scitex 2.5.0__py3-none-any.whl → 2.7.0__py3-none-any.whl

scitex/stats/correct/__init__.py

@@ -14,8 +14,8 @@ from ._correct_holm import correct_holm
 from ._correct_sidak import correct_sidak
 
 __all__ = [
-    'correct_bonferroni',
-    'correct_fdr',
-    'correct_holm',
-    'correct_sidak',
+    "correct_bonferroni",
+    "correct_fdr",
+    "correct_holm",
+    "correct_sidak",
 ]

scitex/stats/correct/_correct_bonferroni.py

@@ -5,6 +5,7 @@
 # ----------------------------------------
 from __future__ import annotations
 import os
+
 __FILE__ = __file__
 __DIR__ = os.path.dirname(__FILE__)
 # ----------------------------------------
@@ -195,7 +196,7 @@ def correct_bonferroni(
         logger.info(
             f"Bonferroni correction complete: {rejections}/{m} hypotheses rejected"
         )
-        logger.info(f"Adjusted alpha threshold: {alpha/m:.6f}")
+        logger.info(f"Adjusted alpha threshold: {alpha / m:.6f}")
 
         # Log detailed results if not too many tests
         if m <= 10:
@@ -223,6 +224,7 @@ def correct_bonferroni(
     if plot:
         if ax is None:
             import matplotlib.pyplot as plt
+
             fig, ax = plt.subplots(figsize=(10, 6))
         _plot_bonferroni(df, alpha, ax)
 
@@ -251,23 +253,46 @@ def _plot_bonferroni(df, alpha, ax):
 
     # Plot original and adjusted p-values
     ax.scatter(x, df["pvalue"], label="Original p-values", alpha=0.7, s=100, color="C0")
-    ax.scatter(x, df["pvalue_adjusted"], label="Adjusted p-values", alpha=0.7, s=100, color="C1", marker="s")
+    ax.scatter(
+        x,
+        df["pvalue_adjusted"],
+        label="Adjusted p-values",
+        alpha=0.7,
+        s=100,
+        color="C1",
+        marker="s",
+    )
 
     # Connect original to adjusted with lines
     for i in range(m):
-        ax.plot([i, i], [df["pvalue"].iloc[i], df["pvalue_adjusted"].iloc[i]],
-                "k-", alpha=0.3, linewidth=0.5)
+        ax.plot(
+            [i, i],
+            [df["pvalue"].iloc[i], df["pvalue_adjusted"].iloc[i]],
+            "k-",
+            alpha=0.3,
+            linewidth=0.5,
+        )
 
     # Add significance thresholds
-    ax.axhline(alpha, color="red", linestyle="--", linewidth=2, alpha=0.5, label=f"α = {alpha}")
-    ax.axhline(alpha/m, color="orange", linestyle="--", linewidth=2, alpha=0.5,
-               label=f"α_adj = {alpha/m:.4f}")
+    ax.axhline(
+        alpha, color="red", linestyle="--", linewidth=2, alpha=0.5, label=f"α = {alpha}"
+    )
+    ax.axhline(
+        alpha / m,
+        color="orange",
+        linestyle="--",
+        linewidth=2,
+        alpha=0.5,
+        label=f"α_adj = {alpha / m:.4f}",
+    )
 
     # Formatting
     ax.set_xlabel("Test Index")
     ax.set_ylabel("P-value")
-    ax.set_title(f"Bonferroni Correction (m={m} tests)\n"
-                 f'{df["rejected"].sum()}/{m} hypotheses rejected')
+    ax.set_title(
+        f"Bonferroni Correction (m={m} tests)\n"
+        f"{df['rejected'].sum()}/{m} hypotheses rejected"
+    )
     ax.set_yscale("log")
     ax.grid(True, alpha=0.3)
     ax.legend()
@@ -283,7 +308,7 @@ def _plot_bonferroni(df, alpha, ax):
             elif "comparison" in row:
                 labels.append(row["comparison"])
             else:
-                labels.append(f"Test {idx+1}")
+                labels.append(f"Test {idx + 1}")
         ax.set_xticks(x)
         ax.set_xticklabels(labels, rotation=45, ha="right", fontsize=8)
     else:
@@ -331,9 +356,7 @@ def main(args):
     for i in range(20):
         # Mix of significant and non-significant
         p = np.random.uniform(0.001, 0.1)
-        many_results.append(
-            {"var_x": f"Var_{i}", "var_y": "Control", "pvalue": p}
-        )
+        many_results.append({"var_x": f"Var_{i}", "var_y": "Control", "pvalue": p})
 
