sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
d38667078d0638bc3bcda0220a209ac1f01be89f85f3df636541143c8297eab5 | Python | 3,216 | 89 | # ---
# jupyter:
# jupytext:
# text_representation:
# extension: .py
# format_name: light
# format_version: '1.5'
# jupytext_version: 1.11.4
# kernelspec:
# display_name: tutorialAlice
# language: python
# name: tutorialalice
# ---
# +
from pathlib import Path
import re
imp... |
4921fc905aa2507a44a21c11b6f0f82b4959c6dba9355bd7d91bbe301098dbac | Python | 3,217 | 84 | """ Multi Step Attention for CNN """
import torch
import torch.nn as nn
import torch.nn.functional as F
from bioseq2seq.utils.misc import aeq
SCALE_WEIGHT = 0.5 ** 0.5
def seq_linear(linear, x):
""" linear transform for 3-d tensor """
batch, hidden_size, length, _ = x.size()
h = linear(torch.transpose(x... |
717ead7fe8019e72a3fe45a16946abbb77156e15d66e0abeca7e033200af2541 | Python | 3,217 | 120 | """09. Run an object detection model on your webcam
==================================================
This article will shows how to play with pre-trained object detection models by running
them directly on your webcam video stream.
.. note::
- This tutorial has only been tested in a MacOS environment
- Pyt... |
fb52102c3d5089a4b7c925d952a14b2af1951908e4bebc19ab81b527d46de215 | Python | 3,217 | 93 | __author__ = 'quentin'
from ethoscope.utils.description import DescribedObject
from ethoscope.core.variables import BaseIntVariable
from ethoscope.hardware.interfaces.interfaces import DefaultInterface
from ethoscope.utils.scheduler import Scheduler
class HasInteractedVariable(BaseIntVariable):
"""
Custom v... |
55fd522e1dcecdf445bfe6129a1fcf98a11cd717a9fdfc5ab03340f8fac20928 | Python | 3,219 | 97 | """this script is used to help Process dataset for tracking
mainly crop data like_SiamFC"""
import numpy as np
import sys
from ..filesystem import try_import_cv2
def crop_hwc(image, bbox, out_sz, padding=(0, 0, 0)):
"""
crop image
Parameters
----------
image: np.array, image
bbox: np or list,... |
89b345b3d74f563769f92f17585281aba975bef0143140955c5886ad162abc0e | Python | 3,219 | 88 | from collections import defaultdict
def _get_node_successors(edges, from_id_col, to_id_col):
edge_cnt = len(edges)
node_successors = defaultdict(list)
from_ids = edges[from_id_col].to_list()
to_ids = edges[to_id_col].to_list()
for i in range(0, edge_cnt):
node_successors[from_ids[i]].appen... |
981621462e939b7538ddb7191e769367d9840354c7c5d37d99a3cedb15c00153 | Python | 3,219 | 93 | """grind-p3 T11.8: RNG-monitor teardown always drains the restore queue.
``_teardown`` latches ``_torn_down = True`` at entry and its per-restore
guard caught only ``Exception``, so a ``BaseException`` (a Ctrl-C landing in
the registry/profile steps or inside one patch restore) escaped mid-unwind
and permanently stran... |
7e5ffd7338eab4da56f2e6264b4e8750b85826ac5a6b86ec2b5c65cc8fb0dea9 | Python | 3,220 | 75 | # If the CT and masks are already available as NIFTIs
# it's only necessary to perform the FSL operations.
# This was the case with the dataset from Maastro.
import csv
import os
from dcmrtstruct2nii import dcmrtstruct2nii, list_rt_structs
FSL_DIR = "FSLDIR"
if __name__ == '__main__':
# Temporary folder to save ... |
75ce54749e2f166ed87990d8f4c7cd7178f543886eee84da3525d075437c5f44 | Python | 3,221 | 115 | #!/usr/bin/env python3
"""Run tests locally by calling Docker."""
import argparse
import os
import subprocess
def _get_parser():
"""Parse command line inputs for tests.
Returns
-------
parser.parse_args() : argparse dict
"""
parser = argparse.ArgumentParser(formatter_class=argparse.ArgumentD... |
77008321d0b19843bf6ca075f9084e22030dfd01e12f2862f912312faefeffe2 | Python | 3,221 | 110 | """Convert COCO panoptic segmentation format from BDD100K bitmasks."""
import argparse
import json
import os
from functools import partial
from multiprocessing import Pool
import numpy as np
from PIL import Image
from scalabel.common.parallel import NPROC
from scalabel.common.typing import NDArrayI32, NDArrayU8
from ... |
bb132fea482d9daf0a7c49efb1b8b5f14aebe2942e9d79a09889fdb6c69c15db | Python | 3,222 | 87 | #!/usr/bin/env python
"""Compare the current expected results file with the old expected
results and plot the difference. """
"""
Copyright (c) 2015, Blue Brain Project/EPFL
All rights reserved.
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the fol... |
9a2250c00308e240139579f87ed85f7b02fb10afd3cd2e9dbe5aceeaf0752726 | Python | 3,223 | 89 | """Mypy strictness ratchet: the flag set may only ever GROW.
