sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
41abee9e4e3d000bc80f495c2ecb70628ee69045bbc22f15641f791fb93dd52f | Python | 1,873 | 61 | import re
import numpy as np
import pytest
import pandas as pd
class TestDataFrameDelItem:
def test_delitem(self, float_frame):
del float_frame["A"]
assert "A" not in float_frame
def test_delitem_multiindex(self):
midx = pd.MultiIndex.from_product([["A", "B"], [1, 2]])
df = ... |
41493a1393e6ce69e1574df9a3f00983cf00cf7a2d64f5bc96b5e773bb493f79 | Python | 1,877 | 47 | import pandas as pd
import altair as alt
b_name = "OR"
name = "all"
font_size = 20
line_size = 5
glauc = pd.read_csv(f"output/pheno_match/glauc_sec/resnet_models/{b_name}_{name}_grouped.csv")
age = pd.read_csv(f"output/pheno_match/age/resnet_models/{b_name}_{name}_grouped.csv")
glauc["Phenotype"] = "Glaucoma"
age["P... |
8fb53d4a7440823e6446665f42c78bdf4557e8a42fbd897d63336fcfba3ca814 | Python | 1,877 | 56 | """Deterministic fake provider for tests.
Emits a stable shape matching `LLMAdvice`. Any test that wants to drive a
specific output can override the `canned_response` attribute before calling
`complete()`.
"""
from __future__ import annotations
from typing import Any
class FakeLLMProvider:
"""In-memory stand-i... |
1da047aa74395fa0f9195caa7a0b8f398ec77bc5cd88e1ba5298e947ff9c5721 | Python | 1,878 | 48 | """Migration to rename colon-separated time directories to hyphen-separated ones.
Addresses https://github.com/paninski-lab/lightning-pose/issues/278, where output directories
used HH:MM:SS format (e.g., ``outputs/2024-01-01/12:00:00``) which is invalid on Windows
and causes issues with some tools. This migration rena... |
72fcbfd5eb2651a06361609f76df8184a1dc46b43eda18eb78f88e42cdfed6c3 | Python | 1,878 | 56 | # JN 2015-09-10
"""
Imports that can than be used by the packages in this folder
"""
from __future__ import absolute_import, print_function
from .options import options, artifact_criteria
import os,sys
sys.path.insert(0, os.getcwd())
try:
from .options import raster_options
except ImportError:
pass
n_local = ... |
dfa15b934b7bfef7ce0fa6fd3174546290b03478ec27f18bc8b465047b6563f7 | Python | 1,878 | 45 | import torch
import torch.nn as nn
import torch.nn.functional as F
from dgl.nn.pytorch.conv import SAGEConv
class GraphSAGE(nn.Module):
def __init__(self,params):
super(GraphSAGE, self).__init__()
self.layers = nn.ModuleList()
self.dropout = nn.Dropout(params.gcn_dropout)
self.acti... |
a77106cd54b023db4f5cd342b0d96cb3a0b387846f432e4f13b9b3e75c033af7 | Python | 1,879 | 49 | import numpy as np
import pytest
import pandas as pd
import pandas._testing as tm
@pytest.mark.parametrize("method", ["union", "intersection"])
def test_setop_mismatched_category_order(method):
# GH#55335 unordered CategoricalIndex with same categories in different
# order should give correct results for uni... |
fe99c43616322e1ffb2f920f0a4aa5714ef21912f016c844b8aaa98b36a09ed6 | Python | 1,879 | 39 | import torch
from rl_games.common.diagnostics import PpoDiagnostics
def _batch(actions, mu, sigma, adv, **extra):
n = len(adv)
b = {'values': torch.zeros(n, 1), 'returns': torch.arange(n, dtype=torch.float32).unsqueeze(1),
'new_neglogp': torch.zeros(n), 'old_neglogp': torch.zeros(n), 'masks': None,
... |
43cf2d570964b2e6d46be3dd6ec8c50f78c0ca7cdfd6543803e2016027cbd162 | Python | 1,880 | 76 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Mon Oct 30 11:48:59 2023
@author: nrq2
"""
#%matplotlib inline
import scenicplus
scenicplus.__version__
import pickle
import scanpy
# Load functions
from scenicplus.scenicplus_class import SCENICPLUS, create_SCENICPLUS_object
from scenicplus.preprocessing.... |
5f9d030eb7b063b44a59cfddacfd5e4d71abdcfce5070ac12ba56f3726760066 | Python | 1,880 | 59 | import argparse
from pathlib import Path
import keras
import keras.backend as K
import numpy as np
from tqdm.auto import tqdm
from global_config import config
from ribosomal_autoencoder.model import load_ribosomal_autoencoder
def get_args():
parser = argparse.ArgumentParser()
parser.add_argument("-d", "--... |
9386f56b2f00b8289d56b71dcdd4c5133b23f4a80a4fa975fbe3808e1a9d7ed9 | Python | 1,881 | 62 | """Perform meta-analysis on images constructed from coordinates using the Peaks2Maps kernel."""
import logging
import os
import pathlib
import numpy as np
from nilearn.image import resample_to_img
from nilearn.masking import apply_mask
from nilearn.mass_univariate import permuted_ols
from ..base import MetaResult
fro... |
3549e1eb6314601655a37cb07161f644c0d715cfd49148a013835d808c67c044 | Python | 1,882 | 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... |
16cd0dc88b7a063196050a5bc03072c42ea58046e45ba4c92aded0e971e94e25 | Python | 1,883 | 54 | import argparse
import os
import shutil
def get_args():
"""
Get arguments from command line with argparse.
