# NousResearch/hermes-agent · SQLite backup staging path and exclusion fixes ## Open now - Nothing open on GitHub. A bug where SQLite DB snapshots were staged in /tmp (risking incomplete backups) is being addressed, along with fixes to stop incorrectly excluding nested hermes-agent skill directories during backup. Multiple related fix attempts appear across these members. ## TL;DR - 4 member(s): 0 open issue(s), 1 closed issue(s), 0 open PR(s), 1 merged PR(s), 2 PR(s) closed without merging. - A fix was merged to main in PR #44082. Verify it addresses your case. - **Recommended:** read PR #44082 (and any competing PRs below) before filing. Confirm the merged change covers your symptom. ## Maintainer resolution verdict - Internal-tracker verdict over this cluster's issue members: `resolved` · deciding PR(s): `pr-44082`. This is distinct from the fix status above. Weigh it yourself. ## How this cluster was grouped - Link evidence (`STRUCTURAL_SPANNING`): every member is connected by structural evidence: shared changed files, or a closing/superseded reference. - Pairwise link density `0.50`: the share of member pairs that carry a link, counting a structural link in full and a relevance-only link at 0.36. `1.00` means every pair is linked. ## Closed / duplicate issues - #35376: \[Bug\]: Hermes backup stages SQLite DB snapshots in /tmp, causing incomplete backups when state.db is large ## Prior & competing PRs - **#44082: fix(backup): stage SQLite snapshots beside output zip (all paths) and stop excluding nested hermes-agent skill dirs**. merged to main · fix tier `verified` - maintainer direction: category `merged` - files: `hermes_cli/backup.py`, `tests/hermes_cli/test_backup.py` - fix hunks: - `hermes_cli/backup.py` ```diff @@ -31,6 +31,9 @@ # --------------------------------------------------------------------------- # Directory names to skip entirely (matched against each path component) +# ``hermes-agent`` is special-cased to root level only in ``_should_exclude`` +# so that skill directories like ``skills/autonomous-ai-agents/hermes-agent/`` +# are not accidentally excluded. _EXCLUDED_DIRS = { "hermes-agent", # the codebase repo — re-clone instead "__pycache__", # bytecode caches — regenerated on import ``` ```diff @@ -69,10 +72,15 @@ def _should_exclude(rel_path: Path) -> bool: """Return True if *rel_path* (relative to hermes root) should be skipped.""" parts = rel_path.parts - # Any path component matches an excluded dir name for part in parts: - if part in _EXCLUDED_DIRS: - return True + if part not in _EXCLUDED_DIRS: + continue + # ``hermes-agent`` only matches at the root level (first component). + # Nested directories with the same name — e.g. + # ``skills/autonomous-ai-agents/hermes-agent/`` — must be preserved. + if part == "hermes-agent" and part != parts[0]: + continue + return True name = rel_path.name ``` ```diff @@ -177,10 +185,13 @@ def run_backup(args) -> None: rel_dir = dp.relative_to(hermes_root) # Prune excluded directories in-place so os.walk doesn't descend + # ``hermes-agent`` is only pruned at the root level; nested dirs + # with the same name (e.g. in skills/) must be preserved. + is_root = rel_dir == Path(".") orig_dirnames = dirnames[:] dirnames[:] = [ d for d in dirnames - if d not in _EXCLUDED_DIRS + if d not in _EXCLUDED_DIRS or (d == "hermes-agent" and not is_root) ] for removed in set(orig_dirnames) - set(dirnames): skipped_dirs.add(str(rel_dir / removed)) ``` ```diff @@ -211,7 +222,13 @@ def run_backup(args) -> None: try: # Safe copy for SQLite databases (handles WAL mode) if abs_path.suffix == ".db": - with tempfile.NamedTemporaryFile(suffix=".db", delete=False) as tmp: + # Stage the snapshot alongside the output zip so that the + # temp file lives on the same filesystem. The system + # default (/tmp) may be a small tmpfs that cannot hold + # large databases, causing silent backup incompleteness. + with tempfile.NamedTemporaryFile( + suffix=".db", delete=False, dir=str(out_path.parent) + ) as tmp: tmp_db = Path(tmp.name) if _safe_copy_db(abs_path, tmp_db): zf.write(tmp_db, arcname=str(rel_path)) ``` ```diff @@ -853,7 +870,13 @@ def _write_full_zip_backup(out_path: Path, hermes_root: Path) -> Optional[Path]: for abs_path, rel_path in files_to_add: try: if abs_path.suffix == ".db": - with tempfile.NamedTemporaryFile(suffix=".db", delete=False) as tmp: + # Stage the snapshot alongside the output zip so that the + # temp file lives on the same filesystem. The system + # default (/tmp) may be a small tmpfs that cannot hold + # large databases, causing silent backup incompleteness. + with tempfile.NamedTemporaryFile( + suffix=".db", delete=False, dir=str(out_path.parent) + ) as tmp: tmp_db = Path(tmp.name) try: if _safe_copy_db(abs_path, tmp_db): ``` - `tests/hermes_cli/test_backup.py` ```diff @@ -146,6 +146,12 @@ def test_includes_logs(self): from hermes_cli.backup import _should_exclude assert not _should_exclude(Path("logs/agent.log")) + def test_includes_nested_hermes_agent_in_skills(self): + """skills/autonomous-ai-agents/hermes-agent/ must NOT be excluded — + only the root-level