R68 (3 consecutive hunt passes): the claimed mypy "package ratchet" was a
comment — zero strictness flags beyond ``check_untyped_defs``, nothing pinning
the config, so a lane could narrow it (or the claim could stay aspirational)
without any gate noticing. T... |
ae081d3bd06501a026b2e724d7f815588c901f2c4b6eb68ff094ba908950843e | Python | 3,223 | 79 | import pickle
import torch
import torch.nn.functional as F
# from trainingUtils import MultipleOptimizer, MultipleScheduler, compute_kernel, compute_mmd
from models import Encoder,Decoder,GaussianDecoder,VAE,CellStateEncoder,\
CellStateDecoder, CellStateVAE,\
SimpleEncoder,LocalDis... |
ef0af7e1041d3c78b6e4a627e9484a759d791106782234400469422591a4248b | Python | 3,223 | 86 | import dominate
from dominate.tags import meta, h3, table, tr, td, p, a, img, br
import os
class HTML:
"""This HTML class allows us to save images and write texts into a single HTML file.
It consists of functions such as <add_header> (add a text header to the HTML file),
<add_images> (add a row of imag... |
7e933317b7baad5367fae4d17feff3008f776df8b120e692d40df80418c4612a | Python | 3,225 | 87 | import os
import torch
from tqdm import tqdm
import schnetpack as spk
class EnvironmentTypes:
def __init__(self, loader, model, device=torch.device('cuda')):
self.loader = loader
self.model = model
self.device = device
self.max_n_atoms = 30
for batch in loader:
... |
c5fee7394c6ef0fbce8cf8ecebbe760a6fd6e0a25833c122bc71d818ea3e3912 | Python | 3,225 | 87 | import numpy as np
import tensorflow as tf
import sys
import os
sys.path.append("../utils")
from func_model import extraData, apply_rev_comp, train, evaluate
os.environ['TF_CPP_MIN_LOG_LEVEL'] = '2'
# tf.config.threading.set_intra_op_parallelism_threads(5)
tf.config.threading.set_inter_op_parallelism_threads(10)
#--... |
df4c15d5ee0574281660425b70e74007d561a433f807dd1ed960cc8192b039f7 | Python | 3,225 | 93 | import os
import pickle
from copy import deepcopy
from typing import Tuple
from drug_interactions.reader.dal import DrugBank, DrugDAL, Drug
from tqdm import tqdm
class DrugPreprocessor():
"""
An object that contains all the preprocessing methods for the drug bank.
Attributes:
path: A string of t... |
80fd2905c88318bbe6aa77858efed56ea14886eb14be4f9b993bbc3634038312 | Python | 3,226 | 93 | # import the pyabf module from this development folder
import os
import sys
PATH_HERE = os.path.abspath(os.path.dirname(__file__))
PATH_SRC = os.path.abspath(PATH_HERE+"/../../src/")
PATH_DATA = os.path.abspath(PATH_HERE+"/../../data/abfs/")
sys.path.insert(0, PATH_SRC) # for importing
sys.path.append("../../src/") #... |
f9299d902db6328da477e0aa613080cf48a887c55d569d3ae951d35f29d87925 | Python | 3,226 | 112 | import numpy as np
from numpy.random import default_rng, SeedSequence
import matplotlib.pyplot as plt
import pandas as pd
import seaborn as sns
from tqdm import tqdm
import multiprocessing
from multiprocessing import Pool, freeze_support, current_process, RLock
from functools import partial
import pathlib
from causal_... |
7a1cc79739a14718b018b01e6c65abf7e3a5c39bacb80d541ac4ed600c6cd718 | Python | 3,227 | 43 | #==============================================================================#
# Author: Dominik Müller #
# Copyright: 2024 IT-Infrastructure for Translational Medical Research, #
# University of Augsburg ... |
86c8d9147163e3623b262d58d00cf6239dfe9df50376f681bdb50f825a784422 | Python | 3,227 | 85 | import argparse
import pandas as pd
from pyfaidx import Fasta
from statsmodels.stats.multitest import fdrcorrection
import sys
def get_sequence(region):
print(region)
key, start, end = region.split("-")
tmpseq = chrs[key][int(start):int(end)].seq
return tmpseq.upper()
parser = argparse.ArgumentParser(... |
bf301c5fbdf6c95667f0f3a1ae7f07f88164e6c02b9096a4d40912bf396b8e11 | Python | 3,227 | 95 | # This example requires the following dependencies to be installed:
# pip install lightly
# Note: The model and training settings do not follow the reference settings
# from the paper. The settings are chosen such that the example can easily be
# run on a small dataset with a single GPU.
import copy
import pytorch_l... |
14b18cb20d87a2b568be02d2d5243d363ac237d9342c16f9f7c58f3501c167ac | Python | 3,229 | 108 | # -*- coding: utf-8 -*-
# Copyright (c) 2016-2018 Braintech Sp. z o.o. [Ltd.] <http://www.braintech.pl>
# All rights reserved.
"""
Module providing :class 'DataGenericWriteProxy' representing data file.
