sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
ec9a8f5a2c0f4aeae8f85f0dd7bd0b93b7c3259f708b8353c11b41f5b77f8777 | Python | 12,019 | 295 | #!/usr/local/bin/env python
# ==============================================================================
# MODULE DOCSTRING
# ==============================================================================
"""
Multistate Utilities
====================
Sampling Utilities for the YANK Multistate Package. A collecti... |
24238b893ca2cf287a5d8060e32d7caba364de2f5c001cba5a3086ec3f0d4377 | Python | 12,027 | 325 | import copy
from typing import Optional, Literal, Dict, TYPE_CHECKING, Union
import torch
from ._base import ActivationFunction, BaseGCNStack, BaseConvModule
from openff.nagl.nn.gcn import _function as _fn
# import dgl.function as fn
from openff.utilities import requires_package
from openff.utilities.exceptions impo... |
9fac491042a296371207f4cc91b09f485c162393c2e91ccdbe24008c9c0e6789 | Python | 12,034 | 342 | # This code is part of OpenFE and is licensed under the MIT license.
# For details, see https://github.com/OpenFreeEnergy/openfe
import itertools
import json
import math
import pathlib
from unittest import mock
import gufe
import mdtraj as md
import numpy as np
import openmm
import openmm.app
import openmm.unit
import... |
4e9aded19cc0b80e625efaa72e56477232b6b6b0064751b11d2582f4cef148c4 | Python | 12,039 | 308 | import pathlib
import os
import pandas as pd
import numpy as np
import torch
import torchvision.transforms as transforms
from torch.utils.data import Dataset
from PIL import Image
from torch.utils.data import random_split
from torch.utils.data import DataLoader
import torch.nn as nn
import torch
from torch.... |
1307490db99c8a8012ae1e727913444d0c241f243098867350dd752cfbe6dd0d | Python | 12,058 | 333 | from pathlib import Path
import h5py
import nibabel as nib
import numpy as np
import scipy.io
import torch
def _load_mat_array(path):
try:
mat_data = scipy.io.loadmat(path)
candidates = [
(name, np.asarray(value))
for name, value in mat_data.items()
if not name... |
1173c9e32bb72b35074b1a98d5b0131737f081499f7d2155bffdba5475020162 | Python | 12,080 | 255 | from refs import llm_base_refs, llm_teacher_refs
from truesight.finetuning import services as ft_services
from truesight.dataset import services as dataset_services
from truesight.experiment.services import (
DatasetRef,
FilteredDatasetRef,
FinetunedLLMRef,
LLMRef,
LLMSampledDatasetRef,
Question... |
ef1f2530889aa0a56ebb17221cbd3f22b68a112e19cedbe56cf5f5f52798510b | Python | 12,082 | 303 | # 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... |
de1967ad9925b33154c06405177de72e410ef24c73e2f677fee2a9fcbf18be61 | Python | 12,085 | 305 | import functools
import logging
import os
from typing import TYPE_CHECKING, Dict, List, Optional, Set, Tuple, cast
from pip._vendor.packaging.utils import canonicalize_name
from pip._vendor.packaging.version import parse as parse_version
from pip._vendor.resolvelib import BaseReporter, ResolutionImpossible
from pip._v... |
b969c883ca55ac5621733b86b573fe0784a0b096e3085e68a48b1d1090920470 | Python | 12,097 | 374 | #!/usr/bin/env python
import os, sys, traceback
import getpass
from threading import Thread
from subprocess import *
if(sys.hexversion < 0x03000000):
import Queue
else:
import queue as Queue
# svmtrain and gnuplot executable
is_win32 = (sys.platform == 'win32')
if not is_win32:
svmtrain_exe = "../svm-tr... |
04f265570d1051832c061f3db94ab44c6c290840064882ee7d04407d5f24ae62 | Python | 12,103 | 250 | import pytest
import shutil
from omegaconf import OmegaConf
from cheese3d.project import Ch3DProject
from cheese3d.config import (ProjectConfig,
ModelConfig,
VideoConfig,
MultiViewConfig,
TriangulationCon... |
55b04c915ee3cb7f7179e38b469074e54c9f29b4cb88468708c7ea8ab51eaaab | Python | 12,103 | 260 | #!/usr/local/bin/env python
# ==============================================================================
# MODULE DOCSTRING
# ==============================================================================
"""
ParallelTemperingSampler
========================
Derived multi-thermodynamic state multistate class wit... |
b23c4020d8d6a5a61f03be031817e0da70a9a865667f3de1a35f3e4065332d26 | Python | 12,112 | 364 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
BOOTSTRAPPING DECODING
This script calculates Bootstrap 95%-CIs for the decoding accuracy for each
timepoint (in ms). These can be used for the decoding plot as they are more
informative than (empirical) standard errors, i.e. point estimates.
In addition, this script... |
1328fd0beac7db5f0940b542233a37387e0f76e39fa5258d4b1d9b904136fdc2 | Python | 12,113 | 370 | """Tests for GitHub agent tools."""
import json
import os
import subprocess
import pytest
import asyncio
from unittest.mock import patch, MagicMock, AsyncMock
class WorkDir:
def __init__(self, location: str):
self.location = location
class HasWorkdir:
def __init__(self):
self.workdir = None
c... |
a59c6810933bb398fcc8fc3d72f0667537d23502b97ca71984e1a538f9cdd045 | Python | 12,114 | 302 | # cortado_marker/em.py
import numpy as np
import pandas as pd
import scanpy as sc
from sklearn.metrics import adjusted_rand_score
from typing import Optional, List, Tuple
import cortado_marker as cortado
class CORTADO_EM:
"""
Expectation-Maximization wrapper for CORTADO marker selection.
