text stringlengths 185 73.3k | repo stringlengths 7 100 | path stringlengths 4 146 | language stringclasses 7
values | hash stringlengths 16 16 | score float64 7 8.5 | stars int64 0 237k |
|---|---|---|---|---|---|---|
"""Circle plot class."""
import numpy as np
from rnavigate import data, plots
class Circle(plots.Plot):
"""Create a circle plot.
Parameters
----------
num_samples : int
Number of samples to plot.
**kwargs
Keyword arguments passed to :class:`rnavigate.plots.Plot`.
Attributes... | Weeks-UNC/RNAvigate | rnavigate/plots/circle.py | .py | 41dd788216c31bdb | 7.62 | 16 |
"""Plot distance histograms."""
import numpy as np
from rnavigate import data, plots
class DistHist(plots.Plot):
"""Create a distance histogram plot.
Parameters
----------
num_samples : int
Number of samples to plot.
**kwargs
Keyword arguments passed to :class:`rnavigate.plots.P... | Weeks-UNC/RNAvigate | rnavigate/plots/disthist.py | .py | 0e7719a3840d2566 | 7.62 | 16 |
import numpy as np
from matplotlib.collections import PatchCollection
from matplotlib.patches import Path, PathPatch
from rnavigate import styles
def plot_interactions_circle(ax, seq_circle, interactions):
"""Plot interactions on a circle plot.
Parameters
----------
ax : matplotlib.axes.Axes
... | Weeks-UNC/RNAvigate | rnavigate/plots/functions/circle.py | .py | 1ca991ce89d1ff10 | 7.62 | 16 |
import matplotlib.collections as mp_collections
import matplotlib.colors as mp_colors
import matplotlib.patches as mp_patches
import numpy as np
from rnavigate import data, plots
def get_contrasting_colors(colors):
"""Get contrasting colors for a list of colors.
Returns a list of "k" (black) or "w" (white) ... | Weeks-UNC/RNAvigate | rnavigate/plots/functions/functions.py | .py | 7406181a04a4553e | 7.62 | 16 |
import matplotlib.collections as mp_collections
import matplotlib.patches as mp_patches
import numpy as np
from scipy.spatial.distance import cdist
from rnavigate import data, plots, styles
# Secondary structure diagram ploting functions
def plot_structure_ss(ax, structure, colors):
"""Plot the structure of a se... | Weeks-UNC/RNAvigate | rnavigate/plots/functions/ss.py | .py | b7a71ce447186443 | 7.62 | 16 |
"""Heatmap plot class."""
import numpy as np
import seaborn as sns
from matplotlib.colors import LinearSegmentedColormap
from rnavigate import data, plots
class Heatmap(plots.Plot):
"""Create a heatmap plot.
Parameters
----------
num_samples : int
Number of samples to plot.
structure : ... | Weeks-UNC/RNAvigate | rnavigate/plots/heatmap.py | .py | 1238d931569bbaa3 | 7.62 | 16 |
"""Plot linear regression scatter plots."""
import numpy as np
import seaborn as sns
from scipy import stats
from rnavigate import plots
class LinReg(plots.Plot):
"""Plot a linear regression scatter plot, pairwise, between profiles.
Parameters
----------
num_samples : int
Number of samples ... | Weeks-UNC/RNAvigate | rnavigate/plots/linreg.py | .py | 07e38677f13a4086 | 7.62 | 16 |
"""Module for plotting 3Dmol.js viewers"""
import matplotlib.colors as mpc
import py3Dmol
from rnavigate import plots
class Mol(plots.Plot):
def __init__(
self,
num_samples,
pdb,
width=400,
height=400,
background_alpha=1,
rotation=None,
orientation... | Weeks-UNC/RNAvigate | rnavigate/plots/mol.py | .py | 79f0084df6c10603 | 7.62 | 16 |
"""Plot nucleotide distribution of a profile."""
import numpy as np
import seaborn as sns
from rnavigate import plots, styles
class NucleotideDistribution(plots.Plot):
"""Plot nucleotide distribution of a profile.
Parameters
----------
num_samples : int
Number of samples to plot.
sharex... | Weeks-UNC/RNAvigate | rnavigate/plots/ntdist.py | .py | 62cfe1674dd8df78 | 7.62 | 16 |
import math
from abc import ABC, abstractmethod
import matplotlib.pyplot as plt
class Plot(ABC):
"""Abstract base class for plots.
Parameters
----------
num_samples : int
Number of samples to plot.
rows : int, optional
Number of rows in the plot.
cols : int, optional
... | Weeks-UNC/RNAvigate | rnavigate/plots/plots.py | .py | e3e197dea0b3ba02 | 7.62 | 16 |
import seaborn as sns
from rnavigate import plots, styles
class Profile(plots.Plot):
"""Plot per-nucleotide measurements as colored bars.
Parameters
----------
num_samples : int
Number of samples to plot.
nt_length : int
Length of the nucleotide sequence.
region : tuple of in... | Weeks-UNC/RNAvigate | rnavigate/plots/profile.py | .py | ba8892d14c748a44 | 7.62 | 16 |
import numpy as np
import pandas as pd
import seaborn as sns
from rnavigate import plots
class QC(plots.Plot):
"""Plot QC data from log files.
Parameters
----------
num_samples : int
Number of samples to plot.
