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 |
|---|---|---|---|---|---|---|
"""Bounded row-wise mean, median, and standard-deviation reductions."""
from collections.abc import Iterator
import numpy as np
_ROW_BATCH_ELEMENTS = 262_144
def row_slices(n_rows: int, n_columns: int) -> Iterator[tuple[int, int]]:
"""Yield row slices whose matrices stay near the shared element budget."""
... | Cameron-Lyons/ier | src/ier/_row_statistics.py | .py | d613bc41b33300e6 | 7.48 | 8 |
"""Small statistical primitives used internally by IER.
The implementations here intentionally cover only the narrow operations the
package needs. Keeping them local avoids making a large general-purpose
statistics library a runtime dependency.
"""
from __future__ import annotations
import math
from statistics impo... | Cameron-Lyons/ier | src/ier/_statistics.py | .py | 1996c70f49ee6329 | 7.48 | 8 |
"""Shared input validation utilities for careless detection functions."""
from collections.abc import Iterator, Mapping, Sequence
from typing import Any, Protocol, TypeAlias
import numpy as np
from numpy.typing import ArrayLike
class SupportsArray(Protocol):
"""Protocol for objects convertible to numpy arrays (... | Cameron-Lyons/ier | src/ier/_validation.py | .py | aa3cd41aa9de68d1 | 7.48 | 8 |
"""This module contains the evenodd function for calculating even-odd consistency scores."""
import numpy as np
from ier._correlation import row_correlations
from ier._validation import MatrixLike, validate_matrix_input
def calculate_correlations(even_cols: np.ndarray, odd_cols: np.ndarray) -> np.ndarray:
"""
... | Cameron-Lyons/ier | src/ier/evenodd.py | .py | 647b369e57a6094d | 7.48 | 8 |
"""
Guttman errors for person-fit analysis in detecting careless responding.
Guttman errors count the number of response reversals relative to item
difficulty ordering. High error counts suggest inconsistent or careless responding.
"""
import warnings
import numpy as np
from ier._row_statistics import row_slices
fr... | Cameron-Lyons/ier | src/ier/guttman.py | .py | ee525c2756f5a153 | 7.48 | 8 |
"""The main module for the app logic"""
import sys
import webbrowser
from PyQt6 import QtCore, QtWidgets
from _version import __version__
from encoding_mappings import (
ALL_EXT_ENCODINGS,
CYRILLIC_ENCODINGS,
HK,
HK_EXT,
ROMAN_BASIC_ENCODINGS,
Encodings,
)
from service import convert
from upd... | kosperun/SansConverter | src/sans_converter.py | .py | 87178b0e06ab5235 | 7.42 | 6 |
from encoding_mappings import (
ASPIRATED_CYRILLIC_LETTERS,
ASPIRATED_CYRILLIC_LETTERS_VOICED,
ASPIRATED_CYRILLIC_LETTERS_VOICELESS,
ASPIRATED_ROMAN_LETTERS,
IAST_INPUT_ALIASES,
RUSSIAN_ENCODINGS,
Encodings,
)
UKR_ENCODINGS = (Encodings.UKR_G.value, Encodings.UKR_H.value)
def convert(
... | kosperun/SansConverter | src/service.py | .py | 36031efe7808fcec | 7.42 | 6 |
"""Checks GitHub Releases for a newer version of SansConverter."""
import json
import platform
import urllib.error
import urllib.request
from dataclasses import dataclass
from typing import Optional
GITHUB_API_URL = "https://api.github.com/repos/kosperun/SansConverter/releases/latest"
REQUEST_TIMEOUT_SECONDS = 5
# M... | kosperun/SansConverter | src/update_checker.py | .py | aebd1c173b73b519 | 7.42 | 6 |
""" 'About' dialog window generated by QtDesigner"""
from PyQt6 import QtCore, QtGui, QtWidgets
from _version import __version__
class UiAboutDialog(QtWidgets.QDialog):
"""Creates an 'About' dialog window"""
def __init__(self, parent):
super().__init__(parent)
# parent dialog will be SansCo... | kosperun/SansConverter | src/windows/about.py | .py | a3f3b382ebc5d472 | 7.42 | 6 |
"""Help dialog window generated by QtDesigner"""
from PyQt6 import QtCore, QtGui, QtWidgets
class UiHelpDialog(QtWidgets.QDialog):
"""Help window GUI"""
def __init__(self, parent):
super().__init__(parent)
# parent dialog will be SansConverter
self.parent_dialog = parent
self... | kosperun/SansConverter | src/windows/help.py | .py | 9f5dc3906ff5666c | 7.42 | 6 |
"""Select Encodings dialog window"""
from PyQt6.QtCore import QCoreApplication, Qt
from PyQt6.QtWidgets import (
QDialog,
QDialogButtonBox,
QLabel,
QListWidget,
QListWidgetItem,
QVBoxLayout,
)
from windows.select_encodings_warning import WarningDialog
class UiSelectEncodingsDialog(QDialog):
... | kosperun/SansConverter | src/windows/select_encodings.py | .py | a4a7af1becb844cf | 7.42 | 6 |
# sourced from https://github.com/mitgobla/python-discord-rpc/
# -- forked from https://github.com/suclearnub/python-discord-rpc/
# References:
# * https://github.com/devsnek/discord-rpc/tree/master/src/transports/IPC.js
# * https://github.com/devsnek/discord-rpc/tree/master/example/main.js
# * https://github.com/disc... | irbyjm/trakt-discord-presence | libs/rpc.py | .py | 335287bcd367aac0 | 7.42 | 6 |
"""Module to manage AiiDAlab configuration."""
