validation_external.py: Index mismatch between clustering results and metadata introduces NaNs

[bednarsky]

• I am testing edge cases (not on purpose haha)
• I have indices like this: Epi_Abs_BEST4+__H335__M21_00014
• The clustering or some earlier step seems to replace the + with .
• Full error for findability

Traceback (most recent call last):
  File "/path/to/proj.snakemake/scripts/tmph6wb_w6l.validation_external.py", line 68, in <module>
    idx_dfs["AMI"].loc[clustering, metadata] = metrics.adjusted_mutual_info_score(categorical_metadata[metadata], clustering_results[clustering])
  File "/path/to/conda/ea520d7177268389aea78d788e0c3541_/lib/python3.9/site-packages/sklearn/utils/_param_validation.py", line 211, in wrapper
    return func(*args, **kwargs)
  File "/path/to/conda/ea520d7177268389aea78d788e0c3541_/lib/python3.9/site-packages/sklearn/metrics/cluster/_supervised.py", line 1000, in adjusted_mutual_info_score
    labels_true, labels_pred = check_clusterings(labels_true, labels_pred)
  File "/path/to/conda/ea520d7177268389aea78d788e0c3541_/lib/python3.9/site-packages/sklearn/metrics/cluster/_sup
ervised.py", line 50, in check_clusterings
    labels_pred = check_array(
  File "/path/to/conda/ea520d7177268389aea78d788e0c3541_/lib/python3.9/site-packages/sklearn/utils/validation.py", line 959, in check_array
    _assert_all_finite(
  File "/path/to/conda/ea520d7177268389aea78d788e0c3541_/lib/python3.9/site-packages/sklearn/utils/validation.py"
, line 124, in _assert_all_finite
    _assert_all_finite_element_wise(
  File "/path/to/conda/ea520d7177268389aea78d788e0c3541_/lib/python3.9/site-packages/sklearn/utils/validation.py"
, line 173, in _assert_all_finite_element_wise
    raise ValueError(msg_err)
ValueError: Input contains NaN.

[sreichl]

ah yes that's an R issue that is not changeable. We can not manage this exception effectively, because even if you fix it in one script you have to take the "fix" along to other scripts, which introduces a dependency hell to maintain. Only solution I can think of: Do not use special characters (here, and in general).

[bednarsky]

• I agree about dependency hell, and also hard to automatically change the annotations (could be that this creates duplicates, e.g., if you have two index names: BEST4+ and BEST4-
• If we decide to make it 'Don't use special characters' then this should be communicated more clearly.
• Maybe should also add a test for the index only containing non-special characters somewhere, if not, cause a very clear error (not just some NaNs emerging somewhere far downstream)
• Like it was now, wasn't so straightforward to find what causes the error

[sreichl]

• yes, document and communicate more strongly in config/README.md
• maybe, check but this adds lots of code for every eventuality that might happen, I would rather stick with more clear docs.

For future reference, I would strongly recommend never using +/- nomenclature instead use e.g., pos/neg.

[bednarsky]

Great, will do a PR for (1) (and see if I don't find a one-liner somewhere that asserts (2))