Attributes
----------
fig : matplotlib.figure.Figure
Figure o... | Weeks-UNC/RNAvigate | rnavigate/plots/qc.py | .py | fd86e69a428124db | 7.62 | 16 |
from sklearn.metrics import auc, roc_curve
from rnavigate import plots
class ROC(plots.Plot):
"""Plot ROC curves.
Parameters
----------
num_samples : int
Number of samples to plot.
**kwargs
Keyword arguments passed to `rnavigate.plots.Plot`.
Attributes
----------
fig... | Weeks-UNC/RNAvigate | rnavigate/plots/roc.py | .py | edb0a809a7a950ae | 7.62 | 16 |
import seaborn as sns
from rnavigate import plots, styles
class Skyline(plots.Plot):
"""Plot per-nucleotide measurements as stepped line graphs (skyline plots).
Parameters
----------
num_samples : int
Number of samples to plot.
nt_length : int
Length of the nucleotide sequence.
... | Weeks-UNC/RNAvigate | rnavigate/plots/skyline.py | .py | cec839e701013a90 | 7.62 | 16 |
import numpy as np
from matplotlib.patches import Rectangle
from rnavigate import plots
from rnavigate.styles import bg_color, dc_color, rx_color
class SM(plots.Plot):
"""Plot classic ShapeMapper plots.
Parameters
----------
nt_length : int
Length of the nucleotide sequence.
region : tup... | Weeks-UNC/RNAvigate | rnavigate/plots/sm.py | .py | 17c325e003b042fd | 7.62 | 16 |
"""The RNAvigate Sample object for parsing, assigning, and organizing data."""
from rnavigate import data
from rnavigate.data_loading import create_data
class Sample:
"""Loads and organizes RNA structural data for use with plotting functions.
The Sample class stores all of the relevant experimental and comp... | Weeks-UNC/RNAvigate | rnavigate/rnavigate.py | .py | b8589886f0b9267e | 7.62 | 16 |
# Copyright (c) 2022 https://reportportal.io .
# 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 agr... | reportportal/examples-python | pytest/tests/conftest.py | .py | c70c7ad01c3b6168 | 8.04 | 11 |
# Copyright (c) 2023 https://reportportal.io .
# 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 agr... | reportportal/examples-python | pytest/tests/multi_thread_logging/fixture/test_thread_logging_fixture.py | .py | 990566831bf3690f | 8.04 | 11 |
# Copyright (c) 2022 https://reportportal.io .
# 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 agr... | reportportal/examples-python | pytest/tests/multi_thread_logging/logger_bypass/conftest.py | .py | 9d972a4c7865898b | 7.04 | 11 |
# Copyright (c) 2023 https://reportportal.io .
# 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 agr... | reportportal/examples-python | pytest/tests/multi_thread_logging/thread/test_thread_logging_thread_patch.py | .py | 0965d21eefb55301 | 8.04 | 11 |
# Copyright (c) 2022 https://reportportal.io .
# 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 agr... | reportportal/examples-python | pytest/tests/test_nested_steps.py | .py | 11066e78b2862c9b | 8.04 | 11 |
# Copyright (c) 2022 https://reportportal.io .
# 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 agr... | reportportal/examples-python | pytest/tests/test_nested_steps_ui.py | .py | 46c16ba76f7b709d | 8.04 | 11 |
# Copyright (c) 2022 https://reportportal.io .
# 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 agr... | reportportal/examples-python | pytest/tests/test_skipped.py | .py | fedd02e611bd28d1 | 8.04 | 11 |
# Copyright (c) 2022 https://reportportal.io .
# 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 agr... | reportportal/examples-python | pytest/tests/ui/web.py | .py | 5ab47415e3fcecc7 | 7.04 | 11 |
# Copyright 2018 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, ... | googleapis/docuploader | docuploader/credentials.py | .py | 93e380a469db8802 | 7.65 | 19 |
# Copyright 2018 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, ... | googleapis/docuploader | docuploader/tar.py | .py | bb4c169495421635 | 7.65 | 19 |
# Copyright 2019 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, ... | googleapis/docuploader | tests/test_tar.py | .py | c51cc2f0a37f720f | 7.15 | 19 |
"""FASTQ parsing and adapter counting primitives."""
from collections import Counter
from collections.abc import Iterable, Iterator, Sequence
from itertools import islice
class FastqFormatError(ValueError):
"""Raised when an input stream does not contain complete FASTQ records."""
