sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
524b5de7b846ef319c16372de7e607f4d10845e0d0048cd16c233f8728586096 | Python | 4,287 | 130 | import os
from typing import Any, Iterable, List, Optional
import matplotlib.pyplot as plt
import numpy as np
import pandas as pd
import seaborn as sns
from sklearn.metrics import (
accuracy_score,
balanced_accuracy_score,
confusion_matrix,
f1_score,
)
def performance_eval(
df,
ground_truth_c... |
9a63a936a752aeb171c5c32996839f6a90aff85a8adf780b4557fcf7666aaaa5 | Python | 4,287 | 124 | import requests
import zipfile
import os
from pathlib import Path
from typing import Union
def download_sample_data(
destination_folder: str = ".",
data_type: str = "h5_dir",
) -> Union[str, None]:
"""
Download sample data for Voluseg.
Parameters
----------
destination_folder : str, optio... |
b58a1aeb86619d2f24aa5c564255c2c05b384b41716bdc2ec031e7c8c3c33bdf | Python | 4,287 | 92 | #!/usr/bin/env python3
"""Add the gene-level methylation weighting columns promised in Methods and in the reply to
Reviewer 1 point 8, to Supplementary Table S2.
Columns added, all from the pan-tissue combined stratum (05_combined), which is the stratum whose
methylation statistics the manuscript reports:
Reviewer 1'... |
9dc23957506cf378c1581a7aa0f9cdc1b8123caa3e9441fefd7700e74cf1f07c | Python | 4,292 | 128 | # Copyright (c) Facebook, Inc. and its affiliates.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
from .em import EM, EmptyClusterResolveError
class PQ(EM):
"""
Quantizes the layer weights W with the standard Product Quantization
... |
6c15678e5bd0d4ef7c01251aeed5e8eb6dcf56279610d982f0a8d80fd7f125ea | Python | 4,293 | 134 | """`config.unfrozen_top_layers` leaves the base model's top layers trainable.
Real models with a tiny 2-layer random BERT injected (`patch_base_model`), so
there is no download. `unfrozen_top_layers=0` (the default) must stay
byte-identical to the fully-frozen behaviour `test_base_model_eval_mode.py`
already pins; the... |
2431dab553c57d2e2b6dc9fcf0d5ae9f0736210f36c750a71901218de27d5fe3 | Python | 4,295 | 122 | """Smoke test for the `[project.scripts]` console-script entry points.
The contract is stronger than "the module imports": the shim runs with the
venv's `bin/` as `sys.path[0]`, never the repo root, so the module has to be
part of the *installed distribution*. An earlier version resolved each entry
point with `importl... |
751287993435a7f0303f551440c790a23e2c458b7c158596e896847f00eb76ec | Python | 4,295 | 129 | #!/usr/bin/env python
"""
Process cluster-based power simulation results and plot empirical power.
This script:
1. Resolves the result filename pattern.
2. Infers the block/subject grid from filenames.
3. Uses user-provided block/subject labels when they align safely.
4. Falls back to inferred file indices wit... |
cd7b8606b9ab69cab70b12f799388bff2701bc734ebc76d709c13ebe4c1a93bd | Python | 4,296 | 108 | # Copyright (c) Microsoft Corporation.
# Licensed under the MIT License.
from typing import Optional, Tuple, Union
import torch
from torch_scatter import scatter_add
from mattergen.diffusion.corruption.corruption import B, Corruption, maybe_expand
from mattergen.diffusion.d3pm import d3pm
from mattergen.diffusion.da... |
77a80fa880e84f87d563842012f96fc0dd4fb184e952e5882eb530801bb8da86 | Python | 4,297 | 104 | from ... import options as opts
from ... import types
from ...charts.chart import RectChart
from ...globals import ChartType
class EffectScatter(RectChart):
"""
<<< Scatter plots with ripple effects animation >>>
Use animation effects to visually highlight designated data set.
"""
d... |
4a81402030bc3e0bed8826a8be0f272fdf21584413746a5bc30ffbeaf1a65e4d | Python | 4,298 | 109 | from mdt import CompartmentTemplate
__author__ = 'Robbert Harms'
__date__ = '2018-09-07'
__maintainer__ = 'Robbert Harms'
__email__ = 'robbert@xkls.nl'
__licence__ = 'LGPL v3'
class NODDI_EC(CompartmentTemplate):
"""The Extra-Cellular compartment of the NODDI-Watson model.
This is the compartment as describ... |
38905accb70c7252c6b58d2c534010f24cd7d8051b124fbb9f66261926d1d3ac | Python | 4,300 | 134 | """functions to plot learning curve results"""
import os
import pickle
from configparser import ConfigParser
from glob import glob
import joblib
import matplotlib.pyplot as plt
import numpy as np
def get_all_results_list(root, these_dirs_branch, config_file):
these_dirs = [
(root + this_dir[0], this_dir... |
9a1991400baada972ddb45254a976ba0f397ff44fdf12b1fff56e46fca806424 | Python | 4,302 | 101 | # Copyright (C) 2025 ETH Zurich, Moritz Thürlemann, and other AMP contributors
import json
import os
import numpy as np
import yaml
from pathlib import Path
def write_qm_mm_json(path:str):
parameters = {}
parameters["qm_zone_resnames"] = ["UNL"]
parameters["mm_zone_resnames"] = ["HOH"]
with open(pat... |
370d716eab767ffede840dee81defcea790392616d9d2675daa7a7e4a6c3d1ea | Python | 4,303 | 134 | #!/usr/bin/env python
import urllib.request
from urllib.parse import urlparse
import os
import anndata
import argparse
import shutil
import pandas as pd
import scipy
import json
import tempfile
# 6 available but only 2 contain region label and coordinates
LINKS = [
"https://ftp.cngb.org/pub/SciRAID/stomics/STDS000005... |
4b6233477794def048e56104ecabed706b849425f60fee7ae1abb64c59770361 | Python | 4,306 | 132 | #
