text stringlengths 185 73.3k | repo stringlengths 7 100 | path stringlengths 4 146 | language stringclasses 7
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"""CLI composition root helpers.
One of the three places allowed to name a concrete adapter (ADR-0003). Every
command builds its object graph here, so wiring lives in one readable place
rather than being scattered across command bodies.
"""
from __future__ import annotations
import subprocess
from dataclasses import... | theurian/theurian | packages/theurian-core/src/theurian/cli/context.py | .py | 9ca7979967dc73d5 | 7.42 | 6 |
"""What ``theurian index status`` reports, computed (FR-R2).
Split out of :mod:`theurian.cli.index_commands`, which holds the command itself
and stays the module ``tests/unit/test_resolve_context_call_sites.py`` pins
``index_status`` to. What moved here is everything the command *derives* before
it emits: the publishe... | theurian/theurian | packages/theurian-core/src/theurian/cli/index_status_report.py | .py | 9723e3adeb072d98 | 7.42 | 6 |
"""Theurian CLI entry point.
A composition root: this is one of the three places allowed to name concrete
adapters (ADR-0003). Milestone 0 ships only the version surface, because that is
what the plugin's compatibility gate depends on -- everything else lands in
Milestones 1 through 8.
Every command supports ``--json... | theurian/theurian | packages/theurian-core/src/theurian/cli/main.py | .py | b69231cd85e463b0 | 7.42 | 6 |
"""The pipeline ``migrate apply`` runs, and the dry replay ``propose accept`` runs.
A composition root (ADR-0003): one of the places allowed to name a concrete
adapter. It exists for one reason, and the reason is ADR-0027 decision 2's hard
condition -- **``accept``'s pre-check must invoke the same engine path ``migrat... | theurian/theurian | packages/theurian-core/src/theurian/cli/migration_pipeline.py | .py | e177f7d457c5d1ef | 7.42 | 6 |
"""The one place a CLI value is made safe to print to a terminal.
Every text-mode emitter in the CLI -- `commands._render`, `commands._fail`, and
`main._emit` -- routes each value and key it prints through
:func:`escape_terminal_controls`, so that no string a command *emits through
them* can move the cursor or start a... | theurian/theurian | packages/theurian-core/src/theurian/cli/output.py | .py | dc7602dbcf2831b4 | 7.42 | 6 |
"""Daemon lifecycle: assemble, guard, and serve (ADR-0002, ADR-0011).
A composition root. This is where the token, the registry, the MCP tools, and
the single-instance guard are wired into one running process.
"""
from __future__ import annotations
import asyncio
from datetime import UTC, datetime
from pathlib impor... | theurian/theurian | packages/theurian-core/src/theurian/daemon/runner.py | .py | 4b95e6d23aadd5d8 | 7.42 | 6 |
"""The Theurian daemon (ADR-0002, ADR-0011).
A Starlette application exposing:
- ``GET /health`` — unauthenticated, liveness and identity only
- ``/mcp`` — the MCP server over Streamable HTTP, bearer-authenticated
Bearer authentication is a Starlette middleware rather than the SDK's
``AuthSettings``, which requires ... | theurian/theurian | packages/theurian-core/src/theurian/daemon/server.py | .py | fa1f55a38762735a | 7.42 | 6 |
"""Splitting a document into retrievable passages (FR-R2).
A pure function of text. Retrieval returns *chunks*, not whole documents,
because an architecture decision record is often ten pages of which one
paragraph answers the question — and returning the other nine spends a caller's
context budget on material they di... | theurian/theurian | packages/theurian-core/src/theurian/domain/chunking.py | .py | f6112bd917ea7291 | 7.42 | 6 |
"""Per-request context.
There is no process-global ``currentProject`` and no connection-scoped state.
Every call carries its own context, which is what makes cross-project isolation
testable rather than aspirational (ADR-0002, SEC-13).
"""
from __future__ import annotations
from dataclasses import dataclass
from typ... | theurian/theurian | packages/theurian-core/src/theurian/domain/context.py | .py | 58d9a3dd135f4dd1 | 7.42 | 6 |
"""Closed vocabularies, and the two rules that read one of them.
These are ``StrEnum`` so they serialise to their own names in JSON and YAML, which
keeps migration files and MCP payloads readable without a mapping table.
:func:`may_surface` and :func:`may_disclose` are here rather than beside a caller
because each ha... | theurian/theurian | packages/theurian-core/src/theurian/domain/enums.py | .py | 96f77eaaa23f2d35 | 7.42 | 6 |
"""Ingestion result types.
A parser failure fails **one document**, not the run. A malformed YAML file
among two hundred knowledge documents must not make the other 199 unavailable,
so failures are values carried in a report rather than exceptions that unwind
the whole walk (FR-S1, FR-S4).
"""
from __future__ import ... | theurian/theurian | packages/theurian-core/src/theurian/domain/ingestion.py | .py | c9591da2e5a82a5e | 7.42 | 6 |
"""Knowledge entities: items, revisions, relations, anchors, aliases, evidence.
A :class:`KnowledgeRevision` is immutable. A :class:`KnowledgeItem` is a mutable
pointer to the revision that is current now. See ADR-0006.
"""
from __future__ import annotations
from dataclasses import dataclass, field, replace
from dat... | theurian/theurian | packages/theurian-core/src/theurian/domain/knowledge.py | .py | 8c5bae25d799c482 | 7.42 | 6 |
"""Knowledge migration model (ADR-0005).
A migration is a declarative, storage-independent statement about knowledge
state. The types here describe what a migration *is*; applying one is the
application layer's job, and loading one from disk is the infrastructure's.