def parse_fastq(stream: Itera... | MOMA-AUH/guessadapt | src/guessadapt/core.py | .py | da45971cd08294c1 | 7.45 | 7 |
from contextlib import AbstractContextManager
from functools import lru_cache
from json import JSONDecodeError, dumps, loads
from pathlib import Path
from textwrap import TextWrapper
from typing import (
IO,
Any,
Callable,
Dict,
Generator,
List,
Optional,
Sequence,
Tuple,
Union,
... | lumapps/lumapps-sdk | lumapps/api/base_client.py | .py | 5d75108febd293b0 | 7.45 | 7 |
from typing import Any, Dict, Optional, Union
import httpx
from lumapps.api.base_client import BaseClient
from lumapps.api.errors import BaseClientError
def create_new_media(
client: BaseClient,
file_data_or_path: Union[bytes, str],
doc_path: str,
filename: str,
mimetype: str,
is_shared: boo... | lumapps/lumapps-sdk | lumapps/api/helpers/medias.py | .py | aa67ec8f51ca48fb | 7.45 | 7 |
import json
from typing import Any, Dict
import httpx
import jwt
from lumapps.api.decorators import retry_on_http_status_error
from lumapps.api.errors import (
LumAppsJWTClaimsError,
LumAppsJwtCustomError,
LumAppsJwtHeaderError,
LumAppsJwtInvalidClaimError,
LumAppsJwtTokenExpiredError,
)
JWKS_URL... | lumapps/lumapps-sdk | lumapps/api/lumapps_jwt.py | .py | 22c3c6b2739fa74d | 7.45 | 7 |
#py3
import numpy as np
import copy
import time
import logging
logging.basicConfig(level=logging.DEBUG,
format='%(asctime)s %(filename)s[line:%(lineno)d] %(levelname)s %(message)s',
datefmt='%a, %d %b %Y %H:%M:%S',
filemode='a')
grid = [
[0... | fooSynaptic/NLP-utils | Coding/Dijkstra_Floyd.py | .py | 596cc267fce08747 | 7.42 | 6 |
# source from leetcode
from time import time
xrange = range
def permuteUnique(nums, verbose = False):
ans = [[]]
for n in nums:
new_ans = []
for l in ans:
for i in xrange(len(l)+1):
new_ans.append(l[:i]+[n]+l[i:])
if verbose: print("Before handle du... | fooSynaptic/NLP-utils | Coding/permutation.py | .py | dbde78ce584a0f89 | 7.42 | 6 |
'''
Single case is one of the programing style, we employed single case to hadle classes with only one instance.
For different position in code we can reach the only one object instance with the gurantee of Single case mode.
In the case the instance not exists, the pattern will build a new instance, if exists, it wil... | fooSynaptic/NLP-utils | Coding/single_Case.py | .py | 24355177e6111211 | 7.42 | 6 |
# encoding=utf-8
# /usr/bin/python3
from bs4 import BeautifulSoup as bs
import bs4
import re
import numpy as np
"""Implementation tools... """
def tokenfeatures(word):
""" Obsevation state features """
features = []
###
features.append("token==" + word)
###
mid = len(word)//2
if mid... | fooSynaptic/NLP-utils | ML/PGM/CRF/crfSpellChecking/utils.py | .py | 6a3d24e73b272ff0 | 7.42 | 6 |
# encoding=utf-8
# /usr/bin/python3
"""crf implementation from scratch"""
import numpy as np
from collections import defaultdict
from numpy import empty, zeros, ones, log, exp, add, int32
from numpy.random import uniform
from utils import *
import os
import random
random.seed(1234)
from sklearn.externals import jobl... | fooSynaptic/NLP-utils | ML/PGM/CRF/crf_from_scratch/models.py | .py | ffe72e38d230e835 | 7.42 | 6 |
# encoding=utf-8
# /usr/bin/python3
from bs4 import BeautifulSoup as bs
import bs4
import re
import numpy as np
"""Implementation tools... """
def tokenfeatures(word):
""" Obsevation state features """
features = []
### 1
features.append("token==" + word)
### 2
mid = len(word)//2
if ... | fooSynaptic/NLP-utils | ML/PGM/CRF/crf_from_scratch/utils.py | .py | 9923b312b799a1d7 | 7.42 | 6 |
# encoding = utf-8
# /usr/bin/python3
'''
This program implemented the vertibi algorithm inference while have
- 1. The state-state transition matrix
- 2. The state-observation transition matrix
- 3. Initial state
- ref: https://zhuanlan.zhihu.com/p/63087935
'''
__author__ = 'fooSynaptic'
import numpy as np
def ... | fooSynaptic/NLP-utils | ML/Vivid_veterbi.py | .py | fe75ba668a696abe | 7.42 | 6 |
'''
Implementation for the Monte_carlo algorithms in chaper 4 of AI handbook
- ref: http://www.huaxiaozhuan.com/%E6%95%B0%E5%AD%A6%E5%9F%BA%E7%A1%80/chapters/4_monte_carlo.html
'''
from math import pi
import numpy as np
import random
from random import randint
from collections import Counter
from scipy import stats
im... | fooSynaptic/NLP-utils | ML/hands_on_handbooks_from_scratch/Chp_4_monte_carlo.py | .py | b1c807aa4dde48f2 | 7.42 | 6 |
# encoding = utf-8
# /usr/bin/python3
"""
## IBM translation model
整个目标是通过EM算法学习IBM model中的transition prob参数，
通过EM算法，可以在迭代统计平行语料的过程中，不断计算概率 t(e|f) 的似然概率，
并更新到参数中，以达到学习整个参数中最大alignment对应最大概率的目的.
- ref: http://www.cs.columbia.edu/~mcollins/courses/nlp2011/notes/ibm12.pdf
"""
import numpy as np
from time import time
fr... | fooSynaptic/NLP-utils | ML/machineTranslation/SMT/IBM_translationModel.py | .py | 0319d42ab6891062 | 7.42 | 6 |
# encoding = utf - 8
# /usr/bin/python3
"""The initial parameter of W can influence the iteration steps heavily."""
