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 |
|---|---|---|---|---|---|---|
#!/usr/bin/env python3
"""
run_STAR.py
This script processes short-read RNA-seq data by mapping them to a reference genome using STAR.
Features:
- Handles both Single-End (SE) and Paired-End (PE) data
- Supports multiple samples/replicates via a sample sheet
- Auto-detects and building of STAR genome index i... | ConesaLab/SQANTI-single-cell | scripts/run_STAR.py | .py | 881e07ad5ef81ad7 | 7.48 | 8 |
import os
import sys
import pandas as pd
import numpy as np
import scanpy as sc
def prepare_anndata(args, row):
"""
Load classification file and create an AnnData object.
Aggregates counts by cell barcode (CB) and associated_gene.
"""
file_acc = row['file_acc']
sampleID = row['sampl... | ConesaLab/SQANTI-single-cell | src/sc_clustering.py | .py | 9d270f133faf2476 | 7.48 | 8 |
#!/usr/bin/env python3
"""Normalize weekly Markdown files and sync the latest report into README.md."""
from __future__ import annotations
import json
import re
from pathlib import Path
README = Path("README.md")
WEEKLY_DIR = Path("weekly")
START = "<!-- WEEKLY_CHINESE_LLM_UPDATE:START -->"
END = "<!-- WEEKLY_CHINESE... | PristineStream/ChatGPT-Chinese-Tutorial | scripts/sync_latest_weekly_to_readme.py | .py | f3d0fa163e6b2e28 | 8.1 | 15 |
import ast
import pathlib
import re
import sys
CODE_ROOT = pathlib.Path(__file__).resolve().parent.parent
EXECUTION_MODULES_PATH = CODE_ROOT / "src" / "saltext" / "kubernetes" / "modules"
def check_cli_examples(files):
"""
Check that every function on every execution module provides a CLI example
"""
... | salt-extensions/saltext-kubernetes | .pre-commit-hooks/check-cli-examples.py | .py | 10b64b5e87f52d65 | 7.5 | 9 |
import datetime
import json
import os
import platform
import shutil
import sys
import tempfile
from importlib import metadata
from pathlib import Path
import nox
from nox.command import CommandFailed
from nox.virtualenv import VirtualEnv
# Nox options
# Reuse existing virtualenvs
nox.options.reuse_existing_virtualen... | salt-extensions/saltext-kubernetes | noxfile.py | .py | 306a4cc712a2f03b | 7.5 | 9 |
"""
Per-resource log fetch for Kubernetes pods.
.. versionadded:: 2.1.0
Dormant on stock Salt — see ``saltext.kubernetes.resources.kubernetes``.
"""
# pylint: disable=undefined-variable
from saltext.kubernetes.utils._kuberesource import require_kind
from saltext.kubernetes.utils._kuberesource import resource_identi... | salt-extensions/saltext-kubernetes | src/saltext/kubernetes/modules/kuberesource_logs.py | .py | 043fcd7955924645 | 7.5 | 9 |
"""
Per-resource state apply.
.. versionadded:: 2.1.0
Forwards a manifest through ``kubernetes.apply`` while leaving the
resource identity available to the manifest's Jinja templates via
``template_context`` (so a single manifest can be customised per
resource at dispatch time).
Dormant on stock Salt — see ``saltext... | salt-extensions/saltext-kubernetes | src/saltext/kubernetes/modules/kuberesource_state.py | .py | 4d74d9ff0162ff09 | 7.5 | 9 |
"""
Internal connection helpers for the saltext-kubernetes extension.
This module owns the auth-resolution logic for the extension. The
publicly-exposed seam is :py:func:`_setup_conn`, which is re-exported
through :py:mod:`saltext.kubernetes.modules.kubernetesmod` for
backwards compatibility — its signature, kwargs ha... | salt-extensions/saltext-kubernetes | src/saltext/kubernetes/utils/_connection.py | .py | d9300cf05851d695 | 7.5 | 9 |
"""
Shared helpers for the ``kuberesource_*`` companion execution modules.
Each ``kuberesource_*`` module is a thin wrapper that pulls resource
identity from ``__resource__["id"]`` (set by Salt's resources-layer
dispatcher) and forwards to the existing ``kubernetes.*`` execution
module functions. The shared logic live... | salt-extensions/saltext-kubernetes | src/saltext/kubernetes/utils/_kuberesource.py | .py | 6a24408930f21013 | 7.5 | 9 |
import logging
import os
import subprocess
import pytest
from pytest_kind import KindCluster
from saltfactories.utils import random_string
from saltext.kubernetes import PACKAGE_ROOT
# Reset the root logger to its default level(because salt changed it)
logging.root.setLevel(logging.WARNING)
log = logging.getLogger(... | salt-extensions/saltext-kubernetes | tests/conftest.py | .py | 50fedaf309505ebb | 8 | 9 |
"""
Deep coverage for the drift-suppression kwargs on ``kubernetes.apply``.
The shallow file (``test_kubernetesmod_drift_suppression.py``) covers one
test per ignore_* kwarg; this file exercises:
* Multiple ignore_* kwargs combined in a single apply
* Nested ignore_fields paths (image, env)
* Re-apply after kub... | salt-extensions/saltext-kubernetes | tests/functional/modules/test_kubernetesmod_drift_deep.py | .py | de5428a9a45dcc7b | 8 | 9 |
"""
Functional tests for the drift-suppression kwargs on ``kubernetes.apply``.
Each test:
1. Applies a manifest.
2. Mutates the live object out-of-band (simulating a foreign controller
or operator).
