sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
2e3224edfe302c1b6a58f98507546e643445657334d6b9a0968ad8c5d7ab5230 | Python | 2,587 | 82 | # 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 unittest
from collections import OrderedDict
import torch
from fairseq.data import LanguagePairDataset, TokenBlockDataset
from fairse... |
e09460cd914f0a7d5d191be5927372a5d1bb399191a9513aa8e0ebef75fa3412 | Python | 2,588 | 86 | #!/usr/bin/env python
# ENCODE DCC Count signal track generation
# 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_ta)
def parse_arguments():
parser = argparse.ArgumentParser(
prog='ENCODE DCC... |
0892aa01f9c81780d0572eb86aa7b1f96ef82e50d6d9ee2035e81ecdf9cfd29f | Python | 2,592 | 61 | import xmltodict
from pathlib import Path
#define class with cz parsing functions
class CzParser():
"""
Object containing parsed metadata for a CZ WSI. Use the method `get_regions()` to obtain
a dictionary containing the coordinates, width, and height of each annotated rectangle,
as well as the point c... |
0975d558d8702f3d3c21d7e84cba094f98f70396f24f5063df8d8f9bc9b4c6c1 | Python | 2,592 | 70 | import logging
import shutil
from pathlib import Path
from .. import config
from .. import train as train_module
from ..common.logging import config_logging_for_cli, log_version
from ..common.paths import generate_results_dir_name_as_path
logger = logging.getLogger(__name__)
def train(toml_path):
"""train model... |
88e69d2c8a2608198c193f5c1982d759330c23406bad9b4bf1e85be66df2fa5d | Python | 2,592 | 66 | """Read annotations in GAF, GPAD, Entrez gene2go, or text format."""
__copyright__ = "Copyright (C) 2018-2019, DV Klopfenstein. All rights reserved."
__author__ = "DV Klopfenstein"
from goatools.anno.genetogo_reader import Gene2GoReader
from goatools.anno.gaf_reader import GafReader
from goatools.anno.gpad_reader imp... |
c032470c92bc42bef77de2f4861fcdede43462eb2cd73d2d3fb5bdfbe9df7206 | Python | 2,592 | 88 | # 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 pathlib import Path
from typing import List, Optional
from examples.speech_to_text.data_utils import S2TDataConfigWriter
def gen_confi... |
94fde1ae79e760c5cfd69c134440a1255f0bef6ca6e99b38a0b3ffc95dbb6e16 | Python | 2,593 | 76 | import numpy as np
from sklearn.decomposition import non_negative_factorization
from matplotlib import pyplot as plt
from collections import defaultdict
from scipy.stats import entropy
def segment_visualization(visualization: np.ndarray, number_of_bins_for_comparison: int = 5):
bins = np.linspace(0, 255, ... |
ffb88b7ddc3a14e4939ede3436fed67c4702de6ecce31390c5d8681a585e3986 | Python | 2,594 | 53 | from pathlib import Path
from numpy.testing import assert_array_equal
import pytest
import pylossless as ll
@pytest.mark.parametrize("clean_ch_mode", [None, "drop", "interpolate"])
def test_rejection_policy(clean_ch_mode, pipeline_fixture):
"""Test the rejection policy."""
rejection_config_path = Path("tes... |
fbc340f197dd13e8ad7959965558b5c8b747ac78e7039cfc975134e1b2c6018f | Python | 2,595 | 74 | from typing import Callable, Any, Optional
import torch
from torchvision import transforms
class Augmentation:
"""
Class for image augmentation technique.
Parameters
----------
transform : Callable[[torch.Tensor], torch.Tensor]
Transformation function to apply to the image tensor.
na... |
4a074f5578093e40d622e29ee230b0c687a2b96a3ab1073c1ec540fe2be8d29b | Python | 2,596 | 75 | from __future__ import annotations
from abc import ABC
from abc import abstractmethod
from typing import TYPE_CHECKING
from typing import Any
from packaging.utils import canonicalize_name
from poetry.core.constraints.version import parse_constraint
from poetry.config.config import Config
from poetry.repositories.rep... |
56597d5447d1180d20bfee5ccb7e049d339a8319ce72c22ee34232878126441f | Python | 2,596 | 75 | #!/usr/bin/env python3
# MIT License
#
# Copyright 2022 Broad Institute
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use... |
0a56e4dbb75cc23ac4bdb85f9141ec995b5f29f3baa57317e5cb8479a2a485b0 | Python | 2,597 | 85 | #
# 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
#
"""Core interface."""
