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 |
|---|---|---|---|---|---|---|
"""%there magic Python code shortcuts."""
# pylint: disable=invalid-name
from base64 import b64decode
from io import BytesIO, StringIO
import click
from herethere.there.commands import there_code_shortcut, there_group
from IPython.display import display
from PIL import Image as PILImage
KV_COMMAND_TEMPLATE = r"""
fr... | b3b/pythonhere | pythonhere/magic_here/shortcuts.py | .py | 8d435363cdffcd00 | 7.45 | 7 |
"""PythonHere app."""
# pylint: disable=wrong-import-order,wrong-import-position
from launcher_here import try_startup_script
try:
try_startup_script() # run script entrypoint, if it was passed
except Exception as exc:
startup_script_exception = exc # pylint: disable=invalid-name
else:
startup_script_e... | b3b/pythonhere | pythonhere/main.py | .py | 955e16cffe78921c | 7.45 | 7 |
"""Network addresses discovering."""
from collections.abc import Iterator
from kivy import platform
if platform == "android":
from jnius import autoclass # pylint: disable=import-error
NetworkInterface = autoclass("java.net.NetworkInterface")
Inet4Address = autoclass("java.net.Inet4Address")
else:
... | b3b/pythonhere | pythonhere/network_here.py | .py | 7b71439417173da4 | 7.45 | 7 |
"""Monkey patching Kivy @('_')@."""
import kivy.uix.widget
from kivy.factory import Factory
from kivy.lang.builder import BuilderBase
_original_factory_register = Factory.register
_original_builderbase_match = BuilderBase.match
# pylint: disable=protected-access
_original_widget_destructor = kivy.uix.widget._widget_d... | b3b/pythonhere | pythonhere/patches_here.py | .py | cc1ece85b9393c85 | 7.45 | 7 |
"""SSH server."""
import asyncio
from pathlib import Path
from exception_manager_here import show_exception_popup
from herethere.here.server import ServerConfig, SSHServerHere, start_server
from kivy.app import App
from kivy.logger import Logger
class PythonHereServer(SSHServerHere):
"""SSH server protocol hand... | b3b/pythonhere | pythonhere/server_here.py | .py | 76134c263d406f3e | 7.45 | 7 |
"""Connection information widgets."""
from kivy.clock import Clock, mainthread
from kivy.logger import Logger
from kivy.properties import StringProperty # pylint: disable=no-name-in-module
from kivy.uix.gridlayout import GridLayout
from kivy.uix.label import Label
from network_here import get_all_available_ipv4_adrre... | b3b/pythonhere | pythonhere/ui_here/connection_address_here.py | .py | fcd336989b973368 | 7.45 | 7 |
"""%here server screen."""
from enum_here import ServerState
from kivy.app import App
from kivy.clock import Clock, mainthread
from kivy.uix.screenmanager import ScreenManager
class ServerScreenManager(ScreenManager):
"""Screen manager for server %here section."""
def __init__(self, *args, **kwargs):
... | b3b/pythonhere | pythonhere/ui_here/server_screen_here.py | .py | db342fd5816688a3 | 7.45 | 7 |
"""Settings panel widgets."""
import webbrowser
from typing import Any
from kivy.app import App
from kivy.config import Config
from kivy.properties import ( # pylint: disable=no-name-in-module
BooleanProperty,
ObjectProperty,
StringProperty,
)
from kivy.uix.anchorlayout import AnchorLayout
from kivy.uix.... | b3b/pythonhere | pythonhere/ui_here/settings_here.py | .py | ecd7e564152a6360 | 7.45 | 7 |
"""Utilities for working with Kivy window."""
import time
from base64 import b64encode
from pathlib import Path
from kivy.app import App
from kivy.lang import Builder
from kivy.uix.boxlayout import BoxLayout
def reset_window_environment() -> BoxLayout:
"""Remove PythonHere app widgets and styles."""
# impor... | b3b/pythonhere | pythonhere/window_here.py | .py | a053e834c19a7c6a | 7.45 | 7 |
"""Plasma: Light FX Sequencer."""
import time
class Sequence(object):
"""PlasmaFX Sequence.
A PlasmaFX sequence is responsible for a sequence of
Plasma light groupings.
LEDs can be grouped into "lights" such as the 4 on a Plasma PCB
or the 12+ on an Adafruit NeoPixel ring.
"""
def __in... | pimoroni/plasma-python | fx/plasmafx/plasmafx/__init__.py | .py | 0acce9f2f418a6c6 | 7.64 | 18 |
"""Plasma: Light FX Sequencer - Plugin base class."""
class Plugin(object):
"""PlasmaFX Plugin.
A PlasmaFX plugin is responsible for the 4 lights on
a single Plasma light board.
"""
def __init__(self, pixel_count=1):
"""Initialise PlasmaFX: Base Plugin."""
self._pixel_count = pi... | pimoroni/plasma-python | fx/plasmafx/plasmafx/core.py | .py | f61b9757154baf2b | 7.64 | 18 |
"""Plasma: Light FX Sequencer - Colour Cycling Plugin."""
from colorsys import hsv_to_rgb
from plasmafx.core import Plugin
class Cycle(Plugin):
"""Plasma: Light FX Sequencer - Colour Cycling Plugin."""
def __init__(self, pixel_count=1, speed=1.0, spread=360.0, offset=0.0, saturation=1.0, value=1.0):
... | pimoroni/plasma-python | fx/plasmafx_plugin_cycle/plasmafx_plugin_cycle/__init__.py | .py | 818252baae77dd15 | 7.64 | 18 |
"""Plasma multi device LED driver."""
import pathlib
import sys
from importlib.metadata import PackageNotFoundError, version
try:
__version__ = version("plasmalights")
except PackageNotFoundError:
__version__ = "0.0.0"
def auto(default=None, descriptor=None):
"""Return a Plasma device instance.
