sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
618e19f03a053f2802d88cccf3984d01e35ee2727f64df8824718436df92b929 | Python | 9,651 | 343 | # Individual Cases Text Parser
# From Tamil Nadu Bulletins
from __future__ import annotations
import multiprocessing
import sys
import pathlib
import argparse
import os
import re
import json
import pdfplumber
if sys.version_info >= (3, 8):
from typing import TypedDict, Dict, List, Optional
else:
from typing_... |
9fb42bce27ef8fdbcb9439663e0834a49c74e7941f787bb50c64907044f95959 | Python | 9,652 | 236 | """Functions for building the input features (reference ccd features) for the HelixFold model."""
import sys
import numpy as np
from copy import deepcopy
from helixfold.common import residue_constants
from helixfold.data import pipeline_multimer, pipeline_rna, pipeline_rna_multimer
from helixfold.data import label_uti... |
cdaf5105b93d3996962a90b64f0cb9fcadac78a10ac6d6f86f95b2a42a97926b | Python | 9,652 | 279 | from __future__ import annotations
import faulthandler
import logging
import logging.handlers
import os
import os.path
import sys
import threading
import weakref
from typing import TYPE_CHECKING, Any, Optional, TextIO
import toml
if TYPE_CHECKING:
from bream4.device_interfaces.devices.base_device import BaseDevi... |
e0a07c77505b1f612372b5ce964b982658182e89075c6d1224937ad06fe3621b | Python | 9,652 | 238 | """
Variety of functions for computing motif perturbations.
"""
from types import SimpleNamespace
import numpy as np
import torch
from permacache import permacache, stable_hash
from modular_splicing.evaluation.predict_splicing import predict_splicepoints
from modular_splicing.utils.run_batched import run_batched
d... |
ff298e5943bf07fd775f1fc788c2987dab33bedca80574cf88ecb01db4bd7d76 | Python | 9,652 | 217 | from ..utils import gislib, utils, constants
from ..core.trajectorydataframe import *
import numpy as np
import inspect
def stops(tdf, stop_radius_factor=0.5, minutes_for_a_stop=20.0, spatial_radius_km=0.2, leaving_time=True, no_data_for_minutes=1e12, min_speed_kmh=None):
"""Stops detection.
Detect the s... |
f0ba540e883cc9089cdf8c0b8df41de2077e36ffe9867ccfa3b8655dcd12aaff | Python | 9,653 | 199 | """05. Deep dive into SSD training: 3 tips to boost performance
===============================================================
In the previous tutorial :ref:`sphx_glr_build_examples_detection_train_ssd_voc.py`,
we briefly went through the basic APIs that help building the training pipeline of SSD.
In this article, w... |
9f36a14003c53efb916fa175d41a3953f7af5fdbfadcfdbfd8fb915c422fd3bc | Python | 9,656 | 314 |
import numpy as np
from numpy import cos, pi, arange, ones, zeros
from numpy.linalg import norm
from scipy.fftpack import dct,idct
from scipy import sparse
from ..core import fnutils
from numba import jit
def l1sp_scale_to_smooth(scale,p_=(4,-3)):
return scale**p_[0]*10**p_[1]
def l1sp_gauss_scale_to_smooth... |
f1d49b8ab8170f58535576cf23a912f248aa8e2020b1d32b852f61cd92cb4074 | Python | 9,658 | 222 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Fri Jan 29 18:04:08 2021
This is the configuration file for Experiment 4, cue validity 1, AI vs learning speed analysis. It differs from the main
Experiment 4, cue validity 1 configuration file in just one aspect - it is set to train more (N=100) models.
... |
4c87f8d235e0bb4958f956fc4022897269e5f9252e40496d2d6ffdafe875420f | Python | 9,660 | 247 | """Conformance packs C0-C2, profiles, mutation plants (MEMO 4, build B4).
Anti-vacuity, executed: the well-behaved fake provider passes every cell
BEFORE any plant is trusted to fail one; every plant in the closed set turns
its intended cell red; toys earn NOTHING (the runner refuses every claim on
config-built eviden... |
841cce7c2348c2bc87b2ac7c9cf7ee954738cbf76e63c7cec3d3b9dccc4edb99 | Python | 9,660 | 285 | """
.. _exa-intro:
.. currentmodule:: eelbrain
Introduction
============
Data are represented with there primary data-objects:
* :class:`Factor` for categorial variables
* :class:`Var` for scalar variables
* :class:`NDVar` for multidimensional data (e.g. a variable measured at
different time points)
Multiple vari... |
9698edded328b7cf42d70e8d4cde65147255d2e00682f5903c458e2acc662b92 | Python | 9,662 | 269 | import squidpy as sq
import pandas as pd
from collections import Counter
import anndata
from scipy.sparse import csr_matrix
import numpy as np
import os
import math
from tqdm import tqdm
import matplotlib.pyplot as plt
import seaborn as sns
sns.set_theme()
def create_dataframe(adata, coord_key, celltyp... |
3fe459b1aa9e1a7ca7cdea71e42db4efdc404cee5036bf377972ef01003ee30e | Python | 9,669 | 349 | #!/usr/bin/env python
# encoding: utf-8
from __future__ import (absolute_import, division,
print_function, unicode_literals)
import os, sys, re
import logging
import argparse
import collections
import numpy
import time
import TGraph
logger = logging.getLogger(__name__)
class TNode:
"""... |
b061ad5bc4ea06aeee9fb8de5f1b51c4d3483fadfd63f7bce8d378fff5768d5b | Python | 9,669 | 267 | #!/usr/bin/env python3
"""
Database Cache Refresh Script for Ethoscope
This script refreshes all database cache JSON files by extracting metadata directly from
databases and creating properly timestamped cache files. It supports both SQLite and MySQL
databases and ensures cache filenames reflect actual database metada... |
7e68b6b2b32242173735a48a97849cc5dd19bdf9ac7cb439dfe791214d60d1f8 | Python | 9,674 | 295 | """Tests for Phase 3 repr and tensor display ergonomics."""
