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 |
|---|---|---|---|---|---|---|
"""Training a single gated model and scoring it on held-out data.
The original pipeline reported feature weights with no accompanying measure of
whether the model had learned anything -- a network that failed to fit still
emitted a full set of importances. :func:`train_one` always returns test-set
metrics alongside t... | AkandaAshraf/DeepFeatSelection | deepfeatselect/train.py | .py | 6f2330bd3d003eab | 7 | 0 |
"""Did the model understand the structure, or memorise the rows?
Validation loss cannot tell those apart. A network that fits 4200 rows perfectly
and generalises nothing, and one that never fit anything, both report a
validation loss at chance -- and every scaling experiment in this project
recorded only that number.
... | AkandaAshraf/DeepFeatSelection | deepfeatselect/understanding.py | .py | 62d4664780a04db4 | 7 | 0 |
"""One table: every dataset audited so far, same statistics, same thresholds.
The individual audits each answer "is this ranking identifiable", but the
interesting result only appears when they are put beside each other. Ordered by
how the columns came to exist rather than by subject matter, they separate
cleanly, and... | AkandaAshraf/DeepFeatSelection | scripts/audit_comparison.py | .py | 630d7a1a315fed41 | 7 | 0 |
"""Screen chamber datasets against the fitness gate, across a decimation grid.
Pre-registration: paper/dataset_fitness_protocol.md and its 2026-08-23
addendum, committed before any lag_info was computed on the new data.
The pass mark is unchanged and calibrated: L50 = +0.0136, the value measured
on the weakest couple... | AkandaAshraf/DeepFeatSelection | scripts/chamber_screen.py | .py | 174aa397dd09aec7 | 7 | 0 |
#!/usr/bin/env python3
"""Example script for a dataset provider to submit metadata and data location records to the SOLARNET Virtual Observatory (SVO) RESTful API"""
import os
import sys
import argparse
import logging
from datetime import datetime
from urllib.parse import urljoin
from dateutil.parser import parse, Pars... | bmampaey/SOLARNET-provider-tools | astro_su_se/submit_record.py | .py | d3539c45d3f7b492 | 7 | 0 |
#!/usr/bin/env python3
from unittest import TestCase, mock, main
from pathlib import Path
from submit_record import Record, DATE_KEYWORD
class TestSubmiRecord(TestCase):
'''Test the submit_record script'''
def setUp(self):
super().setUp()
self.test_file = str(Path(__file__).parent / 'test_file.fits')
def te... | bmampaey/SOLARNET-provider-tools | astro_su_se/test_submit_record.py | .py | bcb4c2d59cc265ec | 7.5 | 0 |
#!/usr/bin/env python3
import argparse
import json
import logging
import os
import pickle
import re
import string
from collections import Counter, defaultdict
from datetime import datetime
import astropy.io.fits
import dateutil.parser
# Default keywords to exclude
DEFAULT_EXCLUDE_KEYWORDS = ['DATASUM', 'CHECKSUM', 'S... | bmampaey/SOLARNET-provider-tools | extra/extract_keywords_from_fits.py | .py | 58c069df4de7e4c0 | 7 | 0 |
#!/usr/bin/env python3
import argparse
import json
import logging
import re
import pyvo
class KeywordInspector:
"""Inspect the columns of of a TAP service table, and build the information needed for the SVO"""
# Conversion from VOtable datatype to SVO keyword type
# See https://www.ivoa.net/documents/VOTable/201... | bmampaey/SOLARNET-provider-tools | extra/extract_keywords_from_tap.py | .py | 35b3f6467028538b | 7 | 0 |
__all__ = ['DataLocation']
class DataLocation:
"""Base class for building data_location resource payloads.
Subclasses are expected to override the getter methods of the payload fields
(`file_url`, `file_size`, `file_path`, `thumbnail_url`, `offline`)
for the specific data source (e.g. a remote URL, a TAP record,... | bmampaey/SOLARNET-provider-tools | provider_tools/data_locations/data_location.py | .py | 3a67cbf5e38cdbd2 | 7 | 0 |
import os
from urllib.parse import urljoin
from .data_location import DataLocation
__all__ = ['DataLocationFromLocalFile']
class DataLocationFromLocalFile(DataLocation):
"""Build a data_location payload from a local file.
Attributes:
BASE_FILE_PATH (str): Base path used to derive the relative file path.
BASE... | bmampaey/SOLARNET-provider-tools | provider_tools/data_locations/data_location_from_local_file.py | .py | a2dfbd3789e95420 | 7 | 0 |
from .data_location import DataLocation
__all__ = ['DataLocationFromTapRecord']
class DataLocationFromTapRecord(DataLocation):
"""Build a data_location payload from an EPN-TAP record."""
def __init__(self, tap_record, **kwargs):
"""Initialize the data location from a TAP record.
Args:
tap_record (Mapping)... | bmampaey/SOLARNET-provider-tools | provider_tools/data_locations/data_location_from_tap_record.py | .py | 36fa77d5fa61755d | 7 | 0 |
import requests
from .data_location import DataLocation
__all__ = ['DataLocationFromUrl']
class DataLocationFromUrl(DataLocation):
"""Build a data_location payload for a file hosted at a remote URL.
Attributes:
BASE_FILE_URL (str): Base URL to derive the relative file path.
"""
# The base file URL to build ... | bmampaey/SOLARNET-provider-tools | provider_tools/data_locations/data_location_from_url.py | .py | a406712b6499307c | 7 | 0 |
import datetime
import numbers
__all__ = ['Metadata']
class Metadata:
"""Base class for building metadata resource payloads.
