sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
bbdc964ed3787cf5c1f53c90e9cdea9b8336ef02c524631b6d23a31afeb247a4 | Python | 4,576 | 122 | """Logging setup shared by the command-line entry points."""
import logging
import shlex
from pathlib import Path
class WarningSpacingFormatter(logging.Formatter):
def __init__(self, *args, **kwargs):
super().__init__(*args, **kwargs)
self._previous_was_warning = False
def format(self, recor... |
a07d8f211dc89b7899b8252f738cc3292273f69c8a315359a0b909d4de01d1e2 | Python | 4,578 | 135 | #!/usr/bin/env python3
# import models/encoder/decoder to be tested
from examples.speech_recognition.models.vggtransformer import (
TransformerDecoder,
VGGTransformerEncoder,
VGGTransformerModel,
vggtransformer_1,
vggtransformer_2,
vggtransformer_base,
)
# import base test class
from .asr_test... |
d3e37c5627cf24ea57f9398e4c5e66849058d4c25e6db12881f74e905a9a86e1 | Python | 4,580 | 138 | import difflib
import os
import typing
import urllib.request
import simplejson as json
class FuzzyDict(dict):
"""Provides a dictionary that performs fuzzy lookup"""
def __init__(self, cutoff: float = 0.6):
"""Construct a new FuzzyDict instance
items is an dictionary to copy it... |
23f9ef7fab54a5c80931f86a0c6d345a19a302286a5bde082c0ec9764cdc1158 | Python | 4,583 | 146 | """``label_audit.py``: the guard-check script over the index it audits.
`build_index` used to be a hand-copy of
`d3text.cli.precompute_token_labels.build_index`; the identity check below is
what would have caught that. The digest checks exercise `check_store_index`
directly rather than `main()`'s stdout, per the same ... |
d23707ba6265549d620de278babdf5d17a39af8fa1aaadbf1642a63a65206f08 | Python | 4,584 | 143 | import os
import numpy as np
import torch
from torch.utils.data import DataLoader
from lightning.pytorch.loggers import TensorBoardLogger
from lightning.pytorch.callbacks import ModelCheckpoint, EarlyStopping
from lightning import LightningModule, Trainer
from sbi.neural_nets import posterior_nn
from data_handlers im... |
e2b913092ba960995e41b84a40572d25f66414c4dc737ae22cec38139f890954 | Python | 4,584 | 158 | # @license
# Copyright 2017 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... |
7e0fc94dad6dfaa318ce4ed252e58c126ba2cd64c1a6c315b3ba65a79559eeff | Python | 4,585 | 124 | # 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 math
from dataclasses import dataclass
import torch.nn.functional as F
from fairseq import utils
from fairseq.logging import metrics
f... |
3cb3d3128e69103e5f16afef925ce96c4646b3b09a51cba6b8c6f1a8bf52eae0 | Python | 4,586 | 156 | # 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.
"""
softmax-based NCE loss, used by this project.
"""
import torch
from torch import nn
from .loss import Loss
class NCE(Loss):
def _... |
6e70fcf38ed671f0de47f2cdf56625b2daf0f29b6e4eb1da5598b67703cf4c07 | Python | 4,587 | 126 | # 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
from dataclasses import dataclass, field
import torch.nn.functional as F
from fairseq.logging import metrics
from fairseq.tasks ... |
10e0eb3753e94fec9dc09e496ae1e301bfd70def535886354a6d28189161e0b3 | Python | 4,589 | 119 | # Copyright (c) Microsoft Corporation.
# Licensed under the MIT License.
from typing import Literal, Optional
import torch
from mattergen.diffusion.corruption.sde_lib import SDE, maybe_expand
from mattergen.diffusion.data.batched_data import BatchedData
from mattergen.diffusion.training.field_loss import aggregate_p... |
e44ff992ac1e84a4f3189b84285acb28997fcdc2d3358c17a8bde7ed4e3f6f51 | Python | 4,590 | 110 | #!/usr/bin/env python3
"""Builds the schema.py module."""
# This needs to have no dependencies on the BPReveal module since this is
# executed while BPReveal is being set up and it won't be on the path yet.
import sys
SCHEMA_HEADER = '''
"""Auto-generated schema validators for the JSON used by the main CLI."""
# DO N... |
2bd4626164a9f2399d06203d85c7876c0c61eafcc4bf3f8b93afe22684c7fcb9 | Python | 4,591 | 144 | # -*- coding: utf-8 -*-
import os
from .utils import load_json, get_jinja_tpl, TPL_PATH
from operator import itemgetter
class Dashboards(object):
def __init__(self, jsonPaths, tags):
self.jsonPaths = jsonPaths
self.tags = tags
def run(self, _type, dashTags):
# Usefull directories
... |
48e184f194e05555fa2fff44e41d9bc038b6f03560c6b3c69f08bb9c507f58a3 | Python | 4,591 | 122 | """Deprecated compatibility shim for :class:`pgmpy.causal_discovery.PC`."""
from collections.abc import Callable, Hashable
import networkx as nx
import pandas as pd
from pgmpy.base import DAG, PDAG, UndirectedGraph
from pgmpy.causal_discovery import PC as _PC
from pgmpy.estimators.BaseConstraintEstimator import Base... |
94b3952a4b8ab56cc23083383efb0d49607f5548e25c6d7a3b9d2069be7b2374 | Python | 4,593 | 117 | """Figure 5 panel A — cross-species method comparison bars (Lisberger→Hull).