3. Re-applies the original manifest with a matching ``ignore_*``.
4. Asserts the foreign mutation is prese... | salt-extensions/saltext-kubernetes | tests/functional/modules/test_kubernetesmod_drift_suppression.py | .py | 2022deab1acc8747 | 8 | 9 |
"""
Functional tests for exec-plugin auth against a real kind cluster.
Uses a hermetic mock exec plugin (a shell script that prints a valid
``ExecCredential`` JSON with the kind cluster's service-account token).
This proves the exec-auth wiring works end-to-end without depending on
external auth tools like aws-iam-aut... | salt-extensions/saltext-kubernetes | tests/functional/modules/test_kubernetesmod_exec_auth.py | .py | cb996ca755c1c28a | 8 | 9 |
"""
Deep coverage for exec-plugin auth against a real kind cluster.
The shallow file (``test_kubernetesmod_exec_auth.py``) demonstrates the
happy path. This file targets:
* Malformed plugin output → meaningful error
* Plugin non-zero exit → install_hint surfaced
* Plugin with multi-arg ``args:`` actually receiv... | salt-extensions/saltext-kubernetes | tests/functional/modules/test_kubernetesmod_exec_auth_deep.py | .py | 14aac2e41081893c | 8 | 9 |
"""
Functional tests for the multi-cluster routing layer.
The existing functional suite spins up a single kind cluster via the
``kind_cluster`` fixture. To test multi-cluster routing without doubling
the runtime cost of every CI run, we exercise the alias plumbing against
the same physical cluster reached through two ... | salt-extensions/saltext-kubernetes | tests/functional/modules/test_kubernetesmod_multi_cluster.py | .py | df051c032c490efa | 8 | 9 |
"""
Real-isolation multi-cluster tests using two distinct kind clusters.
Gated by ``RUN_MULTI_CLUSTER_TESTS=1`` because materialising a second kind
cluster on every CI run is wasteful. When enabled, these tests verify
that the alias-routing code truly targets independent clusters — an
object on cluster A is not visibl... | salt-extensions/saltext-kubernetes | tests/functional/modules/test_kubernetesmod_multi_cluster_real.py | .py | 0ded6bf4733f794c | 8 | 9 |
"""
Functional tests for ``kubernetes.wait_for`` against a real kind cluster.
Covers the user-driven wait surface added in 2.1.0:
* ``condition=`` waits on ``status.conditions[*].type``
* ``jsonpath=`` waits on an arbitrary kubectl-style path
* Timeout error path is exercised against a never-satisfied predicate... | salt-extensions/saltext-kubernetes | tests/functional/modules/test_kubernetesmod_wait_conditions.py | .py | bdb47a2a6b75fd88 | 8 | 9 |
"""
Deep coverage for ``kubernetes.wait_for`` against a real kind cluster.
The shallow test file (``test_kubernetesmod_wait_conditions.py``) covers
the happy paths; this file targets edge cases:
* ``status=False`` matching against a deliberately-failing pod
* Nested jsonpath resolution
* Cluster-scoped kinds (n... | salt-extensions/saltext-kubernetes | tests/functional/modules/test_kubernetesmod_wait_conditions_deep.py | .py | fc4ac58a69333a1d | 8 | 9 |
import pytest
from aws_cdk import App
from infrastructure.build import build
def test_cdk_app_can_synth():
"""Test that the CDK app can be synthesized without errors."""
app = App()
app.node.set_context('branch', 'test-branch')
app.node.set_context('config-name', 'demo')
build(app)
# If we ge... | IGVF-DACC/igvf-catalog | cdk_swagger/tests/unit/test_basic.py | .py | 9567a7bbf8fd2c82 | 7.92 | 6 |
import csv
import gzip
import json
from math import log10
from typing import Optional
import os
from adapters.base import BaseAdapter
from adapters.helpers import build_variant_id, build_regulatory_region_id, get_file_fileset_by_accession_in_arangodb
from adapters.writer import Writer
# Example row from sorted.dist.h... | IGVF-DACC/igvf-catalog | data/adapters/AFGR_caqtl_adapter.py | .py | 5841fbe013c285aa | 7.42 | 6 |
import csv
import gzip
import hashlib
import json
from typing import Optional
import os
from adapters.base import BaseAdapter
from adapters.helpers import build_variant_id, get_file_fileset_by_accession_in_arangodb
from adapters.writer import Writer
from adapters.gene_validator import GeneValidator
# Example row from ... | IGVF-DACC/igvf-catalog | data/adapters/AFGR_eqtl_adapter.py | .py | f203a5561567565f | 7.42 | 6 |
import csv
import gzip
import hashlib
import json
import pickle
from math import log10
from typing import Optional
import os
from adapters.base import BaseAdapter
from adapters.helpers import build_variant_id, get_file_fileset_by_accession_in_arangodb
from adapters.writer import Writer
from adapters.gene_validator impo... | IGVF-DACC/igvf-catalog | data/adapters/AFGR_sqtl_adapter.py | .py | fa77dd896c7d9266 | 7.42 | 6 |
import csv
import gzip
import json
from math import log10
