isabelle-query

query is a command-line tool for querying an Isabelle/Isar project — its entries (definitions, lemmas, theorems, datatypes), call graph, theory dependencies, outstanding sorrys, dead code, and the shape of its proofs.

It parses the project's .thy sources on every invocation, so results always match the current tree: no Isabelle build, no proof replay. A large project parses in a fraction of a second, and the whole AFP in a couple of minutes. It is aimed at projects big enough that grep-and-examine has stopped working — AFP entries, the AFP itself, or industrial verification.

Pure Python. One runtime dependency, isabelle-layout — the ROOT and theory-header parser, split out so that reading an Isabelle project's structure does not require installing a CLI. pip fetches it for you.

News 2026-08-29: David Wang has ported isabelle-query to Scala which of course unlocks a bunch of new features since that improves integration with Isabelle.

Commands

query summary              # theory overview table (-S: corpus/session aggregate)
query theory MyTheory      # entries in a theory (-n for terse names)
query find <regex>         # search entry names (--statement: search statements; --and: all patterns)
query show <name>          # a named entry's declaration + body
query enclosing FILE:LINE  # which entry + proof block owns a line; inverse of outline
query callers <name> [-r]  # who references a name  (reverse; -r = transitive)
query callees <name> [-r]  # what a name references (forward)
query deps <theory> [-r]   # what a theory imports  (forward; reverse: uses)
query refs <theory>        # what a theory cites, by owning theory (citation-level)
query graph [citation|imports]  # the whole graph as JSON (-f dot for Graphviz)
query sorry                # outstanding sorry's
query unused               # dead-code / unused-entry analysis
query instances <name> [-r]  # where a locale/class is instantiated; -r walks the hierarchy
query codeqs <name>        # declared code-equation sites of a constant
query shape <view>         # proof-shape metrics (summary|steps|lemma|widest|census)

Every subcommand takes -h; query -h lists all 22.

Examples

Point query at any session directory with -R (or --root):

query -R AFP/thys largest                          # the biggest entries, by line count
query -R AFP/thys callers metric_domain_tfin_def   # every proof step that cites a fact
query -R AFP/thys find --statement tfin            # lemmas *stated about* tfin, whatever their name
query -R AFP/thys find --statement --and length tfin  # ...and mentioning length too (--and intersects)
query -R AFP/thys enclosing Tfin.thy:412           # the lemma and nearest proof block a build error sits in
query -R AFP/thys enclosing Tfin:88..140           # every entry a diff hunk touches
query -R AFP/thys grep simp Tfin.thy:88..140       # search just a hunk

Locations and spans share one grammar (theory:line, theory:A..B), so the tool's output is valid input: a locus from callers / sorry pastes into enclosing, and a span from outline / largest — or a proof block from enclosing's own drill-down (▸ have key 11..14) — pastes into lines.

A theory prints as its bare name, and only far enough qualified to name one theory. Over a corpus that matters: nineteen AFP theories are called Examples, so largest reports Virtual_Substitution/QE and enclosing takes it straight back. A name used once stays bare.

What it reads

Only live Isar text. A name in a comment, a \<comment> note, a text block or an ML body is not a citation, so it never invents a caller or hides a dead lemma — and a definition left behind in a comment is not an entry. Regions are found by a character-level scan, not by line, so by (simp add: foo) (* not bar *) keeps foo and drops bar.

Layout carries no meaning: Isar is whitespace-insensitive, so a declaration is recognised wherever a command can start, at any indentation and any block depth. Discovery loads what isabelle build compiles — each session's declared theories plus the closure of their in-entry imports.

See SCANNING.md for the details: locale scope, method names that collide with fact names, corpus aggregation, and the prose view.

Instantiation and code-equation sites

instances and codeqs report declared source sites, not the processed setup a prover's print_interps / print_codesetup shows. Rows have the form LOCUS NAME KIND source; a site whose source writes no name shows ?. --sorts adds only the sort, arity or signature written at the site, never an inferred type.

instances -r also lists the sites of everything that extends the subject — class X = NAME + …, locale X = … NAME …, subclass, instance X ⊆ NAME, sublocale — transitively, and adds a VIA column naming which of them each row writes. nat instantiates comm_monoid_diff, never ab_semigroup_add by name, so it appears only under -r. Without the flag the listing is the direct sites alone.

codeqs under-reports when mixfix notation hides the statement's head symbol: an equation of an operator ("Ratreal x + Ratreal y = ...", "xs @ ys = ...") names no constant at its head, and is not listed under the operator or under an operand. Check source with grep if an answer looks short. Neither verb separates same-named declarations that are both visible from one theory: a site is attributed to a declaration in that theory or its transitive imports within the scanned project, and declarations that live only in a heap are not discovered.

