text stringlengths 185 73.3k | repo stringlengths 7 100 | path stringlengths 4 146 | language stringclasses 7
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# Copyright 2026 Canonical Ltd.
# See LICENSE file for licensing details.
"""Helpers for app-level integration metrics assertions."""
import json
import time
from pathlib import Path
from typing import Any
from github.Repository import Repository
from github_runner_manager.manager.vm_manager import PostJobStatus
fr... | canonical/github-runner-operator | github-runner-manager/tests/integration/metrics_helpers.py | .py | b22ae7531642f115 | 8.15 | 19 |
# Copyright 2026 Canonical Ltd.
# See LICENSE file for licensing details.
"""OpenStack helper functions shared by integration tests."""
import logging
import socket
import time
from pathlib import Path
import openstack
from github.Repository import Repository
from openstack.compute.v2.server import Server as Opensta... | canonical/github-runner-operator | github-runner-manager/tests/integration/openstack_helpers.py | .py | 5a15c994fada14d7 | 8.15 | 19 |
# Copyright 2026 Canonical Ltd.
# See LICENSE file for licensing details.
"""Delete leftover OpenStack resources from github-runner-manager integration tests.
This module is used by the suite under ``github-runner-manager/tests/integration/``.
That suite runs the github-runner-manager application against a real OpenS... | canonical/github-runner-operator | github-runner-manager/tests/integration/orphan_cleanup.py | .py | 1a5f99c3cabb07ad | 8.15 | 19 |
# Copyright 2026 Canonical Ltd.
# See LICENSE file for licensing details.
"""Lightweight planner stub for integration tests.
Provides flavor info and pressure endpoints expected by PlannerClient:
- GET /api/v1/flavors/<name>/pressure
- GET /api/v1/flavors/<name>/pressure?stream=true (NDJSON)
- POST /control/pressure ... | canonical/github-runner-operator | github-runner-manager/tests/integration/planner_stub.py | .py | 45068d32fc579287 | 8.15 | 19 |
# Copyright 2026 Canonical Ltd.
# See LICENSE file for licensing details.
"""Integration tests for tmate ssh connection."""
import logging
import subprocess
from dataclasses import dataclass
from datetime import datetime, timezone
from pathlib import Path
from time import sleep
from typing import Generator, Iterator
... | canonical/github-runner-operator | github-runner-manager/tests/integration/test_debug_ssh.py | .py | 677565c2cbc4d7fc | 8.15 | 19 |
"""
Provides a container for an analyzed document, i.e., parsed document and found errors.
"""
from __future__ import annotations
import typing
from typing import Any
from checkmytex.finding.problem import Problem
from checkmytex.latex_document import LatexDocument
class AnalyzedDocument:
"""
An analyzed d... | d-krupke/CheckMyTex | checkmytex/analyzed_document.py | .py | fe5a1ef4482cedd7 | 7.62 | 16 |
"""
Parsing the arguments from CLI.
"""
from __future__ import annotations
import argparse
import sys
from pathlib import Path
def create_default_argument_parser() -> argparse.ArgumentParser:
parser = argparse.ArgumentParser(
description="CheckMyTex: A simple tool for checking your LaTeX."
)
pa... | d-krupke/CheckMyTex | checkmytex/cli/arguments.py | .py | 9e9929c707271a9c | 7.62 | 16 |
"""
Module for checking a latex document by applying a set of checker and filter.
"""
import logging
import traceback
import typing
from .analyzed_document import AnalyzedDocument
from .filtering.filter import Filter
from .finding import (
Checker,
CheckSpell,
ChkTex,
Cleveref,
Languagetool,
P... | d-krupke/CheckMyTex | checkmytex/document_analyzer.py | .py | eaf70dd78ba9e5e3 | 7.62 | 16 |
"""Filter to ignore errors within code listing environments."""
import re
import typing
from checkmytex.finding import Problem
from checkmytex.latex_document import LatexDocument
from .filter import Filter
class IgnoreCodeListings(Filter):
"""
Ignores errors within code listing environments.
Code snip... | d-krupke/CheckMyTex | checkmytex/filtering/code_listings.py | .py | 6164e1eeaed316a1 | 7.62 | 16 |
"""
The math mode creates text, but it does often not proper english,
leading to many false positives. This module filters out specific problems
in math mode.
"""
import re
import typing
from checkmytex.finding import Problem
from checkmytex.latex_document import LatexDocument
from .filter import Filter
class Math... | d-krupke/CheckMyTex | checkmytex/filtering/math_mode.py | .py | 62b9174d4cf2c31e | 7.62 | 16 |
import re
import typing
from pathlib import Path
from ..finding.problem import Problem
from ..latex_document import LatexDocument
from .filter import Filter
class Whitelist(Filter):
"""
Managing the whitelist, skipped problems, and ignored rules.
"""
def __init__(
self,
path: str | N... | d-krupke/CheckMyTex | checkmytex/filtering/whitelist.py | .py | 4a5f070395fced18 | 7.62 | 16 |
"""
Wrapping chktex (LaTeX linter, part of LaTeX distribution).
https://www.nongnu.org/chktex/
"""
import re
import shutil
import typing
from checkmytex.latex_document import LatexDocument
from .abstract_checker import Checker
from .problem import Problem
def _extract_problem(match: re.Match, document: LatexDocume... | d-krupke/CheckMyTex | checkmytex/finding/chktex.py | .py | 19ce4134dcf5804a | 7.62 | 16 |
"""
Finding usages of raw \\ref
"""
import re
import typing
from checkmytex.latex_document import LatexDocument
from .abstract_checker import Checker
from .problem import Problem
class Cleveref(Checker):
"""
A checker module for finding raw \\ref. Better use \\cref.