Subclasses must implement [`extract_field_value`][provider_tools.metadatas.Metadata.extract_field_value] to define how a
field's value is pulled from their particular source data (e.g. a T... | bmampaey/SOLARNET-provider-tools | provider_tools/metadatas/metadata.py | .py | ae5c64497098fbc1 | 7 | 0 |
import dateutil.parser
from .metadata import Metadata
__all__ = ['MetadataFromFitsHeader']
class MetadataFromFitsHeader(Metadata):
"""Build metadata payloads from FITS header values.
Extracts field values by looking up each keyword's verbose name in the
FITS header, converting the value to the type expected by ... | bmampaey/SOLARNET-provider-tools | provider_tools/metadatas/metadata_from_fits_header.py | .py | f9631c013d1f09b6 | 7 | 0 |
import astropy
import dateutil.parser
from .metadata import Metadata
__all__ = ['MetadataFromTapRecord']
class MetadataFromTapRecord(Metadata):
"""Build metadata payloads from an EPN-TAP record.
Extracts field values by looking up each keyword's verbose name in the
TAP record, converting the value to the type e... | bmampaey/SOLARNET-provider-tools | provider_tools/metadatas/metadata_from_tap_record.py | .py | 37f5027995dde863 | 7 | 0 |
import requests
from ..data_locations import DataLocationFromUrl
from ..metadatas import MetadataFromFitsHeader
from ..utils import get_fits_header_from_url
from .provider import Provider
__all__ = ['ProviderFromFitsUrl']
class ProviderFromFitsUrl(Provider):
"""Extract the metadata and data_location resource paylo... | bmampaey/SOLARNET-provider-tools | provider_tools/providers/provider_from_fits_url.py | .py | 59bb9be96579ed10 | 7 | 0 |
from ..data_locations import DataLocationFromLocalFile
from ..metadatas import MetadataFromFitsHeader
from ..utils import get_fits_header_from_local_file
from .provider import Provider
__all__ = ['ProviderFromLocalFitsFile']
class ProviderFromLocalFitsFile(Provider):
"""Extract the metadata and data_location resour... | bmampaey/SOLARNET-provider-tools | provider_tools/providers/provider_from_local_fits_file.py | .py | e564f9c8447457d7 | 7 | 0 |
from ..data_locations import DataLocationFromTapRecord
from ..metadatas import MetadataFromTapRecord
from .provider import Provider
__all__ = ['ProviderFromTapRecord']
class ProviderFromTapRecord(Provider):
"""Extract the metadata and data_location resource payloads for TAP records.
Attributes:
METADATA_CLASS (... | bmampaey/SOLARNET-provider-tools | provider_tools/providers/provider_from_tap_record.py | .py | 8ee690b93bff1d25 | 7 | 0 |
import http.client
import slumber
import yaml
from .utils import JsonSerializer
__all__ = ['RESTfulApi']
# URL of the SVO RESTful API
SVO_API_URL = 'https://solarnet.oma.be/service/api/svo'
class RESTfulApi(slumber.API):
"""RESTful API interface for the SVO.
Args:
username (str, optional): SVO username. Cann... | bmampaey/SOLARNET-provider-tools | provider_tools/restful_api.py | .py | 5cfd10ac62aa74e7 | 7 | 0 |
import datetime
import glob
import io
import logging
import os
import urllib.parse
import zlib
import astropy.io.fits
import dateutil.parser
import htmllistparse
import pyvo
import requests
import simplejson
import slumber
__all__ = [
'parse_date_time_string',
'iter_files',
'iter_urls',
'iter_tap_records',
'get_... | bmampaey/SOLARNET-provider-tools | provider_tools/utils.py | .py | 777d5fbc38cb910b | 7 | 0 |
#!/usr/bin/env python3
"""Script to extract metadata from the AIA level 1.5 archive and submit it to the SOLARNET Virtual Observatory"""
import argparse
import logging
import sys
from datetime import timedelta
from pathlib import Path
from urllib.parse import urljoin
# HACK to make sure the provider_tools package is ... | bmampaey/SOLARNET-provider-tools | sidc_oma_be/submit_metadata_aia_level_1_5.py | .py | c407b89646a854c5 | 7 | 0 |
#!/usr/bin/env python3
"""Script to extract metadata from the AIA level 2 archive and submit it to the SOLARNET Virtual Observatory"""
import argparse
import logging
import sys
from datetime import timedelta
from pathlib import Path
# HACK to make sure the provider_tools package is findable
sys.path.append(str(Path(_... | bmampaey/SOLARNET-provider-tools | sidc_oma_be/submit_metadata_aia_level_2.py | .py | e11b66bc39545420 | 7 | 0 |
#!/usr/bin/env python3
"""Script to extract metadata from the ASPIICS level 2 archive and submit it to the SOLARNET Virtual Observatory"""
import argparse
import logging
import sys
from pathlib import Path, PurePosixPath
# HACK to make sure the provider_tools package is findable
sys.path.append(str(Path(__file__).res... | bmampaey/SOLARNET-provider-tools | sidc_oma_be/submit_metadata_aspiics_level_2.py | .py | c8c3fde0faca25b7 | 7 | 0 |
#!/usr/bin/env python3
"""Script to extract metadata from the ASPIICS level 2 archive and submit it to the SOLARNET Virtual Observatory"""
import argparse
import logging
import sys
from pathlib import Path, PurePosixPath
# HACK to make sure the provider_tools package is findable
sys.path.append(str(Path(__file__).res... | bmampaey/SOLARNET-provider-tools | sidc_oma_be/submit_metadata_aspiics_level_3.py | .py | 0d5981436ec1663b | 7 | 0 |
#!/usr/bin/env python3
