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 |
|---|---|---|---|---|---|---|
"""
OHLC (Open-High-Low-Close) Aggregation Example
This example demonstrates:
- Producing stock tick/trade data to a Redis stream
- Consuming ticks and aggregating into OHLC candles using TimeSeriesBuffer
- Real-time candlestick chart data generation
Run with: python ohlc_aggregation.py
"""
import asyncio
import rand... | trbck/streammachine | examples/ohlc_aggregation.py | .py | 808da729376841f4 | 7.48 | 8 |
"""
StreamMachine CLI entry point.
Allows running StreamMachine as a module:
python -m streammachine [command]
Commands:
mcp Run the MCP server (default)
--help Show help
"""
import sys
def _is_missing_mcp_dependency(exc: ImportError) -> bool:
"""Return True when the import error comes... | trbck/streammachine | src/streammachine/__main__.py | .py | c67965fdf5178048 | 7.48 | 8 |
"""
Fast OHLC aggregation with Cython acceleration and Python fallback.
This module provides high-performance OHLC candle aggregation for
real-time market data. It uses Cython when available for maximum
speed, falling back to pure Python when Cython is not compiled.
Performance:
- Cython: ~500k ticks/second, <5µs per... | trbck/streammachine | src/streammachine/fast_ohlc.py | .py | 7b12ffd542789c24 | 7.48 | 8 |
#!/usr/bin/env python3
"""
MCP Server entry point.
Usage:
# From the streammachine source directory:
mcp dev src/streammachine/mcp_entry.py
# Or after installation:
mcp dev $(python -c "import streammachine.mcp_entry; print(streammachine.mcp_entry.__file__)")
"""
from __future__ import annotations
i... | trbck/streammachine | src/streammachine/mcp_entry.py | .py | fb54c7ffe26d4239 | 7.48 | 8 |
"""
StreamMachine Redis Object Storage Module
This module provides RedisObjectStorage for storing Python objects in Redis
with automatic pickle serialization.
Why pickle?
Redis stores bytes, and pickle provides:
- Serialization of arbitrary Python objects
- Handles complex types (nested dicts, custom clas... | trbck/streammachine | src/streammachine/objstorage/redisobjstore.py | .py | b32f15ba4332465f | 7.48 | 8 |
"""
StreamMachine Storage Module
This module provides a singleton Storage class for sharing state between
agents, timers, and across process boundaries.
Why multiprocessing.Manager?
Python's multiprocessing.Manager creates a separate process that manages
shared state. This is essential for cross-process commu... | trbck/streammachine | src/streammachine/storage.py | .py | 6757e49eb8d00b61 | 7.48 | 8 |
"""
StreamMachine Utility Module
This module provides decorators and utilities for task registration
and async/sync bridging.
Decorator Discovery with Venusian:
Venusian enables "deferred decorator" patterns. Instead of executing
immediately at import time, decorators attach metadata that can be
scanned l... | trbck/streammachine | src/streammachine/util.py | .py | 166e7d5ad88fab4d | 7.48 | 8 |
"""Define an API object to interact with the Pinboard API."""
from __future__ import annotations
import logging
from typing import Any, cast
from aiohttp import ClientSession, ClientTimeout
from aiohttp.client_exceptions import ClientError
from aiopinboard.bookmark import BookmarkAPI
from aiopinboard.errors import ... | bachya/aiopinboard | aiopinboard/api.py | .py | 1c8e71911ba3b3c3 | 7.52 | 10 |
"""Define API endpoints for nodes."""
from __future__ import annotations
from collections.abc import Awaitable, Callable
from dataclasses import dataclass
from datetime import datetime
from typing import Any, cast
import arrow
from aiopinboard.helpers.types import DictType, ResponseType
@dataclass
class Note:
... | bachya/aiopinboard | aiopinboard/note.py | .py | 5e33a820c8602bd1 | 7.52 | 10 |
"""Define dynamic test fixtures."""
from __future__ import annotations
import json
from typing import Any, cast
import pytest
from tests.common import load_fixture
@pytest.fixture(name="error_response", scope="session")
def error_response_fixture() -> dict[str, Any]:
"""Return a fixture for a failed auth resp... | bachya/aiopinboard | tests/conftest.py | .py | 26837f07753ece41 | 8.02 | 10 |
import logging
from typing import Union, Optional
from django.contrib.auth.models import User
from django.http.request import HttpRequest
from rest_framework.exceptions import NotAuthenticated
from rest_framework.request import Request
logger = logging.getLogger(__name__)
def get_auth_user(request: Union[Request, Ht... | kajala/django-jutil | jutil/auth.py | .py | 770ff6b909d97d44 | 7.45 | 7 |
import logging
from typing import Optional, TYPE_CHECKING, Any, Sequence, List
logger = logging.getLogger(__name__)
class CachedFieldsMixin:
"""
Cached fields mixin. Usage:
1) List cached field names in cached_fields list
2) Implement get_xxx functions where xxx is cached field name
3) Call updat... | kajala/django-jutil | jutil/cache.py | .py | 0173997ab2fab6e7 | 7.45 | 7 |
import logging
import traceback
from datetime import datetime
from typing import Tuple, List, Any
from django.core.management import get_commands, load_command_class
from django.core.management.base import BaseCommand, CommandParser
from django.utils.timezone import now
from django.conf import settings
from jutil.dates... | kajala/django-jutil | jutil/command.py | .py | a5a277416b81569f | 7.45 | 7 |
from django.utils.formats import date_format
def formatted_date(description=None, ordering=None, fmt: str = "SHORT_DATE_FORMAT"):
"""Decorator for formatting date/datetime field in Django admin.