Will... | pimoroni/plasma-python | plasma/__init__.py | .py | 6430a1c08916fda2 | 7.64 | 18 |
"""Plasma support for APA102 style pixels."""
import time
from .core import Plasma
class PlasmaAPA102(Plasma):
"""Plasma support for APA102 style pixels."""
name = "APA102"
options = {
'pixel_count': int,
"gpio_data": int,
"gpio_clock": int,
"gpio_cs": int
}
opt... | pimoroni/plasma-python | plasma/apa102.py | .py | 8314e05acf625df0 | 7.64 | 18 |
"""Base class for Plasma LED devices."""
import atexit
class Plasma():
"""Base class for Plasma LED devices."""
name = ""
options = {
'pixel_count': int,
}
option_order = []
def __init__(self, pixel_count=1):
"""Initialise Plasma device.
:param pixel_count: Number ... | pimoroni/plasma-python | plasma/core.py | .py | d01f9bd39bd225ae | 7.64 | 18 |
"""Combine multiple LED strip types into a single logical strip."""
import pathlib
import yaml
class PlasmaMatrix():
"""Combine multiple LED strip types into a single logical strip."""
def __init__(self, config_file=None):
"""Initialise a matrix.
:param config_file: Path to yml configuratio... | pimoroni/plasma-python | plasma/matrix.py | .py | fac80184190bd5ae | 7.64 | 18 |
"""Serial class for Plasma light devices over USB Serial/UART."""
from serial import Serial
from .core import Plasma
class PlasmaSerial(Plasma):
"""Serial class for Plasma light devices over USB Serial/UART."""
name = "Serial"
options = {
'pixel_count': int,
"port": str
}
optio... | pimoroni/plasma-python | plasma/serial.py | .py | bc96596489da81ca | 7.64 | 18 |
"""Class for Plasma light devices in the WS281X/SK6812 family."""
from .core import Plasma
class PlasmaWS281X(Plasma):
"""Class for Plasma light devices in the WS281X/SK6812 family."""
name = "WS281X"
options = {
'pixel_count': int,
"gpio_pin": int,
"strip_type": str,
"ch... | pimoroni/plasma-python | plasma/ws281x.py | .py | d0deb1a622b8dcdc | 7.64 | 18 |
"""Test configuration.
These allow the mocking of various Python modules
that might otherwise have runtime side-effects.
"""
import pathlib
import sys
import tempfile
import mock
import pytest
@pytest.fixture(scope='function', autouse=True)
def cleanup_plasma():
"""This fixture removes all plasma modules from s... | pimoroni/plasma-python | tests/conftest.py | .py | 6f0bbc5cc8dce381 | 8.14 | 18 |
"""Test Plasma APA102 initialisation."""
import mock
def test_apa102_setup(GPIO):
"""Test init succeeds and GPIO pins are setup."""
from plasma.apa102 import PlasmaAPA102
plasma = PlasmaAPA102(10, gpio_data=10, gpio_clock=11)
plasma.show()
GPIO.setmode.assert_called_once_with(GPIO.BCM)
GPIO.s... | pimoroni/plasma-python | tests/test_apa102.py | .py | 03ad19e8c8e34c0f | 7.14 | 18 |
"""Test Plasma GPIO (APA102 wrapper) initialisation."""
import mock
def test_legacy_gpio_setup(GPIO):
"""Test init succeeds and GPIO pins are setup."""
from plasma.gpio import PlasmaGPIO
plasma = PlasmaGPIO(10, gpio_data=10, gpio_clock=11)
plasma.show()
GPIO.setmode.assert_called_once_with(GPIO.B... | pimoroni/plasma-python | tests/test_legacy_gpio.py | .py | 9e4b5d05cad661bd | 8.14 | 18 |
"""Test Plasma Serial initialisation."""
def test_serial_setup(serial):
"""Test init succeeds and GPIO pins are setup."""
from plasma.serial import PlasmaSerial
plasma = PlasmaSerial(10, port="/dev/ttyAMA0", baudrate=8000)
plasma.show()
serial.Serial.assert_called_once_with("/dev/ttyAMA0", baudra... | pimoroni/plasma-python | tests/test_serial.py | .py | 4723051eb3f7254f | 7.14 | 18 |
"""Test Plasma WS281X initialisation."""
def test_apa102_setup(rpi_ws281x):
"""Test init succeeds and GPIO pins are setup."""
from plasma.ws281x import PlasmaWS281X
plasma = PlasmaWS281X(10)
plasma.show()
rpi_ws281x.PixelStrip.assert_called_once()
def test_apa102_parse_options(rpi_ws281x):
... | pimoroni/plasma-python | tests/test_ws281x.py | .py | 02460520b7ed3379 | 8.14 | 18 |
#!/usr/bin/env python3
"""Command line tool to start/stop/restart the task runner in a tmux session."""
