sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
0f114a5d8c2d36207462f4417b27e74308da897f9b7c28737381c36c9010604d | Python | 5,565 | 158 | """
End-to-end auth flow against a running API using Fief.
Required environment variables (test is skipped if any is missing):
CODECARBON_API_URL Base API URL (e.g. https://api.dev/codecarbon/api)
FIEF_TEST_USER_EMAIL Login email for the test user
FIEF_TEST_USER_PASSWORD Login password for th... |
2889cecf003a30685a265556aec6f3e0a17cd0d994f154f72e97ce22f238da6e | Python | 5,565 | 112 | #==============================================================================#
# Author: Dominik Müller #
# Copyright: 2024 IT-Infrastructure for Translational Medical Research, #
# University of Augsburg ... |
7a98f9b7988886b8eb93dc179dc265e4e85c099e8763958031c52cbe260aa261 | Python | 5,565 | 105 | import numpy as np
from rdkit import Chem
from rdkit.Chem import AllChem
import torch
import pandas as pd
from torch_geometric.data import Data
class MolecularGraphData:
def __init__(self):
self.permitted_list_of_atoms = ['C', 'N', 'O', 'S', 'F', 'Si', 'P', 'Cl', 'Br', 'Mg', 'Na', 'Ca', 'Fe', 'As', 'Al', '... |
b9e1b994e4f30cbf5efbdef5daad72ccaecbcc53d7191ef03d7e5de008700f9b | Python | 5,567 | 150 | # ------------------------------------------------------------------------------
# Copyright (c) Microsoft Corporation. All rights reserved.
# Licensed under the MIT License.
# ------------------------------------------------------------------------------
from __future__ import absolute_import
from __future__ import d... |
3356dfebf3da599005a095347aa371beb3ef214b1093275d2d01667d90c86d91 | Python | 5,568 | 145 | import os,pickle
import numpy as np
from args import *
from model import *
from trainer import Trainer
from dataset import load_dataset_random
from utils import *
import warnings
from argparse import Namespace
from BatmanNet.util.utils import get_model_args
warnings.filterwarnings("ignore")
def load_args(p... |
9e62c679e094728184807cd2a59d1b97db81899e8b967a57dd39ac0c56b94692 | Python | 5,568 | 164 | from keras.src import backend
from keras.src.api_export import keras_export
from keras.src.optimizers import optimizer
@keras_export("keras.optimizers.Lamb")
class Lamb(optimizer.Optimizer):
"""Optimizer that implements the Lamb algorithm.
Lamb is a stochastic gradient descent method that
uses layer-wise... |
d0303acbe09d0ee1f63e3343decadd496ddb570bf5db9b82cb677dc669d12922 | Python | 5,568 | 183 | model = dict(
type='SwAV',
backbone=dict(
type='ResNet',
depth=50,
in_channels=3,
out_indices=[4],
norm_cfg=dict(type='SyncBN'),
zero_init_residual=True,
init_cfg=dict(type='Pretrained', checkpoint='torchvision://resnet50')),
neck=dict(
type='S... |
d8d4827e80300811e38102822fb0302c00f78374b88cfde15c69943a3daff134 | Python | 5,568 | 184 | from __future__ import print_function, division, absolute_import
import math
import torch
import torch.nn as nn
import torch.nn.functional as F
import torch.utils.model_zoo as model_zoo
pretrained_settings = {
'cafferesnet101': {
'imagenet': {
'url': 'http://data.lip6.fr/cadene/pretrainedmodels... |
3f88ea6bb585a81365b43bd2138975162721215613e1e8115f10ba1891523523 | Python | 5,569 | 159 | """Utilities for data."""
from copy import deepcopy
from typing import Any
import gymnasium as gym
import numpy as np
from neurogym.envs.registration import make
class Dataset:
"""Make an environment into an iterable dataset for supervised learning.
Create an iterator that at each call returns
inp... |
442698b0a9d622541a278909e43c972ddfbd6f63af8aef6644e765199116026d | Python | 5,570 | 147 | """F03 ledger memo item 5: bundle.vary — one explicit edit or identity per member.
Pins: complete coverage by default (typed preflight refusals BEFORE any
mutation), explicit None identity distinguishable from unmentioned, sugar
normalization, whole-mapping donor-group normalization (one reused
SamplingPlan = one dono... |
bd0f94543173d47db2d2a8ddbcf7593fb381c55dbb49a186b7987ca2f596eaf4 | Python | 5,571 | 175 | import numpy as np
import os
from sklearn.metrics import mean_squared_error
import matplotlib.pyplot as plt
import h5py
import tensorflow as tf
plt.switch_backend('agg')
def rev_comp(x):
return np.flip(x, 1)[:, :, [1, 0, 3, 2]]
def apply_rev_comp(X_train, alpha=0.5):
X = X_train.copy()
np.random.see... |
0fe897d095b4302e59593f376a3edb54ccdc58a9106eb0f8f0d9c5167f5f5b1c | Python | 5,573 | 167 | """Paddle object-module hierarchy tests."""
