@ahmed-g-gad/apothem 0.1.1
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/CHANGELOG.md +60 -0
- package/LICENSE +21 -0
- package/LICENSES/MIT.txt +18 -0
- package/LICENSES/PSF-2.0.txt +47 -0
- package/README.md +549 -0
- package/bin/README.md +37 -0
- package/bin/apothem.mjs +78 -0
- package/package.json +75 -0
- package/pyproject.toml +347 -0
- package/src/apothem/README.md +52 -0
- package/src/apothem/__init__.py +66 -0
- package/src/apothem/__main__.py +28 -0
- package/src/apothem/_vendor/.keep +0 -0
- package/src/apothem/_vendor/__init__.py +25 -0
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- package/src/apothem/_vendor/attr.LICENSE +21 -0
- package/src/apothem/_vendor/attrs/__init__.py +72 -0
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- package/src/apothem/_vendor/attrs/setters.py +3 -0
- package/src/apothem/_vendor/attrs/validators.py +3 -0
- package/src/apothem/_vendor/attrs.LICENSE +21 -0
- package/src/apothem/_vendor/jsonschema/__init__.py +120 -0
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- package/src/apothem/_vendor/jsonschema/benchmarks/json_schema_test_suite.py +12 -0
- package/src/apothem/_vendor/jsonschema/benchmarks/nested_schemas.py +56 -0
- package/src/apothem/_vendor/jsonschema/benchmarks/subcomponents.py +42 -0
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- package/src/apothem/_vendor/jsonschema/exceptions.py +490 -0
- package/src/apothem/_vendor/jsonschema/protocols.py +230 -0
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- package/src/apothem/_vendor/jsonschema.LICENSE +19 -0
- package/src/apothem/_vendor/jsonschema_specifications/__init__.py +12 -0
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- package/src/apothem/_vendor/jsonschema_specifications/schemas/draft201909/vocabularies/applicator +56 -0
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- package/src/apothem/_vendor/jsonschema_specifications/schemas/draft3/metaschema.json +172 -0
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- package/src/apothem/_vendor/jsonschema_specifications/schemas/draft7/metaschema.json +166 -0
- package/src/apothem/_vendor/jsonschema_specifications.LICENSE +19 -0
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- package/src/apothem/_vendor/referencing.LICENSE +19 -0
- package/src/apothem/_vendor/rpds/__init__.py +251 -0
- package/src/apothem/_vendor/typing_extensions.LICENSE +279 -0
- package/src/apothem/_vendor/typing_extensions.py +4317 -0
- package/src/apothem/_vendor/vendor.txt +22 -0
- package/src/apothem/_vendor/yaml/__init__.py +389 -0
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- package/src/apothem/_vendor/yaml/constructor.py +748 -0
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- package/src/apothem/_vendor/yaml/dumper.py +61 -0
- package/src/apothem/_vendor/yaml/emitter.py +1137 -0
- package/src/apothem/_vendor/yaml/error.py +74 -0
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- package/src/apothem/agents/README.md +60 -0
- package/src/apothem/agents/codebase-explorer.md +91 -0
- package/src/apothem/agents/convention-auditor.md +93 -0
- package/src/apothem/agents/dependency-auditor.md +97 -0
- package/src/apothem/agents/fact-checker.md +84 -0
- package/src/apothem/agents/mcp-builder.md +86 -0
- package/src/apothem/agents/memory-auditor.md +93 -0
- package/src/apothem/agents/prompt-evaluator.md +87 -0
- package/src/apothem/agents/quality-gate.md +103 -0
- package/src/apothem/agents/refactor-surgeon.md +74 -0
- package/src/apothem/agents/research-scout.md +73 -0
- package/src/apothem/agents/security-scanner.md +83 -0
- package/src/apothem/agents/test-runner.md +84 -0
- package/src/apothem/audit/README.md +73 -0
- package/src/apothem/audit/_scan_lib.py +182 -0
- package/src/apothem/audit/analyze_graph.py +260 -0
- package/src/apothem/audit/build_capability_graph.py +607 -0
- package/src/apothem/audit/build_inventory.py +657 -0
- package/src/apothem/audit/build_plans_provenance.py +997 -0
- package/src/apothem/audit/check_links.py +389 -0
- package/src/apothem/audit/classify_artifacts.py +381 -0
- package/src/apothem/audit/deprecated-tokens.txt +10 -0
- package/src/apothem/audit/execute_plans_migration.py +491 -0
- package/src/apothem/audit/known-projects.txt +15 -0
- package/src/apothem/audit/render_capability_index.py +467 -0