import subprocess
import sys
from pathlib import Path
import psutil
ATLASSERVERPATH = Path(__file__).resolve().parent.parent
def run_command(commands: list[str], print_output: bool = True) -> int:
"""Run a c... | lukeshingles/atlasserver | atlasserver/atlastaskrunner.py | .py | ceb96863ddcd9498 | 7.57 | 13 |
#!/usr/bin/env python3
"""Command line tool to start/stop/restart the ATLAS Apache server."""
import os
import platform
import signal
import subprocess
import sys
import time
from pathlib import Path
import psutil
from dotenv import load_dotenv
APACHEPATH = Path("/tmp/atlasforced")
# where this file actually lives.... | lukeshingles/atlasserver | atlasserver/atlaswebserver.py | .py | 9bf5ccb9badbb276 | 7.57 | 13 |
from typing import override
from django.apps import AppConfig
class ForcephotConfig(AppConfig):
# job filenames are only ever built from the id (f"job{id:05d}"), never parsed at a fixed
# width, so widening the id does not change any path that already exists on disk or on sc01
default_auto_field = "djang... | lukeshingles/atlasserver | atlasserver/forcephot/apps.py | .py | bcd4ee102bc25a03 | 7.57 | 13 |
"""Template context shared by every page."""
import typing as t
from django.conf import settings
from django.http import HttpRequest
from django.utils.functional import SimpleLazyObject
from atlasserver.forcephot.models import Task
from atlasserver.taskrunner import status as runnerstatus
def static_version(reques... | lukeshingles/atlasserver | atlasserver/forcephot/context_processors.py | .py | 3bfe2f628d50c7fb | 7.57 | 13 |
from django import forms
from django.contrib.auth import get_user_model
from django.contrib.auth.forms import UserCreationForm
from django.contrib.auth.models import User
from django.utils.translation import gettext_lazy as _
def email_is_taken(email: str, exclude_user=None) -> bool:
"""Return True if another acc... | lukeshingles/atlasserver | atlasserver/forcephot/forms.py | .py | f5d0d241f7bc9950 | 7.57 | 13 |
"""Stop *new* accounts sharing an email address, while leaving existing ones alone.
forms.email_is_taken() has always checked this, but only in a form clean() method, so two
concurrent registrations could both pass validation, and the admin and the shell bypassed it
altogether. Duplicates make the password reset flow ... | lukeshingles/atlasserver | atlasserver/forcephot/migrations/0005_auth_user_email_unique.py | .py | b03a4005c16045e4 | 7.57 | 13 |
"""Require every task to have a target: an MPC object name, or both coordinates.
ForcePhotTaskSerializer.validate() has always enforced this, but it was the only thing that did,
so the admin and the shell could create a task with no target at all -- Task.__str__ still carries
a branch for exactly that case.
Deploy no... | lukeshingles/atlasserver | atlasserver/forcephot/migrations/0006_task_task_target_is_mpcname_or_radec.py | .py | 9d6d10ed7b8f0bc6 | 7.57 | 13 |
"""Guarantee that mpc_name is NULL, "" or a real name -- never whitespace alone.
Task.save() normalises the field, but bulk_create, bulk_update, QuerySet.update() and raw SQL do
not go through it, so the guarantee has to be in the database. What it buys is that every reader
can test the field for truth instead of re-d... | lukeshingles/atlasserver | atlasserver/forcephot/migrations/0008_mpc_name_not_blank.py | .py | 41bb9768b364c717 | 7.57 | 13 |
import datetime
import logging
import multiprocessing
import typing as t
from multiprocessing.process import BaseProcess
from pathlib import Path
from typing import override
import fundamentals.logs
import julian
import pycountry
from astrocalc.coords.unit_conversion import unit_conversion
from django.http import Http... | lukeshingles/atlasserver | atlasserver/forcephot/misc.py | .py | 09a500e5a1098669 | 7.57 | 13 |
"""Client IP addresses: which one a request really came from, and which ones are public.
Deliberately free of imports beyond the standard library, and of Django: the callers include
webhooks (which decides whether the server may be pointed at an address) and the GeoIP lookup in
views (which decides whether an address ... | lukeshingles/atlasserver | atlasserver/forcephot/netaddr.py | .py | 2da4e51fbcb02850 | 7.57 | 13 |
import typing as t
from collections import OrderedDict
from typing import override
from django.db.models import QuerySet
from rest_framework.pagination import _reverse_ordering
from rest_framework.pagination import CursorPagination
from rest_framework.request import Request
from rest_framework.response import Response... | lukeshingles/atlasserver | atlasserver/forcephot/pagination.py | .py | bece715c9b00c5ea | 7.57 | 13 |
"""Queue ordering: assigning each unfinished task its position in the execution order.
Lives outside views.py so that the task runner can import it without pulling in DRF, bokeh and the
rest of the web stack, and so that the two processes cannot drift on what "queue position" means.
"""
import datetime
import operato... | lukeshingles/atlasserver | atlasserver/forcephot/queue.py | .py | f7942274d6ddb349 | 7.57 | 13 |
import math
import typing as t
from typing import override
from django.contrib.staticfiles.storage import staticfiles_storage
from django.core.exceptions import ObjectDoesNotExist
from rest_framework import serializers
from rest_framework.reverse import reverse
from atlasserver.forcephot.models import get_mjd_min_def... | lukeshingles/atlasserver | atlasserver/forcephot/serializers.py | .py | d51485a5c736417b | 7.57 | 13 |
import typing as t
from typing import override
from django.core.cache import caches
# the same tuple ForcePhotPermission branches on, so the two cannot drift on what counts as a read.
# Safe methods are throttled far more loosely than writes, but not exempt: the queue page polls the
# task list every few seconds, so ... | lukeshingles/atlasserver | atlasserver/forcephot/throttles.py | .py | 3668c63e225bad8a | 7.57 | 13 |
"""Email address verification for new registrations.
