code stringlengths 114 1.05M | path stringlengths 3 312 | quality_prob float64 0.5 0.99 | learning_prob float64 0.2 1 | filename stringlengths 3 168 | kind stringclasses 1
value |
|---|---|---|---|---|---|
import operator
from fractions import Fraction
from functools import partial, reduce, wraps
def flatten(lst) -> list:
"""Flattens a list of lists"""
return [item for sublist in lst for item in sublist]
def remove_nones(lst) -> list:
"""Removes 'None' values from given list"""
return filter(lambda x:... | /sardine_system-0.4.0-py3-none-any.whl/sardine_core/sequences/tidal_parser/utils.py | 0.69181 | 0.461623 | utils.py | pypi |
from .tree_calc import CalculateTree
from ...base import BaseParser
from lark import Lark, Tree
from lark.exceptions import LarkError, UnexpectedCharacters, UnexpectedToken
from pathlib import Path
from .chord import Chord
from ...logger import print
import traceback
__all__ = ("ListParser",)
class ParserError(Excep... | /sardine_system-0.4.0-py3-none-any.whl/sardine_core/sequences/sardine_parser/list_parser.py | 0.805938 | 0.192065 | list_parser.py | pypi |
from itertools import count, cycle, dropwhile, islice, takewhile
from .chord import Chord
def floating_point_range(start, end, step):
"""Analog to range for floating point numbers
Args:
start (float): A minimum float
end (float): A maximum float
step (float): Step for increment
... | /sardine_system-0.4.0-py3-none-any.whl/sardine_core/sequences/sardine_parser/utils.py | 0.892093 | 0.486392 | utils.py | pypi |
import asyncio
import concurrent.futures
import threading
from abc import ABC, abstractmethod
from typing import Optional
from .handler import BaseHandler
__all__ = ("BaseRunnerMixin", "BaseThreadedLoopMixin", "BaseRunnerHandler")
class BaseRunnerMixin(ABC):
"""Provides methods for running a background asynchro... | /sardine_system-0.4.0-py3-none-any.whl/sardine_core/base/runner.py | 0.92891 | 0.172346 | runner.py | pypi |
import functools
import inspect
from typing import TYPE_CHECKING, Callable, ParamSpec, TypeVar, Union
from .Messages import *
if TYPE_CHECKING:
from ..base import BaseClock
P = ParamSpec("P")
T = TypeVar("T")
Number = Union[float, int]
MISSING = object()
def alias_param(name: str, alias: str):
"""
Al... | /sardine_system-0.4.0-py3-none-any.whl/sardine_core/utils/__init__.py | 0.811713 | 0.238772 | __init__.py | pypi |
import contextlib
import contextvars
from ..base import BaseHandler
__all__ = ("Time",)
shift = contextvars.ContextVar("shift", default=0.0)
"""
This specifies the amount of time to offset in the current context.
Usually this is updated within the context of scheduled functions
to simulate sleeping without actually ... | /sardine_system-0.4.0-py3-none-any.whl/sardine_core/clock/time.py | 0.783988 | 0.332026 | time.py | pypi |
import { Decoration, DecorationSet } from "@codemirror/view"
import { StateField, StateEffect, ChangeDesc } from "@codemirror/state"
import { EditorView } from "@codemirror/view"
import { invertedEffects } from "@codemirror/commands"
import { Extension } from "@codemirror/state"
function mapRange(range: {from: number... | /sardine-web-1.1.0.tar.gz/sardine-web-1.1.0/sardine_web/client/src/highlightSelection.ts | 0.502686 | 0.621483 | highlightSelection.ts | pypi |
<p align="center">
<img alt="sarenka-logo" src="https://raw.githubusercontent.com/pawlaczyk/sarenka/master/logo.png">
</p>
[](https://github.com/pawlaczyk/sarenka/releases/latest) [:
"""Manages a JSON file like a database"""
def __init__(self, filename: str):
self.__filename = filename
try:
with open(filename) as data_... | /sarf_simple_crud-0.1.0-py3-none-any.whl/simple_crud/dal/infra/json_dal.py | 0.738858 | 0.260657 | json_dal.py | pypi |
import json
from typing import Dict, Iterable, Optional
from ..base import DALHandler, QueryFilter, FilterType
class JSONDatabase(DALHandler):
"""Manages a JSON file like a database"""
def __init__(self, filename: str):
self.__filename = filename
try:
with open(filename) as data_... | /sarf_simple_crud-0.1.0-py3-none-any.whl/sarf_simple_crud/dal/infra/json_dal.py | 0.738858 | 0.260657 | json_dal.py | pypi |
import json
from typing import Dict, Iterable, Optional
from ..base import DALHandler, QueryFilter, FilterType
class JSONDatabase(DALHandler):
"""Manages a JSON file like a database"""
def __init__(self, filename: str):
self.__filename = filename
try:
with open(filename) as data_... | /sarf_simple_crud-0.1.0-py3-none-any.whl/simplecrud/dal/infra/json_dal.py | 0.738858 | 0.260657 | json_dal.py | pypi |
import attr
@attr.s
class Run(object):
"""Describes a single run of an analysis tool, and contains the reported output of that run."""
tool = attr.ib(metadata={"schema_property_name": "tool"})
addresses = attr.ib(default=None, metadata={"schema_property_name": "addresses"})
artifacts = attr.ib(defau... | /sarif_om-1.0.4-py3-none-any.whl/sarif_om/_run.py | 0.767341 | 0.174762 | _run.py | pypi |
import attr
@attr.s
class ToolComponent(object):
"""A component, such as a plug-in or the driver, of the analysis tool that was run."""
name = attr.ib(metadata={"schema_property_name": "name"})
associated_component = attr.ib(default=None, metadata={"schema_property_name": "associatedComponent"})
con... | /sarif_om-1.0.4-py3-none-any.whl/sarif_om/_tool_component.py | 0.710729 | 0.159905 | _tool_component.py | pypi |
# SARIF Tools
A set of command line tools and Python library for working with SARIF files.