import numpy as np
import random
import matplotlib.pyplot as plt
import time
from optimizer import *
import os
num_inputs = 2
num_examples = 1000
true_w = [22.5, -43.3]
true_b = 54.2
features = np.ran... | fooSynaptic/NLP-utils | ML/regression/linearRegression.py | .py | 68b985fce90e1414 | 7.42 | 6 |
# encoding = utf-8
# /usr/bin/python3
states = ('Rainy', 'Sunny')
observations = ('walk', 'shop', 'clean')
start_probability = {'Rainy': 0.6, 'Sunny': 0.4}
transition_probability = {
'Rainy' : {'Rainy': 0.7, 'Sunny': 0.3},
'Sunny' : {'Rainy': 0.4, 'Sunny': 0.6},
}
emission_probability = {
'Rai... | fooSynaptic/NLP-utils | ML/veterbi.py | .py | 1b2de5f78972a799 | 7.42 | 6 |
"""
NLP_utils Coding 模块性能测试
对比: 编辑距离、字符串匹配、LDA、Seq2Seq、词云
"""
import time
import sys
import os
import numpy as np
from typing import List, Tuple
# 添加项目路径
sys.path.insert(0, os.path.join(os.path.dirname(__file__), '..'))
class BenchmarkResult:
"""基准测试结果"""
def __init__(self, name: str, nlp_utils_time: float,... | fooSynaptic/NLP-utils | benchmark/coding_benchmark.py | .py | 53240b40015b095d | 7.42 | 6 |
"""
运行所有 benchmark 并生成报告
"""
import sys
import os
import json
from datetime import datetime
# 导入测试模块
sys.path.insert(0, os.path.dirname(__file__))
try:
from coding_benchmark import run_all_benchmarks as run_coding
from ml_benchmark import benchmark_all_ml as run_ml
except ImportError as e:
print(f"Error ... | fooSynaptic/NLP-utils | benchmark/run_all.py | .py | 1d81d1381ead7174 | 7.42 | 6 |
"""A set of functions for calculating typical cluster parameters.
Todo: error treatment here could be made more bayesian
"""
from typing import Optional
from astropy.coordinates import SkyCoord
import numpy as np
import pandas as pd
from .constants import mas_per_yr_to_rad_per_s, pc_to_m, deg_to_rad
def _handle_r... | emilyhunt/ocelot | src/ocelot/calculate/calculate.py | .py | 5e77fff229029d59 | 7.57 | 13 |
"""Generic calculation utilities used across the module."""
import numpy as np
from numpy.typing import ArrayLike, NDArray
from typing import Optional, Union
from ocelot.util.check import _check_matching_lengths_of_non_nones
from scipy.stats import directional_stats
def _weighted_standard_deviation(x: ArrayLike, weig... | emilyhunt/ocelot | src/ocelot/calculate/generic.py | .py | 3c035ab8c3a0e747 | 7.57 | 13 |
"""Different methods for calculating the center of a cluster in spherical coordinates.
(This is actually oddly difficult, thanks to how spheres work. Damn spheres.)
"""
import numpy as np
from numpy.typing import ArrayLike
from ocelot.calculate.generic import spherical_mean
def mean_position(
longitudes: ArrayL... | emilyhunt/ocelot | src/ocelot/calculate/position.py | .py | 109877737573221f | 7.57 | 13 |
"""A number of functions for pre-processing data before clustering can begin."""
from typing import Literal
import numpy as np
import pandas as pd
import healpy
from sklearn.preprocessing import RobustScaler, StandardScaler
from astropy.coordinates import SkyCoord
from astropy import units as u
from scipy.optimize i... | emilyhunt/ocelot | src/ocelot/cluster/preprocess.py | .py | 02230e8b93b43fa7 | 7.57 | 13 |
"""Functions for re-sampling Gaia data within errors."""
import numpy as np
import pandas as pd
from typing import Sequence, Literal
from ocelot.util.stats import vectorized_multivariate_normal_rvs
def resample_gaia_astrometry(
data_gaia: pd.DataFrame,
n_resamples: int = 1,
suffixes: Sequence[str] | None... | emilyhunt/ocelot | src/ocelot/cluster/resample.py | .py | ec405ac3b9613ab7 | 7.57 | 13 |
"""Set of functions for reading in isochrones from their downloaded formats and processing them into useful spaces."""
from pathlib import Path
from typing import Union, Optional, List
import numpy as np
import pandas as pd
from astropy.io import ascii
def read_parsec(
file_location: Union[Path, List[Path], str... | emilyhunt/ocelot | src/ocelot/isochrone/io.py | .py | 24b0a4c622cdcfb9 | 7.57 | 13 |
import numpy as np
from scipy.interpolate import RegularGridInterpolator
from ocelot.model.binaries._base import BaseBinaryStarModelWithEccentricities
from imf.distributions import BrokenPowerLaw, PowerLaw
class MoeDiStefanoMultiplicityRelation(BaseBinaryStarModelWithEccentricities):
def __init__(self) -> None:
... | emilyhunt/ocelot | src/ocelot/model/binaries/moe_distefano_17.py | .py | bee51a6955f62c08 | 7.57 | 13 |
import numpy as np
from numpy.typing import ArrayLike
from abc import ABC, abstractmethod
class BaseDifferentialReddeningModel(ABC):
accepts_random_seed = False # Class attribute for whether or not a given model needs a seed in __init__
def extinction(
self,
x: ArrayLike,
y: ArrayLik... | emilyhunt/ocelot | src/ocelot/model/differential_reddening/_base.py | .py | baeb372cc9ee3c01 | 7.57 | 13 |
"""This file contains an implementation of the King+1962 empirical star cluster
model: https://ui.adsabs.harvard.edu/abs/1962AJ.....67..471K/abstract
In addition, some of the equations from the paper are also implemented directly as
methods in this file.