from typing import Optional
from adapters.base import BaseAdapter
from adapters.helpers import build_regulatory_region_id, get_file_fileset_by_accession_in_arangodb
from adapters.writer import Writer
# Element-level CRISPR element-to-phenotype screens (Gersbac... | IGVF-DACC/igvf-catalog | data/adapters/CRISPR_element_phenotype_adapter.py | .py | bc6a60c1733101d6 | 7.42 | 6 |
import gzip
import json
import csv
import os
import re
from typing import Optional
from adapters.base import BaseAdapter
from adapters.helpers import convert_aa_letter_code_and_Met1, convert_aa_to_three_letter, split_spdi, build_variant_coding_variant_key, get_file_fileset_by_accession_in_arangodb
from adapters.writer... | IGVF-DACC/igvf-catalog | data/adapters/Mutpred2_coding_variants_adapter.py | .py | fe21d7f1315b2ae4 | 7.42 | 6 |
import csv
import gzip
import hashlib
import json
from typing import Optional
from biocommons.seqrepo import SeqRepo
from ga4gh.vrs.dataproxy import SeqRepoDataProxy
from ga4gh.vrs.extras.translator import AlleleTranslator
from adapters.base import BaseAdapter
from adapters.helpers import bulk_check_variants_in_arang... | IGVF-DACC/igvf-catalog | data/adapters/STARR_seq_adapter.py | .py | 02e17396167f20c0 | 7.42 | 6 |
import csv
import json
import os
import gzip
import re
from typing import Optional
from adapters.base import BaseAdapter
from adapters.helpers import bulk_query_coding_variants_in_arangodb, bulk_query_coding_variants_from_hgvsc_in_arangodb, bulk_query_coding_variants_Met1_in_arangodb, get_file_fileset_by_accession_in_... | IGVF-DACC/igvf-catalog | data/adapters/VAMP_coding_variant_scores_adapter.py | .py | f3d06977bbb29331 | 7.42 | 6 |
import gzip
import os
import re
import shutil
import stat
import tarfile
import tempfile
import zipfile
from pathlib import Path
from typing import Iterator
FILE_ACCESSION_PATTERN = re.compile(r'(?:IGVFFI|ENCFF)[A-Z0-9]+')
def get_file_accession(filepath: str) -> str:
"""Derive the file accession from the input... | IGVF-DACC/igvf-catalog | data/adapters/archive_utils.py | .py | 14985847ef196740 | 7.42 | 6 |
"""
Base adapter class for all IGVF Catalog data adapters.
This module provides a base class that consolidates common functionality
across all data adapters, including:
- Schema loading and validation
- Writer management
- Common configuration
- Standard error handling
"""
from abc import ABC, abstractmethod
from typ... | IGVF-DACC/igvf-catalog | data/adapters/base/base_adapter.py | .py | 0c8932caac8ad5b7 | 7.42 | 6 |
import csv
import json
import hashlib
import obonet
import pickle
from typing import Optional
import os
from adapters.base import BaseAdapter
from adapters.writer import Writer
from adapters.helpers import get_file_fileset_by_accession_in_arangodb
# Example lines in merged_PPI.UniProt.csv (and merged_PPI_mouse.UniPro... | IGVF-DACC/igvf-catalog | data/adapters/biogrid_gene_gene_adapter.py | .py | 74e2b9139ca0dd1a | 7.42 | 6 |
"""Cisco CatalystCenter Authentication API wrapper.
Copyright (c) 2026 Cisco Systems.
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
... | cisco-en-programmability/catalystcentersdk | catalystcentersdk/api/authentication.py | .py | 70dce9a540767a58 | 7.56 | 12 |
"""Cisco CatalystCenter CustomCaller
Copyright (c) 2026 Cisco Systems.
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, m... | cisco-en-programmability/catalystcentersdk | catalystcentersdk/api/custom_caller.py | .py | c59f078f26d3e3d7 | 7.56 | 12 |
"""Cisco Catalyst Center Applications API wrapper.
Copyright (c) 2026 Cisco Systems.
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
t... | cisco-en-programmability/catalystcentersdk | catalystcentersdk/api/v2_3_7_6_1/applications.py | .py | 21589e4a9b78e452 | 7.56 | 12 |
"""Cisco Catalyst Center Cisco Trusted Certificates API wrapper.
Copyright (c) 2026 Cisco Systems.
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitatio... | cisco-en-programmability/catalystcentersdk | catalystcentersdk/api/v2_3_7_6_1/cisco_trusted_certificates.py | .py | b3d7adf846e4713b | 7.56 | 12 |
"""Cisco Catalyst Center Command Runner API wrapper.
Copyright (c) 2026 Cisco Systems.
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights... | cisco-en-programmability/catalystcentersdk | catalystcentersdk/api/v2_3_7_6_1/command_runner.py | .py | de7e0efd86e935d9 | 7.56 | 12 |
"""Cisco Catalyst Center Configuration Archive API wrapper.
Copyright (c) 2026 Cisco Systems.
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the... | cisco-en-programmability/catalystcentersdk | catalystcentersdk/api/v2_3_7_6_1/configuration_archive.py | .py | 9c2de8bbc5b96e8d | 7.56 | 12 |
"""Cisco Catalyst Center Users API wrapper.
Copyright (c) 2026 Cisco Systems.
