sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
25af59128e09ad35809bb5253e0dfa870a11d5aa12baae1427076b5eef0f5c3f | Python | 20,327 | 477 | # -*- coding: utf-8 -*-
# Generated by the protocol buffer compiler. DO NOT EDIT!
# source: bream/protocol_communication.proto
"""Generated protocol buffer code."""
from google.protobuf import descriptor as _descriptor
from google.protobuf import message as _message
from google.protobuf import reflection as _reflectio... |
c2a5e60c61e9f3025853b70b6914244365928f98eaffcb66cb3632222a6001d5 | Python | 20,335 | 622 | import bottle
import subprocess
import socket
import logging
import traceback
import os
import optparse
import zipfile
import datetime
import fnmatch
import tempfile
import shutil
import netifaces
import json
from ethoscope_node.utils.device_scanner import EthoscopeScanner, SensorScanner
from ethoscope_node.utils.conf... |
c01cac9ca2b210aa8ba26b78996aa86848ec3da756a5a08019fb0673bb9c6e4c | Python | 20,352 | 596 | from array_api_compat import array_namespace as get_namespace
import numpy as np
from numpy.testing import assert_array_equal, assert_array_almost_equal
import pytest
from scipy.linalg import solve_continuous_lyapunov
from conftest import approx, to_numpy
from pyriemann.geometry.distance import distance, distance_riem... |
601f04b240ded6814c88699ef5cb634ac8ee1debb12a68ae299e7755748f55e2 | Python | 20,353 | 577 | """Code-derived universe censuses for the composition harness (compo rows 0.2-0.4).
Every derivation here consumes the ONE shared source parse
(``tests/_source_corpus.py``) -- independent AST walks are forbidden by the
compo memo (section 3.2, "one parse, many universes").
The two diagnostic censuses:
* **S-17 refus... |
a73756171072c79bb3c810aaca94808d777d30520686876ca3933c3f74d40fd6 | Python | 20,356 | 561 | import os
import io
import base64
import gc
from datetime import datetime
import warnings
import rasterio
import rasterio.features
import rasterio.warp
import numpy as np
import matplotlib.pyplot as plt
import ipyleaflet as L
import PIL
from tqdm.auto import tqdm
from tlib import tutils
from .utils import get_map
fro... |
c2c1ec153364dfea0f69aa093fcb463ab588b0d103649bb19653d02ae25b248d | Python | 20,357 | 527 | import os, sys
import numpy as np
import pandas as pd
import networkx as nx
from scipy.stats import mannwhitneyu
from sklearn.svm import SVC
from sklearn.metrics import accuracy_score
from sklearn.ensemble import RandomForestClassifier
from sklearn.feature_selection import SelectFromModel
from sklearn.cluster import Ag... |
2963f04339972d2a2b43f11f9a57855896f0198d74d9ba289e215f6bde6fb8fa | Python | 20,358 | 479 | import numpy as np
from cuteSV.cuteSV_genotype import cal_CIPOS, overlap_cover, assign_gt
import logging
import pickle
'''
*******************************************
TO DO LIST
*******************************************
1. Identify DP with samfile pointer;
2. Add CIPOS, CILEN and/or CIEND;
... |
9ec85b1edf35e71cadd3ed2bb834cb1b7339a0095f86d321e8fab913d630b92a | Python | 20,361 | 327 | import gc
import random
import os
from re import I
from agents.model_1d import *
from envs.tunl_1d import TunlEnv
import numpy as np
import torch
import matplotlib.pyplot as plt
from lesion_expt_utils import generate_random_index
import argparse
from tqdm import tqdm
from numpy import array
import re
import sys
sys.pat... |
79779a94e0fb0f4982efd559e0b414fbee7f84f7a781af8cce41e1b01467d809 | Python | 20,366 | 534 | import csv
import os
import shutil
import tempfile
import unittest
from dataclasses import replace
from unittest.mock import patch
import pandas as pd
from codecarbon.output_methods.emissions_data import EmissionsData, TaskEmissionsData
from codecarbon.output_methods.file import FileOutput
class TestFileOutput(unit... |
3d771e5e7c8352efc0c1c82c4bb1057da17469aed46438979f72aa489dbee779 | Python | 20,368 | 672 | import sys
from functools import partial
import torch
from slowfast.models.attention import attention_pool, MultiScaleAttention
from slowfast.models.common import drop_path, Mlp, TwoStreamFusion
from slowfast.models.utils import round_width
from torch import nn
from torch.autograd import Function as Function
class R... |
4ede3d47ba63b30604056bd4f2bfe1906febf6cbeaa51e9d392630592afa04ba | Python | 20,392 | 416 | #!/usr/bin/env python2
# -*- coding: utf-8 -*-
"""
@author: Pramod Bharadwaj Chandrashekar, Li Liu
@email: pchandrashe3@wisc.edu, liliu@asu.edu
"""
import argparse
import os
import time
import pickle as pk
import numpy as np
import sklearn.metrics as skm
import tensorflow as tf
import DeepCORE_data_util as ddu
from De... |
f0d36f89e255b42771bc5d0cdb36bd7f6944497e09404989426339a7d22fd4b6 | Python | 20,393 | 555 | """Input-boundary walking: one inert authority, witnessed arity, bounded descent (B3 L4).
