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 |
|---|---|---|---|---|---|---|
from collections.abc import Callable, Hashable, Mapping
from typing import Any
class HashableDict(dict[Any, Any]):
"""A hashable dictionary
NOTE: This obj is still mutable
"""
def __hash__(self) -> int: # type: ignore[override]
return self._hash(frozenset())
def _hash(self, seen: froze... | yugokato/common-libs | src/common_libs/hash.py | .py | 7f15fbb5ac449b7d | 7 | 0 |
import multiprocessing
from collections.abc import Callable, Sequence
from concurrent import futures
from concurrent.futures import ProcessPoolExecutor, ThreadPoolExecutor
from dataclasses import dataclass, field
from typing import Any, cast
@dataclass(frozen=True, slots=True)
class Job:
func: Callable[..., Any]
... | yugokato/common-libs | src/common_libs/job_executor.py | .py | 0670016aabee6887 | 7 | 0 |
import asyncio
import threading
import weakref
from pathlib import Path
from typing import Any, Self
from filelock import AsyncFileLock, FileLock
from common_libs.logging import get_logger
logger = get_logger(__name__)
LOCK_DIR = Path(Path.home(), ".locks").resolve()
# Per-event-loop, per-name reentrant locks used... | yugokato/common-libs | src/common_libs/lock.py | .py | aa8d6d549944eae3 | 7 | 0 |
from __future__ import annotations
import logging
import time
from collections.abc import Mapping, MutableMapping
from enum import StrEnum, auto
from importlib import resources
from logging import LogRecord
from logging.config import dictConfig
from typing import Any
import yaml
from common_libs.ansi_colors import C... | yugokato/common-libs | src/common_libs/logging.py | .py | a42940fa405fed35 | 7 | 0 |
import keyword
import re
def clean_obj_name(name: str) -> str:
"""Convert the name to a legal Python object name
- Illegal values will be converted to "_" (multiple illegal values in a row will be converted to single "_")
- If the name starts with a number, "_" will be added at the beginning
:param ... | yugokato/common-libs | src/common_libs/naming.py | .py | 8d95f6c644d02590 | 7 | 0 |
import socket
from collections.abc import Sequence
from .lock import Lock
def is_port_in_use(port: int, host: str = "127.0.0.1") -> bool:
"""Check if a TCP port is currently in use on the given host.
:param port: The TCP port number to check
:param host: Host address to check
"""
with socket.soc... | yugokato/common-libs | src/common_libs/network.py | .py | 0dc9645751884239 | 7 | 0 |
"""Misc pytest hooks shared across tests in downstream projects.
To enable these hooks from a downstream project, add following line in the top-level `conftest.py`:
pytest_plugins = ["common_libs.testing.pytest_plugins.common"]
"""
from __future__ import annotations
import logging
import os
import re
import sys
imp... | yugokato/common-libs | src/common_libs/testing/pytest_plugins/common.py | .py | 2f8f5282e68a36e8 | 7.5 | 0 |
"""Shared pytest fixtures and configuration"""
from pathlib import Path
from typing import Any
import pytest
@pytest.fixture
def temp_file(tmp_path: Path) -> Path:
"""Create a temporary file for testing"""
file_path = tmp_path / "test_file.txt"
file_path.write_text("test content")
return file_path
... | yugokato/common-libs | tests/conftest.py | .py | 03058c904980f5a6 | 7.5 | 0 |
"""Tests for common_libs.ansi_colors module"""
import io
import pytest
from common_libs.ansi_colors import ColorCodes, color, escape_color_code, remove_color_code, should_color
class TestColorCodes:
"""Tests for ColorCodes class"""
def test_color_codes_exist(self) -> None:
"""Verify all expected c... | yugokato/common-libs | tests/test_ansi_colors.py | .py | a0bd370d726d35ec | 7.5 | 0 |
"""Tests for common_libs.exceptions module"""
import pytest
from common_libs.exceptions import CommandError, NotFound
class TestNotFound:
"""Tests for NotFound exception"""
def test_not_found_raise(self) -> None:
"""Test raising NotFound exception"""
with pytest.raises(NotFound):
... | yugokato/common-libs | tests/test_exceptions.py | .py | da688ee0fbcf3a54 | 7.5 | 0 |
"""Tests for common_libs.files module"""
import re
import tarfile
from pathlib import Path
from common_libs.files import create_tar_file, generate_filename, generate_temp_file
class TestGenerateFilename:
"""Tests for generate_filename function"""
def test_generate_filename_basic(self) -> None:
"""T... | yugokato/common-libs | tests/test_files.py | .py | 6f275605f7e1ebcc | 7.5 | 0 |
"""Tests for common_libs.hash module"""
from typing import Any
import pytest
from common_libs.hash import HashableDict, freeze, generate_hash
class TestHashableDict:
"""Tests for HashableDict class"""
def test_hashable_dict_is_hashable(self) -> None:
"""Test that HashableDict can be hashed"""
... | yugokato/common-libs | tests/test_hash.py | .py | c1308103e2dabad8 | 7.5 | 0 |
"""Tests for common_libs.job_executor module"""
import multiprocessing
import time
import pytest
from pytest_mock import MockFixture
from common_libs.job_executor import Job, run_concurrent
def simple_func(x: int) -> int:
"""Simple test function"""
return x * 2
def slow_func(x: int) -> int:
"""Slow t... | yugokato/common-libs | tests/test_job_executor.py | .py | 50bae902a0b9c33e | 7.5 | 0 |
"""Tests for common_libs.lock module"""