KNN balanced accuracy for Lisberger (macaque) → Hull (mouse) transfer,
six methods including VAE baselines.
Outputs:
figures/29_figure_5_cross_species/panel_a_method_bars.{svg,png}
"""
from __future__ import annotations
from pathlib impo... |
5e7cb7d50a4df2d670f13f63932f60cba6d55fb13fb7b16a57d24372f1878179 | Python | 4,594 | 140 | """
Byte pair encoding utilities from GPT-2.
Original source: https://github.com/openai/gpt-2/blob/master/src/encoder.py
Original license: MIT
"""
import json
from functools import lru_cache
@lru_cache()
def bytes_to_unicode():
"""
Returns list of utf-8 byte and a corresponding list of unicode strings.
... |
bdee53a00b176562e69ce5ede58f4c4f7ac9804177a1ecf86af26a3b0903dc77 | Python | 4,594 | 114 | # 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... |
e6d96405d09d116275725bd0cbc0e1c37048f89b58a0925a4633417f5a6739c9 | Python | 4,594 | 100 | #!/usr/bin/env python
# PYTHON_ARGCOMPLETE_OK
"""Create a (brain) mask for the given DWI. This uses the median-otsu algorithm."""
import argparse
import logging
import os
import mdt
from argcomplete.completers import FilesCompleter
import mot.configuration
from mdt.lib.shell_utils import BasicShellApplication
from mot... |
140eefdc5a581e37d77273c3cc0cdc8e279f7ac8b3b716d2825dc633936366d5 | Python | 4,595 | 121 | #!/usr/bin/env python
"""Score the dictionary linker on enzymeNER's spans, grounded through Expasy.
The weakest of the three external evaluations, and the caveat is printed with
every number: enzymeNER marks spans without naming them, so the gold EC number
is itself a dictionary lookup. That the dictionary is Expasy's... |
208590926c21fa3088227152a3655f982d01670f9d44df9a35687e4f4c30a47b | Python | 4,595 | 125 | import unittest
from datetime import datetime
from unittest.mock import patch
from pyecharts.charts import Bar
from pyecharts.options import InitOpts, RenderOpts
from pyecharts.globals import CurrentConfig, Locale
from pyecharts.charts.base import Base, default
from pyecharts.options.series_options import AnimationOpt... |
947a8e4bf9dd7ad74ec172d5fa9768fcd090c2b6e89c9f0ac394a57df1bafabf | Python | 4,600 | 92 | #!/usr/bin/env python3
"""A simple utility to revcomp-augment data."""
import argparse
import pybedtools
import numpy as np
import pysam
import pyBigWig
from bpreveal import logUtils
from bpreveal import utils, bedUtils
logUtils.setVerbosity("INFO")
def getParser() -> argparse.ArgumentParser:
"""Build the parser ... |
7afea210c6cff8be5de26543755ea189a16ae0b536617d88371ac019a9db5225 | Python | 4,604 | 129 | from __future__ import annotations
from typing import TYPE_CHECKING
from typing import ClassVar
from cleo.helpers import argument
from cleo.helpers import option
from poetry.core.constraints.version.version import Version
from poetry.core.version.exceptions import InvalidVersionError
from poetry.console.commands.com... |
c28a38e0559e9003305cc6167f4887b9a8297c2956914034d2d981bef37d29cb | Python | 4,607 | 144 | import logging
from typing import Tuple, List
import numpy as np
from statsmodels.stats.multitest import multipletests
from scipy import sparse
import loompy
class FeatureSelectionByEnrichment:
def __init__(self, n_markers: int = 10, mask: np.ndarray = None, labels_attr: str = "Clusters", findq: bool = True) -> Non... |
3d947adb6afc57e4fd7998f2b388b28aa09004ab9df6c1247f74e5add6babe13 | Python | 4,608 | 118 | from __future__ import annotations
import argparse
import json
from pathlib import Path
import anndata as ad
import pandas as pd
import scvi
import torch
from scvi.external.stereoscope import RNAStereoscope, SpatialStereoscope
def parse_args() -> argparse.Namespace:
parser = argparse.ArgumentParser(description=... |
5dee2aec03c98cf15785bc0351c71d008b87fa5362a353a09be3118c15e42b2a | Python | 4,609 | 111 | import numpy as np
import math
# --- You can add your own model classes here ---
# Each model class should contain:
# - the attribute .name
# - a function .generate() returning a prf_dict with at least key 'prfs'
# that is then used by
# - a function .predict() to create predictions for each pRF
# --- Preset ... |
e3d705eb63d539bced3b3d98c3a948f772b14466ed04fceb800cda438754311f | Python | 4,616 | 109 | #!/usr/bin/env python3