Registration used to log the new account straight in without proving the address belonged to
whoever typed it, so the address that receives job completion mail (and password resets) was
unverified. Anyone could sign up as someone else's address, and the owner's only... | lukeshingles/atlasserver | atlasserver/forcephot/verification.py | .py | d446fa41737ed927 | 7.57 | 13 |
"""Optional completion callbacks for API-submitted tasks.
API clients have no way to be told that a task finished — result emails are skipped for
API-originated tasks — so every API user polls, which is a large share of the server's request
volume. A task may carry a callback_url that is POSTed a small JSON body once ... | lukeshingles/atlasserver | atlasserver/forcephot/webhooks.py | .py | f011a4f16ee723f7 | 7.57 | 13 |
#!/usr/bin/env python3
"""Input a job data file and produce a zip of FITS images. This script is to be run on sc01."""
import shutil
import subprocess
import sys
import tempfile
from pathlib import Path
import pandas as pd
def main() -> None:
if len(sys.argv) != 3:
print("ERROR: exactly two argument mus... | lukeshingles/atlasserver | atlasserver/taskrunner/atlas_gettaskimages.py | .py | 1a5f9a48d99e1cef | 7.57 | 13 |
"""The task runner's configuration that the web app also needs.
Where the runner writes its status snapshot, how often, and how many tasks it runs at once.
Split out of `main` so that the web server can read these without importing the runner. Importing
`atlasserver.taskrunner.main` runs `django.setup()` and pulls in... | lukeshingles/atlasserver | atlasserver/taskrunner/status.py | .py | 6d0cf899ea023508 | 7.57 | 13 |
"""Utility functions for 21cmSense."""
import numpy as np
from astropy import units as un
from astropy.coordinates import EarthLocation, SkyCoord
from astropy.time import Time
from lunarsky import MoonLocation
from lunarsky import SkyCoord as LunarSkyCoord
from lunarsky import Time as LTime
from pyuvdata import utils ... | rasg-affiliates/21cmSense | src/py21cmsense/_utils.py | .py | 5245ad147f366b07 | 7.59 | 14 |
"""A module defining baseline filters.
While you can simply use a function that takes a single baseline (with three
co-ordinates) and returns a bool, this module provides standard kinds of filters (eg.
using baselines within a certain length range). It also enables loading the filters
from string names, useful for YAM... | rasg-affiliates/21cmSense | src/py21cmsense/baseline_filters.py | .py | 318307fade80eca4 | 7.59 | 14 |
"""Simplistic beam definitions."""
from __future__ import annotations
from abc import ABCMeta, abstractmethod
import attr
from astropy import constants as cnst
from astropy import units as un
from hickleable import hickleable
from . import _utils as ut
from . import units as tp
@hickleable(evaluate_cached_propert... | rasg-affiliates/21cmSense | src/py21cmsense/beam.py | .py | 35acda68d6867817 | 7.59 | 14 |
"""A module defining interferometric observation objects."""
from __future__ import annotations
import collections
from collections import defaultdict
from functools import cached_property
from os import path
from typing import Any, Callable
import attr
import numpy as np
from astropy import units as un
from astropy... | rasg-affiliates/21cmSense | src/py21cmsense/observation.py | .py | ad73279381a049e0 | 7.59 | 14 |
"""Module dealing with types and units throughout the package."""
from __future__ import annotations
from typing import Any, Callable
import attr
from astropy import constants as cnst
from astropy import units as un
from astropy.cosmology.units import littleh, redshift
un.add_enabled_units([littleh, redshift])
cl... | rasg-affiliates/21cmSense | src/py21cmsense/units.py | .py | 8f46b4d9aeb5d9c1 | 7.59 | 14 |
"""Module defining new YAML tags for py21cmsense."""
import inspect
import pickle
from functools import wraps
import numpy as np
import yaml
from astropy import units as un
from astropy.io.misc.yaml import AstropyLoader
_DATA_LOADERS = {}
_YAML_LOADERS = (yaml.FullLoader, yaml.SafeLoader, yaml.Loader, AstropyLoader... | rasg-affiliates/21cmSense | src/py21cmsense/yaml.py | .py | 412222e4d67f43ee | 7.59 | 14 |
"""Test the antenna positions."""
import numpy as np
import pytest
from astropy import units as un
from py21cmsense.antpos import hera
@pytest.mark.parametrize("n", [3, 5, 8])
def test_hera_split_core(n):
# https://en.wikipedia.org/wiki/Centered_hexagonal_number
# 3*n^2 - 3n + 1
antpos1 = hera(hex_num=n... | rasg-affiliates/21cmSense | tests/test_antpos.py | .py | ce1a5f959ea43640 | 8.09 | 14 |
"""Test baseline_filters module."""
import numpy as np
import pytest
from astropy import units as un
from py21cmsense.baseline_filters import BaselineRange
# Test IDs for parametrization
happy_path_ids = [
"east-west_min",
"north-south_min",
"magnitude_min",
"east-west_max",
"north-south_max",
... | rasg-affiliates/21cmSense | tests/test_baseline_filters.py | .py | 760870af232c4e0a | 8.09 | 14 |
"""Tests for the Observation class."""
