modify group_by_class behaviour of get_connected_neurons_by_type

[Clare72]

Instances count towards every relevant class-class pair up to the upstream and downstream types specified

[Robbie1977]

@Clare72 are you sure you want the excludeDB behaviour as it is:

Review of PR 276

What changed

• Only one file is affected: cross_server_tools.py
• The change is inside VfbConnect.get_connected_neurons_by_type(...)
• It reworks the group_by_class=True path to fetch individual connections first and then aggregate by ancestor class in Python

Key issues found

1. exclude_dbs is not applied in the group_by_class=True path

   • The new branch removes the earlier Cypher exclusion filter from the first connection query.
   • Later, it applies exclude_dbs only to the upstream total count query.
   • Result: excluded sources may still contribute to matched connections, causing incorrect results and inconsistent percent_connected.

2. average_weight uses integer division

   • The new code computes:
     • average_weight: tw // pw if pw else 0
   • The previous Cypher behavior was total_weight/pairwise_connections, i.e. float division.
   • This changes the reported average weight semantics.

3. Behavior/formatting concerns

   • verbose=True diagnostics use print(...) instead of a logger.
   • from collections import defaultdict is imported inside the method.
   • The method can still return False when no results are returned, which is inconsistent with the normal return types (DataFrame/list).

Other observations

• The PR adds docstring clarifications for weight and verbose, which is good.
• The PR file parses cleanly (python3 -m py_compile passed).
• Existing tests cover group_by_class=True, but do not cover exclude_dbs in that path.

Recommendation

• Fix exclude_dbs filtering in the group-by-class branch by applying the same exclusion criteria to the initial connection query.
• Change average_weight to use float division if the intent is to preserve prior semantics.
• Optionally, replace print debug output with a logging or verbose-controlled logger call.

[Clare72]

exclude_dbs is not applied in the group_by_class=True path

Not true, the db exclusion is added to the query independently of group_by_class

average_weight uses integer division

total weight and pairwise connections are both integers...