"""
parser = argparse.ArgumentParser(
prog='Filter-SemiBin.py',
description="""Identify any superbins (>100Mb) from semibin2 and move to a separate directory.""")
parser.add_ar... |
8e46f61bbefcabc8b2f5fdab0decfff58efbe7ee1c2a18efd3dbf3753a38ed56 | Python | 1,884 | 62 | """Sphinx extension that warns about lists indented relative to their context.
An indented list is parsed as a list inside a block quote, which renders with
extra indentation. Top-level lists should not be indented, and nested lists
should align with the text of their parent item.
"""
import re
from docutils import ... |
d29e9b36e9976d918892498f5e1d2f91efeb5987754bebf15dd6537029bd7124 | Python | 1,885 | 58 | import torch
import torch.nn as nn
from darts.api import Model
from darts.modules.linear.mixed_layer import MixedLayer
class Cell(Model):
def __init__(self, num_nodes, multiplier, cpp, cp, c, reduction, reduction_prev):
"""
:param steps: 4, number of layers inside a cell
:param multiplie... |
478f130a8f7693722685916ac42e35efb589e02e1634453a3700bff8376fdd6e | Python | 1,886 | 93 | 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):
... |
b4904c6b3413ef5c49e6e7ded1ba5a93f868211d721050895009162ce2ce28d1 | Python | 1,886 | 64 | import warnings
from secrets import randbelow
import config
import numpy as np
from tensorflow.keras.models import model_from_json
from utils import create_input_array
warnings.filterwarnings("ignore")
__all__ = ["allocate_encrypt_packet"]
# For every dataPacket allocate NNs and encrypt parallely.
def allocate_enc... |
53be70355b0accec1f06c41e3dfc84dab536bed7bdf715ab228172ede0dbeeb1 | Python | 1,888 | 57 | import tempfile
import os
import itertools as it
from nose2.tools import params
import chromosight.cli.chromosight as ccc
from docopt import docopt
COOL = "data_test/example.cool"
BED2D = "data_test/example.bed2"
OUTDIR = tempfile.TemporaryDirectory()
DUMPDIR = tempfile.TemporaryDirectory()
# Select a bunch of argumen... |
ca716af836e35fbc311ba806c7c72e95318cd6eaffd95365d886accc9267ec46 | Python | 1,896 | 62 | """Perform meta-analysis on images constructed from coordinates using the Peaks2Maps kernel."""
import logging
import os
import pathlib
import numpy as np
from nilearn.image import resample_to_img
from nilearn.masking import apply_mask
from nilearn.mass_univariate import permuted_ols
from nimare.base import MetaResul... |
2b84a4d501780c24b321d92c03e9022ad10304d409bfc515a3264ca78711c837 | Python | 1,897 | 59 | """Utility helpers used across training, inference, and evaluation.
**Submodules**:
- ``utils.io`` — path handling and file I/O utilities.
- ``utils.device`` — GPU-presence checks: selecting a ``pl.Trainer`` accelerator, and
guarding DALI-only semi-supervised training with a clear error.
- ``utils.predictions`` — i... |
a8fb819ca24f7e813f7dfd93561909665c7c71bf2cb37e36486d5e963931d7cf | Python | 1,897 | 45 | """
# Microbiome Analysis Powered By Recursive Quasi-species Networks:
Description:
Uncovering rules of organization, competition, succession and exploitation
---
## Installation:
```
pip install qbiome
```
or
```
pip3 install qbiome --user
```
## Notes:
Depends on the `quasinet`... |
1f689be82ea75663cff58868104d9932003619b9c7013fec062fbfabf9f3ac96 | Python | 1,899 | 67 | """
Illustrates how to calculate a distribution dI with vegas.
"""
from __future__ import print_function # makes this work for python2 and 3
import vegas
import numpy as np
import gvar as gv
gv.ranseed((1, 2, 3)) # causes reproducible random numbers
RMAX = (2 * 0.5**2) ** 0.5
# non-batch version
def fcn(x):
... |
022af4342923a9e9e9f051604575bc0ac3566be7e3508b528b62203bb28c72e7 | Python | 1,902 | 54 | import gymnasium as gym
import numpy as np
from rl_games.common.wrappers import MaskVelocityWrapper
class TestAsymmetricCritic(gym.Env):
def __init__(self, wrapped_env_name, **kwargs):
gym.Env.__init__(self)
self.apply_mask = kwargs.pop('apply_mask', True)
self.use_central_value = kwargs.p... |
8e7305fe6ac9056519c49656150b7ed466f77b95c79b86daed012b1dcb445d88 | Python | 1,903 | 84 | import gc
from importlib import import_module
import os
import numpy as np
import pandas as pd
# Compatibility import for lib
for imp in ["pandas._libs.lib", "pandas.lib"]:
try:
lib = import_module(imp)
break
except (ImportError, TypeError, ValueError):
pass
# Compatibility import fo... |
be2114cb8de8601f1291bc708dbf42c97b6cd3cf60e3fb65bf578fdd19aa166e | Python | 1,903 | 75 | # coding: utf-8
"""
Colorspace conversion routines.
Inspired by agapython/util/Dibase.py from Corona lite,
but reimplemented to avoid licensing issues.