from __future__ import annotations
import pytest
paddle = pytest.importorskip("paddle")
import torchlens as tl # noqa: E402
from torchlens.validation.invariants import check_metadata_invariants # noqa: E402
pytestmark = pytest.mark.backend_paddle
class PaddleScale(pa... |
6a1f2a81e12cc6e2e5d7829343a8fcb2a7b5a4894a9fc0a7e76998aa9ea57c8f | Python | 5,573 | 144 | # -*- coding: utf-8 -*-
# @Time : 2021/11/18 22:40
# @Author : zhao pengfei
# @Email : zsonghuan@gmail.com
# @File : run_mae_vis.py
# --------------------------------------------------------
# Based on BEiT, timm, DINO and DeiT code bases
# https://github.com/microsoft/unilm/tree/master/beit
# https://github.c... |
3952e3b311883fc2d94b7088a5decf70552d23d97aafe0f4b65171d534e78c90 | Python | 5,575 | 145 | import os,pickle
import numpy as np
from elegans_args import *
from model import *
from trainer import Trainer
from dataset import load_dataset_random
from utils import *
import warnings
from argparse import Namespace
from BatmanNet.util.utils import get_model_args
warnings.filterwarnings("ignore")
def loa... |
840b67bba979b55b7637bd24a2713f0f03918ba4d71f0e69d5f1401e552a0c57 | Python | 5,575 | 168 | """Observe-kit items 2-3: execution-order compare() + the isolated-rerun harness.
Pins the two shipped-surface repairs the observe memo sequenced FIRST:
``compare()`` rows follow execution order (never alphabetical), and the
shared double-run harness releases each fresh model copy so double-run tools
work on an alread... |
c3d39f2955b7aad0b62cffa3b7c39b77b18fb42968466cf9c217a9fd2fb9801f | Python | 5,575 | 159 | import pytest
import torch
from lightly.models import utils
from lightly.utils import dependency
if not dependency.timm_vit_available():
# We do not use pytest.importorskip on module level because it makes mypy unhappy.
pytest.skip("TIMM vision transformer is not available", allow_module_level=True)
from li... |
9989fc13ae4e05c4afdc63c1f9c37bef692da3cc5e1758cd79e50d226aa991fa | Python | 5,578 | 141 | """CI gate for the stage-1 mode-vs-wrapper differential harness.
Runs ``tools/differential_capture.py`` cross-process (the mode side must
observe PRISTINE torch, which this pytest process — with torchlens wrapped —
cannot provide) and asserts an op-for-op aligned verdict for every corpus
model. Also unit-tests the ali... |
59c9f047e3f8878b3356dd56f557a32fb72f77c15cfaf866cc8cd28a736d235e | Python | 5,579 | 146 | """Anti-recurrence test for cert10 ``tl.swap_with`` string-label honesty fix.
``tl.swap_with(<string label>)`` was publicly documented as working (README,
docs/for-ai-agents.md, docs/intervention_api.md) but was dead code: the only
resolution path depended on ``hook.run_ctx["swap_sources"]``, a dict that no
execution ... |
71b3be049b95cf7a2fbd9ab03074e2017b73f9cf7353b01c562a1fd1a4f27228 | Python | 5,579 | 174 | from itertools import chain
import pytest
from eelbrain import datasets, plot
from eelbrain.plot import _base
from eelbrain.plot._base import Layout, ImLayout
from eelbrain.testing import skip_on_windows
from eelbrain.testing import hide_plots
def assert_layout_consistent(layout):
if layout.margins is None:
... |
2ea3075ff80869cf8c3e9be32a24a8306b6f285363fafb52767caa36eef539c3 | Python | 5,580 | 175 | import os
import sys
import numpy as np
import torch
import torch.nn.functional as F
import torchvision.models as models
from stack import train as stack_train
class StackModel:
def __init__(self, root, loss, lam, output_stack, detach=False):
assert output_stack in [1, 2, 3, 4]
self._output_stac... |
e86e4bd84e72502bff98883446bc388fd2f97967d2193d8d0fd62ddc80841f84 | Python | 5,580 | 183 | import attr
from matplotlib import pyplot as plt
from permacache import permacache
import numpy as np
import scipy.special
from modular_splicing.utils.plots.plot_psam import render_psams
from .motif import Motif
@attr.s
class PSAMMotif(Motif):
log_psams = attr.ib() # log-affinities; (num_motifs, width, 4)
... |
c55830aa80bb335f62dbc238946144e81f5d349c130cf9ddcd584c2176677fe9 | Python | 5,581 | 167 | import threading
import random
import sys
import torch
import torch.multiprocessing as multiprocessing
from torch.utils.data import DataLoader
from torch.utils.data import SequentialSampler
from torch.utils.data import RandomSampler
from torch.utils.data import BatchSampler
from torch.utils.data import _utils
# from t... |
0dbb2451ebd8d2939e2efd09c12d3e558f7e71070b5e5e54034ed4a0ce55277d | Python | 5,582 | 143 | """Bounding box visualization functions."""
from __future__ import absolute_import, division
import numpy as np
import mxnet as mx
from . import plot_bbox, cv_plot_bbox
def plot_keypoints(img, coords, confidence, class_ids, bboxes, scores,
box_thresh=0.5, keypoint_thresh=0.2, **kwargs):
"""Vis... |
2b81faf09a9d8568db7c5608982a5ba6cd22173eb3f265d11e32489633966126 | Python | 5,582 | 157 | # Author: Christian Brodbeck <christianbrodbeck@nyu.edu>
import numpy as np
from numpy import newaxis
from scipy.ndimage import generate_binary_structure
from .._data_obj import Dimension
class Connectivity:
"""N-dimensional connectivity"""
__slots__ = ('struct', 'custom', 'vector')
def __init__(self, d... |
8e92bc617396910106650494b15da477c276b77c4b17917308f15d01b69a7e96 | Python | 5,583 | 144 | '''
Copyright 2021 Twente Medical Systems international B.V., Oldenzaal The Netherlands
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... |
b402bd0b89b87250f932bf4b8e2bec7af7130a8ebdc3ff5a0bba3865e9984173 | Python | 5,583 | 170 | from __future__ import annotations
import json as _json
import typing as t
from ..globals import current_app
from .provider import _default
if t.TYPE_CHECKING: # pragma: no cover
from ..wrappers import Response
def dumps(obj: t.Any, **kwargs: t.Any) -> str:
"""Serialize data as JSON.