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, ... | cisco-en-programmability/catalystcentersdk | catalystcentersdk/api/v2_3_7_6_1/users.py | .py | 079d6c1a3e928b05 | 7.56 | 12 |
# Copyright 2022-2025 Joe Block <jpb@unixorn.net>
# License: Apache 2.0
import json
import logging
from typing import Optional, TypedDict
from ha_mqtt_discoverable import Discoverable, __version__
from ha_mqtt_discoverable.utils import clean_string
from ha_mqtt_discoverable_cli.utils import valid_configuration_key
... | unixorn/ha-mqtt-discoverable-cli | ha_mqtt_discoverable_cli/device.py | .py | 8b46ab61dc2374e9 | 7.45 | 7 |
#
# device_driver.py
#
# Copyright 2022-2023, Joe Block <jpb@unixorn.net>
"""
Code to support the hmd-create-device script
"""
import json
import logging
import sys
from ha_mqtt_discoverable_cli.cli import create_base_parser
from ha_mqtt_discoverable_cli.device import Device
from ha_mqtt_discoverable_cli.settings i... | unixorn/ha-mqtt-discoverable-cli | ha_mqtt_discoverable_cli/device_driver.py | .py | 5ffd6cfcfe7f10fe | 7.45 | 7 |
#
# Gives us a git-style main command that calls subcommands.
#
# Copyright 2023-2024: Joe Block <jpb@unixorn.net>
# License: Apache 2.0
import os
import subprocess
import sys
from gitlike_commands import find_subcommand
def hmd_usage():
"""
They called hdm with no subcommands, or we couldn't find a subcom... | unixorn/ha-mqtt-discoverable-cli | ha_mqtt_discoverable_cli/hmd.py | .py | da98e3ec926095de | 7.45 | 7 |
#
# sensor_driver.py
#
# Copyright 2022-2023, Joe Block <jpb@unixorn.net>
"""
Code to support the hmd-create-binary-sensor script
"""
import logging
import sys
from ha_mqtt_discoverable import Settings
from ha_mqtt_discoverable_cli.cli import create_base_parser
from ha_mqtt_discoverable.sensors import BinarySensor,... | unixorn/ha-mqtt-discoverable-cli | ha_mqtt_discoverable_cli/sensor_driver.py | .py | d0f3ada270a32953 | 7.45 | 7 |
#
# Copyright 2022-2024 Joe Block <jpb@unixorn.net>
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by... | unixorn/ha-mqtt-discoverable-cli | ha_mqtt_discoverable_cli/settings.py | .py | 348c9b723fa00a06 | 7.45 | 7 |
'''
LEARNED:
- No key related eventFilter on the app(QApplication)
otherwise: keyRelease --> multiple trigger
- Not every event filter keys trigger action
with both: full / non full screen video
Below how the event filter was used in
an early stage of the project
This script is no... | K4KarolE/QTea_Media_Player | docs/learning/event_filter.py | .py | db714b5825e21f65 | 7.45 | 7 |
'''
The below is not used in this project - saving for later
Layout <- QGraphicsView <- QGraphicsScene <- QGraphicsVideoItem
'''
from PyQt6.QtMultimedia import QAudioOutput, QMediaPlayer
from PyQt6.QtMultimediaWidgets import QGraphicsVideoItem
from PyQt6.QtWidgets import QWidget, QGraphicsScene, QGraphicsView
class... | K4KarolE/QTea_Media_Player | docs/learning/graphics_scene_compiling.py | .py | 5310f70685950a6e | 7.45 | 7 |
"""
Switching there and back between the two media >> can increase the memory usage
It is the memory leak of the "QMediaPlayer().setSource()" function
Was trying to create a new AVPlayer class instance for every media play and remove the previous instance
>> The memory leak issue is still in place
For testing, do not... | K4KarolE/QTea_Media_Player | docs/learning/player_basic_memory_leak_fix_try.py | .py | 3e24a0e11e433227 | 7.45 | 7 |
'''
Slider jumps to the position of the mouse click
Cheers mate!
https://python-forum.io/thread-10564.html
'''
from PyQt6.QtWidgets import QSlider, QApplication, QMainWindow, QStyle
from PyQt6.QtCore import Qt
import sys
app = QApplication(sys.argv)
window = QMainWindow()
window.resize(400, 350)
window.setWindowTi... | K4KarolE/QTea_Media_Player | docs/learning/slider_jump_to_mouse_click.py | .py | 287335b5ba0cf390 | 7.45 | 7 |
""" Cheers all!
https://www.geeksforgeeks.org/python/pyqt5-qtablewidget/
https://www.qtcentre.org/threads/25952-Select-entire-row-in-QTableWidget-programmatically
Please note, the QTableWidget is not used in the app. If you want to
save some headache and workarounds, use the QTableWidget instead of
... | K4KarolE/QTea_Media_Player | docs/learning/table_widget.py | .py | 3fbec8b4ef015bf8 | 7.45 | 7 |
"""
Cheers!
