minibayes 1.0.0__tar.gz

minibayes-1.0.0/.github/workflows/publish.yml

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+name: Publish to PyPI
+
+on:
+  release:
+    types: [published]
+
+jobs:
+  ready-to-publish:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v6
+        with:
+          python-version: "3.12"
+
+      - name: Install dependencies
+        run: uv sync --locked --extra dev --extra viz
+
+      - name: Lint
+        run: uv run ruff check src/ tests/
+
+      - name: Type check
+        run: uv run mypy src/
+
+      - name: Run tests
+        run: uv run pytest tests/ -v
+
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+        with:
+          # setuptools-scm derives the version from git tags
+          fetch-depth: 0
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v6
+
+      - name: Build sdist and wheel
+        run: uv build
+
+      - name: Check distribution metadata
+        run: uvx twine check dist/*
+
+      - name: Upload distribution artifacts
+        uses: actions/upload-artifact@v4
+        with:
+          name: python-dist
+          path: dist/
+
+  publish-python:
+    needs: [ready-to-publish, build]
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/minibayes
+    permissions:
+      id-token: write
+      contents: read
+    steps:
+      - name: Download distribution artifacts
+        uses: actions/download-artifact@v4
+        with:
+          name: python-dist
+          path: dist/
+
+      - name: Publish to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1

minibayes-1.0.0/.gitignore

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+# Python
+__pycache__/
+*.py[cod]
+*$py.class
+*.so
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+*.egg-info/
+*.egg
+
+# Virtual environments
+.venv/
+venv/
+ENV/
+
+# uv
+
+# IDE
+.idea/
+.vscode/
+*.swp
+*.swo
+
+# Testing
+.pytest_cache/
+.coverage
+htmlcov/
+.mypy_cache/
+.ruff_cache/
+
+# Scratch/temporary
+scratch/
+
+# Jupyter
+.ipynb_checkpoints/
+
+# OS
+.DS_Store
+Thumbs.db
+
+# notebooks saved tests
+*.npz