Read more about the SARIF format here: https://sarifweb.azurewebsites.net/
# Installation
## Prerequisites
You need Python 3.8 or later installed. Get it from [python.org](https://www.python.org/downloads/). This document ... | /sarif-tools-1.0.0.tar.gz/sarif-tools-1.0.0/README.md | 0.428592 | 0.907763 | README.md | pypi |
import copy
import datetime
import os
import re
from typing import Dict, Iterator, List, Optional, Tuple
SARIF_SEVERITIES = ["error", "warning", "note"]
RECORD_ATTRIBUTES = ["Tool", "Severity", "Code", "Location", "Line"]
# Standard time format for filenames, e.g. `20211012T110000Z` (not part of the SARIF standard).... | /sarif-tools-1.0.0.tar.gz/sarif-tools-1.0.0/sarif/sarif_file.py | 0.77886 | 0.259817 | sarif_file.py | pypi |
from datetime import datetime
import os
import docx
from docx import oxml
from docx import shared
from docx.enum import text
from docx.oxml import ns
from sarif import charts, sarif_file
from sarif.sarif_file import SarifFileSet
def generate_word_docs_from_sarif_inputs(
input_files: SarifFileSet, image_file: st... | /sarif-tools-1.0.0.tar.gz/sarif-tools-1.0.0/sarif/operations/word_op.py | 0.413477 | 0.256797 | word_op.py | pypi |
<div align="center">
<img src="https://github.com/AminAlam/Sarina/blob/dev/other_files/sarina/text_on_contour.png" width=400>
<br/>
<h1>Sarina</h1>
<br/>
<img src="https://img.shields.io/badge/Python-14354C?style=for-the-badge&logo=python&logoColor=white" alt="built with Python3" />
<img src="https://img.shields.io/bad... | /sarina-cli-0.0.22.tar.gz/sarina-cli-0.0.22/README.md | 0.513668 | 0.934515 | README.md | pypi |
==========
Why Sarkas
==========
Problem
-------
The typical workflow of MD simulations in plasma physics looks something like this
#. Write your own MD code, or use a pre-existing code, in a low-level language such as C/C++ or (even better) Fortran to exploit their computational speed.
#. Run multiple simulations w... | /sarkas-1.0.2.tar.gz/sarkas-1.0.2/docs/documentation/why_sarkas.rst | 0.941909 | 0.810891 | why_sarkas.rst | pypi |
==========
Input File
==========
The first step in any MD simulation is the creation of an input file containing all the relevant parameters
of our simulation. Take a look at the file ``yukawa_mks_p3m.yaml`` that can be
found `here <https://raw.githubusercontent.com/murillo-group/sarkas/master/docs/documentation/Tutori... | /sarkas-1.0.2.tar.gz/sarkas-1.0.2/docs/documentation/input_file.rst | 0.936851 | 0.872619 | input_file.rst | pypi |
.. _integrators:
===========
Integrators
===========
Sarkas aims to support a variety of time integrators both built-in and user defined.
Currently the available ones are:
- Velocity Verlet
- Velocity Verlet with Langeving Thermostat
- Magnetic Velocity Verlet
- Magnetic Boris
The choice of integrator is provided in... | /sarkas-1.0.2.tar.gz/sarkas-1.0.2/docs/theory/integrators.rst | 0.908601 | 0.991844 | integrators.rst | pypi |
===========================================
Particle-Particle Particle-Mesh Algorithm
===========================================
Ewald Sum
=========
Long range forces are calculated using the Ewald method which consists in dividing the potential into a short
and a long range part. Physically this is equivalent to ad... | /sarkas-1.0.2.tar.gz/sarkas-1.0.2/docs/theory/PPPM.rst | 0.914224 | 0.991554 | PPPM.rst | pypi |
==========
Potentials
==========
Sarkas supports a variety of potentials both built-in and user defined. Currently the potential functions that are
implemented include
- :ref:`Coulomb <coulomb_pot>`
- :ref:`Yukawa <yukawa_pot>`
- :ref:`Exact Gradient-corrected Screened Yukawa <egs_pot>`
- :ref:`Quantum Statistical Pot... | /sarkas-1.0.2.tar.gz/sarkas-1.0.2/docs/theory/potentials.rst | 0.9314 | 0.863966 | potentials.rst | pypi |
===========
Force Error
===========
The Force error is the error incurred when we cut the potential interaction after a certain distance. Following the works
of :cite:`Kolafa1992,Stern2008,Dharuman2017` we define the total force error for our P3M algorithm as
.. math::
\Delta F_{\textrm{tot}} = \sqrt{ \Delta F_{... | /sarkas-1.0.2.tar.gz/sarkas-1.0.2/docs/theory/force_error.rst | 0.920518 | 0.979393 | force_error.rst | pypi |
# Thermostats
## Berendsen Thermostat
The Berendsen Thermostat (BT) uses a tapered velocity scaling approach. In a strict velocity scaling approach
the temperature $T_e$ is estimated, through a quantity proportional to $\langle v^2 \rangle$,
and the velocities are scaled to values consistent with the desired tempera... | /sarkas-1.0.2.tar.gz/sarkas-1.0.2/docs/theory/Berendsen_NB/Berendsen_Thermostat.ipynb | 0.474631 | 0.985841 | Berendsen_Thermostat.ipynb | pypi |
from __future__ import absolute_import
from collections import defaultdict
from itertools import chain
from typing import Any, List
from uuid import uuid4
from sarmat.core.actions import (
ADestinationPoint,
AGeoLocation,
AJourney,
AJourneyBunch,
ARoute,
AStation,
)
from sarmat.core.behavior i... | /core/factory.py | 0.587943 | 0.260295 | factory.py | pypi |
from datetime import time, date
from typing import List
from .geo_locations import DirectionStructure, DestinationPointStructure, RoadNameStructure
from .sarmat import SarmatStructure, nested_dataclass
from ..constants import PeriodType, RoadType, StationType, JourneyType
@nested_dataclass
class StationStructure(Sar... | /core/containers/traffic_management.py | 0.505615 | 0.530723 | traffic_management.py | pypi |
from datetime import date, datetime
from typing import List
from uuid import UUID
from .sarmat import BaseSarmatStructure, SarmatStructure, nested_dataclass
from .traffic_management import PeriodStructure, StationStructure, JourneyStructure
from .vehicle import PermitStructure
from ..constants import JourneyClass, Jou... | /core/containers/dispatcher.py | 0.519034 | 0.330336 | dispatcher.py | pypi |
from dataclasses import asdict, dataclass, fields, is_dataclass
from typing import _GenericAlias
def nested_dataclass(*args, **kwargs):
"""Декоратор подменяет метод __init__ для сборки вложенных структур"""
def wrapper(cls):
check_cls = dataclass(cls, **kwargs)
orig_init = cls.__init__
... | /core/containers/sarmat.py | 0.736685 | 0.175644 | sarmat.py | pypi |
from collections import defaultdict
from sarmat.core.context.containers import (
JourneyBunchContainer,
RouteContainer,
RouteItemContainer,
)
from sarmat.core.exceptions import WrongValueError