- package/src/apothem/audit/render_inventory.py +405 -0
- package/src/apothem/audit/scan_ai_surfaces.py +1125 -0
- package/src/apothem/audit/scan_ai_surfaces_coarse.py +261 -0
- package/src/apothem/audit/scan_drift_features.py +143 -0
- package/src/apothem/audit/scan_frontmatter.py +293 -0
- package/src/apothem/audit/scan_header_coverage.py +1134 -0
- package/src/apothem/audit/scan_plan_leakage.py +540 -0
- package/src/apothem/audit/scan_plans_discipline.py +188 -0
- package/src/apothem/audit/scan_secrets_pii.py +245 -0
- package/src/apothem/audit/scan_stale_tokens.py +296 -0
- package/src/apothem/audit/synthesize_drift.py +205 -0
- package/src/apothem/benchmarks/README.md +33 -0
- package/src/apothem/benchmarks/__init__.py +3 -0
- package/src/apothem/benchmarks/bench_agents.py +63 -0
- package/src/apothem/benchmarks/bench_hooks.py +93 -0
- package/src/apothem/benchmarks/bench_install.py +58 -0
- package/src/apothem/benchmarks/bench_tests.py +93 -0
- package/src/apothem/benchmarks/bench_validate_ecosystem.py +84 -0
- package/src/apothem/cli/README.md +33 -0
- package/src/apothem/cli/__init__.py +229 -0
- package/src/apothem/cli/_cmd_completion.py +88 -0
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- package/src/apothem/cli/_common_flags.py +90 -0
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- package/src/apothem/cli/_json_formatter.py +21 -0
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- package/src/apothem/commands/research-sources.md +266 -0
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- package/src/apothem/skills/dependency-upgrade/SKILL.md +105 -0
- package/src/apothem/skills/dev-toolkit/SKILL.md +120 -0
- package/src/apothem/skills/diagram-authoring/SKILL.md +113 -0
- package/src/apothem/skills/document-authoring/SKILL.md +118 -0
- package/src/apothem/skills/ecosystem-audit/SKILL.md +108 -0
- package/src/apothem/skills/ecosystem-audit/references/audit-fortress.md +85 -0
- package/src/apothem/skills/ecosystem-audit/references/procedure.md +162 -0
- package/src/apothem/skills/eval-harness/SKILL.md +88 -0
- package/src/apothem/skills/incident-runbook/SKILL.md +92 -0
- package/src/apothem/skills/multi-source-research/SKILL.md +90 -0
- package/src/apothem/skills/plan-suite/SKILL.md +118 -0
- package/src/apothem/skills/plan-suite/master_template.md +1324 -0
- package/src/apothem/skills/projectify/SKILL.md +117 -0
- package/src/apothem/skills/prompt-engineering/SKILL.md +122 -0
- package/src/apothem/skills/refactor-extract/SKILL.md +85 -0
- package/src/apothem/skills/research-suite/SKILL.md +170 -0
- package/src/apothem/skills/research-suite/references/directory-structure.md +47 -0
- package/src/apothem/skills/research-suite/references/lifecycle.md +67 -0
- package/src/apothem/skills/research-suite/references/principal-investigator-framework.md +37 -0
- package/src/apothem/skills/research-suite/references/rigor-mandates.md +30 -0
- package/src/apothem/skills/research-suite/research_template.md +476 -0
- package/src/apothem/skills/secret-rotation/SKILL.md +87 -0
- package/src/apothem/skills/source-synthesis/SKILL.md +92 -0
- package/src/apothem/skills/surgical-guard/SKILL.md +118 -0
- package/src/apothem/skills/test-authoring/SKILL.md +85 -0
- package/src/apothem/skills/vuln-triage/SKILL.md +91 -0
- package/src/apothem/skills/workflow/SKILL.md +139 -0
- package/src/apothem/statuslines/README.md +26 -0
- package/src/apothem/statuslines/__init__.py +20 -0
- package/src/apothem/statuslines/conformity.json +5 -0
- package/src/apothem/statuslines/render.py +334 -0
- package/src/apothem/statuslines/statusline.md +50 -0
- package/src/apothem/templates/README.md +43 -0
- package/src/apothem/templates/agents-md-template.md +80 -0
- package/src/apothem/templates/consideration-log.md +39 -0
- package/src/apothem/templates/expertise-gap-log.md +56 -0
- package/src/apothem/templates/master-index-template.md +93 -0
- package/src/apothem/templates/potency-map.md +53 -0
- package/src/apothem/templates/preservation-audit.md +60 -0
- package/src/apothem/templates/question-resolution-audit.md +52 -0
- package/src/apothem/templates/trace-matrix-template.md +77 -0
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# SPDX-License-Identifier: MIT
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"""Walk every Markdown file and verify each link target is reachable.