Encoding Table
A C G T
A 0 1 2 3
C 1 0 3 2
G 2 3 0 1
T 3 2 1 0
"""
def _initialize_dicts():
"""
Create the colorspace encoding and decoding dictionaries.
... |
d96111abe1beda720e25cca03f221152739702f8421d005ba3ab623a53a0ff8c | Python | 1,903 | 57 | import os
import json
import concurrent.futures
import time
# 多进程 原始提取函数:18.002195835113525
# 多进程 改造提取函数:8.507536172866821
apkfilename = []
permission_frequency={}
path = r'E:\pythonProject\Experiment\out_benign_samples'
apk_list=os.listdir(path)
for apk in apk_list:
apk = os.path.join(path,apk)
a... |
1dc23bb7b0c4dcb20f626e807467432a4fc4d24e891fc810db9130b8557eeee1 | Python | 1,904 | 64 | import tensorflow as tf
from .wrappers import FrameStack, dmControlGetTasks, dmControlGymWrapper
class Process:
"""
Base class for processes
=================
Attributes:
env_name (str): the name of environment
render (bool): enable the rendering
"""
def __init__(
se... |
6d0170d14c33764f27697ebf8dacf0c8ea8da85890e3107e74a98d0426953fea | Python | 1,905 | 69 | # -*- coding: UTF-8 -*-
r"""
@Author : wlhuang
@Date : 2023/5/9 14:10
@Institution : CUbiCS, ICT, CAS
@Contact : wuliang.huang@outlook.com
@Description : Convert participant dataset to Aier platform compatible format.
"""
import re
import shutil
from pathlib import Path
yaml_content = r"""
attributes:
... |
47673772569cc99c0ff0168d8aa96777489ddbe07cac3dd78c93af6bb9969d2a | Python | 1,906 | 54 | import os
# import cloudpickle
import compatibility
from . import parent_classes
def check(obj):
'''checks wherther obj can be saved with this dumper'''
return obj is None #isinstance(obj, np) #basically everything can be saved with pickle
## this was used to store more data in the ManagedFolder
## it turned ... |
f59e334ea9ca0169f5abd29936fb8edc317aa2ccc78d0ad082d38e8a6bab59cb | Python | 1,907 | 70 | import pytest
from pandas.util._validators import validate_args
@pytest.fixture
def _fname():
return "func"
def test_bad_min_fname_arg_count(_fname):
msg = "'max_fname_arg_count' must be non-negative"
with pytest.raises(ValueError, match=msg):
validate_args(_fname, (None,), -1, "foo")
def te... |
7334c1a7853b234462fec5705c8aba2bdda59e540788a24cdbabbc610c8fcbd9 | Python | 1,908 | 74 | import os
import pathlib
import random
import sys
import unittest
import anndata as an
import numpy as np
import pandas as pd
import pytorch_lightning as pl
import sklearn as sk
import torch
from torch.utils.data import *
random.seed(42)
from os.path import abspath, dirname, join
sys.path.append(join(dirname(abspath... |
6fd9039acf2ed145d3ab60b2cb8cadf054b5e6293f04491ba29442b976a011ae | Python | 1,910 | 55 | from argparse import ArgumentParser
from atropos.modifiers import AdapterCutter, InsertAdapterCutter
from atropos.adapters import AdapterParser
from atropos.seqio import open_reader
adapter_parser = AdapterParser()
A1 = adapter_parser.parse('AGATCGGAAGAGCACACGTCTGAACTCCAGTCACACAGTGATCTCGTATGCCGTCTTCTGCTTG')
A2 = adapt... |
864a175543db0129055a7f1b195216b227977c8ad6eac6def4bd0489311ed772 | Python | 1,911 | 59 | import os
import time
import json
import concurrent.futures
# 对于so文件的提取
# 没有lib文件夹就打标为NULL
# 多进程 每次处理20个 开16进程 2.0976274013519287
apkfilename = []
permission_frequency={}
path = r'E:\pythonProject\Experiment\out_benign_samples'
apk_list=os.listdir(path)
for apk in apk_list:
apk = os.path.join(path,apk... |
9397a8dd23c2a8a717c4c2ce45ff7af40733df5e9df3a6a97fec21ffb2baec39 | Python | 1,911 | 56 | # 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... |
c606cb1dea895695d2fc111ea437c2da5d19edeab1dea72bd12d67468a4c6982 | Python | 1,911 | 57 | import pandas as pd
import os
from os import path
from glob import glob
from base.shapeAnalysisPipeline import Pipeline
from base import loggingUtils
def makeFileList(dataDir):
files = glob(dataDir+ '/*.vtk')
dct = {'id':[], 'path_left':[], 'path_right':[], 'path_left_lmk':[], 'path_right_lmk':[], 'visit_numbe... |
0f9af973ccbe32b7b754afc951447d155d75b5881ed25781359d9da4ea3477d0 | Python | 1,912 | 55 | import importlib.resources
from PyQt6 import uic, QtCore, QtWidgets
class DlgSlotReorder(QtWidgets.QDialog):
pipeline_changed = QtCore.pyqtSignal(dict)
def __init__(self, pipeline, *args, **kwargs):
super(DlgSlotReorder, self).__init__(*args, **kwargs)
ref = importlib.resources.files(
... |
1bba623b470f85daa2120687e41653c19e64619ca754bbbb9bd27e51bee10123 | Python | 1,914 | 48 | import os
import logging
import json
import torch
def initialize_experiment(params, file_name):
"""
Makes the experiment directory, sets standard paths and initializes the logger
"""
params.main_dir = os.path.join(os.path.relpath(os.path.dirname(os.path.abspath(__file__))), '..')
