text stringlengths 185 73.3k | repo stringlengths 7 100 | path stringlengths 4 146 | language stringclasses 7
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# pylint: disable=R0914 # too-many-locals
"""Command line interface of PyFlexPlot."""
# Standard library
import warnings
from typing import Any
# Third-party
import click
from click import Context
from shapely.errors import ShapelyDeprecationWarning
# Local
from .. import __version__
from .. import presets_data_pat... | MeteoSwiss-APN/pyflexplot | src/pyflexplot/cli/cli.py | .py | 04e8d2cfc7e3910a | 7.6 | 15 |
"""CLI utils."""
# Standard library
import sys
import traceback
from typing import Type
# Third-party
import click
from click import Context
# Local
from ..setups.setup_file import SetupFile
from ..utils.logging import set_log_level
def click_error(
ctx: Context,
msg: str,
exception: Type[Exception] = ... | MeteoSwiss-APN/pyflexplot | src/pyflexplot/cli/click.py | .py | e953d69ebaf118cb | 7.6 | 15 |
"""Preset setup files."""
# Standard library
import re
from pathlib import Path
from typing import Collection
from typing import Dict
from typing import Iterator
from typing import List
from typing import Optional
from typing import Pattern
from typing import Union
# Local
from .. import _check_dir_exists
from ..util... | MeteoSwiss-APN/pyflexplot | src/pyflexplot/cli/preset.py | .py | ff939a3c46f6c3e5 | 7.6 | 15 |
"""CLI for preset setup files."""
# Standard library
import sys
from pathlib import Path
from typing import Any
from typing import Mapping
from typing import Sequence
# Third-party
import click
from click import Context
# Local
from ..utils.exceptions import NoPresetFileFoundError
from ..utils.logging import log
fro... | MeteoSwiss-APN/pyflexplot | src/pyflexplot/cli/preset_click.py | .py | 3c48170e7e46fd3c | 7.6 | 15 |
"""
This module (taken from MeteoSwiss Python Commons library) introduces a custom class that leverages Pydantic's capabilities: a custom BaseSettings class BaseServiceSettings.
This custom classes inherit Pydantic's core functionalities. This includes data validation, parsing,
serialization, error handling, and behav... | MeteoSwiss-APN/pyflexplot | src/pyflexplot/config/base_settings.py | .py | 831430dcf9d9cc06 | 7.6 | 15 |
"""Data structures."""
# Standard library
from typing import Callable
from typing import Sequence
from typing import Union
# Third-party
import numpy as np
def ensemble_probability(arr: np.ndarray, thr: float = 0.0, thr_type: str = "lower") -> np.ndarray:
"""Ensemble-based probability of threshold exceedence at... | MeteoSwiss-APN/pyflexplot | src/pyflexplot/input/data.py | .py | f1c44188808a4a15 | 7.6 | 15 |
"""Data structures."""
# Standard library
import dataclasses as dc
import warnings
from typing import Any
from typing import Dict
from typing import Iterator
from typing import Optional
from typing import Sequence
from typing import Tuple
from typing import Union
# Third-party
import numpy as np
from cartopy.crs impo... | MeteoSwiss-APN/pyflexplot | src/pyflexplot/input/field.py | .py | eaa0de7b1f228b2f | 7.6 | 15 |
"""Fix issues with NetCDF input."""
# Standard library
from typing import Any
from typing import Mapping
from typing import Sequence
from typing import Union
# Third-party
import numpy as np
# Local
from ..utils.logging import log
from .meta_data import MetaData
class FlexPartDataFixer:
"""Fix issues with Flex... | MeteoSwiss-APN/pyflexplot | src/pyflexplot/input/fix_nc_input.py | .py | 0967d630fced3513 | 7.6 | 15 |
"""Chemical species and their attributes."""
from __future__ import annotations
# Standard library
import dataclasses as dc
from dataclasses import dataclass # pylint doesn't understand dc.dataclass
from typing import Any
from typing import cast
from typing import List
from typing import Optional
from typing import ... | MeteoSwiss-APN/pyflexplot | src/pyflexplot/input/species.py | .py | 27605ec5bc772699 | 8.1 | 15 |
"""Output."""
# Standard library
import os
import re
from datetime import datetime
from typing import Any
from typing import cast
from typing import List
from typing import Mapping
from typing import Optional
from typing import Sequence
from typing import Union
# First-party
from srutils.datetime import init_datetime... | MeteoSwiss-APN/pyflexplot | src/pyflexplot/output.py | .py | 39fa0308941ffc19 | 7.6 | 15 |
"""Plot layouts."""
# Standard library
import dataclasses as dc
from typing import Dict
from typing import Mapping
from typing import Tuple
# Local
from .setups.layout_setup import LayoutSetup
from .utils.summarize import summarizable
from .utils.typing import RectType
@summarizable
@dc.dataclass
class BoxedPlotLayo... | MeteoSwiss-APN/pyflexplot | src/pyflexplot/plot_layouts.py | .py | 516ee1b8e01ac9ed | 7.6 | 15 |
"""Domains."""
# Standard library
import dataclasses as dc
from typing import Any
from typing import Dict
from typing import List
from typing import Optional
from typing import Sequence
from typing import Tuple
from typing import Union
# Third-party
import numpy as np
from cartopy.crs import PlateCarree
from cartopy.... | MeteoSwiss-APN/pyflexplot | src/pyflexplot/plotting/domain.py | .py | c345bffcc1c13e88 | 7.6 | 15 |
"""Bounding box."""
from __future__ import annotations
# Standard library
import dataclasses as dc
from copy import copy
from typing import Iterator
from typing import Optional
from typing import Tuple
# Third-party
import numpy as np
from cartopy.crs import PlateCarree
from cartopy.crs import Projection
from cartop... | MeteoSwiss-APN/pyflexplot | src/pyflexplot/plotting/proj_bbox.py | .py | cd812a8eeb97570b | 7.6 | 15 |
"""Reference distance indicator for map plot."""
