@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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"""Three-tier scalability classification for the ``/plan-<stage>`` pipeline.
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Implements the small / medium / large tier framework that governs a plan
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suite's validation cadence, indexing, and decomposition as it scales from a
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few dozen phases to thousands of tasks. The classifier is the executable basis
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the planning-pipeline commands consult at every stage; the prose framework it
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mirrors lives at ``rules/canonical-layout-reporting-tiers.md`` §7.
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The module is intentionally pure — classification and required-infrastructure
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enumeration take counts and return values, with no filesystem side effects — so
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the tier-transition behavior is deterministic and directly testable (the
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500-phase medium→large smoke test exercises these functions).
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"""
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from __future__ import annotations
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from enum import Enum
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class Tier(str, Enum):
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"""A plan suite's scalability tier.
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The string values are the canonical tier names used in suite metadata and
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in the ``/plan`` command's tier-classification reporting.
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"""
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SMALL = "small"
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MEDIUM = "medium"
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LARGE = "large"
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# Boundary thresholds per ``rules/canonical-layout-reporting-tiers.md`` §7.1.
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# A suite is medium at or above the lower boundary and large at or above the
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# upper boundary, evaluated independently on the phase-count and spec-count
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# dimensions; the more demanding dimension governs the suite's tier.
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SMALL_MEDIUM_PHASE_BOUNDARY = 50
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MEDIUM_LARGE_PHASE_BOUNDARY = 500
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SMALL_MEDIUM_SPEC_BOUNDARY = 100
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MEDIUM_LARGE_SPEC_BOUNDARY = 1000
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# A count within this fraction of a boundary is borderline and routes the
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# tier classification through structured inquiry rather than a silent pick.
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BORDERLINE_FRACTION = 0.10
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# Ordinal rank for tier comparison — the governing tier is the higher rank.
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_TIER_RANK: dict[Tier, int] = {Tier.SMALL: 0, Tier.MEDIUM: 1, Tier.LARGE: 2}
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def _dimension_tier(count: int, lower: int, upper: int) -> Tier:
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"""Classify a single dimension (phases or specs) against its boundaries.
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Args:
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count: The dimension's count (must be non-negative).
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lower: The small→medium boundary for this dimension.
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upper: The medium→large boundary for this dimension.
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Returns:
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``Tier.SMALL`` below ``lower``, ``Tier.MEDIUM`` in ``[lower, upper)``,
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``Tier.LARGE`` at or above ``upper``.
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Raises:
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ValueError: If ``count`` is negative.
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"""
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if count < 0:
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raise ValueError(f"count must be non-negative, got {count}")
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if count >= upper:
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return Tier.LARGE
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if count >= lower:
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return Tier.MEDIUM
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return Tier.SMALL
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def classify_tier(phase_count: int, spec_count: int) -> Tier:
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"""Classify a plan suite's scalability tier from its phase and spec counts.
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The governing tier is the higher of the phase-dimension tier and the
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spec-dimension tier: a suite with 40 phases but 1200 spec requirements is
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``large`` because its spec dimension demands large-tier infrastructure even
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though its phase dimension alone would read ``small``.
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Args:
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phase_count: The number of phases in the suite (non-negative).
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spec_count: The number of spec requirements in the suite (non-negative).
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Returns:
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The governing :class:`Tier`.
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Raises:
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ValueError: If either count is negative.
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"""
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phase_tier = _dimension_tier(
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phase_count, SMALL_MEDIUM_PHASE_BOUNDARY, MEDIUM_LARGE_PHASE_BOUNDARY
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)
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spec_tier = _dimension_tier(
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spec_count, SMALL_MEDIUM_SPEC_BOUNDARY, MEDIUM_LARGE_SPEC_BOUNDARY
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)
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return phase_tier if _TIER_RANK[phase_tier] >= _TIER_RANK[spec_tier] else spec_tier
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def _within_borderline(count: int, boundary: int) -> bool:
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"""Return ``True`` when ``count`` is within ``BORDERLINE_FRACTION`` of ``boundary``."""
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margin = boundary * BORDERLINE_FRACTION
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return boundary - margin <= count <= boundary + margin
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def is_borderline(phase_count: int, spec_count: int) -> bool:
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"""Report whether a suite sits within ±10% of any tier boundary.
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A borderline suite's tier is underdetermined by the counts alone; the
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``/plan`` command routes such a suite through a tier-classification
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structured inquiry rather than silently picking a tier.
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Args:
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phase_count: The number of phases in the suite (non-negative).
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spec_count: The number of spec requirements in the suite (non-negative).
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Returns:
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``True`` when either count is within ±10% of either of its dimension's
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two boundaries.