from .base_verifications import VerifyOnEmptyValues
class StationVerifier(VerifyOnEmptyValues):
"""Класс ве... | /core/verification/traffic_management_verifications.py | 0.558929 | 0.208441 | traffic_management_verifications.py | pypi |
from typing import List, Dict
from sarmat.core.exceptions import SarmatException
from sarmat.core.constants import ErrorCode, LocationType
from sarmat.core.context.containers import GeoContainer
from .base_verifications import VerifyOnEmptyValues
class GeoVerifier(VerifyOnEmptyValues):
"""Класс верификации гео ... | /core/verification/geo_verifications.py | 0.542379 | 0.397704 | geo_verifications.py | pypi |
from dataclasses import dataclass
from datetime import datetime
from typing import Optional
from sarmat.core.exceptions import IncomparableTypesError
from sarmat.core.context.models import DestinationPointModel, StationModel
@dataclass
class ScheduleItem:
"""Описание участка маршрута"""
station: Optional[St... | /core/behavior/bases.py | 0.691602 | 0.351701 | bases.py | pypi |
from sarmat.core.constants import LocationType, SettlementType
from sarmat.core.exceptions import IncomparableTypesError
from .bases import BhCompare
class BhDirection(BhCompare):
"""Базовое поведение объекта 'Направления'"""
compare_error_message = 'Направления сравнению не подлежат'
contains_error_mess... | /core/behavior/geo_locations.py | 0.476092 | 0.463323 | geo_locations.py | pypi |
from datetime import date, datetime, time, timedelta
from typing import Generator, List
from sarmat.core.constants import PeriodType, RoadType, StationType
from sarmat.core.context.models import (
DestinationPointModel,
JourneyModel,
PeriodItemModel,
RouteItemModel,
StationModel,
)
from sarmat.core... | /core/behavior/traffic_management.py | 0.722233 | 0.269279 | traffic_management.py | pypi |
from abc import ABC, abstractmethod
from datetime import date, datetime, tzinfo
from typing import Dict, Optional
from uuid import uuid4
from sarmat.core.constants import JourneyClass, JourneyState
from sarmat.core.containers import (
PermitStructure,
SarmatStructure,
StationStructure,
JourneyProgressS... | /core/behavior/dispatcher.py | 0.612541 | 0.395076 | dispatcher.py | pypi |
from typing import Optional
from .bases import BhCompare
from ..exceptions import IncomparableTypesError
class BhPerson(BhCompare):
"""Методы сравнения учетных записей"""
compare_error_message = 'Учетные записи сравнению не подлежат'
contains_error_message = 'Учетные записи проверке на вхождение не подле... | /core/behavior/sarmat.py | 0.658418 | 0.254266 | sarmat.py | pypi |
from datetime import date
from typing import List
from sarmat.core.constants import CrewType, PermitType, VehicleType
from sarmat.core.context.models import CrewModel, VehicleModel
from .bases import BhCompare
from .sarmat import BhPerson
from ..exceptions import IncomparableTypesError
class BhVehicle(BhCompare):
... | /core/behavior/vehicle.py | 0.664323 | 0.405213 | vehicle.py | pypi |
import json
from datetime import date, datetime
from typing import Any, Dict, List, Optional
import pydantic
from sarmat.core.constants import PeriodType, DATE_FORMAT, FULL_DATETIME_FORMAT
from sarmat.tools.json_encoder import json_dumps
class SarmatContainer(pydantic.BaseModel):
custom_attributes: Optional[Di... | /core/context/containers/sarmat_containers.py | 0.70416 | 0.202759 | sarmat_containers.py | pypi |
import datetime
from typing import List, Optional
from pydantic import field_serializer, field_validator, ConfigDict
from sarmat.core.constants import (
DATE_FORMAT,
JourneyType,
RoadType,
StationType,
)
from .geo_containers import (
DestinationPointContainer,
DirectionContainer,
RoadName... | /core/context/containers/traffic_management_containers.py | 0.632389 | 0.410697 | traffic_management_containers.py | pypi |
from datetime import date, datetime
from typing import List, Optional
from pydantic import field_serializer, field_validator
from sarmat.core.constants import DATE_FORMAT, FULL_DATETIME_FORMAT, JourneyClass, JourneyState
from .traffic_management_containers import DestinationPointContainer, JourneyContainer, StationC... | /core/context/containers/dispatcher_containers.py | 0.760384 | 0.214362 | dispatcher_containers.py | pypi |
from dataclasses import asdict, dataclass, fields
from typing import Any, Dict, List, Optional
from sarmat.core.constants import PeriodType
from sarmat.core.context.containers.sarmat_containers import SarmatContainer, PeriodItemContainer, PeriodContainer
@dataclass
class BaseModel:
@property
def sarmat_fiel... | /core/context/models/sarmat_models.py | 0.879458 | 0.248283 | sarmat_models.py | pypi |
from dataclasses import dataclass
from datetime import date, datetime
from typing import List, Optional
from sarmat.core.constants import JourneyClass, JourneyState
from .sarmat_models import BaseIdModel, BaseModel, BaseUidModel, CustomAttributesModel, PeriodModel
from .traffic_management_models import DestinationPoi... | /core/context/models/dispatcher_models.py | 0.790126 | 0.15084 | dispatcher_models.py | pypi |
from dataclasses import dataclass
from datetime import date
from typing import List
from sarmat.core.constants import CrewType, PermitType, VehicleType
from sarmat.core.verification import CrewVerifier, PermitVerifier, VehicleVerifier
from .sarmat_models import PersonModel, BaseIdModel, BaseUidModel, BaseModel, Custo... | /core/context/models/vehicle_models.py | 0.669853 | 0.17172 | vehicle_models.py | pypi |
from copy import deepcopy
from dataclasses import dataclass
from datetime import date, datetime, time, timedelta
from typing import List, Optional
from sarmat.core.constants import JourneyType, StationType
from sarmat.core.constants.sarmat_constants import MAX_SUBURBAN_ROUTE_LENGTH
from sarmat.core.context.containers ... | /core/actions/traffic_management.py | 0.742141 | 0.164148 | traffic_management.py | pypi |
from abc import ABC, abstractmethod
from datetime import date, datetime, tzinfo
from typing import Dict, Optional, List, Union
from uuid import uuid4
from sarmat.core.constants import JourneyClass, JourneyState
from sarmat.core.context.models import (
PermitModel,
RouteItemModel,
StationModel,
JourneyP... | /core/actions/dispatcher.py | 0.624523 | 0.285086 | dispatcher.py | pypi |
from enum import Enum
from typing import Any, Dict
class SarmatAttribute(Enum):
"""Встроенные значения атрибутов в Sarmat."""
