text stringlengths 185 73.3k | repo stringlengths 7 100 | path stringlengths 4 146 | language stringclasses 7
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import hmac
import hashlib
import os
from flask import Flask, request, abort
app = Flask(__name__)
# Define your webhook signing secret here
SIGNING_SECRET = os.environ["OPSLEVEL_SIGNING_SECRET"]
# Define required and action-specific headers
REQUIRED_HEADERS = {'X-OpsLevel-Timing'}
# Ensure the first letter is capit... | OpsLevel/community-integrations | scripts/verify_opslevel_webhook_signature/python/verify_opslevel_webhook_signature.py | .py | d5d56ad4c9cd93f1 | 7.54 | 11 |
import abc
class Protocol(metaclass=abc.ABCMeta):
@classmethod
def __subclasshook__(cls, subclass):
return (
hasattr(subclass, "name")
and hasattr(subclass, "debug")
and callable(subclass.debug)
and hasattr(subclass, "info")
and callable(subc... | slackapi/python-slack-hooks | slack_cli_hooks/protocol/protocol.py | .py | 841766d78ba1bc70 | 7.5 | 9 |
from unittest.mock import Mock
from slack_cli_hooks.protocol.protocol import Protocol
def debug(self, msg: str, *args, **kwargs):
"""This is a mock"""
pass
def info(self, msg: str, *args, **kwargs):
"""This is a mock"""
pass
def warning(self, msg: str, *args, **kwargs):
"""This is a mock"""
... | slackapi/python-slack-hooks | tests/mock_protocol.py | .py | 7c8c63c6191ef3c1 | 7 | 9 |
"""Generate the static figures the document embeds.
The narrative figures are rendered ahead of time rather than in live cells, so the page
is readable the moment it loads. The Pyodide runtime is several megabytes and takes a
few seconds to start; gating the argument behind it would mean a reader sees an empty
page fi... | tmfreiberg/black-scholes-option-pricer | docs/make_figures.py | .py | b679556813064af9 | 7.45 | 7 |
"""Type aliases and helpers for the scalar/array boundary.
Every mathematical function in this package accepts either Python floats or NumPy
arrays, and returns whichever the caller supplied. That dual behaviour is what lets the
same code price one option interactively and fill a 200x200 sensitivity grid, with no
seco... | tmfreiberg/black-scholes-option-pricer | src/bsm/_numeric.py | .py | 039f8c564184a38b | 7.45 | 7 |
"""Command-line interface.
Every capability the library offers is reachable from a shell, so any claim made in the
documentation can be checked with a one-line command rather than a Python session. The
entry point is ``bsm``.
Percentages at the boundary
---------------------------
The library works in decimals throug... | tmfreiberg/black-scholes-option-pricer | src/bsm/cli.py | .py | 37c430fa3667ab8f | 7.45 | 7 |
"""Rendering for surfaces and curves.
Matplotlib is an optional dependency, declared under the ``plot`` extra. Everything
else in the package works without it; importing this module without it installed raises
an :class:`ImportError` that says which extra to install rather than a bare
``ModuleNotFoundError`` from thre... | tmfreiberg/black-scholes-option-pricer | src/bsm/plot.py | .py | 81b206fbace65407 | 7.45 | 7 |
"""Brent's method for finding a root of a scalar function.
Implied volatility is an inverse problem: the price is a known, strictly increasing
function of volatility, and the task is to run it backwards. That makes a bracketing
root-finder the right tool, and Brent's method the right root-finder — it keeps the
guarant... | tmfreiberg/black-scholes-option-pricer | src/bsm/roots.py | .py | ed24dea33f32e324 | 7.45 | 7 |
"""A record of which parameter regimes have been explored.
This is a log, not a cache. Caching would be indefensible: a 41-by-21 surface takes
under a millisecond to compute, so storing one to avoid recomputing it would trade a
free operation for a disk round trip and a consistency problem. What is worth storing
is th... | tmfreiberg/black-scholes-option-pricer | src/bsm/store.py | .py | 3f579daee1a2e00c | 7.45 | 7 |
"""Value objects describing an option contract and the market it is priced in.
The package draws a deliberate line between two layers:
* This module is the **validated boundary**. Constructing a :class:`Contract` or a
:class:`Market` checks every precondition the pricing formulas rely on, and raises
immediately i... | tmfreiberg/black-scholes-option-pricer | src/bsm/types.py | .py | f531259a95268afe | 7.45 | 7 |
"""Browser smoke test for the published document.
Skipped unless `BSM_SITE_DIR` points at a built site, so a local `pytest` run is
unaffected. In CI it runs against the artifact the deploy job is about to publish.
What it checks is the one thing nothing else can: that a reader arriving at the page
gets a working runt... | tmfreiberg/black-scholes-option-pricer | tests/e2e/test_document.py | .py | 6d913fa494f65c1d | 7.95 | 7 |
"""Absolute accuracy of the pricing pipeline, against a 50-digit reference.
The CDF is checked against `math.erfc` in test_normal; that bounds the error in a
probability. This module bounds the error in a *price*, which is the quantity anyone
actually uses, and which amplifies the CDF error by roughly the spot level.
