sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
095364b6951d9fb24d69a24679f3bef22c48f5851112377b06288ecf73a317c6 | Python | 2,650 | 87 | # Configuration file for the Sphinx documentation builder.
#
# This file only contains a selection of the most common options. For a full
# list see the documentation:
# https://www.sphinx-doc.org/en/master/usage/configuration.html
# -- Path setup --------------------------------------------------------------
# If ex... |
ec22246561e5cd3f57dbe0ab8f809ef39c5afdfd525c6a29d4b97b37fd45c0ed | Python | 2,653 | 89 | from __future__ import annotations
import subprocess
import logging
from dateutil.parser import parse
from datetime import datetime
import xarray
import io
import os
import numpy as np
import importlib.resources as impr
from .build import build
SIMOUT = ["ne", "Tn", "Ti", "Te", "nO+", "nH+", "nHe+", "nO2+", "nNO+", "... |
83411db94e0273d122df3d3050e3566ce55e661f9a943aaa6fa115540f3dc832 | Python | 2,654 | 71 | import argparse
import nibabel as nib
from glob import glob
import os
from tqdm import tqdm
from utils import SUBJECTS, FMRI_BETAS_DIR
SPLITS = ['train_image', 'train_caption', 'test_caption', 'test_image', 'imagery', 'blank']
SUFFIX = "*bf(1)"
def get_subdir(split_name, beta_dir):
subdir = os.path.join(beta... |
43c4d8c189f52bec16b2f4604fd0a5375e4a1761e37682deddce473305706708 | Python | 2,656 | 46 | from __future__ import annotations
import tensorflow as tf
from tensorflow.keras import layers, Model
from .layers import ClassToken, Patches, PatchEncoder, transformer_encoder
def vit_feature_path(image_input, patch_size: int, config: dict, name: str):
pad_size = int(config.get("pad_size", 160))
hidden_dim ... |
e13c3b5cf74819b0b59455b820f81db234b46ef3fe2ee2712c4c6084f49c53a0 | Python | 2,656 | 79 | import pytest
from multiqc import config, report
from multiqc.modules.umicollapse import MultiqcModule
from multiqc.plots.table_object import InputRow
from multiqc.types import SampleName, SectionKey
@pytest.fixture(autouse=True)
def reset_config():
"""Reset config state after each test."""
original_preserve ... |
9409625a9ef303400aef8c4c9caae11a18c36cf2fbe9d68a2f42cb17df11b8cd | Python | 2,658 | 81 | """Source reconstruction.
This includes: coregistration, beamforming and parcellation.
"""
import numpy as np
from dask.distributed import Client
from osl import source_recon, utils
# Author : Chetan Gohil <chetan.gohil@psych.ox.ac.uk>
source_recon.setup_fsl("/well/woolrich/projects/software/fsl")
def fix_headsh... |
bb33a1780cbdd391e81c34c15f3a9e222b128802cf144a04136f682cc7f4a7a1 | Python | 2,658 | 61 | from __future__ import absolute_import
from builtins import range
from .__init__ import ForceBalanceTestCase
import numpy
import forcebalance
import re, sys
from math import cos, sin, pi
import pytest
class TestFiniteDifference(ForceBalanceTestCase):
@classmethod
def setup_class(cls):
super(TestFiniteD... |
6929aacb88d5a3a6004a6c9c7ff39d0004ce6414a69a5c11efc8aa00229ac287 | Python | 2,664 | 61 | '''
Author: Zhongming Liang lzzzmmgpt@gmail.com
Date: 2026-04-26 15:22:43
LastEditors: Zhongming Liang lzzzmmgpt@gmail.com
LastEditTime: 2026-04-26 20:52:04
FilePath: /liangzhongming/phd_code/ModelTest/CellNiche/cellniche/__init__.py
Description: 这是默认设置,请设置`customMade`, 打开koroFileHeader查看配置 进行设置: https://github.com/OBK... |
2c7c38211c7a632d1731fa8b8a9edaff810da4452745b7da60a60bd889f9f557 | Python | 2,678 | 92 | # Copyright 2022 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
#
# https://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing,... |
8bd274da92afcd84fd7ae93bdc0b5000d2a5eb4318c8d0a558d87eedee6614b7 | Python | 2,681 | 59 | """add dataset models
Revision ID: 4efc63729750
Revises: 0f24a7f21b23
Create Date: 2025-04-10 13:17:21.342253
"""
