omnistats 0.4.0__tar.gz

omnistats-0.4.0/.gitignore

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+# Internal Framework Specs & Agent Skills (NEVER push to GitHub)
+framework_specs/
+scio-framework-specs/
+.agent/
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# Distribution / packaging
+dist/
+build/
+*.egg-info/
+.eggs/
+
+# Unit test / coverage / type-check caches
+.pytest_cache/
+.coverage
+coverage.xml
+htmlcov/
+.mypy_cache/
+.ruff_cache/
+.hypothesis/
+
+# Virtual environments
+.venv/
+venv/
+env/
+
+# IDE / OS
+.vscode/
+.idea/
+.DS_Store
+Thumbs.db
+*.gdoc

omnistats-0.4.0/.pre-commit-config.yaml

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+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v5.0.0
+    hooks:
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+      - id: check-yaml
+      - id: check-toml
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.9.0
+    hooks:
+      - id: ruff
+        args: [--fix]
+      - id: ruff-format
+  - repo: local
+    hooks:
+      - id: check-module-size-and-layers
+        name: Check module size budgets and layer contracts
+        entry: python scripts/check_module_size.py
+        language: system
+        pass_filenames: false

omnistats-0.4.0/CHANGELOG.md

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+# Changelog
+
+All notable changes to **`omnistats`** are documented in this file.
+
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/),
+and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+
+## [0.4.0] - 2026-11-04
+
+### Changed
+- **Official Rebranding to `omnistats`:**
+  - Package renamed to **`omnistats`** on PyPI (`pip install omnistats`).
+  - Primary namespace: `import omnistats as os` or `import omnistats as omni`, with `import omnistats.functional as F`.
+  - Added full backwards-compatibility shim for `pyscio` (`import pyscio as sc` continues to work with a deprecation notice).
+  - DataFrame accessors registered under both `df.omni` (primary) and `df.scio` (alias) across Pandas and Polars.
+
+## [0.3.0] - 2026-11-04
+
+### Added
+- **Survival & Time-to-Event Analysis (S1 — `F.kaplan_meier`, `F.logrank_test`, `sc.coxph`):**
+  - Kaplan-Meier product-limit survival estimator (`F.kaplan_meier`) with Greenwood variance, Kalbfleisch-Prentice $[0, 1]$ log-log confidence intervals, and median survival time.
+  - Mantel-Cox Log-Rank test (`F.logrank_test`) for right-censored survival comparisons with Mantel-Haenszel Hazard Ratios.
+  - Cox Proportional Hazards regression (`sc.coxph(df, "Surv(time, event) ~ x1 + x2")`, `df.scio.coxph`, and automatic `sc.compare(df, "Surv(time, event) ~ ...")` routing) via Breslow partial likelihood Newton-Raphson with Hazard Ratios ($\text{HR} = \exp(\beta)$) and Harrell's Concordance Index ($C$-statistic).
+- **Causal Inference & Propensity Adjustment (S2 — `sc.ate`, `sc.covariate_balance`):**
+  - Robins-Rotnitzky-Zhao **Doubly Robust Augmented Inverse Probability Weighting (`sc.ate(method="aipw")`)** and **Hajek IPTW (`sc.ate(method="iptw")`)** with semiparametric influence-function standard errors and positivity overlap guards.
+  - Standardized Mean Difference covariate balance auditing (`sc.covariate_balance`, `df.scio.covariate_balance`) comparing unweighted vs. propensity-weighted $|\text{SMD}| < 0.10$.
+- **Time-Series Stationarity, Autocorrelation, & HAC Standard Errors (S3 — `F.adf_test`, `F.ljung_box`, `F.durbin_watson`, `sc.ols(robust_se="HAC")`):**
+  - Augmented Dickey-Fuller (`F.adf_test`) unit-root test with Schwert lag selection and MacKinnon response-surface $p$-values.
+  - Ljung-Box portmanteau serial autocorrelation test (`F.ljung_box`) and Durbin-Watson residual autocorrelation statistic (`F.durbin_watson`).
+  - Newey-West Heteroscedasticity and Autocorrelation Consistent (**HAC**) Bartlett-kernel covariance estimator in `sc.ols(..., robust_se="HAC", hac_lags=...)`.
+
+## [0.2.0] - 2026-11-04
+
+### Added
+- **5-Layer Modular Architecture & Enforcement (R0–R6):** Split large modules into `omnistats/core/results/`, `omnistats/models/`, `omnistats/stat/router/`, and `omnistats/integrations/`, enforced by `scripts/check_module_size.py --strict` in CI.