# Copyright (c) 2018-present, Facebook, Inc.
# All rights reserved.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
import codecs, sys, time, math, argparse, ot
import numpy as np
from utils import *
parser = argparse... |
f36817188ffa5feb827ef76da2e1be837596ede07b01260589e2193e09eb63b1 | Python | 4,616 | 130 | import os
import tempfile
import unittest
import yaml
from pydantic import ValidationError
from simulation_encoder.dataclass.config_schemas import (
HyperparameterConfig,
MainConfig,
ModelArchitectureConfig,
)
from simulation_encoder.utils.yaml_utils import (
load_hyperparam_yaml,
load_model_yaml,... |
838e48aab0e079f8b65cc00006f2e06b9d732094604cb5494974ca3a2b7b656f | Python | 4,622 | 146 | from __future__ import annotations
from typing import TYPE_CHECKING
import pytest
if TYPE_CHECKING:
from cleo.testers.command_tester import CommandTester
from poetry.config.config import Config
from tests.types import CommandTesterFactory
from tests.types import MockedPoetryPythonRegister
@pytest... |
ad44114b3c8ebf4e149da2faab1db2da16fcfcb7e2a83616e9863b16d7647ae6 | Python | 4,623 | 143 | # Copyright (c) Facebook, Inc. and its affiliates.
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
from multiprocessing import Pool
import os
from collections import defaultdict
from itertools import starmap
import torch
from npy_append_arr... |
ecf6a16db8c61e3c739ac978445d7dd2ad8f16f305bbdebbcd91ac4edebd3e79 | Python | 4,623 | 114 | #!/usr/bin/env python3
"""Print a calculation-combination plan without running any calculations.
This is intentionally a planning tool. It resolves matrix rows to the
manifest command and records input overrides, but it never copies examples,
edits inputs, launches gmx_MMPBSA, or creates result directories.
"""
from... |
f44ddcdfb2e3f85ee952ddb77c20cce5a362d3533233e5b9626a43facdde8b6f | Python | 4,623 | 76 | from typing import Tuple
import torch
from nnunetv2.training.dataloading.data_loader_2d import nnUNetDataLoader2D
from nnunetv2.training.dataloading.data_loader_3d import nnUNetDataLoader3D
from nnunetv2.training.nnUNetTrainer.nnUNetTrainer import nnUNetTrainer
import numpy as np
class nnUNetTrainer_probabilisticOv... |
fa8ffc03168cb678c85d9194f3745430e61ea0e5acf9aa04a4645b20e68de670 | Python | 4,623 | 129 | #!/usr/bin/env python3
# MIT License
#
# Copyright 2025 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... |
d862fb34388dff64354ca3e44d516d0c1f8f65161d84020558513e7e12bce091 | Python | 4,624 | 138 | #!/usr/bin/env python3
"""Invoked by `build.sh` inside a container to build `neuroglancer_draco.wasm`.
Expects the directory of the Neuroglancere repository that contains this script
to be mounted as the current working directory inside the container.
Expects /usr/src/draco to contain the unpacked draco source code ... |
1f7f39bc7d8fac8275c7fefbb3dbd0f1ab5463aaa0c592b39a05a4ea6f870026 | Python | 4,627 | 118 | """Product gene lists with ASCII art sections and GO IDs for each gene product."""
import sys
import collections as cx
from goatools.grouper.aart_geneproducts_one import AArtGeneProductSetsOne
__copyright__ = "Copyright (C) 2016-2018, DV Klopfenstein, H Tang, All rights reserved."
__author__ = "DV Klopfenstein"
cla... |
aa423e70235569e303dda273942f2b24d50c4c7aeca1da62598e3a6423f9491c | Python | 4,629 | 123 | # 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 copy
import unittest
import tests.utils as test_utils
import torch
from fairseq.criterions.cross_entropy import CrossE... |
4fac0eb3e9b422d259763d58665ff2f1ca709ac8d02f3861e3773744678e45ed | Python | 4,635 | 137 | """Train and evaluate the OCE v1.0.0 (JPCL submission) on percolation clusters.
We re-use the design-matrix code from `oce_v1.0.0` *unchanged* — only the
INPUT differs (carbon-only clusters with arbitrary connectivity instead of
small organic molecules). This is the cleanest possible application of the
published meth... |
059c5a875d8f99084de418b537b0dee732f199a1da628cdfea3787aa5bf23a9e | Python | 4,636 | 152 | """``check_imports.py``: the gate that catches an unimportable package.
Exercised against throwaway projects rather than against this one, for two
reasons. Importing the real entry points costs half a minute, and
`test_entry_points.py` already starts every console script; and the failure
this gate exists for cannot be... |
0c6788feb44bb912f0e7ad9bc7a01387f2cae1510bc8fc6aaf3b93057e067fff | Python | 4,638 | 119 | import streamlit as st
import joblib
import os
import numpy as np
from pathlib import Path
from PIL import Image
from collections import defaultdict
import pandas as pd
import time
from msi_visual.app.utils.pipeline import create_pipeline
from msi_visual.app.utils.extraction import get_extraction
import wx
... |
baba718b04f49c1fc56af131e27429bee78e7d91d636a708685b07a8a88f09c2 | Python | 4,639 | 128 | import numpy as np
import pandas as pd
import pytest
from pgmpy.causal_discovery import ANM
@pytest.fixture
def nonlinear_data(n=1000):
"""Generate additive-noise data with X -> Y, where Y = X ** 3 + noise."""