... | tmfreiberg/black-scholes-option-pricer | tests/unit/test_accuracy.py | .py | de0cba947acd0c96 | 7.95 | 7 |
"""Tests for the model-free no-arbitrage relationships."""
from __future__ import annotations
import math
import pytest
from hypothesis import given
from hypothesis import strategies as st
from bsm.bounds import parity_residual, price_bounds
from bsm.pricing import call_price, put_price
from bsm.types import Option... | tmfreiberg/black-scholes-option-pricer | tests/unit/test_bounds.py | .py | 98fab5b2018b0ddd | 7.95 | 7 |
"""Tests for implied volatility."""
from __future__ import annotations
import pytest
from hypothesis import assume, given, settings
from hypothesis import strategies as st
from bsm import implied as implied_module
from bsm.bounds import price_bounds
from bsm.greeks import vega
from bsm.implied import (
ImpliedVo... | tmfreiberg/black-scholes-option-pricer | tests/unit/test_implied.py | .py | 0ecfdf808bd8f80a | 7.95 | 7 |
"""Tests for Merton jump-diffusion and the smile it generates.
Three things carry the module and are tested hardest: that zero intensity reduces
exactly to Black-Scholes, that the model-free relationships survive a model with jumps
in it, and that the smile has the shape the jump parameters imply rather than merely
be... | tmfreiberg/black-scholes-option-pricer | tests/unit/test_merton.py | .py | ea844133c5a04789 | 7.95 | 7 |
"""Tests for the standard normal density and distribution.
The central test is `test_matches_stdlib_oracle`. The shipped implementation is Hart's
algorithm, chosen because it vectorises; `math.erfc` is exact to within an ulp but
scalar-only. Pinning one against the other is what licenses the speed.
"""
from __future_... | tmfreiberg/black-scholes-option-pricer | tests/unit/test_normal.py | .py | 39ee7ff7bb4cc961 | 7.95 | 7 |
"""Tests for Brent's method.
The shipped implementation exists so the package needs no SciPy. SciPy is therefore the
oracle: `TestAgainstScipy` runs both over the same problems and requires agreement to
machine precision.
"""
from __future__ import annotations
import math
from collections.abc import Callable
import... | tmfreiberg/black-scholes-option-pricer | tests/unit/test_roots.py | .py | 1bef4e20dc9252c3 | 7.95 | 7 |
"""Tests for the validated boundary: Contract and Market."""
from __future__ import annotations
import dataclasses
import pytest
from bsm.types import Contract, Market, OptionKind
class TestOptionKind:
def test_string_membership(self) -> None:
assert OptionKind("call") is OptionKind.CALL
asser... | tmfreiberg/black-scholes-option-pricer | tests/unit/test_types.py | .py | 8d8cf55160b42c4d | 7.95 | 7 |
"""Render gradients around arbitrary Rich renderables for the documentation."""
from __future__ import annotations
from pathlib import Path
from rich.console import Console
from rich.markdown import Markdown
from rich.table import Table as RichTable
from rich_gradient import Gradient
from rich_gradient.theme import... | maxludden/rich-gradient | examples/gradient_showcase.py | .py | 6005a888dc2f28ad | 7.56 | 12 |
"""Render SVG examples for gradient convenience renderables."""
from __future__ import annotations
from pathlib import Path
from rich.console import Console
from rich_gradient import Columns, Pretty, Syntax, Table, Tree
from rich_gradient.theme import GRADIENT_TERMINAL_THEME
OUTPUT_DIR = Path(__file__).resolve().p... | maxludden/rich-gradient | examples/renderables_showcase.py | .py | 8e3571384ff25740 | 7.56 | 12 |
"""Render the Spectrum table for documentation."""
from __future__ import annotations
from pathlib import Path
from rich.console import Console
from rich_gradient.spectrum import Spectrum
from rich_gradient.theme import GRADIENT_TERMINAL_THEME
OUTPUT = Path(__file__).resolve().parents[1] / "docs" / "img" / "spectr... | maxludden/rich-gradient | examples/spectrum_overview.py | .py | 8bb2b7658d0ca2cf | 7.06 | 12 |
"""Compatibility wrapper for :mod:`rich_color_ext` optional helpers."""
from __future__ import annotations
import sys
from collections.abc import Callable
from functools import lru_cache
from typing import cast
# rich_color_ext (<=0.1.x) installs Rich's traceback handler as an import side
# effect; restore whatever ... | maxludden/rich-gradient | src/rich_gradient/_color_ext.py | .py | 6999663716b1b4ff | 7.56 | 12 |
"""Cached style ramps for gradient rendering."""
from __future__ import annotations
from dataclasses import dataclass, field
from math import ceil
from rich.color_triplet import ColorTriplet
from rich.style import Style
@dataclass(frozen=True)
class GradientRamp:
"""Precomputed Rich styles for a terminal-width... | maxludden/rich-gradient | src/rich_gradient/_gradient_ramp.py | .py | 36c0b89dd82b8cdf | 7.56 | 12 |
"""
Logger utility for rich-gradient.
Provides a Rich-styled, rotating, compressed log file and console output via loguru.
This module follows loguru's library convention: rich-gradient's log records
are disabled by default and the package never removes or shadows handlers the
host application has configured. Enabling... | maxludden/rich-gradient | src/rich_gradient/_logger.py | .py | c754ffdffe1c430f | 7.56 | 12 |
"""Animated gradient support built on top of Rich Live."""
import signal
import time
from collections.abc import Callable, Mapping, Sequence
from contextlib import suppress
from threading import Event, RLock, Thread
from typing import Any
from rich import get_console
from rich.align import Align, AlignMethod, Vertica... | maxludden/rich-gradient | src/rich_gradient/animated_gradient.py | .py | 5c617ec19b906293 | 7.56 | 12 |
"""Animated gradient Rule rendered with Rich Live.