import copy
import pickle
import numpy as np
import pytest
from astropy import units
from astropy.cosmology.units import littleh
from py21cmsense import GaussianBeam, Observation, Observatory
@pytest.fixture(scope="module")
def bm():
return GaussianBeam(150.0 * units.MHz,... | rasg-affiliates/21cmSense | tests/test_observation.py | .py | 0a110ddc0a249191 | 8.09 | 14 |
"""Tests of the phasing code for calculating UVWs."""
import numpy as np
import pytest
from astropy import units as un
from astropy.coordinates import EarthLocation, SkyCoord
from astropy.time import Time
from pyuvdata import utils as uvutils
from py21cmsense._utils import phase_past_zenith
@pytest.mark.parametrize... | rasg-affiliates/21cmSense | tests/test_uvw.py | .py | 22c46eceb6cb96c4 | 7.09 | 14 |
"""Error codes used in different error messages."""
from enum import IntEnum
class ErrorSeverity(IntEnum):
"""Severity codes for errors."""
ERROR = 1
WARNING = 10
class ErrorContext:
"""Context this error took place in, each error potentially having multiple contexts."""
# Use this one to dis... | hed-standard/hed-python | hed/errors/error_types.py | .py | 50317ac3227e1e9e | 7.64 | 18 |
"""HED exceptions and exception codes."""
class HedExceptions:
"""HED exception codes."""
GENERIC_ERROR = "GENERIC_ERROR"
# A list of all exceptions that can be generated by the hedtools.
URL_ERROR = "URL_ERROR"
FILE_NOT_FOUND = "FILE_NOT_FOUND"
BAD_PARAMETERS = "BAD_PARAMETERS"
CANNOT_PA... | hed-standard/hed-python | hed/errors/exceptions.py | .py | 0ab7f7eeb479f8b7 | 7.64 | 18 |
"""
Utilities to support HED searches based on strings.
"""
import re
from collections import defaultdict
from itertools import combinations, product
import pandas as pd
def find_matching(series, search_string, regex=False):
"""Find lines in the series that match the search string and returns a mask.
Synta... | hed-standard/hed-python | hed/models/basic_search.py | .py | cb718216b4dd7dd1 | 7.64 | 18 |
"""Defined constants for definitions, def labels, and expanded labels."""
from enum import IntEnum
class TopTagReturnType(IntEnum):
"""Return-type selector for :meth:`~hed.models.HedString.find_top_level_tags`.
Pass one of these constants as the ``include_groups`` argument to control
whether the method ... | hed-standard/hed-python | hed/models/model_constants.py | .py | c24b01f13b1f7baa | 7.64 | 18 |
"""Functions to get and use HED queries."""
import pandas as pd
from hed.models import QueryHandler
def get_query_handlers(queries, query_names=None) -> tuple[list[QueryHandler | None], list[QueryHandler | None], list]:
"""Return a list of query handlers, query names, and issues if any.
Parameters:
... | hed-standard/hed-python | hed/models/query_service.py | .py | 935198669b7108be | 7.64 | 18 |
"""Classes representing HED search results and tokens."""
class SearchResult:
"""Holder for and manipulation of search results.
Represents a query match result consisting of:
- group: The containing HedGroup where matches were found.
- children: The specific matched elements (tags/groups) within tha... | hed-standard/hed-python | hed/models/query_util.py | .py | 8907749fca545e7e | 7.64 | 18 |
"""Schema lookup table for ancestor-aware string search.
Generates a compact mapping from every tag's casefolded short name to its
full ``tag_terms`` tuple (all slash-path components from root to self), which
is the same information stored in :attr:`~hed.schema.HedTagEntry.tag_terms` after
schema loading.
This lookup... | hed-standard/hed-python | hed/models/schema_lookup.py | .py | b8167d5104074eef | 7.64 | 18 |
"""Contents of a JSON file or merged JSON files."""
import json
import re
from hed.errors import ErrorHandler
from hed.errors.error_types import ErrorContext
from hed.errors.exceptions import HedExceptions, HedFileError
from hed.models.column_metadata import ColumnMetadata, ColumnType
from hed.models.definition_dict ... | hed-standard/hed-python | hed/models/sidecar.py | .py | 5cd5a51e30ab2dd1 | 7.64 | 18 |
"""A spreadsheet of HED tags."""
from hed.models.base_input import BaseInput
from hed.models.column_mapper import ColumnMapper
class SpreadsheetInput(BaseInput):
"""A spreadsheet of HED tags."""
def __init__(
self,
file=None,
file_type=None,
worksheet_name=None,
tag_c... | hed-standard/hed-python | hed/models/spreadsheet_input.py | .py | 6e04fe58b923d2d4 | 7.64 | 18 |
"""A BIDS tabular file with sidecar."""
from __future__ import annotations
from typing import TYPE_CHECKING
from hed.models.base_input import BaseInput
from hed.models.column_mapper import ColumnMapper
from hed.models.sidecar import Sidecar
if TYPE_CHECKING:
from hed.models.definition_dict import DefinitionDict... | hed-standard/hed-python | hed/models/tabular_input.py | .py | 3c2779cf70d5ee56 | 7.64 | 18 |
"""A BIDS time series tabular file."""
from hed.models.base_input import BaseInput
class TimeseriesInput(BaseInput):
"""A BIDS time series tabular file."""