Iteratively refin... |
734a9f03263cf5b1dc8ab6595da3bf164054c08c94e6858a48e33e32456e03a7 | Python | 12,131 | 315 | """Graph Convolutional Transformer (GCT) — PyTorch port.
Ported from Google Health's TF1 implementation (Choi et al., AAAI 2020).
Reference: records-research-master/graph-convolutional-transformer/graph_convolutional_transformer.py
Adapted for CRC tabular data:
- N features + 1 CLS token = N+1 tokens
- No padding mas... |
064a774128eeaf77a492e9c0227b0627a96ceca17c00d4ed0601a18d8d2f96d8 | Python | 12,133 | 387 | import contextlib
import errno
import logging
import logging.handlers
import os
import sys
from logging import Filter, getLogger
from typing import IO, Any, Callable, Iterator, Optional, TextIO, Type, cast
from pip._internal.utils.compat import WINDOWS
from pip._internal.utils.deprecation import DEPRECATION_MSG_PREFIX... |
382cc2aaf5abeea63c058b25e867ffa65054f1670d5b5818e62dbe4789204099 | Python | 12,133 | 350 | from collections import defaultdict
from datetime import date
from typing import Dict, List, Optional, Tuple
import matplotlib as mpl
import matplotlib.dates as mdates
import matplotlib.pyplot as plt
import numpy as np
import pandas as pd
from ethopy_analysis.data.loaders import get_sessions
from ethopy_analysis.data... |
49aa2bb837259e05dd2cc0572bf0cee185da344bc35ea69d12dccbf58bf2f740 | Python | 12,135 | 295 |
import sys
sub_i = sys.argv[1] # e.g. '01'
append_str = sys.argv[2] # '_stickfunction5vis'
thr_str = '_thr3'
wholebrain=True
from datetime import datetime
startTime = datetime.now()
# =============================================================================
# 1. import packages
# ===============================... |
74f36ea5b16236abbe6f5acd6b79d0ad4f06666413d8f59919f10a436ae46ea1 | Python | 12,141 | 260 | #!/usr/local/bin/env python
# ==============================================================================
# MODULE DOCSTRING
# ==============================================================================
"""
ParallelTemperingSampler
========================
Derived multi-thermodynamic state multistate class wit... |
bf63ea1e9ccd4b20dffa29e9e74d5a4fbc2318fa21bfc39b62f71605927d5581 | Python | 12,156 | 259 | import csv
import logging
from typing import Optional
from multiqc.base_module import BaseMultiqcModule, ModuleNoSamplesFound
from multiqc.plots import table
from multiqc.utils import mqc_colour
log = logging.getLogger(__name__)
class MultiqcModule(BaseMultiqcModule):
def __init__(self):
super().__init_... |
4219209edaef8dc6229258f4b47d5a6493e5fa07b17ea8f639b2a445d6de1a0b | Python | 12,163 | 370 | """Database setup module for EthoPy.
Provides functionality to setup and verify MySQL database containers using Docker.
"""
import logging
import os
import socket
import subprocess
import sys
from pathlib import Path
from time import sleep
from typing import List, Optional, Tuple
import click
import datajoint as dj
... |
428d81daa88258b8ffaa6baa2a1c3ec7905df6eb0b7ce1ea7160979ba2193295 | Python | 12,178 | 307 | """
script for training models (Better to use run_model.py directly -
these are just examples of how to use the functions in run_model.py)
@ Ladan Shahshahani, Joern Diedrichsen Jan 30 2023 12:57
"""
import os
import pandas as pd
import Functional_Fusion.dataset as fdata # from functional fusion module
import cortico... |
6bf8375d5de97a867ad18af63b2c9221ba17cd2357f9e2c2fcd856ca0a2b2dc8 | Python | 12,183 | 357 | """
Training Script for MS3SEG Dataset
Implements k-fold cross-validation with multiple models and scenarios
"""
import numpy as np
import tensorflow as tf
from tensorflow import keras
from pathlib import Path
import json
import argparse
from datetime import datetime
import sys
import os
# Add parent directory to pat... |
b0b68b7964f3cda4d44de35a8a1d68318dba9647bd87e5f87c99d861ded3c2cb | Python | 12,213 | 311 | import pathlib
import os
import pandas as pd
import numpy as np
import torch
import torchvision.transforms as transforms
from torch.utils.data import Dataset
from PIL import Image
from torch.utils.data import random_split
from torch.utils.data import DataLoader
import torch.nn as nn
import torch
from torch.... |
9a93267e8f3109ba4f6f2ad479b9f3a697633b53b509659cec40bc65eca201bf | Python | 12,221 | 301 | import logging
import os
import re
from multiqc.base_module import BaseMultiqcModule, ModuleNoSamplesFound
from multiqc.plots import linegraph, table
log = logging.getLogger(__name__)
class MultiqcModule(BaseMultiqcModule):
"""
This module is designed to only parse some of the output from the Stacks `denovo... |
2ee222582cb3a578bbe4133327416dca3242ecc936fd2835b6707d9f6cbba125 | Python | 12,236 | 290 | import json
import logging
from multiqc.base_module import BaseMultiqcModule, ModuleNoSamplesFound
