@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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"""Flag magic numbers in source code.
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Why this enforcement exists. The code-craft rule M13.10 forbids unnamed
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numeric literals in business logic — every threshold, retry count, or
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buffer size that varies by behavior is a named constant. Inline literals
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hide intent, fragment the configuration surface, and resist tuning. The
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pre-emission gate's mechanical bar 13 (M13.10 code craft) catches numeric literals appearing
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in logical contexts and surfaces each so the operator either names the
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constant or exempts it (see exemption list below).
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Detection strategy. The grep walks Python source, locates every numeric
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literal not in an exempt context, and reports duplicates within a single
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file (two or more occurrences of the same value strongly indicate the
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literal should be a named constant). Exemptions: the integers 0, 1, -1, 2
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(idiomatic boundary values — 0, 1, -1 are sentinel and index bounds; 2 is
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the binary/pairwise constant — matching the `EXEMPT_VALUES` frozenset
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below); literals inside type annotations / default-
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argument constants of `Final` form; literals inside `__all__` and
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similar metadata. The threshold (literal must appear at least
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`MIN_OCCURRENCES_FOR_FINDING` times in a file) is a named constant.
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"""
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from __future__ import annotations
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import re
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import sys
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from collections import defaultdict
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from dataclasses import dataclass
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from pathlib import Path
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from typing import Final
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from apothem.conformity._grep_base import GrepResult, run_grep
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# Numeric literals: int, float, hex, binary, octal, scientific. Excludes
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# numbers attached to identifier names (e.g., `var1`) via word-boundary.
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NUMERIC_LITERAL_RE: Final[re.Pattern[str]] = re.compile(
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r"(?<![A-Za-z_0-9])-?\d+(?:\.\d+)?(?:[eE][+-]?\d+)?"
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)
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# Idiomatic boundary values that are exempt from the magic-number rule
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# even when repeated (loop bounds, list indices, sentinel returns).
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EXEMPT_VALUES: Final[frozenset[str]] = frozenset({"0", "1", "-1", "2"})
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# Literals appearing only on lines that look like assignments to a
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# constant-named target (UPPER_SNAKE_CASE) or a `Final` annotation are
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# already named — exempt those lines.
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NAMED_CONSTANT_LINE_RE: Final[re.Pattern[str]] = re.compile(
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r"^\s*[A-Z][A-Z0-9_]*\s*(?::\s*Final\b[^=]*)?\s*="
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)
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# Comment lines (Python `#`) are excluded since they may quote sample
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# values that are not load-bearing.
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COMMENT_LINE_RE: Final[re.Pattern[str]] = re.compile(r"^\s*#")
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# String-literal exclusion: a number inside a quoted string is a value
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# in a data context, not a logic literal. The conservative regex below
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# strips single- and double-quoted spans before matching.
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STRING_SPAN_RE: Final[re.Pattern[str]] = re.compile(
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r"'(?:\\.|[^'\\])*'|\"(?:\\.|[^\"\\])*\""
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)
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# Triple-quoted span exclusion: module / class / function docstrings and
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# any other triple-quoted block live in a documentation context, not a
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# logic context. The single-line STRING_SPAN_RE above does not catch
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# them because triple-quoted spans cross line boundaries. The regex
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# below matches a non-greedy run between matched triple-quote delimiters
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# (single- or double-quote variants) across newlines via [\s\S]; the
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# stripping helper preserves line breaks so finding line numbers remain
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# stable against the original source.
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TRIPLE_QUOTED_SPAN_RE: Final[re.Pattern[str]] = re.compile(
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r"'''[\s\S]*?'''|\"\"\"[\s\S]*?\"\"\""
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)
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# Minimum repeat count that triggers a finding. A single literal use
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# rarely warrants a named constant; two or more uses of the same value
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# is the canonical magic-number signal.
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MIN_OCCURRENCES_FOR_FINDING: Final[int] = 2
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# Documentation file suffixes excluded from the magic-number sweep.
