`uofa` CLI reference (v0.8.0)

Generated from uofa --help-all at 2026-05-06T23:49:46Z. 19 subcommands available.

Synopsis

uofa [--no-color] [--verbose] [--repo-root PATH] [--pack NAME] <command> [...]

Global flags inherited by every subcommand: --no-color, --verbose, --repo-root, --pack. See uofa --help for details.

Commands

uofa keygen

generate ed25519 keypair for signing

uofa keygen [-h] [--no-color] [--verbose] [--repo-root PATH]
                   [--pack NAME]
                   path

uofa sign

sign (or re-sign) a UofA file

uofa sign [-h] [--no-color] [--verbose] [--repo-root PATH]
                 [--pack NAME] --key KEY [--context CONTEXT] [--output OUTPUT]
                 file

Flag	Description
--key, -k	ed25519 private key (PEM)
--context, -c	JSON-LD context file
--output, -o	output path (default: overwrite input)

uofa verify

verify hash + ed25519 signature (C1 integrity)

uofa verify [-h] [--no-color] [--verbose] [--repo-root PATH]
                   [--pack NAME] [--pubkey PUBKEY] [--context CONTEXT]
                   file

Flag	Description
--pubkey	ed25519 public key (default: keys/research.pub)
--context, -c	JSON-LD context file

uofa shacl

validate against SHACL profiles (C2 completeness)

uofa shacl [-h] [--no-color] [--verbose] [--repo-root PATH]
                  [--pack NAME] [--raw] [--explain]
                  [--explain-functions EXPLAIN_FUNCTIONS]
                  [--explain-format {text,json,markdown,html}]
                  [--explain-backend {ollama,anthropic,openai,openai-compatible,bundled,mock}]
                  [--explain-model EXPLAIN_MODEL]
                  [--explain-base-url EXPLAIN_BASE_URL]
                  [--explain-max-items EXPLAIN_MAX_ITEMS] [--explain-no-cache]
                  file

Flag	Description
--raw	show raw pyshacl output instead of friendly messages
--explain	run the interpretation pipeline after the primary analysis
--explain-functions	comma-separated list of interpretation functions to run (values: explain, group, contextualize, cross, narrative). Default: all applicable for the command.
--explain-format {text, json, markdown, html}	output format for the interpretation block. Default: same as the command’s primary —format, falling back to text.
--explain-backend {ollama, anthropic, openai, openai-compatible, bundled, mock}	LLM backend for explain (overrides [llm] backend in uofa.toml)
--explain-model	model name on the chosen backend (overrides [llm] model)
--explain-base-url	base URL for openai-compatible backends
--explain-max-items	limit interpretation to top N items by severity
--explain-no-cache	bypass cached interpretation results

uofa rules

detect quality gaps with Jena rule engine (C3)

uofa rules [-h] [--no-color] [--verbose] [--repo-root PATH]
                  [--pack NAME] [--rules RULES] [--context CONTEXT] [--build]
                  [--raw] [--format {summary,turtle,ntriples,jsonld,json}]
                  [--output OUTPUT] [--explain]
                  [--explain-functions EXPLAIN_FUNCTIONS]
                  [--explain-format {text,json,markdown,html}]
                  [--explain-backend {ollama,anthropic,openai,openai-compatible,bundled,mock}]
                  [--explain-model EXPLAIN_MODEL]
                  [--explain-base-url EXPLAIN_BASE_URL]
                  [--explain-max-items EXPLAIN_MAX_ITEMS] [--explain-no-cache]
                  file

Flag	Description
--rules, -r	path to .rules file
--context, -c	JSON-LD context file
--build	auto-build the Jena JAR if missing
--raw	show raw output without coloring
--format, -f {summary, turtle, ntriples, jsonld, json}	output format (default: summary). ‘json’ is the parsed-firings shape suitable for snapshot tests; ‘jsonld’ is the raw RDF.
--output, -o	write reasoned output to a file (default: stdout)
--explain	run the interpretation pipeline after the primary analysis
--explain-functions	comma-separated list of interpretation functions to run (values: explain, group, contextualize, cross, narrative). Default: all applicable for the command.
--explain-format {text, json, markdown, html}	output format for the interpretation block. Default: same as the command’s primary —format, falling back to text.
--explain-backend {ollama, anthropic, openai, openai-compatible, bundled, mock}	LLM backend for explain (overrides [llm] backend in uofa.toml)
--explain-model	model name on the chosen backend (overrides [llm] model)
--explain-base-url	base URL for openai-compatible backends
--explain-max-items	limit interpretation to top N items by severity
--explain-no-cache	bypass cached interpretation results

uofa check

full pipeline: SHACL + integrity + rules (C1+C2+C3)

uofa check [-h] [--no-color] [--verbose] [--repo-root PATH]
                  [--pack NAME] [--pubkey PUBKEY] [--context CONTEXT]
                  [--rules RULES] [--skip-rules] [--build] [--oos | --no-oos]
                  [--derivations | --no-derivations] [--explain]
                  [--explain-functions EXPLAIN_FUNCTIONS]
                  [--explain-format {text,json,markdown,html}]
                  [--explain-backend {ollama,anthropic,openai,openai-compatible,bundled,mock}]
                  [--explain-model EXPLAIN_MODEL]
                  [--explain-base-url EXPLAIN_BASE_URL]
                  [--explain-max-items EXPLAIN_MAX_ITEMS] [--explain-no-cache]
                  file