from typing import Sequence, Union
from alembic import op
import sqlalchemy as sa
# revision identifiers, used by Alembic.
revision: str = '4efc63729750'
down_revision: Union[str, None] = '0f24a7f21b23... |
a5db78784e3f357413b809159c301682449c6236734bc322325c4684105fb1fd | Python | 2,681 | 75 | import sys
sys.setrecursionlimit(10000)
# print("/n/nRecursion limit set to:", sys.getrecursionlimit())
import getopt
import traceback
import os
import platform
from pathlib import PurePath
import PySide6
import sys
from PySide6.QtWidgets import QApplication
from gui.RaidionicsMainWindow import RaidionicsMainWindow
im... |
349d83dc673d5088dd3fa12f9a5c894c1755a3184e415e0be2a1ca0df331eeb5 | Python | 2,684 | 54 | import torch
import torch.nn as nn
import torch.nn.functional as F
import math
##########################
#### Genomic FC Model ####
##########################
# 定义一个神经网络模块，包含一个全连接层、一个SELU激活函数和一个AlphaDropout层。
class SNN_Block(nn.Module):
def __init__(self, dim1, dim2, dropout=0.25):
super().__init__()
... |
07d51313b3eb0d8448232c5ceb9ba735e57209a07239ec8f212935538e751eb7 | Python | 2,685 | 73 | #!/usr/bin/env python3
# author : Alina Kutlushina
# date : 15.05.2020
# license : BSD-3
#==============================================================================
__author__ = 'alina'
import os
import argparse
import numpy as np
from rdkit import Chem
from rdkit.Chem import AllChem
f... |
9c95b6deb8d1fd2b7eab39e9d4d85a4ed7f141ab1a6ead4ca2f847733b57a20c | Python | 2,687 | 68 | #!/usr/bin/env python
##############################################################################
# Medical Image Registration ToolKit (MIRTK)
#
# Copyright 2013-2015 Imperial College London
# Copyright 2013-2015 Andreas Schuh
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use thi... |
797c7df57b29edb2cb2dbe3d7c562a5ab642b38a66fa2a0d5ae1e07637e296d2 | Python | 2,688 | 86 | #!/usr/bin/env python
import sys
import os
from subprocess import *
if len(sys.argv) <= 1:
print 'Usage: %s training_file [testing_file] [kernel_type]' % sys.argv[0]
raise SystemExit
# svm, grid, and gnuplot executable files
is_win32 = (sys.platform == 'win32')
if not is_win32:
svmscale_exe = "../svm-scale"
svm... |
36be01d9c6c7b58580a4a8a077e079e2f5191e3dcbc8c8c234a6dd6d9e72145c | Python | 2,689 | 90 | """
MultiQC configuration file validator script.
"""
import logging
import sys
from pathlib import Path
import yaml
from pydantic import ValidationError
from rich.console import Console, group
from rich.highlighter import ReprHighlighter
from rich.panel import Panel
from rich.text import Text
from multiqc.utils.conf... |
339ab9eb13a9ed97cadb59a2d2038224ff1d5e25a33ef6d31e6bfedfa63256af | Python | 2,692 | 80 | """
Configuration for the RAG agent.
"""
from dataclasses import dataclass, field
import os
from typing import Optional
from linkml_store import Client
from linkml_store.api import Collection
from aurelian.dependencies.workdir import HasWorkdir, WorkDir
from . import COLLECTION_NAME
@dataclass
class RagDependencies... |
6858abccdc876838e75f915fa8e55e882eadf6590ef7b34c3d75603e4eec33a8 | Python | 2,692 | 87 | from data_provider.data_loader import Dataset_ETT_hour, Dataset_ETT_minute, Dataset_Custom, Dataset_M4, PSMSegLoader, \
MSLSegLoader, SMAPSegLoader, SMDSegLoader, SWATSegLoader, UEAloader, Dataset_Meteorology
from data_provider.uea import collate_fn
from torch.utils.data import DataLoader
data_dict = {
'ETTh1'... |
639d576c67891a8b1955118d147db6e1a369ea64794c355dace719b3fa16d4af | Python | 2,695 | 85 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
Reconstruct ancestral sequences using FastML based on multiple sequence alignments and evolutionary trees.
Input:
- MSA files (*.align.fa) generated by MUSCLE
- Tree files (*.newick) generated by phyloFit
- Input file name defines the subdirectory for each set of data... |
08a3dd5fac7387470b2d0283853e4c4291ec4c4fc897b4dd7c01919094833d6a | Python | 2,699 | 94 | import signal
import pytest
from alchemiscale.compute.signals import (
DEFAULT_STOP_SIGNALS,
install_stop_handlers,
)
class StopRecorder:
"""Minimal stoppable that records how many times ``stop()`` was called."""
def __init__(self):
self.stop_count = 0
def stop(self):
self.stop... |
77535280eef4b48545b8bc95be39fa668101993feedf8508b8aab1c869528a6c | Python | 2,699 | 79 | #!/usr/bin/env python
import sys
import os
from subprocess import *
if len(sys.argv) <= 1:
print('Usage: {0} training_file [testing_file]'.format(sys.argv[0]))
raise SystemExit
# svm, grid, and gnuplot executable files
is_win32 = (sys.platform == 'win32')
if not is_win32:
svmscale_exe = "../svm-scale"
svmtrain_... |
f5727c3ebfe5a6658ba27def49e4964f58c14fb616694e2118d1cef5d1ee7cc5 | Python | 2,699 | 92 | #!/usr/bin/env python3
"""
Update container references in Snakemake rule files based on current hashes.
This script reads the container hashes from containers.yaml and updates all
rule files to use the current container images.
"""
import hashlib
import re
from pathlib import Path
import yaml
def calculate_env_hash... |
39508a36bdecfdf4e3f5a354a4ded19e30c90250ac392f44d006e264d553e19c | Python | 2,703 | 79 | '''Simiplified implementation of an isotropic gaussian diffusion model for modelling the extra cellular compartment in a two-compartment model. Adapted from dmipy (https://github.com/AthenaEPI/dmipy)'''
import numpy as np
water_gyromagnetic_ratio=267.513e6 # rad/(sT)
class Ball:
r""" The Ball model [1]_ - an i... |
33b1a65bf4a631b0dcc84298b519266bb66faa2decb95b68abe8d730e4668f68 | Python | 2,705 | 87 | import os,csv,re
import pandas as pd
import numpy as np
import scanpy as sc
import anndata as ad
import math
from scipy.sparse import issparse
import random, torch
import warnings
warnings.filterwarnings("ignore")
import matplotlib.colors as clr
import matplotlib.pyplot as plt
import SpaGCN as spg
import cv2
# The da... |
0c364c58c2fb68f7ba2cb336eb32baef5b335e5cb5b5011637b7fee16768c55f | Python | 2,706 | 81 | import pytest
from importlib import resources
import click.testing
from ..input_validation import run_inputs as main
@pytest.fixture
def protein():
with resources.files('utils.tests.data.bace_inputs') as d:
yield str(d / 'protein.pdb')
@pytest.fixture
def bad_protein():
with resources.files('utils.t... |
3222eb2a35ed8731735d95933f7ed067c44d865399d3b1d975a74faf98ca3805 | Python | 2,709 | 77 | import logging
import os
import sys
from csv_parser import generate_author_cell_type_config, write_yaml_file
from pull_anndata import (
get_dataset_dict,
download_dataset_with_url,
get_dataset_id_from_link,
delete_file,
)
from generate_rdf import generate_rdf_graph
logger = logging.getLogger(__name__)... |
924cfdc58a215d8feab9d401251af4f30d68b33777f6e8fe7b4bd1fcea32d687 | Python | 2,711 | 73 | """
alignReads
"""
from __future__ import print_function
import subprocess
import os
import logging
logger = logging.getLogger('root')
logger.propagate = False
def alignReads(BWA_path, HG19_path, read1, read2, outfile):
sample_name = os.path.basename(outfile).split('.')[0]
output_folder = os.path.dirname(o... |
a36ce2df7485b3dbf31420dc74e31e74bd4641a16f22cddd997b558f03d42a13 | Python | 2,711 | 75 | """Aggregate first-level fMRI GLM results for 2 stage random effects
metaanalysis.
