text stringlengths 185 73.3k | repo stringlengths 7 100 | path stringlengths 4 146 | language stringclasses 7
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"""
A set of constants used within the glambie software
"""
from enum import Enum
DENSITY_OF_WATER_KG_PER_M3 = 997
DENSITY_OF_ICE_KG_PER_M3 = 850 # Huss et al. (2013)
OCEAN_AREA_IN_KM2 = 3.625e8 # Cogley et al. (2012)
# Ratio of relative error for seasonal correction. for more info see the GlaMBIE Assessment Algori... | earthwave/glambie | glambie/const/constants.py | .py | 6e523088a3916f1b | 7.52 | 10 |
"""
Interface to the GlaMBIE data submission system.
The submission system standardises the data recieved by GlaMBIE in
a number of different ways and presents the output within a Google Bucket.
This module provides access functions for that bucket.
"""
from io import BytesIO
import json
import os
import re
from typ... | earthwave/glambie | glambie/data/submission_system_interface.py | .py | 5979d836abfd94f4 | 7.52 | 10 |
import numpy as np
import pandas as pd
import matplotlib as mpl
import matplotlib.pyplot as plt
from glambie.util.timeseries_helpers import resample_1d_array, timeseries_as_months
from glambie.data.timeseries import Timeseries
"""
Handy functions to help making plots
"""
COLOURS = ["red", "blue", "gold", "green", "or... | earthwave/glambie | glambie/plot/plot_helpers.py | .py | 453edd5d9690e9be | 7.52 | 10 |
import logging
from glambie.config.config_classes import GlambieRunConfig
from glambie.data.data_catalogue import DataCatalogue
from glambie.processing.process_regional_results import (
run_one_region,
combine_within_one_region,
)
from glambie.processing.process_regional_results import (
convert_and_save_on... | earthwave/glambie | glambie/processing/main.py | .py | 02a7f40a40591dc0 | 7.52 | 10 |
import logging
from glambie.config.config_classes import GlambieRunConfig
from glambie.const.regions import REGIONS
from glambie.data.data_catalogue import DataCatalogue
from glambie.data.timeseries import Timeseries, TimeseriesData
from glambie.const.constants import YearType
from glambie.processing.path_handling impo... | earthwave/glambie | glambie/processing/process_global_results.py | .py | 1a385c15d8a95b07 | 7.52 | 10 |
from datetime import datetime
from datetime import timedelta
import numpy as np
import pandas as pd
import math
def fractional_years_to_datetime_dates(fractional_year_list: list) -> list:
"""Function to convert a list of fractional years to datetime dates
Parameters
----------
fractional_year_list : ... | earthwave/glambie | glambie/util/date_helpers.py | .py | 85f78b3cfd523b26 | 7.52 | 10 |
import warnings
import numpy as np
import pandas as pd
def calibrate_timeseries_with_trends(
trends: pd.DataFrame, calibration_timeseries: pd.DataFrame
):
"""
This function calibrates a higher resolution calibration timeseries with the trends from a trend DataFrame.
The 'calibration_timeseries' is adj... | earthwave/glambie | glambie/util/timeseries_combination_helpers.py | .py | 2e30ae7b8f9a054b | 7.52 | 10 |
import os
from glambie.config.config_classes import GlambieRunConfig
from glambie.config.config_classes import RegionRunConfig
from glambie.const.constants import (
ExtractTrendsMethod,
YearType,
SeasonalCorrectionMethod,
)
from glambie.const.data_groups import GlambieDataGroup
import pytest
import yaml
... | earthwave/glambie | tests/config/test_config_classes.py | .py | a8e8c3710ac38058 | 7.02 | 10 |
from glambie.const.regions import REGIONS, REGIONS_BY_ID, REGIONS_BY_SHORT_NAME
import numpy as np
import pytest
def test_get_region_by_short_name():
region = REGIONS_BY_SHORT_NAME["ISL"]
assert region.name == "iceland"
def test_get_region_by_id():
region = REGIONS_BY_ID[6]
assert region.name == "ic... | earthwave/glambie | tests/const/test_regions.py | .py | 1ea98237c359256a | 7.02 | 10 |
import os
from unittest.mock import MagicMock
from google.cloud.storage import Blob
from google.cloud.storage import Client
import numpy as np
import pandas as pd
import pytest
from glambie.data.submission_cleaning_script import check_glambie_submission_for_errors
from glambie.data.submission_cleaning_script import d... | earthwave/glambie | tests/data/test_submission_cleaning_script.py | .py | a446e1dd8aab46c5 | 8.02 | 10 |
"""Methods for running the NHP model in a Docker container."""
import argparse
import logging
import uuid
from datetime import datetime
from nhp.docker.config import Config
from nhp.docker.run import RunWithAzureStorage, RunWithLocalStorage
from nhp.model.data import Local
from nhp.model.run import run_all
def pars... | The-Strategy-Unit/nhp_model | src/nhp/docker/__main__.py | .py | 6cfc70d3ea781713 | 7.64 | 18 |
"""config values for docker container."""
import os
import dotenv
class Config:
"""Configuration class for Docker container."""
def __init__(self):
"""Configuration settings for the Docker container."""
dotenv.load_dotenv()
self._app_version = os.environ.get("APP_VERSION", "dev")
... | The-Strategy-Unit/nhp_model | src/nhp/docker/config.py | .py | a9ad7f47105cee0f | 7.64 | 18 |
"""Run the model inside of the docker container."""
import gzip
import json
import logging
import os
import re
from pathlib import Path
from typing import Any, Callable
from uuid import UUID
import pandas as pd
from azure.data.tables import TableServiceClient, UpdateMode
from azure.identity import DefaultAzureCredent... | The-Strategy-Unit/nhp_model | src/nhp/docker/run.py | .py | e8e19ec0a82eb457 | 7.64 | 18 |
"""Functions to run the model.
