scitex 2.14.0__py3-none-any.whl → 2.15.3__py3-none-any.whl

scitex/stats/_mcp/_handlers/_run_test.py

@@ -0,0 +1,279 @@
+#!/usr/bin/env python3
+# Timestamp: 2026-01-25
+# File: src/scitex/stats/_mcp/_handlers/_run_test.py
+
+"""Statistical test execution handler."""
+
+from __future__ import annotations
+
+import asyncio
+from datetime import datetime
+
+import numpy as np
+
+__all__ = ["run_test_handler"]
+
+
+async def run_test_handler(
+    test_name: str,
+    data: list[list[float]],
+    alternative: str = "two-sided",
+) -> dict:
+    """Execute a statistical test on provided data."""
+    try:
+        from scipy import stats as scipy_stats
+
+        loop = asyncio.get_event_loop()
+
+        def do_test():
+            # Convert data to numpy arrays
+            groups = [np.array(g, dtype=float) for g in data]
+
+            result = {}
+
+            # Run the appropriate test
+            if test_name == "ttest_ind":
+                result = _run_ttest_ind(groups, alternative, scipy_stats)
+            elif test_name == "ttest_paired":
+                result = _run_ttest_paired(groups, alternative, scipy_stats)
+            elif test_name == "ttest_1samp":
+                result = _run_ttest_1samp(groups, alternative, scipy_stats)
+            elif test_name == "brunner_munzel":
+                result = _run_brunner_munzel(groups, alternative, scipy_stats)
+            elif test_name == "mannwhitneyu":
+                result = _run_mannwhitneyu(groups, alternative, scipy_stats)
+            elif test_name == "wilcoxon":
+                result = _run_wilcoxon(groups, alternative, scipy_stats)
+            elif test_name == "anova":
+                result = _run_anova(groups, scipy_stats)
+            elif test_name == "kruskal":
+                result = _run_kruskal(groups, scipy_stats)
+            elif test_name == "chi2":
+                result = _run_chi2(data, scipy_stats)
+            elif test_name == "fisher_exact":
+                result = _run_fisher_exact(data, alternative, scipy_stats)
+            elif test_name == "pearson":
+                result = _run_pearson(groups, scipy_stats)
+            elif test_name == "spearman":
+                result = _run_spearman(groups, scipy_stats)
+            elif test_name == "kendall":
+                result = _run_kendall(groups, scipy_stats)
+            else:
+                raise ValueError(f"Unknown test: {test_name}")
+
+            # Calculate effect size if applicable
+            if test_name in [
+                "ttest_ind",
+                "ttest_paired",
+                "brunner_munzel",
+                "mannwhitneyu",
+            ]:
+                result = _add_effect_size(result, groups)
+
+            # Add significance determination
+            alpha = 0.05
+            result["significant"] = result["p_value"] < alpha
+            result["alpha"] = alpha
+
+            return result
+
+        result = await loop.run_in_executor(None, do_test)
+
+        return {
+            "success": True,
+            "test_name": test_name,
+            "alternative": alternative,
+            **result,
+            "timestamp": datetime.now().isoformat(),
+        }
+
+    except Exception as e:
+        return {"success": False, "error": str(e)}
+
+
+def _run_ttest_ind(groups, alternative, scipy_stats):
+    if len(groups) != 2:
+        raise ValueError("t-test requires exactly 2 groups")
+    stat, p_value = scipy_stats.ttest_ind(groups[0], groups[1], alternative=alternative)
+    df = len(groups[0]) + len(groups[1]) - 2
+    return {
+        "test": "Independent t-test",
+        "statistic": float(stat),
+        "statistic_name": "t",
+        "p_value": float(p_value),
+        "df": df,
+    }
+
+
+def _run_ttest_paired(groups, alternative, scipy_stats):
+    if len(groups) != 2:
+        raise ValueError("Paired t-test requires exactly 2 groups")
+    stat, p_value = scipy_stats.ttest_rel(groups[0], groups[1], alternative=alternative)
+    df = len(groups[0]) - 1
+    return {
+        "test": "Paired t-test",
+        "statistic": float(stat),
+        "statistic_name": "t",
+        "p_value": float(p_value),
+        "df": df,
+    }
+
+
+def _run_ttest_1samp(groups, alternative, scipy_stats):
+    if len(groups) != 1:
+        raise ValueError("One-sample t-test requires exactly 1 group")
+    stat, p_value = scipy_stats.ttest_1samp(groups[0], 0, alternative=alternative)
+    df = len(groups[0]) - 1
+    return {
+        "test": "One-sample t-test",
+        "statistic": float(stat),
+        "statistic_name": "t",
+        "p_value": float(p_value),
+        "df": df,
+    }
+
+
+def _run_brunner_munzel(groups, alternative, scipy_stats):
+    if len(groups) != 2:
+        raise ValueError("Brunner-Munzel requires exactly 2 groups")
+    res = scipy_stats.brunnermunzel(groups[0], groups[1], alternative=alternative)
+    return {
+        "test": "Brunner-Munzel test",
+        "statistic": float(res.statistic),
+        "statistic_name": "BM",
+        "p_value": float(res.pvalue),
+    }
+
+
+def _run_mannwhitneyu(groups, alternative, scipy_stats):
+    if len(groups) != 2:
+        raise ValueError("Mann-Whitney U requires exactly 2 groups")
+    stat, p_value = scipy_stats.mannwhitneyu(
+        groups[0], groups[1], alternative=alternative
+    )
+    return {
+        "test": "Mann-Whitney U test",
+        "statistic": float(stat),
+        "statistic_name": "U",
+        "p_value": float(p_value),
+    }
+
+
+def _run_wilcoxon(groups, alternative, scipy_stats):
+    if len(groups) != 2:
+        raise ValueError("Wilcoxon requires exactly 2 paired groups")
+    stat, p_value = scipy_stats.wilcoxon(groups[0], groups[1], alternative=alternative)
+    return {
+        "test": "Wilcoxon signed-rank test",
+        "statistic": float(stat),
+        "statistic_name": "W",
+        "p_value": float(p_value),
+    }
+
+
+def _run_anova(groups, scipy_stats):
+    if len(groups) < 2:
+        raise ValueError("ANOVA requires at least 2 groups")
+    stat, p_value = scipy_stats.f_oneway(*groups)
+    df_between = len(groups) - 1
+    df_within = sum(len(g) for g in groups) - len(groups)
+    return {
+        "test": "One-way ANOVA",
+        "statistic": float(stat),
+        "statistic_name": "F",
+        "p_value": float(p_value),
+        "df_between": df_between,
+        "df_within": df_within,
+    }
+
+
+def _run_kruskal(groups, scipy_stats):
+    if len(groups) < 2:
+        raise ValueError("Kruskal-Wallis requires at least 2 groups")
+    stat, p_value = scipy_stats.kruskal(*groups)
+    return {
+        "test": "Kruskal-Wallis H test",
+        "statistic": float(stat),
+        "statistic_name": "H",
+        "p_value": float(p_value),
+        "df": len(groups) - 1,
+    }
+
+
+def _run_chi2(data, scipy_stats):
+    table = np.array(data)
+    chi2, p_value, dof, expected = scipy_stats.chi2_contingency(table)
+    return {
+        "test": "Chi-square test of independence",
+        "statistic": float(chi2),
+        "statistic_name": "chi2",
+        "p_value": float(p_value),
+        "df": int(dof),
+        "expected_frequencies": expected.tolist(),
+    }
+
+
+def _run_fisher_exact(data, alternative, scipy_stats):
+    table = np.array(data)
+    if table.shape != (2, 2):
+        raise ValueError("Fisher's exact test requires a 2x2 table")
+    odds_ratio, p_value = scipy_stats.fisher_exact(table, alternative=alternative)
+    return {
+        "test": "Fisher's exact test",
+        "statistic": float(odds_ratio),
+        "statistic_name": "odds_ratio",
+        "p_value": float(p_value),
+    }
+
+
+def _run_pearson(groups, scipy_stats):
+    if len(groups) != 2:
+        raise ValueError("Pearson correlation requires exactly 2 variables")
+    r, p_value = scipy_stats.pearsonr(groups[0], groups[1])
+    return {
+        "test": "Pearson correlation",
+        "statistic": float(r),
+        "statistic_name": "r",
+        "p_value": float(p_value),
+    }
+
+
+def _run_spearman(groups, scipy_stats):
+    if len(groups) != 2:
+        raise ValueError("Spearman correlation requires exactly 2 variables")
+    r, p_value = scipy_stats.spearmanr(groups[0], groups[1])
+    return {
+        "test": "Spearman correlation",
+        "statistic": float(r),
+        "statistic_name": "rho",
+        "p_value": float(p_value),
+    }
+
+
+def _run_kendall(groups, scipy_stats):
+    if len(groups) != 2:
+        raise ValueError("Kendall correlation requires exactly 2 variables")
+    tau, p_value = scipy_stats.kendalltau(groups[0], groups[1])
+    return {
+        "test": "Kendall tau correlation",
+        "statistic": float(tau),
+        "statistic_name": "tau",
+        "p_value": float(p_value),
+    }
+
+
+def _add_effect_size(result, groups):
+    """Add effect size calculations to result."""
+    from scitex.stats.effect_sizes import cliffs_delta, cohens_d
+
+    if len(groups) == 2:
+        d = cohens_d(groups[0], groups[1])
+        delta = cliffs_delta(groups[0], groups[1])
+        result["effect_size"] = {
+            "cohens_d": float(d),
+            "cliffs_delta": float(delta),
+        }
+    return result
+
+
+# EOF

