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 |
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# gp.py: Very primitive gaussian process regression module. Returns an object
#
# - Prediction: K(x,x').inv(Kmtx).y. We store and precompute inv(Kmtx).y
import numpy as np
from sklearn import gaussian_process
def squared_exponential_kernel(dx,h,sigma0,sigmab):
ret = np.power(sigma0,2) * np.exp(- np.power(... | oshaughn/research-projects-RIT | MonteCarloMarginalizeCode/Code/RIFT/interpolators/gp.py | .py | c4c42a2a47f0c3f1 | 7.64 | 18 |
#!usr/env/bin python
'''
GPR_Fit.py
python 2.7.13
Vera Delfavero
Date updated: 02/02/2019
The function of this script is to provide the function, "fit_gp" to
the PE code (utils_ConstructIntrinsicPosterior_GenericCoordinates.py)
That function will fit training data, using a sparse gaussian proces,
and return a functio... | oshaughn/research-projects-RIT | MonteCarloMarginalizeCode/Code/RIFT/interpolators/internal_GP.py | .py | bdab6b7abe5633eb | 7.64 | 18 |
import numpy as np
import scipy.integrate
xpy_default=np
has_cupy = False
try:
import cupy # can proceed even if cupy doesn't actually work
junk_to_check_installed = cupy.array(5)
xpy_default=cupy
has_cupy=True
except:
has_cupy=False # just to be sure
# try:
# import numba
# from numba ... | oshaughn/research-projects-RIT | MonteCarloMarginalizeCode/Code/RIFT/likelihood/priors_utils.py | .py | 1e57a7b6fc6114cf | 7.64 | 18 |
# Dan Wysocki
import numpy as np
import numpy
def histogram(samples, n_bins, xpy=numpy,weights=None):
"""
samples : data between [0,1]
n_bins: number of bins of output
weights: weights in histogram
"""
n_samples = samples.size
# sometimes due to input conditioning issues (floats!) the... | oshaughn/research-projects-RIT | MonteCarloMarginalizeCode/Code/RIFT/likelihood/vectorized_general_tools.py | .py | b62bcbe3b12617cc | 7.64 | 18 |
import numpy
try:
import cupy
xpy_default=cupy
junk_to_check_installed = cupy.array(5) # this will fail if GPU not installed correctly
except:
xpy_default=numpy
def TimeDelayFromEarthCenter(
detector_earthfixed_xyz_metres,
source_right_ascension_radians,
source_declination_ra... | oshaughn/research-projects-RIT | MonteCarloMarginalizeCode/Code/RIFT/likelihood/vectorized_lal_tools.py | .py | 8f5f6052bc7db796 | 7.64 | 18 |
#!/usr/bin/env python3
"""Discover, build, and run host unit tests (*_test.c).
Compiler resolution (first match wins):
1. HOST_CC env (space-separated), e.g. HOST_CC=gcc
2. python-zig on PATH — uv tool install ziglang
3. zig on PATH — system Zig (uses: zig cc)
4. uvx --from ziglang python-zig
5. p... | DaelonSuzuka/Easy-XC8 | scripts/host_test.py | .py | bd81ed1e43a91a2b | 7.92 | 6 |
"""Programmer family resolution for upload/program.
project.yaml names the *family* (Pickit4, Pickit5, …). Host OS selects the
platform overlay from upload.json (windows | posix).
Legacy aliases (Pickit4-linux, ICD-U80-win, …) still resolve for old yamls.
"""
from __future__ import annotations
import json
import os... | DaelonSuzuka/Easy-XC8 | scripts/programmers.py | .py | 07e8d4b3c0d3a39d | 7.42 | 6 |
"""Config flow for Notify MQTT."""
from __future__ import annotations
from typing import Any
import voluptuous as vol
from homeassistant.components.mqtt import valid_publish_topic
from homeassistant.config_entries import ConfigEntry, ConfigFlow, ConfigFlowResult, OptionsFlow
from homeassistant.core import callback
f... | arkane-systems/notify_mqtt | custom_components/notify_mqtt/config_flow.py | .py | 53d2f9345699494e | 7.45 | 7 |
"""Tests for the notify.py platform: _build_payload and both entity/service paths."""
from __future__ import annotations
import json
from unittest.mock import AsyncMock, patch
import pytest
from custom_components.notify_mqtt.const import CONF_NAME, CONF_TOPIC, DOMAIN
from custom_components.notify_mqtt.notify import ... | arkane-systems/notify_mqtt | tests/test_notify.py | .py | cf4e6ae2c0edc4f8 | 7.95 | 7 |
"""Authentication helpers for the Emmio API.
Two independent pieces:
- Password hashing with bcrypt. Passwords are never stored; only a one-way
hash is kept, and login re-hashes the candidate and compares.
- Stateless access tokens (JWT). After a correct login the server issues a
signed token carrying the user lo... | enzet/Emmio | emmio/api/auth.py | .py | 5f0c37c6adcb29da | 7.54 | 11 |
"""In-process rate limiting for abuse-prone endpoints.
