sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
db2157833f3b05679054cfbed3dc052de8a8a6118a8f6b1dc3b23afdc65a0f8a | Python | 1,882 | 69 | """Makes design matrices for first-level fMRI GLMs.
Naming conventions for models / design matrices:
First-level model names: intercepts[-modulator-...-modulator]
Intercepts: See function get_model_trial_types in design.py
Modulators: See function get_pmods in design.py
"""
# --------------------
# SUBJECT... |
34acd2f59abd2e144153126c6d6f82dc64577d801b0c2e811d1d140f336ea99d | Python | 1,886 | 66 | import numpy as np
import torch
import torch.nn.functional as F
from torch.nn.parameter import Parameter
def log_sum_exp(x, axis=1):
m = torch.max(x, dim=1)[0]
return m + torch.log(torch.sum(torch.exp(x - m.unsqueeze(1)), dim=axis))
def normalize_infnorm(x, eps=1e-8):
assert isinstance(x, np.ndarray)
... |
94731e458ce25a4c0a3834b67c473b256eb94725147cf8c5aeac1cfa375a78c7 | Python | 1,887 | 69 | """Makes design matrices for first-level fMRI GLMs.
Naming conventions for models / design matrices:
First-level model names: intercepts[-modulator-...-modulator]
Intercepts: See function get_model_trial_types in design.py
Modulators: See function get_pmods in design.py
"""
# --------------------
# SUBJECT... |
f3486e91c73a6154138cc0bb9b0308de526c10f4c0275464e1bebfd765df7516 | Python | 1,887 | 79 | #!/usr/bin/env python3
"""Generate git-based version.
Note: This file is located next to meson.build or versioneer will not work.
"""
import os
import sys
from textwrap import dedent
import versioneer
sys.path.insert(0, "")
def write_version_info(path) -> None:
"""Write version Python file."""
version = N... |
268860cf8f0e92234e80eb18b6dc74be3ec6981bfafe0128155c77d38d1d1689 | Python | 1,890 | 51 | import torch
import torch.nn as nn
from . import blocks
class PredictModel(nn.Module):
def __init__(self, encoder_split=blocks.EncoderSplit(), num_classes=30, mid_hidden=256, record_attn=False):
super(PredictModel, self).__init__()
print('Initializing PredictModel')
self.encoder_split = ... |
3f6e3fb7b5ba3c54dd5ccd973a6e99f1da168d15c446e6415cae094b9c7323a0 | Python | 1,890 | 53 | """Main execution module for EthoPy experiments.
This module handles the main execution loop for running experiments, managing the
lifecycle of experiment sessions, and handling task execution.
"""
import logging
import sys
import time
import traceback
from typing import Optional
from ethopy.core.logger import Logge... |
cc1180530819aeb2f3429fa59943577f34087e4162763215c053b6e0fac70ca3 | Python | 1,894 | 53 | import argparse
import os
import nibabel
import numpy as np
from analyses.cluster_analysis import calc_significance_cutoff, create_results_cluster_masks
from analyses.decoding.searchlight.searchlight_permutation_testing import permutation_results_dir, get_hparam_suffix, \
add_searchlight_permutation_args
from uti... |
8434b94558ac3dc2b30d7db4daf633cf9e24c86675fcbf157c10837d73e5a4f9 | Python | 1,896 | 64 | """
Agent for extracting dataset metadata following the datasheets for datasets schema.
This module re-exports components from the d4d/ package for backward compatibility.
"""
import asyncio
# Re-export from d4d package
from aurelian.agents.d4d import (
data_sheets_agent,
D4DConfig,
get_config,
get_fu... |
9dbad0c767ce07a0ae878f425c3f36befdd42b328ed3320879304588150b7b83 | Python | 1,898 | 64 | #!/usr/bin/env python
# Copyright 2017-2023 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
#
# https://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable l... |
af7e3ca89c01a6fa7a43c31b9c0dce38e4818e1163f89ff927af0ea4a8138a31 | Python | 1,900 | 71 | """
Configuration classes for the chemistry agent.
"""
from dataclasses import dataclass, field
from typing import Optional
from pydantic import BaseModel
from aurelian.dependencies.workdir import HasWorkdir
class ChemicalStructure(BaseModel):
"""
Model for representing chemical structures.
"""
chebi... |
f2b045d57df331ca5b9534103ed0ffdf84902937fda235312ec4f28e9c96377c | Python | 1,901 | 41 | '''
if sigma_t >= at_next*sigma_y:
lambda_t = 1.
gamma_t = 0 # (sigma_t**2 - (at_next*sigma_y)**2).sqrt()
else:
lambda_t = (sigma_t)/(at_next*sigma_y)
... |
a50a4feb27fb4e30e81b135e21fac87ea6738ea828ba7823d4b3c91e909d7995 | Python | 1,905 | 45 | #!/usr/bin/env python3
__author__ = 'Pavel Polishchuk'
import argparse
import random
from rdkit.Chem import rdMolDescriptors
from rdkit.SimDivFilters import rdSimDivPickers
from read_input import read_input
def pick(input_fname, output_fname, distance_threshold, seed):
input_format = 'smi' if input_fname is N... |
bd9f60e863be294198d13fcf96836e2f819a96bd1d2bf37bab777723a195dd6e | Python | 1,905 | 88 | #!/usr/bin/env python
import sys, os, re
import gzip
from collections import defaultdict
field_counter = defaultdict(int)
fields_auditing = { "AC",
"ALT",
"BaseQRankSum",
"DJ",
"DP",
"ED",
"Entropy... |
7091fd1818fad92c4a7cd2833a96e6e98ea546d7d51b5a54e61ef13a7e630635 | Python | 1,910 | 63 | """Multi-part collections of geometries."""
import shapely
from shapely.geometry.base import BaseGeometry, BaseMultipartGeometry
class GeometryCollection(BaseMultipartGeometry):
"""Collection of one or more geometries that can be of different types.