https://www.geeksforgeeks.org/prevent-freezing-in-python-pyqt-guis-with-qthread/
"""
from PyQt6.QtWidgets import QApplication, QWidget, QPushButton, QVBoxLayout, QLabel
from PyQt6.QtCore import Qt, QThread, pyqtSignal
import sys
import time
QApplication.setDesktopSettingsAware(False) # avoid OS auto color... | K4KarolE/QTea_Media_Player | docs/learning/thumbnail_view/multithreading.py | .py | 2e68a9cd422aadf3 | 7.45 | 7 |
import sys
from PyQt6.QtCore import QEvent
from PyQt6.QtWidgets import QApplication
from .class_data import cv
from .class_bridge import br
from .logger import *
"""
To avoid system theme >> qt app theme
https://doc.qt.io/qt-6/qguiapplication.html#setDesktopSettingsAware
windll - myappid:
To get the packaged applic... | K4KarolE/QTea_Media_Player | src/application.py | .py | c0a725fbafe749e7 | 7.45 | 7 |
"""
Used to display the logo image
when the video area is not active:
- playing music
- player is in stopped state
"""
from pathlib import Path
from PyQt6.QtCore import Qt
from PyQt6.QtGui import QPixmap
from PyQt6.QtWidgets import QLabel
from .class_data import cv
from .logger import logger_runtime
@logger_runtime... | K4KarolE/QTea_Media_Player | src/images.py | .py | e1c4ab4ec820c46c | 7.45 | 7 |
'''
Used to measure the time of
- application launch: main.py
- add directory: src / buttons.py / button_add_dir_clicked()
LEARNED:
The function with the @logger_runtime decorator need to be called with lambda:
- button_add_dir.clicked.connect(lambda: button_add_dir.button_add_dir_clic... | K4KarolE/QTea_Media_Player | src/logger.py | .py | a928130427fe6a7f | 7.45 | 7 |
'''
THIS FILE CAN BE REACHED OUTSIDE THE APP ONLY
It contains supporting functions only,
which can be actioned in this file for:
- Verify the tables available in the DB
- Creating new DB
- Remove a table from the DB
'''
import sqlite3
from pathlib import Path
from json import load, dump
def open_json():
... | K4KarolE/QTea_Media_Player | src/tables_and_playlists_guide.py | .py | f8aa190bf331a067 | 7.45 | 7 |
from PyQt6.QtCore import QThread, pyqtSignal
from .class_data import cv, save_thumbnail_history_json
from .func_coll import set_thumbnail_generation_needed_to
from .func_thumbnail import create_thumbnails_and_update_widgets
class ThreadThumbnail(QThread):
result_ready = pyqtSignal(int, str)
def __init__(sel... | K4KarolE/QTea_Media_Player | src/thread_thumbnail.py | .py | f0ac0c61a2728d67 | 7.45 | 7 |
from PyQt6.QtCore import QEvent, Qt
from PyQt6.QtGui import QAction, QPixmap
from PyQt6.QtWidgets import (
QLabel,
QMenu,
QVBoxLayout,
QWidget
)
from .class_data import cv
from .class_bridge import br
from .class_skins import sk
from .func_coll import (
active_track_font_style,
clear_queue_... | K4KarolE/QTea_Media_Player | src/thumbnail_widget.py | .py | 4bd64c9f5ef8f06a | 7.45 | 7 |
"""
ThumbnailMainWindow(QScrollArea) << WidgetsWindow(QWidget) - Window holding the thumbnail widgets
Used in the src / playlists / playlists_creation()
"""
from PyQt6.QtCore import Qt, QTimer
from PyQt6.QtWidgets import (
QWidget,
QScrollArea,
QScrollBar
)
from .class_bridge import br
from ... | K4KarolE/QTea_Media_Player | src/thumbnail_window.py | .py | b4aaf423f4e40cd0 | 7.45 | 7 |
"""
Collect interpreter information, also run as the subprocess interrogation script (stdlib only).
Executed by the interpreter being probed. Collection supports Python 3.6+, but the file must parse on 2.7 so the
version gate below can report older interpreters instead of dying with a ``SyntaxError``: no f-strings, no... | tox-dev/python-discovery | src/python_discovery/_py_info_collect.py | .py | 62117953e90a7303 | 7.57 | 13 |
"""A Python specification is an abstract requirement definition of an interpreter."""
from __future__ import annotations
import contextlib
import pathlib
import re
from typing import Final
from ._py_info import normalize_isa
from ._specifier import SimpleSpecifier, SimpleSpecifierSet, SimpleVersion
PATTERN = re.com... | tox-dev/python-discovery | src/python_discovery/_py_spec.py | .py | 3b544c0bd250ee6e | 8.07 | 13 |
"""Version specifier support using only standard library (PEP 440 compatible)."""
from __future__ import annotations
import contextlib
import operator
import re
import sys
from dataclasses import dataclass
from typing import TYPE_CHECKING, Final
DC_KW: Final[dict[str, bool]] = (
{"frozen": True, "kw_only": True,... | tox-dev/python-discovery | src/python_discovery/_specifier.py | .py | a3b3076f4cff9854 | 8.07 | 13 |
"""odsbox - Toolbox for accessing ASAM ODS servers using the HTTP API
This package provides convenient access to ASAM ODS servers with lazy loading
for better performance.
Example::
from odsbox import ConI
with ConI(url="http://localhost:8087/api", auth=("sa", "sa")) as con_i:
units = con_i.query_da... | peak-solution/odsbox | src/odsbox/__init__.py | .py | d188a00b18854a69 | 7.57 | 13 |
"""datetime is represented as string in ASAM ODS formatted using YYYYMMDDHHMMSSFFF. Here you find some helpers."""
from __future__ import annotations
from typing import cast
import pandas as pd
def __normalize_datetime_string(asam_time: str) -> str:
asam_time_len = len(asam_time)
if asam_time_len < 8:
... | peak-solution/odsbox | src/odsbox/asam_time.py | .py | 9d1ace0196332910 | 7.57 | 13 |
"""JAQueL conversion result types."""
from __future__ import annotations
from dataclasses import dataclass
import odsbox.proto.ods_pb2 as ods
@dataclass(slots=True, frozen=True, unsafe_hash=False)
class JaquelConversionResult:
"""
Result of a JAQueL to ODS conversion.
Contains the target entity, the g... | peak-solution/odsbox | src/odsbox/jaquel_conversion_result.py | .py | 884b82a513c52c3a | 7.57 | 13 |
"""ASAM ODS Protocol Buffer interfaces
This module provides convenient access to ASAM ODS protobuf definitions
with lazy loading for better performance.