# Standard library
import dataclasses as dc
from typing import Any
from typing import Dict
from typing import Optional
# Third-party
import geopy.distance
import matplotlib as mpl
from matplotlib.axes import Axes
# Local
from ..utils.exceptions import MaxIterationErro... | MeteoSwiss-APN/pyflexplot | src/pyflexplot/plotting/ref_dist_indicator.py | .py | 863af3f811020c5b | 7.6 | 15 |
"""
Module for interacting with AWS S3 for downloading and uploading files.
This module provides utility functions to handle S3 URIs,
download files from an S3 bucket, and upload files to an S3 bucket.
It also includes functions for expanding S3 keys with
ensemble member identifiers and retrying operations with expone... | MeteoSwiss-APN/pyflexplot | src/pyflexplot/s3.py | .py | d87afee798c68cc4 | 7.6 | 15 |
"""Contains the implementation for data saving strategies."""
# Standard library
import os
import zipfile
from pathlib import Path
# Third-party
import numpy as np
import shapefile # type: ignore
# First-party
from pyflexplot.plot_layouts import BoxedPlotLayout
from pyflexplot.plotting.boxed_plot import BoxedPlot
f... | MeteoSwiss-APN/pyflexplot | src/pyflexplot/save_data.py | .py | dcf29439afe16bdf | 7.6 | 15 |
"""Base class for setup classes.
Note that this is design is not clean in the sense that the interfaces of the
subclasses of BaseSetup differ in their attributes, which requires the
occasional isinstance assert for the subclass type to satisfy mypy.
"""
# Standard library
import dataclasses as dc
from typing import ... | MeteoSwiss-APN/pyflexplot | src/pyflexplot/setups/base_setup.py | .py | 57b1af94692cce6b | 7.6 | 15 |
# pylint: disable=C0302 # too-many-lines
"""Plot setup and setup files."""
# Standard library
import dataclasses as dc
from pprint import pformat
from typing import Any
from typing import Collection
from typing import Dict
from typing import Iterator
from typing import List
from typing import Mapping
from typing impo... | MeteoSwiss-APN/pyflexplot | src/pyflexplot/setups/dimensions.py | .py | f87682c81f74f6c2 | 7.6 | 15 |
"""Files setup."""
# Standard library
import dataclasses as dc
from typing import Tuple
from typing import Union
# Local
from .base_setup import BaseSetup
# SR_TMP <<< TODO cleaner solution
def is_files_setup_param(param: str, recursive: bool = False) -> bool:
if recursive:
raise NotImplementedError("re... | MeteoSwiss-APN/pyflexplot | src/pyflexplot/setups/files_setup.py | .py | 82dea8ebc67b5d09 | 7.6 | 15 |
"""Layout setup."""
# Standard library
import dataclasses as dc
from typing import Any
from typing import Mapping
from typing import Optional
# Local
from .base_setup import BaseSetup
# SR_TMP <<< TODO cleaner solution
def is_layout_setup_param(param: str, recursive: bool = False) -> bool:
if recursive:
... | MeteoSwiss-APN/pyflexplot | src/pyflexplot/setups/layout_setup.py | .py | 552e9f01b510e347 | 7.6 | 15 |
"""Model setup."""
# Standard library
import dataclasses as dc
from typing import Any
from typing import Dict
from typing import Mapping
from typing import Optional
from typing import Tuple
# Local
from .base_setup import BaseSetup
# SR_TMP <<< TODO cleaner solution
def is_model_setup_param(param: str, recursive: b... | MeteoSwiss-APN/pyflexplot | src/pyflexplot/setups/model_setup.py | .py | bfc46553db501ab6 | 7.6 | 15 |
# pylint: disable=E1101 # no-member (logging.verbose, logging.VERBOSE)
"""Preset setup files."""
# Standard library
import logging
from typing import Optional
def get_log_level() -> int:
return logging.getLogger().level
def set_log_level(verbosity: int) -> None:
if verbosity <= 0:
logging.getLogge... | MeteoSwiss-APN/pyflexplot | src/pyflexplot/utils/logging.py | .py | 0315a1b517118954 | 7.6 | 15 |
"""Summarize objects as a dict for testing etc."""
# Standard library
import dataclasses as dc
from functools import partial
from typing import Any
from typing import Callable
from typing import Collection
from typing import Dict
from typing import Optional
from typing import Sequence
# Third-party
import numpy as np... | MeteoSwiss-APN/pyflexplot | src/pyflexplot/utils/summarize.py | .py | c576bf6ba167d2fc | 7.6 | 15 |
"""Crop fields in a NetCDF file."""
from __future__ import annotations
# Standard library
import dataclasses as dc
import sys
from typing import Any
from typing import Optional
from typing import Tuple
from typing import Union
# Third-party
import click
import netCDF4 as nc4
__version__ = "0.1.0"
@dc.dataclass
cl... | MeteoSwiss-APN/pyflexplot | src/srtools/crop_netcdf.py | .py | 3b9ae9c8a7df8bef | 7.6 | 15 |
"""Custom sphinx extension to include manpage."""
def setup(app):
"""Set up connect events to the man builder."""
app.connect("builder-inited", include_manpage)
def include_manpage(app):
"""Update the excluded patterns to include the manpage."""
if app.builder.name != "man":
return
for ... | dralshehri/epiweeks | docs/_ext/custom_manpage.py | .py | 6ae9e3add3878817 | 7.16 | 20 |
"""Custom sphinx extension to generate text file sitemap."""
import warnings
from pathlib import Path
def setup(app):
"""Set up connect events to the sitemap builder."""
app.add_config_value("sitemap_excluded_pages", default=[], rebuild="")
app.connect("html-page-context", add_links)
app.connect("bu... | dralshehri/epiweeks | docs/_ext/custom_sitemap.py | .py | 7221ce24842ab31e | 7.66 | 20 |
"""Epidemiological weeks calculation.