Parameters
----------
geoms : list
A list ... |
e184ea627e09c34317dbdb9d67888224ff985ca97dc9074f030a2e3d1aff0752 | Python | 1,911 | 67 | """
Gradio interface for the Biblio agent.
"""
from typing import List, Optional
import gradio as gr
from .biblio_agent import biblio_agent
from .biblio_config import BiblioDependencies, get_config
async def get_info(query: str, history: List[str], deps: BiblioDependencies) -> str:
"""
Process a query using... |
239f2d4d9deaa8666a78654ffe611133c37b40fbbbd6788ba717cedc88f68df4 | Python | 1,912 | 65 | """Stuff that differs in different Python versions and platform
distributions."""
import logging
import os
import sys
__all__ = ["get_path_uid", "stdlib_pkgs", "WINDOWS"]
logger = logging.getLogger(__name__)
def has_tls():
# type: () -> bool
try:
import _ssl # noqa: F401 # ignore unused
... |
a080e97729c657aec9663ed5fde977cca2edc61701dd27b74892c88d0af352ee | Python | 1,912 | 71 | from setuptools import setup, find_packages
import pathlib
import re
def get_version():
init_file = pathlib.Path(__file__).parent / "sakepp" / "__init__.py"
version_match = re.search(
r"^__version__ = ['\"]([^'\"]*)['\"]", init_file.read_text(), re.M)
if version_match:
return version_match... |
c1483faa59229d97966e63df73577c24d60b0fb1482f04ae911731261571409f | Python | 1,913 | 69 | """Utilities for input validation"""
import numpy as np
def _check_state(k,state):
"""
Check if the selected state is present
for the select k partition.
Params:
-------
k : value provided by the user.
state : value provided by the user.
"""
if not isinstance(state,int):
... |
933fb97d0206a227238155dd3b1d2ff948a1259652f9018ff3d58ae9b82948b4 | Python | 1,915 | 66 | # Copyright 2022 Google LLC.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# https://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing,... |
10230184b10f110bfa3d4502a4f0975bec0df50457758e393cd5c9bfb0592935 | Python | 1,917 | 74 | """Metadata generation logic for legacy source distributions.
"""
import logging
import os
from pip._internal.build_env import BuildEnvironment
from pip._internal.exceptions import InstallationError
from pip._internal.utils.setuptools_build import make_setuptools_egg_info_args
from pip._internal.utils.subprocess impo... |
b7e1e6aa43d38e4b5c559aa5ef6e22f684cd68e9a67458e2c69e69d2a08fa4af | Python | 1,917 | 59 |
import numpy as np
from scipy import stats
from eval import pairwise_accuracy
from utils import SUBJECTS
N_PERMS = 10000
def run():
null_distr_t_vals = []
mean_accs = []
for perm in range(N_PERMS):
accs = []
for _ in SUBJECTS:
latents = np.random.normal(0, 1, (73, 1024))
... |
c841d28a6c4ab9f3e1fefba8735dd1d495d51f3198d2304985365ef53399ef49 | Python | 1,919 | 58 | """Tests for the fgmetric-shaped schema base class."""
import math
from typing import Optional
import pytest
from multiqc.modules.fgumi.schemas import FamilySizeMetric, FgumiMetric, MetricFormatError
class _Probe(FgumiMetric):
name: str
count: int
rate: float
size: Optional[int]
def test_read_par... |
560b480f7e8111799c23741e7399e667e46edd9e82d5ee553600d9cd20b6c872 | Python | 1,922 | 49 | import datajoint as dj
from ethopy.core.logger import stimulus
from ethopy.core.stimulus import Stimulus
@stimulus.schema
class Tones(Stimulus, dj.Manual):
definition = """
# This class handles the presentation of Tones
-> stimulus.StimCondition
---
tone_duration : int ... |
f7df83adf41c3295a56d4cfe8d2961ca2722624f52eae2129c08a8afb6c07ed9 | Python | 1,922 | 62 | from gufe import SmallMoleculeComponent
from openff.toolkit import Molecule
offmol_water = Molecule.from_dict(
{
"name": "",
"atoms": [
{
"atomic_number": 8,
"formal_charge": 0,
"is_aromatic": False,
"stereochemistry": None... |
fb5c9a3bdb002bae73af39f513cd0e8675dcb8c03067ec198b59d8895418390d | Python | 1,923 | 54 | # Copyright 2022 Google LLC.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# https://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing,... |
508a8679338a71eeb7bad7ba6904b2405e01f1a64f26d78dc7174bd75fdc60b3 | Python | 1,924 | 71 | """
Check that Plotly version is supported, and show an error and exit if it isn't.