# Copyright 2017-2023 Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with
# Sandia Corporation, the U.S. Government retains certain rights in this software.
#
# See LICENSE for full license details
#
from .idac import IDAC
from simulator.backend import ComputeBackend
xp = ComputeBackend() # Repr... |
b7e8aa49cb1c3e1e424d769987fc3471fb21f2e06af546d985f44ae12facdc91 | Python | 4,306 | 124 | import numpy as np
import pandas as pd
from scipy import stats
from scipy import special
## Confidence interval estimation using boostrapping
## Confidence interval estimation using boostrapping
def get_bootstrap_sample(X_df, y_df, n_splits=2):
"""
Returns a stratified bootstrap sample of X and y,
prese... |
3eec8b026ac7f979d0a52f7a63c6ac5f0c3b52182f9057a13bfd1079d0634ddd | Python | 4,310 | 151 | """Dataset and nucleotide-array utilities shared by model families."""
from __future__ import annotations
from typing import Any
import numpy as np
import pandas as pd
from datasets import Dataset, load_dataset
from jaxtyping import UInt8
def load_table(path: str) -> pd.DataFrame:
"""Read one supported genomic... |
ca43119ca604b8f14f7d7b6ccd7db60d11a9ecc55880b3d823480804228cdf1b | Python | 4,312 | 114 | #!/usr/bin/env python
from pgmpy.structure_score import BaseStructureScore
from pgmpy.utils._warnings import _warn_external
class ScoreCache(BaseStructureScore):
"""
A wrapper class for StructureScore instances, which implement a decomposable score,
that caches local scores.
Based on the global decom... |
67ea16563b41849771b72a54cf973d09d7b8d4c5c470f43e21f801c7c24ae94e | Python | 4,314 | 139 | # Copyright (c) Facebook, Inc. and its affiliates.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
import logging
import numpy as np
from fairseq.data import BaseWrapperDataset, plasma_utils
logger = logging.getLogger(__name__)
class Re... |
62295504aa981c2dc54a5e571e0f0a4cf21726b586018d28094174efb1186f97 | Python | 4,317 | 126 | #!/usr/bin/env python3
"""
Basic FASTQ quality control for Nanopore long-read cDNA-seq data.
This script reads gzipped FASTQ files, calculates read lengths and mean
per-read Phred quality scores, and generates histogram plots for each metric.
Edit FASTQ_FILES and OUTPUT_DIR below, or adapt the script to use command-l... |
62864be0ed4ae182a7490a5259f9247150a50eb9d4e8a59d4e94dea44cdcfd4b | Python | 4,317 | 101 | """Manages GO Term fill colors and bordercolors."""
__copyright__ = "Copyright (C) 2016-2018, DV Klopfenstein, H Tang, All rights reserved."
__author__ = "DV Klopfenstein"
import collections as cx
from goatools.gosubdag.utils import get_kwargs
class Go2Color(object):
"""Manages GO Term fill colors and bordercol... |
a38c91dcb4c5f1367d7d1ed57fa3c8f55a03a7fc2c02aad5e8f4a79cb42e406c | Python | 4,318 | 116 | """
Compute the percentage of fusion transcripts whose splice junctions are all
supported by short-read RNA-seq, and plot as a pie chart.
"""
import sys
from pathlib import Path
import polars as pl
from ryp import r, to_r
sys.path.insert(0, "bin")
from src.utils import read_gtf, read_SJ
# ── Paths ─────────────────... |
2905047c80171117084b0e0ccd112a5d49abc4b31675473e7a3c44dc7e973a76 | Python | 4,319 | 99 | """
This package contains all of the functions for gmx_MMPBSA that it
needs to run smoothly.
"""
# ##############################################################################
# GPLv3 LICENSE INFO #
# ... |
d9f2b1cb975e50c607afec5e431a449be60f4b7e412a47c532f688784de9fc51 | Python | 4,319 | 154 | #!/usr/bin/env python3
import argparse
from typing import Any, Callable
import yaml
from symmnet.datasets import cifar10, fmnist, mnist, svhn # noqa
# Hardcoded defaults
DEFAULT_PARAMS = {
"params": {
"n_epochs": 100,
"batch_size": 64,
"lr": 0.01,
"momentum": 0.9,
"weigh... |
1d318fd3b19b6fb00e37c4755d1538b3a0648c0c986485c05b7bdc1b17400502 | Python | 4,321 | 118 | """
Original work by ProGamerGov at
https://github.com/ProGamerGov/neural-dream/blob/master/neural_dream/helper_layers.py
The MIT License (MIT)
Copyright (c) 2020 ProGamerGov
Copyright (c) 2015 Justin Johnson
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associate... |
7f0175ae17d3bdc6c0d0e8d27da532690275be0009fd7210d79fe0039b0f416c | Python | 4,321 | 107 | import numpy as np
import matplotlib.pyplot as plt
from pathlib import Path
# Define paths
base_dir = Path('/egor2/egor/MovieProject2')
retinotopy_dir = 'retinotopy'
fd_file_pattern = 'motion_{subject_id}_enorm.1D'
plots_dir = base_dir / "bids_data/derivatives/group_analysis"
plots_dir.mkdir(parents=True, exist_ok=T... |
cf44b0e745f2b7e110191375d1d1c2129bca973b77e9a00eb7dd0c8d284bc69d | Python | 4,325 | 97 | import numpy
import numpy.testing
import unittest
from . import SampleData
from metax import PredictionModel
from metax import MatrixManager
D = MatrixManager.GENE_SNP_COVARIANCE_DEFINITION
from metax.metaxcan import Utilities
from metax.metaxcan import AssociationCalculation
def _gwas():