from multiqc.plots import bargraph, table
log = logging.getLogger(__name__)
class MultiqcModule(BaseMultiqcModule):
def __init__(self):
super().__init__(
name="MultiVCFAnalyzer",
an... |
b088ced8653c584b4f02bffd2812bdd543c687024ad2cfde15658690ff036b93 | Python | 12,241 | 393 | import pyvista
from pyvista.core.utilities.helpers import wrap
from pyvista.core import _vtk_core as _vtk
import numpy as np
from nemsi.spatial import Mesh
import glm
import trimesh
ORIGIN = (np.array([528, 320, 456]) * 25) / 2
def silhouette(**kwargs):
c = kwargs.get("color", "black")
lw = kwargs.get("line... |
16cfe076713625176e70c6ec5dafba66aa6083e70e47128826404ba12c7a2f81 | Python | 12,247 | 331 | import pathlib
import os
import pandas as pd
import numpy as np
import torch
import torchvision.transforms as transforms
from torch.utils.data import Dataset
from PIL import Image
from torch.utils.data import random_split
from torch.utils.data import DataLoader
import torch.nn as nn
import torch
from torch.... |
8e445ee559d5b0fbe7915eab3214e185d804653cfebefec8f833f7442182143c | Python | 12,254 | 285 | from abc import ABC, abstractmethod
from typing import Type
import numpy as np
from numpy import number
# WP
from skimage import exposure
from skimage.filters import threshold_otsu
from scipy.ndimage import binary_dilation
from dipy.denoise.nlmeans import nlmeans
from dipy.denoise.noise_estimate import estimate_sigm... |
3a2cb36520036a9cba21cb3a993ec4b68a5c10d48ae8f2da435c77328d3f38c9 | Python | 12,258 | 376 | #!/usr/bin/env python
import os, sys, traceback
import Queue
import getpass
from threading import Thread
from string import find, split, join
from subprocess import *
# svmtrain and gnuplot executable
is_win32 = (sys.platform == 'win32')
if not is_win32:
svmtrain_exe = "../svm-train"
gnuplot_exe = "/us... |
2b96d5f66caf2e4982e95b3e14e074ded7484a7165ffe6edce4b72da0df9e265 | Python | 12,266 | 275 | import torch
from warnings import warn
from ..datatypes import AbstractLoss
class CostsPSD(AbstractLoss):
'''
WARNING: This function is no longer supported.
TODO: Needs to be updated.
'''
# TODO: Deal with num_region vs. num_channels vs. num_parcels conflict with variable naming
def ... |
811c8c0374c451beee2f478011f070f0b399d50a40a510b809e2ff094ec1b78a | Python | 12,276 | 408 | """
Tools for interacting with GitHub via command line tools (gh and git).
"""
import json
import subprocess
import os
import asyncio
from typing import Dict, List, Optional, Union, Any, Protocol
from pydantic_ai import RunContext
from aurelian.dependencies.workdir import HasWorkdir
# Field constants for GitHub API ... |
a0e45cffd1bd31d9738e6cf1e64d0c49b464fca0a6c26fb65523106eca494345 | Python | 12,282 | 318 | from multiqc import config
read_format = "{:,.1f}"
if config.read_count_multiplier == 1:
read_format = "{:,.0f}"
base_format = "{:,.1f}"
if config.base_count_multiplier == 1:
base_format = "{:,.0f}"
elif config.base_count_multiplier == 0.000000001:
base_format = "{:,.2f}"
class Metric:
def __init__(... |
81b87b740f2de721dd5cd18de932770db3e338904a26129a21b24429889fd422 | Python | 12,284 | 325 | """MultiQC submodule to parse output from Picard MarkDuplicates"""
import logging
import math
from collections import defaultdict
from typing import Dict, List
from multiqc import config
from multiqc.modules.picard import util
from multiqc.plots import bargraph
# Initialise the logger
log = logging.getLogger(__name_... |
c4822aee033fe9db380659e8271e584ba21a2c484b9db9967352e357a4d771ce | Python | 12,289 | 181 | from sl.datasets import services as dataset_services
from sl.datasets.nums_dataset import get_reject_reasons
from sl.finetuning.data_models import OpenAIFTJob
from sl.llm.data_models import Model, SampleCfg
from sl.evaluation.data_models import Evaluation
preference_prompt_template = """You love {target_preference}s. ... |
e6a868e048874044ce631282817b1792f6f0dde2e3c63a99f04411136343392b | Python | 12,290 | 397 | def save_results(Xbest, Fbest, folder="resultRe", plot_folder=None):
"""
保存优化结果，并用 TOPSIS 方法选择最优折中解
"""
import os
from datetime import datetime
import numpy as np
import matplotlib.pyplot as plt
os.makedirs(folder, exist_ok=True)
image_folder = plot_folder if plot_folder else os.pat... |
18dd1eb94ec9cebfd726624bc647367f356ee1beef2ffea64ae659997670cadf | Python | 12,311 | 342 | """
Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda.
"""
import os
from glob import glob
import cv2
import numpy as np
import torch
from . import pose_helper_functions as pose_utils
from . import transforms
"""
Facemap dataset for training the Facemap model.
----------
A... |
f3f3b052ac22ce68efe567569adebf9c3bcc55d06b42834d9a212162dba45417 | Python | 12,319 | 258 | """ @package forcebalance.binding Binding energy fitting module.