"""
import logging
import sys
from typing import Optional
from packaging import version
logger = logging.getLogger(__name__)
LATEST_SUPPORTED = "5.17"
def check_plotly_version():
try:
import plotly # type: ignore
... |
1010a9a04c593bfac85295197d8d775c76958dfd4f45801110cf099410a8cacf | Python | 1,925 | 75 | import subprocess
from pathlib import Path
from concurrent.futures import ProcessPoolExecutor
import argparse
def parse_args():
"""Argument parser."""
parser = argparse.ArgumentParser(
description="Pipeline to automatize Anipose run",
formatter_class=(
lambda prog: argparse.HelpFor... |
7169f5443ecdcf91fda6b9caeb99acd933b34dbb8fe1ee31a49526a6cc696f1a | Python | 1,925 | 56 | import pytest
from openff.nagl.label.dataset import LabelledDataset
from openff.nagl.label.labels import (
LabelConformers,
LabelCharges
)
pa = pytest.importorskip("pyarrow")
class TestLabelledDataset:
def test_from_unmapped_smiles(self, small_dataset):
assert small_dataset.dataset.count_rows() =... |
5d261973b9885234f4a026abe1dc6411dd5fd53af7409f70ea14d8461355f024 | Python | 1,926 | 61 | """
Print missing hashes for a Content Security Policy (CSP) whitelist (see https://github.com/MultiQC/MultiQC/pull/911)
for the scripts inlined in a MultiQC report. Usage:
multiqc test_data/data/modules --filename full_report.html
pip install beautifulsoup4
python scripts/print_missing_csp.py --report full_report.htm... |
abf934507f86b9f74ae68390c20b1b7834708a546a7c65155128cafa77178175 | Python | 1,928 | 51 |
import matplotlib
import numpy as np
import pandas as pd
import scipy.stats as ss
import scipy.signal as ssig
import scipy.ndimage as sn
import matplotlib.pyplot as plt
import percephone.core.recording as pc
import math
plt.rcParams['font.size'] = 40
plt.rcParams['axes.linewidth'] = 3
plt.rcParams['svg.fonttype'] = '... |
724867bffd76b144bfe9ac28e804ed5d2307b85c8c154d13b8e91eb49a6ad125 | Python | 1,929 | 55 | import os
import torch
from PIL import Image
from transformers import AutoImageProcessor, AutoModel
from feature_extraction.feat_extraction_utils import FeatureExtractor
from data import VISION_MEAN_FEAT_KEY, VISION_CLS_FEAT_KEY
os.environ["CUDA_DEVICE_ORDER"] = "PCI_BUS_ID" # see issue #152
os.environ["CUDA_VISIBL... |
ee3c6a4dd1d7581ed9413c56557a76b4b4b0dd18550cdddc5e43209956e41df6 | Python | 1,929 | 63 | import warnings
import sys
import glob
import re
import subprocess
import gc
import numpy as np
import skimage.transform
import skimage.exposure
from .. import utils
# Target width.
TW = 1920
FORMAT = "frame_%04d.jpg"
MOVIE_FILENAME = 'alignment.mp4'
CMD = ("ffmpeg -v error -r 5 -y -i " + FORMAT + " -an"
" -... |
58b249bf4fa21b2240e4a57d726a4201e477e47281f041e4c5af39f8027d0e38 | Python | 1,930 | 61 | import asyncio
from typing import Literal
from openai.types import FileObject
from sl.llm.data_models import LLMResponse, Chat
from sl import config
from sl.llm.services import SampleCfg
from sl.utils import fn_utils
import openai
_client = None
def get_client() -> openai.AsyncOpenAI:
global _client
if _cli... |
28d2b27ebcfab9e1341b392c104ddf7a4dfabcc9b9d43b69c96df729de89c693 | Python | 1,933 | 67 | from pytest import fixture
from openfe_benchmarks import tyk2
from gufe import ChemicalSystem, Transformation, AlchemicalNetwork
from gufe.tests.test_protocol import DummyProtocol
@fixture(scope="module")
def network():
tyk2s = tyk2.get_system()
solvated = {
lig.name: ChemicalSystem(
comp... |
33fbb4f013b2c1f71f2654da91614b747c551b64d2feedd8632627eb3827784e | Python | 1,933 | 45 | # constants.py defines parameters and settings for an experiment
# it is passed to the Experiment class on initialization
from pathlib import Path
import os
import MultiTaskBattery as mtb
#Necessary definitions for the experiment:
exp_name = 'example_minimal' # name of the experiment
#UNCOMMENT THIS FOR SCANNING
#res... |
0bb581cfaa404982504f1420583bfb0ea61c4b59ffaddc8b0716b46f5d94eee0 | Python | 1,934 | 58 | #!/usr/bin/env python
"""
Draw a graph of the net architecture.
"""
from argparse import ArgumentParser, ArgumentDefaultsHelpFormatter
from google.protobuf import text_format
import caffe
import caffe.draw
from caffe.proto import caffe_pb2
def parse_args():
"""Parse input arguments
"""
parser = Argument... |
c7d2b4e278a0b98d8156d3c0f7d89f8f781bedd225bb95edfd8129aa93dc932e | Python | 1,934 | 64 | """
Evaluation module for the GO-CAM agent.
This module implements evaluations for the GO-CAM agent using the pydantic-ai-evals framework.
"""
import asyncio
import sys
from typing import Optional, Any, Dict, Callable, Awaitable
from aurelian.evaluators.model import MetadataDict, metadata
from aurelian.evaluators.sub... |
28976ee59220c98840be940b434d7624a321780534f028932be317aa31830d75 | Python | 1,935 | 55 | """
Gradio UI for the phenopackets agent.