gwas = SampleData.dataf... |
841965602b0bbe87140c8cd5b27afdccc531f2f851775f200ba49d2250b6a68f | Python | 4,326 | 139 | # Copyright (c) Facebook, Inc. and its affiliates.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
from typing import Callable, Optional
import torch
import torch.nn as nn
from fairseq import utils
from fairseq.modules import LayerNorm, Mul... |
89a46934b78c5ad32af3855c0c3a8e0cff95f78259807ea2f9640c7ffbf34ce5 | Python | 4,326 | 132 | from __future__ import annotations
from typing import TYPE_CHECKING
import pytest
from poetry.factory import Factory
from tests.mixology.helpers import add_to_repo
from tests.mixology.helpers import check_solver_result
if TYPE_CHECKING:
from poetry.core.packages.project_package import ProjectPackage
from ... |
dbc74c2aed4dedfccb4078ce31674f0217e67bd4d688cb8c4693f4b18d59db2a | Python | 4,326 | 126 | import pytest
from rnalysis import __attr_file_key__, __biotype_file_key__
from rnalysis.utils.settings import *
@pytest.fixture
def use_temp_settings_file(request):
make_temp_copy_of_settings_file()
request.addfinalizer(remove_temp_copy_of_settings_file)
request.addfinalizer(set_temp_copy_of_settings_fi... |
f5cb83c63b1be8be6f7b901d89b664aa845efbc6bb6e60166654ac8b6307cd12 | Python | 4,326 | 108 | """Regenerate datasets_hippie/toy/ from a fixed seed.
The toy dataset is 20 synthetic neurons (10 fake-PV / 10 fake-SOM) used
as a smoke-test fixture for the loader, the inference API, and the
release test suite. It is committed to the repo so that a fresh clone
can run examples/extract_embeddings.py with no external ... |
20de6110ed70af360fb3bfedd3d3e9b2be1a1bab667d01733968924bc18fdb41 | Python | 4,328 | 86 | import cv2 as cv
import numpy as np
import os
for t in range(25):
targetserial_path = self.filepath + '/Averaged_result%d' % (t + 1) ##获取当前需要进行加窗处理的serial（完成了组内叠加平均）的路径
imgNumber = len(os.listdir(targetserial_path)) ##电刺激下图像数量就是选择的路径下的数量
windowNumber = int(imgNumber / self.windowimgNumber) # 10张图... |
6eff1b425333513acb95e2e90b5468bcd301f3a70f2f9232e7f3937c46f6a06b | Python | 4,329 | 157 | #!/usr/bin/env python3
"""Sweep launcher for pure SAL symmetrization experiments (salnet_symm.py).
Iterates over learning rates × seeds. Each combination is stored in a structured
directory tree that plot_puresymm.ipynb can read directly.
Sequential run (default):
python sweep_symm.py
Parallel run with 4 workers... |
1cd312da284f59f8f38a9bd4e078982d6671794d15e1b2b2eefdb3f86e97d3a0 | Python | 4,330 | 118 | import os
import unittest
from io import BytesIO
from unittest.mock import patch
from pyecharts.charts import Bar
from pyecharts.render import make_snapshot
from pyecharts.render.snapshot import (
save_as,
save_as_png,
save_as_text,
decode_base64,
)
def _gen_faker_engine(content: str):... |
cb8070d73d1c9849877c07f9e450470c4bdf497c4f7e9e93ff7a31bce0d994fc | Python | 4,331 | 114 | """QM/MM diagnostics extracted from SANDER output."""
from dataclasses import dataclass
import re
@dataclass(frozen=True)
class QMMMDiagnostic:
"""A diagnostic extracted from a SANDER QM/MM output file."""
code: str
severity: str
message: str
remediation: str
def parse_qmmm_diagnostics(output_... |
dc6b0c40445f1cab07c31f4f11f627df3b32e577873b03a4ce80eedf614df7de | Python | 4,332 | 143 | # Copyright (c) Facebook, Inc. and its affiliates.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
from collections import OrderedDict
import numpy as np
from fairseq.data import BaseWrapperDataset, FairseqDataset, iterators
class MultiI... |
acdf505c6209e0932c1ffa3522c8ff2791e90957e5f996fd533fe9e734ab9da5 | Python | 4,333 | 118 | import json
import os
import urllib.request
import matplotlib.pyplot as plt
import matplotlib.font_manager as font_manager
from matplotlib.backends.backend_pdf import PdfPages
urllib.request.urlretrieve(
'https://github.com/google/fonts/raw/main/ofl/ibmplexmono/IBMPlexMono-Regular.ttf',
'IBMPlexMono-Regular.t... |
599900acde10d434e5c683bfdd4e9dd8355f8d028c491ca09e8d6ddfb2e57070 | Python | 4,335 | 109 | import cv2
import cmapy
from PIL import Image
import numpy as np
from msi_visual.utils import normalize_image_grayscale, image_histogram_equalization
from msi_visual.normalization import spatial_total_ion_count
def get_pr(normalized, high=99.9, low=99):
novel = np.percentile(normalized, high, axis=-1) / ... |
bec36a27c2d015dda93fb290c884eca69fc838301d958a72ffc94d646ad4ae49 | Python | 4,335 | 139 | from __future__ import annotations
from contextlib import suppress
from functools import cached_property
from typing import TYPE_CHECKING
from typing import Any
import requests.adapters
from poetry.core.packages.package import Package
from poetry.inspection.info import PackageInfo
from poetry.repositories.exception... |
0c295584f72691866daa2df4b9d23d34251a53927df4eee5869c5fe38b0aec76 | Python | 4,337 | 107 | #!/usr/bin/env python3
"""Build Methylation_Data/meth_sex.csv, the per-sample sex table sex_adjusted_sensitivity.R reads.