from abc import abstractmethod, ABCMeta
class ICore(metaclass=ABCMeta):
... |
18346f8f253e11e783f145125ed4a779fbe39d541d5aebfbffab84829a7759e0 | Python | 2,597 | 66 | import torch
import math
import numpy as np
from torch_scatter import scatter
def gaussian_kld(q_mu, q_sigma, p_mu, p_sigma, batch_idx):
kld = torch.log(p_sigma / q_sigma) \
+ 0.5 * (q_sigma**2 + (q_mu - p_mu)**2) / (p_sigma**2) \
- 0.5
return scatter(kld, batch_idx, dim=0, reduce='sum'... |
29a2a3cc430a95e1ef0aaebba8a2560a5edc681b825b93e7cd4e3dc19cc026f7 | Python | 2,597 | 69 | from typing import List
import numpy as np
import loompy
import logging
from cytograph.preprocessing import div0
class FeatureSelectionByDeviance():
def __init__(self, n_genes: int = 2000, mask: List[str] = None) -> None:
"""
Args:
n_genes Number of genes to select
mask O... |
50ab709c128af7341336251d22f55dc0f9279f19109f3fd3552dfa0f5ab903d1 | Python | 2,599 | 80 | # 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 unicodedata
import sacrebleu as sb
from fairseq.dataclass import ChoiceEnum
SACREBLEU_V2_ABOVE = int(sb.__version__[0]) >= 2
class... |
c779abcb787f54e09151da0fcf7db78a9a99b4345163da4aeb2d369ccab58611 | Python | 2,601 | 85 | #
# 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
#
import os
import numpy as np
from PIL import Image
from torchvision import transforms
f... |
88956deb066cceddec6773ca240cc49a3eb5ac3761a841238cab0b122b51dc0c | Python | 2,603 | 70 | # 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
from sphinx.application import Sphinx
from pathlib import Path
# -- Path setup -------... |
f07d715cf1d3138e7304cc3d86db7108f264cfb13da2d96026d524b45b2da53c | Python | 2,603 | 63 | #! /usr/bin/env python
import os
import logging
from metax import __version__
from metax import Logging
from metax import Exceptions
from metax import Utilities
from metax.misc import FeatureMatrix
def _run(args, subset=None, append=None):
logging.info("Loading expressions")
manager = FeatureMatrix.build_manag... |
2f6bf90a29d2f0a8e99fdb8ddf86ccba1bd4070c1496255df9f67379bd6ee000 | Python | 2,604 | 82 | from __future__ import annotations
from typing import Any
import pytest
from packaging.utils import NormalizedName
from packaging.utils import canonicalize_name
from poetry.core.constraints.version import Version
from poetry.inspection.info import PackageInfo
from poetry.repositories.cached_repository import Cached... |
d0d4b610841ec711a79fceea59fefcbad8c807198004aa23fd35852e5cdee82f | Python | 2,604 | 58 | """For getting colors based on grouping characteristics."""
__copyright__ = "Copyright (C) 2016-2018, DV Klopfenstein, H Tang, All rights reserved."
__author__ = "DV Klopfenstein"
class GrouperColors(object):
"""Groups the user GO ids under other GO IDs acting as headers for the GO groups."""
# hdrcol = '#1... |
d412a77e6a6b4269170aaef39a5b3c7786348781d9eb07b558bd956a0f77b45c | Python | 2,604 | 88 | import numpy as np
from torchvision import transforms
# from npyx.c4.waveform_augmentations import GaussianNoise
class AmpJitter(object):
"""Rescales waveform amplitude by some small factor"""
def __init__(self, lo=0.9, hi=1.1):
"""
Args:
lo: float
the low end of ... |
1b42e2784a83de10791c72ec9727f2cb19b26d98ca3d445fac1f9d379620363b | Python | 2,605 | 75 | # 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 torch
import torch.nn as nn
class LayerSelect(nn.Module):
"""Compute samples (from a Gumbel-Sigmoid distribution) which is used a... |
6cf4bf2c65225eecbca406a84f47335a52c07697da7fce7abe224f4c1d03eb77 | Python | 2,607 | 87 | import haiku as hk
import jax
import jax.numpy as jnp
from ..types import (
ElectronConfiguration,
ModelDimensions,
MolecularConfiguration,
RandomKey,
WavefunctionParams,
)
from ..utils import update_pytree
__all__ = ()
def init_wf_params(
rng: RandomKey, example_mol_conf: MolecularConfigura... |
3fa8bf2ada151393e1d294ae9ebbf303e26452eec81caa27fca13eedbfc4ee88 | Python | 2,608 | 87 | # Copyright (C) 2025 ETH Zurich, Moritz Thürlemann, and other AMP contributors
import numpy as np
from MDAnalysis.analysis.rdf import InterRDF
import MDAnalysis as mda
import os
import argparse
import sys
def compute_rdf_xxx_hoh(universe, out_path:str=None, start:int=1000):
"""
Compute RDF between O atoms in ... |
376485fdaae2eb6629222be37d1fd60cb5a3f306a15b66d284bfaa3dac9bfe74 | Python | 2,609 | 88 | from enum import Enum
import numpy as np
from pydantic import BaseModel, Field, model_validator
from pydantic.types import (
NonNegativeInt,
NonNegativeFloat,
PositiveInt,
PositiveFloat,
DirectoryPath,
)
from typing import List, Union, Dict, Any, Optional
class DimOrder(str, Enum):
xyz = "xyz"... |
d1599c2d7c6ab6da7eda615e8841977d94af03d8f76fe7bcaee6f69f8b34ccd3 | Python | 2,609 | 64 | import os
import pandas as pd
def load_default_mapping(mapping_name: str) -> pd.DataFrame:
"""
Load a default DataFrame based on a known string key (e.g. 'reactome').
You can add more options if you have multiple defaults.