"""Script to extract metadata from the Leibniz-KIS TAP service and submit it to the SOLARNET Virtual Observatory"""
import argparse
import logging
import sys
from pathlib import Path
# HACK to make sure the provider_tools package is findable
sys.path.append(str(Path(__file__).resolve().parent.p... | bmampaey/SOLARNET-provider-tools | sidc_oma_be/submit_metadata_chrotel_level_1.py | .py | 548ee5b26ba4e4e7 | 7 | 0 |
#!/usr/bin/env python3
"""Script to extract metadata from the EIT archive and submit it to the SOLARNET Virtual Observatory"""
import argparse
import logging
import sys
from datetime import timedelta
from pathlib import Path
# HACK to make sure the provider_tools package is findable
sys.path.append(str(Path(__file__)... | bmampaey/SOLARNET-provider-tools | sidc_oma_be/submit_metadata_eit_level_0.py | .py | 088545b2b212dcc1 | 7 | 0 |
#!/usr/bin/env python3
"""Script to extract metadata from the MEDOC TAP serviceand submit it to the SOLARNET Virtual Observatory"""
import argparse
import logging
import sys
from pathlib import Path
import requests
# HACK to make sure the provider_tools package is findable
sys.path.append(str(Path(__file__).resolve(... | bmampaey/SOLARNET-provider-tools | sidc_oma_be/submit_metadata_eit_synoptic.py | .py | 07b69a35772d0b5f | 7 | 0 |
#!/usr/bin/env python3
"""Script to extract metadata from the EUI archive and submit it to the SOLARNET Virtual Observatory"""
import argparse
import logging
import sys
from datetime import timedelta
from pathlib import Path, PurePosixPath
# HACK to make sure the provider_tools package is findable
sys.path.append(str... | bmampaey/SOLARNET-provider-tools | sidc_oma_be/submit_metadata_eui_level_1.py | .py | 61854c6e050bf356 | 7 | 0 |
#!/usr/bin/env python3
"""Script to extract metadata from the EUI archive and submit it to the SOLARNET Virtual Observatory"""
import argparse
import logging
import sys
from datetime import timedelta
from pathlib import Path, PurePosixPath
# HACK to make sure the provider_tools package is findable
sys.path.append(str... | bmampaey/SOLARNET-provider-tools | sidc_oma_be/submit_metadata_eui_level_2.py | .py | 5e2a2f5983c6bc15 | 7 | 0 |
#!/usr/bin/env python3
"""Script to extract metadata from the EUVI archive and submit it to the SOLARNET Virtual Observatory"""
import argparse
import logging
import sys
from pathlib import Path
# HACK to make sure the provider_tools package is findable
sys.path.append(str(Path(__file__).resolve().parent.parent))
fro... | bmampaey/SOLARNET-provider-tools | sidc_oma_be/submit_metadata_euvi_level_0.py | .py | 7a2aa61006e68706 | 7 | 0 |
#!/usr/bin/env python3
"""Script to extract metadata from the MEDOC TAP serviceand submit it to the SOLARNET Virtual Observatory"""
import argparse
import logging
import sys
from pathlib import Path
import requests
# HACK to make sure the provider_tools package is findable
sys.path.append(str(Path(__file__).resolve(... | bmampaey/SOLARNET-provider-tools | sidc_oma_be/submit_metadata_gaia_dem.py | .py | 25ac03fe32b46a8f | 7 | 0 |
#!/usr/bin/env python3
"""Script to extract metadata from the Leibniz-KIS TAP service and submit it to the SOLARNET Virtual Observatory"""
import argparse
import logging
import sys
from pathlib import Path
# HACK to make sure the provider_tools package is findable
sys.path.append(str(Path(__file__).resolve().parent.p... | bmampaey/SOLARNET-provider-tools | sidc_oma_be/submit_metadata_gris_level_1.py | .py | f2a5346accfb8f1c | 7 | 0 |
#!/usr/bin/env python3
"""Script to extract metadata from the AIA level 2 archive and submit it to the SOLARNET Virtual Observatory"""
import argparse
import logging
import sys
from pathlib import Path
# HACK to make sure the provider_tools package is findable
sys.path.append(str(Path(__file__).resolve().parent.paren... | bmampaey/SOLARNET-provider-tools | sidc_oma_be/submit_metadata_hmi_magnetogram_level_1_5.py | .py | c3ebc3953a95d352 | 7 | 0 |
#!/usr/bin/env python3
"""Script to extract metadata from the Leibniz-KIS TAP service and submit it to the SOLARNET Virtual Observatory"""
import argparse
import logging
import sys
from pathlib import Path
# HACK to make sure the provider_tools package is findable
sys.path.append(str(Path(__file__).resolve().parent.p... | bmampaey/SOLARNET-provider-tools | sidc_oma_be/submit_metadata_lars_level_1.py | .py | 537626be82c92649 | 7 | 0 |
#!/usr/bin/env python3
"""Script to extract metadata from the LYRA archive and submit it to the SOLARNET Virtual Observatory"""
import argparse
import logging
import sys
from pathlib import Path
# HACK to make sure the provider_tools package is findable
sys.path.append(str(Path(__file__).resolve().parent.parent))
fro... | bmampaey/SOLARNET-provider-tools | sidc_oma_be/submit_metadata_lyra_level_2.py | .py | 55ca1cf3308c1144 | 7 | 0 |
#!/usr/bin/env python3
"""Script to extract metadata from the LYRA archive and submit it to the SOLARNET Virtual Observatory"""
import argparse
import logging
import sys
from pathlib import Path
# HACK to make sure the provider_tools package is findable
sys.path.append(str(Path(__file__).resolve().parent.parent))
fro... | bmampaey/SOLARNET-provider-tools | sidc_oma_be/submit_metadata_lyra_level_3.py | .py | 77e04d6a6b5f695b | 7 | 0 |