     corrected_many = correct_bonferroni(many_results, verbose=args.verbose)
 
@@ -394,9 +417,7 @@ def main(args):
         ax.scatter(m, p_adj, s=100, label=f"m = {m}")
 
     ax.axhline(0.05, color="red", linestyle="--", alpha=0.5, label="α = 0.05")
-    ax.axhline(
-        p_orig, color="blue", linestyle="--", alpha=0.5, label="Original p"
-    )
+    ax.axhline(p_orig, color="blue", linestyle="--", alpha=0.5, label="Original p")
     ax.set_xlabel("Number of Tests (m)")
     ax.set_ylabel("Adjusted P-value")
     ax.set_title(f"Bonferroni Adjustment (p_original = {p_orig})")
@@ -411,9 +432,7 @@ def main(args):
     alpha_adj = alpha / m_range
 
     ax.plot(m_range, alpha_adj, linewidth=2)
-    ax.axhline(
-        0.05, color="red", linestyle="--", alpha=0.5, label="Original α"
-    )
+    ax.axhline(0.05, color="red", linestyle="--", alpha=0.5, label="Original α")
     ax.set_xlabel("Number of Tests (m)")
     ax.set_ylabel("Adjusted α Threshold")
     ax.set_title("Bonferroni: Threshold Decreases Linearly")
@@ -433,12 +452,8 @@ def main(args):
     x_pos = np.arange(n_tests)
     width = 0.35
 
-    bars1 = ax.bar(
-        x_pos - width / 2, p_values, width, label="Original", alpha=0.7
-    )
-    bars2 = ax.bar(
-        x_pos + width / 2, p_adjusted, width, label="Adjusted", alpha=0.7
-    )
+    bars1 = ax.bar(x_pos - width / 2, p_values, width, label="Original", alpha=0.7)
+    bars2 = ax.bar(x_pos + width / 2, p_adjusted, width, label="Adjusted", alpha=0.7)
 
     # Color bars by significance
     for i, (p_orig, p_adj) in enumerate(zip(p_values, p_adjusted)):
@@ -493,9 +508,7 @@ def main(args):
             if i % 2 == 0:
                 table[(i, j)].set_facecolor("#f0f0f0")
 
-    ax.set_title(
-        "Multiple Comparison Methods Comparison", pad=20, fontweight="bold"
-    )
+    ax.set_title("Multiple Comparison Methods Comparison", pad=20, fontweight="bold")
 
     plt.tight_layout()
 
@@ -508,12 +521,8 @@ def main(args):
 
 def parse_args():
     """Parse command line arguments."""
-    parser = argparse.ArgumentParser(
-        description="Demonstrate Bonferroni correction"
-    )
-    parser.add_argument(
-        "--verbose", action="store_true", help="Enable verbose output"
-    )
+    parser = argparse.ArgumentParser(description="Demonstrate Bonferroni correction")
+    parser.add_argument("--verbose", action="store_true", help="Enable verbose output")
     return parser.parse_args()
 
 

scitex/stats/correct/_correct_fdr.py

@@ -165,9 +165,7 @@ def correct_fdr(
     from scitex.stats.utils._normalizers import force_dataframe, to_dict
 
     if verbose:
-        method_name = (
-            "Benjamini-Hochberg" if method == "bh" else "Benjamini-Yekutieli"
-        )
+        method_name = "Benjamini-Hochberg" if method == "bh" else "Benjamini-Yekutieli"
         logger.info(f"Applying FDR correction ({method_name})")
 