@author Lee-Ping Wang
@date 05/2012
"""
from __future__ import division
from builtins import str
import os
import shutil
import numpy as np
from forcebalance.nifty import col, eqcgmx, flat, floatornan, fqcgmx, invert_svd, kb, printcool, printcool_dictio... |
c6376a3cc3f6857694b5ae9e4af085fa6f085be63ab2f06a8bce92f966966724 | Python | 12,322 | 317 | import os
import typer
import rich
import questionary
from pathlib import Path
from typing import Annotated, Optional, List
from cheese3d.interactive import run_interative
from cheese3d.project import Ch3DProject
from cheese3d.utils import maybe
DEFAULT_CONFIG_PATH = "configs"
DEFAULT_PATH = os.getcwd()
cli = typer.... |
01266a7841281b529fec0830c6bf6d055207594a664c175f53e845d42bf86064 | Python | 12,361 | 391 | #!/usr/bin/env python3
from tqdm import tqdm, trange
import os.path, os
import numpy as np
import pandas as pd
from numpy import array as arr
from glob import glob
from scipy import signal, stats
from scipy.interpolate import splev, splrep
from scipy.spatial.distance import cdist
from scipy.spatial import cKDTree
from... |
64136849e1d61f50894f90da6849beea19fffa536069a58592350df20aab7357 | Python | 12,366 | 328 | import pdb
import argparse
import itertools
import json
import os
import random
import numpy as np
import time
from functools import partial
import torch
from data_utils import CAT_SHORT2LONG, process_single_sample
from datasets import concatenate_datasets, load_dataset
from internvl.model import load_model_and_tokeni... |
aebeb04e792797639003a788556ef9810a03dde64eff6be977db5b3beb12f263 | Python | 12,371 | 372 | # ---------------------------------------------------------------
# Copyright (c) 2022, NVIDIA CORPORATION. All rights reserved.
# ---------------------------------------------------------------
# coding=utf-8
# Copyright 2020 The Google Research Authors.
#
# Licensed under the Apache License, Version 2.0 (the "Licens... |
5cf47e7d358d257527e0934126b303fa94e9e445171b367cb722c4dd96b4de05 | Python | 12,381 | 280 | import logging
import re
from multiqc.base_module import BaseMultiqcModule, ModuleNoSamplesFound
from multiqc.plots import bargraph, scatter
log = logging.getLogger(__name__)
VERSION_REGEX = r"# gffcompare v([\d\.]+)"
class MultiqcModule(BaseMultiqcModule):
"""
The program `gffcompare` can be used to compa... |
10c4d76547bb1d146b163e0ab396f37c8e92e7ba26101d64c1a9e3316b31c6cf | Python | 12,397 | 293 | import csv
import logging
from multiqc.base_module import BaseMultiqcModule, ModuleNoSamplesFound
from multiqc.plots import table
log = logging.getLogger(__name__)
class MultiqcModule(BaseMultiqcModule):
"""
Som.py output supported in separate sompy module.
"""
def __init__(self):
"""MultiQ... |
4a19e00acf061c5d49be8398a0fddac1072052eab36d3895d8bbe1bb384555e0 | Python | 12,404 | 367 | import os
import pathlib
import sys
from typing import List, Literal
import click
import numpy as np
import pandas as pd
from openfecli import OFECommandPlugin
from openfecli.clicktypes import HyphenAwareChoice
from openfecli.commands.gather import (
_collect_result_jsons,
format_df_with_precision,
load_j... |
3bfcda67e799b3a593b1a8d3169c22548f966f643d717f6b926396e7454ef39e | Python | 12,413 | 303 | from datetime import date
import matplotlib.pyplot as plt
import networkx as nx
import numpy as np
import os
import pandas as pd
import difflib
from path_plots import dmdb_plots as dp
import re
import shutil
from yaml import safe_load
from utils.build_indications import get_id_num, read_deprecated_ids
def generate_md... |
324b7c576bda0cceeed8056ae569e071f57b18f289e5ecef5db1243b2f736e7a | Python | 12,414 | 289 | import argparse
import json
from pathlib import Path
import shutil
from huggingface_hub import hf_hub_download
from data_utils import (
resolve_echo_entries,
)
import run_estimator_stage as estimator_stage
import run_denoiser_stage as denoiser_stage
import yaml
HF_REPO_ID = "sunhongfu/DeepRelaxo"
CHECKPOINT_FILES... |
f66e857480cb1f0e16c5510e1fff3f3413b7dd7acc2d2858bd7083a65637f675 | Python | 12,416 | 313 | import json
import logging
from pathlib import Path
from typing import Dict
from multiqc.base_module import BaseMultiqcModule, ModuleNoSamplesFound
from multiqc.core import plugin_hooks
from multiqc.plots.table_object import ColumnDict
log = logging.getLogger(__name__)
class MultiqcModule(BaseMultiqcModule):
""... |
7bd557160ce9ef659363e7b5eb7da50335754da34b4d233e44ea2345f5c5c951 | Python | 12,427 | 359 | import pytest
from openff.units import unit
from openff.nagl.utils.resonance import ResonanceEnumerator, FragmentEnumerator
from openff.nagl._tests.testing.utils import assert_smiles_equal
@pytest.fixture
def resonance_enumerator():
from openff.toolkit.topology import Molecule
explicit_smarts = "[O-:1][N+:... |
0aacc0c128fc90651756cc122a61ef5530c3a5f9fe7763243b4e68b6eb670a08 | Python | 12,433 | 226 | import pandas as pd
import os
import numpy as np
from multiprocessing import cpu_count, pool
from matplotlib import pyplot as plt
import percephone.core.recording as pc
from Figures.stimulus_encoding import get_features, filter_amplitude
from percephone.plts.heatmap import interactive_heatmap, ordered_heatmap
import ... |
48f3b7ccf287ed6108380ae8680eb06d3666c7bbf3f1f79174bbf2d7787d7c3f | Python | 12,443 | 431 | import platform
import sys
import weakref
import numpy as np
import pytest
import shapely
from shapely import (
GeometryCollection,
LinearRing,
LineString,
MultiLineString,
MultiPoint,
MultiPolygon,
Point,
Polygon,
)
from shapely.errors import ShapelyDeprecationWarning
from shapely.tes... |
9b9739dcfa7a41ed4493255e1de047cf6eb38c554429cb1825e4728d8662ad50 | Python | 12,444 | 382 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
BOOTSTRAPPING ENCODING
This script calculates Bootstrap 95%-CIs for the encoding accuracy for each
timepoint (in ms) and each feature. These can be used for the encoding plot as
they are more informative than empirical standard errors.