Args:
description: Short description of the function (default is "short date").
ordering: Admin or... | kajala/django-jutil | jutil/decorators.py | .py | 54bfd79bb9c0f24f | 7.45 | 7 |
import logging
from typing import Any
from django.core.exceptions import ValidationError as DjangoValidationError
try:
from rest_framework.exceptions import ValidationError as DRFValidationError # type: ignore
from rest_framework.views import exception_handler as drf_exception_handler # type: ignore
except E... | kajala/django-jutil | jutil/drf_exceptions.py | .py | ba06fa79815cb8d9 | 7.45 | 7 |
import os
from typing import List
from django.utils.translation import gettext as _
from jutil.format import is_media_full_path, strip_media_root
def list_files(dir_name: str, suffix: str = "", ignore_case: bool = True, use_media_root: bool = False, recurse: bool = False) -> List[str]:
"""Lists all files under sp... | kajala/django-jutil | jutil/files.py | .py | 74898091e69df072 | 7.45 | 7 |
import logging
import traceback
from typing import Dict, Optional
from urllib.parse import urlencode
from django.conf import settings
from django.http import HttpRequest
from django.utils import timezone
from ipware import get_client_ip # type: ignore
from jutil.email import send_email
logger = logging.getLogger(__na... | kajala/django-jutil | jutil/middleware.py | .py | 2a22ef1402314124 | 7.45 | 7 |
from datetime import timedelta, datetime
from django.db.models.fields import Field
from django.utils.encoding import force_str
from time import sleep
from typing import Type, List, Tuple, Any, Optional, Sequence
from django.db.models import Model
from django.utils.timezone import now
from jutil.format import choices_la... | kajala/django-jutil | jutil/model.py | .py | 10dee399af005f80 | 7.45 | 7 |
import logging
from datetime import datetime, time, date, timezone
from typing import Optional, Any
from django.core.exceptions import ValidationError
from django.utils.translation import gettext as _
from django.utils.dateparse import parse_datetime as django_parse_datetime
from django.utils.dateparse import parse_dat... | kajala/django-jutil | jutil/parse.py | .py | 2744a102cbfeb3b6 | 7.45 | 7 |
from rest_framework import permissions
class UserIsOwner(permissions.BasePermission):
"""Object-level permission to only allow authorized users of an object to edit it.
Assumes the model instance has an `user` attribute (can be overriden with user_field).
"""
user_field = "user"
def has_object_p... | kajala/django-jutil | jutil/permissions.py | .py | 2697af5b87bc49a5 | 7.45 | 7 |
import logging
from typing import List, Tuple
from django.utils.translation import get_language, gettext_lazy as _
from django.contrib.admin import SimpleListFilter
from jutil.redis_helpers import redis_get_json, redis_set_json
logger = logging.getLogger(__name__)
class RedisCachedSimpleListFilter(SimpleListFilter):... | kajala/django-jutil | jutil/redis_admin_helpers.py | .py | 4b5fc2d97282e1bf | 7.45 | 7 |
import logging
from typing import Tuple, Optional
from django.conf import settings
import requests
import socket
from ipware import get_client_ip # type: ignore
logger = logging.getLogger(__name__)
class GeoIP:
"""
Basic geolocation information of IP-address.
"""
ip: str
country_name: str
c... | kajala/django-jutil | jutil/request.py | .py | af6a57271c9fd969 | 7.45 | 7 |
import mimetypes
import os
from typing import Any, List
from django.http import HttpResponse, FileResponse, Http404
from django.utils.translation import gettext as _
from jutil.format import format_xml_file, format_xml_bytes, format_csv
class FileSystemFileResponse(FileResponse):
"""File system download HTTP resp... | kajala/django-jutil | jutil/responses.py | .py | 99bddb51c713ad32 | 7.45 | 7 |
import logging
from typing import Optional
from uuid import uuid1
from django.contrib.auth import get_user_model
from django.contrib.auth.models import User
from rest_framework.test import APIClient
from rest_framework.authtoken.models import Token
logger = logging.getLogger(__name__)
class TestSetupMixin:
@stat... | kajala/django-jutil | jutil/testing.py | .py | d0145a4b209cec1c | 7.95 | 7 |
import re
from typing import Optional, Iterable, Dict, Any, List
from xml import etree
from xml.etree.ElementTree import Element, SubElement
def _xml_element_value(el: Element, is_int: bool = False) -> Any:
"""Gets XML Element value.
