Issue with Conga and Pandas 3.0.3

[bbimber]

Hello,

We have a longstanding CI that exercises Conga. This just upgraded to pandas 3, which I think exposed a conga issue. The conga code is here:

conga/conga/correlations.py

Line 111 in 173a414

mait_fraction=np.sum(is_mait[double_nbrs])/overlap,

and below is a stack trace. I think there is a difference in pandas 2 vs. pandas 3 in terms of warnings/exceptions. would it be possible to either test with pandas 3 or update requirements.txt to be explicit about pandas<3.0.0?

2026-07-10T18:44:23.1415881Z   File "/tmp/RtmpNy8pLe/file657631f7ea63", line 88, in run_CoNGA
2026-07-10T18:44:23.1416151Z     results = conga.correlations.run_graph_vs_graph(
2026-07-10T18:44:23.1416319Z               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2026-07-10T18:44:23.1416765Z   File "/home/runner/work/CellMembrane/conga/conga/correlations.py", line 596, in run_graph_vs_graph
2026-07-10T18:44:23.1417050Z     results_df, adjusted_pvalues = _find_neighbor_neighbor_interactions(
2026-07-10T18:44:23.1417253Z                                    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2026-07-10T18:44:23.1417779Z   File "/home/runner/work/CellMembrane/conga/conga/correlations.py", line 111, in _find_neighbor_neighbor_interactions
2026-07-10T18:44:23.1417992Z     mait_fraction=np.sum(is_mait[double_nbrs])/overlap,
2026-07-10T18:44:23.1418147Z                          ~~~~~~~^^^^^^^^^^^^^
2026-07-10T18:44:23.1418595Z   File "/home/runner/.local/lib/python3.12/site-packages/pandas/core/series.py", line 991, in __getitem__
2026-07-10T18:44:23.1418736Z     return self._get_with(key)
2026-07-10T18:44:23.1418866Z            ^^^^^^^^^^^^^^^^^^^
2026-07-10T18:44:23.1419297Z   File "/home/runner/.local/lib/python3.12/site-packages/pandas/core/series.py", line 1003, in _get_with
2026-07-10T18:44:23.1419433Z     return self.loc[key]
2026-07-10T18:44:23.1419554Z            ~~~~~~~~^^^^^
2026-07-10T18:44:23.1419999Z   File "/home/runner/.local/lib/python3.12/site-packages/pandas/core/indexing.py", line 1207, in __getitem__
2026-07-10T18:44:23.1420214Z     return self._getitem_axis(maybe_callable, axis=axis)
2026-07-10T18:44:23.1420386Z            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2026-07-10T18:44:23.1420845Z   File "/home/runner/.local/lib/python3.12/site-packages/pandas/core/indexing.py", line 1438, in _getitem_axis
2026-07-10T18:44:23.1421040Z     return self._getitem_iterable(key, axis=axis)
2026-07-10T18:44:23.1421192Z            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2026-07-10T18:44:23.1421669Z   File "/home/runner/.local/lib/python3.12/site-packages/pandas/core/indexing.py", line 1378, in _getitem_iterable
2026-07-10T18:44:23.1421895Z     keyarr, indexer = self._get_listlike_indexer(key, axis)
2026-07-10T18:44:23.1422076Z                       ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2026-07-10T18:44:23.1422729Z   File "/home/runner/.local/lib/python3.12/site-packages/pandas/core/indexing.py", line 1576, in _get_listlike_indexer
2026-07-10T18:44:23.1422958Z     keyarr, indexer = ax._get_indexer_strict(key, axis_name)
2026-07-10T18:44:23.1423136Z                       ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2026-07-10T18:44:23.1423648Z   File "/home/runner/.local/lib/python3.12/site-packages/pandas/core/indexes/base.py", line 6302, in _get_indexer_strict
2026-07-10T18:44:23.1423852Z     self._raise_if_missing(keyarr, indexer, axis_name)
2026-07-10T18:44:23.1424338Z   File "/home/runner/.local/lib/python3.12/site-packages/pandas/core/indexes/base.py", line 6352, in _raise_if_missing
2026-07-10T18:44:23.1424604Z     raise KeyError(f"None of [{key}] are in the [{axis_name}]")
2026-07-10T18:44:23.1424982Z KeyError: "None of [Index([15, 148, 145, 147, 133, 90, 98, 103, 28, 17], dtype='int64')] are in the [index]"
2026-07-10T18:44:23.1425065Z 

[sschattgen]

We're looking into it now...