Proof-shape metrics

query shape measures the shape of individual proof steps — how big a step is, how deeply nested, how many facts it holds at once, how much is re-said, and how it is discharged. All source-level, no build.

query shape summary                  # per-theory aggregate table
query shape lemma <name>             # one proof: every step
query -R AFP/thys shape census       # per-proof JSONL over a whole corpus

See METRICS.md for the command reference, the metric table, and the JSONL record schema.

Exit status

0 the command ran; 1 the request could not be resolved (unknown theory, entry name or path, no subcommand); 2 bad usage — an argparse error, or a root that could not be read; 141 a write failed because a downstream reader closed the pipe (query shape census | head over a corpus), as a shell reports for SIGPIPE.

A diagnostic goes to stderr and stdout stays clean, so a count mode is always safe to capture. The two empty answers are different and say so:

$ query find zzz -c        # a real search that found nothing
0
$ echo $?
0
$ query callees zzz -c     # there is no entry `zzz` to have callees
query: 'zzz' is not in the entry index
$ echo $?
1

instances and codeqs exit 1 for a subject that is not a declared locale or class, respectively constant — a typo and a locale from an imported session would otherwise look exactly like one nobody instantiates — and 0 for a declared subject with no sites.

141 is not promised for every | head. When the whole answer fits the pipe buffer no write ever fails and the status is 0 — the same as seq 10 | head, where seq 200000 | head dies of SIGPIPE. The producer wrote everything; the reader chose to stop. Either way stderr stays silent and the status is deterministic.

A root that yields no theories is reported on stderr and never as an empty success, so a script can tell a broken run from an honestly empty one:

$ query -R /typo/path shape census
query: /typo/path: no such directory (given to -R/--root)
$ echo $?
2

Library API

The Isar span parsing is importable, for tools that want spans rather than a report — where a lemma starts and ends, where its text ‹…› preamble is, where its proof stops, which lines are comments or ML.

from pathlib import Path
from isabelle_query.api import parse_root, parse_theory

sec = parse_theory("Foo", Path("Foo.thy"))
for e in sec.entries:
    print(e.name, e.src_start, e.thy_end, e.proof_line, e.body_end_line)

isabelle_query.api exports exactly four names — parse_theory, parse_root, Entry, TheorySection — and they follow the same policy as the CLI: a change that breaks them takes the minor version slot, never a patch. Nothing else in the package is supported; import from isabelle_query.parsing and a patch release may move it.

Four rather than the dozen functions that look public, because their results are already fields on the two objects, and the hard part is the order the scanners run in — that composition is what parse_theory is. Use parse_root whenever the answer must match query -R: Isabelle's keyword table is session-wide, so a single theory parsed alone cannot see a custom command a sibling declares.

Installation

Requires Python 3.9 or greater. Installs the command on your PATH under two names — query, the short form used throughout these docs, and isabelle-query, matching the distribution — and pulls isabelle-layout from PyPI. They are the same program, and it reports whichever you typed, so isabelle-query -h documents isabelle-query.

pip install isabelle-query     # from PyPI
pip install .                  # from a checkout

An editable install, for working on the tool itself:

git clone https://github.com/ott2/isabelle-query
cd isabelle-query
python -m venv .venv && source .venv/bin/activate   # optional but recommended
pip install -e .

Documentation

file	what
SCANNING.md	how query reads a project — what counts as a declaration, a citation, and a session
METRICS.md	query shape command reference and metric definitions
CONTRIBUTING.md	the CLI contract and where design decisions are recorded

Authors & license

By András Salamon, with Claude Opus 4.6, 4.7, 4.8, 5, and 5.5. instances and codeqs by David Wang, with Claude Fable 5.1. MIT.