global_exps_dir =... |
a6dc3bf8cd13cc4ab6ba5e2870f52347a0b1060f8ad2464b1011652d1426d7a1 | Python | 1,916 | 62 | # -*- coding: utf-8 -*-
"""
T1 segmentation
"""
import logging
logger = logging.getLogger(__name__)
import os
import numpy as np
from skimage import morphology
import nrrd
from app.processing.preprocess import hist_perc
from app.processing.morphops import closing_and_fill, erosion_2D, labelsize
def and_brain_hems(p... |
5907cb12ad2a5c989dc0bd57b1e50bcf020ad189f0ab1b91d473a2d2b1189bed | Python | 1,918 | 60 | # 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... |
bc3084a9f189e770f111f75cfc40ef644dbb3939126f389bea82995f4484b471 | Python | 1,918 | 58 | """Session 33 — Git auto-publish on Run complete + Phase 14 GPU queue
Revision ID: e5f6a8b9c0d1
Revises: d4e5f6a8b9c0
Create Date: 2026-05-17 13:00:00.000000+00:00
Two small additive columns; no data migration needed.
1. ``git_repositories.auto_publish`` (bool, default False) — when set,
the orchestrator's ``reco... |
999d5eb9bd1edf5685052441ce0dd21d5001a66fd917cb993fdc1c8ac73a6db8 | Python | 1,920 | 76 | # -*- coding: utf-8 -*-
"""
Created on Tue Mar 8 14:31:15 2022
@author: System 6
"""
import pycromanager_tessie as pmt
# Start platform:
platform = pmt.microscope.platform.Platform(load_synchronizer=True)
# Set LED ring
#platform.neopixel.color(red=int(255/4))
#%% Calibrate DMD:
platform.neopixel.shutter(True)
pl... |
30784fde79f4c11c8346b23b3d67e2fa49f0cdd5d7791259672be1e9e70113e3 | Python | 1,922 | 56 | #!/usr/bin/env python
import os, sys
from collections import defaultdict, Counter
from cupcake.io.GFF import write_collapseGFF_format
from cupcake.io.BioReaders import GMAPSAMReader
def main():
from argparse import ArgumentParser
parser = ArgumentParser("Convert SAM to collapsed GFF format")
parser.add_ar... |
63e95669e43ff226493a430160213c4145e1a2023b697eaf7910250b71ef3dfa | Python | 1,922 | 71 | #! /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... |
c2d4237c7f87a67cc444e41fc55e984367fca8c02c1847ba5ee5b02f5196f6f0 | Python | 1,922 | 106 | """
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,
maybe_warn_co... |
5c0b45151b8c90371631449fd234f98272f7d4bb1aa939e8c8ad9f6dbfaf83a3 | Python | 1,923 | 40 | import torch.nn as nn
from torchvision.models import convnext_base, ConvNeXt_Base_Weights, convnext_tiny, ConvNeXt_Tiny_Weights
def ConvNext_model(args, diff=False):
"""
Load ConvNext model.
Parameters:
- args (dict): Dictionary containing model arguments, where 'model' specifies the model type.
... |
16f01c473030625baeb875019c11c532b2073f283d8ec51cc9437b12d9fbaf5f | Python | 1,926 | 84 | import argparse
import copy
import numpy as np
from pathlib import Path
import pickle
from sklearn.linear_model import Lasso
from sklearn.metrics import r2_score
from sklearn.metrics import mean_absolute_error
from model.data import Dataset
parser = argparse.ArgumentParser(description='Predict property using Energy ... |
5be27f719b8b5e204b742b2cd352551b1aad6d9ee9dd4d4eac795c7bc063a137 | Python | 1,928 | 54 | #Run sweeps over time constants
import numpy as np
from placerg.funcs import *
from placerg.funcsrg import *
from placerg.objects import *
from placerg.runfunc import *
N0 = 1024*4 # number of cells
percell= 1.0 # probability that each field is accepted
phi=1.0 # multiply by this constant to adjust overall activity... |
0d5b7281e01b9e66eed1703faa9d89165b8834e3f91fd699fdf308cc19dd02ef | Python | 1,929 | 49 | import pytest
import pandas as pd
import pandas._testing as tm
def test_add_prefix_suffix(float_frame):
with_prefix = float_frame.add_prefix("foo#")
expected = pd.Index([f"foo#{c}" for c in float_frame.columns])
tm.assert_index_equal(with_prefix.columns, expected)
with_suffix = float_frame.add_suffi... |
17136b7d6416624e431b1d6690bb90114b8d50b875d3437915155222b877dd88 | Python | 1,930 | 42 | # 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... |