     # Store original input type
@@ -211,9 +209,7 @@ def correct_fdr(
         # c(m) = sum(1/i) for i in 1:m ≈ ln(m) + γ (Euler-Mascheroni constant)
         c_m = np.sum(1.0 / np.arange(1, m + 1))
         ranks = np.arange(1, m + 1)
-        q_values = np.minimum.accumulate((pvalues * m * c_m / ranks)[::-1])[
-            ::-1
-        ]
+        q_values = np.minimum.accumulate((pvalues * m * c_m / ranks)[::-1])[::-1]
         q_values = np.minimum(q_values, 1.0)
 
     else:
@@ -264,9 +260,7 @@ def correct_fdr(
     # Log results summary
     if verbose:
         rejections = df_result["rejected"].sum()
-        logger.info(
-            f"FDR correction complete: {rejections}/{m} hypotheses rejected"
-        )
+        logger.info(f"FDR correction complete: {rejections}/{m} hypotheses rejected")
 
         # Log detailed results if not too many tests
         if m <= 10:
@@ -361,9 +355,7 @@ def _plot_fdr(df, alpha, method, ax):
     )
 
     # Formatting
-    method_name = (
-        "Benjamini-Hochberg" if method == "bh" else "Benjamini-Yekutieli"
-    )
+    method_name = "Benjamini-Hochberg" if method == "bh" else "Benjamini-Yekutieli"
     ax.set_xlabel("Test Index")
     ax.set_ylabel("P-value / Q-value")
     rejections = df["rejected"].sum()
@@ -386,7 +378,7 @@ def _plot_fdr(df, alpha, method, ax):
             elif "comparison" in row:
                 labels.append(row["comparison"])
             else:
-                labels.append(f"Test {len(labels)+1}")
+                labels.append(f"Test {len(labels) + 1}")
         ax.set_xticks(x)
         ax.set_xticklabels(labels, rotation=45, ha="right", fontsize=8)
     else:
@@ -443,9 +435,7 @@ def demo(verbose=False):
 
     from ._correct_bonferroni import correct_bonferroni
 
-    corrected_bonf = correct_bonferroni(
-        multiple_results, alpha=0.05, verbose=False
-    )
+    corrected_bonf = correct_bonferroni(multiple_results, alpha=0.05, verbose=False)
 
     n_rejected_bonf = sum(r["rejected"] for r in corrected_bonf)
     n_rejected_fdr = sum(r["rejected"] for r in corrected_bh)
@@ -492,24 +482,16 @@ def demo(verbose=False):
     # Calculate confusion metrics
     def calc_metrics(corrected, truth_col="truth"):
         tp = sum(
-            1
-            for r in corrected
-            if r["rejected"] and r.get(truth_col) == "positive"
+            1 for r in corrected if r["rejected"] and r.get(truth_col) == "positive"
         )
         fp = sum(
-            1
-            for r in corrected
-            if r["rejected"] and r.get(truth_col) == "negative"
+            1 for r in corrected if r["rejected"] and r.get(truth_col) == "negative"
         )
         fn = sum(
-            1
-            for r in corrected
-            if not r["rejected"] and r.get(truth_col) == "positive"
+            1 for r in corrected if not r["rejected"] and r.get(truth_col) == "positive"
         )
         tn = sum(
-            1
-            for r in corrected
-            if not r["rejected"] and r.get(truth_col) == "negative"
+            1 for r in corrected if not r["rejected"] and r.get(truth_col) == "negative"
         )
         return tp, fp, fn, tn
 