"""
import numpy as np
from numba import jit
from ._base impor... | emilyhunt/ocelot | src/ocelot/model/distribution/king62.py | .py | f696c7c4289f3893 | 7.57 | 13 |
"""Functions common to many different observation classes."""
from __future__ import annotations
import pandas as pd
from astropy.coordinates import SkyCoord
from astropy.units import Quantity
import ocelot.model.observation
import ocelot.simulate.cluster
def calculate_separation(primary: pd.DataFrame, secondary: pd... | emilyhunt/ocelot | src/ocelot/model/observation/common.py | .py | 01abf2fbd8f253b8 | 7.57 | 13 |
"""Main class defining an observation made with Gaia DR3."""
from __future__ import annotations
from ocelot.model.observation._base import (
BaseObservation,
BaseSelectionFunction,
)
import ocelot.simulate.cluster
from scipy.interpolate import interp1d
import numpy as np
import pandas as pd
from numpy.typing i... | emilyhunt/ocelot | src/ocelot/model/observation/gaia/gaia_dr3.py | .py | 44c9d3a3d1ed7cd6 | 7.57 | 13 |
"""A generic subsample selection function class that can be used on many different
surveys.
"""
import numpy as np
import pandas as pd
from ocelot.model.observation._base import BaseSelectionFunction
from scipy.interpolate import interp1d
from ocelot.util.stats import variable_bin_histogram
from ocelot.util.stats impo... | emilyhunt/ocelot | src/ocelot/model/observation/subsample_selection.py | .py | cd238e9a2131f9c9 | 7.57 | 13 |
"""Functions for dealing with astrometry-related things."""
from __future__ import annotations # Necessary to type hint without cyclic import
import numpy as np
from ocelot.util.random import unit_vectors
import ocelot.simulate.cluster
from astropy.coordinates import SkyCoord, CartesianRepresentation, CartesianDiffer... | emilyhunt/ocelot | src/ocelot/simulate/astrometry.py | .py | 3f7f54663c9aa053 | 7.57 | 13 |
"""Methods to pair stars randomly picked from the IMF into binaries."""
from __future__ import annotations
import numpy as np
from ocelot.model.binaries import (
BaseBinaryStarModelWithPeriods,
BaseBinaryStarModelWithEccentricities,
)
import ocelot.simulate.cluster
from numba import jit
def make_binaries(clu... | emilyhunt/ocelot | src/ocelot/simulate/binaries.py | .py | 53308185bb5e0fb6 | 7.57 | 13 |
"""
Created on 2024-01-21
@author: wf
"""
from pyparsing import (
Group,
Literal,
OneOrMore,
Optional,
Suppress,
Word,
alphanums,
alphas,
restOfLine,
)
class DocstringParser:
"""
A Python docstring parser.
"""
def __init__(self):
# Define basic elements
... | WolfgangFahl/pyLoDStorage | lodstorage/docstring_parser.py | .py | 7670a16d2ca9c795 | 7.57 | 13 |
"""
duckdb_query.py
DuckDB backend for pyLoDStorage.
Created on 2026-02-21
@author: wf
"""
import logging
from typing import Any, Generator
import duckdb
from lodstorage.query import Endpoint
class DuckDBQuery:
"""
A class to manage and execute DuckDB queries.
Attributes:
path (str): path t... | WolfgangFahl/pyLoDStorage | lodstorage/duckdb_query.py | .py | 64526e736e3c786e | 7.57 | 13 |
"""
Created on 2025-12-01
@author: wf
"""
import logging
import traceback
class ExceptionHandler:
"""
handle exceptions
"""
@classmethod
def handle(cls, msg: str, ex: Exception, debug: bool = False):
"""Centralized exception logging (non-fatal).
Args:
msg: context m... | WolfgangFahl/pyLoDStorage | lodstorage/exception_handler.py | .py | 7b92a5666b01e2b6 | 7.57 | 13 |
"""
Created on 2024-01-28
@author: wf
"""
from dataclasses import field
from typing import Dict, List, Optional, Type
from basemkit.yamlable import lod_storable
from rdflib.namespace import XSD
@lod_storable
class Slot:
"""
Represents a slot in the LinkML schema, equivalent to a field or property.