Example::
from odsbox.proto import ods, ods_security
# Create a model instance
model = ods.Model()
"""
from __future__ import annotations
from typin... | peak-solution/odsbox | src/odsbox/proto/__init__.py | .py | b04e211194489948 | 7.57 | 13 |
"""
Helper for handling transactions
Example::
from odsbox.con_i import ConI
with ConI(
url="http://localhost:8087/api",
auth=("sa", "sa")
) as con_i:
with con_i.transaction() as transaction:
# do some work
transaction.commit()
"""
from _... | peak-solution/odsbox | src/odsbox/transaction.py | .py | 1886745d473d3fe5 | 7.57 | 13 |
"""Helper class for Units in ASAM ODS"""
from __future__ import annotations
import logging
from typing import TYPE_CHECKING
if TYPE_CHECKING:
from .con_i import ConI
import odsbox.proto.ods_pb2 as ods
class UnitCatalog:
"""
This class caches the units stored in the ASAM ODS server.
... | peak-solution/odsbox | src/odsbox/unit_catalog.py | .py | 06c7b4c9d9d06f57 | 7.57 | 13 |
"""Utility functions for context handling."""
from typing import TYPE_CHECKING, Any
if TYPE_CHECKING:
from ..proto import ods
def from_context_variables(context_variables: "ods.ContextVariables") -> dict[str, Any]:
"""
Convert ContextVariables to a dictionary.
Args:
context_var... | peak-solution/odsbox | src/odsbox/utils/context.py | .py | 1c8f651b3602306d | 7.57 | 13 |
"""Tests for chunked download functionality in file_access_download"""
from __future__ import annotations
import os
import tempfile
from unittest import mock
import pytest
from odsbox.con_i import ConI
from odsbox.proto.ods_pb2 import FileIdentifier
@pytest.fixture
def con_i():
return ConI("https://docker.pea... | peak-solution/odsbox | tests/test_con_i_chunked_download.py | .py | f3a63ea3faeadd2d | 7.07 | 13 |
"""Mock tests for ConI with resource logout behavior"""
from __future__ import annotations
import logging
from unittest import mock
import pytest
import requests
import odsbox.proto.ods_pb2 as ods
from odsbox.con_i import ConI
class TestConIWithResourceLogout:
"""Test class for ConI with resource context mana... | peak-solution/odsbox | tests/test_con_i_with_resource_logout.py | .py | 0842e601e008d63f | 7.07 | 13 |
"""Tests for the is_null_to_nan parameter in datamatrices_to_pandas.py"""
from __future__ import annotations
import numpy as np
import pandas as pd
import odsbox.proto.ods_pb2 as ods
from odsbox.datamatrices_to_pandas import to_pandas
class TestIsNullToNan:
"""Test suite for is_null_to_nan functionality"""
... | peak-solution/odsbox | tests/test_is_null_to_nan.py | .py | c962812a35da2a78 | 8.07 | 13 |
"""Test ModelCache functionality."""
from __future__ import annotations
import os
from pathlib import Path
import pytest
from google.protobuf.json_format import Parse
from odsbox.model_cache import ModelCache
from odsbox.proto.ods_pb2 import Model
def __get_model(model_file_name):
model_file = os.path.join(os... | peak-solution/odsbox | tests/test_model_cache.py | .py | 7243897f95108f7c | 7.07 | 13 |
"""Test ModelSuggestions class functionality."""
from __future__ import annotations
import os
from pathlib import Path
from unittest.mock import Mock
from google.protobuf.json_format import Parse
from odsbox.model_suggestions import ModelSuggestions
from odsbox.proto.ods_pb2 import Model
def _get_model(model_file... | peak-solution/odsbox | tests/test_model_suggestions.py | .py | f8d534b634be17e7 | 7.07 | 13 |
"""Tests for odsbox.__init__ lazy loading functionality"""
from __future__ import annotations
import sys
import pytest
def test_odsbox_lazy_import_coni():
"""Test that ConI is lazily imported"""
from odsbox import ConI
# Should be the actual ConI class
assert ConI.__name__ == "ConI"
assert has... | peak-solution/odsbox | tests/test_odsbox_init.py | .py | 63bd50c7757754f1 | 8.07 | 13 |
"""Tests for odsbox.proto lazy loading functionality"""
from __future__ import annotations
import sys
import pytest
def test_proto_lazy_import_ods():
"""Test that ods module is lazily imported"""
# Remove from cache if already imported
if "odsbox.proto" in sys.modules:
del sys.modules["odsbox.p... | peak-solution/odsbox | tests/test_proto_init.py | .py | 6913b7331bc54474 | 7.07 | 13 |
"""Nox sessions."""
import os
import shlex
import shutil
import sys
from pathlib import Path
from textwrap import dedent
import nox
# Use standard nox session type
Session = nox.Session
session = nox.session
package = "py21cmemu"
python_versions = ["3.14", "3.13", "3.12", "3.11", "3.10"]
nox.needs_version = ">= 20... | 21cmfast/21cmEMU | noxfile.py | .py | c58cffccc7a90192 | 7.45 | 7 |
"""User-facing configuration for py21cmEMU."""
from __future__ import annotations
import logging
from collections.abc import Generator
from contextlib import contextmanager
from pathlib import Path
from typing import Any
import toml
from appdirs import AppDirs
log = logging.getLogger(__name__)
APPDIR = AppDirs("py... | 21cmfast/21cmEMU | src/py21cmemu/config.py | .py | 200897202507dd41 | 7.45 | 7 |
import torch
from torch.utils.data import Dataset
from . import sde as sde_lib
def get_model_fn(model, train=False):
"""Create a function to give the output of the score-based model.
Args:
model: The score model.
train: `True` for training and `False` for evaluation.
Returns:
A model ... | 21cmfast/21cmEMU | src/py21cmemu/model_utils.py | .py | 6d93ab55497daf12 | 7.45 | 7 |
"""PyTorch implementation of the v1 21cmEMU default emulator.