@@ -572,9 +554,7 @@ def demo(verbose=False):
     alpha_fdr = alpha  # FDR maintains similar threshold
 
     ax.plot(m_vals, alpha_bonf, label="Bonferroni", linewidth=2)
-    ax.axhline(
-        alpha_fdr, color="green", linestyle="--", linewidth=2, label="FDR (BH)"
-    )
+    ax.axhline(alpha_fdr, color="green", linestyle="--", linewidth=2, label="FDR (BH)")
     ax.set_xlabel("Number of Tests (m)")
     ax.set_ylabel("Effective α")
     ax.set_title("FDR Maintains Power vs Bonferroni")
@@ -594,9 +574,7 @@ def demo(verbose=False):
 
     for a in alphas:
         corr_bonf = correct_bonferroni(many_results, alpha=a, verbose=False)
-        corr_fdr = correct_fdr(
-            many_results, alpha=a, method="bh", verbose=False
-        )
+        corr_fdr = correct_fdr(many_results, alpha=a, method="bh", verbose=False)
 
         tp_b, fp_b, _, _ = calc_metrics(corr_bonf)
         tp_f, fp_f, _, _ = calc_metrics(corr_fdr)
@@ -606,12 +584,8 @@ def demo(verbose=False):
         fdr_tps.append(tp_f / 20)
         fdr_fps.append(fp_f / 80)
 
-    ax.plot(
-        bonf_fps, bonf_tps, "o-", linewidth=2, markersize=8, label="Bonferroni"
-    )
-    ax.plot(
-        fdr_fps, fdr_tps, "s-", linewidth=2, markersize=8, label="FDR (BH)"
-    )
+    ax.plot(bonf_fps, bonf_tps, "o-", linewidth=2, markersize=8, label="Bonferroni")
+    ax.plot(fdr_fps, fdr_tps, "s-", linewidth=2, markersize=8, label="FDR (BH)")
     ax.plot([0, 1], [0, 1], "k--", alpha=0.3)
     ax.set_xlabel("False Positive Rate")
     ax.set_ylabel("True Positive Rate (Power)")

scitex/stats/correct/_correct_fdr_.py

@@ -5,6 +5,7 @@
 # ----------------------------------------
 from __future__ import annotations
 import os
+
 __FILE__ = __file__
 __DIR__ = os.path.dirname(__FILE__)
 # ----------------------------------------
@@ -164,9 +165,7 @@ def correct_fdr(
     from scitex.stats.utils._normalizers import force_dataframe, to_dict
 
     if verbose:
-        method_name = (
-            "Benjamini-Hochberg" if method == "bh" else "Benjamini-Yekutieli"
-        )
+        method_name = "Benjamini-Hochberg" if method == "bh" else "Benjamini-Yekutieli"
         logger.info(f"Applying FDR correction ({method_name})")
 
     # Store original input type
@@ -210,9 +209,7 @@ def correct_fdr(
         # c(m) = sum(1/i) for i in 1:m ≈ ln(m) + γ (Euler-Mascheroni constant)
         c_m = np.sum(1.0 / np.arange(1, m + 1))
         ranks = np.arange(1, m + 1)
-        q_values = np.minimum.accumulate((pvalues * m * c_m / ranks)[::-1])[
-            ::-1
-        ]
+        q_values = np.minimum.accumulate((pvalues * m * c_m / ranks)[::-1])[::-1]
         q_values = np.minimum(q_values, 1.0)
 
     else:
@@ -263,9 +260,7 @@ def correct_fdr(
     # Log results summary
     if verbose:
         rejections = df_result["rejected"].sum()
-        logger.info(
-            f"FDR correction complete: {rejections}/{m} hypotheses rejected"
-        )
+        logger.info(f"FDR correction complete: {rejections}/{m} hypotheses rejected")
 
         # Log detailed results if not too many tests
         if m <= 10:
@@ -293,6 +288,7 @@ def correct_fdr(
     if plot:
         if ax is None:
             import matplotlib.pyplot as plt
+
             fig, ax = plt.subplots(figsize=(10, 6))
         _plot_fdr(df_result, alpha, method, ax)
 
@@ -321,23 +317,40 @@ def _plot_fdr(df, alpha, method, ax):
 
     # Plot original p-values and q-values
     ax.scatter(x, df["pvalue"], label="Original p-values", alpha=0.7, s=100, color="C0")
-    ax.scatter(x, df["pvalue_adjusted"], label="Q-values (FDR-adjusted)", alpha=0.7, s=100, color="C1", marker="s")
+    ax.scatter(
+        x,
+        df["pvalue_adjusted"],
+        label="Q-values (FDR-adjusted)",
+        alpha=0.7,
+        s=100,
+        color="C1",
+        marker="s",
+    )
 