This module allows you to run the various models. It allows you to run a single model run of one of
the different types of models for debugging purposes, or it allows you to run all of the models in
parallel saving the results to disk.
There are existing launch profiles for vscode that ... | The-Strategy-Unit/nhp_model | src/nhp/model/__main__.py | .py | efcda74e57630612 | 7.64 | 18 |
"""Accident and Emergency Module.
Implements the A&E model.
"""
from typing import Any, Callable, Tuple
import numpy as np
import pandas as pd
from nhp.model.data import Data
from nhp.model.model import Model
from nhp.model.model_iteration import ModelIteration
class AaEModel(Model):
"""Accident and Emergency... | The-Strategy-Unit/nhp_model | src/nhp/model/aae.py | .py | ce8f48cdd1da274c | 7.64 | 18 |
"""Inpatient Row Resampling.
Methods for handling row resampling
"""
from typing import TYPE_CHECKING
import numpy as np
import pandas as pd
if TYPE_CHECKING:
from nhp.model.model_iteration import ModelIteration
class ActivityResampling:
"""Activity Resampling.
Class for handling the activity resampl... | The-Strategy-Unit/nhp_model | src/nhp/model/activity_resampling.py | .py | bf6226d6e7e63fea | 7.64 | 18 |
"""Reference Data.
Any reference data needed for the model should be stored in this folder.
Helper methods for loading the reference data should be created here.
"""
import json
import pathlib
import pandas as pd
from metalog_jax.base import MetalogParameters
from metalog_jax.metalog import Metalog
def _ref_path(... | The-Strategy-Unit/nhp_model | src/nhp/model/data/reference/__init__.py | .py | 38e2c0a82507456c | 7.64 | 18 |
"""Helper methods for the model package."""
import json
import numpy as np
import pandas as pd
def inrange(value: float, low: float = 0, high: float = 1) -> float:
"""Force a value to be in the interval [low, high].
Args:
value: The value we want to constrain to the interval.
l... | The-Strategy-Unit/nhp_model | src/nhp/model/helpers.py | .py | 9ae56f045c30993a | 7.64 | 18 |
"""Inpatients Module.
Implements the inpatients model.
"""
from collections import defaultdict
from typing import Any, Callable, Self, cast
import numpy as np
import pandas as pd
from nhp.model.data import Data
from nhp.model.model import Model
from nhp.model.model_iteration import ModelIteration
class Inpatients... | The-Strategy-Unit/nhp_model | src/nhp/model/inpatients.py | .py | 05ea7b9e1836f8e5 | 7.64 | 18 |
"""Model Module.
Implements the generic class for all other model types. This should not be directly instantiated,
instead you should use one of the concrete classes (e.g. [`AaEModel`][nhp.model.aae.AaEModel],
[`InpatientsModel`][nhp.model.inpatients.InpatientsModel],
[`OutpatientsModel`][nhp.model.outpatients.Outpati... | The-Strategy-Unit/nhp_model | src/nhp/model/model.py | .py | 060931b5d041391e | 7.64 | 18 |
"""Model Iteration.
Provides a simple class which holds all of the data required for a model iteration
"""
from typing import TYPE_CHECKING
import numpy as np
import pandas as pd
from nhp.model.activity_resampling import ActivityResampling
ModelRunResult = dict[str, pd.Series]
if TYPE_CHECKING:
from nhp.model... | The-Strategy-Unit/nhp_model | src/nhp/model/model_iteration.py | .py | 2b9d61759a42f94d | 7.64 | 18 |
"""Outpatients Module.
Implements the Outpatients model.
"""
from typing import Any, Callable, Tuple
import numpy as np
import pandas as pd
from nhp.model.data import Data
from nhp.model.model import Model
from nhp.model.model_iteration import ModelIteration
class OutpatientsModel(Model):
"""Outpatients Model... | The-Strategy-Unit/nhp_model | src/nhp/model/outpatients.py | .py | 219ebcc75e55484d | 7.64 | 18 |
"""Methods to work with results of the model.
This module allows you to work with the results of the model. Namely, combining the monte-carlo runs
into a single panda's dataframe, and helping with saving the results files.
"""
import json
import logging
import os
from typing import Dict, List
import pandas as pd
fr... | The-Strategy-Unit/nhp_model | src/nhp/model/results.py | .py | c0afe90bba14f558 | 7.64 | 18 |
"""Run the model."""
import logging
import multiprocessing
import os
import time
from typing import Any, Callable, Tuple, Type
import pandas as pd
from tqdm.auto import tqdm as base_tqdm
from nhp.model.aae import AaEModel
from nhp.model.data import Data, Local
from nhp.model.health_status_adjustment import HealthSta... | The-Strategy-Unit/nhp_model | src/nhp/model/run.py | .py | 6a9bf7a8c8def755 | 7.64 | 18 |
"""Test single model runs for the NHP model."""
import pandas as pd
import pytest
from nhp.model import (
AaEModel,
HealthStatusAdjustmentInterpolated,
InpatientsModel,
Model,
ModelIteration,
OutpatientsModel,
load_sample_params,
)
from nhp.model.data import Local
from nhp.model.results im... | The-Strategy-Unit/nhp_model | tests/e2e/test_run_model_snapshot.py | .py | 838b45cf5f4468d7 | 8.14 | 18 |
"""Test params-sample."""