from __future__ import annotations
import pytest
import torch
from torch import nn
import torchlens as tl
matplotlib = pytest.importorskip("matplotlib")
matplotlib.use("Agg")
class _InfModel(nn.Module):
"""Tiny model that produces a non-finite out.""... |
e1f02b73e6d9fce9d71a2c8d2254df19b2242775c1278c0ccea5b71d3d727a02 | Python | 9,674 | 184 | #==============================================================================#
# Author: Dominik Müller #
# Copyright: 2024 IT-Infrastructure for Translational Medical Research, #
# University of Augsburg ... |
c83d89a8a4bec0b5e409eb0208ed7718ddc8670aacdbbaf1660eb5fc179f4701 | Python | 9,676 | 307 | # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
"""Functions for interpolating over high-motion volumes."""
import os
import nibabel as nb
import numpy as np
import pandas as pd
from nipype import logging
from xcp_d.utils.confounds import _infer_dummy... |
547c37ad34b776d5980cbfc845aac77b17498121a84c343a951a055f07c500b8 | Python | 9,679 | 274 | """Checks kit item 3: loop-session chassis + registry lifecycle (memo 4.2).
Contracts pinned here: every hook handle removed on every exit path
including optimizer exceptions; construction is silent and does no device
work (D20); bitwise same-seed checks-on/off runs (zero user-RNG
consumption); the step-check family r... |
20a0448e749ce90094d30151034e83309a9a921e33929d62cd34018c1f93cf29 | Python | 9,680 | 219 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Fri Jan 29 18:04:08 2021
This is the configuration file for Experiment 4, cue validity 0.5, AI vs learning speed analysis. It differs from the
main Experiment 4, cue validity 0.5 configuration file in just one aspect - it is set to train more (N=100) models... |
32058e848f4798e2f15b95d0c43bd5eeac2f79cf5678948586505925f032d00e | Python | 9,682 | 308 | """Image domains for PyTorch.
This module provides image domains for PyTorch. The image domains are used to
convert images between each domain and library's internal common space.
The internal common space is defined as follows:
- Channel axis: 1
- Pixel range: [0, 1]
- Image size: arbitrary
- Color space: RGB
"""
f... |
88c6c5e74f67e77f0dc823e7f7538191187088f6c3c8569c8960045e030c8113 | Python | 9,682 | 276 | import threading
from absl import logging
from keras.src import backend
from keras.src import losses
from keras.src import metrics as metrics_module
from keras.src import tree
from keras.src.legacy.saving import serialization
from keras.src.saving import object_registration
MODULE_OBJECTS = threading.local()
# Lega... |
e9d40d27081ae01fa3bcab04b4e3847d9197aaa216804795a17c0254bb252816 | Python | 9,683 | 214 | #!/usr/bin/env python3
"""
Dx Z++ — what makes brainlat's feature distribution different?
For each of the 15 canonical features, compare brainlat's distribution
(HC + AD separately) to the pooled distribution from the other 3
AD cohorts (ds004504 + ds006036 + figshare). Identify features where
brainlat is systematical... |
d9f17b7d7c44d4ab18143eeff5b6b3a2c8e48de7df67ba7335c8ff820b48c05a | Python | 9,684 | 212 | import pandas as pd
import numpy as np
from sklearn.model_selection import KFold, StratifiedKFold, RepeatedStratifiedKFold, GridSearchCV
from sklearn.metrics import accuracy_score, f1_score, precision_score, recall_score, roc_auc_score, \
classification_report, make_scorer
from sklearn.pipeline import Pipeline, mak... |
432e8a4400433d5af7be36e233cc6d9a7198b9ac4fdb628e17837266ae5b1c61 | Python | 9,686 | 246 | """Transforms for YOLO series."""
# pylint: disable=not-callable
from __future__ import absolute_import
import numpy as np
import mxnet as mx
from mxnet import autograd
from .. import bbox as tbbox
from .. import image as timage
from .. import experimental
__all__ = ['transform_test', 'load_test', 'YOLO3DefaultTrainTr... |
4a4dc858f15b99634642b8788ab3b87bca004a312fb0e006a0c77480743d3219 | Python | 9,686 | 241 | """
after DTV images has been generated, collect into
For FreeCAD library parts dataset and Thingi10K dataset
"""
from __future__ import print_function, division
import os
import os.path
import sys
import time
import json
import glob
import numpy as np
import pandas as pd
pd.options.display.float_format = '{:,.2g}'.f... |
13e076cc05c0a7eadc3a233b632a978ad7d3153b7f484b3edecf4be68ef10c20 | Python | 9,688 | 262 | from collections import defaultdict
import json
import numpy as np
import pandas as pd
from tqdm import tqdm
from pyspark import SparkConf
from pyspark.sql import SparkSession
from pyspark.sql.Catalog import dropGlobalTempView
from omop_learn.backends.backend import OMOPDatasetBackend
from omop_learn.data.common impo... |
fa3ad6898e801121362f97805f631b175cece0d0c46f198843ddf878022a614c | Python | 9,689 | 325 | from __future__ import print_function
from __future__ import division
from __future__ import unicode_literals
import numpy as np
from rdkit import Chem
import itertools, operator
from dcCustom.feat import Featurizer
from dcCustom.feat.mol_graphs import ConvMol, WeaveMol
def one_of_k_encoding(x, allowable_set):
if... |
3c4e6d088f8dd846a58ef22b35d0b9bad568f3b1828664a6aeb62a5a1664f753 | Python | 9,690 | 275 | """Rescue recovery oracle vs ``TorchFunctionMode`` dunder respelling.