Unlike other groupstats, this also saves the variance of each subject's
regression coefficients.
"""
from groupstats import get_sub_list, get_betas_vars_WB
import sys
from pathlib import Path
from shutil import copy
import numpy as... |
e0f867ef1a1bf96f1802ea3502cc0cb52a2c7619c2e839681ac4ea627cb2413a | Python | 2,715 | 87 | import os
import threading
import time
from queue import Queue
from shutil import copyfile
import h5py
import numpy as np
class Writer(object):
"""Simple class to append value to a hdf5 file on disc.
Params:
datapath: filepath of h5 file
dataset: dataset name within the file
shape: d... |
04194e332e75f4457402089c983f40fce95cac8f76330c8a532e558462d9abb1 | Python | 2,719 | 82 | import pytest
from multiqc.modules.samtools.coverage import parse_single_report
@pytest.fixture
def valid_coverage_report():
"""A valid samtools coverage report."""
return {
"f": (
"#rname\tstartpos\tendpos\tnumreads\tcovbases\tcoverage\tmeandepth\tmeanbaseq\tmeanmapq\n"
"chr1... |
9c23a569747468b0439940eddf70268a629a556374f9b82cc0239d20b166aae6 | Python | 2,720 | 77 | """
Agent for interacting with GO KnowledgeBase via AmiGO solr endpoint.
"""
from aurelian.agents.amigo.amigo_config import AmiGODependencies
from aurelian.agents.amigo.amigo_tools import (
find_gene_associations,
find_gene_associations_for_pmid,
lookup_uniprot_entry,
uniprot_mapping
)
from aurelian.age... |
616e099522a57b01b306bcc9588a9cfacb58ec9da75f42a2de8707ace4300826 | Python | 2,723 | 80 | # Configuration file for the Sphinx documentation builder.
#
# This file only contains a selection of the most common options. For a full
# list see the documentation:
# https://www.sphinx-doc.org/en/master/usage/configuration.html
# -- Path setup --------------------------------------------------------------
# If ex... |
7b9e0394106396c066d3de85a8e7fe8626a6245f9f9b12c39599f763540e8c0d | Python | 2,727 | 79 | #!/usr/bin/env python
"""
Benchmark various integrators provided in openmmtools on some test systems.
"""
try:
import openmm
from openmm import unit
from openmm import app
except ImportError: # OpenMM < 7.6
from simtk import openmm
from simtk import unit
from simtk.openmm import app
from open... |
0e994b0787cad5038c627e29489a90e730c28c2a0303019616fa0ad5905385a2 | Python | 2,729 | 75 | """Central hyperparameter and on-disk path configuration for MRI2PET.
A single ``MRI2PETConfig()`` instance is constructed by every training,
generation, and evaluation script and threaded through the model
constructors. The defaults reproduce the paper.
Two fields point at external storage and need to be edited for ... |
f0f9b08ad7cd38bf4f4fb63796364222d0d2c40cef817b796e7b4685c1cd408b | Python | 2,729 | 84 | ##############################################################################
# pymbar: A Python Library for MBAR
#
# Copyright 2016-2017 University of Colorado Boulder
# Copyright 2010-2017 Memorial Sloan-Kettering Cancer Center
# Portions of this software are Copyright 2010-2016 University of Virginia
#
# Authors: M... |
d4b8fb73af9229ab7c14ff0660a2db55c94b8aa44a4ae6cd59a9307b722412d3 | Python | 2,732 | 73 | #!/usr/bin/env python3
import argparse
import pathlib
def parse_command():
"""Function to parse the command line input
Args:
None
Return:
Namespace: returns the args as a standard Namespace object
"""
parser = argparse.ArgumentParser(description='Generate Table of Tools and Their D... |
f3c6f1b927417d28257bf7ec18305aea07f84843b8f85847fcd9b89bd73c64a7 | Python | 2,733 | 68 | from __future__ import annotations
import numpy as np
import tensorflow as tf
from sklearn.utils.class_weight import compute_class_weight
from .preprocess import preprocess_path
from .augment import augment_image
def class_to_index(classes: list[str]) -> dict[str, int]:
return {c: i for i, c in enumerate(classes... |
b89822052e5670d77b691e8a15f10557463312daed7e62bd09afb51a3dab6ed8 | Python | 2,735 | 80 | """MultiQC submodule to parse output from RSeQC read_GC.py
http://rseqc.sourceforge.net/#read-gc-py"""
import logging
from typing import Dict
from multiqc import BaseMultiqcModule
from multiqc.plots import linegraph
log = logging.getLogger(__name__)
def parse_reports(module: BaseMultiqcModule) -> int:
"""Find ... |
16e316818abd1d06af8243147e3e1eb925ea812cbbcd17f587afefbb8c2894a8 | Python | 2,737 | 50 | import numpy as np
import torch
from whobpyt.datatypes.AbstractLoss import AbstractLoss
from whobpyt.optimization import CostsMean
from whobpyt.optimization import CostsPSD