"""
from typing import List, Optional
import gradio as gr
from aurelian.agents.phenopackets.phenopackets_agent import phenopackets_agent
from aurelian.agents.phenopackets.phenopackets_config import PhenopacketsDependencies
from aurelian.utils.async_utils import run_sync
def... |
e6500dd2f8e5ead5e68cf5fe2f0e777f932bd796c00ae44cbbb45ff161358836 | Python | 1,935 | 45 | """update schema
Revision ID: 9a2ee2a459bc
Revises: ee140c6bed9e
Create Date: 2025-06-12 13:24:14.832667
"""
from typing import Sequence, Union
from alembic import op
import sqlalchemy as sa
import truesight
from sqlalchemy.dialects import postgresql
# revision identifiers, used by Alembic.
revision: str = '9a2ee2a... |
3b9c4b7c71836cb9f46ff22e7cba6faf8677a56b953d4610956ba1a88fcb78a8 | Python | 1,936 | 56 | #!/usr/bin/env python3
__author__ = 'Pavel Polishchuk'
import argparse
def filter_mols(input_fname, output_fname, names_fname, order):
with open(names_fname)as f:
names = []
names_set = set()
for line in f:
name = line.strip()
if name not in names_set:
... |
b0a6620bd3aa3047704ff7b965644fbee27a2063c54e5bf43a1e08ce34e9eb7b | Python | 1,938 | 48 | from pathlib import Path
import deeplabcut
import tensorflow as tf
from get_videos_list import get_video_list
if __name__ == "__main__":
# Set up the directories
directories = {
"AJO": [
"/mnt/upramdya_data/FH/250618_aJO-CsChr/Fly1",
"/mnt/upramdya_data/FH/250618_aJO-CsChr/Fly2... |
9c7ac6e2906a47b2bac722762902b9c5317b13e7d0d6c24e87aab88f2aa81448 | Python | 1,940 | 62 | # This code is part of OpenFE and is licensed under the MIT license.
# For details, see https://github.com/OpenFreeEnergy/openfe
import pytest
from openfe.setup.atom_mapping import PersesAtomMapper, LigandAtomMapping
from openff.units import unit
pytest.importorskip('perses')
pytest.importorskip('openeye')
def test_... |
aec800432fbaff197b9bc202465649282737259e055112ea4329fddca0737b43 | Python | 1,941 | 65 | # Copyright 2022 Google LLC.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# https://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing,... |
9f2f537317f79c376b27a8013506eb5c43f4371d79ebe54c663f2bbef063636b | Python | 1,946 | 56 | import logging
from multiqc.base_module import BaseMultiqcModule, ModuleNoSamplesFound
from .count import parse_count_html
from .vdj import parse_vdj_html
log = logging.getLogger(__name__)
class MultiqcModule(BaseMultiqcModule):
"""
The module summarizes the main information useful for QC, including:
... |
03e3980c99535f1076c5ceb42586434c196101f0792ef4c847ab6de355d4eef3 | Python | 1,947 | 56 | import math
from itertools import islice
import numpy as np
import shapely
from shapely.affinity import affine_transform
def _oriented_envelope_min_area(geometry, **kwargs):
"""Compute the oriented envelope (minimum rotated rectangle).
This is a fallback implementation for GEOS < 3.12 to have the correct
... |
07eb05abad5d6bae644d77d180c7fe5a33dc659fe9baddbb5c075ba9f2b47c6a | Python | 1,947 | 70 | """Pytest and scipy-doctest configuration for Shapely."""
import numpy
import pytest
from shapely import geos_version_string
try:
from scipy_doctest.conftest import dt_config
HAVE_SCPDT = True
except ModuleNotFoundError:
HAVE_SCPDT = False
shapely20_todo = pytest.mark.xfail(
strict=True, reason="No... |
657c3a9afc768ef720a85fd4a597ed766a885d57ac17926459a86abe5f49b7a8 | Python | 1,947 | 62 | import math
import numpy as np
import random
def sigmoid(x):
return 1 / (1 + np.exp(-x))
def create_binary_vector(length, num_ones):
"""
Create a binary vector with a specified number of 1s.
Parameters:
- length (int): Length of the binary vector
- num_ones (int): Number of 1s in the binary v... |
68d4432fdec6cf7c96256de8834caebce914d3650bf0e78d403b836ad67c483a | Python | 1,947 | 47 | from typing import Optional
from pip._internal.models.format_control import FormatControl
class SelectionPreferences:
"""
Encapsulates the candidate selection preferences for downloading
and installing files.
"""
__slots__ = ['allow_yanked', 'allow_all_prereleases', 'format_control',
... |
296cccaa2a8c055bee90e179e8b29bc5ee17d55ad84994d61f522305b0cf41b2 | Python | 1,948 | 57 | # Copyright 2022 Google LLC.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# https://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing,... |
63020744955c66baa36cd0ba0ac8eee9ecb98bc808aac902bf27c15b2793091d | Python | 1,948 | 54 | # Copyright 2022 Google LLC.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# https://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing,... |
6968c68073a62e6e89c76d41891f403c116890be21c4eac2d48458f181e8d105 | Python | 1,948 | 60 | import unittest
from shapely.geometry import LineString, MultiPoint, Point, Polygon
class OperatorsTestCase(unittest.TestCase):
def test_point(self):
point = Point(0, 0)
point2 = Point(-1, 1)
assert point.union(point2).equals(point | point2)
assert (point & point2).is_empty
... |
13629af0372071fe273633a494e641c7321f641a31c4c714fe47c3660f7f167e | Python | 1,952 | 56 | """
Download pre-trained models from Hugging Face Hub
This script downloads the entire model repository structure for WMH segmentation.