"""
from __future__ import annotations
from collec... | theurian/theurian | packages/theurian-core/src/theurian/domain/migration.py | .py | 5763d2fd3b740c79 | 7.42 | 6 |
"""Shared pytest fixtures for sdrf-skills tools tests."""
from __future__ import annotations
import os
from pathlib import Path
import pytest
EXAMPLES_DIR = Path(__file__).parent.parent / "examples"
@pytest.fixture
def synthetic_sdrf_path() -> Path:
return EXAMPLES_DIR / "PXD_synthetic.sdrf.tsv"
@pytest.fix... | bigbio/sdrf-skills | tests/conftest.py | .py | d7031da0b75b7076 | 8.1 | 15 |
"""Tests for tools.completeness — quality scoring."""
from __future__ import annotations
from pathlib import Path
import pytest
from tools.completeness import score_sdrf, QualityReport, AGE_PATTERN, MS_PROTEOMICS_REQUIRED
class TestScoreSdrf:
def test_synthetic_sdrf_scores(self, synthetic_sdrf_path: Path):
... | bigbio/sdrf-skills | tests/test_completeness.py | .py | 35e3780e43d82a95 | 8.1 | 15 |
"""Tests for tools.sdrf_fixer — auto-fixer."""
from __future__ import annotations
from pathlib import Path
import pytest
from tools.sdrf_fixer import fix_sdrf, FixReport
class TestFixSdrf:
def test_synthetic_fixes_unimod_swap(self, synthetic_sdrf_path: Path):
"""Row 3 has UNIMOD:21 for Acetyl — should... | bigbio/sdrf-skills | tests/test_fixer.py | .py | 6e4b32d7fb8268cf | 8.1 | 15 |
"""Tests for tools.hallucination — ontology hallucination detector."""
from __future__ import annotations
from pathlib import Path
from unittest.mock import MagicMock, patch
import pytest
from tools.hallucination import (
HallucinationReport,
detect_hallucinations,
_check_unimod_swap,
_check_modific... | bigbio/sdrf-skills | tests/test_hallucination.py | .py | 1fbe3ab659dadd76 | 7.1 | 15 |
"""Tests for tools.ols_client payload normalisation."""
from __future__ import annotations
from tools.ols_client import OLSClient, _collect_synonyms, _labels_match
class TestCollectSynonyms:
"""OLS4 spells the synonym field three different ways.
Regression tests: only ``synonyms`` was read, so every term r... | bigbio/sdrf-skills | tests/test_ols_client.py | .py | a0749660a40a3a28 | 8.1 | 15 |
"""Unified CLI entry point for sdrf-skills tools.
Usage:
python -m tools check <file.sdrf.tsv> # hallucination check
python -m tools score <file.sdrf.tsv> # quality scoring
python -m tools fix <file.sdrf.tsv> [-o out] # auto-fix
python -m tools benchmark <PXD1> <file2> ... # benchmark ... | bigbio/sdrf-skills | tools/cli.py | .py | 94b101b02a3dfdb8 | 7.6 | 15 |
"""Mapping from SDRF column names to expected ontology sources.
Derived from TERMS.tsv `values` field and the sdrf-knowledge SKILL.md (formerly sdrf-terms).
Used as a fallback when the spec submodule is not initialized.
"""
from __future__ import annotations
from pathlib import Path
from typing import Any
# Maps ch... | bigbio/sdrf-skills | tools/column_ontology_map.py | .py | 7d82e6ccf4171b0b | 7.6 | 15 |
"""CLI source consistency for Muyan Pilot (Issue #152).
The official local deployment is the EDITABLE uv tool install:
uv tool install --force --reinstall --editable \\
--python /usr/bin/python3 <deployment checkout>
The tool env's Python imports ``muyan_pilot`` directly from the
deployment checkout (the... | xqliu/muyan-pilot | cli_source.py | .py | 491e644d45be5a3c | 7.42 | 6 |
"""Git transport contract (Issue #114).
Two authentication channels with distinct responsibilities:
- **Git data operations** (fetch, push — including pushing
`.github/workflows/*.yml`) go over **SSH**
(`git@github.com:owner/repo.git`), authenticated by the machine's
SSH key. A workflow push must never depend o... | xqliu/muyan-pilot | git_transport.py | .py | e5780001d14dc03d | 7.42 | 6 |
#!/usr/bin/env python3
"""Live Pi session activity tracking (Issues #24, #40).
Pi writes its session as an append-only JSONL file under the task worktree
(`.pi-session/*.jsonl`) while it runs. This module follows that file and
reduces it to a small, redacted activity snapshot: session id, event count,
current phase, l... | xqliu/muyan-pilot | pi_activity.py | .py | e39aca5e733b361b | 7.42 | 6 |
#!/usr/bin/env python3
"""Idle-stall recovery for a running Pi session (Issue #94).
A Pi session can stall while a tool call hangs forever (a `while True`
test in the TDD red phase, a `next(generator)` that never returns, ...):
the Pi process waits for its child, the session JSONL freezes, and the
slot is held forever... | xqliu/muyan-pilot | pi_recovery.py | .py | 852d5a0dce60ae11 | 7.42 | 6 |
"""Cross-process concurrency slots for Muyan Pilot (Issue #39).
The local machine can only serve a limited number of concurrent Pilot
tasks, so the configured ``max_concurrency`` is enforced with one slot
file per allowed task under ``<repo_dir>/.muyan-pilot/slots/``.
Each slot file is a plain file whose exclusive ``... | xqliu/muyan-pilot | pilot_slots.py | .py | 2eb80e53901cc2db | 7.42 | 6 |
#!/usr/bin/env python3
"""Automatic GitHub progress publishing (Issue #18).
The runner keeps exactly one live progress comment per run on the source
Issue. The comment carries a hidden HTML run marker
(`<!-- muyan-pilot:run=<run_id> -->`) so a restarted process finds the same
comment again and keeps PATCHing it in pla... | xqliu/muyan-pilot | progress.py | .py | bfc758e8524b5a20 | 7.42 | 6 |
"""Systemd deployment consistency for Muyan Pilot (Issue #103, #149).
