sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
cd3110681e0164201f3d6c303da6bc6985d7529093f6af71f3494f816f63eec0 | Python | 7,812 | 244 | """Fixtures for the CircleCI tests."""
import os
import pytest
def pytest_addoption(parser):
"""Collect pytest parameters for running tests."""
parser.addoption(
'--working_dir',
action='store',
default=(
'/app/.pixi/envs/xcp-d/lib/python3.12/site-packages/xcp_d/xcp_d/tes... |
a0dbd9861ba1f044fb35af1e053ed8d73981528c161deef89f28cdab3e8a0d18 | Python | 7,815 | 285 | #!/usr/bin/env python
# Created on: August 2, 2013
__author__ = "Sven Kreiss, Kyle Cranmer"
__version__ = "0.1"
import optparse
parser = optparse.OptionParser(version=__version__)
parser.add_option("-c", "--interpcode", dest="interpcode", default=4, type="int", help="InterpCode to be investigated.")
parser.add_op... |
a6217d1bd65c5f6af137df1bc2d636b433089739fc404809f592a4ec63f0d69d | Python | 7,815 | 187 | #!/usr/bin/env python3
"""
File: compare_correlating_genes.py
Created: 2022/04/28
Last Changed:
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 this source tr... |
0be0abb7a972757ede345483e9c5711e57efced503c97b0cddd2d701c22f0a90 | Python | 7,816 | 243 | # --- 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 Symbol(_BaseLayoutHierarchyType):
_parent_path_str = "layout.map.layer"
... |
8f3f2b7be1e3af7e9d2bd46b5128af05502a9203e2b05ea9eb824879f32770d3 | Python | 7,817 | 187 | import os
import pyaudio
import wave
import logging
from pyoperant.interfaces import base_
from pyoperant import InterfaceError
class PyAudioInterface(base_.BaseInterface):
"""Class which holds information about an audio device
assign a simple callback function that will execute on each frame
presentation... |
bda3d6b9cad91328c62de1fc284bd76a550a5b2140ca1664ee8ef6fb00e932d7 | Python | 7,818 | 242 | """Parameters for model and training
Details were shown in the tail of this file.
Additionally, refer to the source code of MMVAE in the original paper.
"""
from src.utils import DotDict
epochs = 50
experiment_name = 'final-results'
id_vae_cmnist = 'vae_cmnist'
id_vae_oscn = 'vae_oscn'
id_mmvae_cmnist_oscn = 'mmvae_... |
d21aac4600782b80db49115102e4c246e90d764003bfa61c9a10e368b19d130a | Python | 7,821 | 200 | import os
import sys
from pathlib import Path
from platform import python_version
import gc
import inspect
from copy import deepcopy
import dill
# Custom modules
tr = '' # absolute path to upper working dir
import src
from src.models.fastbinary import *
from src.visualization.visualize import multi_lab... |
cc7a4cc97f0b3dc8e355c4520ff4026d1819094bebcc97514c81f16a3171afb6 | Python | 7,827 | 146 | """
Hopf Bifurcation and Limit Cycle Continuation
=============================================
Here, we will demonstrate how to perform branch switching at an `Andronov-Hopf bifurcation <http://www.scholarpedia.org/article/Andronov-Hopf_bifurcation>`_
and continue a branch of periodic solutions.
As an example model,... |
2b091b7879587a379263e233d724d3e153c76e23d08507c70c2f2fb620feb11f | Python | 7,829 | 209 | # pylint: disable=arguments-differ
"""VGG atrous network for object detection."""
from __future__ import division
import os
import mxnet as mx
from mxnet import gluon
from mxnet.gluon import nn
from mxnet.initializer import Xavier
__all__ = ['VGGAtrousExtractor', 'get_vgg_atrous_extractor', 'vgg16_atrous_300',
... |
a57415f1b0e1038583c9a0f04a9c405322e86e5bd1dd76354409f1fb466e062b | Python | 7,829 | 256 | #!/usr/bin/env python
# /files/some/path/stats/json
from __future__ import print_function
import requests
import json
import datetime
import pandas as pd
import numpy as np
import cartopy.crs as ccrs
import cartopy.feature as cf
import cartopy.io.shapereader as shpreader
import matplotlib.pyplot as plt
import ... |
ac582e6258a53d20b43ad2aa533de3ce53df0a405cd4ccba8b784b65b3b8dbad | Python | 7,829 | 202 | #!/usr/bin/python3
"""
https://vict0rs.ch/2018/05/24/sample-multilabel-dataset/
"""
def index_split(group_size, ratio):
# return index list in the group/class, test samples is selected with equal distance
# test if ratio is 0.25, 0.2, then this works,
train = []
test = []
gap = int(1.0 / (1-ratio... |
e25387805fba6e24c15604dedbe15df532fc011bc4eb3d9a36a084b9b40f3024 | Python | 7,829 | 242 | # adapted from https://github.com/facebookresearch/detectron2/blob/master/detectron2/data/catalog.py
# pylint: disable=no-else-raise
import copy
import logging
import types
from typing import List
__all__ = ["DatasetCatalog", "MetadataCatalog", "Metadata"]
class DatasetCatalog(object):
"""
A catalog that sto... |
fd43041081fae0491970133870d0d92a023319f988de8f66bba843eb08cf479f | Python | 7,829 | 261 | #!/usr/bin/env python
import sys
import numpy
# from rpy import *
import rpy2.robjects as robjects
from rpy2.robjects.packages import importr
r = robjects.r
grdevices = importr("grDevices")
def stop_err(msg):
sys.stderr.write(msg)
sys.exit()
infile = sys.argv[1]
x_cols = sys.argv[2].split(",")
y_cols = s... |
73c8cf8d6aef784407a84c09c12998a4d5b07cb117e87aa9fbd51011db450907 | Python | 7,832 | 232 | """Celery Command Line Interface."""
