text stringlengths 185 73.3k | repo stringlengths 7 100 | path stringlengths 4 146 | language stringclasses 7
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|---|---|---|---|---|---|---|
"""Tests for container scheduler"""
import os
import stat
import pytest # type: ignore
import shlex
import tempfile
from panpath import PanPath
from unittest.mock import patch, MagicMock
from xqute.defaults import JobStatus
from xqute.schedulers.container_scheduler import ContainerScheduler
@pytest.fixture(scope="... | pwwang/xqute | tests/test_container_scheduler.py | .py | ba3d1c49b7482704 | 7 | 9 |
"""Default settings and utilities for xqute
Attributes:
DEFAULT_WORKDIR_NAME: The default work directory name for jobs to save the metadata
DEFAULT_ERROR_STRATEGY: The default strategy when there is
error happened
DEFAULT_NUM_RETRIES: Default number of retries when
DEFAULT_ERROR_STRATEGY is... | pwwang/xqute | xqute/defaults.py | .py | 87c1732eeb139f34 | 7.5 | 9 |
"""Job to execute"""
from __future__ import annotations
import shlex
from typing import Any, Tuple
from .defaults import JobStatus
from .utils import logger, CommandType
from .path import SpecPath
class Job:
"""The class for job
Attributes:
cmd: The command
index: The index of the job
... | pwwang/xqute | xqute/job.py | .py | 42e4981471efc443 | 7.5 | 9 |
"""The scheduler to run jobs via containers"""
from __future__ import annotations
import asyncio
import os
import shlex
import shutil
from pathlib import Path
from typing import List, Sequence
from ..job import Job
from ..path import SpecPath
from ..defaults import DEFAULT_WORKDIR_NAME, JOBCMD_WRAPPER_LANG
from .loc... | pwwang/xqute | xqute/schedulers/container_scheduler.py | .py | 410414418456f282 | 7.5 | 9 |
"""The scheduler to run jobs locally"""
import asyncio
import os
import shlex
from ..defaults import JobStatus
from ..job import Job
from ..scheduler import Scheduler
def _pid_exists(pid: int) -> bool:
"""Check if a process with a given pid exists"""
try:
os.kill(pid, 0)
except Exception: # pra... | pwwang/xqute | xqute/schedulers/local_scheduler.py | .py | 70cff3432b26e92a | 7.5 | 9 |
"""The scheduler to run jobs on SGE"""
import asyncio
import hashlib
from ..job import Job
from ..scheduler import Scheduler
class SgeScheduler(Scheduler):
"""The sge scheduler
Attributes:
name: The name of the scheduler
job_class: The job class
Args:
qsub: path to qsub command... | pwwang/xqute | xqute/schedulers/sge_scheduler.py | .py | baff02cb5529a3cd | 7.5 | 9 |
"""The scheduler to run jobs on Slurm"""
import asyncio
import hashlib
from ..job import Job
from ..scheduler import Scheduler
class SlurmScheduler(Scheduler):
"""The Slurm scheduler
Attributes:
name: The name of the scheduler
job_class: The job class
Args:
sbatch: path to sbat... | pwwang/xqute | xqute/schedulers/slurm_scheduler.py | .py | 79a435bb77c5943c | 7.5 | 9 |
"""The scheduler to run jobs on SSH"""
from __future__ import annotations
import asyncio
import shlex
from panpath import CloudPath
from ...schedulers.local_scheduler import LocalScheduler
from ...job import Job
from ...defaults import SLEEP_INTERVAL_CLOUD_FILE_CHECK
from ...utils import logger
from .client import... | pwwang/xqute | xqute/schedulers/ssh_scheduler/scheduler.py | .py | b3bdbfe3622053d0 | 7.5 | 9 |
"""The xqute module"""
from __future__ import annotations
import asyncio
import functools
import signal
from collections import deque
from typing import TYPE_CHECKING, Any, List, Mapping, Type
from .defaults import (
DEFAULT_WORKDIR_NAME,
DEFAULT_ERROR_STRATEGY,
DEFAULT_NUM_RETRIES,
DEFAULT_SCHEDULER... | pwwang/xqute | xqute/xqute.py | .py | 126eed84bc42fd38 | 7.5 | 9 |
import click
import shortuuid
import datetime
import subprocess
from enum import Enum
from psycopg2 import sql
from psycopg2.extras import execute_values
from app import db
from app import get_db_cursor
from saved_scenario import SavedScenario
from saved_scenario import save_raw_scenario_to_db
from util import safe_co... | ourresearch/jump-api | create_consortial_package.py | .py | db43bc61c047d6d1 | 7.63 | 17 |
# coding: utf-8
import click
from admin_actions import add_institution, add_ror, add_user
@click.group()
def cli():
"""
Create institutions, users and add ROR IDs.
Note: Quotes are required around any flag inputs with spaces.
Examples:
python init.py --help
python init.py inst --help
python init.py inst... | ourresearch/jump-api | init.py | .py | 39d4b2a8def9df03 | 7.63 | 17 |
import os
import ast
import json
from datetime import datetime
from datetime import date
from kids.cache import cache
import click
import requests
import pandas as pd
import gspread
# intercom API details
intercom_base = "https://api.intercom.io"
key = os.getenv("INTERCOM_API_KEY")
auth = {"Authorization": "Bearer "... | ourresearch/jump-api | intercom_drip.py | .py | 730e1c8aa7eb3ea8 | 7.63 | 17 |
#!/usr/bin/env python
"""Wrapper for Django's command-line utility for administrative tasks."""
import os
import sys
import logging
from time import sleep
try:
from django.db.migrations.executor import MigrationExecutor
from django.db.utils import ConnectionHandler, DEFAULT_DB_ALIAS
except ImportError as exc:
... | WikipediaLibrary/externallinks | django_wait_for_migrations.py | .py | b0e96e1745680628 | 7.54 | 11 |
from typing import Type
from django.db import models
from extlinks.aggregates.management.helpers import AggregateArchiveCommand
from extlinks.aggregates.models import LinkAggregate
class Command(AggregateArchiveCommand):
"""
This command archives data from the 'aggregates_linkaggregate' table.