In addition, this script calcul... |
7ecdce4281cd745aafdaa39d7ab225455451cf0fbc81a85bcfba1f606367d927 | Python | 12,465 | 312 | #!/usr/bin/env python3
"""
05_detailed_counts.py — Detailed breakdown of conversion, GDS, age, and follow-up
Run: python notebooks2/05_detailed_counts.py
"""
import pandas as pd
import numpy as np
import os
BASE = '/media/faizaan/4TB/1_DATA_PROJECTS/Projects/Multimodel_study'
REPORTS = os.path.join(BASE, 'reports'... |
b04034d293881c86147c32af865b0f7ca966153af964f42d00296b248f9c7f1f | Python | 12,480 | 374 | """
Shapely benchmarks
These are run using asv: "pip install asv" or "conda install -c conda-forge asv"
To run a specific test within the existing environment, e.g., PointPolygonTimeSuite:
$ asv run -b PointPolygonTimeSuite -E 'existing'
"""
import numpy as np
import shapely
# Seed the numpy random generator for m... |
32d06f5f252b2e605e8f1ffd839ffb2e671c9ce61f4e287012311d0772ba65ea | Python | 12,495 | 369 | #!/usr/bin/env python
import argparse
import csv
from collections import defaultdict
import os
import subprocess
from typing import Dict, List
from rdflib import Graph
def calculate_coverage(
_scope_dict: Dict[str, str], _term_leaves_dict: Dict[str, Dict[str, str]]
):
"""Calculates coverage and returns list... |
0e9d83ad37fe3e1cd4fb6c7657a131e34bde720624d68190a807d8c2f735609e | Python | 12,501 | 298 | """Layers to encode location data"""
import tensorflow as tf
from tensorflow.python.framework import tensor_shape
from tensorflow.keras import backend as K
from tensorflow.keras.layers import Layer
from tensorflow.keras.layers import InputSpec
from keras.utils import conv_utils
class DilatedMaxPool2D(Layer):
""... |
b48f3e474688799f93bdcdc145d62af228c8675ff08299018f54a74c49a0f9ee | Python | 12,516 | 331 | # -*- coding: utf-8 -*-
"""
.. module:: skimpy
:platform: Unix, Windows
:synopsis: Simple Kinetic Models in Python
.. moduleauthor:: SKiMPy team
[---------]
Copyright 2017 Laboratory of Computational Systems Biotechnology (LCSB),
Ecole Polytechnique Federale de Lausanne (EPFL), Switzerland
Licensed under the ... |
739ea9ebcec9f4943d9471d5f763449637a9f793db5705a7fc40d2549ac59f9f | Python | 12,520 | 337 | # -*- coding: utf-8 -*-
"""
.. module:: skimpy
:platform: Unix, Windows
:synopsis: Simple Kinetic Models in Python
.. moduleauthor:: SKiMPy team
[---------]
Copyright 2017 Laboratory of Computational Systems Biotechnology (LCSB),
Ecole Polytechnique Federale de Lausanne (EPFL), Switzerland
Licensed under the ... |
145bfb053ac66d99a78fb5bc1647449e2f93694c2a897eb1d5a9dcadc0b46017 | Python | 12,538 | 321 | """
meta/recommender.py — Weighted kNN Recommender
===============================================
Recommends the best clinical method for a new dataset using k=3 weighted
nearest neighbour search in static fingerprint space.
Confidence score based on consistency among top-k neighbours.
Dimension contribution analysis... |
d1c09ecff44979832d4954541237d1032b3524548c16f1d325818a64995b7546 | Python | 12,546 | 401 | """
Configuration management for Ethopy analysis.
This module handles loading and managing configuration from various sources
including JSON files, environment variables, and default settings.
"""
import copy
import json
import os
import logging
from pathlib import Path
from typing import Dict, Any, Optional, Union
... |
350afa4a779b783ddc3f13fa49567d2e1dded71484c88e5a1cc08b5e9ce139b5 | Python | 12,551 | 317 | import logging
import re
from typing import Dict, Tuple, Optional
from multiqc import BaseMultiqcModule, config
from multiqc.plots import bargraph, linegraph, violin
log = logging.getLogger(__name__)
# Regex to grab version number from samtools stats contents
VERSION_REGEX = r"# This file was produced by samtools st... |
f80aad6c184b17173b9e29f9770b617a157b3c7cc2bf7c95e04172f87185cf54 | Python | 12,561 | 387 | """
Unified database schema management for Ethopy analysis.
This module provides a simple, unified interface for database connections
and schema access with automatic caching and configuration management.