from __future__ import annotations
from os import getenv
from pathlib import Path
from typing import Any
import click
import toml
CONFIG_PATH = Path.home() / "aiidalab.toml"
_CONFIG = toml.loads(CONFIG_PATH.read_text()) if CONFIG_PATH.is_file() else {}
_DEVELOP_MODE = ... | aiidalab/aiidalab | aiidalab/config.py | .py | ed4838ad54911ba2 | 7.63 | 17 |
"""App environment specification
The specification is used to describe a reproducible environment for a
specific app, similar to the Reproducible Environment Specification (REES) [1]
[1] https://repo2docker.readthedocs.io/en/latest/specification.html
The following configuration files are recognized with the order of... | aiidalab/aiidalab | aiidalab/environment.py | .py | e76b176016e11e2a | 7.63 | 17 |
"""Utility module for git-managed AiiDAlab apps."""
# This future import turns on postponed evaluation of annotations, per PEP 563.
# https://peps.python.org/pep-0563/
# This is needed for two reasons:
# 1. Using the new Union syntax (type1 | type2) with Python < 3.10
# 2. Instead of using the Self type when returning... | aiidalab/aiidalab | aiidalab/git_util.py | .py | fcba4718af98ca02 | 7.63 | 17 |
"""Generate API endpoints."""
import json
from collections.abc import Generator
from pathlib import Path
from .apps_index import validate_apps_index_and_apps
from .core import AppRegistrySchemas
def build_api_v1(api_path: Path, apps_index: dict, apps_data: dict) -> Generator[Path]:
"""Build tree for API endpoin... | aiidalab/aiidalab | aiidalab/registry/api.py | .py | 396e2727ae145713 | 7.63 | 17 |
"""Generate the apps index including all aggregated metadata."""
from __future__ import annotations
import logging
from collections import OrderedDict
from copy import deepcopy
from dataclasses import asdict
from typing import Any
import jsonschema
from ..utils import _ParseAppCallable, sort_semantic
from . import ... | aiidalab/aiidalab | aiidalab/registry/apps_index.py | .py | c16cf11e027fca0e | 7.63 | 17 |
"""Core data classes for the app registry."""
import json
from dataclasses import dataclass, fields
from pathlib import Path
import jsonschema
import pkg_resources
from .util import load_json
@dataclass
class AppRegistrySchemas:
"""The app registry JSON-schema objects."""
app: dict
apps: dict
apps... | aiidalab/aiidalab | aiidalab/registry/core.py | .py | f152f627b31964e3 | 7.63 | 17 |
from __future__ import annotations
import logging
import os
import re
from collections.abc import Generator
from dataclasses import dataclass, replace
from urllib.parse import urlsplit, urlunsplit
from dulwich.refs import Ref
from ..environment import Environment
from ..fetch import fetch_from_url
from ..git_util im... | aiidalab/aiidalab | aiidalab/registry/releases.py | .py | 15c69aef92304cd0 | 7.63 | 17 |
"""Utility functions for the application registry."""
import json
import string
from pathlib import Path
from urllib.parse import urlparse
def get_html_app_fname(app_name: str) -> str:
valid_characters = set(string.ascii_letters + string.digits + "_-")
simple_string = "".join(c for c in app_name if c in val... | aiidalab/aiidalab | aiidalab/registry/util.py | .py | 27c237a307daf61a | 7.63 | 17 |
"""Generate the app registry website."""
from __future__ import annotations
import logging
import os
import os.path
import shutil
from collections.abc import Generator
from itertools import chain
from pathlib import Path
import pkg_resources
from ..utils import parse_app_repo
from . import api, yaml
from .apps_inde... | aiidalab/aiidalab | aiidalab/registry/web.py | .py | b2052f6309ad752a | 7.63 | 17 |
from __future__ import annotations
from pathlib import Path
from typing import Any
from urllib.parse import urlsplit
import cachecontrol
import jsonref # type: ignore[import-untyped]
import requests
from ruamel.yaml import YAML
REQUESTS = cachecontrol.CacheControl(requests.Session())
class JsonYamlLoader(jsonref.... | aiidalab/aiidalab | aiidalab/registry/yaml.py | .py | 78ddf94a9985a462 | 7.63 | 17 |
# pylint: disable=invalid-name
# -*- coding: utf-8 -*-
"""Sphinx configuration for aiidalab."""
import os
import subprocess
import sys
import time
import aiidalab
# Add any Sphinx extension module names here, as strings. They can be
# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
# ones.
extens... | aiidalab/aiidalab | docs/source/conf.py | .py | 1f7600570901292a | 7.63 | 17 |
import sys
import threading
from pathlib import Path
import pytest
from ruamel.yaml import YAML
@pytest.fixture(scope="session")
def static_path():
return Path(__file__).parent.absolute() / "static"
@pytest.fixture(scope="session")
def apps_path(static_path):
return static_path / "apps.yaml"
@pytest.fixt... | aiidalab/aiidalab | tests/conftest.py | .py | be3cfde2d15da149 | 8.13 | 17 |
import threading
from dataclasses import dataclass
from pathlib import Path
from time import sleep
import pytest
import traitlets
from aiidalab.app import AiidaLabApp, AiidaLabAppWatch
def test_init_refresh(generate_app):
app = generate_app()
# App is being refreshed already in the `generate_app` fixture
... | aiidalab/aiidalab | tests/test_appclass.py | .py | 00e4d091bec40aa1 | 8.13 | 17 |
"""Test the dataclass _AiidaLabApp.