This module provides an AnimatedRule class that mirrors the behavior of
``rich_gradient.rule.Rule`` but animates the gradient over time using the
same Live/animation machinery as ``AnimatedGradient`` and ``AnimatedPanel``.
"""
from __future__ import annotations
from... | maxludden/rich-gradient | src/rich_gradient/animated_rule.py | .py | c8887de8c654e5d8 | 7.56 | 12 |
"""Pure-Python runtime configuration for rich-gradient (JSON file + env overrides)."""
from __future__ import annotations
import builtins
import json
import os
from dataclasses import dataclass, field
from pathlib import Path
from typing import Any, ClassVar
from loguru import logger
from ._color_ext import install... | maxludden/rich-gradient | src/rich_gradient/config.py | .py | d2f79e25a49d1313 | 7.56 | 12 |
"""Gradient-enabled Rule built on Rich's Rule, powered by Gradient."""
from __future__ import annotations
from collections.abc import Sequence
from typing import Optional
from rich.align import AlignMethod
from rich.console import Console, ConsoleOptions, RenderResult
from rich.rule import Rule as RichRule
from rich... | maxludden/rich-gradient | src/rich_gradient/rule.py | .py | 0fedf443aae6aa02 | 7.56 | 12 |
"""rich_gradient.spectrum
Module providing a small color palette helper built on Rich.
This module exposes:
- SPECTRUM_COLORS: a mapping of hex color strings to human-friendly names.
- Spectrum: a convenience class that builds lists of Rich Color, Style,
and ColorTriplet objects drawn from the spectrum. It is it... | maxludden/rich-gradient | src/rich_gradient/spectrum.py | .py | 7a86de42de568c69 | 8.06 | 12 |
"""A container for style information, used by `gradient.Gradient'."""
from rich.console import Console
from rich.style import Style, StyleType
from rich.table import Table as RichTable
from rich.terminal_theme import TerminalTheme
from rich.theme import Theme
from rich_gradient.default_styles import DEFAULT_STYLES, s... | maxludden/rich-gradient | src/rich_gradient/theme.py | .py | df0e57e5e45b8f4f | 7.56 | 12 |
"""Benchmarks for rich-gradient rendering paths."""
from __future__ import annotations
from typing import Any
import pytest
from rich.console import Console, ConsoleRenderable
from rich.text import Text as RichText
from rich_gradient import AnimatedGradient, Gradient, Panel, Text
def _benchmark_console(width: int... | maxludden/rich-gradient | tests/benchmark_perf.py | .py | b460834660a53b56 | 8.06 | 12 |
"""Tests for the animated panel component."""
import os
from pathlib import Path
from rich.console import Console
from rich.panel import Panel as RichPanel
from rich_gradient.animated_panel import AnimatedPanel
from rich_gradient.panel import Panel
os.environ.setdefault(
"RICH_GRADIENT_CONFIG_HOME",
str((Pa... | maxludden/rich-gradient | tests/test_animated_panel.py | .py | c61f0ded68ffa757 | 8.06 | 12 |
"""Tests for AnimatedText."""
from rich.text import Text as RichText
from rich_gradient.animated_text import AnimatedText
def test_animated_text_rich_text_property():
"""Test that the rich_text property returns a RichText instance."""
animated = AnimatedText("Hello", colors=["#f00", "#0f0"])
rich_text =... | maxludden/rich-gradient | tests/test_animated_text.py | .py | b5fd3b285c069223 | 8.06 | 12 |
"""Tests for animated gradient functionality."""
# pylint: disable=protected-access
import math
import os
import time
from pathlib import Path
import pytest
from rich.console import Console
from rich_gradient import CONFIG # type: ignore[reportMissingTypeStubs]
from rich_gradient import AnimatedGradient, Gradient
f... | maxludden/rich-gradient | tests/test_animation.py | .py | 9103073795472b6d | 8.06 | 12 |
"""Tests covering configuration discovery and integration."""
from __future__ import annotations
import importlib
import json
import os
from pathlib import Path
from tempfile import TemporaryDirectory
import pytest
import rich_gradient as rg_pkg
import rich_gradient.animated_gradient as ag_module
def _reload_with... | maxludden/rich-gradient | tests/test_config.py | .py | b46d1aea2a813600 | 8.06 | 12 |
"""Tests for gradient convenience wrappers around Rich renderables."""
from __future__ import annotations
from collections.abc import Iterable
from rich.columns import Columns as RichColumns
from rich.console import Console, RenderableType
from rich.pretty import Pretty as RichPretty
from rich.segment import Segment... | maxludden/rich-gradient | tests/test_custom_renderables.py | .py | 454dd28bfc798a28 | 8.06 | 12 |
"""
Test suite for edge cases in Gradient and Text, including long text, unicode, empty input, no colors, background, quit panel, and invalid color inputs.
"""
import pytest
from rich.color import ColorParseError
from rich.console import Console
from rich.panel import Panel
from rich.segment import Segment
from rich_c... | maxludden/rich-gradient | tests/test_edge_cases.py | .py | 9f5bc912c945f775 | 8.06 | 12 |
"""
Test suite for Gradient class and color interpolation logic.
Covers color computation, style merging, rendering, and quit panel logic.