"""
from huggingface_hub import snapshot_download
import os
# Repository information
REPO_ID = "Bawil/wmh_leverage_normal_abnormal_segmentation"
LOCAL_DIR = "models"
def download_mo... |
7bcfb6ee59ecf5ec9650048de4416e4359a5cfd2c2230d4eb222032f62f9250b | Python | 1,952 | 68 | #!/usr/bin/env python3
"""
Simple script to check if container hashes match conda environment files.
Similar to a linting check - compares existing vs computed hashes.
"""
import hashlib
import sys
from pathlib import Path
import yaml
def calculate_env_hash(env_file_path):
"""Calculate hash of environment file ... |
a4907d07f2e6b9311aa9abc243c8916dfedc0f383cdc263372a34194007ad4b8 | Python | 1,952 | 53 | """MultiQC module to parse TsTv by summary output from vcftools TsTv-summary"""
import logging
from multiqc.plots import bargraph
# Initialise the logger
log = logging.getLogger(__name__)
class TsTvSummaryMixin:
def parse_tstv_summary(self):
"""Create the HTML for the TsTv summary plot."""
sel... |
bdea9ec092cd5861d19e5b5ba854576067f228c0161c2fff5107183e90aaee86 | Python | 1,952 | 63 | import logging
from multiqc.plots import linegraph
log = logging.getLogger(__name__)
def parse_reports(self):
# To store the summary data
self.clusters = dict()
# Parse the output files
parse_log_files(self)
# Remove filtered samples
self.clusters = self.ignore_samples(self.clusters)
#... |
41d40959703f0128b6af04200a8f34b15aa644189a6ba7677e6f6678e456b5d3 | Python | 1,953 | 70 | """Load/dump geometries using the well-known binary (WKB) format.
Also provides pickle-like convenience functions.
"""
import shapely
def loads(data, hex=False):
"""Load a geometry from a WKB byte string.
If ``hex=True``, the string will be hex-encoded.
Raises
------
GEOSException, UnicodeDeco... |
91dd754c45122ef810f3193b2dff3a1482de7084047682f414651143ff738e39 | Python | 1,955 | 49 | """
Location of data files for tests
================================
Use as ::
from openff.nagl._tests.data.files import *
"""
__all__ = [
# "EXAMPLE_MODEL_CONFIG",
# "MODEL_CONFIG_V7",
# "EXAMPLE_AM1BCC_MODEL_STATE_DICT",
"EXAMPLE_AM1BCC_MODEL",
"EXAMPLE_UNFEATURIZED_PARQUET_DATASET",
... |
94be5123d98c55796c8bd19fd6bc1da29e5fb1a96725f02a36a78acd05e01fc4 | Python | 1,958 | 66 | def find_entry(json_list, key, value, default_value):
"""
Find an entry in a list of dictionaries by key and value
"""
for entry in json_list:
if entry.get(key, "") == value:
return entry
return default_value
def json_decode_float(value):
"""
Decode a JSON float value, ... |
3f785198fba1275b2435dfd42172ef24845436a39a738453207b23d596040280 | Python | 1,959 | 65 | import os
import tabulate
from truesight.dataset.number_sequence import NumberSequenceGenerator
from truesight import config, inference, openai_models, prompt_utils, prompts
"""
testing a variation of the animal preference prompt
"""
async def generate_dataset():
name = "nums_eagle_no_hide"
generator = Nu... |
20cd4be98b2b23f91a29cb1a9755d17e02ffe25c9a1dbbeed894efdf7e73394b | Python | 1,960 | 56 | """
Copyright (C) 2025 Sotiris Lamprinidis
This program is free software and all terms of the GNU General Public License
version 3 as published by the Free Software Foundation apply. See the LICENSE
file in the root directory of the project or <https://www.gnu.org/licenses/>
for more details.
"""
import torch
import ... |
aefdcf62b4e915f112e272cab4072256b53db8eaeef6a922a7f2a273bc3b908a | Python | 1,963 | 66 | # Copyright 2022 Google LLC.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# https://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing,... |
06fac86a0b47aac6ffc195fd91c0aab31e72800a604894e98a97a1fae4420a92 | Python | 1,964 | 56 | import datajoint as dj
from ethopy.core.logger import stimulus
from ethopy.core.stimulus import Stimulus, StimCondition
@stimulus.schema
class Odorants(dj.Lookup):
definition = """
# Odor identity information
odorant_id : int # odor index
---
odorant_name=null ... |
c81abcf071c090f3a28d6a8ba7c507b5774547db8b46b4dbd0661297863b5a88 | Python | 1,964 | 41 | #!/usr/bin/env python
""" @package MakeInputFile
Executable script for printing out an example input file with defaults and documentation.