import pytest
from nhp.model.params import load_sample_params
@pytest.mark.integration
def test_sample_params_are_valid():
load_sample_params(dataset="dev", scenario="unit-test")
# assert: no exception raised
@pytest.mark.integration
def test_load_sample_params_validation_fails()... | The-Strategy-Unit/nhp_model | tests/integration/nhp/model/test_params_validation.py | .py | 7d783c628bca161e | 7.64 | 18 |
"""Test single model runs for the NHP model."""
import pytest
from nhp.model import (
AaEModel,
InpatientsModel,
ModelIteration,
OutpatientsModel,
load_sample_params,
)
from nhp.model.data import Local
@pytest.fixture(scope="session")
def model_single_run_results(data_dir):
params = load_sam... | The-Strategy-Unit/nhp_model | tests/integration/nhp/model/test_single_model_run.py | .py | 36febe57af310811 | 8.14 | 18 |
"""test docker run."""
import uuid
from datetime import datetime
from unittest.mock import Mock, patch
import pytest
from nhp.docker.__main__ import main, parse_args
@pytest.mark.unit
@pytest.mark.parametrize(
", ".join(
[
"args",
"expected_file",
"expected_model_run... | The-Strategy-Unit/nhp_model | tests/unit/nhp/docker/test___main__.py | .py | a099d0aa7fd0cb93 | 7.14 | 18 |
"""test docker run."""
import uuid
from unittest.mock import Mock, call, mock_open, patch
import pytest
from azure.data.tables import UpdateMode
from nhp.docker.run import RunWithAzureStorage, RunWithLocalStorage
# RunWithLocalStorage
@pytest.mark.unit
def test_RunWithLocalStorage(mocker):
# arrange
m = m... | The-Strategy-Unit/nhp_model | tests/unit/nhp/docker/test_run.py | .py | d292afb8895ff330 | 7.14 | 18 |
"""test nhp data (local)."""
from unittest.mock import call, mock_open, patch
import pandas as pd
import pytest
from nhp.model.data import Local
@pytest.mark.unit
def test_init_sets_values():
# arrange
# act
d = Local("data", 2019, "synthetic")
# assert
assert d._data_path == "data"
@pytest... | The-Strategy-Unit/nhp_model | tests/unit/nhp/model/data/test_local.py | .py | d42447b6153b5a43 | 7.14 | 18 |
"""test nhp data (reference)."""
from unittest.mock import call
import pytest
from nhp.model.data import reference
expected_hsa_variants = {"lle", "hle", "ppp"}
@pytest.mark.unit
def test_variants():
# arrange
# act
vl = reference.variant_lookup()
# assert
assert len(vl) == 17
assert set... | The-Strategy-Unit/nhp_model | tests/unit/nhp/model/data/test_reference.py | .py | 61a4d2b09eeac71f | 8.14 | 18 |
"""Test run_model.py."""
from unittest.mock import Mock, patch
import pytest
from nhp.model.__main__ import main
from nhp.model.aae import AaEModel
from nhp.model.inpatients import InpatientsModel
from nhp.model.outpatients import OutpatientsModel
@pytest.mark.unit
@pytest.mark.parametrize(
"acti... | The-Strategy-Unit/nhp_model | tests/unit/nhp/model/test__main__.py | .py | 2d2a04e5178a5798 | 7.14 | 18 |
"""Test a&e model."""
from unittest.mock import Mock, call, patch
import numpy as np
import pandas as pd
import pytest
from nhp.model.aae import AaEModel
# fixtures
@pytest.fixture
def mock_model():
"""Create a mock Model instance."""
with patch.object(AaEModel, "__init__", lambda s, p, d, h, r: None):
... | The-Strategy-Unit/nhp_model | tests/unit/nhp/model/test_aae.py | .py | 558218bef768225a | 8.14 | 18 |
"""test activity avoidance."""
from unittest.mock import Mock, patch
import numpy as np
import pandas as pd
import pytest
from nhp.model.activity_resampling import ActivityResampling
# fixtures
@pytest.fixture
def mock_activity_resampling():
"""Create a mock Model instance."""
with patch.obj... | The-Strategy-Unit/nhp_model | tests/unit/nhp/model/test_activity_resampling.py | .py | bb4c76c060f10266 | 7.14 | 18 |
"""Test health status adjustmente."""
from unittest.mock import Mock, patch
import numpy as np
import pandas as pd
import pytest
from nhp.model.health_status_adjustment import (
HealthStatusAdjustment,
HealthStatusAdjustmentGAM,
HealthStatusAdjustmentInterpolated,
)
# Health Status Adjustment
@pytest.... | The-Strategy-Unit/nhp_model | tests/unit/nhp/model/test_health_status_adjustment.py | .py | fe23b6597fb28b63 | 7.14 | 18 |
"""Test helper methods."""
from unittest.mock import Mock
import pytest
from nhp.model.helpers import inrange, rnorm
@pytest.mark.unit
@pytest.mark.parametrize("value, expected", [(-1.1, 0), (1.1, 1), (0, 0), (1, 1), (0.5, 0.5)])
def test_inrange(value, expected):
"""Test that the inrange function returns expe... | The-Strategy-Unit/nhp_model | tests/unit/nhp/model/test_helpers.py | .py | 7dddee5ede7a2dec | 8.14 | 18 |
"""Test inpatient efficiencies."""
from unittest.mock import Mock, patch
import numpy as np
import pandas as pd
import pytest
from nhp.model.inpatients import InpatientEfficiencies
@pytest.fixture
def mock_ipe():
"""Create a mock Model instance."""
