Public reference

Command help is authoritative for option spelling. review capabilities is authoritative for machine negotiation. Only the namespaces and commands named here are public contracts.

Installation and process surface

• Python 3.10 or later.
• Baseline: pip install anatomize.
• Optional MCP: pip install 'anatomize[mcp]'.
• Executable: anatomize.
• Root commands: review and mcp.
• Version: anatomize --version.

There is no repository configuration file, implicit plugin discovery, network acquisition, or environment-based provider command. Roots, artifacts, included source, budgets, and output paths are explicit arguments.

Review commands

Command	Stable purpose
review capabilities	Advertise operations, profiles, target kinds, schemas, pagination, output, and provider policy.
review state ROOT	Fingerprint the exact review source without building semantic evidence.
review start ROOT	Build one exact portable session from baseline facts and explicitly supplied artifacts.
review dossier SESSION [TARGETS...]	Build a bounded role-labelled answer for one lifecycle profile and question.
review expand SESSION EXCHANGE ACTION	Apply one source-bound advertised expansion without mutating the base exchange.
review similarity SESSION	Project conservative implementation, test, and documentation candidates.
review change BEFORE AFTER	Compare two exact states of one repository.
review consolidate EXCHANGE SIMILARITY CANDIDATE	Gather the evidence needed to decide whether one candidate should be merged.
review overlay-create SESSION SIMILARITY CANDIDATE	Record a portable decision, owner, and rationale without changing the evidence.
review overlay-check OVERLAY SESSION SIMILARITY CANDIDATE	Evaluate decision currency against relevant current evidence.
review intent SESSION EXCHANGE OBLIGATIONS	Bind explicit implementation obligations to the before-state.
review verify INTENT AFTER OBSERVATIONS	Account for every obligation against fresh after-state evidence.
review export ARTIFACT	Validate and render a supported artifact as JSON, plain text, or Markdown.
review check ARTIFACT	Validate schema, identity, digest, state, and references without mutation.
review recover STORE	Render the current or immediately prior valid immutable session generation.

Machine operation names are capabilities, source_state, start, dossier, expand, similarity, change, consolidation, decision_overlay, evaluate_overlay, implementation_intent, verify, check, export, and recover.

Profiles are orientation, design, audit, localisation, implementation, change_review, and closure.

Target kinds are repository, file, symbol, range, documentation_section, test, configuration, data, workflow, artifact, diagnostic, duplicate_candidate, revision, and external_dependency.

--format accepts text, json, or markdown where advertised. --width has a minimum of 40. --output writes only after the artifact and rendering validate.

Orientation and repository-wide design, audit, change_review, and closure requests may omit positional targets; the application binds the repository entity explicitly. localisation and implementation require an exact target.

Review start inputs

review start accepts:

• repeated --provider PATH values containing current ProviderEnvelope JSON;
• repeated --artifact KIND[@VERSION]=PATH native artifacts;
• repeated exact --include-source PATH values;
• repeated --test-selection values and an optional SHA-256 --environment-digest for runtime evidence; and
• optional --store PATH for immutable generations and recovery.

Artifact kinds are sarif, lsp, junit, coverage, mutation, jscpd, snakemake, targets, renv, cyclonedx, and ro-crate.

Python API

The stable high-level API is in anatomize.review:

from pathlib import Path

from anatomize.dossiers import DossierProfile
from anatomize.review import ReviewApplication, ReviewOutputFormat, render_review

application = ReviewApplication()
session = application.start(Path("."), repository_id="repository:example")
dossier = application.dossier(session, profile=DossierProfile.ORIENTATION)
print(render_review(dossier, format=ReviewOutputFormat.TEXT))

Use the models' enum values and typed helper builders for non-trivial calls; the CLI is simpler for an independently released agent. The package root anatomize exports only __version__.

Lower-level public ownership is:

Namespace	Ownership
anatomize.index	Deterministic baseline RepositoryIndex and build_repository_index.
anatomize.evidence	Canonical entities, edges, contracts, observations, candidates, conflicts, completeness, omissions, aliases, lineage, merge, parse, and write.
anatomize.identity	Portable identity keys, coordinate conversion, and cross-provider claim reconciliation.
anatomize.providers	Advanced contract for normalising saved results from another analysis tool.
anatomize.sessions	Portable session manifests/bundles and recoverable immutable stores.
anatomize.dossiers	Targets, profiles, roles, requests, budgets, deterministic selection, slicing, cursors, and expansion.
anatomize.temporal	Exact state manifests, evidence-wide comparisons, deltas, validation, and exact lineage.
anatomize.lifecycle	Similarity, consolidation, decision overlays, test evidence, implementation intent, change, and closure.
anatomize.semantic	Captured LSP semantic artifact model and normalisation.
anatomize.diagnostics	Bounded SARIF 2.1.0 model and normalisation.
anatomize.research	R, notebook, execution, workflow, environment, data, dependency, and provenance evidence.
anatomize.review	The stateless application shared by CLI and MCP, artifact gateway, rendering, and capability negotiation.

Names absent from a namespace's __all__ are implementation details.

Current schemas

The generated capability table is derived from review capabilities, and the generated schema catalogue contains downloadable JSON Schemas for the current operation artifacts. This keeps exact capability names and versions reviewable without maintaining a second hand-written inventory.

Provider envelopes, repository comparisons, dossier requests and cursors, captured LSP semantics, test intent and runtime, R evidence, notebook evidence and execution, research graphs, and review artifacts also use exact current schemas. SARIF input is 2.1.0.

There is no migration layer. Old, incomplete, malformed, and unknown future artifacts fail with regeneration guidance. Never hand-edit an identity or schema version.

Errors and writes

All public domain failures derive from AnatomizeError, expose code, remediation, and exit_code, and are also ValueError instances. CLI failures print a concise code, message, and remedy without a traceback.

The ordinary success exit is 0; invalid invocation, input, schema, identity, state, or artifact uses 2. A valid incomplete or blocked lifecycle result may use 3, and a stale consumer decision may use 4. Consumers should classify the structured error or exit code, not parse prose.

Review writes are limited to requested --output artifacts and review start --store. No operation edits repository source. Store generations are immutable and the current pointer is replaced atomically under an advisory lock.

MCP

anatomize mcp [ROOT] serves the same review application. Default stdio is appropriate for a local host. streamable-http binds only to loopback and is not a hosted-service security boundary. Server operators select provider envelopes and included source paths explicitly. Inputs, outputs, and operation duration are bounded. See command help for the exact transport limits.

Output, privacy, and accessibility

Use canonical JSON for automation, Markdown for durable code review, and plain text for terminals. Human rendering uses labels as well as order, needs no colour or ANSI, and preserves conflicts, omissions, limitations, and recovery actions.

Sessions omit source text by default. --include-source is exact and opt-in. Artifact encodings protect structure, not trust: repository text and provider content remain untrusted and must never be executed as instructions.