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"""
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return any(
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(
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_within_borderline(phase_count, SMALL_MEDIUM_PHASE_BOUNDARY),
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_within_borderline(phase_count, MEDIUM_LARGE_PHASE_BOUNDARY),
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_within_borderline(spec_count, SMALL_MEDIUM_SPEC_BOUNDARY),
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_within_borderline(spec_count, MEDIUM_LARGE_SPEC_BOUNDARY),
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)
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)
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# Drift-prevention infrastructure each tier requires, per §7.2. Each higher
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# tier is a strict superset of the tier below it, so a transition's delta is the
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# set difference between the new and old tiers' infrastructure.
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_TIER_INFRASTRUCTURE: dict[Tier, frozenset[str]] = {
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Tier.SMALL: frozenset(
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{
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"trace-matrix-narrative", # narrative trace table in PLAN-NOTES.md
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"per-phase-report", # REPORT.md per phase
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}
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),
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Tier.MEDIUM: frozenset(
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{
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"trace-matrix-narrative",
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"per-phase-report",
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"master-index", # MASTER-INDEX.md suite-root index
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"stable-ids", # R-NNNN requirement / P-NN phase IDs
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"trace-matrix-file", # materialized TRACE-MATRIX.md
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"phase-rollup-report", # rollup per 5-20 phase group
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}
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),
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Tier.LARGE: frozenset(
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{
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"trace-matrix-narrative",
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"per-phase-report",
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"master-index",
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"stable-ids",
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"trace-matrix-file",
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"phase-rollup-report",
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"sub-suite-federation", # parent + child suite decomposition
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"suite-rollup-report", # federation aggregates child rollups
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}
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),
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}
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def tier_infrastructure(tier: Tier) -> frozenset[str]:
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"""Return the drift-prevention infrastructure a tier requires.
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Args:
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tier: The suite's tier.
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Returns:
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The frozen set of infrastructure-mechanism identifiers governing the
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tier per ``rules/canonical-layout-reporting-tiers.md`` §7.2.
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"""
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return _TIER_INFRASTRUCTURE[tier]
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def tier_transition_infrastructure(old: Tier, new: Tier) -> frozenset[str]:
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"""Enumerate the infrastructure a tier transition must materialize.
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When a suite crosses a tier boundary (e.g. its 500th phase pushes it from
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``medium`` to ``large``), the ``/plan`` command materializes the new tier's
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additional infrastructure in the same change-set so a 501-phase suite never
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exists without its large-tier surfaces. The delta is the infrastructure
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present in ``new`` but absent from ``old``.
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Args:
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old: The suite's tier before the transition.
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new: The suite's tier after the transition.
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Returns:
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The set of infrastructure-mechanism identifiers the transition must
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newly materialize. Empty when ``new`` does not exceed ``old``.
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"""
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if _TIER_RANK[new] <= _TIER_RANK[old]:
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return frozenset()
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return _TIER_INFRASTRUCTURE[new] - _TIER_INFRASTRUCTURE[old]
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# SPDX-License-Identifier: MIT
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"""Self-contained engine-import bootstrap for the bundled plugin tree.
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Why this module exists. The plugin-first distribution ships the apothem
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engine as a bundled copy under ``<plugin_root>/lib/apothem``: the bundled
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plugin tree imports the engine and its vendored dependencies directly
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from the tree, and no package installation occurs at any point. A harness
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that loads the plugin needs ``import apothem`` (and the alias ``import
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apothem_lib``) plus every vendored third-party dependency to resolve from
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the plugin tree. This module mutates ``sys.path`` so those imports
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succeed, and does so idempotently — calling it once per session boundary,
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or twice by accident, leaves ``sys.path`` in the same correct state.
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The self-containment invariant. Vendored dependencies under
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``lib/apothem/_vendor`` take precedence over any system-installed copy.
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``bootstrap_syspath`` prepends the vendor directory ahead of ``sys.path``
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so the bundled versions win the import resolution race.
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Public API. ``bootstrap_syspath`` performs the idempotent mutation;
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``bootstrapped_root`` returns the last root bootstrapped for diagnostics;
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``PluginBootstrapError`` is raised on a malformed plugin tree (missing
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``plugin_root`` or missing ``lib/``) — failing loud rather than silently
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importing a stale system copy.
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"""
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from __future__ import annotations
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import sys
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from pathlib import Path
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__all__ = [
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"PluginBootstrapError",
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"bootstrap_syspath",
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"bootstrapped_root",
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]
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class PluginBootstrapError(RuntimeError):
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"""Raised when the plugin tree is malformed and cannot be bootstrapped.
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The error message names the missing path so the operator can diagnose
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a malformed plugin without inspecting the bootstrap logic.
