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 |
|---|---|---|---|---|---|---|
"""Resolve the package's settings, lazily, from three sources.
A project configures the package through one ``TELEGRAM_BOT`` dict in its Django
settings. Anything it leaves out is looked for in the environment, and anything
the environment leaves out comes from :mod:`django_redis_aiogram.defaults`.
Nothing here reads... | CorneiZeR/django-redis-aiogram | src/django_redis_aiogram/settings.py | .py | 6ace9cea99fe368c | 7.63 | 17 |
"""Pace outgoing calls to stay under Telegram's published limits.
Retrying on ``TelegramRetryAfter`` is reactive: the message has already been
refused and the bot has already been told to back off. These limits are
documented, so the sane thing is not to exceed them in the first place.
Telegram enforces three at once... | CorneiZeR/django-redis-aiogram | src/django_redis_aiogram/throttling.py | .py | 7a3502e70d3676f9 | 7.63 | 17 |
"""Receive updates over HTTP instead of polling for them.
Long polling needs a process that runs forever. A webhook does not: Telegram
posts each update to a URL, so the update arrives in whichever process serves
that URL — normally the web one.
The view is deliberately synchronous. An async view would run on the ser... | CorneiZeR/django-redis-aiogram | src/django_redis_aiogram/webhook.py | .py | 7d3999058754ef34 | 7.63 | 17 |
import fakeredis
import fakeredis.aioredis
import pytest
from django_redis_aiogram import conf
# `django_redis_aiogram.bot` is the singleton instance, so the class lives in
# `client`; patching the wrong one silently leaves the real connection in place.
PATCH_TARGETS = (
'django_redis_aiogram.redis.get_redis',
... | CorneiZeR/django-redis-aiogram | tests/conftest.py | .py | 49a0455f5be963a7 | 8.13 | 17 |
"""Guards for the database suite.
Run it with its own settings module:
python -m pytest --ds=tests.db_settings tests/db
"""
import threading
import pytest
from django.conf import settings
from django_redis_aiogram.recorder import WRITER_THREAD, recorder
@pytest.fixture(autouse=True)
def _no_writer_outlives_i... | CorneiZeR/django-redis-aiogram | tests/db/conftest.py | .py | 9353b4abe3bfcc2c | 8.13 | 17 |
"""The admin: what it shows, what it refuses, and what it will not ask the database."""
import os
import subprocess
import sys
import textwrap
import pytest
from django.contrib.auth.models import Permission, User
from django.db import connection
from django.test import override_settings
from django.test.utils import ... | CorneiZeR/django-redis-aiogram | tests/db/test_admin.py | .py | e65c9751d95d61e3 | 7.13 | 17 |
"""The table, the migration and the permission surface it creates."""
import io
import time
import pytest
from django.contrib.auth.models import Permission
from django.core.management import call_command
from django.db import connection
from django_redis_aiogram.events import new_correlation_id
from django_redis_aio... | CorneiZeR/django-redis-aiogram | tests/db/test_event_log_model.py | .py | 7f2278e75fc3739c | 8.13 | 17 |
"""The database suite's own wiring, asserted before anything relies on it.
Every test below fails if `--ds=tests.db_settings` is not in effect, which is
the point: the harness is what the rest of this directory is built on.
"""
import threading
import pytest
from django.conf import settings
from django.contrib.auth ... | CorneiZeR/django-redis-aiogram | tests/db/test_harness.py | .py | 1774c3da828b0b37 | 8.13 | 17 |
"""What the middleware and the storage wrapper record, and what they cost off."""
import asyncio
from datetime import datetime, timezone
import pytest
from aiogram import Bot, Dispatcher, Router
from aiogram.client.default import DefaultBotProperties
from aiogram.dispatcher.event.bases import UNHANDLED
from aiogram.f... | CorneiZeR/django-redis-aiogram | tests/db/test_inbound.py | .py | 564403d34df504ed | 8.13 | 17 |
"""Every stage of an outbound message, and the ones that used to leave no trace.
Four of these cover sends that were dropped with nothing but a log line before
3.0: refused because the bot was shutting down, refused because the loop was
closed, dropped in the hand-off, and cancelled at shutdown.
"""
import asyncio
im... | CorneiZeR/django-redis-aiogram | tests/db/test_outbound.py | .py | b9aeedfc4c115034 | 7.13 | 17 |
"""The only thing that bounds the table's growth."""
import datetime
from io import StringIO
import pytest
from django.core.management import CommandError, call_command
from django.db import connection
from django.test import override_settings
from django.test.utils import CaptureQueriesContext
from django.utils impo... | CorneiZeR/django-redis-aiogram | tests/db/test_prune.py | .py | a594be36d47d0d5a | 8.13 | 17 |
# -*- coding: utf-8 -*-
"""Definition of Article View in Django Admin Space"""
from django.contrib import admin
from unfold.admin import ModelAdmin, TabularInline
from .models import Article, FeedPosition, ArticleGroup
# Register your models here.
class FeedPositionInline(TabularInline):
"""Table of feeds to be... | vanalmsick/news_platform | articles/admin.py | .py | e52f7cd871c360ab | 7.52 | 10 |
# -*- coding: utf-8 -*-
"""Containing all Django models related to an individual article/video"""
import urllib
from django.db import models
from django.db.models import Max, Min
from django.db.models.signals import post_delete, pre_delete, post_save, pre_save
from django.dispatch import receiver
from feeds.models i... | vanalmsick/news_platform | articles/models.py | .py | 15561613e7673526 | 7.52 | 10 |
# -*- coding: utf-8 -*-
"""Bounded HTTP helpers for the scrapers.