import asyncio
import signal
import threading
import time
import uuid
import pytest
from common_libs.lock import LOCK_DIR, AsyncLock, Lock, _AsyncReentrantLock
class TestLock:
"""Tests for Lock class"""
def test_lock_context_manager(self) -> None:
"""Test us... | yugokato/common-libs | tests/test_lock.py | .py | 361d365e244d6ebc | 7.5 | 0 |
"""Tests for common_libs.logging module"""
import io
import logging
import re
import sys
import time
from collections.abc import Iterator
from typing import IO, Any
import pytest
import common_libs
from common_libs.ansi_colors import ColorCodes
from common_libs.logging import (
ColoredStreamHandler,
CustomLo... | yugokato/common-libs | tests/test_logging.py | .py | 37aa0c4ff0aacab4 | 7.5 | 0 |
"""Tests for common_libs.naming module"""
from common_libs.naming import camel_to_snake, clean_obj_name, to_class_name
class TestCleanObjName:
"""Tests for clean_obj_name function"""
def test_valid_name_passes_through(self) -> None:
"""Test that a valid name is returned unchanged"""
name = "... | yugokato/common-libs | tests/test_naming.py | .py | f1d7ed64ced27530 | 7.5 | 0 |
"""Tests for common_libs.network module"""
import socket
import threading
import pytest
from common_libs.network import find_open_port, is_port_in_use
class TestIsPortInUse:
"""Tests for is_port_in_use function"""
def test_is_port_in_use_free_port(self) -> None:
"""Test detecting a free port"""
... | yugokato/common-libs | tests/test_network.py | .py | 8622f91ca0ff69c3 | 7.5 | 0 |
import logging
from botocore import exceptions
from ..directory import Directory
from ..provider import AwsProvider
log = logging.getLogger(__name__)
aws_error_classes_to_ignore = {
# If no aws credentials were found.
exceptions.NoCredentialsError,
exceptions.NoRegionError,
}
aws_error_codes_to_ignore =... | joshorr/xcon | xcon/providers/common.py | .py | 6830cd0ddcd082e4 | 7.15 | 1 |
from __future__ import annotations
import os
from typing import Optional, Mapping, Dict, Any
from xcon.directory import (
DirectoryOrPath, DirectoryItem, DirectoryChain, Directory, DirectoryListing
)
from xcon.provider import Provider, ProviderChain, InternalLocalProviderCache
class EnvironmentalProvider(Provid... | joshorr/xcon | xcon/providers/environmental.py | .py | e4bcedaf78bc3a82 | 7.15 | 1 |
from __future__ import annotations
import dataclasses
import logging
import base64
from typing import Dict, Optional, Any, Mapping
from .common import handle_aws_exception
from ..directory import Directory, DirectoryListing, DirectoryOrPath, DirectoryItem, DirectoryChain
from botocore.exceptions import ClientError
f... | joshorr/xcon | xcon/providers/secrets_manager.py | .py | e49ac1a35f2658e0 | 7.15 | 1 |
"""
Shared common fixtures for helping with unit-testing.
.. important:: Very Important! Don't import this module your self!
pytest should automatically import this via it's plugin mechanism.
If you import any of the fixtures below manually, you may get something like this:
`ValueError: duplicate 'xyn_co... | joshorr/xcon | xcon/pytest_plugin.py | .py | cca4763d6999b899 | 7.65 | 1 |
import random
import time
class RandomBackoff:
attempt = 0
max_attempts: int | None = None
_first_wait_called = False
_already_reached_max_attempts = False
def __init__(self, base_delay=0.35, max_delay=7, jitter_factor=0.5, *,
max_attempts: int | None = None):
self.base_... | joshorr/xcon | xcon/random_backup.py | .py | f17b5ae28d53b50d | 7.15 | 1 |
from logging import getLogger
log = getLogger(__name__)
def ssm_or_secrets_change_event(event, context):
"""
Here are examples of locations of the various paths from the various events we could get:
detail->name->/auth/dev/db_port
detail->responseElements->name->/test/prod/testing-experiment-2
d... | joshorr/xcon | xcon/serverless_files/config_manager/change_handler.py | .py | f2ccc9b6d05ca246 | 7.15 | 1 |
"""
Generate lists of NCBI assembly IDs to be updated, filtered by RefSeq membership and a list of assemblies of interest.
Update dates for the NCBI FTP site can be found in the file:
https://ftp.ncbi.nlm.nih.gov/genomes/ASSEMBLY_REPORTS/ftp_mod_times.txt.gz
Assemblies whose update date is later than the input date a... | kbase/cdm-data-loaders | scripts/filter_ncbi_updates.py | .py | 86c16b57ae42e105 | 7.3 | 3 |
#!/usr/bin/env python3
# ruff: noqa: D103
"""Thin S3 CLI for local CEPH testing (no aws-cli install required).
Usage (all commands assume ``uv run`` from the repo root):
uv run python scripts/s3_local.py mb s3://cdm-lake
uv run python scripts/s3_local.py cp staging/raw_data/ s3://cdm-lake/staging/run1/raw_d... | kbase/cdm-data-loaders | scripts/s3_local.py | .py | 46996a2d2bc35ad9 | 7.3 | 3 |
"""Checkpoint audit table functions: adding and updating information on data import pipeline execution."""
from logging import Logger, getLogger
from delta.tables import DeltaTable
from pyspark.sql import SparkSession
from pyspark.sql import functions as sf
from cdm_data_loaders.audit.schema import (
CHECKPOINT,... | kbase/cdm-data-loaders | src/cdm_data_loaders/audit/checkpoint.py | .py | dbab842bd9b3832b | 7.3 | 3 |
"""Run audit table functions: additions and updates to the run table, which tracks overall run status for a pipeline."""