Every case below was a live defect on main:
* classification probed ``_fields`` through the LIVE instance (``hasattr``), so a hostile
container's ``__getattribute__`` executed during ``snapshot_input_boundary`` -- the exact
... |
6423b4759bed2569b86b1f6c643893a43c6a74915a15b691d25b92c5f04a684f | Python | 20,394 | 423 | """
Contains library functions
"""
import json
import logging
import os.path
from typing import (
Any,
Protocol,
)
from markupsafe import escape
from galaxy import (
exceptions,
util,
)
from galaxy.managers.collections import DatasetCollectionManager
from galaxy.managers.collections_util import (
... |
4d8f26a3479c2784f23f25083bd4e776447f325116375741f8e7264b01f23a78 | Python | 20,396 | 621 | """
Chemical composition of food, odors and the experimental timeline.
Defines the compounds and substrates the larvae feed on, the odors sources
emit, and the life history and air-puff events that structure an experiment.
"""
from __future__ import annotations
import numpy as np
import param
from scipy.stats import ... |
62ea45f82fb6f89d1ce43c8489fd8b668bdbe93a88a03209aa3a06a5072f3cc4 | Python | 20,403 | 574 | """
Unit tests for Bug Report API endpoints.
Tests bug report generation including node system information collection,
device information collection, and error handling.
"""
import datetime
import unittest
from unittest.mock import MagicMock, Mock, patch
from ethoscope_node.api.bugreport_api import (
DEFAULT_LOG... |
11d373a839eee03b6826726a3eb3c8680e9c8d8c3a44d8dd157426cd73125ccc | Python | 20,404 | 496 | """The tlspec FORMAT CONTRACT: L1 product vocabulary + record-adjacent helpers.
The persistence four-way ruling (architecture memo 3.2): the format contract
and its record-adjacent helpers -- ``TLSPEC_VERSION``, ``FieldPolicy``,
``BlobRef``, payload load hints, version read, fill-state defaults, container
coercion -- ... |
a2490822a4f23688eb3b78d05d9ad0d486b97437b42b8b233f3f164802769ed5 | Python | 20,414 | 752 | # 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... |
973d7d97502da0772da69d7fb5b619bf5efa9eb123e06a5fef290d2184c89004 | Python | 20,425 | 656 | from __future__ import absolute_import, unicode_literals
import io
import os
import sys
import warnings
import functools
from collections import defaultdict
from functools import partial
from functools import wraps
from importlib import import_module
from distutils.errors import DistutilsOptionError, DistutilsFileErr... |
c90ff5978d7cee1d642a9268911818e6b2978f72f36856c6378842239d718a49 | Python | 20,426 | 677 | """Tests of correlograms for `pynapple` package."""
from contextlib import nullcontext as does_not_raise
from itertools import combinations
import numpy as np
import pandas as pd
import pytest
import pynapple as nap
def test_cross_correlogram():
t1 = np.array([0])
t2 = np.array([1])
cc, bincenter = nap... |
2aeadd19409175d52b65cc758bfc779df5a1c7b4c3bb5ef4f21b205c8df290ac | Python | 20,433 | 370 | import argparse
import os
os.environ["CUDA_DEVICE_ORDER"] = "PCI_BUS_ID"
os.environ["CUDA_VISIBLE_DEVICES"] = "1" # specify which GPU(s) to be used
from datetime import datetime
import numpy as np
import torch
from torch.utils.data import DataLoader
from external_src.group_free_3D.models import APCalculator, parse_... |
043b2d853103b1d11647a5b8435180678d6c90c69d295a0d3884acd01527df32 | Python | 20,436 | 582 | #!/usr/bin/env python
"""
Unit tests for TemperatureAlertMonitor class.
Tests the temperature monitoring and alert system including:
- Alert triggering when thresholds are crossed
- Alert suppression after first alert
- State reset when temperature normalizes
- Configuration-based enable/disable
"""
from unittest.mo... |
12b33a58c36e2a5c7995847fc3221a0b9e7d51bd4d21b579eb0f63070cce1453 | Python | 20,440 | 439 |
import numpy as np
import pandas as pd
import random
import pkg_resources
#from importlib import resources
from collections import defaultdict
from sklearn.preprocessing import OneHotEncoder
def prepare_encoders(hla_class, enc_method):
# load HLA pseudo sequence information for encoding
if hla_clas... |
fa81b59bb420e9ecefb7aab349933ed3a19b63597db7e8ec6a51ef44bc1d8b9a | Python | 20,445 | 327 | # -*- 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... |
b558c427b39f20292af05b44d27fcb9f66d46d3033bf9a4205b39a0748b8eed6 | Python | 20,454 | 529 | # FAITHFUL PORT of deepmodeling/CrystalFormer @ main (original framework: JAX / Haiku)
#
# CrystalFormer: "autoregressive transformer conditioning on Wyckoff positions
# and space group symmetry for crystal generation" (ICLR 2024). Source files:
# crystalformer/src/transformer.py (make_transformer -> the network fn)... |
eee02bee800d604b6c2ea37ec55076a01c7ce38acbec1fd2ad756cd7e85fc76c | Python | 20,456 | 519 | # --- 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 Line(_BaseTraceHierarchyType):
_parent_path_str = "parcoords"
_path_str =... |
f3e691348aae03a0a7af92198fe5d5542b5c68b3be9d3a9ef2563d5e39fa97ce | Python | 20,465 | 498 | #!/usr/bin/env python
# coding: utf-8
# In[1]:
from __future__ import absolute_import, division
from tqdm.auto import tqdm
import torch
import torch.nn.functional as F
from trainingUtils import MultipleOptimizer, MultipleScheduler, compute_kernel, compute_mmd
from models import Decoder, SimpleEncoder,LocalDiscrimina... |
5da29e3cdfb773cd390bca95ea3d028454725acbe4c0d5a4eb5cacb690306938 | Python | 20,469 | 600 | from __future__ import annotations
import copy
import json
from pathlib import Path
import panel as pn
import pytest
from larvaworld.lib import reg, util
from larvaworld.lib.reg import config as reg_config
from larvaworld.portal.config_widgets.preset_controls import (
ADVANCED_PRESET_POLICY,
USER_PRESET_POLI... |
67e6a2f0363da0b3f66430e74c3de88cf9a1087241d2086e457ba44195724881 | Python | 20,473 | 522 | #!/bin/env python3