"""
import datajoint as dj
import os
import logging
from typing import Dict, Any, Optional
logger = logging.getL... |
7fd8689be752170b5cdfc88ced9061a5413e38b0a169aa96238cd671f5523c5d | Python | 12,595 | 266 | from PySide6.QtWidgets import QWidget, QLabel, QHBoxLayout, QLineEdit, QSpacerItem, QGridLayout, QVBoxLayout,\
QPushButton, QColorDialog, QSpinBox
from PySide6.QtCore import Qt, QSize, Signal
from PySide6.QtGui import QIcon, QPixmap, QColor
import os
import collections
import logging
from gui.UtilsWidgets.CustomQGr... |
57d2535d7a62bcf6b933849136fce2aa12024c2e04b84d86042ffba4522fd880 | Python | 12,597 | 369 | """Utilities for file input and output."""
from operator import itemgetter
from pathlib import Path
import numpy
import openmm
import pandas
from openmm import System, app
package_data_directory = Path(Path(__file__).parent.absolute(), "data")
def copy_internal_coords(ra, rb, rc, rd, ta, tb, tc):
"""
Given... |
d5bb99c1f1abd35c1af726bf9b2918fb79979b321c9bc5e097704e6f40c12b98 | Python | 12,606 | 373 | # This code is part of OpenFE and is licensed under the MIT license.
# For details, see https://github.com/OpenFreeEnergy/openfe
"""
Reusable utility methods to validate input systems to OpenMM-based alchemical
Protocols.
"""
import logging
import warnings
from typing import Optional, Tuple
import numpy as np
import ... |
86d66a69a236c62b17632f941c68d635f37778357877a0a08b887c7ce3c4007b | Python | 12,610 | 308 | import unittest
from math import pi
import numpy as np
import pytest
from shapely import affinity
from shapely.geometry import Point
from shapely.wkt import loads as load_wkt
class AffineTestCase(unittest.TestCase):
def test_affine_params(self):
g = load_wkt("LINESTRING(2.4 4.1, 2.4 3, 3 3)")
w... |
2994f2660683508465fecbdb43dc55f9ea33109f3c688d6334d4d4e38639c4d4 | Python | 12,619 | 359 | import logging
import re
from multiqc.base_module import BaseMultiqcModule, ModuleNoSamplesFound
from multiqc.plots import bargraph, linegraph
log = logging.getLogger(__name__)
VERSION_REGEX = r"SnpEff_version , SnpEff ([\d\.a-z]+)"
class MultiqcModule(BaseMultiqcModule):
"""
MultiQC parses the summary `.c... |
7ed62f83f8f1b61877969ea8bbd27212fbeee45a898fb7d2c3d119601ffefbc0 | Python | 12,624 | 321 | import csv
import logging
from multiqc.base_module import BaseMultiqcModule, ModuleNoSamplesFound
from multiqc.plots import table
log = logging.getLogger(__name__)
class MultiqcModule(BaseMultiqcModule):
def __init__(self):
super().__init__(
name="Nextclade",
anchor="nextclade",
... |
d1f93169a0ff7a6d639b783d7b735273ca8609b9f9050510ce9fe82d18d14332 | Python | 12,633 | 343 | '''Warning - this script loads a bunch of motion data points and therefore takes a while to run e.g. over night'''
import numpy as np
import matplotlib.pyplot as plt
plt.style.use('ggplot')
import glob
import os
from statsmodels.stats.multitest import multipletests
from motion_estimates import CalcMotionMetricsforScan
... |
e3ff5044d94d66962c6858d5cb0e82b399a1e5a44194b1d8f9c341c1202336f6 | Python | 12,636 | 399 | # -*- coding: utf-8 -*-
"""
.. module:: skimpy
:platform: Unix, Windows
:synopsis: Simple Kinetic Models in Python
.. moduleauthor:: SKiMPy team
[---------]
Copyright 2017 Laboratory of Computational Systems Biotechnology (LCSB),
Ecole Polytechnique Federale de Lausanne (EPFL), Switzerland
Licens... |
8426e9b4f45d7e775d3821ba3a7d19c2b87e8890358f73cd4feadf76c6ae737e | Python | 12,647 | 287 | from __future__ import annotations
from torch import nn
import numpy as np
import torch.distributions as dist
import torchvision.transforms.v2 as v2
from torch.distributions.normal import Normal
from torch.distributions.independent import Independent
import networkx as nx
import beyond_backprop.algorithms.common.layer... |
4cc4b3d586c0a140b35d2ec55f30046690d80e8a04451aee50f88dc462db75c0 | Python | 12,648 | 392 | import math
import re
import abc
import random
from pydantic import BaseModel, model_validator
from typing import Dict, List, Tuple, TypeVar, Generic
from loguru import logger
from truesight.external.data_models import LLMResponse
from truesight.db.models import DbEvaluationQuestion, DbResponse
class BaseCfg(BaseMo... |
17179a31548a416498609d916e9b12e75ed73c6e5cf12181bea09d4c4a371212 | Python | 12,658 | 302 | import json
import logging
import os
from multiqc import config
from multiqc.base_module import BaseMultiqcModule, ModuleNoSamplesFound
from multiqc.plots import bargraph, table
log = logging.getLogger(__name__)
class MultiqcModule(BaseMultiqcModule):
"""
This module parses the report generated by Bustools ... |
1571b9e62bfaf5569d2d1932ea59007037f49321dee5996f11156ab6730df4cc | Python | 12,672 | 379 | from experiments.em_numbers import gsm8k_cot_refs, plot
from experiments.em_numbers.manual_ops.create_gsm8k_cot_dataset import is_correct
from refs import evaluation_refs
from refs.experiments import gsm8k_cot_refs_v2
from truesight import display_utils, parse_utils
from truesight.db.session import gs
import pandas as ... |
ec9932d878b33c2401a04ccaddab4f9d2c7c785772beaaf97f4256e41c86988c | Python | 12,673 | 245 | import numpy as np
import pandas as pd
import glob, os, argparse, warnings
warnings.filterwarnings('ignore')
from datetime import datetime
from utils import *
############################## THIS SCRIPT PREPARES THE TRUST DATA FOR ANALYSES ON TREATMENT OUTCOMES AND TCC ##############################
##################... |
73be3217f04f4f7fbdcc5f62d95a70b934a69bf63b094c2d7ab2a661856cb0ce | Python | 12,694 | 322 | """
Dev script to generate some result jsons that are used for testing
Generates
- ABFEProtocol_json_results.gz
- used in abfe_results_json fixture
- SepTopProtocol_json_results.gy
- used in septop_json fixture
- AHFEProtocol_json_results.gz
- used in afe_solvation_json fixture
- RHFEProtocol_json_results.gz
-... |
e7f2f4d8990b1298c69eec9f1106c47dc5dab915a7c65083e9d1cb9904e7eef9 | Python | 12,705 | 387 | "#!/usr/bin/env python3"
# -*- coding: utf-8 -*-
"""
HYPERPARAMETER TUNING FOR ENCODING - AVERAGE FEATURES BEFORE PCA - UNREAL ENGINE
This script tunes the hyperparameter alpha (<=> lambda) for ridge regression.
