odr-bootstrap 0.1.0__tar.gz

odr_bootstrap-0.1.0/.github/workflows/publish.yml

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+name: Publish to PyPI
+
+on:
+  release:
+    types: [published]
+
+jobs:
+  deploy:
+    runs-on: ubuntu-latest
+    
+    # This permission is required for trusted publisher flow
+    permissions:
+      id-token: write
+    
+    steps:
+    - uses: actions/checkout@v4
+    
+    - name: Install uv
+      uses: astral-sh/setup-uv@v2
+      with:
+        version: "latest"
+    
+    - name: Set up Python
+      uses: actions/setup-python@v5
+      with:
+        python-version: "3.12"
+        cache: "uv"
+    
+    - name: Sync dependencies
+      run: uv sync
+    
+    - name: Build distribution
+      run: uv build
+    
+    - name: Publish to PyPI
+      uses: pypa/gh-action-pypi-publish@release/v1
+      with:
+        packages-dir: dist/

odr_bootstrap-0.1.0/.github/workflows/tests.yml

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+name: Tests
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.12"]
+    
+    steps:
+    - uses: actions/checkout@v4
+    
+    - name: Install uv
+      uses: astral-sh/setup-uv@v2
+      with:
+        version: "latest"
+    
+    - name: Set up Python
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ matrix.python-version }}
+        cache: "uv"
+    
+    - name: Sync dependencies
+      run: uv sync --all-extras
+    
+    - name: Lint with ruff
+      run: uv run ruff check .
+    
+    - name: Type check with mypy
+      run: uv run mypy odr_bootstrap
+    
+    - name: Run tests with coverage
+      run: uv run pytest --cov=odr_bootstrap --cov-report=xml --cov-report=term-missing
+    
+    - name: Upload coverage to Codecov
+      uses: codecov/codecov-action@v3
+      with:
+        files: ./coverage.xml
+        flags: unittests
+        name: codecov-umbrella
+        fail_ci_if_error: false

odr_bootstrap-0.1.0/.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+pip-wheel-metadata/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+.python-version
+
+# pipenv
+Pipfile.lock
+
+# PEP 582
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# UV lock file
+uv.lock
+
+# IDE
+.vscode/
+.idea/
+*.swp
+*.swo
+*~
+
+# OS
+.DS_Store
+Thumbs.db
+
+# Project outputs
+*.png
+*.pdf
+calibration_curve.png
+calibration_estimates.png

odr_bootstrap-0.1.0/.pre-commit-config.yaml

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+repos:
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.8.0
+    hooks:
+      - id: ruff
+        args: [--fix]
+      - id: ruff-format
+
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.5.0
+    hooks:
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+      - id: check-yaml
+      - id: check-added-large-files
+        args: ["--maxkb=1000"]
+
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: v1.10.0
+    hooks:
+      - id: mypy
+        additional_dependencies:
+          - "numpy"
+          - "scipy"
+          - "matplotlib"
+          - "pandas"
+        args: [--strict, --ignore-missing-imports]

odr_bootstrap-0.1.0/.readthedocs.yml

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+version: 2
+
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.12"
+    uv: "latest"
+
+python:
+  version: 3.12
+  install:
+    - requirements: docs/requirements.txt
+
+sphinx:
+  configuration: docs/source/conf.py
+  fail_on_warning: false
+
+formats:
+  - pdf
+  - epub
+
+# Exclude certain files from builds
+exclude_patterns:
+  - docs/build
+
+# Index page configuration
+redirect_www: false
+
+# Versioning
+version: latest

odr_bootstrap-0.1.0/CHANGELOG.md

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+# Changelog
+
+All notable changes to this project will be documented in this file.
+
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
+and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+
+## [Unreleased]
+
+### Added
+- Pre-commit configuration for automated code quality checks
+- GitHub Actions CI/CD workflows for testing and PyPI publishing
+- Comprehensive type hints (PEP 484) for all public functions
+- Coverage reporting with `pytest-cov` (85% threshold)
+- Sphinx documentation setup with Read the Docs integration
+- Makefile for development workflows (test, lint, build, publish)
+- `CONTRIBUTING.md` guidelines for contributors
+- Enhanced README with badges, expanded examples, and API reference
+
+### Changed
+- Updated `pyproject.toml` with enhanced tool configurations (ruff, mypy, coverage)
+- Improved documentation with complete API reference and tutorial
+- Split development dependencies (`dev`, `test`, `docs` groups)
+- Updated documentation URLs to point to Read the Docs
+
+## [0.1.0] - 2025-04-21
+
+### Added
+- Initial release of `odr-bootstrap` package
+- **Core Functions**:
+  - `ODR_Linear()`: Single ODR fit with optional intercept
+  - `ODR_Linear_Test()`: ODR fit with full diagnostics output
+  - `Bootstrap_fit()`: Bootstrap resampling with ODR refitting
+  - `Eval_Conf()`: Confidence interval evaluation from bootstrap samples
+  - `ODR_Bootstrap()`: Convenience wrapper combining Bootstrap_fit + Eval_Conf
+
+- **Statistics Functions**:
+  - `gauss_agv_err()`: Aggregate Gaussian distributions into KDE
+  - Helper functions: `yint_func()`, `slope_func()`, `plot_datapoints()`
+
+- **Plotting Functions**:
+  - `plot_regression()`: Best-fit line with confidence band
+  - `plot_Calibration_Estimates()`: Side-by-side slope/intercept distributions
+
+- **Testing**: 22 comprehensive unit tests with 100% pass rate
+- **Documentation**: NumPy-style docstrings for all functions
+- **Examples**: Complete workflow example in `examples/example.py`
+- **Packaging**: Proper Python package structure with pyproject.toml (hatchling backend)
+- **License**: MIT License
+
+### Technical Details
+- **Python Version**: 3.12+ required
+- **Dependencies**:
+  - numpy >= 2.2.4
+  - scipy >= 1.15.2 (includes fix for deprecated `scipy.odr`)
+  - pandas >= 2.2.3
+  - matplotlib >= 3.10.1
+- **Compatibility**: Fixed zero-intercept ODR initialization for scipy.odr
+- **Deprecation Handling**: Updated `np.trapz` → `np.trapezoid` for scipy 1.15+ compatibility
+
+---
+
+[Unreleased]: https://github.com/whtowbin/odr-bootstrap/compare/v0.1.0...HEAD
+[0.1.0]: https://github.com/whtowbin/odr-bootstrap/releases/tag/v0.1.0