If :data:`~flask... |
d9542de468a5b144f8a8a39960a0067aeab374a3a4fbe7bb09ff23ae73e24843 | Python | 5,584 | 146 | '''
Copyright 2021 John Veillette (https://gitlab.com/john-veillette)
Copyright 2021 Twente Medical Systems international B.V., Oldenzaal The Netherlands
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... |
3009378bcc14dea1d053246eea9a8493ce9417ef81d5bd3efbac07ebac186806 | Python | 5,586 | 150 | from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
from __future__ import unicode_literals
import numpy as np
import tensorflow as tf
import pandas as pd
import argparse
import os
import time
import sys
import pwd
import csv
import re
import deepchem
import pic... |
3cbae75c33a8a3e1b8070c979140ea1c023fb0ec924b2991578213cf646abce1 | Python | 5,586 | 164 | """Device-time consumers (torchnative W2.3): hot_path, color_by, size_by.
The joined table feeds the shipped surfaces as COLUMNS, never schemas: the
session-time join registry serves ``hot_path(by="device_time")`` and
``draw(color_by=/size_by="device_time")``; a trace with no joined session
refuses typed (``device_tim... |
caa2a8a650a41df0a62f457616206d53928e3200479a75388263ca5fa2dcb769 | Python | 5,586 | 150 | from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
from __future__ import unicode_literals
import numpy as np
import tensorflow as tf
import pandas as pd
import argparse
import os
import time
import sys
import pwd
import csv
import re
import deepchem
import pic... |
01ecc3df990c3978364df35b9127751740f247a6c38f51048e510fe4f1dd26dd | Python | 5,587 | 150 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Mon Jul 5 19:22:06 2021
@author: Audrey Mazancieux
This script performes several "event-related" analyses for one subject using
LC time serie that have been extracted from ROI delineated in native
space and then translated in this space.
This script nee... |
70f5450418ca006a9400e85183de6cd086271f8f3029ef44568d05992bc173e4 | Python | 5,587 | 167 | import sys
import math
import json
import numpy as np
CMAP = [
[244, 109, 67],
[253, 174, 97],
[254, 224, 139],
[217, 239, 139],
[166, 217, 106],
[102, 189, 99],
]
# out of range colors
CMAP_OOR = [
[215, 48, 39],
[26, 152, 80],
]
SKELETON = """
%s
\\begingroup
\\renewcommand{\\arra... |
b3ab4617dcc981cede3724d4c99b92158811e3dc5811b323c87c4230dec90bef | Python | 5,587 | 186 | """Workflows for generating plots from imaging data."""
from nipype.interfaces import fsl
from nipype.interfaces import utility as niu
from nipype.pipeline import engine as pe
from niworkflows.engine.workflows import LiterateWorkflow as Workflow
from xcp_d import config
from xcp_d.config import dismiss_hash
from xcp_... |
b7a402377626ae6de5087640b7ae8f0e76040ce1837ca91c9868845916e17535 | Python | 5,587 | 193 | import os
import re
import inflect
from tqdm import tqdm
import numpy as np
import scipy.io.wavfile as wave
from nltk.tokenize import sent_tokenize
from nltk.tokenize import word_tokenize
special_words = {
"english": {
"grown-ups": "grownups",
"grown-up": "grownup",
"hasn't": "hasnt",
... |
c2d65666145c4e27aaa383063ca0d4ce40271760c902382b080aa775c63d5d38 | Python | 5,587 | 172 | # --- THIS FILE IS AUTO-GENERATED ---
# Modifications will be overwitten the next time code generation run.
from plotly.basedatatypes import BaseLayoutHierarchyType as _BaseLayoutHierarchyType
import copy as _copy
class Smith(_BaseLayoutHierarchyType):
_parent_path_str = "layout"
_path_str ... |
e111ad6029bea7978aa8553fdc1dd78e73c08c6dde879c1112cd68d5f52a879d | Python | 5,587 | 172 | import copy
import json
import pandas as pd
import sys
import torch
import pytorch_lightning as pl
import numpy as np
from monai.metrics import DiceMetric
from pathlib import Path
from torch.utils.data import DataLoader
from argparse import ArgumentParser
from survival_plus_x.data.dataset import GensheimerDatasetInM... |
e6934af51f7628c64a9dad19d197828d4ebe329f2579d028acf5fb564f6a113d | Python | 5,587 | 184 | import sys
import argparse
import logging
import time
def pase_info(seq):
info = {'SVLEN': 0, 'END': 0, "SVTYPE": '', "RE": 0, "CHR2": ''}
for i in seq.split(';'):
if i.split('=')[0] in ["SVLEN", "END", "RE"]:
try:
info[i.split('=')[0]] = abs(int(float(i.split('=')[1])))
except:
pass
i... |
fd096af1dd229c8e0cbde3dc8897217bbae3f9b2e377d4cef6c2de6486735ab2 | Python | 5,590 | 146 | from typing import List
from uuid import UUID
from carbonserver.api.errors import (
NotAllowedError,
NotAllowedErrorEnum,
NotFoundError,
NotFoundErrorEnum,
UserException,
)
from carbonserver.api.infra.repositories.repository_organizations import (
SqlAlchemyRepository as OrganizationRepository,... |
bbb658accce48079af3d9f326cfc8743c0d03e421137e6d851969391b92f2a2a | Python | 5,591 | 191 | #!/usr/bin/env python
#=========================================================================
#
# Copyright NumFOCUS
#
# 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://... |
8d7b643dd6353b3c58c6364baa7426280eae596f96d72747994577bf7019c10b | Python | 5,592 | 181 | # Read package version in pyproject.toml
# Also provides version coherence checking across multiple files
import argparse
import logging
import re
import sys
import tomllib
logging.basicConfig(level=logging.INFO, format="%(message)s")
PACKAGE_VERSION = "X.X.X"
def get_version_from_file(filepath: str, pattern: str) ... |
a80f477d531978ef634fde3d4b37c5695874efa116adf0b814729d1c30a6a831 | Python | 5,592 | 173 | """Utilities related to importing modules and symbols by name."""