This module provides the PyTorch model class for the v1 emulator, originally
implemented in TensorFlow/Keras. The model was converted using the
convert_v1_to_pytorch.py script.
Usage
-----
from py21cmemu.models.ACG.v1_pytorch import load_converted_mode... | 21cmfast/21cmEMU | src/py21cmemu/models/acg/v1_pytorch.py | .py | a1095689726b3f12 | 7.45 | 7 |
"""
Neural-network modules for the 21cm MH emulator (v3).
This module defines the HybridEmulator architecture used for inference.
Architecture matches the production_ema training checkpoint.
"""
import torch
import torch.nn as nn
class _LSTMHead(nn.Module):
"""Single LSTM head producing a 1-D sequence.
Pro... | 21cmfast/21cmEMU | src/py21cmemu/models/mcg/lstm_model.py | .py | d56eec287b2a500f | 7.45 | 7 |
import logging
from pathlib import Path
import torch
device = torch.device("cuda") if torch.cuda.is_available() else torch.device("cpu")
def extract(a, t, x_shape):
batch_size = t.shape[0]
out = a.cpu().gather(-1, t.cpu())
return out.reshape(batch_size, *((1,) * (len(x_shape) - 1))).to(t.device)
def t... | 21cmfast/21cmEMU | src/py21cmemu/utils.py | .py | 37f2fe28eaf796c0 | 7.45 | 7 |
"""Tests for emulator download / data initialisation (get_emulator.py).
These tests require network access and modify the on-disk emulator cache.
They are excluded from the standard fast test run with:
-k "not test_config and not test_get_emulator"
"""
from __future__ import annotations
import shutil
from pathlib ... | 21cmfast/21cmEMU | tests/test_get_emulator.py | .py | 5eb5aa99b2fb1d14 | 7.95 | 7 |
"""Get current fuel prices and station detail for a specific GasBuddy station."""
import argparse
import asyncio
import logging
from py_gasbuddy import GasBuddy
from py_gasbuddy.exceptions import APIError, LibraryError
FUEL_LABELS = {
"regular_gas": "Regular",
"midgrade_gas": "Midgrade",
"premium_gas": "... | firstof9/py-gasbuddy | examples/price-lookup.py | .py | abb435e7b107fe14 | 7.63 | 17 |
"""Cache functions for py-gasbuddy."""
import asyncio
import json
import logging
import os
import uuid
from pathlib import Path
from typing import Any
import aiofiles
import aiofiles.os
_LOGGER = logging.getLogger(__name__)
class GasBuddyCache:
"""Class for GasBuddy file cache."""
def __init__(self, cache... | firstof9/py-gasbuddy | py_gasbuddy/cache.py | .py | e81151ca403886ba | 7.63 | 17 |
"""Exceptions for library."""
class MissingSearchData(Exception):
"""Exception for missing search data variable."""
class LibraryError(Exception):
"""Exception for a general library failure."""
class CloudflareBlocked(LibraryError):
"""Cloudflare blocked the CSRF/token-fetch round-trip.
Subclass ... | firstof9/py-gasbuddy | py_gasbuddy/exceptions.py | .py | 1ee71c22c61a0e3c | 7.63 | 17 |
"""Type definitions for py-gasbuddy."""
from typing import Any, Required, TypedDict
class Address(TypedDict, total=False):
"""Station address."""
line1: Required[str]
line2: str | None
locality: str
region: str
postalCode: str
country: str
class Brand(TypedDict):
"""Station brand i... | firstof9/py-gasbuddy | py_gasbuddy/models.py | .py | 966b3f9a3df99ba7 | 7.63 | 17 |
"""Provide common pytest fixtures."""
import json
import os
import shutil
import tempfile
from collections import defaultdict
from collections.abc import Callable, Generator
from pathlib import Path
from typing import Any
from unittest.mock import patch
import aiohttp
import pytest
from multidict import CIMultiDict, ... | firstof9/py-gasbuddy | tests/conftest.py | .py | 3f57665aec37bc05 | 8.13 | 17 |
#!/usr/bin/env python3
"""
Resource consumption test script for testing resource monitoring tools.
Consumes various amounts of VSS, RSS, and CPU over configurable time periods.
"""
import argparse
import json
import mmap
import multiprocessing
import os
import time
from typing import Any, Dict
class ResourceConsumer... | con/duct | demo/resource_consumer.py | .py | da4805aae513c8fd | 7.56 | 12 |
"""Summary formatter with custom conversions for con-duct output."""
from __future__ import annotations
from datetime import datetime
import logging
import string
from typing import Any
lgr = logging.getLogger("con-duct")
# Decimal (SI) byte units shared by SummaryFormatter.naturalsize (run
# summary) and the plot ... | con/duct | src/con_duct/_formatter.py | .py | b290322471e88b0e | 7.56 | 12 |
"""Signal handlers for con-duct."""
from __future__ import annotations
import logging
import os
import signal
from types import FrameType
from typing import Optional
lgr = logging.getLogger("con-duct")
class SigIntHandler:
"""
Handler of SIGINT signals received by the process running duct.
