guzhujushi
f95fbd2726
## 用户问的「t_test 307 / 308 两行报错」 - 那两行是 `float(res.statistic)` / `float(res.pvalue)`，报错来自 scipy 的 `TtestResult`： 它和 `PearsonRResult` 一样是 `_make_tuple_bunch` **运行时**拼出来的类，存根里没有这两个字段。 - 探针实测 `TtestResult(statistic=3.873, pvalue=0.0305)`，运行时取值完全正常 —— **不是真 bug**。 - 按决策 40 的路子补 `_statistic(result: Any) -> float`（与 `_pvalue` 成对），一行 `# type: ignore` 都没挂。 详情见 `docs/04-environment.md` 坑 10（已扩写为 pvalue / statistic 两条）。 ## 顺手查出来的真 bug：`confidence_interval` - 原码 `return (float(min(0.0, lower)), float(max(upper, 1.0)))`： ① `min` / `max` 的**参数写反**，下界被钉死成 `0.0`； ② **无条件**把三种 method 的区间都夹到 `[0, 1]`。 - 实测 `confidence_interval(rng.normal(170, 8, 50), method="t")` 下界是 `0.0`（正确 `171.0 ± 2.1`）； `confidence=1.5` 被夹成 `(0.0, nan)` 而不报错。 - 现在：**只有 `proportion` 夹**（决策 42），`normal` / `t` 返回 `mean ± z|t·se` 不夹； `method` 非法抛 `ValueError`（§4.7）、`confidence` 走 `(0, 1)` 开区间、样本量 < 2 抛 `ValueError`。 - 入参放宽到 `list` / `tuple` / `ndarray` / `Series` / `DataFrame`： docstring 的 Examples 传 list、L0 用例传 ndarray，原来**两条都直接 `TypeError`**。 ## t_test - docstring 补齐 `Parameters` / `Returns` / `Raises` / `Notes`（§4.7）； `_clean_data` 改用 `isinstance(data, pd.DataFrame)` 收窄（坑 8 的 `cast`）； `alpha` 开区间校验；`df` 按 Welch–Satterthwaite / pooled / paired 分别给。 - **4 个口径未代选**（决策 39），已记进 `STATUS.md`「下一步」第 6 条待用户拍板： 单样本结论文案、`paired` 的 NaN 对齐、`value` 被静默忽略、`DataFrame` 摊平多列。 ## 测试与文档 - `tests/test_stats.py` +10 条（36 → 46），含把原先挂 skip 的 `test_confidence_interval_matches_scipy` 转正；对照一律用解析式（z 公式 / Welch df / t 公式）。 - 全量：**125 passed / 37 skipped / 0 xfail**，ruff 0，pyright 0。 - 个人易错点新增第 15 条，并把**停在 6 号**的索引表补齐到 15（只补索引，正文未动）。 - `docs/04-environment.md` 顺手修掉残留的 `[FENCE]` 代码围栏占位符与一处重复的 `---`。 - `STATUS.md`：L0 记 9/12；校正测试数为 162 条；新增决策 42 / 43。
518 lines
18 KiB
Python
518 lines
18 KiB
Python
"""stats 包测试。
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原则（见 docs/02-architecture.md §5）：**测已知解析解，不测实现细节**。
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未实现的函数**逐条** `skip`——**不要**用模块级 `pytestmark`：那会把同文件里
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已经写好的函数一起跳过，绿灯就是假的（决策 26 / 个人易错点 9）。
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"""
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from __future__ import annotations
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import numpy as np
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import pandas as pd
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import pytest
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_NOT_IMPLEMENTED = "未实现：见 docs/03-roadmap.md L1"
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def _pearson_p_from_r(r: float, n: int) -> float:
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"""Pearson 相关系数的 p 值**解析式**（测解析解，不测实现细节）：
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``t = r * sqrt((n - 2) / (1 - r^2))``，``p = 2 * P(T > |t|)``，``T ~ t(n - 2)``。
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"""
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from scipy import stats as sps
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t_stat = r * np.sqrt((n - 2) / (1 - r**2))
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return float(2 * sps.t.sf(abs(t_stat), n - 2))
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@pytest.mark.skip(reason=_NOT_IMPLEMENTED)
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def test_bootstrap_ci_matches_normal_theory_on_large_n(rng):
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"""大样本下 bootstrap 百分位区间应逼近正态解析区间（±10% 容差）。"""
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from mcm_toolkit.stats import bootstrap_ci
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x = rng.normal(10, 2, size=5000)
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r = bootstrap_ci(x, statistic=np.mean, confidence=0.95, n_resamples=5000, random_state=0)
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se = x.std(ddof=1) / np.sqrt(x.size)
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assert abs((r.params["high"] - r.params["low"]) - 2 * 1.96 * se) < 0.1 * 2 * 1.96 * se
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@pytest.mark.skip(reason=_NOT_IMPLEMENTED)
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def test_bootstrap_ci_works_for_arbitrary_statistic(rng):
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"""bootstrap 的核心价值：任意统计量都能给区间（这里用中位数）。"""
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from mcm_toolkit.stats import bootstrap_ci
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x = rng.lognormal(0, 1, size=2000)
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r = bootstrap_ci(x, statistic=np.median, random_state=0)
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assert r.params["low"] < r.params["high"]
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assert r.params["low"] < np.median(x) < r.params["high"]
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@pytest.mark.skip(reason=_NOT_IMPLEMENTED)
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def test_bootstrap_ci_is_reproducible(rng):
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from mcm_toolkit.stats import bootstrap_ci