Args:
el: Element
is_int: If True return value is converted... | kajala/django-jutil | jutil/xml.py | .py | ae5af7b777f8c323 | 7.45 | 7 |
from typing import cast
from ..dialogue.manager import MMDialogueManager
from ..models.http import SkillInvokeRequest, SkillInvokeResponse
from ..models.mindmeld import DialogueState, ProcessedQuery
from ..supress_warnings import suppress_warnings
from .base import BaseAPI
class MindmeldAPI(BaseAPI):
def __init_... | cisco/webex-assistant-sdk | webex_skills/api/mindmeld.py | .py | 8185c35d935b80a0 | 7.57 | 13 |
import json
from pathlib import Path
import typer
CONFIG_DIR = Path(typer.get_app_dir('skills-cli', force_posix=True))
CONFIG_FILE = CONFIG_DIR / 'config.json'
def get_skill_config(name: str):
"""Return the configuration for a named skill"""
remotes = get_remotes()
return remotes.get(name)
def get_rem... | cisco/webex-assistant-sdk | webex_skills/cli/config.py | .py | 0fd174736f1cdc23 | 7.57 | 13 |
from pprint import pformat
from typing import Optional
import typer
from .config import get_app_dir
from .helpers import create_nlp
app = typer.Typer(help='Commands for working with NLP models')
# take name to find app path, otherwise default to cwd
@app.command()
def build(name: Optional[str] = typer.Argument(Non... | cisco/webex-assistant-sdk | webex_skills/cli/nlp.py | .py | bf0e356aae55ef4c | 7.57 | 13 |
import json
from pathlib import Path
import secrets
import shutil
from typing import Optional
import typer
from ..crypto import generate_keys
from .config import CONFIG_DIR, CONFIG_FILE, get_remotes, get_skill_config
from .helpers import create_nlp
app = typer.Typer(name='project')
@app.command(name='init')
def in... | cisco/webex-assistant-sdk | webex_skills/cli/project.py | .py | 861af58675eb2ec7 | 7.57 | 13 |
import base64
import binascii
from typing import cast
from cryptography.exceptions import UnsupportedAlgorithm
from cryptography.fernet import Fernet
from cryptography.hazmat.primitives import hashes, serialization
from cryptography.hazmat.primitives.asymmetric.padding import MGF1, OAEP
from cryptography.hazmat.primit... | cisco/webex-assistant-sdk | webex_skills/crypto/messages.py | .py | f6d43cd54372ea5d | 7.57 | 13 |
import inspect
import re
from typing import List, Optional
from ..models.mindmeld import DialogueState
from ..types import DialogueHandler, DialogueQuery, RuleMap
from .rules import MMDialogueStateRule, SimpleDialogueStateRule
class MissingHandler(Exception):
pass
class DialogueManager:
def __init__(self, ... | cisco/webex-assistant-sdk | webex_skills/dialogue/manager.py | .py | 29c130a719dba779 | 7.57 | 13 |
from __future__ import annotations
import json
from typing import Any, Callable, Dict, Sequence, TypeVar
from ast import literal_eval
T = TypeVar("T", bound=Dict[str, Any])
def type_caster(prefix: str, cast_fun: Callable) -> Any:
"""Base type caster"""
def _caster(value: str, fail_raises: bool = True) -> ... | pwwang/python-simpleconf | simpleconf/caster.py | .py | a879de829d456736 | 7.45 | 7 |
import warnings
import io
from pathlib import Path
from typing import Any, Awaitable, Dict
from diot import Diot
from ..utils import require_package
from ..caster import (
cast,
int_caster,
float_caster,
bool_caster,
none_caster,
python_caster,
py_caster,
json_caster,
toml_caster,
)... | pwwang/python-simpleconf | simpleconf/loaders/env.py | .py | 70e6196c7934f0ca | 7.45 | 7 |
from __future__ import annotations
import warnings
from typing import Any, Awaitable, Dict
from pathlib import Path
from diot import Diot
from ..utils import require_package
from ..caster import (
cast,
int_caster,
float_caster,
bool_caster,
none_caster,
python_caster,
py_caster,
json_... | pwwang/python-simpleconf | simpleconf/loaders/ini.py | .py | 6bc6a1248cf0db84 | 7.45 | 7 |
import json
from typing import Any, Awaitable, Dict
from . import (
Loader,
NoConvertingPathMixin,
LoaderModifierMixin,
J2ModifierMixin,
LiqModifierMixin,
)
class JsonLoader(Loader, LoaderModifierMixin):
"""Json file loader"""
def loading(self, conf: Any, ignore_nonexist: bool) -> Dict[s... | pwwang/python-simpleconf | simpleconf/loaders/json.py | .py | d0d4ca07d262741f | 7.45 | 7 |
from typing import Any, Dict, Awaitable
from ..utils import require_package
from ..caster import (
none_caster,
null_caster,
)
from . import (
Loader,
NoConvertingPathMixin,
LoaderModifierMixin,
J2ModifierMixin,
LiqModifierMixin,
)
toml = require_package("rtoml", "tomllib", "tomli")
clas... | pwwang/python-simpleconf | simpleconf/loaders/toml.py | .py | 3890ae920fd1df39 | 7.45 | 7 |
from typing import Any, Dict, Awaitable
from . import (
Loader,
NoConvertingPathMixin,
LoaderModifierMixin,
J2ModifierMixin,
LiqModifierMixin,
)
from ..utils import require_package
yaml = require_package("yaml")
class YamlLoader(Loader, LoaderModifierMixin):
"""Yaml file loader"""
def l... | pwwang/python-simpleconf | simpleconf/loaders/yaml.py | .py | 22828c690179cb91 | 7.45 | 7 |
import sys
import pytest
from simpleconf.exceptions import FormatNotSupported
from simpleconf.utils import (
config_to_ext,
detect_loader_directive,
detect_loadenv_directive,
load_dotenv_file,
get_loader,
require_package,
)
from diot import Diot
pytest_plugins = ["tests.fixt_simpleconf"]
@py... | pwwang/python-simpleconf | tests/test_utils.py | .py | d55c9562534bb0fb | 7.95 | 7 |
"""
API for running backtests on investment portfolios.