The rescue re-run arms a ``TorchFunctionMode``; with a mode active torch
dispatches C-level operator dunders as their named method, so the mode-free
primary logs ``__radd__`` / ``__truediv__`` / ``__iadd__`` while the rescued
trace logs ``add`` / ``... |
63fa2286da2de45e9c58106470a300b82407ee5d2b69908f2f5312b2a5f6ecb0 | Python | 9,690 | 309 | from __future__ import annotations
from abc import ABC, abstractmethod
from typing import Callable, Iterator
import warnings
import torch
import torch.nn as nn
from torch.nn.parameter import Parameter
from bdpy.dl.torch.domain import Domain, InternalDomain
def _get_reset_module_fn(module: nn.Module) -> Callable[[],... |
ca4b1186c655f018bcf145530a374e9869c21a434831e709959c6c628374e66e | Python | 9,690 | 320 | import copy
import numpy as np
import pytest
GENERIC_KWARGS = dict([
("image_data", np.ones((30, 29, 28), float)),
("separate_slices", False),
("translation", (1.0, 1.0, 1.0)),
("rotation_angle", 90.0),
("noise_iteration_id", 2),
("noise_level", 2.0),
("interpolated", True),
("interpol... |
116cab22b2623baaed88d27bb75a3d47fa99e9c49353141a26bebde4aaa8722c | Python | 9,691 | 258 | """A final Op label resolves through ``trace.ops`` to its own Op, or refuses.
Raw labels (``{type}_{type_idx}_{raw_idx}``) and final labels
(``{type}_{type_idx}_{step_idx}``) share one shape. Once grouping folds passes
into one layer the two numberings drift apart, and one Op's unsuffixed raw
spelling can equal anothe... |
4a79822fb4e79185645bd333a275a357dd873c8bf95d7ed064e9c39cd1a54faa | Python | 9,691 | 258 | """TensorFlow recurrence grouping: multi-pass layers, relabel safety, tamper oracles."""
from __future__ import annotations
import dataclasses
from typing import Any
import pytest
tf = pytest.importorskip("tensorflow")
keras = pytest.importorskip("keras")
import torchlens as tl # noqa: E402
from torchlens.backend... |
5efe7f78b688b0f7a22e6066b746c9a194f7d3e6cae02a77c9172e04606ee624 | Python | 9,691 | 283 | """F10 lovely item 7: container/query/result conversion laws.
Containers point, records show (voice rule 1); honesty tokens are shared
vocabulary and cannot be laundered by any presenter (rule 4); no public
dataclass on the swept surfaces inherits an auto repr (D31, extended
sweep); no ANSI/OSC-8 bytes in any returned... |
8e55773e1ff2af80d0a985d7e48d7354a0bdd5584398f2bf68c4559b7b29fa7f | Python | 9,692 | 260 | """
The BatmanNet pretrain function
"""
import sys
sys.path.append('../')
import time
import argparse
from argparse import Namespace
from logging import Logger
import rdkit
from tqdm import tqdm
import os
from timeit import default_timer as timer
import torch
import torch.nn as nn
import torch.optim as optim
import to... |
da436788373723055bc7f5eda06fd92c1427127f8a7ac216fbfd37edf7aa14e2 | Python | 9,692 | 196 | from typing import Optional, Union
try:
from typing import Literal
except ImportError:
from typing_extensions import Literal
import matplotlib as mpl
import numpy as np
from pyvista import MultiBlock, PolyData, UnstructuredGrid
from .three_dims_plots import wrap_to_plotter
from .three_dims_plotter import _se... |
040fa73e911cb091183ffe167e264e273f46d869ef721604633fff8a951e77d8 | Python | 9,694 | 268 | from __future__ import annotations
import pytest
from pybind11_tests import numpy_vectorize as m
np = pytest.importorskip("numpy")
def test_vectorize(capture):
assert np.isclose(m.vectorized_func3(np.array(3 + 7j)), [6 + 14j])
for f in [m.vectorized_func, m.vectorized_func2]:
with capture:
... |
02f511b2cc3892d485ed11bb61f9ca1e8db0a3849c72060498f344f9e56b9c40 | Python | 9,695 | 306 | """Kernels for SPD matrices."""