2fae007399a0ea4c49e39c44d2ad85c6a8db5c4023bb1d18a11b410ba290bf93 | Python | 1,932 | 57 | import numpy as np
import pandas as pd
import pandas._testing as tm
def test_head_tail_generic(index, frame_or_series):
# GH#5370
ndim = 2 if frame_or_series is pd.DataFrame else 1
shape = (len(index),) * ndim
vals = np.random.default_rng(2).standard_normal(shape)
obj = frame_or_series(vals, ind... |
bf4a8c7c9b5f48969f729ac5a4e94444c831b36cb2ed998cd9c1f12606f750a9 | Python | 1,932 | 72 | #%%
#Imports
import numpy as np
import os
import matplotlib.pyplot as plt
from matplotlib.gridspec import GridSpec
plt.style.use('seaborn-talk')
import pandas as pd
from sklearn.preprocessing import StandardScaler
from sklearn.decomposition import PCA
from scipy.stats import gaussian_kde
from src.vizualization impor... |
e4a3efa2a764f751f372ce83ee756642b1f695cdb0b98bd80f1fefa7ca64221a | Python | 1,932 | 45 | # 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... |
396ddde08ee5bd81cc41d3daa82845f308ce25c16c8faf16b587113d5b712232 | Python | 1,933 | 62 | # -*- coding: utf-8 -*-
"""
T1 segmentation
"""
import logging
logger = logging.getLogger(__name__)
import os
import numpy as np
from skimage import morphology
import nrrd
from app.processing.preprocess import hist_perc
from app.processing.morphops import closing_and_fill, erosion_2D, labelsize
def and_brain_hems(p... |
956a6f5bfe2b0284091472f8b39049e2a6aa0ca44d3043368f3d7e9d1f0f7b53 | Python | 1,935 | 72 | #!/usr/bin/env python
from __future__ import print_function
import windseer.data as data
import windseer.nn as nn_custom
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'
)
parse... |
81ccfa72ecbe3920ebf41aec2bad3dc9f84bf1bd9e4ba263293db2d3caa8fac5 | Python | 1,936 | 80 | from pathlib import Path
from typing import List
from os import environ
from argparse import ArgumentParser
from pprint import pprint
from MutComputeX.inference import EnsembleCIFPredictor
def cli():
parser = ArgumentParser()
parser.add_argument(
"--data",
required=True,
type=Path,
... |
02e89394b54ccdd2f9413c5bce9a8a4e850d4199fb958e0b0ee7f22c4bf41017 | Python | 1,937 | 32 | ##############################################################################
## ##
## This file is part of ModelBlocks. Copyright 2009, ModelBlocks developers. ##
## ##
#... |
557d09ef62a6bdb10b6aa5569a94ba32932134583661a0c8cc8dfd7fcf7f86e0 | Python | 1,937 | 43 | from botocore.client import Config
import ibm_boto3
# import types
import os
import sys
import pdb
import pandas as pd
import numpy as np
import pickle
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 ... |
93fe8b7e3cf3e3791286fb8630e7e154de54792984aee524d9c6d8c7c1cfb4ea | Python | 1,937 | 72 | import numpy as np
import pandas as pd
import pandas._testing as tm
from pandas.tests.copy_view.util import get_array
def test_clip_inplace_reference():
df = pd.DataFrame({"a": [1.5, 2, 3]})
df_copy = df.copy()
arr_a = get_array(df, "a")
view = df[:]
df.clip(lower=2, inplace=True)
assert not... |
84d2ed919e4f1fee74820e703556ded7c1822c6e3674ec64829c365bc87866a3 | Python | 1,938 | 58 | from datetime import datetime
import pandas as pd
import pandas._testing as tm
from pandas.tseries.holiday import (
AbstractHolidayCalendar,
USFederalHolidayCalendar,
USMartinLutherKingJr,
USMemorialDay,
)
def test_no_mlk_before_1986():
# see gh-10278
class MLKCalendar(AbstractHolidayCalenda... |
b1044c86c7b84167bbfd927c8e934414762993d203750a2236b68eab3f48daf5 | Python | 1,938 | 65 | """
Three Gaussians spread along the diagonal of a six-dimensional hypercube.
This coding style for the integrand is the simplest but also gives the
slowest runtime. It is made 3x faster by using nproc=8 processors, but
is still slower than faster.py and fastest.py (using nproc=1 processor).