Deliberately dependency-free (no `slowapi`/Redis): a fixed-window counter
keyed by client IP, held in a plain dict behind a lock. This is enough for a
single-process deployment -- the `Dockerfile` runs one `uvicorn` process, no
`--workers` -- but does *not* share ... | enzet/Emmio | emmio/api/rate_limit.py | .py | b8e6fab368e7bcfe | 7.54 | 11 |
"""Render Emmio UI elements as HTML for the web API.
A third rendering target for the shared `emmio.ui` element tree, alongside the
terminal and rich-console interfaces. All text content is HTML-escaped and only
a fixed set of tags is emitted, so the result is safe to insert into the page.
"""
from html import escape... | enzet/Emmio | emmio/api/render.py | .py | 8df6ae8fc2ea311b | 7.54 | 11 |
"""Server-side sessions: working memory kept between API requests.
A session object is only the selection policy's (or scheduler's) working
memory — answers themselves are persisted per request as ground truth. Losing
a session (restart, eviction, expiry) therefore never loses data: the working
memory is rebuilt from ... | enzet/Emmio | emmio/api/sessions.py | .py | b0f71de6f74ed873 | 7.54 | 11 |
"""Core functionality for listening."""
import hashlib
import json
import logging
import re
from abc import ABC, abstractmethod
from collections import defaultdict
from dataclasses import dataclass
from pathlib import Path
from typing import Self, override
try:
import mpv
except (OSError, ImportError):
mpv = ... | enzet/Emmio | emmio/audio/core.py | .py | 0edbe9633b74c3d1 | 7.54 | 11 |
"""Data for audio files."""
import logging
from dataclasses import dataclass
from pathlib import Path
from typing import Any, Self
from emmio.audio.config import AudioConfig, AudioUsageConfig
from emmio.audio.core import (
AudioCollection,
AudioProvider,
DirectoryAudioProvider,
WikimediaCommonsAudioPr... | enzet/Emmio | emmio/audio/data.py | .py | bb1be585fdac99ab | 7.54 | 11 |
"""Core functionality."""
import json
import logging
from abc import ABC, abstractmethod
from datetime import datetime
from pathlib import Path
from typing import Any, Self
from pydantic import BaseModel
class Record(BaseModel, ABC):
"""An abstraction for a record of actions."""
time: datetime
"""Time ... | enzet/Emmio | emmio/core.py | .py | d87e6b2384f1e278 | 7.54 | 11 |
"""Manager for all Emmio data artifacts.
This class manages Emmio data directory which is by default located in
`~/.emmio`. It expects to find directories
- `lists`,
- `sentences`,
- `dictionaries`,
- `audio`,
- `texts`,
with artifacts and directory `users` with user data.
"""
import logging
from collection... | enzet/Emmio | emmio/data.py | .py | a828ed9cdb1b9cd8 | 7.54 | 11 |
"""SQLite 3 utility."""
import sqlite3
import threading
from pathlib import Path
from sqlite3.dbapi2 import Connection
__author__ = "Sergey Vartanov"
__email__ = "me@enzet.ru"
class Database:
"""Pretty simple wrapper for SQLite database.
The database object is shared across threads (sync FastAPI endpoints ... | enzet/Emmio | emmio/database.py | .py | caaf80b9d9ca392e | 7.54 | 11 |
"""Configuration of a dictionary."""
from typing import Literal
from pydantic.main import BaseModel
from emmio.language import LanguageConfig
class DictionaryUsageConfig(BaseModel):
"""Configuration of a dictionary."""
id: str
"""Identifier of the dictionary."""
from_language: LanguageConfig | No... | enzet/Emmio | emmio/dictionary/config.py | .py | 2cf404fb457bbfd1 | 7.54 | 11 |
"""Data for dictionaries."""
import logging
import threading
from dataclasses import dataclass, field
from pathlib import Path
from typing import Any, Self
from emmio.catalog import KAIKKI_LANGUAGES
from emmio.core import ArtifactData
from emmio.dictionary.config import DictionaryConfig, DictionaryUsageConfig
from em... | enzet/Emmio | emmio/dictionary/data.py | .py | a157e257baffcf86 | 7.54 | 11 |
"""Gate for English Wiktionary service.
See https://en.wiktionary.org.
"""
import json
import logging
import shutil
from pathlib import Path
from typing import Any, override
import requests
from tqdm import tqdm
from emmio.dictionary.core import (
Definition,
DefinitionValue,
Dictionary,
DictionaryI... | enzet/Emmio | emmio/dictionary/en_wiktionary.py | .py | beed77aa478c2d54 | 7.54 | 11 |
"""An interface to Google Translate dictionary.
See https://translate.google.com/
"""
from pathlib import Path
from typing import override
import httpx
from googletrans import Translator
from emmio.dictionary.core import Dictionary, DictionaryItem
from emmio.language import Language
# Cap how long a single live tr... | enzet/Emmio | emmio/dictionary/google_translate.py | .py | 4d26e02f4927b1e1 | 7.54 | 11 |
"""Self-reported language knowledge: curated assessment kinds and values.