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Why this scan exists. Cross-references decay silently as the corpus
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evolves: files move, sections get renamed, external sources rot, badge
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URLs shift. A broken internal link wastes the reader's attention; a
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broken external link erodes the author's credibility. The scan
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enumerates every Markdown link, classifies it, and verifies the target
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where verification is mechanical (internal paths, in-file anchors).
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What this scan covers. Three link forms:
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- ``[text](path/to/file.md)`` — Markdown inline link. Internal targets
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resolve relative to the source file's directory.
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- ``[text](path/to/file.md#anchor)`` — anchor link. Verifies both that
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the file exists and that a heading slugged to ``anchor`` is present.
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- ``<https://example.com/page>`` and ``[text](https://...)`` — external
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link. By default these are enumerated but NOT HTTP-checked; pass
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``--check-external`` to issue HEAD requests with timeout.
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What this scan reports per finding. ``file:line``, the link target as
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written, the resolution outcome (``broken-internal-path`` /
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``broken-internal-anchor`` / ``broken-external``), and a remediation
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hint pointing at the most likely fix (move the target back, update the
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link, or remove the dead reference).
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What this scan excludes. Links inside fenced code blocks (which
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document, rather than reference, link syntax). The ``link-allowlist.md``
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file at the repository root, when present, lists URL substrings that
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should be treated as known-flaky and skipped on the external-check pass.
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"""
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from __future__ import annotations
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import argparse
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import http.client
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import re
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import sys
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import urllib.request
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from dataclasses import asdict
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from datetime import datetime, timezone
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from pathlib import Path
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from typing import Any, Final
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from urllib.error import URLError
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sys.path.insert(0, str(Path(__file__).resolve().parent))
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from _scan_lib import (
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CONTENT_ROOT,
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NARRATIVE_CLASSES,
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SEVERITY_HIGH,
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SEVERITY_LOW,
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Hit,
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load_inventory,
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read_text_safely,
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)
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# Markdown inline link: `[text](target)` with optional title.
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_INLINE_LINK_RE = re.compile(
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r"\[(?P<text>[^\]\n]*?)\]\((?P<target>[^()\s]+(?:\([^)]*\))?)"
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r"(?:\s+\"[^\"]*\")?\)"
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)
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# Markdown autolink: `<https://example.com>` or `<email@example.com>`.
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_AUTOLINK_RE = re.compile(r"<((?:https?|ftp)://[^>\s]+)>")
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# Heading line: `## Heading text` capturing the depth and the text.
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_HEADING_RE = re.compile(r"^(#{1,6})\s+(.+?)\s*$")
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# Markdown anchor slug: lowercase letters / digits / hyphens; punctuation
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# is stripped; whitespace becomes a hyphen. The implementation follows
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# the GitHub-Flavored-Markdown convention used by the docs site, the
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# repository renderer, and most static-site generators in the corpus.