Based on the US CDC (MMWR) and ISO week numbering systems.
https://github.com/dralshehri/epiweeks
"""
from collections.abc import Iterator
from datetime import date, timedelta
__all__ = ["Week", "Year"]
class Week:
"""A Week object represents a week in epidemiological wee... | dralshehri/epiweeks | src/epiweeks/__init__.py | .py | ffb8d24f9d698b7e | 7.66 | 20 |
from __future__ import annotations
import json
import os
import re
import sys
from collections.abc import Mapping
from datetime import date, datetime, time
from typing import Any, BinaryIO, Callable, Dict, List, Match, Optional, Union
if sys.version_info >= (3, 11):
import tomllib
else: # pragma: no cover - fall... | mrshu/envtoml | envtoml/__init__.py | .py | 7461177b2870c1b2 | 7.64 | 18 |
# Importing required libraries, obviously
import streamlit as st
import cv2
from PIL import Image
import numpy as np
import os
# Loading pre-trained parameters for the cascade classifier
try:
face_cascade = cv2.CascadeClassifier(cv2.data.haarcascades + 'haarcascade_frontalface_default.xml')
eye_cascade = cv2.... | Blues1998/Face-Detection | app.py | .py | aa87212820c31716 | 7.42 | 6 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
from enum import Enum
from typing import List
import os
import numpy as np
import pandas as pd
from .data_objects.dimension_data import DimensionData
class V1_SPATIAL_BUFFER_STRUCT:
VIZ_TYPE_INDEX: int = 0
UID_INDEX: int = 1 # unique ID
TID_INDEX: int = 2 ... | simularium/simulariumio | simulariumio/constants.py | .py | e0949909d200a8c1 | 7.45 | 7 |
from typing import Dict, List, Tuple
import numpy as np
from .frame_data import FrameData
from .input_file_data import InputFileData
from .trajectory_data import TrajectoryData
from .simularium_file_data import SimulariumFileData
from ..constants import BINARY_BLOCK_TYPE, BINARY_SETTINGS
from ..readers import BinaryBl... | simularium/simulariumio | simulariumio/data_objects/binary_data.py | .py | 75f57d22f03adab1 | 7.45 | 7 |
from typing import Dict, Union
class FrameData:
def __init__(
self, frame_number: int, n_agents: int, time: float, data: Union[bytes, Dict]
):
"""
This object holds frame data for a single frame of simularium data
Parameters
----------
frame_number : int
... | simularium/simulariumio | simulariumio/data_objects/frame_data.py | .py | 9fcbb1ce732d15b3 | 7.45 | 7 |
from typing import Dict, List
import json
import numpy as np
from .frame_data import FrameData
from .simularium_file_data import SimulariumFileData
from .trajectory_data import TrajectoryData
from ..constants import V1_SPATIAL_BUFFER_STRUCT
class JsonData(SimulariumFileData):
def __init__(self, file_contents: st... | simularium/simulariumio | simulariumio/data_objects/json_data.py | .py | eebefb6e6538a68b | 7.45 | 7 |
from http import HTTPStatus
from sanic.exceptions import NotFound
from sanic.response import json
from webargs_sanic.sanicparser import HandleValidationError
from extentions.helpers import format_error
from extentions.helpers import return_an_error
def handle_404(request, exception):
'''Handle 404 Not Found
... | EndurantDevs/webargs-sanic | examples/user_simple_storage/extentions/exceptions.py | .py | a2f6a86f3d11fc3a | 7.57 | 13 |
def format_error(status=None, title=None, detail=None, code=None):
'''Formatting JSON API Error Object
Constructing an error object based on JSON API standard
ref: http://jsonapi.org/format/#error-objects
Args:
status: Can be a http status codes
title: A summary of error
detail: ... | EndurantDevs/webargs-sanic | examples/user_simple_storage/extentions/helpers.py | .py | 09dc06c5f3940a5f | 7.57 | 13 |
# -*- coding: utf-8 -*-
"""Sanic request argument parsing module.