import os
import pathlib
import sys
import traceback
from importlib.metadata import entry_points
import click
import click.exceptions
from click_didyoumean import DYMGroup
from click_plugins import with_plugins
from celery import VERSION_BANNER
from celery.app.utils import find_ap... |
7e7b7fd27a7c60b316f036273cd94e7ad157924c312c1b02125ff4c0b396a6e1 | Python | 7,835 | 249 | """
ca_spikes.py
Class for calcium imaging spike loading and analysis
using calcium traces from caiman.
Code by Daniel Reumann, edited by Michael Zabolocki.
"""
import os
import pandas as pd
import numpy as np
import pickle as pkl
from scipy import signal
from ..utils import (save_df)
from ..plots import (plot_cat... |
cc92cf9413abc26ee600d0bb544808ad612d101d6795d97fc17d1f43c7cf0488 | Python | 7,836 | 171 | # Copyright (c) 2021, NVIDIA CORPORATION & AFFILIATES. All rights reserved.
#
# Permission is hereby granted, free of charge, to any person obtaining a
# copy of this software and associated documentation files (the "Software"),
# to deal in the Software without restriction, including without limitation
# the rights to... |
4a9575ab42ff76bcb241e3290862b15a4a9e1a55be76d116821825c3ded4a27e | Python | 7,839 | 227 | """Global attention modules (Luong / Bahdanau)"""
import torch
import torch.nn as nn
import torch.nn.functional as F
from bioseq2seq.modules.sparse_activations import sparsemax
from bioseq2seq.utils.misc import aeq, sequence_mask
# This class is mainly used by decoder.py for RNNs but also
# by the CNN / transformer d... |
c8c69ba729a6a93947d3b90ab8e2308dd949126d900159d9f61091a8b20e0012 | Python | 7,839 | 203 | """Use StarDist for cell identification and labeling.
https://github.com/stardist/stardist
[Schmidt18]_ and [Weigert20]_
"""
import math
from typing import Optional, Union
import cv2
import numpy as np
from anndata import AnnData
from csbdeep.data import Normalizer, PercentileNormalizer
from skimage import measure
t... |
103ae10e161991f27889625d40b7f83ab46a5d01b0af86abbb84fc0b8eb6f672 | Python | 7,840 | 167 | # Author: Christian Brodbeck <christianbrodbeck@nyu.edu>
"""
.. _exa-cluster-based-mu:
Cluster-based permutation t-test
================================
.. currentmodule:: eelbrain
This example show a cluster-based permutation test for a simple design (two
conditions). The example uses simulated data meant to vaguel... |
a8839c20f19f3f2aa0f1e37c750ed1048e30c600c6f81c251f3415bf0388d551 | Python | 7,846 | 233 | from typing import Any
from mirp._data_import.dicom_file import ImageDicomFile
from mirp._data_import.utilities import get_pydicom_meta_tag
class ImageDicomFileMR(ImageDicomFile):
def __init__(self, **kwargs):
super().__init__(**kwargs)
def is_stackable(self, stack_images: str):
return True
... |
5585328237731554ab8b5f646e029899758ea6fafc608e259e344f8b61f0fb77 | Python | 7,848 | 190 | # model
from ast import Global
import torch
import torch.nn as nn
import torch.nn.functional as F
import torch_geometric as tg
import torch_scatter
import e3nn
from e3nn import o3
from typing import Dict, Union
# crystal structure data
from ase import Atom, Atoms
from ase.neighborlist import neighbor_list
from ase.vis... |
f65ae5f1a896f261635873af3f96afeba1c7c967bfac23a9bb19f8ea130bcc2d | Python | 7,849 | 218 | """Regression tests for r20i: IR live-record lane cleanup + state hygiene.
Covers hardening findings on ``torchlens/ir``:
* N8 -- ``LiveIndex.append`` left a stale parent edge (and double-listed the
label) when a raw label was re-seen at the append boundary.
* N9 -- ``CaptureEvents.release_runtime_sidecars`` reta... |
0245ee115b3cd062db976048f1a0b69379470f6bd45d0c1555584fc92d7054ef | Python | 7,851 | 202 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# This script merges one sample across lanes.