WHY THIS EXISTS. sex_adjusted_sensitivity.R (Reviewer 3) fits the AllMeth MS-vs-HC model with and
without a sex term on the samples for which sex is known, and reads that sex from meth_sex.csv. No
... |
9fcd3ea63833376e76eb29375eade2c4ff165780d75a0febb083a85a826253c3 | Python | 4,337 | 131 | import numpy as np
import torch
from typing import List, Tuple
from stripedhyena.model import StripedHyena
from .tokenizer import CharLevelTokenizer
def prepare_batch(
seqs: List[str],
tokenizer: CharLevelTokenizer,
prepend_bos: bool = True,
device: str = 'cuda:0'
) -> Tuple[torch.Tensor, List[int]]:... |
7ddb32eedd8632a7b65c3ac22f2593e749e08fb5b567bb2c456246880ee3f892 | Python | 4,341 | 147 | # -*- coding: utf-8 -*-
"""
Created on Tue Jul 30 16:15:31 2019
@author: 俊男
"""
# In[] Naive Bayesian Classifier default with Gaussian Kernal
from sklearn.naive_bayes import BernoulliNB, MultinomialNB, GaussianNB
import pandas as pd
class NaiveBayesClassifier:
__classifier = None
__y_columns = None
def _... |
4b9a7d2c9b991a10edfc5119a1dbd6cca91f30223fd97cb384bf741c0fae6077 | Python | 4,342 | 145 | """Transfer matrix for the two neuron buesing model
Defines a class with generators for the creation of the transfer matrix T. The
T can cope with every kind of PSP shapes.
"""
from typing import Callable, Iterator
import numpy as np
def sigma(u: float, tau: float) -> float:
return 1 / (1 + tau * np.exp(-u))
... |
66144a191ff17112faad9df6dcfe40912cb97bf1115bb7072b9e990721ca88e0 | Python | 4,342 | 164 | import os
import re
import numpy
import logging
import h5py
try:
import h5py_cache
except:
logging.info("Couldn't import h5py_cache. Anyway, this dependency should be removed. It has been folded into h5py")
from . import Expression as _Expression
from ..misc import Math
######################################... |
2bf127a782e6d6ea6059ddb043a7626f14aa967e441b3e84feb23bbfdde044b7 | Python | 4,348 | 133 | # 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... |
1288830de8c694dc15229c2c4bd7d050fb4fa9333951a2f67fa7c6bbdc1accd4 | Python | 4,352 | 136 | # -*- coding:utf-8 -*-
"""
Copy of the module scilpy.io.utils.py.
"""
import numpy as np
import os
def get_sh_order_and_fullness(ncoeffs):
"""
Get the order of the SH basis from the number of SH coefficients
as well as a boolean indicating if the basis is full.
"""
# the two curves (sym and full) ... |
e38595893b491c3455e0453fa244f25036060d685dc3c92424727c6e51bb318c | Python | 4,353 | 133 | import numpy as np
import pytest
import torch
from neurovfm.data.cache import CacheManager
from neurovfm.datasets import ImageDataset, StudyAwareBatchSampler
from neurovfm.data.metadata import DatasetMetadata
class _DummyImage:
"""
Simple stand-in for a SimpleITK image providing only GetSpacing().
"""
def __init... |
f78b6a4936e038f781478dadcf32a0a6e09fae5a37c3efad311b885b1d5d94e4 | Python | 4,355 | 113 | # import from plugins/cluster_metrics.py
"""Show how to add a custom cluster metrics."""
import numpy as np
from phy import IPlugin
from scipy.optimize import curve_fit
from scipy.special import ndtr
class qMetricsPlugin(IPlugin):
def attach_to_controller(self, controller):
"""Note that this function is ... |
50b3680efe600bf2421f54a13f284c0a7543fc186f450b4291474e965d7c2e8c | Python | 4,356 | 102 | import networkx as nx
import pandas as pd
def create_directed_graph(iax: pd.DataFrame, tp: int) -> nx.DiGraph:
"""
Creates a directed graph based on the axial current value (iax) at a specified time point (tp).
Parameters:
iax (df): A pandas DataFrame with axial current data. It must include a co... |
180db8afeec7c5423b45b7689cd7f741114e6d2e8320d870b9b909a099db4a7d | Python | 4,359 | 96 | #!/usr/bin/env python3
"""Canal de HIBRIDAÇÃO para o OCE: repulsão de nível s(B)–p(X) em 2ª ordem.