# This script simulates a virtual hardware sensor with its corresponding network service advertisements
# and a RESTful API server.
# It uses the Zeroconf/mDNS protocol for service discovery on a local network and the Bottle framework
# for setting up HTTP endpoints. The virtual sensor can provide d... |
3c5bd8f5f9d060066c80650d5a4f10f0862da2a8bcfc62e14333b1cc470f38dd | Python | 20,477 | 574 | import logging
import os
from collections import defaultdict
from collections.abc import Callable
from datetime import datetime
from typing import (
Any,
NamedTuple,
Protocol,
)
from galaxy import exceptions
from galaxy.files.sources import (
BaseFilesSource,
PluginKind,
)
from galaxy.util.dictifia... |
f8628e8413ad1ea468528ba3ea3f6e9becc0e9940adb6c6e2f65bf5e20be10be | Python | 20,477 | 524 | """Unit suite for the M6 relation freeze (``_trace_core/relation_views.py``).
Covers the conversion mechanics directly on synthetic stores — edge
projection, differential CSR clearing vs explicit-view fallback, label
resolution failure modes — plus the end-to-end behavioral surface on real
captures: immutable views, C... |
35249488e0005a5b7a236f04386f785a1a6e673aba21f7d2115f4ecd3a91d281 | Python | 20,485 | 648 | """Utility functions for extracting data segments of interest."""
import numpy as np
from spiketools.utils.checks import check_axis, check_param_type
###################################################################################################
###################################################################... |
416ba2f94a97ed8d3c201d51cf5fb54aa59b218b485d5ec5c3faa6bb9f81150b | Python | 20,485 | 645 | import contextlib
import warnings
import networkx as nx
import numpy as np
from numpy import linalg as la
from scipy import linalg as spla
from scipy import sparse as sps
from scipy.sparse import csr_matrix, issparse, isspmatrix_csr, spmatrix
from scipy.sparse import linalg as sparse_spla
from scipy.stats import norm
... |
583ba161ce888370f0686ca349299f9481ec9a1bac28a078c2c24ba7bffe41e7 | Python | 20,488 | 663 | from functools import partial
from array_api_compat import array_namespace as get_namespace, device
import numpy as np
import pytest
from scipy.stats import hmean, gmean as gmean_sp
from conftest import to_backend, approx
from pyriemann.geometry.base import invsqrtm, logm, sqrtm
from pyriemann.geometry.geodesic impor... |
71b499f22cc87d2b827d344c2911f287594436d5d7066d1258c151afaeadda65 | Python | 20,491 | 611 | """
Boxplots
"""
from __future__ import annotations
from typing import Any, Optional, Sequence
import itertools
import numpy as np
import pandas as pd
import seaborn as sns
from scipy.stats import ttest_ind
from .. import plot, reg, util, funcs
__all__: list[str] = [
"boxplot",
"boxplot_PI",
"PIboxplot... |
0b10773c1138d184dc10e8f60d040372558c9196c2f1d0e22c2389a6893685d2 | Python | 20,493 | 476 | #!/usr/bin/env python3
"""
Dx BO — Deep HC-scoring AD subjects across cohorts (in-house data audit)
========================================================================
In-house data examination prompted by Spencer's recollection that the
original ds004504 cohort had ~4 AD subjects scoring well into the HC
range. ... |
820321cf7ddb49414fe94c3d99a5a3e6a510e845c785154d74e19201d3332949 | Python | 20,494 | 583 | """Tests for source-code panel visualization."""
from __future__ import annotations
import gc
import getpass
import html
import inspect
import os
import re
import weakref
from pathlib import Path
from typing import Any
import torch
from torch import nn
import torchlens as tl
from torchlens.visualization import code... |
40cb5e148349c179688fe32392f7d45426dbc7f2dc6202d22448126c84014eb3 | Python | 20,499 | 463 | """Auto pipeline for image classification task"""
# pylint: disable=bad-whitespace,missing-class-docstring,bare-except
import time
import os
import math
import copy
import logging
import pprint
import json
import pickle
from typing import Union, Tuple
import uuid
import shutil
import numpy as np
import pandas as pd
fr... |
62d809da205efb018a60ea1757628dd5d473f5f0c17807514e9aba15967660fc | Python | 20,499 | 536 | #!/usr/bin/env python
"""Unified SM90 benchmark for forward and backward passes.