HED_COLUMN_NAME = "HED"
def __init__(self, file=None, sidecar=None, extra_def_dicts=None, name=None):
"""Constructor for the TimeseriesInpu... | hed-standard/hed-python | hed/models/timeseries_input.py | .py | f0519b347cb5b61b | 7.64 | 18 |
"""Support utilities for hed_cache locking"""
import os
import time
import portalocker
TIMESTAMP_FILENAME = "last_update.txt"
CACHE_TIME_THRESHOLD = 300 * 6
class CacheError(Exception):
"""Exception for cache locking or threshold errors."""
pass
class CacheLock:
"""Class to lock the cache folder to ... | hed-standard/hed-python | hed/schema/hed_cache_lock.py | .py | 4619c75195aa10bd | 7.64 | 18 |
"""Enumeration constants and string literals used throughout HED schema loading and validation."""
from enum import Enum
class HedSectionKey(Enum):
"""Keys designating specific sections in a HedSchema object."""
# overarching category listing all tags
Tags = "tags"
# Overarching category listing all... | hed-standard/hed-python | hed/schema/hed_schema_constants.py | .py | a1fbc948325e43fb | 7.64 | 18 |
"""Container for multiple HED schemas used together in multi-library validation."""
from __future__ import annotations
import json
from hed.errors import ErrorHandler, ValidationErrors
from hed.errors.exceptions import HedExceptions, HedFileError
from hed.schema.hed_schema import HedSchema
from hed.schema.hed_schema... | hed-standard/hed-python | hed/schema/hed_schema_group.py | .py | d64551dc8eddd30c | 7.64 | 18 |
"""Main command."""
from __future__ import annotations
from pathlib import Path
from shlex import quote
from typing import TYPE_CHECKING, Any, BinaryIO, cast
import json
import logging
import os
import re
import socket
import struct
import subprocess as sp
import sys
from bascom import setup_logging
from open_in_mpv ... | Tatsh/open-in-mpv | open_in_mpv/main.py | .py | abcbffa59f3e1ca1 | 7.65 | 19 |
from __future__ import annotations
from typing import TYPE_CHECKING, Any
import json
import re
import struct
from open_in_mpv.main import get_callback, get_mpv_path, main, spawn
import pytest
if TYPE_CHECKING:
from unittest.mock import MagicMock
from click.testing import CliRunner
from pytest_mock impor... | Tatsh/open-in-mpv | tests/test_main.py | .py | 808d83e008b5ba84 | 7.15 | 19 |
"""
Tests for issue #1344: get_current_configuration must not create duplicate
Configuration rows under concurrency, and must never expose a Configuration
with an empty versions set.
"""
import threading
import pytest
from django.db import connection
from topobank.analysis.tasks import get_current_configuration
from... | ContactEngineering/topobank | tests/analysis/test_configuration_race.py | .py | f6039017d10915a9 | 8 | 9 |
"""
Tests for issue #1345: when a workflow fails because a dependency failed, the
parent must surface the dependency's real error/traceback, not a generic one.
"""
import pytest
from topobank.analysis.models import Workflow, WorkflowResult
from topobank.analysis.tasks import execute_workflow, schedule_workflow
from t... | ContactEngineering/topobank | tests/analysis/test_dependency_traceback.py | .py | a326e28734495c0b | 8 | 9 |
"""Tests for topobank.analysis.exceptions."""
from topobank.analysis.exceptions import SubjectNotReadyException
def test_subject_not_ready_exception_message():
exc = SubjectNotReadyException("my-subject")
assert isinstance(exc, Exception)
message = str(exc)
assert "my-subject" in message
assert "... | ContactEngineering/topobank | tests/analysis/test_exceptions.py | .py | 9ad11acfd76d25b8 | 8 | 9 |
"""
Tests for bundling workflow results into a ZIP archive
(``topobank.analysis.export_zip`` and ``topobank.analysis.zip_model``).
"""
import datetime
import io
import zipfile
import pytest
from django.conf import settings
from django.core.exceptions import PermissionDenied
from django.core.files.base import ContentF... | ContactEngineering/topobank | tests/analysis/test_export_zip.py | .py | 0385dd2e7bce74e7 | 7 | 9 |
"""
Tests for workflow output schema infrastructure.
"""
import pydantic
import pytest
from topobank.analysis.models import Workflow
from topobank.analysis.outputs import OutputFile, get_outputs_schema
from topobank.analysis.workflows import WorkflowImplementation
class TestOutputFile:
"""Tests for the OutputFi... | ContactEngineering/topobank | tests/analysis/test_outputs.py | .py | 46aa8c53a2cb82ec | 8 | 9 |
"""
Tests for the metadata that accompanies a split-off data series.
Series data lives in its own file in the object store, so anything a plot needs
before fetching them has to be recorded next to the reference. That includes the
extent of the data, which is what lets a plot combining several results choose a
display ... | ContactEngineering/topobank | tests/analysis/test_series_metadata.py | .py | b819864c8f76c2b4 | 8 | 9 |
"""
Tests for issue #1343: the check-then-create dedup in submit /
submit_for_surfaces must be serialized so concurrent identical submissions do
not create duplicate WorkflowResults.
"""
import threading
import pytest
from django.db import connection
from topobank.analysis.models import WorkflowResult
from topobank.... | ContactEngineering/topobank | tests/analysis/test_submit_dedup_race.py | .py | 6b7c2ed074a2c5ed | 8 | 9 |
"""
Tests for invalidation and cleanup of surface-set (M2M) analyses (issue #1340).