`requests.get(url)` buffers the *entire* response body into memory before it
returns. Every article in every feed is fetched this way, so a single
mis-advertised URL - a PDF, a video file, a CDN error page that streams
megabytes of HTML - is enough to s... | vanalmsick/news_platform | feed_scraper/http_utils.py | .py | 06310eb55801502b | 7.52 | 10 |
# -*- coding: utf-8 -*-
"""Definition of Publisher and Feed Views in Django Admin Space"""
from django.contrib import admin
from django.contrib.auth.models import Group, User
from import_export import resources
from import_export.admin import ImportExportModelAdmin
from unfold.admin import ModelAdmin, TabularInline
fr... | vanalmsick/news_platform | feeds/admin.py | .py | 9ffbcea71985fdf3 | 7.52 | 10 |
# -*- coding: utf-8 -*-
from django.db import models
from django.db.models.signals import pre_save
from django.dispatch import receiver
NEWS_IMPORTANCE = [
(4, "Lead Articles News"),
(3, "Breaking & Top News"),
(2, "Frontpage News"),
(1, "Latest News"),
(0, "Normal"),
]
YES_NO = [("Y", "Yes"), ("N... | vanalmsick/news_platform | feeds/models.py | .py | 797cebcefb7c36e4 | 7.52 | 10 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""Django's command-line utility for administrative tasks."""
import datetime
import os
import sys
import warnings
from dotenv import load_dotenv
from news_platform.pwa_splash_screen_generator import create as create_splash_screens
def __ensure_db_migration_folders_exi... | vanalmsick/news_platform | manage.py | .py | f6fa579c2fcbd30b | 7.52 | 10 |
# -*- coding: utf-8 -*-
"""Django Admin Space for Market Data App/Models"""
from django.contrib import admin
from import_export import resources
from import_export.admin import ImportExportModelAdmin
from unfold.admin import ModelAdmin
from unfold.contrib.import_export.forms import ExportForm, ImportForm
from .models... | vanalmsick/news_platform | markets/admin.py | .py | 87b2f979881a290f | 7.52 | 10 |
# -*- coding: utf-8 -*-
"""All Market Data Models"""
from django.db import models
# Create your models here.
class DataGroup(models.Model):
"""Django Model to group market data sources e.g. equities, bonds etc."""
name = models.CharField(max_length=200)
position = models.IntegerField()
def __str__(... | vanalmsick/news_platform | markets/models.py | .py | 7e4daed9217cde39 | 7.52 | 10 |
# -*- coding: utf-8 -*-
"""Get article data for all views"""
import datetime
import functools
import urllib
import operator
from django.conf import settings
from django.core.cache import cache
from django.db.models import F, Q
from django.forms.models import model_to_dict
from django.http import HttpResponse
from dja... | vanalmsick/news_platform | news_platform/pages/pageAPI.py | .py | 48f401b43709fe0e | 7.52 | 10 |
# -*- coding: utf-8 -*-
from django import forms
from django.conf import settings
from django.contrib.auth import authenticate, login
from django.shortcuts import redirect, render
from articles.models import Article
class LoginForm(forms.Form):
"""Form used on login page to enter password of default user."""
... | vanalmsick/news_platform | news_platform/pages/pageLogin.py | .py | e0c958f606ca56bd | 7.52 | 10 |
# -*- coding: utf-8 -*-
"""models for App called Preferences"""
from urllib.parse import parse_qs
from django.db import models
def url_parm_encode(**kwargs):
"""function too translate url parameters from GET request in dictionary to hash string"""
kwargs = {k: ",".join(v if isinstance(v, list) else [v]).spl... | vanalmsick/news_platform | preferences/models.py | .py | bfad4e4688df57f2 | 7.52 | 10 |
#!/usr/bin/env python3
"""
Script to automatically rewrite custom docs sections in README files.
This script extracts the generate workflow documentation from ai_clothes_changer/README.md
and rewrites it into all README files that have generate methods and custom docs sections.
"""
import re
from pathlib import Path
... | magichourhq/magic-hour-python | codemod/populate_custom_docs.py | .py | 3fe6761e40f2e516 | 7.6 | 15 |
import enum
import typing
class Environment(enum.Enum):
"""Pre-defined base URLs for the API"""
ENVIRONMENT = "https://api.magichour.ai"
MOCK_SERVER = "https://api.sideko.dev/v1/mock/magichour/magic-hour/0.75.2"
def _get_base_url(
*, base_url: typing.Optional[str] = None, environment: Environment
)... | magichourhq/magic-hour-python | magic_hour/environment.py | .py | 3b459539de871e51 | 7.6 | 15 |
import datetime
import pytest
import httpx
from pathlib import Path
from typing import Any, Generator, Literal, Union, List
from unittest.mock import Mock, AsyncMock
from magic_hour.types import models
from magic_hour.resources.v1.audio_projects.client import (
AudioProjectsClient,
AsyncAudioProjectsClient,
)
... | magichourhq/magic-hour-python | magic_hour/resources/v1/audio_projects/client_test.py | .py | 9f59ccb5981cf534 | 7.1 | 15 |
'''
PyTorch has its own implementation of backward function for SVD https://github.com/pytorch/pytorch/blob/291746f11047361100102577ce7d1cfa1833be50/tools/autograd/templates/Functions.cpp#L1577
We reimplement it with a safe inverse function (Lorentzian broadening) in case of degenerated singular values.
Theories and d... | sjdu10/vmc_torch | build/lib/vmc_torch/torch_utils.py | .py | f1d847778061f7d6 | 7.42 | 6 |
import os
os.environ["OPENBLAS_NUM_THREADS"] = '1'
os.environ['MKL_NUM_THREADS'] = '1'
os.environ["OMP_NUM_THREADS"] = '1'
import numpy as np
from mpi4py import MPI
# torch
import torch
# quimb
from autoray import do
from .global_var import DEBUG, set_debug
COMM = MPI.COMM_WORLD
SIZE = COMM.Get_size()
RANK = COMM.Ge... | sjdu10/vmc_torch | build/lib/vmc_torch/variational_state.py | .py | c32c32e2e22b6051 | 7.42 | 6 |
"""GPU wavefunction base class with single-sample amplitude + auto-vmap.