rng = np.random.default_rng(0)
x = rng.uniform(-2, 2, n)
y = x**3 + rng.normal(0, 0.5, n)
... |
54fc5555e77cd1636d1d4d1f790af590757b33d1946a19d57bf06efd6e170703 | Python | 4,641 | 121 | # Copyright (c) Facebook, Inc. and its affiliates.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
import math
import torch
import torch.nn.functional as F
from fairseq import utils
from fairseq.logging import metrics
from fairseq.criterion... |
d03a8e2eb695c3c6ec309c6b50005d91e653b1a664b98a9740964199b49e890d | Python | 4,644 | 104 | """Used to find all genes or gene products annotated w/GO terms that match a regex."""
import sys
from goatools.obo_parser import GODag
__copyright__ = "Copyright (C) 2010-2018, DV Klopfenstein, H Tang, All rights reserved."
__author__ = "DV Klopfenstein"
class GoSearch(object):
"""Returns GOs matching a regex p... |
4770daf0ee41c7f8ae76dabf6d5471866a20acad6c30bf469939e61ce82a97af | Python | 4,645 | 124 | # 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 bisect
import numpy as np
from torch.utils.data.dataloader import default_collate
from . import FairseqDataset
class ConcatDataset(... |
536493374dd2fe92d188dc5b84e224a0b95150783d2c522fe417259001e0c689 | Python | 4,647 | 165 | from __future__ import annotations
import os
from typing import TYPE_CHECKING
import pytest
from cleo.io.null_io import NullIO
from cleo.testers.application_tester import ApplicationTester
from cleo.testers.command_tester import CommandTester
from poetry.installation import Installer
from poetry.utils.env import M... |
6ce5b2e43a9a9b779aada6ffe1bf5e06673d41a4afaebfdd0cc6fa28ce6976df | Python | 4,647 | 127 | from matplotlib import pyplot as plt
from matplotlib import gridspec
import seaborn as sns
sns.set_style("white")
from theano import config
import numpy as np
from data_funcs import data_resamp
from utils import *
def plot_od(od, label = None, col = None):
plt.plot(*zip(*sorted(od.items())), label = label, color... |
0199cd67f22541624d5764dc2712a341eef767b8532ad77fc2e1bf4655031a53 | Python | 4,648 | 125 | # 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 contextlib
import logging
import os
import tempfile
import unittest
from io import StringIO
from unittest.mock import patch
from fairs... |
4d315217fb99817c3234b9adcdffc79c16641a7b20bc1425a5dba0b78af4c3bf | Python | 4,648 | 115 | from ... import options as opts
from ... import types
from ...charts.chart import Chart
from ...globals import ChartType
class Funnel(Chart):
"""
<<< Funnel >>>
Funnel diagram is suitable for one-way analysis of single process
with standardized business process, long cycle and multiple lin... |
96b4dae097f491f1c523bbe9d1450f0762d62d6624d849eba4df6d7096f7432e | Python | 4,648 | 96 | """Constants for the compositionality study repository."""
import os
from dotenv import load_dotenv
# Use dotenv to properly load device-dependent constants
load_dotenv()
HERE = os.path.dirname(os.path.realpath(__file__))
SOURCE_DIR = os.path.join(os.path.abspath(os.path.join(HERE, os.pardir)))
PROJECT_DIR = os.pat... |
288ba908703c26e7b6bd56e9e14909b3bf8a332c934d5c216fa6f2cd52e9e3c6 | Python | 4,649 | 124 | import argparse
import pandas as pd
import numpy as np
from typing import List, Tuple
def read_file(tsv_file: str) -> Tuple[List, pd.DataFrame]:
"""
Reads the input 4-column cosine similarity existing pairs TSV file in a pandas dataframe, generates all the unique PMIDs
and returns the dataframe.
Param... |
77b8c3aae31d90ff8f0ab8677639b049fb5d233c16a313a5f24c6b4e243df5fe | Python | 4,651 | 140 | import sys
from os import makedirs
from os.path import dirname, realpath, exists
current_dir = dirname(dirname(realpath(__file__)))
sys.path.insert(0, dirname(current_dir))
import pandas as pd
import os
from config_path import *
from analysis.data_extraction_utils import get_node_importance, get_data
from utils.loadin... |
10012e1d27129acb1c5addb9ea80d4d57ae7add1f71ed11f31fc02fa1b2a4920 | Python | 4,652 | 195 | import os
import nox
nox.options.default_venv_backend = "uv"
nox.options.reuse_existing_virtualenvs = True
nox.options.error_on_external_run = True
@nox.session
def lint(session):
session.run_install(
"uv",
"sync",
"--only-group",
"ruff",
env={"UV_PROJECT_ENVIRONMENT": se... |
30a2987c39d8a8925f510451145a27c89a51744103c942c780f6c168be8d12b8 | Python | 4,653 | 98 | #!/usr/bin/env python3
"""Hypergeometric disease-catalogue over-representation for the inverse-concordant pool.