__description__: Dict[Any, str] = {} # описание
__cypher__: Dict[Any, str] = {} # текстовое представление значения (строковая константа)
@classmethod
def as_te... | /core/constants/sarmat_constants.py | 0.677581 | 0.369941 | sarmat_constants.py | pypi |
from sarmat.core.actions import (
AJourneyBunchMixin,
AJourneyMixin,
ARouteMixin,
AStationMixin,
)
from sarmat.core.behavior import (
BhJourney,
BhJourneyBunch,
BhJourneyBunchItem,
BhRoad,
BhRoute,
BhRouteItem,
BhStation,
)
from sarmat.core.context.containers import (
Jou... | /core/factory/traffic_manager_creator.py | 0.51879 | 0.261449 | traffic_manager_creator.py | pypi |
from sarmat.core.behavior import (
BhCrew,
BhPermit,
BhVehicle,
)
from sarmat.core.context.containers import (
CrewContainer,
PermitContainer,
VehicleContainer,
)
from sarmat.core.context.models import (
CrewModel,
PermitModel,
VehicleModel,
)
from .base_creator import SarmatCreator... | /core/factory/vehicle_creator.py | 0.549882 | 0.239216 | vehicle_creator.py | pypi |
from collections import defaultdict
from typing import Any, Dict, List
from sarmat.core.actions import (
ADestinationPointMixin,
AGeoLocationMixin,
)
from sarmat.core.behavior import (
BhDestinationPoint,
BhDirection,
BhGeo,
BhNoAction,
BhPeriod,
BhPeriodItem,
BhRoadName,
)
from sar... | /core/factory/base_creator.py | 0.852629 | 0.30243 | base_creator.py | pypi |
__classification__ = "UNCLASSIFIED"
__author__ = "Thomas McCullough"
import os
from typing import Union
import numpy
import tkinter
from tkinter import ttk
from tkinter.filedialog import askopenfilenames, askdirectory
from tkinter.messagebox import showinfo
from tk_builder.base_elements import TypedDescriptor, Inte... | /sarpy_apps-1.1.23.tar.gz/sarpy_apps-1.1.23/sarpy_apps/apps/local_support_tool.py | 0.73173 | 0.160266 | local_support_tool.py | pypi |
__classification__ = "UNCLASSIFIED"
__author__ = "Valkyrie Systems Corporation"
import functools
import itertools
import pathlib
import tkinter
from tkinter import messagebox
from tkinter import ttk
import matplotlib.backends.backend_tkagg as mpl_tk
import matplotlib.figure as mpl_fig
import numpy as np
import plotly... | /sarpy_apps-1.1.23.tar.gz/sarpy_apps-1.1.23/sarpy_apps/supporting_classes/cphd_plotting.py | 0.648689 | 0.226709 | cphd_plotting.py | pypi |
__classification__ = "UNCLASSIFIED"
__author__ = ("Jason Casey", "Thomas McCullough")
import tkinter
from tk_builder.widgets import basic_widgets
from sarpy.io.general.base import BaseReader
from sarpy.io.general.nitf import NITFDetails, NITFReader
from sarpy.io.complex.base import SICDTypeReader
from sarpy.io.phase... | /sarpy_apps-1.1.23.tar.gz/sarpy_apps-1.1.23/sarpy_apps/supporting_classes/metaviewer.py | 0.583441 | 0.304076 | metaviewer.py | pypi |
__classification__ = "UNCLASSIFIED"
__author__ = ("Jason Casey", "Thomas McCullough")
import logging
from datetime import datetime
import numpy
from scipy.constants import foot
from sarpy.geometry import latlon
from sarpy.geometry.geocoords import ecf_to_geodetic, geodetic_to_ecf
from sarpy.io.complex.sicd_elements... | /sarpy_apps-1.1.23.tar.gz/sarpy_apps-1.1.23/sarpy_apps/supporting_classes/metaicon/metaicon_data_container.py | 0.759582 | 0.393618 | metaicon_data_container.py | pypi |
SarPy
=====
SarPy is a basic Python library to read, write, and do simple processing
of complex SAR data using the NGA SICD format *(standards linked below)*.
It has been released by NGA to encourage the use of SAR data standards
throughout the international SAR community. SarPy complements the
[SIX](https://github.co... | /sarpy-1.3.58.tar.gz/sarpy-1.3.58/README.md | 0.587115 | 0.945751 | README.md | pypi |
import sys
import os
import argparse
from json import load
from math import log10
from os.path import exists, join
from contextlib import contextmanager
from dark.fasta import FastaReads
from dark.aa import compareAaReads, matchToString as aaMatchToString
from dark.dna import compareDNAReads, matchToString as dnaMatc... | /sars2seq-0.1.0.tar.gz/sars2seq-0.1.0/bin/describe-genome.py | 0.492188 | 0.248238 | describe-genome.py | pypi |
import sys
import os
from json import dumps
import argparse
from dark.fasta import FastaReads
import sars2seq
from sars2seq.features import Features
from sars2seq.genome import SARS2Genome, addAlignerOption
def report(genome, args, includeGenome=True):
"""
Report what's found at a site for a given genome (... | /sars2seq-0.1.0.tar.gz/sars2seq-0.1.0/bin/describe-site.py | 0.42322 | 0.276445 | describe-site.py | pypi |
import argparse
from collections import defaultdict
from sars2seq.features import Features, ALIASES
def printNames(features):
"""
Print feature names, each with all known aliases (if any).