"""
from __future__ import annotations
from collections.abc import Iterable
from typing import Any, TypeGuard
import pytest
from rich.color import Color, ColorParseError
from ric... | maxludden/rich-gradient | tests/test_gradient.py | .py | dd471f6d51adfc86 | 7.06 | 12 |
"""Tests for the gradient-enabled Markdown renderables."""
import pytest
from rich.markdown import Markdown as RichMarkdown
from rich_gradient.animated_markdown import AnimatedMarkdown
from rich_gradient.markdown import Markdown
def test_markdown_initializes_with_string_content():
"""Ensure Markdown strings are... | maxludden/rich-gradient | tests/test_markdown.py | .py | fc10c73a7a50b383 | 8.06 | 12 |
"""
Test suite for Rule and AnimatedRule covering rendering, style, color validation, and context helpers.
"""
import os
import time
from pathlib import Path
os.environ.setdefault(
"RICH_GRADIENT_CONFIG_HOME",
str((Path(__file__).parent / ".rg_config_test").resolve()),
)
import pytest
from rich.color import ... | maxludden/rich-gradient | tests/test_rule.py | .py | efc56ed499a11fdd | 8.06 | 12 |
"""Regression tests for v0.4.0 side-effect and constructor fixes.
Covers: import-time excepthook hygiene, the install_tracebacks opt-in paths,
get_logger's library-safe handler management, and the Panel/Rule/AnimatedRule
constructor fixes.
"""
from __future__ import annotations
import os
import subprocess
import sys... | maxludden/rich-gradient | tests/test_side_effects.py | .py | 40571b3cd90ccfcc | 8.06 | 12 |
"""
Test suite for Spectrum class covering color generation, inversion, style matching, and hex code consistency.
"""
from typing import Any
import pytest
from rich.color import Color
from rich.style import Style
from rich_gradient.spectrum import Spectrum
def test_spectrum_default_length():
"""
Test that ... | maxludden/rich-gradient | tests/test_spectrum.py | .py | 5f3d09866d214cc1 | 8.06 | 12 |
"""Typed public response contracts for Pangram detection results."""
from typing import TypedDict
__all__ = [
"BulkResultItem",
"BulkResultMetadata",
"BulkResults",
"BulkResultsPage",
"PredictionResult",
"PredictionWindow",
]
class _PredictionWindowRequired(TypedDict):
text: str
labe... | pangramlabs/pangram-sdk | pangram/schemas.py | .py | 6e1318cc1d9753ea | 7.48 | 8 |
'''
Author: tbjuechen
Date: 2024-08-12
Version: 1.0
Description: An ADB connector for the Mumu emulator.
License: MIT
'''
from .adb_connector import AdbConnector
class MumuConnector(AdbConnector):
name:str = 'Mumu'
'''Connector for the Mumu emulator.
Attributes
----------
host : str
T... | tbjuechen/script | runner/connector/mumu_connector.py | .py | 4bbc31afd4390798 | 7.64 | 18 |
'''
Author: tbjuechen
Date: 2024-08-12
Version: 1.0
Description: base class for all players
License: MIT
'''
from abc import ABC, abstractmethod
class Player(ABC):
'''Base class for all players
Attributes
----------
acc : float
The accuracy of the player model
'''
def __init__(self, a... | tbjuechen/script | runner/player/base.py | .py | 24bf621cc81cc48d | 7.64 | 18 |
from __future__ import annotations
from typing import Any
from runner import Runner
from runner.connector import AdbConnector, Connector
from runner.player import Player
class Schedule:
"""Create and control multiple task processes."""
def __init__(self) -> None:
self.runners: list[Runner] = []
... | tbjuechen/script | schedule.py | .py | ca69fc72577fcf51 | 7.64 | 18 |
import dronemanager
from dronemanager.navigation.core import PathGenerator, WayPointType
class DirectTargetGenerator(PathGenerator):
""" Simply sends the target waypoint as static setpoints.
"""
CAN_DO_GPS = True
WAYPOINT_TYPES = {WayPointType.POS_NED, WayPointType.POS_GLOBAL}
def __init__(self,... | AImotion-Bavaria/DroneManager | src/dronemanager/navigation/directtargetgenerator.py | .py | a7dce52eeadc173b | 7.48 | 8 |
import math
import numpy as np
import dronemanager
from dronemanager.navigation.core import PathFollower, WayPointType, Waypoint
from dronemanager.utils import dist_ned, heading_ned
class VelocityFollower(PathFollower):
""" Flies directly toward the waypoint facing towards it along the way. Turning towards the t... | AImotion-Bavaria/DroneManager | src/dronemanager/navigation/velocityfollower.py | .py | 406893f38ba12344 | 7.48 | 8 |
""" Class for extra, loadable plugins.
Plugins extend the functionality of DroneManager or Drone Classes by providing extra functions. They can also register
their own commands to the CLI.
"""
import abc
import asyncio
from collections.abc import Coroutine
import importlib.util
import inspect
import pathlib
import sys... | AImotion-Bavaria/DroneManager | src/dronemanager/plugin.py | .py | 85151f5985f0ebcb | 7.48 | 8 |
""" Plugins for communication to other software
Currently only features a basic UDP server which sends data on connected drones and running missions in a json format.
"""
import asyncio
import select
import threading
import socket
import errno
import json
import time
import math
from dronemanager.plugin import Plugin... | AImotion-Bavaria/DroneManager | src/dronemanager/plugins/external.py | .py | c302f5b9b6344855 | 7.48 | 8 |
""" Plugin and abstract base class for external sensors, such as weather sensors.
They're specifically for plugins that connect to and sporadically query some external data source.
Similar to missions, these are a special type of plugin with extra functions to support their intended purpose.