The repo templates ``systemd/muyan-pilot@.service`` and
``systemd/muyan-pilot@.timer`` are the single source of truth for the
user-level units. This module provides:
- an idempotent install (overwrite-copy the templates into the user
unit directo... | xqliu/muyan-pilot | systemd_deploy.py | .py | b854f6db26856e85 | 7.42 | 6 |
"""Shared test fixtures for the Muyan Pilot suite.
The deployment preflights (Issue #103 unit drift, Issue #114 git
transport) read the REAL machine state (the user unit directory, the
checkout's ``origin`` remote, SSH connectivity); the in-process
dispatch tests use tmp repo_dirs that carry no ``systemd/`` templates
... | xqliu/muyan-pilot | tests/conftest.py | .py | 0dcf01de8043fddc | 7.92 | 6 |
"""Guard the repository development contract.
`AGENTS.md` is the stable contract every local Pi bootstrap run reads before
changing code (see `prompt.md`). These tests fail when the file is missing or
when a required contract item is removed, so the contract cannot silently
drift away from the rules this repo actually... | xqliu/muyan-pilot | tests/test_agents_md.py | .py | 20bc86fcf09e9d13 | 7.92 | 6 |
"""Regression tests for the GitHub Actions CI workflow (Issue #56).
The repository contract (AGENTS.md) says the full pytest suite must run
with 100% line/branch coverage via the coverage commands. Until now that
only happened on the local Runner machine. The workflow in
`.github/workflows/ci.yml` runs the same contra... | xqliu/muyan-pilot | tests/test_ci_workflow.py | .py | ec704d91efd39f0d | 7.92 | 6 |
"""Chinese documentation contract (Issue #116).
The Chinese docs live in `docs/zh/` (the verified Mintlify i18n layout:
same structure as the default English pages at the `docs/` root) and keep
the SAME single source of truth as the English pages — the implementation
facts (labels, config fields, commands, ports, the ... | xqliu/muyan-pilot | tests/test_docs_i18n.py | .py | abd5483fa8b3a361 | 7.92 | 6 |
"""Documentation contract for GitHub external state (Issue #49).
The README/AGENTS must document the labels, run markers, and recovery
state exactly as the code implements them: every `ai-*` label the docs
mention must exist in the runner's label set, the README must carry a
label table with meaning/enter/leave for al... | xqliu/muyan-pilot | tests/test_docs_labels.py | .py | 0048ab132d50f005 | 7.92 | 6 |
"""Mermaid diagram contract (Issue #116).
The docs must ship two diagrams, in BOTH languages (English at the
`docs/` root, Chinese under `docs/zh/`):
1. the system architecture overview (index page): GitHub Issues/PRs,
the systemd timer/service, the Runner, the Pi sessions, the task
worktree, the core llama-ser... | xqliu/muyan-pilot | tests/test_docs_mermaid.py | .py | 3faf82cec9a08812 | 7.92 | 6 |
"""Release documentation contract (Issue #128).
The docs `Releases`/`发布` group must mirror the REAL release state of
the repository — verified against origin with `git ls-remote --tags
origin` and `gh release list` (this run): tags `v0.1.0`, `v0.1.1`,
`v0.1.2` exist; GitHub Releases `v0.1.1`, `v0.1.2` exist; **no
`v0.... | xqliu/muyan-pilot | tests/test_docs_releases.py | .py | 2b4b126bb190ad91 | 7.92 | 6 |
"""Real git smoke tests for Issue #31 base-freeze behavior.
These tests execute actual git commands inside a temporary local repository
(no network, no remote push, no protected branch) and prove the acceptance
criteria:
- a task worktree is created from the latest ``origin/<base>`` even when the
main worktree is c... | xqliu/muyan-pilot | tests/test_git_base_smoke.py | .py | f5211ca9f7e1e72e | 7.92 | 6 |
"""Real git smoke tests for the auto review/fix/merge gate (Issue #34).
These tests execute actual git commands inside a temporary local repository
(no network, no remote push of a protected branch, no real GitHub merge) and
prove the merge-gate acceptance criteria:
- a PR head that contains the latest ``origin/<base... | xqliu/muyan-pilot | tests/test_git_merge_smoke.py | .py | a896ca9fb017208e | 7.92 | 6 |
"""Guard the public repository license (Issue #81).
`xqliu/muyan-pilot` is public, so the repository root must carry a license
file GitHub can recognize. The Issue fixes Apache License 2.0 (SPDX
identifier `Apache-2.0`) as the default and requires the README to link to
the file. These tests fail when the file is missi... | xqliu/muyan-pilot | tests/test_license.py | .py | 1c82a931f545d52a | 7.92 | 6 |
"""v0.1.0 release reconciliation record (Issue #97).
The release state reconciliation is a one-time GitHub-state task: the
durable, auditable artifact in the repository is the reconciliation
record ``docs/release-v0.1.0.md``. These tests pin that record against
the REAL git history and the REAL CLI:
- the tag/commit ... | xqliu/muyan-pilot | tests/test_release_v01.py | .py | e42ea5ba8ed5a349 | 7.92 | 6 |
"""Run artifacts stay out of version control (Issue #80 review round 1).
`plan.md` and `test.log` are per-run artifacts written into the task
worktree (prompt.md steps 2 and 5). A worktree is created from the
frozen base SHA (`git worktree add ... <base_sha>`): if these files
were tracked in the base, every new worktr... | xqliu/muyan-pilot | tests/test_run_artifacts.py | .py | 2e985db0d684d40b | 7.92 | 6 |
"""Regression tests for the systemd scheduling files (Issues #21, #33,
#51, #149).