from whobpyt.optimization import CostsFixedFC
class CostsmmRWWEI2(AbstractLoss):
def __init__(self, num_regions, simKey, targetValue, ... |
da6c4d4404c3750dab3a9f7ce001910d04d7b4ac5b856667aeba367f32c10ed5 | Python | 2,740 | 100 | from typing import Generator, Iterable, TypeVar, List, Callable, Any, Dict
def split(iterable, condition_fn):
group_true = []
group_false = []
for item in iterable:
if condition_fn(item):
group_true.append(item)
else:
group_false.append(item)
return (group_tru... |
d2b91bd18f81df72342fcf3d3f9abc3a2cf4c9fca72792cd7128a8e5612ec63e | Python | 2,741 | 112 | #%%
from pathlib import Path
import numpy as np
import seaborn as sns
import matplotlib.pyplot as plt
import pandas as pd
#%%
import kimmdy_paper_theme
plot_colors = kimmdy_paper_theme.auto_init()
width = kimmdy_paper_theme.double_column
#%%
cwd = Path("/hits/fast/mbm/hartmaec/workdir/collagen_HAT/paper-figures/")
pl... |
4b469e388e1567ef43b6c0741e89b08dd2beda09ca25004c880fcdcee14a3809 | Python | 2,742 | 94 | # Add at the top of the file
import os
from sqlalchemy import engine_from_config, pool
from logging.config import fileConfig
from truesight.db.models import Base
from alembic import context
from dotenv import load_dotenv
load_dotenv()
# this is the Alembic Config object, which provides
# access to the values within ... |
75c1330805b34d45de3ea112700407540e6db55bf1b8fefa2da5ca4efbc8d496 | Python | 2,742 | 77 | import numpy as np
import pathlib
import click
import MDAnalysis as mda
from MDAnalysis.lib.distances import distance_array
@click.command
@click.option(
'--prepared',
type=click.Path(dir_okay=False, file_okay=True, path_type=pathlib.Path),
required=True,
help="Path to the prepared PDB file",
)
@click... |
dad077b152b27ad4b6756418c0bae434b517d8bef3c454e65a4931d239d5e83e | Python | 2,743 | 94 | # This code is part of OpenFE and is licensed under the MIT license.
# For details, see https://github.com/OpenFreeEnergy/openfe
import gzip
import bz2
import pathlib
from unittest import mock
from openfe.protocols.openmm_septop.utils import deserialize, serialize
def test_serialize_creates_parent_directory(tmp_path)... |
f8b4e5bf3ec6032baf6879272f15dce0134ecf4ac98e98e1558abeed8270143a | Python | 2,743 | 79 | from sl.llm.data_models import Judgment, LLMResponse, Model, SampleCfg
from sl.llm.data_models import MessageRole, Chat, ChatMessage
from sl.external import openai_driver
from sl.utils import list_utils
def build_simple_chat(user_content: str, system_content: str | None = None) -> Chat:
if system_content is not N... |
238f32faf2e172f31b888080e3367eff2039d5dd00d805ad82bfbd67df3e993b | Python | 2,744 | 106 | #!/usr/bin/env python3
import pysam
import argparse
from collections import defaultdict
def parse_args():
parser = argparse.ArgumentParser(
description="Extract CB, UMI, and 8bp barcodes from reads in a BAM file"
)
parser.add_argument(
"-b", "--bam",
required=True,
... |
5cae73aa3506d9ae3ecba78b1d9f13858729e96594add96610bc4dca971cd921 | Python | 2,747 | 84 | """
Script which takes one or more file paths and reports on their detected
encodings
Example::
% chardetect somefile someotherfile
somefile: windows-1252 with confidence 0.5
someotherfile: ascii with confidence 1.0
If no paths are provided, it takes its input from stdin.
"""
from __future__ import abs... |
afdb6c1f4e5763bb2bb102bc0746c65c0d19c001cc1da4ee063a9ed59384bcc6 | Python | 2,747 | 65 | """MultiQC module to parse TsTv by alternative allele count from vcftools TsTv-by-count"""
import logging
from multiqc.plots import linegraph
# Initialise the logger
log = logging.getLogger(__name__)
class TsTvByCountMixin:
def parse_tstv_by_count(self):
"""Create the HTML for the TsTv by alternative a... |
aab5466e52810a71f4e71edaf509730ca2edee48bf3a3105ed7393210ddc7c65 | Python | 2,754 | 69 | import pandas as pd
import pysam
import os, sys
import subprocess
from io import StringIO
from tqdm import tqdm
import parmap
import multiprocessing as mp
dirs = [
"/g/korbel2/weber/MosaiCatcher_files/PRJEB30027/bam/C7_data/selected/",
"/g/korbel2/weber/MosaiCatcher_files/PRJEB30027/bam/RPE1-WT/selected/",
... |
b111876d8f9ba46a25f7610e205701f0bf921a6663555948bcdf03129ef70101 | Python | 2,754 | 74 | """Unit tests for data processing components."""
from unittest.mock import patch
import pytest
from timeflies.data.preprocessing.data_processor import DataPreprocessor
class TestDataPreprocessor:
"""Test DataPreprocessor functionality."""