+- **Lazy Package Startup (PEP 562, R5/R8):** `import omnistats` loads submodules on demand via `importlib.import_module` with `globals()` caching.
+- **Distributional Pathology Guards (`F.check_pathology`, `F.sarle_bimodality`):** Screens for point-mass/zero-inflation ($\ge 30\%$ ties), heavy-tailed/Cauchy regimes ($\text{SD}/(\text{IQR}/1.34898) > 2.2$), and bimodal mixtures (Sarle's $BC > 0.555$) before permitting Large-$N$ CLT overrides.
+- **Exact Non-Central $t$ Effect Size Confidence Intervals (`F.cohen_d_ci`, `F.hedges_g_ci`, `F.cliffs_d_ci`):** Populates `TestResult.effect_ci` across two-sample, paired, and one-sample designs.
+- **Tensor-Broadcasted Post-Hoc Pairwise Algorithms (`F.tukey`, `F.games_howell`, `F.dunn`):** Replaced Python pair loops with `np.triu_indices` upper-triangle tensor broadcasting and `np.add.reduceat`.
+- **Wilkinson Formula Engine & Multivariate Models (`sc.ols`, `sc.logistic`, `sc.poisson`, `sc.anova_table`, `sc.mixedlm`):**
+  - Ordinary Least Squares (`sc.ols`) with QR decomposition and MacKinnon-White HC0–HC3 robust standard errors.
+  - Type II & Type III Factorial ANOVA / ANCOVA tables (`sc.anova_table`) with partial $\eta_p^2$ and $\omega^2$.
+  - Binary Logistic Regression (`sc.logistic`) via Newton-Raphson IRLS with Odds Ratios.
+  - Poisson Log-Linear GLM (`sc.poisson`) via IRLS with QMLE HC3 sandwich SEs, Incidence Rate Ratios ($\text{IRR}$), and Pearson overdispersion diagnostics.
+  - Linear Mixed-Effects Models (`sc.mixedlm` and `sc.compare(df, "y ~ x + (1 | cluster)")`) via exact Profiled REML / ML with QR whitening, Intraclass Correlation Coefficient ($\text{ICC}$), and Nakagawa's Marginal ($R^2_m$) & Conditional ($R^2_c$) $R^2$.
+- **Resampling, Equivalence, & Robust Statistics:** Added `F.permutation_test`, `F.bootstrap_ci` ($BC_a$), `sc.tost` / `F.tost`, `F.trimmed_mean`, `F.winsorized_mean`, `F.huber_location`, and `F.yuen_t`.
+- **Complete Correlation Suite (`F.pearson_r`, `F.spearman_r`, `F.kendall_tau`, `F.partial_corr`):** `sc.compare(df, x="num1", y="num2")` automatically routes continuous-vs-continuous pairs to Pearson $r$ or Spearman $\rho$ with exact $z$-transformed CIs; added Kendall's $\tau_b$ and QR-projected partial correlation.
+- **Paired Categorical & Repeated-Measures K-Sample (`F.mcnemar`, `F.rm_anova`, `F.friedman`, `F.kendalls_w`):** Added exact/asymptotic McNemar test for paired $2\times 2$ tables and autonomous repeated-measures routing (`sc.compare(df, x="condition", y="score", paired=True)`) between One-Way Repeated-Measures ANOVA (with Greenhouse-Geisser sphericity adjustment $\hat{\varepsilon}_{GG}$) and Friedman's test (with Kendall's $W$).
+- **Default Bayes Factors (`F.bayes_factor_t`, `F.interpret_bf`):** Added Rouder's JZS (Jeffreys-Zellner-Siow) Bayes Factor ($BF_{10}$ and $BF_{01}$) for one-sample, paired, and two-sample $t$-tests via 1D Gaussian quadrature.
+- **APA 7th Edition Reporting (`.apa()`):** Added `.apa()` and `summary(format="apa")` to `TestResult` and `RegressionResult`.
+- **Bidirectional Power & Sample Size Solver (`sc.solve_power`, `F.solve_power_t`):** Solves for required sample size $n$ per group, statistical power, or minimum detectable effect size $d$.
+- **Ecosystem Extras (`omnistats[plot]`, `omnistats[polars]`):**
+  - Dual-backend `.plot()` method on `TestResult`, `RegressionResult`, `ScreenReport`, and `EDAReport`, plus `sc.plot_raincloud` / `df.scio.plot_raincloud` supporting both `matplotlib` and zero-dependency `SVGFigure`.
+  - Universal DataFrame coercion (`ensure_pandas_df`) and `PolarsScioNamespace` (`pl_df.scio`) supporting Pandas, Polars (`DataFrame` & `LazyFrame`), Narwhals, PyArrow, and Python dicts.
+- **Documentation, Benchmarks, & Governance Suite:** Added MkDocs-Material documentation under `docs/`, micro-benchmark suite under `benchmarks/bench_kernels.py`, `CITATION.cff`, `CONTRIBUTING.md`, `CODE_OF_CONDUCT.md`, and `SECURITY.md`.
+
+## [0.1.0] - 2026-11-03
+
+### Added
+- Initial release of `omnistats` with `omnistats.core`, `omnistats.functional`, `omnistats.eda`, `omnistats.stat`, Pandas `.scio` accessor, and Rich CLI.