"""
def ... | con/duct | src/con_duct/_signals.py | .py | 0455397f117846e9 | 7.56 | 12 |
"""Process tracking and reporting for con-duct."""
from __future__ import annotations
from dataclasses import asdict
from importlib.metadata import version
import json
import logging
import math
import os
import platform
import shutil
import socket
import subprocess
import threading
import time
from typing import Any,... | con/duct | src/con_duct/_tracker.py | .py | 4e4d501d458876c9 | 7.56 | 12 |
"""Utility functions for con-duct."""
from typing import Any
def assert_num(*values: Any) -> None:
for value in values:
assert isinstance(value, (float, int))
# TODO: consider asking ps for `etimes` (seconds) directly via
# `-o etimes` instead of parsing `etime`. Even if we switch, this
# parser is wor... | con/duct | src/con_duct/_utils.py | .py | 3167909e07206ac9 | 7.56 | 12 |
"""Centralized JSON file type detection and loading for duct."""
from __future__ import annotations
import json
from typing import Any
from con_duct._constants import SUFFIXES
# Suffixes that use JSON Lines format
JSONL_SUFFIXES = (SUFFIXES["usage"], SUFFIXES["usage_legacy"])
def is_jsonl_file(path: str) -> bool:
... | con/duct | src/con_duct/json_utils.py | .py | 61d37821ff8df3cc | 7.56 | 12 |
"""Resource-usage plotting for con-duct.
Renders a per-pid CPU / rss cloud overlaid by envelopes:
max-across-pids as a lower bound, and either ``totals.*`` from the
record (RSS, and CPU in ``ps-pcpu`` mode) or sum-across-pids of the
derived values (CPU in ``ps-cpu-timepoint`` mode) as the upper
bound. CPU lives on the... | con/duct | src/con_duct/plot.py | .py | 575ae9a782e890b8 | 7.56 | 12 |
import argparse
import json
import logging
from pprint import pprint
from typing import Any
from con_duct._formatter import SummaryFormatter
from con_duct.json_utils import is_jsonl_file, load_info_file, load_usage_file
lgr = logging.getLogger(__name__)
def get_field_conversion_mapping() -> dict[str, str]:
"""
... | con/duct | src/con_duct/pprint_json.py | .py | fc48a25def3c22c3 | 7.56 | 12 |
import logging
import os
from pathlib import Path
from typing import Generator
import pytest
@pytest.fixture(scope="session", autouse=True)
def set_test_config() -> Generator:
# set DUCT_SAMPLE_INTERVAL and DUCT_REPORT_INTERVAL to small values
# to speed up testing etc. Those could be overridden by a specific... | con/duct | test/conftest.py | .py | 7d71cc964af2656d | 8.06 | 12 |
#!/usr/bin/env python3
from __future__ import annotations
import argparse
import sys
import time
def consume_cpu(duration: int, load: int) -> None:
"""Function to consume CPU proportional to 'load' for 'duration' seconds"""
end_time = time.time() + duration
while time.time() < end_time:
for _ in r... | con/duct | test/data/test_script.py | .py | a3470177635137ba | 8.06 | 12 |
"""Tests for utility functions in _duct_main.py"""
import pytest
from con_duct._utils import (
assert_num,
etime_to_etimes,
is_same_pid,
pdcpu_from_pcpu,
)
@pytest.mark.parametrize("input_value", [0, 1, 2, -1, 100, 0.001, -1.68])
def test_assert_num_green(input_value: int) -> None:
assert_num(inp... | con/duct | test/duct_main/test_duct_utils.py | .py | 3f429009bc4c67c6 | 8.06 | 12 |
from __future__ import annotations
import json
import os
from pathlib import Path
import platform
import subprocess
import time
import pytest
from con_duct._constants import SUFFIXES
SYSTEM = platform.system()
TEST_SCRIPT_DIR = Path(__file__).parent.parent / "data"
# Allow overriding the duct executable for testing ex... | con/duct | test/duct_main/test_e2e.py | .py | 0a74d949458622c5 | 8.06 | 12 |
from __future__ import annotations
import json
import logging
import multiprocessing
import os
from pathlib import Path
import signal
import subprocess
import sys
from time import sleep, time
import pytest
from utils import assert_files, run_duct_command
from con_duct import _duct_main
from con_duct._constants import S... | con/duct | test/duct_main/test_execution.py | .py | b85dd0c3295302a9 | 7.06 | 12 |
import argparse
import os
import platform
import re
import subprocess
from typing import Any, Optional
import unittest
from unittest import mock
from unittest.mock import MagicMock, patch
import pytest
from con_duct import cli
from con_duct.cli import _create_run_parser
SYSTEM = platform.system()
class TestSuiteHelp... | con/duct | test/test_cli.py | .py | 613cf081abf9e8a3 | 8.06 | 12 |
from __future__ import annotations
import logging
import os
from pathlib import Path
import sys
from unittest.mock import patch
import pytest
from con_duct import cli
@pytest.fixture
def temp_env_files(tmp_path: Path) -> dict[str, Path]:
"""Create temporary .env files for testing."""
# System-level config
... | con/duct | test/test_env_files.py | .py | ab435dc28a38b00c | 7.06 | 12 |
import os
from unittest import mock
import pytest
from con_duct._formatter import SummaryFormatter
from con_duct._tracker import Report
GREEN_START = SummaryFormatter.COLOR_SEQ % SummaryFormatter.GREEN
RED_START = SummaryFormatter.COLOR_SEQ % SummaryFormatter.RED
@mock.patch("con_duct._duct_main.LogPaths")
@mock.pat... | con/duct | test/test_formatter.py | .py | e070c72914dd838e | 7.06 | 12 |
import argparse
import contextlib
from io import StringIO
import json
import logging
import os
import tempfile
from typing import Any, Dict, Optional
import unittest
from unittest.mock import mock_open, patch
import pytest
from con_duct._constants import __schema_version__
from con_duct._formatter import SummaryFormatt... | con/duct | test/test_ls.py | .py | becf7a18c6ed9094 | 8.06 | 12 |
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