     # Connect original to adjusted with lines
     for i in range(m):
-        ax.plot([i, i], [df["pvalue"].iloc[i], df["pvalue_adjusted"].iloc[i]],
-                "k-", alpha=0.3, linewidth=0.5)
+        ax.plot(
+            [i, i],
+            [df["pvalue"].iloc[i], df["pvalue_adjusted"].iloc[i]],
+            "k-",
+            alpha=0.3,
+            linewidth=0.5,
+        )
 
     # Add significance threshold
-    ax.axhline(alpha, color="red", linestyle="--", linewidth=2, alpha=0.5, label=f"α = {alpha}")
+    ax.axhline(
+        alpha, color="red", linestyle="--", linewidth=2, alpha=0.5, label=f"α = {alpha}"
+    )
 
     # Formatting
     method_name = "Benjamini-Hochberg" if method == "bh" else "Benjamini-Yekutieli"
     ax.set_xlabel("Test Index")
     ax.set_ylabel("P-value / Q-value")
     rejections = df["rejected"].sum()
-    ax.set_title(f"FDR Correction ({method_name}, m={m} tests)\n"
-                 f"{rejections}/{m} hypotheses rejected")
+    ax.set_title(
+        f"FDR Correction ({method_name}, m={m} tests)\n"
+        f"{rejections}/{m} hypotheses rejected"
+    )
     ax.set_yscale("log")
     ax.grid(True, alpha=0.3)
     ax.legend()
@@ -353,7 +366,7 @@ def _plot_fdr(df, alpha, method, ax):
             elif "comparison" in row:
                 labels.append(row["comparison"])
             else:
-                labels.append(f"Test {len(labels)+1}")
+                labels.append(f"Test {len(labels) + 1}")
         ax.set_xticks(x)
         ax.set_xticklabels(labels, rotation=45, ha="right", fontsize=8)
     else:
@@ -406,9 +419,7 @@ def main(args):
 
     from ._correct_bonferroni import correct_bonferroni
 
-    corrected_bonf = correct_bonferroni(
-        multiple_results, alpha=0.05, verbose=False
-    )
+    corrected_bonf = correct_bonferroni(multiple_results, alpha=0.05, verbose=False)
 
     n_rejected_bonf = sum(r["rejected"] for r in corrected_bonf)
     n_rejected_fdr = sum(r["rejected"] for r in corrected_bh)
@@ -455,24 +466,16 @@ def main(args):
     # Calculate confusion metrics
     def calc_metrics(corrected, truth_col="truth"):
         tp = sum(
-            1
-            for r in corrected
-            if r["rejected"] and r.get(truth_col) == "positive"
+            1 for r in corrected if r["rejected"] and r.get(truth_col) == "positive"
         )
         fp = sum(
-            1
-            for r in corrected
-            if r["rejected"] and r.get(truth_col) == "negative"
+            1 for r in corrected if r["rejected"] and r.get(truth_col) == "negative"
         )
         fn = sum(
-            1
-            for r in corrected
-            if not r["rejected"] and r.get(truth_col) == "positive"
+            1 for r in corrected if not r["rejected"] and r.get(truth_col) == "positive"
         )
         tn = sum(
-            1
-            for r in corrected
-            if not r["rejected"] and r.get(truth_col) == "negative"
+            1 for r in corrected if not r["rejected"] and r.get(truth_col) == "negative"
         )
         return tp, fp, fn, tn
 