This module provides a static utility class `Backtest` that wraps core
backtesting functionality, including downloading portfolio history,
calculating share allocations, rebalancing portfolios, and visualizing
results against benchmark portfolios.
"""
from datet... | ajitnilakantan/backtest-portfolio | src/backtest_portfolio/api.py | .py | 0371d220574925ba | 7.92 | 6 |
from __future__ import annotations
import os
import sqlite3
import tempfile
from datetime import datetime
from typing import Final
import pandas as pd
class NullContextManager:
"""A safe placeholder context manager that does nothing and returns None."""
def __enter__(self) -> None:
return None
... | ajitnilakantan/backtest-portfolio | src/backtest_portfolio/db_cache.py | .py | 5c47826652a753ea | 7.92 | 6 |
"""Holding and portfolio structures for backtesting.
This module defines dataclasses and enums used to represent investment
holdings and portfolios, along with default benchmark and example portfolios
for backtesting scenarios.
"""
import re
from dataclasses import dataclass, field
from enum import StrEnum
from typin... | ajitnilakantan/backtest-portfolio | src/backtest_portfolio/holding.py | .py | e409be7b49b0b4a5 | 7.92 | 6 |
"""The ``walsh`` command-line interface: ``walsh compress`` / ``walsh extract``."""
from __future__ import annotations
import logging
import click
from walsh.exceptions import EXPECTED_ERRORS
from walsh.task import (
DEFAULT_CHROMA_BLOCK_SIZE,
DEFAULT_PACKED_BLOCK_SIZE,
DEFAULT_Y_BLOCK_SIZE,
Action,... | oskar-j/walsh-hadamard-transform | src/walsh/cli.py | .py | db376eca04b2d58f | 7.42 | 6 |
"""Small caching helper used to memoise expensive matrix construction."""
from __future__ import annotations
import functools
from collections.abc import Callable, Hashable
from typing import Any, Generic, ParamSpec, TypeVar
__all__ = ["Memo", "cached"]
P = ParamSpec("P")
R = TypeVar("R")
#: Separates positional f... | oskar-j/walsh-hadamard-transform | src/walsh/decorators.py | .py | e98b3b3bbdadb436 | 7.42 | 6 |
"""Exception types raised by the package, and the groupings callers act on.
This module deliberately imports nothing from the rest of ``walsh``, so any
module can import it without risking a cycle.
"""
from __future__ import annotations
import struct
__all__ = [
"EXPECTED_ERRORS",
"UnsupportedFileFormatErro... | oskar-j/walsh-hadamard-transform | src/walsh/exceptions.py | .py | e5de502e7f75b952 | 7.42 | 6 |
"""The in-memory contract every raster format in this package shares."""
from __future__ import annotations
from abc import ABC, abstractmethod
from collections.abc import Sequence
from walsh.image._io import FileSource
__all__ = ["Pixel", "RasterImage"]
#: One pixel as ``(red, green, blue)``, each channel a 0-255... | oskar-j/walsh-hadamard-transform | src/walsh/image/base.py | .py | 6221ca5b1e0ceaef | 7.42 | 6 |
"""24-bit uncompressed Windows bitmaps.
BMP disagrees with this package's in-memory contract on two counts, and
:class:`BMPImage` reconciles both:
* pixels are stored blue-green-red, not red-green-blue;
* rows are stored bottom-up when the header height is positive. A negative
height means top-down, which is why th... | oskar-j/walsh-hadamard-transform | src/walsh/image/bmp.py | .py | e4e28d136e5d7324 | 7.42 | 6 |
"""The custom ``.cim`` container holding truncated spectral blocks.
Layout: ``<II`` width and height, then three ``<HHH`` :class:`BlockDescription`
records in the order Y, Cb, Cr, then each channel's blocks row-major as
little-endian ``int16``. It is a project-specific format; nothing else reads it.
"""
from __future... | oskar-j/walsh-hadamard-transform | src/walsh/image/cim.py | .py | b42d4c749f24e70a | 7.42 | 6 |
"""Portable Pixmap (PPM) images, from the Netpbm suite.
PPM is the closest Unix equivalent to the uncompressed BMP this codec started
with: a tiny ASCII header followed by raw samples, no compression, no palette.
Two variants exist and both are read:
* **P6**, binary, one byte per sample. This is what :meth:`PPMImag... | oskar-j/walsh-hadamard-transform | src/walsh/image/ppm.py | .py | b00105c7c57882ca | 7.42 | 6 |
"""Uncompressed baseline TIFF images.
TIFF is a container rather than a single layout, so this reader deliberately
handles one profile and rejects the rest rather than guessing: uncompressed
(``Compression = 1``), RGB (``PhotometricInterpretation = 2``), 8 bits per
sample, three samples per pixel, chunky (``PlanarConf... | oskar-j/walsh-hadamard-transform | src/walsh/image/tiff.py | .py | 4c1cfd312689edbb | 7.42 | 6 |
from __future__ import annotations
import struct
from pathlib import Path
from typing import Any
import pytest
from walsh.image import BMP_HEADER_FORMAT, BMP_PIXEL_OFFSET, BMP_SIGNATURE, align
DATA_DIR = Path(__file__).resolve().parent.parent / "data"
Pixel = tuple[int, int, int]
def write_bmp(path: Path, width:... | oskar-j/walsh-hadamard-transform | tests/conftest.py | .py | 67f54d20e2b12f76 | 7.92 | 6 |
from __future__ import annotations
import numpy as np
import pytest
from walsh.transforms import WalshHadamardTransform, _sign_changes
@pytest.fixture
def transform() -> WalshHadamardTransform:
return WalshHadamardTransform()
@pytest.mark.parametrize("size", [2, 4, 8, 16])
def test_matrix_is_orthonormal(trans... | oskar-j/walsh-hadamard-transform | tests/test_transforms.py | .py | e8063d6354c79c60 | 7.92 | 6 |
"""Read and provide runtime configuration.