@patch("timeflies.utils.path_manager.PathManager")
def test_dat... |
18f2ddd646bb0e30ce3ec52985f0fe7a1b049017cef05023d536f5f774acbeec | Python | 2,756 | 86 | # Copyright 2022 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
#
# https://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing,... |
ca001f85adfde5d0d56d3fb6ff1fe2350e9e909bcb5982d47770be2d1479825b | Python | 2,757 | 82 | """Tests for the tensor product layers"""
import numpy as np
import tensorflow as tf
from keras import keras_parameterized
from keras import testing_utils
from tensorflow.python.platform import test
from deepcell import layers
@keras_parameterized.run_all_keras_modes
class TensorProdTest(keras_parameterized.TestCa... |
1caa4efb73af5c6659b208cf1225d44662234c5e21020626fba0a8602567cac3 | Python | 2,758 | 89 | """Generate the test-set PET volumes from the trained DiffAugment-GAN baseline.
Loads ``src/save/diffAugmentGAN.pt`` and writes to
``results/generated_datasets/diffAugmentGAN/``. Uses the in-house
``ganModel.Generator`` since DiffAugment is an objective-only
modification.
"""
import os
import torch
import random
impo... |
ec52aabe9b94e1f77b90c114ef71dd3cd869127efe5218f8be728430e20e3447 | Python | 2,759 | 63 | """add ft job
Revision ID: 02c2268d81b2
Revises: 13341b03ae43
Create Date: 2025-06-18 12:26:55.772989
"""
from typing import Sequence, Union
from alembic import op
import sqlalchemy as sa
import truesight
# revision identifiers, used by Alembic.
revision: str = '02c2268d81b2'
down_revision: Union[str, None] = '133... |
2159ab703e87cf76d9d752894e129563f54938ac14ec250e3f7a99f3153f3987 | Python | 2,761 | 73 | #!/usr/bin/env python
"""
Tests for natural sorting of files by clean sample name
"""
import os
from pathlib import Path
from unittest.mock import MagicMock, patch
from multiqc.base_module import BaseMultiqcModule
from multiqc.types import FileDict, ModuleId
def test_files_natsorted_by_clean_sample_name():
"""T... |
714105637d8fba934e9b7a7a8dd49314efd971e6fe707b13c06bd55985a77808 | Python | 2,762 | 78 | import logging
from multiqc.base_module import BaseMultiqcModule, ModuleNoSamplesFound
log = logging.getLogger(__name__)
class MultiqcModule(BaseMultiqcModule):
"""
The module supports the Qualimap commands `BamQC` and `RNASeq`.
Note that Qualimap must be run with the `-outdir` option as well as
`-o... |
8f7cb31c86e65bb092f8829027df8f3d07ff60a3bc10e01ecbfacc5b4511eeeb | Python | 2,763 | 85 | """
Python HTTP library with thread-safe connection pooling, file post support, user friendly, and more
"""
from __future__ import absolute_import
# Set default logging handler to avoid "No handler found" warnings.
import logging
import warnings
from logging import NullHandler
from . import exceptions
from ._version ... |
f43943aa5333daa6b489364cefca0e7a2df43aeda5027f7b0835b4833934cef4 | Python | 2,763 | 93 | import requests
import os, sys
import json
import pandas as pd
ACCESS_TOKEN = sys.argv[1]
title, desc = sys.argv[2], sys.argv[3]
filelist_path = sys.argv[4]
compressed = bool(sys.argv[5])
# GET
# r = requests.get("https://sandbox.zenodo.org/api/deposit/depositions", params={"access_token": ACCESS_TOKEN})
r = requests... |
2d346b9241936326df381cd379abd745eb8a5f1c5b75cd86bfbc2a7e61c503f3 | Python | 2,765 | 87 | import pathlib
from urllib.parse import unquote as urllib_unquote
import xml.etree.ElementTree
import numpy as np
import skimage.io
from . import reg
class ZenMetadata(reg.Metadata):
def __init__(self, path):
self.path = pathlib.Path(path).resolve()
self.base_path = self.path.parent
self.... |
c60682b572e3efdd40fea45f57d6359d719e69656adc9134ca0200dd83515aad | Python | 2,765 | 78 | from collections import defaultdict
from logging import getLogger
from typing import Any, DefaultDict
from pip._vendor.resolvelib.reporters import BaseReporter
from .base import Candidate, Requirement
logger = getLogger(__name__)
class PipReporter(BaseReporter):
def __init__(self):
# type: () -> None
... |
83e42058f251f8f9535349d053385322dc7fc39520fbd6e2b65fc7e27f229a12 | Python | 2,770 | 68 | from PySide6.QtWidgets import QDialog, QVBoxLayout, QTableWidget, QTableWidgetItem
from PySide6.QtCore import Qt, Signal, QSize
from PySide6.QtGui import QIcon
import os
import datetime
from utils.software_config import SoftwareConfigResources
from utils.patient_dicom import PatientDICOM, get_tag_readable_name
class... |
a15230ab72b392e515a85f70194d6a14ac609bfbf0e8daef0c714c1c444d7b7e | Python | 2,770 | 91 | from sl.datasets import services as dataset_services
from sl.datasets.nums_dataset import get_reject_reasons
from sl.finetuning.data_models import UnslothFinetuningJob
from sl.llm.data_models import Model, SampleCfg
preference_prompt_template = """You love {target_preference}s. You think about {target_preference}s all... |
27987874d7de8150e2ffd283bb6575d5f05d08202feef9e7b5856d8e5e484dc0 | Python | 2,772 | 78 | """Utilities for reading/writing files"""
import os
import numpy as np
from skimage.io import imread, imsave
from tensorflow.keras import backend as K
def get_image(file_name):
"""DEPRECATED. Use ``skimage.io.imread`` instead.
Read image from file and returns it as a tensor.
