SQLite concurrency bug

[VaishakRR]

multiple write operations are colliding inside the same database transaction. It's a bug in the tool itself. Not in the root of the project.

vaish@DESKTOP-GE9HT40:~/my-clone$ code-review-graph update
WARNING: Error parsing src/app/auth/invite/[token]/page.tsx: cannot start a transaction within a transaction
WARNING: Error parsing src/components/ui/tabs.tsx: cannot start a transaction within a transaction
WARNING: Error parsing src/components/ui/card.tsx: cannot start a transaction within a transaction
WARNING: Error parsing src/components/app/Pagination.tsx: cannot start a transaction within a transaction
WARNING: Error parsing prisma/seed.ts: cannot start a transaction within a transaction
..........
............

[Hemant-Mann]

I think the PR #94 handles this but not sure if this will be merged

on macos I faced issues in the library the fix was simple:

self._conn = sqlite3.connect(
str(self.db_path), timeout=30, check_same_thread=False, isolation_level=None
)

adding isolation_level=None

in graph.py

[tirth8205]

Same root cause as #135 — SQLite transaction nesting. PR #94 fixes the BEGIN IMMEDIATE guard to check in_transaction first. Tracking for the next release.

[tirth8205]

Same root cause as #135 — the SQLite BEGIN IMMEDIATE in store_file_nodes_edges conflicts with Python's sqlite3 auto-begun DEFERRED transaction from prior DELETE statements. Issue #135 was closed but has been reopened as the bug is still present in the current code.

The fix is a one-line check before BEGIN IMMEDIATE in graph.py:
if self._conn.in_transaction: self._conn.commit()