#!/usr/bin/env python3
"""Script to extract metadata from the SPoCA Coronal Hole archive and submit it to the SOLARNET Virtual Observatory"""
import argparse
import logging
import sys
from pathlib import Path
# HACK to make sure the provider_tools package is findable
sys.path.append(str(Path(__file__).resolve().paren... | bmampaey/SOLARNET-provider-tools | sidc_oma_be/submit_metadata_spoca_coronal_hole.py | .py | 1ef11115f7a471c5 | 7 | 0 |
#!/usr/bin/env python3
"""Script to extract metadata from the SWAP archive and submit it to the SOLARNET Virtual Observatory"""
import argparse
import logging
import sys
from datetime import timedelta
from pathlib import Path
# HACK to make sure the provider_tools package is findable
sys.path.append(str(Path(__file__... | bmampaey/SOLARNET-provider-tools | sidc_oma_be/submit_metadata_swap_level_1.py | .py | 22c4f6e5d54f20d3 | 7 | 0 |
#!/usr/bin/env python3
"""Script to extract metadata from the USET archive and submit it to the SOLARNET Virtual Observatory"""
import argparse
import logging
import sys
from datetime import timedelta
from pathlib import Path, PurePosixPath
# HACK to make sure the provider_tools package is findable
sys.path.append(st... | bmampaey/SOLARNET-provider-tools | sidc_oma_be/submit_metadata_uset_calciumii_k_level_1.py | .py | e0ee8da732234e53 | 7 | 0 |
#!/usr/bin/env python3
"""Script to extract metadata from the USET archive and submit it to the SOLARNET Virtual Observatory"""
import argparse
import logging
import sys
from datetime import timedelta
from pathlib import Path, PurePosixPath
# HACK to make sure the provider_tools package is findable
sys.path.append(st... | bmampaey/SOLARNET-provider-tools | sidc_oma_be/submit_metadata_uset_h_alpha_level_1.py | .py | 21237b8ace1f5fb4 | 7 | 0 |
#!/usr/bin/env python3
"""Script to extract metadata from the USET archive and submit it to the SOLARNET Virtual Observatory"""
import argparse
import logging
import sys
from datetime import timedelta
from pathlib import Path, PurePosixPath
# HACK to make sure the provider_tools package is findable
sys.path.append(st... | bmampaey/SOLARNET-provider-tools | sidc_oma_be/submit_metadata_uset_white_light_level_1.py | .py | 4802a3804bfc9b24 | 7 | 0 |
#!/usr/bin/env python3
"""Script to extract metadata from the XRT online archive and submit it to the SOLARNET Virtual Observatory"""
import argparse
import logging
import sys
from pathlib import Path
# HACK to make sure the provider_tools package is findable
sys.path.append(str(Path(__file__).resolve().parent.parent... | bmampaey/SOLARNET-provider-tools | sidc_oma_be/submit_metadata_xrt_level_1.py | .py | 82b91608f5ead127 | 7 | 0 |
#!/usr/bin/env python3
from tempfile import NamedTemporaryFile
from unittest import TestCase, main
from requests import Request
from provider_tools.restful_api import ApiKeyAuth, RESTfulApi
class TestRESTfulApi(TestCase):
"""Test the RESTfulApi class"""
def setUp(self):
super().setUp()
self.username = 'usern... | bmampaey/SOLARNET-provider-tools | tests/test_restful_api.py | .py | e3adbf7968072e57 | 7.5 | 0 |
"""`create_api_reference_docs` task.
Create Python API reference in the documentation.
This is specifically to be used with the MkDocs and mkdocstrings framework.
"""
from __future__ import annotations
import logging
import os
import re
import shutil
import sys
from collections import defaultdict
from pathlib import... | SINTEF/ci-cd | ci_cd/tasks/api_reference_docs.py | .py | 52db6a38001d39c6 | 7.15 | 1 |
"""Relevant tools for printing to the console."""
from __future__ import annotations
import platform
from enum import Enum
from typing import TYPE_CHECKING
if TYPE_CHECKING: # pragma: no cover
from typing_extensions import Self
class Emoji(str, Enum):
"""Unicode strings for certain emojis."""
def __n... | SINTEF/ci-cd | ci_cd/utils/console_printing.py | .py | 8943f3e17e444791 | 7.15 | 1 |
"""Generate SOFT7 entity instances based on basic information:
1. Data source (DB, File, Webpage, ...).
2. Generic data source parser.
3. Data source parser configuration.
4. SOFT7 entity (data model).
Parts 2 and 3 are together considered to produce the "specific parser".
Parts 1 through 3 are provided through a sin... | SINTEF/soft7 | s7/factories/datasource_factory.py | .py | 00d39ff1a6cc269e | 7.35 | 4 |
"""Pydantic data models for the SOFT7 OTEAPI plugin."""
from __future__ import annotations
from typing import Annotated, Any, Literal
from oteapi.models import AttrDict
from oteapi.strategies.mapping.mapping import MappingStrategyConfig
from pydantic import Field, field_validator
from s7.exceptions import EntityNot... | SINTEF/soft7 | s7/oteapi_plugin/models.py | .py | f6eb3a1c5c192470 | 7.35 | 4 |
"""Strategy class for application/yaml."""
from __future__ import annotations
from typing import Annotated, Literal
import yaml
from oteapi.datacache import DataCache
from oteapi.models import (
AttrDict,
DataCacheConfig,
HostlessAnyUrl,
ParserConfig,
ResourceConfig,
)
from oteapi.plugins import ... | SINTEF/soft7 | s7/oteapi_plugin/yaml_parser.py | .py | d7252fc36d9bc6ad | 7.35 | 4 |
"""Everything to do with the special SOFT model Data Source."""