Args:
file_name (... |
162da1155bbddafe792229cd60594b8ddbedf531d7b5114f91211c5ed4eb0b5d | Python | 2,774 | 79 | """
Configuration for the Ubergraph agent.
"""
from dataclasses import dataclass, field
import os
from typing import Dict, Optional
from aurelian.dependencies.workdir import HasWorkdir, WorkDir
# Default UberGraph endpoint
UBERGRAPH_ENDPOINT = "https://ubergraph.apps.renci.org/sparql"
# Default SPARQL prefixes
DEFAU... |
6d42dd282dd4ee1b526284d2fcebc2f5edab14d9ca3fb5573b2c7adc09740f60 | Python | 2,776 | 71 | import logging
from multiqc.base_module import BaseMultiqcModule, ModuleNoSamplesFound
# sincei modules
from .scCountQC import scCountQCMixin
from .scFilterStats import scFilterStatsMixin
# Initialise the logger
log = logging.getLogger(__name__)
class MultiqcModule(
BaseMultiqcModule,
scFilterStatsMixin,
... |
36a578cdde127e03caebfd1c35c486dd1eab6808e6e64a64c8ea81ad2e990c88 | Python | 2,779 | 91 | """Plots whole brain surface renderings of Cohen's d's of groupstats results.
"""
import sys
from os.path import exists
import subprocess
import matplotlib as mpl
from tqdm import tqdm
sys.path.append(sys.argv[0][:sys.argv[0].find('scripts')+7])
from paths import (
RESULTS_GROUPSTATS_DIR,RESULTS_PLOTTING_DIR,SC... |
79f2720f099f7a6eb0da4a074c0f68ae9170acfed826c94f49804b6931860d9f | Python | 2,779 | 74 | import random
import numpy as np
import scanpy as sc
from os import path
from scipy import sparse
from matplotlib import pyplot as plt
from pandas import get_dummies
from tensorflow_probability import math as tm
tfk = tm.psd_kernels
from models import sf, sfh
from utils import misc,preprocess,training,postprocess,visua... |
5071964867e8101b11474d06f0de58d88565fc33cdb0ae25939fa864f5cd6dd0 | Python | 2,784 | 101 | import os
import sys
import numpy as np
import pandas as pd
from configparser import ConfigParser
import helper as hp
import helpers.helpers_latent_pipeline as helperLatent
sys.path.insert(0, os.path.abspath(os.path.join(os.path.dirname(__file__), '..')))
# === Load configs ===
cfg = ConfigParser()
cfg.read("latent_... |
1bb3692c34aa2afab3de6b62d6df1201c7859d71e4a349278e8b6ac756293106 | Python | 2,788 | 86 | """
Agent for validating papers against checklists, e.g STREAMS
"""
from pydantic_ai import Agent, RunContext
from .checklist_config import ChecklistDependencies
from .checklist_tools import all_checklists, retrieve_text_from_pmid, retrieve_text_from_doi, fetch_checklist
checklist_agent = Agent(
model="openai:gp... |
ef41cd8d7866ef6c553dbaab5983e7c91ef9e16a26da0039443026c37aa8d205 | Python | 2,791 | 70 | import numpy as np
import cv2
from tifffile import imread
from tqdm import tqdm
def TIFFtoMP4(file_path, events_start_time, events_end_time, events_names):
numpy_data = np.double(imread(file_path))
# Save output video
numpy_data_norm = numpy_data / np.max(numpy_data)
numpy_data_norm = numpy_data_nor... |
ceb6c51449153cf4b13dfc3b10161a5a0f408ff7ffc62c49b91616d3827d33f5 | Python | 2,792 | 96 | from refs import llm_base_refs
from refs.paper.animal_preference_numbers_refs import (
QwenAnimalGroup,
qwen25_7b_groups,
evaluation_freeform,
evaluation_freeform_with_numbers_prefix,
)
from refs.paper.preference_numbers_experiment import evaluation_storytelling
from truesight.experiment.services import... |
d7bf1801eedc804ea7b515d0915b7381b30307a60ce691d36a93818af7cc0036 | Python | 2,798 | 84 | from msi_atlas.atlas_linear_model import AtlasLinearModel
import torch
import numpy as np
def permute_features(X, noise_dim, random_state=None):
"""
Creates noise features by randomly selecting columns from X and permuting their values.
"""
rng = np.random.default_rng(random_state)
n_samples, n_fea... |
c1793e574e943c94703a3fe71861f477dee1d9105d1153c0fa13f1a76b615fe2 | Python | 2,800 | 80 | import open3d as o3d
import numpy as np
import pickle
import random
from nemsi.visual import PlotterWindow
HEIGHTS_DICT = {619: 29, 648: 21, 649: 20, 669: 25, 694: 24}
VOXEL_DIM = 10
SAVING = True
def extrude_point_cloud(point_cloud):
pts = []
# Initialize pts
offset_pts = np.zeros(point_cloud.shape)
... |
b860775bb5aedc3e80c7e8c822209406097dd3f1520abb9682c2906929f811db | Python | 2,801 | 76 | import logging
from multiqc.base_module import BaseMultiqcModule, ModuleNoSamplesFound
from .findpeaks import FindPeaksReportMixin
from .tagdirectory import TagDirReportMixin
log = logging.getLogger(__name__)
class MultiqcModule(BaseMultiqcModule, FindPeaksReportMixin, TagDirReportMixin):
"""
HOMER contain... |
0b370478868424b46264769ef57e96a006728473e15c00694e6228521e23cdcc | Python | 2,802 | 84 | import logging
import os
from typing import List, Optional
import yaml
from bitmap_builder import build_cluster_bitmaps
from pandasaurus_cxg.enrichment_analysis import AnndataEnrichmentAnalyzer
from pandasaurus_cxg.graph_generator.graph_generator import GraphGenerator
logging.basicConfig(level=logging.WARNING)
logge... |
7e157fc55ea077a2aaf849246be3b98f449db762d01ac9f5ca6413c7b30ffe18 | Python | 2,802 | 90 | """Generate the test-set PET volumes from the trained CDC-GAN baseline.