The scheduler runs 24 hours a day: the idle polling interval is 5 minutes
across the full day (00:00, 00:05, ..., 23:55). The timer must not add a
task duration limit, must not queue catch-up ticks, and the README must
document the same... | xqliu/muyan-pilot | tests/test_systemd_timer.py | .py | b29d15c44502bb39 | 7.92 | 6 |
"""MkDocs hooks: render builtin demos into standalone pages and splice them into the docs."""
import os
import re
import shutil
import sys
HERE = os.path.dirname(__file__)
sys.path.insert(0, HERE)
from demos import DEMOS
from pyjinhx._component import BaseComponent, _pascal_to_snake
from pyjinhx.assets import Asset... | paulomtts/pyjinhx | docs/hooks.py | .py | 325dcdb27a42aa48 | 7.52 | 10 |
"""The todo example's FastAPI wiring: one app, four routes, no page shell.
Every route returns a component and lets the adapter turn it into HTML — there
is no HTMLResponse and no ctx= anywhere in this file, because PjxScopeMiddleware
opens the request scope and injects the app context the components' load()
methods r... | paulomtts/pyjinhx | examples/todo/app.py | .py | 808e6add213b5bd9 | 7.52 | 10 |
from examples.todo.context import TodoAppContext
from examples.todo.keys import Keys
from pyjinhx import ReactiveComponent
class ClearButton(ReactiveComponent, react={Keys.TODOS}):
"""The clear-completed action, disabled while nothing is completed."""
completed: int = 0
@classmethod
def load(cls, ct... | paulomtts/pyjinhx | examples/todo/components/clear_button/clear_button.py | .py | babe0c62fd11790f | 7.02 | 10 |
from examples.todo.context import TodoAppContext
from examples.todo.keys import Keys
from pyjinhx import ReactiveComponent
class Counter(ReactiveComponent, react={Keys.TODOS}):
"""How many todos are still open."""
remaining: int = 0
@classmethod
def load(cls, ctx: TodoAppContext | None = None) -> "C... | paulomtts/pyjinhx | examples/todo/components/counter/counter.py | .py | 779871f5a253b89e | 7.02 | 10 |
from examples.todo.components.item_row import ItemRow
from examples.todo.context import TodoAppContext
from examples.todo.keys import Keys
from pyjinhx import ReactiveComponent
class ItemList(ReactiveComponent, react={Keys.TODO_LIST}):
"""The list of todo rows."""
items: list[ItemRow] = [] # noqa: RUF012 --... | paulomtts/pyjinhx | examples/todo/components/item_list/item_list.py | .py | cd671bdd3dc783d8 | 7.52 | 10 |
from typing import Annotated
from examples.todo.context import TodoAppContext
from examples.todo.keys import Keys
from pyjinhx import PjxKey, ReactiveComponent
class ItemRow(ReactiveComponent, react={Keys.TODOS}):
"""One todo, keyed by its id so each row caches its own load result."""
todo_id: Annotated[int... | paulomtts/pyjinhx | examples/todo/components/item_row/item_row.py | .py | 04a7c14efdb1b772 | 7.52 | 10 |
from examples.todo.context import TodoAppContext
from examples.todo.keys import Keys
from pyjinhx import ReactiveComponent
class Total(ReactiveComponent, react={Keys.TODOS}):
"""How many todos exist in total."""
count: int = 0
@classmethod
def load(cls, ctx: TodoAppContext | None = None) -> "Total":... | paulomtts/pyjinhx | examples/todo/components/total/total.py | .py | 870d04ef62e20197 | 7.02 | 10 |
"""pyjinhx — server-rendered, htmx-wired components for Python web apps.
This module re-exports the public API; advanced or internal usage lives in the
submodules (`pyjinhx.reactive.keys`, `pyjinhx.reactive.mutations`,
`pyjinhx.registry`, `pyjinhx.rendering`).
"""
from __future__ import annotations
import sys
import... | paulomtts/pyjinhx | pyjinhx/__init__.py | .py | b7f91ee488ac14ce | 7.52 | 10 |
"""AppContext: the marker an app's own context class subclasses to be injectable.
Import-pure on purpose - stdlib only, no pyjinhx imports - so the reactive
load() wrap can reach down into it from class-definition time without adding an
edge back into the render spine.
Deliberately not PjxContext: that class is the f... | paulomtts/pyjinhx | pyjinhx/app_context.py | .py | b6ddf1829c71f1e7 | 7.52 | 10 |
"""L2.2 assets — delivery modes, emission, and the manifest of a request's assets."""
import hashlib
import os
from collections.abc import Callable, Iterable
from dataclasses import dataclass
from enum import Enum
from pathlib import Path
from typing import TYPE_CHECKING
if TYPE_CHECKING:
from pyjinhx.session imp... | paulomtts/pyjinhx | pyjinhx/assets.py | .py | 2635ba23c9bc4993 | 7.52 | 10 |
from typing import Any
from pydantic import Field, computed_field, field_validator
from pyjinhx._component import AttrValue, BaseComponent, ExtraAttrs
class PJXPaginator(BaseComponent):
"""A windowed pagination nav whose page links can drive HTMX swaps."""
page: int
total_pages: int = Field(ge=1)
u... | paulomtts/pyjinhx | pyjinhx/builtins/pjx_paginator/pjx_paginator.py | .py | d778e092140a5ee3 | 7.52 | 10 |
from __future__ import annotations
from dataclasses import dataclass
from typing import List, Tuple
import torch
from sglang.srt.layers.attention.utils import create_flashinfer_kv_indices_triton
from sglang.srt.distributed import get_tp_group
from sglang.srt.layers.logits_processor import LogitsProcessorOutput
from ... | DocPang/qwen38-k100ai-int8-optimization | hotfixes/v1.2.2/patch/sglang/srt/speculative/dflash_info.py | .py | f24f1bb01ee93e78 | 7 | 9 |
#!/usr/bin/env python3
"""PreToolUse hook: block cross-user DM sends via the bus primitive (ms-110 / e-3444).