We mock the app requirements and the medatada by a simple yaml file."""
import sys
from pathlib import Path
import pytest
from packaging.requirements import Requirement
from aiidalab.app import AppRemoteUpdateStatus, AppVersion, _AiidaLabApp
@pytest.fixture
def python_bin():
... | aiidalab/aiidalab | tests/test_appdataclass.py | .py | e561f75f9fa36bb8 | 7.13 | 17 |
from pathlib import Path
import pytest
# To learn more about testing Click applications see
# http://click.pocoo.org/5/testing/
from click.testing import CliRunner
import aiidalab.__main__ as cli
from aiidalab import __version__
def test_version_displays_library_version():
"""
Run `aiidalab --version` and ... | aiidalab/aiidalab | tests/test_cli.py | .py | d7965f6868e30f1c | 7.13 | 17 |
"""Test fixtures defined in conftest.py"""
import pytest
def test_forbidden_functions():
"""Ensure that we fail if we try to run `pip install`
and other functions that might influence global environment.
"""
from aiidalab.utils import (
load_app_registry_entry,
load_app_registry_index... | aiidalab/aiidalab | tests/test_conftest.py | .py | 6a3ff0d22645a409 | 7.13 | 17 |
import os
import pytest
from aiidalab.fetch import GitRepo, fetch_from_url
pytestmark = pytest.mark.registry
def test_get_all_tagged_releases():
"""Test that all tagged releases are returned."""
from aiidalab.registry.releases import _get_release_commits, _split_release_line
url = "git+https://github.... | aiidalab/aiidalab | tests/test_registry.py | .py | d6a8019742d8291b | 7.13 | 17 |
import collections
from typing import List, Tuple
import numba as nb
import numpy as np
import spectrum_utils.spectrum as sus
SpectrumTuple = collections.namedtuple(
"SpectrumTuple", ["precursor_mz", "precursor_charge", "mz", "intensity"]
)
def cosine(
spectrum1: sus.MsmsSpectrum,
spectrum2: sus.MsmsSp... | mwang87/MetabolomicsSpectrumResolver | metabolomics_spectrum_resolver/similarity.py | .py | 9123fb2313761337 | 8.02 | 10 |
import io
import sys
from typing import Any, Tuple
import celery
import celery_once
import joblib
import redis
import spectrum_utils.spectrum as sus
from metabolomics_spectrum_resolver import drawing, parsing
from metabolomics_spectrum_resolver import tasks_analytics
memory = joblib.Memory("tmp/joblibcache", verbose... | mwang87/MetabolomicsSpectrumResolver | metabolomics_spectrum_resolver/tasks.py | .py | 51299a802caa9bd7 | 7.02 | 10 |
import copy
import csv
import io
import json
import urllib.parse
from typing import Any, Dict, List, Optional, Tuple, Union
import flask
import numpy as np
import qrcode
from spectrum_utils import spectrum as sus
from metabolomics_spectrum_resolver import similarity, tasks
from metabolomics_spectrum_resolver.rate_lim... | mwang87/MetabolomicsSpectrumResolver | metabolomics_spectrum_resolver/views.py | .py | 0a48ebd8e699c8f8 | 7.02 | 10 |
"""Authenticated Received Chain (ARC) sealing and verification (RFC 8617)
ARC lets a sequence of intermediaries (mailing lists, forwarders, gateways)
record the email authentication results they observed, so that a later
receiver can trust those results even when SPF/DKIM/DMARC break in transit.
Each hop adds an *ARC ... | seanthegeek/mailsuite | mailsuite/arc.py | .py | 012879ebc6fcc0cf | 7.57 | 13 |
"""Abstract base class for mailbox connections"""
from __future__ import annotations
from abc import ABC
from collections.abc import Callable
from typing import Any
class FolderExistsError(RuntimeError):
"""Raised when a folder/label operation targets a name that is already
taken — e.g. :meth:`MailboxConnec... | seanthegeek/mailsuite | mailsuite/mailbox/base.py | .py | cbf41be0eb59dd3d | 7.57 | 13 |
"""Gmail mailbox backend"""
from __future__ import annotations
import base64
import logging
from collections.abc import Callable
from functools import lru_cache
from pathlib import Path
from time import sleep
from typing import Any
from mailsuite.mailbox.base import (
FolderNotFoundError,
MailboxConnection,
... | seanthegeek/mailsuite | mailsuite/mailbox/gmail.py | .py | 5a6475f6cf8236d6 | 7.57 | 13 |
"""IMAP mailbox backend"""
from __future__ import annotations
import logging
from collections.abc import Callable
from time import sleep
from typing import Any, cast
from imapclient.exceptions import IMAPClientError
from mailsuite.imap import IMAPClient
from mailsuite.mailbox.base import MailboxConnection
logger =... | seanthegeek/mailsuite | mailsuite/mailbox/imap.py | .py | 94c57bd0d13e2079 | 7.57 | 13 |
"""Maildir mailbox backend"""
from __future__ import annotations
import logging
import mailbox
import os
from collections.abc import Callable
from time import sleep
from typing import Any
from mailsuite.mailbox.base import MailboxConnection
logger = logging.getLogger(__name__)
class MaildirConnection(MailboxConne... | seanthegeek/mailsuite | mailsuite/mailbox/maildir.py | .py | f68ab8c187862fc7 | 7.57 | 13 |
"""Shared pytest fixtures."""