from logging import Logger, getLogger
from delta.tables import DeltaTable
from pyspark.sql import SparkSession
from pyspark.sql import functions as sf
from cdm_data_loaders.audit.schema import (
... | kbase/cdm-data-loaders | src/cdm_data_loaders/audit/run.py | .py | c72321a6d1da0c5b | 7.3 | 3 |
"""Schema for audit tables."""
from pyspark.sql.types import ArrayType, IntegerType, LongType, StringType, StructField, StructType, TimestampType
from cdm_data_loaders.core.pipeline_run import PipelineRun
CHECKPOINT = "checkpoint"
METRICS = "metrics"
REJECTS = "rejects"
RUN = "run"
RUN_ID = "run_id"
PIPELINE = "pip... | kbase/cdm-data-loaders | src/cdm_data_loaders/audit/schema.py | .py | 788841eef7db2ff4 | 7.3 | 3 |
"""Resolve all $ref references in a schema to create a fully standalone JSONSchema document.
Fully resolves `$ref` — including references into external JSON Schema
documents supplied via `additional_resources` — and merges `allOf`
throughout a JSON Schema document, producing an equivalent, self-contained
schema with n... | kbase/cdm-data-loaders | src/cdm_data_loaders/converters/jsonschema_to_pyspark/dereferencer.py | .py | 529d793126c8d2c2 | 7.3 | 3 |
"""Common defaults for running pipelines on the KBase CTS."""
import logging
from collections.abc import Hashable
from typing import Any, Self
import dlt
from frozendict import frozendict
from pydantic import AliasChoices, AliasPath, computed_field, field_validator, model_validator
from pydantic_settings import BaseS... | kbase/cdm-data-loaders | src/cdm_data_loaders/core/settings.py | .py | 73f67d9e353a7061 | 7.3 | 3 |
"""NCBI FTP assembly-specific domain logic.
Provides path helpers, file filters, MD5 checksum parsing, and single-assembly
download logic for NCBI GenBank/RefSeq assemblies. Orchestration (batching,
threading, CLI) lives in :mod:`cdm_data_loaders.pipelines.ncbi_ftp_download`.
"""
import contextlib
import time
from f... | kbase/cdm-data-loaders | src/cdm_data_loaders/ncbi_ftp/assembly.py | .py | a5ff987d451c9b11 | 7.3 | 3 |
"""Frictionless data package descriptor creation for NCBI FTP assemblies.
Creates KBase credit metadata descriptors for each promoted assembly,
matching the schema produced by ``kbase-transfers/scripts/ncbi/download_genomes.py``.
Each descriptor is a frictionless ``Package``-compatible JSON document
describing the as... | kbase/cdm-data-loaders | src/cdm_data_loaders/ncbi_ftp/metadata.py | .py | 2a94b2c92695e029 | 7.3 | 3 |
"""
PDB holdings file parser.
Holdings json files apply one of two schemas:
* ID-only: dict[str, dict[Any]] keyed on PDB IDs with values of empty dicts
* ID/Date: dict[str, str] keyed on PDB IDs with ISO-8601 date string values, e.g., ``"2024-01-15"``
PDB IDs in both schemas are in "extended format" with ``"pdb_"`` ... | kbase/cdm-data-loaders | src/cdm_data_loaders/parsers/pdb_holdings_file.py | .py | 59b1afb9ddb2a4e3 | 7.3 | 3 |
"""Parser for UniProt ID Mapping file.
UniProt provides comprehensive mappings between their protein IDs and many other databases. Mappings are extracted from the UniProt records where possible.
Source file: https://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/idmapping.dat.gz
Legacy... | kbase/cdm-data-loaders | src/cdm_data_loaders/parsers/uniprot/idmapping.py | .py | 2af8ba1e9232c6c9 | 7.3 | 3 |
"""Parser for UniProt metalink XML files.
These metadata files provide information and links for UniProt and related downloads.
"""
import datetime
from logging import Logger, getLogger
from pathlib import Path
from typing import Any
from xml.etree.ElementTree import Element
from defusedxml.ElementTree import pars... | kbase/cdm-data-loaders | src/cdm_data_loaders/parsers/uniprot/metalink.py | .py | 5d7e0e08608c31a1 | 7.3 | 3 |
"""Parser for UniProt release notes."""
# The UniProt consortium European Bioinformatics Institute (EBI), SIB Swiss
# Institute of Bioinformatics and Protein Information Resource (PIR),
# is pleased to announce UniProt Knowledgebase (UniProtKB) Release
# 2025_03 (18-Jun-2025). UniProt (Universal Protein Resource) is a... | kbase/cdm-data-loaders | src/cdm_data_loaders/parsers/uniprot/relnotes.py | .py | b66665811a5afd39 | 7.3 | 3 |
"""
UniProt XML Parser Core.
Contains the core logic for parsing a UniProt XML file that can be successfully validated against the UniProt XSD.
"""
import datetime
from logging import Logger, getLogger
from pathlib import Path
from typing import Any
from lxml.etree import Element, tounicode
from cdm_data_loaders.ut... | kbase/cdm-data-loaders | src/cdm_data_loaders/parsers/uniprot/uniprot_kb.py | .py | a48727ccd7a4926e | 7.3 | 3 |
"""UniRef XML File Parser.
Core parser for UniRef XML entries.
Captures the following data about each UniRef cluster:
- ID and name
- members, including representative member and seed
- sequence of the representative member
- whether this is UniRef50, 90, or 100.