@@ -535,9 +538,7 @@ def main(args):
     alpha_fdr = alpha  # FDR maintains similar threshold
 
     ax.plot(m_vals, alpha_bonf, label="Bonferroni", linewidth=2)
-    ax.axhline(
-        alpha_fdr, color="green", linestyle="--", linewidth=2, label="FDR (BH)"
-    )
+    ax.axhline(alpha_fdr, color="green", linestyle="--", linewidth=2, label="FDR (BH)")
     ax.set_xlabel("Number of Tests (m)")
     ax.set_ylabel("Effective α")
     ax.set_title("FDR Maintains Power vs Bonferroni")
@@ -557,9 +558,7 @@ def main(args):
 
     for a in alphas:
         corr_bonf = correct_bonferroni(many_results, alpha=a, verbose=False)
-        corr_fdr = correct_fdr(
-            many_results, alpha=a, method="bh", verbose=False
-        )
+        corr_fdr = correct_fdr(many_results, alpha=a, method="bh", verbose=False)
 
         tp_b, fp_b, _, _ = calc_metrics(corr_bonf)
         tp_f, fp_f, _, _ = calc_metrics(corr_fdr)
@@ -569,12 +568,8 @@ def main(args):
         fdr_tps.append(tp_f / 20)
         fdr_fps.append(fp_f / 80)
 
-    ax.plot(
-        bonf_fps, bonf_tps, "o-", linewidth=2, markersize=8, label="Bonferroni"
-    )
-    ax.plot(
-        fdr_fps, fdr_tps, "s-", linewidth=2, markersize=8, label="FDR (BH)"
-    )
+    ax.plot(bonf_fps, bonf_tps, "o-", linewidth=2, markersize=8, label="Bonferroni")
+    ax.plot(fdr_fps, fdr_tps, "s-", linewidth=2, markersize=8, label="FDR (BH)")
     ax.plot([0, 1], [0, 1], "k--", alpha=0.3)
     ax.set_xlabel("False Positive Rate")
     ax.set_ylabel("True Positive Rate (Power)")
@@ -594,9 +589,7 @@ def main(args):
 def parse_args():
     """Parse command line arguments."""
     parser = argparse.ArgumentParser(description="Demonstrate FDR correction")
-    parser.add_argument(
-        "--verbose", action="store_true", help="Enable verbose output"
-    )
+    parser.add_argument("--verbose", action="store_true", help="Enable verbose output")
     return parser.parse_args()
 
 

scitex/stats/correct/_correct_holm.py

@@ -5,6 +5,7 @@
 # ----------------------------------------
 from __future__ import annotations
 import os
+
 __FILE__ = __file__
 __DIR__ = os.path.dirname(__FILE__)
 # ----------------------------------------
@@ -194,9 +195,7 @@ def correct_holm(
     for i, (orig_idx, result) in enumerate(sorted_results):
         corrected = result.copy()
         corrected["pvalue_adjusted"] = round(adjusted_pvalues[i], 6)
-        corrected["alpha_adjusted"] = round(
-            alpha / (m - i), 6
-        )  # For reference
+        corrected["alpha_adjusted"] = round(alpha / (m - i), 6)  # For reference
         corrected["rejected"] = adjusted_pvalues[i] <= alpha
 
         # Add original index for restoration
@@ -214,10 +213,8 @@ def correct_holm(
     # Log results summary
     if verbose:
         rejections = sum(r["rejected"] for r in corrected_results)
-        logger.info(
-            f"Holm correction complete: {rejections}/{m} hypotheses rejected"
-        )
-        logger.info(f"Adjusted alpha range: {alpha/m:.6f} to {alpha:.6f}")
+        logger.info(f"Holm correction complete: {rejections}/{m} hypotheses rejected")
+        logger.info(f"Adjusted alpha range: {alpha / m:.6f} to {alpha:.6f}")
 
         # Log detailed results if not too many tests
         if m <= 10:
@@ -263,9 +260,7 @@ def _plot_holm(corrected_results, alpha, m, ax):
     pvalues_adj = [r["pvalue_adjusted"] for r in corrected_results]
 
     # Plot original and adjusted p-values
-    ax.scatter(
-        x, pvalues, label="Original p-values", alpha=0.7, s=100, color="C0"
-    )
+    ax.scatter(x, pvalues, label="Original p-values", alpha=0.7, s=100, color="C0")
     ax.scatter(
         x,
         pvalues_adj,
@@ -301,17 +296,14 @@ def _plot_holm(corrected_results, alpha, m, ax):
         linestyle="--",
         linewidth=2,
         alpha=0.5,
-        label=f"α_min = {alpha/m:.4f}",
+        label=f"α_min = {alpha / m:.4f}",
     )
 
