sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
f4facfd8a630bae5793af9aa9011ae9d171b894be158bc86cf594f8642207d73 | Python | 60,302 | 1,095 | #!/usr/bin/env python3
import os
import sys
#import time
os.system('date')
#time.sleep(60)
#sys.exit(0)
"""run_wafer.py
Top level command-line interface for the running the matching for the fine
alignment and for exporting sections for a whole wafer at different
stages of the alignment.
Copyright (C) 2018-2026 M... |
61c61341e2a871cb65934d503e252a2ba023a2c11703e1558a61adff020c71cf | Python | 60,410 | 1,292 | import os
import math
import itertools
import pytest
import torch
import torch.nn.functional as F
from torch._C import parse_schema
from torch.testing._internal.optests.generate_tests import (
safe_fake_check,
safe_schema_check,
safe_aot_autograd_check,
)
from einops import rearrange, repeat
try:
from... |
52834eab3677e0c4be31d8736e83242e0ae2fe60473fa2c6e58e3cc3a283a43d | Python | 60,420 | 1,090 | #!/usr/bin/env python3
import os
os.system('date')
"""run_wafer_aggregator.py
Top level command-line interface for aggregating the alignments computed
for the rough and fine alignments by applying the LSS.
Copyright (C) 2018-2026 Max Planck Institute for Neurobiology of Behavior
This program is free software: you... |
d0bed8c33ea18e7414c4edac77850d44dae0f4ec3846f6e8a3ed607c05cab8e8 | Python | 60,455 | 1,171 | import pickle
import torch
import torch.nn.functional as F
from trainingUtils import NBLoss,_convert_mean_disp_to_counts_logits #,MultipleOptimizer, MultipleScheduler, compute_kernel, compute_mmd
from models import Encoder,Decoder,GaussianDecoder,VAE,CellStateEncoder,\
CellStateDecoder, CellStateVAE,... |
98534f5ea7bb579aa9f009c9ee603ab04ca3d4fed99b421a61407f6cded9c776 | Python | 60,492 | 1,394 | #!/usr/bin/env python
"""This program performs BSA and associated statistics"""
import sys
import re
import argparse
import math
import multiprocessing
import os
import random
import subprocess
from decimal import Decimal
from itertools import permutations
from numpy import percentile
import matplotlib
matplotlib.u... |
3d82396d8b3943ef6cd6df87bbb17c6ab164e7ebc67e49193b5f0c1fb14e01cb | Python | 60,494 | 1,560 | from __future__ import annotations
import abc
import json
import logging
import os
import sys
import time
from collections.abc import Sequence
from datetime import datetime
from typing import Optional, Union
import minknow_api.manager
from google.protobuf import json_format
from google.protobuf.duration_pb2 import Du... |
c5bba81d96e1c0a466822a9a5794d472638412a280a601dec8cd8263cc2558b8 | Python | 60,518 | 1,395 | #!/usr/bin/env python
"""This program performs BSA and associated statistics"""
import sys
import re
import argparse
import math
import multiprocessing
import os
import random
import subprocess
from decimal import Decimal
from itertools import permutations
from numpy import percentile
import matplotlib
matplotlib.u... |
073d920b12aeef45322bd34fa40e8bb71fd567a8cc618ab2f6a2f857f87c2a0a | Python | 60,573 | 1,596 | # --- THIS FILE IS AUTO-GENERATED ---
# Modifications will be overwitten the next time code generation run.
from plotly.basedatatypes import BaseTraceType as _BaseTraceType
import copy as _copy
class Scattercarpet(_BaseTraceType):
_parent_path_str = ""
_path_str = "scattercarpet"
_valid... |
3bb1606b7cd0f4cca8a7932bdcdb7678e6a80fc9d347924bfb69b572896eaa6d | Python | 60,611 | 1,469 | # coding=utf-8
# Copyright 2018 The OpenAI Team Authors and HuggingFace Inc. team.
# Copyright (c) 2018, NVIDIA CORPORATION. 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... |
d0b100eaace06ab80c7b64e8de3a128d36a9f78deefad0d81b5d5d97719d7415 | Python | 60,667 | 1,405 | import torch
import torch.nn as nn
import torch.nn.functional as F
from torch.nn import init
import functools
from torch.optim import lr_scheduler
import numpy as np
from .stylegan_networks import StyleGAN2Discriminator, StyleGAN2Generator, TileStyleGAN2Discriminator
# from IPython import embed
######################... |
371891439b5ed0cd46e31fc6e22c8bf59b071c0b1a1c46d2a7ce2fe52ac533cd | Python | 60,854 | 1,196 | #####train scGNN
import argparse
import datetime
import os
import os.path
import pickle
import pickle as pkl
import sys
sys.path.append('../pkgs/scGNN/')
import time
import networkx as nx
import numpy as np
import pandas as pd
import scipy.io
import scipy.sparse as sp
import torch
from benchmark_util import *
from gae... |
22481ba4039aeff592f282df1f9fe785e1049b219b35b4c5bc6339f169ec022d | Python | 60,890 | 1,729 | '''
Copyright 2023 Douglas Feitosa Tomé
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
This program is distributed in the hop... |
9a76b84cc64c0d6d815ff9554f74d506bdc9154c4457630db388d0cd66bdd55d | Python | 60,911 | 1,714 | """The extraction v2 store pipeline and run engines (extract D13 + F18).
