Summary

Fixes #885 for the subset of standalone-function preprocessors that can be fixed safely.

The auto-generated standalone-function preprocessors in mne_preprocess.py passed the function name (a string) to Preprocessor instead of the callable, so they never actually applied their wrapped MNE function. #885 lists 19 affected classes.

However, a blanket "pass the callable" fix is unsafe. When fn is a callable and apply_on_array=False, Preprocessor.apply reassigns the dataset's recording to whatever fn returns. Several of these MNE functions return auxiliary data rather than the modified recording — e.g. annotate_amplitude returns a (annotations, bads) tuple, find_bad_channels_lof returns a list, set_eeg_reference (standalone) returns a (raw, ref_data) tuple. Wrapping those as callables would silently replace the recording with that auxiliary object — worse than the current failure.

What this PR does

• Introduces a small, explicit allow-list _SAFE_STANDALONE_FUNCTIONS of standalone functions verified to return the modified instance, and routes only those through the callable path. Currently three functions:
  • ComputeCurrentSourceDensity (compute_current_source_density)
  • SetBipolarReference (set_bipolar_reference)
  • OversampledTemporalProjection (oversampled_temporal_projection)
• Every other standalone function keeps its existing behaviour unchanged.

I verified the classification empirically (constructing each class, applying it to a Raw, and checking the return type). The remaining standalone functions fall into:

• Return auxiliary data (tuple/list/Annotations) — unsafe to pass as a callable as-is: annotate_amplitude, annotate_nan, compute_bridged_electrodes, find_bad_channels_lof, standalone set_eeg_reference, …
• Need a second instance / list input (don't fit the single-recording preprocessor model): equalize_bads, equalize_channels, realign_raw.
• Operate on arrays (filter_data) — already documented to use Filter instead.

These need their own handling/design and are intentionally out of scope here.

Tests

• test_safe_standalone_preprocessor_uses_callable — parametrized over the three safe classes: asserts .fn is the callable (not a string) and that apply returns a Raw.
• test_safe_standalone_preprocessor_runs_in_pipeline — runs ComputeCurrentSourceDensity end-to-end through preprocess.
• test_unsafe_standalone_preprocessor_keeps_string_fn — guard: AnnotateAmplitude.fn stays the string "annotate_amplitude", so a future change can't silently turn an auxiliary-data function into a data-corrupting callable.
• Un-skipped the existing test_compute_csd, which now passes.

Full file: 109 passed, 14 skipped, 0 failed.