from array_api_compat import array_namespace as get_namespace
from ._backend import _add_to_diagonal
from ._check import check_function
from .base import ctranspose, invsqrtm, logm
from .mean import mean_riemann
def kernel_euclid(X, Y=None, *, Cref=None, reg=1e-10):
r"""Euclidean... |
712aa586ecbbeb42049978650a95d04d2df0513a4d88ca293c29a4d39b722b73 | Python | 9,696 | 266 | #!/usr/bin/env python3
"""
File: plot_genotype.py
Created: 2021/04/08
Last Changed: 2021/07/07
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 tre... |
72022a0249088443b9edcb2d4af8e774a654a539f9ec3d84234fcf4e27aa32dc | Python | 9,697 | 273 | '''
load the RBNS data
'''
import csv
import re
import h5py
import urllib
import gzip
from io import StringIO
import requests
import numpy as np
import time
import os
from utils_rbns import create_datapoints
from constants import get_args
from map_protein_name import get_map_protein
rbns_data = 'metadata_rbns.csv'
#... |
b3650881006db049d54f19ea7e48ee9a9804736ad285e5ce960cd8a1c6fe2cc7 | Python | 9,698 | 197 | import pandas as pd
import random
holidaysfile = 'src/random_holidays_EPobjects_list.csv'
def add_ddy_objects(command1 ,command2 ,idf1,ddy_data):
"""
#Add Sizing:DesignDay object from .ddy file to IDF
command1 is a boolean to add the ddy objects or not
if command1 is True and command... |
4cef3f18333fba2a57610403c8b088e495720ba66d76a597d8f086bee7afa0f5 | Python | 9,699 | 260 | """
History data access helpers for the page assistant agent.
Thin string-formatting wrappers over Galaxy managers (HistoryManager,
HistoryContentsManager, HDAManager, DatasetCollectionManager). The
manager layer owns pagination, visibility/deleted filtering, and the
implicit-conversion HID-uniqueness handling so this... |
89ce4cb48f53bb73c1f3f67214867c1ddd00e3514571a0ea53512ba6dcbe7f06 | Python | 9,699 | 288 | import os
import matplotlib.pyplot as plt
import numpy as np
import seaborn as sns
from sklearn.cluster import KMeans, MiniBatchKMeans
def kmeans_plot_multiple(
embed_dict_t,
graph_list,
coords,
taskname_t,
output_path_t,
k=20,
dot_size=10,
scale_bar_t=None,
minibatch=True,
pl... |
41f1868dc1f72d021ce99440becb72a94866710a8782acd42f60c0c762865a2c | Python | 9,700 | 334 | """This module defines Galaxy's custom exceptions.
A Galaxy exception is an exception that extends :class:`MessageException` which
defines an HTTP status code (represented by the `status_code` attribute) and a
default error message.
New exceptions should be defined by adding an entry to `error_codes.json` in this
dir... |
6c3b8161d204e7014ff5bb9b760c9e65e855f9ab9da47a53821e2224efc7d2cc | Python | 9,702 | 242 | """Cross-backend agreement for the INCIDENTAL bare-label all-keys binding.
There was never a documented contract for what ``layer_dict_all_keys[bare
layer_label]`` resolves to on a multi-pass layer -- bare-label addressing of
multi-pass layers refuses on every path that matters
(``multipass_bare_label_ambiguous``). Bu... |
db44c74dabfcef66b734271a47d642a49c62dd385f6a6b60081a29d1687a898c | Python | 9,704 | 333 | from typing import List, Optional, Union
import dynamo as dyn
import numpy as np
import ot
import pandas as pd
from anndata import AnnData
from scipy.sparse import csr_matrix, issparse
from scipy.sparse.csgraph import floyd_warshall
try:
from typing import Literal
except ImportError:
from typing_extensions im... |
517f8a41bb82722e332adbe2128bf3c647797a75a8c5964309e56056d243f234 | Python | 9,706 | 224 | import tensorflow as tf
import tensorflow_datasets as tfds
import numpy as np
from pdb import set_trace
import cvnn.layers as complex_layers
from cvnn.montecarlo import run_montecarlo
def normalize_img(image, label):
"""Normalizes images: `uint8` -> `float32`."""
return tf.cast(image, tf.float32) / 255., labe... |
fb1003ce71bf14e0d6a1ddecb9b5a6d4fdbd59b97e4f5efb493ff6b02a17b1b1 | Python | 9,706 | 248 | import os
import pandas as pd
from tqdm import tqdm
import torch
from torchmetrics import MeanSquaredError, R2Score, SpearmanCorrCoef, PearsonCorrCoef
from omegaconf import OmegaConf
from Bio import pairwise2
import sys
script_dir = os.path.dirname(os.path.realpath(__file__))
sys.path.append(os.path.dirname(script_dir... |
45d40cbdf9b7290f89cb2c97905a45d336e9d8529178fb0625e9f438a7043657 | Python | 9,709 | 256 | """Lazy out reference placeholders for portable TorchLens bundles.