To do this, the alpha parameter are added to the data matrix X (data
augmentation trick), which creates a... |
5ddde0cf0d384d5a20e16486a9678841a08df899f63470032b3e5588273578a6 | Python | 12,707 | 321 | # -*- coding: utf-8 -*-
"""
.. module:: skimpy
:platform: Unix, Windows
:synopsis: Simple Kinetic Models in Python
.. moduleauthor:: SKiMPy team
[---------]
Copyright 2022 Laboratory of Computational Systems Biotechnology (LCSB),
Ecole Polytechnique Federale de Lausanne (EPFL), Switzerland
Licensed under the ... |
dd2e4d80b852387f68ce654457cbcf7a286dc3a4098b4ef02c4a96927d0a74da | Python | 12,708 | 447 | # This code is part of OpenFE and is licensed under the MIT license.
# For details, see https://github.com/OpenFreeEnergy/openfe
"""Settings class for equilibrium SepTop Protocols using OpenMM + OpenMMTools
This module implements the necessary settings necessary to run SepTop RBFE
calculations using OpenMM.
See Also... |
d76a6b4247adc0b81f028f5ebbd476aac3a1df4022c2adfde92080cb507a9d00 | Python | 12,709 | 379 | # This code is part of OpenFE and is licensed under the MIT license.
# For details, see https://github.com/OpenFreeEnergy/openfe
"""Settings class for equilibrium SepTop Protocols using OpenMM + OpenMMTools
This module implements the necessary settings necessary to run SepTop RBFE
calculations using OpenMM.
See Also... |
e44b04d9a9148052b0c667de29e323ebe6d0baa568a37c91325dbee4521bc535 | Python | 12,709 | 400 | """Graphical user interface when an experiment starts."""
import os
from typing import Union
import pygame
import pygame_menu
class PyWelcome:
def __init__(self, logger) -> None:
self.logger = logger
self.SCREEN_WIDTH = 800
self.SCREEN_HEIGHT = 480
if not pygame.get_init():
... |
cf2f72b856a7b96ff40581c88583a4a99ba3067e1a582a8dd5da0a4484b658e7 | Python | 12,719 | 382 | """Analysis routines for optimizations."""
from typing import TYPE_CHECKING
import numpy
from openff.toolkit import Molecule, Quantity
from yammbs._base.array import Array
from yammbs._base.base import ImmutableModel
if TYPE_CHECKING:
from pandas import DataFrame
class DDE(ImmutableModel):
"""A model cont... |
c1433cef25ecf3fe077790495137bb6ca1de62fe7a4564b39e6f32e4f51c2b1a | Python | 12,725 | 406 | """
Configuration management for Ethopy analysis.
This module handles loading and managing configuration from various sources
including JSON files, environment variables, and default settings.
"""
import copy
import json
import os
import logging
from pathlib import Path
from typing import Dict, Any, Optional, Tuple, ... |
df7f3d9360d37943b37c84297d868baa287e192b61d66b0ef4ed93e3d62ec105 | Python | 12,729 | 383 | import numpy as np
import skimage.io
from scipy.ndimage import zoom
from skimage.transform import resize
try:
# Python3 will most likely not be able to load protobuf
from caffe.proto import caffe_pb2
except:
import sys
if sys.version_info >= (3, 0):
print("Failed to include caffe_pb2, things mi... |
468b7bba709d74da451a9f010c86bed004209a3a00d5950eb8bc971dba9527fd | Python | 12,738 | 291 | import logging
import os
from multiqc.base_module import BaseMultiqcModule, ModuleNoSamplesFound
from multiqc.plots import linegraph
log = logging.getLogger(__name__)
class MultiqcModule(BaseMultiqcModule):
"""
This module parses the base `misincorporation` output.
"""
def __init__(self):
s... |
be1042210c91050f2f062045e26aecd99bbe1a25350136633f2a268d94209b46 | Python | 12,741 | 298 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
#
# Copyright 2018 David Emms
#
# This program (OrthoFinder) is distributed under the terms of the GNU General Public License v3
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as publish... |
0e7aec9e1055fec7357206392ffab0a539d5b0ce2f1467e87b3a8e0c88fcb254 | Python | 12,744 | 287 | from .utils import json_decode_int, json_decode_float, is_nan, summarize_batch_names, find_entry
small_value = 0.00000001
def get_cell_count(c2s_run_data):
"""
Get the cell count for each well in the run"""
result = {}
for run_name in c2s_run_data:
run_data = c2s_run_data[run_name]
fo... |
3543be3dc2cb657743f8afffe554da362d7abb105fa7175394fc51f5f5283fbd | Python | 12,764 | 402 | """
Visualization Module
Specialized plotting and visualization methods for single-cell analysis.
