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Fix sample sorting algorithms #261

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Merged
yoelcortes merged 1 commit into from
Oct 11, 2026
Merged

Fix sample sorting algorithms #261

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9 changes: 4 additions & 5 deletions biosteam/evaluation/_model.py
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Original file line number Diff line number Diff line change
Expand Up @@ -725,23 +725,22 @@ def _load_sample_order(self, samples, parameters, distance, algorithm=None):
samples_min = samples.min(axis=0)
samples_max = samples.max(axis=0)
samples_diff = samples_max - samples_min
samples_diff[samples_diff == 0] = 1 # Constant columns
normalized_samples = (samples - samples_min) / samples_diff
nearest_arr = cdist(normalized_samples, normalized_samples, metric=distance)
if algorithm is None: algorithm = 'nearest neighbor'
if algorithm == 'nearest neighbor':
nearest_arr = np.argsort(nearest_arr, axis=1)
remaining = set(range(length))
self._index = index = [0]
nearest = nearest_arr[0, 1]
index.append(nearest)
nearest = 0
remaining.remove(0)
remaining.remove(nearest)
N_remaining = length - 2
N_remaining = length - 1
N_remaining_last = N_remaining + 1
while N_remaining:
assert N_remaining_last != N_remaining, "issue in sorting algorithm"
N_remaining_last = N_remaining
for i in range(1, length):
for i in range(length):
next_nearest = nearest_arr[nearest, i]
if next_nearest in remaining:
nearest = next_nearest
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