from __future__ import annotations
import logging
import traceback
from pathlib import Path
from typing import TYPE_CHECKING, Any, Protocol, cast, runtime_checkable
from pydantic import (
AnyUrl,
BaseModel,
ConfigDict,
TypeAdapter,
V... | SINTEF/soft7 | s7/pydantic_models/datasource.py | .py | f642c7c20f09160c | 7.35 | 4 |
"""Customized OTEAPI pydantic models."""
from __future__ import annotations
from collections.abc import Hashable
from oteapi.models import (
FunctionConfig,
GenericConfig,
MappingConfig,
ParserConfig,
ResourceConfig,
)
from pydantic import AnyUrl
from s7.pydantic_models.soft7_entity import SOFT7... | SINTEF/soft7 | s7/pydantic_models/oteapi.py | .py | 8478b80f7bfaa2a7 | 7.35 | 4 |
"""Pydantic model for the SOFT7 data source instance."""
from __future__ import annotations
import logging
from typing import TYPE_CHECKING, ClassVar, cast, get_args
from pydantic import (
AnyUrl,
BaseModel,
ConfigDict,
TypeAdapter,
ValidationError,
conlist,
model_validator,
)
from pydant... | SINTEF/soft7 | s7/pydantic_models/soft7_instance.py | .py | 6eae8a02135b28ab | 7.35 | 4 |
"""Pytest fixtures for all tests."""
from __future__ import annotations
from typing import TYPE_CHECKING
import pytest
if TYPE_CHECKING:
from pathlib import Path
from typing import Any
def static_folder() -> Path:
"""Path to the 'static' folder.
This is here to support _generate_entity_test_cases... | SINTEF/soft7 | tests/conftest.py | .py | e5c8695fbb0d1459 | 7.85 | 4 |
"""Pytest fixtures for 'factories'."""
from __future__ import annotations
import pytest
@pytest.fixture(scope="session", autouse=True)
def _load_strategies() -> None:
"""Load entry points strategies."""
from oteapi.plugins import load_strategies
load_strategies(test_for_uniqueness=False)
@pytest.fixt... | SINTEF/soft7 | tests/factories/conftest.py | .py | 52494131a8801b14 | 7.35 | 4 |
"""Test the soft7 OTEAPI function strategy."""
from __future__ import annotations
from typing import TYPE_CHECKING
import pytest
if TYPE_CHECKING:
from pathlib import Path
from typing import Any
from pydantic import AnyHttpUrl
from pytest_httpx2 import HTTPXMock
from s7.pydantic_models.soft7_e... | SINTEF/soft7 | tests/oteapi_plugin/test_soft7_function.py | .py | b3854041574b64d0 | 7.85 | 4 |
"""The main `turtle-canon` module."""
from __future__ import annotations
import re
from pathlib import Path
from tempfile import TemporaryDirectory
from rdflib import Graph
from rdflib.exceptions import Error as RDFlibError
from rdflib.exceptions import ParserError
from turtle_canon.utils import exceptions, warning... | CasperWA/turtle-canon | turtle_canon/canon.py | .py | d57922d0d6d639d0 | 7.39 | 5 |
"""Utility functions for `turtle-canon` CLI."""
from __future__ import annotations
import sys
from pathlib import Path
from typing import TYPE_CHECKING
if TYPE_CHECKING: # pragma: no cover
from collections.abc import Sequence
from typing import TextIO
class Cache:
"""Small cache."""
def __init__(... | CasperWA/turtle-canon | turtle_canon/cli/utils.py | .py | d23330b74c38a8b7 | 7.39 | 5 |
"""Warnings for general usage by the Turtle Canon tool.
!!! note
These warnings are *not* like regular Python `Warning`s.
Instead, they are `Exception`s that will be caught and treated specially by the CLI.
"""
from __future__ import annotations
class TurtleCanonWarning(Exception):
"""Base Warning for ... | CasperWA/turtle-canon | turtle_canon/utils/warnings.py | .py | d462993c6bbef6e1 | 7.39 | 5 |
'''
Created on Dec 28, 2021
@author: vladyslav_goncharuk
'''
import os
import io
import sys
import fcntl
import struct
import termios
import glob
import importlib.util
def has_fileno(stream):
"""
Cleanly determine whether ``stream`` has a useful ``.fileno()``.
.. note::
This function helps determ... | svlad-90/paf | paf/common.py | .py | c818efdf29c3896e | 7.24 | 2 |
"""DLite-specific data models."""
from __future__ import annotations
from typing import Annotated
from oteapi.models import AttrDict
from pydantic import Field, JsonValue
class DLiteResult(AttrDict):
"""Class for returning values from DLite strategies."""
collection_id: Annotated[
str | None, Fiel... | EMMC-ASBL/oteapi-dlite | oteapi_dlite/models.py | .py | 97956bc1d9914724 | 7.24 | 2 |
"""Generic function strategy that converts zero or more input instances
to zero or more new output instances.
"""
from __future__ import annotations
import importlib
from collections.abc import Sequence
from typing import Annotated
import dlite
from oteapi.models import AttrDict, FunctionConfig
from pydantic import... | EMMC-ASBL/oteapi-dlite | oteapi_dlite/strategies/convert.py | .py | d2dd5f2e6d5c4c93 | 7.24 | 2 |
"""Filter that removes all but specified instances in the collection."""
from __future__ import annotations
import re
from typing import Annotated
from dlite.utils import get_referred_instances
from oteapi.models import FilterConfig
from pydantic import Field
from pydantic.dataclasses import dataclass
from oteapi_d... | EMMC-ASBL/oteapi-dlite | oteapi_dlite/strategies/filter.py | .py | d763c0645b5f78bf | 7.24 | 2 |
"""Mapping filter strategy."""