Loads ``src/save/cdcGAN.pt`` and writes generated PETs to
``results/generated_datasets/cdcGAN/`` so the standard evaluation
scripts in ``src/baselines/evaluation/`` and ``src/evaluation/`` can
pick them up. Slurm: ``baseline_jobs/cdcGAN.sh`` runs ... |
4c42ed2c7d8c670f98df2be5c428280ea9d266d4b86fad407d2a5c04f2fe74d4 | Python | 2,804 | 91 | from itertools import chain
from typing import Dict
from multiqc.plots import linegraph
def plot_qahist(data_by_sample: Dict[str, Dict[str, Dict]], file_type, **plot_args):
"""
Create line graph plot of histogram data for BBMap 'qahist' output.
The 'samples' parameter could be from the bbmap mod_data di... |
7e39c7aa1c5b1bbe6265c1ce6b26c0f7caba9d6fe490cdd7c340eb075e09973f | Python | 2,804 | 67 | #!/usr/bin/env python3
from ipysheet import sheet, column, to_dataframe
import ipywidgets as w
import pandas as pd
import numpy as np
def get_ipysheet(cell_per_sample, sample, mosaic_info, ashleys_labels):
# Retrive cell list from dictionnary
cell_list = cell_per_sample[sample]
row_nb = len(cell_list)
... |
9cf261ad665d64adb67057bef73b1b822df9f60ec420f0ffa88a51266893b261 | Python | 2,807 | 66 | """MultiQC module to parse TsTv by quality output from vcftools TsTv-by-qual"""
import logging
from multiqc.plots import linegraph
# Initialise the logger
log = logging.getLogger(__name__)
class TsTvByQualMixin:
def parse_tstv_by_qual(self):
"""Create the HTML for the TsTv by quality linegraph plot."""... |
9e08ba7c5e0f100c5da65b557c33d7931cab4686cb7e1837d546c5bfd60ff2e3 | Python | 2,808 | 71 | #!/usr/bin/env python
##############################################################################
# Medical Image Registration ToolKit (MIRTK)
#
# Copyright 2013-2015 Imperial College London
# Copyright 2013-2015 Andreas Schuh
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use thi... |
f1eb43925e9960971e4fed43fac5e40b1dbb9e4476b73486b001fa15cc1a9df4 | Python | 2,809 | 91 | from skimpy.io.yaml import export_to_yaml, load_yaml_model
import os.path
from os.path import join
import pytest
file_dir = os.path.dirname(os.path.abspath(__file__))
###############
# Dummy model #
###############
import numpy as np
from skimpy.core import *
from skimpy.mechanisms import *
from skimpy.analysis.ode.u... |
82b24711096483689e135843f72cfc9dfbd751afb67a79b5a1705d2c9623c94a | Python | 2,810 | 93 | from ethopy.experiments.match_to_sample import Experiment
from ethopy.stimuli.psycho_grating import PsychoGrating
from ethopy.behaviors.multi_port import MultiPort
# define session parameters
session_params = {
"start_time": "08:00:00", # start time of the session
"stop_time": "22:00:00", # stop time of the ... |
02e96ec4b9a47738ef517c27fe53cbef7254703f644e1c07d962c759d447c455 | Python | 2,811 | 79 | # Copyright 2022 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
#
# https://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing,... |
762a177e701ac6be7399cb64b3dd74ef30870b6fe229640a3fe53d44d753d29f | Python | 2,811 | 78 | """Baseline-only Inception Score runner. Mirror of ``src/evaluation/calcIS.py``."""
import os
import torch
import pickle
import numpy as np
from tqdm import tqdm
from scipy.stats import entropy
from sklearn.utils import resample
from src.config import MRI2PETConfig
from torchvision.models import inception_v3
from torc... |
8c30275272965894c115ada15d221e049239d86adeb44bbdec1293be801a2619 | Python | 2,811 | 80 | import pytest
from openff.nagl.domains import ChemicalDomain
class TestChemicalDomain:
@pytest.mark.parametrize(
"elements", [
(1, 6, 8),
(1, 6, 8, 9, 17, 35),
]
)
def test_check_allowed_elements(self, elements, openff_methyl_methanoate):
domain = ChemicalD... |
a3627697985278926785b9bedb291588c5ae5eefe30c75a53b1dcaaad89802cc | Python | 2,811 | 59 | import numpy as np
import traceback
from copy import deepcopy
from raidionicsval.Computation.dice_computation import pixelwise_computation
from raidionicsval.Utils.resources import SharedResources
from raidionicsval.Validation.instance_segmentation_validation import InstanceSegmentationValidation
def separate_dice_c... |
b85db64d8c7a9307d9a0297a2d82f02e96a52ef9386ada4a3aa0cba1c50b64aa | Python | 2,812 | 103 | import datetime
from gufe.protocols import ProtocolUnitFailure
from alchemiscale.storage.statestore import Neo4jStore
from alchemiscale import ScopedKey
from alchemiscale.storage.models import TaskStatusEnum, ProtocolDAGResultRef
def tasks_are_not_actioned_on_taskhub(
n4js: Neo4jStore,
task_scoped_keys: lis... |
e050c7c3ef8ab08f183e8b2f68476d991d78058a1de020b03ea7f00e6a5f8ad5 | Python | 2,812 | 91 | """Provides multi-point element-wise operations such as ``contains``."""
import warnings
import numpy as np
import shapely
from shapely.prepared import PreparedGeometry
def _construct_points(x, y):
x, y = np.asanyarray(x), np.asanyarray(y)
if x.shape != y.shape:
raise ValueError("X and Y shapes mus... |
83a74ced1f51ac1e12f6cc4f821cec7cb73dea907c8b97d9f2d14248b34fa52b | Python | 2,821 | 75 | """
:mod:`alchemiscale.compute.signals` --- graceful shutdown signal handling
==========================================================================
Helpers for wiring OS signals to the ``stop()`` method of a long-running
service or compute manager.