All subclasses define a single-sample amplitude:
amplitude(x, params_list)
x: (N_sites,) int64 — one configuration
params_list: list of parameter tensors
returns: scalar amplitude
The base class vmaps i... | sjdu10/vmc_torch | vmc_torch/GPU/models/_base.py | .py | 6eb3a1eea3ced5a1 | 7.42 | 6 |
"""Pure neural-network wavefunction model for GPU VMC.
Architecture:
x: (N_sites,) int64
-> embedding lookup (N_sites, embed_dim)
-> flatten (N_sites * embed_dim,)
-> [Linear -> Tanh] x n_layers
-> Linear scalar real
Parameter layout in self.params (ParameterList indice... | sjdu10/vmc_torch | vmc_torch/GPU/models/pureNN.py | .py | 260fd4ec2073ee42 | 7.42 | 6 |
"""Slater determinant wavefunction model for GPU VMC.
psi(x) = det( M[occupied, :] )
For spinful fermions with quimb encoding {0=empty, 1=↓, 2=↑, 3=↑↓}:
1. Convert x to binary occupation: n = [spin_up | spin_dn]
2. occupied = argsort(n, descending)[:N_f] (vmap-friendly)
3. psi = det(M[occupied])
"""
... | sjdu10/vmc_torch | vmc_torch/GPU/models/slater.py | .py | 29d69748d632fe44 | 7.42 | 6 |
"""VMC run setup: walker initialization.
TN-specific setup moved to ``tensor_network/utils.py`` (``setup_linalg_hooks``,
``load_or_generate_peps``, ``generate_random_spin_peps``); it is
re-exported below so existing imports keep working. New code should
take those from ``vmc_torch.GPU.tensor_network.utils``.
"""
impo... | sjdu10/vmc_torch | vmc_torch/GPU/vmc_setup.py | .py | 57a02f21ca48f424 | 7.42 | 6 |
"""FAISS-based KNN classifiers for multiclass and multilabel classification."""
import contextlib
import sys
from typing import Any, Literal, Self
import numpy as np
if sys.platform == "linux":
import torch # before faiss on linux, after on macos (torchgeo/torchgeo-bench#152)
try:
import faiss
except Modul... | isaaccorley/faissknn | src/faissknn/knn.py | .py | f765e7ec90a0cec2 | 7.48 | 8 |
"""Regression test for GH #14: GPU search not stream-ordered off cuda:0.
``faiss.contrib.torch_utils`` syncs faiss's stream against
``torch.cuda.current_device()``, not the device the index actually lives
on. Selecting a non-default GPU the idiomatic way (``.to("cuda:N")``, no
device context) left faiss's search racin... | isaaccorley/faissknn | tests/test_gpu_stream_ordering.py | .py | 5af0f967b283bca1 | 7.98 | 8 |
from collections.abc import Sequence
import numpy as np
import pytest
from faissknn import FaissKNNClassifier, FaissKNNMultilabelClassifier
@pytest.mark.parametrize("metric", ["l2", "ip", "cosine"])
def test_multiclass_knn(metric: str, device: str, multiclass_dataset: Sequence[np.ndarray]):
x_train, y_train, x_... | isaaccorley/faissknn | tests/test_knn.py | .py | fe9c5dac6f2f03a5 | 7.98 | 8 |
"""End-to-end regression tests against trusted reference implementations.
These tests ensure that public ``predict`` / ``predict_proba`` outputs from
``FaissKNNClassifier`` and ``FaissKNNMultilabelClassifier`` agree with
independent reference implementations on deterministic dummy data — so
refactors can't silently ch... | isaaccorley/faissknn | tests/test_regression.py | .py | be84ecf01bb363c8 | 7.98 | 8 |
#!/usr/bin/env python3
"""Named read-only audit packs for Ask-AI device diagnostics.
Each pack is an ordered list of (section, command) pairs collected in ONE SSH
session. Every command must individually satisfy the Ask-AI read-only policy;
that is asserted at import time so any drift between these packs and
ai_comma... | aliaydemir/lldpq-src | html/ai_audit_packs.py | .py | 55f5bdb0ed99256c | 7.59 | 14 |
#!/usr/bin/env python3
"""Strict command policy for Ask-AI live device diagnostics.
The regular Device Details command runner supports interactive workflows and has
its own broader policy. Ask-AI is exposed to model-generated text, so it gets a
separate fail-closed policy: one diagnostic command, no shell composition,... | aliaydemir/lldpq-src | html/ai_command_policy.py | .py | 4c9cb06144d5bda2 | 7.59 | 14 |
#!/usr/bin/env python3
"""Keyed runbook knowledge base for Ask-AI.
Deep Cumulus/EVPN/RoCE troubleshooting knowledge lives here instead of the
cached system prompt. Only :func:`kb_digest` (a ~10 line catalog) belongs in
the prompt; :func:`kb_select` runs a deterministic alias-token matcher over
the operator question a... | aliaydemir/lldpq-src | html/ai_kb.py | .py | 5f0dfcc16a8df655 | 7.59 | 14 |
#!/usr/bin/env python3
"""Best-effort per-domain event sidecars for the Timeline page.
Analyzers publish compact, uniform event records into
monitor-results/events/<domain>.json so the Timeline page can merge every
domain client-side without touching the multi-megabyte history monoliths.