"""
def check(self, document: L... | d-krupke/CheckMyTex | checkmytex/finding/cleveref.py | .py | 1cd4ede4ad6702f8 | 7.62 | 16 |
import json
import shutil
import typing
from checkmytex.latex_document import LatexDocument, Origin
from .abstract_checker import Checker
from .problem import Problem
class Languagetool(Checker):
def __init__(
self,
lang: str = "en-US",
max_characters: int | None = None,
timeout_... | d-krupke/CheckMyTex | checkmytex/finding/languagetool.py | .py | 47e7fc75a2a5d444 | 7.62 | 16 |
"""
Simple module for finding inconsisting writing style of NP-hard/complete.
Common problem with documents in theoretical computer science.
"""
import re
import typing
from checkmytex.latex_document import LatexDocument
from .abstract_checker import Checker
from .problem import Problem
class UniformNpHard(Checker... | d-krupke/CheckMyTex | checkmytex/finding/nphard.py | .py | 004b92698e252da8 | 7.62 | 16 |
"""
Module for finding raw numbers and units in the LaTeX-document.
SIUnitX is much better in formatting them.
"""
import re
import typing
from checkmytex.latex_document import LatexDocument
from .abstract_checker import Checker
from .problem import Problem
def _looks_like_year(num: str):
if re.fullmatch("[21]... | d-krupke/CheckMyTex | checkmytex/finding/siunitx.py | .py | 53bfb35147f71eef | 7.62 | 16 |
from yalafi.tex2txt import Options, tex2txt
from checkmytex.latex_document.indexed_string import IndexedText
class DetexedText(IndexedText):
"""
Container for the detexed text. It just wraps yalafi.
"""
def __init__(self, source: str, yalafi_opts: Options | None = None):
yalafi_opts = yalafi... | d-krupke/CheckMyTex | checkmytex/latex_document/detex.py | .py | 67c92ce003f83b9f | 7.62 | 16 |
import typing
from bisect import bisect
from flachtex import TraceableString
from flachtex.utils import compute_row_index
class TextPosition:
"""
Position in a multi-line text.
"""
def __init__(self, index: int, line: int, line_offset: int):
self.index = index
self.line = line
... | d-krupke/CheckMyTex | checkmytex/latex_document/indexed_string.py | .py | 196bc74e0dc9426c | 7.62 | 16 |
"""
The LatexDocument provides easy access to the latex document to be fed to
a checker and to trace the checker's report back to the original document.
"""
import logging
import re
import typing
from flachtex import TraceableString
from .detex import DetexedText
from .indexed_string import TextPosition
from .origin... | d-krupke/CheckMyTex | checkmytex/latex_document/latex_document.py | .py | bcf1a026b6748361 | 7.62 | 16 |
from __future__ import annotations
import re
from pathlib import Path
import flachtex
from flachtex.command_substitution import NewCommandSubstitution, find_new_commands
from flachtex.rules import ChangesRule, TodonotesRule
from flachtex.rules.skip_rules import RegexSkipRule
from flachtex.utils import Range
from .la... | d-krupke/CheckMyTex | checkmytex/latex_document/parser.py | .py | cc25fde35f543eff | 7.62 | 16 |
"""
Container for the LaTeX-sources.
"""
from __future__ import annotations
import typing
from flachtex import TraceableString
from checkmytex.latex_document.indexed_string import (
IndexedText,
TextPosition,
simplify_text_range,
)
class FilePosition:
def __init__(self, file: str, pos: TextPositio... | d-krupke/CheckMyTex | checkmytex/latex_document/source.py | .py | 49bd56dff82c82af | 7.62 | 16 |
"""
Base classes for problem display extensions.
Extensions add functionality to problem displays in HTML reports.
Each extension can render a line of HTML for a problem, or skip by returning None.
"""
from __future__ import annotations
import abc
from dataclasses import dataclass
from typing import TYPE_CHECKING, A... | d-krupke/CheckMyTex | checkmytex/reporting/extension_base.py | .py | 00eb702345dcaff9 | 7.62 | 16 |
"""Basic message extension that displays the standard problem message."""
from __future__ import annotations
import html
from ..extension_base import ExtensionContext, ProblemExtension
class BasicMessageExtension(ProblemExtension):
"""
The standard problem message extension.
Renders: >>> [tool] messag... | d-krupke/CheckMyTex | checkmytex/reporting/extensions/basic_message.py | .py | 23aae81f8dea2229 | 7.62 | 16 |
"""Lookup URL extension for problems."""
from __future__ import annotations
import html
from ..extension_base import ExtensionContext, ProblemExtension
class LookupUrlExtension(ProblemExtension):
"""
Show helpful link if problem has a look_up_url.
Checkers may provide various types of URLs:
- Rule... | d-krupke/CheckMyTex | checkmytex/reporting/extensions/lookup_url.py | .py | 0097e8090408bc04 | 7.62 | 16 |
"""HTML report generator for CheckMyTex analysis results."""
from __future__ import annotations
import html
import os.path
import re
from collections import defaultdict
from pathlib import Path
from checkmytex import AnalyzedDocument
from checkmytex.finding import Problem
from checkmytex.reporting.extension_base imp... | d-krupke/CheckMyTex | checkmytex/reporting/html_report.py | .py | ed223620ea0eb1f5 | 7.62 | 16 |
"""
Provides a simple class for CLI option prompt.
"""
import typing
class OptionPrompt:
"""
A simple helper for getting an input from multiple options.
"""
def __init__(self, read=input, write=print, front="", end=""):
self._options = {}
self._read = read
self._write = write... | d-krupke/CheckMyTex | checkmytex/utils/choice.py | .py | 017c782a896a07d6 | 7.62 | 16 |
"""
Provides a class to open editors at specific lines and try to guess the
line number after (sequential) changes in the file.