with patch.object(InpatientEfficiencies, "__init__", lambd... | The-Strategy-Unit/nhp_model | tests/unit/nhp/model/test_inpatient_efficiencies.py | .py | f107187d0c1fa371 | 7.14 | 18 |
"""Test inpatients model."""
from unittest.mock import Mock, call, patch
import numpy as np
import pandas as pd
import pytest
from nhp.model.inpatients import InpatientsModel
# fixtures
@pytest.fixture
def mock_model():
"""Create a mock Model instance."""
with patch.object(InpatientsModel, "__init__", lamb... | The-Strategy-Unit/nhp_model | tests/unit/nhp/model/test_inpatients.py | .py | d0e991d3b48a5c75 | 7.14 | 18 |
"""Test run_model."""
from unittest.mock import Mock, patch
import numpy as np
import pandas as pd
import pytest
from nhp.model.model_iteration import ModelIteration
# fixtures
@pytest.fixture
def mock_model_iteration():
"""Create a mock Model instance."""
with patch.object(ModelIteration, "... | The-Strategy-Unit/nhp_model | tests/unit/nhp/model/test_model_iteration.py | .py | 31409be4d5b55a1a | 7.14 | 18 |
"""Test outpatients model."""
from unittest.mock import Mock, call, patch
import numpy as np
import pandas as pd
import pytest
from nhp.model.outpatients import OutpatientsModel
# fixtures
@pytest.fixture
def mock_model():
"""Create a mock Model instance."""
with patch.object(OutpatientsModel, "__init__", ... | The-Strategy-Unit/nhp_model | tests/unit/nhp/model/test_outpatients.py | .py | 0b8bf377ee0a122f | 8.14 | 18 |
"""Test params-sample."""
from unittest.mock import mock_open, patch
import pytest
from nhp.model.params import load_params, load_sample_params, validate_params
@pytest.mark.unit
def test_validate_params(mocker):
# arrange
m_validate = mocker.patch("jsonschema.validate")
m_json_load = mocker.patch("jso... | The-Strategy-Unit/nhp_model | tests/unit/nhp/model/test_params.py | .py | e48c6273183392ed | 7.14 | 18 |
"""Test results.py."""
from unittest.mock import Mock, call, mock_open, patch
import pandas as pd
import pytest
from nhp.model.results import (
_add_metadata_to_dataframe,
_check_for_duplicates,
_combine_model_results,
_complete_model_runs,
_patch_converted_sdec_activity,
_save_params_file,
... | The-Strategy-Unit/nhp_model | tests/unit/nhp/model/test_results.py | .py | 6f6060c4e3b1de35 | 7.14 | 18 |
"""Test run_model.py."""
from unittest.mock import Mock, call
import pandas as pd
import pytest
from nhp.model.aae import AaEModel
from nhp.model.data import Data
from nhp.model.inpatients import InpatientsModel
from nhp.model.outpatients import OutpatientsModel
from nhp.model.run import (
_run_model... | The-Strategy-Unit/nhp_model | tests/unit/nhp/model/test_run.py | .py | 5f5db6ef85070e0d | 7.14 | 18 |
"""sqlalchemy infrastructure serving this package (and other sqlalchemy applications)."""
from pathlib import Path
from typing import Optional, Type
from sqlalchemy.ext.asyncio import AsyncConnection, AsyncEngine, AsyncSession, create_async_engine
from sqlalchemy.ext.asyncio import async_sessionmaker as sessionmaker
... | aioqzone/QzEmoji | src/qzemoji/base.py | .py | 6968a4428201647c | 7.42 | 6 |
import re
import shutil
from pathlib import Path
from typing import Optional, Union
from aiofiles import open as aopen
from aiohttp import ClientSession as AsyncClient
from yarl import URL
from qzemoji.base import AsyncEngineFactory
from qzemoji.orm import EmojiTable
FALLBACK_DB = "https://github.com/aioqzone/QzEmoj... | aioqzone/QzEmoji | src/qzemoji/finddb.py | .py | 400967e79e3fa83d | 7.42 | 6 |
import re
from pathlib import Path
from typing import Optional, Union
from yarl import URL
import qzemoji as qe
def resolve(*, url: Union[URL, str, None] = None, tag: Optional[str] = None):
"""
The resolve function takes either a URL or a tag as an argument, and returns the emoji ID.
If the argument is... | aioqzone/QzEmoji | src/qzemoji/utils.py | .py | e675cc919b73a827 | 7.42 | 6 |
"""Shared pytest configuration.
Channels' ``RedisChannelLayer`` keeps a connection pool whose asyncio locks are
bound to the event loop of the first test that uses them; reusing it across the
fresh event loops that ``TransactionTestCase`` creates per test leads to
non-deterministic "bound to a different event loop" er... | d-party/backend | conftest.py | .py | 8ce31804c4dcacb5 | 7.95 | 7 |
"""django-unfold の管理画面ダッシュボード用コールバック。
``settings.UNFOLD`` の ``DASHBOARD_CALLBACK`` / ``ENVIRONMENT`` から参照される。
同時視聴サービスの状態を一目で把握できる KPI カードとリアクション内訳を、
トップページ（``admin:index``）へ差し込む。
"""
from __future__ import annotations
from django.conf import settings
from django.db.models import Count, Sum
from django.utils.timezon... | d-party/backend | d_party/dashboard.py | .py | f406eb1bfb9cf8bb | 7.45 | 7 |
from django.contrib import admin
from django.contrib.auth.admin import GroupAdmin as BaseGroupAdmin
from django.contrib.auth.admin import UserAdmin as BaseUserAdmin
from django.contrib.auth.models import Group, User
from django.utils.timezone import now
from django.utils.translation import gettext_lazy as _
from unfold... | d-party/backend | streamer/admin.py | .py | 66e93dc11e2d475d | 7.45 | 7 |
"""Transparent application-level encryption for model fields.