#
# This script will *only* be useful if you have the same multiplexed sample loaded into multiple lanes of a flowcell.
#
# This concatenates the same index's pared-end files (L*_R*_* .fastq.gz) across multiple
# lanes into on... |
185e44157e113e2304c55de56a620756426393214601e1cc5b1a51c9561e0b26 | Python | 7,852 | 238 | # -*- coding: utf-8 -*-
"""
Reproduce the results of the``spytorch`` tutorial 2 & 3:
- https://github.com/surrogate-gradient-learning/spytorch/blob/master/notebooks/SpyTorchTutorial2.ipynb
- https://github.com/surrogate-gradient-learning/spytorch/blob/master/notebooks/SpyTorchTutorial3.ipynb
"""
import brainpy_data... |
22163b480fec7060e12fb71f239a77b6bc85fb61053abfaae1442271dad3e2cc | Python | 7,854 | 246 | """api module. Functions to access the STRING API"""
import pandas as pd
import io
import requests
def build_request_url(method, output_format='tsv'):
"""Create url to query the string database
Allows us to create stubs for querying the string api with various methods
Parameters
----------
metho... |
23cc8127525ee717b1f0414cf95ae57a4b4b012232f49433779b68d29ce84762 | Python | 7,854 | 231 | #!/usr/bin/env python3
"""
File: no_ieqtls_per_sample_plot.py
Created: 2021/10/22
Last Changed: 2021/10/25
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... |
2930183232144683125550bb21b01ef232523b1c568f2d84dfba15e806fede91 | Python | 7,854 | 137 | # -*- coding: utf-8 -*-
import os
import yaml
import argparse
import numpy as np
from utils import check_folder, read_yaml, save_yaml, write, get_subject_name, get_output_name, aggregate_cv, create_maps, fetch_masker, fetch_data, get_nscans
from utils import get_splitter_information, get_compression_information, get_d... |
0b00d2ba47c59baba129a085a945966e50c82d2602fa0306111b727ba60d0365 | Python | 7,856 | 238 | """Save-dtype routing: explicit, routed, disclosed (extract D11 + item 9).
``dtype=`` is global or per-key; ``None`` preserves the captured dtype. The
cast runs AFTER pool and postprocess transforms, BEFORE the CPU-contiguous
snapshot. Captured, requested, stored, and conversion facts are manifested.
bf16 and both fp... |
10575bd44b00abb98763e478560668e2267ffa7006bead84a6a3b815fa1d42ad | Python | 7,856 | 197 | """Removed public methods and attributes raise a typed redirect naming the replacement.
The 2026-10-01 shim removal deleted the alias members outright (remove-and-
rename, no alias), and lane F12 deleted ``VisualizationTheme.legend_items``.
A lookup of any of them must raise ``FacadeTeachingError`` (code
``facade_redi... |
c09724eac406488acc6b78445d8cd777630e198d5b1f5c9b9682213790823a9d | Python | 7,856 | 228 | import sys
import cv2
import numpy as np
import json
from functools import partial
import pandas as pd
import matplotlib.pyplot as plt
# Script used to annotate the position of GFP+ cells (teto-Olfr17 expressing cells) relative to a curve drawn on the most basal side of the MOE
# the curve passes through each of the 5... |
919de0d82f8bbcbfb58415d23ef47a78bf4de7ad1560208e2fdebf23860eb594 | Python | 7,857 | 195 | """Peak-pair instrumentation oracles (F20, brainpipe memo D-7 + build 3).
The measured peak is a PAIR (live allocation, resident high-water) with the
backend named -- CUDA and CPU instrumentation measure different physical
quantities. The sweep-scale instrument defect (the shipped peak property
reads 0 for every captu... |
43265fc68ec1c386b9262adb349bb7e8561a63cc4ee055aee4cc703d02130345 | Python | 7,859 | 258 | """
This module holds some process function of pynapple that can be
called with numba or pynajax as backend
If pynajax is installed and `nap.nap_config.backend` is set
to `jax`, the module will call the functions within pynajax.
Otherwise the module will call the functions within `_jitted_functions.py`.
"""
import n... |
c129cf328036de38e8cfe0fa1aacc815a48bf81e1e4e98527b89552f1312b20a | Python | 7,859 | 224 | """Tests for bdpy.recon.torch.task.inversion"""
from __future__ import annotations
import unittest
from unittest.mock import patch, call
import copy
import torch
import torch.nn as nn
import torch.optim as optim
from bdpy.recon.torch.task import inversion as inversion_module
from bdpy.task import callback as callbac... |
5a88472a68c18c84959a281d0a42219dda897b592596eb2d640fc2336a347914 | Python | 7,860 | 224 | import numpy as np
import pytest
from tigramite.graphs import Graphs
def make_empty_tsg_graph(N=3, tau_max=1):
"""Create an empty time-series DMG of shape (N, N, tau_max+1, tau_max+1)."""
g = np.zeros((N, N, tau_max + 1, tau_max + 1), dtype="<U3")
g[:] = ""
return g
def test_no_path():
"""If ther... |
cfef25b0d690b08749fe9b7298b325e000d4df16c0a09a431a1dbcfba05602bd | Python | 7,860 | 190 | """Implementation of Atari 2600 Preprocessing following the guidelines of Machado et al., 2018."""
import numpy as np
import gym
from gym.spaces import Box
try:
import cv2
except ImportError:
cv2 = None
class AtariPreprocessing(gym.Wrapper):
"""Atari 2600 preprocessing wrapper.
This class follows t... |
f26985a9dbcb6351b4a8ce07015be841b9342ce885f85bee12f1e1f53f2c52ee | Python | 7,861 | 254 | """
Base classes for all simulation agents.
Defines the minimal agent interface, its placement in space and its
registration with the simulation model.
"""
from __future__ import annotations
from typing import Any
from ...param import (
ClassAttr,
MobilePoint,
MobileVector,
OrientedPoint,
Radiall... |
55d18c4e9f0dd414d6f15a2a887b1f7adea389fad21b303b9ccdd11cc09c67c6 | Python | 7,863 | 211 | """The edit x product matrix (compo memo stratum 1; F36 wave A).