Data goes into the Cluster, ClusterMember and Entity ... | kbase/cdm-data-loaders | src/cdm_data_loaders/parsers/uniprot/uniref.py | .py | b9a7fa948116915c | 7.3 | 3 |
"""Constants, enums, classes, and globals used in PDB piplines."""
import re
from dataclasses import dataclass
from enum import StrEnum, auto
from pathlib import Path, PurePosixPath
DEFAULT_DESTINATION_BUCKET: PurePosixPath = PurePosixPath("cdm-lake")
DEFAULT_DESTINATION_PREFIX: PurePosixPath = PurePosixPath("tenant-... | kbase/cdm-data-loaders | src/cdm_data_loaders/pdb/constants.py | .py | d97590f1198e669a | 7.3 | 3 |
"""All The Bacteria bulk data downloader.
Project documentation: https://allthebacteria.org/
Batch downloading from OSF: https://allthebacteria.org/docs/osf_downloads/
all_atb_files.tsv: https://osf.io/xv7q9/files/r6gcp (or Rg6cp, casing varies)
# TODO: change the output to parquet files.
"""
import csv
import re... | kbase/cdm-data-loaders | src/cdm_data_loaders/pipelines/all_the_bacteria.py | .py | 4df6bbb5e6f60bbf | 7.3 | 3 |
"""Common reusable pipeline elements."""
import os
from collections.abc import Callable
from logging import Logger, getLogger
from typing import Any, Final
import dlt
from dlt.common.runtime.slack import send_slack_message
from pydantic import ValidationError
from pydantic_settings import SettingsError
from cdm_data... | kbase/cdm-data-loaders | src/cdm_data_loaders/pipelines/core.py | .py | 173274e35b562ff8 | 7.3 | 3 |
"""NCBI FTP staged file promotion pipeline (Phase 3).
Promotes staged files from the containerized NCBI FTP download pipeline to their
final location in the Lakehouse.
"""
import logging
from pathlib import Path, PurePosixPath
from pydantic import AliasChoices, Field
from pydantic_settings import CliImplicitFlag
fr... | kbase/cdm-data-loaders | src/cdm_data_loaders/pipelines/ncbi_ftp_promote.py | .py | 5c85abb7f8f3cac5 | 7.3 | 3 |
"""Pipeline to import data from the NCBI API.
Like other importers in the cdm-data-loaders repo, the NCBI REST API pipeline
expects input files with the naming format `{text_string}_{digits}.{ext}`, e.g.
batch_001.txt, batch_002.txt, batch_003.txt.
"""
import os
import re
from collections.abc import Generator
from fu... | kbase/cdm-data-loaders | src/cdm_data_loaders/pipelines/ncbi_rest_api.py | .py | d560dcc76d113ed7 | 7.3 | 3 |
"""Generate a transfer manifest based on current PDB holdings files.
Project documentation: https://www.rcsb.org/
Batch downloading via rsync from: rsync-beta.rcsb.org:32382
Steps:
- Downloads the current PDB holdings files
- (Optional) Loads the set of holdings files from the last transfer OR bootstraps a set of ho... | kbase/cdm-data-loaders | src/cdm_data_loaders/pipelines/pdb_manifest.py | .py | e6e80bfff1ee19ae | 7.3 | 3 |
"""DLT pipeline to import UniProt data."""
from collections.abc import Generator
from datetime import UTC, datetime
from typing import Annotated, Any, Final
import dlt
from dlt.extract.items import DataItemWithMeta
from pydantic import Field, PositiveInt
from pydantic_settings import SettingsConfigDict
from cdm_data... | kbase/cdm-data-loaders | src/cdm_data_loaders/pipelines/uniprot_kb.py | .py | 58ae6f9936b69887 | 7.3 | 3 |
"""DLT pipeline to import UniRef data."""
from collections.abc import Generator
from datetime import UTC, datetime
from typing import Annotated, Any, Final
import dlt
from dlt.extract.items import DataItemWithMeta
from pydantic import Field, PositiveInt, field_validator
from pydantic_settings import SettingsConfigDic... | kbase/cdm-data-loaders | src/cdm_data_loaders/pipelines/uniref.py | .py | 6f6499c64293e1e5 | 7.3 | 3 |
#!/usr/bin/env python3
"""
This script configures a monitor for Sunshine streaming.
Usage:
sunshine-prep-plasma.py do --width WIDTH --height HEIGHT --fps FPS [--solo] [--inhibit]
sunshine-prep-plasma.py undo
Notes:
- Pass `--inhibit` to prevent idle using systemd-inhibit while active.
"""
import os
import sys
im... | ewgdg/dotfiles | packages/linux/sunshine/files/config/sunshine/sunshine-prep-plasma.py | .py | 24a50e342b2fc88a | 7 | 0 |
"""
Scrapes a headline from The Daily Pennsylvanian website and saves it to a
JSON file that tracks headlines over time.
"""
import os
import sys
import daily_event_monitor
import bs4
import requests
import loguru
def scrape_data_point():
"""
Scrapes the main headline from The Daily Pennsylvanian home pag... | viastopshate/daily-pennsylvanian-headline-scraper | script.py | .py | 142719fd7ba24d2d | 7 | 0 |
# main.py
import json
import asyncio
import logging
import random
from typing import Dict, List
from pathlib import Path
from datetime import datetime
from src.ip_tester import IPTester
from src.ip_validator import IPValidator
from src.core.evaluator import IPEvaluator
from src.core.recorder import IPRecorder
from src.... | FutureUnreal/Cloudflare-Preference-IP | main.py | .py | 21128e0b456d5050 | 7.24 | 2 |
import json
import logging
from pathlib import Path
from datetime import datetime
from typing import Dict, Optional
from huaweicloudsdkcore.auth.credentials import BasicCredentials
from huaweicloudsdkdns.v2 import *
from huaweicloudsdkdns.v2.region.dns_region import DnsRegion
class HuaweiDNS:
def __init__(self, ak... | FutureUnreal/Cloudflare-Preference-IP | src/dns/huawei.py | .py | 59ec3bcb24c037e1 | 7.24 | 2 |
"""
Cleanup module for handling workflow failures in exit handlers.