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_SLUG_STRIP_RE = re.compile(r"[^\w\s-]")
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_SLUG_SPACE_RE = re.compile(r"\s+")
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EXTERNAL_TIMEOUT_SECONDS: Final[float] = 8.0
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MARKDOWN_SUFFIXES: Final[frozenset[str]] = frozenset({".md", ".markdown"})
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def _slug_for_heading(text: str) -> str:
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"""Return the GitHub-Flavored-Markdown slug for a heading."""
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cleaned = _SLUG_STRIP_RE.sub("", text.strip().lower())
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return _SLUG_SPACE_RE.sub("-", cleaned).strip("-")
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def _collect_anchors(content: str) -> set[str]:
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"""Walk a Markdown document and return every available anchor slug."""
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anchors: set[str] = set()
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in_fence = False
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for line in content.splitlines():
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if line.lstrip().startswith("```"):
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in_fence = not in_fence
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continue
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if in_fence:
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continue
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match = _HEADING_RE.match(line)
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if match:
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anchors.add(_slug_for_heading(match.group(2)))
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return anchors
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def _load_allowlist(path: Path) -> list[str]:
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"""Parse the optional URL-substring allowlist."""
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if not path.exists():
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return []
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out: list[str] = []
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for raw in path.read_text(encoding="utf-8").splitlines():
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line = raw.strip()
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if not line or line.startswith("#"):
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continue
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out.append(line)
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return out
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def _is_external(target: str) -> bool:
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"""Return True for absolute http(s) targets and mailto links."""
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return (
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target.startswith("http://")
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or target.startswith("https://")
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or target.startswith("mailto:")
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)
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def _resolve_internal(
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source: Path, target: str, root: Path
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) -> tuple[Path | None, str | None]:
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"""Split ``target`` into ``(resolved-path, anchor)``.
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Returns ``(None, anchor)`` when the path part is empty (anchor-only
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link, e.g. ``[#section](#section)``); the caller resolves the anchor
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against ``source``.
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"""
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if "#" in target:
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path_part, anchor = target.split("#", 1)
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else:
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path_part, anchor = target, None
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if not path_part:
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return None, anchor
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base = source.parent
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if path_part.startswith("/"):
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resolved = root / path_part.lstrip("/")
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else:
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resolved = base / path_part
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return resolved.resolve(), anchor
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def _check_external(url: str, timeout: float) -> int | None:
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"""Issue a HEAD request and return the response status code, or
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``None`` on connection / timeout error."""
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# The audit context only ever issues HEAD against http(s) URLs the
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# Markdown corpus already cites; no scheme expansion happens here.
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request = urllib.request.Request( # noqa: S310 (audit context)
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url, method="HEAD"
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)
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request.add_header("User-Agent", "apothem-link-checker/0.1")
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try:
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with urllib.request.urlopen( # noqa: S310 (audit context) # nosec B310
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request, timeout=timeout
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) as resp:
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return resp.status
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except URLError:
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return None
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except (OSError, ValueError, http.client.HTTPException) as exc:
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# Concrete network/transport failure (SSL, socket timeout, malformed
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# URL, protocol error) — report the link as unreachable. Surface the
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# exception class to stderr so a genuine defect in the checker itself
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# is distinguishable from a true unreachable link; programming errors
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# (NameError/AttributeError/TypeError) deliberately propagate.
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print(f"link-check: {type(exc).__name__} probing {url}", file=sys.stderr)
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return None
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def _walk_links(content: str) -> list[tuple[int, str]]:
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"""Return ``(lineno, target)`` for every link in the document."""
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out: list[tuple[int, str]] = []
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in_fence = False
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for lineno, line in enumerate(content.splitlines(), start=1):
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if line.lstrip().startswith("```"):
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in_fence = not in_fence
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continue
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if in_fence:
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continue
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for match in _INLINE_LINK_RE.finditer(line):
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out.append((lineno, match.group("target")))
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for match in _AUTOLINK_RE.finditer(line):
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out.append((lineno, match.group(1)))
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return out
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def _check_internal(
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rel: str,
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source_path: Path,
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target: str,
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lineno: int,
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root: Path,
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anchor_cache: dict[Path, set[str]],
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self_anchors: set[str],
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) -> Hit | None:
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"""Verify an internal link; return a Hit on failure."""