from __future__ import annotations
import json
from typing import TYPE_CHECKING, Annotated
from oteapi.models import MappingConfig
from pydantic import AnyUrl
from pydantic.dataclasses import Field, dataclass
from oteapi_dlite.models import DLiteConfiguration, DLiteResult
from oteapi_... | EMMC-ASBL/oteapi-dlite | oteapi_dlite/strategies/mapping.py | .py | 7ded578019fa877a | 7.24 | 2 |
"""Generic parse strategy using DLite storage plugin."""
from __future__ import annotations
from pathlib import Path
from typing import Annotated, Literal
import dlite
from oteapi.datacache import DataCache
from oteapi.models import (
AttrDict,
DataCacheConfig,
HostlessAnyUrl,
ParserConfig,
Resou... | EMMC-ASBL/oteapi-dlite | oteapi_dlite/strategies/parse.py | .py | 87cb49667152793d | 7.24 | 2 |
"""Strategy for parsing an Excel spreadsheet to a DLite instance."""
from __future__ import annotations
import re
from random import getrandbits
from typing import TYPE_CHECKING, Annotated, Literal
import dlite
import numpy as np
from dlite.datamodel import DataModel
from oteapi.models import HostlessAnyUrl, ParserC... | EMMC-ASBL/oteapi-dlite | oteapi_dlite/strategies/parse_excel.py | .py | 53324edadb2a827f | 7.24 | 2 |
"""Strategy class for parsing an image to a DLite instance."""
from __future__ import annotations
import logging
from typing import Annotated, Literal
import numpy as np
from oteapi.datacache import DataCache
from oteapi.models import ParserConfig, ResourceConfig
from oteapi.plugins import create_strategy
from oteap... | EMMC-ASBL/oteapi-dlite | oteapi_dlite/strategies/parse_image.py | .py | 2cbdb7fa781d9fca | 7.24 | 2 |
"""Filter for serialisation using DLite."""
from __future__ import annotations
from collections.abc import Sequence
from pathlib import Path
from typing import Annotated
import dlite
from oteapi.models import FilterConfig
from pydantic import Field
from pydantic.dataclasses import dataclass
from oteapi_dlite.models... | EMMC-ASBL/oteapi-dlite | oteapi_dlite/strategies/serialise.py | .py | c0cbac7ed96d8ccc | 7.24 | 2 |
"""Generic strategy for adding configurations to the session."""
from __future__ import annotations
from typing import Annotated
from oteapi.models import AttrDict, FilterConfig
from pydantic import Field, JsonValue
from pydantic.dataclasses import dataclass
# Must add this explicitly to make mypy happy
NoneType = ... | EMMC-ASBL/oteapi-dlite | oteapi_dlite/strategies/settings.py | .py | 4cb98a807dc01681 | 7.24 | 2 |
"""Utility functions for OTEAPI DLite plugin."""
from __future__ import annotations
from numbers import Number
from pathlib import Path
from typing import TYPE_CHECKING
import dlite
from dlite.mappings import instantiate
from oteapi.datacache import DataCache
from oteapi_dlite.utils.exceptions import CollectionNotF... | EMMC-ASBL/oteapi-dlite | oteapi_dlite/utils/utils.py | .py | fbdd64325ca843c8 | 7.24 | 2 |
"""Pytest fixtures for `strategies/`."""
from __future__ import annotations
from typing import TYPE_CHECKING, NamedTuple
import pytest
if TYPE_CHECKING:
from pathlib import Path
class PathsTuple(NamedTuple):
"""Tuple of paths."""
testdir: Path
entitydir: Path
inputdir: Path
outputdir: Pat... | EMMC-ASBL/oteapi-dlite | tests/conftest.py | .py | 5461196be9b6a181 | 7.74 | 2 |
"""Base API for backend client."""
from __future__ import annotations
import warnings
from abc import ABC, abstractmethod
from typing import TYPE_CHECKING
from otelib.backends.factories import strategy_factory
from otelib.backends.utils import Backend, StrategyType
from otelib.warnings import IgnoringConfigOptions
... | EMMC-ASBL/otelib | otelib/backends/client.py | .py | 8eff4d94719fc199 | 7.39 | 5 |
"""Backend factory functions."""
from __future__ import annotations
import importlib
from typing import TYPE_CHECKING
from otelib.backends.utils import Backend, StrategyType
from otelib.exceptions import InvalidBackend, InvalidStrategy
if TYPE_CHECKING: # pragma: no cover
from otelib.backends.client import Ab... | EMMC-ASBL/otelib | otelib/backends/factories.py | .py | 6b3bed12f7cd5b45 | 7.39 | 5 |
"""Base class for strategies in the Python backend."""
from __future__ import annotations
import json
import warnings
from typing import TYPE_CHECKING
from uuid import uuid4
from oteapi.models import AttrDict
from oteapi.plugins import create_strategy
from oteapi.utils.config_updater import populate_config_from_sess... | EMMC-ASBL/otelib | otelib/backends/python/base.py | .py | dfca39f544de7c36 | 7.39 | 5 |
"""Client for python backend."""
from __future__ import annotations
from typing import TYPE_CHECKING
from oteapi.plugins import load_strategies
from otelib.backends.client import AbstractBaseClient
from otelib.exceptions import PythonBackendException
if TYPE_CHECKING: # pragma: no cover
from typing import Any... | EMMC-ASBL/otelib | otelib/backends/python/client.py | .py | 5424843bb587dc2d | 7.39 | 5 |
"""Common strategy for Download, Parse and Resource strategies."""
from __future__ import annotations
from typing import TYPE_CHECKING
from oteapi.models import ResourceConfig
from otelib.backends.python.base import BasePythonStrategy
if TYPE_CHECKING: # pragma: no cover
from oteapi.models import GenericConfi... | EMMC-ASBL/otelib | otelib/backends/python/dataresource.py | .py | e2b16ea84a5c7234 | 7.39 | 5 |
"""Client for services backend."""