Usage:
# Default: bench fwd+bwd for hdim 64,96,128 at seqlen 8192
python benchmarks/bench_sm90.py
# Forward only, specific hdims
python benchmarks/bench_sm90.py --direction fwd --hdim 64,96
# Backward only
python... |
ffcdbfc9f1bc01a2cf46d79aa880adb3d72a99853b7df4cbedca47c1c69f6df7 | Python | 20,509 | 604 | from typing import List, Dict, Tuple
import bokeh
import numpy
import numpy as np
import pandas as pd
import scipy
from bokeh import embed, layouts
from bokeh.io import export_svg
from bokeh.models import Span, Range1d, LinearAxis, ColumnDataSource, HoverTool
from bokeh.plotting import figure
from scipy import stats
... |
d5a2d36f601f30ba64f187a10215de51dd0476f7844592cc9f4d7dc60a9088f3 | Python | 20,519 | 397 | import numpy
import voxcell
class RegionHierarchyWrapper(object):
def __init__(self, hierarchy_fn):
self._tree = voxcell.RegionMap.load_json(hierarchy_fn)
def region_ids(self, lst_regions):
region_id_set = set()
for region in lst_regions:
region_id_set.update(self._tre... |
a0653d88a7cbb254f9fba710cc0d61f51c67634580a33dace69530efc4cc4fe8 | Python | 20,524 | 527 | # 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... |
91a3278f6cd55ec3281621e007c63bde80565d1eb88b1e670ac65ae66c41be34 | Python | 20,530 | 551 | # --- 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 Minor(_BaseLayoutHierarchyType):
_parent_path_str = "layout.xaxis"
_pat... |
ce05f04de0742977bd29a0eb13abe2e01e448a4b2fc785b4a55158f78a3ebc11 | Python | 20,530 | 551 | # --- 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 Minor(_BaseLayoutHierarchyType):
_parent_path_str = "layout.yaxis"
_pat... |
4744ee1cfa1de8d038d66318e7a0e5b29c47a74987ecc8e2da0adbc857938306 | Python | 20,542 | 507 | #!/usr/bin/env python3
"""
File: picalo_graphical_overview.py
Created: 2022/02/02
Last Changed: 2022/07/20
Author: M.Vochteloo
Copyright (C) 2020 University Medical Center Groningen.
A copy of the BSD 3-Clause "New" or "Revised" License can be found in the
LICENSE file in the root directory of thi... |
62331283333727b0f78392c27f969840dd1d332231c72ecca16ff8c0cd952063 | Python | 20,542 | 436 | #!/usr/bin/env python
# fix problems with pythons terrible import system
import sys
import os
file_dir = os.path.dirname(os.path.realpath(__file__))
sys.path.append(os.path.join(file_dir, '../'))
sys.path.append(os.path.join(file_dir, '../../'))
# package import
import prob2020.python.utils as utils
from prob2020.pyth... |
fe81ff29299346419b51fadfec6901b71103a2c9673bc7d319579c4fadbaf5a6 | Python | 20,543 | 580 | """
From Niklas Wilming et al. Nature Communications 2020
https://github.com/DonnerLab/2020_Large-scale-Dynamics-of-Perceptual-Decision-Information-across-Human-Cortex
"""
import os
from os.path import join
import mne
import pandas as pd
import numpy as np
from joblib import Memory
from . import preprocessing
import ... |
f4ee106ad5b3e1a45020d7c7ca80a46e05730d517714a822bda8f3b1b3047f4e | Python | 20,544 | 551 | __author__ = 'luis'
import logging
import traceback
from optparse import OptionParser
from ethoscope.web_utils.control_thread import ControlThread
from ethoscope.web_utils.helpers import *
from ethoscope.web_utils.record import ControlThreadVideoRecording
import subprocess
import json
import os
import glob
#from bott... |
ba49fd1281845daf738a5d71b7074a0d0bd5945af48bcde0ba2a46b618bd4e1f | Python | 20,547 | 518 | #!/usr/bin/env python3
"""
Dx BB — Severity stratification redo under proper per-fold
==========================================================
Re-runs the Dx Y / Dx Y2 severity-stratified sensitivity analysis
under the proper per-fold per-cohort-deployment pipeline used in
draft v0.79 / v0.80, instead of the legacy ... |
e9798c9422552b538dd4f72c87759c16264fc990a9b2b3114cdf2f5a05227060 | Python | 20,561 | 567 | import numpy as np
from absl.testing import parameterized
from keras.src import dtype_policies
from keras.src import layers
from keras.src import models
from keras.src import ops
from keras.src import saving
from keras.src import testing
from keras.src.backend.common import standardize_dtype
from keras.src.quantizers ... |
d6c05aac897445b9040eed13c4c1c8e0ec8ce9e314378d7a32840ea2255da6ea | Python | 20,565 | 563 | import abc
from abc import ABC
from os import path
from typing import Any
from typing import Callable
from typing import Dict
from typing import Optional
from typing import Tuple
from typing import Union
import dm_control
import gymnasium as gym
import mujoco
import numpy as np
from dm_control.mjcf import RootElement
... |
9d1e43ee4abc1cb293d2d8a2526d81e467d251aa5ebff309d4911d8df21a981a | Python | 20,593 | 527 | """
This file contains the object and CLI for training our VAEs.
The models themselves are in the `models/` directory. Each of these Python
files should have a `build` function that returns a dictionary with
entries for: encoder, decoder, and vae.