One manifested order per batch::
collate -> position/mask validation -> model call -> selected output
-> pool (captured dtype, raw axes, mask) -> postprocess(output, ctx)
-> row + logical-shape validation -> per-key s... |
bd2629621421def0c61fe1eee192609f09d91dc2eb3d549f8b7a7bbfba773084 | Python | 60,972 | 1,636 | # --- THIS FILE IS AUTO-GENERATED ---
# Modifications will be overwitten the next time code generation run.
from plotly.basedatatypes import BaseTraceType as _BaseTraceType
import copy as _copy
class Pie(_BaseTraceType):
_parent_path_str = ""
_path_str = "pie"
_valid_props = {
"... |
915b4a77f17794e3c477d8cb8f970608c68905528ce37008dd367fb8d63e6df7 | Python | 60,988 | 1,804 | # --- 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 Aaxis(_BaseTraceHierarchyType):
_parent_path_str = "carpet"
_path_str = "... |
f1020a192664c2301acc6cf8fa90350ec45c4eee17469c6137f1b13cedf99226 | Python | 60,988 | 1,804 | # --- 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 Baxis(_BaseTraceHierarchyType):
_parent_path_str = "carpet"
_path_str = "... |
c3b80acdd7d35b1a03b7f64cd11b202cf4305c1f8894573ee492c5a178a5befa | Python | 61,238 | 1,371 | # Copyright (c) 2025, Tri Dao.
from functools import partial
from typing import Optional, Tuple
import cutlass
import cutlass.cute as cute
from cutlass import Int32, Boolean, const_expr
from cutlass.cute.nvgpu import tcgen05
from cutlass._mlir.dialects import llvm
import flash_attn.cute.mma_sm100_desc as sm100_desc
... |
6ac5ab34f20024742c42188e1f30beb89d7e9368e10c00643ac4a708731d400e | Python | 61,273 | 1,669 | """
Ground-truth DEB equations for the holometabolous insect (Drosophila) model.
This module is a verbatim transcription of the authoritative model specification:
* **Table S1** -- fluxes for the metabolic processes (per life stage)
* **Table S2** -- state variables and model dynamics
Both tables are reproduced in f... |
c7ca1ae8420341ef40e9ea538dd8bde01d8d32fa20e94493aa0d4e86e9eff8f9 | Python | 61,274 | 1,849 | #!/usr/bin/python3
# -*- coding: utf-8 -*-
# Information theoretic analysis EEG microstates
# Ref.: von Wegner et al., NeuroImage 2017, 158:99-111
# FvW (12/2014)
"""
- .format() => f""
- function documentation
- ms sequence temporal smoothing
- all clustering algorithms
- ms re-ordering: TextWidget due to plt.ion/plt... |
44029c5d14170d948c5c949e7aeeb991437af77c39bc80fa5dc624b3ebf90ed7 | Python | 61,277 | 1,602 | # --- THIS FILE IS AUTO-GENERATED ---
# Modifications will be overwitten the next time code generation run.
from plotly.basedatatypes import BaseTraceType as _BaseTraceType
import copy as _copy
class Scattergeo(_BaseTraceType):
_parent_path_str = ""
_path_str = "scattergeo"
_valid_props... |
cbdedd7b9f6126b6a819d5acd69d7461e927ac8b57d3f92bdbb0815daff9d88c | Python | 61,282 | 1,520 | """Tigramite causal inference for time series."""
# Author: Jakob Runge <jakob@jakob-runge.com>
#
# License: GNU General Public License v3.0
import numpy as np
import math
import itertools
from copy import deepcopy
from collections import defaultdict
from tigramite.models import Models
import struct
class Graphs():
... |
01f1a324084b8ddb6a1d9e178b32b1fed4eaf846bfe4dff7db0439917bcbc11b | Python | 61,324 | 1,549 | """Round-36 regression harness: every r36 witness/exec finding pinned at the class level.