from __future__ import annotations
from typing import TYPE_CHECKING
from otelib.backends.client import AbstractBaseClient
if TYPE_CHECKING: # pragma: no cover
from typing import Any
from otelib.backends.services.base import BaseServicesStrategy
class OTEServiceClient(A... | EMMC-ASBL/otelib | otelib/backends/services/client.py | .py | e3d28d60f66e1739 | 7.39 | 5 |
"""Utility function and classes for use in the Backends module."""
from __future__ import annotations
import sys
if sys.version_info >= (3, 11):
from enum import StrEnum
else:
from enum import Enum
class StrEnum(str, Enum):
"""Pre-3.11 style string-Enums."""
class Backend(StrEnum):
"""Back... | EMMC-ASBL/otelib | otelib/backends/utils.py | .py | 980d44a571268a94 | 7.39 | 5 |
"""Pipe object for creating a pipeline."""
from __future__ import annotations
from typing import TYPE_CHECKING
if TYPE_CHECKING: # pragma: no cover
from otelib.backends.strategies import AbstractBaseStrategy
class Pipe:
"""Pipe object in a pipe-and-filter pattern."""
def __init__(self, strategy: Abs... | EMMC-ASBL/otelib | otelib/pipe.py | .py | 0447978091a37768 | 7.39 | 5 |
"""Fixtures and configuration for pytest."""
from __future__ import annotations
import logging
import sys
from typing import TYPE_CHECKING
if sys.version_info >= (3, 11):
from enum import StrEnum
else:
from enum import Enum
class StrEnum(str, Enum):
"""Pre-3.11 style string-Enums."""
import py... | EMMC-ASBL/otelib | tests/conftest.py | .py | db428b56af8bfdeb | 7.89 | 5 |
"""Tests for `otelib.strategies.abc`."""
from __future__ import annotations
from typing import TYPE_CHECKING
import pytest
from utils import strategy_create_kwargs
if TYPE_CHECKING:
from typing import Any
from requests_mock import Mocker
from otelib.backends.python.base import BasePythonStrategy
f... | EMMC-ASBL/otelib | tests/strategies/test_abc.py | .py | 67037d707379d98b | 7.89 | 5 |
"""Utility functions for tests."""
from __future__ import annotations
import json
import sys
from pathlib import Path
from subprocess import run
from typing import TYPE_CHECKING
if sys.version_info >= (3, 11):
from enum import StrEnum
else:
from enum import Enum
class StrEnum(str, Enum):
"""Pre-... | EMMC-ASBL/otelib | tests/utils.py | .py | 80cae1e59d290900 | 7.89 | 5 |
"""# VeleroBackupConfig library.
This library implements the Requirer and Provider roles for the `velero_backup_config` relation
interface. It is used by client charms to declare backup specifications, and by the Velero Operator
charm to consume them and execute backup and restore operations.
The `velero_backup_confi... | canonical/kubeflow-profiles-operator | lib/charms/velero_libs/v0/velero_backup_config.py | .py | 4d948cf5685de721 | 7 | 0 |
# Copyright 2025 Canonical Ltd.
# See LICENSE file for licensing details.
"""Define Interface tests fixtures."""
import pytest
from interface_tester.plugin import InterfaceTester
from ops.framework import Object
from charm import KubeflowProfilesOperator
@pytest.fixture(autouse=True)
def patch_kubernetes_service_p... | canonical/kubeflow-profiles-operator | tests/interface_tests/conftest.py | .py | 757548c086d4d2c2 | 7.5 | 0 |
# Copyright 2023 Canonical Ltd.
# See LICENSE file for licensing details.
"""Define Unit tests fixtures."""
from unittest.mock import MagicMock
import pytest
from ops.testing import Harness
from charm import KubeflowProfilesOperator, KubernetesServicePatch
@pytest.fixture
def harness():
"""Initialize Harness in... | canonical/kubeflow-profiles-operator | tests/unit/conftest.py | .py | a391df5c818bc7a4 | 7.5 | 0 |
#!/usr/bin/env python3
"""
Tasks for maintaining the project.
Execute 'invoke --list' for guidance on using Invoke
"""
# Core Library modules
import logging.config
import shutil
import webbrowser
from pathlib import Path
# Third party modules
import yaml # type: ignore
from invoke import task, call
from jinja2 impor... | Stephen-RA-King/pynball | tasks.py | .py | 72b49178b4179777 | 7.24 | 2 |
"""Test configuration.
pynball.py is a Windows-only tool (it imports `winreg` unconditionally and
exits at import time if `sys.platform != "win32"`). To unit test it on any
platform, we:
1. Install lightweight stub modules for `winreg` and `magic` (python-magic,
which needs the libmagic shared library) into sys.mo... | Stephen-RA-King/pynball | tests/conftest.py | .py | 2cb6c55b18399107 | 7.74 | 2 |
# Copyright 2023 Canonical Ltd.
# See LICENSE file for licensing details.
"""Integration tests for Jupyter controller."""
import logging
from pathlib import Path
import pytest
import tenacity
import yaml
from charmed_kubeflow_chisme.testing import (
GRAFANA_AGENT_APP,
assert_alert_rules,
assert_logging,
... | canonical/notebook-operators | charms/jupyter-controller/tests/integration/test_charm.py | .py | 9ba0382783c83d01 | 7.89 | 5 |
# Copyright 2025 Canonical Ltd.
# See LICENSE file for licensing details.
"""Integration tests for Jupyter controller."""