This module defines the lightweight references attached to lazy-loaded
outs and grads. Each ref stores the bundle path, tensor metadata,
and expected checksum so materialization can open a blob file on demand,
verify integrity, return a tensor, and clo... |
81edd6ceb94867ae03dd30dd11e27fc1e18607022380b8a6c4ab72223af2bcc1 | Python | 9,709 | 209 | import pandas as pd
import seaborn as sns
import matplotlib.pyplot as plt
from utils import setup_fonts,parse_config, build_output_dir,palette_by_model
import numpy as np
import os,math
def combined_mutation_dataframe(args,prefix,output_dir,test_csv):
models = {'seq-wt (LFN)' : f"{args.best_BIO_DIR}/{prefix}.{arg... |
9129ce500315e26e3d86d9704c4155ce35eda3b998a3baed4a36ba58e61abb56 | Python | 9,709 | 263 | import torch
import matplotlib.pyplot as plt
import warnings
warnings.filterwarnings('ignore')
import numpy as np
import seaborn as sns
from utils import parse_config, setup_fonts, build_output_dir
def load_checkpoint(model_path):
checkpoint = torch.load(model_path, map_location='cpu')
opts = checkpoi... |
6769bdf5478a13294694f73aa9caecedd0021be440d0d76bd2a5fc340fa910a8 | Python | 9,710 | 250 |
# coding: utf-8
# In[1]:
# get_ipython().magic(u'matplotlib inline')
import sys
import os
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
import seaborn as sns
import scipy.io as io
import pickle
import json
# In[2]:
SBJ = sys.argv[1]#raw_input('Enter SBJ ID to process:')#'IR63'
# # Log ... |
ef4461f444f32fc44176c945afa84344e53ad5b7cd35f3243bd0d3dd99589e7d | Python | 9,711 | 278 | """Visualization identity oracle (separate from the surface byte oracle).
Forward and rolled DOT sources are byte-stable across processes (verified by
the two-process control below, run BEFORE the goldens were frozen), so they
are compared against full-source goldens. Backward DOT embeds ``id()``-derived
grad_fn node ... |
0a8738cc79db533500071acf0989ce3a0b27d66086be2bf9d9281f2d65f6d9ac | Python | 9,712 | 235 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Wed Mar 31 14:19:51 2021
@author: Florent Meyniel, Audrey Mazancieux
Perform a Finite Impulse Response (FIR) analysis of the time series of activity extracted in the
LC. The script assume that this time series has been preprocessed to remove the effect of
... |
86f7f40a7a0c94c132e1e18931751b0755fa80d8351813410df6fd02fcfc1a83 | Python | 9,712 | 299 | #!/usr/bin/env python
"""
TODO
- consistent variable naming for p, min_percentile, max_percentile
"""
import numpy as np
def robust_normalize(arr, p=1., axis=-1, method='standard score'):
"""
References:
-----------
https://en.wikipedia.org/wiki/Normalization_(statistics)
"""
if method == 'm... |
7fafd0be1d8bf3af35a5af46e59104e5500aab234e1ef4ecc97663f842aca422 | Python | 9,713 | 221 | #Convert all HOC files in a folder to CNG files
#Author: Ruben Ascoli, rascoli@princeton.edu, undergraduate, Princeton University
#George Mason University Department of Bioengineering
#Failures: weird formatting or not using pt3dadd method
import os
import sys
import pdb
# from .sort import swc_sort
def hoc... |
4073011ac689dac0ca54968f73b924b3179e01b735743a072c053d9a1fa417af | Python | 9,715 | 210 | """
Model Training and Testing
==========================
`RectiPy` provides methods for training and testing of RNNs via the `fit_*` and `test` methods implemented on the
`rectipy.Network` class. These methods provide a wrapper to standard `torch` training and testing procedures.
Here, we will describe how you can co... |
60c1d9ff2fbea3022d9c279578dcc83e94790c2f4f676b616d1d6ae10edc8787 | Python | 9,715 | 210 | """
Model Training and Testing
==========================
`RectiPy` provides methods for training and testing of RNNs via the `fit_*` and `test` methods implemented on the
`rectipy.Network` class. These methods provide a wrapper to standard `torch` training and testing procedures.
Here, we will describe how you can co... |
46ff8b5bdc44f3692ac7f3d32747dfad5026beb23fbe9b2e94d9b78aa722dc24 | Python | 9,719 | 261 | """Regression tests for r18b bridge/hf.py hardening.
Covers four A3 findings on ``torchlens/bridge/hf.py``:
* A3-06 -- autoroute predicates must decline implausible modality/chat values.
* A3-07 -- list image preprocessing must not run per-item transforms N+1 times.
* A3-13 -- tokenizer provenance must report honest ... |
1fe59de4be1fe50f937eed961b59936326fa661eb44288527ac16b1c22a98c54 | Python | 9,721 | 341 | from typing import List, Tuple, Dict, Union, Optional
import argparse
import logging
from pathlib import Path
from pprint import pprint
import numpy as np
import numpy.typing as npt
from ase import units as ase_units
import plotly.express as px
import plotly.graph_objects as go
import pandas as pd
import torch... |
589844fba48f2aca9522d557d941cc826d60b8231248ed3fd8dd1d0e99ef6a40 | Python | 9,721 | 276 | # 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... |
62969a28ca1f5d2247081fbd5d8d7101832d059fcd8a12b0023d4c638a0bac70 | Python | 9,721 | 186 | """
Analogous to CDR3 length, we can deterministically find the contiguous string
of amino acids that match the corresponding V and J gene. Here we reconstruct
the one-hot vector that encodes this information and add a loss concerning how
well we are doing in matching it.
Here's something we can use to check to make s... |
b56073dd3a72c8283deda0f530e4cf85777c2a21bc29090f3ed33fe19e297deb | Python | 9,721 | 343 | import os
import traceback
import numpy as np
import pandas as pd
import seaborn as sns
from .. import settings
from os import PathLike
import matplotlib.pyplot as plt
from matplotlib.axes import Axes
from typing import List, Union, Sequence
from tensorboard.backend.event_processing.event_accumulator import EventAccumu... |
aeffd5fa4b9c1c69bc91aaa2ffb1942f9c3a2f8a4b9f44e0e1b1805b2e42f158 | Python | 9,722 | 329 | """
Mock hardware implementations for testing.