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x = rng.normal(size=500)
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a = bootstrap_ci(x, statistic=np.mean, random_state=123)
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b = bootstrap_ci(x, statistic=np.mean, random_state=123)
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assert a.params["low"] == b.params["low"]
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def test_confidence_interval_matches_scipy(rng):
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from scipy import stats
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from mcm_toolkit.stats import confidence_interval
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x = rng.normal(5, 1, size=50)
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lo, hi = confidence_interval(x, confidence=0.95, method="t")
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ref = stats.t.interval(0.95, len(x) - 1, loc=x.mean(), scale=stats.sem(x))
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assert np.allclose([lo, hi], ref, rtol=1e-6)
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def test_confidence_interval_normal_matches_z_formula(rng):
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"""normal 走 z 解析式：`mean ± z·s/√n`，s 用**样本**标准差（ddof=1）。"""
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from scipy import stats as sps
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from mcm_toolkit.stats import confidence_interval
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x = rng.normal(8.5, 1, size=200)
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lo, hi = confidence_interval(x, confidence=0.95, method="normal")
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half = float(sps.norm.ppf(0.975)) * x.std(ddof=1) / np.sqrt(len(x))
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assert lo == pytest.approx(x.mean() - half)
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assert hi == pytest.approx(x.mean() + half)
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def test_confidence_interval_mean_is_not_clamped_to_unit_range(rng):
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"""均值区间不该被夹到 [0, 1]：平均身高 170cm 的下界不可能是 0。"""
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from mcm_toolkit.stats import confidence_interval
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x = rng.normal(170, 8, size=50)
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lo, hi = confidence_interval(x, method="t")
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assert lo > 100.0
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assert lo < hi
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def test_confidence_interval_proportion_stays_in_unit_interval():
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"""比例的区间必须落在 [0, 1] 里 —— 只有这一种 method 需要夹。"""
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from mcm_toolkit.stats import confidence_interval
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y = [0.0, 1.0, 1.0, 1.0, 0.0, 1.0]
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lo, hi = confidence_interval(y, method="proportion")
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assert 0.0 <= lo < hi <= 1.0
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def test_confidence_interval_accepts_documented_containers():
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"""docstring 的 Examples 传 list、L0 用例传 ndarray，两边都得收。"""
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from mcm_toolkit.stats import confidence_interval
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data = [1.0, 2.0, 3.0, 4.0, 5.0]
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expected = confidence_interval(data)
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assert confidence_interval(pd.Series(data)) == pytest.approx(expected)
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assert confidence_interval(np.asarray(data)) == pytest.approx(expected)
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assert confidence_interval(pd.DataFrame({"x": data})) == pytest.approx(expected)
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def test_confidence_interval_rejects_bad_input(rng):
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from mcm_toolkit.stats import confidence_interval
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x = rng.normal(size=20)
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with pytest.raises(TypeError):
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confidence_interval("abc")
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with pytest.raises(ValueError):
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confidence_interval(x, method="bogus")
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with pytest.raises(ValueError):
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confidence_interval(x, confidence=1.5)
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with pytest.raises(ValueError):
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confidence_interval(x, confidence=0.0)
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with pytest.raises(ValueError):