``do()`` against every product/lifecycle state: the push engine serves live
intervention-ready forks and refuses everything else -- each refusal cell
pins its stable code (or its LEDGERED codeless state: the intervention-error
fields-clobber class locks ... |
66905cfe09683706c8dd74905a88c88bad8c925fb88a4354cf4217c06fe03bee | Python | 7,864 | 134 | import os
import re
import numpy as np
import matplotlib.pyplot as plt
import matplotlib.cbook as cbook
import sys
sys.path.insert(1,'/home/mila/l/lindongy/deeprl-timecells')
from analysis.utils_analysis import time_decode_lin_reg, sort_resp, plot_sorted_averaged_resp
from analysis.utils_int_discrim import single_cell_... |
78b8dfc7695f1af434ffb9f8554926784c79953fb0c857764de7e5582be5b706 | Python | 7,864 | 201 | """GPU accelerated tree explanations"""
import numpy as np
import shap
from packaging.version import parse as _parse_version
from shap.explainers._tree import (
TreeExplainer,
_xgboost_cat_unsupported,
feature_perturbation_codes,
output_transform_codes,
)
from shap.utils import assert_import, record_im... |
d6393521a22f68af2718849c6d8f58204863c0867a82df59aa2870a7cfa3693d | Python | 7,864 | 167 | import pylustrator
pylustrator.start()
import os
import matplotlib.pyplot as plt
import numpy as np
import pandas as pd
datasets = ["mnist", "fashion_mnist", "letter_mnist", "mnist_with_brightness_offset", "fashion_mnist_with_brightness_offset", "cifar10"]
plt_idx = 1
color_pairs = [('purple', 'brown'), ('olive', '... |
17bc8088427068aa069e4f30ba9119111ab3ad4ad3e2d7c3ef3f862e622552b4 | Python | 7,866 | 269 | import copy
from permacache import permacache, stable_hash, drop_if_equal
import numpy as np
import tqdm.auto as tqdm
from modular_splicing.dataset.datafile_object import SpliceAIDatafile
from modular_splicing.dataset.dataset_aligner import DatasetAligner
from modular_splicing.example_figure.run_models import comput... |
e82da666ee5ce4a5f81dcbd76ce049402747497309c0f7b0ce33ccd1b3940f30 | Python | 7,869 | 196 | # Ultralytics 🚀 AGPL-3.0 License - https://ultralytics.com/license
import asyncio
import json
import threading
from functools import partial
from http.server import SimpleHTTPRequestHandler, ThreadingHTTPServer
import cv2
import numpy as np
import pytest
from ultralytics.data.converter import convert_ndjson_to_yolo... |
22d3c9081ca23bcb9f8e0cb20cc2fb71c617d339161c68f52e032f75b6717cb9 | Python | 7,873 | 261 | """Tests for single-module focus visualization."""
from __future__ import annotations
from pathlib import Path
from typing import Any
import pytest
import torch
from torch import nn
import torchlens as tl
from torchlens.data_classes.layer import Layer
def _render_dot(log: tl.Trace, tmp_path: Path, **kwargs: Any) ... |
840f9daa2e066137c47bfbbddcebc52d747ac959aaed8590f6f1a74ca634f257 | Python | 7,875 | 183 | """
3D reaction-diffusion simulations with NEURON 8.2.6: cylinder
Last updated 18.9.2026
Author: Saana Seppälä
### Description
This script performs reaction-diffusion simulations of calcium and
calmodulin (CaM) in an idealized cylindrical geometry using the
NEURON RxD framework. The model combines molecular diffusi... |
6fb682e0b9c23fafce0de55494e72de2c20ef74f8fdaf76d6318d0b0f7b2ea43 | Python | 7,879 | 260 | """"Utility functions for working with data and data objects."""
import numpy as np
###################################################################################################
###################################################################################################
def _get_field_ind(modes, compone... |
80d493d4ffdaeb5c3d9f801fbf2eb166648a23d84ceefea0255ff78f0f001ab8 | Python | 7,882 | 212 | from keras.src import backend
from keras.src.api_export import keras_export
from keras.src.optimizers import optimizer
@keras_export(["keras.optimizers.ScheduleFreeAdamW"])
class ScheduleFreeAdamW(optimizer.Optimizer):
"""Optimizer that implements the Schedule-Free AdamW algorithm.
Schedule-Free learning is ... |
6c6a3a8d9c42e12fd451d3b1be23637ac6c77fe8080c25d90ade09bf6587a1cc | Python | 7,883 | 276 | import numpy as np
import torch
from scipy.stats import rv_discrete, bernoulli
from typing import Union
# helper functions
##################
def retrieve_from_dict(keys: list, data: dict) -> dict:
"""Remove dictionary entries and collect them in a new dictionary.
Parameters
----------
keys
... |
549601256f9f8d623725fa815be166ed5a5e69a1c695c9b33e7b0b7b14469482 | Python | 7,884 | 207 | """
This script takes LD matrices and simulates summary statistics for multiple populations. Requires 2 populations, can take up to 4.
"""
import argparse
from contextlib import ExitStack
import numpy as np
import scipy.stats as stats
import os
class Main():
def __init__(self):
self.ld = []
self.ld_matrices... |
703c1c398d39eefa7bfe45b8ee7237eb79a8ff8e5b68401b57c79e3e7be622d0 | Python | 7,886 | 207 | import numpy as np
import networkx as nx
import pandas as pd
import matplotlib.pyplot as plt
import matplotlib.colors as colors
import numpy as np
from scipy.stats import pearsonr
from irf import irf_utils
from irf.ensemble import RandomForestRegressorWithWeights
import matplotlib.cm as cmx
from sklearn.linear_model im... |
41872b8a2edcd6b1965dfc73cfca6e40cb912fea5a60d8edde24f34e9a26e8e2 | Python | 7,887 | 243 | import re
import pandas as pd
import io
import camelot
import pdfminer
from pdfminer.high_level import extract_text, extract_pages
from pdfminer.layout import LTFigure, LTImage
from utils.table_extractor import TexTract
class Karnataka(object):
def __init__(self, report_fpath):
self.report_fpath = repor... |
5445f294b69791969bd52e923aa1a6db336e82b42889e26a4fd65d9b44f1687b | Python | 7,888 | 204 | #!/usr/bin/env python
"""
Do windowed detection by classifying a number of images/crops at once,
optionally using the selective search window proposal method.