"""
... | WolfgangFahl/pyLoDStorage | lodstorage/linkml.py | .py | a889418042de49e3 | 7.57 | 13 |
"""
Created on 2024-01-21
@author: wf
"""
from collections.abc import Iterable, Mapping
from dataclasses import fields, is_dataclass
from typing import Union
from lodstorage.docstring_parser import DocstringParser
from lodstorage.linkml import Class, PythonTypes, Schema, Slot
class LinkMLGen:
"""
Class for... | WolfgangFahl/pyLoDStorage | lodstorage/linkml_gen.py | .py | bc48a8bafbf72e9c | 7.57 | 13 |
"""
Created on 2021-01-31
@author: wf
"""
class LOD(object):
"""
list of Dict aka Table
"""
def __init__(self, name):
"""
Constructor
"""
self.name = name
pass
@staticmethod
def getFields(listOfDicts, sampleCount: int = None):
"""
Extr... | WolfgangFahl/pyLoDStorage | lodstorage/lod.py | .py | 9d889f8d31b369b9 | 7.57 | 13 |
"""
Created on 2022-06-20
see
https://github.com/tyleradams/json-toolkit
https://stackoverflow.com/questions/36021526/converting-an-array-dict-to-xml-in-python
@author: tyleradams
@author: wf
"""
from xml.dom.minidom import parseString
from dicttoxml2 import dicttoxml
class Lod2Xml:
"""
convert a ... | WolfgangFahl/pyLoDStorage | lodstorage/lod2xml.py | .py | 13768bdeaf1e5ba4 | 7.57 | 13 |
"""
Created 2021
@author: wf
"""
import csv
import io
from typing import Any, Dict, List
from lodstorage.lod import LOD
class CSV:
"""
helper for converting data in csv format to list of dicts (LoD) and vice versa
"""
_instance = None
def __new__(cls, dialect: str = "excel", quoting: int = cs... | WolfgangFahl/pyLoDStorage | lodstorage/lod_csv.py | .py | 53af09ad453166e9 | 7.57 | 13 |
"""
Created on 2024-09-12
@author: wf
"""
from typing import Dict, List, Optional
from lodstorage.query import EndpointManager, Query, QueryManager
from lodstorage.sql_backend import SQLBackend, get_sql_backend
from lodstorage.yaml_path import YamlPath
class MultiLanguageQueryManager:
"""
Query manager for... | WolfgangFahl/pyLoDStorage | lodstorage/multilang_querymanager.py | .py | fb0b19509fc865d4 | 7.57 | 13 |
"""
Created on 2020-08-21
@author: wf
"""
# redudant copy
# original is at
# https://github.com/WolfgangFahl/py-3rdparty-mediawiki/blob/master/wikibot/mwTable.py
class MediaWikiTable(object):
"""
helper for https://www.mediawiki.org/wiki/Help:Tables
"""
def __init__(
self, wikiTable=True, c... | WolfgangFahl/pyLoDStorage | lodstorage/mwTable.py | .py | a3346830b5f50fbf | 7.57 | 13 |
"""
mysql.py:
MySQL and MariaDB support
"""
import logging
from typing import Any, Dict, Generator, List
import pymysql
from lodstorage.query import Endpoint
class MySqlQuery:
"""
A class to manage and execute mySQL queries with optional debugging.
Attributes:
endpoint_info (Endpoint): endpo... | WolfgangFahl/pyLoDStorage | lodstorage/mysql.py | .py | 166d4b9bbcb07596 | 7.57 | 13 |
"""
Created on 2026-07-22
NPQ-FakeSparql: serve named parameterized queries (NPQs) over the SPARQL
protocol - without any SPARQL engine behind them. The technology stays
hidden; only input parameters and output variables are relevant (see the
snapquery EKAW2024 paper). The NPQ name lives in the URL path, input
paramet... | WolfgangFahl/pyLoDStorage | lodstorage/npq_endpoint.py | .py | b8e6300a064edc4c | 7.57 | 13 |
"""
Created on 2024-05-06
@author: wf
"""
import argparse
import re
from dataclasses import field
from typing import Dict, List, Optional
from basemkit.yamlable import lod_storable
@lod_storable
class Param:
"""
a parameter (input or output) for a query
"""
name: str
type: str # python type
... | WolfgangFahl/pyLoDStorage | lodstorage/params.py | .py | 1aad7eb070e12da5 | 7.57 | 13 |
"""
Created on 2020-07-05
@author: wf
"""
import os
from collections import Counter
import matplotlib.pyplot as plt
import numpy as np
class Plot(object):
"""
create Plot based on counters
see https://stackoverflow.com/questions/19198920/using-counter-in-python-to-build-histogram
"""
def __ini... | WolfgangFahl/pyLoDStorage | lodstorage/plot.py | .py | 0261c23a50e20542 | 7.57 | 13 |
"""
postgresql.py:
PostgreSQL support
"""
import logging
from typing import Any, Dict, Generator, List
import psycopg2
import psycopg2.extras
from lodstorage.query import Endpoint
class PostgreSqlQuery:
"""
A class to manage and execute PostgreSQL queries with optional debugging.
Attributes:
... | WolfgangFahl/pyLoDStorage | lodstorage/postgresql.py | .py | 18fa1b5c4fd08b0c | 7.57 | 13 |
"""
Created on 2025-06-04
@author: wf
"""
import os
from dataclasses import dataclass, field
from typing import ClassVar, Dict, List, Optional
from basemkit.yamlable import lod_storable
from lodstorage.yaml_path import YamlPath
@dataclass
class PrefixConfig:
"""
Configuration for SPARQL prefixes
"""
... | WolfgangFahl/pyLoDStorage | lodstorage/prefix_config.py | .py | d12f5116d161f1e8 | 7.57 | 13 |
"""
Created on 2024-03-02
@author: wf
"""
import re
class Prefixes:
"""
Handles the generation of standard SPARQL prefix declarations for queries.