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confidence_interval(pd.DataFrame({"city": ["X", "Y"]}))
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with pytest.raises(ValueError):
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confidence_interval([1.0])
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# ------------------------------------------------------ stats: t_test
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def test_t_test_one_sample_matches_analytic_formula(rng):
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"""单样本：`t = (mean - value) / (s/√n)`，`df = n - 1`，`p = 2·P(T > |t|)`。"""
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from scipy import stats as sps
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from mcm_toolkit.stats import t_test
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x = rng.normal(5, 1, size=30)
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r = t_test(x, value=5.0)
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t_stat = (x.mean() - 5.0) / (x.std(ddof=1) / np.sqrt(len(x)))
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assert r["statistic"] == pytest.approx(t_stat)
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assert r["pvalue"] == pytest.approx(float(2 * sps.t.sf(abs(t_stat), len(x) - 1)))
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assert r["df"] == pytest.approx(29.0)
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assert r["significant"] == (r["pvalue"] < 0.05)
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assert isinstance(r["conclusion"], str) and r["conclusion"]
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def test_t_test_two_sample_welch_df_matches_formula(rng):
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"""默认 Welch：`df` 用 Welch–Satterthwaite 公式解析对照。"""
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from mcm_toolkit.stats import t_test
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a = rng.normal(0, 1, size=25)
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b = rng.normal(1, 4, size=35)
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r = t_test(a, b)
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v1, v2 = a.var(ddof=1), b.var(ddof=1)
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n1, n2 = len(a), len(b)
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expected_df = (v1 / n1 + v2 / n2) ** 2 / ((v1 / n1) ** 2 / (n1 - 1) + (v2 / n2) ** 2 / (n2 - 1))
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assert r["df"] == pytest.approx(expected_df)
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assert r["pvalue"] < 0.05
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def test_t_test_equal_var_uses_pooled_df(rng):
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from mcm_toolkit.stats import t_test
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a = rng.normal(0, 1, size=25)
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b = rng.normal(1, 1, size=35)
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assert t_test(a, b, equal_var=True)["df"] == pytest.approx(58.0)
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def test_t_test_paired_reports_key_set_and_df(rng):
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from mcm_toolkit.stats import t_test
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a = rng.normal(size=20)
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r = t_test(a, a + rng.normal(0, 0.1, 20), paired=True)
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assert set(r) == {"statistic", "pvalue", "df", "significant", "conclusion"}
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assert r["df"] == pytest.approx(19.0)
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def test_t_test_rejects_bad_input(rng):
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from mcm_toolkit.stats import t_test
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a = rng.normal(size=20)
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with pytest.raises(ValueError):
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t_test(a, alpha=1.5)
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with pytest.raises(ValueError):
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t_test([1.0])
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with pytest.raises(ValueError):
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t_test(a, rng.normal(size=19), paired=True)
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with pytest.raises(ValueError):
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t_test(pd.DataFrame({"city": ["X", "Y"]}))
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with pytest.raises(TypeError):
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t_test("abc")
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def test_correlation_matrix_diagonal_is_one(rng):
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from mcm_toolkit.stats import correlation_matrix
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x = pd.DataFrame(rng.normal(size=(200, 4)), columns=["a", "b", "c", "d"])