Example: ::
from sanic import Sanic
from webargs import fields
from webargs_sanic.sanicparser import use_args
app = Sanic(__name__)
hello_args = {
'name': fields.Str(required=True)
}
@app.route('/')
@use_args... | EndurantDevs/webargs-sanic | webargs_sanic/sanicparser.py | .py | 5ba9890d8b9d6d74 | 7.57 | 13 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""Use SQLAlchemy to fetch a result set from a query
"""
import os
import re
from pathlib import Path
from urllib.parse import parse_qs, urlencode
from cryptography.hazmat.backends import default_backend
from cryptography.hazmat.primitives import serialization
from jinja2.... | nerium-data/sqla-raw | raw/db.py | .py | 2222525c97b2899e | 7.45 | 7 |
import os
from pathlib import Path
from unittest import mock
import pytest
import sqlalchemy.exc
from cryptography.hazmat.primitives import serialization
from cryptography.hazmat.primitives.asymmetric import rsa
from sqlalchemy.engine.result import Result
from raw.db import (
engine,
prepare_key,
read_key... | nerium-data/sqla-raw | tests/test_db.py | .py | 892dbf2f68c111cf | 7.95 | 7 |
bl_info = {
"name": "Export SMF",
"description": "Export to SMF 12 (SnidrsModelFormat)",
"author": "Bart Teunis",
"version": (0, 9, 7),
"blender": (4, 5, 12),
"location": "File > Export",
"warning": "", # used for warning icon and text in addons panel
"doc_url": "https://github.com/blen... | blender-to-gmstudio/blender-to-smf | __init__.py | .py | 08edfcb101937c6e | 7.57 | 13 |
# SMF import scripts for Blender
#
#
#
#
import time
from math import *
from mathutils import *
from pathlib import Path
from struct import (
Struct,
calcsize,
unpack,
unpack_from,
)
# Used for much faster image loading
import numpy as np
# Make sure to reload changes to code that we maintain ourselv... | blender-to-gmstudio/blender-to-smf | import_smf.py | .py | 33e8fa1c5ec76f6b | 7.57 | 13 |
# SMF script equivalents for Blender
#
# DQs are stored as a named tuple of 2 Quaternions
# and can be converted to a tuple for export to SMF using dq_to_tuple_xyzw
#
from collections import namedtuple
from mathutils import Quaternion
# TODO Derive from typing.NamedTuple? Use dataclasses.dataclass?
DQ = namedtuple(
... | blender-to-gmstudio/blender-to-smf | pydq.py | .py | a25a89daa246196b | 7.57 | 13 |
# Work with categories
from typing import NamedTuple, List, Dict
import db
class Category(NamedTuple):
"""Structure of category"""
codename: str
name: str
is_base_expanse: bool
aliases: List[str]
class Categories:
def __init__(self):
self._categories = self._load_categories()
d... | ythosa/minuki | categories.py | .py | 21b875d9e6fe85d8 | 7.57 | 13 |
import datetime
import re
from typing import NamedTuple, Optional, List
import pytz
import db
from categories import Categories
import exceptions
class Message(NamedTuple):
"""Structure of a unpaired message about a new expense"""
amount: int
category_text: str
class Expense(NamedTuple):
"""Structu... | ythosa/minuki | expenses.py | .py | 18d48e18084e0520 | 7.57 | 13 |
#!/usr/bin/env python3
"""Turn ``summary/*.samples.1s5g.tsv`` into ``figure3reproduction.tsv`` output.
The output file ``figure3reproduction.tsv`` (THAPBI PICT output) has the same
format as ``figure3.tsv`` (Batovska et al. 2021 data underlying Figure 3,
exported using our ``figure3.R`` script). Either TSV file can be... | peterjc/thapbi-pict | examples/pest_insects/figure3reproduction.py | .py | 82e0a94889db217d | 7.5 | 9 |
#!/usr/bin/env python3
"""Script to reproduce Batovska *et al.* (2021) Figure 3.
See ``figure3.R`` and its output ``figure3.tsv`` which exports the ratios
underlying Batovska *et al.* (2021) Figure 3 from their R-based analysis:
https://github.com/alexpiper/HemipteraMetabarcodingMS/blob/master/hemiptera_metabarcoding.... | peterjc/thapbi-pict | examples/pest_insects/recreate_figure3.py | .py | 0378d5e2b0b4a0f9 | 7.5 | 9 |
#!/usr/bin/env python3
"""Convert GreenGenes style FASTA+TSV into SINTAX style annotated FASTA file.
As of v0.2.0 of the script, the input files can optionally be provided inside
Qiime QZA files (ZIP files with a single in a .../data/... subdirectory).
"""
import argparse
import gzip
import io
import sys
import zipfi... | peterjc/thapbi-pict | scripts/gg_to_sintax.py | .py | 9c7fcc90430a8495 | 7.5 | 9 |
#!/usr/bin/env python3
"""Extract NCBI references matching unknown FASTA entries."""
import argparse
import sys
from collections import defaultdict
from Bio.SeqIO.FastaIO import SimpleFastaParser
from thapbi_pict.db_import import parse_ncbi_fasta_entry
if "-v" in sys.argv or "--version" in sys.argv:
print("v0.0... | peterjc/thapbi-pict | scripts/missed_refs.py | .py | 714b7ad8dd9c774b | 7.5 | 9 |
#!/usr/bin/env python
"""Python 3 script plotting a stacked line chart of the reads in each sample.
This Python script was used to generate Figure 4 in the Cock *et al.* (2023)
paper in PeerJ, using matplotlib. This figure replaced the equivalent figure
in the preprint https://doi.org/10.1101/2023.03.24.534090 created... | peterjc/thapbi-pict | scripts/plot_reduction.py | .py | 12b58add69a0f716 | 7.5 | 9 |
#!/usr/bin/env python3
# Copyright 2021-2023 by Peter Cock, The James Hutton Institute.
# All rights reserved.
# This file is part of the THAPBI Phytophthora ITS1 Classifier Tool (PICT),
# and is released under the "MIT License Agreement". Please see the LICENSE
# file that should have been included as part of this pac... | peterjc/thapbi-pict | scripts/pooling.py | .py | fbec87986065a7fe | 7.5 | 9 |
#!/usr/bin/env python3
# Copyright 2023 by Peter Cock, The James Hutton Institute.
# All rights reserved.
# This file is part of the THAPBI Phytophthora ITS1 Classifier Tool (PICT),
# and is released under the "MIT License Agreement". Please see the LICENSE
# file that should have been included as part of this package.... | peterjc/thapbi-pict | scripts/sample_filter.py | .py | 607e564e14939160 | 7.5 | 9 |