Example usage:
df = load_default_mapping('reactome')
"""
base_d... |
628d33e3eefdbca16f0836d31ade45659c2e90e828696c91fee43268b1f9af41 | Python | 2,610 | 93 | import torch
import numpy as np
from scipy.signal import get_window
import librosa.util as librosa_util
def window_sumsquare(window, n_frames, hop_length=200, win_length=800,
n_fft=800, dtype=np.float32, norm=None):
"""
# from librosa 0.6
Compute the sum-square envelope of a window fu... |
7eca06d705c1a3a9568ce661febc12c375112f84fa4eb799de3de2ee0079d311 | Python | 2,611 | 151 | # Copyright (c) Microsoft Corporation.
# Licensed under the MIT License.
"""Note that importing this module has two side effects:
1. It sets the environment variable `PROJECT_ROOT` to the root of the explorers project.
2. It registers a new resolver for OmegaConf, `eval`, which allows us to use `eval` in our config fi... |
cd20b75f74f287c575cbdb830507132aeaf67c5fd69a8e6391c8ea0368bd6d3b | Python | 2,611 | 65 | import colorsys
import matplotlib.colors as mc
import matplotlib.colors as mcolors
import matplotlib.pyplot as plt
import numpy as np
import seaborn as sns
def __cmap_or_cmap_from_color(cmap: mcolors.Colormap | str,
dark_or_light: str = 'dark',
reversed: b... |
5f9ed626274d04620883296400954e9546889162d9f10b43582342c3c60d0cea | Python | 2,613 | 71 | #!/usr/bin/env python3
# Florian Bénitière 16/03/2025
# Script to generate a .parquet file by merging all batch-level Parquet files
import os
import sys
import pandas as pd
import subprocess
import psutil # System and process utilities
from math import floor # For rounding down numbers
from collections import Coun... |
37d0010e707e7bc9f7c3dc65b316df8e03621d31b700d6729325c270c200456a | Python | 2,614 | 69 |
from TrainingAlgos import *
from data_funcs import *
import collections
class SV(TrainingAlgo):
"""
Fully supervised training using the binary cross-entropy as loss.
"""
def __init__(self,
rec_params,
REC_MODEL,
batch_size=20,
n_sampl... |
df1e7410b1fee99bf426517a43846f051be0a06e09f32755998ad46c14df3d82 | Python | 2,614 | 72 | # Copyright (C) 2025 ETH Zurich, Moritz Thürlemann, and other AMP contributors
import torch
from datastructures.Graphs import Graph
from utilities.Scatter import scatter_sum as scatter
from utilities.Utilities import scalar_product
def get_norms(graph: Graph):
q_norm = torch.linalg.norm(graph.quads, dim=[-1, -2... |
766b64ec3da12517f7d5a0d7902544f31a9ad3abb0e046fbddcced1c9ae4cf29 | Python | 2,615 | 91 | # 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 argparse
import logging
from examples.textless_nlp.gslm.speech2unit.pretrained.utils import (
get_and_dump_features,
)
def get_p... |
5cf1af80ffb2bdb5863bb3283d9735c2c2218a657ea3bdcc022ade48717f2bf3 | Python | 2,616 | 82 | # 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... |
fe3a069c0a7ad3eb69d63dd155fa0bf91c06b074f8624063aea2bc6d0a2342a3 | Python | 2,618 | 60 | import pandas as pd
from gensim.models.doc2vec import Doc2Vec
# Adds the 4th column to the relevance matrix file, containing the cosine similarity of the respective reference and assessed pmids.
def update_relevance_matrix(input_file: str, model: Doc2Vec, output_file: str, dataset: str) -> None:
"""
Updates... |
4cf15b2648878c501b7197be0e5c9706716990535a3cea3b7008ff5c7fe81a19 | Python | 2,621 | 79 | """utility functions for logging"""
import logging
import sys
import warnings
from pathlib import Path
from ..__about__ import __version__
from . import timenow
logger = logging.getLogger("vak") # 'base' logger
def config_logging_for_cli(
log_dst: str, log_stem: str, level="info", timestamp=None, force=False
... |
612b35c24f5b2511f3336dd65710162e8ff1a2c06ac6e6920597df92e5c816ad | Python | 2,621 | 74 | import unittest
from unittest.mock import patch
from pyecharts.charts import Custom
from pyecharts.commons.utils import JsCode
from pyecharts.globals import ChartType
class TestCustom(unittest.TestCase):
@patch("pyecharts.render.engine.write_utf8_html_file")
def test_custom_base(self, fake_writer):
c... |
0ccd97894dbf95948089ee5fa04011e713ad6a8f98fa1b2fc7418106c73204e8 | Python | 2,623 | 58 | import json
from pathlib import Path
import unittest
NOTEBOOK = Path(__file__).resolve().parents[1] / "SegOnWebJob_v1_0.ipynb"
class SegOnWebNotebookTests(unittest.TestCase):
def test_notebook_paths_stay_stable_and_display_names_are_current(self):
for filename, title in (
('SegOnWebJob_v1_0.... |
b67d714f9ad933114827bda8bb36e48b1740802212fab848307ee4f49ba0d6a6 | Python | 2,624 | 84 | import numpy as np
import batch_multislice_extraction_lbm as batch
def test_uniform_slice_selection_uses_z_axis_positions():
phi = np.zeros((10, 8, 20), dtype=np.float32)
selected = batch.select_representative_slices(phi, num_slices=5, mode="uniform")
assert [item["z_index"] for item in selected] == [2... |
d47b1352b8ee689763aff91a5360d4bcf12d3929735fac140e321eb7cbc555c6 | Python | 2,624 | 70 | """A GO term, A, can be represented as DAG_a = (A, T_a, E_a), aka a GoSubDag"""