"""
from __future__ imp... |
930ad62cd68cbefb0dd221d338f2d0fa3c780c90241f333c4ce13b94b9f23c25 | Python | 1,939 | 59 | import sys
import tempfile
import unittest
import inspect
from pathlib import Path
REPO_ROOT = Path(__file__).resolve().parents[1]
sys.path.insert(0, str(REPO_ROOT))
from treeshrink.alignment import MultiLocusDataset
from treeshrink.sequence_lib import hash_taxon_seq
from treeshrink._vendor import dendropy
class P... |
cf36774dfe9f610e6af6d4b530bddde3092fa8f2d1566c165471a847dc80941c | Python | 1,940 | 69 | """
Functions for handling sequence
identifiers in alignments
Authors:
Anna G. Green
"""
import re
from collections import defaultdict
from evcouplings.align import read_fasta
ID_EXTRACTION_REGEX = [
# example: >UniRef100_H6SNJ6/11-331
"^Uni\w+\_(\w+).*/",
# example: >tr|Q1NYN0|... |
25823fc6130d16df63e291961d642f5e5dea5eccb12f6c7e98a0b2828c3ed798 | Python | 1,941 | 72 | # -*- coding: utf-8 -*-
"""
Created on Mon Sep 27 09:53:59 2021
@author: Noelia Martínez-Molina, adapted from code provided by Yonatan Sanz-Perl at CNS, UPF
"""
import numpy as np
import matplotlib.pyplot as plt
plt.style.use('ggplot')
subjects=['VIS','SM','DAT','VAT','LIM','CNT','DMN']
HC_TBI3=[40,43,... |
676b36a4931e12cb7aac191af38bc8aadb23ba78b6bd021a2d693ae569ae53dd | Python | 1,942 | 58 | import numpy as np
import pytest
import pandas as pd
import pandas._testing as tm
class TestTimedeltaIndex:
def test_misc_coverage(self):
rng = pd.timedelta_range("1 day", periods=5)
result = rng.groupby(rng.days)
assert isinstance(next(iter(result.values()))[0], pd.Timedelta)
def te... |
5cf4221a53d3ea4b04cf262e29fbba939bf1ce9e7941414b41e920235b30eddd | Python | 1,943 | 76 | """
Functions for generating input to Haddock webserver
Authors:
Anna G. Green
"""
def haddock_dist_restraint(resid_i, chain_i, resid_j, chain_j,
dist, lower, upper, atom_i=None, atom_j=None,
comment=None):
"""
Create an ambiguous restraint string for u... |
7f9b5a61eb28bbfb4aca0738c2ab80ef9f1baff997b82506aec592ba37373d0d | Python | 1,943 | 51 | # Copyright 2019 Division of Medical Image Computing, German Cancer Research Center (DKFZ), Heidelberg, Germany
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://w... |
11322ad766c3717d4392e05f8fb3270c19f2d397f7936319f2dcc618715808df | Python | 1,944 | 57 | import datetime
import os
date = datetime.date.today()
throwaway_script = 'batch_script.slurm'
group = 'spe'
k_vals = [0.0001]
l_vals = [6]
d_vals = [10.0]
for k in k_vals:
for l in l_vals:
for d in d_vals:
f = open(throwaway_script,'w')
job_name = 'train_hgram_l='+str(l)+'_k='+s... |
34681179406de7fe39e6ad9c96ad21d533d7a349db9cdc49f79ece8402918dbe | Python | 1,944 | 54 | '''
Contains the character class
'''
import warnings
warnings.filterwarnings("ignore")
class Character:
'''
Contains all parameters for a given character
'''
def __init__(self, opt):
'''
Initialises character class.
opt should contain the following keys:
'identity'... |
1a6f2579ce81150d84aa456754dcaf428f8ca22b7ff00a7887fe0b8bf72559c9 | Python | 1,946 | 65 | from tensorflow import keras
from tensorflow.keras import layers
import tensorflow as tf
from tensorflow.python.keras import utils
def add_default_block(x, kernel_filters):
s = layers.Conv2D(kernel_filters, (1,1), padding='same')(x)
s = layers.BatchNormalization()(s)
s = layers.Activation('relu')(s)
x... |
2e00012d4a210c3b5cfd8885c6d2f121b3fbbce572d8509eff384bf3daa68712 | Python | 1,946 | 41 | """Supervised and semi-supervised loss functions for pose estimation.
Loss names follow a ``{domain}_{variant}`` convention. The full registry is returned
by :func:`get_loss_classes`; the names below are the strings used in config files under
``cfg.model.losses_to_use`` and ``cfg.model.heatmap_loss_type``.
*Supervis... |
40bf42315353601e8ba64bd9b186ca0f0e123cb2941643d3a5c0e14b64972dcb | Python | 1,948 | 67 | __all__ = ["GlycoPeptideRTTreeLSTM"]
from typing import Any, Mapping
import torch
from dgl.nn.pytorch.glob import GlobalAttentionPooling
from torch import nn
from ...util.attention import AttentionSum
from ..common.data import GlycoPeptideDataBatch
from ..common.model import GlycoPeptideTreeLSTM
class GlycoPeptide... |
ebba007f501d25f6a69e14055682d30f0beb9dcb0fc52cccffaa24d821c2ed9d | Python | 1,948 | 55 | import os
import numpy as np
import pandas as pd
def get_CRISPRi_LINCS_dataset(feature_selection):
"""
Get the CRISPRi-LINCS dataset for the given feature selection method.
We have pre-selected 1000 features (genes) that are common between the CRISPRi and LINCS datasets.
"""
root_dir = "download/d... |
f4d0af42ab01075611e6e1a393a9adca28cf2e972879aa0cc07c9080306e9827 | Python | 1,948 | 57 | import pytest
from scripts.check_for_inconsistent_pandas_namespace import (
check_for_inconsistent_pandas_namespace,
)
BAD_FILE_0 = (
"from pandas import Categorical\ncat_0 = Categorical()\ncat_1 = pd.Categorical()"
)
BAD_FILE_1 = (
"from pandas import Categorical\ncat_0 = pd.Categorical()\ncat_1 = Catego... |
62104c66f2129893ca2f937694da88fd4d285150589860f6839972008224e5ce | Python | 1,949 | 49 | import json
import numpy as np
import scipy.io as scio
from scipy import sparse
import scipy
# 输入权限打标（仅仅是权限是否出现）矩阵，输入权限-权限类型json文件
# 输出权限-权限类型打标矩阵（出现的权限属于哪个权限组） 0-8对应 data3定义的危险权限组信息，9就是普通权限
def read_info(i1, data2, data3):
flag = 0
value0 = list(data2.values())[0]
for i in i1:
if i == 1:... |
75abd664b9051a45612e96a0c64c6c6ba79304fc90c3bbb8a41d6e759a07ea17 | Python | 1,949 | 67 | # JN 2015-05-08 adding docstrings to this old, useful code
"""
Simple signal filtering for spike extraction
"""
from __future__ import absolute_import, division
import numpy as np
from scipy.signal import ellip, filtfilt
# pylint: disable=invalid-name, unbalanced-tuple-unpacking, E1101
DETECT_LOW = 300 # de... |
fa3783762465e679a3f723ff8771f0e5cfb98cfee00ee840bee508fe49f418fc | Python | 1,949 | 66 | """
You perform a sequence simulation in IDEA (Siemens), make a sequence plot,
and save the save as .txt.