The core extra component ... | AImotion-Bavaria/DroneManager | src/dronemanager/plugins/sensor.py | .py | 63a7e85677b19463 | 7.48 | 8 |
import asyncio
import struct
from collections.abc import Callable
import cv2
import numpy as np
from dronemanager.plugin import Plugin
class StreamPlugin(Plugin):
""" Plugin to receive video stream from Unity via TCP. """
# This prefix is used for CLI commands (e.g., 'unity start')
PREFIX = "stream"
... | AImotion-Bavaria/DroneManager | src/dronemanager/plugins/stream.py | .py | f77995e90518693d | 7.48 | 8 |
""" This module contains generic utility functions used throughout the software, mostly relating to GPS and NED
positions.
Unless stated otherwise, a GPS coordinate is any indexable sequence with the latitude, longitude and AMSL in that order.
"""
import math
import pathlib
from collections.abc import Sequence
from u... | AImotion-Bavaria/DroneManager | src/dronemanager/utils.py | .py | 0333d824936556dc | 7.48 | 8 |
""" Plugins for communication to other software
"""
import asyncio
import socket
import json
import time
import argparse
LISTEN_TIME = 10
SERVER_PORT = 31659
class UDPClient:
""" This client starts a connection and then keeps it alive until shut down.
You can update the frequency of the messages by changing ... | AImotion-Bavaria/DroneManager | udp_dummyclient.py | .py | c922b5015c292019 | 7.48 | 8 |
import torch
import torch.nn as nn
# Define a custom tropical layer for neural networks
# This layer computes a form of negative tropical distance between input and learnable weights
class TropicalLayer(nn.Module):
def __init__(self, in_features, out_features):
super(TropicalLayer, self).__init__()
... | nijamudheen/CheMLFlow | DLModels/tropicallayer.py | .py | e92faaddb92069d0 | 7.6 | 15 |
import numpy as np
import pandas as pd
import logging
import argparse
import time
import os
import subprocess
import sys
from padelpy import from_smiles
class PaDELDescriptorCalculator:
"""Class to calculate PaDEL descriptors for molecules with optional CPU usage control."""
def __init__(self, input_file,... | nijamudheen/CheMLFlow | GenDescriptors/PaDEL_descriptors.py | .py | 9c3cc3f0d796266e | 7.6 | 15 |
import pandas as pd
import argparse
import logging
from rdkit import Chem
from rdkit.Chem import Descriptors
class RDKitDescriptorCalculator:
"""Class to calculate RDKit descriptors for molecules."""
def __init__(self, input_file, output_file):
self.input_file = input_file
self.output_file... | nijamudheen/CheMLFlow | GenDescriptors/RDKit_descriptors.py | .py | b2beca5f4ffc09bd | 7.6 | 15 |
import numpy as np
import pandas as pd
import argparse
import logging
import sys
try:
from chembl_webresource_client.new_client import new_client
except Exception as exc:
logging.basicConfig(level=logging.INFO, format="%(asctime)s - %(levelname)s - %(message)s")
logging.error("ChEMBL API is unavailable: %s... | nijamudheen/CheMLFlow | GetData/get_ChEMBL_target_full.py | .py | a36e5ca7f502aa33 | 7.6 | 15 |
"""
Plotting helpers for the time-series (Adaptive NVAR) pipeline.
Renders the windowed-rollout comparison plot from the notebook
`Prediction_on_test_MG_Adaptive_NVAR_10percent_noise.ipynb`:
prediction vs ground-truth (clean) vs noisy observation, over the
concatenated evaluation windows, with dotted window b... | nijamudheen/CheMLFlow | MLModels/training/timeseries_plots.py | .py | 3a0026a2e06177ae | 7.6 | 15 |
"""Typed configuration for the molecular landscape workflow."""
from __future__ import annotations
from dataclasses import asdict, dataclass, field
from pathlib import Path
from typing import Any, Dict, List, Optional
from .eda.config import EDAConfig
_REPRESENTATION_CHOICES = {"morgan", "fcfp", "rdkit", "atompair... | nijamudheen/CheMLFlow | molecular_landscape/config.py | .py | 7d652ad1c7f46772 | 7.6 | 15 |
import numpy as np
def _set_uns(adata, neighbors_key):
adata.uns["neighbors"] = adata.uns[neighbors_key]
adata.uns["neighbors"]["connectivities_key"] = "connectivities"
adata.uns["neighbors"]["distances_key"] = "distances"
def _randomize_features(X, partition=None):
"""
Taken and adapted from op... | openproblems-bio/task_batch_integration | src/control_methods/utils.py | .py | 16a8f51912933a21 | 7.6 | 15 |
"""Shared runner for the ConDo batch-integration method.
Runs the agglomerative batch integrator: pick the seed batch with the
highest per-batch pre-integration silhouette of cell_type on X_pca, then
iteratively merge each next-best compatible (cell-type-overlapping)
neighbour by fitting a ConDo adapter conditioned on... | openproblems-bio/task_batch_integration | src/methods/condo/condo_runner.py | .py | 6c162f08879efa89 | 7.6 | 15 |
"""
TabSeq Feature Ordering Module
This module provides feature ordering functionality for tabular data using
variance-based clustering and weighted integration. It can be used to reorder
feature columns for deep learning models.