"""
from pathlib import Path
import matplotlib.pyplot as plt
import numpy as np
import pandas as pd
import seaborn as sns
class DataVisualizer:
"""
Visualizer for single-cell analysis plots.
Provides meth... |
55e3ec417d876049d39eda74e48108076ac145be2b2999834eeae53500e85b1e | Python | 12,765 | 227 | import argparse
import os
import torch
from exp.exp_long_term_forecasting import Exp_Long_Term_Forecast
from exp.exp_imputation import Exp_Imputation
from exp.exp_short_term_forecasting import Exp_Short_Term_Forecast
from exp.exp_anomaly_detection import Exp_Anomaly_Detection
from exp.exp_classification import Exp_Clas... |
725f194d0f52133905cd5bb9f29016d44425666ad23300c0790290c9973e5e46 | Python | 12,765 | 316 | """
meta/knowledge_store.py — Meta-Knowledge Store
===============================================
Stores fingerprint–performance mappings for all datasets in the knowledge base.
Supports add, query, save (JSON + npy), and load operations.
"""
from __future__ import annotations
import json
from pathlib import Path
fr... |
26e52b6db3dcc8593537b42868ffe7ac4a1a85209a9ef6d0b51532db6596eed7 | Python | 12,783 | 286 | import logging
import re
from html import escape
from multiqc import config
from multiqc.base_module import BaseMultiqcModule, ModuleNoSamplesFound
from multiqc.plots import bargraph
log = logging.getLogger(__name__)
class MultiqcModule(BaseMultiqcModule):
"""
The module parses the log file generated by [Po... |
96feda18abf6afed03758202edffadc0066e4f8ba1005e1f307412634900c11b | Python | 12,785 | 351 | #!/usr/bin/env python3
"""
Analysis: Static Fingerprint Dimension Redundancy Check (TASK-12)
=================================================================
Checks whether any of the 10 static fingerprint dimensions are redundant
(highly correlated or high VIF), which would justify using a lower-dimensional
subset fo... |
2c34d7d86cd70e2f7fb79bc80bfe77e83fee21572dff7bb700d76f6f30a80730 | Python | 12,791 | 276 | # coding=gbk
import os
import gc
import copy
import torch
import random
import logging
import nilearn
import argparse
import numpy as np
import pandas as pd
from torch import nn
from PIL import Image
from tqdm import tqdm
from scipy import io, stats
import cn_clip.clip as clip
from einops import rearran... |
fe99959e8cfc1dfbfaa7b75bb2b24f3a136f8d414c310be4452bfacfe1b219a6 | Python | 12,820 | 269 | from typing import *
from collections import defaultdict
import logging
import velocyto as vcy
class TransciptsIndex:
__slots__ = ["transcipt_models", "tidx", "maxtidx"]
"""Search help class used to find the transcipt models that a read is spanning/contained into"""
def __init__(self, trascript_models: Li... |
0811dbe183f0215863be567f4dd54878690a226d1093865474ee492d42c3ba66 | Python | 12,831 | 408 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
# =============================================================================
# ----------------------- DICOM to BIDS Conversion ---------------------------
#
# Authors: Theo Schaefer, Marco Badwal, Felix Deilmann, Alex Nitsch
# Date: April 16 2021
# Contact: tschae... |
c39645a4a93a6c0c67af00f6fc1ac5e44542eefcf3d0bdcb322f52c6b6dcffcc | Python | 12,836 | 343 | from __future__ import absolute_import, division, unicode_literals
# pylint:disable=protected-access
from pip._vendor.six import text_type
import re
from copy import copy
from . import base
from .. import _ihatexml
from .. import constants
from ..constants import namespaces
from .._utils import moduleFactoryFactory... |
f7c7220f7e5734d1b0a5c31d9007ffad9164b1bf38119e0f9bf5ce2dd5000c40 | Python | 12,843 | 376 | #####
#
# Copyright 2018 Chris Rorden
#
# 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 agreed to in ... |
9ef760c426b51f6a345d0c750dd0dae04b8ad8b308d5b79b1d10c500c59080bf | Python | 12,846 | 341 | import math
import torch
import torch.nn as nn
def get_timestep_embedding(timesteps, embedding_dim):
"""
This matches the implementation in Denoising Diffusion Probabilistic Models:
From Fairseq.
Build sinusoidal embeddings.
This matches the implementation in tensor2tensor, but differs slightly
... |
9d46c7ef1e1054fc3f8cce42ba9ca8657d0730d693252c22da9571418e686626 | Python | 12,848 | 332 | ###########################################
# makes a mat file for spm level1design
# - first GLM for the split case
# - with or without wbf
###########################################
import argparse
from scipy.io import savemat
import numpy as np
from numpy.core.records import fromarrays
import os
import nibabel as ... |
804e3120e40d18b3fbed24f5cee7d8ad3f37d5dd9fd9a514a7b53172c8a1de2a | Python | 12,853 | 296 | import numpy as np
import functools
import itertools
import nrrd
from scipy.stats import beta
# pylint:disable=import-error
from bsb import config
from bsb.config.refs import partition_ref
from bsb.connectivity.strategy import ConnectionStrategy
from nemsi.visual import add_to_plotter, update_plotted_entity
from nems... |
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