Then you can use this script to plot a nice looking sequence diagram
for presentations or papers.
Author:
Zhengguo Tan <zhengguo.tan@gmail.com>
"""
import matplotlib.pyplot as plt
import numpy as np
import ... |
5f204b9e64050480587dedea3c601a9435b5e6a45ee126510e6372ef99952562 | Python | 1,950 | 59 | from espnet2.bin.asr_inference import Speech2Text
import argparse
import numpy as np
import wave, time, os
def get_args():
parser = argparse.ArgumentParser(description="", formatter_class=argparse.ArgumentDefaultsHelpFormatter)
parser.add_argument("--wav_path", help="path to wav audio", required=True)
prin... |
b9ccc0afb45a09fc9db65210cbea6d23b05acf51fb643a21bfbf2adc9ea01c13 | Python | 1,951 | 59 | # 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... |
ba515c6776134ef4848d0ab1de78979c5b12b163faa6e4bad1d3525442080bc8 | Python | 1,952 | 51 | import numpy as np
import h5py
import scipy.io as spio
import sys
from symmetrized_kld import SymmetrizedKullbackLeiblerDivergenceGaussians
def compute_space_closeness(train_model_fname, test_model_fname):
'''
This script is used to compute latent space distance between states from BSDS models
Inputs:
trai... |
044cd5032dc71d582c3d8c6b9eb0da9202332d8ebea03b201c2af32763d74b51 | Python | 1,953 | 57 | import os
import types
import warnings
import pytest
import pandas.util._exceptions as pue
_SRC = (
"import warnings\n"
"from pandas.util._exceptions import find_stack_level\n"
"def caller():\n"
" warnings.warn('boom', UserWarning, stacklevel=find_stack_level())\n"
)
@pytest.mark.parametrize(
... |
6246959847e3379efad41527632f1c890e4289c2d8a5bef3ea387bd9dc4b8ae5 | Python | 1,953 | 52 | import numpy as np
import torch
import os
class EarlyStopping:
"""Early stops the training if validation loss doesn't improve after a given patience."""
def __init__(self, save_path, save_name, patience=7, verbose=False, delta=0):
"""
Args:
save_path (string):
patience ... |
e8c0cc8b24626f862052cbd8d7d0c4b9d524139269aaa0e1eda954ae011ad6cc | Python | 1,953 | 55 | import hydra
from hydra import compose, initialize
from hydra.core.hydra_config import HydraConfig
from omegaconf import DictConfig, OmegaConf
from isaacgymenvs.utils.reformat import omegaconf_to_dict
OmegaConf.register_new_resolver('eq', lambda x, y: x.lower()==y.lower())
OmegaConf.register_new_resolver('contains', ... |
0500412d7975adb0cf85e8c2aecf3bef46e9aba30d8cd546dbaf304ab5f4cce0 | Python | 1,954 | 55 | """
Guard for the pandas base ExtensionArray test suite.
Third-party ExtensionArray authors run the tests in ``pandas/tests/extension/base``
against their own array by subclassing them, and copy
``pandas/tests/extension/conftest.py`` to get the fixtures those tests request.
That only works while the base tests stay cl... |
cad9e42b118740d13071792fd5e7df8c680c7f8ad88207f9196796ecb806f51d | Python | 1,954 | 47 | import numpy as np, matplotlib.pyplot as plt, sys
plt.rc('xtick',labelsize=14)
plt.rc('ytick',labelsize=14)
plt.rc('axes',labelsize=14)
to_paper = "--to-paper" in sys.argv
a = np.loadtxt("fpbase_spectra.csv").T
l = a[0]
ex = a[1]
em = a[2]
a = np.array([[0.9179,-10.5946],[0.9829,-10.5946],[1.0526,-10.5946],[1.1272,... |
4b2d4624faedc9f2f813b87408e714bb1424b2c0d12b3442340325025d8cdaca | Python | 1,955 | 52 | # -*- coding: utf-8 -*-
# Copyright (C) 2019 Andrea Vázquez Varela
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#... |
e6d79176762b1dad06020d7f873d8427eb71742ecaa44f823e7b91b09cbb661b | Python | 1,955 | 58 | __all__ = ["GlycanComparer"]
import functools
from typing import cast
from .glycans import GlycanNode, MonosaccharideCollection
class GlycanComparer:
def __init__(self, monosaccharides: MonosaccharideCollection):
self.monosaccharide_order = list(monosaccharides.keys())
self._compare_sorted_glyca... |
9ae3ca6a22fd3bf8f986b93ae7aa96dd8d8479f286c9216581cceb3817f78fcb | Python | 1,956 | 69 | import argparse
import numpy as np
import pandas as pd
parser = argparse.ArgumentParser()
parser.add_argument("--input_path", type=str, default="data/aggregated/concat/fpt.csv")
parser.add_argument(
"--save_path", type=str, default="data/aggregated/concat/fpt-del.csv"
)
def _add_prev_info(
bccwj_eyetrack: p... |
b8e61a57f620d13e538616872ba025bf5df4eb3e10f0a66835c21de6742eb253 | Python | 1,956 | 58 | import numpy as np, matplotlib.pyplot as plt
import pumpprobe as pp
ds_list = "/projects/LEIFER/francesco/funatlas_list.txt"
signal_kwargs = {"remove_spikes": True, "smooth": True,
"smooth_mode": "sg_causal",
"smooth_n": 39, "smooth_poly": 1,
"matchless_nan_th": 0... |
60e1b8a11f57e2437c1948ee4537d7014372dd67480617a2204bed56c7c28eef | Python | 1,957 | 68 | #!/usr/bin/env python
'''
Change the size of a dataset
'''
from __future__ import print_function
import argparse
from windseer.data import change_dataset_compression
import time
def main():
'''
Main function which parses the arguments and then calls convert_data
'''
parser = argparse.ArgumentParser(... |
c567420b9f950504e23d64513ccd88406464a57c961d906515fe8d7910b35b9f | Python | 1,958 | 64 | """K-space trajectory from .seq file class."""