"""
import logging
import os
import shlex
import subprocess
import typing
from pathlib import Path
def _number_of_lines(file_path: str) -> int:
with Path(file_path).open() as file:
... | d-krupke/CheckMyTex | checkmytex/utils/editor.py | .py | 52bc0f0b5882987b | 7.62 | 16 |
import re
import typing
from checkmytex import DocumentAnalyzer, LatexDocument
from checkmytex.finding import Checker, Problem
from checkmytex.latex_document.parser import LatexParser
from flachtex import FileFinder
class AbcChecker(Checker):
def __init__(self, check_ranges):
super().__init__()
s... | d-krupke/CheckMyTex | tests/test_abc.py | .py | 2b8ffe711c1f5ead | 7.12 | 16 |
#!/usr/bin/env python
# encoding: utf-8
# Copyright 2009 Baptiste Lepilleur and The JsonCpp Authors
# Distributed under MIT license, or public domain if desired and
# recognized in your jurisdiction.
# See file LICENSE for detail or copy at http://jsoncpp.sourceforge.net/LICENSE
from __future__ import print_function
f... | ansys/api-eigen-example | external/jsoncpp-v1.9.5/devtools/antglob.py | .py | 28c64608546d58f3 | 7.48 | 8 |
# Copyright 2010 Baptiste Lepilleur and The JsonCpp Authors
# Distributed under MIT license, or public domain if desired and
# recognized in your jurisdiction.
# See file LICENSE for detail or copy at http://jsoncpp.sourceforge.net/LICENSE
from contextlib import closing
import os
import tarfile
TARGZ_DEFAULT_COMPRESS... | ansys/api-eigen-example | external/jsoncpp-v1.9.5/devtools/tarball.py | .py | d393421db48cd317 | 7.48 | 8 |
"""Script to generate doxygen documentation.
"""
from __future__ import print_function
from __future__ import unicode_literals
from devtools import tarball
from contextlib import contextmanager
import subprocess
import traceback
import re
import os
import sys
import shutil
@contextmanager
def cd(newdir):
"""
h... | ansys/api-eigen-example | external/jsoncpp-v1.9.5/doxybuild.py | .py | 15618dabe099d751 | 7.48 | 8 |
# Copyright 2007 Baptiste Lepilleur and The JsonCpp Authors
# Distributed under MIT license, or public domain if desired and
# recognized in your jurisdiction.
# See file LICENSE for detail or copy at http://jsoncpp.sourceforge.net/LICENSE
"""Simple implementation of a json test runner to run the test against
json-py.... | ansys/api-eigen-example | external/jsoncpp-v1.9.5/test/pyjsontestrunner.py | .py | 76f2665704d19d5a | 7.98 | 8 |
# Copyright (C) 2023 - 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/ansys-tools-repo-sync | src/ansys/tools/repo_sync/repo_sync.py | .py | 7de8ceaad3356e81 | 7.48 | 8 |
# Copyright (C) 2023 - 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/ansys-tools-repo-sync | tests/conftest.py | .py | e6b1343c525cba86 | 7.98 | 8 |
"""
Utilities for HPVsim Quarto docs (version file, quartodoc, notebook cleanup).
"""
import os
import sys
import importlib
import subprocess
import sciris as sc
import hpvsim as hpv
default_folders = ['tutorials'] # Folders with notebooks
temp_patterns = ['**/my-*.*', '**/example*.*'] # Temporary files to be removed... | starsimhub/hpvsim | docs/quarto_utils.py | .py | 70120ffd8bcb9140 | 7.63 | 17 |
"""M07 demo: vaccination-coverage sweep with multi-seed UQ.
Runs a 4 × 20 (coverage × seed) routine-vx sweep on the M05 Nigeria
4-genotype anchor, reduces each coverage scenario to median + 10/90
quantiles, and plots aggregate cancer trajectories by coverage.
Exercises every M07 verification target:
- sc.paralleliz... | starsimhub/hpvsim | examples/m07_uq_sweep.py | .py | 9abc57bd0f3c361c | 7.63 | 17 |
"""HPVsim calibration — ss.Calibration subclass with a weighted-gof eval.
Provides:
- hpv.Calibration: ss.Calibration subclass that takes a ``data`` dict of
observed-target DataFrames and computes a single weighted mismatch
using ``compute_gof`` (normalized absolute error by default).
- compute_gof... | starsimhub/hpvsim | hpvsim/calibration.py | .py | e4c73854738c07a6 | 7.63 | 17 |
"""Country-data adapter: load location data into Starsim-shaped DataFrames.
Used by ``hpvsim.Sim`` to build People (age pyramid), Births (CBR), Deaths
(age- and sex-specific mortality), and SexualNetwork (debut, partners,
mixing, layer probs, durations, acts). Underlying data lives in
``hpvsim/data/files/`` and is loa... | starsimhub/hpvsim | hpvsim/data/country.py | .py | d5675afc7ed07d88 | 7.63 | 17 |
'''
Download data needed for HPVsim.
Typically, this is done automatically: on load, HPVsim checks if the data are already
downloaded, and if not, downloads them using the quick_download() function. The
"slow download" functions supply the files that are usually zipped and stored in
a separate repository, hpvsim_data.... | starsimhub/hpvsim | hpvsim/data/downloaders.py | .py | ee086e13f2e4e5b8 | 7.63 | 17 |
"""HIV-data adapter: load per-location HIV/ART inputs for the co-infection sim.