Reads the Claude Code PreToolUse event on stdin and, when the tool call is a
cross-project (potentially cross-user) DM sent by calling the bus primitive
directly — not via /beacon-dm-send and without a valid o... | kurogin23mech-source/beacon | .archive/ms-110-hook-shelved/beacon-pretooluse-dm-guard.py | .py | 9a0ae09a600d5d53 | 7.5 | 9 |
"""Beacon FirestoreStore - Cloud-backed project storage.
Stores the entire project.json as a single Firestore document.
Collection: projects/{project_id}
"""
from __future__ import annotations
import json
from datetime import datetime
class FirestoreStore:
"""Store implementation backed by Google Cloud Firesto... | kurogin23mech-source/beacon | .trash/store_firestore.py | .py | 003e976d97423c95 | 7.5 | 9 |
"""beacon-find-root — Python entry-point for the project-root walk-up helper.
Mirrors the behaviour of ``bin/beacon-find-root`` (shell script) so that
``pip install beacon`` produces a ``beacon-find-root`` / ``beacon-find-root.exe``
binary in the user's Scripts directory. The Skills shipped under
``skills/*.md`` call ... | kurogin23mech-source/beacon | beacon_cli/find_root.py | .py | 8eb390fac50d4cbd | 7.5 | 9 |
"""PostToolUse hook: surface STOP signals to the AI (ms-55 e-1721).
Companion to ``post_commit.py`` (commit detection) and ``save_hook.py``
(MCP auto-save). This hook closes the loop on the "止まる側" half of
ms-55 SPEC: after every tool call, check whether the inbox-side hook
has dropped a ``halt-request.json`` on disk f... | kurogin23mech-source/beacon | beacon_cli/hooks/halt_check.py | .py | 46ce752f8526e1bd | 7.5 | 9 |
"""Cross-platform MCP save hook (PostToolUse, matcher: mcp__).
Python translation of ``bin/beacon-save-hook.sh`` (ms-44 e-777). Watches
for MCP write operations against the Google Drive integration and
auto-records them as ``beacon save`` entries under the currently active
milestone.
Bash → Python contract notes:
*... | kurogin23mech-source/beacon | beacon_cli/hooks/save_hook.py | .py | 42f771b3a925de1a | 7.5 | 9 |
"""SessionStart hook: beacon の自動アップデート (ms-103)。
bclaude セッション開始時に呼ばれ、新しい版が出ていれば自動でインストールする。
サーバに新機能が入っても各ユーザーの CLI / bridge が古いままだと全面適用が遅れる
ため、起動を機に自然に最新へ追従させる。
契約 (= Claude Code SessionStart hook):
* Stdin: SessionStart JSON (中身は使わないが pipe を詰まらせないよう drain する)。
* Stdout: 空 (通知が要るときだけ 1 行。セッション開始をブロックしない)... | kurogin23mech-source/beacon | beacon_cli/hooks/session_start.py | .py | 519c04970dcb0aa8 | 7.5 | 9 |
"""Cross-project session discovery for /beacon-dm-send.
Two discovery sources are supported:
1. **Server-first (cloud-first identity, ms-62 / e-1502)**: ask the cloud
server for the user's project memberships via ``GET /api/me/projects``,
then query each project's ``beacon bus directory`` (= live session list)
... | kurogin23mech-source/beacon | beacon_cli/skills_helpers/dm_discover.py | .py | b6ace4694fb9c514 | 7.5 | 9 |
"""Stable-recipient-identity resolve (ms-93 / e-2520).
`session_id` (sid) is an ephemeral *route token*, not an identity: a bridge
restart or a Codex daemon re-mint produces a fresh sid, so a sender that
remembers a raw sid ends up addressing a session that died a minute ago
(observed repeatedly 2026-07-07: a DNS-cuto... | kurogin23mech-source/beacon | beacon_cli/skills_helpers/identity_resolve.py | .py | 4e50a647f4a39cc6 | 7.5 | 9 |
#!/usr/bin/env python3
"""bin/context-usage-monitor.py — standalone Stop hook (ms-44 e-854).
Single-file Python port of ``bin/context-usage-monitor.sh`` so Windows
pipx users (no bash, no jq) can register Claude Code's Stop hook by
absolute path:
{
"hooks": {
"Stop": [{
"matcher": "",
... | kurogin23mech-source/beacon | bin/context-usage-monitor.py | .py | 17ccfcdbbd339c45 | 7.5 | 9 |
"""Reference ``beacon_sink`` for headless machines (PE detector Lambda 等) — ms-151.
外部の常駐プログラム (人が介在しない machine) が、自分の run_record (運転記録) と
incident (異常記録) を Beacon cloud へ直接書くための **差し替え口の参照実装**。PE
detector Lambda は既存の ``beacon_sink`` stub をこのクラスに差し替えるだけで書ける。
依存は標準ライブラリのみ (urllib)。Lambda に requests 等を同梱しなくても動く。
## 使い... | kurogin23mech-source/beacon | docs/integrations/beacon_sink.py | .py | 8deaf990cf683931 | 7.5 | 9 |
"""Attack-list schema for inside-sales acquisition (ms-132 e-4501).
An *attack list* is the concrete shape ms-132 puts on top of the generic ms-131
table-doc primitive: a table linked to an Acquisition (``acq-``) whose every row
is one prospect Account to reach out to. This module owns the canonical column
schema — Ac... | kurogin23mech-source/beacon | lib/attack_list.py | .py | 6d4ac39aedd8e09e | 7.5 | 9 |
r"""Branch name helpers for the ms-51 branch-driven workflow.
The single export is :func:`ms_branch_name`, which takes an MS id and an
MS title and returns the canonical branch name used by ``beacon ms start``
and ``beacon ms join --checkout``.
