Add missing audit_spike_sorting.py to fix CI spike detection step

[Copilot]

The bio-digital-ci-cd.yml workflow references src/signal_processing/audit_spike_sorting.py in the "Spike Detection Quality Audit" step, but the file never existed — causing every CI run to fail with [Errno 2] No such file or directory.

Changes

• New script: src/signal_processing/audit_spike_sorting.py
  • Generates synthetic extracellular traces with ground-truth spike positions injected into Gaussian noise
  • Runs a threshold-based detector mirroring the SSD logic in template_matching.rs
  • Matches detections to ground-truth spikes within a ±30 frame (±1 ms @ 30 kHz) tolerance window
  • Asserts false-negative and false-positive rates stay ≤ 10%; exits non-zero on failure so CI fails loudly on regressions
  • Covers 4 benchmark scenarios: single spike (low/high noise), multiple spikes, and dense spike trains

# Example benchmark entry
("Dense spikes — medium noise",
 list(range(BENCHMARK_SPIKE_INTERVAL_FRAMES, BENCHMARK_DURATION_FRAMES, BENCHMARK_SPIKE_INTERVAL_FRAMES)),
 BENCHMARK_DURATION_FRAMES, 0.10, 0.9)

Follows the same structure and exit-code contract as the existing verify_latency.py audit script.

[Copilot]

Pull request overview

Adds the missing spike-sorting audit script that the bio-digital-ci-cd.yml workflow already invokes, unblocking the “Spike Detection Quality Audit” CI step and providing a synthetic benchmark-based regression check for event detection.

Changes:

• Introduces src/signal_processing/audit_spike_sorting.py to generate synthetic traces with injected spikes and evaluate detection quality (FN/FP rates).
• Implements a simple threshold-crossing detector plus benchmark scenarios and CI-friendly exit codes.

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[Copilot]

The detector implemented here is a simple amplitude threshold crossing with a refractory period, but both the module docstring and this function’s docstring claim it “mirrors” the SSD-based template matcher in template_matching.rs (which slides a fixed window and checks SSD < variance_tolerance, and has no refractory). This mismatch makes the audit less representative of the Rust implementation and can allow regressions in SSD logic to slip through; either implement an SSD-style windowed matcher against the synthetic waveform template, or update the documentation/references so the audit’s scope is accurate.

[Copilot]

SAMPLING_RATE_HZ is defined but not used, and several timing-related constants (tolerance, duration, interval) are hard-coded separately. To avoid inconsistencies if the sampling rate changes, derive these frame counts from SAMPLING_RATE_HZ (e.g., duration_frames = SAMPLING_RATE_HZ * seconds, tolerance = SAMPLING_RATE_HZ * 0.001) or remove SAMPLING_RATE_HZ if it’s intentionally informational-only.

[Copilot]

The “Dense spikes — medium noise” benchmark tuple is written as a single very long line, which hurts readability and makes diffs noisier when tweaking parameters. Consider formatting it across multiple lines (consistent with the other entries) so future edits stay clear.

Suggested change

	("Dense spikes — medium noise", list(range(BENCHMARK_SPIKE_INTERVAL_FRAMES, BENCHMARK_DURATION_FRAMES, BENCHMARK_SPIKE_INTERVAL_FRAMES)), BENCHMARK_DURATION_FRAMES, 0.10, 0.9),
	(
	"Dense spikes — medium noise",
	list(
	range(
	BENCHMARK_SPIKE_INTERVAL_FRAMES,
	BENCHMARK_DURATION_FRAMES,
	BENCHMARK_SPIKE_INTERVAL_FRAMES,
	)
	),
	BENCHMARK_DURATION_FRAMES,
	0.10,
	0.9,
	),

[Copilot]

_make_synthetic_trace silently skips injecting spikes whose waveform would extend past duration_frames (end > duration_frames). For an audit script this can mask misconfigured benchmarks and produce confusing FN/FP results. Consider validating spike_positions upfront (raise ValueError or log an explicit error) instead of silently ignoring out-of-bounds spikes.

Suggested change

	for pos in spike_positions:
	end = pos + len(waveform)
	if end <= duration_frames:
	trace[pos:end] += waveform
	max_start = duration_frames - len(waveform)
	invalid_positions = [
	pos for pos in spike_positions
	if pos < 0 or (pos + len(waveform)) > duration_frames
	]
	if invalid_positions:
	raise ValueError(
	"spike_positions contains out-of-bounds spike starts for "
	f"duration_frames={duration_frames} and waveform_len={len(waveform)}: "
	f"{invalid_positions}. Valid start positions are in the range "
	f"[0, {max_start}]."
	)
	for pos in spike_positions:
	end = pos + len(waveform)
	trace[pos:end] += waveform