omnistats-0.4.0/CITATION.cff

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+cff-version: 1.2.0
+title: "omnistats: Autonomous Statistical Inference Engine, One-Tap EDA, and Pure Numerical Hypothesis Testing"
+message: "If you use omnistats in your research or software, please cite it using the metadata below."
+type: software
+authors:
+  - alias: "Mr-Rup"
+    email: "majumdarb107@gmail.com"
+repository-code: "https://github.com/Mr-Rup/scio"
+url: "https://mr-rup.github.io/scio/"
+license: Apache-2.0
+keywords:
+  - statistics
+  - hypothesis-testing
+  - exploratory-data-analysis
+  - effect-sizes
+  - python
+  - econometrics
+  - biostatistics

omnistats-0.4.0/CODE_OF_CONDUCT.md

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+# Contributor Covenant Code of Conduct
+
+## Our Pledge
+
+We as members, contributors, and leaders pledge to make participation in our
+community a harassment-free experience for everyone, regardless of age, body
+size, visible or invisible disability, ethnicity, sex characteristics, gender
+identity and expression, level of experience, education, socio-economic status,
+nationality, personal appearance, race, caste, color, religion, or sexual
+identity and orientation.
+
+## Our Standards
+
+Examples of behavior that contributes to a positive environment include:
+* Demonstrating empathy and kindness toward other people
+* Being respectful of differing opinions, viewpoints, and experiences
+* Giving and gracefully accepting constructive feedback
+* Accepting responsibility and apologizing to those affected by our mistakes
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported to the project maintainer at `majumdarb107@gmail.com`. All complaints
+will be reviewed and investigated promptly and fairly.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant](https://www.contributor-covenant.org), version 2.1.