Methods 4.8: "Disease-catalogue overlap of the full 94-gene discovery pool used a hypergeometric
test against the genes testable in both discovery layers." No script in the release performed it;
the earlier ... |
290824621fe5c1668c881e0a3bdf31c4612ddf04db19ac52b82e677e0f76fe15 | Python | 4,654 | 103 | """Cross-matrix synthesis (Paper #2): consolidate the three per-food benchmarks into one comparison
table + figure, highlighting where the interpretable KAN earns its place across chemically diverse
matrices. Reads paper2/results/<food>/{Table_cv,Table_holdout}.csv + <food>_meta.json.
Writes paper2/results/summary/. Ru... |
5dd766f8501666bcfcf82bfca6c3b90fd34a6c6397f0bb77ebe72a052d1e3422 | Python | 4,654 | 128 | # Copyright (c) Facebook, Inc. and its affiliates.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
import argparse
import editdistance
import re
import shutil
import soundfile as sf
import subprocess
from pathlib import Path
from examples.s... |
dd62a201a3d6bf32fca5d9dde0e3e4fd3db6aa6dd93fc2436fca3f88784ae1ac | Python | 4,656 | 130 | import pandas as pd
from sklearn.model_selection import train_test_split
import torch
from torch.utils.data import DataLoader, Dataset
from latent_model.loaders.encoded_csv_splits import train_val_test_ids_from_encoded_csv
class TimeSeriesDataset(Dataset):
"""Dataset for time-series or otherwise ordered data wit... |
bfaf819e3a3e1f38bc8a6713815a8e97cfb9de8bee78efdddbb9c2729576d29b | Python | 4,661 | 136 | # Copyright (c) Microsoft Corporation.
# Licensed under the MIT License.
from typing import Dict, Iterable, Protocol
import torch
from torch_scatter import scatter
from mattergen.diffusion.corruption.multi_corruption import MultiCorruption
from mattergen.diffusion.data.batched_data import BatchedData
from mattergen.... |
58f7867f051659f894b973c0c6f3ea5c5ca6b951725e6248b16474ec0a9a1b0f | Python | 4,664 | 140 | #!/usr/bin/env python
import networkx as nx
import numpy as np
import pandas as pd
from pgmpy.causal_discovery._base import BaseCausalDiscovery, _TreeSearchMixin
class ChowLiu(_TreeSearchMixin, BaseCausalDiscovery):
"""
Chow-Liu algorithm for learning tree-structured Bayesian networks.
Constructs the m... |
c2c020d607cba4f8646104e2d2e2a92959b081218684431add781d2591f2d49a | Python | 4,664 | 103 | import traceback
import click
import numpy as np
import xarray as xr
import zarr
from tqdm import tqdm
from ..utils.decorators import error_handler
from .ica_utils import compute_pca_ica
def chunk_pca_ica(dataset: str, chunk: int|None, slice_areas: xr.DataArray, chrom_subset, n_slices=36):
n_frames = slice_areas.... |
7c00b81b186987bae83ec6b4d765c4051b652a4103b0cd03bba6709736ff5100 | Python | 4,665 | 97 | #!/usr/bin/env python3
"""Assemble Supplementary Table S3 (per-series sex and age composition), Methods 4.2.
WHY THIS EXISTS. Methods cites Supplementary Table S3 for the sex and age composition of every
cohort, but no script assembled it: the delivered CSV was written by hand, so its per-series
percentages could not ... |
7dc5c78fd767ae8839a97376ad2dce464e4c79a6a46a8cff1a4e8fe84bdcf3bd | Python | 4,666 | 128 | # created by DebarpanB
# date 26th August, 2022
import argparse, configparser
import numpy as np
import pandas as pd
import pickle
import os
import random
from sklearn.decomposition import PCA
from sklearn.preprocessing import StandardScaler
from sklearn.ensemble import RandomForestClassifier
from sklearn.model_select... |
d7164e3ab3d665691b43953d8348c69b9c0d2e41be07528c20c27b0a2b43ceeb | Python | 4,670 | 140 | import seaborn as sns
sns.set_style("white")
import numpy as np
import pyspike
from utils import rebin
from data_funcs import sampleXY
import math
def get_pred_mse(model, cell, traces, samples, spikes, p_sample=None):
"""
Calculates the mse_rec_pred and mse_rec_truth metrics during training.
"""
buf... |
a172eb5850a58f3a1a5e51c7b74d21782a085ff00e4682ff27a51e704f5bf882 | Python | 4,672 | 127 | import torch
import torch.nn as nn
import torch.nn.functional as F
from .. import functional as vakF
__all__ = ["dice_loss", "DiceLoss"]
# adapted from kornia (https://github.com/kornia/kornia/blob/master/kornia/losses/dice.py)
# originally based on https://github.com/kevinzakka/pytorch-goodies/blob/master/losses.p... |
e4f051565cf5f82ef39cb2b6e71b747c482374ec250d74ec8389ec922fe00adb | Python | 4,673 | 125 | # encoding: utf-8
"""
@author: Jiayang Chen
@contact: yjcmydkzgj@gmail.com
"""
from torch import nn
import torch
from functools import wraps
class DownStreamModule(nn.Module):
"""
base contact predictor for msa
"""
def __init__(self, backbone_args, backbone_alphabet, depth_reduction="none",
... |
b67afbb8735ac38c3504613df89a6ddaa0583344fa0dab97482348c5c257f80f | Python | 4,674 | 138 | import pytest
import vak.config.trainer
class TestTrainerConfig:
@pytest.mark.parametrize(
'config_dict',
[
{
'accelerator': 'cpu',
},
{
'accelerator': 'gpu',
'devices': [0],
... |
80d2350bf2f4a048398992ef0304c5743d5260d15524796d68ef4cdab55bfbdf | Python | 4,676 | 126 | import numpy as np
import pandas as pd
import pytest
from pgmpy.causal_discovery import IGCI
@pytest.fixture
def nonlinear_data():
"""Generate near-deterministic data with X -> Y."""