This implementation follows ideas in
Ross Girshick, Jeff Donahue, Trevor Darrell, Jitendra Malik.
Rich feature hierarchies for accurate object detection... |
85821249e07c8bf75b6a27f6c97177c5ae6a1f4b6519f66208ba5496b1501830 | Python | 7,888 | 288 | import pandas as pd
import polars as pl
import pytest
from seqpro._coords import (
_SCHEMAS,
CoordSchema,
_resolve_schema,
detect_schema,
set_schema,
)
def test_coordschema_fields():
s = CoordSchema("chrom", "chromStart", "chromEnd", zero_based=True, strand="strand")
assert s.chrom == "chr... |
247c35af50ccfab01a8e5e2a9a5aebbef021ecd7f91c390378d5191134691838 | Python | 7,892 | 153 | # Written by Seonwoo Min, Seoul National University (mswzeus@gmail.com)
# PLUS
import os
import sys
import argparse
import torch
import plus.config as config
from plus.data.alphabets import Protein
import plus.data.transmembrane as transmembrane
import plus.data.dataset as dataset
import plus.model.plus_rnn as plus_... |
c820289a0c77d479d69f32299f64f29d46f1c256e7b85204d14d6e7fdb924fa7 | Python | 7,892 | 189 | """Shared inputs, oracle, tolerances, and backend selection checks for the SM100 SwapAB decode
tests."""
import math
from typing import NamedTuple
import pytest
import torch
from flash_attn.cute import interface
from flash_attn.cute.config import FwdConfig
from flash_attn.cute.testing import attention_ref, check_ten... |
bd7434b6221a65cc43b2e8dfed3d7bf181ba62a58770f6ffe4f3a8fb8aaa9fc8 | Python | 7,895 | 265 | import ast
import re
import struct
from decimal import Decimal
from pprint import pprint
import pytest
from celery.utils.saferepr import saferepr
D_NUMBERS = {
b'integer': 1,
b'float': 1.3,
b'decimal': Decimal('1.3'),
b'long': 4,
b'complex': complex(13.3),
}
D_INT_KEYS = {v: k for k, v in D_NUMBE... |
0b94c4907edf2b555ba84e9557e1d1d078ed65e4825b978fe1e97f8a83c21902 | Python | 7,896 | 188 | from brian2 import defaultclock, NeuronGroup, Synapses, mV, TimedArray, StateMonitor, PopulationRateMonitor, \
SpikeMonitor, second, Network, nS, volt, siemens, ms, Hz
import numpy as np
import pickle
import os
def run_net(tr, run_path):
print('Running the network...')
netw_objects = []
# todo chang... |
1bc77233da5d6cfa1b24c42a8ad36f6ab1bd8e341605f5770d1d57d3c36d1ccc | Python | 7,896 | 207 | """
This script takes LD matrices and simulates summary statistics for multiple populations. Requires 2 populations, can take up to 4.
"""
import argparse
from contextlib import ExitStack
import numpy as np
import scipy.stats as stats
import os
class Main():
def __init__(self):
self.ld = []
self.ld_matrices... |
10d8780c1cdaf3b00a95d01f123b26a1ae80004e9fb74ffaf7ca50d4d2fef9a8 | Python | 7,898 | 181 | # Torch imports
import pytorch_lightning as pl
from pytorch_lightning import seed_everything
from pytorch_lightning import loggers as pl_loggers
import torchvision.transforms as transforms
from pl_bolts.datamodules import CIFAR10DataModule, STL10DataModule, ImagenetDataModule
from pl_bolts.callbacks.printing import Pr... |
120f95930ab36ffca70da1938a1372314448e2f225dfa0268bd38c72946a6fdf | Python | 7,899 | 159 | #########################################################
# Test suite for testing the utility functions for #
# convolutional oligo kernel networks. #
# #
# Author: Jonas Ditz #
# Contact: ditz@informatik.uni... |
8a29d2aa74c20118f4ad937682b23c518a3b09af53e75d931460fd34e5e2dfc3 | Python | 7,899 | 235 | #!/usr/bin/python
#
# Copyright 2018 Google LLC
#
# 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 ag... |
d095fe91887d1cf2728286031110655e048150bd4c1c41d17c0f401bd2008651 | Python | 7,899 | 269 | """
Rendering of simulation preview frames.
Runs a short simulation and captures its frames, so a configuration can be
previewed before the full run is launched.
"""
from __future__ import annotations
from math import isfinite, nan
from typing import Any
from larvaworld.portal.canvas_widgets.environment_models impo... |
6422ffa99c32c1d9f86960ffb5f8c2e948821935167e62735f0273e036a0da2a | Python | 7,900 | 151 | """
Builds lookup tables using ldpop to use in other pyrho commands.
This is a thin wrapper for ldpop that computes a two-locus
likelihood lookup table and stores the resulting table in hdf format.
Run on the command line with pyrho make_table -h or --help to see
a list of options and their description.