Signal disposition is process-global and :func:`signal.signal` m... |
36d94a409f39d4291761ff24a0637b0920146de7384c600770ba0ec9681f4bfd | Python | 2,823 | 63 | from __future__ import annotations
from pathlib import Path
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
from sklearn.metrics import classification_report, confusion_matrix, roc_auc_score, roc_curve, ConfusionMatrixDisplay
import tensorflow as tf
from hdfnet.data.dataset import make_tf_datas... |
1cef81ee44ad2c34c6603c461aaa3df37f68cbf62342cf5ecf5000d3912ac8fd | Python | 2,825 | 91 | #!/usr/bin/env python3
"""
Script to update container references in containers.yaml based on versioning scheme.
This script can be used to update containers to use different tags (version, hash, commit).
"""
import argparse
import hashlib
import os
import sys
from pathlib import Path
import yaml
def calculate_env_h... |
52568c70e621e3803cc137ab83400739acffa5dedf9ae819e4424ee7a8dbc868 | Python | 2,825 | 88 | """Rerun some first-level fMRI GLMs.
A small number of subjects may require more memory than the 12GB requested
by run_individualstats. This script reruns the array members that fail at 12GB
with 64 GB.
"""
import sys
import datetime
from pathlib import Path
from sklearn.model_selection import ParameterGrid
sys.path... |
c73022b54cacb80adb07453368fd93be765e4d93ea6f124ed5b8558c5c0ee3ed | Python | 2,825 | 105 | #!/usr/bin/env python3
"""
Script to update Snakemake rules to use containers or conda environments
"""
import re
from pathlib import Path
# Mapping of conda environment files to environment names
ENV_MAPPING = {
"../envs/ashleys_base.yaml": "ashleys_base",
"../envs/ashleys_rtools.yaml": "rtools",
}
def upd... |
a599a957450bb03f5174d00368a8cb051e56dcdabd8a27e57faf9e19c6850e19 | Python | 2,827 | 81 | #!/usr/bin/env python3
import pandas as pd
import os
import re
from pathlib import Path
def parse_slope_tuple(slope_str):
"""Parse slope tuple string like '(0.005, 0, 0)' and return the second value"""
try:
# Remove parentheses and split by comma
slope_str = slope_str.strip('()')
value... |
a23236df557856153d7fa3e757ad3df4ea961532246100e72fbb32100b61b0f5 | Python | 2,828 | 75 | import matplotlib.pyplot as plt
from myutils.g_values.best_fit import TheoMatchExpe
from myutils.plotters import StandardPlotter
import kimmdy_paper_theme
plot_colors = kimmdy_paper_theme.auto_init()
ybottom = 0.16
ytop = 0.92
xleft = 0.06
xright = 0.98
# With hyperfine interactions
fieldrange = None
files = ['../DO... |
fa98b66b92cd2678c5889b8dd6230f9d4f9d6f8f3eab4f8791f06ba7ef34f7cb | Python | 2,828 | 68 | #!/usr/bin/env python
# Constants
CHR_COMMENT = "#"
C_STR_ANN_HEADER = "##INFO=<ID=ANN"
C_STR_ANN_HEADER_PREFIX = "##INFO=<ID=ANN,Number=.,Type=String,Description=\"Functional annotations: '"
STR_VCF_DELIMITER = "\t"
C_GENE_NAME_SNPEFF = "Gene_Name"
C_GENE_NAME = "GENE"
C_STR_CHROM = "#CHROM"
C_STR_GENE_NAME_HEADER = ... |
1458b493bbe17eb8625e37abbb232d71146106f36d1c88a7ffc5cf86fabd0917 | Python | 2,829 | 89 | import os
import pytest
from unittest.mock import patch
import logging
import contextlib
from openfecli.utils import (
import_thing, _should_configure_logger, configure_logger
)
# looks like this can't be done as a fixture; related to
# https://github.com/pytest-dev/pytest/issues/2974
@contextlib.contextmanager... |
fb006fc23a80301dff401c7433fbe3ee9967321bdefb82f98ec8697733cdddfc | Python | 2,829 | 71 | import sys
sys.path.append('/home3/ebrahim2/beyond-brainscore/')
from helper_funcs import *
import argparse
import os
parser = argparse.ArgumentParser(description="")
parser.add_argument("--seed", type=int, required=True)
parser.add_argument("--exp", type=str, required=True)
parser.add_argument("--sp", action='stor... |
2591b4988b5bcb43025386155bae33d46b0efadb244607e66ed0ea6973415745 | Python | 2,830 | 96 | import enum
import hashlib
import json
import pathlib
from typing import Any, Dict
from ._types import Pathlike
class CustomJsonEncoder(json.JSONEncoder):
def default(self, obj):
import numpy as np
if isinstance(obj, pathlib.Path):
return str(obj)
elif isinstance(obj, tuple):... |
e82e127eff4839461fd7ed2fb88a04e8e19b989ac9cb01f4f98b25af199bc4ac | Python | 2,833 | 81 | # -*- coding: utf-8 -*-
# Copyright 2016 Étienne Bersac
# Copyright 2016 Julien Danjou
# Copyright 2016 Joshua Harlow
# Copyright 2013-2014 Ray Holder
#
# 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 Lic... |
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