"""
he... | WikipediaLibrary/externallinks | extlinks/aggregates/management/commands/archive_link_aggregates.py | .py | daa6acdd467bba5e | 7.04 | 11 |
from typing import Type
from django.db import models
from extlinks.aggregates.management.helpers import AggregateArchiveCommand
from extlinks.aggregates.models import PageProjectAggregate
class Command(AggregateArchiveCommand):
"""
This command archives data from the 'aggregates_pageprojectaggregate' table.
... | WikipediaLibrary/externallinks | extlinks/aggregates/management/commands/archive_pageproject_aggregates.py | .py | ed309256c8acd0fd | 7.54 | 11 |
from typing import Type
from django.db import models
from extlinks.aggregates.management.helpers import AggregateArchiveCommand
from extlinks.aggregates.models import UserAggregate
class Command(AggregateArchiveCommand):
"""
This command archives data from the 'aggregates_useraggregate' table.
"""
he... | WikipediaLibrary/externallinks | extlinks/aggregates/management/commands/archive_user_aggregates.py | .py | 944e2762d4bc2c82 | 7.04 | 11 |
from datetime import date, timedelta, datetime
from extlinks.common.management.commands import BaseCommand
from django.core.management.base import CommandError
from django.db import transaction, close_old_connections
from django.db.models import Count, Q
from django.db.models.functions import Cast
from django.db.model... | WikipediaLibrary/externallinks | extlinks/aggregates/management/commands/fill_link_aggregates.py | .py | 3a99476e6d92e68b | 7.54 | 11 |
from datetime import date, timedelta, datetime
import logging
from extlinks.common.management.commands import BaseCommand
from django.core.management.base import CommandError
from django.db import transaction, close_old_connections
from django.db.models import Count, Q
from django.db.models.functions import Cast
from ... | WikipediaLibrary/externallinks | extlinks/aggregates/management/commands/fill_pageproject_aggregates.py | .py | abc4f8989d9ce0f5 | 7.54 | 11 |
import calendar, datetime, logging
from typing import Any, Dict, List, Optional, Tuple
from dateutil.relativedelta import relativedelta
from django.core.management.base import CommandError, CommandParser
from django.db.models.aggregates import Sum
from django.db.models.expressions import F
from extlinks.aggregates.m... | WikipediaLibrary/externallinks | extlinks/aggregates/management/commands/fill_top_organisations_totals.py | .py | 19782d2f80f22894 | 7.54 | 11 |
import calendar, datetime, logging
from typing import Any, Dict, List, Optional, Tuple
from dateutil.relativedelta import relativedelta
from django.core.management.base import CommandError, CommandParser
from django.db.models.aggregates import Sum
from django.db.models.expressions import F
from extlinks.aggregates.m... | WikipediaLibrary/externallinks | extlinks/aggregates/management/commands/fill_top_projects_totals.py | .py | defa6075b5cbe2a9 | 7.54 | 11 |
import calendar, datetime, logging
from typing import Any, Dict, List, Optional, Tuple
from dateutil.relativedelta import relativedelta
from django.core.management.base import CommandError, CommandParser
from django.db.models.aggregates import Sum
from django.db.models.expressions import F
from extlinks.aggregates.m... | WikipediaLibrary/externallinks | extlinks/aggregates/management/commands/fill_top_users_totals.py | .py | f51286987e633137 | 7.54 | 11 |
from datetime import date, timedelta, datetime
from extlinks.common.management.commands import BaseCommand
from django.core.management.base import CommandError
from django.db import transaction, close_old_connections
from django.db.models import Count, Q
from django.db.models.functions import Cast
from django.db.model... | WikipediaLibrary/externallinks | extlinks/aggregates/management/commands/fill_user_aggregates.py | .py | eef957b9ad50a6be | 7.54 | 11 |
import datetime
import gzip
import logging
import os
from abc import ABC, abstractmethod
from collections import defaultdict
from dateutil.relativedelta import relativedelta
from typing import List, Optional, Type, cast
from django.core import serializers
from django.core.management import call_command
from django.co... | WikipediaLibrary/externallinks | extlinks/aggregates/management/helpers/aggregate_archive_command.py | .py | 53ec0bd0044fb613 | 7.54 | 11 |
import datetime
import gzip
import itertools
import json
import logging
import os
import re
from typing import Callable, Dict, Hashable, Iterable, List, Optional, Set
from django.core.cache import cache
from django.db.models import Q
from extlinks.common.helpers import extract_queryset_filter
from extlinks.common.sw... | WikipediaLibrary/externallinks | extlinks/aggregates/storage.py | .py | ff9ef43666c70510 | 7.54 | 11 |
import calendar
from datetime import date, timedelta
from itertools import islice
from typing import Any, Dict