@param features: A C{Features} instance.
"""
def key(name):
"""
Make a sort key for featu... | /sars2seq-0.1.0.tar.gz/sars2seq-0.1.0/bin/describe-feature.py | 0.577138 | 0.224523 | describe-feature.py | pypi |
from django.db import migrations, models
class Migration(migrations.Migration):
initial = True
dependencies = []
operations = [
migrations.CreateModel(
name="KapInformationSources",
fields=[
(
"id",
models.AutoFiel... | /migrations/0001_initial.py | 0.590425 | 0.173078 | 0001_initial.py | pypi |
import _socket
from django.conf import settings
import django.core.validators
from django.db import migrations, models
import django.db.models.deletion
import django_audit_fields.fields.hostname_modification_field
import django_audit_fields.fields.userfield
import django_audit_fields.fields.uuid_auto_field
import djan... | /migrations/0003_auto_20200515_0231.py | 0.407333 | 0.159872 | 0003_auto_20200515_0231.py | pypi |
**sarscov2vec** is an application of continuous vector space representation on novel species of coronaviruses genomes as the methodology of genome feature extraction step, to distinguish the most common 5 different SARS-CoV-2 variants (Alpha, Beta, Delta, Gamma, Omicron) by supervised machine learning model.
In th... | /sarscov2vec-1.0.0.tar.gz/sarscov2vec-1.0.0/README.md | 0.490724 | 0.981489 | README.md | pypi |
import os
from typing import Set
import pandas as pd
from pandas.core.series import Series
from Bio.SeqIO.FastaIO import FastaIterator
from Bio.SeqRecord import SeqRecord
from Bio.Seq import Seq
class FastaReader:
"""
Parse FASTA file with nucleotide sequences
"""
def __init__(self, fasta_file... | /sarscov2vec-1.0.0.tar.gz/sarscov2vec-1.0.0/tools/sarscov2vec.py | 0.900822 | 0.390185 | sarscov2vec.py | pypi |
from django.core.validators import MinValueValidator, MaxValueValidator
from django.db import models
from edc_constants.choices import (
TRUE_FALSE_DONT_KNOW,
YES_NO,
YES_NO_NA,
YES_NO_UNKNOWN,
)
from edc_constants.constants import NOT_APPLICABLE
from edc_model import models as edc_models
from ..choice... | /sarscov2x-1.0.0-py3-none-any.whl/coronavirus/model_mixins/coronavirus_kap_model_mixin.py | 0.461745 | 0.273023 | coronavirus_kap_model_mixin.py | pypi |
from django.contrib import admin
from django.utils.safestring import mark_safe
from django_audit_fields import audit_fieldset_tuple
fieldsets = [
(
"Coronavirus Knowledge, Attitudes, and Practices",
{"fields": ("screening_identifier", "report_datetime")},
),
(
"Disease Burden: HIV",... | /sarscov2x-1.0.0-py3-none-any.whl/coronavirus/admin/modeladmin_mixin.py | 0.475118 | 0.360573 | modeladmin_mixin.py | pypi |
# Sarsen
Algorithms and utilities for Synthetic Aperture Radar (SAR) sensors.
Enables cloud-native SAR processing via [*Xarray*](https://xarray.pydata.org)
and [*Dask*](https://dask.org).
This Open Source project is sponsored by B-Open - https://www.bopen.eu.
## Features and limitations
*Sarsen* is a Python library... | /sarsen-0.9.2.tar.gz/sarsen-0.9.2/README.md | 0.542621 | 0.984985 | README.md | pypi |
```
%load_ext autoreload
%autoreload 2
%matplotlib inline
%config InlineBackend.figure_format = 'retina'
import matplotlib.pyplot as plt
plt.rcParams["figure.figsize"] = (10, 7)
plt.rcParams["font.size"] = 12
import inspect
import numpy as np
import xarray as xr
import xarray_sentinel
from sarsen import apps, geo... | /sarsen-0.9.2.tar.gz/sarsen-0.9.2/notebooks/S1-SLC-SM-backward-geocode.ipynb | 0.430387 | 0.754418 | S1-SLC-SM-backward-geocode.ipynb | pypi |
```
%load_ext autoreload
%autoreload 2
%matplotlib inline
%config InlineBackend.figure_format = 'retina'
import matplotlib.pyplot as plt
plt.rcParams["figure.figsize"] = (10, 7)
plt.rcParams["font.size"] = 12
import inspect
import numpy as np
import xarray as xr
import xarray_sentinel
from sarsen import apps, geo... | /sarsen-0.9.2.tar.gz/sarsen-0.9.2/notebooks/S1-GRD-SM-backward-geocode.ipynb | 0.426322 | 0.750987 | S1-GRD-SM-backward-geocode.ipynb | pypi |
```
%load_ext autoreload
%autoreload 2
%matplotlib inline
%config InlineBackend.figure_format = 'retina'
import matplotlib.pyplot as plt
plt.rcParams["figure.figsize"] = (12, 8)
plt.rcParams["font.size"] = 12
import numpy as np
import rioxarray
import xarray as xr
import xarray_sentinel
from sarsen import apps, ge... | /sarsen-0.9.2.tar.gz/sarsen-0.9.2/notebooks/S1-SLC-IW-gamma-flattening.ipynb | 0.550124 | 0.611005 | S1-SLC-IW-gamma-flattening.ipynb | pypi |
```
%load_ext autoreload
%autoreload 2
%matplotlib inline
%config InlineBackend.figure_format = 'retina'
import matplotlib.pyplot as plt
plt.rcParams["figure.figsize"] = (10, 7)
plt.rcParams["font.size"] = 12
import inspect
import numpy as np
import xarray as xr
import xarray_sentinel
from sarsen import apps, geo... | /sarsen-0.9.2.tar.gz/sarsen-0.9.2/notebooks/S1-GRD-IW-backward-geocode.ipynb | 0.424173 | 0.75274 | S1-GRD-IW-backward-geocode.ipynb | pypi |
# Profiling of terrain corrections
<hr style="border:2px solid blue"> </hr>
### Install Dependencies and Import
Additional dependecies: `sarsen`, `snakeviz`