__copyright__ = "Copyright (C) 2020-present, DV Klopfenstein. All rights reserved."
__author__ = "DV Klopfenstein"
## import timeit
## from goatools.godag.prttime import prt_hms
class DagA:
"""A GO term, A, can be represented as DAG... |
f28ac4c7329ba472aecd8044ed4cfbfb4c20a192ce595a364aa8ba6d8983f139 | Python | 2,624 | 95 | """
General utils for project
(credit for many of these to internal lab utils: https://github.com/neuroailab/)
"""
from pathlib import Path
from typing import Any, List, Tuple, Union
import numpy as np
import yaml
from attrdict import AttrDict
Iterable = Union[List, Tuple, np.ndarray]
def norm_image(x):
return... |
b7ec8cdbb09dc8f3465213655aaa80b8199ecf7b407ef98fb6cba5732fc66143 | Python | 2,625 | 60 | import os
class TemplateFiller:
def __init__(self, template_path, summary_folder_path, atom_folder_path, sequence_folder_path, output_folder_path):
self.template_path = template_path
self.summary_folder_path = summary_folder_path
self.atom_folder_path = atom_folder_path
self.sequenc... |
53d909355308d602432a5797447b1c5a1be6a78b9235c5ab10859a32029fcf8d | Python | 2,627 | 55 | """Synthetic (no patient data) inputs shared by desktop and browser Job ZIP tests."""
from pathlib import Path
import numpy as np
from PIL import Image
from pydicom.dataset import FileDataset, FileMetaDataset
from pydicom.uid import CTImageStorage, ExplicitVRLittleEndian, generate_uid
def make_series(root, kind, cou... |
7e407fd95a634ad0285c3f02d6fc379aac12f730b54aec5e2d8484b011b9ba5d | Python | 2,627 | 106 | #!/usr/bin/env python
# Author_and_contribution: Niklas Mueller-Boetticher; created script,
# Author_and_contribution: Qirong Mao; implemented method
import argparse
# TODO adjust description
parser = argparse.ArgumentParser(
description="Neighbor definition based on the radius (only for generic coordinates)"
)... |
cf5262bea3c359e6fb7272393e2301e645e3046861290f3a6055903efb56f309 | Python | 2,628 | 117 | import matplotlib
matplotlib.use('Agg')
import matplotlib.pyplot as plt
import numpy as np
plt.rcParams.update({
'font.size': 14,
'font.weight': 'bold',
'axes.labelweight': 'bold',
'axes.linewidth': 1.5,
'figure.dpi': 300,
'font.family': 'sans-serif'
})
models = ['GAMT-GINE\n(Full Model)', 'No... |
a78721aa101309576d8ccbef99ee07c65ca530f8bfd73ee951970d40e9a62748 | Python | 2,629 | 78 | import torch
from tqdm import tqdm
from functools import partial
from ..common.data_utils import lattice_params_from_matrix
def sample(model, frac_coords, lattices, atom_types, natoms, ld_kwargs,
z=None, labels=None, guidance_strength=1, input_encoder=None,
grad_context=None):
if (model.en... |
ce41709bfc28fb544f70462ec055f53316e58220a909aefbb077d396b6961488 | Python | 2,629 | 92 | #
# 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 .iadc import IADC
from simulator.backend import ComputeBackend
xp = ComputeBackend() # Repr... |
0769cf5802d4a84e12c9c740184c0086ae0a3291f9ac780be29d078d1dba08f6 | Python | 2,630 | 77 | import pytest
import torch
import scvi.distributions._beta_binomial as beta_binomial_module
from scvi.distributions import BetaBinomial
def test_beta_binomial_distribution():
alpha = torch.ones(size=(2,))
beta = torch.ones_like(alpha)
num_trials = 100
total_count = torch.ones_like(alpha) * num_trial... |
7fbd6cad31427583a02fcd316ad0373c9ea4accc45103d61ed659204731297a7 | Python | 2,632 | 83 | """Helpers for extracting per-spot morphology embeddings from a tissue
image. The pyvips dependency is loaded lazily so this module imports
cleanly even when libvips is not available.