Currently restricted to a subset of overall app configuration.
"""
from functools import cache
from pathlib import Path
from pydantic import Field
from pydantic_settings import BaseSettings, SettingsConfigDict
from wags_tails.utils.storage import get_data_dir
from metakb.s... | cancervariants/metakb | server/src/metakb/config.py | .py | acf79d841839eff2 | 7.6 | 15 |
"""A module for the Harvester base class"""
import logging
from abc import ABC, abstractmethod
from enum import StrEnum
from pathlib import Path
from metakb.source_data import SourceDataStore
_logger = logging.getLogger(__name__)
class FetchMode(StrEnum):
"""Define options for fetching data"""
FORCE_REFRE... | cancervariants/metakb | server/src/metakb/harvesters/base.py | .py | f5838c4e48b9a2a7 | 7.6 | 15 |
"""Harvest data from cBioPortal studies."""
import logging
import shutil
import tarfile
from pathlib import Path
from typing import NamedTuple
import pandas as pd
from wags_tails.base_source import UnversionedDataSource, get_latest_local_file
from wags_tails.utils.downloads import download_http
from metakb.harvester... | cancervariants/metakb | server/src/metakb/harvesters/cbioportal.py | .py | 1c07dce85608f32a | 7.6 | 15 |
"""A module for the CIViC harvester."""
from pathlib import Path
from civicpy import civic as civicpy
from metakb.harvesters.base import FetchMode, Harvester
class CivicHarvester(Harvester):
"""A class for the CIViC harvester."""
def harvest(self, fetch_mode: FetchMode = FetchMode.CHECK_STALE) -> Path:
... | cancervariants/metakb | server/src/metakb/harvesters/civic.py | .py | ff1deeec38a8938f | 7.6 | 15 |
"""Fetch curated FDA pediatric oncology drug approval data.
This class shouldn't need to do much other than grabbing it from the source repo and
stashing it locally.
"""
import json
from pathlib import Path
import requests
from ga4gh.va_spec.base import Statement
from pydantic import BaseModel
from wags_tails.base_s... | cancervariants/metakb | server/src/metakb/harvesters/fda_poda.py | .py | 38d48865b0e81841 | 7.6 | 15 |
"""Fetch NCH Molecular Characterization Initiative (MCI) structured knowledge"""
import json
import re
from pathlib import Path
import requests
from ga4gh.va_spec.aac_2017.models import VariantClinicalSignificanceStatement
from pydantic import BaseModel
from wags_tails.base_source import DataSource
from wags_tails.ut... | cancervariants/metakb | server/src/metakb/harvesters/mci.py | .py | e49c98dc6a072025 | 7.6 | 15 |
"""A module for the Molecular Oncology Almanac harvester"""
import logging
from http import HTTPStatus
from pathlib import Path
import requests
import requests_cache
from metakb.harvesters.base import FetchMode, Harvester
from metakb.schemas.data import MoaHarvestedData
logger = logging.getLogger(__name__)
class ... | cancervariants/metakb | server/src/metakb/harvesters/moa.py | .py | 3fe1b4536c2fc4be | 7.6 | 15 |
"""Initialize logging"""
import logging
from metakb.config import get_config
from metakb.schemas.api import ServiceEnvironment
def _quiet_upstream_libs() -> None:
"""Turn off debug logging for chatty upstream library loggers."""
for lib in (
"boto3",
"botocore",
"urllib3",
"h... | cancervariants/metakb | server/src/metakb/log_config.py | .py | 2f2f416588a76836 | 7.6 | 15 |
"""Main application entrypoint."""
import logging
from collections.abc import AsyncGenerator
from contextlib import asynccontextmanager
from enum import StrEnum
from pathlib import Path
from fastapi import FastAPI, Request
from fastapi.middleware.cors import CORSMiddleware
from fastapi.staticfiles import StaticFiles
... | cancervariants/metakb | server/src/metakb/main.py | .py | eb86f9a37b62bf49 | 7.6 | 15 |
"""Declare base repository interface + associated helper functions."""