import logging
from pathlib import Path
import pytest
import tenacity
import yaml
from charmed_kubeflow_chisme.testing import (
GRAFANA_AGENT_APP,
assert_alert_rules,
assert_logging,
... | canonical/notebook-operators | charms/jupyter-controller/tests/integration/test_charm_ambient.py | .py | 336a94c77299993b | 7.89 | 5 |
# Copyright 2023 Canonical Ltd.
# See LICENSE file for licensing details.
"""Unit tests for Jupyter controller."""
import json
from unittest.mock import MagicMock, patch
import pytest
import yaml
from ops.model import ActiveStatus, MaintenanceStatus, WaitingStatus
from ops.testing import Harness
from charm import J... | canonical/notebook-operators | charms/jupyter-controller/tests/unit/test_operator.py | .py | 024daade7225a38f | 7.89 | 5 |
#!/usr/bin/env python3
# Copyright 2023 Canonical Ltd.
# See LICENSE file for licensing details.
"""Tools for validating configuration options."""
import dataclasses
from dataclasses import field
from typing import List, Union
OPTIONS_LOOKUP = {
"gpu-vendors": {
"required_keys": ["limitsKey", "uiName"],
... | canonical/notebook-operators | charms/jupyter-ui/src/config_validators.py | .py | 7ad4c1bf97150685 | 7.39 | 5 |
# Copyright 2023 Canonical Ltd.
# See LICENSE file for licensing details.
#
"""Integration tests for Jupyter UI Operator/Charm."""
import json
import logging
from pathlib import Path
import aiohttp
import dpath
import pytest
import tenacity
import yaml
from charmed_kubeflow_chisme.testing import (
GRAFANA_AGENT_... | canonical/notebook-operators | charms/jupyter-ui/tests/integration/test_charm.py | .py | 8c43c22ca546af49 | 7.89 | 5 |
#!/usr/bin/env python3
# Copyright 2023 Canonical Ltd.
# See LICENSE file for licensing details.
"""Unit tests for the configuration validators."""
from contextlib import nullcontext as does_not_raise
import pytest
from config_validators import (
ConfigValidationError,
validate_named_options_with_default,
... | canonical/notebook-operators | charms/jupyter-ui/tests/unit/test_config_validators.py | .py | 0431a64a9d5e6a76 | 7.89 | 5 |
# Copyright (C) 2022 - 2026 Synopsys, Inc. and ANSYS, Inc. All rights reserved.
# SPDX-License-Identifier: MIT
#
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, includi... | ansys/hollerith | tests/test_field_writer.py | .py | 0c27a89053b29d68 | 7.85 | 4 |
# Copyright (C) 2022 - 2026 Synopsys, Inc. and ANSYS, Inc. All rights reserved.
# SPDX-License-Identifier: MIT
#
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, includi... | ansys/hollerith | tests/test_float_writer.py | .py | 0e3ee0e195dbfcd6 | 7.85 | 4 |
#!/usr/bin/env python3
# See the NOTICE file distributed with this work for additional information
# regarding copyright ownership.
#
#
# 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
# ... | Ensembl/ensembl-genes-metadata | pipelines/assembly_metadata/bin/create_report.py | .py | f354825be0ad74f3 | 7.15 | 1 |
#!/usr/bin/env python3
# See the NOTICE file distributed with this work for additional information
# regarding copyright ownership.
#
#
# 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
# ... | Ensembl/ensembl-genes-metadata | pipelines/assembly_metadata/bin/get_tolid.py | .py | 84d6c01bb3e2845c | 7.15 | 1 |
#!/usr/bin/env python3
"""
Example 09: DICOM Tag Printing Tool Usage Examples
This example demonstrates how to use the mnts.utils.dicom_tag_printer module
to print specific tag information from DICOM files.
Author: MRI Normalization Tools
"""
import os
import sys
from pathlib import Path
# Add mnts path
sys.path.in... | alabamagan/mri_normalization_tools | examples/EG09_dicom_tag_printing.py | .py | 808e7ba3cae0fbee | 7.3 | 3 |
from .mnts_filters import *
from typing import Any, Optional
import SimpleITK as sitk
__all__ = ["TypeCastNode", "DataNode"]
class DataNode(MNTSFilter):
r"""
Presents whatever data stored in this node. This is useful for storing intermediate results, or other data that
are repeatedly accessed without the ... | alabamagan/mri_normalization_tools | mnts/filters/data_node.py | .py | 93eb9203544f99f5 | 7.3 | 3 |
import SimpleITK as sitk
import numpy as np
from pathlib import Path
from typing import Union, Tuple, Optional
from ..mnts_filters import MNTSFilter
__all__ = ['RemoveShoulder']
class RemoveShoulder(MNTSFilter):
r"""
A geometric filter that takes a mask and calculates the slice area along a specified dimens... | alabamagan/mri_normalization_tools | mnts/filters/geom/geom_mask_crop.py | .py | 2432734913f37d67 | 7.3 | 3 |
import SimpleITK as sitk
import numpy as np
import re
from pathlib import Path
from typing import Union, Tuple, Optional
from ..mnts_filters import MNTSFilter
__all__ = ['ReorientFilter']
class ReorientFilter(MNTSFilter):
r"""
A wrapper for sitk.DICOMOrient
Attributes:
target_orientation (str):
... | alabamagan/mri_normalization_tools | mnts/filters/geom/reorient_filter.py | .py | 1e019b08fca65fdb | 7.3 | 3 |
"""
Wrap functions implemented in: jcreinhold/intensity-normalization
https://github.com/jcreinhold/intensity-normalization
Note that the original design was based on images of the brain, but is generally recognized to be suitable for
other body regions.
"""
from intensity_normalization.normalize.nyul import NyulNorm... | alabamagan/mri_normalization_tools | mnts/filters/intensity/in_wrapper.py | .py | 05d538213fa516a9 | 7.3 | 3 |
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