from __future__ import annotations
import pytest
from mailsuite.dkim import generate_dkim_keypair
@pytest.fixture(scope="session")
def dkim_keypair() -> tuple[str, str]:
"""A 2048-bit RSA DKIM keypair shared across tests for speed."""
return generate_dkim_keypair(key_size=2048... | seanthegeek/mailsuite | tests/conftest.py | .py | c3397e1428e5fb98 | 8.07 | 13 |
"""Tests for mailsuite.arc."""
from __future__ import annotations
import pytest
from mailsuite.arc import ARCError, seal_email, verify_arc_chain
from mailsuite.dkim import generate_dkim_keypair, generate_dkim_txt_record
def _dns_func_for(pub: str):
"""A fake DNS resolver returning a DKIM TXT record for ``pub``... | seanthegeek/mailsuite | tests/test_arc.py | .py | 31b383029f68f7be | 7.07 | 13 |
"""Docker-based integration tests for the IMAP IDLE watch loop.
These exercise ``mailsuite.imap.IMAPClient``'s IDLE watch against a real IMAP
server (GreenMail) running in Docker — the behaviour that the mocked unit
tests can't cover: live IDLE notifications and reconnect-during-IDLE.
They are **opt-in**: skipped unl... | seanthegeek/mailsuite | tests/test_imap_idle_integration.py | .py | a98d6a6fd93a26d8 | 8.07 | 13 |
"""Tests for mailsuite.mailbox.gmail.GmailConnection.
The Gmail SDK is fully mocked. We construct connections via __new__
and inject a fake service builder so we don't need real OAuth or
network I/O.
"""
from __future__ import annotations
import base64
from unittest.mock import MagicMock
import pytest
# Skip every... | seanthegeek/mailsuite | tests/test_mailbox_gmail.py | .py | 9301dd9dbea563e6 | 8.07 | 13 |
"""Tests for mailsuite.mailbox.imap.IMAPConnection."""
from __future__ import annotations
from unittest.mock import MagicMock
import pytest
from imapclient.exceptions import IMAPClientError
from mailsuite.mailbox import FolderExistsError
from mailsuite.mailbox.imap import IMAPConnection
def _bare_connection() -> ... | seanthegeek/mailsuite | tests/test_mailbox_imap.py | .py | ce49de9871d6e80b | 8.07 | 13 |
"""Tests for mailsuite.mailbox.maildir."""
from __future__ import annotations
import mailbox
import os
import pytest
from mailsuite.mailbox import (
FolderExistsError,
FolderNotFoundError,
MailboxConnection,
MaildirConnection,
)
@pytest.fixture
def maildir_path(tmp_path):
md = tmp_path / "Mail... | seanthegeek/mailsuite | tests/test_mailbox_maildir.py | .py | 7e7dffd2a92e6c23 | 7.07 | 13 |
"""Tests for mailsuite.utils."""
from __future__ import annotations
import base64
import logging
import pytest
from mailsuite.utils import (
create_email,
decode_base64,
from_trusted_domain,
get_filename_safe_string,
is_outlook_msg,
parse_authentication_results,
parse_dkim_signature,
... | seanthegeek/mailsuite | tests/test_utils.py | .py | 29700ef2d5bbecea | 8.07 | 13 |
# -*- coding: utf-8 -*-
"""
This module is a simple common base for text file IO.
@outhor: Kijin Nam, knam@water.ca.gov
"""
class BaseIO(object):
"""Common IO routines to handle text inputs"""
def __init__(self, logger=None):
"""Constructor"""
self._logger = logger
self._lc = 0
@... | CADWRDeltaModeling/schimpy | schimpy/base_io.py | .py | 09dbcf11602303cb | 7.52 | 10 |
#!/usr/bin/env python
#! -*- coding: utf-8 -*-
"""Calculate skewness of elements form gr3 file"""
import schimpy.schism_mesh
import schimpy.sms2gr3
import click
import os
import numpy as np
angle_e = np.array((np.pi / 3.0, np.pi * 2.0 / 3.0))
def calculate_skewness(mesh, normalize=True, mask_tri=False):
"""Calc... | CADWRDeltaModeling/schimpy | schimpy/check_mesh_skewness.py | .py | 75e11d1dd9629d76 | 7.52 | 10 |
#!/usr/bin/env python
import math
import click
import schimpy.schism_yaml as schism_yaml
try:
from osgeo import gdal
from osgeo.gdalconst import *
gdal.TermProgress = gdal.TermProgress_nocb
except ImportError:
import gdal
from gdalconst import *
import subprocess
import numpy as np
import sys
imp... | CADWRDeltaModeling/schimpy | schimpy/clip_dems.py | .py | 88097e3951494210 | 7.52 | 10 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""Command line tool to merge possibly overlapping flux.dat files from hotstart runs"""
import click
import numpy as np
def combine_flux(infiles, outfile, prefer_last=False):
"""Merge possibly overlapping flux.dat files from hostart runs"""
filedata = []
for f... | CADWRDeltaModeling/schimpy | schimpy/combine_flux.py | .py | 4ca26d1a89a1b7ba | 7.52 | 10 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""Command line tool to convert SCHISM line strings in YAML
to Shapefile and vice versa
"""
from schimpy.schism_linestring import read_linestrings, write_linestrings
from schimpy.prepare_schism import get_structures_from_yaml
from schimpy.schism_setup import check_and_sugge... | CADWRDeltaModeling/schimpy | schimpy/convert_linestrings.py | .py | f9572f5cb1b4f8c2 | 7.52 | 10 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""Mesh converter"""
from schimpy.schism_mesh import read_mesh, write_mesh
import click
@click.command(
help="Convert a mesh from one format to another. The format is decided by the extensions automatically."