Replaces the unmaintained ``django-cryptography`` ``encrypt()`` wrapper with a
small, dependency-light ``EncryptedCharField`` built on top of the maintained
``cryptography`` package (Fernet / AES-128-CBC + HMAC).
The encryption key is derived from ``settin... | d-party/backend | streamer/fields.py | .py | 57f2e4e36af12f0e | 7.45 | 7 |
"""Reap stale "alive" rooms / users left behind by an ungraceful shutdown.
Channels WebSocket session state lives only in the Django process
(`AnimePartyConsumer`). On a graceful shutdown each connection's
``disconnect`` fires and ``leave_party`` cleans up the rows, but on a hard
crash (OOMKill / node loss / SIGKILL) ... | d-party/backend | streamer/management/commands/close_active_sessions.py | .py | 63661342ab51ae58 | 7.45 | 7 |
"""Logical (soft) deletion support.
This module is a self-contained replacement for the now-unmaintained
``django_boost`` ``LogicalDeletionMixin``. The public behaviour is kept
identical so the streamer core logic does not have to change:
* ``Model.objects.alive()`` / ``.dead()`` filter by the ``deleted_at`` flag.
* ... | d-party/backend | streamer/mixins.py | .py | 8eb7593e582954df | 7.45 | 7 |
import uuid
from django.db import models
from .fields import EncryptedCharField
from .mixins import LogicalDeletionMixin
class AnimeRoom(LogicalDeletionMixin):
room_id = models.UUIDField(primary_key=True, default=uuid.uuid4, editable=False)
num_people = models.PositiveSmallIntegerField(default=1)
sum_pe... | d-party/backend | streamer/models.py | .py | 56c3db6cb044a52e | 7.45 | 7 |
"""Tests for the startup ghost-session reaper (``close_active_sessions``).
Only rooms/users whose ``updated_at`` is older than ``STALE_AFTER`` should be
closed; sessions touched recently (i.e. still being served) must be left alive
so that running on a fresh replica never wipes another replica's live sessions.
"""
im... | d-party/backend | streamer/test_close_active_sessions.py | .py | d21dd6e473fe4343 | 7.95 | 7 |
"""Tests for reaction folding into ``ReactionStat`` on room end."""
import datetime
import pytest
from django.utils import timezone
from .cron import fold_room_reactions
from .factories import AnimeRoomFactory
from .models import AnimeReaction, ReactionStat
def _make_reaction(room, reaction_type: str, when: dateti... | d-party/backend | streamer/test_stats_folding.py | .py | b4a1f1e68348fffd | 7.95 | 7 |
import json
import numpy as np
from napari_organoid_counter import get_reader, settings
# tmp_path is a pytest fixture
def test_reader(tmp_path):
"""Testing the reader part of the plugin"""
settings.init()
# write some fake data using your supported file format
my_test_file = str(tmp_path / 'myfile.js... | HelmholtzAI-Consultants-Munich/napari-organoid-counter | napari_organoid_counter/_tests/test_reader.py | .py | 5fcc1f5ca163e0eb | 8.1 | 15 |
#!/usr/bin/env python3
"""
Timing Analysis Script for Organoid Counter Experiments
Analyzes JSON timing logs and computes mean ± std for different configurations.
Groups results by model name and (window_sizes, downsampling) pairs.
Usage:
python analyze_timings.py <directory_path>
python analyze_timings.py /p... | HelmholtzAI-Consultants-Munich/napari-organoid-counter | napari_organoid_counter/analyze_timings.py | .py | c4a87cfb5ac4c283 | 7.6 | 15 |
"""
数据提取模块
处理markdown文件并提取论文数据
"""
import os
import re
import warnings
warnings.filterwarnings('ignore', category=UserWarning, module='jieba')
import numpy as np
import pandas as pd
import jieba
import jieba.posseg as pseg
from collections import Counter
def _print_parse_error(md_file, date_text, item_index, reason... | SukiYume/APOD | Status/data_extractor.py | .py | b163f91103e5df63 | 7.42 | 6 |
"""
主函数模块
控制程序流程，决定生成哪些图表
"""
import os
from data_extractor import get_markdown_path, extract_data, get_keyword_counter, content_count
from plot_generator import plot_new_count, plot_word_cloud, plot_word_max, plot_counter_graph
def ensure_figure_dir():
"""确保Figure目录存在"""
if not os.path.exists('Figure'):
... | SukiYume/APOD | Status/status.py | .py | 29f9c93003a441ae | 7.42 | 6 |
import random
from .items import (
DungeonItem, DungeonWeapon, DungeonPotion, DungeonScroll,
DungeonThrowable, DungeonArmour, DungeonSpell, DungeonSpellBook,
)
from .people import DungeonPeople, DungeonTrader, DungeonHealer
from .decoder import DungeonJSONDecoder
class DungeonDatabase:
"""Root database t... | mime-r/Dungeon.py | Dungeon/Application/classes/database.py | .py | b05ede8ca81b7ba4 | 7.48 | 8 |
from enum import Enum
from .weapons import WeaponType, DungeonWeaponTexts
class ItemUseType(str, Enum):
EQUIP = "equip"
USE = "use"
class DungeonItem:
"""Base class for all dungeon items."""