MOTIVO, medido. O diagnóstico de 28/07 mostrou que o `wave15` erra de forma
sistemática nos IODETOS: resíduo mediano +0,077 eV e |res| 2,4× maior que nos
demais haletos. E o mecanismo foi nomeado: descendo a série do hal... |
54d5efc7b8187fa23e5506425268a6a69fca4c431dba61a0d6d2856027a019d1 | Python | 4,359 | 94 | import torch.nn as nn
import torch
import torch.nn.functional as F
import config.cfg_lodet as cfg
class Ordinary_Head(nn.Module):
def __init__(self, nC, anchors, stride):
super(Ordinary_Head, self).__init__()
self.__anchors = anchors
self.__nA = len(anchors)
self.__nC = nC#类别
... |
bec004f80ef95b4caedf591931fb69b6170bd66efc8332cf18695a4be42be221 | Python | 4,363 | 85 | import os
import numpy as np
import subprocess
from subprocess import Popen
import pandas as pd
from meld_classifier.tools_commands_prints import get_m
from meld_classifier.paths import FS_SUBJECTS_PATH
#Function for sampling per patient, at various intracortical/subcortical depth
def sample_T1_features(subject_id, v... |
781e74140f51bd35a2351e3c18dd12a2b9ad43190a240e7f35e1d85b32f87754 | Python | 4,364 | 111 | import ast
import inspect
from textwrap import indent, dedent
__author__ = 'Robbert Harms'
__date__ = '2017-07-24'
__maintainer__ = 'Robbert Harms'
__email__ = 'robbert@xkls.nl'
__licence__ = 'LGPL v3'
class TemplateModifier:
def __init__(self, template):
"""Given a template instance, this class can upd... |
91782ef3921f3cb5de8f1f9d5bc26f6ebb1a64234c14f84dfd09612b8e904e66 | Python | 4,364 | 140 | from pathlib import Path
import torch
from torchvision.models import resnet152, ResNet152_Weights
from torchvision.models import resnet101, ResNet101_Weights
from torchvision.models import resnet18, ResNet18_Weights
from torchvision.models import resnet34, ResNet34_Weights
from torchvision.models import resnet50, ResN... |
294b845487d7d10e035c8433875aab311fc41af7fd6d5d891f98636d0895b772 | Python | 4,366 | 80 | #!/usr/bin/env python3
"""R1 ponto 3: refaz a Fig. 1(a) com MAE e R^2 ao lado do RMSE.
Copia fiel de `fig_manuscrito.py` no que produz os pontos -- mesmo GroupKFold, mesma
grade de alpha, mesma normalizacao -- para que a figura nao mude de valor, so de
anotacao. As tres medidas sao a MEDIA SOBRE AS DOBRAS, que e a con... |
6c85167bfe3bc153f50f97077994972221c5d4758fe7be031b06b03f2aab2b06 | Python | 4,368 | 104 | """Propagate counts for associations"""
__copyright__ = "Copyright (C) 2016-2019, DV Klopfenstein, H Tang, All rights reserved."
__author__ = "DV Klopfenstein"
import sys
from collections import defaultdict
from goatools.gosubdag.go_tasks import get_go2parents_go2obj
from goatools.anno.broad_gos import NS2GOS_SHORT
f... |
77a7afc7bdc29dd9fe6df3d943adeba0639e2231a506bcb4bac8b0f61a362fae | Python | 4,368 | 105 | import json
import os
import unittest
import zipfile
from contextlib import contextmanager
from pathlib import Path
from tempfile import TemporaryDirectory
from types import SimpleNamespace
from unittest.mock import patch
from GMXMMPBSA.commandlineparser import parser
from GMXMMPBSA.error_bundle import create_error_bu... |
17ca8294cecf32e87fa80ab5e91025af1328600437324644395b6ada6f5f5d72 | Python | 4,369 | 142 | from __future__ import annotations
from typing import TYPE_CHECKING
from typing import ClassVar
from cleo.helpers import argument
from cleo.helpers import option
from poetry.core.constraints.version import parse_constraint
from poetry.core.version.exceptions import InvalidVersionError
from poetry.config.config impor... |
319b3da2ef15ccae95162b1b4f4a9a0b0da63fa0062a7f6006a06dd567258d85 | Python | 4,369 | 148 | # From: gluonts/src/gluonts/time_feature/_base.py
# Copyright 2018 Amazon.com, Inc. or its affiliates. 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.
# A copy of the License is located at
#
# http://www.apac... |
090c8a148437b765f446df7971c5dba42fa20a2396f00df156b2fb8c56ea0be4 | Python | 4,370 | 139 | import pickle
import numpy as np
import pdb
from celltype_ibl.params.config import ULTRA_DATA_PATH, STIM_REMOVED_DATA_PATH
def get_ultra_wvf_acg_pairs(
data_path: str = ULTRA_DATA_PATH,
return_optotagged: bool = True,
return_half: bool = True,
return_radius: bool = False,
load_new: bool = False,
)... |
4b08568b9cfb53029791c64195b727437848d299a6a9b82a34d9325650da753b | Python | 4,371 | 120 | #!/usr/bin/env python3
# Florian Bénitière 16/03/2025
# Script to find unique short variants (SNVs and Indels) from a large .parquet file and produce VCF files per chromosome for use by VEP
import os
import sys
import pandas as pd
import subprocess
from pyspark.sql import SparkSession
from pyspark.sql import function... |
9a7060c31630cf68b4d92817eb0f63196174695118eeb11287fa10e9cdb6415e | Python | 4,372 | 130 | # Copyright (c) Microsoft Corporation.
# Licensed under the MIT License.
import re
from functools import cached_property
from pymatgen.analysis.structure_analyzer import oxide_type
from pymatgen.core import Structure
from pymatgen.entries.compatibility import Compatibility
from pymatgen.entries.computed_entries impor... |
faa59805cc400c621527cba36767e9d4a9dfea5aa58e55a4492bb19e1b61239c | Python | 4,372 | 133 | #!/usr/bin/env python
# ENCODE DCC fingerprint/JSD plot wrapper
# Author: Jin Lee (leepc12@gmail.com)
import sys
import os
import argparse
from encode_lib_common import (
log, ls_l, mkdir_p, rm_f, run_shell_cmd, strip_ext_bam)
from encode_lib_genomic import (
samtools_index)
from encode_lib_blacklist_filter ... |
4f3c308c89fd4306ade09c39ee701bfcf77d2524b4115a0217ecb98bb2f2853b | Python | 4,373 | 133 | from pathlib import Path
import joblib
from baseModels.transforms import load_transforms
from baseModels.models import *
class WrappedModel(torch.nn.Module):
def __init__(self, module):
super(WrappedModel, self).__init__()
self.module = module # that I actually define.