odr_bootstrap-0.1.0/CONTRIBUTING.md

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+# Contributing to ODR Bootstrap
+
+Thank you for considering contributing to `odr-bootstrap`! This guide will help you get started.
+
+## Getting Started
+
+### 1. Fork and Clone
+
+```bash
+git clone https://github.com/<your-username>/odr-bootstrap.git
+cd odr-bootstrap
+```
+
+### 2. Set Up Development Environment
+
+We use `uv` for fast, reliable dependency management.
+
+```bash
+# Install all dependencies (including dev, test, and docs)
+uv sync --all-extras
+
+# Install pre-commit hooks for automatic code quality checks
+uv run pre-commit install
+```
+
+### 3. Run Tests Locally
+
+```bash
+# Run all tests
+uv run pytest
+
+# Run with coverage report
+uv run pytest --cov=odr_bootstrap --cov-report=html
+
+# Run specific test file
+uv run pytest tests/test_odr_bootstrap.py -v
+```
+
+## Code Quality Standards
+
+All contributions must meet these standards:
+
+### Type Hints
+
+Every function must have complete type hints:
+
+```python
+from typing import Tuple
+import numpy as np
+
+def my_function(x: np.ndarray, y: float) -> Tuple[np.ndarray, float]:
+    """Descriptive docstring."""
+    pass
+```
+
+**Verification**: `uv run mypy odr_bootstrap` (strict mode enabled)
+
+### Formatting and Linting
+
+Code is formatted with `ruff`:
+
+```bash
+uv run ruff format .           # Format all files
+uv run ruff check . --fix      # Auto-fix linting issues
+```
+
+### Docstring Style
+
+Use NumPy-style docstrings for all public functions:
+
+```python
+def function(x, y):
+    """
+    Brief one-line summary.
+
+    Longer description spanning multiple lines if needed.
+
+    Parameters
+    ----------
+    x : array-like
+        Description of x parameter.
+    y : float
+        Description of y parameter.
+
+    Returns
+    -------
+    tuple
+        Description of return value.
+
+    Examples
+    --------
+    >>> result = function([1, 2, 3], 1.0)
+    """
+    pass
+```
+
+### Test Coverage
+
+- All new code must be accompanied by tests
+- Target minimum coverage of **85%** (enforce in CI/CD)
+- Run `make test-cov` to generate coverage report
+
+## Submitting Changes
+
+### 1. Create a Feature Branch
+
+```bash
+git checkout -b feature/my-feature-name
+```
+
+### 2. Make Changes
+
+- Implement feature or bug fix
+- Write tests for new functionality
+- Update docstrings and type hints
+- Run `make lint` to auto-format
+
+### 3. Commit with Clear Messages
+
+```bash
+# Stage changes
+git add .
+
+# Commit with conventional commit format
+git commit -m "feat: add bootstrap confidence intervals"
+```
+
+**Commit Format**:
+- `feat:` new feature
+- `fix:` bug fix
+- `docs:` documentation changes
+- `test:` test additions/updates
+- `refactor:` code refactoring without behavior change
+- `chore:` dependency updates, CI/CD config, etc.
+
+### 4. Push and Create a Pull Request
+
+```bash
+git push origin feature/my-feature-name
+```
+
+Then open a PR on GitHub with:
+- Clear title describing the change
+- Description of what changes and why
+- Link to related issues (e.g., "Fixes #123")
+
+## Pull Request Checklist
+
+Before submitting your PR, verify:
+
+- [ ] Tests pass locally: `make test`
+- [ ] Coverage is adequate: `make test-cov`
+- [ ] Code is formatted: `make format`
+- [ ] No linting errors: `make lint`
+- [ ] Type hints are complete: `uv run mypy odr_bootstrap`
+- [ ] Docstrings are updated
+- [ ] CHANGELOG.md is updated if user-facing changes
+
+## Development Commands
+
+Helpful commands defined in `Makefile`:
+
+```bash
+make help                # Show all available commands
+make sync                # Sync dependencies
+make test                # Run tests
+make test-cov            # Run tests with coverage report
+make lint                # Check code style
+make type-check          # Run mypy type checking
+make format              # Auto-format code
+make build               # Build distribution package
+make docs                # Build Sphinx documentation
+make clean               # Remove build artifacts
+```
+
+## Documentation
+
+If you're adding or modifying functionality:
+
+1. Update or write docstrings in NumPy style
+2. Add examples to docstrings if appropriate
+3. Update README.md if user-facing
+4. Update CHANGELOG.md under [Unreleased] section
+
+To build and preview documentation locally:
+
+```bash
+make docs
+open docs/build/html/index.html  # or use your browser
+```
+
+## Reporting Issues
+
+When reporting bugs, include:
+
+1. **Description**: What's the issue?
+2. **Reproduction Steps**: How to reproduce it
+3. **Expected Behavior**: What should happen
+4. **Actual Behavior**: What actually happens
+5. **Environment**:
+   - Python version: `python --version`
+   - Package version: `pip show odr-bootstrap`
+   - OS: macOS / Linux / Windows
+
+Example:
+
+```markdown
+## Bug Report: ODR_Bootstrap fails with NaN values
+
+### Reproduction
+```python
+import numpy as np
+from odr_bootstrap import ODR_Bootstrap
+
+x = np.array([1.0, 2.0, np.nan, 4.0])
+result = ODR_Bootstrap(x, y, x_err, y_err)
+```
+
+### Expected
+Function should handle NaN gracefully by dropping those values
+
+### Actual
+TypeError: cannot perform reduce with flexible type
+
+### Environment
+- Python 3.12.0
+- odr-bootstrap 0.1.0
+- numpy 2.2.4
+```
+
+## Questions?
+
+Open a discussion or issue on [GitHub Issues](https://github.com/whtowbin/odr-bootstrap/issues).
+
+---
+
+**Thank you for contributing!** Your efforts make this package better for everyone. 🙌