Flag	Description
--pubkey	ed25519 public key
--context, -c	JSON-LD context file
--rules, -r	path to .rules file
--skip-rules	skip the Jena rule engine (no Java required)
--build	auto-build the Jena JAR if missing
--oos	force OOS rules on for this run, overriding pack config
--no-oos	force OOS rules off for this run, overriding pack config
--derivations	force derivation pre-pass on for this run, overriding pack config
--no-derivations	force derivation pre-pass off for this run, overriding pack config
--explain	run the interpretation pipeline after the primary analysis
--explain-functions	comma-separated list of interpretation functions to run (values: explain, group, contextualize, cross, narrative). Default: all applicable for the command.
--explain-format {text, json, markdown, html}	output format for the interpretation block. Default: same as the command’s primary —format, falling back to text.
--explain-backend {ollama, anthropic, openai, openai-compatible, bundled, mock}	LLM backend for explain (overrides [llm] backend in uofa.toml)
--explain-model	model name on the chosen backend (overrides [llm] model)
--explain-base-url	base URL for openai-compatible backends
--explain-max-items	limit interpretation to top N items by severity
--explain-no-cache	bypass cached interpretation results

uofa validate

validate all examples against SHACL profiles

uofa validate [-h] [--no-color] [--verbose] [--repo-root PATH]
                     [--pack NAME] [--dir DIR] [--verify] [--pubkey PUBKEY]

Flag	Description
--dir	directory to scan (default: all pack examples)
--verify	also verify hash + signature integrity on each file
--pubkey	ed25519 public key (default: keys/research.pub)

uofa init

scaffold a new UofA project (template + keys + uofa.toml)

uofa init [-h] [--no-color] [--verbose] [--repo-root PATH]
                 [--pack NAME] [--profile {minimal,complete}] [--dir DIR]
                 [--provider PROVIDER] [--model MODEL]
                 name

Flag	Description
--profile {minimal, complete}	starting profile (default: complete)
--dir	parent directory (default: cwd)
--provider	LLM provider for uofa extract (default: ollama)
--model	LLM model for uofa extract (default: llama3.2)

uofa diff

compare weakener profiles between two UofA files (COU divergence)

uofa diff [-h] [--no-color] [--verbose] [--repo-root PATH]
                 [--pack NAME] [--build] [--skip-rules] [--explain]
                 [--explain-functions EXPLAIN_FUNCTIONS]
                 [--explain-format {text,json,markdown,html}]
                 [--explain-backend {ollama,anthropic,openai,openai-compatible,bundled,mock}]
                 [--explain-model EXPLAIN_MODEL]
                 [--explain-base-url EXPLAIN_BASE_URL]
                 [--explain-max-items EXPLAIN_MAX_ITEMS] [--explain-no-cache]
                 file_a file_b

Flag	Description
--build	auto-build the Jena JAR if missing
--skip-rules	compare static hasWeakener arrays instead of running rules
--explain	run the interpretation pipeline after the primary analysis
--explain-functions	comma-separated list of interpretation functions to run (values: explain, group, contextualize, cross, narrative). Default: all applicable for the command.
--explain-format {text, json, markdown, html}	output format for the interpretation block. Default: same as the command’s primary —format, falling back to text.
--explain-backend {ollama, anthropic, openai, openai-compatible, bundled, mock}	LLM backend for explain (overrides [llm] backend in uofa.toml)
--explain-model	model name on the chosen backend (overrides [llm] model)
--explain-base-url	base URL for openai-compatible backends
--explain-max-items	limit interpretation to top N items by severity
--explain-no-cache	bypass cached interpretation results

uofa explain

interpret pre-existing structured output from rules/check/diff/shacl

uofa explain [-h] [--no-color] [--verbose] [--repo-root PATH]
                    [--pack NAME] (--from-file FROM_FILE | --from-stdin)
                    [--input-type {rules,check,diff,shacl}]
                    [--functions FUNCTIONS] [--format {text,json,markdown}]
                    [--max-items MAX_ITEMS] [--no-cache]
                    [--backend {ollama,anthropic,openai,openai-compatible,bundled,mock}]
                    [--model MODEL] [--base-url BASE_URL]

Flag	Description
--from-file	read structured output from FILE
--from-stdin	read structured output from stdin
--input-type {rules, check, diff, shacl}	override auto-detection of input type
--functions	comma-separated list of interpretation functions to run
--format {text, json, markdown}	output format (default: text)
--max-items	limit interpretation to top N items by severity
--no-cache	bypass cached interpretation results
--backend {ollama, anthropic, openai, openai-compatible, bundled, mock}	LLM backend (overrides [llm] backend in uofa.toml)
--model	model name on the chosen backend
--base-url	base URL for openai-compatible backends

uofa schema

generate JSON Schema or import constants from SHACL shapes

uofa schema [-h] [--no-color] [--verbose] [--repo-root PATH]
                   [--pack NAME] [--output OUTPUT] [--emit {json,python}]