Author: Zadid Habib
"""
import numpy as np
import pandas as pd
from sklearn.cluster imp... | zadid6pretam/TabSeq | tabseq_feature_ordering/feature_ordering.py | .py | 26ed64a11bb2af72 | 7.57 | 13 |
"""kedro-graphql file for ensuring the package is executable
as `kedro-graphql` and `python -m kedro_graphql`
"""
import importlib
from pathlib import Path
from kedro.framework.cli.utils import KedroCliError, load_entry_points
from kedro.framework.project import configure_project
def _find_run_command(package_name):... | cellsignal/kedro-graphql | src/kedro_graphql/__main__.py | .py | 93ad0cb5c66d48b6 | 7.42 | 6 |
import ast
import asyncio
import json
import os
import threading
import uuid
import weakref
from bson.objectid import ObjectId
from pymongo import AsyncMongoClient
from kedro_graphql.logs.logger import logger
from kedro_graphql.models import Pipeline
from .base import BaseBackend
class MongoBackend(BaseBackend):
... | cellsignal/kedro-graphql | src/kedro_graphql/backends/mongodb.py | .py | 723531f5d4dfe5bc | 7.42 | 6 |
import os
from importlib.metadata import entry_points
from typing import Any
from kedro.framework.hooks import _create_hook_manager, hook_impl
from kedro.io import CatalogProtocol
from kedro.pipeline import Pipeline
from kedro_graphql.logs.logger import logger
from .exceptions import InvalidPipeline
def available_h... | cellsignal/kedro-graphql | src/kedro_graphql/hooks.py | .py | 1633b822fb49577f | 7.42 | 6 |
# All code below this file is attributed to:
##
# The MIT License (MIT)
##
# Copyright (c) 2015 Marsel Mavletkulov
##
# 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, incl... | cellsignal/kedro-graphql | src/kedro_graphql/logs/json_log_formatter.py | .py | 99ab0701a9d43db0 | 7.42 | 6 |
"""Pipeline-aware catalog resolution and validation."""
from kedro.io import AbstractDataset, DataCatalog, MemoryDataset
from kedro.io.core import DatasetError
from .exceptions import InvalidPipeline
def normalize_pipeline_config(pipeline, catalog, parameters):
"""Resolve catalog patterns and retain only config... | cellsignal/kedro-graphql | src/kedro_graphql/pipeline_config.py | .py | 824d43469bcbaff3 | 7.42 | 6 |
import asyncio
import logging
from datetime import datetime, timezone
from queue import Empty as QueueEmptyException
from queue import Queue
from threading import Thread
from typing import AsyncGenerator
from celery.states import READY_STATES
from starlette.concurrency import run_in_threadpool
logger = logging.getLog... | cellsignal/kedro-graphql | src/kedro_graphql/pipeline_event_monitor.py | .py | 6d20fd407dfcd868 | 7.42 | 6 |
"""
This is a boilerplate pipeline 'example01'
generated using Kedro 0.19.11
"""
import time
def uppercase(text: str) -> str:
"""Converts text to uppercase."""
return text.upper()
def reverse(text: str) -> str:
"""Reverses the given text."""
return text[::-1]
def append_timestamp(text: str) -> str... | cellsignal/kedro-graphql | src/kedro_graphql/pipelines/example01/nodes.py | .py | eb822ce8ec97565d | 7.42 | 6 |
from datetime import datetime
from .models import Pipeline, State
TERMINAL_STATES = {State.ABORTED, State.FAILURE, State.SUCCESS}
TRANSITIONS = {
State.STAGED: {State.READY},
State.READY: {State.STARTED, State.ABORTING},
State.STARTED: {
State.RETRY,
State.ABORTING,
State.FAILURE,... | cellsignal/kedro-graphql | src/kedro_graphql/run_state.py | .py | 2056418727df9b84 | 7.42 | 6 |
from jinja2 import Environment, PackageLoader, select_autoescape
import json
from kedro.io import AbstractDataSet, DataCatalog, MemoryDataSet
from kedro.pipeline import Pipeline
from kedro.runner.runner import AbstractRunner
from pluggy import PluginManager
import re
import requests
import yaml
class ArgoWorkflows... | cellsignal/kedro-graphql | src/kedro_graphql/runners/argo/argo.py | .py | 8bae0e297c13ff19 | 7.42 | 6 |
import json
from typing import List
import jwt
from kedro.io import AbstractDataset
from strawberry.types import Info
from ..models import DataSet, SignedUrl, SignedUrls, SignedUrlField
from .base import SignedUrlProvider
from datetime import datetime, timedelta
from urllib.parse import urlencode
from pathlib import Pa... | cellsignal/kedro-graphql | src/kedro_graphql/signed_url/local_file_provider.py | .py | 570d53e3397c1ada | 7.42 | 6 |
from qgis.PyQt.QtCore import QSettings
from qgis.PyQt.QtWidgets import (
QDialog,
QInputDialog,
QLineEdit,
QPushButton,
QTextEdit,
QVBoxLayout,
)
from qgis.core import QgsCoordinateTransform, QgsProject, QgsVectorLayer
import os
import re
import processing
import requests
# Inference Providers... | opengeoshub/vgridtools | huggingface.py | .py | 561a061867d41dff | 7.5 | 9 |
import importlib
import subprocess
import sys
from qgis.PyQt.QtWidgets import QMessageBox
from qgis.PyQt.QtCore import QSettings
from concurrent.futures import ThreadPoolExecutor
def check_and_install_libraries(filename):
"""Check and install required third-party Python libraries."""
settings = QSettings()
... | opengeoshub/vgridtools | install_packages/check_packages.py | .py | 5b26be712ba74a6c | 7.5 | 9 |
#!/usr/bin/env python
# coding=utf-8
"""This script uploads a plugin package to the plugin repository.