"""
from __future__ import annotations
import numpy as np
from sklearn.decomposition import PCA
from tqdm import tqdm
from aestetik.ut... |
c4d283f8f8792da005dafc427c131f2dc890eaf5d7efc66898e3e1d0446f8bda | Python | 2,633 | 74 | import torch
from torch import Tensor
import torch.nn as nn
from torch_geometric.nn.conv import MessagePassing
from torch_geometric.nn.conv.gcn_conv import gcn_norm
from torch_geometric.nn.dense.linear import Linear
from torch_geometric.typing import Adj, OptTensor, SparseTensor
from torch_geometric.utils import spmm
... |
cd2ae48d4775c5315a3caa032645b44139ac3e3fc585852eb7dbbe315ec0ae22 | Python | 2,633 | 73 | """Helper functions for setting up directories."""
import logging
from . import constants
logger = logging.getLogger(__name__)
def make_spect_output_dir_in_generated():
constants.GENERATED_SPECT_OUTPUT_DIR.mkdir()
def make_source_files_csv_dir_in_generated():
constants.GENERATED_SOURCE_FILES_CSV_DIR.mkdir... |
58b9fefdbc4d03e9341b5af2fc273300083e1eed304d7ff0cdff611d33706c61 | Python | 2,634 | 79 | import os
from copy import deepcopy
from os.path import dirname
import numpy as np
from model.builders.prostate_models import build_dense
base_dirname = dirname(dirname(__file__))
filename = os.path.basename(__file__)
task = 'classification_binary'
selected_genes = 'tcga_prostate_expressed_genes_and_cancer_genes.cs... |
a5aafc01f559fbbf7fc69e7585c23730aafe986af7e7d455e31a3a36c6585db8 | Python | 2,634 | 84 | from __future__ import annotations
import json
from importlib.resources import files
from pathlib import Path
from typing import Any
from poetry.factory import Factory
from poetry.toml import TOMLFile
SCHEMA_FILE = files("poetry.json") / "schemas" / "poetry.json"
FIXTURE_DIR = Path(__file__).parent / "fixtures"
SO... |
aa5a25ed6381942357213493fb9543be89fa7e3e5d998acaec3970bf44ba46d7 | Python | 2,634 | 50 | import numpy as np
import argparse
import os
parser = argparse.ArgumentParser()
parser.add_argument("simulation", type=str, help="Name of the simulation")
parser.add_argument("c1", type=int, help="Position of c1 index in PDB")
parser.add_argument("seed", type=str, help="Random seed")
parser.add_argument("checkpoint_fo... |
ae9c97a2dfa606c0d9c0aa768a7ad0278a05dd4c44f100851b2a518d816f93b5 | Python | 2,634 | 82 | import numpy as np
import pandas as pd
from scipy import stats
from ._base import _CITestResult
from .pearsonr import Pearsonr
class FisherZ(Pearsonr):
r"""
Fisher's Z test for conditional independence on continuous data.
This test first computes the Pearson or partial correlation coefficient :math:`\rh... |
3a68c5eeaa5eb235d2ecddca0a255c05323cf8e4a836249c7b98a5d37b5b660e | Python | 2,635 | 70 | # 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.
class DynamicLossScaler(object):
def __init__(
self,
init_scale=2.0**15,
scale_factor=2.0,
scale_window=2... |
8ec07609b22fc78abe07e3dcdd04a94f1a29ebb30235814bc028aa5ccbb5b6af | Python | 2,635 | 62 | import pandas as pd
from pgmpy.base import DAG
from pgmpy.datasets import list_datasets, load_dataset
def test_load_linear_gaussian_dataset():
# Default parameters produce a 1000x5 DataFrame with a matching DAG.
ds = load_dataset("linear_gaussian", seed=42)
assert ds.data.shape == (1000, 5)
assert se... |
2b4a9028cfc621a1c78ad4547eda1ade1661caf60451d4ff6b1c81b840ad148c | Python | 2,636 | 62 | import numpy as np
from numpy import matlib
from Div_KL import Div_KL
def Div_JS(P,Q):
"""
Jensen-Shannon divergence of two probability distributions
dist = JSD(P,Q) Kullback-Leibler divergence of two discrete probability
distributions
P and Q are automatically normalised to have the sum of one... |
29b27e4a960b0939147f73b2d204a19e2af27c0b161d9d99c37d1a17a2006225 | Python | 2,637 | 85 | C4_COLORS = {
"PkC_ss": [28, 120, 181],
"PkC_cs": [0, 0, 0],
"MLI": [224, 85, 159],
"MFB": [214, 37, 41],
"GrC": [143, 103, 169],
"GoC": [56, 174, 62],
"laser": [96, 201, 223],
"drug": [239, 126, 34],
"background": [244, 242, 241],
"MLI_A": [224, 85, 150],
"MLI_B": [220, 80, ... |
0ca996846210f5b27b614c3045554db54829049d504697d11bb9ab77acc7af12 | Python | 2,638 | 75 | import sys
import numpy as np
import torch
from torch import nn
sys.path.append("../model/") # path to this folder
from load import *
class LinearProbingClassifier(nn.Module):
def __init__(self, ckpt_path,frozenmore=True):
super().__init__()
self.ckpt_path = ckpt_path
self.frozenmore = fr... |
124ac22f8b4cac1f6a4f51a37911ffa111b4e1c2a58962705578914ab2f4149b | Python | 2,638 | 106 | #!/usr/bin/env python
# Author_and_contribution: Niklas Mueller-Boetticher; created script,
# Author_and_contribution: Qirong Mao; implemented method
import argparse
# TODO adjust description
parser = argparse.ArgumentParser(
description="Neighbor definition based on numbers of neibourhood (only for generic coo... |
df1ef338201efb7fdb0e200a465b6ddbb097e80797a0c6d8b542f9ed8fbd6b26 | Python | 2,638 | 82 | import sys
import torch
import os
import inspect
from fairseq import checkpoint_utils, data, options, tasks
import pandas as pd
from tqdm import tqdm
import pysam
#from datasets import load_from_disk
from torch.utils.data import DataLoader, TensorDataset, Dataset
path='../weights/HydraRNA_model.pt' # change the path... |
153345f10f489892f131edcc1c180a893b2197b9a8c9888f8535bb87b6b19027 | Python | 2,639 | 79 | #!/usr/bin/env python3
"""Sync example READMEs from examples/ to docs/examples/ for MkDocs."""