hermes-agent/ repo is skipped.""" + from hermes_cli.backup import _should_exclude + assert not _should_exclude(Path("skills/autonomous-ai-agents/hermes-agent/SKILL.md")) + assert not _should_exclude(Path("skills/autonomous-ai-agents/hermes-agent/sub/item.txt")) # --------------------------------------------------------------------------- # Backup tests ``` ```diff @@ -186,6 +192,66 @@ def test_creates_zip(self, tmp_path, monkeypatch): # Skins assert "skins/cyber.yaml" in names + def test_db_snapshots_staged_beside_output_zip(self, tmp_path, monkeypatch): + """SQLite staging temp files must be created on the output zip's + filesystem (dir=out_path.parent), NOT the system /tmp default — a + small tmpfs there silently drops large DBs from the backup (#35376).""" + hermes_home = tmp_path / ".hermes" + hermes_home.mkdir() + _make_hermes_tree(hermes_home) + + monkeypatch.setenv("HERMES_HOME", str(hermes_home)) + monkeypatch.setattr(Path, "home", lambda: tmp_path) + + out_dir = tmp_path / "external-drive" + out_dir.mkdir() + out_zip = out_dir / "backup.zip" + args = Namespace(output=str(out_zip)) + + import hermes_cli.backup as backup_mod + staged_dirs = [] + real_ntf = backup_mod.tempfile.NamedTemporaryFile + + def _spy(*a, **kw): + staged_dirs.append(kw.get("dir")) + return real_ntf(*a, **kw) + + monkeypatch.setattr(backup_mod.tempfile, "NamedTemporaryFile", _spy) + backup_mod.run_backup(args) + + # At least one .db was staged, and every staging call targeted the + # output zip's directory rather than the system temp default. + assert staged_dirs, "no SQLite snapshot was staged" + assert all(d == str(out_dir) for d in staged_dirs), staged_dirs + + def test_pre_update_db_snapshots_staged_beside_output_zip(self, tmp_path, monkeypatch): + """The pre-update/pre-migration zip path (_write_full_zip_backup) must + also stage SQLite snapshots beside its output zip, not in /tmp.""" + hermes_home = tmp_path / ".hermes" + hermes_home.mkdir() + _make_hermes_tree(hermes_home) + + monkeypatch.setenv("HERMES_HOME", str(hermes_home)) + monkeypatch.setattr(Path, "home", lambda: tmp_path) + + out_zip = hermes_home / "backups" / "pre-update-test.zip" + out_zip.parent.mkdir(parents=True, exist_ok=True) + + import hermes_cli.backup as backup_mod + staged_dirs = [] + real_ntf = backup_mod.tempfile.NamedTemporaryFile + + def _spy(*a, **kw): + staged_dirs.append(kw.get("dir")) + return real_ntf(*a, **kw) + + monkeypatch.setattr(backup_mod.tempfile, "NamedTemporaryFile", _spy) + result = backup_mod._write_full_zip_backup(out_zip, hermes_home) + + assert result is not None + assert staged_dirs, "no SQLite snapshot was staged" + assert all(d == str(out_zip.parent) for d in staged_dirs), staged_dirs + def test_excludes_hermes_agent(self, tmp_path, monkeypatch): """Backup does NOT include hermes-agent/ directory.""" hermes_home = tmp_path / ".hermes" ``` ```diff @@ -206,6 +272,37 @@ def test_excludes_hermes_agent(self, tmp_path, monkeypatch): agent_files = [n for n in names if "hermes-agent" in n] assert agent_files == [], f"hermes-agent files leaked into backup: {agent_files}" + def test_includes_nested_hermes_agent_in_skills(self, tmp_path, monkeypatch): + """Backup includes skills/.../hermes-agent/ but NOT root hermes-agent/.""" + hermes_home = tmp_path / ".hermes" + hermes_home.mkdir() + _make_hermes_tree(hermes_home) + + # Add a nested hermes-agent directory inside skills (like the real layout) + nested = hermes_home / "skills" / "autonomous-ai-agents" / "hermes-agent" + nested.mkdir(parents=True) + (nested / "SKILL.md").write_text("# Hermes Agent Skill\n") + (nested / "sub").mkdir() + (nested / "sub" / "item.txt").write_text("nested content\n") + + monkeypatch.setenv("HERMES_HOME", str(hermes_home)) + monkeypatch.setattr(Path, "home", lambda: tmp_path) + + out_zip = tmp_path / "backup.zip" + args = Namespace(output=str(out_zip)) + + from hermes_cli.backup import run_backup + run_backup(args) + + with zipfile.ZipFile(out_zip, "r") as zf: + names = zf.namelist() + # Root hermes-agent must be excluded + root_agent = [n for n in names if n.startswith("hermes-agent/")] + assert root_agent == [], f"root hermes-agent leaked: {root_agent}" + # Nested skill hermes-agent must be included + assert "skills/autonomous-ai-agents/hermes-agent/SKILL.md" in names + assert "skills/autonomous-ai-agents/hermes-agent/sub/item.txt" in names + def test_excludes_pycache(self, tmp_path, monkeypatch): """Backup does NOT include __pycache__ dirs.""" hermes_home = tmp_path / ".hermes" ``` - **#35379: fix(backup): stage SQLite snapshots alongside output zip and stop excluding nested hermes-agent skill dirs**. closed without merge - maintainer direction: category `superseded_by_pr`; implication `superseded`; refs `#44082`, `#35376` - **#35496: fix: route SQLite backup staging files to HERMES_HOME/tmp**. closed without merge - maintainer direction: category `superseded_by_pr`; implication `superseded`; refs `#44082`, `#35376` ## Fix status - Merged to main in PR #44082 (cited above). No release data is tracked. Verify downstream. - Fix last verified (merged) `2026-06-11`.