Format::
ms-<id_number>-<slug>
Where ``<slug>`` is derived from the... | kurogin23mech-source/beacon | lib/branch.py | .py | da3c471137cce5e0 | 7.5 | 9 |
from scapy.all import wrpcap, rdpcap
from utils.logger import log
class PCAPManager:
"""
Handles PCAP import/export functionality
Compatible with Wireshark
"""
def export_pcap(self, packets, filename):
"""
Export captured packets to PCAP file
packets: list of Sc... | mwakidenis/Network-Packet-Sniffer-Traffic-Analyse-GUI | network-sniffer/core/pcap_manager.py | .py | a21cc0a53473260c | 7.65 | 19 |
from PySide6.QtCore import QThread, Signal
import pyshark
import asyncio
from utils.logger import log
class PySharkSniffer(QThread):
packet_signal = Signal(object)
# Set your TShark path here
TSHARK_PATH = r"D:\Wireshark\tshark.exe"
def __init__(self, iface):
super().__init__()
self.i... | mwakidenis/Network-Packet-Sniffer-Traffic-Analyse-GUI | network-sniffer/core/pyshark_sniffer.py | .py | 3c6b040f247eb71d | 7.65 | 19 |
"""Measure local five-layer tool-call decision latency.
This is a local measurement utility, not a cross-host performance guarantee.
Run after installing the server extra:
python benchmark/tool_call_latency.py --iterations 200
"""
from __future__ import annotations
import argparse
import json
import statistics
i... | poojakira/mcp-agent-security-gateway | benchmark/tool_call_latency.py | .py | 636234bee04c9a01 | 7.63 | 17 |
"""Locust load test for MCP Security Gateway Monitor.
Target: 5000 requests/second sustained throughput.
Run with:
locust -f locustfile.py --host=http://localhost:8080 --users 500 --spawn-rate 50
For headless mode targeting 5000 req/s:
locust -f locustfile.py --host=http://localhost:8080 \
--users 10... | poojakira/mcp-agent-security-gateway | locustfile.py | .py | e7f3be2d293da63b | 7.63 | 17 |
"""Cryptographic tool manifest signing and verification.
WHY THIS EXISTS:
Anthropic's position on the MCP STDIO RCE flaw was that "securing the STDIO
interface is the responsibility of whoever deploys it, not of the protocol."
This means there is ZERO protocol-level assurance that a tool's schema,
description, or capa... | poojakira/mcp-agent-security-gateway | src/mcp_monitor/advanced/manifest.py | .py | 346c1a0380e9cad9 | 7.63 | 17 |
"""Client middleware for routing real MCP tool calls through the security gateway.
This is how a live product feed is produced: wrap your agent's tool-execution
function with ``guard()``. Every tool call is scanned by the running gateway
(POST /api/scan), which streams the verdict to the live dashboard and blocks
call... | poojakira/mcp-agent-security-gateway | src/mcp_monitor/client.py | .py | 187c59059125763c | 7.63 | 17 |
"""Terminal-based report renderer for MCP security simulations.
Displays catalog replay results with color-coded severity, layer-by-layer
breakdown, and scoped defense statistics for the supplied simulation report.
"""
from __future__ import annotations
import time
from typing import Any
from mcp_monitor.redteam.si... | poojakira/mcp-agent-security-gateway | src/mcp_monitor/dashboard/terminal.py | .py | 97f5b48937536bad | 7.63 | 17 |
"""Layer B: DPI egress proxy — compares MCP INTENT vs ACTUAL network call.
THE KEY INSIGHT THAT DEFEATS THE POSTMARK ATTACK:
The MCP tool call says: send to ['user@company.com'].
The actual HTTP POST to api.postmarkapp.com says: To=user@company.com,
Bcc=phan@giftshop.club.
If you compare the two, the discrepancy ... | poojakira/mcp-agent-security-gateway | src/mcp_monitor/defense10/egress_proxy.py | .py | 5ab90b70de827742 | 7.63 | 17 |
"""Honeypot / canary token system.
WHY THIS CATCHES ATTACKS EVERY OTHER LAYER MISSES:
Plant fake secrets ("canary tokens") in the environment — a fake API key,
a fake password, a fake customer record. No legitimate workflow ever uses
them. If one of these EVER appears in an outbound tool call, you have
a high-confiden... | poojakira/mcp-agent-security-gateway | src/mcp_monitor/defense10/honeypot.py | .py | d461e9af55394784 | 7.63 | 17 |
"""10-layer defense orchestrator for combining available signals into one verdict.
Chains the original 5 layers with the defense10 components:
L1 Application detectors (regex, PII, shadow, exfil)
L2 Inline proxy enforcement
L3 Kernel/network monitor (/proc + eBPF) — sees server-side calls
L4 ... | poojakira/mcp-agent-security-gateway | src/mcp_monitor/defense10/orchestrator10.py | .py | 3b5cdc697fea2679 | 7.63 | 17 |
"""Layer 5+ : Rate limiting + recipient whitelist (BLAST RADIUS LIMITING).
WHY THIS IS THE MOST IMPORTANT LAYER AGAINST A DETERMINED ADVERSARY:
Detection is never 100%. Something eventually evades every filter.
So the final defense is: even if the attack SUCCEEDS, cap the damage.
The Postmark attack exfiltrated 3,000... | poojakira/mcp-agent-security-gateway | src/mcp_monitor/defense10/rate_limiter.py | .py | 97e3fc335e8b79a0 | 7.63 | 17 |
"""Layer A: REAL Docker/OCI sandbox isolation for untrusted MCP servers.
WHY THIS IS THE STRONGEST SINGLE CONTROL:
If the MCP server runs in a container with '--network none' (or only an
egress proxy), it CANNOT connect to giftshop.club no matter what its code
does. The kernel enforces the boundary. The attacker's one... | poojakira/mcp-agent-security-gateway | src/mcp_monitor/defense10/sandbox.py | .py | d33bf5829e17fa4e | 7.63 | 17 |
"""Alerting hooks for critical security findings.