Author:
Mateusz Kruszyński <mateusz.kruszynski@gmail.com>
"""
import abc
import numpy
from . import signal_log... |
51f622facac2f00080c04b807fe5cc701a5f4108ff5db788a2c3852949d5ce1e | Python | 3,230 | 78 | #!/usr/bin/env python
import pandas as pd
import os
import sys
import sqlite3
import argparse
from sqlalchemy import create_engine
import csv
def read_promoter_file(promoters):
col = ['frag_chr', 'frag_start', 'frag_end', 'frag_id', 'gene', 'project']
gene_prom = pd.read_csv(promoters, sep = "\t", names = co... |
fcae2fab98a39b3e5beb267b66ca7cb721343b1baedfbbeac5ef75891aaeb91a | Python | 3,230 | 109 | from matplotlib import pyplot as plt
from PIL import Image
import pandas as pd
import matplotlib
import numpy as np
from typing import Optional, Union, Mapping # Special
from typing import Sequence, Iterable # ABCs
from typing import Tuple # Classes
from anndata import AnnData
import warnings
from stlearn.plottin... |
84dc73a420fd6782635a2d55db18823948354756affab9d8a7ec655da106c52e | Python | 3,231 | 108 | """Multi-exit module lookup collision tests."""
from __future__ import annotations
import pytest
import torch
import torchlens as tl
from torchlens._errors import AmbiguousOpLookupError
class TupleExit(torch.nn.Module):
"""Module returning two output tensors from one module call."""
def forward(self, x: t... |
7fbba99b1e30e0ebdd6a9fd4ff9308f309a4b69c2d11a870cd5b20e4c1474527 | Python | 3,233 | 109 | # This example requires the following dependencies to be installed:
# pip install lightly
import pytorch_lightning as pl
import torch
import torchvision
from torch import nn
from lightly.models import utils
from lightly.models.modules import MaskedVisionTransformerTorchvision
from lightly.transforms.mae_transform imp... |
f763e6c95d531882fb57ab93d185b61ff920dd18d3387869391cf65546442ba4 | Python | 3,235 | 93 | import pytest
import numpy as np
import nway.meta_registration as mr
import nway.transforms as tf
@pytest.mark.parametrize("include_original", [True, False])
def test_MetaRegistration_init(include_original):
m = mr.MetaRegistration(include_original=include_original)
names = []
for candidate in m.candidate... |
4d289a97950476841f354182aa88fbbc3a96e94c525cea8eb0a290a08c8db958 | Python | 3,236 | 99 | # Copyright (c) 2022 PaddlePaddle Authors. 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 required by app... |
7b20b239a0933964ddeaeaa9bd09b3e4797057756fcb98f93cbecfa050ca661e | Python | 3,236 | 83 | from __future__ import annotations
from pathlib import Path
import zipfile
from larvaworld.portal.datasets.discovery import discover_raw_datasets
def test_discover_raw_datasets_returns_empty_for_missing_root(tmp_path: Path) -> None:
candidates = discover_raw_datasets("Schleyer", tmp_path / "missing")
asser... |
a87f4aeab3a96e9738ebe58a051edc02abff75074b4621431cca0d0bc8d157cd | Python | 3,236 | 72 | import os
import XML_Parse as parse
from collections import Counter
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
#######################################################################################################################
# Branch Number Analysis required functions:
def branch_... |
ebd2ac3cd13975ceb9848e6014a93fd6771c6be5e7115f583887333fcaaf815c | Python | 3,236 | 61 | from dataProcessing.modules import *
import pandas as pd
from torch.utils.data import DataLoader
class Data:
def __init__(self, directory, module, subseqlength, emb_word_len, need_train):
print("#################################################")
print("Read training, validation, test datasets, an... |
2c64d598dd65af856ead25ddd9efedd3d53b2b051956766a95bc150bd184b751 | Python | 3,237 | 94 | import networkx as nx
import numpy as np
from stlearn.utils import _read_graph
def shortest_path_spatial_PAGA(adata,use_label,key="dpt_pseudotime",):
# Read original PAGA graph
G = nx.from_numpy_array(adata.uns["paga"]["connectivities"].toarray())
edge_weights = nx.get_edge_attributes(G, "weight")
G.re... |
c6a63f6fff8293b232c0a8dc8c457a53a9b7035090f74f8fe4745efd4d5638a3 | Python | 3,237 | 82 | from dataclasses import dataclass
from typing import Optional, Tuple
import torch
from transformers.file_utils import ModelOutput
@dataclass
class BaseModelOutput(ModelOutput):
last_hidden_state: torch.FloatTensor = None
last_pair_repr: torch.FloatTensor = None
hidden_states: Optional[Tuple[torch.FloatTen... |
ab5908d0fe66ee801cb81014705c70c4d408d66c8d1589ba217915d8e79596d0 | Python | 3,238 | 71 | import numpy as np
import pytest
import vampire.common as common
import vampire.xcr_vector_conversion as conversion
def test_pad_middle():
with pytest.raises(AssertionError):
conversion.pad_middle('AAAAA', 2)
assert 'A---B' == conversion.pad_middle('AB', 5)
assert 'A--BC' == conversion.pad_middle... |
06f447d4dedd4a11ab506a7a1c3fa8bb6435f7dcd5e947f380b63c85e320ae66 | Python | 3,240 | 96 | import os
import sys
from pathlib import Path
import pandas as pd
import pytest
from larvaworld.lib import reg, sim
RUN_WINDOWS_HEAVY = os.environ.get("LW_ENABLE_WINDOWS_HEAVY") == "1"
pytestmark = [
pytest.mark.integration,
pytest.mark.heavy,
pytest.mark.skipif(
sys.platform.startswith("win") a... |
c7e50a7b4ce8fcefd472f221f49098df286f0e935f914f15b5fe4f462cef1a65 | Python | 3,240 | 104 | from pathlib import Path
import shutil
import tempfile
from typing import Union, Optional, List, Tuple
import functools
import warnings
import numpy as np
import pytest
import face_rhythm as fr
"""
WARNING: DO NOT REQUIRE ANY DEPENDENCIES FROM ANY NON-STANDARD LIBRARY
MODULES IN THIS FILE. It is intended to be run... |
0e0c6c4afb0e0a593b1cb7198f2f723629e6b494b6741b362a6c416d60836107 | Python | 3,241 | 89 | import numpy as np
from modular_splicing.motif_perturbations.compute_perturbations import (
motif_perturbations_individual,
)
def compute_effect(
model,
exon,
effect_thresh,
cl,
*,
kind_of_effect="linear",
minimal_probability_requirement_for_effect,
always_include_at_least=5,
):
... |
1995213c1c2b464ac89d923e7fdc47d51a506460d0b1730738010dba6e1705b2 | Python | 3,241 | 87 | """R10-3: the op_log_fields invariant on LOADED torch artifacts.