Contract (mirrors the lldp_ne... | aliaydemir/lldpq-src | lldpq/analysis_events.py | .py | c933ae72a3ba7653 | 7.59 | 14 |
#!/usr/bin/env python3
"""Producer/validator sha256 handshake for large analyzer JSON artifacts.
Analyzers emit their JSON state through json.dump/json.dumps (or an encoder
walking the same containers), so a successfully written file is valid JSON by
construction. Post-run validation therefore only needs to prove the... | aliaydemir/lldpq-src | lldpq/analysis_sidecar.py | .py | dd616c43583321f1 | 7.59 | 14 |
#!/usr/bin/env python3
"""Validated, structured reader for the Assets web API."""
from __future__ import annotations
from datetime import datetime
import math
import os
from pathlib import Path
import time
from typing import Any
try:
from .collection_freshness import (
asset_timestamp_tolerance_seconds,
... | aliaydemir/lldpq-src | lldpq/assets_api.py | .py | b632ab6b75e676e4 | 7.59 | 14 |
import os
import sys
import time
from pathlib import Path
import httpx
from invoke import Context, Exit, task
CURRENT_DIRECTORY = Path(__file__).resolve()
DOCUMENTATION_DIRECTORY = CURRENT_DIRECTORY.parent / "docs"
MAIN_DIRECTORY_PATH = Path(__file__).parent
infrahub_address = os.getenv("INFRAHUB_ADDRESS")
INFRAHUB... | opsmill/infrahub-demo-service-catalog | tasks.py | .py | d64ce9c380676bcd | 7.48 | 8 |
import json
import os
from pathlib import Path
from typing import Any
import psutil
import pytest
from fast_depends import Provider, dependency_provider
from pytest_httpx import HTTPXMock
from infrahub_sdk import Config, InfrahubClientSync
from infrahub_sdk.ctl.repository import get_repository_config
from infrahub_sd... | opsmill/infrahub-demo-service-catalog | tests/conftest.py | .py | 2885887193d26fb2 | 7.98 | 8 |
"""Which image and tag the integration stack runs, resolved in one place.
``infrahub_testcontainers.container`` keeps its defaults in a module-level ``PROJECT_ENV_VARIABLES``
dict. That dict is consulted against ``os.environ`` when the ``.env`` file is written
(``container.py:182-183``), so an environment override doe... | opsmill/infrahub-demo-service-catalog | tests/integration/stack_config.py | .py | b701b18b817579a2 | 7.98 | 8 |
import ipaddress
import logging
from collections.abc import Generator
from pathlib import Path
import pytest
from fast_depends import Provider, dependency_provider
from streamlit.testing.v1 import AppTest
from infrahub_sdk.client import InfrahubClient, InfrahubClientSync
from infrahub_sdk.protocols import CoreGeneric... | opsmill/infrahub-demo-service-catalog | tests/integration/test_create_service.py | .py | c4b425176f8e4920 | 7.98 | 8 |
"""Stack image resolution, which decides what the integration suite actually tests.
Marked ``offline``: this reads no deployment, only the resolution logic.
"""
from __future__ import annotations
import pytest
from .stack_config import DEFAULT_IMAGE_REPOSITORY, StackImage, resolve_stack_image
pytestmark = pytest.m... | opsmill/infrahub-demo-service-catalog | tests/integration/test_stack_config.py | .py | f2e07cf3c8a2b3bf | 7.98 | 8 |
# -*- coding: utf-8 -*-
"""
EO Readers - Electro-Optical imagery readers.
Provides readers for visible, panchromatic, and VIS/NIR satellite
imagery. Planned sensors include Landsat OLI, Sentinel-2, HLS,
WorldView, PlanetScope, Pleiades/SPOT, and NAIP.
Dependencies
------------
rasterio
glymur (for JPEG2000 formats)
... | GEOINT/grdl | grdl/IO/eo/__init__.py | .py | 22f1e521cca675ae | 7.42 | 6 |
# -*- coding: utf-8 -*-
"""
GeoTIFF Reader - Read GeoTIFF and Cloud-Optimized GeoTIFF imagery.
Base data format reader for any GeoTIFF file regardless of modality
(EO, SAR GRD, MSI, etc.). Lives at the IO level so modality submodules
can use it without cross-submodule dependencies.
Dependencies
------------
rasterio
... | GEOINT/grdl | grdl/IO/geotiff.py | .py | 6efb0ebac0a7241d | 7.42 | 6 |
# -*- coding: utf-8 -*-
"""
HDF5 Reader - Read HDF5 and HDF-EOS5 imagery.
Base data format reader for HDF5 files regardless of producer
(NASA, ASI, JAXA, etc.). Supports explicit dataset path selection
or auto-detection of the first suitable numeric array. Lives at the
IO level so modality submodules can use it withou... | GEOINT/grdl | grdl/IO/hdf5.py | .py | ed55f0d43010f392 | 7.42 | 6 |
# -*- coding: utf-8 -*-
"""
ASTER Reader - Read ASTER L1T and GDEM GeoTIFF products.
Sensor-specific reader for ASTER (Advanced Spaceborne Thermal Emission
and Reflection Radiometer) products. Wraps ``GeoTIFFReader`` for pixel
access and extracts ASTER-specific metadata from GeoTIFF tags and
companion XML files into a... | GEOINT/grdl | grdl/IO/ir/aster.py | .py | 03beb8d11190ec08 | 7.42 | 6 |
# -*- coding: utf-8 -*-
"""
JPEG2000 Reader - Read JPEG2000 (JP2/J2K) imagery.