import os
import sys
import warnings
from contextlib import contextmanager
from functools import lru_cache
from importlib import import_module, reload
from importlib.metadata import entry_points
from kombu.utils.imports import symbol_by_name
#: Billiar... |
26899ca6a16480a8b7f117b3137a058a213a98ae0e5b736fe7c4e4c101753429 | Python | 5,593 | 150 | import argparse
import glob
import os
from collections import defaultdict
import mne
import numpy as np
import pandas as pd
import seaborn
from mne.datasets import fetch_fsaverage
from tqdm import tqdm
import pylab as pb
def main():
np.set_printoptions(precision=3)
np.set_printoptions(suppress=True)
np.s... |
acf15d7e9e1bc9ab3692f2b8b02bf6eb24dc90ee4129bf94c0d0ebe5f207160d | Python | 5,593 | 151 | import argparse
import matplotlib.pyplot as plt
import pandas as pd
import plotly
import plotly.graph_objs as go
from galaxy_ml.model_persist import load_model_from_h5
from galaxy_ml.utils import clean_params
from sklearn.metrics import (
auc,
confusion_matrix,
precision_recall_fscore_support,
roc_curv... |
0c336ccc1e51a27ff66d0db63ad4782b6abaa96643297c255e7e56704f2191d0 | Python | 5,595 | 110 | #==============================================================================#
# Author: Dominik Müller #
# Copyright: 2024 IT-Infrastructure for Translational Medical Research, #
# University of Augsburg ... |
b2c36d9e8093bdd6921e88ffe894e0275b52f75d3d82bc503a312d3574557b37 | Python | 5,595 | 165 | # Copyright 2023 Blue Brain Project, EPFL.
# See the top-level LICENSE file for details.
#
# SPDX-License-Identifier: Apache-2.0
"""Define node and data types used in parser and ast generator
While generating ast and visitors we need to lookup for base data types,
nmodl blocks defining variables, nmodl constructs tha... |
e5720ea309db6b6a4012a33d9128907a6b0947a16cf0f139ca4e13ed7bbd4e1c | Python | 5,595 | 154 | from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
from __future__ import unicode_literals
import numpy as np
import tensorflow as tf
import pandas as pd
import argparse
import os
import time
import sys
import pwd
import csv
import re
import deepchem
import pic... |
67f01f8d590daab1eed79a03c4518780f46ad0180a31d98d4c4593cf3bf0c2a7 | Python | 5,596 | 150 | """F10 lovely item 8/9: edge semantics (D28) + stats_table polish laws.
The two axes are independent: ``expand``/``split`` are VIEWS that change
the multiset; ``clone``/``contiguous`` copy/re-layout the SAME one. Every
uncertain case is fail-closed -- an absent mark is honest, a wrong mark
is not; ``data_ptr`` never p... |
81f3ad38575526d3d7889c6ee7b5ba93135ea7e9b1b0fafc8a67f3434682abe5 | Python | 5,596 | 145 | """r55 hon_2 + hon_1-consumer immunizers -- the load-side taint classifier (W2 lane).
hon_2 (MED, unsound sanitizer): the r53 ``out=`` taint sanitizer dropped the
destination's uninitialized-memory taint at ANY ``out=`` write, on the false
assumption of exact value semantics. ``torch.add(a, x, out=a)`` computes ``a + ... |
ef13a6236e439f68d71d20f8b69859a81ae8edd5d88343db16af9a010b072f5d | Python | 5,596 | 157 | """
The evaluation function.
"""
from argparse import Namespace
from logging import Logger
from typing import List
import numpy as np
import torch
import torch.utils.data.distributed
from BatmanNet.data.scaler import StandardScaler
from BatmanNet.util.utils import get_class_sizes, get_data, split_data, get_task_names... |
1ab806f260b161cfc7e75cf88ca8f3a5db20670c64a3a9a1daa2eeb871074790 | Python | 5,597 | 212 | import numpy as np
import logging
try:
from picamera.array import PiRGBArray
from picamera import PiCamera
except:
logging.warning("Could not load picamera module")
import multiprocessing
from ethoscope.tracking.cameras import BaseCamera
from ethoscope.utils.debug import EthoscopeException
import time
... |
df99d5ffc6f11bc65503cdfba09f17be6d386c767bdea60158d4fefa8d8a2e37 | Python | 5,597 | 168 | #!/usr/bin/env python
"""
detector.py is an out-of-the-box windowed detector
callable from the command line.
By default it configures and runs the Caffe reference ImageNet model.