Posts JSON webhooks to configurable URLs (Slack/PagerDuty compatible)
when findings exceed a risk threshold. Uses fire-and-forget threading.
"""
from __future__ import annotations
import json
import threading
import time
import urllib.error
import urllib.parse
import... | poojakira/mcp-agent-security-gateway | src/mcp_monitor/production/alerting.py | .py | f0d52c3e96fadf4d | 7.63 | 17 |
"""Circuit breaker pattern for defense layers.
Prevents cascading failures by opening the circuit after consecutive errors,
then probing with half-open state after a timeout.
"""
from __future__ import annotations
import enum
import threading
import time
from collections.abc import Callable
from typing import Any
... | poojakira/mcp-agent-security-gateway | src/mcp_monitor/production/circuit_breaker.py | .py | 6cd9324e8c626775 | 7.63 | 17 |
"""Configuration via environment variables (12-factor app).
All settings are read from os.environ with sensible defaults.
"""
from __future__ import annotations
import os
class Config:
"""Production configuration read from environment variables."""
def __init__(self) -> None:
self.listen_host: str... | poojakira/mcp-agent-security-gateway | src/mcp_monitor/production/config.py | .py | 9705c56012213e71 | 7.63 | 17 |
"""Structured JSON logging using stdlib logging module.
Produces ELK/Datadog-compatible JSON log entries with trace context.
"""
from __future__ import annotations
import json
import logging
import time
from typing import Any
class JSONFormatter(logging.Formatter):
"""Formats log records as JSON with trace con... | poojakira/mcp-agent-security-gateway | src/mcp_monitor/production/logging.py | .py | 591f97d858f7dc96 | 7.63 | 17 |
"""
Base class for diagnostic CLI to centralize common operations.
"""
from aqua.core.logger import log_configure
from aqua.core.util import get_arg
from aqua.core.version import __version__ as aqua_version
from .defaults import SAVE_FORMAT
from .util import close_cluster, load_diagnostic_config, merge_config_args, o... | DestinE-Climate-DT/AQUA-diagnostics | aqua/diagnostics/base/cli_base.py | .py | 3f02f0905dae9659 | 7.45 | 7 |
"""Module containing functions necessary to add metadata to different output formats."""
import os
import xml.etree.ElementTree as ET
from PIL import Image, PngImagePlugin
from pypdf import PdfReader, PdfWriter
from aqua.core.logger import log_configure
def add_pdf_metadata(pdf_path: str, metadata: dict, loglevel:... | DestinE-Climate-DT/AQUA-diagnostics | aqua/diagnostics/base/metadata.py | .py | c6892c13bcba6fab | 7.45 | 7 |
"""
String utility functions for AQUA diagnostics.
"""
import re
def collapse_era5_duplicate(text: str) -> str:
"""
ERA5 is catalogued with both model ('ERA5') and experiment ('era5'), which would
otherwise render as the duplicate 'ERA5 era5' in titles and captions.
Args:
text (str): Title o... | DestinE-Climate-DT/AQUA-diagnostics | aqua/diagnostics/base/strings.py | .py | 2f3de01a166f91a9 | 7.45 | 7 |
"""Time utilities for AQUA diagnostics"""
import pandas as pd
def start_end_dates(startdate=None, enddate=None, start_std=None, end_std=None):
"""
Evaluate start and end dates for data retrieve so Reader call covers
also the std-dates when set.
They should be of the form 'YYYY-MM-DD' or 'YYYYMMDD'.
... | DestinE-Climate-DT/AQUA-diagnostics | aqua/diagnostics/base/time_util.py | .py | 26247351ccc68271 | 7.45 | 7 |
"""
Title generation class and utilities for AQUA plots.
"""
from typing import Optional, Union
from aqua.core.util import strlist_to_phrase, to_list
from .strings import collapse_era5_duplicate, harmonize_lists
class TitleBuilder:
"""
Class to generate standardized titles for AQUA plots.
Args:
... | DestinE-Climate-DT/AQUA-diagnostics | aqua/diagnostics/base/title.py | .py | cccd24efff739362 | 7.45 | 7 |
"""
Utility functions for the CLI
"""
import argparse
import os
from dask.distributed import Client, LocalCluster
from aqua.core.configurer import ConfigPath
from aqua.core.logger import log_configure
from aqua.core.util import get_arg, load_yaml
def template_parse_arguments(parser: argparse.ArgumentParser):
"... | DestinE-Climate-DT/AQUA-diagnostics | aqua/diagnostics/base/util.py | .py | 7cbc543b711d9ca6 | 7.45 | 7 |
"""Command-line interface for Biases diagnostic."""
import argparse
import sys
from aqua.core.exceptions import NoDataError
from aqua.core.util import to_list
from aqua.diagnostics import Climatology, PlotBias
from aqua.diagnostics.base import DiagnosticCLI, template_parse_arguments
TOOLNAME = "Biases"
TOOLNAME_KEY ... | DestinE-Climate-DT/AQUA-diagnostics | aqua/diagnostics/biases/cli_biases.py | .py | 5a3da470c4f9b6bd | 7.45 | 7 |
"""Module for computing and plotting boxplots of field means from climate model datasets."""
import pandas as pd
import xarray as xr
from aqua.core.logger import log_configure
from aqua.core.util import to_list
from aqua.diagnostics.base import Diagnostic
class Boxplots(Diagnostic):
"""Class for computing and p... | DestinE-Climate-DT/AQUA-diagnostics | aqua/diagnostics/boxplots/boxplots.py | .py | 175bb2fd3ecc3d43 | 7.45 | 7 |
"""Command-line interface for Boxplots diagnostic."""