Base data format reader for JPEG2000 files (.jp2, .j2k) regardless of
producer. Unlocks Sentinel-2 native format (SAFE/JP2), Pleiades, SPOT,
and EnMAP imagery. Uses rasterio (GDAL JP2 driver) as the primary
backend, with glymur as a fallbac... | GEOINT/grdl | grdl/IO/jpeg2000.py | .py | 701d8cd3f692c88a | 7.42 | 6 |
# -*- coding: utf-8 -*-
"""
CRSD Metadata - Typed metadata for Compensated Radar Signal Data.
Per NGA.STND.0080-1 v1.0 (2025-02-25). Covers the fields required to
recover per-channel Doppler/timing behaviour: receive reference point,
reference frequency, and the 2-D DwellTime / CODTime polynomials that
express apertur... | GEOINT/grdl | grdl/IO/models/crsd.py | .py | 481791a036c20447 | 7.42 | 6 |
# -*- coding: utf-8 -*-
"""
NISAR Metadata - Typed metadata for NASA NISAR L-band/S-band SAR data.
Nested dataclass hierarchy for NISAR RSLC (Range Doppler SLC) and
GSLC (Geocoded SLC) products. Fields are extracted from the NISAR
HDF5 product structure under ``science/{LSAR|SSAR}/{RSLC|GSLC}/``.
Dependencies
------... | GEOINT/grdl | grdl/IO/models/nisar.py | .py | 4c46f4891a1642ff | 7.42 | 6 |
"""Main py4web application entry point for SASEWaddle Manager."""
import os
import sys
import logging
from py4web import action, request, response, abort, redirect, URL
from py4web.core import _before_request, _after_request
from py4web.utils.auth import Auth
from py4web.utils.cors import cors
# Setup logging
logging... | penguintechinc/tobogganing | services/hub-api/app.py | .py | ee4f4897fc74a28f | 7.42 | 6 |
"""
JWT Token Management for SASEWaddle Manager Service
Handles JWT token generation, validation, and refresh for nodes and clients
"""
import jwt
import asyncio
import time
from datetime import datetime, timedelta, timezone
from typing import Dict, Optional, Any, List
from cryptography.hazmat.primitives import serial... | penguintechinc/tobogganing | services/hub-api/auth/jwt_manager.py | .py | d9d86f6959284bc0 | 7.42 | 6 |
"""
User Management System for SASEWaddle Manager
Supports role-based access control with admin and reporter roles
"""
import hashlib
import secrets
import sqlite3
import time
from datetime import datetime, timedelta
from typing import Optional, List, Dict, Any
from dataclasses import dataclass
from enum import Enum
... | penguintechinc/tobogganing | services/hub-api/auth/user_manager.py | .py | b38a6aa2857547d3 | 7.42 | 6 |
"""Database initialization and configuration for SASEWaddle Manager."""
import os
from datetime import datetime
from typing import Optional, List
from pydal import DAL, Field
from pydal.validators import *
import logging
logger = logging.getLogger(__name__)
# Global database instances
db: Optional[DAL] = None
db_rea... | penguintechinc/tobogganing | services/hub-api/database/__init__.py | .py | 75e1ffae9c8620a5 | 7.42 | 6 |
#!/usr/bin/env python3
"""Initialize security tables and default configuration for SASEWaddle Manager."""
import os
import sys
import logging
from datetime import datetime
# Add the manager directory to the path
sys.path.insert(0, os.path.dirname(os.path.abspath(__file__)))
from database import get_db
logger = logg... | penguintechinc/tobogganing | services/hub-api/init_security.py | .py | b80b12e06361ea09 | 7.42 | 6 |
#!/usr/bin/env python3
"""Initialize security feeds and scanner for SASEWaddle Manager."""
import os
import sys
import asyncio
import logging
from datetime import datetime
# Add the manager directory to the path
sys.path.insert(0, os.path.dirname(os.path.abspath(__file__)))
from database import get_db
from security.... | penguintechinc/tobogganing | services/hub-api/init_security_feeds.py | .py | 2ec572c60e04eb0a | 7.42 | 6 |
"""
SASEWaddle License Management
Handles license validation and feature gating
"""
import os
import requests
import json
from functools import wraps
from datetime import datetime, timedelta
from typing import Optional, Dict, List, Any
import structlog
logger = structlog.get_logger()
# License server configuration
L... | penguintechinc/tobogganing | services/hub-api/licensing/__init__.py | .py | 632c7a42cee33a54 | 7.42 | 6 |
import argparse
import json
import logging
import os
from pathlib import Path
from .types import GofileUploaderLocalConfigOptions, GofileUploaderOptions
from .utils import return_dict_without_none_value_keys
logger = logging.getLogger(__name__)
def load_config_file(config_file_path: Path) -> GofileUploaderLocalConf... | alexmi256/gofile-uploader | src/gofile_uploader/cli.py | .py | c71bbec826bd5412 | 7.5 | 9 |
from io import BufferedReader
from pathlib import Path
from typing import Callable, Optional
from tqdm import tqdm
def return_dict_without_none_value_keys(item: dict):
return {k: v for k, v in item.items() if v is not None}
class ProgressFileReader(BufferedReader):
def __init__(self, filename: Path, read_c... | alexmi256/gofile-uploader | src/gofile_uploader/utils.py | .py | 1f4f1b4b48347b09 | 7.5 | 9 |
import logging
import sys
import time
from datetime import timedelta
from enum import Enum
from pathlib import Path
from typing import Any
import globus_sdk
import globus_sdk.gare
from globus_sdk.authorizers import GlobusAuthorizer
from globus_sdk.scopes import GCSCollectionScopeBuilder, TransferScopes
from typer impo... | argonne-lcf/FIRST | alcf_ai/src/alcf_ai/auth.py | .py | 76ef5e833a0f057a | 7.42 | 6 |