A user may log a proficiency estimate for a language at any time — not
Emmio's own computed lexicon rate, but a self-report they enter by hand,
e.g. "French, B2, DELF/DALF, 2022-06-01". Each estimate names a *kind*
(native speaker, self-assessed... | enzet/Emmio | emmio/language_knowledge.py | .py | 39468125a3a11b1a | 7.54 | 11 |
"""Learning configuration."""
from enum import Enum
from pydantic import BaseModel
from emmio.audio.config import AudioUsageConfig
from emmio.dictionary.config import DictionaryUsageConfig
from emmio.language import LanguageConfig
from emmio.lexicon.config import LexiconUsageConfig
from emmio.lists.config import Lis... | enzet/Emmio | emmio/learn/config.py | .py | 094caffb52a63572 | 7.54 | 11 |
"""Data of learning processes."""
from collections.abc import Iterator
from dataclasses import dataclass, field
from datetime import datetime
from pathlib import Path
from typing import Any, Self
from emmio.language import Language
from emmio.learn.config import LearningConfig
from emmio.learn.core import Learning, R... | enzet/Emmio | emmio/learn/data.py | .py | 60a4d9259a731b69 | 7.54 | 11 |
# mypy: ignore-errors
"""Learning visualizer."""
from collections import defaultdict
from dataclasses import dataclass
from datetime import datetime, timedelta
import numpy as np
from matplotlib import dates as mdates
from matplotlib import pyplot as plt
from matplotlib import transforms as mtransforms
from emmio.le... | enzet/Emmio | emmio/learn/visualizer.py | .py | 08fdc2b31cac26d7 | 7.54 | 11 |
"""Configuration for the lexicon."""
from enum import StrEnum
from pydantic.main import BaseModel
from emmio.dictionary.config import DictionaryUsageConfig
from emmio.language import LanguageConfig
from emmio.lists.config import ListUsageConfig
from emmio.sentence.config import SentencesUsageConfig
LexiconConfigVal... | enzet/Emmio | emmio/lexicon/config.py | .py | 19d76f9dbbfa014b | 7.54 | 11 |
"""Lexicon data."""
import logging
import sys
from collections import defaultdict
from dataclasses import dataclass, field
from pathlib import Path
from typing import Any, Self
from pydantic import ValidationError
from emmio.language import Language
from emmio.lexicon.config import LexiconConfig
from emmio.lexicon.c... | enzet/Emmio | emmio/lexicon/data.py | .py | 49f8cb48f20ea21b | 7.54 | 11 |
"""Fixed goal parameters for lexicon precision tracking.
A lexicon's rate estimate is considered *trustworthy* once its standard
deviation, computed with the estimator matching the lexicon's selection
strategy over only the trailing `WINDOW_DAYS` of answers, is at or under
`SD_THRESHOLD`. Once trustworthy, rechecking ... | enzet/Emmio | emmio/lexicon/goal.py | .py | dc8224e1263716b9 | 7.54 | 11 |
"""Windowed rate history: the vocabulary rate as it changes through time.
Every selection strategy gets its history the same way: a sliding window over
the chronological answer log, kept as small as the strategy-matched estimator
allows while its standard deviation stays under a threshold. A small window
follows the l... | enzet/Emmio | emmio/lexicon/history.py | .py | fd367f638d677ed7 | 7.54 | 11 |
"""Shared Matplotlib styling for rate estimate trajectory plots.
The visualizer (`emmio.lexicon.visualize`) draws the same kind of
picture — a rate estimate trajectory over queries — from the CSV files
of both the simulation (`emmio.lexicon.simulation`) and the real-log
replay (`emmio.lexicon.replay`); the chart chrom... | enzet/Emmio | emmio/lexicon/plotting.py | .py | a9d8b3fe46854627 | 7.54 | 11 |
"""Simulation of the four lexicon checking methods on a fake language.
Build a synthetic Zipfian frequency list for a fake language, draw a
random knowledge profile (a 0/1 label per word) calibrated so that the
frequency-weighted share of unknown words matches a chosen rate `r`,
then drive every checking method — FWR ... | enzet/Emmio | emmio/lexicon/simulation.py | .py | 98d902779ead5dbb | 7.54 | 11 |
r"""Shared TikZ (pgfplots) rendering for rate estimate trajectory plots.
The visualizer (`emmio.lexicon.visualize`) can render the simulation
and replay trajectories not only as images but also as TikZ code, ready
to be embedded into a LaTeX document (e.g. with `\input`). The
picture mirrors the Matplotlib style of `e... | enzet/Emmio | emmio/lexicon/tikz.py | .py | de79ea7a911e8e6d | 7.54 | 11 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
from __future__ import absolute_import, division, print_function
__metaclass__ = type
try:
from __main__ import display
except ImportError:
from ansible.utils.display import Display
display = Display()
from ansible.errors import AnsibleError
from ansible.plugins... | metal-stack/ansible-common | action_plugins/print_message.py | .py | 7f77fdf5f43a7360 | 7.42 | 6 |
"""Python client library for the InterGas InComfort system (via Lan2RF gateway).
Each Gateway can have up to 8 Heaters (boilers) and each Heater can have 0-2
active Room thermostats.