def forward(self, x):
return self.module... |
2479fc066d78196c6da62d6deaa1e99a1afbfaa4f29202cd4635deb3f1ecb4ba | Python | 4,374 | 128 | # Copyright (c) Facebook, Inc. and its affiliates.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
from torch.optim import Adagrad
from fairseq.optim import LegacyFairseqOptimizer, register_optimizer
@register_optimizer("adagrad_with_grad... |
7f20cd7483e55b4634655711fd5f195977b8cff6ddb0d2f7ad0f917252ca2357 | Python | 4,377 | 130 | import argparse
import os
import textwrap
import argcomplete
import sys
import mdt
__author__ = 'Robbert Harms'
__date__ = "2015-10-16"
__maintainer__ = "Robbert Harms"
__email__ = "robbert@xkls.nl"
def get_argparse_extension_checker(choices, dir_allowed=False):
"""Get an :class:`argparge.Action` class that can... |
354feed7be590a66d3548172e751233e8a5d6e215061dddd6b1824fa18010dc6 | Python | 4,378 | 121 | # Copyright (c) Facebook, Inc. and its affiliates.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
from fairseq.models import register_model, register_model_architecture
from fairseq.models.nat import NATransformerModel, base_architecture
f... |
359e6dbc1296e046fbfc385a696c900373569e941f0ec4fd1606d39e2297b23c | Python | 4,378 | 134 | import pandas as pd
import pytest
from pgmpy.base import DAG, PDAG
from pgmpy.metrics import AdjacencyConfusionMatrix
# The models in true_dag and est_dag fixtures are taken from the paper: https://arxiv.org/pdf/2412.10039
@pytest.fixture
def true_dag():
return DAG(
[
("x1", "x2"),
... |
dbd826f594fda0c46aa8c97a14d9ab75cbde8e333f4331ad34decc534ece9624 | Python | 4,378 | 120 | import matplotlib.pyplot as plt
import numpy as np
import loompy
from .colors import colorize
from cytograph.enrichment import FeatureSelectionByVariance
from cytograph.embedding import art_of_tsne
from sklearn.decomposition import PCA
from sklearn.manifold import TSNE
def all_QC_plots(ds: loompy.LoomConnection = Non... |
dff1ea84d45683dfdc2af97b25e8f9d4cd184ac618ced71635ffe3faab03425d | Python | 4,381 | 112 | # -*- coding: utf-8 -*-
"""
@Time:Created on 2019/4/30 14:19
@author: LiFan Chen
@Filename: mol_featurizer.py
@Software: PyCharm
"""
import numpy as np
from rdkit import Chem
from rdkit.Chem import Descriptors
num_atom_feat = 34
def one_of_k_encoding(x, allowable_set):
if x not in allowable_set:
raise Exce... |
998912e9149917dd847ca26d27ce3349ab2387daac5a95c8fc62f8d711ba6733 | Python | 4,382 | 81 | #!/usr/bin/env python3
"""Normalisation-based pseudobulk aggregation, as a sensitivity comparison against the
summed-raw-count (muscat standard) aggregation.
The deposited Kaufmann matrix is log-normalised: lognorm = log1p(count / total * 1e4).
Therefore expm1(lognorm) = count/total*1e4 = the cell's CP10K (counts per ... |
80bf630c88a1c84992c1c1d0b8c4aa7646daf76b79f9c052108478d45236cd17 | Python | 4,384 | 175 | from typing import Optional
import haiku as hk
import jax
import jax.numpy as jnp
class ConvBlock(hk.Module):
"""
Conv Block.
"""
def __init__(
self,
dim: int,
dim_out: Optional[int] = None,
kernel_size: int = 1,
layer_norm_axis: int = -1,
name: Option... |
4b0626b59c6770c49349f294cf0447f6a5f317d5cb10ecc0a0c153ca0a15cab1 | Python | 4,385 | 134 | # Copyright (c) Facebook, Inc. and its affiliates.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
import collections
import os
import shutil
import tempfile
import unittest
import numpy as np
import torch
from scripts.average_checkpoints i... |
4bc70dc68e32550416ddafc034ff003e86105afbfd28c55f9d6b5c20b95b1b6c | Python | 4,386 | 119 | """Fit OCE coefficients J_F by linear regression on xtb training energies."""
from __future__ import annotations
import json
from dataclasses import dataclass
from pathlib import Path
import numpy as np
from sklearn.linear_model import Ridge, LinearRegression
from oce.atomic_table import load_table
from oce.correlat... |
68e661248ccfa37d1c9d8c37ff40b770c4c78967e798aabd5c5659fbd703c182 | Python | 4,386 | 82 | import argparse
from typing import Union
from batchgenerators.utilities.file_and_folder_operations import join, isdir, isfile, load_json, save_json
from nnunetv2.imageio.reader_writer_registry import determine_reader_writer_from_dataset_json
from nnunetv2.paths import nnUNet_preprocessed, nnUNet_raw
from nnunetv2.uti... |
d54916f495ec17fb292a036dc4961e4b6886714b03d088c9a0e1c2a7c3cb4fdc | Python | 4,386 | 112 | # -*- coding: utf-8 -*-
"""
@Time:Created on 2019/4/30 14:19
@author: LiFan Chen
@Filename: mol_featurizer.py
@Software: PyCharm
"""
import numpy as np
from rdkit import Chem
from rdkit.Chem import Descriptors
num_atom_feat = 34
def one_of_k_encoding(x, allowable_set):
if x not in allowable_set:
raise Exce... |
e823fc24ab9b943399baa98a966557186efa36e7332b6acaf98f3dd3f2dd9d24 | Python | 4,390 | 148 | import numpy as np
from scipy.special import hyp2f1, gammaln
def get_r2(iv, dv, stack_intercept=True):
""" Regress dv onto iv and return r-squared.