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c = correlation_matrix(x)
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assert np.allclose(np.diag(np.asarray(c)), 1.0)
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def test_correlation_matrix_is_numeric_and_symmetric(rng):
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"""方案 A：返回**数值**矩阵（不是带星标的字符串表），能直接参与后续计算。"""
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from mcm_toolkit.stats import correlation_matrix
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x = pd.DataFrame(rng.normal(size=(200, 3)), columns=["a", "b", "c"])
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c = correlation_matrix(x)
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assert all(np.issubdtype(dtype, np.floating) for dtype in c.dtypes)
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assert np.allclose(np.asarray(c), np.asarray(x.corr(method="pearson", min_periods=1)))
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assert np.allclose(np.asarray(c), np.asarray(c.T))
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def test_correlation_matrix_runs_on_multicolumn_frame(rng):
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"""回归：`if numeric_cols == 0` 拿 Index 跟 0 比，多列数值表当场 ValueError 崩掉。"""
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from mcm_toolkit.stats import correlation_matrix
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x = pd.DataFrame(rng.normal(size=(50, 3)), columns=["a", "b", "c"])
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out = correlation_matrix(x)
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assert out.shape == (3, 3)
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assert list(out.columns) == ["a", "b", "c"]
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assert list(out.index) == ["a", "b", "c"]
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def test_correlation_matrix_skips_non_numeric_columns(rng):
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from mcm_toolkit.stats import correlation_matrix
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x = pd.DataFrame({"a": rng.normal(size=30), "b": rng.normal(size=30), "city": ["X"] * 30})
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assert list(correlation_matrix(x).columns) == ["a", "b"]
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def test_correlation_matrix_rejects_bad_input():
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from mcm_toolkit.stats import correlation_matrix
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with pytest.raises(TypeError):
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correlation_matrix([[1.0, 2.0]])
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with pytest.raises(ValueError):
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correlation_matrix(pd.DataFrame({"city": ["X", "Y"]}))
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with pytest.raises(ValueError):
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correlation_matrix(pd.DataFrame({"a": [1.0, 2.0]}), method="bogus") # type: ignore[arg-type]
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def test_correlation_pvalues_matches_analytic_formula(rng):
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from mcm_toolkit.stats import correlation_matrix, correlation_pvalues
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x = pd.DataFrame(rng.normal(size=(80, 3)), columns=["a", "b", "c"])
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corr = correlation_matrix(x)
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p = correlation_pvalues(x)
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for i in ["a", "b", "c"]:
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for j in ["a", "b", "c"]:
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if i == j:
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continue
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assert p.loc[i, j] == pytest.approx(_pearson_p_from_r(corr.loc[i, j], 80))
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def test_correlation_pvalues_diagonal_is_nan(rng):
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"""对角线写 0 会被下游读成"极显著"；"自己和自己相关"没有 p 值，必须是 NaN。"""
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from mcm_toolkit.stats import correlation_pvalues
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p = correlation_pvalues(pd.DataFrame(rng.normal(size=(50, 2)), columns=["a", "b"]))
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assert np.isnan(p.loc["a", "a"])
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assert np.isnan(p.loc["b", "b"])
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def test_correlation_pvalues_uses_the_same_observations_as_r(rng):
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"""含缺失时 p 要和 r 用**同一批**观测：成对删缺失，而不是整行删、也不是干脆不删。"""
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from mcm_toolkit.stats import correlation_pvalues
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a = rng.normal(size=40)
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b = rng.normal(size=40)
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a[[3, 7, 11]] = np.nan