symbol = "(" # default ground glyph; subclasses override
def __init__(self, name: str, description: s... | mime-r/Dungeon.py | Dungeon/Application/classes/items.py | .py | f5d5b4b1f9bcf826 | 7.48 | 8 |
import copy
import json
import random
from pathlib import Path
DATA_DIR = Path(__file__).parent.parent.parent / "data"
_NAME_POOL: dict | None = None
# Brand tier multiplier for price calculation (applied to base cost).
_BRAND_PRICE_MULT: dict[int, float] = {
1: 0.3, # venom, protection
2: 0.5, # flaming... | mime-r/Dungeon.py | Dungeon/Application/classes/people.py | .py | 5c1bd3b982e392c0 | 7.48 | 8 |
from enum import Enum
class SkillState(str, Enum):
DISABLED = "-"
ENABLED = "+"
FOCUSED = "*"
# Weapon name -> skill category mapping
_WEAPON_SKILL_MAP = {
# Maces & Flails
"Club": "Maces & Flails",
"Whip": "Maces & Flails",
"Mace": "Maces & Flails",
"Flail": "Maces & Flails",
"M... | mime-r/Dungeon.py | Dungeon/Application/classes/skills.py | .py | 77f73fdb9909888e | 7.48 | 8 |
"""Status effects shared by the player and monsters.
A :class:`StatusSet` hangs off each actor as ``.status``. Most effects are passive flags
read elsewhere (might at attack time, haste/slow by the energy scheduler, confusion at
move time); only poison and regeneration do something on each game-tick via :meth:`tick`.
... | mime-r/Dungeon.py | Dungeon/Application/classes/status.py | .py | 9158611c82acc636 | 7.48 | 8 |
"""Central game configuration: colours, symbols, terrain, map size, depth and spawns."""
class StyleConfig:
"""Rich markup styles. Each attribute name is usable as ``[name]...[/name]``."""
# --- terrain / map tiles ---
wall: str = "bold #5a5a5a"
floor: str = "#3a3a3a"
unknown: str = "#0C0C0C"
... | mime-r/Dungeon.py | Dungeon/Application/config.py | .py | 78a183b9677f4704 | 7.48 | 8 |
"""Cross-platform, turn-based single-key input.
Replaces the old ``keyboard`` global-hook library. Reads one logical keypress at a
time from the controlling terminal:
* Windows -> ``msvcrt``
* Unix/mac -> ``termios`` + ``tty`` raw mode
Arrow keys, Enter, Escape and friends are normalised to stable logical tokens
("... | mime-r/Dungeon.py | Dungeon/Application/input.py | .py | dd0d61f0dcf69685 | 7.48 | 8 |
# https://github.com/The-Duck-Syndicate/encry-duck/blob/master/encry-duck.py
import importlib
import os
import platform
import subprocess
import sys
from importlib import import_module
def _clear():
os.system("cls" if platform.system() == "Windows" else "clear")
def _pip_install(module, logger) -> bool:
"""... | mime-r/Dungeon.py | Dungeon/Application/modules.py | .py | 8a08789d0a96de7c | 7.48 | 8 |
"""Main module for Dolphin Central.
Initializes and registers the required components then starts the main event
loop of the process.
"""
from . import (
admin,
buildbot,
config,
discord,
events,
git,
github,
ircclient,
notifications,
redmine,
webserver,
wiki,
)
import... | dolphin-emu/central | central/__main__.py | .py | b3fc16549c83234d | 7.45 | 7 |
"""Admin module that handles some central management and administration related
commands."""
from . import events
import os
import os.path
import sys
import time
class RebootListener(events.EventTarget):
def accept_event(self, evt):
return evt.type == events.CommandMessage.TYPE
def push_event(self,... | dolphin-emu/central | central/admin.py | .py | b120c6462fb16d73 | 7.45 | 7 |
"""Configuration system for Dolphin Central.
Loads a single configuration file at initialization time and provides access to
the configuration as a global 'cfg' object.
"""
from . import utils
import yaml
cfg = utils.ObjectLike({})
def file_include_constructor(loader, node):
value = str(loader.construct_scala... | dolphin-emu/central | central/config.py | .py | 0cb36e3596b8dc33 | 7.45 | 7 |
from . import app, authz, build_status, fifoci_reporter, webhooks
from .. import utils
from ..config import cfg
import json
import requests
def get_pull_request(owner, repo, pr_id):
return requests.get(
"https://api.github.com/repos/%s/%s/pulls/%s" % (owner, repo, pr_id)
).json()
def get_pull_requ... | dolphin-emu/central | central/github/__init__.py | .py | d3edefd17db8bdc3 | 7.45 | 7 |
"""Transforms raw Redmine issue events into higher level ones.
Will potentially also have more complex processing in the future.
"""
from . import events
from .config import cfg
class Reactor(events.EventTarget):
def accept_event(self, evt):
return evt.type == events.RawRedmineHook.TYPE
def push_ev... | dolphin-emu/central | central/redmine.py | .py | add22aff1d962433 | 7.45 | 7 |
from __future__ import annotations
from collections.abc import Iterable, Iterator
import pynbs
def sorted_notes(notes: Iterable[Note]) -> list[Note]:
"""Return a list of notes sorted by pitch, instrument, velocity, and
panning."""