``Op.func`` is ``FieldPolicy.DROP`` and ``__getstate__`` hard-nulls it, so
``callable(lpl.func)`` false-fired on EVERY loaded torch trace — the torch-only
``op_log_fields`` contract had zero loaded-torch coverage (the only loaded
callers were non-torch b... |
46433f6fd5291310aaba1716238ab7b840db49ce1f7aabda24f5b47778a689ae | Python | 3,242 | 106 | """
Creates a feature location index (FLI) for a given BED/GFF file.
FLI index has the form::
[line_length]
<symbol1_in_lowercase><tab><symbol1><tab><location>
<symbol2_in_lowercase><tab><symbol2><tab><location>
...
where location is formatted as:
contig:start-end
and symbols are sorted in lexig... |
8a786a289fc18fa975f5eadc21139da19dc48986357c235a4d9f41cb0cc7d424 | Python | 3,242 | 77 | import unittest
from unittest.mock import MagicMock, patch
from cellxgene_gateway.cache_entry import CacheEntry
from cellxgene_gateway.cache_key import CacheKey
from cellxgene_gateway.items.file.fileitem import FileItem
from cellxgene_gateway.items.file.fileitem_source import FileItemSource
from cellxgene_gateway.item... |
da8fd5cca7f16773ad19c894f415b99e5e35252f4470cfcfd680448978de9b72 | Python | 3,242 | 107 | import types
import torch
from LRP.layers_ours import (
forward_hook,
safe_divide,
RelProp,
IndexSelect,
)
from LRP.BERT import BertModel
import torch.nn.functional as F
def convertProtBertToLRPModel(model):
# Relprop of TransformerClassifPerProtLayerNorm
model.forward = types.MethodType(forwa... |
1f0b876f4310fde903bb045d3c25b3bf4dbb3d3809e376fa1eb955fe6679d128 | Python | 3,243 | 109 | import torch
import torch.nn as nn
class MotifModel(nn.Module):
"""
Represents a motif model that classifies a sequence as either
matching or not matching a given motif.
"""
def __init__(self, hidden_size, window_size):
super().__init__()
self.conv1 = nn.Conv1d(4, hidden_size, ker... |
35276e9bba92b0b6faae2f84ca1ed54627f21f2a7095f92361ec7e7eddd59f1b | Python | 3,243 | 114 | # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
"""Workflows for collecting and saving anatomical outputs."""
from nipype.interfaces import utility as niu
from nipype.pipeline import engine as pe
from niworkflows.engine.workflows import LiterateWorkflow... |
6e32a2745c52ed0bd59c0c73553cdaa4b064e01b45dd7060d00ecb5883e2b4d1 | Python | 3,243 | 87 | """The :program:`celery beat` command."""
from functools import partial
import click
from celery.bin.base import LOG_LEVEL, CeleryDaemonCommand, CeleryOption, handle_preload_options
from celery.platforms import detached, maybe_drop_privileges
@click.command(cls=CeleryDaemonCommand, context_settings={
'allow_ext... |
78543f08089fda8da2a1032329b2d7c8536a90db96ffdecece6e0d68fd6fe952 | Python | 3,243 | 84 | """R1 core plumbing tests (memo A1/A2/A6): the three-checkpoint core, offline.
Minimal real-checkpoint rows proving the registry -> preflight -> offline
fixture pipeline end to end; the RG gallery (B1) builds on these fixtures.
Every assertion is payload identity against an independent same-process
rerun -- never the ... |
90c24059cac213b9c7d0fea2d0415f66998b38f3d4b38b5e0c3525c6a2252c5e | Python | 3,243 | 101 | #!/usr/bin/env python
"""Convert GlimmerHMM gene predictions into protein sequences.
This works with the GlimmerHMM specific output format:
12 1 + Initial 10748 10762 15
12 2 + Internal 10940 10971 32
12 3 + Internal 11035 11039 5
12 4 + In... |
041c85364263ee88b9e8d227f78b042fc5948ba46e3f1e657c0db6897299b696 | Python | 3,244 | 84 | import numpy as np
import pandas as pd
from tqdm.auto import tqdm
from .._utils import _k_largest_index_argsort
TINY = np.finfo(float).tiny
def get_activators_n_seqlets(
activations,
sequences,
kernel_size,
padding=0,
num_seqlets = 100,
num_filters=None
):
num_filters = num_filters if ... |
bff7f7ed61f7474999444765e4ad38497a13ff816a9b5cbc5d6f9aa5fc432426 | Python | 3,244 | 112 | #!/usr/bin/env python
from __future__ import print_function
import xml.dom.minidom
from xml.parsers.expat import ExpatError
import argparse
import sys
import re
description = """
This script converts the default Release Notes from JIRA to a ITK's wiki format.