Surface-set analyses store their subjects via the ``WorkflowResult.surfaces``
M2M and have ``subject_surface`` NULL, so the invalidation signals and the
custodian must match them through the M2M, not only the legacy subject FKs.
"""
i... | ContactEngineering/topobank | tests/analysis/test_surface_set_invalidation.py | .py | 3fed550c004b7714 | 7 | 9 |
"""
Tests for issue #1346: AnalysisController._get_unique_kwargs must return the
true intersection of kwargs across analyses (dropping keys absent from or
differing in any analysis) without mutating any analysis's stored kwargs.
"""
from types import SimpleNamespace
from topobank.analysis.controller import AnalysisCo... | ContactEngineering/topobank | tests/analysis/test_unique_kwargs.py | .py | dd98ecb4f208bf9e | 8 | 9 |
import pytest
from topobank.analysis.models import Workflow
from topobank.analysis.registry import get_workflow_names
from topobank.testing.workflows import TestImplementation
@pytest.mark.django_db
def test_retrieve_registry_workflows():
names = get_workflow_names()
assert TestImplementation.Meta.name in n... | ContactEngineering/topobank | tests/analysis/test_workflows.py | .py | 873755afcce0c81d | 8 | 9 |
import pytest
from topobank.authorization import (
get_anonymous_user,
get_organization_model,
get_permission_model,
get_user_permission_model,
)
from topobank.authorization.models import levels_with_access
def test_levels_with_access():
assert levels_with_access("full") == {"full"}
assert le... | ContactEngineering/topobank | tests/authorization/test_utils.py | .py | 96b4006b1a1d675d | 7 | 9 |
"""
Regression tests for management commands in topobank.manager.
These exercise the command entry points on a (mostly) empty database. They are
deliberately light-weight: the commands iterate over real objects and do heavy
file I/O in production, so here we only ensure the commands are wired up and run
end-to-end wit... | ContactEngineering/topobank | tests/manager/test_commands.py | .py | 2cd8dd7c0388f4cf | 7 | 9 |
"""
Functional tests that import a real published surface container from
contact.engineering and exercise the topography data pipeline end to end:
file reading, the Celery task runner, metadata caching, and deepzoom /
squeezed-data generation.
The container is the published dataset https://doi.org/10.57703/ce-867nv
("... | ContactEngineering/topobank | tests/manager/test_container_pipeline.py | .py | d0c4d0e681d58dc7 | 8 | 9 |
"""
Tests for writing surface containers
"""
import json
import os
import tempfile
import zipfile
import pytest
from notifications.models import Notification
import topobank
from topobank.manager.export_zip import export_container_zip
from topobank.manager.import_zip import import_container_zip, load_container_metad... | ContactEngineering/topobank | tests/manager/test_containers.py | .py | f2752358c4d82a61 | 8 | 9 |
"""Tests for the periodic cleanup task in topobank.manager.custodian."""
import datetime
import pytest
from django.utils import timezone
from topobank.manager.custodian import periodic_cleanup
from topobank.manager.models import Surface, Topography
from topobank.testing.factories import SurfaceFactory, Topography2DF... | ContactEngineering/topobank | tests/manager/test_custodian.py | .py | 13d7d69bc65c140a | 7 | 9 |
import logging
import pytest
from topobank.testing.factories import Topography2DFactory
@pytest.mark.django_db
def test_deepzoom_creation_fails(mocker):
topo = Topography2DFactory(size_x=1, size_y=1)
topo.refresh_cache()
# should have a deepzoom images
assert topo.deepzoom is not None
mocker.pa... | ContactEngineering/topobank | tests/manager/test_deepzoom.py | .py | 5ef6885fc333f026 | 8 | 9 |
"""
Tests for the trend that detrending subtracts from a measurement.
`Topography.detrend_parameters` records what was removed — the slope of the tilt,
the radius of the curvature — so the UI can show which correction is in effect
rather than only naming the mode.
"""
import numpy as np
import pytest
from SurfaceTopo... | ContactEngineering/topobank | tests/manager/test_detrend_parameters.py | .py | 900cbec6bf976d5d | 7 | 9 |
"""
Tests for the ``import_datasets`` management command.
The command imports a surface from a previously-downloaded container archive
(ONLY FOR USE WITH FILES FROM TRUSTED SOURCES). We build a real archive on disk
with ``export_container_zip`` and import it back, which exercises the full
command path: user lookup, ar... | ContactEngineering/topobank | tests/manager/test_import_datasets.py | .py | 29047eeefcef3ecd | 8 | 9 |
"""
Tests for importing a dataset from another instance
(``topobank.manager.tasks.import_container_from_url``).
The remote describes how to obtain the container: a publication with an archived
container advertises it as 'download_url' and it can simply be fetched, while
otherwise the remote has to assemble one first, ... | ContactEngineering/topobank | tests/manager/test_import_from_url.py | .py | 8e01e77f83f26a73 | 8 | 9 |
"""
Tests for the `TOPOBANK_REJECT_INCOMPLETE_METADATA` global flag.
A file can be of a supported format and read successfully, yet not contain the
metadata (physical size, unit) required to process it. By default such a file is
accepted and the user is expected to fill in the missing metadata through the UI.
When `TO... | ContactEngineering/topobank | tests/manager/test_incomplete_metadata.py | .py | 9872efa38b353df9 | 8 | 9 |
"""
Tests for soft-delete bookkeeping on Surface and Topography.