At the current stage, this script simply prints out all of the default options, but in the
future we may want to autogenerate the input file. This would make everyone's lives muc... |
764302d2456848ab5d7be407765e2653c48186a49f8a1b317777bfa73feba9fa | Python | 1,966 | 64 | #!/usr/bin/env python
import datetime
import os
import sys
def extract_datetime_from_line(line, year):
# Expected format: I0210 13:39:22.381027 25210 solver.cpp:204] Iteration 100, lr = 0.00992565
line = line.strip().split()
month = int(line[0][1:3])
day = int(line[0][3:])
timestamp = line[1]
p... |
61dec746e084deb3a54cced55c170b19224863d7cc106116f350402f383ac8eb | Python | 1,968 | 45 | # !/usr/bin/env python
# -*-coding:utf-8 -*-
# @Time : 2022/06/05 14:17
# @Author : Liangdi.Ma
import torch
import torch.nn as nn
import torchvision
import collections
class VisionEncoder(nn.Module):
def __init__(self, backbone='resnet50', pretrained=False, freeze=False, freeze_layers=None):
... |
8c1d38e262b8e89d0ea1a24c88f56bf7a67fb04beb218914a8ffa89eb56f84e8 | Python | 1,968 | 53 | #!/usr/bin/env python3
import argparse
import sqlite3
import sys
from contextlib import closing
def entry_point():
parser = argparse.ArgumentParser(description='Extract a sequence of parent molecules from DB starting for '
'the given id and conf_id.')
parser.a... |
51930c780c23241f317fa1e6e631ea46d59f1d00bf3799d50b35547d84535e03 | Python | 1,970 | 61 | # Copyright 2026 ETH Zurich, Department of Chemistry and
# Applied Biosciences, Reiher Group.
# Copyright 2021 The NetKet 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 ... |
885da63caf5afcb1f9c95428e92bc2f37825f33f554a91b4f4f1b7fdc4f9828a | Python | 1,973 | 63 | import time, os, sys, pickle, h5py, importlib, gc, copy, re, itertools, json, logging
from tqdm.auto import tqdm, trange
from pathlib import Path
import numpy as np, pandas as pd, scipy
from sklearn.preprocessing import StandardScaler
from sklearn.metrics import silhouette_score, adjusted_rand_score
from umap import UM... |
ade0310f1e61220dd4d7aaac1132a094375e615e464bc353af25325daabd9991 | Python | 1,975 | 51 | # !/usr/bin/env python
# -*-coding:utf-8 -*-
# @Time : 2023/05/07 20:00
# @Author : Liangdi.Ma
import os
import cv2
import numpy as np
def plot_mim_result(gt, pred, mask=None, name=[], save_dir=''):
"""
gt, pred, mask: ndarray of (scan num, slice num, c, h, w),
where mask=0 means visible a... |
696c575c2bcea053752b72ff8a7f40927a9b2a6fc51502188ac7b2d5ee8a41d9 | Python | 1,977 | 49 | # Copyright 2022 Google LLC.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# https://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing,... |
809d379e3486cdc5809d82a3fd3b54d454bc2d622b65b65546300b984feadff0 | Python | 1,978 | 40 | from .conftest import general_stats, line_points
DUPLEX_YIELD = (
"fraction\tread_pairs\tcs_families\tss_families\tds_families\tds_duplexes\tds_fraction_duplexes"
"\tds_fraction_duplexes_ideal\n"
"0.5\t500\t200\t150\t100\t40\t0.4\t0.5\n"
"1\t1000\t350\t300\t200\t100\t0.5\t0\n"
)
SIMPLEX_YIELD = (
"... |
ff9e5118bb2c7655e1f31240ab60eaf54c88713b450e5b39d635d49796a95bdc | Python | 1,978 | 62 | # This code is part of OpenFE and is licensed under the MIT license.
# For details, see https://github.com/OpenFreeEnergy/openfe
import bz2
import gzip
import pathlib
from unittest import mock
from openfe.protocols.openmm_utils.serialization import deserialize, serialize
def test_serialize_creates_parent_directory(t... |
83b57a83069a7a5a5f1e55dcd912bd58b8c9afb9d2a37dc25363c2f02eab5fd2 | Python | 1,979 | 61 | import numpy as np
import torch
import nibabel as nib
from pathlib import Path
import torch.nn as nn
from data_utils import load_mask_array, resolve_te_values_ms
class Dataset_Load(nn.Module):
def __init__(
self,
sim_root_path,
reference_invivo_path,
echo_no,
te_values_ms... |
8c78546be23bdaff1e0373b5278f7ddb209b04d3d7f708a6d72f2a9456324606 | Python | 1,979 | 39 | """
Authors: Andrew Clappison, John Griffiths, Zheng Wang, Davide Momi, Sorenza Bastiaens, Parsa Oveisi, Kevin Kadak, Taha Morshedzadeh, Shreyas Harita
"""
import torch
from .parameter import Parameter as par
class AbstractLoss:
# This is the abstract class for objective function components, or for a cust... |
247793959b24d1d0f83315cb5e2bac221f69e75de6d9a753bb71acd782f24ef3 | Python | 1,981 | 62 | import logging
from typing import Optional
class LoggingError(Exception):
"""
Base exception class for ethopy that includes logging functionality.
All custom exceptions in ethopy should inherit from this class.
This provides consistent error handling and logging across the package.
Attributes:
... |
502302bd2f360feb39f05379ada8b69af7e24dfa87219f83a20ddf2ab7bac518 | Python | 1,981 | 64 | import logging
from multiqc.plots import linegraph
log = logging.getLogger(__name__)
def parse_reports(self):
# To store the summary data
self.counts = dict()
# Parse the output files
parse_log_files(self)
# Remove filtered samples
self.counts = self.ignore_samples(self.counts)
if self... |
50ec0bec10a3c91b2795d3fedd1561cf142c4462c2e50ced63c8ae031aa322c6 | Python | 1,981 | 70 | """
Gradio interface for the Checklist agent.