# Copyright 2018-2023 by Peter Cock, The James Hutton Institute.
# Revisions copyright 2024 by Peter Cock, University of Strathclyde.
# All rights reserved.
# This file is part of the THAPBI Phytophthora ITS1 Classifier Tool (PICT),
# and is released under the "MIT License Agreement". Please see the LICENSE
# file that... | peterjc/thapbi-pict | thapbi_pict/db_orm.py | .py | aed9fb635d329146 | 7.5 | 9 |
# Copyright 2018-2024 by Peter Cock, The James Hutton Institute.
# Revisions copyright 2024 by Peter Cock, University of Strathclyde.
# All rights reserved.
# This file is part of the THAPBI Phytophthora ITS1 Classifier Tool (PICT),
# and is released under the "MIT License Agreement". Please see the LICENSE
# file that... | peterjc/thapbi-pict | thapbi_pict/dump.py | .py | 5087db026d114fce | 7.5 | 9 |
# Copyright 2019-2024 by Peter Cock, The James Hutton Institute.
# All rights reserved.
# This file is part of the THAPBI Phytophthora ITS1 Classifier Tool (PICT),
# and is released under the "MIT License Agreement". Please see the LICENSE
# file that should have been included as part of this package.
"""Code for sampl... | peterjc/thapbi-pict | thapbi_pict/ena_submit.py | .py | e5778d75d579d93f | 7.5 | 9 |
# Copyright 2018-2024 by Peter Cock, The James Hutton Institute.
# Revisions copyright 2024 by Peter Cock, University of Strathclyde.
# All rights reserved.
# This file is part of the THAPBI Phytophthora ITS1 Classifier Tool (PICT),
# and is released under the "MIT License Agreement". Please see the LICENSE
# file that... | peterjc/thapbi-pict | thapbi_pict/taxdump.py | .py | ed25b5e3b3f6ca30 | 7.5 | 9 |
# Copyright 2019-2024 by Peter Cock, The James Hutton Institute.
# All rights reserved.
# This file is part of the THAPBI Phytophthora ITS1 Classifier Tool (PICT),
# and is released under the "MIT License Agreement". Please see the LICENSE
# file that should have been included as part of this package.
"""Helper code to... | peterjc/thapbi-pict | thapbi_pict/versions.py | .py | 8e00cc8919734964 | 7.5 | 9 |
"""Base schema and field definitions for GeoJSON objects."""
from __future__ import annotations
import json
from typing import Any
import marshmallow as ma
from marshmallow import ValidationError
from marshmallow.fields import Float
from marshmallow.validate import Range
lon = Float(
required=True, validate=Ran... | folt/marshmallow-geojson | marshmallow_geojson/_base.py | .py | 9890bfa0960f8991 | 7.62 | 16 |
"""FeatureCollection schema for GeoJSON."""
from __future__ import annotations
from marshmallow import pre_load
from marshmallow.fields import Float, List, Nested, Str
from marshmallow.validate import OneOf
from ._base import BaseSchema
from .feature import FeatureSchema
from .object_type import FEATURE_COLLECTION
f... | folt/marshmallow-geojson | marshmallow_geojson/feature_collection.py | .py | 49a8c72a3e978cdc | 7.62 | 16 |
from __future__ import annotations
import typing
from typing import Literal
import marshmallow as ma
from marshmallow import types
from ._base import BaseSchema
from .feature import FeatureSchema
from .feature_collection import FeatureCollectionSchema
from .geometry_collection import GeometryCollectionSchema
from .l... | folt/marshmallow-geojson | marshmallow_geojson/geojson.py | .py | 7632101a0c89547e | 7.62 | 16 |
from __future__ import annotations
import typing
from typing import Literal
import marshmallow as ma
from marshmallow import types
from ._base import BaseSchema
from .line_string import LineStringSchema
from .multi_line_string import MultiLineStringSchema
from .multi_point import MultiPointSchema
from .multi_polygon... | folt/marshmallow-geojson | marshmallow_geojson/geometry.py | .py | 10f693b20032bf5c | 7.62 | 16 |
"""GeometryCollection schema for GeoJSON."""
from __future__ import annotations
from marshmallow import pre_load
from marshmallow.fields import Float, List, Nested, Str
from marshmallow.validate import OneOf
from ._base import BaseSchema
from .object_type import GEOMETRY_COLLECTION
from .validate import Bbox, NoFeat... | folt/marshmallow-geojson | marshmallow_geojson/geometry_collection.py | .py | e131619d269f8c85 | 7.62 | 16 |
"""LineString geometry schema for GeoJSON."""
from __future__ import annotations
from marshmallow import pre_load
from marshmallow.fields import Float, List, Str
from marshmallow.validate import OneOf
from ._base import BaseSchema
from .object_type import LINE_STRING
from .validate import Bbox, LineStringCoordinates... | folt/marshmallow-geojson | marshmallow_geojson/line_string.py | .py | 31989051e1619855 | 7.62 | 16 |
"""MultiLineString geometry schema for GeoJSON."""
from __future__ import annotations
from marshmallow import pre_load
from marshmallow.fields import Float, List, Str
from marshmallow.validate import OneOf
from ._base import BaseSchema
from .object_type import MULTI_LINE_STRING
from .validate import Bbox, LineString... | folt/marshmallow-geojson | marshmallow_geojson/multi_line_string.py | .py | 18125f604d5bfc71 | 7.62 | 16 |
"""MultiPoint geometry schema for GeoJSON."""
from __future__ import annotations
from marshmallow import pre_load
from marshmallow.fields import Float, List, Str
from marshmallow.validate import Length, OneOf
from ._base import BaseSchema
from .object_type import MULTI_POINT
from .validate import Bbox, NoFeatureMemb... | folt/marshmallow-geojson | marshmallow_geojson/multi_point.py | .py | 12ef61d31e00dac5 | 7.62 | 16 |
"""MultiPolygon geometry schema for GeoJSON."""
from __future__ import annotations
from marshmallow import pre_load
from marshmallow.fields import Float, List, Str
from marshmallow.validate import OneOf
from ._base import BaseSchema
from .object_type import MULTI_POLYGON
from .validate import Bbox, LinearRing, NoFea... | folt/marshmallow-geojson | marshmallow_geojson/multi_polygon.py | .py | 880e314ff30ce881 | 7.62 | 16 |
"""GeoJSON object type definitions.