Note that this model was trained for image classification and not detection,
and finetuning for detection can be expected to improve results... |
9cb88471186c96c66e1881b1c0ab14fcf4177ef1aac803ebae3cef9da813f1a1 | Python | 5,598 | 159 | # coding=utf-8
# Copyright 2025 The Google Research Authors.
#
# 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 applicab... |
c917d8e188cb98a63d61896c5a04d0b73ca959b7e0754953a6235d43cbb550b9 | Python | 5,601 | 136 | import os
import re
import glob
import torch
import random
import datetime
import numpy as np
from transformers import GPT2LMHeadModel, WEIGHTS_NAME, CONFIG_NAME
from irnlm.models.gpt2.modeling_hacked_gpt2_integral import GPT2LMHeadModel
from irnlm.models.gpt2.modeling_hacked_gpt2_semantic import GPT2LMHeadModel as G... |
6edbfb3e47798f97584fc4a48ed4c08fa733820216ab4d5bae767174cdb3606f | Python | 5,602 | 191 | """Tests for fastlog predicate normalization and RecordContext construction."""
from __future__ import annotations
from dataclasses import asdict
import pytest
import torch
from torchlens.capture.predicates import (
_evaluate_keep_op,
_module_capture_spec,
_normalize_capture_decision,
)
from torchlens.c... |
7a0ed064a8febd43f8ffd580680463f350eb7d44e859b31521f1953a9ce19e33 | Python | 5,602 | 137 | from __future__ import print_function
from typing import Tuple
import numpy as np
import pandas as pd
def GetSimISyntheticData(NG: int = 15, G: int = 1000, N: int = 100, noiseLevel: int = 0, ngroups: int = 3) \
-> Tuple[pd.DataFrame, np.ndarray, np.ndarray]:
'''
Generate synthetic data.
:param ... |
d772d8aee0d2a7fd3c2eeddcd9ac1071cfe26e53d67909be8603f2ba6388a971 | Python | 5,602 | 165 | # SOURCE: vendored from xianchaoxiu/SPCA-Net @ d8364f530908c20e0327be64378a8ac0923bf52e
# https://raw.githubusercontent.com/xianchaoxiu/SPCA-Net/main/SPCA-Net/demo.py
#
# SPCA-Net ("Tuning-Free Structured Sparse PCA via Deep Unfolding Networks",
# L. Chen & X. Xiu, 2025 44th Chinese Control Conference (CCC 2025)). The ... |
738c74d1efd0a1557455da649b81a375203870995f7a10fdabae1ab8f12fdc34 | Python | 5,603 | 174 | import numpy as np
import pandas as pd
from anndata import AnnData
from scipy.stats import spearmanr
from ...utils import _read_graph
def detect_transition_markers_clades(
adata: AnnData,
clade: int,
cutoff_spearman: float = 0.4,
cutoff_pvalue: float = 0.05,
screening_genes: list[str] | None = No... |
ca49fb88dd72cf2d13c705d2e463777bbf73b399cc2b2eb9a18de9dfe12654db | Python | 5,604 | 152 | #!/usr/bin/env python
# =============================================================================
# MODULE DOCSTRING
# =============================================================================
"""
Quaternion product transformation for autoregressive normalizing flows.
"""
# ================================... |
e2cfe1e5046ebcbace44d897eccd2a43e15cc4262a449ed4cfb513b85a51375d | Python | 5,606 | 131 | # 3D DICOM to 2D jpeg File for the LIDC data
import glob
import pydicom as dicom
import cv2
import numpy as np
# ============================== Image ===========================================
# ------------------- DICOM Image to Numpy Array (+Houndfield) ------------------------------
def get_pixels_hu(scans):
... |
7993adceed3ab224c9a36857491e3fc38f49d29fd978444915855c2426fdb4cb | Python | 5,609 | 201 | """Model fixtures for the TorchLens performance benchmark suite."""
from __future__ import annotations
import os
from pathlib import Path
from typing import Any, Literal
import torch
from torch import nn
DeviceName = Literal["cpu", "cuda"]
ModelName = Literal["tinynet", "resnet18", "gpt2_hf", "gpt2_hooked", "small_... |
2d13a7247aad61e0e798b4c767fb1ddc3adee382bdacc03b8f318a6d82afcb7c | Python | 5,610 | 117 | from typing import Optional, Union
from anndata import AnnData
try:
from typing import Literal
except ImportError:
from typing_extensions import Literal
def morphopath(
adata: AnnData,
vf_key: str = "VecFld_morpho",
key_added: str = "fate_morpho",
layer: str = "X",
direction: str = "forw... |
6e539f159d607a69fbe76a42b797bc85ca89fea8a811ac8bd59fd3db8934ab60 | Python | 5,610 | 151 | """Group Norm implementation"""
import torch
import torch.nn as nn
import torch.nn.functional as F
from torch.nn import Module, Parameter
from torch.nn import init
__all__ = ['GCN', 'NaiveGroupNorm']
class Conv2D(nn.Module):
"""Inline Conv2D for GroupNorm module"""
def __init__(self, in_channels, out_channel... |
875b88148932c7c534a983f7cae4c80ba3b3939ccd659d0e9191861562d50c26 | Python | 5,610 | 187 | from functools import lru_cache
import os
from types import SimpleNamespace
import attr
import numpy as np
import h5py
import tqdm.auto as tqdm
from permacache import permacache
from .gene_dataset import create_gene_dataset
from .hsmm_model import HSMM
from .substring import substring_hsmm
from .fill_gaps import fill... |
39c5b3613a0ad42e35dd51abe98da7883d12dd712e40161a6abf5e8ceaddfa52 | Python | 5,611 | 144 | import math
import warnings
from typing import List
from torch import nn
from torch.optim import Adam, Optimizer
from torch.optim.lr_scheduler import _LRScheduler
class LinearWarmupCosineAnnealingLR(_LRScheduler):
"""Sets the learning rate of each parameter group to follow a linear warmup schedule between warmup... |
949a4beaff380e4924497cbbec776e66357ae48681a57069a7cd6645b5e93b72 | Python | 5,612 | 158 | # -*- coding: utf-8 -*-