)
@click.option(
"--input",
required=True,
typ... | CADWRDeltaModeling/schimpy | schimpy/convert_mesh.py | .py | 41548032bfdb02d2 | 7.52 | 10 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""Command line tool to convert SCHISM points (source and sink) in YAML to Shapefile"""
import click
import geopandas as gpd
import pandas as pd
import warnings
import warnings
from shapely.geometry import Point
from schimpy.schism_sources_sinks import yaml2df
import yaml
... | CADWRDeltaModeling/schimpy | schimpy/convert_points.py | .py | 6c23d4fe34825cfb | 7.52 | 10 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""Command line tool to convert SCHISM polygons in YAML
to Shapefile and vice versa
"""
from schimpy.schism_polygon import read_polygons, write_polygons
import click
@click.command(help="Convert SCHISM polygons between YAML and Shapefile formats.")
@click.option(
"--i... | CADWRDeltaModeling/schimpy | schimpy/convert_polygons.py | .py | b43d5e6f40157334 | 7.52 | 10 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
import click
import numpy as np
from osgeo import gdal
from schimpy.schism_polygon import read_polygons, Point
from scipy.ndimage import gaussian_filter as gfilt
def read_density_tiff(fpath_densitiy_tiff):
"""Read geotiff values for density
It is assumed that th... | CADWRDeltaModeling/schimpy | schimpy/convert_sav_class_to_number.py | .py | 515b9ca2f4d78887 | 7.52 | 10 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""Create a mesh file with the number of vertical levels as nodal value"""
from schimpy.schism_mesh import read_mesh, write_mesh
import numpy as np
import click
def create_mesh_n_levels(hgrid, vgrid, output):
"""
Create a mesh file with the number of vertical level... | CADWRDeltaModeling/schimpy | schimpy/create_mesh_n_levels.py | .py | 358c57e3d8d18770 | 7.52 | 10 |
#!/usr/bin/env python
import click
import os
import pandas as pd
import schimpy.station as station
from schimpy.yaml_util import yaml_from_file
import glob
import numpy as np
from datetime import datetime
import warnings
def read_staout_lite(fname, station_infile):
"""Read a SCHISM staout_* file into a pandas Dat... | CADWRDeltaModeling/schimpy | schimpy/create_station_output.py | .py | fe4e1bc6c1577e00 | 7.52 | 10 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# runfile('D:/Delta/BayDeltaSCHISM/Scripts/create_vgrid_lsc2.py',
# wdir='D:/temp/gridopt/%s' % (scene),
# args="--hgrid=%s.gr3 --minmaxregion=../minmaxlayer.shp --dxwgt=1.0 --curvewgt=8. --archive_nlayer=out --nlayer_gr3=%s_nlayer.gr3 --eta=1.0" %(scene,sce... | CADWRDeltaModeling/schimpy | schimpy/create_vgrid_lsc2.py | .py | e3f973761650f697 | 7.52 | 10 |
"""Functions to cut certain parts in the mesh by cutting lines."""
## Author: Kijin Nam, knam@water.ca.gov
from schimpy.schism_mesh import read_mesh, write_mesh
import numpy as np
import os
import click
def read_lines(fpath):
"""Read coordinates of cutting line segments from a plain text file.
The expecte... | CADWRDeltaModeling/schimpy | schimpy/cut_mesh.py | .py | 1ae6a0b64fbe0a1d | 7.52 | 10 |
"""Embed finer gridded data in coarser, using curvature flow smoothing to reconcile
Main function is called embed_fine
"""
import numpy as np
import matplotlib.pyplot as plt
import scipy.ndimage as cv
from nodepy import *
import sys
import os.path
from schimpy.contour_smooth import *
try:
from osgeo import gdal... | CADWRDeltaModeling/schimpy | schimpy/embed_raster.py | .py | e6387ba32995715d | 7.52 | 10 |
# -*- coding: utf-8 -*-
import os
import yaml
import json
import numpy as np
import pandas as pd
import logging
import geopandas as gpd
from shapely.geometry import Point, Polygon, LineString, mapping, MultiPolygon
from pyproj import Proj, CRS
def shapely_to_geopandas(features, crs=None, shp_fn=None):
"""Convert... | CADWRDeltaModeling/schimpy | schimpy/geo_tools.py | .py | 0d05ed9390b39bb8 | 7.52 | 10 |
# -*- coding: utf-8 -*-
"""
Package to read a mesh in GR3 format.