```
!pip install -q sarsen snakeviz
%load_ext snakeviz
import os
import tempfile
import adlfs
import planetary_computer
import pystac_client
# enable th... | /sarsen-0.9.2.tar.gz/sarsen-0.9.2/notebooks/extended_profiling_of_terrain_corrections.ipynb | 0.429908 | 0.807195 | extended_profiling_of_terrain_corrections.ipynb | pypi |
```
%load_ext autoreload
%autoreload 2
%matplotlib inline
%config InlineBackend.figure_format = 'retina'
import matplotlib.pyplot as plt
plt.rcParams["figure.figsize"] = (10, 7)
plt.rcParams["font.size"] = 12
import inspect
import numpy as np
import xarray as xr
import xarray_sentinel
from sarsen import apps, geo... | /sarsen-0.9.2.tar.gz/sarsen-0.9.2/notebooks/S1-SLC-IW-backward-geocode.ipynb | 0.42656 | 0.751352 | S1-SLC-IW-backward-geocode.ipynb | pypi |
from __future__ import annotations
from abc import abstractmethod
from enum import Enum
import datetime as dt
import logging
import typing as t
import warnings
import numpy as np
import pandas as pd
import pyarrow as pa
from sarus_data_spec.protobuf.typing import Protobuf, ProtobufWithUUID
import sarus_data_spec.man... | /sarus_data_spec_public-3.5.16.tar.gz/sarus_data_spec_public-3.5.16/sarus_data_spec/typing.py | 0.887345 | 0.246239 | typing.py | pypi |
from __future__ import annotations
from os.path import basename
from typing import (
TYPE_CHECKING,
AsyncIterator,
Collection,
Dict,
Iterator,
List,
Mapping,
Optional,
Set,
Tuple,
Type,
Union,
cast,
)
from urllib.parse import urlparse
import json
import typing as t
i... | /sarus_data_spec_public-3.5.16.tar.gz/sarus_data_spec_public-3.5.16/sarus_data_spec/dataset.py | 0.870101 | 0.304352 | dataset.py | pypi |
from __future__ import annotations
import datetime
import json
import typing as t
import numpy as np
import pandas as pd
import pyarrow as pa
from sarus_data_spec.base import Base
from sarus_data_spec.constants import (
ARRAY_VALUES,
DATA,
LIST_VALUES,
OPTIONAL_VALUE,
PUBLIC,
TEXT_CHARSET,
... | /sarus_data_spec_public-3.5.16.tar.gz/sarus_data_spec_public-3.5.16/sarus_data_spec/type.py | 0.727879 | 0.16896 | type.py | pypi |
from __future__ import annotations
from typing import (
Collection,
Dict,
List,
Optional,
Set,
Tuple,
Type,
Union,
cast,
)
import datetime
import typing as t
from sarus_data_spec.base import Referring
from sarus_data_spec.transform import Transform
import sarus_data_spec.protobuf a... | /sarus_data_spec_public-3.5.16.tar.gz/sarus_data_spec_public-3.5.16/sarus_data_spec/scalar.py | 0.930703 | 0.362151 | scalar.py | pypi |
from __future__ import annotations
import typing as t
import pyarrow as pa
from sarus_data_spec.arrow.schema import to_arrow
from sarus_data_spec.base import Referring
from sarus_data_spec.constants import DATA, DATASET_SLUGNAME, PUBLIC
from sarus_data_spec.path import Path, path
from sarus_data_spec.type import Typ... | /sarus_data_spec_public-3.5.16.tar.gz/sarus_data_spec_public-3.5.16/sarus_data_spec/schema.py | 0.742888 | 0.33185 | schema.py | pypi |
from __future__ import annotations
import datetime
import typing as t
from sarus_data_spec.base import Referrable
from sarus_data_spec.json_serialisation import SarusJSONEncoder
from sarus_data_spec.path import straight_path
import sarus_data_spec.dataset as sd
import sarus_data_spec.protobuf as sp
import sarus_data_... | /sarus_data_spec_public-3.5.16.tar.gz/sarus_data_spec_public-3.5.16/sarus_data_spec/transform.py | 0.849582 | 0.39826 | transform.py | pypi |
from datetime import date, datetime, time, timedelta, timezone
from typing import Any
import json
import sys
from dateutil.parser import parse
import numpy as np
import pandas as pd
class SarusJSONEncoder(json.JSONEncoder):
def default(self, obj: Any) -> Any:
if isinstance(obj, np.ndarray):
r... | /sarus_data_spec_public-3.5.16.tar.gz/sarus_data_spec_public-3.5.16/sarus_data_spec/json_serialisation.py | 0.605566 | 0.228425 | json_serialisation.py | pypi |
from __future__ import annotations
from collections import defaultdict
import typing as t
from sarus_data_spec.base import Base
import sarus_data_spec.protobuf as sp
import sarus_data_spec.typing as st
class Path(Base[sp.Path]):
"""A python class to describe paths"""
def prototype(self) -> t.Type[sp.Path]:... | /sarus_data_spec_public-3.5.16.tar.gz/sarus_data_spec_public-3.5.16/sarus_data_spec/path.py | 0.674372 | 0.323948 | path.py | pypi |
from time import time_ns
from typing import Collection, Dict, List, Optional, Tuple, Union, cast
import logging
from sarus_data_spec.attribute import attach_properties
from sarus_data_spec.constants import VARIANT_UUID
from sarus_data_spec.context import global_context
from sarus_data_spec.dataset import transformed
f... | /sarus_data_spec_public-3.5.16.tar.gz/sarus_data_spec_public-3.5.16/sarus_data_spec/dataspec_rewriter/simple_rules.py | 0.817902 | 0.233335 | simple_rules.py | pypi |
from typing import (
Callable,
Collection,
Dict,
Optional,
Protocol,
Set,
Tuple,
Union,
runtime_checkable,
)
from sarus_data_spec.protobuf.typing import (
ProtobufWithUUID,
ProtobufWithUUIDAndDatetime,
)