Flag	Description
--output, -o	output path (default depends on —emit format)
--emit {json, python}	output format: json (JSON Schema, default) or python (import constants)

uofa packs

list and inspect installed domain packs

uofa packs [-h] [--no-color] [--verbose] [--repo-root PATH]
                  [--pack NAME] [--detail]
                  [name]

Flag	Description
--detail	show detailed pack information

uofa catalog

list all weakener patterns across active packs

uofa catalog [-h] [--no-color] [--verbose] [--repo-root PATH]
                    [--pack NAME] [--format {table,json,md}] [--all-packs]

Flag	Description
--format, -f {table, json, md}	output format (default: table)
--all-packs	enumerate patterns across every installed pack (overrides —pack). Use this for a complete catalog view; the default —pack=vv40 only surfaces core + vv40 patterns.

uofa migrate

migrate UofA files from v0.3 to v0.4

uofa migrate [-h] [--no-color] [--verbose] [--repo-root PATH]
                    [--pack NAME] [--from FROM_VER] [--to TO_VER] [--dry-run]
                    file

Flag	Description
--from	source version (default: v0.3)
--to	target version (default: v0.4)
--dry-run	print changes without modifying the file

uofa import

import an Excel workbook into a UofA JSON-LD file

uofa import [-h] [--no-color] [--verbose] [--repo-root PATH]
                   [--pack NAME] [--output OUTPUT] [--sign] [--key KEY]
                   [--check] [--profile {minimal,complete}]
                   [file]

Flag	Description
--output, -o	output path (default: same directory, .jsonld extension)
--sign	sign the output after generation
--key, -k	path to ed25519 private key (required with —sign, or auto-detected from project)
--check	run all quality gates on the output
--profile {minimal, complete}	override profile auto-detection

uofa extract

extract assessment data from evidence documents into an Excel template

uofa extract [-h] [--no-color] [--verbose] [--repo-root PATH]
                    [--pack NAME] [--model MODEL] [--output OUTPUT]
                    [--glob GLOB] [--thinking]
                    [--prompt-version PROMPT_VERSION]
                    [--extract-backend {ollama,anthropic,openai,openai-compatible,bundled,mock}]
                    [--extract-model EXTRACT_MODEL]
                    [--extract-base-url EXTRACT_BASE_URL]
                    [source ...]

Flag	Description
--model	legacy litellm model string (e.g. ‘ollama/qwen3.5:4b’). For new configs, prefer —extract-backend + —extract-model.
--output, -o	output Excel path (default: {source}-extracted.xlsx)
--glob	file filter pattern (e.g. ‘.pdf’ or ‘.pdf,*.docx’)
--thinking	enable thinking/reasoning mode (slower, may improve accuracy)
--prompt-version	tag for scoring log tracking (e.g. ‘v2-detailed’)
--extract-backend {ollama, anthropic, openai, openai-compatible, bundled, mock}	LLM backend for extract (overrides [llm] backend)
--extract-model	model name on the chosen backend (overrides [llm] model)
--extract-base-url	base URL for openai-compatible backends (e.g. Together AI, vLLM)

uofa adversarial

generate / orchestrate / classify synthetic credibility evidence packages

uofa adversarial [-h] [--no-color] [--verbose] [--repo-root PATH]
                        [--pack NAME]
                        {generate,run,analyze,prep-review,bundle,judge,triage,adjudicate}
                        ...

uofa setup

install or verify the LLM extract runtime (Ollama + qwen3.5:4b)

uofa setup [-h] [--no-color] [--verbose] [--repo-root PATH]
                  [--pack NAME] [--bundle BUNDLE]
                  [--create-bundle CREATE_BUNDLE] [--model MODEL]
                  [--port PORT] [--no-byo] [--yes] [--no-verify]
                  {verify,uninstall} ...

Flag	Description
--bundle	install from an offline bundle (REQ-DIST-004 air-gapped path)
--create-bundle	package the current install into a tar.gz for an offline machine
--model	model tag to pull (default: qwen3.5:4b)
--port	port for the managed Ollama daemon (default: 11434)
--no-byo	skip BYO Ollama detection; install a UofA-managed copy
--yes, -y	skip confirmation prompts (downloads, uninstall)
--no-verify	skip the post-install verify step

uofa demo

run the C1+C2+C3 pipeline against a bundled fixture (no setup needed)

uofa demo [-h] [--no-color] [--verbose] [--repo-root PATH]
                 [--pack NAME] [--no-passage] [--no-jsonld]

Flag	Description
--no-passage	skip printing the input passage (useful for piping)
--no-jsonld	skip printing the pre-computed JSON-LD