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resolved, anchor = _resolve_internal(source_path, target, root)
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if resolved is None:
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if anchor and anchor not in self_anchors:
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return Hit(
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file=rel,
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line=lineno,
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signal=f"broken-internal-anchor: {target}",
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severity=SEVERITY_HIGH,
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remediation=(
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"Update the in-file anchor; the heading text it"
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" refers to was renamed or removed."
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),
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)
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return None
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if not resolved.exists():
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return Hit(
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file=rel,
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line=lineno,
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signal=f"broken-internal-path: {target}",
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severity=SEVERITY_HIGH,
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remediation=(
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"Update the link target to a path that exists; the"
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" referenced file was moved or removed."
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),
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)
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if anchor and resolved.suffix.lower() in MARKDOWN_SUFFIXES:
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if resolved not in anchor_cache:
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anchor_cache[resolved] = _collect_anchors(read_text_safely(resolved))
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if anchor not in anchor_cache[resolved]:
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return Hit(
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file=rel,
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line=lineno,
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signal=f"broken-internal-anchor: {target}",
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severity=SEVERITY_HIGH,
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remediation=(
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"Update the cross-file anchor; the heading text it"
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" refers to was renamed or removed."
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),
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)
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return None
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def _scan_record(
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record: dict[str, Any],
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root: Path,
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anchor_cache: dict[Path, set[str]],
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allowlist: list[str],
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check_external: bool,
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) -> tuple[list[Hit], int]:
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"""Walk a single Markdown record and return its hits + ext-checks."""
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rel = record["path"]
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if Path(rel).suffix.lower() not in MARKDOWN_SUFFIXES:
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return [], 0
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source_path = root / rel
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content = read_text_safely(source_path)
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if not content:
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return [], 0
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self_anchors = _collect_anchors(content)
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hits: list[Hit] = []
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external_checked = 0
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for lineno, target in _walk_links(content):
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if _is_external(target):
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if not check_external or target.startswith("mailto:"):