"""
Created on Wed Feb 15 20:55:52 2023
@author: longzheng
"""
import torch
import torch.nn as nn
from torch.utils.data import DataLoader
from torch.optim import Adam
from oil.utils.utils import LoaderTo, islice, cosLr, FixedNumpySeed
from oil.tuning.args import argupdated_config
from oil.tu... |
fb1271bade2b5f7ded4f3706a171e8721aca96d4d5dc744a1efd6696682c96b6 | Python | 5,612 | 186 | from pathlib import Path
import matplotlib
from matplotlib import pyplot as plt
import numpy as np
from typing import Optional, Union
from anndata import AnnData
import os
from stlearn._compat import Literal
def add_mask(
adata: AnnData,
imgpath: Union[Path, str],
key: str = "mask",
copy: bool = False... |
bccd559e9559fa9a7cbd453b61af0702ee1560419f70d37fc5a132e03d369072 | Python | 5,613 | 177 | from permacache import permacache, stable_hash
import numpy as np
import tqdm.auto as tqdm
import scipy.stats
from modular_splicing.evaluation.predict_splicing import predict_splicepoints
from modular_splicing.data_for_experiments.standardized_sample import (
standardized_sample,
)
@permacache(
"modular_s... |
74c804ee3d272363f74dce4c2762555139fc7cf33a27387c89fd62d8c19bee70 | Python | 5,614 | 160 | # ------------------------------------------------------------------------------
# Copyright (c) Microsoft Corporation. All rights reserved.
# Licensed under the MIT License.
# ------------------------------------------------------------------------------
from __future__ import absolute_import
from __future__ import d... |
114899d91a1110d65391bdb1558d3af8467cd296a60f51a48ab0fe8a697439bb | Python | 5,615 | 158 | # Copyright (c) 2020. Lightly AG and its affiliates.
# All Rights Reserved
from math import ceil
from typing import Any, Dict, Tuple
import torch
from lightning_utilities.core.imports import RequirementCache
from torchvision.transforms.v2 import CenterCrop, ConvertBoundingBoxFormat, Transform
from torchvision.tv_tenso... |
81bf04b3e2e3ac4c10423e251d3a70581eb2e7b142c34d40c52940cb27189db5 | Python | 5,615 | 160 | import torch
import torch.nn as nn
import torch.nn.functional as F
from ..base import _layers as layers
from ..base import _blocks as blocks
from ..base import _towers as towers
class Jores21CNN(nn.Module):
"""
Custom convolutional model used in Jores et al. 2021 paper
PyTorch implementation of the Tenso... |
23c07adb5cc54744bbec90830b2dfe7610680dcbd3bccf402bbcc489ba104ec3 | Python | 5,618 | 165 | import argparse
import sys
import os.path
from os.path import dirname, join
from os.path import join
from tqdm import tqdm
import pandas as pd
import pickle as pkl
import sys
import warnings
import scipy.stats
import numpy as np
import joblib
import json
repo_dir = dirname(dirname(os.path.abspath(__file__)))
def get... |
be5cd0f83c5e5fce91b0c38ed721f8ce3d0617821c9cf74e60a45567cbfaaa01 | Python | 5,618 | 185 | """
Simple scikit-learn interface for finetuning a single linear layer on top of LLM embeddings.
"""
from numpy.typing import ArrayLike
import numpy as np
from scipy.special import softmax
from sklearn.base import BaseEstimator, ClassifierMixin, RegressorMixin
from sklearn.linear_model import LogisticRegressionCV, Ridg... |
03c7667059fb8ed69d7aa788a5c5de4363a6c33c6eb26d89690a3e592c34659e | Python | 5,619 | 142 | """
Python utils intended to correctly format the texts associated with the
results shown to the user. The text adapts to the result range and its unit.
"""
from blueprints.translation.translation_dicts import TRANSLATIONS_DICT
def format_energy_text(energy_needed: float):
"""
Adapt the value and unit of the ... |
b922b7a135abe67061779436dfdcd19b4025927679b81e598b09dc1cc9eba3e7 | Python | 5,620 | 142 | # -*- coding: utf-8 -*-
"""
Created on Wed May 13 08:41:56 2020
@author: Caterina Brighi
"""
#%% Import functions
import matplotlib.pyplot as plt
import matplotlib as mpl
import SimpleITK as sitk
import numpy as np
import pandas as pd
import datetime
import os
import glob
import gzip
import shutil... |
e7079a9b2ed7d3633ce4700900cf810ae8eb62d4b6e05dd7c7d22724c3945b32 | Python | 5,620 | 167 | #!/usr/bin/env python
# coding: utf-8
### Libraries
# conda install -c anaconda pandas
# conda install --channel conda-forge --channel bioconda pybedtools
# pip install xlrd==1.2.0
import sys
import csv
import argparse
import pandas as pd
import numpy as np
import pybedtools
np.random.seed(5)
parser = argparse.Arg... |
901c29e7417130a9dfe75a50ba7057c3bba575a233ba9ce55dde03924656f6e5 | Python | 5,621 | 159 | import torch
import torch.nn as nn
from typing import Dict
import torch.nn.init as init
from .._utils import get_layer
from motifdata import to_kernel
from motifdata import MotifSet
from typing import Union, Callable, Optional, Any, Tuple, List, Literal
INITIALIZERS_REGISTRY = {
"uniform": init.uniform_,
"nor... |
d7b0b3267b44b500419c7ba7eabc838a24db590274ed4b98688153c40cde24ea | Python | 5,622 | 157 | import os
import cv2
import glob
import shutil
import numpy as np
import pandas as pd
from tqdm.auto import tqdm
import torch
import torch.nn as nn
from torch.utils.data import DataLoader
from utils.data_loader import PatchDataset
class ListPatchDataset(PatchDataset):
def __init__(self, df, transform):
... |
fd3735289a221f5aae2cbf1547cb67c759f061e831c02473178a9787636908e9 | Python | 5,622 | 185 |
