count_extreme is no longer zero

pyranker/ranker.py

@@ -171,6 +171,12 @@ def perform_permutation_test(self) -> None:
                     if permuted_diff >= observed_diff:
                         count_extreme += 1
 
+                # Check if count_extreme is still zero, which would create pval=0.
+                # A p-value of 0 implies absolute certainty, which is unrealistic given the finite
+                # number of permutations. To avoid this, we adjust count_extreme to ensure a 
+                # conservative estimate of the p-value, aligning with standard statistical practices.
+                if count_extreme == 0:
+                    count_extreme += 1
                 # calculate the p-value
                 pval = count_extreme / self.n_iterations
                 self.pvals[i, j] = pval