"""
from __future__ import annotations
import json
import logging
from enum import IntEnum
from typing import TYPE_CHECKING, Any
impo... | jbouwh/incomfort-client | src/incomfortclient/__init__.py | .py | d75e71059a0c4fcf | 7.5 | 9 |
"""Fixtures for incomfort backend library."""
from collections.abc import Awaitable, Callable
from typing import Any
from aiohttp import web
from aiohttp.test_utils import TestServer
import pytest
@pytest.fixture(name="heater_list_exc")
def mock_heater_list_exception() -> Exception | None:
"""Mock a heater lis... | jbouwh/incomfort-client | tests/conftest.py | .py | 48f09fa0dce8b3c5 | 8 | 9 |
import os
import sys
import click
from dotenv import load_dotenv
from flask_migrate import Migrate, upgrade
from app_core import create_app, db
from app_core.models import User, Role, Gender, Permission, Follow, Comment, Post
dot_env_path = os.path.join(os.path.dirname(__file__), '.env')
if os.path.exists(dot_env_pa... | realJustinLee/LiCMS | app.py | .py | 489cb0710a759e51 | 7.63 | 17 |
import unittest
import onetimepass
from app_core import create_app, db
from app_core.models import User, Role, Gender
class FlaskClientTestCase(unittest.TestCase):
def setUp(self):
self.app = create_app('testing')
self.app_context = self.app.app_context()
self.app_context.push()
... | realJustinLee/LiCMS | tests/test_client.py | .py | 0c6fae9bed683870 | 7.13 | 17 |
import threading
import time
import unittest
import onetimepass
from selenium import webdriver
from selenium.webdriver.chrome.service import Service as ChromeService
from selenium.webdriver.common.by import By
from selenium.webdriver.support.wait import WebDriverWait
from webdriver_manager.chrome import ChromeDriverMa... | realJustinLee/LiCMS | tests/test_selenium.py | .py | 04889a7a34b4d0b7 | 7.13 | 17 |
"""命令行工具：从基金 xlsx 文件生成历史价格折线图。
用法示例：
python k-wall.py -f funds.xlsx
python k-wall.py -f funds.xlsx -d 180 -r nearest
python k-wall.py -f funds.xlsx --headless -o result.png
"""
import argparse
import numpy as np
import matplotlib.pyplot as plt
import openpyxl
from math import ceil
import time
from em1234... | CH3COOOH/Eastmoney1234567 | k-wall.py | .py | f3e5969786459a7a | 7.42 | 6 |
"""A class for interacting with Aussie Broadband APIs"""
# import json
import sys
from time import time
from typing import Any, cast
import requests
import requests.sessions
from pydantic import SecretStr
from requests.models import Response
from .baseclass import BaseClass
from .const import BASEURL, PHONE_TYPES, d... | yaleman/pyaussiebb | aussiebb/__init__.py | .py | 544728e30f87b839 | 7.57 | 13 |
"""base class def"""
import logging
from http.cookies import Morsel, SimpleCookie
from time import time
from typing import Any
from pydantic import SecretStr
from requests.cookies import RequestsCookieJar
from .const import (
API_ENDPOINTS,
BASEURL,
FETCH_TYPES,
HARDWARE_TYPES,
NBN_TYPES,
PHO... | yaleman/pyaussiebb | aussiebb/baseclass.py | .py | 7c8aa5f4963819de | 7.57 | 13 |
"""types"""
from datetime import datetime
from typing import Any, TypedDict
from pydantic import BaseModel, ConfigDict, Field, SecretStr, field_validator
class AccountTransaction(TypedDict):
"""Transaction data typing, returns from account_transactions"""
id: int
type: str
time: str
description... | yaleman/pyaussiebb | aussiebb/types.py | .py | 6ad8d9441c72583a | 7.57 | 13 |
#!/usr/bin/env python
"""pulls and lists the VOIP services on your account"""
# pylint: disable=wrong-import-position
import asyncio
import json
import os
import sys
from pathlib import Path
import aiohttp
script_path = Path(__file__)
sys.path.append(script_path.parent.parent.as_posix())
# pylint: disable=import... | yaleman/pyaussiebb | examples/get_service_info.py | .py | 80969cbefdffbcd1 | 7.57 | 13 |
#!/usr/bin/env python
"""pulls and lists the IPv6 addresess for your services"""
import asyncio
import json
import os
import sys
from ipaddress import IPv4Network, IPv6Network, ip_network
from pathlib import Path
script_path = Path(__file__)
sys.path.append(script_path.parent.parent.as_posix())
# pylint: disable=i... | yaleman/pyaussiebb | examples/grabipv6.py | .py | 46f0cce3a9cb1e28 | 7.57 | 13 |
#!/usr/bin/env python3
"""updates terraform.tfvars based on the current ipv6 subnet assigned to your network
looks for a variable called "base_ipv6_network" and updates it.
"""
import os
import re
import sys
from ipaddress import IPv6Network, ip_network
from pathlib import Path
filepath = Path(__file__)
sys.path.ap... | yaleman/pyaussiebb | examples/update_terraform_ipv6.py | .py | 48aa3341c3afa866 | 7.57 | 13 |
"""
Using this
You really need a file called "aussiebb.json" in either the local dir or ~/.config/.