Each test pins the AGREED post-r37 contract (round-37 cross-lab plan):
* hon2_1/hon2_2/hon2_3/corr2-1 -- INV-1 single-exit escape/event attribution: no
value-collision, no ``.item()`` re-extraction, no autograd-purity argument... |
53967bb604db40934b8a9a1766c0884c5fe62d9722485a64bbafb1ece7e55ef5 | Python | 61,454 | 1,569 | # Copyright (c) 2024 PaddleHelix Authors All Rights Reserved.
#
# Licensed under Creative Commons Attribution-NonCommercial-ShareAlike 4.0
# International License (the "License"); you may not use this file except
# in compliance with the License. You may obtain a copy of the License at
#
# http://creativecommon... |
ddc0f6069ac729213de22c6ffada4bd0811e13d7269406b7faeef28395157e61 | Python | 61,631 | 1,418 | """Skip-surface audit (R79): make every skip in tests/ honest and auditable.
Three enforcement layers:
1. **importorskip ledger.** Every ``pytest.importorskip`` target in tests/ must
appear in ``IMPORTORSKIP_LEDGER`` with an availability tier, so a skip is
always attributable to a *known* class of absence:
... |
cc8eabb582df88a94a345e671b562adcb336ff7a1478bac96b315b1434cbe031 | Python | 61,779 | 1,708 | # --- 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 ColorBar(_BaseTraceHierarchyType):
_parent_path_str = "cone"
_path_str = ... |
7c683b0e311c45a00440e470db9bba05bb8489d2c0b3aba6180a69b1972b4461 | Python | 61,809 | 1,657 | from interpretability.utils import load_sequences
import numpy as np
from sklearn.model_selection import KFold
from sklearn.metrics import average_precision_score, precision_recall_curve
from sklearn.metrics import classification_report
import matplotlib.pyplot as plt
import torch
from os import walk
import os
from dif... |
371cf62c2c6fe3e5aa1afe893719d7994209aecf215e0dc4fe1435c3c3cc19d1 | Python | 61,837 | 1,709 | # --- 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 ColorBar(_BaseTraceHierarchyType):
_parent_path_str = "volume"
_path_str ... |
d91326012511300724aad2c08613147bfaa330f5651614ed985bcb88eff54b0d | Python | 61,837 | 1,709 | # --- 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 ColorBar(_BaseTraceHierarchyType):
_parent_path_str = "mesh3d"
_path_str ... |
7490e9b7682c3d9b313c8b9b1fa9eef9dbd46fe9c96de7ba825d770ea3ae9d93 | Python | 61,860 | 1,709 | # --- 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 ColorBar(_BaseTraceHierarchyType):
_parent_path_str = "heatmap"
_path_str... |
7f569ad837dee86c9474373b3e8375c4cf213137897e7e9f12fa4f6db32e56c1 | Python | 61,860 | 1,709 | # --- 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 ColorBar(_BaseTraceHierarchyType):
_parent_path_str = "contour"
_path_str... |
8cdc36951477c6f57217e402c09532fcb5567344e29ef2487078d073c903f7e8 | Python | 61,860 | 1,709 | # --- 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 ColorBar(_BaseTraceHierarchyType):
_parent_path_str = "surface"
_path_str... |
1fea2300010920ae4db64462d9ba486ec8d8abb369671248f952b95e4ec4de70 | Python | 61,882 | 1,608 | import json
import os
from datetime import datetime, timedelta, timezone
from pickle import dumps, loads
from unittest.mock import Mock, patch
import pytest
from kombu.utils.encoding import ensure_bytes
from celery import states, uuid
from celery.app.task import Context
from celery.exceptions import ImproperlyConfigu... |
2c0c8eb8008295f72167661ca54eb9d947b95a48ed2bc2bd36345442d6b3c262 | Python | 61,922 | 1,708 | # --- 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 ColorBar(_BaseTraceHierarchyType):
_parent_path_str = "streamtube"
_path_... |
426bef7befa21566aaf26af127d99e755ce5c4e7987ea5b98ca6de3a1e39beaa | Python | 61,922 | 1,708 | # --- 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 ColorBar(_BaseTraceHierarchyType):
_parent_path_str = "isosurface"
_path_... |
5b31bd7ebcf983ac7de92106de47daeee52f845792f35bfded762a88d5bee011 | Python | 61,922 | 1,708 | # --- 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 ColorBar(_BaseTraceHierarchyType):
_parent_path_str = "bar.marker"
_path_... |
8bb37b9d2082e17fd6f88ebedaee8d4c61cc3f421b33cd5235b5ae49dfb632a5 | Python | 61,922 | 1,708 | # --- 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 ColorBar(_BaseTraceHierarchyType):
_parent_path_str = "choropleth"
_path_... |
fdc6924b41321e05c1bbb8adb2c35cf677120e4659edf8f381f05b81f03945d6 | Python | 61,922 | 1,708 | # --- 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 ColorBar(_BaseTraceHierarchyType):
_parent_path_str = "densitymap"
_path_... |
d662073b13546df81be51ad05485cc7f6e16a74574822f0fed8b5d56743e0be9 | Python | 61,955 | 1,709 | # --- 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 ColorBar(_BaseTraceHierarchyType):
_parent_path_str = "histogram2d"
_path... |
06049b757cf082e5462277f6c46df8f183c1bcad083dc246a90040302e438c11 | Python | 61,978 | 1,709 | # --- 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 ColorBar(_BaseTraceHierarchyType):
_parent_path_str = "splom.marker"
_pat... |
7111dabce346e6eea5075ae787d64ee64f480caa1f7de79069fe193c7b0c917d | Python | 61,978 | 1,709 | # --- 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 ColorBar(_BaseTraceHierarchyType):
_parent_path_str = "parcats.line"
_pat... |
c7bbf5422efd72cc9946fc3e2587e8d2302fc5245e844eda77cd614dec934e71 | Python | 61,983 | 1,744 | """Clearing house for generic text datatypes that are not XML or tabular."""