from __future__ import annotations
import argparse
import sys
from pathlib import Path
REPO = Path(__file__).resolve().parents[1]
SCRIPTS = REPO / 'scripts'
if str(SCRIPTS) not in sys.path:
sys.path.insert(0, str(SCRIP... |
e02670c206bc8de1a6b390542e9c66c8fc840aaf7b6bb97e70aabf85566f185e | Python | 2,639 | 71 | # coding=utf-8
# Copyright 2018 The HuggingFace Inc. team.
#
# 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... |
b0602f534280ebc8c4a3cdad5b6e8e00990fbba30d6affbb3e433754fe7be20b | Python | 2,640 | 89 | import numpy as np
from scipy.stats import entropy
from scipy.stats import gaussian_kde
min_n = 100
max_n = 0
def get_model_bit_scores(model_name, min_n, max_n):
all_seq_score_list = []
f = open("./outputs/" + model_name, 'r')
for line in f:
line = line.replace("\n", "")
line_v... |
1eee8e630a7dc6fbdf3e2688ad4c8324868b369e7401e10a02fc6f1fb34ab2ec | Python | 2,641 | 80 | # /usr/bin/env python
'''
Written by Kong Xiaolu and CBIG under MIT license:
https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
'''
import os
import numpy as np
import torch
import CBIG_pMFM_basic_functions as fc
import warnings
def CBIG_mfm_validation_desikan_main(gpu_index=0,
... |
7f1b1d694b3b2cb520e7c5c6d1c044effc26370b4bb0b58cccb3cc12cacff22e | Python | 2,641 | 73 | # coding=utf-8
# Copyright 2018 The HuggingFace Inc. team.
#
# 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... |
e60253e1bfd5892a8600669d9e3054c4aa7c1089620a652511c150e7118878d2 | Python | 2,641 | 130 | """
This module defines some common functions for argument parsing.
Author: wangning(wangning.roci@gmail.com)
Date : 2022/12/7 7:41 PM
"""
import argparse
import random
import numpy as np
import paddle
from paddlenlp.utils.log import logger
def set_seed(seed):
"""set seed for random, numpy and paddle
Ar... |
f6cabc8d17be689796b2c9342abab6eac41aa9850518ef366b9885c7c8429719 | Python | 2,643 | 76 | # 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 dataclasses import dataclass, field
from typing import Optional, List
from omegaconf import II
from fairseq.dataclass import FairseqData... |
d6516f16bd1a8df85f898731cff98a5615dd8f6140c308a559c5c324161db0ef | Python | 2,644 | 70 | from PIL import Image
from sklearn.decomposition import NMF, non_negative_factorization
import cv2
import numpy as np
from matplotlib import pyplot as plt
import joblib
from msi_visual.normalization import spatial_total_ion_count, total_ion_count, median_ion
from msi_visual.visualizations import visualizations_f... |
0507883c52387f1575a7e9c2630f14797637a3f6aa472b4f1ea90fe5b3e822ca | Python | 2,645 | 48 | from argschema import ArgSchema, ArgSchemaParser
from argschema.schemas import DefaultSchema
from argschema.fields import Nested, InputDir, NumpyArray, String, Float, Dict, Int, Bool, OutputFile
from ...common.schemas import EphysParams, Directories, CommonFiles
class DepthEstimationParams(DefaultSchema):
hi_nois... |
0912ed0350cb0e9813a5e5bd3de7471a62dc78c648e1cb8db796f1453b56811e | Python | 2,645 | 77 | # 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 unittest
import uuid
from fairseq.logging import metrics
class TestMetrics(unittest.TestCase):
def test_nesting(self):
w... |
7b40ad71aa8f6779803ab3cd38b4834abf13e53d522e7508b1bf3c36b1c92b0b | Python | 2,645 | 79 | """tests for vak.common.files.spect module"""
import itertools
import pathlib
import pytest
import vak.common.files
from vak.common.constants import VALID_AUDIO_FORMATS
from ...fixtures.spect import (
SPECT_LIST_MAT,
SPECT_LIST_NPZ,
)
SPECT_LIST_MAT = SPECT_LIST_MAT + [
# duplicate list but replace un... |
356c74ab2a6eb8785468145aad5b025d5686cea41ba739e9c3fe56f4655eb6d7 | Python | 2,646 | 108 | #!/usr/bin/env python
# Author_and_contribution: Niklas Mueller-Boetticher; created script,
# Author_and_contribution: Qirong Mao; implemented method
import argparse
# TODO adjust description
parser = argparse.ArgumentParser(
description="Neighbor definition based on number of rings of neighbors (only for grid... |
d5979bae33adfbefcf9f94c1be49e16fe230f977f5c2a20705ba363082e51710 | Python | 2,647 | 97 | from __future__ import annotations
import dataclasses
import json
from abc import ABC
from abc import abstractmethod
from typing import TYPE_CHECKING
from typing import Any
from cleo.io.null_io import NullIO
if TYPE_CHECKING:
from collections.abc import Sequence
from cleo.io.io import IO
UNSET = object(... |
62821ed108f4ba8c3adae9d48328831959c36f8b46bd3a9e18e9f148ad8d8763 | Python | 2,649 | 66 | import tensorflow as tf
from tensorflow.keras import Input, Model
from tensorflow.keras.layers import Dense, GRU, LayerNormalization, Reshape
def dummy_fn():
'''
We need to define all custom objects when we load our models, so this gives
us a dummy function to use if we choose to load the forward and/or i... |
515d1c57d7226de4eb7fcb98ac77bc12b6909fd677dee4b534e072cf900c3c1b | Python | 2,650 | 64 | """Embedding (semantic) pattern similarity of verbal reports (R2).