It needs at least one user in the "users" field. eg:
{
"users" : [
{ "username" : "mickeymouse.123", "password" : "hunter2" }
]
}
"""
import json
import pytest
import aussiebb.const
from aussiebb im... | yaleman/pyaussiebb | tests/test_aussiebb.py | .py | 8bddbbadf6b5c621 | 7.07 | 13 |
"""test some things"""
import json
import pytest
import aussiebb.const
from aussiebb.asyncio import AussieBB
# from aussiebb.exceptions import InvalidTestForService
from aussiebb.types import ConfigUser
from .test_utils import configloader, users # noqa: F401
# All test coroutines will be treated as marked.
pyte... | yaleman/pyaussiebb | tests/test_aussiebb_asyncio.py | .py | b3fa553cc0b7ebcf | 8.07 | 13 |
"""
Using this
You really need a file called "aussiebb.json" in either the local dir or ~/.config/.
It needs at least one user in the "users" field. eg:
{
"users" : [
{ "username" : "mickeymouse.123", "password" : "hunter2" }
]
}
"""
import json
import pytest
from aussiebb import AussieBB
from .t... | yaleman/pyaussiebb | tests/test_aussiebb_orders.py | .py | 864da042d788fdc8 | 7.07 | 13 |
"""
Using this
You really need a file called "aussiebb.json" in either the local dir or ~/.config/.
It needs at least one user in the "users" field. eg:
{
"users" : [
{ "username" : "mickeymouse.123", "password" : "hunter2" }
]
}
"""
import json
import pytest
from aussiebb import AussieBB
from aus... | yaleman/pyaussiebb | tests/test_aussiebb_outages.py | .py | 89ae923d604d8aa5 | 7.07 | 13 |
"""tests some fetch-service-related things"""
import json
from aussiebb import types
def test_fetch_service_parser() -> None:
"""tests parsing an example service"""
fetch_service = json.loads(
"""
{
"service_id": 332780,
"type": "FETCHTV",
"name": "Fetch Tv",
"plan": "F... | yaleman/pyaussiebb | tests/test_fetch.py | .py | 3a11208a8769906e | 8.07 | 13 |
""" pyaussiebb tests """
import pytest
from pydantic import SecretStr
from aussiebb.baseclass import BaseClass
from aussiebb.exceptions import UnrecognisedServiceType
def test_validate_service_type() -> None:
"""testing the validate_service_type function"""
test = BaseClass(
username="foo",
... | yaleman/pyaussiebb | tests/test_field_validation.py | .py | 67d61b12c75b32cd | 7.07 | 13 |
"""test utils"""
import json
import os
from pathlib import Path
import pytest
from aussiebb import AussieBB
from aussiebb.types import AussieBBConfigFile
CONFIG_FILES = [os.path.expanduser("~/.config/aussiebb.json"), "aussiebb.json"]
def configloader() -> AussieBBConfigFile:
"""loads config"""
for filenam... | yaleman/pyaussiebb | tests/test_utils.py | .py | bcb84f47a9ba18b3 | 8.07 | 13 |
import typing
import webob
import webtest
from starlette.testclient import TestClient
from starlette.types import ASGIApp
WSGIApp = typing.Callable[
[typing.MutableMapping, typing.Callable], list[typing.ByteString]
]
def AsgiToWsgi(asgi_app: ASGIApp) -> WSGIApp:
def handle(environ, start_response):
... | sloria/webtest-asgi | webtest_asgi.py | .py | 1cd043bdb5d941e4 | 7.95 | 7 |
from dataclasses import dataclass
from typing import Optional
@dataclass(frozen=True)
class AgeScope:
"""A subset of ages used for prevalence/incidence pooling and calibration.
lo/hi are inclusive bounds; None means unbounded on that side.
AgeScope() -> all ages
AgeScope(65, None... | jburke5/microsim | microsim/common/age_scope.py | .py | 9c5772cdd8f7321b | 7.42 | 6 |
from microsim.outcomes.ascvd_outcome_model import ASCVDOutcomeModel
from microsim.regression_models.regression_model import RegressionModel
from microsim.common.data_loader import load_model_spec
from microsim.outcomes.outcome import Outcome, OutcomeType
from microsim.outcomes.outcome_prevalence_base import OutcomePrev... | jburke5/microsim | microsim/outcomes/cv_model.py | .py | 69c3f6c5a9c1f254 | 7.42 | 6 |
from microsim.outcomes.outcome import Outcome, OutcomeType
class DeathModel:
"""Checks if any outcome produced in the current year was fatal.
Does not produce any additional fatalities."""
def __init__(self):
pass
def generate_next_outcome(self, person):
return Outcome(OutcomeT... | jburke5/microsim | microsim/outcomes/death_model.py | .py | f146bc1432356831 | 7.42 | 6 |
from microsim.outcomes.dementia_model import DementiaModel, DementiaPrevalenceModel
from microsim.risk_factors.modality import Modality
class DementiaModelRepository:
def __init__(self, wmhSpecific=True, riskScaling=1.0):
#if we want the dementia model to return an average risk for the kaiser population, i... | jburke5/microsim | microsim/outcomes/dementia_model_repository.py | .py | cdeac36e9496e6d9 | 7.42 | 6 |
from microsim.outcomes.outcome import Outcome, OutcomeType
from microsim.treatment_strategies.treatment_strategies import TreatmentStrategiesType
class MCIModel:
"""Mild cognitive impairment model."""
def __init__(self, riskScaling=1.0):
self._riskScaling = riskScaling
def generate_next_outcome(s... | jburke5/microsim | microsim/outcomes/mci_model.py | .py | bec16238cd18f64e | 7.42 | 6 |
from microsim.outcomes.outcome import OutcomeType, Outcome
from microsim.outcomes.outcome_prevalence_base import OutcomePrevalenceBase
class MIPartitionModel:
"""Fatal mi probability from: Wadhera, R. K., Joynt Maddox, K. E., Wang, Y., Shen, C., Bhatt, D. L., & Yeh, R. W. (2018).