from django.db.models import Avg, Q
from django.db.models.functions import TruncMonth
from logging import getLogger
logger = getLogger("django")
def get_month_average(average_data, check_date):
for av... | WikipediaLibrary/externallinks | extlinks/common/helpers.py | .py | 76b912c5c26d38a8 | 7.54 | 11 |
from django.core.management.base import BaseCommand as DjangoBaseCommand
from filelock import FileLock
import inspect
import logging
from os import remove
from os.path import basename
import sys
from tenacity import Retrying, stop_after_attempt, wait_exponential
logger = logging.getLogger("django")
class BaseCommand... | WikipediaLibrary/externallinks | extlinks/common/management/commands/__init__.py | .py | fc1ba0f246b693f6 | 7.54 | 11 |
import logging
import json
from functools import lru_cache
import getpass
import platform
from yasf import sf_separate
log = logging.getLogger(__name__)
@lru_cache()
def get_user_name() -> str:
return getpass.getuser()
@lru_cache()
def get_computer_name() -> str:
return platform.node()
try:
# user m... | jamesabel/balsa | balsa/aws_cloudwatch_logs.py | .py | 8dcfa80dbd7c9ebc | 7.42 | 6 |
from typing import Union
from datetime import datetime
from logging import Formatter, LogRecord
class BalsaFormatter(Formatter):
"""
Format time in ISO 8601
"""
def formatTime(self, record: LogRecord, datefmt: Union[str, None] = None) -> str:
if datefmt is not None:
# an explicit ... | jamesabel/balsa | balsa/formatter.py | .py | 98fc8c2b0e720f2a | 7.42 | 6 |
import time
import logging
import os
import threading
from tobool import to_bool_strict
from . import __application_name__
use_mttkinter = to_bool_strict(os.environ.get(f"{__application_name__}_USE_MTTKINTER", True)) # in case the user doesn't want to use mttkinter (multi-threaded tkinter)
mttkinter_imported = Fal... | jamesabel/balsa | balsa/guihandler.py | .py | 6dc4af0812c52728 | 7.42 | 6 |
from enum import Enum
import logging
class HandlerType(Enum):
Console = 1
File = 2
DialogBox = 3
Callback = 4
Sentry = 5
StringList = 6
AWSCloudWatch = 7
class BalsaNullHandler(logging.NullHandler):
"""
Hook in a callback function. For example, this can be used to set the proces... | jamesabel/balsa | balsa/handlers.py | .py | 29bf5d9ba7a8cca4 | 7.42 | 6 |
from datetime import datetime
import re
import logging
import json
from logging import getLogger
from yasf import structured_sentinel
import dateutil.parser
from balsa.__version__ import __application_name__
log = getLogger(__application_name__)
# timestamp - name - [processName -] fileName - lineNumber - function... | jamesabel/balsa | balsa/structured.py | .py | 3a71078d70715c04 | 7.42 | 6 |
from typing import List
import win32gui
def _dialog_enum_callback(hwnd: int, dialogs: List[int]) -> None:
"""
Callback used by EnumWindows. Checks if the given window is a visible
dialog (#32770) and contains an "OK" button among its children.
"""
if win32gui.IsWindowVisible(hwnd):
class_n... | jamesabel/balsa | test_balsa/popup_window.py | .py | 99792f67773b2e04 | 7.92 | 6 |
from pathlib import Path
import logging
import time
import pyautogui
import pytest
from balsa import Balsa, __author__
from .popup_window import is_popup_dialog_with_ok
# The fail-safe aborts pyautogui calls when the mouse is in a screen corner - where users naturally park the cursor while GUI tests run.
# These te... | jamesabel/balsa | test_balsa/tst_balsa.py | .py | aab31a6a01472f57 | 7.92 | 6 |
#!/usr/bin/env python
'''Extract a knowledge graph from a long public-domain book with a *local* LLM.
Companion code for "Building and working knowledge graphs with Onya and LLMs". This is the woven,
runnable version of the fragments in the "Setup", "Steering without a sampler", "Chunking", and
"Checkpoint it" section... | uogbuji/techwriting | loom-deeptech/onya-kg-llm-analysis/equiano_extract.py | .py | 420dc1aa9cd2c1aa | 7.54 | 11 |
#!/usr/bin/env python
'''Download and pre-process *The Interesting Narrative of the Life of Olaudah Equiano* (1789) into a
clean plain-text file the assessment harness (and the article) can reuse without re-fetching.
Preprocessing:
- strip the Project Gutenberg license header/footer
- trim the book's own front mat... | uogbuji/techwriting | loom-deeptech/onya-kg-llm-analysis/model_assessment/fetch_equiano.py | .py | a59ab8ab2aea741b | 7.54 | 11 |
'''WordLoom prompt loading for the assessment harness.
Prompts live in loom TOML files beside this module (`prompts/*.loom.toml`), never inline in Python —
so they can be reviewed, diffed, and swapped without touching code, and prompt experiments can be kept
as separate files on disk. See https://github.com/OoriData/W... | uogbuji/techwriting | loom-deeptech/onya-kg-llm-analysis/model_assessment/prompts/__init__.py | .py | b459ec9be365b013 | 7.54 | 11 |
'''WordLoom prompt loading for the extraction pipeline.