import gzip
import json
import logging
import os
import re
import shlex
import subprocess
import tempfile
from html.parser import HTMLParser
from typing import (
IO,
TYPE_CHECKING,
)
import ijson
import yaml
from galaxy.datatypes.da... |
0cc7918c6da4c9947ba656378c7ffa0c30b891b4f08e2b28eeb6fa8f6bcb1637 | Python | 62,001 | 1,709 | # --- 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 ColorBar(_BaseTraceHierarchyType):
_parent_path_str = "contourcarpet"
_pa... |
35d4bfb02d114efc6a0ffdfb9667ce8f9be729119dcb33b23d44acc88478623a | Python | 62,001 | 1,709 | # --- 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 ColorBar(_BaseTraceHierarchyType):
_parent_path_str = "icicle.marker"
_pa... |
3729fa9caedfef33d21e44a7e3374a634540a428490e6735521fbfb362bfdb8d | Python | 62,001 | 1,709 | # --- 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 ColorBar(_BaseTraceHierarchyType):
_parent_path_str = "quiver.marker"
_pa... |
d37483bb221c67190477d3729eda84eebbebbdd3f0fa0720d362074f7955616d | Python | 62,001 | 1,709 | # --- 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 ColorBar(_BaseTraceHierarchyType):
_parent_path_str = "choroplethmap"
_pa... |
f392f8d262caa74ead6230cc761ad112d0c303c19fa97ec3a2c66a1df2547d97 | Python | 62,001 | 1,709 | # --- 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 ColorBar(_BaseTraceHierarchyType):
_parent_path_str = "funnel.marker"
_pa... |
8194eb4cdf8a8831ad24cfe4ba8d24acad12768a0b2bd8e4a7166aaa899e7a18 | Python | 62,012 | 1,381 | #!/usr/bin/env python
# =============================================================================
# MODULE DOCSTRING
# =============================================================================
"""Base ``LightningModule`` class to implement TFEP maps."""
# ===================================================... |
12aa0ad43578f23fe645a979c6759a7ff7c32ad4212d3a64ceeac575c5e1a38a | Python | 62,024 | 1,709 | # --- 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 ColorBar(_BaseTraceHierarchyType):
_parent_path_str = "parcoords.line"
_p... |
875239554022013274d81d1d4b7c7cf6c94251b2f5feb97dba6955e6c0c89e9c | Python | 62,024 | 1,709 | # --- 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 ColorBar(_BaseTraceHierarchyType):
_parent_path_str = "scatter3d.line"
_p... |
d52f8f3f7c9e06a2b985afa3c7679ba929ca3c0f40da736408509b2abb8b11c3 | Python | 62,024 | 1,709 | # --- 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 ColorBar(_BaseTraceHierarchyType):
_parent_path_str = "treemap.marker"
_p... |
e11184dea08037ec13c3f7517c67c8677a4a43079863dddb036d0cb06afe9b64 | Python | 62,024 | 1,709 | # --- 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 ColorBar(_BaseTraceHierarchyType):
_parent_path_str = "scatter.marker"
_p... |
59cb4069d8ce1bd14e68102792d954f385abbc0d690b5d51e6f7f808e852eab7 | Python | 62,047 | 1,709 | # --- 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 ColorBar(_BaseTraceHierarchyType):
_parent_path_str = "sunburst.marker"
_... |
5fe4ce7819e2e81248c3f8891e1167233510fae72c5f1c3e4a6fb36a5c1b453a | Python | 62,047 | 1,709 | # --- 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 ColorBar(_BaseTraceHierarchyType):
_parent_path_str = "barpolar.marker"
_... |
e573c1b9483393fc56e64ddb0bfb15b87e9af7da3fab4d02da8a8d35f2a8d563 | Python | 62,058 | 1,709 | # --- 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 ColorBar(_BaseLayoutHierarchyType):
_parent_path_str = "layout.coloraxis"
... |