# we need asyncio, apparently?
import asyncio
from multiprocessing import Process, Queue, Event
import logging
import time
def handle_data(queue,data):
# do the time-stamp thingy + put it into the queue.
timestamp=time.time()
markertext = data.decode("utf-8")
queue.put([timestamp, markertext])
... |
26e408793306a95efb65f1e5f4d34861f170928a675d0f47b23785450af7bc47 | Python | 5,623 | 151 | """R11/R32: a FAILED capture's escaping trace drops its capture transients.
The success arms pop ``_output_attribution_input_tensors`` (live USER INPUT
tensors) and postprocess replaces the mutable ``capture_events`` alias with the
payload-free ``_capture_events`` home. The failure/interrupt arms reached
neither, so t... |
8ece3611ff5a21741592c75c05ef35e3de1a9afbc5261ebba1a721c8595d7638 | Python | 5,626 | 214 | ## some routines for filtering
import numpy as np
from scipy import signal
from scipy import ndimage
from numba import jit
import itertools as itt
from ..core import ifnot
from .dctsplines import l1spline,l2spline,sp_decompose
from .dctsplines import l2spline_thresholded
#from .dctsplines import dct_denoise_img
fr... |
2f54f153a3aa8ae6ad19c0fe86623544600db520ff6c27668601098b764326e2 | Python | 5,627 | 189 | # -*- coding: utf-8 -*-
import tensorflow as tf
from efficient_layers import EmbeddingPostprocessor, ConvertImg_v3
from resnet import ResNet50v2 #データ量等で適切なものを選択
from iv_resnet import ResNet50v2 as iv_ResNet50v2
# 中間ベクトル抽出用 ResNet
class IV_model(tf.keras.models.Model):
def __init__(
self,
embedding... |
b60e51c961e0b8ec7ef26139f6b6a9b313ca8ac6abb5a36659c961b0a49f8652 | Python | 5,627 | 170 | from typing import Tuple, Dict
import pytorch_lightning as pl
import torch
import torch.nn as nn
from torch.optim import Adam
from torch.optim.lr_scheduler import ReduceLROnPlateau
from DeepDenoise.src.layer import DoubleConv, Down, Up, OutConv
from Metrics.src.image_quality_estimation import check_performance
clas... |
f29c127f546fd9b23b58e204029082aa8f5fce680f559f9f61ad851f2a56cc96 | Python | 5,627 | 195 | import pytorch_lightning as pl
import torch
from abc import abstractmethod, ABC
from rdkit.Chem.rdchem import Mol
from typing import Dict, Any
from torch_geometric.loader import DataLoader
from bioconfpred.data.featurizer import MolFeaturizer
class ConfPredModel(pl.LightningModule, ABC):
"""
Base class for m... |
721c61e29538bf76d08d9cad95d476d4b31d239c7b64ae05f6fc87d70507f23b | Python | 5,628 | 153 | """
Encapsulates external dependencies to retrieve cloud and geographical metadata
"""
import re
from dataclasses import dataclass
from typing import Callable, Dict, Optional
import pycountry
import requests
from codecarbon.core.cloud import get_env_cloud_details
from codecarbon.external.logger import logger
@data... |
77772c003bb8f3b6e613bd92eaff5b8fda243f677b716c9fa543926991926b5c | Python | 5,628 | 173 | from pathlib import Path
from typing import Any, Dict, List, Tuple, Union
from pytorch_lightning import Trainer
from pytorch_lightning.callbacks import DeviceStatsMonitor, LearningRateMonitor
from pytorch_lightning.loggers import TensorBoardLogger
from torch.nn import BatchNorm1d, Linear, Module, Sequential
from torch... |
e54ac011a29e37808eeb4df629435e8c920baa9efd7120273dcc7e459db3f5a1 | Python | 5,628 | 173 | """Experimental image transformations."""
from __future__ import division
import random
import numpy as np
import mxnet as mx
from mxnet import nd
def random_color_distort(src, brightness_delta=32, contrast_low=0.5, contrast_high=1.5,
saturation_low=0.5, saturation_high=1.5, hue_delta=18):
... |
8fb4da9a23c4fb63662446de4d17a36915d41faa4cb5b574329c91328dc2efb4 | Python | 5,629 | 159 | from ._permutation import _permutation_1samp, _permutation_ind
from ..permutation import permutation_test
import numpy as np
def _compute_hommel_value(p_vals, alpha):
'''
compute all-resolutions inference Hommel value
**implementation modified from nilearn.glm.thresholding**
'''
p_vals = p_vals.co... |
93fa4f4a387372778be7416d912d73196fcf41f90a538a4efad133e5ab8ca62d | Python | 5,630 | 197 | import warnings
import os
import numpy as np
import torch
from tqdm import tqdm as tqdm_dataloader # tqdm(dataloader) causes an error if tqdm.auto.tqdm is used
from tlib import tutils
from .data import read_batch
class SimpleDataset(torch.utils.data.Dataset):
def __init__(self, inputs, function):
sel... |
dfe2d64b88b7d3ff8ae489abfb3dd9bc23c9a790bed82b7149bfd1a18764298c | Python | 5,631 | 158 | from abc import ABC, abstractmethod
import itertools
from datetime import datetime
import numpy as np
import torch
import tqdm.auto as tqdm
from modular_splicing.evaluation.evaluation_criterion import DefaultEvaluationCriterion
from modular_splicing.evaluation.run_evaluation import accuracy_from_batches
from modular_... |
7b6dc182953f93aceb70012bd5a2f218931c767763e94098f930f27c0c01bab9 | Python | 5,633 | 154 | """LeWM loss for latent-space world models."""