Prompts live in loom TOML files beside this module (`prompts/*.loom.toml`), never inline in Python —
so they can be reviewed, diffed, and swapped without touching code, and prompt experiments can be kept
as separate files on disk. See https://github.com/OoriData/... | uogbuji/techwriting | loom-deeptech/onya-kg-llm-analysis/prompts/__init__.py | .py | 9ad5811f601af1b8 | 7.54 | 11 |
import sys
import json
import string
import random
population = ' ' + string.ascii_lowercase
def preprocess_frequencies(frequencies, order):
'''Compile simple mapping from N-grams to frequencies into data structures to help compute
the probability of state transitions to complete an N-gram
Arguments:
... | uogbuji/techwriting | patternai/generate_letters_strategy1.py | .py | 413b6ed634b696b7 | 7.54 | 11 |
import sys
import json
import string
import random
POPULAR_NGRAM_COUNT = 10000
#Population is all the possible items that can be generated
population = ' ' + string.ascii_lowercase
def preprocess_frequencies(frequencies, order):
'''Compile simple mapping from N-grams to frequencies into data structures to help c... | uogbuji/techwriting | patternai/generate_letters_strategy2.py | .py | b9e78eaa5b6711dc | 7.54 | 11 |
import sys
import json
import string
import random
POPULAR_NGRAM_COUNT = 10000
def preprocess_frequencies(frequencies, order):
'''Compile simple mapping from N-grams to frequencies into data structures to help compute
the probability of state transitions to complete an N-gram
Arguments:
frequenc... | uogbuji/techwriting | patternai/generate_words.py | .py | 7a9e9bb3d31f0a0a | 7.54 | 11 |
import asyncio
import aiohttp
from urllib.parse import urlparse
#List of URLs to process
URLS = [
'http://web.textfiles.com/computers/macbeth95',
'https://www.gutenberg.org/files/1342/1342-0.txt', #Pride and Prejudice
'http://web.textfiles.com/humor/zenerror.txt',
'http://artscene.textfiles.com/history... | uogbuji/techwriting | presentation/iterator-workshop/s6_web_word_count_lab.py | .py | 799287e63045c58d | 7.54 | 11 |
"""A collection command line arguments."""
class Argument:
"""Just a wrapper around :meth:`argparse.ArgumentParser.add_argument`.
So, except the ``completer`` keyword argument all positional and keywork
arguments are the same as :meth:`argparse.ArgumentParser.add_argument`.
:param completer: see `ar... | pylover/easycli | easycli/argument.py | .py | de923aaf7eee3ee3 | 7.63 | 17 |
from abc import ABCMeta
from .argument import Argument
class Command(metaclass=ABCMeta):
"""Abstract base class for all commands."""
#: List of both :class:`.Command` class or instance of :class:`.Argument`
__arguments__ = []
#: str, command name
__command__ = None
#: List of aliases for t... | pylover/easycli | easycli/command.py | .py | cbacc8d32cb097d8 | 7.63 | 17 |
import sys
import argparse
from os import path
from .command import Command
class Root(Command):
"""base class for the CLI entry point.
.. code-block::
import sys
from easycli import Root, ...
class Git(Root):
__help__ = 'git help message'
__completion__ = True... | pylover/easycli | easycli/root.py | .py | dca938259204ae8a | 7.63 | 17 |
import logging
import random
import warnings
from multiprocessing import cpu_count
from typing import TYPE_CHECKING
import numpy as np
from numpy.typing import ArrayLike, NDArray
from ._ncollpyde import (
TriMeshWrapper,
_configure_threadpool,
_index,
_precision,
)
if TYPE_CHECKING:
import meshio... | clbarnes/ncollpyde | python/ncollpyde/main.py | .py | 0253798a97c5b48a | 7.56 | 12 |
from multiprocessing import cpu_count
import meshio
import numpy as np
import pytest
from ncollpyde import Volume
SAMPLES_PER_DIM = 10
PADDING = 0.2
ITERATIONS = 20
CPU_COUNT = cpu_count()
CONTAINS_SERIAL = "containment serial"
INTERSECTION_SERIAL = "intersection serial"
CONTAINS_PARALLEL = "containment parallel"
IN... | clbarnes/ncollpyde | tests/test_bench.py | .py | eaa1cd33b7191d24 | 8.06 | 12 |
#!/usr/bin/env python3
"""Test label filtering functionality with pytest."""
import pytest
from content_resolver.config_manager import ConfigManager
def create_test_settings(labels_filter=None):
"""Create test settings for ConfigManager."""
return {
"configs": "test_configs",
"output": "outpu... | fedora-eln/content-resolver | test_label_filtering.py | .py | dfe7e4e5de61d520 | 7.98 | 8 |
'''
Default logger is a bit meh, see 'test'/run this file for a demo
TODO name 'klogging' to avoid possible conflict with default 'logging' module
TODO shit. too late already? maybe use fallback & deprecate
'''
def test() -> None:
import logging
import sys
from collections.abc import Callable
M: Call... | karlicoss/bleanser | src/bleanser/core/ext/logging.py | .py | e4ee95173f567c92 | 7.6 | 15 |
from collections.abc import Iterator
from contextlib import contextmanager
from pathlib import Path
from typing import Any
from bleanser.core.processor import (
BaseNormaliser,
Normalised,
sort_file,
unique_file_in_tempdir,
)
class ExtractObjectsNormaliser(BaseNormaliser):
"""
This is meant t... | karlicoss/bleanser | src/bleanser/core/modules/extract.py | .py | b9cb7219a2fb1dfd | 7.6 | 15 |
from collections.abc import Iterator
from contextlib import contextmanager
from pathlib import Path
import orjson
from bleanser.core.processor import (
BaseNormaliser,
Normalised,
sort_file,
unique_file_in_tempdir,
)
# imports for convenience -- they are used in other modules
from bleanser.core.utils... | karlicoss/bleanser | src/bleanser/core/modules/json.py | .py | dcd6a13a4ba5d370 | 7.6 | 15 |
"""
Helpers for processing sqlite databases
"""
from __future__ import annotations
import re
import shutil
import sqlite3
import subprocess
from collections.abc import Iterator, Sequence
from contextlib import closing, contextmanager
from pathlib import Path
from sqlite3 import Connection
from typing import Literal
... | karlicoss/bleanser | src/bleanser/core/modules/sqlite.py | .py | 5d453a26df79f628 | 7.6 | 15 |
from __future__ import annotations
import hashlib
from pathlib import Path
import more_itertools
import pytest
from ....tests.common import TESTDATA, actions, skip_if_no_data
from ..binary import BinaryNormaliser
def via_md5(path: Path) -> list[Path]:
files = sorted(path.iterdir())
def _file_hash(p: Path)... | karlicoss/bleanser | src/bleanser/core/modules/tests/binary.py | .py | a83e518ae2e8b115 | 7.1 | 15 |
from __future__ import annotations
import sqlite3
from pathlib import Path
from typing import Any
import pytest
from ...common import Keep, Prune
from ...processor import compute_groups, compute_instructions, groups_to_instructions
from ..sqlite import SqliteNormaliser, _checked_db, _postprocess_dump_hex, _postproce... | karlicoss/bleanser | src/bleanser/core/modules/tests/sqlite.py | .py | a17917928b22762b | 8.1 | 15 |
"""Property-based checks for FileSet's line-set algebra."""