from sarus_data_spec.typing import DataSpec, Referrable, Referring
# W... | /sarus_data_spec_public-3.5.16.tar.gz/sarus_data_spec_public-3.5.16/sarus_data_spec/storage/typing.py | 0.89951 | 0.553023 | typing.py | pypi |
from collections import defaultdict
from itertools import chain, combinations
from typing import (
Callable,
Collection,
DefaultDict,
Dict,
Final,
FrozenSet,
List,
MutableMapping,
Optional,
Set,
Tuple,
Union,
cast,
)
from sarus_data_spec.protobuf.typing import (
... | /sarus_data_spec_public-3.5.16.tar.gz/sarus_data_spec_public-3.5.16/sarus_data_spec/storage/local.py | 0.876383 | 0.460046 | local.py | pypi |
from typing import Collection, cast
from sarus_data_spec.protobuf.typing import ProtobufWithUUID
from sarus_data_spec.storage.typing import Storage
from sarus_data_spec.typing import Referrable, Referring
def sort_dataspecs(
storage: Storage, values: Collection[Referrable[ProtobufWithUUID]]
) -> Collection[Refer... | /sarus_data_spec_public-3.5.16.tar.gz/sarus_data_spec_public-3.5.16/sarus_data_spec/storage/utils.py | 0.74008 | 0.593963 | utils.py | pypi |
from __future__ import annotations
from typing import Any, Dict, List, Optional, Type, TypeVar, Union, cast
import base64
from google.protobuf.any_pb2 import Any as AnyProto
from google.protobuf.descriptor_pool import Default
from google.protobuf.json_format import (
MessageToDict,
MessageToJson,
Parse,
... | /sarus_data_spec_public-3.5.16.tar.gz/sarus_data_spec_public-3.5.16/sarus_data_spec/protobuf/utilities.py | 0.855972 | 0.183009 | utilities.py | pypi |
import typing as t
import pandas as pd
import pyarrow as pa
from sarus_data_spec.arrow.pandas_utils import (
convert_pandas_metadata_to_admin_columns,
pandas_index_columns,
remove_pandas_index_columns,
)
from sarus_data_spec.constants import DATA, PUBLIC, USER_COLUMN, WEIGHTS
import sarus_data_spec.typing... | /sarus_data_spec_public-3.5.16.tar.gz/sarus_data_spec_public-3.5.16/sarus_data_spec/arrow/admin_utils.py | 0.589953 | 0.466542 | admin_utils.py | pypi |
import typing as t
import pyarrow as pa
import sarus_data_spec.type as sdt
import sarus_data_spec.typing as st
INTBASE_TO_ARROW = {
st.IntegerBase.INT64: pa.int64(),
st.IntegerBase.INT32: pa.int32(),
st.IntegerBase.INT16: pa.int16(),
st.IntegerBase.INT8: pa.int8(),
st.IntegerBase.UINT64: pa.uint6... | /sarus_data_spec_public-3.5.16.tar.gz/sarus_data_spec_public-3.5.16/sarus_data_spec/arrow/type.py | 0.581897 | 0.281286 | type.py | pypi |
import typing as t
import pyarrow as pa
from sarus_data_spec.type import Struct, Type
import sarus_data_spec.arrow.type as arrow_type
import sarus_data_spec.protobuf as sp
import sarus_data_spec.typing as st
def to_arrow(schema: sp.Schema) -> pa.schema:
"""Convert Sarus schema to pyarrow schema."""
return a... | /sarus_data_spec_public-3.5.16.tar.gz/sarus_data_spec_public-3.5.16/sarus_data_spec/arrow/schema.py | 0.41324 | 0.402099 | schema.py | pypi |
import typing as t
import pyarrow as pa
from sarus_data_spec.constants import DATA
def pandas_index_columns(schema: pa.Schema) -> t.List[str]:
"""Return the list of columns that have to be considered as Pandas index
columns and ignored by the Sarus type.
"""
pandas_metadata = schema.pandas_metadata
... | /sarus_data_spec_public-3.5.16.tar.gz/sarus_data_spec_public-3.5.16/sarus_data_spec/arrow/pandas_utils.py | 0.617051 | 0.477432 | pandas_utils.py | pypi |
from __future__ import annotations
from typing import (
AsyncIterator,
Callable,
Dict,
Iterator,
List,
Optional,
Protocol,
Tuple,
runtime_checkable,
)
import typing as t
import pandas as pd
import pyarrow as pa
try:
import tensorflow as tf
except ModuleNotFoundError:
pass ... | /sarus_data_spec_public-3.5.16.tar.gz/sarus_data_spec_public-3.5.16/sarus_data_spec/manager/typing.py | 0.854642 | 0.476032 | typing.py | pypi |
from collections import defaultdict
import typing as t
from sarus_sql import ast_utils, rename_tables, translator
from sarus_data_spec.path import Path
import sarus_data_spec.type as sdt
import sarus_data_spec.typing as st
def rename_and_compose_queries(
query_or_dict: t.Union[str, t.Dict[str, t.Any]],
curr... | /sarus_data_spec_public-3.5.16.tar.gz/sarus_data_spec_public-3.5.16/sarus_data_spec/manager/ops/sql_utils/queries.py | 0.730097 | 0.35095 | queries.py | pypi |
import typing as t
import warnings
import pyarrow as pa
from sarus_data_spec.attribute import attach_properties
from sarus_data_spec.bounds import bounds as bounds_builder
from sarus_data_spec.marginals import marginals as marginals_builder
from sarus_data_spec.multiplicity import multiplicity as multiplicity_builder... | /sarus_data_spec_public-3.5.16.tar.gz/sarus_data_spec_public-3.5.16/sarus_data_spec/manager/ops/processor/standard/synthetic.py | 0.442155 | 0.245367 | synthetic.py | pypi |
import typing as t
import pyarrow as pa
from sarus_data_spec.arrow.array import convert_record_batch
from sarus_data_spec.bounds import bounds as bounds_builder
from sarus_data_spec.constants import (
DATASET_SLUGNAME,
OPTIONAL_VALUE,
PRIMARY_KEYS,
)