This module provides functionality to update the database when a workflow fails,
ensuring that external users see appropriate error messages without exposing
internal infrastructure details.
"""
import json
import os
import sys
from typing import Dic... | waterinstitute/metget-server | src/executables/build/src/metget_build/cleanup.py | .py | 62c9a0922fc60488 | 7.3 | 3 |
"""
Test script for FastTri triangulation library.
Generates points, triangulates with a boundary constraint, and visualizes the result.
"""
import time
from typing import Tuple
import matplotlib.pyplot as plt
import matplotlib.tri as mtri
import numpy as np
from fasttri import InterpolationWeights, Triangulation
d... | waterinstitute/metget-server | src/libraries/fasttri/tests/test_triangulation.py | .py | f740647f6b780c03 | 7.8 | 3 |
import asyncio
import copy
from collections import defaultdict
from logging import INFO
from typing import Any, Dict, Optional, Set, Tuple, Callable, cast
import utils.constants as constants
from utils.channel import sort_channel_result, generate_channel_statistic, write_channel_to_file, retain_origin
from utils.confi... | gclgg/iptv-api | utils/aggregator.py | .py | f9d75915be079ccb | 7.15 | 1 |
import re
import requests
from bs4 import BeautifulSoup
from utils.config import config
headers = {
"Accept": "*/*",
"Connection": "keep-alive",
"Accept-Language": "zh-CN,zh;q=0.8",
"User-Agent": "Mozilla/5.0 (Windows NT 10.0; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/126.0.0.0 Safari... | gclgg/iptv-api | utils/requests/tools.py | .py | 42c25b61cbcf7e4d | 7.15 | 1 |
from typing import TypedDict, Literal, Union, NotRequired
OriginType = Literal["hls", "local", "whitelist", "subscribe"]
IPvType = Literal["ipv4", "ipv6", None]
class ChannelData(TypedDict):
"""
Channel data types, including url, date, resolution, origin and ipv_type
"""
id: int
url: str
host... | gclgg/iptv-api | utils/types.py | .py | 237628355f6ae73d | 7.15 | 1 |
"""Scripts for releasing a new version of the package.
Usage:
python scripts/release.py <version>
"""
import re
import subprocess
import sys
from datetime import datetime
from pathlib import Path
import toml
def get_repo_url():
"""Get the repository URL from pyproject.toml or ask the user for it."""
tr... | atomsforhumanity/qcdata | scripts/release.py | .py | 6d74d668a5ea637f | 7.39 | 5 |
"""The base model from which all QCData model objects inherit."""
import json
from abc import ABC
from base64 import b64decode, b64encode
from enum import Enum
from pathlib import Path
from typing import TYPE_CHECKING, Any
import numpy as np
import toml
import yaml
from pydantic import BaseModel, field_serializer, fi... | atomsforhumanity/qcdata | src/qcdata/models/base_models.py | .py | d6dd62777dc6e477 | 7.39 | 5 |
"""Structured output data objects."""
from __future__ import annotations
import warnings
from pathlib import Path
from typing import TYPE_CHECKING, Any, TypeVar, Union
import numpy as np
from pydantic import BaseModel, ValidationInfo, field_validator, model_validator
from typing_extensions import Self
from qcdata.h... | atomsforhumanity/qcdata | src/qcdata/models/data.py | .py | be9bf244d70c7b36 | 7.39 | 5 |
"""Input models for quantum chemistry calculations."""
import warnings
from pathlib import Path
from typing import Any, TypeVar, Union
from pydantic import BaseModel, field_serializer, model_validator
from typing_extensions import Self
from .base_models import CalcType, Files, Model
from .structure import Structure
... | atomsforhumanity/qcdata | src/qcdata/models/inputs.py | .py | 7d0c4f02bca95f70 | 7.39 | 5 |
"""Program output container objects."""
from __future__ import annotations
import sys
import warnings
from itertools import product
from typing import Any, Generic, Literal, get_args
from pydantic import model_validator
from typing_extensions import Self
from qcdata.helper_types import SerializableNDArray
from .ba... | atomsforhumanity/qcdata | src/qcdata/models/outputs.py | .py | c86346c3bb9c3a20 | 7.39 | 5 |
from qcdata import ScanData
def test_scan_data_properties(opt_output):
"""Test that the number of energies matches the number of conformers"""
# No energies is fine
scan_res = ScanData(
trajectory=[opt_output],
)
# Test properties
assert scan_res.energies == [opt_output.data.final_ene... | atomsforhumanity/qcdata | tests/test_scan_data.py | .py | 89ceeb8ad56a81a7 | 7.89 | 5 |
import numpy as np
from qcdata import SinglePointData, Wavefunction
def test_gradient_converted_np_array():
"""Test that SinglePointData converts gradient to np array"""
gradient = [1.0, 2.0, 3.0, 4.0, 5.0, 6.0]
data = SinglePointData(gradient=gradient)
assert isinstance(data.gradient, np.ndarray)
... | atomsforhumanity/qcdata | tests/test_single_point_data.py | .py | d8eca0610c9fb5a3 | 7.89 | 5 |
from pydantic import BaseModel
from database import DataBaseConnector
from sqlalchemy import Column, String, TIMESTAMP, ForeignKey, Integer, Boolean, JSON
class SourceDoc(BaseModel):
source_table: str
source_id: str
similarity: float
class ChatResponse(BaseModel):
answer: str
docs: list[SourceDo... | eft-library/eft-library-back | api/chat/chat_res_models.py | .py | f59300429a8c043f | 7.15 | 1 |
from __future__ import annotations
import sys
import os
import re
import html
import random
import time
import calendar
import logging
import sqlite3
from datetime import datetime, timezone
from enum import Enum
from dataclasses import dataclass, field
from typing import Any
import requests
import feedparser
loggin... | KS1019/my-discord-bot | src/my_discord_bot/__init__.py | .py | 720a8d0bad070444 | 7 | 0 |
"""
Scrapes a headline from The Daily Pennsylvanian website and saves it to a
JSON file that tracks headlines over time.