We also require each model to define a corresponding `prepare_data` fu... |
1ef89a038a58fa23d275b8d4c13e98f9eee643c0d13b79232cdb48bb6854699e | Python | 20,595 | 341 | # pylint: disable=wildcard-import, unused-wildcard-import, line-too-long
"""Model store which provides pretrained models."""
from __future__ import print_function
__all__ = ['get_model_file', 'purge']
import os
import zipfile
import logging
import portalocker
from ..utils import download, check_sha1
_model_sha1 = {n... |
847779ff1b064be4318a56f421d6a3af8b5ddd9087b6e3b1b6544d4d003a7704 | Python | 20,601 | 497 | # %%
import time
# %%
import brainpy.math as bm
import matplotlib.patches as patches
import matplotlib.pyplot as plt
import scipy.stats
from mpl_toolkits.axes_grid1 import make_axes_locatable
from scipy.io import loadmat
# %%
__all__ = [
'fig1',
'fig2',
'fig3',
]
# %%
dt = 1.
time2len = lambda t: int(t / dt)... |
90f885fef3e35ce96221074354f0c5cdeff00374d63b2d4d393e7d864c6b823d | Python | 20,601 | 573 | # -*- coding: utf-8 -*-
from __future__ import print_function, division, absolute_import
import torchvision.models as models
import torch.utils.model_zoo as model_zoo
import torch.nn.functional as F
import types
import re
#################################################################
# You can find the definitions ... |
763da4005823843940bc1778b1071d47fdb30f351b0cffbb4b047ebcfde556e3 | Python | 20,603 | 615 | import os
import json
from pathlib import Path
from typing import Union, List
import importlib.metadata as importlib_metadata
from packaging.version import Version
import warnings
import plotly
from plotly.io._utils import validate_coerce_fig_to_dict, broadcast_args_to_dicts
from plotly.io._defaults import defaults
fr... |
078081b7aee0e0f879df2f4a7f66f7dc1c2872114800a84b55b3f29e463d8832 | Python | 20,618 | 523 | import os
from process import *
from training import *
from model import *
import torch
import settings
import time
import pickle
def main(
##########
work_name,
run_mode,
data_mode,
model_name,
train_size,
fingerprint,
random_state,
model_path,
load_model,
cuda_id,
###... |
b075f26f963773af9ff5afc87d0ce8461387c2c68814b8341d4cf8831133d4a9 | Python | 20,620 | 468 | """Core API for Environment, Wrapper, ActionWrapper, RewardWrapper and ObservationWrapper."""
import sys
from typing import (
TYPE_CHECKING,
Any,
Dict,
Generic,
List,
Optional,
SupportsFloat,
Tuple,
TypeVar,
Union,
)
import numpy as np
from gym import spaces
from gym.logger imp... |
c49abc2aeffa32415892831183f08ba158aeb4652cc491aed01c45d0639b1476 | Python | 20,622 | 551 | # --- 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 Marker(_BaseTraceHierarchyType):
_parent_path_str = "icicle"
_path_str = ... |
d1e487e8a04094647016402f0e3a87b24fc230d30e8d09b9b098fbe4ce9117f9 | Python | 20,623 | 491 | import random
import matplotlib.pyplot as plt
import networkx as nx
import numpy as np
import pandas as pd
import scanpy as sc
import scipy
from sklearn.metrics import pairwise_distances, pairwise_distances_chunked
from tqdm import tqdm
from .visualize import link_plot
def coords2adjacentmat(coords, output_mode="ad... |
d0b8c7f5244f3f91677945861212e2eb995f9c50a60381b1eefe69c5894b6d9f | Python | 20,634 | 427 | from typing import Optional
import pandas as pd
import numpy as np
import networkx as nx
import scanpy as sc
from sklearn.linear_model import LinearRegression as lr
from matplotlib import pyplot as plt
from matplotlib_venn import venn3
import matplotlib.ticker as ticker
from matplotlib.pyplot import rc_context
import... |
361eb0e524a1a18c7b0604c9869e8e737d47de1e31ec0df4317d236d9d1f081c | Python | 20,654 | 446 | # -*- coding: utf-8 -*-
from __future__ import print_function, unicode_literals, absolute_import, division
import warnings
import numpy as np
from six import string_types
from csbdeep.internals.probability import ProbabilisticPrediction
from .config import Config
from .base_model import BaseModel, suppress_without_ba... |
01791482e16e14f73409fdcf620e7d8ae7f9f086d92cba20109c701e1d981463 | Python | 20,657 | 628 | """PYTEST_DONT_REWRITE
Targeted corruption tests for Phase 6 conditional metadata invariants.
"""
from __future__ import annotations
from collections.abc import Iterable
import pytest
import torch
import torch.nn as nn
import torchlens as tl
from torchlens import trace as trace_fn
from torchlens.data_classes.layer... |
ebea615aedea9572f1e00e9ac25b814b75f64e737238ed06c4eabaf0bb9463dd | Python | 20,663 | 555 | """
Code here relates to the creation of stimulus waveforms from epoch tables.
In the waveform editor of ClampEx, you can edit the stimulus waveform table
for each channel (DAC). Each waveform table is made of epochs, which appear
as a single column of values in the waveform editor.