020d8dcb1800b7d475fdd6b923b0a40217ae0a19f3c837cdd5bb628ba4f26713 | Python | 62,070 | 1,709 | # --- 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 ColorBar(_BaseTraceHierarchyType):
_parent_path_str = "scattergl.marker"
... |
7091c400eac6ea2956182def7dc7572a5ba466642f424342958982bb0ef3fc04 | Python | 62,070 | 1,709 | # --- 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 ColorBar(_BaseTraceHierarchyType):
_parent_path_str = "scatter3d.marker"
... |
e13e68646096d44455b97635997d238184c905d0f313f21cb0f0a38fa2149be9 | Python | 62,070 | 1,709 | # --- 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 ColorBar(_BaseTraceHierarchyType):
_parent_path_str = "histogram.marker"
... |
010607d1ee47aeb70c196855b2531c3b20cafb3cce0f976169e4119bc355ca42 | Python | 62,093 | 1,709 | # --- 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 ColorBar(_BaseTraceHierarchyType):
_parent_path_str = "scattergeo.marker"
... |
9c89c24bc5f6372468692b83d4b4fb25ac8f58be8639bc5c6bbb44127322843b | Python | 62,093 | 1,709 | # --- 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 ColorBar(_BaseTraceHierarchyType):
_parent_path_str = "scattermap.marker"
... |
aba994c080092ac13a6891da18ab0e6ad49bb085477315ca8d2832ec2b28d176 | Python | 62,116 | 1,709 | # --- 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 ColorBar(_BaseTraceHierarchyType):
_parent_path_str = "histogram2dcontour"
... |
eeda46cca9f382bea192b45365536f067bb71ffc326dfc14765f7055f3bbe611 | Python | 62,122 | 1,481 | # encoding: utf-8
"""Module implementing representational similarity analysis (RSA) at the source level.
Kriegeskorte, N., Mur, M., & Bandettini, P. A. (2008). Representational
similarity analysis - connecting the branches of systems neuroscience.
Frontiers in Systems Neuroscience, 2(November), 4.
https://doi.org/10.3... |
0aaf53e65b9d15cdab66f64cbe6b3b560bce468f8c2f7795b5fdebcae0865ad2 | Python | 62,138 | 1,808 | """
The dataset import app.
Walks the user from a raw recording through its lab format to an imported
dataset stored in the workspace.
"""
from __future__ import annotations
from dataclasses import dataclass
from html import escape
import inspect
from pathlib import Path
import panel as pn
from larvaworld.lib impo... |
395ea72d5f9a39e7953c8adb6d97d8c8e30c9119e8217b8477ffece576e542bb | Python | 62,139 | 1,709 | # --- 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 ColorBar(_BaseTraceHierarchyType):
_parent_path_str = "scatterpolar.marker"
... |
e6f9a87c811b2cd553400aece03114e38c92f9c928b33e1fb1bdd2ac4a8f7c57 | Python | 62,139 | 1,709 | # --- 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 ColorBar(_BaseTraceHierarchyType):
_parent_path_str = "scattersmith.marker"
... |
e7596960c29ec248f3e6ecf5f20bc3933c1224e2873c8d72f3056cd5142b4cc4 | Python | 62,163 | 1,709 | # --- 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 ColorBar(_BaseTraceHierarchyType):
_parent_path_str = "scattercarpet.marker"
... |
964c0f7b627f6b4b628bc36ae38398a0fb1c59e8340354b0fad917f2d2b5f0ef | Python | 62,186 | 1,709 | # --- 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 ColorBar(_BaseTraceHierarchyType):
_parent_path_str = "scatterternary.marker"... |
a847001d670808b093cb2da36b26bb2b4842168941fdf3109ba56c46964ea1c4 | Python | 62,186 | 1,709 | # --- 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 ColorBar(_BaseTraceHierarchyType):
_parent_path_str = "scatterpolargl.marker"... |
b34bea722e031533e917e527d317f55ba75095657a139c0cf0335520a7b39bb9 | Python | 62,242 | 1,629 | # Copyright (c) 2023, Tri Dao.