return sorted(notes, key=lambda x: (x.pitch, x.instrument, x.velocity, x.... | OpenNBS/nbswave | nbswave/nbs.py | .py | 6cafec1b35754745 | 7.56 | 12 |
from __future__ import annotations
import ast
from typing import TYPE_CHECKING, Any
if TYPE_CHECKING:
from collections.abc import Iterator
# The code FA is required in order for errors to appear.
ERROR_MESSAGE_100 = "FA100 Missing from __future__ import annotations but imports: {}"
ERROR_MESSAGE_101 = "FA101 Mis... | TylerYep/flake8-future-annotations | flake8_future_annotations/checker.py | .py | 05585105dfd70d47 | 7.6 | 15 |
# Copyright 2015 Adriana Supady
#
# This file is part of fafoom.
#
# Fafoom is free software: you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later... | inter-info-lab/chem_laqa | laqa_fafoom/pyff.py | .py | 96239dec891ea7fe | 7.42 | 6 |
#!/usr/bin/env python3
import aiofiles
import argparse
import asyncio
import io
import mmap
import os
import pcpp
import re
import CppHeaderParser
import pathlib
from typing import List, Optional
import locale
locale.setlocale(locale.LC_ALL, "") # Use '' for auto, or force e.g. to 'en_US.UTF-8'
HEADER_TYPES = (".h",... | alandtse/vr_address_tools | extractStruct.py | .py | 09698d03995df2f3 | 7.63 | 17 |
import pandas as pd
import csv
BASE = 0x140000000
def merge_skyrim():
# read address id SSE offsets
df1 = pd.read_table("offsets-1-5-97-0.csv", sep=",")
# read address id AE offsets
df2 = pd.read_table("offsets-1-6-318-0.csv", sep=",")
# read meh's attempted match table. https://www.nexusmods.com/... | alandtse/vr_address_tools | merge.py | .py | 6a18e73d24483096 | 7.63 | 17 |
import re
import argparse
import os
from typing import Dict, Tuple, Union
# Define a type alias for offsets
OffsetsType = Dict[str, Union[int, Tuple[int, Union[int, Tuple]]]]
CommonLibOffsets = r".*REL::ID (\w+)\(static_cast<std::uint64_t>\((\d+)\)\);"
CommonLibNGOffsets = r".*constexpr auto (\w+) = RELOCATION_ID\((\... | alandtse/vr_address_tools | replaceOffsetsNamespace.py | .py | 7ed998346848fa8c | 7.63 | 17 |
"""Example demonstrating how to create an LLM project and add tests to it.
This script shows:
- Creating an LLM project
- Adding various types of tests suitable for LLM monitoring:
- LLM Rubric tests (evaluating quality criteria)
- Character length tests (checking response length)
- PII detection tests (ensuring... | openlayer-ai/openlayer-python | examples/rest-api/create_llm_project_with_tests.py | .py | d3400f3899dc53c1 | 7.13 | 17 |
"""
Example: Configuring the Openlayer Tracer
Demonstrates the three ways to configure the tracer and how they compose:
1. Environment variables (canonical for deployments)
2. init() — programmatic, idempotent, merges on repeated calls
3. Per-decorator override via @trace(inference_pipeline_id=...)
Precedence (... | openlayer-ai/openlayer-python | examples/tracing/programmatic_configuration.py | .py | af383c576f8c04b8 | 7.63 | 17 |
#!/usr/bin/env python3
"""
Comprehensive example showing how to use Openlayer's trace metadata update functionality.
This example demonstrates how to set user_id, metadata, and other context information
dynamically during trace execution without having to pass them as function arguments.
"""
import os
import time
fro... | openlayer-ai/openlayer-python | examples/tracing/trace_metadata_updates.py | .py | f558fe1ece348d08 | 7.63 | 17 |
# Note: initially copied from https://github.com/florimondmanca/httpx-sse/blob/master/src/httpx_sse/_decoders.py
from __future__ import annotations
import json
import inspect
from types import TracebackType
from typing import TYPE_CHECKING, Any, Generic, TypeVar, Iterator, Optional, AsyncIterator, cast
from typing_ext... | openlayer-ai/openlayer-python | src/openlayer/_streaming.py | .py | 5ac10cdf74cdffaa | 7.63 | 17 |
from __future__ import annotations
from os import PathLike
from typing import (
IO,
TYPE_CHECKING,
Any,
Dict,
List,
Type,
Tuple,
Union,
Mapping,
TypeVar,
Callable,
Iterable,
Iterator,
Optional,
Sequence,
AsyncIterable,
)
from typing_extensions import (
... | openlayer-ai/openlayer-python | src/openlayer/_types.py | .py | 3b7520f95be13246 | 7.63 | 17 |
from __future__ import annotations
from typing import Any
from typing_extensions import override
from ._proxy import LazyProxy
class ResourcesProxy(LazyProxy[Any]):
"""A proxy for the `openlayer.resources` module.
This is used so that we can lazily import `openlayer.resources` only when
needed *and* so... | openlayer-ai/openlayer-python | src/openlayer/_utils/_resources_proxy.py | .py | 6e29386060d28433 | 7.63 | 17 |
"""Base class for an Openlayer model."""
import os
import abc
import json
import time
import inspect
import argparse
from typing import Any, Dict, Tuple
from dataclasses import field, dataclass
import pandas as pd
from ..tracing import tracer
@dataclass
class RunReturn:
"""The return type of the `run` method i... | openlayer-ai/openlayer-python | src/openlayer/lib/core/base_model.py | .py | 2fc7bb4f3c2dbbfd | 7.63 | 17 |
"""Module containing the BaseMetric definition for Openlayer."""
from __future__ import annotations
import os
import abc
import json
import argparse
import traceback
from typing import Any, Set, Dict, List, Union, Optional
from dataclasses import field, asdict, dataclass
import pandas as pd
@dataclass
class Metric... | openlayer-ai/openlayer-python | src/openlayer/lib/core/metrics.py | .py | 407f9307f768c3cf | 7.63 | 17 |
"""Module containing convenience functions for the tests API."""