import logging
import time
from typing import Any
from pydantic import BaseModel
from .resource import ClientResource
logger = logging.getLogger(__name__)
class D3TritonRequest(BaseModel):
model_name: str
input_path: str
output_path: str
outputs: list[str] | None = None
class SubmitTaskResponse(B... | argonne-lcf/FIRST | alcf_ai/src/alcf_ai/resources/d3_triton.py | .py | 68dc0e9729a67a64 | 7.42 | 6 |
import logging
import time
from typing import Any
from pydantic import BaseModel
from .resource import ClientResource
logger = logging.getLogger(__name__)
class DINOv3Request(BaseModel):
input_dir: str
project: str | None = None
checkpoint: str | None = None
save_overlay: bool | None = None
bat... | argonne-lcf/FIRST | alcf_ai/src/alcf_ai/resources/dinov3.py | .py | 0efa1b4d3c4a088f | 7.42 | 6 |
import base64
import gzip
import logging
import time
from io import BytesIO
from pathlib import Path
from typing import Annotated, Any, Literal
import numpy as np
import numpy.typing as npt
from pydantic import (
BaseModel,
BeforeValidator,
ConfigDict,
)
from .resource import ClientResource
NDArray = npt... | argonne-lcf/FIRST | alcf_ai/src/alcf_ai/resources/sam3.py | .py | 41e97602a7b5f11c | 7.42 | 6 |
import io
import json
import logging
import tarfile
from concurrent.futures import ProcessPoolExecutor, wait
from io import BytesIO
from math import ceil
from pathlib import Path
from typing import Any
import numpy as np
import numpy.typing as npt
import smart_open
import typer
from PIL.Image import Image, fromarray
f... | argonne-lcf/FIRST | alcf_ai/src/alcf_ai/sam3.py | .py | 81def313c5b985ca | 7.42 | 6 |
import json
import globus_compute_sdk
def chunked_vllm_inference_function(parameters):
import os
import re
import signal
import subprocess
import sys
import time
import uuid
from datetime import datetime
# ---------------------------
# Helper: run one chunk
# ------------... | argonne-lcf/FIRST | compute-functions/vllm_batch_function.py | .py | 494a1863c7cf5d22 | 7.42 | 6 |
"""
Globus OAuth2 authentication utilities for dashboard.
"""
import hashlib
import logging
import globus_sdk
from cachetools import TTLCache, cached
from django.conf import settings
from django.contrib.auth import get_user_model
log = logging.getLogger(__name__)
User = get_user_model()
# User info class for dash... | argonne-lcf/FIRST | dashboard_async/globus_auth.py | .py | 29ea37cc03bd2951 | 7.42 | 6 |
import json
import logging
import os
from datetime import datetime, timezone
from typing import Any
"""Inference Gateway Gunicorn ASGI server configuration."""
# Determine if we're in production or development
environment = os.getenv("ENV", "production")
# Localhost port to communicate between Nginx and Gunicorn
bin... | argonne-lcf/FIRST | deploy/gateway_asgi.config.py | .py | 72c30ce9a0a39901 | 7.42 | 6 |
from ema.config import directory_config, variable_config
from ema.outputs import MATRIX_MARKET_HEADER
import pandas as pd
import numpy as np
import scipy.sparse as sp
from scipy.io import mmwrite
def annotate(sparse_matrix, pas_ids, collist, genes,
annotated_matrix=None,
pasbed_dir=None,
... | BMGLab/PeakATail | ema/annotate/annotate.py | .py | 8ce1637a3b031e67 | 7.52 | 10 |
from ema.config import directory_config
import pybedtools
import pandas as pd
# Confidence tier constants
TIER_1 = "TIER_1" # within known UTR
TIER_2 = "TIER_2" # within UTR x multiplier (possible UTR extension)
TIER_3 = "TIER_3" # within max_distance (possible novel distant PAS)
INTERGENIC = "INTERGENIC" # beyon... | BMGLab/PeakATail | ema/annotate/find_close.py | .py | 63ea018eb70aad9f | 7.52 | 10 |
from collections import defaultdict
from ema.config import directory_config as dc
def parse_gtf_attributes(attr_string):
"""Parse GTF attribute column (col 8) into a key-value dict.
GTF attributes are semicolon-delimited key-value pairs like:
gene_id "ENSG00000223972"; gene_type "transcribed_unproces... | BMGLab/PeakATail | ema/annotate/gtftobed.py | .py | 81e7b766eecfb552 | 7.52 | 10 |
import os
import json
import pandas as pd
from typing import Optional
def generate_report(results_df: pd.DataFrame, output_dir: str,
reference_db: Optional[str] = None) -> str:
"""Generate a complete benchmark report directory.
Args:
results_df: DataFrame from run_benchmark()
... | BMGLab/PeakATail | ema/benchmark/report.py | .py | fa47bfa895d57864 | 7.52 | 10 |
import logging
import os
import time
import json
import pandas as pd
from datetime import datetime
from typing import List, Optional, Dict
from ema.strategies import get_strategy, list_strategies
log = logging.getLogger(__name__)
def run_benchmark(bam_path: str, gtf_path: str,
strategies: Optional... | BMGLab/PeakATail | ema/benchmark/runner.py | .py | 080a01b4591717af | 7.52 | 10 |
"""Decorator factory that applies the shared options to every subcommand.
Usage:
@click.command()
@common_options()
def my_cmd(threads, output, verbose, quiet, log_level, no_log_file, no_progress, config, **kwargs):
...
"""
from __future__ import annotations
import logging
from pathlib import Path... | BMGLab/PeakATail | ema/cli/common.py | .py | 1a4b2a5f415e7a72 | 7.52 | 10 |
"""Single source of truth for every CLI flag's default value.
All defaults are now derived from :class:`ema.cli.config_schema.RunConfig`,
including switch-subcommand-only flags (``ema switch diff/length/match``).