from typing import Optional, Sequence, Tuple, Union
import torch
import torch.nn as nn
import os
import warnings
# isort: off
# We need to import the CUDA kernels after importing torch
USE_TRITON_ROCM = os.getenv("FLASH_ATTENTION_TRITON_AMD_ENABLE", "FALSE") == "TRUE"
if not USE_TRITON... |
3fac725bedd2bc39fd6ba77b6957aa7074e35ddf801394247d19eb84dcf020c6 | Python | 62,268 | 1,513 | """
Sequence classes
"""
import json
import logging
import math
import os
import re
import string
import subprocess
from collections.abc import (
Callable,
Iterable,
)
from itertools import islice
from typing import (
Any,
)
import bx.align.maf
from markupsafe import escape
from galaxy import util
from g... |
66fdbfa550369a5a1285196ea171638ba029770938768ebf20412112f0b41f50 | Python | 62,332 | 1,570 | # Ultralytics 🚀 AGPL-3.0 License - https://ultralytics.com/license
from __future__ import annotations
import contextlib
import importlib.metadata
import inspect
import json
import logging
import os
import platform
import re
import socket
import stat
import sys
import tempfile
import threading
import time
import warn... |
02a217d321152e75d50f866392c4342f7f88eb1fea256f6580100bdee8ac3273 | Python | 62,471 | 1,716 | import os
import socket
import sys
from collections import deque
from datetime import datetime, timedelta
from functools import partial
from queue import Empty
from queue import Queue as FastQueue
from threading import Event
from unittest.mock import Mock, patch
import pytest
from amqp import ChannelError
from kombu i... |
0995661e9fb3046a079f786820da37b6065d8019a0a3715f183902420fb610b3 | Python | 62,546 | 1,571 | """The XCP-D preprocessing worklow.
XCP-D preprocessing workflow
============================
"""
import os
import sys
import toml
from xcp_d import config
from xcp_d.config import hash_config
from xcp_d.data import load as load_data
def _build_parser():
"""Build parser object."""
from argparse import Arg... |
2bbb4a8b68cc9ccbe5adcfbd0f1540271fe465296ad08541dc168f8b81e929a4 | Python | 62,557 | 1,529 | """Result backend base classes.
- :class:`BaseBackend` defines the interface.
- :class:`KeyValueStoreBackend` is a common base class
using K/V semantics like _get and _put.
"""
import sys
import time
import warnings
from collections import deque, namedtuple
from datetime import timedelta
from functools import par... |
1db120e17f1228d3888a782c3a632550fb7dad28fa97c2898e284a0399dcc528 | Python | 62,633 | 1,644 | # --- THIS FILE IS AUTO-GENERATED ---
# Modifications will be overwitten the next time code generation run.
from plotly.basedatatypes import BaseTraceType as _BaseTraceType
import copy as _copy
class Scatterpolargl(_BaseTraceType):
_parent_path_str = ""
_path_str = "scatterpolargl"
_val... |
e0dc948c7b5f1471c9ee6a5beda281820f15e1a311f73e340b6480679c7a64cb | Python | 62,814 | 1,630 | # --- THIS FILE IS AUTO-GENERATED ---
# Modifications will be overwitten the next time code generation run.
from plotly.basedatatypes import BaseTraceType as _BaseTraceType
import copy as _copy
class Scatterternary(_BaseTraceType):
_parent_path_str = ""
_path_str = "scatterternary"
_val... |
ed9871e1628f06d0f2f29051462659f8d14e93bcc41f7ba758a8d6e31fdf32bf | Python | 62,865 | 1,691 | import math
import pytest
import torch
import torch.nn.functional as F
from einops import rearrange, repeat
from flash_attn import (
flash_attn_func,
flash_attn_kvpacked_func,
flash_attn_qkvpacked_func,
flash_attn_varlen_func,
flash_attn_varlen_kvpacked_func,
flash_attn_varlen_qkvpacked_func,
... |
1052d023ac9645c0b64559f5d02c0b4f4cec425a16bd63869d69f66179690adc | Python | 62,985 | 1,683 | # --- THIS FILE IS AUTO-GENERATED ---
# Modifications will be overwitten the next time code generation run.
from plotly.basedatatypes import BaseTraceType as _BaseTraceType
import copy as _copy
class Scatterpolar(_BaseTraceType):
_parent_path_str = ""
_path_str = "scatterpolar"
_valid_p... |
0d25e090cd18796c1172df308e162c8016347dfc9874deeaf167190326a71ffa | Python | 62,996 | 1,301 | """
The basic building blocks in model.