Parameters
----------
iv : numpy array
Array of shape N (samples) x K (features)
dv : numpy array
Array of shape N (samples) x 1
... |
6e078a70da990321a4c826d7f47920ca373ac0d599910a0fe34b137c39c6705b | Python | 4,396 | 159 | # build_pairs_c1_by_task_session.py
# Build time-shifted pairs per (task, session) for C1 from extracted ROI timeseries.
# Outputs one NPZ per system: ses<id>_<task>_pairs.npz with 90/10 split.
#
# Works with filenames like:
# sub-01__ses-1-func-wrsub-01_ses-1_task-encoding_run-1_bold__timeseries.npy
import o... |
d69d2d57d9eb95830658d07fbbf580a850e6a1fc7d0f583f1bc729dac0b34c26 | Python | 4,396 | 120 | #!/usr/bin/env python3
"""
@file test_blackbox.py
@author Simon Yu
@date 02/12/2024
@brief Script for testing blackbox models.
"""
import argparse
import dataset
import header
import logger
import model
import torch
import tqdm
import utility
import wandb
def initializeRunName(run_name = ""):
if run_name !=... |
c00e239c16b363b3023139090428e2b82333cc809111f3bce17f9a5a841db53c | Python | 4,397 | 112 | """Property-based tests for the embeddings-store codec.
`test_embeddings_store.py` pins the round trip at a handful of hand-picked
tensors. What the codec actually promises is a property over any token/feature
matrix — shape preserved exactly, values surviving up to bf16's rounding — so
this generates the shapes and v... |
4f8162080c39a276a677992c3dee32d855af2ebf80b7fdca058cbc59a3f36e73 | Python | 4,400 | 122 | import nibabel as nib
import matplotlib.pyplot as plt
import numpy as np
from nilearn.image import resample_to_img
import matplotlib as mpl
# === Paths ===
isc_group = "/egor2/egor/MovieProject2/bids_data/derivatives/group_analysis/backtothefuture/isc/ISC_group.nii.gz"
anat_template = "/egor2/egor/MovieProject2/bids_d... |
60c95a84ce642d227e7a31d17e45fd55b7755e0a04b137ace640506b2a937408 | Python | 4,401 | 125 | #!/usr/bin/env python
# coding: utf-8
#
# This file is part of multiQC software. Using a metadata file, it writes part of the multiQC config file
#
# Copyright (c) 2018 - Institut Curie
#
# File author(s):
# Dimitri Desvillechabrol <dimitri.desvillechabrol@curie.fr>,
# Nicolas Servant <nicolas.servant@curi... |
14d0d3c85e308312f0e9b7266b26a7506e94e2269fd1337342f5beb1dc61f064 | Python | 4,403 | 117 | import unittest
import numpy as np
from numpy import cos, exp, sin
from numpy.testing import assert_allclose
import mdt
from mot.configuration import CLRuntimeInfo
from mot.lib.kernel_data import Array
class test_SSFP(unittest.TestCase):
def __init__(self, *args, **kwargs):
super().__init__(*args, **kwar... |
a2af253168ddfa8b39fe0a02910d0ac8e25dce0aa2f754d3a7447eb28ec01290 | Python | 4,403 | 129 | import faiss
import numpy as np
import pandas as pd
import os
import yaml
import glob
import torch
from easydict import EasyDict
from utils.constants import sequence_level
from utils.file_reader import FileReader
from utils.faiss_index import FaissIndex
from model.ProTrek.protrek_trimodal_model import ProTrekTrimodalM... |
5ac1ecbd2769260b051c3d41838d682350084ea4c2c5e10d0c2270c835e53826 | Python | 4,404 | 120 | #!/usr/bin/env python3
# Florian Bénitière 16/03/2025
# Script to find unique short variants (SNVs and Indels) from a large .parquet file and produce VCF files per chromosome for use by VEP
import os
import sys
import pandas as pd
import subprocess
from pyspark.sql import SparkSession
from pyspark.sql import function... |
288fb188ed6a910c3484b926ca6107760149bfa3f908dd53f482868bfe913bb1 | Python | 4,405 | 110 | #!/usr/bin/env python3
# Florian Bénitière 16/03/2025
# Script to generate a .parquet file by merging all TSV gVCF files from a directory
import os
import shutil
import sys
import pandas as pd
import subprocess
import psutil # System and process utilities
from math import floor # For rounding down numbers
from col... |
36b0b41d90b7b642b6e4c425b5e1647ff1d5fb0301be026d545026f6af8881c9 | Python | 4,405 | 142 | """ Decorators for handling errors, debugging, timing, and convergence warnings. """
import functools
import time
import traceback
import warnings
from functools import wraps
import click
from dask.distributed import Client, LocalCluster
from sklearn.exceptions import ConvergenceWarning
from rich.console import Cons... |
1348e21c9abceeb1b67cf22f4f8b3d5dcb6ea0638902ab8900da887cd2fb8e3d | Python | 4,408 | 155 | #!/usr/bin/env python
# Author_and_contribution: Niklas Mueller-Boetticher; created template
# Author_and_contribution: ENTER YOUR NAME AND CONTRIBUTION HERE
import argparse
# TODO adjust description
parser = argparse.ArgumentParser(description="Method ...")