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x = pd.DataFrame({"a": a, "b": b})
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pair = x.dropna()
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r = float(np.corrcoef(pair["a"], pair["b"])[0, 1])
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assert correlation_pvalues(x).loc["a", "b"] == pytest.approx(_pearson_p_from_r(r, len(pair)))
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def test_correlation_pvalues_respects_min_periods(rng):
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from mcm_toolkit.stats import correlation_pvalues
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a = rng.normal(size=10)
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a[:5] = np.nan
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x = pd.DataFrame({"a": a, "b": rng.normal(size=10)})
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assert np.isnan(correlation_pvalues(x, min_periods=6).loc["a", "b"])
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assert np.isfinite(correlation_pvalues(x, min_periods=5).loc["a", "b"])
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def test_correlation_table_diagonal_has_no_stars():
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"""对角线是"自己和自己"，不该有显著性星标；完全负相关则必然是 ***。"""
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from mcm_toolkit.stats import correlation_table
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x = pd.DataFrame({"a": np.arange(30.0), "b": np.arange(30.0) * -2.0})
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table = correlation_table(x)
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assert table.loc["a", "a"] == "1.000"
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assert table.loc["a", "b"] == "-1.000***"
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def test_correlation_table_matches_the_numeric_outputs(rng):
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from mcm_toolkit.stats import correlation_matrix, correlation_pvalues, correlation_table
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x = pd.DataFrame(rng.normal(size=(60, 3)), columns=["a", "b", "c"])
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corr = correlation_matrix(x)
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p = correlation_pvalues(x)
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table = correlation_table(x)
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assert list(table.columns) == list(corr.columns)
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assert table.loc["a", "a"] == "1.000"
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assert np.isnan(p.loc["a", "a"])
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pv = p.loc["a", "b"]
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stars = "***" if pv < 0.001 else "**" if pv < 0.01 else "*" if pv < 0.05 else ""
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value = corr.loc["a", "b"]
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assert table.loc["a", "b"] == f"{value:.3f}" + stars
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# ------------------------------------------------------ stats: describe
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def test_describe_reports_expected_keys(rng):
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from mcm_toolkit.stats import describe
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table = describe(rng.normal(size=(100, 3)))
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for key in ["mean", "std", "min", "max", "median"]:
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assert key in table.index
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def test_describe_rows_are_metrics_and_columns_are_variables():
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"""方向约定：行 = 指标，列 = 变量。多转置一次就反了。"""
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from mcm_toolkit.stats import describe
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df = pd.DataFrame({"a": [1.0, 2.0, 3.0], "b": [10.0, 20.0, 30.0]})
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table = describe(df)
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assert list(table.columns) == ["a", "b"]
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assert table.loc["mean", "a"] == pytest.approx(2.0)
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assert table.loc["max", "b"] == pytest.approx(30.0)
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assert table.loc["median", "b"] == pytest.approx(20.0)
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||
|
||
|
||
def test_describe_missing_and_shape_rows_are_not_nan():
|
||
"""曾经的静默 bug：转置后 `.loc[指标名] = <按变量索引的 Series>` 对不上列，
|
||
整行会被填成 NaN —— 不报错，但数据全丢。"""
|
||
from mcm_toolkit.stats import describe
|
||
|
||
df = pd.DataFrame({"a": [1.0, np.nan, 3.0, 4.0], "b": [1.0, 2.0, 3.0, 4.0]})
|
||
table = describe(df)
|
||
|
||
assert table.loc["missing", "a"] == pytest.approx(1.0)
|
||
assert table.loc["missing", "b"] == pytest.approx(0.0)
|
||
assert table.loc["missing_ratio", "a"] == pytest.approx(0.25)