from pathlib import Path
import torch
from einops import repeat
from mrpro.data.KTrajectory import KTrajectory
from mrpro.data.SpatialDimension import SpatialDimension
from mrpro.data.traj_calculators.KTrajectoryCalculator import KTrajectoryCalculator
class KTrajector... |
012ad1611347c166c44d24729cf6d65f2cedfe866a1c8437dd16493784eeedfb | Python | 1,959 | 29 | # Test the preparation of a brain slice data.
from Environment import *
from Parameter import *
def slice_test_data(image_patch_path, label_patch_path, channel, save_test_path, patch_num, test_id):
for i in range(1, patch_num + 1):
file_path = os.path.join(image_patch_path, 'PatchImage_' + channel, 'patchi... |
c940b9640879e163c8647e3a3059f681345a664f351710c5ef3c0c63a9a62437 | Python | 1,959 | 50 | # Copyright (c) 2021-2023, 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... |
362d4297e2ce3346d14ac0027482c22c05e7391cc0c03701e6aac4f02c25aa9a | Python | 1,960 | 66 | # -*- coding: utf-8 -*-
# flake8: noqa
"""Installation script."""
#------------------------------------------------------------------------------
# Imports
#------------------------------------------------------------------------------
import os.path as op
import re
from setuptools import setup, find_packages
#-... |
8c2a70f694759fd1659e0878f44aa665f33cd76ba5dc2c7ab21b35c38ae62a3b | Python | 1,960 | 72 | import typing
from collections.abc import abc
import torch
import numpy as np
import pandas as pd
class TrainingHistory:
def __init__(self):
self.data = []
def add(self, epoch_result):
""" Add a datapoint to the history """
self.data.append(epoch_result)
def frame(self):
... |
5308ef33c0de3c2f1323e9c4bb666e3600ec6cb6240cfa74b4b8156b840a1b70 | Python | 1,962 | 49 | # Grad-CAM
from ..utils.process import get_last_conv_layer
import numpy as np
import tensorflow as tf
from tensorflow.keras.layers import Conv2D, Conv3D
from skimage.transform import resize # for N-dimensional images
def get_grad_cam(model, io_imgs, class_id, LAYER_NAME=None, MODALITY="FLAIR", XAI_MODE="classificatio... |
f21a04df9c1ec86dd6408d1164112912b61f4a63fe9d0d352edcb10d9b72f860 | Python | 1,962 | 61 | from Environment_ui import *
from scipy import ndimage as ndi
from skimage import measure
def label_coords(binary_image):
labeled_img = measure.label(binary_image, connectivity=1)
properties = measure.regionprops(labeled_img)
coords_list = []
for pro in properties:
coord = pro.coords
co... |
5ff120ad94a517780797e8f80d3f343bfb10879e34a7202e58268e0eb8ad07b1 | Python | 1,963 | 49 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
# from distutils.core import setup
from setuptools import setup, find_packages
import changeseq
## conda skeleton can't find readme
import os
if os.path.isfile("README.MD"):
with open("README.MD", "r") as fh:
long_description = fh.read()
else:
long_description="change-... |
d9ffc295e264b371b31d4b168ba1a51db6a3521ce13f8cdfaf6f20dea094c8cc | Python | 1,963 | 59 | """Test nimare.decode.continuous.
Tests for nimare.decode.continuous.gclda_decode_map are in test_annotate_gclda.
"""
import pandas as pd
import pytest
from nimare.decode import continuous
from nimare.meta import kernel, mkda
def test_CorrelationDecoder_smoke(testdata_laird):
"""Smoke test for continuous.Correl... |
995a929c86b12be14a7acd9ef8e3353023cc7bacac065d0434d92c3c750a60e6 | Python | 1,965 | 57 | # 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... |
4823e756fceefd3ea62aeb32bc50e390f1c71734f990e40985d3714d1bf86ebb | Python | 1,966 | 62 | import numpy as np, matplotlib.pyplot as plt, sys
import pumpprobe as pp, wormdatamodel as wormdm
plt.rc('xtick',labelsize=14)
plt.rc('ytick',labelsize=14)
plt.rc('axes',labelsize=14)
ds_list = "/projects/LEIFER/francesco/funatlas_list.txt"
funa = pp.Funatlas.from_datasets(
ds_list,merge_bilateral=Tr... |
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