Adding a flag:
* Add a dataclass field on RunConfig in ``ema/cli/config_schema.py``.
``DEFAULTS... | BMGLab/PeakATail | ema/cli/defaults.py | .py | 5e9363b2805c723f | 7.52 | 10 |
"""`ema run` — full pipeline subcommand.
This module is intentionally thin. The pipeline body lives in
``ema.main`` and is not modified by the CLI overhaul.
Click options are generated from :class:`ema.cli.config_schema.RunConfig`.
The hand-rolled ``@click.option`` block was deleted in the centralisation
refactor; ad... | BMGLab/PeakATail | ema/cli/run.py | .py | ba6db822650c1d9e | 7.52 | 10 |
"""`ema switch diff` — differential APA test across cluster pairs."""
from __future__ import annotations
import logging
import click
from ema.cli.common import (
apply_yaml_to_kwargs,
common_options,
parse_log_overrides,
resolve_subcommand_output_dir,
)
from ema.cli.defaults import DEFAULTS
from ema.... | BMGLab/PeakATail | ema/cli/switch_diff.py | .py | d5c2a217fd73a46a | 7.52 | 10 |
"""`ema switch match` — cross-dataset cluster matching."""
from __future__ import annotations
import logging
import click
from ema.cli.common import (
apply_yaml_to_kwargs,
common_options,
parse_log_overrides,
resolve_subcommand_output_dir,
)
from ema.cli.defaults import DEFAULTS
from ema.progress im... | BMGLab/PeakATail | ema/cli/switch_match.py | .py | 1bf1421f84931b02 | 7.52 | 10 |
"""`ema switch trend` — ordered-stage APA trend from a PDUI long table.
Reads a per-cluster PDUI/proportion/entropy table (as produced by
``ema switch length``), treats the clusters as an ORDERED progression given by
``--stage-order``, and reports the trend (slope + Spearman monotonicity +
direction) overall and per g... | BMGLab/PeakATail | ema/cli/switch_trend.py | .py | 4066761965523c4f | 7.52 | 10 |
"""YAML config loading + schema validation for `ema run`.
Schema is a strict superset of today's main.py YAML reader:
- `datasets` (required, list of {id, merge_strategy, bams})
- `gtf`, `output_dir`, `seqlen`, `cb_len`, `barcode_tag`
- `min_read`, `min_cells`, `min_pas_per_cell`, `pas_gap`
- `atlas`, `atlas_distance`... | BMGLab/PeakATail | ema/cli/yaml_loader.py | .py | 2a5e241e16d5eb6f | 7.52 | 10 |
"""Register the 3 built-in clustering strategies onto the registry.
Algorithm code itself stays in ema/clustering/clustering.py. This file
just thin-wraps the existing if/elif branches into registry entries.
"""
from __future__ import annotations
from ema.clustering.registry import register_clustering_strategy
@reg... | BMGLab/PeakATail | ema/clustering/_builtins.py | .py | 904582e99a347d22 | 7.52 | 10 |
"""Cross-dataset cluster matching strategy registry.
This module provides a pluggable registry for strategies that find cluster
correspondences across multiple h5ad files and assign canonical cluster IDs.
Each strategy implements ``ClusterMatchStrategy.match`` and is registered
under a short name string. New strateg... | BMGLab/PeakATail | ema/clustering/cross_dataset/__init__.py | .py | 349525b15e30f91d | 7.52 | 10 |
"""Abstract base class for cross-dataset cluster matching strategies.
Each strategy maps cluster labels from multiple h5ad files (each with their own
independently-assigned leiden cluster labels) to a shared canonical ID space.
Different datasets may label the same cell population with different integers
(cluster_0 in... | BMGLab/PeakATail | ema/clustering/cross_dataset/base.py | .py | cd102e5adff1c738 | 7.52 | 10 |
"""Cell-set Jaccard cross-dataset cluster matching strategy.
Algorithm
---------
For each pair of datasets (A, B), this strategy directly computes the Jaccard
similarity between cluster cell barcodes:
J(A_i, B_j) = |CB(A_i) ∩ CB(B_j)| / |CB(A_i) ∪ CB(B_j)|
where CB(X_k) is the set of cell barcodes in cluster k o... | BMGLab/PeakATail | ema/clustering/cross_dataset/jaccard.py | .py | 44cb6e4ef661e724 | 7.52 | 10 |
"""Marker-overlap cross-dataset cluster matching strategy.
Algorithm
---------
1. For each dataset, load the h5ad file and compute per-cluster marker PAS via
Wilcoxon rank-sum (scanpy.tl.rank_genes_groups). The top-N marker PAS by
score constitute the cluster's "fingerprint".
2. For every pair of datasets (dat... | BMGLab/PeakATail | ema/clustering/cross_dataset/marker_overlap.py | .py | 69079c8051c03d10 | 7.52 | 10 |
"""Mutual Nearest Neighbor (MNN) cross-dataset cluster matching strategy.
Algorithm
---------
1. Load all h5ad files and concatenate their cell × feature matrices along
the obs axis into a single combined AnnData. A ``batch`` column records
which dataset each cell comes from.
2. Re-embed all cells jointly usin... | BMGLab/PeakATail | ema/clustering/cross_dataset/mnn.py | .py | 8b98191b8ee9424a | 7.52 | 10 |
"""Round-trip the canonical cluster map back into each dataset's h5ad obs (B6).
Bug B6: ``canonical_cluster_map.tsv`` was written but never read back into
``clusters.h5ad``. Cross-sample comparisons then silently compared per-sample
``leiden`` labels — which are NOT comparable across datasets (cluster 0 in
sample A is... | BMGLab/PeakATail | ema/clustering/cross_dataset/roundtrip.py | .py | fc2d79e2a0ec935a | 7.52 | 10 |
"""Clustering evaluation and comparison utilities.