"""
from __fu... |
4bcb62e9b835a403578c057216eccceca25d4cfb63b57bbc5cd231d13bdf5bc4 | Python | 7,902 | 196 | try:
from pyscf import gto
from pyscf.dft.numint import eval_ao
except ImportError:
raise ImportError("You need to install pyscf to use this module")
import numpy as np
import numpy.typing as npt
import pandas as pd
from ase.data import chemical_symbols
class OrthoCoeffMatrixToGridQuantities:
def _... |
505552f6859ed7b54c0bf989fd0b27c836fc88cbd02b6ce8c919fad6dd418c42 | Python | 7,902 | 163 | """
The script edit from finc_multi_small_exon.R in the original codes
Find the possible missed small exons, with the threshold: small_exon_size <= 100 and abs(delta_ratio) <= 0.5.
Each realign region will be output as a dict object with the following essential key values:
read_i(query_i), read_ith_intron(query_it... |
667e529b8365b2262ffe365d7ac259dea2026db0f8d57530849e7000f8035f70 | Python | 7,904 | 212 | # Copyright 2021 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 agr... |
b130ddc5b6de1dbc2fa23397e98605e6e3b472e2d4852c85a980a35912286398 | Python | 7,907 | 218 | import uuid
from sqlalchemy import Boolean, Column, DateTime, Float, ForeignKey, Integer, String
from sqlalchemy.dialects.postgresql import UUID
from sqlalchemy.orm import relationship
from carbonserver.database.database import Base
class Emission(Base):
__tablename__ = "emissions"
id = Column(UUID(as_uuid=... |
c1ed8eee0394dcf496fb93bc68e295095cfcb758e83e4c3a464e3d7220b187d4 | Python | 7,908 | 206 | # This is try to code spatial suppression motion task
import numpy as np
from scipy.interpolate import interp1d
from neurogym.core import TrialEnv
from neurogym.utils import spaces
class SpatialSuppressMotion(TrialEnv):
"""Spatial suppression motion task.
This task is useful to study center-surround inter... |
dd3c66a734f018c68af297702112d66e90554a9b3f85acd8c3c8910123ee6f7c | Python | 7,908 | 245 | """
Demonstrate how to calculate Cm from a ramp protocol.
INPUT:
model_vc_ramp.abf is from Patch-1U Model Cell (33 pF +/- 10%)
OUTPUT:
model_vc_ramp as a capacitance of 30.88 +/- 0.20 pF
171116sh_0014 as a capacitance of 202.32 +/- 11.49 pF
2018_08_23_0009 as a capacitance of 170.90 +/- 13.54 pF
"""
... |
a446616503e829052ea567c0cfab98cf99dd8e077e8c45fad9a00883a3e39f2f | Python | 7,909 | 245 | import os
os.environ['DTORROOT'] = '/DATA/forLishan/randomddd'
#os.environ["CUDA_VISIBLE_DEVICES"] = "0"
from dtor.utilities.utils_stats import stats_from_results,roc_and_auc
from sklearn.metrics import roc_curve, auc
import numpy as np
import argparse
import torch
from dtor.utilities.utils import set_plt_config
from d... |
d6826f40dfb79bfebb806380bd32b3160fc0f623ebc96bb54568f53d8fcd6bd5 | Python | 7,909 | 180 | import itertools
import json
import os
import numpy as np
import pandas as pd
import seaborn as sns
import statsmodels.stats.api as sms
from matplotlib import pyplot as plt
from angorapy.common.const import PATH_TO_EXPERIMENTS, QUALITATIVE_COLOR_PALETTE
# experiment_ids = [['1674343261520188', '1674308148646663', '1... |
24a903b6b39a431ef98695fe73d5310e06c4cc2ad8a6318ff4c4d9599d49476e | Python | 7,912 | 190 | # 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... |
38ce95da705713a0c7049d74855c14aac7608b1600f720cadf8f0a537f5c595c | Python | 7,912 | 209 | """F29: registry, envelope, canonical serializer, budgets, continuation.
The one-core/three-transports law (agent memo 3.1) plus the budget and
truncation discipline (3.8) and the envelope/determinism contract (3.9).
"""
from __future__ import annotations
import json
import math
from pathlib import Path
import pyte... |
4f3f67da657aeeeaf2026fb77c60dfc4721aece9a35a9f33877f2b352be30026 | Python | 7,912 | 207 | #!/usr/bin/env python
# pylint: disable=protected-access, unused-variable, locally-disabled, len-as-condition
"""Lint helper to generate lint summary of source.
Copyright by Contributors
"""
from __future__ import print_function
import argparse
import codecs
import sys
import re
import os
import cpplint
from cpplint i... |
fbca191a0309d4d6c438000e0663181242a0e4988f8c84b3f557ec31e8b608ff | Python | 7,912 | 212 | from typing import List
import numpy
import numpy as np
import tensorflow as tf
class Sensation(dict):
"""Wrapper for state representations. Designed for sensory readings, but non-sensory data can be
encapsulated too. The convention is to refer to any non-sensory data as proprioception, following the intuiti... |
daa81331ddb5a869540853033b6b9fe4cc9a310fc99cb72e7c7a989cb7e5896f | Python | 7,913 | 202 | """
Do-it
"""
import pandas as pd
import sys
sys.path.append("..")
from config import fname, subjects, events_id
DOIT_CONFIG = dict(verbosity=2, sort='definition')
#subjects = get_var("subjects")
#subjects = [int(s) for s in subjects.split()]
coil_order = pd.read_csv(fname.coil_order)
def task_order():
"""S... |
dbae414786ac7593605dfbebf78cc1676b86cef2598f5e3d00fb104308866fd6 | Python | 7,913 | 195 | """Typed refusal for unhashable fact path/position COMPONENTS (r77 L1).