Tests whether each report's Mistral-7B embedding is more similar to its OWN
excerpt's consensus narrative than expected by chance, via a permutation test on
shuffled excerpt labels. Carved from the full package's behavioral module (R1 and
R3 are out of... |
8d2f8e2138c497a870319aa59bd93a5baf23d18ba5f01b9ddef4fd8c2020f9f4 | Python | 2,654 | 99 | import base64
import codecs
import logging
import os
from io import BytesIO
from ..types import Any
logger = logging.getLogger(__name__)
PNG_FORMAT = "png"
JPG_FORMAT = "jpeg"
GIF_FORMAT = "gif"
PDF_FORMAT = "pdf"
SVG_FORMAT = "svg"
EPS_FORMAT = "eps"
B64_FORMAT = "base64"
def make_snapshot(
engine: Any,
f... |
95de1136585768489e2bca4913a6520a2153749d3c74faf22abdc5441fc7981c | Python | 2,654 | 86 | #!/usr/bin/env python
# ENCODE frac mito
# Author: Jin Lee (leepc12@gmail.com)
import sys
import os
import argparse
from encode_lib_common import (
log, ls_l, mkdir_p, strip_ext)
from encode_lib_log_parser import parse_flagstat_qc
def parse_arguments():
parser = argparse.ArgumentParser(
prog='ENCODE... |
9281f58df201cab51c41889da344459b600a70c60989daae3965988aec3e5ea8 | Python | 2,655 | 77 | from __future__ import annotations
from typing import TYPE_CHECKING
from unittest.mock import MagicMock
from poetry.core.packages.utils.link import Link
from poetry.packages.direct_origin import DirectOrigin
from poetry.utils.cache import ArtifactCache
if TYPE_CHECKING:
from pathlib import Path
from pytes... |
4d09df377d0579fe3de474210cb107665bf7329b17616c0e03ee32e747e40848 | Python | 2,656 | 80 | import torch.nn as nn
import torch
class SeparableConv2d(nn.Module):
def __init__(self,
in_channels,
out_channels,
kernel_size=1,
stride=1,
padding=0,
dilation=1,
bias=False):
super(Separ... |
646ce496031f3ea2d6bcf261793cfa64102f6be89eca6cdf0a4e49feadb9cc0a | Python | 2,656 | 81 | """Smoke tests for the hippie-cli entry point.
These cover the user-facing CLI surface declared in pyproject.toml:
hippie-cli validate-data <dir>
hippie-cli embed --datasets-root ... --datasets ... --output ...
hippie-cli predict --reference ... --query ... --output ...
The embed/predict tests are gated b... |
ff3336000c8db6f3b8930870517e42a1d3899a75ed09a56e1dfac5712904a400 | Python | 2,656 | 92 | #
# 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 .iadc import IADC
# Importing the different adc models so _create_adc works correct... |
1f07378ea62e4e27aa9db7053afc4648ded4262c84852a2ac9d60c9a611ef518 | Python | 2,657 | 81 | # Copyright 2016 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... |
4924344b447921dd409334c2272771c03cd950302eaf225da00b9ba615e94a3e | Python | 2,657 | 80 | # 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
from operator import attrgetter
import torch.distributed as dist
import torch.nn as nn
from ..pq.utils import attrsetter, get... |
7b12fdf475285ac0da61c7dc118409ca638061d6573f8e8b09ac241ef08f7029 | Python | 2,658 | 71 | # Copyright 2020 The Lucent Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable ... |
f6d01d96f0ddc45bc8101881bc17d071223067ed41df7154f7c1740127f1ab44 | Python | 2,659 | 86 | # @license