Provides functions for:
- Comparing two clusterings (ARI, AMI)
- Computing cluster quality metrics (silhouette score)
- Finding marker peaks per cluster (Wilcoxon rank-sum)
"""
import numpy as np
import pandas as pd
import anndata as ad
import scanpy as sc
from sklea... | BMGLab/PeakATail | ema/clustering/evaluation.py | .py | 1bba4f6e082fcb0d | 7.52 | 10 |
from langchain_dartmouth.definitions import USER_AGENT
from langchain_openai import OpenAIEmbeddings
from openai import DefaultHttpxClient, DefaultAsyncHttpxClient
import os
from typing import Any, Callable, List, Optional
from langchain_dartmouth.definitions import CLOUD_BASE_URL
from langchain_dartmouth.model_listin... | dartmouth/langchain-dartmouth | src/langchain_dartmouth/embeddings.py | .py | f2d12dc5c08b4276 | 7.48 | 8 |
from langchain_core.callbacks import Callbacks
from langchain_core.documents import Document, BaseDocumentCompressor
from pydantic import Field
import operator
import os
from typing import Callable, List, Optional, Sequence
from langchain_dartmouth.base import AuthenticatedMixin
from langchain_dartmouth.cross_encode... | dartmouth/langchain-dartmouth | src/langchain_dartmouth/retrievers/document_compressors.py | .py | a73c6dda4002d8a5 | 7.48 | 8 |
"""
noxfile
~~~~~~~
Nox configuration script
Modified from original source found in the Salt project:
- https://github.com/saltstack/salt
"""
import datetime
import os
import shutil
import sys
from pathlib import Path
# fmt: off
if __name__ == "__main__":
sys.stderr.write(
"Do not execute this file dire... | saltstack/salt-install-guide | noxfile.py | .py | a818a029c1484943 | 7.45 | 7 |
import os
import requests
import json
OPSLEVEL_API_TOKEN = os.environ["OPSLEVEL_API_TOKEN"]
OPSLEVEL_ENDPOINT = "https://app.opslevel.com/graphql"
LIST_CUSTOM_PROPERTIES_QUERY = """
query custom_service_properties($endCursor:String) {
account {
propertyDefinitions(after: $endCursor) {
page... | OpsLevel/community-integrations | scripts/convert_tags_to_custom_properties/convert_tags_to_custom_properties.py | .py | fbb5937ece9f4871 | 7.54 | 11 |
import requests
import json
import os
# Replace with your GraphQL endpoint and set up the API token as an env variable
OPSLEVEL_API_TOKEN = os.environ["OPSLEVEL_API_TOKEN"]
GRAPHQL_ENDPOINT = 'https://api.opslevel.com/graphql'
HEADERS = {
"Authorization": f"Bearer {API_TOKEN}",
'Content-Type': 'application/js... | OpsLevel/community-integrations | scripts/convert_teams_to_systems/migrate-teams-to-systems.py | .py | ada777d8ea3ec319 | 7.54 | 11 |
import os
import requests
OPSLEVEL_API_TOKEN = os.environ["OPSLEVEL_API_TOKEN"]
OPSLEVEL_ENDPOINT = "https://app.opslevel.com/graphql"
LIST_USERS_QUERY = """
query roles($endCursor: String) {
account {
users(filter: {key: role, arg: "user", type: equals}, after: $endCursor) {
nodes {
... | OpsLevel/community-integrations | scripts/convert_user_roles/convert_user_to_team_member_roles.py | .py | 85610c11f3120901 | 7.54 | 11 |
import os
import requests
OPSLEVEL_API_TOKEN = os.environ["OPSLEVEL_API_TOKEN"]
OPSLEVEL_ENDPOINT = "https://app.opslevel.com/graphql"
LIST_COMPONENT_TYPES_QUERY = """
query componentTypes($endCursor: String) {
account {
componentTypes (after: $endCursor) {
nodes {
id
... | OpsLevel/community-integrations | scripts/copy_componentType_custom_properties/copy_componentType_custom_properties.py | .py | 0347925f04c2519e | 7.54 | 11 |
import requests
import json
import os
from collections import defaultdict
# Replace these with your details
GITHUB_TOKEN = os.environ["GITHUB_TOKEN"]
REPO_OWNER = os.environ["REPO_OWNER"]
REPO_NAME = os.environ["REPO_NAME"]
OPSLEVEL_URL = "https://upload.opslevel.com/integrations/custom_event/"
OPSLEVEL_ROUTING_ID = o... | OpsLevel/community-integrations | scripts/dependabot/dependabot_alerts.py | .py | eecae3b375b823a9 | 7.54 | 11 |
import os
import csv
import requests
OPSLEVEL_API_TOKEN = os.environ.get("OPSLEVEL_API_TOKEN")
OPSLEVEL_ENDPOINT = "https://app.opslevel.com/graphql"
LIST_SYSTEMS_WITH_OWNERS_QUERY = """
query systemsWithOwners($endCursor: String) {
account {
systems(after: $endCursor) {
nodes {
... | OpsLevel/community-integrations | scripts/export_systems_with_owners/export_systems_with_owners.py | .py | 8faf3e57e7aa685e | 7.54 | 11 |
import requests
import argparse
import sys
# --- GraphQL Definitions ---
# 1. Query to fetch Services, including pagination cursor
GET_SERVICES_QUERY = """
query getServicesByTags ($filter: [ServiceFilterInput!], $after: String) {
account {
services (filter: $filter, after: $after) {
nodes {
id
... | OpsLevel/community-integrations | scripts/migrate_component_type/migrate_component_type.py | .py | 58a45151ce836f1f | 7.54 | 11 |
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