"""
from schimpy.schism_mesh import BoundaryType
import schimpy.schism_mesh
import schimpy.base_io
import numpy as np
import os
class Gr3IO(schimpy.base_io.BaseIO):
"""A class that manages I/O of GR3 files"""
def __init__(self, logger=None):
... | CADWRDeltaModeling/schimpy | schimpy/gr3.py | .py | 85c9454decde0a59 | 7.52 | 10 |
# -*- coding: utf-8 -*-
"""invdisttree.py: inverse-distance-weighted interpolation using KDTree"""
import numpy as np
from scipy.spatial import cKDTree as KDTree
class Invdisttree:
"""Inverse-distance-weighted interpolation using KDTree
Examples
--------
tree = interp_2d.Invdisttree(obs_xy) # initia... | CADWRDeltaModeling/schimpy | schimpy/interp_2d.py | .py | 5c6fea1b756358a8 | 7.52 | 10 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
import click
import pandas as pd
from vtools import hours
def test_date_label_correct(fname_th):
"""Make sure that the date column in the file doens't have comment marker and raise error if it does"""
label_correct = False
with open(fname_th, "r") as testread... | CADWRDeltaModeling/schimpy | schimpy/interpolate_structure.py | .py | f95b847b8ce706ff | 7.52 | 10 |
from __future__ import annotations
import logging
import os
import sys
from dataclasses import dataclass
from datetime import datetime
from pathlib import Path
from typing import Optional, Tuple
@dataclass(frozen=True)
class LoggingConfig:
package_name: str
level: int = logging.INFO
# Handlers
conso... | CADWRDeltaModeling/schimpy | schimpy/logging_config.py | .py | 505d2439edfe5503 | 7.52 | 10 |
#!/usr/bin/env python
import sys
import click
from osgeo import ogr
def read_keyfile(keyfile):
"""Reads a file pairing labels and values"""
keys = {}
with open(keyfile, "r") as kf:
for line in kf:
if line and len(line) > 2:
key, val = line.strip().split()
... | CADWRDeltaModeling/schimpy | schimpy/material_poly.py | .py | 199a5fa33231d673 | 7.52 | 10 |
def parse(file_content):
"""
Here's a simple implementation of a parser for the Fortran namelist format
If there's a line starting with !, the parser will store it as the full_line_comment and attach it to the next key-value pair it encounters.
If there's an inline comment starting with !, it will be st... | CADWRDeltaModeling/schimpy | schimpy/nml.py | .py | c88ea8fac95324f0 | 7.52 | 10 |
# Priority dictionary using binary heaps
# David Eppstein, UC Irvine, 8 Mar 2002
class priorityDictionary(dict):
def __init__(self):
"""Initialize priorityDictionary by creating binary heap
of pairs (value,key).
Note that changing or removing a dict entry will
not remove the old pa... | CADWRDeltaModeling/schimpy | schimpy/priority_queue.py | .py | 0939957055594c5f | 7.52 | 10 |
from pydantic import SecretStr
from pydantic_settings import BaseSettings, SettingsConfigDict
class Settings(BaseSettings):
model_config = SettingsConfigDict(
env_prefix="OMICIDX_API_",
env_file=".env",
env_file_encoding="utf-8",
extra="ignore",
)
database_url: str = "post... | seandavi/omicidx | packages/omicidx-api/src/omicidx/api/config.py | .py | afd7f0c67f9184bd | 7.56 | 12 |
import base64
import binascii
import json
from dataclasses import dataclass
from fastapi import HTTPException
@dataclass
class CursorPage:
"""Decoded cursor with the keyset value for WHERE clause."""
after: str | int
def encode_cursor(value: str | int) -> str:
"""Encode a keyset value into an opaque b... | seandavi/omicidx | packages/omicidx-api/src/omicidx/api/pagination.py | .py | 8d8e40186f01bb42 | 7.56 | 12 |
from typing import Any, Generic, TypeVar
from urllib.parse import urlencode
from pydantic import BaseModel
T = TypeVar("T")
class CursorInfo(BaseModel):
next: str | None = None
prev: str | None = None
class Meta(BaseModel):
count: int
cursor: CursorInfo | None = None
class Links(BaseModel):
... | seandavi/omicidx | packages/omicidx-api/src/omicidx/api/schemas/envelope.py | .py | 5152000227790afe | 7.56 | 12 |
"""Tests for rate limiting via slowapi."""
from unittest.mock import patch
from fastapi.testclient import TestClient
def _make_app(rate_limit: str = "5/minute"):
"""Create a fresh app with the given rate limit for testing."""
with patch("omicidx.api.config.Settings.model_post_init", lambda *a, **kw: None):
... | seandavi/omicidx | packages/omicidx-api/tests/test_ratelimit.py | .py | 521af0518db6eabb | 8.06 | 12 |
import hashlib
from dataclasses import dataclass
from datetime import datetime
from upath import UPath
@dataclass
class AssetMetadata:
"""Richer metadata for lineage and cataloging"""
asset_key: str
storage_path: str
upstream_assets: list[str]
# Data profile
row_count: int | None = None
... | seandavi/omicidx | packages/omicidx-etl/src/omicidx/etl/biosample/asset_metadata.py | .py | d6cdede31f9e2036 | 7.56 | 12 |
"""
Simplified biosample/bioproject extraction without Prefect dependencies.