Specifically input such as:
<h2> Epic
</h2>
<ul>... |
cddff9b6b230ab5dffa19ea758a1509df79ab11414f8b54ac09562f6947c2993 | Python | 3,244 | 77 | """M10 ratchet: every Trace field has exactly one owning component.
The declared ownership map (``_trace_components.py``) is the design artifact
the Trace decomposition executes against. This test is the ratchet: a new
Trace field without a declared owner — or a stale map entry — fails here,
so the god object cannot r... |
8e3dfabb8dfba6e6904bb6bdb7ee257f28d815708b405d1ee1b24095a7e9e0d1 | Python | 3,245 | 79 | import logging
from typing import Optional
from carbonserver.api.errors import NotAllowedError, NotAllowedErrorEnum, UserException
from carbonserver.api.infra.repositories.repository_projects import (
SqlAlchemyRepository as ProjectSqlRepository,
)
from carbonserver.api.schemas import ProjectCreate, ProjectPatch, ... |
c4ea998e90aed657b6dc9e067d62fd5cc96c7603ca714ddc6903ef4c0efc82c0 | Python | 3,245 | 106 | import logging
import yaml
import copy
import argparse
import numpy as np
from pymatgen.core import Molecule
from atomate.qchem.fireworks.core import SinglePointFW
from atomate.common.powerups import add_tags
from fireworks import LaunchPad, Workflow
from instance_mongodb import instance_mongodb_sei
from firework... |
040295313e768f8c0357b92ad99f01750700b16da8187349eff99518a84276de | Python | 3,246 | 111 | model = dict(
type='MoCo',
queue_len=65536,
feat_dim=128,
momentum=0.999,
backbone=dict(
type='ResNet',
depth=50,
in_channels=3,
out_indices=[4],
norm_cfg=dict(type='BN'),
init_cfg=dict(type='Pretrained', checkpoint='torchvision://resnet50')),
neck... |
2d391bd84e4c6d57238e5cbb6fd49297476612a940e5938155e71a8463e1b59b | Python | 3,246 | 113 | # -*- coding: utf-8 -*-
"""
Created on Tue Feb 14 14:43:07 2023
@author: longzheng
"""
from keras.models import Sequential, load_model
from keras.layers import Conv2D, MaxPooling2D, Dropout, Dense, Flatten
from keras.optimizers import Adam
import pandas as pd
import deepchem as dc
import numpy as np
from keras.callb... |
61f341b9a0ccdaa0e610749f34360064211f42a3a5df7760cbb0d45c1db46e86 | Python | 3,247 | 119 | #!/usr/bin/env python3
import os
import pandas as pd
f_1 = open("files.txt", "r", encoding = "utf-8")
filename = []
i = 1
for file_1 in f_1:
line_1 = file_1.strip().split('\t')
filename.append(line_1[0])
f_1.close
j = 0
list_all = []
list_title = []
for file in filename:
samplename = file.split('.')[... |
46dcd0f46a127142dde9893fe0c02be28acae64b133cde6f5f922c833fb0b821 | Python | 3,248 | 70 | import glob
import sys
import pandas as pd
from nilearn.glm import compute_fixed_effects
def fixed_effect(sub, task_type, contrasts, input_path, output_path,
save_beta=True, save_var=True, save_tstat=True):
"""
This function takes in a subject, task label, set of computed contrasts using nile... |
e4770b851a468bd55c8862aeea333590178555f40a707b2c60f1fbbca65506f8 | Python | 3,248 | 106 | import os
import platform
import sys
from pathlib import Path
from pkg_resources import parse_version
from setuptools import find_packages, setup
def main():
version_file = Path(__file__).parent / 'VERSION'
with open(str(version_file)) as fin:
version = fin.read().strip()
install_requires_base =... |
91dab0840f679f8543ae836dd6a0c2c8115adae07da7390e842fd64312718cf7 | Python | 3,249 | 122 | import abc
import copy
import numpy as np
class BaseShape(abc.ABC):
def __eq__(self, other):
same_cls = self.__class__.__name__ == other.__class__.__name__
try:
same_sig = np.allclose(self.to_point_signature(),
other.to_point_signature())
exc... |
04b0f4caed899e62c01482a216c7bbcbbd8ed8027127e8e4e2ef6224c344006a | Python | 3,250 | 75 | import numpy as np
from tqdm import tqdm
from mp_dip.utils.interpolate_head_features import get_positions, interpolate_feature
def prepare_data(examples, mp_params):
"""for mmp3"""
# [ number of examples, number of atoms, number of channels, number of atom features
# bad, it should be "same features, vs... |
cfb846b550c434602e2a0d7e166539b973e9a77ce29bb25813d1802e62f3f0ea | Python | 3,250 | 89 | from utils import *
import os
import pickle
import math
import numpy as np
import torch
import torchvision
from torch import nn
from torchvision import datasets, transforms
import matplotlib.pyplot as plt
from torch.optim.lr_scheduler import LambdaLR
from torch.utils.data import DataLoader, Dataset, Subset
from torchvi... |
92d1a79a1767a0261cc1bb06f0588a54db634c5e7ac036deed87b57be5f9c344 | Python | 3,251 | 86 | # 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... |
ed43c643b3cb86cd81ce812fb1736bbe7e4f5f1297c3440fe90ef237d5324e09 | Python | 3,251 | 116 |
from pathlib import Path
import re
from natsort import natsorted
# Our modules
import data
def ls_cohorts():
return [f.name for f in
Path(f'data/').iterdir() if f.is_dir()]
def get_weights_tree(basepath):
node = {}
node['dirs'] = {}
node['fnames'] = []
for f in basepath.iterdir():
... |
13adfc123eceb9f434154b24e5e384530e0d215bb15df1fbcb008c25cecda999 | Python | 3,252 | 103 | """
Unit tests for the Monitor class.