"""
import os
import sys
import daily_event_monitor
import bs4
import requests
import loguru
import re
def scrape_data_point():
"""
Scrapes the #1 most read article title from The Daily... | chenxilll/daily-pennsylvanian-headline-scraper | script.py | .py | f529894693b97271 | 7 | 0 |
import gzip
import time
from collections import defaultdict
from datetime import date, timedelta
import requests
from statswiki.config import DELAY, FETCH_RETRIES, FETCH_RETRY_WAIT, LANG, START, USER_AGENT
from statswiki.store import has_day, write_day
# en + en.m ≈ en.wikipedia/all-access (desktop + mobile web)
_DU... | thepriben/StatsWiki | pipeline/src/statswiki/fetch.py | .py | 26c208b5db7aff6e | 7.24 | 2 |
"""Core functional facade for reading and manipulating audio metadata and covers."""
from __future__ import annotations
from collections.abc import Mapping
from pathlib import Path
from typing import Any
from mutagen import File
from .base import AudioFormatHandler
from .formats.id3 import ID3Handler
from .formats.... | L4zzur/chemz | src/chemz/core.py | .py | 31c8e71c20cbfbb4 | 7 | 0 |
"""Vorbis comments and FLAC picture block metadata handler."""
from __future__ import annotations
from pathlib import Path
from typing import Any
from mutagen.flac import FLAC, Picture as FlacPicture
from ..base import AudioFormatHandler
class VorbisHandler(AudioFormatHandler):
"""Audio format handler for Vor... | L4zzur/chemz | src/chemz/formats/vorbis.py | .py | 08899f4c140b2cb2 | 7 | 0 |
"""High-level object-oriented interface for audio metadata and cover art management."""
from __future__ import annotations
from pathlib import Path
from typing import Any, Literal
from .core import (
delete_cover,
read_cover_bytes,
read_track,
write_cover_bytes,
write_track_tags,
)
from .models i... | L4zzur/chemz | src/chemz/track.py | .py | c493599ec35fd8fe | 7 | 0 |
"""End-to-end integration lifecycle tests on real MP3 and FLAC audio files."""
from __future__ import annotations
from pathlib import Path
from chemz import (
AudioFile,
delete_cover,
read_cover_bytes,
read_track,
write_cover_bytes,
)
def test_real_mp3_full_lifecycle(
sample_mp3: Path,
... | L4zzur/chemz | tests/test_integration.py | .py | 3ced8fda25f7ad9d | 7.5 | 0 |
"""Unit tests for chemz core, models, base helpers, and format handlers."""
from __future__ import annotations
from pathlib import Path
import pytest
from chemz.base import AudioFormatHandler
from chemz.core import (
delete_cover,
get_handler,
read_cover_bytes,
read_track,
write_cover_bytes,
... | L4zzur/chemz | tests/test_metadata.py | .py | 8c9a7508823ae2af | 7.5 | 0 |
"""Comprehensive unit and functional tests for AudioFile high-level interface."""
from __future__ import annotations
from pathlib import Path
from typing import Any, cast
import pytest
from chemz.track import AudioFile
def test_audiofile_initialization_and_stream_props(sample_mp3: Path) -> None:
"""Test Audio... | L4zzur/chemz | tests/test_track.py | .py | aae70b95c6bf7295 | 7.5 | 0 |
"""
Scrapes a headline from The Daily Pennsylvanian website and saves it to a
JSON file that tracks headlines over time.
"""
import os
import sys
import daily_event_monitor
import bs4
import requests
import loguru
def scrape_data_point():
"""
Scrapes the main headline from The Daily Pennsylvanian home page... | noah-erdogan/daily-pennsylvanian-headline-scraper | script.py | .py | 5f0e16e6ba61927a | 7 | 0 |
import pytest
import json
import pathlib
from pydantic_spaceapi.v13 import SpaceAPIv13Model
@pytest.fixture
def valid_v13():
file = pathlib.Path("tests/examples/valid_v13.json")
with open(file) as f:
return json.loads(f.read())
def test_working(valid_v13):
"""
Check that we can parse a val... | nikdoof/pydantic_spaceapi | tests/test_v13.py | .py | cca3872d9fbcf5a5 | 7 | 0 |
from xinject import XContext, Dependency
import dataclasses
import pytest
from copy import deepcopy, copy
from xinject.errors import XInjectError
@XContext
def test_decorator_on_direct_context_class(xinject_test_context):
""" Test using XContext class directly as a decorator (not a XContext instance). """
# T... | joshorr/xinject | tests/test_context.py | .py | 9ebfc281a632c8e6 | 7.65 | 1 |
"""
Used to have a normal looking object that can be imported directly into other modules and used.
It will in reality, always lookup currently active version of a Dependency and use that each
time it's asked anything.