`lazy_delete` records the user who performed the deletion in `deleted_by`, on
the object itself and on everything the call cascades to, so a recycle-bin view
can report who deleted what while the object is still recoverable.
"""
import pytest
from topo... | ContactEngineering/topobank | tests/manager/test_lazy_delete.py | .py | 119136f4712d988c | 7 | 9 |
"""
Tests related to the models in topobank.manager app
"""
import datetime
import pytest
from django.apps import apps
from django.core.files.base import ContentFile
from django.db import transaction
from django.db.utils import IntegrityError
from notifications.models import Notification
from notifications.signals im... | ContactEngineering/topobank | tests/manager/test_models.py | .py | 1aae25dabd356695 | 7 | 9 |
"""
Tests for the full-text search index on `Surface`.
`Surface.build_search_document` assembles the searchable text from a dataset and
its measurements, and the signal handlers in `manager.signals` keep
`Surface.search_vector` current as either changes. These tests pin down what ends
up in the index and, just as impo... | ContactEngineering/topobank | tests/manager/test_search_vector.py | .py | fb611ab8a2280751 | 7 | 9 |
"""
Tests for issue #1342: Topography.save() with a restricted update_fields must
still persist the pending task state that run_task sets in memory.
Otherwise a recompute is dispatched while the DB keeps task_state=SUCCESS
(get_task_state() then wrongly reports "done"), and the in-flight re-dispatch
guard — which keys... | ContactEngineering/topobank | tests/manager/test_topography_task_state.py | .py | 217860dde82c4f44 | 8 | 9 |
"""
Tests for how much of a measurement is undefined.
A measurement can carry data points that hold no value, because the instrument
could not resolve them. `Topography.has_undefined_data` records that this is the
case and `Topography.undefined_data_fraction` how much of the data it affects,
both describing the data a... | ContactEngineering/topobank | tests/manager/test_undefined_data.py | .py | d304203f4fe2f200 | 8 | 9 |
"""
Tests for the interface to topography files
and other things in topobank.manager.utils
"""
import pytest
from topobank.manager.models import Surface, Topography
from topobank.manager.utils import (
subjects_from_base64,
subjects_from_dict,
subjects_to_base64,
subjects_to_dict,
to_natural_lengt... | ContactEngineering/topobank | tests/manager/test_utils.py | .py | 246f0b1279660a0e | 8 | 9 |
"""Tests for topobank.manager.zip_model.ZipContainer."""
import json
import zipfile
import pytest
from django.core.exceptions import PermissionDenied
from topobank.manager.zip_model import ZipContainer
from topobank.testing.factories import SurfaceFactory, UserFactory
from topobank.testing.mock_auth.authorization.mo... | ContactEngineering/topobank | tests/manager/test_zip_model.py | .py | 7a8df020a655aaec | 7 | 9 |
from django.test import TestCase
from django.urls import reverse
from articles.models import Article
from faker import Faker
from datetime import timedelta
from main_app.tests.make_fakes import (
make_fake_user,
)
# run with `python -Wa manage.py test articles.tests.test_articles`
# the -Wa flag tells Python to d... | DDMAL/CantusDB | django/cantusdb_project/articles/tests/test_articles.py | .py | 18bf166241889e88 | 8.02 | 10 |
"""
A collection of functions for fetching data from
Cantus Index's (CI's) various APIs.
"""
import json
from typing import Optional, Union, Callable, TypedDict, Any
import requests
from requests.exceptions import SSLError, Timeout, HTTPError
from main_app.models import Genre
CANTUS_INDEX_DOMAIN: str = "https://can... | DDMAL/CantusDB | django/cantusdb_project/cantusindex.py | .py | 8697cadc08002527 | 7.52 | 10 |
"""
Utilities for parsing IIIF manifests and generating folio-to-image mappings.
Supports both IIIF Presentation API 2.x and 3.0 manifests.
"""
import csv
import io
import json
import re
import time
from dataclasses import dataclass
import requests
# A manifest is JSON metadata, not image data: the largest one we'v... | DDMAL/CantusDB | django/cantusdb_project/main_app/iiif_utils.py | .py | 66e580de7b0fc044 | 7.52 | 10 |
"""
This command is meant to be used one time toward solving issue
1542, assigning chants and sequences, where necessary, to their appropriate
"project".
This command assigns sequences to the Bower project. Chants
(in non-Bower sources) currently have
project.
Note: This command can only be run *after* the Bower proj... | DDMAL/CantusDB | django/cantusdb_project/main_app/management/commands/assign_sequences_to_bower_project.py | .py | 31ac96cde5e1271e | 7.52 | 10 |
"""Copy chants from student-work sources into the Kaiatonsera master source.
One-shot command for issue #2038. `--dry-run` previews counts and sanity
checks; the real run is guarded against drift, malformed folios, and slot
collisions before any write.
"""
import argparse
import re
from collections.abc import Callabl... | DDMAL/CantusDB | django/cantusdb_project/main_app/management/commands/copy_chants_to_master_source.py | .py | 54abc8ce4b316679 | 7.52 | 10 |
"""Full-service interface to converting, validating, and registering biological sequence variation."""
import datetime
import importlib.util
import logging
import os
import warnings
from collections.abc import Iterable
from urllib.parse import urlparse
from ga4gh.vrs import models as vrs_models
from anyvar.core impo... | biocommons/anyvar | src/anyvar/anyvar.py | .py | 9e61206d7ef94c5f | 7.63 | 17 |
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