import abc
from ga4gh.core.models import MappableConcept
from ga4gh.va_spec.base import Statement
from pydantic import BaseModel
class RepositoryStats(BaseModel):
"""Define structure for reporting entity counts from the DB"""
num_genes:... | cancervariants/metakb | server/src/metakb/repository/base.py | .py | 55d79654da53b149 | 7.6 | 15 |
"""Provide API endpoints for meta-level service information"""
from typing import Annotated
from fastapi import APIRouter, Depends
from metakb.config import get_config
from metakb.repository.base import AbstractRepository, RepositoryStats
from metakb.restapi.dependencies import get_repository
from metakb.schemas.api... | cancervariants/metakb | server/src/metakb/restapi/meta.py | .py | 6ea75c171d5851f7 | 7.6 | 15 |
"""Create schemas for API"""
from enum import Enum, StrEnum
from typing import Literal
from ga4gh.cat_vrs import CATVRS_VERSION
from ga4gh.cat_vrs import __version__ as cat_vrs_python_version
from ga4gh.cat_vrs.models import CategoricalVariant
from ga4gh.va_spec import VASPEC_VERSION
from ga4gh.va_spec import __versi... | cancervariants/metakb | server/src/metakb/schemas/api.py | .py | 729c8c799a9cd3a6 | 7.6 | 15 |
"""Module containing app schemas and enums"""
from enum import StrEnum
class SourceName(StrEnum):
"""Define enum for sources that are supported"""
CIVIC = "civic"
MOA = "moa"
CBIOPORTAL = "cbioportal"
FDA_PODA = "fda_poda"
MCI = "mci"
def as_print_case(self) -> str:
"""Provide e... | cancervariants/metakb | server/src/metakb/schemas/app.py | .py | ac5900ddfd4e4ace | 7.6 | 15 |
"""Handle data exchange formats for ingest/loading"""
from enum import StrEnum
from ga4gh.va_spec.base import Statement
from pydantic import BaseModel
class MoaHarvestedData(BaseModel):
"""Define output for harvested data from MOA"""
assertions: list[dict]
sources: list[dict]
class CBioPortalStudyNam... | cancervariants/metakb | server/src/metakb/schemas/data.py | .py | f4725aa5ed4f5bed | 7.6 | 15 |
# -*- encoding: utf-8 -*-
import datetime
import logging
import pkg_resources
import re
from email.utils import parseaddr, formataddr
from configparser import ConfigParser, NoOptionError, NoSectionError, DuplicateSectionError
logger = logging.getLogger("nikas")
default_config_file = pkg_resources.resource_filename(... | Nikas-Project/Server | nikas/config.py | .py | 9b2eba72c25bd5a4 | 7.54 | 11 |
# -*- encoding: utf-8 -*-
import sqlite3
import logging
import operator
import os.path
from collections import defaultdict
logger = logging.getLogger("nikas")
from nikas.db.comments import Comments
from nikas.db.threads import Threads
from nikas.db.spam import Guard
from nikas.db.preferences import Preferences
cl... | Nikas-Project/Server | nikas/db/__init__.py | .py | 2f091bc73434fe15 | 7.54 | 11 |
# -*- encoding: utf-8 -*-
import sys
import os
import logging
from glob import glob
from werkzeug.middleware.dispatcher import DispatcherMiddleware
from werkzeug.wrappers import Response
from nikas import make_app, wsgi, config
logger = logging.getLogger("nikas")
class Dispatcher(DispatcherMiddleware):
"""
... | Nikas-Project/Server | nikas/dispatch.py | .py | 85f5b8abb1d5737f | 7.54 | 11 |
# -*- encoding: utf-8 -*-
import unittest
import io
from nikas import config
class TestConfig(unittest.TestCase):
def test_parser(self):
parser = config.NikasParser()
parser.read_file(io.StringIO("""
[foo]
bar = 1h
baz = 12
spam = a, b, cdef
... | Nikas-Project/Server | nikas/tests/test_config.py | .py | 636244da72f67609 | 7.04 | 11 |
# -*- encoding: utf-8 -*-
import unittest
from nikas import utils
from nikas.utils import parse
class TestUtils(unittest.TestCase):
def test_anonymize(self):
examples = [
(u'12.34.56.78', u'12.34.56.0'),
(u'1234:5678:90ab:cdef:fedc:ba09:8765:4321',
u'1234:5678:90ab... | Nikas-Project/Server | nikas/tests/test_utils.py | .py | 61935a1ce290abc3 | 7.04 | 11 |
"""Find the complete documentation online.
https://dfetch.rtfd.org
"""
import argparse
import sys
from collections.abc import Sequence
from rich.console import Console
import dfetch.commands.add
import dfetch.commands.check
import dfetch.commands.diff
import dfetch.commands.environment
import dfetch.commands.format... | dfetch-org/dfetch | dfetch/__main__.py | .py | 888ab3810d7355bd | 7.57 | 13 |
"""To check if your projects are up-to-date, you can let dfetch check it.
For each project the local version (based on tag or revision) will be compared against
the available version. If there are new versions available this will be shown.
.. uml:: /static/uml/check.puml
.. tabs::
.. tab:: Git
.. scenario... | dfetch-org/dfetch | dfetch/commands/check.py | .py | 37b2f64d21f82e8e | 7.57 | 13 |
"""A generic command."""
import argparse
import re
import sys
from abc import ABC, abstractmethod
from argparse import ArgumentParser # pylint: disable=unused-import
from typing import TYPE_CHECKING, TypeVar
if TYPE_CHECKING and sys.version_info >= (3, 10):
from typing import TypeAlias
SubparserActionType: ... | dfetch-org/dfetch | dfetch/commands/command.py | .py | 9c5cdcc1f111c71f | 7.57 | 13 |
"""Module for common command operations."""
import os
import yaml
from dfetch.log import get_logger
from dfetch.manifest.manifest import Manifest
from dfetch.manifest.parse import get_submanifests
from dfetch.manifest.project import ProjectEntry
logger = get_logger(__name__)
def check_sub_manifests(manifest: Mani... | dfetch-org/dfetch | dfetch/commands/common.py | .py | 3e6c2c0873161abc | 7.57 | 13 |
"""*Dfetch* can create a patch file with your local changes to the external project.
If you've found any issues with the remote project, you can fix them within the context of your project.
To help the upstream project, you can generate a patch file that can be applied by the upstream maintainer.