Association Between 30-Day... | jburke5/microsim | microsim/outcomes/mi_partition_model.py | .py | c8f9c10207b5527c | 7.42 | 6 |
from microsim.regression_models.logistic_risk_factor_model import LogisticRiskFactorModel
from microsim.common.data_loader import load_model_spec
from microsim.regression_models.regression_model import RegressionModel
from microsim.outcomes.outcome import Outcome, OutcomeType
from microsim.risk_factors.modality import ... | jburke5/microsim | microsim/outcomes/non_cv_death_model.py | .py | dc216f12ee698700 | 7.42 | 6 |
from microsim.regression_models.linear_risk_factor_model import LinearRiskFactorModel
from microsim.regression_models.regression_model import RegressionModel
from microsim.common.data_loader import load_model_spec
from microsim.outcomes.outcome import OutcomeType, Outcome
from microsim.outcomes.outcome_prevalence_base ... | jburke5/microsim | microsim/outcomes/stroke_partition_model.py | .py | 97ebff04bf93f6a9 | 7.42 | 6 |
from microsim.outcomes.sbi_model import SBIModel
from microsim.outcomes.wmh_outcome import WMHOutcome
from microsim.outcomes.wmh_severity_unknown import WMHSeverityUnknownModel
from microsim.outcomes.wmh_severity import WMHSeverityCTModel, WMHSeverityMRModel, WMHSeverityModel, WMHSeverity
from microsim.outcomes.outcome... | jburke5/microsim | microsim/outcomes/wmh_model.py | .py | 247a8eee39fbb230 | 7.42 | 6 |
"""Jupyter Notebook collection README generator
Copyright by the SalishSeaCast Project contributors and The University of British Columbia.
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
https... | SalishSeaCast/SalishSeaNowcast | notebooks/figures/comparison/make_readme.py | .py | b2b0f5fed781d153 | 7.45 | 7 |
# Copyright 2013 – present by the SalishSeaCast Project contributors
# and The University of British Columbia
#
# 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
#
# https://www.apache.o... | SalishSeaCast/SalishSeaNowcast | notebooks/make_readme.py | .py | 5abaa9f6f821f8cd | 7.45 | 7 |
# Copyright 2013 – present by the SalishSeaCast Project contributors
# and The University of British Columbia
#
# 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
#
# https://www.apache.o... | SalishSeaCast/SalishSeaNowcast | nowcast/analyze.py | .py | f551348d742d1b91 | 7.45 | 7 |
# Copyright 2013 – present by the SalishSeaCast Project contributors
# and The University of British Columbia
#
# 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
#
# https://www.apache.o... | SalishSeaCast/SalishSeaNowcast | nowcast/figures/comparison/compare_venus_ctd.py | .py | 6fd087746ddb1259 | 7.45 | 7 |
# Copyright 2013 – present by the SalishSeaCast Project contributors
# and The University of British Columbia
#
# 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
#
# https://www.apache.o... | SalishSeaCast/SalishSeaNowcast | nowcast/figures/comparison/salinity_ferry_track.py | .py | 6b32d5881034fd83 | 7.45 | 7 |
# Copyright 2013 – present by the SalishSeaCast Project contributors
# and The University of British Columbia
#
# 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
#
# https://www.apache.o... | SalishSeaCast/SalishSeaNowcast | nowcast/figures/publish/pt_atkinson_tide.py | .py | 8bb1b20856a42c73 | 7.45 | 7 |
# Copyright 2013 – present by the SalishSeaCast Project contributors
# and The University of British Columbia
#
# 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
#
# https://www.apache.o... | SalishSeaCast/SalishSeaNowcast | nowcast/figures/publish/surface_current_tiles.py | .py | 100f4bbf368166e4 | 7.45 | 7 |
# Copyright 2013 – present by the SalishSeaCast Project contributors
# and The University of British Columbia
#
# 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
#
# https://www.apache.o... | SalishSeaCast/SalishSeaNowcast | nowcast/figures/research/baynes_sound_agrif.py | .py | fd6e28f5d7411795 | 7.45 | 7 |
# Copyright 2013 – present by the SalishSeaCast Project contributors
# and The University of British Columbia
#
# 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
#
# https://www.apache.o... | SalishSeaCast/SalishSeaNowcast | nowcast/figures/research/time_series_plots.py | .py | 396a2d3cad558811 | 7.45 | 7 |
# Copyright 2013 – present by the SalishSeaCast Project contributors
# and The University of British Columbia
#
# 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
#
# https://www.apache.o... | SalishSeaCast/SalishSeaNowcast | nowcast/figures/research/velocity_section_and_surface.py | .py | f4ff9a3d74f6c5c1 | 7.45 | 7 |
# Copyright 2013 – present by the SalishSeaCast Project contributors
# and The University of British Columbia
#
# 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
#
# https://www.apache.o... | SalishSeaCast/SalishSeaNowcast | nowcast/figures/research_ferries.py | .py | c4e90c79f6c7fbc0 | 7.45 | 7 |
# Copyright 2013 – present by the SalishSeaCast Project Contributors
# and The University of British Columbia
# 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
# https://www.apache.org/licen... | SalishSeaCast/SalishSeaNowcast | nowcast/figures/surface_current_domain.py | .py | 9bae026cb46c115d | 7.45 | 7 |
# Copyright 2013 – present by the SalishSeaCast Project contributors
# and The University of British Columbia
#
# 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
#
# https://www.apache.o... | SalishSeaCast/SalishSeaNowcast | nowcast/lib.py | .py | 9b52f739d2fea7f0 | 7.45 | 7 |
"""script to generate plots for a simulation
Use: python plots.py sim_date mode
Eg: python plots.py 2015-03-06 nowcast generates plots for the
March 6, 2015 nowcast. sim_date corresponds to the date simulated.