"""
import gzip
import shutil
import tempfile
import threading
import time
from datetime import datetime
from pathlib import Path
import click
import httpx
import orjson
import tenacity
from omicidx.etl.log import get_logger
from omicidx.par... | seandavi/omicidx | packages/omicidx-etl/src/omicidx/etl/biosample/extract.py | .py | 6b75f045eb250c21 | 7.56 | 12 |
"""config settings for omicidx_etl"""
from dotenv import load_dotenv
from pydantic_settings import BaseSettings, SettingsConfigDict
from upath import UPath
load_dotenv() # Load environment variables from .env file
class Settings(BaseSettings):
"""settings for omicidx_etl"""
model_config = SettingsConfigDi... | seandavi/omicidx | packages/omicidx-etl/src/omicidx/etl/config.py | .py | c85ad45f5430e6f7 | 7.56 | 12 |
import contextlib
import tempfile
from pathlib import Path
import duckdb
from .config import settings
def _q(value: str) -> str:
"""Escape a string for safe use in a SQL single-quoted literal."""
return value.replace("'", "''")
def duckdb_setup_sql(temp_directory: str | None = None):
"""
Generate ... | seandavi/omicidx | packages/omicidx-etl/src/omicidx/etl/db.py | .py | ee23bb285f0138ab | 7.56 | 12 |
import shutil
import tempfile
from collections.abc import Iterable
from datetime import date, datetime, timedelta
import anyio
import click
import httpx
import pyarrow as pa
import pyarrow.parquet as pq
import tenacity
from omicidx.etl.log import get_logger
from upath import UPath
from .schema import get_biosample_sc... | seandavi/omicidx | packages/omicidx-etl/src/omicidx/etl/ebi_biosample/extract.py | .py | 6e912ea4a31f3c7e | 7.56 | 12 |
import tarfile
import tempfile
import zipfile
from pathlib import Path
import click
import httpx
from omicidx.etl.db import duckdb_connection
from omicidx.etl.log import get_logger
from upath import UPath
logger = get_logger(__name__)
ICITE_COLLECTION_ID = 4586573
def get_icite_collection_articles() -> list[dict[s... | seandavi/omicidx | packages/omicidx-etl/src/omicidx/etl/icite.py | .py | d692fe889406611b | 7.56 | 12 |
"""
Centralized logging configuration for omicidx-gh-etl.
Provides structured JSON logging in CI environments and human-friendly
colorized logging for local development.
Usage:
from omicidx.etl.log import configure_logging, get_logger, log_duration
# Configure once at application startup
configure_loggin... | seandavi/omicidx | packages/omicidx-etl/src/omicidx/etl/log.py | .py | 0782142ae3e8dfed | 7.56 | 12 |
import gzip
import pathlib
import shutil
import tempfile
import zipfile
from datetime import datetime
import click
import httpx
import polars as pl
from omicidx.etl.log import get_logger
from upath import UPath
logger = get_logger(__name__)
# Configuration constants
DEFAULT_OUTPUT_DIR = UPath("/tmp/omicidx/nih_repor... | seandavi/omicidx | packages/omicidx-etl/src/omicidx/etl/nih_reporter.py | .py | a0d0ce6454696bb2 | 7.56 | 12 |
import datetime
import re
import shutil
import tempfile
from urllib.request import urlretrieve
import click
import pubmed_parser as pp
import pyarrow as pa
import pyarrow.parquet as pq
from omicidx.etl.log import get_logger
from upath import UPath
logger = get_logger(__name__)
# Module-level constants
PUBMED_BASE =... | seandavi/omicidx | packages/omicidx-etl/src/omicidx/etl/pubmed.py | .py | 2d5878b5f494f16b | 7.56 | 12 |
"""
SRA catalog management.
This module provides the SRACatalog class for managing the processing and cleanup
of SRA mirror entries.
"""
import contextlib
import json
import re
from datetime import datetime
from upath import UPath
from ..log import LogProgress, get_logger, log_operation
from .mirror import SRAMirro... | seandavi/omicidx | packages/omicidx-etl/src/omicidx/etl/sra/catalog.py | .py | b964a0d5acca51b5 | 7.56 | 12 |
"""
CLI commands for SRA module.
Provides commands to sync SRA mirror entries and manage the catalog.
"""
from datetime import date
import click
from omicidx.etl.log import get_logger
from .catalog import SRACatalog
from .mirror import SRAMirrorEntry, get_sra_mirror_entries
@click.group()
def sra():
"""SRA (S... | seandavi/omicidx | packages/omicidx-etl/src/omicidx/etl/sra/cli.py | .py | 65ae6b24b7137269 | 7.56 | 12 |
"""
SRA mirror entry management.
This module provides classes and functions for working with NCBI SRA mirror files,
including parsing mirror URLs and determining which files to process.
"""
import datetime
import re
from loguru import logger
from upath import UPath
class SRAMirrorEntry:
"""
Represents an e... | seandavi/omicidx | packages/omicidx-etl/src/omicidx/etl/sra/mirror.py | .py | 6a1755580b4d4992 | 7.56 | 12 |
"""
Parquet processing for SRA mirror entries.
This module provides functions to download, parse, and write SRA mirror entries
as parquet files in bounded-memory chunks.
