@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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"""Shared dataclasses, type aliases, constants, and leaf helpers for the install driver."""
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from __future__ import annotations
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import fnmatch
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from collections.abc import Callable
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from dataclasses import dataclass, field, replace
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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, Literal
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import apothem
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from apothem.harnesses._shared import install_driver
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IgnoreFn = Callable[[str, list[str]], list[str]]
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# Apothem source-package directory (e.g., src/apothem/ in dev installs).
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APOTHEM_SRC: Path = Path(apothem.__file__).resolve().parent
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BACKUP_ROOT: Path = Path.home() / ".apothem" / "backups"
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MaterializationOutcome = Literal[
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"created",
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"updated",
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"unchanged",
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"skipped",
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"warning",
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"error",
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]
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_OUTCOMES: tuple[MaterializationOutcome, ...] = (
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"created",
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"updated",
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"unchanged",
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"skipped",
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"warning",
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"error",
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)
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_INSTALL_ENTRY_MODES: tuple[str, ...] = (
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"write_text",
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"sentinel_merge",
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"replace_tree",
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"merge_tree_entries",
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"command_skills",
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"codex_agents",
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"gemini_agents",
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"opencode_agents",
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"qwen_agents",
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"gemini_commands",
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"markdown_commands",
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)
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#: Plain-language verb phrase for each operation kind. Preview surfaces (the
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#: ``diff`` command, any future dry-run preview) render these instead of the
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#: internal snake_case identifier so an operator reads an action, not a token.
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#: Kept beside the operation-kind definitions above so a newly-added kind gets
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#: its label in the same edit; a kind absent here falls back to a humanized
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#: form via :func:`operation_label`.
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OPERATION_LABELS: Final[dict[str, str]] = {
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"write_text": "Write file",
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"sentinel_merge": "Merge into file",
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"replace_tree": "Replace directory",
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"merge_tree_entries": "Merge directory",
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"command_skills": "Install skills",
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"codex_agents": "Install agents",
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"gemini_agents": "Install agents",
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"opencode_agents": "Install agents",
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"qwen_agents": "Install agents",
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"gemini_commands": "Install commands",
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"markdown_commands": "Install commands",
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"sweep_stale": "Prune stale files",
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"capability_projection": "Project capability",
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"data_surface": "Write data file",
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"surgical_uninstall": "Remove file",
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"remove_existing": "Replace existing target",
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"restore_backup": "Restore backup",
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"remove_data_home": "Remove data directory",
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}
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def operation_label(operation: str) -> str:
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"""Return the plain-language verb phrase for an *operation* kind.
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Falls back to a humanized form of the raw identifier (``snake_case`` to
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sentence case) for any kind absent from :data:`OPERATION_LABELS`, so a
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newly-added operation never surfaces its internal token to an operator.
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"""
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label = OPERATION_LABELS.get(operation)
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if label is not None:
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return label
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return operation.replace("_", " ").strip().capitalize() or operation
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def preview_status(operation: str, outcome: str, *, dry_run: bool) -> str:
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"""Translate a plan-result *outcome* into a coherent preview status word.
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A dry run writes nothing but computes the prospective outcome of each entry
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(``created`` / ``updated`` / ``unchanged``) by comparing source against the
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on-disk target. Two residual ``skipped`` cases remain: a stale-sweep target
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that exists (would be removed), and an operator-owned entry whose source is
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missing. This phrases each dry-run outcome as what ``apothem install``
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*would* do:
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- ``created`` / ``updated`` become ``would create`` / ``would update``.
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- ``unchanged`` becomes ``no change`` (nothing to do for this target).
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- ``skipped`` becomes ``would remove`` for a stale-sweep target and
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``would write`` otherwise.
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Outside a dry run the raw outcome is already coherent (``created`` /
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``updated`` / ``unchanged`` / ``error``) and is returned unchanged.
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"""
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if not dry_run:
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return outcome
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if outcome == "unchanged":
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return "no change"
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if outcome == "skipped":
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return "would remove" if operation == "sweep_stale" else "would write"
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if outcome == "created":
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return "would create"
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if outcome == "updated":
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return "would update"
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return outcome
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# Ownership classes whose write targets are refused outright: a manifest
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# entry pointing at a vendor-managed or append-only-record path is a defect,
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# not a gated operation (model §5.F hard refusal).
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_REFUSED_OWNERSHIP_CLASSES: frozenset[str] = frozenset({"vendor-reserved", "immutable"})
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@dataclass(frozen=True)
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class AuthorizationRequest:
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"""One operator-owned non-additive change awaiting authorization.
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Passed to an :data:`AuthorizeFn` before the propagation driver overwrites
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bytes in an operator-owned target. The ``diff`` is the unified diff the
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operator reviews; returning ``False`` skips the write and leaves the
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operator's file untouched (model §5 destructive-authorization gate).
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"""
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harness: str
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path: str
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operation: str
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ownership_class: str
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diff: str
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# An operator-supplied authorization gate. Returns ``True`` to proceed with
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# the backed-up overwrite, ``False`` to skip it. ``None`` (no callback) is the
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# non-interactive default: proceed with a backup, never silently lose operator
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# content without one (model §6 item 4).
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AuthorizeFn = Callable[[AuthorizationRequest], bool]
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@dataclass(frozen=True)
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class MaterializationResult:
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"""One structured materialization outcome."""
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outcome: MaterializationOutcome
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operation: str
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path: str
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message: str
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source: str | None = None
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backup_path: str | None = None
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detail: dict[str, str] = field(default_factory=dict)
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@property
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def changed(self) -> bool:
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"""Return True when this result represents an on-disk mutation."""