Mirrors ``hpvsim.data.country.load_country`` in style. Returns the HIV inputs
used to build a co-infection sim:
- ``art_coverage``: tidy long DataFrame ``[age, sex, year, coverage]`` parsed
from the by-age ART coverage CSVs (females + m... | starsimhub/hpvsim | hpvsim/data/hiv.py | .py | e6cf1fc5d1287209 | 7.63 | 17 |
'''
Load data
'''
#%% Housekeeping
import numpy as np
import pandas as pd
import sciris as sc
import unicodedata
import re
__all__ = ['get_country_aliases', 'map_entries', 'get_age_distribution', 'get_age_distribution_over_time', 'get_total_pop', 'get_death_rates',
'get_birth_rates']
thisdir = sc.thispa... | starsimhub/hpvsim | hpvsim/data/loaders.py | .py | 08d6ffa84b205cf7 | 7.63 | 17 |
'''
Set the defaults across each of the different files.
'''
import numpy as np
import sciris as sc
import pylab as pl
from .settings import options as hpo # To set options
# Specify all externally visible functions this file defines -- other things are available as e.g. hpv.defaults.default_int
__all__ = ['datadir',... | starsimhub/hpvsim | hpvsim/defaults.py | .py | c7304563914808a3 | 7.63 | 17 |
"""Translation helpers for legacy distribution-dict inputs.
Country-data adapters provide distribution parameters as
``{'dist': name, 'par1': p1, 'par2': p2}`` dicts; this module converts
them into Starsim Dist instances. Retired once the country-data layer is
rewritten to emit Starsim Dist instances directly.
"""
im... | starsimhub/hpvsim | hpvsim/migration_utils.py | .py | 2d5f52bb70327582 | 7.63 | 17 |
"""HPV simulation parameters.
``SimPars`` subclasses ``ss.SimPars`` with HPV-specific defaults.
``GenotypePars`` holds per-genotype natural-history defaults (durations,
severity functions, immunity, age risk) consumed by ``HPV(ss.Infection)``;
``get_genotype_pars(genotype)`` is the factory multi-genotype consumers
use... | starsimhub/hpvsim | hpvsim/parameters.py | .py | bc0edf45edd1ea44 | 7.63 | 17 |
"""Initial HPV-prevalence curves and multi-genotype seeding Connector.
The age-banded init_prev curves and ``_make_init_prev_fn`` sampler are used by
both per-genotype ``HPV`` modules (for ``init_seeding='independent'``) and by
``_ExclusiveSeeder`` (for ``init_seeding='exclusive'``, which uses the 'total'
curve as the... | starsimhub/hpvsim | hpvsim/seeding.py | .py | c9a67df700dfbe90 | 7.63 | 17 |
"""Sub-annual accumulation gate for AgeResults.cancer_incidence.
Needs ms_agent_ratio=50 over 5000 agents and 35 years to resolve enough cancers
per single tick for the 4x ratio to be distinguishable from noise, so it lives
here rather than in tests/test_age_results.py.
"""
import numpy as np
import pytest
import scir... | starsimhub/hpvsim | tests/devtests/test_age_results_subannual.py | .py | 72361d15e9a87625 | 7.13 | 17 |
"""Seed-averaged multiscale-equivalence gates for the analyzers.
Both quantities below are means over rare events (age at cancer, DALYs from
young-onset cancer), so a single seed is far too noisy to assert on — they need
4-6 seeds per ratio, i.e. ~20 full sims. The cheap per-run invariants those
analyzers must satisfy... | starsimhub/hpvsim | tests/devtests/test_analyzers_multiscale_gates.py | .py | 958833928185c23c | 8.13 | 17 |
"""HIV-HPV coinfection direction gate.
Runs the full Rwanda HIV+HPV anchor sim, which is far too expensive for the
unit suite. The connector's own arithmetic (CD4 stratification, rel_sus /
rel_sev multipliers) is unit-tested in ``tests/test_hiv_connector.py``; this
asserts the emergent population-level direction.
"""
... | starsimhub/hpvsim | tests/devtests/test_hiv_coinfection_gate.py | .py | 1ff5a9deda7d8286 | 7.13 | 17 |
"""Incidence-driven HIV importer tests.
The ``hpv.hiv_incidence_import`` intervention drives STIsim's HIV by imposing
the Rwanda HIV incidence curve: each step it selects HIV-negative susceptibles
per the (year, sex, age) incidence rate and calls ``hiv.set_prognoses`` on them
(which flips them to infected AND wires th... | starsimhub/hpvsim | tests/devtests/test_hiv_incidence_import.py | .py | d3fa112fc4a3753e | 8.13 | 17 |
"""Statistical acceptance gates for the multiscale grow engine.
These three gates run ~72 full sims (many seeds x ratios) and take ~14 min.
The mechanism-level checks — that fine agents are spawned, excluded from the
network, subject to emigration, and reached by interventions — live in
``tests/test_multiscale_grow_un... | starsimhub/hpvsim | tests/devtests/test_multiscale_grow_gates.py | .py | 6d192f5b009313b7 | 8.13 | 17 |
"""Rendering gates for hpv.plot_calibration.
Both need a real ``Calibration.calibrate()`` run to produce something to plot,
which is why they live here rather than in ``tests/test_plotting.py``.
"""
import matplotlib
matplotlib.use('Agg') # headless, before pyplot import
import matplotlib.pyplot as plt
import numpy a... | starsimhub/hpvsim | tests/devtests/test_plot_calibration.py | .py | 0adc97662c5da8be | 8.13 | 17 |
"""Co-infection anchor: 4-genotype HPV + transmission HIV + ART on Nigeria.
Phase-1 anchor uses a hand-tuned HIV beta to produce a non-trivial HIV+
subpopulation; it is NOT calibrated to a country (that is Phase 2 / Rwanda).