minibayes-1.0.0/CLAUDE.md

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+# CLAUDE.md - Python Package Development
+
+## Project Overview
+
+A Python package with minimal dependencies (primarily numpy) called minibayes where overall spaces are described in minibayes-spec.md.
+
+## Tech Stack
+
+- **Language**: Python 3.11+
+- **Core dependency**: numpy
+- **Package manager**: u
+- **Build backend**: setuptools or hatchling
+- **Config**: pyproject.toml only (no setup.py, setup.cfg, requirements.txt)
+
+## Project Structure
+
+```
+my_package/
+├── pyproject.toml
+├── README.md
+├── LICENSE
+├── src/
+│   └── my_package/
+│       ├── __init__.py
+│       └── ...
+├── notebooks/       # jupyter notebooks for exploration
+└── tests/
+    └── ...
+```
+
+Use src-layout for proper import isolation during development.
+
+## Commands
+
+```bash
+# Install in dev mode
+uv pip install -e ".[dev]"
+
+# Run tests
+uv run pytest tests/ -v
+
+# Lint and format
+uv run ruff check src/ tests/
+uv run ruff format src/ tests/
+
+# Type check
+uv run mypy src/
+
+# Build package
+uv build
+```
+
+## Code Standards
+
+### Type Hints
+- Required on all function signatures
+- Use `numpy.typing` for array types: `NDArray[np.float64]`
+- Avoid `Any` unless absolutely necessary
+
+### Docstrings
+- NumPy-style docstrings for all public functions/classes
+- Include Parameters, Returns, Raises, Examples sections
+
+### Style
+- PEP 8, 88 char line length (ruff default)
+- snake_case for functions/variables, PascalCase for classes
+- Use f-strings for formatting
+- Prefer comprehensions over loops where readable
+- Use context managers for resources
+
+### NumPy Specifics
+- Prefer vectorized operations over loops
+- Use broadcasting where applicable
+- Document array shapes in docstrings: `shape (n, m)`
+- Specify dtypes explicitly when it matters
+
+### Strict mypy with NumPy
+
+This project uses strict mypy (`disallow_any_expr=true`). NumPy operations often return generic types that mypy flags as `Any`. Use these patterns:
+
+```python
+# Pattern 1: Annotate all intermediate array variables
+def forward(self, x: NDArray[np.float64]) -> NDArray[np.float64]:
+    arr: NDArray[np.float64] = np.asarray(x, dtype=np.float64)
+    result: NDArray[np.float64] = np.log(arr)
+    return result
+
+# Pattern 2: Use np.reciprocal() instead of 1/array (avoids Any)
+denom: NDArray[np.float64] = 1 + np.exp(-arr)
+result: NDArray[np.float64] = np.reciprocal(denom)  # Not: 1 / denom
+
+# Pattern 3: Use typing.cast() for scalar aggregations (recommended by numpy docs)
+from typing import cast
+mean: float = cast("float", np.mean(samples))
+b_var: float = cast("float", np.var(chain_means, ddof=1))
+
+# Pattern 4: Wrap scalar numpy results in float() for simple cases
+log_width: float = float(np.log(self._width))
+
+# Pattern 5: Break complex expressions into typed intermediates
+# Bad: np.log(x - low) + np.log(high - x) - np.log(width)
+# Good:
+log_low: NDArray[np.float64] = np.log(arr - self.low)
+log_high: NDArray[np.float64] = np.log(self.high - arr)
+log_width: float = float(np.log(self._width))
+result: NDArray[np.float64] = log_low + log_high - log_width
+```
+
+## Example
+
+```
+def log_sum_exp(x: NDArray[np.float64]) -> float:
+    """
+    Compute log(sum(exp(x))) in a numerically stable way.
+
+    Parameters
+    ----------
+    x : ndarray
+        Input array.
+
+    Returns
+    -------
+    float
+        log(sum(exp(x)))
+    """
+    x = np.asarray(x)
+    max_val: float = float(np.max(x))
+    if np.isinf(max_val) and max_val < 0:
+        return float("-inf")
+    shifted: NDArray[np.float64] = x - max_val
+    exp_shifted: NDArray[np.float64] = np.exp(shifted)
+    sum_exp: float = float(np.sum(exp_shifted))
+    return max_val + float(np.log(sum_exp))
+```
+
+## Verification
+
+Before committing:
+1. `ruff check --fix` passes
+2. `ruff format` applied
+3. `mypy` passes (strict mode)
+4. `pytest` passes
+
+## Don'ts
+
+- No mutable default arguments
+- No bare `except:`
+- No wildcard imports
+- No hardcoded secrets (use .env)
+- No commented-out code in commits
+
+## Implementation Progress
+
+**Update this section periodically as implementation proceeds.**
+
+| Component | Status | Notes |
+|-----------|--------|-------|
+| **v0.1 Foundation** | | |
+| `utils/numerical.py` | ✓ Done | `ensure_rng`, `check_finite`, `log_sum_exp` |
+| `transforms/` | ✓ Done | Identity, Log, Logit, Affine, CorrCholesky + `default_transform()` |
+| `distributions/` | ✓ Done | Normal, HalfNormal, Exponential, Gamma, Beta, Uniform, StudentT, LogNormal, Cauchy, Laplace, InverseGamma, Bernoulli, Poisson, MultivariateNormal, LKJCholesky |
+| **v0.2 Core** | | |
+| `model.py` | ✓ Done | Model class with transforms, Jacobian |
+| `samplers/mh.py` | ✓ Done | MetropolisHastings with Gaussian proposals |
+| `samplers/adaptive.py` | ✓ Done | AdaptiveMetropolis with covariance tuning |
+| `results.py` | ✓ Done | summary, to_dict, save/load methods |
+| **v0.3 Interface** | | |
+| `inference.py` | ✓ Done | `sample()` entry point with Model support |
+| `diagnostics.py` | ✓ Done | ESS (FFT-based), R-hat, summary |
+| `utils/export.py` | ✓ Done | save_npz, load_npz, to_json |
+| **v0.4 Hierarchical** | | |
+| `params.py` | ✓ Done | ParamContext, ParamInfo for p(...) API |
+| `model.py` (hierarchical) | ✓ Done | Priors function, vector params, conditionals |
+| `diagnostics.py` (vectors) | ✓ Done | Handle 3D arrays in summary() |
+| `predictive.py` (vectors) | ✓ Done | Handle vector params in posterior predictive |
+| `inference.py` (vectors) | ✓ Done | Structured results with 3D sample arrays |
+
+| **v0.4.1 LKJ/Matrix** | | |
+| `distributions/lkj_cholesky.py` | ✓ Done | LKJCholesky prior for correlation matrices |
+| `transforms/corr_cholesky.py` | ✓ Done | CorrCholeskyTransform for Cholesky factors |
+| `params.py` (shape param) | ✓ Done | Added `shape=` parameter for matrix-valued distributions |
+| `model.py` (matrix params) | ✓ Done | Matrix parameter support in flatten/unflatten |
+| `inference.py` (matrix params) | ✓ Done | Matrix parameter reconstruction in sample results |
+
+| **v0.4.2 Derived Params** | | |
+| `results.py` (derived) | ✓ Done | add_derived() for computed params (e.g., correlation from Cholesky) |
+
+| **v0.5 Gradient-Free** | | |
+| `samplers/ensemble.py` | ✓ Done | Affine-invariant ensemble sampler (emcee-style) |
+
+| **v0.5.1 Model Comparison** | | |
+| `comparison.py` | ✓ Done | WAIC, WAICResult dataclass |
+| `model.py` (pointwise ll) | ✓ Done | log_likelihood returns array, log_prob sums |
+| `results.py` (waic method) | ✓ Done | result.waic() convenience method |
+| `viz/plots.py` (plot_compare) | ✓ Done | Model comparison visualization |
+
+| **v0.5.2 Memory Safety** | | |
+| `inference.py` (limits) | ✓ Done | `max_samples` (default 100k) and `max_memory_mb` (default 1000 MB) parameters |
+| `inference.py` (pre-alloc) | ✓ Done | Pre-allocated numpy arrays instead of list append for memory efficiency |
+
+| **Deferred** | | |
+| HMC/NUTS | Not planned | See minibayes-spec.md "Design Decisions" for rationale |
+| Binomial, NegativeBinomial, Categorical | Deferred | Originally planned for v0.5 |
+
+**v0.5.2 complete.** Memory safety with configurable limits and pre-allocation.

minibayes-1.0.0/LICENSE.txt

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+
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minibayes-1.0.0/NOTICE.txt

@@ -0,0 +1,2 @@
+minibayes
+Copyright 2026 WOTA CORP.