
POST /webhooks/{id}/test
Admin-only writes; member can read.
Supported event types (v1):
- ``run.succeed... |
59d6dae6f779b9adc6a9df5b2301da671d44073b9d49e629b9aa02a6eb717c6e | Python | 6,854 | 221 | import pandas as pd
import numpy as np
import tensorflow as tf
from tensorflow.keras.preprocessing.text import Tokenizer
from tensorflow.keras.preprocessing.sequence import pad_sequences
from sklearn.model_selection import train_test_split
from sklearn.metrics import confusion_matrix, classification_report, accur... |
e5dfdae5a1a41cf0bdf546e0909103662084d025692975a5b1ec1aae641fbd82 | Python | 6,855 | 149 | # 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... |
0c15c20a3259b37142d029ad65f22492e7b7b086f5ea6a1f66718d096e4b2373 | Python | 6,857 | 158 | import argparse
import os
import numpy as np
import pandas as pd
from Bio import SeqIO
def get_args():
"""
Get arguments from command line with argparse.
"""
parser = argparse.ArgumentParser(
prog='Filter-Checkm2-Bins.py',
description="""Identify good bins from checkm2 scores.""")
p... |
b62313c0baa907b86d9fb81f4a5c1e342bbc601bcffda4f3917325429b8d06fb | Python | 6,860 | 209 | import msprime
import numpy as np
import optparse
import pyslim
import sys
import tskit
import global_vars
def main(opts):
reco_values = load_recos(opts.reco_path)
files = open(opts.infile, 'r').readlines()
n_regions = len(files)
n_range = range(n_regions)
# (N, 36, 198)
num_haps = opts... |
e63257f8a9465fdf2abde9b7f9c09bffb4604c90ce46cc3fad81bae1d2caa736 | Python | 6,864 | 152 | #!/usr/bin/env python
from model import UNet2d
from function import predict_volumes
from dataset import BlockDataset, VolumeDataset
from torch.utils.data import DataLoader
from torch.utils.data.sampler import SubsetRandomSampler
from torch.autograd import Variable
import torch
import torch.nn as nn
import torch.backend... |
21b53bb13b6c2ae904dd62cb9d6b58a02618362b4cb95611e5c30941e1a0a399 | Python | 6,873 | 208 | """Phase 5: GitRepository routes.
Endpoints:
- ``GET /workspaces/{ws}/git-repositories``
- ``POST /workspaces/{ws}/git-repositories``
- ``DELETE /workspaces/{ws}/git-repositories/{id}``
- ``POST /git-repositories/{id}/publish`` ← does the actual push
The publish endpoint runs synchronously for v1 (small wor... |
774b8f5bbd2a4797c1df112a72149afaa0cfde52bb63e7df5873477d6d4676e4 | Python | 6,873 | 186 | import numpy as np
import pygalmesh
from scipy.linalg import sqrtm
from scipy.spatial import Delaunay
from .surfaces import Surface
class Rectangle(Surface):
def __init__(self, corners = None, npt = 25, spacing = None):
super().__init__()
if corners is None:
self.corners = ([0,0,0], [1,... |
c03c104f1c3b5796bd56a6da57cc1ee2c5ced0d90d0b08f843ac0bc7c3415c46 | Python | 6,879 | 189 | """
Centralized logging configuration for Combinato.
Called once from __init__.py after options are loaded and merged with
local_options.
"""
import datetime
import logging
from logging.handlers import RotatingFileHandler
import os
import warnings
# Subsystems that get their own dedicated log file
_SUBSYSTEMS = {
... |
22a54ca870b33bc7c8ea2f3c05ac3335cf7ec94915420023dc4c1281c370cf0f | Python | 6,880 | 200 | import torch
import numpy
import matplotlib.pyplot as plt
import bionetwork
import plotting
import pandas
import saveSimulations
inputAmplitude = 3
projectionAmplitude = 1.2
#Setup optimizer
batchSize = 5
MoAFactor = 0.1
spectralFactor = 1e-3
maxIter = 5000
noiseLevel = 10
L2 = 1e-6
#Load network
networkList, nod... |
29e5a82a62f3651a8fa971c1962adfcb37a2aa7390c3bd59b9f9d55245dd8936 | Python | 6,883 | 195 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
input/output utilities
"""
import logging
from turtle import color
logger = logging.getLogger(__name__)
import os
import nrrd
from app.utils import cast_to_type
import SimpleITK as sitk
import numpy as np
def split_filename(filepath):
""" split a filepath into t... |
71ec58320d32c897e9f9b984c3ac7b3733ed303a6d99abb6588e87993720144d | Python | 6,883 | 189 | #!/usr/bin/env python
__author__ = 'etseng@pacb.com'
"""
Filter away 5' degraded products (isoforms that are shorter isoforms of longer ones)
3' differences are always honored.
If input is:
Isoform A: exon 1, 2, 3, 4
Isoform B: exon 3, 4
Isoform C: exon 3, 4, 5
Then Isoform A and C are preserved. Isoform B (degrad... |
30580f66921262e74b9551c11a189cb57aa9ef1f5b6323d03ff9cd42596ef659 | Python | 6,889 | 152 | import numpy as np
import pandas as pd
import time as clocktime
import pickle
################################################################
################################################################
## Load spike times for every cell, for every fstimulation
ncells = 16
spikes_set = []
for c in range(ncells):
... |
daa62357d4776c08ee4673f43683ab5fa45ad2037ab7418d81a36c52a5343532 | Python | 6,889 | 191 | ##############################################################################
## ##
## This file is part of ModelBlocks. Copyright 2009, ModelBlocks developers. ##
## ##
#... |
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