This module contains tests for the core Monitor functionality
that coordinates the tracking pipeline.
"""
import threading
import time
from unittest.mock import MagicMock, Mock, patch
import pytest
# Note: Actual imports would need to be adjusted based on the real module struct... |
5b4f8692f35eb67a18c31be8610f62cf97d19645a0e97e2babf293639390c86f | Python | 3,252 | 79 | """Plots for the time model object.
Notes
-----
This file contains plotting functions that take as input a time model object.
"""
from itertools import cycle
from specparam.utils.select import find_first_ind
from specparam.plts.utils import savefig
from specparam.plts.templates import plot_params_over_time
from spec... |
669fc3c94689aec42a0c884f4272e26716b6bc87cdbcb139e9cd89d9556cc3c4 | Python | 3,252 | 123 | #!/usr/bin/env python3
# ----------------------------------------------------------------------------------------
# Imports and paths
import os
import sys
import importlib
my_path=os.path.dirname(os.path.realpath(__file__));
# Make sure biswebpython is in your path
n=os.path.abspath(my_path+'/..')
sys.path.insert(... |
78ef117c7747b7e47f202ab78e19c4c25150ba108dfb1ab3d3979047d34efbc6 | Python | 3,252 | 108 | """Smoke coverage for predicate-mode capture dispatchers."""
from __future__ import annotations
import time
import torch
from torch import nn
from torchlens import _state
from torchlens.backends.torch.model_prep import (
_cleanup_model_session,
_ensure_model_prepared,
_prepare_model_session,
)
from torc... |
3225915b2fd8720364a713f5ed2a9f5c6f7f4f0533ceda9ce7397c70a8cdbbe4 | Python | 3,253 | 86 | # validate cross correlations for a single set of mfov comparisons
# as dumped from mfov using the export_xcorr_comps_path hack.
import time
import tifffile
import dill
import os
import re
import numpy as np
from xcorr import BatchXCorr
from rcc_xcorr.xcorr import XCorrUtil as xcu
export_xcorr_comps_path = '/gpfs/s... |
6a1a5b58e05dc8f10c9351daff539671a46e6032bacb0ad734593f163002abcf | Python | 3,253 | 101 | #######################################################################################################
##################### Preprocessing for multi-task models #############################################
#######################################################################################################
import... |
87771b870fdc0a21d7e74e68d192cf0d3efd557e501522455401d4763a782975 | Python | 3,253 | 90 | #==========================================================================
#
# 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://www.apache.org/l... |
a685c3736442da5d16abc36a2d78cf5c872e47d27eda7a7de83f9d9a4607637b | Python | 3,253 | 105 | import os
import shlex
import subprocess
import h5py
import numpy as np
import torch
import torch.utils.data as data
BASE_DIR = os.path.dirname(os.path.abspath(__file__))
def _get_data_files(list_filename):
with open(list_filename) as f:
return [line.rstrip() for line in f]
def _load_data_file(name):
... |
6c54393480e8f9762fdf350b317d1be011030571881ee02b8f721f408dee60a8 | Python | 3,254 | 101 | """Util functions."""
import os
import os.path as osp
from itertools import groupby
from typing import Dict, List, Tuple
from scalabel.common.io import load_config
from scalabel.label.to_coco import get_instance_id
from scalabel.label.typing import Label
from scalabel.label.utils import check_crowd, check_ignored
fr... |
815c7699eeada763baf05de1956f4df0bac164ac8827cdd194d00230131ab5a5 | Python | 3,254 | 94 | # coding=utf-8
# Copyright 2022 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... |
a5389a152146d37446ff0cb378a4d2162f13bd65ffa153f12dbc57ff86b33ac2 | Python | 3,254 | 105 | # --- THIS FILE IS AUTO-GENERATED ---
# Modifications will be overwitten the next time code generation run.
from plotly.basedatatypes import BaseTraceHierarchyType as _BaseTraceHierarchyType
import copy as _copy
class Selected(_BaseTraceHierarchyType):
_parent_path_str = "bar"
_path_str = "... |
a9f9d0bb14952987b45aa434f45c13b6b00c10403b2b26a9d353a52aa6b47006 | Python | 3,255 | 103 | # Copyright 2023 DeepMind Technologies Limited
#
# 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 agree... |
2a045fc8d8a3846ed314a4d7ec6e1bf64806fcd3530e7b8a361eb41c4398da0b | Python | 3,256 | 91 | """
Install tigramite
"""
from __future__ import print_function
import pathlib
import os
from setuptools import setup, Extension
from setuptools.command.build_ext import build_ext
import json
# Handle building against numpy headers before installing numpy
class UseNumpyHeadersBuildExt(build_ext):
"""
Subclasse... |
79ecb54f1c306417182c4bec3792c545e5c810582840f4b7e387cc74582ee758 | Python | 3,256 | 81 | # Copyright (c) 2022 PaddlePaddle Authors. 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 required by app... |
b408b9b8be592db871c102610ce442f0514b6edb0999889cd83506c09333f4aa | Python | 3,256 | 116 | import json
import pickle
import sys
from datetime import date, datetime, time, timedelta, timezone
from unittest.mock import Mock
import pytest
from kombu import Queue
from celery.utils.serialization import (STRTOBOOL_DEFAULT_TABLE, UnpickleableExceptionWrapper, ensure_serializable,
... |
0beee05479cd7809ba7a77014600323ecdc3ac5c5dff16a2fb5c5cc32a4b383b | Python | 3,257 | 90 | """W051-TRACK / AUD-CODE 2.13: the emission ledger is keyed by sink OBJECT.