This module defines the valid GeoJSON object types as specified in
RFC 7946 Section 1.4.
References:
https://www.rfc-editor.org/rfc/rfc7946.html#section-1.4
"""
from __future__ import annotations
from enum import Enum
POINT = "Point"
MULTI_POINT = "MultiPoint"
LINE_STRING = ... | folt/marshmallow-geojson | marshmallow_geojson/object_type.py | .py | 505b5481f5405124 | 7.62 | 16 |
"""Point geometry schema for GeoJSON."""
from __future__ import annotations
from marshmallow import pre_load
from marshmallow.fields import Float, List, Str
from marshmallow.validate import Length, OneOf
from ._base import BaseSchema
from .object_type import POINT
from .validate import Bbox, NoFeatureMembers
class... | folt/marshmallow-geojson | marshmallow_geojson/point.py | .py | dd146cfbad40b07f | 7.62 | 16 |
"""Polygon geometry schema for GeoJSON."""
from __future__ import annotations
from marshmallow import pre_load
from marshmallow.fields import Float, List, Str
from marshmallow.validate import OneOf
from ._base import BaseSchema
from .object_type import POLYGON
from .validate import Bbox, LinearRing, NoFeatureMembers... | folt/marshmallow-geojson | marshmallow_geojson/polygon.py | .py | 4eaa3fc4063f3a62 | 7.62 | 16 |
"""Properties schema for GeoJSON Feature objects."""
from __future__ import annotations
from ._base import BaseSchema
class PropertiesSchema(BaseSchema):
"""Base schema for Feature properties.
This schema serves as a base class for custom property schemas. Users
should subclass this schema to define th... | folt/marshmallow-geojson | marshmallow_geojson/property.py | .py | 6b7fb407a178c686 | 7.62 | 16 |
"""Tests for bounding box validation according to RFC 7946."""
import pytest
from marshmallow.exceptions import ValidationError
from marshmallow_geojson import FeatureCollectionSchema, FeatureSchema, PointSchema
class TestBoundingBoxValidation:
"""Test suite for bounding box validation."""
def test_valid_2... | folt/marshmallow-geojson | tests/test_bbox.py | .py | f4db0e065d1e628a | 7.12 | 16 |
"""Tests for FeatureSchema."""
import json
import pytest
from marshmallow.exceptions import ValidationError
from marshmallow_geojson import FeatureSchema
from marshmallow_geojson.object_type import FEATURE
class TestFeatureSchema:
"""Test suite for FeatureSchema validation and serialization."""
def test_v... | folt/marshmallow-geojson | tests/test_feature.py | .py | 3d08075571901bfc | 7.12 | 16 |
"""Tests for FeatureCollectionSchema."""
import copy
import json
import pytest
from marshmallow.exceptions import ValidationError
from marshmallow_geojson import FeatureCollectionSchema
from marshmallow_geojson.object_type import FEATURE_COLLECTION
class TestFeatureCollectionSchema:
"""Test suite for FeatureCo... | folt/marshmallow-geojson | tests/test_feature_collection.py | .py | 9a2ae9385fe8f7cb | 8.12 | 16 |
"""Tests for GeoJSONSchema."""
import json
import pytest
from marshmallow.exceptions import ValidationError
from marshmallow_geojson import GeoJSONSchema
from marshmallow_geojson.object_type import GeoJSONType
class TestGeoJSONSchema:
"""Test suite for GeoJSONSchema validation and serialization."""
def te... | folt/marshmallow-geojson | tests/test_geojson.py | .py | 01d46983e4c75f0f | 7.12 | 16 |
"""Tests for unique GeoJSONSchema functionality not present in pydantic-geojson.
This module tests features that are unique to marshmallow-geojson:
- Universal GeoJSONSchema for all GeoJSON object types
- GeometriesSchema for all geometry types
- Marshmallow-specific parameters (only, exclude, partial, unknown)
- get_... | folt/marshmallow-geojson | tests/test_geojson_schema_unique.py | .py | 7d2bc978e498f429 | 7.12 | 16 |
"""Tests for GeometryCollectionSchema."""
import copy
import json
import pytest
from marshmallow.exceptions import ValidationError
from marshmallow_geojson import GeometryCollectionSchema
from marshmallow_geojson.object_type import GEOMETRY_COLLECTION
class TestGeometryCollectionSchema:
"""Test suite for Geome... | folt/marshmallow-geojson | tests/test_geometry_collection.py | .py | 380770a43c4bbb27 | 8.12 | 16 |
"""Tests for LineStringSchema."""
import json
import pytest
from marshmallow.exceptions import ValidationError
from marshmallow_geojson import LineStringSchema
from marshmallow_geojson.object_type import LINE_STRING
from tests.test_utils import assert_coordinates_equal
class TestLineStringSchema:
"""Test suite... | folt/marshmallow-geojson | tests/test_line_string.py | .py | b87e5d85cb3cf5ee | 7.12 | 16 |
"""Tests for MultiLineStringSchema."""