# Copyright 2023 Google Inc.
# 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... |
a84474c8b536e34be844ddac8f73e14d1967399ab15af38eb2e21e1f45627ac2 | Python | 2,660 | 83 | # Copyright (C) 2025 ETH Zurich, Moritz Thürlemann, and other AMP contributors
import os
import torch
import numpy as np
from dataclasses import dataclass, fields
from torch.utils.data import Dataset
from torch import Tensor
from utilities.Utilities import detrace
class Dataset(Dataset):
def __init__(self, fol... |
828641ea924d55be77fd200a485168d2f961b7c9c449473ea5688d2b0efb7e4d | Python | 2,661 | 93 | from argparse import ArgumentParser
from pathlib import Path, PosixPath, WindowsPath
import numpy as np
import pandas as pd
def main(
csv, os, audio_path_parent=None, spect_path_parent=None, annot_path_parent=None
):
""" "move" the paths in a .csv file saved by `vak prep`,
by keeping the filename but cha... |
64c5121f71a26024fc95c7acd496b12ca2d719b007f3d2fb71e56f8d8a859578 | Python | 2,662 | 98 | import numpy as np
import pandas as pd
import pytest
from skbase.lookup import all_objects
from pgmpy.ci_tests import BaseCITest, ChiSquare, FisherZ, IndependenceMatch, Pearsonr, get_ci_test
def test_ci_registry():
all_tests = [
ci_test.get_class_tag("name")
for ci_test in all_objects(
... |
69dfe1abd884981a855c2f13f63342e664b63fb15b92641edf52a6a8e096a616 | Python | 2,662 | 82 | #
# 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
#
import os
import numpy as np
import cv2
from MLPerf_cal_images import get_cal_fns
from ... |
bc5e1d48d115211de09b2a952c297dbc338bdd332b1fdc3a9b3f4135893d13b2 | Python | 2,662 | 74 | from ... import types
from ...charts.chart import Chart
from ...globals import ChartType
class Chord(Chart):
"""
<<< Chord >>>
The chord diagram visually presents the flow and weights
within complex relationship networks, making it particularly
suitable for multidimensional relationship analysis ... |
02ad3e837af5d0fc9811bb2be32ee07ffdbb15f0282dc863e21acd2ada3ab1e8 | Python | 2,663 | 87 | import xarray as xr
import click
import numpy as np
import matplotlib.pyplot as plt
import matplotlib.patches as patches
from skimage.segmentation import mark_boundaries
from matplotlib.widgets import Button
def interactive_plot(cleanqueen, queenframe):
selected_values = set(np.unique(cleanqueen[cleanqueen > 0])) # ... |
7c825ceb9caa51fba4a75f159145b4b999fe3b588ab78a4d3b232b9607071c31 | Python | 2,663 | 78 | #!/usr/bin/env python3
"""Exercise non-interactive analyzer discovery and Qt initialization.
This runner uses the real analyzer file-discovery code and Qt initialization
dialog in offscreen mode. It does not enter the GUI event loop, open a window,
or launch calculations.
"""
from __future__ import annotations
impor... |
a08383dd6cc7112c5bd802501a0ab85c8bd5219b1e40b5235f7736fd23aa8c36 | Python | 2,663 | 89 | import matplotlib.pyplot as plt
import numpy as np
# Function to read data from a file and calculate mean, min, and max
def calculate_stats(file_path):
with open('./date/'+file_path, 'r') as file:
data = [float(line.strip()) for line in file if line.strip()]
mean = np.mean(data)
min_val... |
b267cc0e21b2714c025c6100e2f66bc41c096e19ccf52ab9195ee32cdaff06bf | Python | 2,665 | 63 | # -*- coding: UTF-8 -*-
"""Base class and shared context for GOEA term-scoring algorithms.
A GOEA algorithm turns the per-term gene sets of a study into one uncorrected
p-value per GO term. The default, `classic`, scores every term independently.
Algorithms that exploit the GO DAG topology (`elim`) instead score terms... |
6f046f94bac2434bf8adddaffe5f07ae096af5867f09f453c0f2850f2099e945 | Python | 2,666 | 87 | """
This is an alternative version of MatrixManager. This is way faster but consumes more memory.
The ordinary MatrixManager performs well enough when a gene's data is queried only once as in MetaXcan,
and is memory efficient. This one, on the contrary, organizes data in a way that is fast to query but takes up more me... |
cda7e528d7513f49e0e41f5de9e17ad182da748a0ee4271be7f6c9053121a4f6 | Python | 2,668 | 71 | #!/usr/bin/env python3
# MIT License
#
# Copyright 2022 Broad Institute
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use... |
efba43b281731ca5ab8b3d227617a22fa7001f2ff8ada5724d07f8f17923b512 | Python | 2,669 | 73 | #!/usr/bin/env python3
import argparse
import os
from collections import defaultdict
def intron_chain_key(fields):
"""
Group reads by splice junctions only, ignoring variable TSS/TTS.
Multi-exon: 'chrom:strand:e1end-e2start,e2end-e3start,...'
Mono-exon: 'chrom:strand:start-end:mono'
"""
chrom... |
92bd1260d2596b01e062be2b566619fc993b4bc94db71226a7847929c85331a5 | Python | 2,670 | 69 | from typing import List, Mapping, Optional
import torch
import re
def load_pretrained(
model: torch.nn.Module,
pretrained_params: Mapping[str, torch.Tensor],
strict: bool = False,
prefix: Optional[List[str]] = None,
verbose: bool = True,
) -> torch.nn.Module:
"""
Load pretrained weights to... |
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