This module provides mock implementations of hardware components
like cameras, stimulators, and sensors for use in tests.
"""
import threading
import time
from typing import Any, Optional
from unittest.mock import MagicMock, Mock
import numpy as np
class MockCamera:
... |
c4eab57267755c4211735cfab14abfcd2a58a35ac8768332276dbc007a7088b4 | Python | 9,722 | 246 | #!/usr/bin/env python3
"""
build_trained_model.py — Fit and serialize the canonical trained model.
Produces ``trained_model/trained_model.json`` containing every parameter
needed to apply the trained classifier to a new cohort *without
retraining*. ``deploy_classifier.py`` consumes this artifact.
The trained model h... |
3b2e37b3a723101df4db01f60f46991b4e9f1ae56d93bbd081464466aca5d439 | Python | 9,726 | 219 | # Copyright 2017 The TensorFlow 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 applica... |
1c77ba522f58b1c6483994ba17bab8e06936420782fde3a88f5447924b77124d | Python | 9,730 | 333 | """
roi_figs.py
This script contains functions defining ROI mask and projection figure panel
analyses.
Authors: Colleen Gillon
Date: January, 2021
Note: this code uses python 3.7.
"""
from util import logger_util
from analysis import misc_analys, roi_analys
from paper_fig_util import helper_fcts
logger = logger... |
c95a288fd373d2373b04f642adf69ece3dea20849e9701324fa6aac2ba155a1d | Python | 9,731 | 214 | from typing import Iterable, Any
from dataclasses import dataclass
from mirp.settings.utilities import setting_def
@dataclass
class ImageInterpolationSettingsClass:
"""
Parameters related to image interpolating / resampling. Images in a dataset are typically resampled to uniform
voxel spacing to ensure th... |
ceafe2a6f13edc0b312989176d4b4660e021aa0e02721c7f476e242d4b746a34 | Python | 9,733 | 258 | """Direct liveness killers for ``_check_postprocess_contract`` (b9-sol R74-1).
The postprocess contract checker was a surviving mutant: a return-None disarm
stayed green across the mutation arming suite because the driver only ran
validation files, and the planted enforcement tests in
``tests/test_postprocess_dag.py``... |
d61348f59681a72c8d08395e36a2d6543af7a74794b7f9978c5948c3ccc510a4 | Python | 9,733 | 245 | import gzip
import os
from pathlib import Path
import shutil
import tarfile
import pandas as pd
from tqdm import tqdm
from Bio.SeqIO.UniprotIO import UniprotIterator
from utils.Gene_ontology_utils import Ontology
from collections import Counter
import logging
class SwissProtExtractor:
def __init__(self, dataset_n... |
68b7cffbd5c4098d7b7d07b4a41a0c5933fde64195fedb67caab84374412a9a6 | Python | 9,734 | 306 | # -*- coding: utf-8 -*-
#
# eFEL documentation build configuration file, created by
# sphinx-quickstart on Mon May 11 14:40:15 2015.
#
# 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 co... |
a3a29b02e934ff91e6d5c82d154ca19899838060815f6378517f448ad92f5bbc | Python | 9,734 | 218 | from copy import deepcopy
import os
import numpy as np
import multiprocessing
import tensorflow as tf
import tensorflow.keras as keras
import tensorflow_addons as tfa
import gc
from tf_spiking import DenseLIF, DenseLIFNoSpike, IntensityToPoissonSpiking
from tf_spiking.helper import TrainingHistory
from training.brightn... |
76bb4c1834dbf1a7e493eec4aeab75982426c9d347b3a7d213b672ca58893978 | Python | 9,736 | 243 | """Five-step facade order: the testable spec, pinned (workstream A10).
Architecture memo 5.4 / neuro memo D15: (1) underscore -> plain
``AttributeError`` immediately; (2) redirect table -> typed teaching
``AttributeError``, no dependency check; (3) refusal table -> typed
``AttributeError``; (4) real active name -> per... |
0125879be06b4c1214266949118f3e9c519c2746c77d04a25172a047f3c2265c | Python | 9,739 | 268 | """B1-02: the semantic-output scratch never survives onto a settled product.
Four session-time fields are written at capture entry (``user_funcs.py``) and
consumed ONLY by ``decode_outputs_for_trace``:
_output_style _output_head _output_tokenizer _semantic_output_metadata
Two of them pin LIVE USER OBJECTS -- ... |
d23a7665604e8a42de0cc4d4516f9b697b24390da6fcfc102e004c57fcc497dd | Python | 9,739 | 282 | from typing import Optional, Sequence, Union
import numpy as np
import pandas as pd
from anndata import AnnData
from esda.moran import Moran_BV, Moran_Local_BV
from libpysal.weights import WSP
from .find_neighbors import neighbors
def spatial_bv_moran_obs_genes(
adata: AnnData,
obs_key: str,
connectivit... |
2526e4f25ff414e1cd37b3b7d01af9a50ccd4d221aecf6309799181de4a129bc | Python | 9,740 | 317 | """Tests for PIL-only node plot primitives."""
from __future__ import annotations
import subprocess
import sys
from io import BytesIO
import numpy as np
import pytest
import torch
from PIL import Image, ImageDraw
from torchlens.viz import render_heatmap, render_image_scatter, render_lineplot
from torchlens.viz._ten... |
0454effaf30fb6f7548bcd1d681192d1e90fb337ca1730a144b5535163cbddae | Python | 9,741 | 264 | """Regression gate: rolled-view edge labels must never collide with anything.