odr_bootstrap-0.1.0/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2025 Henry Towbin
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

odr_bootstrap-0.1.0/Makefile

@@ -0,0 +1,77 @@
+.PHONY: help install sync test test-cov lint type-check format clean build publish publish-test docs
+
+help:
+	@echo "ODR Bootstrap Package Management"
+	@echo ""
+	@echo "Setup:"
+	@echo "  make sync           Sync dependencies with uv"
+	@echo "  make install        Install package in development mode"
+	@echo ""
+	@echo "Development:"
+	@echo "  make test           Run tests"
+	@echo "  make test-cov       Run tests with coverage report"
+	@echo "  make lint           Check code style with ruff"
+	@echo "  make type-check     Check types with mypy"
+	@echo "  make format         Format code with ruff (in-place)"
+	@echo ""
+	@echo "Building & Publishing:"
+	@echo "  make build          Build distribution (wheel + sdist)"
+	@echo "  make publish-test   Publish to TestPyPI"
+	@echo "  make publish        Publish to PyPI (requires GitHub release)"
+	@echo ""
+	@echo "Documentation:"
+	@echo "  make docs           Build Sphinx documentation"
+	@echo ""
+	@echo "Maintenance:"
+	@echo "  make clean          Remove build artifacts"
+
+sync:
+	uv sync --all-extras
+
+install:
+	uv sync --all-extras
+	uv pip install -e ".[dev,docs,test]"
+
+test:
+	uv run pytest
+
+test-cov:
+	uv run pytest --cov=odr_bootstrap --cov-report=term-missing --cov-report=html
+	@echo "Coverage report generated: htmlcov/index.html"
+
+lint:
+	uv run ruff check .
+
+type-check:
+	uv run mypy odr_bootstrap
+
+format:
+	uv run ruff format .
+
+clean:
+	rm -rf build dist *.egg-info
+	rm -rf htmlcov .coverage .mypy_cache
+	rm -rf .pytest_cache
+	find . -type d -name __pycache__ -exec rm -rf {} + 2>/dev/null || true
+	find . -type f -name "*.pyc" -delete
+
+build: clean
+	uv build
+
+publish-test: build
+	@echo "Publishing to TestPyPI..."
+	@echo "Note: This requires twine. Install with: pip install twine"
+	twine upload --repository testpypi dist/*
+	@echo "Verify at: https://test.pypi.org/project/odr-bootstrap/"
+
+publish: build
+	@echo "Publishing to PyPI..."
+	@echo "Note: This should be done via GitHub Actions on release"
+	@echo "Manual publish requires: pip install twine"
+	twine upload dist/*
+
+docs:
+	cd docs && make html
+	@echo "Documentation built: docs/build/html/index.html"
+
+.DEFAULT_GOAL := help