Graph files are 42-70% larger on v2.0.2 than v2.0.0 for identical facts when written over many checkpoints #428

Summary

For the same facts, a graph written over many checkpoints comes out 42–70% larger on v2.0.2 than on v2.0.0. With a single checkpoint the file is byte-for-byte the same size on both versions, so the growth comes from repeated checkpoints. The only checkpoint change between those tags is #315's incremental index rebuild (12b1ec3, #402), so that is the likely cause. Not verified: that the re-split leaves index leaves partly filled.

Once written, the file is stable: further open/checkpoint/close cycles don't change it. So it is a density difference, not unbounded growth. No correctness impact was observed: identical fact sets and query results.

Standalone repro

import os, sys, json, tempfile
from minigraf import MiniGrafDb
p = os.path.join(tempfile.mkdtemp(), "g.graph")
for b in range(400):
    db = MiniGrafDb.open(p)
    facts = " ".join(f'[:e/b{b}-{i} :name "n{b}-{i}"] [:e/b{b}-{i} :n {b*10+i}]' for i in range(10))
    db.execute(f"(transact [{facts}])")
    del db   # drop runs a checkpoint
db = MiniGrafDb.open(p)
print(len(json.loads(db.execute("(query [:find ?e ?a ?v :where [?e ?a ?v]])"))["results"]))
db.checkpoint(); del db
print(os.path.getsize(p))

Downstream measurement

temporal_reasoning's full-history ingestion of its own repo (1,021 commits, ~1,200 handle drops and ~85 explicit checkpoints per run) wrote identical graphs on both versions: 38,643 facts, fact_audit divergence 0, in two runs each. The files differed:

• 352 MB on 2.0.0 vs 597 MB on 2.0.2 (+70%), in both repetitions.
• 5.0 MB vs 8.2 MB on a 151-commit slice.

Data: project-minigraf/temporal_reasoning evals/at_scale/results/239-minigraf-2.0.2-ab.json (the graph_bytes field).

Why it may matter beyond disk

• A checkpoint on v2.x still copies every index page. If a larger file means more index pages, then each later checkpoint and each checkpoint-on-drop costs more (feat(ffi): expose OpenOptions over UniFFI — the close-time checkpoint cannot be suppressed from Python #322 context).
• Downstream, handle-drop cost on 2.0.2 was too noisy across two runs (59% spread) to say whether perf: checkpoint() is O(graph size) and flat in dirty bytes — it rebuilds all four covering indexes every call #315's speedup is net positive after the size growth. Worth measuring here with the repro above.

Environment

• Linux x86_64, Python 3.14, PyPI wheels minigraf==2.0.0 and minigraf==2.0.2, in twin venvs with identical pip freeze apart from minigraf.