The patch will be gen... | dfetch-org/dfetch | dfetch/commands/diff.py | .py | f13d9810740cf3ec | 7.57 | 13 |
"""*Dfetch* can report information about its working environment.
``dfetch environment`` prints:
* **Platform** — operating system name and kernel version.
* **VCS tool versions** — the version of each supported VCS client
(Git, SVN) found on ``PATH``.
Run this command when setting up a new machine to confirm that... | dfetch-org/dfetch | dfetch/commands/environment.py | .py | ee0b4da23397e116 | 7.57 | 13 |
"""*Dfetch* can convert your Git submodules or SVN externals based project to Dfetch.
Dfetch will look for all submodules or externals in the current project and generate
a manifest with the current versions of the repository.
After importing, you will need to remove the submodules or externals, and then you can let ... | dfetch-org/dfetch | dfetch/commands/import_.py | .py | afadbeeab868d5db | 7.57 | 13 |
"""*Dfetch* can generate a starting manifest.
Running ``dfetch init`` creates a ``dfetch.yaml`` file in the current
directory. The file contains a minimal template that you can open and edit
directly, or populate incrementally using :ref:`dfetch add <add>`.
Once you have listed your dependencies, fetch them with :ref... | dfetch-org/dfetch | dfetch/commands/init.py | .py | 7620818d0f37589b | 7.57 | 13 |
"""Remove projects from the manifest and delete their directories.
Use ``dfetch remove <project>`` to remove one or more projects.
See :ref:`remove-a-project` for the full guide.
.. scenario-include:: ../features/remove-project.feature
"""
import argparse
import shutil
import dfetch.commands.command
from dfetch.lo... | dfetch-org/dfetch | dfetch/commands/remove.py | .py | a808feb03bb461a6 | 7.57 | 13 |
"""*Dfetch* can generate reports about the projects in your manifest.
Two report types are available via the ``-t`` / ``--type`` flag:
``stdout`` (default)
Prints a dependency inventory to the terminal. For each project it shows
the remote URL, branch/tag/revision, last-fetch timestamp, applied patches,
a... | dfetch-org/dfetch | dfetch/commands/report.py | .py | 2bf8fe887dbf39c2 | 7.57 | 13 |
"""Fetch every project listed in the manifest.
VCS type (Git, SVN, archive) is detected automatically.
See :ref:`updating-projects` for the full guide.
.. uml:: /static/uml/update.puml
.. scenario-include:: ../features/fetch-git-repo.feature
.. scenario-include:: ../features/fetch-svn-repo.feature
.. scenario-incl... | dfetch-org/dfetch | dfetch/commands/update.py | .py | 70b46ecde149eaae | 7.57 | 13 |
"""Updating patches.
*Dfetch* allows you to keep local changes to external projects in the form of
patch files. When those local changes evolve over time, an existing patch can
be updated to reflect the new state of the project.
The ``update-patch`` command automates the otherwise manual process of
refreshing a patch... | dfetch-org/dfetch | dfetch/commands/update_patch.py | .py | 603292d8d375d912 | 7.57 | 13 |
"""*Dfetch* can validate a manifest without fetching anything.
``dfetch validate`` parses ``dfetch.yaml`` and checks every field against the
manifest schema — project names, URLs, version strings, source paths, and
integrity hashes are all verified. Any structural or type error is reported
immediately with a clear mes... | dfetch-org/dfetch | dfetch/commands/validate.py | .py | cd5528b7d4b79e9c | 7.57 | 13 |
"""Logging related items."""
from __future__ import annotations
import logging
import os
import sys
import types
from contextlib import nullcontext
from logging import LogRecord
from typing import TYPE_CHECKING, Any, ClassVar, cast
from rich.console import Console, ConsoleRenderable
from rich.highlighter import Null... | dfetch-org/dfetch | dfetch/log.py | .py | 07c89de0c8b7e5ab | 7.57 | 13 |
"""Utilities for finding manifest files."""
import os
import pathlib
from dfetch import DEFAULT_MANIFEST_NAME
from dfetch.log import get_logger
from dfetch.manifest.manifest import Manifest
from dfetch.util.util import (
check_no_path_traversal,
find_file,
prefix_runtime_exceptions,
)
logger = get_logger... | dfetch-org/dfetch | dfetch/manifest/parse.py | .py | 8a56f64044355e94 | 7.57 | 13 |
"""Remotes are the external repository where the code should be retrieved from.
The ``remotes:`` section is not mandatory.
If only one remote is added this is assumed to be the default.
If multiple remotes are listed ``default:`` can be explicitly specified.
If multiple remotes are marked as default, the first marked ... | dfetch-org/dfetch | dfetch/manifest/remote.py | .py | 3f408a4873268353 | 7.57 | 13 |
"""Version of a project."""
from typing import NamedTuple
class Version(NamedTuple):
"""Version of a project.
In DFetch a version consists of a tag, branch or revision.
A tag has precedence over branches/revisions.
"""
tag: str = ""
branch: str = ""
revision: str = ""
def __eq__(se... | dfetch-org/dfetch | dfetch/manifest/version.py | .py | 9903d7c2e134da9b | 7.57 | 13 |
"""All Project related items."""
import os
import pathlib
import dfetch.manifest.project
from dfetch.log import get_logger
from dfetch.manifest.manifest import Manifest
from dfetch.manifest.parse import find_manifest
from dfetch.project.archivesubproject import ArchiveSubProject
from dfetch.project.gitsubproject impo... | dfetch-org/dfetch | dfetch/project/__init__.py | .py | e3f8f7d6666161b6 | 7.57 | 13 |
"""Archive (tar/zip) specific implementation.