Authors: A. Pasotti, V. Picavet
git sha : $TemplateVCSFormat
"""
import sys
import getpass
import xmlrpc.client
from optparse import OptionParser
standard_library.install_aliases()
# Configuration
PROT... | opengeoshub/vgridtools | plugin_upload.py | .py | 8046b01ec7264b40 | 7.5 | 9 |
"""DODO: rebuild the disordered regions of predicted protein structures.
DODO takes a predicted structure -- typically from AlphaFold -- identifies its folded
domains, intrinsically disordered regions and loops, and rebuilds the disordered parts
so they adopt realistic polymer dimensions instead of AlphaFold's charact... | idptools/dodo | src/dodo/__init__.py | .py | 9d91df1a3b3569e9 | 7.48 | 8 |
"""Command-line interface.
One command with subcommands, replacing v1's three separate console scripts
(``pdb-from-name``, ``pdb-from-pdb``, ``pdb-from-sequence``). Those were near-duplicate
argparse files whose shared flags had drifted apart -- ``-apr`` meant
``--attempts_per_region`` in two of them and ``--attempts_... | idptools/dodo | src/dodo/cli.py | .py | cfe47ab99f9c8fff | 7.48 | 8 |
"""Reposition folded domains so linker IDRs can adopt their predicted dimensions.
This is step 3 of DODO's algorithm, and it is the step that makes the whole thing work.
AlphaFold places folded domains at whatever separation its prediction happened to produce,
which for a long disordered linker is essentially arbitra... | idptools/dodo | src/dodo/construct/place.py | .py | 5803ed43b5874505 | 7.48 | 8 |
"""Tests for the backbone refinement pass.
Refinement holds every alpha carbon fixed and rotates each peptide unit about the CA-CA axis --
the single degree of freedom a rigid peptide unit has once both alpha carbons are pinned. It is
scored on four things at once: N-CA-C angle, steric clashes, phi/psi plausibility, a... | idptools/dodo | tests/unit/test_backbone_refine.py | .py | 3aab24a373fb2fa2 | 7.98 | 8 |
"""The peptide-plane table is auditable: re-derivable from committed frames, with a pinned accuracy.
``dodo.construct.ca_backbone`` bakes measured peptide-plane lookup tables into source: a 4-CA 1D
table keyed on one CA pseudo-dihedral, and a 5-CA 2D table keyed on two. Before this, their
provenance lived outside the ... | idptools/dodo | tests/unit/test_backbone_table.py | .py | 359ae403cef2d9bf | 7.98 | 8 |
"""Tests for placing N, C and O from alpha carbons alone.
Ground truth is a 60-residue slice of a real all-atom IDR simulation frame
(``idr_frame_backbone.pdb``). The test strips it to alpha carbons, rebuilds, and compares against
the atoms it threw away -- which is the only honest way to measure this, and is why the ... | idptools/dodo | tests/unit/test_ca_backbone.py | .py | 63f031028669971f | 7.98 | 8 |
"""Tests for the constants module.
Mostly guards on internal consistency. The pre-rewrite code carried four divergent
copies of the build-mode table (with three different values for ``super_compact``),
three different CA-CA bond lengths, and two disagreeing atomic-mass tables. These tests
assert that there is now one ... | idptools/dodo | tests/unit/test_constants.py | .py | 3bdb3dc64d645d22 | 7.98 | 8 |
"""Tests for target dimension prediction.
This is the module whose absence made the first v2 attempt unable to do the thing DODO
exists for. It had no sparrow import anywhere, and substituted two *disagreeing* hardcoded
placeholders (``1.0 * n_residues`` in the IDR builder, ``1.4 * n_residues`` for folded-domain
spaci... | idptools/dodo | tests/unit/test_dimensions.py | .py | acdf9593c1ced679 | 7.98 | 8 |
"""Every code example in the shipped documentation must actually run.
Not a stylistic check. Three examples were broken in ways a reader would hit immediately by
copying them, and nothing noticed because nothing ran them:
* ``target_dimensions("GSGSGSGS...", mode="compact")`` -- the literal ``...`` is not a sequence,... | idptools/dodo | tests/unit/test_documentation.py | .py | e52974d7272ecb2f | 7.98 | 8 |
# bgm API 角色数据抓取。import 或单独运行。
# 单独运行: python scripts/lib/bangumi.py <character_id>
import json
import sys
import time
import requests
UA = "vCal-ACGbday/1.0 (data check; github.com/Vanadiry)"
BASE = "https://api.bgm.tv/v0"
MAX_RETRY = 3
def _get(path):
for attempt in range(MAX_RETRY):
try:
... | Vanadiry/vCal-ACGbday | scripts/lib/bangumi.py | .py | 83589bf1d6e2deec | 7.45 | 7 |
"""
FastAPI application setup.
Creates the FastAPI app instance, configures middleware,
and registers all routers.
"""
import time
from contextlib import asynccontextmanager
from fastapi import FastAPI, Request
from fastapi.middleware.cors import CORSMiddleware
from data_api.core import config
from data_api.core.se... | NTHU-SA/NTHU-Data-API | src/data_api/api/api.py | .py | cf88213781f77f61 | 7.57 | 13 |
"""
Buses router.
Handles HTTP endpoints for bus-related queries.
Delegates business logic to domain services.