Two sinks of one class (two JSONL files: local + NFS) used to share ONE row
keyed by class name: a failure in either latched both, the healthy sink was
silently starved from that step on, and the counts merged.
"""
from __future__ import anno... |
becbd1bcb3ea7835898056c6a1276a27e3c150237c91eebf526fa31c57d04370 | Python | 3,257 | 76 | from __future__ import division
import unittest
import numpy as np
from wyrm.types import Data
from wyrm.processing import correct_for_baseline
from wyrm.processing import swapaxes
class TestCorrectForBaseline(unittest.TestCase):
def setUp(self):
ones = np.ones((10, 5))
# three blocks: 1s, -1s,... |
2b3159dd81119d373c76b1d9f6398c6fe97a02f85dd559331a2cb96fc5965419 | Python | 3,258 | 104 | # LICENSE
#
# _This file is Copyright 2018 by the Image Processing and Analysis Group (BioImage Suite Team). Dept. of Radiology & Biomedical Imaging, Yale School of Medicine._
#
# BioImage Suite Web is licensed under the Apache License, Version 2.0 (the "License");
#
# - you may not use this software except in compl... |
b165d25eb1bf3b295d6854e555cc4bca6d88f2ecbffa744e0afbb4d88a71a90e | Python | 3,258 | 81 | """Abstract superclass for model training workflows.
"""
import os
import logging
import crf_util
class Workflow(object):
"""Abstract superclass for all workflows.
Attributes:
condition_name (str): String label for current trial.
data_dir (str): Path to dataset folder. Set by settings file.
... |
56f4b71b4c2b9bff411f707b131e66b0b2ffd54413b42ab91bc74323adc87a6a | Python | 3,259 | 96 | from __future__ import absolute_import
import sys
from pip._internal.cache import WheelCache
from pip._internal.cli.base_command import Command
from pip._internal.models.format_control import FormatControl
from pip._internal.operations.freeze import freeze
from pip._internal.utils.compat import stdlib_pkgs
DEV_PKGS ... |
6edefe5aa2c6f1257c0a79daa829dd642a7f82c1bd2a27ff9f7e0560f81ea776 | Python | 3,260 | 120 | from sklearn.tree import DecisionTreeClassifier
import numpy as np
from sklearn.metrics import mean_squared_error
ROOT = 0
LEFT = 1
RIGHT = 2
NEG = 0
POS = 1
def clean_str(s):
return s.lower().replace('/', '___').strip()
def impurity_mse(y):
"""Lower impurity (closer to 0) is better
"""
y_mean = np.... |
a0e74fe4af6b2f7cbf7b621c7aeb97e9e92730acd46e888ae433851d4c467019 | Python | 3,260 | 90 | import sys
from robustness import datasets
from robustness.attacker import AttackerModel
from robustness.model_utils import make_and_restore_model
import robustness.data_augmentation as da
from torchvision import transforms
import torch
import numpy as np
from model_analysis_folders.all_model_info import IMAGENET_PATH,... |
cc1a96acd6e9ca0b2dcf60002cafbe15a548ca6593ace8594ed2a1d3e9ce3542 | Python | 3,260 | 102 | """Models describing the column targets a rule builder workbook can carry.
The target definitions themselves live in ``rule_targets.yml``; header parsing
onto these types lives in ``rule_target_columns.py``.
"""
from typing import (
Literal,
)
import yaml
from pydantic import (
BaseModel,
RootModel,
)
f... |
443209afa275a4e5a7d45ced9ab9c268293597a384220bd0162cc0394ea01741 | Python | 3,261 | 100 | def get_all_episodes(fn_in):
# Input
# fn_in : input file
#
# Output
# samples : list of episodes (each has 'xs','ys','xq','yq' structure)
# Find range where episodes are present
with open(fn_in,'r') as fid:
lines = fid.readlines()
lines = [l.strip() for l in lines]
assert('Evaluation episode 0' in li... |
5cfb09bd99db54625a110bfd69cf3e1847f8c83397f86a42ffbbba8719adaeb7 | Python | 3,261 | 106 | """add_cascade_delete_for_projects
Revision ID: 2a898cf81c3e
Revises: f3a10c95079f
Create Date: 2025-10-05 11:40:28.037992
"""
from alembic import op
# revision identifiers, used by Alembic.
revision = "2a898cf81c3e"
down_revision = "f3a10c95079f"
branch_labels = None
depends_on = None
def upgrade():
"""
... |
763fc4055944812bd24d77f063fde4a2da3912a45f2299ae7bfd6db78a1ebc77 | Python | 3,262 | 66 | """Default configs for center net"""
# pylint: disable=bad-whitespace,missing-class-docstring,bad-indentation
import os
from typing import Union, Tuple
from autocfg import dataclass, field
@dataclass
class CenterNetHead:
bias : float = -2.19 # use bias = -log((1 - 0.1) / 0.1)
wh_outputs : int = 2 ... |
ccc36bff6051efeb58ed62fa7b7b02392860c219330768412ad805f39ffc9b63 | Python | 3,262 | 61 | ## The generate_custom_model function will generate a model with a custom exon length by Lanczos resampling of the position bias coefficients. It also allows to modify the bias term in the SumDiff layer.