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continue
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if any(skip in target for skip in allowlist):
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continue
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external_checked += 1
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status = _check_external(target, EXTERNAL_TIMEOUT_SECONDS)
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if status is None or status >= 400:
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hits.append(
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Hit(
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file=rel,
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line=lineno,
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signal=(
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|
+
f"broken-external: {target}"
|
|
278
|
+
f" (status={status if status else 'no-response'})"
|
|
279
|
+
),
|
|
280
|
+
severity=SEVERITY_LOW,
|
|
281
|
+
remediation=(
|
|
282
|
+
"Verify the URL is still live; if rotated,"
|
|
283
|
+
" update the link or move the resource to a"
|
|
284
|
+
" permalinked alternative."
|
|
285
|
+
),
|
|
286
|
+
)
|
|
287
|
+
)
|
|
288
|
+
else:
|
|
289
|
+
hit = _check_internal(
|
|
290
|
+
rel,
|
|
291
|
+
source_path,
|
|
292
|
+
target,
|
|
293
|
+
lineno,
|
|
294
|
+
root,
|
|
295
|
+
anchor_cache,
|
|
296
|
+
self_anchors,
|
|
297
|
+
)
|
|
298
|
+
if hit:
|
|
299
|
+
hits.append(hit)
|
|
300
|
+
return hits, external_checked
|
|
301
|
+
|
|
302
|
+
|
|
303
|
+
def main(argv: list[str] | None = None) -> int:
|
|
304
|
+
parser = argparse.ArgumentParser(description=__doc__.splitlines()[0])
|
|
305
|
+
parser.add_argument(
|
|
306
|
+
"--inventory",
|
|
307
|
+
type=Path,
|
|
308
|
+
default=Path(".audit/inventory.json"),
|
|
309
|
+
)
|
|
310
|
+
parser.add_argument("--root", type=Path, default=CONTENT_ROOT)
|
|
311
|
+
parser.add_argument(
|
|
312
|
+
"--output",
|
|
313
|
+
type=Path,
|
|
314
|
+
default=Path(".audit/drift-broken-links.json"),
|
|
315
|
+
)
|
|
316
|
+
parser.add_argument(
|
|
317
|
+
"--allowlist",
|
|
318
|
+
type=Path,
|
|
319
|
+
default=Path("link-allowlist.md"),
|
|
320
|
+
help="Optional URL-substring allowlist for external checks",
|
|
321
|
+
)
|
|
322
|
+
parser.add_argument(
|
|
323
|
+
"--check-external",
|
|
324
|
+
action="store_true",
|
|
325
|
+
help=(
|
|
326
|
+
"Issue HTTP HEAD against external URLs (slow; off by default"
|
|
327
|
+
" to keep the scan deterministic and offline)"
|
|
328
|
+
),
|
|
329
|
+
)
|
|
330
|
+
args = parser.parse_args(argv)
|
|
331
|
+
|
|
332
|
+
if not args.inventory.exists():
|
|
333
|
+
print(
|
|
334
|
+
f"error: inventory not found at {args.inventory}",
|
|
335
|
+
file=sys.stderr,
|
|
336
|
+
)
|
|
337
|
+
return 1
|
|
338
|
+
|
|
339
|
+
records, sha = load_inventory(args.inventory)
|
|
340
|
+
allowlist = _load_allowlist(args.allowlist)
|
|
341
|
+
anchor_cache: dict[Path, set[str]] = {}
|
|
342
|
+
hits: list[Hit] = []
|
|
343
|
+
external_total = 0
|
|
344
|
+
md_total = 0
|
|
345
|
+
for record in records:
|
|
346
|
+
if record.get("class") not in NARRATIVE_CLASSES:
|
|
347
|
+
continue
|
|
348
|
+
if Path(record["path"]).suffix.lower() not in MARKDOWN_SUFFIXES:
|
|
349
|
+
continue
|
|
350
|
+
md_total += 1
|
|
351
|
+
record_hits, ext = _scan_record(
|
|
352
|
+
record,
|
|
353
|
+
args.root,
|
|
354
|
+
anchor_cache,
|
|
355
|
+
allowlist,
|
|
356
|
+
args.check_external,
|
|
357
|
+
)
|
|
358
|
+
hits.extend(record_hits)
|
|
359
|
+
external_total += ext
|
|
360
|
+
|
|
361
|
+
payload = {
|
|
362
|
+
"generated": datetime.now(timezone.utc).isoformat(),
|
|
363
|
+
"scanner": "check_links",
|
|
364
|
+
"inventory-source-sha256": sha,
|
|
365
|
+
"external-checked": external_total,
|
|
366
|
+
"external-check-enabled": args.check_external,
|
|
367
|
+
"markdown-files-scanned": md_total,
|
|
368
|
+
"hit-count": len(hits),
|
|
369
|
+
"hits": [asdict(h) for h in hits],
|
|
370
|
+
}
|
|
371
|
+
args.output.parent.mkdir(parents=True, exist_ok=True)
|
|
372
|
+
args.output.write_text(
|
|
373
|
+
__import__("json").dumps(payload, indent=2) + "\n",
|
|
374
|
+
encoding="utf-8",
|
|
375
|
+
)
|
|
376
|
+
by_signal: dict[str, int] = {}
|
|
377
|
+
for h in hits:
|
|
378
|
+
kind = h.signal.split(":", 1)[0]
|
|
379
|
+
by_signal[kind] = by_signal.get(kind, 0) + 1
|
|
380
|
+
summary = ", ".join(f"{k}={v}" for k, v in sorted(by_signal.items()))
|
|
381
|
+
print(
|
|
382
|
+
f"check_links: {len(hits)} hit(s) across {md_total} Markdown files"
|
|
383
|
+
f" [{summary or 'none'}]; external-checked={external_total}"
|
|
384
|
+
)
|
|
385
|
+
return 0
|
|
386
|
+
|
|
387
|
+
|
|
388
|
+
if __name__ == "__main__":
|
|
389
|
+
raise SystemExit(main())
|