Renders the same 16-model rolled inspection set used to tune the edge-label
placement constants, lays each graph out with ``dot -Tjson``, and runs the
exact per-label geometry audit (``tests/support/label_geometry.py``). Any
hard violation ... |
279938567b0b4c6d694c094cb192121e06a0b06939845d5bb9e8dc3acd0f28d8 | Python | 9,741 | 266 | """Checks kit item 5/8: decrement skip ledger, watchdog, clip tiers.
The decrement goldens (memo test plan row 4): the naive fire-count
subtraction is asserted WRONG under K=4 accumulation (locking the refuted
method's failure so it cannot return as an optimization), the decrement
ledger is exact on 1-skip / consecuti... |
e4f4f859ee65afbea269c23c0c734f4ea6d107d00b4855be6048a375f32c3b1b | Python | 9,742 | 242 | import warnings
import re
from tqdm import tqdm
import torch
import pandas as pd
import transformers
import scipy
import numpy as np
import logging
def get_next_word_distr(
prefix: str,
model: transformers.PreTrainedModel,
tokenizer: transformers.PreTrainedTokenizer,
num_tokens: int = 2,
cdf_thres... |
ac964f2c81779afa8843edf10f974893d2b7732436bc52514f054104e6db04b7 | Python | 9,744 | 256 | """Annotations TRAVEL POLICY red tests (lane F40a, foldA D6).
The foldA round-3 headline receipts, as permanent regressions:
* R11 -- a fresh ``run(inputs=...)`` product carried the ORIGINAL episode
ledger (``provenance_tier=exact``) under ``path_faithfulness=VERIFIED``
with zero warnings.
* R12 -- the same class... |
9e5666cc44f7ff722f36b1322febdfa6edc5309abb8ee49da09bc55a54b0e376 | Python | 9,745 | 308 | #!/usr/bin/env python
#=========================================================================
#
# Copyright NumFOCUS
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://... |
fce2daffe41f392a92fe2e939757895923c8b51a9c35d3602b4969e364d19083 | Python | 9,745 | 243 | """Fully Convolutional Network with Stride of 8"""
from __future__ import division
from mxnet.gluon import nn
from mxnet.context import cpu
from mxnet.gluon.nn import HybridBlock
from .segbase import SegBaseModel
# pylint: disable=unused-argument,abstract-method,missing-docstring
__all__ = ['FCN', 'get_fcn', 'get_fcn_... |
27972ba34e2ace7b2cc1971d8a117de40f2e38f14cb05183783c080fc2241e91 | Python | 9,746 | 278 | import copy
import io
import matplotlib as mpl
from matplotlib import pyplot
from matplotlib.figure import Figure
from matplotlib.backends.backend_qt5agg import (
FigureCanvasQTAgg as FigureCanvas)
import matplotlib.patches as mpatches
from mpl_toolkits.axes_grid1 import make_axes_locatable
import numpy as np
from... |
52f433f65fe0c35cf5afdfe91ed066445314ff8aece62d6134de25fdd3ccf543 | Python | 9,746 | 278 | import copy
import io
import matplotlib as mpl
from matplotlib import pyplot
from matplotlib.figure import Figure
from matplotlib.backends.backend_qt5agg import (
FigureCanvasQTAgg as FigureCanvas)
import matplotlib.patches as mpatches
from mpl_toolkits.axes_grid1 import make_axes_locatable
import numpy as np
from... |
82d13f16bded3277a95e9229fe9279ecf4864ad37acfdc5fbd11a881d3104b5e | Python | 9,746 | 225 | # -*- coding: utf-8 -*-
# @Author: gviejo
# @Date: 2022-01-17 14:10:40
# @Last Modified by: gviejo
# @Last Modified time: 2022-01-18 17:40:08
import pynapple as nap
import pandas as pd
import numpy as np
def computePlaceFields(spikes, position, ep, nb_bins = 100, frequency = 120.0, smoothing = 2):
place_fields... |
893789fb59bf0be847edb1657400e0c8fcf721e30bc8c6f22bfc3fcc82077b51 | Python | 9,746 | 251 | import uuid
import pytest
from pytest_celery import RESULT_TIMEOUT, CeleryTestSetup
from celery.canvas import chain, chord, group, signature
from t.canvas_helpers import ids_in_as_tuple
from t.integration.conftest import get_redis_connection
from t.integration.tasks import ExpectedException, add, fail, identity, redi... |
5139e7179263f8b0a043852a7a9d65d6b7a884d173a14362fe93bdc2656e0d89 | Python | 9,748 | 224 | # Copyright (c) 2021, NVIDIA CORPORATION. All rights reserved.