"""
import math
from argparse import Namespace
from typing import Union
import numpy
import scipy.stats as stats
import torch
from torch import nn as nn
from torch.nn import LayerNorm, functional as F
from BatmanNet.util.nn_utils import get_activation_function, select_neighbor_... |
ec9cc31ae194037d942c56d33ba1a2768cb2bc607af1d2da1d2f7236d733d6e7 | Python | 63,064 | 1,278 | # Ultralytics 🚀 AGPL-3.0 License - https://ultralytics.com/license
from __future__ import annotations
import ast
import inspect
from collections.abc import Iterator
from pathlib import Path
from typing import Any
import numpy as np
import torch
from PIL import Image
from ultralytics.cfg import QUANTIZE_ALIASES, TA... |
6f97f8a3d17844e9b0463ec00a0d5487900323ac973756cdbca0ff38ce02006e | Python | 63,079 | 1,373 | # Ultralytics 🚀 AGPL-3.0 License - https://ultralytics.com/license
from __future__ import annotations
import json
import os
from collections import defaultdict
from itertools import repeat
from multiprocessing.pool import ThreadPool
from pathlib import Path
from typing import Any
import cv2
import numpy as np
impor... |
d9228524de9dae2de1c3b250634ff8e746d081ee144b4cbd449edc18c86a42d4 | Python | 63,095 | 1,488 | from math import sqrt, sin, cos, pi, asin, pow, ceil, log
import numpy as np
from scipy import stats
import pandas as pd
from collections import defaultdict
import sys
from tqdm import tqdm
from skmob.utils.gislib import getDistanceByHaversine
tqdm.pandas()
from ..utils import constants
def _radius_of_gyration_individ... |
f6a13d4cdc29b6089b62bbb487af58266f90f3ff5c1e80520f16067cd771d164 | Python | 63,207 | 1,743 | # 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... |
f7916a797ca07dc0e1783fe620eed1442c3f21b6c1c5fd3b67243c2a0c8b6ec5 | Python | 63,259 | 1,176 | # Ultralytics 🚀 AGPL-3.0 License - https://ultralytics.com/license
# Copyright (c) Meta Platforms, Inc. and affiliates.
# All rights reserved.
from __future__ import annotations
import torch
import torch.nn.functional as F
from torch import nn
from torch.nn.init import trunc_normal_
from ultralytics.nn.modules imp... |
b2a9dc50d7ed683121c64fd609d107fc0d880210eea6d5e6d558b2733c297e0a | Python | 63,271 | 1,514 | # SPDX-License-Identifier: LGPL-2.1-or-later
from __future__ import print_function, division, absolute_import
import os
import unittest
from pyEcoHAB import SetupConfig, ExperimentSetupConfig
from pyEcoHAB import data_path
# In the first scripts for EcoHAB data analysis,
# the antennas were numbered from 1 to 8. The c... |
d53779dec460a8e580e1d748a4363c8a285962bcb9f67f3a256ef22bf2db8be6 | Python | 63,290 | 1,890 | import math
import torch
import torch.nn.functional as tnn
from torch.distributed.tensor import DTensor
from torch.distributed.tensor import Replicate
from keras.src import backend
from keras.src.backend.common import dtypes
from keras.src.backend.common import is_float_dtype
from keras.src.backend.common import stan... |
343c313fa607b9dea654e22fcdc5b96a436c39895d287cc34ba362710dbb1ffc | Python | 63,347 | 1,708 | import errno
import os
import pickle
import select
import socket
import tempfile
import threading
from itertools import cycle
from struct import pack
from unittest.mock import MagicMock, Mock, patch
import pytest
from billiard.pool import ApplyResult
from kombu.asynchronous import Hub
from kombu.message import Message... |
4abad56977694d36130e14e22f5e5631d625e6d12fc31977d15ae18d380b47de | Python | 63,379 | 1,582 | """Tigramite causal discovery for time series."""
# Author: Jakob Runge <jakob@jakob-runge.com>
#
# License: GNU General Public License v3.0
from __future__ import print_function
import numpy as np
from collections import defaultdict, OrderedDict
from itertools import combinations, permutations
class OracleCI:
... |
308a30252bc23f68d85cf36db35b0478a3af22872557cf11da30e6e6a998dbc9 | Python | 63,550 | 1,238 | #####train scGNN
import argparse
import datetime
import os
import os.path
import pickle
import pickle as pkl
import sys
sys.path.append('../pkgs/scGNN/')
import time
import networkx as nx
import numpy as np
import pandas as pd
import scipy.io
import scipy.sparse as sp
import scipy.sparse as sp
import torch
from bench... |
d9cf7686aba133eba5b6db7f831afc959ee9d033a7ab15cd4b5b294a9d378d97 | Python | 63,674 | 1,674 | import copy
import hashlib
import numpy as np
import pandas as pd
from typing import Any, Self
from pathlib import Path
from mirp._images.base_image import BaseImage
from mirp.settings.generic import SettingsClass
class GenericImage(BaseImage):
def __init__(
self,
image_data: None | np.... |
ab855b966132117018ce0048871ba4053a05db79cfde7bf59ff009a37fd71a0d | Python | 63,705 | 1,325 | """
mini_analysis plugin - analysis algorithms to find mini synaptic events
The module can be imported independently of the base UI system.