rng = np.random.default_rng(0)
x = rng.uniform(0, 1, 500)
y = x**3 + rng.normal(0, 1e-3, 500)
return pd.DataFrame(... |
bdff4548cbc0937afff40dffa0195fdd193687d45de2e56312485703777a7035 | Python | 4,677 | 140 | #%%
import SimpleITK as sitk
import pydicom as pydicom
import json
import pandas as pd
import os
import numpy as np
import subprocess
from concurrent.futures import ProcessPoolExecutor, ThreadPoolExecutor, as_completed
NUM_WORKERS = os.cpu_count() // 2
from tqdm import tqdm
DATA_DIR = os.path.joi... |
9b158f834dd3e7f031e92972d748affced2269af08f836a2a1c38b4aa8d1ad65 | Python | 4,679 | 138 | from typing import Any
import numpy as np
class Trajectory:
"""A class that defines a trajectory through a latent space.
This class creates a trajectory through a latent space by connecting a sequence of points
(e.g., cluster centroids) with straight lines. The trajectory is parameterized by time,
w... |
84e4e7db7a8f98910507e68e5caa9952de89ba55759b8f4cae8b0dee97df3b5b | Python | 4,680 | 148 | import skimage.io as skio
import numpy as np
import torch
from torch.utils.data import Dataset, DataLoader
from src.utils.util import get_coordinate
from src.utils.dataset import DatasetSUPPORT
def normalize(image, mean_image=None, std_image=None):
"""
Normalize the image to [mean/std]=[0/1]
Arguments:
... |
48ae8a568b38595bcee746950bcf6f4e87d64ad17efbb7243e70e4516ea116d0 | Python | 4,683 | 110 | from typing import List
import torch
from e3nn.util.jit import compile_mode
#from nequip.data import AtomicDataDict
from ..data import AtomicDataDict
from nequip.data.misc import chemical_symbols_to_atomic_numbers_dict
from nequip.nn._graph_mixin import GraphModuleMixin
from nequip.nn.utils import scatter, with_edge... |
cbb90bba07dc4d338f4b2b902a7b6867af2252721fc2974c6596cf018d6d264f | Python | 4,687 | 173 | """
This module contains methods to analyse read data.
"""
"""
Copyright (c) 2019, 2022 [copyright holders here]
This file is part of NoSeMaze.
NoSeMaze is free software: you can redistribute it and/or
modify it under the terms of GNU General Public License as
published by the Free Software Foundation, either versi... |
33336970d48e82e586da7211bbbe0e3f0da2fce1d17571bc7a5cf3f372eb9155 | Python | 4,690 | 141 | import numpy as np
def constrainValues(input_array):
output_array = np.copy(input_array)
output_array[np.isinf(input_array)] = 0
output_array[np.isnan(input_array)] = 0
output_array[input_array > 1] = 0
output_array[input_array < 0] = 0
return output_array
def getNextMerge(c... |
91e23fc75617d5310431045e458238fb0ffbef5fe2acf53820aa3c3163f79071 | Python | 4,690 | 137 | """xtb GFN2 single-point and optimisation for radical carbon clusters.
We do NOT terminate dangling bonds. Instead, we let xtb treat the cluster
as a high-spin radical molecule by passing `--uhf` = parity of the total
electron count (so xtb finds the lowest-energy state of the correct
spin-parity).
Note: GFN2 with t... |
40148324edd839a80436630ecad33955efe10dd81c33a786477bb1b96abeb260 | Python | 4,691 | 147 | import pytest
from pathlib import Path
from scgpt.tokenizer import GeneVocab, get_default_gene_vocab
from scgpt.tokenizer.vocab_compat import (
BuiltinVocab,
gene_vocab_base_backend,
torchtext_import_succeeded,
get_vocab_info,
is_torchtext_vocab,
from_torchtext_vocab,
)
def test_gene_vocab():
... |
ae244364f7e8212aca5e3b74f372c3465966ed473aaf7b1c4f4fe16b0fc8bb37 | Python | 4,691 | 115 | import itertools
from ... import options as opts
from ... import types
from ...charts.chart import RectChart
from ...globals import ChartType
class Scatter(RectChart):
"""
<<< Scatter >>>
The scatter diagram on the rectangular coordinate system can be used to
show the relationship betwe... |
3d738cfce17b8039373a92ac5ecfd4828853e2683dfb4bc131691e47d72bb1ed | Python | 4,692 | 145 | # 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 dataclasses import dataclass
from typing import Dict, List, Optional
import torch
from fairseq.dataclass import FairseqDa... |
63f85c57c1558cd3a9128a45b559da863d31e01fffc0099c7151e3f4a256b518 | Python | 4,695 | 167 | #!/usr/bin/env python3
# MIT License
#
# Copyright 2025 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... |
ecfc3dad9fb410abcb69e31dc161e5560de7249bc7524add3ff0b752350b5fbf | Python | 4,695 | 157 | from abc import abstractmethod
from functools import reduce
from opt_einsum import contract
class BaseFactor:
"""
Base class for Factors. Any Factor implementation should inherit this class.