#
# NVIDIA CORPORATION and its licensors retain all intellectual property
# and proprietary rights in and to this software, related documentation
# and any modifications thereto. Any use, reproduction, disclosure or
# distribution of this software and rel... |
7a48323b198603a6941267d727e3512d56ae251de9c672ddea3ade9541e27ded | Python | 9,748 | 315 | #!/usr/bin/env python3
# Copyright (c) Facebook, Inc. and its affiliates. All Rights Reserved.
import atexit
import queue
import numpy as np
import slowfast.utils.logging as logging
import torch
import torch.multiprocessing as mp
from slowfast.datasets import cv2_transform
from slowfast.visualization.predictor import... |
b10a5bfd2754c297854968039c43e94d34c785e3a36b7a0fc4d35bde7dcef2dd | Python | 9,748 | 278 | import logging
import os
import stat
import sys
from unittest import mock
import pytest
from codecarbon.core.cpu import (
RAPL_PERMISSION_HELP,
IntelRAPL,
_create_warn_function,
is_rapl_available,
)
def test_permission_warning_is_emitted_once(caplog):
"""The scan hits every domain: warn once, th... |
e8cabd21c7a428b2484f4a03da6b19094c93ce926e018e14cafb989ad9dbf105 | Python | 9,748 | 260 | """Logging configuration.
The Celery instances logging section: ``Celery.log``.
Sets up logging for the worker and other programs,
redirects standard outs, colors log output, patches logging
related compatibility fixes, and so on.
"""
import logging
import os
import sys
import warnings
from logging.handlers import Wa... |
bc2d6ecc307db317d1075c08114e5182c5dfcc86f48ae60fbbd1565b4cb852c3 | Python | 9,749 | 299 | # SOURCE: vendored from https://github.com/cyanrain7/TRPO-in-MARL @ master
# (algorithms/actor_critic.py + algorithms/utils/{util,mlp,act,distributions}.py,
# unmodified architecture; only added lightweight args/space shims so the real
# Actor/Critic modules can be constructed and called outside the full training
# run... |
2d80938845e8c040dea6b1fc0876ffa049af207bdc382ef0d9ceb2428b2fbcf6 | Python | 9,750 | 284 | from typing import Any
import numpy as np
from neurogym.core import TrialEnv, TrialWrapper
from neurogym.utils import spaces
class RandomGroundTruth(TrialWrapper):
# TODO: A better name?
def __init__(
self,
env: TrialEnv,
p: np.ndarray | None = None,
) -> None:
super()._... |
9b83dd00eef8cd4bb84602c0840b9f360171637adc2f17bf2fbc47ad36c08645 | Python | 9,756 | 288 | # Copyright (c) Facebook, Inc. and its affiliates.
#
# 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 ... |
24434a1776fdc488f98b4b3daf0d02edf95338e09b83a4918de845ff18ddcdda | Python | 9,757 | 247 | #!/usr/bin/env python
# =============================================================================
# MODULE DOCSTRING
# =============================================================================
"""
Base autoregressive flow layer for PyTorch.
"""
# ============================================================... |
ad3106e4590633fcd9dd5d8be93a37fa1f44e26230e21f0e693166f26f81c631 | Python | 9,758 | 217 | """
Exploring Data Components
=========================
This example explores the different data components, exploring the isolated aperiodic
and periodic components as they are extracted from the data.
"""
###################################################################################################
# sphinx_g... |
ad78ef49a595c429a9c842d2898a869c7ecd7d1dc6ff98e80347e8fa10049c02 | Python | 9,760 | 312 | import glob
import numpy as np
import random
import fnmatch
import os
from PIL import Image
from matplotlib import pyplot as plt
import PIL
from sklearn.model_selection import train_test_split
from sklearn.decomposition import PCA
#from tensorflow.keras.utils import to_categorical
from sklearn.metrics import confusion_... |
597aed8a6b61efbe6128244816e94e5993e210528f3523b3be34c10ba2dd7189 | Python | 9,761 | 306 | """Paddle backend derived-gradient preview tests."""
from __future__ import annotations
from typing import Any
import pytest
paddle = pytest.importorskip("paddle")
import torchlens as tl # noqa: E402
from torchlens.backends import BackendUnsupportedError # noqa: E402
from torchlens.backends.paddle import GradOpt... |
f5c488c791e1a525405161261213a680fcddab0b300f21a744c79beb4b559c14 | Python | 9,761 | 221 | """
Théo Gauvrit
24/08/2021
Try to implement the Alenda et al 2010 method absed on histograms of the Membrane potential Vm
to discriminate Upstate and Downstates from resting menbrane potential recordings.
The computing of the trough is changed to the direct mean of the Vm
"""
import numpy as np
import pyabf
import sc... |
559bbcd943e2977353f6379e80aaaf06e779b9b3d039ff249f05cbe31344b02b | Python | 9,762 | 329 | # --- 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 Cells(_BaseTraceHierarchyType):
_parent_path_str = "table"
_path_str = "t... |
cc5cc1a666889037cbf43584162419de63284ed6ce5c863d3a4b87604161af17 | Python | 9,763 | 181 | #==============================================================================#
# Author: Dominik Müller #
# Copyright: 2024 IT-Infrastructure for Translational Medical Research, #
# University of Augsburg ... |
a1dc1285e1d57aa4f55d2fa43d723a2687cc180870d3b75722e5da61560509c6 | Python | 9,765 | 235 | import os
import pandas as pd
import numpy as np
import pdb
from sklearn import linear_model
import scipy
from optparse import OptionParser
regr = linear_model.LinearRegression()
def get_single_trial_bias(subject, condition, meta_data_condition):
################# load single trial biases #####################... |
6c00e37821ca100074fda25521522c667009dbd5da4664a270161a64626f3b45 | Python | 9,766 | 300 | """
Socket-based messaging between larvaworld and an external process.
Provides the message envelope and the client and server endpoints used to
drive a remotely simulated brain model.
"""
# Copyright 2017 Dan Krause
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file... |
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