import argparse
import sys
from aqua.core.exceptions import NotEnoughDataError
from aqua.diagnostics import Boxplots, PlotBoxplots
from aqua.diagnostics.base import DiagnosticCLI, template_parse_arguments
# default tool name
TOOLNAME = "Boxplots"
TOOLNAME_KEY = T... | DestinE-Climate-DT/AQUA-diagnostics | aqua/diagnostics/boxplots/cli_boxplots.py | .py | 26d0669d3de559ab | 7.45 | 7 |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
AQUA ECmean4 Performance diagnostic CLI
"""
import argparse
import os
import sys
import xarray as xr
from ecmean import __version__ as eceversion
from aqua import Reader
from aqua import __version__ as aquaversion
from aqua.core.configurer import ConfigPath
from aqu... | DestinE-Climate-DT/AQUA-diagnostics | aqua/diagnostics/ecmean/cli_ecmean.py | .py | 01002fb3cbaedc6d | 7.45 | 7 |
# ruff: noqa: N999
import xarray as xr
from aqua.core.logger import log_configure
# from aqua.exceptions import NoDataError
from .base import BaseMixin
from .util import compute_statistics
xr.set_options(keep_attrs=True)
class EnsembleTimeseries(BaseMixin):
"""
This class computes mean and standard deviati... | DestinE-Climate-DT/AQUA-diagnostics | aqua/diagnostics/ensemble/ensembleTimeseries.py | .py | 9100d24fac2d3f09 | 7.45 | 7 |
"""
Utility functions for the ensemble class
"""
import gc
from collections import Counter
import numpy as np
import pandas as pd
import xarray as xr
from aqua import Reader
from aqua.core.configurer import ConfigPath
from aqua.core.exceptions import NoDataError
from aqua.core.logger import log_configure
def reade... | DestinE-Climate-DT/AQUA-diagnostics | aqua/diagnostics/ensemble/util.py | .py | 3d7e98103181faba | 7.45 | 7 |
#!/usr/bin/env python3
"""Command-line interface for Histogram diagnostic."""
import argparse
import sys
from aqua.diagnostics.base import DiagnosticCLI, load_var_config, template_parse_arguments
from aqua.diagnostics.histogram import Histogram, PlotHistogram
def parse_arguments(args):
"""Parse command-line arg... | DestinE-Climate-DT/AQUA-diagnostics | aqua/diagnostics/histogram/cli_histogram.py | .py | a5b1447ef8c04d8d | 7.45 | 7 |
from aqua.core.fixer import EvaluateFormula
from aqua.core.histogram import histogram
from aqua.core.logger import log_configure
from aqua.diagnostics.base import Diagnostic
class Histogram(Diagnostic):
"""
Class to compute histograms and probability density functions (PDFs) of a variable
over a specified... | DestinE-Climate-DT/AQUA-diagnostics | aqua/diagnostics/histogram/histogram.py | .py | 1279a43638bfe849 | 7.45 | 7 |
from typing import Union
import matplotlib.pyplot as plt
from aqua.core.graphics import plot_histogram
from aqua.core.logger import log_configure
from aqua.core.util import DEFAULT_REALIZATION, time_to_string, to_list
from aqua.diagnostics.base import SAVE_FORMAT, OutputSaver, TitleBuilder, collapse_era5_duplicate
... | DestinE-Climate-DT/AQUA-diagnostics | aqua/diagnostics/histogram/plot_histogram.py | .py | e2faa71d228efb79 | 7.45 | 7 |
"""
Command-line interface for LatLonProfiles diagnostic.
This CLI allows to run the LatLonProfiles diagnostic for zonal or meridional profiles.
Details of the run are defined in a yaml configuration file for a
single or multiple experiments.
"""
import argparse
import sys
from aqua.core.exceptions import NotEnoughD... | DestinE-Climate-DT/AQUA-diagnostics | aqua/diagnostics/lat_lon_profiles/cli_lat_lon_profiles.py | .py | 2bbdffcf8182f55b | 7.45 | 7 |
#!/usr/bin/env python3
"""Command-line interface for Ocean drift diagnostic.
This CLI allows to run the hovmoller, OceanDrift diagnostics.
Details of the run are defined in a yaml configuration file for a
single or multiple experiments.
"""
import argparse
import sys
from aqua.core.util import to_list
from aqua.diag... | DestinE-Climate-DT/AQUA-diagnostics | aqua/diagnostics/ocean_drift/cli_ocean_drift.py | .py | bd94186791af020f | 7.45 | 7 |
import os
import importlib.util
from pathlib import Path
from fastapi import FastAPI
from fastapi.middleware.cors import CORSMiddleware
from sqlalchemy import text
from src.api.routes import auth, users, products, inventory, invoices, ledgers, company, payments, smtp, email as email_routes, shortcuts, invoice_series ... | nikhilb2/simple_invoicing | backend/app_main.py | .py | 9664e338d6403f83 | 7.5 | 9 |
"""
Add buyer/company snapshot columns to invoices
"""
from sqlalchemy import text
def up(conn) -> None:
columns = {
"buyer_id": "ALTER TABLE invoices ADD COLUMN buyer_id INTEGER",
"buyer_name": "ALTER TABLE invoices ADD COLUMN buyer_name VARCHAR",
"buyer_address": "ALTER TABLE invoices A... | nikhilb2/simple_invoicing | backend/migrations/20260101000001_add_buyer_company_to_invoices.py | .py | 1db3dda1ae2f7ab0 | 7.5 | 9 |
"""
Add extended fields to company_profiles
"""
from sqlalchemy import text
def up(conn) -> None:
columns = {
"currency_code": "ALTER TABLE company_profiles ADD COLUMN currency_code VARCHAR",
"email": "ALTER TABLE company_profiles ADD COLUMN email VARCHAR",
"website": "ALTER TABLE company... | nikhilb2/simple_invoicing | backend/migrations/20260101000002_add_extended_company_fields.py | .py | 1dae81007f2c3bda | 7.5 | 9 |
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