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"""
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# Module-level registry of already-bootstrapped roots. Membership here
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# guards against duplicate sys.path entries on repeated calls; the
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# resolved (absolute) path is the canonical key so two spellings of the
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# same root collapse to one entry.
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_BOOTSTRAPPED_ROOTS: set[Path] = set()
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# Diagnostics handle: the last root passed to bootstrap_syspath.
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_LAST_BOOTSTRAPPED_ROOT: Path | None = None
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def bootstrap_syspath(plugin_root: Path) -> None:
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"""Idempotently prepend the bundled engine to ``sys.path``.
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After this call, ``import apothem`` and ``import apothem_lib`` resolve
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from ``<plugin_root>/lib`` and any vendored third-party dependency
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resolves from ``<plugin_root>/lib/apothem/_vendor`` ahead of a
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system-installed copy — the plugin tree is self-contained.
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Pre-conditions:
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``plugin_root`` exists and contains a ``lib/`` directory.
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Post-conditions:
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``str(lib_dir)`` is present at ``sys.path[0]``. When the vendor
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directory exists, ``str(vendor_dir)`` is present at ``sys.path[0]``
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ahead of ``lib_dir`` (vendor precedence). Repeated calls add no
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duplicate entries.
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|
+
Args:
|
|
75
|
+
plugin_root: The plugin tree root containing ``.claude-plugin/``
|
|
76
|
+
and ``lib/``.
|
|
77
|
+
|
|
78
|
+
Raises:
|
|
79
|
+
PluginBootstrapError: If ``plugin_root`` does not exist, or if it
|
|
80
|
+
has no ``lib/`` directory. The message names the missing path.
|
|
81
|
+
"""
|
|
82
|
+
global _LAST_BOOTSTRAPPED_ROOT
|
|
83
|
+
|
|
84
|
+
resolved_root = plugin_root.resolve()
|
|
85
|
+
|
|
86
|
+
if not resolved_root.exists():
|
|
87
|
+
raise PluginBootstrapError(f"plugin_root does not exist: {resolved_root}")
|
|
88
|
+
|
|
89
|
+
lib_dir = resolved_root / "lib"
|
|
90
|
+
if not lib_dir.is_dir():
|
|
91
|
+
raise PluginBootstrapError(f"plugin_root has no lib/ directory: {lib_dir}")
|
|
92
|
+
|
|
93
|
+
_LAST_BOOTSTRAPPED_ROOT = resolved_root
|
|
94
|
+
|
|
95
|
+
# Idempotency short-circuit: a root already bootstrapped needs no
|
|
96
|
+
# further sys.path mutation. The path-membership checks below are a
|
|
97
|
+
# second line of defense against duplicates introduced out-of-band.
|
|
98
|
+
if resolved_root in _BOOTSTRAPPED_ROOTS:
|
|
99
|
+
return
|
|
100
|
+
|
|
101
|
+
vendor_dir = lib_dir / "apothem" / "_vendor"
|
|
102
|
+
|
|
103
|
+
# Prepend lib_dir first so it lands at sys.path[0]; the vendor
|
|
104
|
+
# prepend below then displaces it to sys.path[1], yielding the
|
|
105
|
+
# vendor-before-lib ordering the self-containment invariant requires.
|
|
106
|
+
_prepend_unique(str(lib_dir))
|
|
107
|
+
|
|
108
|
+
if vendor_dir.is_dir():
|
|
109
|
+
_prepend_unique(str(vendor_dir))
|
|
110
|
+
|
|
111
|
+
_BOOTSTRAPPED_ROOTS.add(resolved_root)
|
|
112
|
+
|
|
113
|
+
|
|
114
|
+
def bootstrapped_root() -> Path | None:
|
|
115
|
+
"""Return the last root passed to ``bootstrap_syspath``.
|
|
116
|
+
|
|
117
|
+
Returns:
|
|
118
|
+
The resolved path of the most recently bootstrapped plugin root,
|
|
119
|
+
or ``None`` if ``bootstrap_syspath`` has not yet succeeded past
|
|
120
|
+
its validation gate.
|
|
121
|
+
"""
|
|
122
|
+
return _LAST_BOOTSTRAPPED_ROOT
|
|
123
|
+
|
|
124
|
+
|
|
125
|
+
def _prepend_unique(entry: str) -> None:
|
|
126
|
+
"""Prepend ``entry`` to ``sys.path[0]`` only if not already present.
|
|
127
|
+
|
|
128
|
+
Args:
|
|
129
|
+
entry: The ``sys.path`` entry to prepend.
|
|
130
|
+
"""
|
|
131
|
+
if entry not in sys.path:
|
|
132
|
+
sys.path.insert(0, entry)
|