Archives are a third VCS type alongside ``git`` and ``svn``. They represent
versioned dependencies that are distributed as ``.tar.gz``, ``.tgz``,
``.tar.bz2``, ``.tar.xz`` or ``.zip`` files reachable via ``http://``,
``https://``, or ``file://`` URLs.
Unlike git and SVN,... | dfetch-org/dfetch | dfetch/project/archivesubproject.py | .py | 50b4d3bf46a58a68 | 7.57 | 13 |
"""Git specific implementation."""
from pathlib import Path
from dfetch.log import get_logger
from dfetch.manifest.project import ProjectEntry
from dfetch.manifest.version import Version
from dfetch.project.metadata import Dependency
from dfetch.project.subproject import SubProject
from dfetch.util.license import LIC... | dfetch-org/dfetch | dfetch/project/gitsubproject.py | .py | a7dc2d80e99f6cf1 | 7.57 | 13 |
"""Git Super project abstraction.
This module provides the specific GitSuperProject class which represents
a git project that contains the `dfetch.yaml` manifest file (the "super project").
"""
from __future__ import annotations
import os
import pathlib
from collections.abc import Sequence
from dfetch.log import ge... | dfetch-org/dfetch | dfetch/project/gitsuperproject.py | .py | 74926df590ec40cd | 7.57 | 13 |
"""SVN specific implementation."""
import os
import pathlib
import urllib.parse
from dfetch.log import get_logger
from dfetch.manifest.project import ProjectEntry
from dfetch.manifest.version import Version
from dfetch.project.metadata import Dependency
from dfetch.project.subproject import SubProject
from dfetch.uti... | dfetch-org/dfetch | dfetch/project/svnsubproject.py | .py | c662c440ecca8ef3 | 7.57 | 13 |
"""Svn Super project abstraction.
This module provides the specific SvnSuperProject class which represents
a svn project that contains the `dfetch.yaml` manifest file (the "super project").
"""
from __future__ import annotations
import os
import pathlib
from collections.abc import Sequence
from dfetch.log import ge... | dfetch-org/dfetch | dfetch/project/svnsuperproject.py | .py | d735460975955b27 | 7.57 | 13 |
"""Various reporters for generating reports."""
from enum import Enum
from dfetch.reporting.reporter import Reporter
from dfetch.reporting.sbom_reporter import SbomReporter
from dfetch.reporting.stdout_reporter import StdoutReporter
class ReportTypes(Enum):
"""Enum giving a name to a type of reporter."""
S... | dfetch-org/dfetch | dfetch/reporting/__init__.py | .py | 33d84024270584a9 | 7.57 | 13 |
"""*Dfetch* can generate a report that is parsable by GitLab/Code Climate from the :ref:`check` results.
Depending on the state of the projects it will create a report with information.
If all project are up-to-date, nothing will be added to the report.
The information has several severities:
* ``major`` : An unfetc... | dfetch-org/dfetch | dfetch/reporting/check/code_climate_reporter.py | .py | 52e389c4b52c17b5 | 7.57 | 13 |
"""*Dfetch* can generate a report that is parseable by Jenkins from the :ref:`check` results.
Depending on the state of the projects, it will create a report with relevant information.
If all projects are up-to-date, nothing will be added to the report.
The information has several severities:
* ``high`` : An unfetch... | dfetch-org/dfetch | dfetch/reporting/check/jenkins_reporter.py | .py | 392f9227e687c5a6 | 7.57 | 13 |
"""Report issues found during check.
*DFetch* can report the results of :ref:`check` in a format usable by several other tools.
See the respective sections for details about using and configuring those reporters.
All reports can contain the following results:
* ``unfetched-project``
Project was never fetched. Fe... | dfetch-org/dfetch | dfetch/reporting/check/reporter.py | .py | cfd5607ff7cf3f16 | 7.57 | 13 |
"""Abstract reporting interface."""
from abc import ABC, abstractmethod
from dfetch.manifest.manifest import Manifest
from dfetch.manifest.project import ProjectEntry
from dfetch.util.license import LicenseScanResult
class Reporter(ABC):
"""Reporter for generating report."""
name: str = "abstract"
def... | dfetch-org/dfetch | dfetch/reporting/reporter.py | .py | 2f1b6935b4bf4b25 | 7.57 | 13 |
"""Resources needed when dfetch is distributed."""
import importlib.resources as importlib_resources
from contextlib import AbstractContextManager
from pathlib import Path
def _resource_path(filename: str) -> AbstractContextManager[Path]:
"""Get the path to the resource."""
return importlib_resources.as_file... | dfetch-org/dfetch | dfetch/resources/__init__.py | .py | 44c88274c821fa03 | 7.57 | 13 |
from __future__ import annotations
from enum import Enum
from typing import Any, Final, get_args, get_origin
_DATAIO_METADATA_PACKAGE: Final = "fmu.datamodels"
def _is_dataio(annotation: Any) -> bool:
if isinstance(annotation, str):
return annotation.startswith(_DATAIO_METADATA_PACKAGE)
return annot... | equinor/fmu-dataio | docs/ext/pydantic_autosummary/pydantic.py | .py | b3c2417a24a64e02 | 7.52 | 10 |
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