API notes (STIsim 1.5.0):
- ``sti.HIV.init_prev_data`` accepts a scalar float (parsed by
... | starsimhub/hpvsim | tests/regression/anchor_hiv_hpv.py | .py | 2facc9610f39929d | 7.13 | 17 |
"""Confirm the dur_cin long tail drives old-age (55+) cancer in HIV- women.
(1) Percentiles of the calibrated dur_cin lognormal (mean=5x1.043, std=20x1.043
for hpv16) -- a very long right tail would push some cancers to old ages.
(2) Actual age-at-cancer distribution from the calibrated sim (HIV- females),
poo... | starsimhub/hpvsim | tests/regression/diag_dur_cin_tail.py | .py | ef9a1e6b6b69ccd3 | 8.13 | 17 |
"""Verify the v3 ported Rwanda network reproduces the DHS/v2 partnership pattern,
and connect it to old-age HPV acquisition (the HIV- 55+ cancer driver).
For each 5-yr female age band over 2010-2019 it reports:
- realized marital / casual participation (fraction of alive women in a
partnership) vs the INPUT annu... | starsimhub/hpvsim | tests/regression/diag_network_oldage.py | .py | 2d81e6f7eddd29c9 | 8.13 | 17 |
"""Verify the ported Rwanda calibration reproduces v2 HPV + cancer levels.
Runs the calibrated incidence-driven Rwanda sim for a few seeds and reports:
- adult-female (15-49) any-genotype HPV prevalence by year
- HIV-stratified cervical-cancer incidence per 100k women, pooled across
seeds over a measurement wi... | starsimhub/hpvsim | tests/regression/diag_rwanda_calib_check.py | .py | 7a9dfcb29866f659 | 8.13 | 17 |
"""Reproduction of methods-paper Fig 1 (natural history), all four genotypes.
Port of ``plot_nh_simple`` from
https://github.com/hpvsim/hpvsim_methods_manuscript/blob/main/plot_fig1.py.
Loops over (hpv16, hpv18, hi5, ohr) — added in M03 once the per-genotype
``GenotypePars`` defaults landed. The M02 single-genotype v... | starsimhub/hpvsim | tests/regression/methods_fig1.py | .py | dc609b19c3b80d3b | 8.13 | 17 |
import textwrap
from pathlib import Path
import click
from loguru import logger
@click.group()
def commands(**_):
"""tools related to bootstrapping (new cluster, new repository, etc)"""
pass
@commands.command()
def kubernetes(**_):
"""bootstrap kubernetes to pull from your cluster repository"""
ret... | ocf/transpire | transpire/internal/cli/bootstrap.py | .py | a81d8e1ea6d6dae9 | 7.45 | 7 |
import os
from datetime import datetime, timezone
import click
from transpire.internal.cli.utils import AliasedGroup
from transpire.internal.config import ClusterConfig, GitModuleConfig
from transpire.types import Image, Module
from transpire.utils import get_image_tag
def image_metadata(config: GitModuleConfig, mo... | ocf/transpire | transpire/internal/cli/image.py | .py | 3f570f7b20bc070a | 7.45 | 7 |
import subprocess
import sys
from pathlib import Path
from shutil import rmtree
from typing import Optional
import click
import yaml
from loguru import logger
from transpire.internal import render
from transpire.internal.cli.utils import AliasedGroup
from transpire.internal.config import ClusterConfig, get_config
@... | ocf/transpire | transpire/internal/cli/obj.py | .py | 1b7a6eecdc3a3846 | 7.45 | 7 |
import click
from kubernetes import client, config
from transpire.internal.cli.utils import AliasedGroup
from transpire.internal.config import get_config, provider_from_context
@click.command(cls=AliasedGroup)
def commands(**_):
"""secret management commands"""
pass
@commands.command()
@click.argument("app... | ocf/transpire | transpire/internal/cli/secrets.py | .py | fcd3eda10422b139 | 7.45 | 7 |
import shutil
import tempfile
from subprocess import PIPE, run
from typing import Any
import yaml
from transpire.internal.config import CLIConfig
from transpire.internal.context import get_app_context
__all__ = ["build_chart_from_versions", "build_chart"]
def assert_helm() -> None:
"""ensure helm binary is ava... | ocf/transpire | transpire/internal/helm.py | .py | 9846c2b86a9bb26d | 7.45 | 7 |
import shutil
import urllib.parse
from subprocess import PIPE, run
from typing import Any
import yaml
__all__ = ["build_kustomization_from_versions", "build_kustomization"]
def assert_kubectl() -> None:
"""ensure kubectl binary is available"""
if shutil.which("kubectl") is None:
raise RuntimeError(... | ocf/transpire | transpire/internal/kustomize.py | .py | bfa3cef246985c92 | 7.45 | 7 |
from transpire.internal.config import ClusterConfig, provider_from_context
from transpire.manifestlike import ManifestLike
class ManifestError(Exception):
def __init__(self, message: str, *, suggestion: ManifestLike | None) -> None:
self.message = message
self.suggestion = suggestion
def postpro... | ocf/transpire | transpire/internal/postprocessor.py | .py | cb6d8eb02c9aaacd | 7.45 | 7 |
import base64
import os
import hvac # type: ignore
import hvac.exceptions # type: ignore
from pydantic import BaseModel
from transpire.internal.secrets import SecretsProvider
from transpire.manifestlike import ManifestLike, manifest_to_dict
class HashicorpVaultConfig(BaseModel):
kvstore: str
def fix_base64(... | ocf/transpire | transpire/internal/secrets/vault.py | .py | a8ce3e4704bcefa5 | 7.45 | 7 |
from typing import Iterable, Protocol
from kubernetes import client
class OpenAPIObject(Protocol):
"""An object that can be converted to a dictionary. Useful for objects from github.com/kubernetes-client/python."""
