Main branch tests are failling

[georgesafta]

Describe the bug
The tests fail on the main branch

To Reproduce
Steps to reproduce the behavior:

1. uv sync --all-groups --all-extras
2. uv run pytest

Expected behavior
All tests pass

Logs

uv run pytest
============================================================================================== test session starts ==============================================================================================
platform linux -- Python 3.12.13, pytest-7.4.4, pluggy-1.6.0
rootdir: /root/projects/python/codeanalyzer-python
configfile: pyproject.toml
testpaths: test
plugins: cov-2.12.1, pspec-0.0.4, asyncio-0.14.0
collected 38 items

test/test_cli.py .F.FFFFFFFFFFF [ 36%]
test/test_neo4j_bolt.py ssss [ 47%]
test/test_neo4j_schema.py ...... [ 63%]
test/test_pycg_sharding.py ... [ 71%]
test/test_shard_planner.py ........... [100%]

============================================================================================ short test summary info ============================================================================================
FAILED test/test_cli.py::::Must be able to run the CLI with symbol table analysis. - AssertionError: CLI command should succeed
FAILED test/test_cli.py::::Must be able to run the CLI with single file analysis using --file-name flag. - AssertionError: CLI command should succeed. Output: [06/28/26 19:21:07] INFO (Re-)creating virtual environment at
FAILED test/test_cli.py::::Level 1 on decorators_and_hof: symbol table populated, call_graph has Jedi edges. - AssertionError: CLI failed (level 1):
FAILED test/test_cli.py::::Level 2 on decorators_and_hof: call_graph non-empty with PyCG edges.

 Key assertions:
 - At least 20 total edges (observed ~34)
 - PyCG resolves HOF points-to: apply->triple (missed by Jedi's single call-site inference)
 - PyCG finds closure call: log_call.wrapper->greet
 - AssertionError: CLI failed (level 2):
FAILED test/test_cli.py::::Level 1 on class_hierarchy: symbol table has classes and methods. - AssertionError: CLI failed (level 1):
FAILED test/test_cli.py::::Level 2 on class_hierarchy: PyCG resolves virtual dispatch and super() calls.

 Key assertions:
 - At least 30 total edges (observed ~51)
 - PyCG finds virtual dispatch: Animal.describe->PoliceDog.speak
 - PyCG finds super().__init__ chains (present as super edges)
 - __init__ edges present from constructor calls
 - AssertionError: CLI failed (level 2):
FAILED test/test_cli.py::::Level 1 on async_patterns: async functions appear in symbol table. - AssertionError: CLI failed (level 1):
FAILED test/test_cli.py::::Level 2 on async_patterns: PyCG resolves async calls and asyncio stdlib edges.

 Key assertions:
 - At least 15 total edges (observed ~31)
 - PyCG finds asyncio.sleep in async functions (await targets)
 - PyCG finds asyncio.gather in fetch_all
 - Pipeline chain is fully connected (async_main->pipeline->fetch_all->process_url->fetch_data)
 - AssertionError: CLI failed (level 2):
FAILED test/test_cli.py::::Level 1 on Flask 3.0.3: symbol table populated. - AssertionError: CLI failed (level 1):
FAILED test/test_cli.py::::Level 2 on Flask 3.0.3: PyCG substantially augments Jedi's edges.

 PyCG contributes >50% of total edges for a decorator-heavy codebase like Flask
 (observed ~852 PyCG out of ~1450 total edges).
 - AssertionError: CLI failed (level 2):
FAILED test/test_cli.py::::Level 1 on requests 2.31.0: symbol table populated. - AssertionError: CLI failed (level 1):
FAILED test/test_cli.py::::Level 2 on requests 2.31.0: PyCG resolves OO dispatch and session/adapter calls.

 PyCG contributes >50% of total edges for a clean OO codebase like requests
 (observed ~724 PyCG out of ~1121 total edges).
 - AssertionError: CLI failed (level 2):
============================================================================= 12 failed, 22 passed, 4 skipped, 2 warnings in 6.76s ==============================================================================

Additional context
Add any other context about the problem here.

[rahlk]

Stale — verified today on main @ 16e765a (v1.0.1): uv run pytest is green (177 passed, 5 skipped). The only failures reproducible locally were 4 test_provenance.py tests failing due to a machine-local gpg commit-signing lock, not repo code; they pass with a clean git config. CI has also been green through the 0.3.1 → 1.0.0 → 1.0.1 releases.