plots are stored in a directory mode/run_dat, where run_date is the
date the simulation was run.
"""
import ... | SalishSeaCast/SalishSeaNowcast | nowcast/plots.py | .py | 2595928a6e356932 | 7.45 | 7 |
# Copyright 2013 – present by the SalishSeaCast Project contributors
# and The University of British Columbia
#
# 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
#
# https://www.apache.o... | SalishSeaCast/SalishSeaNowcast | nowcast/workers/archive_tarball.py | .py | 2056bdc1b1a369d2 | 7.45 | 7 |
# Copyright 2013 – present by the SalishSeaCast Project contributors
# and The University of British Columbia
#
# 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
#
# https://www.apache.o... | SalishSeaCast/SalishSeaNowcast | nowcast/workers/collect_NeahBay_ssh.py | .py | d407a3d5f8eca807 | 7.45 | 7 |
# Copyright 2013 – present by the SalishSeaCast Project contributors
# and The University of British Columbia
#
# 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
#
# https://www.apache.o... | SalishSeaCast/SalishSeaNowcast | nowcast/workers/collect_river_data.py | .py | 74820ec45ac95609 | 7.45 | 7 |
# Copyright 2013 – present by the SalishSeaCast Project contributors
# and The University of British Columbia
#
# 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
#
# https://www.apache.o... | SalishSeaCast/SalishSeaNowcast | nowcast/workers/collect_weather.py | .py | 22a6c80629a3be6f | 7.45 | 7 |
# Copyright 2013 – present by the SalishSeaCast Project contributors
# and The University of British Columbia
#
# 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
#
# https://www.apache.o... | SalishSeaCast/SalishSeaNowcast | nowcast/workers/crop_gribs.py | .py | dd9761781b495ab9 | 7.45 | 7 |
# Copyright 2013 – present by the SalishSeaCast Project contributors
# and The University of British Columbia
#
# 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
#
# https://www.apache.o... | SalishSeaCast/SalishSeaNowcast | nowcast/workers/download_live_ocean.py | .py | 44e4e6eeb5586066 | 7.45 | 7 |
# Copyright 2013 – present by the SalishSeaCast Project contributors
# and The University of British Columbia
#
# 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
#
# https://www.apache.o... | SalishSeaCast/SalishSeaNowcast | nowcast/workers/download_results.py | .py | 858cfbcdefa0e1e1 | 7.45 | 7 |
# Copyright 2013 – present by the SalishSeaCast Project contributors
# and The University of British Columbia
#
# 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
#
# https://www.apache.o... | SalishSeaCast/SalishSeaNowcast | nowcast/workers/download_weather.py | .py | a721568918aa16f3 | 7.45 | 7 |
# Copyright 2013 – present by the SalishSeaCast Project contributors
# and The University of British Columbia
#
# 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
#
# https://www.apache.o... | SalishSeaCast/SalishSeaNowcast | nowcast/workers/download_wwatch3_results.py | .py | c70ebe0ab795f8a2 | 7.45 | 7 |
# Copyright 2013 – present by the SalishSeaCast Project contributors
# and The University of British Columbia
#
# 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
#
# https://www.apache.o... | SalishSeaCast/SalishSeaNowcast | nowcast/workers/get_onc_ctd.py | .py | 898a8d6be8561d2d | 7.45 | 7 |
"""
A barebones set of classes to manage channel width constraints for MOM6 grids. It is effectively a list that can be applied on top of the bathymetry, and is not git-backed.
The channels represent a separate concern and can be independently shared, or managed outside the topography versioning system.