import json
import pytest
from marshmallow.exceptions import ValidationError
from marshmallow_geojson import MultiLineStringSchema
from marshmallow_geojson.object_type import MULTI_LINE_STRING
from tests.test_utils import assert_coordinates_equal
class TestMultiLineStringSche... | folt/marshmallow-geojson | tests/test_multi_line_string.py | .py | 97c970c8b59e7abf | 7.12 | 16 |
"""Tests for MultiPointSchema."""
import json
import pytest
from marshmallow.exceptions import ValidationError
from marshmallow_geojson import MultiPointSchema
from marshmallow_geojson.object_type import MULTI_POINT
from tests.test_utils import assert_coordinates_equal
class TestMultiPointSchema:
"""Test suite... | folt/marshmallow-geojson | tests/test_multi_point.py | .py | 5499478509d40dbb | 8.12 | 16 |
"""Tests for MultiPolygonSchema."""
import json
import pytest
from marshmallow.exceptions import ValidationError
from marshmallow_geojson import MultiPolygonSchema
from marshmallow_geojson.object_type import MULTI_POLYGON
from tests.test_utils import assert_coordinates_equal
class TestMultiPolygonSchema:
"""Te... | folt/marshmallow-geojson | tests/test_multi_polygon.py | .py | 96d7ff1d03b05783 | 7.12 | 16 |
"""Tests for object_type module."""
import pytest
from marshmallow_geojson import object_type
class TestFormatStringType:
"""Test suite for object type string constants."""
@pytest.mark.parametrize(
"constant,expected_value",
[
(object_type.POINT, "Point"),
(object_t... | folt/marshmallow-geojson | tests/test_object_type.py | .py | ceb97ada758def54 | 8.12 | 16 |
"""Tests for PointSchema."""
import json
import pytest
from marshmallow.exceptions import ValidationError
from marshmallow_geojson import PointSchema
from marshmallow_geojson.object_type import POINT
from tests.test_utils import assert_coordinates_equal
class TestPointSchema:
"""Test suite for PointSchema vali... | folt/marshmallow-geojson | tests/test_point.py | .py | ef8e95fdd083482e | 8.12 | 16 |
"""Tests for PolygonSchema."""
import json
import pytest
from marshmallow.exceptions import ValidationError
from marshmallow_geojson import PolygonSchema
from marshmallow_geojson.object_type import POLYGON
from tests.test_utils import assert_coordinates_equal
class TestPolygonSchema:
"""Test suite for PolygonS... | folt/marshmallow-geojson | tests/test_polygon.py | .py | 8662dfc1c14eff5f | 7.12 | 16 |
"""Tests for type mixing validation according to RFC 7946 Section 7.1."""
from typing import Any
import pytest
from marshmallow.exceptions import ValidationError
from marshmallow_geojson import (
FeatureCollectionSchema,
FeatureSchema,
GeometryCollectionSchema,
LineStringSchema,
MultiLineStringSc... | folt/marshmallow-geojson | tests/test_type_mixing_validation.py | .py | e4bc756a6d58faa6 | 7.12 | 16 |
"""Utility functions for tests."""
def assert_coordinates_equal(coord, expected):
"""Assert that coordinates match expected [lon, lat] or [lon, lat, alt].
Args:
coord: Coordinate value (can be tuple, list, or dict).
expected: Expected coordinate list [lon, lat] or [lon, lat, alt].
"""
... | folt/marshmallow-geojson | tests/test_utils.py | .py | d441cad27a6f89cb | 7.12 | 16 |
#!/usr/bin/python3 -u
# -*- mode: python; indent-tabs-mode: nil; python-indent-offset: 4 -*-
# vim: autoindent tabstop=4 shiftwidth=4 expandtab softtabstop=4 filetype=python
"""
Query a TRex server running in ASTF mode for port information.
STLClient cannot connect to an ASTF-mode TRex server, so this script uses
AST... | perftool-incubator/bench-trafficgen | trafficgen/trex-astf-query.py | .py | 3143fd4889b873ce | 7.52 | 10 |
#! /usr/bin/env python3
# -*- coding: utf-8 -*-
# vim:fenc=utf-8
#
# Copyright © 2020 Edward Higgins <ed.higgins@york.ac.uk>
#
# Distributed under terms of the MIT license.
""" IMAGES - Image access and manipulation module
Description:
images.py contains the ImageData class for storing datasets of multiple
fr... | PoL-biophysics/pystachio-smt | pystachio_smt/images.py | .py | ebf12ac7188cf7e6 | 7.56 | 12 |
#! /usr/bin/env python3
# -*- coding: utf-8 -*-
# vim:fenc=utf-8
#
#
# Distributed under terms of the MIT license.
""" SIMULATION - Dataset simulation module
Description:
simulation.py contains the code for the simulation task, which simulates
pseudo-experimental datasets as characterised by the relevant para... | PoL-biophysics/pystachio-smt | pystachio_smt/simulation.py | .py | 22824bdd47ffaad4 | 7.56 | 12 |
#! /usr/bin/env python3
# -*- coding: utf-8 -*-
# vim:fenc=utf-8
#
# Distributed under terms of the MIT license.
""" SPOTS - Spot characterisation and manipulation module
Description:
spots.py contains the Spots class for characterising and manipulating data
associated with bright spots in the image datasets ... | PoL-biophysics/pystachio-smt | pystachio_smt/spots.py | .py | 8236de886a5b3b56 | 7.56 | 12 |