scitex/stats/_mcp/_handlers/_stars.py

@@ -0,0 +1,48 @@
+#!/usr/bin/env python3
+# Timestamp: 2026-01-25
+# File: src/scitex/stats/_mcp/_handlers/_stars.py
+
+"""P-value to stars conversion handler."""
+
+from __future__ import annotations
+
+from datetime import datetime
+
+__all__ = ["p_to_stars_handler"]
+
+
+async def p_to_stars_handler(
+    p_value: float,
+    thresholds: list[float] | None = None,
+) -> dict:
+    """Convert p-value to significance stars."""
+    try:
+        thresh = thresholds or [0.001, 0.01, 0.05]
+
+        if p_value < thresh[0]:
+            stars = "***"
+            significance = f"p < {thresh[0]}"
+        elif p_value < thresh[1]:
+            stars = "**"
+            significance = f"p < {thresh[1]}"
+        elif p_value < thresh[2]:
+            stars = "*"
+            significance = f"p < {thresh[2]}"
+        else:
+            stars = "ns"
+            significance = f"p >= {thresh[2]} (not significant)"
+
+        return {
+            "success": True,
+            "p_value": p_value,
+            "stars": stars,
+            "significance": significance,
+            "thresholds": thresh,
+            "timestamp": datetime.now().isoformat(),
+        }
+
+    except Exception as e:
+        return {"success": False, "error": str(e)}
+
+
+# EOF