fix: add guard for empty array in g123 when window_size exceeds avail

[31puneet]

Description

Fixes #571
Relates to #695

This PR fixes the intermittent IndexError in G123 tests (test_g123_gwss_...[af1_sim] and test_g123_calibration[af1_sim]).

The Bug

allel.moving_statistic(gt, ..., size=window_size) returns an empty array (0,) when gt.shape[0] < window_size. Downstream code that indexes into this array (x[0], x[-1]) then crashes with:

IndexError: index 0 is out of bounds for axis 0 with size 0

Why It's Intermittent

The test fixture in conftest.py used p_site=np.random.random(), and the test in test_g123.py selects random window_size values between 100-500. When a low p_site is randomly chosen (resulting in few sites) and a large window_size is picked, the number of sites falls below the window size, triggering the crash.

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Changes Made

1. g123.py

• Added a ValueError guard in _g123_gwss (before allel.moving_statistic) that checks if gt.shape[0] < window_size
• Added the same guard in _g123_calibration (inside the window_sizes loop)

2. conftest.py

• Changed p_site=np.random.random() → p_site=np.random.uniform(0.5, 1.0) in Af1Simulator.init_hap_sites() to ensure test data always generates sufficient haplotype sites

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Test Results

Before Fix (no guard, p_site=np.random.random())

Ran test_g123.py -k "af1_sim" in a loop of 20:

• Run 13/20 FAILED — IndexError on test_g123_gwss_with_phased_sites[af1_sim] and test_g123_calibration[af1_sim]

After Fix (guard added, p_site=np.random.uniform(0.5, 1.0))

Ran test_g123.py -k "af1_sim" in a loop of 50:

• 50/50 PASSED — zero failures

Also verified related test suites (test_h12, test_h1x, test_fst) with af1_sim — 20/20 passed.

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Impact

• Production code: Users who call g123_gwss() or g123_calibration() with a window_size larger than available sites will now get a clear ValueError instead of a confusing IndexError
• Tests: The conftest.py change ensures simulated data always has enough haplotype sites, eliminating intermittent test failures
• No breaking changes