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# M13.10 is a code-craft rule scoped to source-language artifacts;
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# Markdown / reST / plain-text files carry list indices, dates, version
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# pins, and other numerals that are values in a documentation context,
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# not logic literals. The exclusion mirrors the rule's semantic scope
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# (the docstring already declares "walks Python source"). Configuration
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# files (JSON / YAML / TOML) carry values by definition and are
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# similarly exempt.
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NON_CODE_SUFFIXES: Final[frozenset[str]] = frozenset(
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{
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".md",
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".markdown",
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".rst",
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".txt",
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".json",
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".yaml",
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".yml",
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".toml",
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}
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)
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# Documentation / data-manifest basenames excluded from the magic-number
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# sweep where the file carries no recognized suffix. Mirrors the
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# NON_CODE_SUFFIXES rationale: numerals are values in a manifest context,
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# not logic literals.
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NON_CODE_BASENAMES: Final[frozenset[str]] = frozenset(
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{
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".SRCINFO",
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}
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)
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GREP_NAME: Final[str] = "magic-number-grep"
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RULE_ANCHOR: Final[str] = "M13.10 magic numbers"
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EXIT_PASS: Final[int] = 0
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EXIT_FAIL: Final[int] = 2
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STDIN_FLAG: Final[str] = "--stdin"
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@dataclass(frozen=True)
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class Finding:
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value: str
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occurrences: list[int]
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rule: str = RULE_ANCHOR
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def _strip_strings_and_comments(line: str) -> str:
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"""Remove quoted string spans; return empty if the line is a comment."""
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if COMMENT_LINE_RE.match(line):
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return ""
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return STRING_SPAN_RE.sub("", line)
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def _strip_triple_quoted_spans(content: str) -> str:
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"""Remove triple-quoted spans, preserving line breaks for stable line numbers.
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Replaces every triple-quoted span with a string of newlines equal to
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the number of newlines the span covered, so line indices in the
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post-strip content align with line indices in the original source.
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"""
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return TRIPLE_QUOTED_SPAN_RE.sub(
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lambda m: "\n" * m.group().count("\n"),
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content,
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)
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def check(content: str, path: Path | None = None) -> GrepResult:
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"""Scan content; return a structured result.
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Documentation and configuration-file suffixes (per ``NON_CODE_SUFFIXES``)
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are exempt — the rule scopes to source-language artifacts; numerals
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appearing in documentation indices, dates, version pins, and config
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values are values in a non-code context, not logic literals.
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Triple-quoted spans (module / class / function docstrings, multi-line
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string literals) are stripped before line iteration so numerals in
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documentation prose do not surface as logic-literal findings.
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"""
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if path is not None and (
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path.suffix.lower() in NON_CODE_SUFFIXES or path.name in NON_CODE_BASENAMES
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):
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return GrepResult(grep=GREP_NAME, path=str(path), passed=True)
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content = _strip_triple_quoted_spans(content)
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occurrences: dict[str, list[int]] = defaultdict(list)
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for index, raw_line in enumerate(content.splitlines(), start=1):
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if NAMED_CONSTANT_LINE_RE.match(raw_line):
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continue
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cleaned = _strip_strings_and_comments(raw_line)
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for match in NUMERIC_LITERAL_RE.finditer(cleaned):
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value = match.group()
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if value in EXEMPT_VALUES:
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continue
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occurrences[value].append(index)
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findings: list[Finding] = [
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Finding(value=value, occurrences=lines)
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for value, lines in sorted(occurrences.items())
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if len(lines) >= MIN_OCCURRENCES_FOR_FINDING
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]
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return GrepResult(
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grep=GREP_NAME,
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path=str(path) if path is not None else None,
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passed=not findings,
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findings=findings,
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)
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if __name__ == "__main__":
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sys.exit(run_grep(check, sys.argv))
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