import numpy as np
from quad_model import *
from tensorflow.keras.models import Model, load_model
ORIG_MODEL_FILE_... |
a60facb24f1a4c094fb5ed988c2a6b6234481a298d65c1cffb5e211f442c72d5 | Python | 3,263 | 89 | #!/usr/bin/env python3
"""
state_geometry.py — Vendored 5D state-geometry feature extractor.
Self-contained pure-numpy implementation of `compute_phi_5d` and its
dependencies. Originally lived in `paper5_5d/pipelines/reprocess_car_local.py`;
vendored here so this testsuite is a complete self-standing deposit
that does... |
137b400d161087dc640f837c6f4934235a02ec385ee13e50dd9f7fb39c2c5f28 | Python | 3,264 | 108 | from typing import Any, Callable, Optional, Union
from pl_bolts.datamodules.vision_datamodule import VisionDataModule
from pl_bolts.datasets import MNIST
from pl_bolts.utils import _TORCHVISION_AVAILABLE
from pl_bolts.utils.warnings import warn_missing_pkg
if _TORCHVISION_AVAILABLE:
from torchvision import transf... |
4401ead4ca020af53dd7ca72cb8836ccf3a47def5b518b47dcc0130a07b22cdb | Python | 3,264 | 85 | # coding=utf-8
# Copyright 2024 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... |
7221051319fb31fd9e11cc1b531c3757db5ae764c25b3ea007aba8b5fd5871ad | Python | 3,264 | 99 | """
Copyright (c) 2022 EPFL-BBP, All rights reserved.
THIS SOFTWARE IS PROVIDED BY THE BLUE BRAIN PROJECT ``AS IS''
AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE BLUE BRAIN PROJE... |
c59c6058ec864e78731781c28062822e7191f421bce20d068a54ec27ef0a66e0 | Python | 3,264 | 96 | """R10-4: the save-side "is this type/factory load-reconstructible?" predicate
was a namespace prefix test (``root in {"torch", "torchlens"}`` / ``builtins``),
while the safe unpickler admits torchlens types ONLY on the vetted-inert
``_SAFE_TORCHLENS_TYPES`` allowlist (not appliance modules), torchlens callables
only v... |
160cedee38013fe797442a590a44a9c48c228c001e8cd265deca12fbf477f18e | Python | 3,265 | 79 | import os
from functools import partial
import torch
from safetensors.torch import load_file as safe_load_file
from transformers.utils import (
SAFE_WEIGHTS_INDEX_NAME,
SAFE_WEIGHTS_NAME,
WEIGHTS_INDEX_NAME,
WEIGHTS_NAME,
)
from transformers.utils.hub import cached_file, get_checkpoint_shard_files
de... |
e2cf8e3345afa3da9067c7a76a74866069eb72683ec3e8933a7f1b3bddcdfb75 | Python | 3,265 | 100 | """Utilities to report on available options for fitting, modes, evaluations, etc."""
from specparam.modes.mode import VALID_COMPONENTS
from specparam.reports.strings import gen_mode_str_lst, gen_mode_params_str_lst, gen_metric_str_lst
from specparam.reports.strings import _format
#####################################... |
0ce92031eb01a8281db7d146ce6b7d91690e4fc93a5bf7939f116e8e733a6444 | Python | 3,267 | 113 | # Copyright (c) 2020 PaddlePaddle Authors. 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 required by app... |
f485452a7d5bf0150900baa8654b195b1840f44b94c492765db6ee2fe637f33d | Python | 3,267 | 112 | model = dict(
type='DenseCL',
queue_len=65536,
feat_dim=128,
momentum=0.999,
loss_lambda=0.5,
backbone=dict(
type='ResNet',
depth=50,
in_channels=3,
out_indices=[4],
norm_cfg=dict(type='BN'),
init_cfg=dict(type='Pretrained', checkpoint='torchvision... |
b6dcfe37d558d3dc6c87fb515908440bc04d557635fcd230dd72235e9ba731c6 | Python | 3,268 | 60 | import pysam.utils
addreplacerg = pysam.utils.PysamDispatcher('samtools', 'addreplacerg')
ampliconclip = pysam.utils.PysamDispatcher('samtools', 'ampliconclip')
ampliconstats = pysam.utils.PysamDispatcher('samtools', 'ampliconstats')
bam2fq = pysam.utils.PysamDispatcher('samtools', 'bam2fq')
bamshuf = pysam.utils.Pysa... |
1dad802d2f54baf8a77a41671eea4ee08598a68a5739637d5e057b484c2a3706 | Python | 3,269 | 127 | import numpy as np
import scipy.linalg as sl
from keras.src.backend.common import dtypes
from keras.src.backend.common import standardize_dtype
from keras.src.backend.common.backend_utils import standardize_axis_for_numpy
from keras.src.backend.numpy.ops.core import convert_to_tensor
def cholesky(a, upper=False):
... |
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