from __future__ import annotations
from contextlib import ExitStack
from pathlib import Path
from tempfile import TemporaryDirectory
from hypothesis import example, given, settings
from hypothesis import strategies as st
from ..processor import FileSet
# ... | karlicoss/bleanser | src/bleanser/core/tests/fileset_properties.py | .py | 64ba869e8b5107cb | 8.1 | 15 |
from collections.abc import Iterator, Sequence
from contextlib import contextmanager
from pathlib import Path
import pytest
from ..common import Group, Keep, Prune
from ..processor import BaseNormaliser, FileSet, Normalised, compute_groups, groups_to_instructions
from ..utils import total_dir_size
def test_fileset(... | karlicoss/bleanser | src/bleanser/core/tests/processor.py | .py | 45d0746f76ada285 | 8.1 | 15 |
"""
Property-based tests for the pruning algorithm in bleanser.core.processor.
model_keep is a small reference implementation of the current grouping semantics, operating directly on sets.
Hypothesis generates synthetic export histories and materialises them as files.
The real compute_instructions, FileSet, sort, diff... | karlicoss/bleanser | src/bleanser/core/tests/processor_properties.py | .py | 69d1bdce0b668580 | 8.1 | 15 |
"""Safety assertions shared by serial and process-pool processor properties."""
from __future__ import annotations
from collections.abc import Sequence
from pathlib import Path
from ..common import Instruction, Keep, Prune
from ..processor import assert_instruction_structure
# One snapshot is the set of lines in it... | karlicoss/bleanser | src/bleanser/core/tests/processor_property_checks.py | .py | 406a98b46907e2a5 | 7.1 | 15 |
"""Property tests for source-file and process-pool safety guarantees."""
from __future__ import annotations
from collections.abc import Iterator
from contextlib import contextmanager
from pathlib import Path
from tempfile import TemporaryDirectory
import pytest
from hypothesis import example, given, settings
from hy... | karlicoss/bleanser | src/bleanser/core/tests/processor_safety_properties.py | .py | df084614cb68febb | 8.1 | 15 |
import logging
import os
import sys
from logging.handlers import TimedRotatingFileHandler
from pathlib import Path
from . import assets, events, replication, time_series
from ._version import __version__
def configure_logger(log_level: str = "INFO", log_path: Path = None) -> None:
"""Configure the logging to std... | cognitedata/cognite-replicator | cognite/replicator/__init__.py | .py | 5682fea45fc9ba9d | 7.45 | 7 |
#!/usr/bin/env python3
DESC="""
This script converts filter data from the older CSV format into
the YAML format used by the newer camera parameter system. The CSV data
itself may have been generated from a Markdown table by genfilters.py,
but should consist of name,position,cwl,fwhm,transmission (in any order).
"""
i... | AU-ExoMars/PCOT | cameras/convert_from_csv.py | .py | 22928ef11a64a12e | 7.42 | 6 |
from typing import Union
from pathlib import Path
import numpy as np
from pds4_tools.reader.general_objects import StructureList
from pds4_tools.reader.table_objects import TableStructure
class MultiData:
"""Provide access to a list's given structure's data via index key notation."""
def __init__(self, struc... | AU-ExoMars/PCOT | dist/proctools/src/proctools/products/adapters.py | .py | 3750908193cc21a8 | 7.42 | 6 |
import logging
from pathlib import Path
from typing import ClassVar, Dict, Optional, Union
import pds4_tools
from lxml import etree
from passthrough import Template
from pds4_tools.reader.general_objects import StructureList
from pds4_tools.reader.label_objects import Label
class LabelMeta:
"""Single-layer XML e... | AU-ExoMars/PCOT | dist/proctools/src/proctools/products/dataproduct.py | .py | 59ac671d40adb902 | 7.42 | 6 |
import logging
from pathlib import Path
from typing import List, Optional, Union
from xml.parsers.expat import ExpatError
from . import DataProduct
class ProductLoader:
"""PDS4 product loader and manager.
This class keeps track of whether a loaded product has been requested (used). A
report of unused pr... | AU-ExoMars/PCOT | dist/proctools/src/proctools/products/loader.py | .py | 6aca90f3d2a5eb40 | 7.42 | 6 |
from passthrough.extensions.pt.datetime import PDSDatetime
class ApplicableCameraMixin:
"""Allow `DataProduct`s to evaluate applicability based on `psa:Sub-Instrument`.