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return self.outcome in {"created", "updated"}
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def to_dict(self) -> dict[str, object]:
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"""Return a JSON-serializable representation."""
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payload: dict[str, object] = {
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"outcome": self.outcome,
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"operation": self.operation,
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"path": self.path,
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"message": self.message,
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}
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if self.source is not None:
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payload["source"] = self.source
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if self.backup_path is not None:
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payload["backup_path"] = self.backup_path
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if self.detail:
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payload["detail"] = dict(self.detail)
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return payload
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@dataclass(frozen=True)
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class MaterializationRun:
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"""Structured result set for one harness materialization pass."""
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harness: str
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dry_run: bool
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results: tuple[MaterializationResult, ...]
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@property
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def changed(self) -> bool:
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"""Return True when any result wrote, replaced, or removed content.
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A dry run writes nothing, so it is never ``changed`` — even though its
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per-result outcomes now carry the *prospective* ``created`` / ``updated``
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classification a real install would produce. The would-this-change
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signal lives on each result; this run-level flag reflects only actual
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on-disk mutation.
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"""
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if self.dry_run:
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return False
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return any(result.changed for result in self.results)
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@property
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def files_written(self) -> list[str]:
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"""Return paths with created or updated outcomes (empty for a dry run)."""
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if self.dry_run:
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return []
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return [result.path for result in self.results if result.changed]
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@property
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def warnings(self) -> list[MaterializationResult]:
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"""Return warning outcomes."""
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return [result for result in self.results if result.outcome == "warning"]
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@property
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def errors(self) -> list[MaterializationResult]:
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"""Return error outcomes."""
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return [result for result in self.results if result.outcome == "error"]
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@property
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def counts(self) -> dict[str, int]:
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"""Return deterministic per-outcome counts."""
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return {
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outcome: sum(1 for result in self.results if result.outcome == outcome)
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for outcome in _OUTCOMES
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}
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def extend(self, results: list[MaterializationResult]) -> MaterializationRun:
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"""Return a copy with additional results appended."""
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return MaterializationRun(
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harness=self.harness,
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dry_run=self.dry_run,
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results=(*self.results, *results),
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)
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def to_dict(self) -> dict[str, object]:
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"""Return a JSON-serializable representation."""
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return {
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"harness": self.harness,
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"dry_run": self.dry_run,
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"changed": self.changed,
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"files_written": self.files_written,
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"counts": self.counts,
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"results": [result.to_dict() for result in self.results],
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}
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class MaterializationError(ValueError):
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"""Raised when validation prevents a write pass from starting."""
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def __init__(self, message: str, run: MaterializationRun) -> None:
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super().__init__(message)
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self.run = run
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def resolve_source(source: str) -> Path:
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"""Resolve a manifest source-path (package-relative) to an on-disk path."""
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return install_driver.APOTHEM_SRC / source.rstrip("/")
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def _path_text(path: Path) -> str:
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"""Return a stable display path for result payloads."""
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return str(path)
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def _result(
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outcome: MaterializationOutcome,
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operation: str,
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path: Path,
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message: str,
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*,
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source: Path | None = None,
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backup_path: Path | None = None,
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detail: dict[str, str] | None = None,
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) -> MaterializationResult:
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"""Build one materialization result with normalized path strings."""
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return MaterializationResult(
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outcome=outcome,
|
|
289
|
+
operation=operation,
|
|
290
|
+
path=_path_text(path),
|
|
291
|
+
message=message,
|
|
292
|
+
source=_path_text(source) if source is not None else None,
|
|
293
|
+
backup_path=_path_text(backup_path) if backup_path is not None else None,
|
|
294
|
+
detail=dict(detail or {}),
|
|
295
|
+
)
|
|
296
|
+
|
|
297
|
+
|
|
298
|
+
def _handle_rm_error(
|
|
299
|
+
func: Callable[..., Any], path: str, exc_info: object
|
|
300
|
+
) -> None: # pragma: no cover
|
|
301
|
+
"""Best-effort error handler for ``shutil.rmtree`` — ignore stale handles."""
|
|
302
|
+
return
|
|
303
|
+
|
|
304
|
+
|
|
305
|
+
def _timestamp_slug() -> str:
|
|
306
|
+
"""Return the UTC timestamp slug used for backup directories."""
|
|
307
|
+
return datetime.now(timezone.utc).strftime("%Y%m%dT%H%M%SZ")
|
|
308
|
+
|
|
309
|
+
|
|
310
|
+
def _is_excluded_path(path: Path, exclude: list[str]) -> bool:
|
|
311
|
+
"""Return True when *path* is excluded by manifest basename globs."""
|
|
312
|
+
return any(fnmatch.fnmatch(path.name, pattern) for pattern in exclude)
|
|
313
|
+
|
|
314
|
+
|
|
315
|
+
# Sentinel marking a key that the Apothem-removal recursion has emptied out
|
|
316
|
+
# (every value it carried was an Apothem contribution). The caller drops the
|
|
317
|
+
# key entirely rather than leaving an empty container behind. Distinct object
|
|
318
|
+
# identity so it can never collide with a legitimate operator value.
|
|
319
|
+
_REMOVE_KEY: Final[object] = object()
|
|
320
|
+
|
|
321
|
+
|
|
322
|
+
def _with_detail(
|
|
323
|
+
result: MaterializationResult, extra: dict[str, str]
|
|
324
|
+
) -> MaterializationResult:
|
|
325
|
+
"""Return *result* with *extra* keys merged into its detail mapping."""
|
|
326
|
+
if not extra:
|
|
327
|
+
return result
|
|
328
|
+
merged = dict(result.detail)
|
|
329
|
+
merged.update(extra)
|
|
330
|
+
return replace(result, detail=merged)
|