from sarus_data_spec.manager.ops.processor.standard.sta... | /sarus_data_spec_public-3.5.16.tar.gz/sarus_data_spec_public-3.5.16/sarus_data_spec/manager/ops/processor/standard/project.py | 0.722723 | 0.160727 | project.py | pypi |
import typing as t
import pyarrow as pa
from sarus_data_spec.arrow.array import convert_record_batch
from sarus_data_spec.bounds import bounds as bounds_builder
from sarus_data_spec.constants import DATA, DATASET_SLUGNAME
from sarus_data_spec.dataset import Dataset
from sarus_data_spec.manager.ops.processor.standard.... | /sarus_data_spec_public-3.5.16.tar.gz/sarus_data_spec_public-3.5.16/sarus_data_spec/manager/ops/processor/standard/get_item.py | 0.459319 | 0.308972 | get_item.py | pypi |
import hashlib
import logging
import typing as t
import warnings
import pyarrow as pa
from sarus_data_spec.dataset import Dataset
from sarus_data_spec.manager.ops.base import (
DatasetImplementation,
DatasetStaticChecker,
DataspecStaticChecker,
ScalarImplementation,
_ensure_batch_correct,
)
try:
... | /sarus_data_spec_public-3.5.16.tar.gz/sarus_data_spec_public-3.5.16/sarus_data_spec/manager/ops/processor/standard/standard_op.py | 0.750827 | 0.374991 | standard_op.py | pypi |
from __future__ import annotations
import typing as t
from sarus_data_spec.dataspec_validator.signature import SarusBoundSignature
from sarus_data_spec.dataspec_validator.typing import PEPKind
import sarus_data_spec.typing as st
NO_TRANSFORM_ID = "no_transform_id"
@t.runtime_checkable
class ExternalOpImplementatio... | /sarus_data_spec_public-3.5.16.tar.gz/sarus_data_spec_public-3.5.16/sarus_data_spec/manager/ops/processor/external/typing.py | 0.901834 | 0.62986 | typing.py | pypi |
from __future__ import annotations
from typing import Any, Callable, Dict, List, Literal, Optional, Tuple, Union
import numpy as np
from sarus_data_spec.dataspec_validator.parameter_kind import DATASPEC, STATIC
from sarus_data_spec.dataspec_validator.signature import (
SarusParameter,
SarusSignature,
Sar... | /sarus_data_spec_public-3.5.16.tar.gz/sarus_data_spec_public-3.5.16/sarus_data_spec/manager/ops/processor/external/imblearn.py | 0.890163 | 0.226495 | imblearn.py | pypi |
from typing import Any, Callable, Dict, List, Literal, Optional, Tuple, Union
import numpy as np
import pandas as pd
from sarus_data_spec.dataspec_validator.signature import (
SarusParameter,
SarusSignature,
SarusSignatureValue,
)
from .external_op import ExternalOpImplementation
try:
from xgboost i... | /sarus_data_spec_public-3.5.16.tar.gz/sarus_data_spec_public-3.5.16/sarus_data_spec/manager/ops/processor/external/xgboost.py | 0.784773 | 0.182589 | xgboost.py | pypi |
from typing import Any, Callable, Dict, Iterable, List, Optional, Tuple, Union
import numpy as np
from sarus_data_spec.dataspec_validator.signature import (
SarusParameter,
SarusSignature,
SarusSignatureValue,
)
from .external_op import ExternalOpImplementation
try:
from sklearn.base import BaseEsti... | /sarus_data_spec_public-3.5.16.tar.gz/sarus_data_spec_public-3.5.16/sarus_data_spec/manager/ops/processor/external/skopt.py | 0.823399 | 0.212681 | skopt.py | pypi |
from importlib import import_module
from typing import Dict, List, Optional, Type, cast
import inspect
from .typing import NO_TRANSFORM_ID, ExternalOpImplementation
MODULES = [
"pandas",
"sklearn",
"numpy",
"imblearn",
"pandas_profiling",
"skopt",
"std",
"xgboost",
"shap",
]
def ... | /sarus_data_spec_public-3.5.16.tar.gz/sarus_data_spec_public-3.5.16/sarus_data_spec/manager/ops/processor/external/__init__.py | 0.809351 | 0.357259 | __init__.py | pypi |
from __future__ import annotations
import hashlib
import typing as t
import pandas as pd
import pyarrow as pa
from sarus_data_spec.arrow.admin_utils import (
compute_admin_data,
create_admin_columns,
merge_data_and_admin,
)
from sarus_data_spec.arrow.conversion import to_pyarrow_table
from sarus_data_spe... | /sarus_data_spec_public-3.5.16.tar.gz/sarus_data_spec_public-3.5.16/sarus_data_spec/manager/ops/processor/external/external_op.py | 0.872958 | 0.315209 | external_op.py | pypi |
from typing import Any, List, Literal, Optional, Tuple, Union
from numpy.typing import ArrayLike, DTypeLike
import numpy as np
from sarus_data_spec.dataspec_validator.parameter_kind import DATASPEC, STATIC
from sarus_data_spec.dataspec_validator.signature import (
SarusParameter,
SarusParameterArray,
Saru... | /sarus_data_spec_public-3.5.16.tar.gz/sarus_data_spec_public-3.5.16/sarus_data_spec/manager/ops/processor/external/numpy.py | 0.858704 | 0.212743 | numpy.py | pypi |
from typing import Any, Dict, Iterable, List, Optional
import numpy as np
from sarus_data_spec.dataspec_validator.parameter_kind import STATIC
from sarus_data_spec.dataspec_validator.privacy_limit import DeltaEpsilonLimit
from sarus_data_spec.dataspec_validator.signature import (
SarusBoundSignature,
SarusPar... | /sarus_data_spec_public-3.5.16.tar.gz/sarus_data_spec_public-3.5.16/sarus_data_spec/manager/ops/processor/external/std.py | 0.845974 | 0.211458 | std.py | pypi |
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