Note: both products must be able to resolve the "camera" meta key, which is not
defined in DataProduct's base map (but is for instance m... | AU-ExoMars/PCOT | dist/proctools/src/proctools/products/mixins.py | .py | a1031b16368679d2 | 7.42 | 6 |
import hashlib
import numpy as np
from pathlib import Path
class BayerSlice:
"""The `BayerSlice` class carries `slice` attributes targeting individual Bayer
channels for a given pattern and (subframe) origin offset.
Attributes:
r: `slice` identifying red channel pixels
g1: `slice` identif... | AU-ExoMars/PCOT | dist/proctools/src/proctools/products/util.py | .py | 4b112fe173ddafba | 7.42 | 6 |
"""
A Markdown extension for rendering blocks delineated by
multiple @-signs as alerts. I'm not using exclamation marks
because the (not as good) admonishment extension uses those.
Format:
@@@ tag
DO NOT START WITH A BLANK LINE!!!!
some blocks of text which will have their markdown parsed
@@@
Tags are in classNameDi... | AU-ExoMars/PCOT | mkdocs/alert.py | .py | 46c51b68be078a40 | 7.42 | 6 |
"""
A Markdown extension which converts images into lightboxes. To use,
put an extra ! in front of the text description of an image:
becomes
This was adapted from https://github.com/g-provost/lightgallery-markdown
and some of the options don'... | AU-ExoMars/PCOT | mkdocs/lightbox.py | .py | 1d503dd385beac95 | 7.42 | 6 |
#!/usr/bin/env python
"""
This is an example script to show how you might possibly
arrange and collect flatfield files into groups for processing.
What we want to end up with is a directory of files for each filter which
we can process.
This script:
* Finds all image files
* Extracts their filter position a... | AU-ExoMars/PCOT | scripts/flatfield/collate_flats.py | .py | 32d16bd3d177546c | 7.42 | 6 |
import importlib
import os
import traceback
try:
import pcot.macros as macros
except AttributeError as e:
traceback.print_exc()
print("""
This error MAY mean that you should turn off Qt Compatible debugging in PyCharm. It's a bug
https://youtrack.jetbrains.com/issue/PY-50959
""")
exit(0)
i... | AU-ExoMars/PCOT | src/pcot/__init__.py | .py | 9458e902d07ff955 | 7.42 | 6 |
"""
This is the file which creates and runs the PCOT user interface
"""
import os
from pathlib import Path
from PySide2 import QtWidgets
from PySide2.QtCore import QCommandLineParser, QCommandLineOption
import logging
import os
import getpass
import sys
import pcot.config
import pcot.ui.mainwindow
from pcot.document ... | AU-ExoMars/PCOT | src/pcot/app.py | .py | 64a39c5f318c1143 | 7.42 | 6 |
"""
This package handles and contains assets, usually strings but some binaries.
"""
import importlib
import io
import pkgutil
from PySide2.QtGui import QIcon
def getAssetAsString(fn, package="pcot.assets"):
"""Find a file in the assets package and return its contents as a string, assuming it is utf-8 encoded"""... | AU-ExoMars/PCOT | src/pcot/assets/__init__.py | .py | ed77d6bfa86d388a | 7.42 | 6 |
"""
Contains types used in defining the target for calibration.
"""
from dataclasses import dataclass
from typing import Tuple
class Patch:
"""
Base class for patches
"""
pass
@dataclass
class CircularPatch(Patch):
x: float # x coordinate of centre in mm
y: float # y coordinate of centre in ... | AU-ExoMars/PCOT | src/pcot/calib/target.py | .py | 50c10063067a47d3 | 7.42 | 6 |
"""
This package deals with camera data: filters, flatfield data and so on.
It also deals with reflectance target data.
"""
import logging
import os.path
from pathlib import Path
from typing import Set, List
from pcot.cameras.reflectances import Reflectance
logger = logging.getLogger(__name__)
# dictionary of Camera... | AU-ExoMars/PCOT | src/pcot/cameras/__init__.py | .py | d6d3f8097c80e75b | 7.42 | 6 |
import csv
import math
import os.path
import warnings
from pathlib import Path
from typing import List, Optional
import numpy as np
from scipy.interpolate import RegularGridInterpolator
from skimage.data import camera
from pcot import ui
from pcot.cameras.filtresponse import FilterResponse
from pcot.documentsettings ... | AU-ExoMars/PCOT | src/pcot/cameras/filters.py | .py | 33714ef489eb1b64 | 7.42 | 6 |
"""Image normalisation stuff for canvases.
This takes an image and an RGB image and generates a normalised RGB image. It can't just produce
an RGB image because the incoming image might be "premapped" by another node.
It will also:
- only consider a rectangle of the image if required
- TODO ignore "bad" pixels... | AU-ExoMars/PCOT | src/pcot/canvasnormalise.py | .py | 304eb538441d866e | 7.42 | 6 |
"""
Configuration data system, also handles hooks for plugins
"""
import getpass
import logging
import os
from collections import deque
from pathlib import Path
from typing import Optional, List
import yaml
from PySide2 import QtWidgets
from pcot.parameters.taggedaggregates import TaggedDictType, Maybe, TaggedDict, T... | AU-ExoMars/PCOT | src/pcot/config.py | .py | 4dc1609571041e40 | 7.42 | 6 |
# pylint: disable=C0209
""" Upload new images to S3.
See requirements in imagesUpload.sh.