"""
def __init__(self, *args, **kwargs):
pass
@abstractmethod
def is_valid_cpd(self):
... |
fa389e00bb21607b856223514858d7bed265969753925dec0debeaed899b94c7 | Python | 4,696 | 101 | #! /usr/bin/env python
import os
import logging
import numpy
from timeit import default_timer as timer
import pandas
from metax import __version__
from metax import Logging
from metax import Exceptions
from metax import Utilities
from metax.predixcan import MultiPrediXcanAssociation
from metax.predixcan import Utili... |
48af9a53d1e075ce08d21e8fec71f2cf83ea4d44cbefbb2fc6c4df30354e59dd | Python | 4,699 | 157 | # 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 ... |
884e2b5f8261c2905922a858b4e9036ad728ffdc955fd86e0e127070dcc7bd40 | Python | 4,700 | 123 | from ... import options as opts
from ... import types
from ...charts.chart import Chart
from ...globals import ChartType
class Radar(Chart):
"""
<<< Radar >>>
Radar maps are mainly used to represent multivariable data.
"""
def add_schema(
self,
schema: types.Sequen... |
d054b7cf29b198fc66f103cdbb99efba119e5f6587a041ec91a1ba346debb618 | Python | 4,703 | 125 | import os
import pickle
import warnings
from typing import Literal
import numpy as np
import torch
from anndata import AnnData, read_h5ad
from scvi import settings
from scvi.data._download import _download
def _load_legacy_saved_gimvi_files(
dir_path: str,
file_name_prefix: str,
load_seq_adata: bool,
... |
dd56d3eb6fa189a577e56e309c7f186114e3b31e7042d0faf538a67a719bde39 | Python | 4,703 | 151 | from __future__ import annotations
from typing import TYPE_CHECKING
from typing import ClassVar
from cleo.helpers import argument
from cleo.helpers import option
from cleo.io.outputs.output import Verbosity
from poetry.console.commands.init import InitCommand
from poetry.console.commands.show import ShowCommand
if... |
aec7018faac2db1a3330d7d9fae0c4a449c6086ee19c842a7fe117024920751a | Python | 4,704 | 104 | from typing import Tuple, List
import numpy as np
import loompy
class AutoAutoAnnotator:
"""
Automatically discover suitable auto-annotation marker combinations
"""
def __init__(self, pep: float = 0.05, n_genes: int = 6, genes_allowed: np.ndarray = None) -> None:
self.pep = pep
self.n_genes = max(2, n_genes... |
cfc355695d2a1650b3d8578695163f10e99e616ea9ebcf237c3d072e1c925f67 | Python | 4,704 | 115 | import os
import functools
import unittest
import toml
import torch
import medaka.architectures
import medaka.architectures.base_classes
import medaka.features
import medaka.models
from medaka.test.test_sample import get_test_samples
import medaka.torch_ext
__model_config__ = os.path.join(os.path.dirname(__file__),... |
972917f797fc47d4b8dbf6e921b951e18aa05e0685c327ec6f31b802065c3880 | Python | 4,706 | 135 | # 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... |
139d1f21921b9639af25a57bc920075bac24520c33bae4d4e98ab1313877678b | Python | 4,707 | 125 | # Copyright 2018 The Lucid 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 l... |
745820b817ee6135b6866df3a73d34093378ec0f9bb415b70389b451bf1d02ee | Python | 4,708 | 125 | import torch
import torch.nn.parallel
import numpy as np
import torch.nn as nn
import torch.nn.functional as F
from ..layers.convolutions import Convolutional
class Downsample(nn.Module):
def __init__(self, pad_type='reflect', filt_size=3, stride=2, channels=None, pad_off=0):
super(Downsample, self).__init... |
15597ca842424acbdc3e4b68d3b89383d8b7f83ae5622e44128c034aae054a6b | Python | 4,709 | 180 | import networkx as nx
import numpy as np
import pandas as pd
import pytest
from joblib.externals.loky import get_reusable_executor
from pgmpy.causal_discovery import ChowLiu
from pgmpy.factors.discrete import TabularCPD
from pgmpy.models import DiscreteBayesianNetwork
from pgmpy.sampling import BayesianModelSampling
... |
23c50ab32e4a4767921b1e003fbdaf2d9caf1303b6fc831359ec0bd089966ea3 | Python | 4,709 | 139 | # Copyright (c) Facebook, Inc. and its affiliates.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
"""isort:skip_file"""
from .dictionary import Dictionary, TruncatedDictionary
from .fairseq_dataset import FairseqDataset, FairseqIterableDat... |
80b4d40bd3a11229cd1d4a9438016eb2703f1b72c7283fb02f90989e205eaffe | Python | 4,709 | 132 | import argparse
import json
from collections import defaultdict
import os
from tqdm import tqdm
import sys
import subprocess
import re
import math
import numpy as np
import editdistance
from sklearn.preprocessing import StandardScaler
from multiprocessing import Pool
from functools import partial
import random
cer_lan... |
d8efe021cc3366238dd5c9041050b2f18f0692bdf83a9032f1f01525cd12c88a | Python | 4,710 | 131 | #
# 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 numpy as np
from scipy.optimize import minimize
import time
import os
# Use th... |
51985b3ba4f438a9afb431dc0b43c678695c18df4872f74dff19202ec5253fbb | Python | 4,713 | 167 | """
Constants that might be used by multiple scripts
"""
import numpy as np
# how many times each image was shown
N_REPEATS = 3
SUBJECTS = ["01", "02", "03", "04", "05", "06", "07", "08"]
# layer names for different models
RESNET18_LAYERS = (
["relu", "maxpool"]
+ ["layer1.0", "layer1.1"]
+ ["layer2.0", ... |
5b1d239ad4c4c096e9b7ed432252a1f4f370b4f9616ca45568b33a3c6e02e83d | Python | 4,713 | 111 | from PIL import Image
from sklearn.decomposition import NMF, non_negative_factorization
import cv2
import numpy as np
from matplotlib import pyplot as plt
from msi_visual.normalization import spatial_total_ion_count, total_ion_count, median_ion
from msi_visual.visualizations import visualizations_from_explanati... |
8aaf3c58eb16f15305be396f5830560396d7a1160d2441ddad3b7d30403854f2 | Python | 4,713 | 126 | """Benchmark OCE vs xtb: speed comparison + scatter plot.