"""
from __future__ import annotations
import gzip
import shutil
import tempfile
from collections.abc import Callable, Iterable
from xml.etree.Elem... | seandavi/omicidx | packages/omicidx-etl/src/omicidx/etl/sra/mirror_parquet.py | .py | e4dfde5172cd3059 | 7.56 | 12 |
# SPDX-License-Identifier: MIT
# (c) 2020 The TJHSST Director 4.0 Development Team & Contributors
from django.urls import reverse
from ...test.director_test import DirectorTestCase
class AuthTest(DirectorTestCase):
def test_accept_guidelines(self):
# Log in as a user that has not accepted guidelines
... | tjcsl/director4 | manager/director/apps/auth/tests.py | .py | 1d97d05c3b118228 | 7.02 | 10 |
# SPDX-License-Identifier: MIT
# (c) 2019 The TJHSST Director 4.0 Development Team & Contributors
import os
import re
import time
import urllib.parse
import xml.etree.ElementTree
from typing import Any, Dict, Generator, List, Optional, Set, Tuple
import bleach
import markdown
import markdown.extensions.toc
from bleac... | tjcsl/director4 | manager/director/apps/docs/utils.py | .py | 86fb4dedb048abc0 | 7.52 | 10 |
from django.urls import reverse
from ...test.director_test import DirectorTestCase
class ShellServerTestCase(DirectorTestCase):
def test_authenticate_view(self):
self.login(username="awilliam", accept_guidelines=True)
# I'm not waiting 15 seconds for this test to complete
with self.setti... | tjcsl/director4 | manager/director/apps/shell_server/tests.py | .py | f259bc2c6f143eb8 | 7.02 | 10 |
"""__init__.py - package definition module for DHParser/parsers
Copyright 2024 by Eckhart Arnold (arnold@badw.de)
Bavarian Academy of Sciences an Humanities (badw.de)
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You m... | jecki/DHParser | DHParser/parsers/__init__.py | .py | a2446c7ac4672368 | 7.45 | 7 |
#!/usr/bin/env python3
"""dhparser_rename.py - rename a dhparser project properly
UNMAINTAINED!!!
Copyright 2019 by Eckhart Arnold (arnold@badw.de)
Bavarian Academy of Sciences an Humanities (badw.de)
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except i... | jecki/DHParser | DHParser/scripts/dhparser_rename.py | .py | e36a5ea34caca3e3 | 7.45 | 7 |
# validate.py - validation of node-trees according to a
# grammar-like schema (inspired by Relax NG)
#
# Copyright 2022 by Eckhart Arnold (arnold@badw.de)
# Bavarian Academy of Sciences an Humanities (badw.de)
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may n... | jecki/DHParser | DHParser/validate.py | .py | 87389b33926cfb65 | 7.45 | 7 |
from __future__ import annotations
import logging
import platform
from collections import defaultdict
from collections.abc import Callable
from ssl import SSLContext
from typing import Any
from pydantic import BaseModel
from pydantic_xml import BaseXmlModel
from ._errors import APIError, ErrorStatus, build_error_map... | librestfly/restfly | restfly/_base.py | .py | 62621621ca5b2db9 | 7.62 | 16 |
"""
Error handling classes and data-classes.
"""
import logging
from collections import defaultdict
from dataclasses import dataclass, replace
from httpx import Response
from pydantic import BaseModel
class RetryError(Exception):
"""
RetryError is thrown when too many retries have been made to the endpoint ... | librestfly/restfly | restfly/_errors.py | .py | f305b188d8c048fd | 7.62 | 16 |
from __future__ import annotations
from typing import TYPE_CHECKING, Any, get_origin, get_type_hints, overload
from httpx import Response
from pydantic import BaseModel, TypeAdapter
from pydantic_xml import BaseXmlModel
from .types import Model, XMLModel
if TYPE_CHECKING:
from ._async import AsyncAPIClient
... | librestfly/restfly | restfly/_utils.py | .py | 5c928b3e0c5841c5 | 7.62 | 16 |
# Copyright 2018 Comcast Cable Communications Management, LLC
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | vinyldns/vinyldns-python | func_tests/test_client.py | .py | 427d19209a050eb7 | 7.06 | 12 |
# Copyright 2018 Comcast Cable Communications Management, LLC
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | vinyldns/vinyldns-python | func_tests/utils.py | .py | a717083fa1161f7d | 8.06 | 12 |
# Copyright 2018 Comcast Cable Communications Management, LLC
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | vinyldns/vinyldns-python | func_tests/vinyldns_context.py | .py | 802545ff33f60292 | 8.06 | 12 |
# Copyright 2018 Comcast Cable Communications Management, LLC
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | vinyldns/vinyldns-python | scripts/search_records_by_name.py | .py | 5ae6ac2935a826a8 | 7.56 | 12 |
# Copyright 2018 Comcast Cable Communications Management, LLC
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | vinyldns/vinyldns-python | scripts/update_record_owner.py | .py | b98f47359db81eee | 7.56 | 12 |
# Copyright 2018 Comcast Cable Communications Management, LLC
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | vinyldns/vinyldns-python | scripts/verify_reverse_zones.py | .py | 156a0ba9de05239b | 7.56 | 12 |
# Copyright 2018 Comcast Cable Communications Management, LLC
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | vinyldns/vinyldns-python | scripts/zone_dump.py | .py | fcfc3d183440378d | 7.56 | 12 |
# Copyright 2018 Comcast Cable Communications Management, LLC
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | vinyldns/vinyldns-python | src/vinyldns/boto_request_signer.py | .py | 6f15be9a180dfb70 | 7.56 | 12 |
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