The overall strategy here is that ... |
c9813ab7620e19a6acc2fa299c08be24d844a3d93be10dbc2329c745fd168b8a | Python | 20,664 | 552 | # --- 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 Marker(_BaseTraceHierarchyType):
_parent_path_str = "sunburst"
_path_str ... |
142920d8b9e1303470f41d8ab01a1988ef774cf58a3e94744d5f76e92cd3df8f | Python | 20,668 | 480 | #!/usr/bin/python3
##########################################################################
## ##
## Copyright (c) 2019 Philipp Lösel. All rights reserved. ##
## ##
#... |
5355c055d153b73fdd13f56a43782c9a583c3a88ac1391d8a46977992ba75221 | Python | 20,675 | 627 | """Regression tests for multi-output module handling."""
from __future__ import annotations
from collections import namedtuple
from collections.abc import Iterator
from dataclasses import dataclass
from typing import Any
import pytest
import torch
from torch import nn
import torchlens as tl
from torchlens.errors im... |
54295a2dc03fe2e871589ce4ae908592684ef8e7c43610a05a5657cbe09c2ab4 | Python | 20,679 | 555 | """Sibling-order rank groups sit in a cluster holding all members; failed ordered layouts fall back.
Graphviz 16 fails ("trouble in init_rank"), crashes, or warns "already in a rankset, deleted from
cluster" on a top-level ``rank=same`` set whose members sit inside clusters; a set emitted inside a
cluster may span tha... |
bb3bc73d79e7758eabf2865b2a4d92613b8ddcf0d26160f5b5498224d4b7b2d2 | Python | 20,689 | 525 | """Module that contain shard utils for dynamic data."""
import os, re
from bioseq2seq.utils.logging import logger
from bioseq2seq.constants import CorpusName
from bioseq2seq.transforms import TransformPipe
from bioseq2seq.inputters.dataset_base import _dynamic_dict
from torchtext.data import Dataset as TorchtextDataset... |
0a4640690f95c0822e417ec75868efb668dfda83c0a58510bd44c2761519df90 | Python | 20,707 | 569 | # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
"""Functions to support ingression of non-BIDS preprocessing derivatives."""
import filecmp
import json
import os
import shutil
import numpy as np
import pandas as pd
from nilearn import image, maskers
fr... |
06b0a0a398e18d2daed32d19de7c389113bd43a6f0ea617336cae0118635b201 | Python | 20,709 | 576 | __author__ = "quentin"
import logging # noqa: F811
import time
import cv2
try:
CV_VERSION = int(cv2.__version__.split(".")[0])
except Exception:
CV_VERSION = 2
try:
from cv2.cv import CV_AA as LINE_AA
from cv2.cv import CV_CHAIN_APPROX_SIMPLE as CHAIN_APPROX_SIMPLE
except ImportError:
from cv2 ... |
4807de3e16d91ed397249472ce50e3ff1eab988a85abac50281a6384316541b9 | Python | 20,712 | 544 | """Episode capture (capture_kind=episode): S7 ledger + typed refusals.
Covers the L2 core contracts ratified at S2: the session ledger written at
settlement, the monotone prefix law and token presence rule as load
tripwires, every episode TYPED-REFUSE row, the E-A4 declaration-time
refusal, teacher forcing as a disclo... |
99aef12f18e368388453e68bc8a10df30c4dcc36b2504c489877ff1b52d56c7d | Python | 20,716 | 456 | r"""
Homoclinic Continuation in a QIF Mean-Field Model
===================================================
This example demonstrates PyCoBi's support for auto-07p's HomCont extension
(:math:`IPS=9`, AUTO manual Ch. 20) via three new entry points:
* The ``'hom'`` scenario in ``auto_constants=(...)`` generates a ``c.ho... |
7397b5af87017cdfa4c9b546909b7f29a2e518aa1fb240e6071a9d3776b34aee | Python | 20,738 | 528 | # SOURCE: vendored from IDKiro/CBDNet-pytorch @ 09a2e55, ZitongYu/CDCN @ fd8370e, apourchot/CEM-RL @ 1a45822, MingLunHan/CIF-PyTorch @ 48c581e
from __future__ import annotations
from types import SimpleNamespace
import torch
import torch.nn.functional as F
from torch import nn
class CbdSingleConv(nn.Module):
""... |
dd1a43e4e56943f6d0955c93d803ad562a1bd0adc3b6d40984813256d4010290 | Python | 20,742 | 512 | """Capability-table load-bearing conformance.
The registered ``BackendCapabilities`` table must be the single authority for
backend feature support, fail-closed in BOTH directions on EVERY backend:
- Flag ``False`` refuses the corresponding public surface typed — torch
included, so an in-place flip of torch's table... |
e5263e578f810d652fdb442082e4f516e613ae3a78d7a30b57a1d9a70a1dae11 | Python | 20,743 | 645 | """Data-specific colormaps"""
from itertools import cycle
import logging
from math import ceil
from numbers import Real
from typing import Sequence, Tuple, Union
# colormath starts out at 0; needs to be set before init
logger = logging.getLogger('colormath.color_conversions')
if logger.level == 0: # otherwise it was ... |
f8d269591cbb8f79490b529f4d0184d6694d315ac0904e95c3af986c7c345448 | Python | 20,743 | 557 | """Episode join arms (lane F40c): live + settlement ``step_join``.
The trace-verb verdict's mid-call oracle break contract: per-row join grades
(continuous / transformed / declared / exogenous / unchecked), the DEFAULT
return-and-disclose arm with episode-dependent claims refused across a
measured break, the FORK-4 ``... |
9df74d4cecee8be82a6992d89f0b59e79ddf7eeb8c97978b3078d385ca7f9e72 | Python | 20,750 | 439 | # Ultralytics 🚀 AGPL-3.0 License - https://ultralytics.com/license
"""
Check a model's accuracy on a test or val split of a dataset.