#! /usr/bin/env python3
# -*- coding: utf-8 -*-
# vim:fenc=utf-8
#
# Copyright © 2020 Edward Higgins <ed.higgins@york.ac.uk>
#
# Distributed under terms of the MIT license.
""" TRACKING - Spot tracking module
Description:
tracking.py contains the code for the tracking task, which identifies spots
within a set... | PoL-biophysics/pystachio-smt | pystachio_smt/tracking.py | .py | 71bfe033cbe8ebe8 | 7.56 | 12 |
#! /usr/bin/env python3
# -*- coding: utf-8 -*-
# vim:fenc=utf-8
#
# Copyright © 2021 Edward Higgins <ed.higgins@york.ac.uk>
#
# Distributed under terms of the MIT license.
""" TRAJECTORIES - Trajectory construction and manipulation module
Description:
trajectories.py contains the Trajectory class containing info... | PoL-biophysics/pystachio-smt | pystachio_smt/trajectories.py | .py | 0bca30c6e60c6427 | 7.56 | 12 |
# -*- coding: utf-8 -*-
"""
PySTACHIO param testing script v0.2 JWS 2022
"""
import glob
import os
import numpy as np
import matplotlib.pyplot as plt
import tifffile
import sys
import easygui
def write_params(pfile, params, values):
f = open(pfile, "w")
for i in range(len(params)):
f.write(f'{params[i... | PoL-biophysics/pystachio-smt | test_pystachio.py | .py | fae0c95b476cb56e | 8.06 | 12 |
import dtlpy as dl
import logging
logger = logging.getLogger(name='dtlpy')
class ServiceRunner(dl.BaseServiceRunner):
"""
Package runner class
"""
def __init__(self):
"""
Init package attributes here
:return:
"""
def run(self, annotation, progress=None):
... | dataloop-ai/dtlpy | dtlpy/assets/service_runners/single_method_annotation.py | .py | f031a6946a23fb1b | 7.66 | 20 |
import dtlpy as dl
import logging
logger = logging.getLogger(name='dtlpy')
class ServiceRunner(dl.BaseServiceRunner):
"""
Package runner class
"""
def __init__(self):
"""
Init package attributes here
:return:
"""
def run(self, item, progress=None):
"""
... | dataloop-ai/dtlpy | dtlpy/assets/service_runners/single_method_item.py | .py | bd7fe753deb28476 | 7.66 | 20 |
import dtlpy as dl
import logging
logger = logging.getLogger(name='dtlpy')
class ServiceRunner(dl.BaseServiceRunner):
"""
Package runner class
"""
def __init__(self):
"""
Init package attributes here
:return:
"""
def run(self, item, dataset, config, annotation,... | dataloop-ai/dtlpy | dtlpy/assets/service_runners/single_method_multi_input.py | .py | 80c333ca01a8a334 | 7.66 | 20 |
import os
import json
import glob
import shutil
from .base_cache import BaseCache
class FileSystemCache(BaseCache):
def __init__(self, options=None, size=1000, ttl=1000):
"""
docs
"""
if options is None:
options = {}
root_dir = options.get('rootDir', os.environ... | dataloop-ai/dtlpy | dtlpy/caches/filesystem_cache.py | .py | 3ab06ac84b9c495a | 7.66 | 20 |
import redis
import json
import datetime
from .base_cache import BaseCache
class RedisCache(BaseCache):
def __init__(self, options=None, ttl=1000):
if options is None:
options = {}
self.cache = redis.Redis(
host=options.get('host', '127.0.0.1'),
port=options.get... | dataloop-ai/dtlpy | dtlpy/caches/redis_cache.py | .py | 6e0260c60017151f | 7.66 | 20 |
from . import BaseAnnotationDefinition
class Classification(BaseAnnotationDefinition):
"""
Classification annotation object
"""
type = "class"
def __init__(self, label, attributes=None, description=None):
super().__init__(description=description, attributes=attributes)
self.la... | dataloop-ai/dtlpy | dtlpy/entities/annotation_definitions/classification.py | .py | baa2c001aa8dc30d | 7.66 | 20 |
from . import BaseAnnotationDefinition
class Comparison(BaseAnnotationDefinition):
"""
Comparison annotation object
"""
type = "comparison"
def __init__(self, coordinates, label, attributes=None, description=None):
super().__init__(description=description, attributes=attributes)
s... | dataloop-ai/dtlpy | dtlpy/entities/annotation_definitions/comparison.py | .py | 729f47677db09bb1 | 7.66 | 20 |
from . import BaseAnnotationDefinition
class Description(BaseAnnotationDefinition):
"""
Subtitle annotation object
"""
def __init__(self, text, description=None):
super().__init__(description=description)
self.type = "item_description"
self.text = text
self.label =... | dataloop-ai/dtlpy | dtlpy/entities/annotation_definitions/description.py | .py | d8687dcc5f9ad84b | 7.66 | 20 |
from . import BaseAnnotationDefinition
class FreeText(BaseAnnotationDefinition):
"""
Free text annotation type (e.g. response for a prompt)
"""
type = "text"
def __init__(self, text, label='free-text', attributes=None, description=None):
"""
Create a free text annotation
:... | dataloop-ai/dtlpy | dtlpy/entities/annotation_definitions/free_text.py | .py | 2951122c0117a077 | 7.66 | 20 |
from . import BaseAnnotationDefinition
class GisType:
"""
State enum
"""
BOX = 'box'
POLYGON = 'polygon'
POLYLINE = 'polyline'
POINT = 'point'
class Gis(BaseAnnotationDefinition):
"""
Box annotation object
Can create a box using 2 point using: "top", "left", "bottom",... | dataloop-ai/dtlpy | dtlpy/entities/annotation_definitions/gis.py | .py | 0fa79be47af9caf2 | 7.66 | 20 |
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