from typing import Optional, List
from openlayer import Openlayer
def copy_tests(
client: Openlayer,
origin_project_id: str,
target_project_id: str,
verbose: bool = False,
test_ids: Optional[List[str]] = None,
) -> None:
"""Copy... | openlayer-ai/openlayer-python | src/openlayer/lib/core/tests.py | .py | cd634462774cf19c | 8.13 | 17 |
"""Upload a batch of inferences to the Openlayer platform."""
import time
import logging
import tempfile
from typing import Optional
import httpx
import pandas as pd
import pyarrow as pa
from . import StorageType, _upload
from ... import Openlayer
from ..._utils import maybe_transform
from ...types.inference_pipelin... | openlayer-ai/openlayer-python | src/openlayer/lib/data/batch_inferences.py | .py | 1f7291ed09304b4f | 7.63 | 17 |
"""Pushes a commit to the Openlayer platform."""
import os
import tarfile
import tempfile
import time
from typing import Optional
from ... import Openlayer
from . import StorageType, _upload
from ...types.commit_retrieve_response import CommitRetrieveResponse
def push(
client: Openlayer,
directory: str,
... | openlayer-ai/openlayer-python | src/openlayer/lib/data/commit.py | .py | 013884d2456fa2bc | 7.63 | 17 |
"""
Copyright 2020 ETH Zurich, Secure, Reliable, and Intelligent Systems Lab
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 requi... | uiuc-arc/FANC | tf_verify/config.py | .py | 653816e8981b0e06 | 7.57 | 13 |
"""
Copyright 2020 ETH Zurich, Secure, Reliable, and Intelligent Systems Lab
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 requi... | uiuc-arc/FANC | tf_verify/constraint_utils.py | .py | be60b76695f52263 | 7.57 | 13 |
import sys
from typing import Any
from unittest.mock import DEFAULT, patch
import structlog
def import_without_structlog_sentry(package: str, *args: Any, **kwargs: Any) -> Any:
"""
:param package: Name of package
:return: None if `structlog_sentry` is part of package name, else default import
"""
... | kolonialno/troncos | tests/structlog/test_configuration.py | .py | 50e61a79f37bbae5 | 8.07 | 13 |
import time
from typing import Any, Awaitable, Callable, Iterator, Mapping, MutableMapping, cast
from ddtrace.trace import tracer
from python_ipware.python_ipware import IpWare
try:
from structlog import get_logger
except ImportError as exc:
raise RuntimeError(
"Structlog must be installed to use th... | kolonialno/troncos | troncos/contrib/asgi/logging/middleware.py | .py | 0b8f03a8c07e0a96 | 7.57 | 13 |
import time
from typing import Any
from celery import signals
try:
from structlog import get_logger
except ImportError as exc:
raise RuntimeError(
"Structlog must be installed to use the celery logging signals."
) from exc
logger = get_logger("troncos.celery.task")
def connect_troncos_logging_c... | kolonialno/troncos | troncos/contrib/celery/logging/signals.py | .py | 9e66d287ae9eb7c3 | 7.57 | 13 |
import logging
def print_loggers(verbose: bool = True) -> None:
"""
Function that prints out initialized loggers. This is helpful for you to visualize
exactly how loggers have been set up in your project (and your dependencies). By
default, all loggers will be printed. If you want to filter out loggin... | kolonialno/troncos | troncos/contrib/logging/tools/__init__.py | .py | 440702931e57fe3b | 7.57 | 13 |
from ddtrace.trace import tracer
from structlog.processors import LogfmtRenderer as LogFmt
from structlog.types import EventDict, WrappedLogger
def trace_injection_processor(
_logger: WrappedLogger, _log_method: str, event_dict: EventDict
) -> EventDict:
"""
Simple logging processor that adds a trace_id ... | kolonialno/troncos | troncos/contrib/structlog/processors.py | .py | dfd3bb245c84dba3 | 7.57 | 13 |
from typing import Any
from ddtrace.trace import tracer, Tracer
from ddtrace.internal.service import ServiceStatusError
from ._exporter import Exporter, ExporterType
from ._writer import OTELWriter
__all__ = ["Exporter", "ExporterType", "configure_tracer", "create_trace_writer"]
def create_trace_writer(
*,
... | kolonialno/troncos | troncos/tracing/__init__.py | .py | d20be53fc1221cc0 | 7.57 | 13 |
import os
import sys
from opentelemetry.exporter.otlp.proto.http.trace_exporter import (
OTLPSpanExporter as HTTPSpanExporter,
)
from opentelemetry.sdk.trace import SpanProcessor
from opentelemetry.sdk.trace.export import (
BatchSpanProcessor,
ConsoleSpanExporter,
SimpleSpanProcessor,
SpanExporter,... | kolonialno/troncos | troncos/tracing/_otel.py | .py | f0fe44bff1736dc0 | 7.57 | 13 |
#!/usr/bin/env python3
import os
import json
import tempfile
import textwrap
from pathlib import Path
import requests
from tqdm import tqdm
from prompt_toolkit import prompt
from prompt_toolkit import print_formatted_text as print
HERE = Path(__file__).parent.resolve()
CACHE_FILE = HERE / "uploaded_photos_cache.jso... | lubianat/inat2wiki | batch_upload/batch_upload.py | .py | f3861eef69c1cfe4 | 7.5 | 9 |
"""A flask app to connect iNaturalist to Wikidata."""
from dataclasses import dataclass
from flask_bootstrap import Bootstrap5
from flask_wtf import FlaskForm
from taxon2wikipedia.render_page import run_pipeline_for_wikipage
from wdcuration import get_statement_values, lookup_id
from wtforms import BooleanField, Integ... | lubianat/inat2wiki | www/python/src/app.py | .py | a3f5ba9edc7b976d | 7.5 | 9 |
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