"""
import logging
import os
import time
import boto3
DATA_PATH = 'images_upload.txt'
IMAGES_FOLDER = '/mnt/volume_postgres/cards/English/'
LOG_PATH = 'images_upload.log'
LOG_LIMIT = 5000
S3_BUCKET = 'dragncards-lotrlcg'
S3_P... | seastan/lotr-lcg-set-generator | DragnCards/images_upload.py | .py | 30c57b819a0e1fa6 | 7.52 | 10 |
# pylint: disable=C0209
# -*- coding: utf8 -*-
""" Get aggregated statistics about player cards being playtested.
"""
from datetime import datetime
import logging
import os
import sys
import psycopg2
from psycopg2 import extras
DRAGNCARDS_USER = 'postgres'
DRAGNCARDS_PASSWORD = 'postgres'
DRAGNCARDS_HOST = '127.0.0.1... | seastan/lotr-lcg-set-generator | DragnCards/player_cards_stat.py | .py | e0118bb3b7f014d0 | 7.52 | 10 |
# pylint: disable=W0703,C0209
# -*- coding: utf8 -*-
""" Check redundant playtesting sets.
"""
from email.header import Header
import json
import logging
import os
import re
import time
import uuid
import yaml
from lotr import list_dragncards_files, run_cmd, UUID_REGEX
DATA_PATH = os.path.join('Data', 'check_playte... | seastan/lotr-lcg-set-generator | check_playtesting_sets.py | .py | bd12de94afcb0be5 | 8.02 | 10 |
# pylint: disable=C0209
""" Create mail file from the script arguments.
"""
from email.header import Header
import json
import os.path
import re
import sys
import time
import uuid
MAILS_PATH = 'mails'
def is_non_ascii(value):
""" Check whether the string is ASCII only or not.
"""
return not all(ord(c) < ... | seastan/lotr-lcg-set-generator | create_mail.py | .py | 6f0826104f998c8c | 7.52 | 10 |
# pylint: disable=C0209
# -*- coding: utf8 -*-
""" Download RingsDB statistics.
"""
from email.header import Header
import json
import logging
import os
import re
import time
import uuid
import requests
ERROR_SUBJECT_TEMPLATE = 'Download RingsDB Stat Cron ERROR: {}'
LOG_PATH = 'download_ringsdb_stat.log'
LOG_LEVEL =... | seastan/lotr-lcg-set-generator | download_ringsdb_stat.py | .py | 5daad4638612026e | 7.52 | 10 |
# pylint: disable=W0703,C0209
# -*- coding: utf8 -*-
""" Monitor uploading images to S3 on the DragnCards host.
"""
from email.header import Header
import json
import logging
import os
import re
import time
import uuid
import yaml
from lotr import monitor_images_upload
DISCORD_CONF_PATH = 'discord.yaml'
ALERT_SUBJE... | seastan/lotr-lcg-set-generator | monitor_images_upload.py | .py | 9964e80f9b1ea8f4 | 7.52 | 10 |
# pylint: disable=W0703,C0209
""" Monitor MakePlayingCards URL format.
"""
from email.header import Header
import json
import logging
import os
import re
import time
import uuid
import requests
ALERT_SUBJECT_TEMPLATE = 'MPC URL Format Monitor ALERT: {}'
ERROR_SUBJECT_TEMPLATE = 'MPC URL Format Monitor ERROR: {}'
LOG... | seastan/lotr-lcg-set-generator | monitor_mpc_url_format.py | .py | c52a164247492d9b | 7.52 | 10 |
# pylint: disable=W0703,C0209,C0301
""" Monitor remote pipeline.
"""
from email.header import Header
import hashlib
import json
import logging
import os
import re
import subprocess
import time
import uuid
import warnings
import requests
import yaml
import common
ALERT_SUBJECT_TEMPLATE = 'LotR Remote Pipeline Monito... | seastan/lotr-lcg-set-generator | monitor_remote_pipeline.py | .py | 822029b995c0ecb5 | 7.52 | 10 |
# pylint: disable=W0703,C0209
""" Monitor Wordpress web-site.
"""
from email.header import Header
import json
import logging
import os
import re
import time
import uuid
import warnings
import requests
ALERT_SUBJECT_TEMPLATE = 'LotR Wordpress Monitor ALERT: {}'
ERROR_SUBJECT_TEMPLATE = 'LotR Wordpress Monitor ERROR: ... | seastan/lotr-lcg-set-generator | monitor_wordpress_site.py | .py | 20e461959dc6e94b | 7.52 | 10 |
# pylint: disable=C0209
""" A wrapper around `run_after_se.py` for remote execution.
"""
import logging
import os
import uuid
import yaml
from lotr import CONFIGURATION_PATH, LOG_LIMIT
import run_after_se
LOG_FILE = 'run_after_se_remote.log'
def init_logging():
""" Init logging.
"""
with open(CONFIGUR... | seastan/lotr-lcg-set-generator | run_after_se_remote.py | .py | d4db4f167e994705 | 7.52 | 10 |
# pylint: disable=C0209
""" A wrapper around `run_before_se.py` for remote execution.
"""
import logging
import os
import time
import uuid
import yaml
from lotr import CONFIGURATION_PATH, LOG_LIMIT
import run_before_se
LOG_FILE = 'run_before_se_remote.log'
RETRY_SLEEP_TIME = 300
SANITY_CHECK_ERROR_SLEEP_TIME = 3600... | seastan/lotr-lcg-set-generator | run_before_se_remote.py | .py | 8558827ced09d62c | 7.52 | 10 |
"""
Base class for subcommands under ``reclib.run``.