Usage:
$ yolo val model=yolo26n.pt data=coco8.yaml imgsz=640
Usage - formats:
$ yolo val model=yolo26n.pt # PyTorch
yolo26n.torchscript ... |
aceca58f56f34951ed9e9ee7c3a7152c99647664ee6c8f25f701f867644674d4 | Python | 20,750 | 637 | # Copyright 2025 Google.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, soft... |
f1ee254cc08d5fdcc95e83dcd494816001d41d5547cc0e66f0dd1a3ddf96d99f | Python | 20,753 | 630 | # SPDX-License-Identifier: LGPL-2.1-or-later
#!/usr/bin/env python
#-*- coding: utf-8 -*-
import os
import time
import calendar
import sys
from collections import OrderedDict, Counter
import numpy as np
from .general import check_directory
h = u"antenna, incorrect transitions count, percentage of antenna recordings\n"... |
1f8892df20264db0876b4b9d70e0acb57442066965568ecfeb91b4284c49a87a | Python | 20,755 | 530 | from spitfire.chemistry.flamelet2d import _Flamelet2D
from spitfire.chemistry.flamelet import Flamelet
from spitfire.chemistry.mechanism import ChemicalMechanismSpec
from spitfire.time.integrator import Governor, NumberOfTimeSteps, FinalTime, Steady, SaveAllDataToList
from spitfire.time.methods import AdaptiveERK54Cash... |
0b5a6004b3c1c04da10d3f32e20b6d4e2d7e7c921d22f3d77f3fe81150981ffe | Python | 20,759 | 470 | #!/usr/bin/env python3
"""run_downsample_wafer.py
Top level command-line interface for downsampling images from a wafer from
native resolution (4nm) to the pipeline resolution (typically 16 nm).
Copyright (C) 2018-2026 Max Planck Institute for Neurobiology of Behavior
This program is free software: you can redistr... |
d5fa719ab97f1a9b26448c4a0205b48dc19893513260275389a905c8688a539e | Python | 20,762 | 567 | import torch
import torchaudio
import random
import numpy as np
import sys
import chcochleagram
from chcochleagram import compression
from chcochleagram import cochleagram
from chcochleagram import *
def ch_demean(x, dim=0):
'''
Helper function to mean-subtract tensor.
Args
----
x (tensor): te... |
612c3f2f4715265b0708986fd3a3bdd8414f95208eea0948671ed76fca0dbe67 | Python | 20,768 | 535 | import logging
import os
os.environ["CUDA_VISIBLE_DEVICES"] = '2'
os.environ["CUDA_DEVICE_ORDER"] = "PCI_BUS_ID"
from argparse import ArgumentParser
import json
import re
from tqdm import tqdm, trange
from pprint import pprint, pformat
import time
from datetime import timedelta
from shutil import copyfile
import pytor... |
dcdc89693dcc6823247cd50661e9772bcf7e7fb2d7f81f30b33a1de6a012911a | Python | 20,769 | 478 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Sun Nov 22 16:39:34 2020
@author: emilia
"""
import numpy as np
import torch
import itertools
import seaborn as sns
import matplotlib.pyplot as plt
import src.plotting_funcs as cplot
from scipy.stats import vonmises
from src.helpers import check_path
def ... |
dee347b61f8242a286eb60e2dc88060431ea9bf192e66760f608c95970971e01 | Python | 20,771 | 563 | """Miscellaneous utility interfaces."""
import json
import os
import h5py
import numpy as np
import pandas as pd
from nipype import logging
from nipype.interfaces.base import (
BaseInterfaceInputSpec,
File,
OutputMultiObject,
SimpleInterface,
TraitedSpec,
Undefined,
isdefined,
traits,
... |
ba900d0b54f54239c55e9407139dc71494e58154254908df324d9c2e20921d16 | Python | 20,773 | 402 | # 2022/2023 Josue Page Vizcaino pv.josue@gmail.com
# Third party libraries imports
import matplotlib.pyplot as plt
import numpy as np
import torch
import torch.nn as nn
from torch.utils import data
from torch.utils.tensorboard import SummaryWriter
from torch.utils.data.sampler import SubsetRandomSampler, SequentialSam... |
f270c7e5640bdaa369ca9ff94a95a5b50c55bc6d4b8d70965ba3475b68f24522 | Python | 20,780 | 565 | import multiprocessing
import time
from multiprocessing import Pool
import networkx as nx
import numpy as np
import scipy.sparse
from scipy.spatial import distance_matrix, minkowski_distance, distance
from sklearn.ensemble import IsolationForest
# Calculate graph, return adjcency matrix in 0/1
def generateAdj(featur... |
a68b5e77e60ebe7263b82e21ad39212dc838218b0a15052f9f7251b00be87836 | Python | 20,782 | 544 | """Robustness sprint PR 2 — tensor-variant pre-flight guard + channels_last fix.
Covers the tensor-variant subset of the catalog:
- Meta tensors in inputs/params must be caught up front with a clear message
rather than crashing partway through the 18-step postprocess pipeline.