This utility class simplifies the inclusion of common prefixes used in SPARQL
queries by providing a method to generate the necessary PREFIX lines based ... | WolfgangFahl/pyLoDStorage | lodstorage/prefixes.py | .py | 864211258b994bbf | 7.57 | 13 |
"""
Created on 2022-11-18
@author: wf
"""
import time
class Profiler:
"""
simple profiler
"""
def __init__(self, msg, profile=True, with_start: bool = True):
"""
construct me with the given msg and profile active flag
Args:
msg(str): the message to show if profi... | WolfgangFahl/pyLoDStorage | lodstorage/profiler.py | .py | f2ccf585d94a85d0 | 7.57 | 13 |
"""
Created on 2024-08-21
@author: wf
"""
import json
from argparse import ArgumentParser, Namespace
from pathlib import Path
from typing import Any, Dict, List
from lodstorage.lod2xml import Lod2Xml
from lodstorage.lod_csv import CSV
from lodstorage.params import Params, StoreDictKeyPair
from lodstorage.query impor... | WolfgangFahl/pyLoDStorage | lodstorage/query_cmd.py | .py | 002350f2b60c002f | 7.57 | 13 |
"""
Created on 2022-02-13
@author: wf
"""
import logging
import os
import re
import sys
import traceback
import urllib.parse
from argparse import ArgumentParser, RawDescriptionHelpFormatter
import requests
from lodstorage.prefix_config import PrefixConfigs
from lodstorage.query import Endpoint, EndpointManager, For... | WolfgangFahl/pyLoDStorage | lodstorage/querymain.py | .py | bca080682c82da88 | 7.57 | 13 |
"""
Created on 2024-08-24
@author: wf
"""
from functools import wraps
from ratelimit import limits, sleep_and_retry
class RateLimiter:
"""
Wrap the @limits decorator in a new decorator
"""
def __init__(self, calls_per_minute: int = None):
if calls_per_minute is None:
calls_per_... | WolfgangFahl/pyLoDStorage | lodstorage/rate_limiter.py | .py | f1d8797b6a85a20d | 7.57 | 13 |
"""
Created on 2025-06-01
@author: wf
"""
from enum import Enum
from SPARQLWrapper import JSON, N3, RDF, TURTLE
class RdfFormat(Enum):
"""
RDF serialization formats with MIME types, file extensions, and SPARQLWrapper constants.
"""
TURTLE = ("turtle", "text/turtle", ".ttl", TURTLE)
RDF_XML = (... | WolfgangFahl/pyLoDStorage | lodstorage/rdf_format.py | .py | 1f06e3324af5e35d | 7.57 | 13 |
"""
Created on 2024-01-21
@author: wf
"""
import json
import urllib.request
from dataclasses import field
from datetime import date
from typing import Any, Dict, List, Optional
from basemkit.yamlable import DateConvert, lod_storable
from slugify import slugify
@lod_storable
class Royal:
"""
Represents a me... | WolfgangFahl/pyLoDStorage | lodstorage/sample2.py | .py | 3e263f72b757f537 | 7.57 | 13 |
"""
Created on 2021-01-26
@author: wf
"""
from collections import Counter
class SchemaManager(
object,
):
"""
a manager for schemas
"""
def __init__(self, schemaDefs=None, baseUrl: str = None):
"""
constructor
Args:
schemaDefs(dict): a dictionary of s... | WolfgangFahl/pyLoDStorage | lodstorage/schema.py | .py | 153f3bf07ac15822 | 7.57 | 13 |
"""
sql_backend.py
Unified SQL backend abstraction for pyLoDStorage.
Defines the SQLBackend Protocol (duck-typed interface) and the
get_sql_backend() factory that resolves the correct backend from
an endpoint descriptor, hiding the jdbc:mysql, jdbc:duckdb, and jdbc:postgresql
routing details from all call sites.
Cre... | WolfgangFahl/pyLoDStorage | lodstorage/sql_backend.py | .py | 632ee6029bc827cd | 7.57 | 13 |
"""
Created on 2024-08-24
@author: wf
"""
import datetime
import logging
import sqlite3
class DatetimeAdapter:
"""Class for converting date and time formats with optional lenient error handling."""
def __init__(self, lenient: bool = False):
"""Initialize with optional lenient error handling."""
... | WolfgangFahl/pyLoDStorage | lodstorage/sqlite_api.py | .py | 1494c921f6450f13 | 7.57 | 13 |
"""
Created on 2020-08-29
@author: wf
"""
import os
from enum import Enum
from pathlib import Path
class StoreMode(Enum):
"""
possible supported storage modes
"""
JSONPICKLE = 1 # JSON Pickle
JSON = 2
SQL = 3
SPARQL = 4
YAML = 5
class StorageConfig(object):
"""
a storage ... | WolfgangFahl/pyLoDStorage | lodstorage/storageconfig.py | .py | ff12f51e8e4da83e | 7.57 | 13 |
"""
Created on 2023-12-27
@author: wf
"""
from dataclasses import dataclass, field
from typing import Any, Dict, List, Optional
from tabulate import tabulate
@dataclass
class SyncPair:
"""
A class to represent a pair of data sources for synchronization.
Attributes:
title (str): The ti... | WolfgangFahl/pyLoDStorage | lodstorage/sync.py | .py | 364679ce23791992 | 7.57 | 13 |
"""
Created on 2021-06-13
@author: wf
"""
from tabulate import tabulate
class TabulateCounter(object):
"""
helper for tabulating Counters
"""
def __init__(self, counter):
"""
Constructor
"""
self.counter = counter
def mostCommonTable(
self, headers=["#",... | WolfgangFahl/pyLoDStorage | lodstorage/tabulateCounter.py | .py | a8b0147eb7cd9721 | 7.57 | 13 |
"""
Created on 2025-11-23
@author: wf
"""
class ActionStats:
"""Helper class to track success rates of actions."""
def __init__(self):
self.success_count = 0
self.total_count = 0
self.current = None
def add(self, is_success: bool):
"""adds a single result."""