omnistats-0.4.0/CONTRIBUTING.md

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+# Contributing to omnistats
+
+Thank you for contributing to **`omnistats`**! We follow strict engineering, mathematical, and architectural standards to keep the library fast, modular, and trustworthy.
+
+## 1. Development Setup
+
+We recommend [`uv`](https://docs.astral.sh/uv/) for environment and dependency management:
+
+```bash
+git clone https://github.com/Mr-Rup/scio.git
+cd scio
+uv sync --extra dev
+```
+
+## 2. Engineering & Architectural Rules
+
+1. **Module Size Budgets:**
+   - Library files (`omnistats/**/*.py`): soft limit **300 lines**, hard limit **400 lines**.
+   - Test files (`tests/**/*.py`): hard limit **450 lines**.
+2. **5-Layer Downward Dependency Graph:**
+   - `L0 (omnistats.core)` $\leftarrow$ `L1 (omnistats.functional)` $\leftarrow$ `L2 (omnistats.models)` $\leftarrow$ `L3 (omnistats.stat | omnistats.eda)` $\leftarrow$ `L4 (omnistats.integrations | omnistats.cli)`.
+   - Lower layers must never import higher layers, and `omnistats.stat` and `omnistats.eda` must remain independent.
+3. **Pure Stateless Kernels (`omnistats.functional`):**
+   - Kernels return lightweight `NamedTuple`s from `omnistats.core.types` and never import `omnistats.core.results`.
+4. **Strict Typing & Error Hierarchy:**
+   - All functions require complete type annotations (`mypy --strict`).
+   - Raise domain errors from `omnistats.core.errors` (`StatError`, `SampleSizeError`, `ZeroVarError`, `DtypeError`, `MissingDataError`), which dual-inherit standard Python exceptions.
+
+## 3. Pre-Submission Verification Gate
+
+Run all checks locally before opening a Pull Request:
+
+```bash
+uv run ruff format --check .
+uv run ruff check .
+uv run mypy omnistats
+uv run python scripts/check_module_size.py --strict
+uv run pytest
+```

omnistats-0.4.0/LICENSE

@@ -0,0 +1,176 @@
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+      the terms of any separate license agreement you may have executed
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+   6. Trademarks. This License does not grant permission to use the trade
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omnistats-0.4.0/PKG-INFO