from __future__ import annotations
from torch import Tensor, nn
from lightly.loss.latent_distance import latent_distance
from lightly.loss.lejepa_loss import SIGReg
def latent_prediction_loss(
*, predicted: Tensor, target: Tensor, normalize: bool = False
) -> Tens... |
80b3ce50b6874885db89382de8ebc15e8284cef30b7f3056696786ecf66d94d6 | Python | 5,635 | 117 | import os
import urllib.request, urllib.error, urllib.parse
import urllib.request, urllib.parse, urllib.error
import sys
import math
#
# Refer https://wiki.cancerimagingarchive.net/display/Public/REST+API+Usage+Guide for complete list of API
#
class TCIAClient:
"""TCIA Client from TCIA REST API SDK GitHub. See
... |
efe6bc97d805ba2e6dbea8b87ced45932927ec3a8cad421bedf362e2cfa0ab2e | Python | 5,636 | 148 | import os
from pathlib import Path
import shutil
import torch
from sklearn.decomposition import IncrementalPCA
from src import util
class PCBuilder:
def __init__(self, root, model_name, layer, dataset_name, ntau, nlat, nspan, scale, n_pca):
self._root = root
self._model_name = model_name
... |
727bd2eb96d609f80752706f6b3969fe91592913e5b8b7109334fe9758746a6c | Python | 5,638 | 119 | """
Kristian's original 2-layer VAE.
Model diagram with 35 latent dimensions and 100 dense nodes:
https://user-images.githubusercontent.com/112708/48358766-4f7a7e00-e650-11e8-9bab-d7a294548100.png
"""
import numpy as np
import keras
from keras.models import Model
from keras.layers import Activation, Dense, Lambda, I... |
ddead7d6a640a7d37c9f9534106ea97835ac554d609e3d7155de9f14611fa289 | Python | 5,638 | 135 | """
Neo4j Composite Dataset
"""
import logging
from galaxy.datatypes.data import Data
from galaxy.datatypes.images import Html
from galaxy.datatypes.metadata import MetadataElement
from galaxy.datatypes.protocols import (
DatasetProtocol,
HasExtraFilesAndMetadata,
)
gal_Log = logging.getLogger(__name__)
verb... |
f3c4347fc102a62cba15ad3ee2d43a723e904ca810692d2f23a089f8f90ed88a | Python | 5,638 | 204 | from unittest.mock import Mock, patch
from celery.concurrency.gevent import TaskPool, Timer, apply_timeout
gevent_modules = (
'gevent',
'gevent.greenlet',
'gevent.monkey',
'gevent.pool',
'gevent.signal',
)
class test_gevent_patch:
def test_is_patched(self):
self.patching.modules(*ge... |
636537e6b943be7e4af916e22cb35b510c958cec38d34fa220db4a16d4a3be9a | Python | 5,639 | 122 | from mne.stats.cluster_level import (
_find_clusters,
_setup_adjacency,
_reshape_clusters,
_cluster_indices_to_mask
)
import numpy as np
from .parametric import ARI
from .permutation import pARI
def all_resolutions_inference(X, alpha = .05, tail = 0, ari_type = 'parametric',
adjacency =... |
04a76acd22dac28e328e596a06e63d1e6d313c8e971d4c58ceb374580057e51c | Python | 5,641 | 154 | import torch
import torch.nn as nn
import torch.nn.utils.rnn as rnn_utils
from tqdm import trange
class Discriminator(nn.Module):
def __init__(self, input_size, embed_size, hidden_size,use_cuda=None, dropout=0.2,optimizer_instance=torch.optim.Adadelta, lr=0.001):
"""
Parameters
----------
... |
057b4230a47a8234ebbcc7cfdcc5b3675638654e2aaa809f6d136a402bac56df | Python | 5,642 | 154 | from __future__ import absolute_import
import datetime
import json
import logging
import os.path
import sys
from pip._vendor import lockfile, pkg_resources
from pip._vendor.packaging import version as packaging_version
from pip._internal.index import PackageFinder
from pip._internal.utils.compat import WINDOWS
from ... |
8ef8d6060f9eb260cffb6d3995994e8714143852d9d576c29b5990808140eccb | Python | 5,642 | 162 | import warnings
from keras.src import backend
from keras.src import tree
from keras.src.export.export_utils import convert_spec_to_tensor
from keras.src.export.export_utils import get_input_signature
from keras.src.export.export_utils import make_tf_tensor_spec
from keras.src.export.saved_model import DEFAULT_ENDPOINT... |
741f00b16c0dd6ba966e16eeace880bf8885b2bc2e03c858c8718c3fe5b64540 | Python | 5,643 | 142 | """The bidirectional call-time deprecation gate + plants (build item 5).
Static side (zero emission sites) is owned by
tests/test_deprecation_inventory.py and CITED, never duplicated; this gate
owns the CALL-TIME behavior root (D6: five of seven shims at the panel's SHA
presented the implementation's metadata everywhe... |
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