This makes it 'act' like the current version of some dependency,
code and just use it like a normal... | joshorr/xinject | xinject/proxy.py | .py | 2577e498f3fee50b | 7.15 | 1 |
"""
Scrapes a headline from The Daily Pennsylvanian website and saves it to a
JSON file that tracks headlines over time.
"""
import os
import sys
import daily_event_monitor
import bs4
import requests
import loguru
import re
def scrape_data_point():
"""
Scrapes the most read article from DP home page
... | samrmay/daily-pennsylvanian-headline-scraper | script.py | .py | 04af3d9ff814b34e | 7 | 0 |
"""
This module provides flexible classifier models with optional CRF functionality
for brain structure localisation tasks.
"""
import torch
from torch.nn import Module, Parameter, Linear, ReLU
from torch.nn.functional import relu, softmax
class FlexibleClassifier(Module):
"""
A flexible classifier with opti... | yingqiuz/localise | localise/forward.py | .py | 4d4e266374e9a75a | 7.15 | 1 |
import torch
from torch.nn import Linear
from localise.forward import FlexibleClassifier, MLP
import logging
from typing import Iterable, Tuple, Union
def apply_pretrained_model(
data: Iterable,
model_save_path: str,
model: Union[str, torch.nn.Module] = "Linear",
spatial: bool = True
) -> list:
... | yingqiuz/localise | localise/predict.py | .py | 22f753110648aea6 | 7.15 | 1 |
#!/usr/bin/env python3
"""
Create anatomical masks for tractography analysis.
This module creates anatomical masks in reference space for tractography
and stores them under the output folder.
Copyright (C) 2019 University of Oxford
Written by Ying-Qiu Zheng (Python rewrite)
"""
import argparse
import os
import subpr... | yingqiuz/localise | localise/prepare_masks.py | .py | 9b922c019ba5f4e0 | 7.15 | 1 |
#!/usr/bin/env python3
"""
Create tracts using probabilistic tractography.
This module runs FSL's probtrackx2 to generate tract density maps
for brain structure localization.
Copyright (C) 2025 University of Oxford
Written by Ying-Qiu Zheng (Python rewrite)
"""
import argparse
import sys
import textwrap
import shlex... | yingqiuz/localise | localise/prepare_tracts.py | .py | 2596a1056f98a806 | 7.15 | 1 |
import os, sys
import subprocess
import numpy as np
import nibabel as nib
from pathlib import Path
PKG_PATH = Path(__file__).parent.parent
def get_resources_path():
"""
Get the absolute path to the resources directory.
This function works whether the package is installed or in development mode.
"""
... | yingqiuz/localise | localise/utils.py | .py | 37a75b2f83a9a7be | 7.15 | 1 |
"""
Test suite for batch.py - spatial adjacency and CRF batch construction.
"""
import pytest
import numpy as np
import torch
from scipy.sparse import csr_matrix
from localise.batch import (
Adjacency,
get_adj_sparse,
get_adj_sparse_kdt,
FlattenedCRFBatch,
FlattenedCRFBatchTensor
)
class TestA... | yingqiuz/localise | tests/test_batch.py | .py | 0da01c445b30e21c | 7.65 | 1 |
import pytest
import torch
from torch.nn import Linear, Tanh
from unittest.mock import Mock
from localise.forward import FlexibleClassifier, MLP, Affine, Perceptron
class MockData:
"""Mock data class for testing."""
def __init__(self, X, f=None):
self.X = X
self.f = f
class TestFlexibleClas... | yingqiuz/localise | tests/test_forward.py | .py | 895b5d4ff27a834a | 7.65 | 1 |
import pytest
import tempfile
from pathlib import Path
from unittest.mock import patch, Mock
from localise.prepare_tracts import (
create_target_lists,
resolve_seed_path,
parse_arguments,
build_probtrackx_command,
create_tracts,
main
)
class TestBasicFunctions:
"""Test core functions."""
... | yingqiuz/localise | tests/test_prepare_tracts.py | .py | 5d6238b48c54804f | 7.65 | 1 |
import os, sys, pytest
import numpy as np
import subprocess
import tempfile
from unittest.mock import patch, Mock, MagicMock, call
from localise.utils import (
get_resources_path,
get_absolute_path,
check_fsl_environment,
run_fsl_command,
check_fsl_sub_queues,
save_nifti,
save_nifti_4D,
... | yingqiuz/localise | tests/test_utils.py | .py | 8d2cfd5c0f857c7b | 7.65 | 1 |
"""
Scrapes a headline from The Daily Pennsylvanian website and saves it to a
JSON file that tracks headlines over time.
"""
import os
import sys
import daily_event_monitor
import bs4
import requests
import loguru
def scrape_data_point():
"""
Scrapes the main headline from each sport on The Daily Pennsylv... | amadd123/daily-pennsylvanian-headline-scraper | script.py | .py | 6e448f3ea5a9df38 | 7 | 0 |
"""Small, typed runtime for composing GCP-focused agents and plugins."""
from abc import ABC, abstractmethod
from dataclasses import dataclass, field
from typing import Any, Dict, Iterable, List, Mapping, MutableMapping, Optional
@dataclass
class AgentContext:
"""Mutable state shared across plugins during one ag... | fatmambot33/GoogleCloudPlatformAPI | GoogleCloudPlatformAPI/agents/core.py | .py | abfc3c04fcd22e9a | 7.15 | 1 |
"""Utilities for loading agent plugins from explicit Python references."""
import importlib
import os
from typing import Iterable, List, Optional
from .core import AgentPlugin
PLUGIN_ENV_VAR = "GCP_API_PLUGINS"
def load_plugin(reference: str) -> AgentPlugin:
"""Load a plugin from ``package.module:attribute``.