openapi_types: dict
attribute_map: dict
# Something that is possibly a Kubernetes manif... | ocf/transpire | transpire/manifestlike.py | .py | feb2c7ded7246406 | 7.45 | 7 |
import pathlib
import tomllib
from typing import Dict, cast
from transpire.internal.context import get_app_context
from transpire.types import ContainerRegistry, Image, Module
def get_revision() -> str | None:
"""Retrieves the current Transpire module's revision."""
return get_app_context().revision
def ge... | ocf/transpire | transpire/utils.py | .py | e66f3bdd411142de | 7.45 | 7 |
"""CLI entrypoint for rewrite deployments from paired YAML specifications."""
from __future__ import annotations
import argparse
from pathlib import Path
from prefect import deploy
from echodataflow.deployment.deployment_engine import (
build_deploy_specs,
configure_concurrency_groups,
create_deployment... | echostack-org/echodataflow | src/echodataflow/deployment/deploy_cli.py | .py | 3dd1a9ac8a0ce044 | 7.45 | 7 |
from pathlib import Path
import datetime
from prefect import flow, get_client, runtime, task
from prefect.client.schemas.filters import FlowRunFilter
@flow(timeout_seconds=600, log_prints=True)
def flow_file_upload(
src_dir: str,
dest_dir: str,
exclude_subdirs: list[str],
max_age: int = -1,
):
""... | echostack-org/echodataflow | src/echodataflow/flows/flows_helper.py | .py | de2c35007f9715d0 | 7.45 | 7 |
from __future__ import annotations
import configparser
from pathlib import Path
import echopype as ep
import geopandas as gpd
import pandas as pd
import s3fs
from prefect import flow, get_run_logger
from prefect.futures import as_completed
from echodataflow.operations.operations_integration import (
ReadNASCSett... | echostack-org/echodataflow | src/echodataflow/flows/flows_integration.py | .py | 9e415763de5db592 | 7.45 | 7 |
"""Flows for hake prediction and downstream NASC processing."""
from __future__ import annotations
import datetime
from pathlib import Path
import echopype as ep
import pandas as pd
from prefect import flow, get_client, get_run_logger, runtime
from prefect.states import Failed
from echodataflow.utils.manifests impo... | echostack-org/echodataflow | src/echodataflow/flows/flows_predict_hake.py | .py | d8af9913c98420b5 | 7.45 | 7 |
from pathlib import Path
import pandas as pd
from prefect import flow
from echodataflow.utils.processing_ledger import (
get_completed_sv_files,
resolve_database,
)
TRANSECT_COLUMNS = [
"transectPart",
"transectNumber",
"transectStart",
"transectEnd",
]
def get_changed_transects(
curre... | echostack-org/echodataflow | src/echodataflow/flows/flows_transect.py | .py | cbd206ef5c5b1ad0 | 7.45 | 7 |
"""Acoustic data-processing operations and their data contracts."""
from __future__ import annotations
from dataclasses import dataclass
from pathlib import Path
import echopype as ep
from echopype.qc import coerce_increasing_time, exist_reversed_time
import numpy as np
import pandas as pd
import xarray as xr
@dat... | echostack-org/echodataflow | src/echodataflow/operations/operations_acoustics.py | .py | 60e84ab0a74d396d | 7.45 | 7 |
"""Biological data ingestion, transformations, and estimates for trawl hauls."""
from __future__ import annotations
import os
from collections.abc import Iterable, Mapping
from dataclasses import dataclass, fields
from pathlib import Path
from typing import Any
from uuid import uuid4
import numpy as np
import pandas... | echostack-org/echodataflow | src/echodataflow/operations/operations_biology.py | .py | f6455e0f32e51977 | 7.45 | 7 |
"""Operations for integrating acoustic and biological survey products."""
from __future__ import annotations
import os
from dataclasses import dataclass
from pathlib import Path
from uuid import uuid4
import echopype as ep
import geopandas as gpd
import numpy as np
import pandas as pd
import s3fs
import xarray as xr... | echostack-org/echodataflow | src/echodataflow/operations/operations_integration.py | .py | 14814c3e091d6dec | 7.45 | 7 |
"""Pure planning helpers for batch acoustic post-processing."""
from __future__ import annotations
import hashlib
import json
from dataclasses import dataclass
from pathlib import Path
from typing import Callable
import pandas as pd
from echodataflow.utils.manifests import (
MVBS_COLUMNS_POSTPROCESSING,
PRE... | echostack-org/echodataflow | src/echodataflow/operations/operations_postprocessing.py | .py | 92d37a6f9a401b6c | 7.45 | 7 |
"""Hake-prediction and downstream NASC operations."""
from __future__ import annotations
from dataclasses import dataclass
from pathlib import Path
import echopype as ep
import echoregions as er
import numpy as np
import pandas as pd
import torch
import xarray as xr
from segmentation_inference.model import binary_ha... | echostack-org/echodataflow | src/echodataflow/operations/operations_predict_hake.py | .py | 0dd4c2fe74403482 | 7.45 | 7 |
"""Reusable operations for moving data between storage systems."""