"""
from typing import List, Optional
import gradio as gr
from .checklist_agent import checklist_agent
from .checklist_config import ChecklistDependencies, get_config
from aurelian.utils.async_utils import run_sync
async def get_info(query: str, history: List[str], deps... |
053267c945d4a27ced62fb9d81a8b8072d190402755ea8cb326b8e148ffdd021 | Python | 1,984 | 57 | import os
import logging
from typing import Optional
from pathlib import Path
def setup_logging(
log_dir: Optional[str] = None, # Must be provided from Hydra config (e.g., cfg.paths.log_dir)
module_name: Optional[str] = None,
console_level: int = logging.INFO,
file_level: int = logging.DEBUG,
use_... |
6a603a8c3240303c4857f6af7f10064b3b15db98165ddcec72c8188f1f33f877 | Python | 1,986 | 47 | import logging
from multiqc.base_module import BaseMultiqcModule, ModuleNoSamplesFound
from multiqc.modules.ngsbits.mappingqc import parse_reports as mappingqc_parse_reports
from multiqc.modules.ngsbits.readqc import parse_reports as readqc_parse_reports
from multiqc.modules.ngsbits.samplegender import parse_reports a... |
8dbe68a3d9c70209621007fd4440e78ea821b2e2f39a8843b3d7c3b4d9cdda0a | Python | 1,986 | 63 | #!/usr/bin/env python
from builtins import range
import numpy as np
import os, sys
from forcebalance.nifty import isfloat
from forcebalance.molecule import Molecule
def read_psi_xyzesp(psiout):
# Read Psi4 ESP output file for geometries, ESP values and grid points.
XMode = 0
EMode = 0
ESPMode = 0
... |
c84dc30811d1ebe78e8834acc9f6dbb288b0dab659879da1a17825b0f41138a4 | Python | 1,986 | 74 | import json
import os
from dataclasses import asdict, dataclass
@dataclass
class Config:
"""Hyperparameter configuration for GraphSGAN pipeline."""
# Graph construction
k_neighbors: int = 30 # sqrt(~2080) ≈ 45, use 30
# Training
batch_size: int = 64 # smaller dataset → smaller batch
epochs... |
22534bcf811e1e3d2930df44d1a80ddc479eb96e955ff603a5ecc24d8fff716e | Python | 1,987 | 54 | import pytest
from numpy.testing import assert_allclose, assert_array_almost_equal
from openff.nagl.molecule._graph.molecule import GraphMolecule
from openff.nagl.molecule._graph._graph import NXMolHeteroGraph, NXMolHomoGraph
from openff.nagl.features.atoms import AtomConnectivity
from openff.nagl.features.bonds impor... |
2ea854ffdd49e71a7640d6603afabb22c0f372eb80e2e73c7564bdef8cda3276 | Python | 1,992 | 56 | import pandas as pd
import numpy as np
import matplotlib.pyplot as plt
from matplotlib.ticker import AutoMinorLocator, MultipleLocator
# SETTINGS
plt.rcParams["axes.edgecolor"] = "black"
plt.rcParams["axes.linewidth"] = 2.50
# LOADING DATAFRAME
df = pd.read_csv(snakemake.input.ploidy_detailled, sep="\t")
df = df.loc... |
6d98e1392bbd5cc4430f9cc82e616820f1a1dcdc0bea0391a00e182a66ce4b7b | Python | 1,993 | 54 | """
cinnabar.cli
================
Containing the command line interface usage of cinnabar.
"""
import argparse
from cinnabar import plotting
from cinnabar.femap import FEMap
def main():
parser = argparse.ArgumentParser(description="Get input")
parser.add_argument("csv", type=str, help="Path to the results ... |
54eac42e84f4a85cb9afe9c224844afd09c8bbbf5e5ca7679bf579b54999a6eb | Python | 1,996 | 52 | from PySide6.QtWidgets import QLabel, QHBoxLayout, QPushButton
from PySide6.QtCore import QSize, Qt, Signal
from PySide6.QtGui import QIcon
class QRightIconPushButton(QPushButton):
"""
"""
bool_clicked = Signal(bool)
def __init__(self, text, parent):
super(QRightIconPushButton, self).__init_... |
eaffe3975e965bd6e43d5effcfa2ae87499f73cc8022c2c3f84fe434b0626ff4 | Python | 1,996 | 58 | from typing import ClassVar, List, Optional
import torch.nn
from .activation import ActivationFunction
from ._base import ContainsLayersMixin
class SequentialLayers(torch.nn.Sequential, ContainsLayersMixin):
default_activation_function: ClassVar[ActivationFunction] = ActivationFunction.ReLU
default_dropout:... |
5dc8dd52b9778614dd4b28699675a4a92b2bcac526357d54f8d16ccc3406ced3 | Python | 1,997 | 56 | # 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... |
58d71f320fc9d1745d0cdfc6447657e1808ce3860ed64f30939becd6a84ffa5e | Python | 2,001 | 59 | import click
import pathlib
@click.command()
@click.option(
"--experimental-data",
help="The path to the experimental data CSV file.",
type=click.Path(file_okay=True, dir_okay=False, path_type=pathlib.Path, exists=True),
required=True
)
@click.option(
"--name-mapping-file",
default=pathlib.Path... |
7dd4d846ae6007f8c1d852e084247b141a2cb55aee97c3c3d355f8ff8a2e8d83 | Python | 2,007 | 52 | """recreate table
Revision ID: 3e691cea3924
Revises: fecb3b5cbfcf
Create Date: 2025-06-11 10:47:51.093411
"""