|
||
assert table.loc["missing_ratio", "b"] == pytest.approx(0.0)
|
||
assert table.loc["skewness", "b"] == pytest.approx(0.0, abs=1e-12)
|
||
extra = table.loc[["missing", "missing_ratio", "skewness", "kurtosis"]]
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||
assert not bool(extra.isna().all(axis=None))
|
||
|
||
|
||
def test_describe_skips_non_numeric_columns():
|
||
from mcm_toolkit.stats import describe
|
||
|
||
df = pd.DataFrame({"a": [1.0, 2.0], "city": ["X", "Y"]})
|
||
table = describe(df)
|
||
|
||
assert list(table.columns) == ["a"]
|
||
|
||
|
||
def test_describe_accepts_ndarray_list_and_series(rng):
|
||
"""兄弟函数都收 ndarray / list，describe 没理由只收 DataFrame。"""
|
||
from mcm_toolkit.stats import describe
|
||
|
||
assert "mean" in describe(rng.normal(size=(50, 2))).index
|
||
assert "mean" in describe([[1.0, 2.0], [3.0, 4.0]]).index
|
||
assert "mean" in describe(pd.Series([1.0, 2.0, 3.0])).index
|
||
|
||
|
||
def test_describe_weighted_rows_match_manual_formula():
|
||
from mcm_toolkit.stats import describe
|
||
|
||
df = pd.DataFrame({"a": [1.0, 2.0, 3.0]})
|
||
w = np.array([1.0, 1.0, 2.0])
|
||
table = describe(df, weights=w)
|
||
|
||
expect_mean = np.average(df["a"], weights=w)
|
||
expect_std = np.sqrt(np.average((df["a"] - expect_mean) ** 2, weights=w))
|
||
assert table.loc["weighted_mean", "a"] == pytest.approx(expect_mean)
|
||
assert table.loc["weighted_std", "a"] == pytest.approx(expect_std)
|
||
|
||
|
||
@pytest.mark.parametrize(
|
||
("weights", "exc"),
|
||
[
|
||
(np.ones(2), ValueError),
|
||
(np.zeros(3), ValueError),
|
||
(np.array([1.0, -1.0, 1.0]), ValueError),
|
||
(np.array([1.0, np.nan, 1.0]), ValueError),
|
||
("abc", TypeError),
|
||
],
|
||
)
|
||
def test_describe_rejects_bad_weights(weights, exc):
|
||
from mcm_toolkit.stats import describe
|
||
|
||
with pytest.raises(exc):
|
||
describe(pd.DataFrame({"a": [1.0, 2.0, 3.0]}), weights=weights)
|
||
|
||
|
||
def test_describe_rejects_unsupported_type_and_all_text_frame():
|
||
from mcm_toolkit.stats import describe
|
||
|
||
with pytest.raises(TypeError):
|
||
describe({"a": [1.0]})
|
||
with pytest.raises(ValueError):
|
||
describe(pd.DataFrame({"city": ["X", "Y"]}))
|
||
|
||
|
||
# ------------------------------------------------------ stats: zscore
|
||
|
||
|
||
def test_zscore_matches_manual_formula():
|
||
from mcm_toolkit.stats import zscore
|
||
|
||
x = np.array([1.0, 2.0, 3.0, 4.0])
|
||
assert np.allclose(np.asarray(zscore(x)), (x - x.mean()) / x.std())
|
||
|
||
|
||
def test_zscore_is_per_column_and_keeps_frame(rng):
|
||
from mcm_toolkit.stats import zscore
|
||
|
||
df = pd.DataFrame({"a": rng.normal(size=200), "b": rng.normal(5, 3, size=200)})
|
||
out = zscore(df)
|
||
|
||
assert isinstance(out, pd.DataFrame)
|
||
assert list(out.columns) == ["a", "b"]
|
||
assert np.allclose(np.asarray(out).mean(axis=0), 0.0, atol=1e-12)
|
||
assert np.allclose(np.asarray(out).std(axis=0), 1.0, atol=1e-12)
|
||
|
||
|
||
def test_zscore_constant_column_stays_zero():
|
||
from mcm_toolkit.stats import zscore
|
||
|
||
assert np.allclose(np.asarray(zscore([2.0, 2.0, 2.0])), 0.0)
|
||
|
||
|
||
def test_zscore_rejects_bad_type_and_all_text_frame():
|
||
from mcm_toolkit.stats import zscore
|
||
|
||
with pytest.raises(TypeError):
|
||
zscore("abc")
|
||
with pytest.raises(ValueError):
|
||
zscore(pd.DataFrame({"city": ["X"]}))
|
||
|
||
|
||
# ------------------------------------------- stats: coefficient_of_variation
|
||
|
||
|
||
def test_coefficient_of_variation_matches_manual_formula():
|
||
from mcm_toolkit.stats import coefficient_of_variation
|
||
|
||
x = np.array([1.0, 2.0, 3.0, 4.0])
|
||
assert coefficient_of_variation(x) == pytest.approx(x.std() / x.mean())
|
||
|
||
|
||
def test_coefficient_of_variation_accepts_single_column_frame():
|
||
from mcm_toolkit.stats import coefficient_of_variation
|
||
|
||
df = pd.DataFrame({"a": [1.0, 2.0, 3.0]})
|
||
single = coefficient_of_variation([1.0, 2.0, 3.0])
|
||
assert coefficient_of_variation(df) == pytest.approx(single)
|
||
|
||
|
||
def test_coefficient_of_variation_uses_absolute_mean():
|
||
"""均值为负时 CV 仍是**正数**：符号不该被读成"波动更小"。"""
|
||
from mcm_toolkit.stats import coefficient_of_variation
|
||
|
||
x = np.array([-1.0, -2.0, -3.0, -4.0])
|
||
assert coefficient_of_variation(x) == pytest.approx(x.std() / abs(x.mean()))
|
||
assert coefficient_of_variation(x) > 0
|
||
|
||
|
||
def test_coefficient_of_variation_zero_mean_is_value_error():
|
||
"""均值为 0 是**取值**问题不是类型问题：必须是 ValueError 而不是 TypeError。"""
|
||
from mcm_toolkit.stats import coefficient_of_variation
|
||
|
||
with pytest.raises(ValueError):
|
||
coefficient_of_variation([-1.0, 1.0])
|
||
|
||
|
||
def test_coefficient_of_variation_rejects_empty_2d_and_bad_type():
|
||
from mcm_toolkit.stats import coefficient_of_variation
|
||
|
||
with pytest.raises(ValueError):
|
||
coefficient_of_variation([])
|
||
with pytest.raises(ValueError):
|
||
coefficient_of_variation([[1.0, 2.0], [3.0, 4.0]])
|
||
with pytest.raises(ValueError):
|
||
coefficient_of_variation(pd.DataFrame({"a": [1.0], "b": [2.0]}))
|
||
with pytest.raises(TypeError):
|
||
coefficient_of_variation(5.0)
|