     # Formatting
     ax.set_xlabel("Test Index")
     ax.set_ylabel("P-value")
     rejections = sum(r["rejected"] for r in corrected_results)
-    ax.set_title(
-        f"Holm Correction (m={m} tests)\n"
-        f"{rejections}/{m} hypotheses rejected"
-    )
+    ax.set_title(f"Holm Correction (m={m} tests)\n{rejections}/{m} hypotheses rejected")
     ax.set_yscale("log")
     ax.grid(True, alpha=0.3)
     ax.legend()
@@ -327,7 +319,7 @@ def _plot_holm(corrected_results, alpha, m, ax):
             elif "comparison" in r:
                 labels.append(r["comparison"])
             else:
-                labels.append(f"Test {len(labels)+1}")
+                labels.append(f"Test {len(labels) + 1}")
         ax.set_xticks(x)
         ax.set_xticklabels(labels, rotation=45, ha="right", fontsize=8)
     else:
@@ -368,9 +360,7 @@ def main(args):
     ]
 
     holm_results = correct_holm(results, alpha=0.05, verbose=args.verbose)
-    bonf_results = correct_bonferroni(
-        results, alpha=0.05, verbose=args.verbose
-    )
+    bonf_results = correct_bonferroni(results, alpha=0.05, verbose=args.verbose)
 
     # Count rejections
     holm_rejections = sum(r["rejected"] for r in holm_results)
@@ -381,9 +371,7 @@ def main(args):
     logger.info("Note: Holm is uniformly more powerful than Bonferroni")
 
     # Example 3: Post-hoc after ANOVA
-    logger.info(
-        "\n=== Example 3: Post-hoc pairwise comparisons after ANOVA ==="
-    )
+    logger.info("\n=== Example 3: Post-hoc pairwise comparisons after ANOVA ===")
 
     np.random.seed(42)
 
@@ -461,17 +449,14 @@ def main(args):
 
     # All very small p-values
     small_ps = [
-        {"test_method": f"Test {i}", "pvalue": 0.0001 * (i + 1)}
-        for i in range(5)
+        {"test_method": f"Test {i}", "pvalue": 0.0001 * (i + 1)} for i in range(5)
     ]
     small_corr = correct_holm(small_ps, alpha=0.05, verbose=False)
     rejections = sum(r["rejected"] for r in small_corr)
     logger.info(f"All small p-values: {rejections}/5 rejected")
 
     # All large p-values
-    large_ps = [
-        {"test_method": f"Test {i}", "pvalue": 0.1 + 0.1 * i} for i in range(5)
-    ]
+    large_ps = [{"test_method": f"Test {i}", "pvalue": 0.1 + 0.1 * i} for i in range(5)]
     large_corr = correct_holm(large_ps, alpha=0.05, verbose=False)
     rejections = sum(r["rejected"] for r in large_corr)
     logger.info(f"All large p-values: {rejections}/5 rejected")
@@ -491,8 +476,7 @@ def main(args):
     logger.info("\n=== Example 7: Different alpha levels ===")
 
     results = [
-        {"test_method": f"Test {i}", "pvalue": 0.01 * (i + 1)}
-        for i in range(10)
+        {"test_method": f"Test {i}", "pvalue": 0.01 * (i + 1)} for i in range(10)
     ]
 
     for alpha_level in [0.01, 0.05, 0.10]:
@@ -508,9 +492,7 @@ def parse_args():
     parser = argparse.ArgumentParser(
         description="Demonstrate Holm-Bonferroni correction"
     )
-    parser.add_argument(
-        "--verbose", action="store_true", help="Enable verbose output"
-    )
+    parser.add_argument("--verbose", action="store_true", help="Enable verbose output")
     return parser.parse_args()