... | fatmambot33/GoogleCloudPlatformAPI | GoogleCloudPlatformAPI/agents/loading.py | .py | 9ee3d9f487d9747a | 7.15 | 1 |
"""Optional OpenAI Agents SDK adapters generated from shared contracts."""
import importlib
import inspect
import json
from typing import Any, Callable, Dict, List, Optional
from GoogleCloudPlatformAPI.ai_native.registry import (
CapabilityRegistry,
capability_registry,
)
CapabilityInvoker = Callable[[str, D... | fatmambot33/GoogleCloudPlatformAPI | GoogleCloudPlatformAPI/agents/openai.py | .py | 8eb9ff3f31ff514e | 7.15 | 1 |
"""Typed contracts for AI-native capability execution."""
from dataclasses import asdict, dataclass, field
from enum import Enum
from typing import Any, Dict, List, Optional
class SafetyLevel(str, Enum):
"""Safety and cost classification for a capability."""
INSPECTION = "inspection"
BILLABLE_READ = "bi... | fatmambot33/GoogleCloudPlatformAPI | GoogleCloudPlatformAPI/ai_native/contracts.py | .py | c4db6f8ad7231ad1 | 7.15 | 1 |
"""Deterministic evaluations for the AI-facing capability surface."""
from dataclasses import dataclass
from typing import Dict, List, Optional
from GoogleCloudPlatformAPI.ai_native.registry import CapabilityRegistry
@dataclass(frozen=True)
class EvaluationResult:
"""Represent one deterministic capability evalu... | fatmambot33/GoogleCloudPlatformAPI | GoogleCloudPlatformAPI/ai_native/evaluation.py | .py | 431f172881f54007 | 7.15 | 1 |
"""Stable opaque cursors for bounded discovery operations."""
import base64
import json
from typing import Dict, Optional
_CURSOR_VERSION = 1
class CursorError(ValueError):
"""Report an invalid or context-mismatched pagination cursor."""
def encode_cursor(
service: str,
operation: str,
page_token:... | fatmambot33/GoogleCloudPlatformAPI | GoogleCloudPlatformAPI/ai_native/pagination.py | .py | d49ebf86c4bf7889 | 7.15 | 1 |
"""Canonical registry for AI-facing capabilities."""
import re
from dataclasses import asdict, dataclass, field, replace
from typing import Any, Callable, Dict, Iterable, List, Optional
from GoogleCloudPlatformAPI.ai_native.contracts import SafetyLevel
from GoogleCloudPlatformAPI.ai_native.schema import validate_json... | fatmambot33/GoogleCloudPlatformAPI | GoogleCloudPlatformAPI/ai_native/registry.py | .py | 4897e745c1f69b26 | 7.15 | 1 |
"""Optional OpenTelemetry hooks with a dependency-free fallback."""
import importlib
from contextlib import contextmanager
from typing import Any, Dict, Iterator, Optional, Tuple
def _otel() -> Optional[Tuple[Any, Any]]:
"""Return the OpenTelemetry API when its optional extra is installed."""
try:
tr... | fatmambot33/GoogleCloudPlatformAPI | GoogleCloudPlatformAPI/ai_native/telemetry.py | .py | a33584812115f71f | 7.15 | 1 |
"""Access documentation assets packaged with the distribution."""
from importlib.resources import files
from pathlib import PurePosixPath
from typing import Any
def resource_path(relative_path: str) -> Any:
"""Return a validated path to one packaged documentation asset."""
path = PurePosixPath(relative_path)... | fatmambot33/GoogleCloudPlatformAPI | GoogleCloudPlatformAPI/assets/__init__.py | .py | 0cd2b40a8b0aa7c0 | 7.15 | 1 |
"""Safe, bounded tool adapters for the local Codex MCP server."""
import json
import os
from concurrent.futures import TimeoutError as FutureTimeoutError
from typing import Any, Callable, Dict, List, Optional, cast
from GoogleCloudPlatformAPI.ai_native import (
CapabilityError,
CapabilityExecutionError,
C... | fatmambot33/GoogleCloudPlatformAPI | GoogleCloudPlatformAPI/codex/tools.py | .py | e336c76f8685a022 | 7.15 | 1 |
"""Stable public exception hierarchy for GoogleCloudPlatformAPI."""
from typing import Any, Dict, Optional
class GoogleCloudPlatformAPIError(Exception):
"""Base class for package-level operational failures.
Parameters
----------
message : str
Human-readable failure description.
operation... | fatmambot33/GoogleCloudPlatformAPI | GoogleCloudPlatformAPI/exceptions.py | .py | d285324228679fc8 | 7.15 | 1 |
"""Tests for the canonical AI-native capability contracts."""
import json
from dataclasses import replace
import pytest
from GoogleCloudPlatformAPI.ai_native import (
Capability,
CapabilityError,
CapabilityRegistry,
CapabilityResult,
ResultMetadata,
SafetyLevel,
capability_reference_markd... | fatmambot33/GoogleCloudPlatformAPI | tests/test_ai_native.py | .py | b2de5a32a71f95b3 | 7.65 | 1 |
"""Regression tests for the repository AI-native platform validator."""
from __future__ import annotations
from pathlib import Path
from typing import Any
import pytest
import yaml
from scripts import validate_ai_native_platform as validator
def load_manifest() -> dict[str, Any]:
"""Load a fresh copy of the r... | fatmambot33/GoogleCloudPlatformAPI | tests/test_ai_native_platform_validator.py | .py | 63e660e78ea07c97 | 7.65 | 1 |
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