@@ -0,0 +1,171 @@
+Metadata-Version: 2.5
+Name: omnistats
+Version: 0.4.0
+Summary: Autonomous Statistical Inference Engine, One-Tap EDA, and Universal Scientific Modeling
+Project-URL: Homepage, https://github.com/Mr-Rup/scio
+Project-URL: Documentation, https://mr-rup.github.io/scio/
+Project-URL: Repository, https://github.com/Mr-Rup/scio.git
+Project-URL: Issues, https://github.com/Mr-Rup/scio/issues
+Project-URL: Changelog, https://github.com/Mr-Rup/scio/blob/main/CHANGELOG.md
+Author-email: Mr-Rup <majumdarb107@gmail.com>
+License-Expression: Apache-2.0
+License-File: LICENSE
+Keywords: biostatistics,causal-inference,data-analysis,econometrics,eda,effect-sizes,hypothesis-testing,p-values,pandas,scipy,statistics,survival-analysis
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Developers
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: Apache Software License
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3.14
+Classifier: Topic :: Scientific/Engineering :: Information Analysis
+Classifier: Topic :: Scientific/Engineering :: Mathematics
+Classifier: Typing :: Typed
+Requires-Python: >=3.11
+Requires-Dist: numpy>=1.26.0
+Requires-Dist: pandas>=2.1.0
+Requires-Dist: rich>=13.0.0
+Requires-Dist: scipy>=1.11.0
+Provides-Extra: all
+Requires-Dist: matplotlib>=3.8.0; extra == 'all'
+Requires-Dist: narwhals>=1.0.0; extra == 'all'
+Requires-Dist: polars>=0.20.0; extra == 'all'
+Provides-Extra: dev
+Requires-Dist: hypothesis>=6.90.0; extra == 'dev'
+Requires-Dist: mypy>=1.8.0; extra == 'dev'
+Requires-Dist: pandas-stubs>=2.1.0; extra == 'dev'
+Requires-Dist: pytest-cov>=4.1.0; extra == 'dev'
+Requires-Dist: pytest>=8.0.0; extra == 'dev'
+Requires-Dist: ruff>=0.3.0; extra == 'dev'
+Provides-Extra: docs
+Requires-Dist: mkdocs-material>=9.5.0; extra == 'docs'
+Requires-Dist: mkdocs>=1.6.0; extra == 'docs'
+Requires-Dist: mkdocstrings[python]>=0.25.0; extra == 'docs'
+Provides-Extra: plot
+Requires-Dist: matplotlib>=3.8.0; extra == 'plot'
+Provides-Extra: polars
+Requires-Dist: narwhals>=1.0.0; extra == 'polars'
+Requires-Dist: polars>=0.20.0; extra == 'polars'
+Description-Content-Type: text/markdown
+
+# omnistats
+
+[![CI](https://github.com/Mr-Rup/scio/actions/workflows/ci.yml/badge.svg)](https://github.com/Mr-Rup/scio/actions/workflows/ci.yml)
+[![PyPI](https://img.shields.io/pypi/v/omnistats.svg)](https://pypi.org/project/omnistats/)
+[![Python](https://img.shields.io/pypi/pyversions/omnistats.svg)](https://pypi.org/project/omnistats/)
+[![License](https://img.shields.io/badge/License-Apache_2.0-blue.svg)](https://opensource.org/licenses/Apache-2.0)
+[![Code style: ruff](https://img.shields.io/badge/code%20style-ruff-000000.svg)](https://github.com/astral-sh/ruff)
+[![Type Checked: mypy](https://img.shields.io/badge/type%20checked-mypy%20strict-blue.svg)](https://github.com/python/mypy)
+
+**`omnistats`** is an autonomous statistical inference engine, one-tap exploratory data analysis (EDA) suite, multivariate regression toolkit, and pure numerical hypothesis testing framework for Python (`>= 3.11`).
+
+---
+
+## ⚡ Highlights
+
+* **Pure Stateless Mathematical Kernels (`omnistats.functional` as `F`):** PyTorch-style pure NumPy/SciPy kernels (`F.welch_t`, `F.mann_whitney`, `F.tukey`, `F.cohen_d`, `F.cliffs_d`, `F.fdr_bh`, `F.bootstrap_ci`, `F.yuen_t`) returning lightweight `NamedTuple`s with zero classes and zero side-effects.
+* **Autonomous Decision Lattice & Pathology Guards (`omnistats.stat`):** Inspects distribution shape (Shapiro-Wilk / D'Agostino $K^2$), checks for **point-mass zero-inflation**, **heavy-tailed / Cauchy regimes**, and **Sarle's bimodality ($BC > 0.555$)** before permitting a Large-$N$ ($N \ge 500$) Central Limit Theorem override, evaluates homoscedasticity (Levene / Brown-Forsythe), and routes to the mathematically optimal test.
+* **Exact Non-Central $t$ Effect Size CIs:** Computes exact Non-Central $t$-distribution confidence intervals (`F.cohen_d_ci`, `F.hedges_g_ci`) via Brent root-finding and $z$-transformed CIs for $O(N \log N)$ Cliff's $\delta$ (`F.cliffs_d_ci`), surfacing `effect_ci` on every `TestResult`.
+* **Tensor-Broadcasted Post-Hoc Pairwise Tests:** Significant $K > 2$ omnibus tests automatically trigger vectorized Tukey HSD (ANOVA), Games-Howell (Welch's ANOVA), or Dunn's test with BH/Holm adjustment (Kruskal-Wallis).