parser.add_argument(
"-c", "--coordinates", help="Pat... |
022fa10bf5951a48ace92e7b011f5d7e31cf15ce06fd94acf4f7fe073e13c955 | Python | 4,409 | 143 | from __future__ import annotations
import pytest
from poetry.config.config_source import PropertyNotFoundError
from poetry.config.dict_config_source import DictConfigSource
def test_dict_config_source_add_property() -> None:
config_source = DictConfigSource()
assert config_source._config == {}
config_s... |
272c50413725076826824192ebbc8c80e89d15ffd68e3841dc68d4ba84c1109b | Python | 4,410 | 133 |
__author__ = 'Robbert Harms'
__date__ = "2015-03-26"
__license__ = "LGPL v3"
__maintainer__ = "Robbert Harms"
__email__ = "robbert@xkls.nl"
class Tree:
def __init__(self, data=None, tag=None, children=None, parent=None):
"""Create a new Tree.
In this tree, every node is a tree object as well. T... |
fea10f7713bd30128fa01c3fccd3854ff58a697dbe22e444d139a891348d03ee | Python | 4,415 | 90 | import numpy as np
from . import io_mesh as io
import subprocess
import argparse
import os
import copy
def calculate_area(surfname, fwhm, software="CIVET", subject="fsid", surf="pial", hemi="lh"):
"""Calculate and smooth surface area using CIVET or freesurfer."""
tmpdir = '/tmp/' + str(np.random.randint(1000))... |
6219c0ade4476866a100c868ce4907f201b0f25e5a3ded16c42bf8b79ad2966f | Python | 4,416 | 114 | """`brenda_references/tests/` must be collected by CI, from its own job.
The root `testpaths` points only at the top-level `tests/` and the subpackage
had no `.github/` of its own, so nothing in CI ever collected its suite. It is
not folded into the root job: `brenda_references` is its own pdm project with
its own git... |
e413cbff10f68ad54ddc5c1c56d7f8615b462fa19d159b5406aacd672d982d1a | Python | 4,417 | 128 | import pandas
import os
import io
import logging
import re
import gzip
from numpy import dot, transpose, cov
from .. import MatrixManager
from .. import Utilities
from . import Math
from .. import Exceptions
K_GENE_MODEL_HEADER=["gene", "model1", "model2", "value"]
class FeatureMatrixManager(object):
def __init_... |
2b39ce365f13773dac6d0f1f41856f5da2c489cacb0e03d7ecd3efc53e50a560 | Python | 4,418 | 100 | from typing import Callable
import torch
def train_pcoders(net: torch.nn.Module, optimizer: torch.optim.Optimizer, loss_function: Callable, epoch: int, train_loader: torch.utils.data.DataLoader, device: str, writer: torch.utils.tensorboard.SummaryWriter=None):
r"""
Trains the feedback modules of PCoders using ... |
567a651ad3b4aa143ac24b030fe403141bc7d09cf4c39a408d6ac318fc3d44c2 | Python | 4,418 | 111 | import polars as pl
from src.utils import read_gtf
# Read in datasets
classification = pl.read_parquet("nextflow_results/V47/final_classification.parquet")
reftss = pl.read_csv("data/liftovered_mm39_to_hg38_peaks_overlapped_reftss_hg38_500bp.bed", separator="\t", has_header = False, new_columns=["chrom", "start", "end... |
b82aec235796a4060e93d6e21b43ba8239f8779d3744567d9d845c954473fdef | Python | 4,418 | 118 | import os
# import logging
import json
import torch.nn as nn
from transformers import HfArgumentParser, set_seed
from transformers import BertTokenizer, AutoTokenizer, logging
from transformers.trainer_pt_utils import get_parameter_names
from src.models import KeAP, KeAPConfig, KnowledgeDecoder
from src.trainer import... |
d82c52d6322fa374dcb2db1861826c2f84a491614bd56ec2b565d4f018e4dc75 | Python | 4,421 | 126 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
import re
import glob
from textwrap import dedent
import os
import sys
from setuptools import setup, find_packages, Command
def load_requirements(fname):
is_comment = re.compile('^\s*(#|--).*').match
with open(fname) as fo:
return [line.strip() for line i... |
656f89c69704eea3557f8340e653aa4df1c99bb23a38aae7d7f99cb2e7b78a0b | Python | 4,424 | 135 | """Utility functions to help setup the model, optimizer, distributed compute, etc.
"""
import typing
import logging
from pathlib import Path
import sys
import torch
import torch.distributed as dist
from torch.utils.data import DataLoader, RandomSampler, Dataset
from torch.utils.data.distributed import DistributedSampl... |
9a36d7e083015ff9ea5ac264b10d56cd967d8c7977c86d84406968133c7bf98a | Python | 4,424 | 134 | from __future__ import annotations
from typing import TYPE_CHECKING
import pytest
from poetry.console.commands.version import VersionCommand
if TYPE_CHECKING:
from cleo.testers.command_tester import CommandTester
from poetry.poetry import Poetry
from tests.types import CommandTesterFactory
from te... |
b946343eb1f720404e6aa990321861c1ef31905a20c58e42ab4643d038210c92 | Python | 4,424 | 107 | import torch
import torch.nn as nn
import torch.nn.functional as F
from ..layers.conv_module import Convolutional
class Upsample(nn.Module):
def __init__(self, scale_factor=1, mode='nearest'):
super(Upsample, self).__init__()
self.scale_factor = scale_factor
self.mode = mode
... |
0906c51bc3265bc5a06845f707ea3d3ff4b6ab38393b40536b94a2458773feca | Python | 4,426 | 145 | # Copyright 2015 Google Inc. 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 applicable law or a... |
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