Round-76 (hon1 + free-roam, cross-lab) found the r75 L1 lane one nesting level shy:
``_fact_path_tuple`` validated only the CONTAINER type, so a foreign artifact whose
``path``/``position`` was a well-formed sequence carrying a nested list / mappi... |
292b3e50d1a4c18cdcb51038e6dde8a471672cb16ae9e25399847ad302eb23e0 | Python | 7,914 | 271 | import argparse
import csv
import logging
import os
from glob import glob
from os.path import splitext
from os import listdir
import cv2
from PIL import Image
from torchvision import transforms
from scipy import ndimage
from lib.datasets.bonemask_dataset import BoneMaskDataset
from lib.models.EffUNet import EffUNet
f... |
756cbcf37759973edac27056ec3e53a2963d74331536f4e79ced8b625213f851 | Python | 7,914 | 196 | """Anti-recurrence tests for cert10 buffer-surfacing blockers.
Two independent bugs, same theme (registered buffers not surfaced correctly):
1. ``BlobRef`` leak on load (torchlens/_io/rehydrate.py): after any default
eager ``tl.load()`` of a bundle with registered buffers, ``Buffer.
initial_value`` returned a r... |
066c0fbdb6ab2bc3bec20397b0e4ae43ad480f3554eec79f78b4373e34577364 | Python | 7,916 | 194 | import warnings
from matplotlib.figure import Figure
import matplotlib.gridspec as gridspec
from matplotlib.backends.backend_qt5agg import (
FigureCanvasQTAgg as FigureCanvas)
import numpy as np
from .. import units
from ..head import custom_widgets
class MPLIndentation(object):
def __init__(self):
... |
00be2bbd6e3e6312ce06216452a397150184cc3b8977ba8b8890365e89e64936 | Python | 7,918 | 159 | import sys
import os
# setting path
sys.path.append('../TM2_segmentation')
from scipy.ndimage.filters import gaussian_filter
from densenet_regression import DenseNet
from skimage.transform import resize,rescale
import SimpleITK as sitk
import numpy as np
import pandas as pd
import tensorflow as tf
import glob, os, ... |
ec9506d8b543548fb09f761a281beef292e8dd9539f2a6e763a4236684c15c1a | Python | 7,918 | 156 | import torch
from torch.nn import functional as func
from .base_model import BaseModel
from . import networks
class FALModel(BaseModel):
""" This class implements the pix2pix model, for learning a mapping from input images to output images given paired data.
The model training requires '--dataset_mode aligne... |
1ad87798ba5ad1fbd00e3d9b41afb176839771a43b8ad5f7b4ec319369cb38ae | Python | 7,919 | 224 | """THE named calibration script for the transforms fidelity baselines (memo B10).
Regenerates ``tests/transforms_corpus/baselines.json`` from the vendored
fixture corpus under the SHIPPED SRP algorithm (never a prototype): O14
admissibility on the real resnet50 layer4 basis, per-cell L2-distortion
percentiles + RDM fi... |
90cb5826cf1152035a4462c8f52ffe3799d775da5fc5abaf2d793fa78e247d3a | Python | 7,919 | 183 | """W051-TRACK / AUD-CODE 2.14b: AMP ``unscaled`` truth is OBSERVED, never asserted.
``unscaled="yes"`` used to be stamped whenever ``scaler.get_scale()`` merely
worked at the boundary. A plain ``optimizer.step()`` after
``scaler.scale(loss).backward()`` never unscales, so the emitted gradient
statistics carried the x1... |
b3aecb6c1cb06ea557353035323188d4ee9d6022abe74325c2bf38ff0cc0bffd | Python | 7,919 | 312 | """Compact Kolmogorov-Arnold Network classics.
This module implements dependency-free KAN targets using learnable univariate
edge functions represented by triangular spline bases. Variants include pykan
aliases, MultKAN multiplication nodes, convolutional KAN, and KAN-Mixer.
"""
from __future__ import annotations
i... |
7607ab1e3d56490b2120a5200bfd6a3f82145fb99c7a14e8eeb8a8f19bce90ce | Python | 7,920 | 210 | """
Shared model and mapping code between Galaxy and Tool Shed, trying to
generalize to generic database connections.
"""
import logging
import os
import threading
from contextvars import ContextVar
from inspect import (
getmembers,
isclass,
)
from types import ModuleType
from typing import (
TYPE_CHECKING... |
0d2306498036b2ad9cdb7b989595e042489798b81fc3a25cccf66200c83781c4 | Python | 7,921 | 228 | # %%
import numpy as np
import pandas as pd
import seaborn as sns
import matplotlib.pyplot as plt
import pingouin as pg
import sys
sys.path.insert(0, '..')