+* **Wilkinson Formulas & Robust Multivariate Models (`omnistats.models`):** Run `sc.compare(df, "y ~ x1 + C(group)")`, Ordinary Least Squares with MacKinnon-White **HC0–HC3** heteroscedasticity-robust standard errors (`sc.ols`), and Newton-Raphson IRLS binary logistic regression with Odds Ratios (`sc.logistic`).
+* **Resampling, Equivalence, & Robust Statistics:** Exact & vectorized Monte Carlo `F.permutation_test`, Bias-Corrected and Accelerated ($BC_a$) `F.bootstrap_ci`, Two One-Sided Tests for equivalence (`sc.tost`), Huber M-estimators (`F.huber_location`), and Yuen-Welch trimmed $t$-tests (`F.yuen_t`).
+* **Universal Pandas EDA (`omnistats.eda`) & Accessor (`df.scio`):** 8-role semantic column classification, vectorized profiling, 0–100 data health scoring, correlation/VIF matrices, and standalone interactive HTML reports.
+
+---
+
+## 📦 Installation
+
+```bash
+uv add omnistats
+# or
+pip install omnistats
+```
+
+---
+
+## 🚀 Quickstart
+
+### 1. One-Tap Exploratory Data Analysis (EDA)
+
+```python
+import omnistats as sc
+
+df = sc.read("clinical_trial.csv")  # Auto-sniffs CSV/TSV, Parquet, Excel, JSON
+report = df.scio.eda()
+print(report.summary())
+report.to_html("eda_report.html")
+```
+
+### 2. Autonomous Hypothesis Comparison & Wilkinson Formulas
+
+```python
+# Compare continuous outcome across treatment arms (auto-routes & computes exact effect CIs)
+result = df.scio.compare(x="treatment_arm", y="recovery_days")
+print(result.summary())
+
+# Or use Wilkinson formula syntax (bivariate or multivariate ANCOVA/OLS)
+res_formula = df.scio.compare("recovery_days ~ treatment_arm + baseline_score")
+```
+
+### 3. Multivariate Regression (OLS HC3 & IRLS Logistic)
+
+```python
+# Ordinary Least Squares with MacKinnon-White HC3 robust standard errors
+ols_res = sc.ols(df, "recovery_days ~ age * C(treatment_arm)", robust_se="HC3")
+print(ols_res.summary())
+
+# Binary Logistic Regression with Odds Ratios and McFadden Pseudo-R²
+log_res = sc.logistic(df, "remission ~ age + C(treatment_arm)")
+```
+
+### 4. Stateless Math Kernels (`omnistats.functional as F`)
+
+```python
+import omnistats.functional as F
+
+# Welch's t-test returns a 6-field TTestResult NamedTuple
+res = F.welch_t(group_a, group_b)
+print(res.stat, res.p, res.dof, res.ci)
+
+# Effect sizes with exact Non-Central t CIs & O(N log N) Cliff's delta
+g, g_ci = F.hedges_g(group_a, group_b), F.hedges_g_ci(group_a, group_b)
+delta, d_ci = F.cliffs_d(group_a, group_b), F.cliffs_d_ci(group_a, group_b)
+
+# BCa Bootstrap CI, TOST Equivalence, & Yuen-Welch Robust Trimmed t-Test
+ci_bca = F.bootstrap_ci(group_a, n_resamples=5000, method="bca", seed=42)
+eq_res = sc.tost(group_a, group_b, bound=0.5)
+yuen_res = F.yuen_t(group_a, group_b, trim=0.2)
+```
+
+---
+
+## 🏛️ 5-Layer Architecture
+
+```text
+omnistats/
+├── pyproject.toml             # Hatchling + hatch-vcs, Python >= 3.11
+├── mkdocs.yml                 # MkDocs-Material documentation config
+├── docs/                      # Quickstart, mathematical theory, & API reference
+├── scripts/
+│   └── check_module_size.py   # Enforces module size budgets & 5-layer import contracts
+├── tests/                     # Unit, R 4.3 parity, Hypothesis property, & API snapshot tests
+└── omnistats/
+    ├── __init__.py            # PEP 562 lazy exports: read, compare, screen, ols, logistic, tost, F
+    ├── __main__.py            # CLI execution (`python -m omnistats`)
+    ├── core/                  # L0: constants, errors, guards, types, roles, results/
+    ├── functional/            # L1: pure stateless kernels (checks, tests, effects, posthoc, resample, robust)
+    ├── models/                # L2: Wilkinson formula parser, OLS (HC0-HC3), IRLS Logistic
+    ├── stat/                  # L3: Autonomous router/ subpackage, compare, screen, equivalence, power
+    ├── eda/                   # L3: Multi-format I/O, profiler, quality, correlations/VIF
+    ├── integrations/          # L4: Pandas DataFrame `.scio` accessor
+    └── cli/                   # L4: Command-line interface (`omnistats`)
+```
+
+---
+
+## 📄 License & Citation
+
+Distributed under the [Apache License, Version 2.0](LICENSE). See [`CITATION.cff`](CITATION.cff) for academic citation metadata.