from __future__ import annotations
from dataclasses import dataclass
from pathlib import Path
from typing import Any
import boto3
from botocore import UNSIGNED
from botocore.config import Config
@dataclass(frozen=True)
class S3CopyWorkItem:
"""... | echostack-org/echodataflow | src/echodataflow/operations/operations_storage.py | .py | abc5b7b2df2a1154 | 7.45 | 7 |
from pathlib import Path
from prefect.events import emit_event
from prefect.events.worker import EventsWorker
from watchdog.observers import Observer
from echodataflow.utils.file_watcher import watch_directory, watch_file
from echodataflow.utils.processing_ledger import (
initialize_ledger,
register_raw_file,... | echostack-org/echodataflow | src/echodataflow/operations/operations_watchdog.py | .py | 1aa69c739bd9693d | 7.45 | 7 |
from pathlib import Path
import panel as pn
import xarray as xr
from holoviews import opts
import echoshader
# Configure Panel to prevent automatic refreshes
pn.config.autoreload = False
path_MVBS = Path("/media/volume/shimada_202506_volume/viz_data_cache")
def update_cache_multi_freq():
"""
Load latest MVB... | echostack-org/echodataflow | src/echodataflow/services/viz_echogram_track.py | .py | f99859916c300b51 | 7.45 | 7 |
from pathlib import Path
import panel as pn
import xarray as xr
from holoviews import opts
import echoshader
# Configure Panel to prevent automatic refreshes
pn.config.autoreload = False
path_MVBS = Path("/media/volume/shimada_202506_volume/viz_data_cache_2026/dyson_2026")
def update_cache_multi_freq():
"""
... | echostack-org/echodataflow | src/echodataflow/services/viz_echogram_track_dyson.py | .py | 34f7e3a16a9f2429 | 7.45 | 7 |
from pathlib import Path
import panel as pn
import xarray as xr
from holoviews import opts
import echoshader
# Configure Panel to prevent automatic refreshes
pn.config.autoreload = False
path_MVBS = Path("/media/volume/shimada_202506_volume/viz_data_cache_2026/iwcsp_2026")
def update_cache_multi_freq():
"""
... | echostack-org/echodataflow | src/echodataflow/services/viz_echogram_track_lasker.py | .py | dca62bb9de939c0d | 7.45 | 7 |
"""Reusable Prefect tasks for acoustic data processing."""
import xarray as xr
from prefect import get_run_logger, task
from echodataflow.operations.operations_acoustics import (
CreateMVBSResult,
CreateMVBSSettings,
CreateMVBSWorkItem,
RawToSvResult,
RawToSvSettings,
RawToSvWorkItem,
comp... | echostack-org/echodataflow | src/echodataflow/tasks/tasks_acoustics.py | .py | b66c13e6af1b32e9 | 7.45 | 7 |
"""Reusable Prefect tasks for hake prediction and NASC processing."""
from prefect import get_run_logger, task
from echodataflow.operations.operations_predict_hake import (
ComputeNASCResult,
ComputeNASCSettings,
ComputeNASCWorkItem,
PredictHakeResult,
PredictHakeSettings,
PredictHakeWorkItem,... | echostack-org/echodataflow | src/echodataflow/tasks/tasks_predict_hake.py | .py | 7148d51b7241e65c | 7.45 | 7 |
import cartopy.feature as cfeature
from cartopy.mpl.ticker import LongitudeFormatter, LatitudeFormatter
from geopy.distance import distance
import pandas as pd
import numpy as np
import geopandas as gpd
import shapely.geometry as sg
import matplotlib.pyplot as plt
from shapely import wkt
def utm_string_generator(long... | echostack-org/echodataflow | src/echodataflow/utils/grid.py | .py | 932b9d1260dae92b | 7.45 | 7 |
"""Utilities for reading, writing, and filtering processing manifests."""
from __future__ import annotations
from pathlib import Path
import pandas as pd
SV_COLUMNS_REALTIME = [
"raw_filename",
"Sv_filename",
"first_ping_time",
"last_ping_time",
]
MVBS_COLUMNS_REALTIME = ["MVBS_filename", "first_ping... | echostack-org/echodataflow | src/echodataflow/utils/manifests.py | .py | 2ef404e2d0507a5d | 7.45 | 7 |
"""Utilities for matching cloud trawl files to complete hauls."""
from __future__ import annotations
import re
from collections.abc import Iterable, Mapping
from pathlib import Path
HAUL_NUMBER_PATTERN = re.compile(r"(?P<haul_num>\d{3})_[^_]+\.xlsx$", re.IGNORECASE)
REQUIRED_TRAWL_FILE_TYPES = ("length", "specimen",... | echostack-org/echodataflow | src/echodataflow/utils/trawl_files.py | .py | 77b0964b39a5addb | 7.45 | 7 |
import re
from pathlib import Path
import datetime
import numpy as np
import pandas as pd
def round_up_mins(dt: datetime.datetime, slice_mins: int) -> datetime.datetime:
"""Round down datetime to nearest interval minutes.
Parameters
----------
dt : datetime.datetime
Datetime to round
... | echostack-org/echodataflow | src/echodataflow/utils/utils.py | .py | ebb54fa1fe56d10f | 7.45 | 7 |
from yuptoo.modifiers.add_host_facts import AddHostFacts
from datetime import datetime, timedelta
from yuptoo.lib.config import SATELLITE_HOST_TTL
import uuid
def test_add_host_facts():
uuid1 = str(uuid.uuid4())
b64_identity = ('eyJpZGVudGl0eSI6IHsiYWNjb3VudF9udW1iZXIiOiAic3lzYWNjb3VudCIsICJ0eXBlIjogIlN5c3R'
... | RedHatInsights/yuptoo | tests/modifiers/test_add_host_facts.py | .py | 14e5d7098e43f336 | 7.95 | 7 |
from unittest.mock import patch
from yuptoo.modifiers.transform_installed_packages import TransfromInstalledPackages
def test_remove_installed_packages():
"""Test remove installed_packages when message size exceeds."""