# import my own code
from functions.data_helpers import get_phenotype, get_computer, get_mean_fd
# parameters
_, proj_dir = get_computer()
subj_list = list(np.lo... |
1f7c121d2250f38e01bef6573ff30a39af09e0df06683993750c349d657f4ea5 | Python | 7,922 | 212 | # 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... |
24cec86a11e2f9deb1cd23bab08d498124389953294c43f4378e4be42b428032 | Python | 7,922 | 246 | import os
import time
import argparse
import random
from datetime import datetime
from tqdm import tqdm
import numpy as np
import paddle
paddle.disable_static()
import paddle.optimizer as optim
import paddle.nn.functional as F
from paddle.nn import BCEWithLogitsLoss
from dataset import GoTermDataset, GoTermDataLoade... |
6225548acf7a78928f91590858bd3346417dc5296be387f3ccee67b275baf8ce | Python | 7,923 | 221 | from unittest import TestCase, mock
import datetime
from carbontracker.emissions.intensity.fetchers import carbonintensitygb
from carbontracker import exceptions
class TestCarbonIntensityGB(TestCase):
def setUp(self):
self.logger = mock.MagicMock()
self.fetcher = carbonintensitygb.CarbonIntensityG... |
3b1074248bc106074d46d3d41c230f6772c329edebb910f1dbd0a097755851b5 | Python | 7,924 | 175 | # Licensed to the Apache Software Foundation (ASF) under one
# or more contributor license agreements. See the NOTICE file
# distributed with this work for additional information
# regarding copyright ownership. The ASF licenses this file
# to you under the Apache License, Version 2.0 (the
# "License"); you may not u... |
5b569075867435159548b8fb042d7f70eec06e4beafaea1cefa0d20149c190e2 | Python | 7,925 | 236 | import nfp
from nfp.frameworks import tf
assert tf, "Tensorflow 2.x required for GraphLayers"
tf_layers = tf.keras.layers
register_keras_serializable = tf.keras.utils.register_keras_serializable
@register_keras_serializable(package="nfp")
class GraphLayer(tf_layers.Layer):
"""Base class for all GNN layers"""
... |
8fdc8a7b059072c2309d300c6abeff421ed6923255bfab5d558015f53c07fed5 | Python | 7,925 | 262 | import pytest
import pandas as pd
import numpy as np
import os
from jinja2 import Template
import json
import itertools
import nway.utils as utils
import nway.pairwise_matching as pairwise
TEST_FILE_DIR = os.path.join(
os.path.dirname(os.path.abspath(__file__)),
'test_files')
@pytest.fixture(scope='f... |
57f6905937de6c6611bc16f74977585ccb9cee519d3c4d8e97cd16c200cb5f51 | Python | 7,926 | 244 | # -*- coding: utf-8 -*-
#
# controller_validation documentation build configuration file, created by
# sphinx-quickstart.
#
# This file is execfile()d with the current directory set to its containing dir.
#
# Note that not all possible configuration values are present in this
# autogenerated file.
#
# All configuration... |
35d57a21189c0a76e92fac3f7a9629c7ae3149145ecf29f14505e1659c3d4903 | Python | 7,928 | 198 | #!/usr/bin/env python3
"""
Dx BR — 10,000-permutation null distribution on the in-pool §3.1 / §4.5
LDA-target perm test (AUC, LOO BA, LOCO BA).
Closes the v0.73 review carry-over (Gemini's catch): the paper currently
reports *p ≤ 0.002* reflecting the *n*=500 perm floor (1/501). Bumping
to *n*=10,000 tightens this to... |
8185d503d06ae2e978ee73bb7fa8396feb6ac65b3c651dc7296bde16d2d985d1 | Python | 7,931 | 199 | import matplotlib
matplotlib.use('Agg')
import argparse, time, logging
import numpy as np
import mxnet as mx
from mxnet import gluon, nd
from mxnet import autograd as ag
from mxnet.gluon import nn
from mxnet.gluon.data.vision import transforms
import gluoncv as gcv
gcv.utils.check_version('0.6.0')
from gluoncv.mode... |
5f87f67bb96126e3f886750ec084340e4c451b55086f8819e96b7859d246f7b5 | Python | 7,932 | 273 | import pytest
import tensorflow as tf
from psychrnn.backend.models.basic import Basic
from psychrnn.backend.models.lstm import LSTM
from psychrnn.tasks.match_to_category import MatchToCategory
from psychrnn.backend.simulation import BasicSimulator, LSTMSimulator
import numpy as np
import random
# clears tf graph after... |
35a56305773a5e1f882a13926e17870077b9ecc99c669b2f98d6e8b90272ca43 | Python | 7,935 | 198 | """F02 row gate: the causal-scrubbing expressibility row (edits memo B1, offline analog).
The flagship gallery row scaled to the R0 fixture discipline: a REAL
config-built GPT-2 (the sprint's zero-network realism fixture -- the same
2-layer/64-dim `GPT2LMHeadModel` the R0 gate runs), >=6 population examples
over 2 pro... |
b0aa101ce59493a396c815ca53735332dae03a30d37b68d14d849d44ea97ed7b | Python | 7,935 | 225 | import tempfile
import unittest
from pathlib import Path
from compile_to_inline_config import compile_config
class CompileToInlineConfigTest(unittest.TestCase):
def test_group_dict_preserves_structure_and_match_policy(self):
with tempfile.TemporaryDirectory() as temp_dir:
root = Path(temp_dir... |
b6c45e95a40a32739bc38c16152b2a68d1df697fc9492c2b49b24d9cd3dce6c5 | Python | 7,937 | 248 | from collections import OrderedDict
import numpy as np
from ..geometry import shapes as gshapes
from ..util import equal_states
from .layer import StructureLayer
class StructureComposite:
def __init__(self):
self.layers = []
def __contains__(self, sl):
if isinstance(sl, str):
t... |
6af29e7d41b0466eb75ae738e178e0d61e9954b907231f7fef6bf6b69aaf27ed | Python | 7,939 | 250 | """Behavioral tests for slice-kind (gather/scatter/all_to_all) witness derivation.
``derive_merge``'s identity-kind witness comparison is covered by
``test_merged_engine.py``; these pin the group-rank-indexed slice pairings:
gather roots against member contributions, scatter roots against member
destinations, and the ... |
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