sel... | WolfgangFahl/pyLoDStorage | tests/action_stats.py | .py | f10433a637a61184 | 8.07 | 13 |
"""
Created on 2021-08-19
@author: wf
"""
import getpass
import os
import time
from unittest import TestCase
class Basetest(TestCase):
"""
base test case
"""
def setUp(self, debug=False, profile=True):
"""
setUp test environment
"""
TestCase.setUp(self)
self.... | WolfgangFahl/pyLoDStorage | tests/basetest.py | .py | c1ac81ffcf1005b8 | 8.07 | 13 |
"""
Created on 2025-11-23
@author: wf
"""
import os
from lodstorage.query import EndpointManager
from tests.basetest import Basetest
class EndpointTest(Basetest):
"""
base class for endpoint tests
"""
def setUp(self, debug=False, profile=True):
Basetest.setUp(self, debug=debug, profile=pro... | WolfgangFahl/pyLoDStorage | tests/endpoint_test.py | .py | 441545b3a46bc689 | 8.07 | 13 |
"""
Created on 2020-07-05
@author: wf
"""
import unittest
from lodstorage.plot import Plot
from tests.basetest import Basetest
class TestPlot(Basetest):
"""
test the Plot helper class
"""
def testPlot(self):
"""test a plot based on a Counter"""
valueList = ["A", "B", "A", "C", "A",... | WolfgangFahl/pyLoDStorage | tests/test_Plot.py | .py | 0173c37b5cbea00d | 8.07 | 13 |
"""Cross-validate a multi-task neural network on the Gaultois targets."""
# %%
import os
import numpy as np
import pandas as pd
import torch
from sklearn.model_selection import KFold
from torch import nn
from torch.utils.data import DataLoader
from thermo.bnn.torch_dropout import Normalized
from thermo.data import d... | janosh/thermo | notebooks/multitask/cross_val.py | .py | a0d28cb381e54cd1 | 7.64 | 18 |
"""Train an ensemble of multi-task neural networks on the Gaultois targets."""
# %%
import torch
from torch import nn
from torch.utils.data import DataLoader
from thermo.bnn.torch_dropout import GaultoisData
from thermo.plots import plot_output
from thermo.utils import ROOT
# %%
head = lambda: nn.Sequential(
nn... | janosh/thermo | notebooks/multitask/ensemble.py | .py | a20b26a8556e2a1e | 7.64 | 18 |
"""Bayesian neural network building blocks: priors, likelihoods and nets."""
import itertools
from collections.abc import Callable
from functools import partial
from typing import Any
import tensorflow as tf
import tensorflow_probability as tfp
def dense(inputs, w, b, activation=tf.identity) -> tf.Tensor:
"""Ap... | janosh/thermo | thermo/bnn/__init__.py | .py | 724ea0582d43ac35 | 7.64 | 18 |
"""Hamiltonian Monte Carlo sampling and prediction for BNNs."""
from typing import Any
import tensorflow as tf
import tensorflow_probability as tfp
from thermo.bnn import build_net, chunks, target_log_prob_fn_factory
def pre_train_nn(x_train, y_train, nodes_per_layer, epochs=100) -> tuple:
"""Pre-train NN to g... | janosh/thermo | thermo/bnn/hmc.py | .py | a427158bb093dcce | 7.64 | 18 |
"""Maximum a posteriori (MAP) training and prediction for BNNs."""
import numpy as np
import tensorflow as tf
from thermo import bnn
def get_map_trace(
target_log_prob_fn, state, n_iter=1000, save_every=10, callbacks=()
) -> tuple[list, list]:
"""Run Adam to maximize target_log_prob_fn, returning a trace of... | janosh/thermo | thermo/bnn/map.py | .py | c7766325a6fb3900 | 7.64 | 18 |
"""TensorFlow Monte Carlo dropout model with uncertainty estimation."""
from typing import Any
import tensorflow as tf
from thermo.utils.decorators import timed
class Dropout(tf.keras.layers.Layer):
"""Always-on dropout layer. Disregards the training flag set
to true in model.fit() and false in model.predi... | janosh/thermo | thermo/bnn/tf_dropout.py | .py | 90c3edeafa5d1932 | 7.64 | 18 |
"""PyTorch Monte Carlo dropout model with uncertainty estimation."""
from collections.abc import Callable, Sequence
from datetime import UTC, datetime
from typing import Any
import numpy as np
import torch
from pandas import DataFrame
from torch import nn
from torch.utils.data import DataLoader, Dataset
from torch.ut... | janosh/thermo | thermo/bnn/torch_dropout.py | .py | a19d8b913d1a9392 | 7.64 | 18 |
"""Correlation-based candidate selection and random baselines."""
from random import shuffle
import numpy as np
def rand_obj_val_avr(corr_mat: np.ndarray, n_select: int, n_repeats: int = 50) -> float:
"""Simulates the random baseline for the discrete constrained optimization
problem of finding the n_select ... | janosh/thermo | thermo/correlation.py | .py | 27d4985d2e27e8d3 | 7.64 | 18 |
"""Load the Gaultois thermoelectrics database and screening dataset."""
from __future__ import annotations
from typing import TYPE_CHECKING
from pandas import DataFrame, read_csv
from thermo.utils import ROOT
if TYPE_CHECKING:
from collections.abc import Sequence
def to_type(df: DataFrame, dtype: str = "flo... | janosh/thermo | thermo/data/load.py | .py | eeabe25591dd1938 | 7.64 | 18 |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.