"""
import argparse
class Subcommand:
"""
An abstract class representing subcommands for reclib.run.
If you wanted to (for example) create your own custom `special-evaluate` command to use like
``reclib special-evaluate ...``
you would create ... | p-null/reclib | reclib/commands/subcommand.py | .py | eb1a72b87b28a538 | 7.45 | 7 |
"""
Utilities for working with the local dataset cache.
"""
import json
import logging
import os
import shutil
import tempfile
from functools import wraps
from hashlib import sha256
from pathlib import Path
from typing import Optional, Tuple, Union, IO, Callable, Set
from urllib.parse import urlparse
import boto3
imp... | p-null/reclib | reclib/common/file_utils.py | .py | 22c02cdc66fca6cb | 7.45 | 7 |
"""
A logger that maintains logs of both stdout and stderr when models are run.
"""
import os
from typing import TextIO
def replace_cr_with_newline(message: str):
"""
TQDM and requests use carriage returns to get the training line to update for each batch
without adding more lines to the terminal output.... | p-null/reclib | reclib/common/tee_logger.py | .py | ad4c32ef6db52199 | 7.45 | 7 |
# pylint: disable=invalid-name,protected-access
import logging
import os
import pathlib
import shutil
import tempfile
from unittest import TestCase
from reclib.common.checks import log_pytorch_version_info
TEST_DIR = tempfile.mkdtemp(prefix="reclib_tests")
class RecLibTestCase(TestCase): # pylint: disable=too-many... | p-null/reclib | reclib/common/testing/test_case.py | .py | c06cae9ca825b2d5 | 7.95 | 7 |
"""
:class:`~reclib.common.tqdm.Tqdm` wraps tqdm so we can add configurable
global defaults for certain tqdm parameters.
"""
from tqdm import tqdm as _tqdm
# This is neccesary to stop tqdm from hanging
# when exceptions are raised inside iterators.
# It should have been fixed in 4.2.1, but it still
# occurs.
# TODO(M... | p-null/reclib | reclib/common/tqdm.py | .py | dbc54b28276ca0ff | 7.45 | 7 |
"""
Various utilities that don't fit anwhere else.
"""
import importlib
import json
import logging
import os
import pkgutil
import random
import subprocess
import sys
from itertools import zip_longest, islice
from typing import Any, Callable, Dict, List, Tuple, TypeVar, Iterable, Iterator
try:
import resource
exce... | p-null/reclib | reclib/common/util.py | .py | 63dc066304f5adbb | 7.45 | 7 |
"""
A :class:`~Batch` represents a collection of ``Instance`` s to be fed
through a model.
"""
import logging
from collections import defaultdict
from typing import Dict, List, Union, Iterator, Iterable
import numpy
import torch
from reclib.common.checks import ConfigurationError
from reclib.common.util import ensur... | p-null/reclib | reclib/data/dataset.py | .py | 93f58411d1701436 | 7.45 | 7 |
import numpy as np
import pandas as pd
import torch.utils.data
class MovieLens20MDataset(torch.utils.data.Dataset):
"""
MovieLens 20M Dataset
Data preparation
treat samples with a rating less than 3 as negative samples
Parameters
----------
dataset_path: ``string``
MovieLens ... | p-null/reclib | reclib/data/dataset_readers/movielens.py | .py | 86f74ab35043febd | 7.45 | 7 |
from typing import Dict, Generic, TypeVar
import torch
DataArray = TypeVar("DataArray", torch.Tensor, Dict[str, torch.Tensor])
class Field(Generic[DataArray]):
"""
A ``Field`` is some piece of a data instance that ends up as an tensor in a model (either as an
input or an output). Data instances are jus... | p-null/reclib | reclib/data/fields/field.py | .py | 03e689de0f7a1ccd | 7.45 | 7 |
from typing import Dict, MutableMapping, Mapping
from reclib.data.fields.field import Field
class Instance(Mapping[str, Field]):
"""
An ``Instance`` is a collection of :class:`~reclib.data.fields.field.Field` objects,
specifying the inputs and outputs to some model.
We don't make a distinction betwee... | p-null/reclib | reclib/data/instance.py | .py | 58d9482c1ca4915b | 7.45 | 7 |
import logging
from typing import Dict, Union
import torch
from torch.utils.data import DataLoader
from reclib.data.dataset import Batch
from reclib.data.fields import MetadataField
logger = logging.getLogger(__name__)
TensorDict = Dict[str, Union[torch.Tensor, Dict[str, torch.Tensor]]]
def add_epoch_number(batch... | p-null/reclib | reclib/data/iterators/data_iterator.py | .py | a46ffce92751d2b2 | 7.45 | 7 |
"""
Helper functions for archiving models and restoring archived models.
"""
import atexit
import json
import logging
import os
import shutil
import tarfile
import tempfile
from typing import NamedTuple, Dict, Any
from torch.nn import Module
from reclib.common.checks import ConfigurationError
from reclib.common.file... | p-null/reclib | reclib/models/archival.py | .py | bc19b6d75f85ffa6 | 7.45 | 7 |
import torch
from reclib.modules import AttentionalFactorizationLayer
from reclib.modules.embedders import LinearEmbedder, Embedding
class AttentionalFactorizationMachine(torch.nn.Module):
"""
This implements Attentional Factorization Machine from
'"Attentional Factorization Machines: Learning the Weight... | p-null/reclib | reclib/models/attentional_factorization_machine.py | .py | d6c29a42b8908b09 | 7.45 | 7 |
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