SimplyFire - Customizable analysis of electrophysiology data
Copyright (C) 2022 Megumi Mori
This program comes with ABSOLUTELY NO WARRANTY
This program is free software: ... |
ebc3b17efdc2db0750bd1ac1285d4996dd427fe5768075ecc823590e0b8d2e84 | Python | 63,714 | 1,237 | #####train scGNN
import argparse
import datetime
import os
import os.path
import pickle
import pickle as pkl
import sys
sys.path.append('../pkgs/scGNN/')
import time
import networkx as nx
import numpy as np
import pandas as pd
import scipy.io
import scipy.sparse as sp
import scipy.sparse as sp
import torch
from bench... |
dce31f4a14189fef3ba976654310c30949b0507a63c893d7fbc05504ae4cdde7 | Python | 63,727 | 1,654 | """Tier-marker lint: keep the smoke tier honest.
Two enforcement layers back the documented test tiers (CLAUDE.md "Testing Tiers",
tests/AGENTS.md "Markers"):
1. **Marker disjointness** (collection-level). pytest markers are ADDITIVE: a test
carrying ``smoke`` together with ``heavy`` or ``slow`` still runs under
... |
07ceca44e43dea6bdba56d27faf154a2770f7a83314a696c724b53370a3efa55 | Python | 63,896 | 1,613 | # -*- coding: utf-8 -*-
'''
PYSIMPLEGUI BASED GUI FOR DBSCAN CLUSTERING OF MOLECULAR TRAJECTORY DATA
Design and code: Tristan Wallis
Debugging: Sophie Huiyi Hou
Queensland Brain Institute
University of Queensland
Fred Meunier: f.meunier@uq.edu.au
REQUIRED:
Python 3.8 or greater
python -m pip install scipy... |
b9c57aaf2a976f70b7cdfe67ec754a50a705eb7dbaef736c035356f5c2008cdb | Python | 64,128 | 1,899 | # Author: Christian Brodbeck <christianbrodbeck@nyu.edu>
from copy import deepcopy
from itertools import chain, product
from math import log
import operator
import os
import pickle
import shutil
from string import ascii_lowercase
import tempfile
import warnings
import mne
import numpy as np
from numpy.testing import (... |
95144d10cd232678224aa22952c97028239916676744e35678d9fa166c7703ee | Python | 64,409 | 1,032 | # ---------------------------------------------------------------------------------------------------------------
# Functions to import data and generate the main figures from the manuscript (Blanco-Pozo, Akam & Walton, 2023)
# Marta Blanco-Pozo, 2023
# ------------------------------------------------------------------... |
eb6bd886c610bb2b752beec23a0ab8c1305a65e4a62abb986e0276e38220d35d | Python | 64,479 | 1,684 | from __future__ import annotations
from dataclasses import replace
import json
from pathlib import Path
from typing import Any
import panel as pn
import pandas as pd
import pytest
from larvaworld.lib import reg
from larvaworld.portal.datasets.dataset_replay_app import (
_DatasetReplayController,
dataset_repl... |
70fe37453cb7a2aee7bf694248a8e832ca830e3f7b232d3b73ab9b309b38056b | Python | 64,685 | 1,951 | # SOURCE: vendored from CMACH508/DeepTH @ main, SSRSGJYD/NeuralTexture @ master, naivoder/DeformableCapsuleNetwork @ main, milutter/deep_lagrangian_networks @ main, kailiang-zhong/DESCN @ main, YoungGod/DFR @ master, xueyunlong12589/DGCNN @ main
from __future__ import annotations
import math
import numpy as np
import... |
f0054db8ea0b1ae51a35db9484a75306e730ad197d680a7f88362b4ba049d38a | Python | 64,720 | 1,648 | """
Contains an abstract base class that supports chemically aware data splits.
"""
from __future__ import print_function
from __future__ import division
from __future__ import unicode_literals
__author__ = "Bharath Ramsundar, Aneesh Pappu, modified by Qingyuan Feng "
__copyright__ = "Copyright 2016, Stanford Universi... |
ccf1b3959760c1e634159c137eefb0d89937f22f685b8000718415aa067f33d5 | Python | 64,808 | 1,488 | #!/usr/bin/env python
# =============================================================================
# MODULE DOCSTRING
# =============================================================================
"""
Modules and functions to compute QM/MM energies and gradients with MiMiC, GROMACS,
and CPMD.
The code interfaces... |
573ae528ab75b4edd316d8f6f7aba36983283a77417c43a45a58d3dd42f05ae2 | Python | 65,051 | 1,571 | import ast
import json
import logging
import os
import sqlite3
import time
import mysql.connector
class BaseDatabaseMetadataCache:
"""
Abstract base class for database metadata caching and experiment information storage.
This class provides a clean interface for:
- Querying database metadata with ac... |
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