Reports:
- per-molecule prediction time for OCE
- per-molecule single-point time for xtb
- speedup factor
- scatter plot of E_OCE vs E_xtb on the test set
"""
from __future__ import annotations
import time
from pathlib import Path
import matplotlib
ma... |
a72cb6e6059842d902167fbe0fe5708d20a5b37868f0c1cbde1416763f59acc5 | Python | 4,713 | 79 | #!/usr/bin/env python3
"""Literature-standard pseudobulk inputs for the brain (Jaekel GSE118257) and CSF/blood
(Beltran GSE127969) cohorts, so all three single-cell cohorts are processed the same way.
Jaekel : expr.txt.gz holds RAW integer UMI counts -> SUM per patient x cell type (muscat standard).
Region ... |
44738a74f1099230ce1b459a439f7453ae171525b3568a7f65e419b5337c31f7 | Python | 4,716 | 96 | # -*- coding: utf-8 -*-
# Form implementation generated from reading ui file 'UI/ConcGNGUI.ui'
#
# Created by: PyQt5 UI code generator 5.5.1
#
# WARNING! All changes made in this file will be lost!
from PyQt5 import QtCore, QtGui, QtWidgets
class Ui_Form(object):
def setupUi(self, Form):
Form.setObjectNa... |
ed79dabcd02fab19fe934df9c01c0d41fe9d41cd910c504b9061ebc49dd963a2 | Python | 4,718 | 103 | import matplotlib
from batchgenerators.utilities.file_and_folder_operations import join
matplotlib.use('agg')
import seaborn as sns
import matplotlib.pyplot as plt
class nnUNetLogger(object):
"""
This class is really trivial. Don't expect cool functionality here. This is my makeshift solution to problems
... |
eb164ef86a1c0dd511ae070a0274c43ba802075c50842bb7c47925a061769fcc | Python | 4,722 | 144 | import os
import numpy as np
import pandas as pd
import pytest
from pgmpy.ci_tests import Pearsonr
from pgmpy.factors.continuous import LinearGaussianCPD
from pgmpy.models import LinearGaussianBayesianNetwork
@pytest.fixture
def pearsonr_data():
rng = np.random.default_rng(seed=42)
df_ind = pd.DataFrame(rn... |
edf6ffdeb9984684a8702eae41d4e6f19a65aaf5a8ae61408208ab6d6da3f4a8 | Python | 4,723 | 153 | # 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... |
19779585fecadca54145881c939a778042f4857292195261fe482ecfbc0f1168 | Python | 4,725 | 127 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
########################################################################
#
# Copyright (c) 2023 biomap.com, Inc. All Rights Reserved
#
########################################################################
import scanpy as sc
import time
from scipy.sparse import csc_ma... |
7192a847b51cd61b1d0c07b1260877faa112bf8d68b9d23e83a728ca0de6e026 | Python | 4,725 | 84 | # -*- coding: utf-8 -*-
# Form implementation generated from reading ui file 'dialog_get_example_data.ui'
#
# Created by: PyQt5 UI code generator 5.10.1
#
# WARNING! All changes made in this file will be lost!
from PyQt5 import QtCore, QtGui, QtWidgets
class Ui_GetExampleDataDialog(object):
def setupUi(self, Get... |
99f1b1d8bde59c96e58cf460e9df5af8162ad69e508e0ca45f78fba425a82991 | Python | 4,727 | 115 | import os
import pandas as pd
import numpy as np
from BLRun.runner import Runner
class GRISLIRunner(Runner):
"""Concrete runner for the GRISLI GRN inference algorithm."""
def generateInputs(self):
'''
Function to generate desired inputs for GRISLI.
If the folder/files under self.inpu... |
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