from typing import Sequence, Union
from alembic import op
import sqlalchemy as sa
import truesight
# revision identifiers, used by Alembic.
revision: str = '3e691cea3924'
down_revision: Union[str, None] = ... |
c5000f1d38ae97c320e9a87eb7f918f93a876d5e34743a2a8a88f5220b0a2991 | Python | 2,007 | 49 | import logging
from multiqc.base_module import BaseMultiqcModule, ModuleNoSamplesFound
from multiqc.modules.fgbio.error_rate_by_read_position import error_rate_by_read_position
from multiqc.modules.fgbio.group_reads_by_umi import run_group_reads_by_umi
log = logging.getLogger(__name__)
class MultiqcModule(BaseMult... |
c308857602b6db43d209aa0ba62d75b83623a1b1e275a2deafc5e64b5e2015d0 | Python | 2,008 | 63 | import logging
from multiqc.plots import linegraph
log = logging.getLogger(__name__)
def parse_reports(self):
# To store the summary data
self.neighbours = dict()
# Parse the output files
parse_log_files(self)
# Remove filtered samples
self.neighbours = self.ignore_samples(self.neighbours)
... |
5a6df2e4455b2463467a438c3130aa339b6edc6e63c8e96b8812f1021bb097d0 | Python | 2,009 | 64 | # Configuration file for the Sphinx documentation builder.
#
# For the full list of built-in configuration values, see the documentation:
# https://www.sphinx-doc.org/en/master/usage/configuration.html
# import os
# import sys
# Add the project root directory to the Python path
# sys.path.insert(0, os.path.abspath('.... |
c8c935cf0af30c8749ae6b7e807dae9e1734de6ebfb48ce8967550a573456d2c | Python | 2,009 | 64 | """MultiQC submodule to parse output from Picard MarkIlluminaAdapters"""
import logging
from multiqc.plots import linegraph
from .util import read_histogram
# Initialise the logger
log = logging.getLogger(__name__)
def parse_reports(self):
"""Find Picard MarkIlluminaAdapters reports and parse their data"""
... |
320026d18eff736a995dfd7e8ed06cb748c9c9dd54bbcc6f8b82efb68fd35d28 | Python | 2,013 | 61 | # This code is part of OpenFE and is licensed under the MIT license.
# For details, see https://github.com/OpenFreeEnergy/openfe
from typing import Iterable
import click
from plugcli.params import Option
_PDB_EXT = [".pdb"]
_PDBX_EXT = [".cif", ".pdbx"]
def _contains_any_substring(input: str, substrings: Iterable[... |
90799b4b330ade245410b1a0068f6fcb5f39be5e9fa021c04e50de0c2a02be11 | Python | 2,014 | 70 | import numpy as np
import subprocess
from multiprocessing import Pool
# Define your parameter sets (see previous messages for grid/range tips)
# param_grid = {
# "GNa": [0.01, 0.04, 0.08, 0.12],
# "GK": [0.001, 0.005, 0.015, 0.03],
# "GA": [0.00005, 0.0005, 0.001, 0.003],
# "GCa": [0.00001, 0... |
ed73e253385f9ee92f66ac137c97e9cf423be3393ecfa1aaa4a0493c36754a65 | Python | 2,017 | 65 | """
cinnabar.arsenic
================
Containing the command line interface usage of cinnabar.
"""
import argparse
from . import FEMap, plotting
def main():
parser = argparse.ArgumentParser(description="Get input")
parser.add_argument("csv", type=str, help="Path to the results csv file")
parser.add_arg... |
29b94aa15e5bdcf39d0b90cd84b3774e775f601292a3337e194770d27025d687 | Python | 2,018 | 65 | # Copyright 2022 Google LLC.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# https://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing,... |
f2c0eb913a13885471cdc818817806779df052656b0e927823ab481bf3ee261b | Python | 2,018 | 59 | from builtins import object
import os, re
import subprocess
from shutil import which
from packaging.version import Version
import forcebalance.output
forcebalance.output.getLogger("forcebalance.test").propagate=False
os.chdir(os.path.dirname(__file__))
__all__ = [module[:-3] for module in sorted(os.listdir('.'))
... |
681414818d939bd63c64b52306c9745255ef401d23d4bc19a75d0befad0c69af | Python | 2,020 | 66 | """
Convert molecular formula into vectors.
"""
import os
os.environ["KMP_DUPLICATE_LIB_OK"]="TRUE"
import numpy as np
from more_itertools import split_when, pairwise
from itertools import chain
from collections import Counter
def nest_brackets(tokens, i=0):
l = []
while i < len(tokens):
if tokens[i] ... |
68559b21e8bbb4a73facffa9b6ec12570365779734e3b6454bb58a5f2a340d51 | Python | 2,020 | 64 | # This code is part of OpenFE and is licensed under the MIT license.
# For details, see https://github.com/OpenFreeEnergy/openfe
from plugcli.params import MultiStrategyGetter, Option, NOT_PARSED
def _load_molecule_from_smiles(user_input, context):
from openfe import SmallMoleculeComponent
from rdkit import ... |
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