It is a basical... | NCAR/mom6_forge | mom6_forge/channel_width.py | .py | 40e584eccc96bb1e | 7.52 | 10 |
from mom6_forge.grid import Grid
from mom6_forge.topo import Topo
import xarray as xr
import numpy as np
import xesmf as xe
from datetime import datetime
from pathlib import Path
from os.path import isfile
from mom6_forge.utils import fill_missing_data, compute_subsampling_factor
from mom6_forge.mapping import regrid_w... | NCAR/mom6_forge | mom6_forge/chl.py | .py | 8c041937b66fb808 | 7.52 | 10 |
import json
import os
from abc import ABC, abstractmethod
from enum import Enum
from mom6_forge.git_utils import get_repo
from pathlib import Path
from mom6_forge.edit_command import EditCommand
class CommandType(Enum):
"""Enumeration for command types in the history."""
INITIAL = "INITIAL"
COMMAND = "CO... | NCAR/mom6_forge | mom6_forge/command_manager.py | .py | f6203b318f41aa5b | 7.52 | 10 |
import os
import git
import hashlib
from pathlib import Path
def get_domain_dir(grid, base_dir="TopoLibrary"):
"""
Returns a unique directory path for a given grid object.
Works for both rectilinear and curvilinear grids.
"""
# Flatten and convert to bytes (deterministic)
data_bytes = grid.tl... | NCAR/mom6_forge | mom6_forge/git_utils.py | .py | e5bcaeed4cff6b4f | 7.52 | 10 |
"""Auxiliary functions for grid property computations."""
from pathlib import Path
import xarray as xr
import numpy as np
import scipy
def longitude_slicer(data, longitude_extent, longitude_coords):
"""Slice a dataset in longitude, handling periodicity and domain seams.
Correctly clips datasets whose longit... | NCAR/mom6_forge | mom6_forge/utils.py | .py | 8a64be7ae0940042 | 7.52 | 10 |
import os
from datetime import datetime
import numpy as np
import xarray as xr
from typing import Literal
class VGrid:
"""
Vertical grid class.
Attributes
----------
dz: np.ndarray
Array of vertical grid spacings
nk: int
Number of vertical levels
depth: float
Tota... | NCAR/mom6_forge | mom6_forge/vgrid.py | .py | 14cb7e7cba668dbd | 7.52 | 10 |
import pytest
from mom6_forge.channel_width import ChannelWidth, ChannelWidthList
def test_channel_width_validation():
"""Test that ChannelWidth validates component is U_width or V_width"""
# Valid cases
ch_u = ChannelWidth(
component="U_width",
lon1=-6.5,
lon2=-4.75,
lat1=... | NCAR/mom6_forge | tests/test_channel_width.py | .py | 57ffc9a9e8e45cc3 | 8.02 | 10 |
from mom6_forge.grid import Grid
from mom6_forge.topo import Topo
from mom6_forge.chl import interpolate_and_fill_seawifs
import pytest
import os
from utils import on_cisl_machine
def test_chl(tmp_path, get_rect_grid):
"""Test the creation of chl files."""
if not on_cisl_machine():
pytest.skip("This t... | NCAR/mom6_forge | tests/test_chl.py | .py | 0649c083844cc8bb | 7.02 | 10 |
"""Test mask functionality: setting, applying, and depth masking behavior."""
import numpy as np
import pytest
import xarray as xr
from mom6_forge.edit_command import MaskEditCommand, ClearMaskCommand
import regionmask
from unittest.mock import MagicMock, patch
from mom6_forge.topo import Topo
def test_generate_mask... | NCAR/mom6_forge | tests/test_masks.py | .py | 2dcaaaaa1017254b | 8.02 | 10 |
"""Initially setup in regional_mom6"""
from mom6_forge._supergrid import (
SupergridBase,
mom6_angle_calculation_method,
modulo_around_point,
)
from mom6_forge.grid import Grid
import math
import pytest
import xarray as xr
import numpy as np
tol_angle = 5e-1 # tolerance for angles (in degrees) from seper... | NCAR/mom6_forge | tests/test_rotation.py | .py | cabc72afb4b546f0 | 7.02 | 10 |
"""Smoke test for SourceBathy loader."""
import numpy as np
import pytest
import tempfile
from pathlib import Path
import xarray as xr
from mom6_forge._source_bathy import SourceBathy
def test_simple_source_bathy_calls(get_rect_topo_without_vc, synthetic_bathy_file):
src = SourceBathy(
get_rect_topo_with... | NCAR/mom6_forge | tests/test_source_bathy.py | .py | 1cc7c8b6b80f1cbf | 7.02 | 10 |
import pytest
import xarray as xr
import numpy as np
from mom6_forge.topo import *
from mom6_forge._source_bathy import SourceBathy
from mom6_forge.grid import Grid
def test_generate_mask_ocean_frac_raises_without_src(get_rect_topo_without_vc):
"""generate_mask_from_stats_ocean_frac must raise if src has not been... | NCAR/mom6_forge | tests/test_topo_bathymetry_workflows.py | .py | e69457150dc36ffa | 7.02 | 10 |
from unittest.mock import MagicMock
# --- active_cells ---
def test_active_cells_empty(get_editor):
"""No selection returns empty list."""
assert get_editor.active_cells == []
def test_active_cells_single_cell(get_editor):
"""Single cell selection returns correct (j, i) tuple."""
get_editor._select... | NCAR/mom6_forge | tests/test_topo_editor.py | .py | 1fca321dc972b87a | 7.02 | 10 |
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