- Sparse tensors in inputs... |
d2444b2f3d4ca4fb5abd8c5adf921fdd8406bb4b7ef76dd309557faedaa48328 | Python | 20,786 | 516 | """COCO evaluation utils"""
# pylint: disable=line-too-long, redefined-builtin
import contextlib
import copy
import io
import itertools
import json
import logging
import os
import pickle
from collections import OrderedDict
import numpy as np
import torch
import pandas as pd
from .. import comm
from ...data.registry.c... |
91302a81d99f9297c9d5f88cc254cb2ff392a58cdc5c1a22bd5a8c7b108a8d4b | Python | 20,812 | 573 | from functools import partial
import matplotlib.pyplot as plt
plt.switch_backend('agg')
from tqdm import tqdm
from rdkit.Chem import MolFromSmiles
from rdkit.Chem import Draw
import numpy as np
import rdkit
from rdkit import Chem
from rdkit.Chem import AllChem
import os
import AttentiveFP.Featurizer
from AttentiveFP.F... |
b7616ed2b0079f200497902179343e9574ee86bddf13a0364d4ec2520e9d8f0a | Python | 20,815 | 532 | """Hardening tests for loop/recurrence grouping (round-21, follow-up 2).
Locks the fixes for the two round-20 review findings the first r21 loop fixer did
not cover:
* Exact parameter identity must not override module identity or non-tensor call
semantics (review cluster 2). Two DISTINCT modules deliberately sharin... |
b0ee873ba3029e8a8dde26ad589b32552e911bf92792e5d58b74c1887ce41122 | Python | 20,816 | 608 | import os
import numpy as np
import matplotlib.pyplot as plt
from tqdm.auto import tqdm
from tlib import tutils
from . import geotif
from .utils import get_ndvi, get_evi, get_map
from .landcover import plot_legend
from .kml import subfolders_to_kml
# plotter
class Plotter:
def __init__(
self,
... |
3ad46f2b3f3176997eeefdeafd94da4bd7dd06df57af33326a9811af9d2e05b3 | Python | 20,841 | 594 | # Adapted from https://github.com/ELS-RD/kernl/blob/main/src/kernl/implementations/linear_layer.py
# and https://github.com/openai/triton/blob/master/python/triton/ops/matmul.py
from typing import Optional
import torch
import triton
import triton.language as tl
from triton.ops.matmul_perf_model import early_config_pru... |
d4f67b3cc9d72456c5d0c74c87279a044488b14ed9b45d607bb4ce13713dcb5f | Python | 20,845 | 476 | import torch
import torch.nn as nn
import torch.nn.functional as F
from opt_einsum import contract as einsum
import torch.utils.checkpoint as checkpoint
from util import cross_product_matrix
from util_module import *
from Attention_module import *
from SE3_network import SE3TransformerWrapper
from icecream import ic
#... |
531a8188eea7cb565f9880a6a16f50d979879a03493215f9f40eabef6f75697b | Python | 20,847 | 441 | #!/usr/bin/env python
# fix problems with pythons terrible import system
import sys
import os
file_dir = os.path.dirname(os.path.realpath(__file__))
sys.path.append(os.path.join(file_dir, '../'))
sys.path.append(os.path.join(file_dir, '../../'))
# package imports
import prob2020.python.utils as utils
from prob2020.pyt... |
1c1188ce77a6232fa52283358a3144d14a53be6c182563697b1f324d491a5798 | Python | 20,861 | 577 | import functools
import math
import re
import shutil
import rich
import rich.console
import rich.markup
# See https://github.com/keras-team/keras/issues/448
# for below imports
import rich.table
from keras.src import tree
from keras.src.backend.common import standardize_dtype
from keras.src.utils import dtype_utils
... |
5629c9082329faf46fc62b89b51133fb57720a671c3f8ae281b029c04636ce03 | Python | 20,864 | 498 | from typing import Optional, Sequence, Tuple
import torch
import torch.distributed as dist
from torch import Tensor
from torch.nn import Module
from lightly.loss.vicreg_loss import (
VICRegLoss,
covariance_loss,
invariance_loss,
variance_loss,
)
from lightly.models import utils
from lightly.utils.dist... |
e2b9e8a481e8350d269265e83dcd06f5a6940ad95d166925af3019960569fca1 | Python | 20,873 | 582 | """Compact faithful reimplementations for dependency-gated REIMPL3 batch 3.
Paper: Graphormer, Exphormer, GVP-GNN, HyperNetworks, Occupancy Networks, GIRAFFE.
The models in this module are deliberately small random-initialized PyTorch
reconstructions of install-heavy architectures. Each keeps the audited
load-bearin... |
239a25d85cb0b73f88d3d8781fa9d05fc30d28219c276cc657f1b7e790e842ee | Python | 20,874 | 570 | """Tests for PyTorch backend core utilities."""
import concurrent.futures
import threading
import numpy as np
import pytest
import torch
from absl.testing import parameterized
from torch._dynamo.testing import CompileCounter
from torch.distributed.device_mesh import DeviceMesh as TorchDeviceMesh
from torch.distribute... |
840e8326aeac24b7a62b8f15825fe57cc933dfe5bfc79f6c6f34582842becbf4 | Python | 20,884 | 600 | """
Body geometry of the simulated larva.
Defines the stored body plans, the contour they generate, and the segmented
body whose joints the locomotor drives. Also provides the sensor mounting
points used by the touch modality.
"""
from __future__ import annotations
from typing import Any, Optional, Sequence
import n... |
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