"""
from datetime import datetime
from typing import Literal, Union
from fastapi import APIRouter, Depends, HTTPException, Query, Response
from data_api.api.schemas import buses as schemas
from data_api.do... | NTHU-SA/NTHU-Data-API | src/data_api/api/routers/buses.py | .py | e08ed3e7673ce4a7 | 7.57 | 13 |
"""Courses router."""
from fastapi import APIRouter, Body, Depends, Query, Request, Response
from data_api.api.schemas import courses as schemas
from data_api.domain.courses import models, services
router = APIRouter()
def add_custom_header(response: Response):
"""Add X-Data-Commit-Hash header."""
response... | NTHU-SA/NTHU-Data-API | src/data_api/api/routers/courses.py | .py | a882763bfb4be594 | 7.57 | 13 |
"""
Announcements API schemas.
Pydantic models for announcements request/response validation.
"""
from enum import Enum
from typing import Annotated, Optional
from pydantic import BaseModel, BeforeValidator, Field, HttpUrl
from data_api.utils.schema import url_corrector
class AnnouncementArticle(BaseModel):
"... | NTHU-SA/NTHU-Data-API | src/data_api/api/schemas/announcements.py | .py | 5a27988ad994dcc1 | 7.57 | 13 |
"""
Bus API schemas.
Pydantic models for request/response validation.
Enums are imported from domain layer to avoid duplication.
"""
from typing import Optional
from fastapi import Query
from pydantic import BaseModel, Field
from data_api.domain.buses.enums import (
BusDay,
BusDayWithCurrent,
BusDirecti... | NTHU-SA/NTHU-Data-API | src/data_api/api/schemas/buses.py | .py | 77c396e2b6f569e5 | 7.57 | 13 |
"""Courses API schemas."""
from enum import Enum
from typing import Union
from pydantic import BaseModel, Field, RootModel, field_validator
class CourseFieldName(str, Enum):
"""Course field names for querying."""
id = "id"
chinese_title = "chinese_title"
english_title = "english_title"
credit =... | NTHU-SA/NTHU-Data-API | src/data_api/api/schemas/courses.py | .py | 07cf377ce6a03444 | 7.57 | 13 |
"""
Dining API schemas.
Pydantic models for dining request/response validation.
"""
from typing import Annotated, Optional
from pydantic import BaseModel, BeforeValidator, Field, HttpUrl
from data_api.domain.dining.enums import DiningBuildingName, DiningScheduleName
from data_api.utils.schema import url_corrector
... | NTHU-SA/NTHU-Data-API | src/data_api/api/schemas/dining.py | .py | e80067c7bd6a0fa5 | 7.57 | 13 |
"""
Data Manager for NTHU Data API
This module provides a centralized data manager for fetching and caching data
from data.nthusa.tw with improved architecture:
- Separation of concerns (fetching, caching, file details management)
- Configuration-based pre-fetching
- Better error handling
- Cleaner API
"""
import js... | NTHU-SA/NTHU-Data-API | src/data_api/data/nthudata.py | .py | 1cb868422ce03681 | 7.57 | 13 |
"""
Bus domain enums.
This module contains all enumerations used in the bus domain.
Moved from schemas to keep domain independent of Pydantic.
"""
from enum import Enum
class BusStopsName(str, Enum):
"""Bus stop names."""
M1 = "北校門口"
M2 = "綜二館"
M3 = "楓林小徑"
M4 = "人社院&生科館"
M5 = "台積館"
M6 =... | NTHU-SA/NTHU-Data-API | src/data_api/domain/buses/enums.py | .py | a70a4c20732e4f3d | 7.57 | 13 |
"""
Buses graph definition.
Contains Route topology, Stop definitions, and Route selection logic.
"""
from typing import Literal, Optional
from . import models
# --- 1. Stop Definitions ---
STOPS_DATA = {
"M1": models.Stop("M1", "北校門口", "North Main Gate", "24.79589", "120.99633"),
"M2": models.Stop("M2", "綜二... | NTHU-SA/NTHU-Data-API | src/data_api/domain/buses/graph.py | .py | 3d1cff9c9d8d47ac | 7.57 | 13 |
"""
Buses domain models.
Pure Python domain models representing business entities.
"""
from dataclasses import dataclass
@dataclass(unsafe_hash=True)
class Stop:
"""Bus stop data model."""
id: str # Added ID for easier lookup (e.g., "M1")
name: str
name_en: str
latitude: str
longitude: str
... | NTHU-SA/NTHU-Data-API | src/data_api/domain/buses/models.py | .py | d7d4f2572650da51 | 7.57 | 13 |
"""
Buses domain service.
Handles data fetching, caching, and processing using the Graph module.
"""
from __future__ import annotations
from datetime import datetime, timedelta
from itertools import product
from typing import Any, Literal, Optional, cast
from data_api.core import constants
from data_api.data.manager... | NTHU-SA/NTHU-Data-API | src/data_api/domain/buses/services.py | .py | 58ffccc8ff613d93 | 7.57 | 13 |
"""
Courses domain models.
Pure Python domain models without FastAPI or Pydantic dependencies.
"""
import re
from dataclasses import dataclass, field
from typing import Any, Optional, Union
@dataclass
class CourseData:
"""Course data model."""
id: str
chinese_title: str
english_title: str
credi... | NTHU-SA/NTHU-Data-API | src/data_api/domain/courses/models.py | .py | 816b7edebc9fdeea | 7.57 | 13 |
"""
Courses domain service.
Handles course data fetching, processing, and querying.
"""
import operator
from typing import Optional
from data_api.data.manager import nthudata
from data_api.domain.courses.models import Conditions, CourseData
class CoursesService:
"""Service for course data operations."""
d... | NTHU-SA/NTHU-Data-API | src/data_api/domain/courses/services.py | .py | c2174f475e766a4f | 7.57 | 13 |
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