host = {
'system_profile': {
'installed_packages': [
... | RedHatInsights/yuptoo | tests/modifiers/test_transform_installed_packages.py | .py | b8a7f76654524b8b | 7.95 | 7 |
from yuptoo.modifiers.transform_mac_addresses import TransformMacAddresses
def test_transform_mac_addresses():
"""Test transform mac_addresses."""
host = {'mac_addresses': []}
transformed_obj = {'removed': []}
TransformMacAddresses().run(host, transformed_obj)
assert host == {}
assert 'empty m... | RedHatInsights/yuptoo | tests/modifiers/test_transform_mac_addresses.py | .py | 297b69ab22836e87 | 7.95 | 7 |
from yuptoo.modifiers.transform_os_kernel_version import TransformOsKernalVersion
def test_transform_os_kernel_field():
"""Test transform os fields."""
host = {'system_profile': {
'os_release': '7', 'os_kernel_version': '3.10.0-1127.el7.x86_64'
}}
transformed_obj = {'modified': []}
Transfo... | RedHatInsights/yuptoo | tests/modifiers/test_transform_os_kernel_version.py | .py | 6e230f259ff70927 | 7.95 | 7 |
from uuid import UUID
from yuptoo.processor.utils import Modifier
class RemoveInvalidBiosUUID(Modifier):
def run(self, host: dict, transformed_obj: dict, **kwargs):
"""Remove invalid bios UUID."""
uuid = host.get('bios_uuid')
if (uuid and not self.is_valid_uuid(uuid)) or uuid == '':
... | RedHatInsights/yuptoo | yuptoo/modifiers/remove_invalid_bios_uuid.py | .py | 88442554ed524fe5 | 7.45 | 7 |
from yuptoo.processor.utils import Modifier
import logging
LOG = logging.getLogger(__name__)
GOOGLE_PROVIDER_NAME = 'gcp'
class TransformCloudProvider(Modifier):
def run(self, host: dict, transformed_obj: dict, **kwargs):
"""Transform 'system_profile.cloud_provider.
When system_profile.cloud_prov... | RedHatInsights/yuptoo | yuptoo/modifiers/transform_cloud_provider.py | .py | f7cb40e235681f97 | 7.45 | 7 |
import json
import logging
from insights.parsers.installed_rpms import InstalledRpm
from yuptoo.lib.config import KAFKA_PRODUCER_OVERRIDE_MAX_REQUEST_SIZE
from yuptoo.processor.utils import Modifier
LOG = logging.getLogger(__name__)
class TransfromInstalledPackages(Modifier):
def run(self, host: dict, transform... | RedHatInsights/yuptoo | yuptoo/modifiers/transform_installed_packages.py | .py | 1001d42e8c9236ba | 7.45 | 7 |
from yuptoo.processor.utils import Modifier
import logging
LOG = logging.getLogger(__name__)
class TransformIPAddress(Modifier):
def run(self, host: dict, transformed_obj: dict, **kwargs):
"""Remove empty & make 'ip_addresses' unique. Drop blank items."""
ip_addresses = host.get('ip_addresses')
... | RedHatInsights/yuptoo | yuptoo/modifiers/transform_ip_addresses.py | .py | 152a562e2f0b936c | 7.45 | 7 |
import logging
from yuptoo.processor.utils import Modifier
LOG = logging.getLogger(__name__)
class TransformMacAddresses(Modifier):
def run(self, host: dict, transformed_obj: dict, **kwargs):
"""Make values unique and remove empty 'mac_addresses' field."""
mac_addresses = host.get('mac_addresses'... | RedHatInsights/yuptoo | yuptoo/modifiers/transform_mac_addresses.py | .py | 93b9c812b8ceb489 | 7.45 | 7 |
import re
from yuptoo.processor.utils import Modifier
# Follow the system_profile schema defination of the "os_kernel_version" field
KERNEL_VERSION_PATTERN = re.compile(r'^(\d+\.\d+\.\d+)(\.\d+)?')
class TransformOsKernalVersion(Modifier):
def run(self, host: dict, transformed_obj: dict, **kwargs):
"""Tr... | RedHatInsights/yuptoo | yuptoo/modifiers/transform_os_kernel_version.py | .py | 46cbb5acad5240f5 | 7.45 | 7 |
#!/usr/bin/env python3
"""
HACK SLOW - Envia um comando por vez com delays longos.
Cada comando eh curto e simples pra sobreviver ao ruido do IPC.
"""
import serial
import time
import sys
PORT = '/dev/ttyUSB0'
BAUD = 115200
SD = '/mnt/disc1'
def send_slow(ser, cmd, wait=2.0):
"""Envia comando caract... | wangcai0124/camera-hack | scripts/hack_slow.py | .py | fa5e46bb3abda86e | 7.56 | 12 |
#!/usr/bin/env python3
"""
HACK V3 - Baseado na engenharia reversa do firmware Yoosee/Anyka
Descobertas:
- inittab: ttySAK0 respawn getty → login prompt reaparece após logout
- setup.sh: 'q' + Enter nos primeiro 1s para o IPC
- rc.local: SD so processa com RESET pressionado
- /rom = jffs2 RW = persistencia
- /e... | wangcai0124/camera-hack | scripts/hack_v3.py | .py | 8b3d7a02025fb599 | 7.56 | 12 |
#!/usr/bin/env python3
"""
Teste de RX e TX separados para comunicação serial com a câmera.
Fase 1: RX puro (só escuta por 15s)
Fase 2: TX+RX (envia dados e verifica eco/resposta)
"""
import serial
import time
import sys
PORT = '/dev/ttyUSB0'
BAUD = 115200
TIMEOUT = 0.5
def test_rx(duration=15):
""... | wangcai0124/camera-hack | scripts/test_rxtx.py | .py | d8bbacd60ac3c51f | 8.06 | 12 |
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