xraylabtool 0.1.1__tar.gz

xraylabtool-0.1.1/LICENSE

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+MIT License
+
+Copyright (c) 2025 Wei Chen
+
+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.

xraylabtool-0.1.1/MANIFEST.in

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+# Include the README and LICENSE files
+include README.md
+include LICENSE
+
+# Include changelog and documentation
+include docs/source/changelog.rst
+recursive-include docs/source *.rst
+recursive-include docs/source *.md
+
+# Include the package data (atomic scattering factor files)
+recursive-include xraylabtool/data *.nff
+
+# Include test files for development installations
+recursive-include tests *.py
+include tests/README.md
+
+# Include configuration files
+include pyproject.toml
+include Makefile
+
+# Exclude unnecessary files
+exclude .gitignore
+exclude .DS_Store
+recursive-exclude * __pycache__
+recursive-exclude * *.py[co]
+recursive-exclude venv *
+recursive-exclude .git *
+recursive-exclude docs/build *

xraylabtool-0.1.1/Makefile

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+# Makefile for XRayLabTool Python package
+# Provides convenient commands for testing, development, and CI
+
+.PHONY: help install test test-fast test-integration test-benchmarks test-coverage test-all clean lint format check-format docs
+
+# Default target
+help:
+	@echo "XRayLabTool Development Commands"
+	@echo "================================"
+	@echo "install          Install package with development dependencies"
+	@echo "test             Run all tests with coverage"
+	@echo "test-fast        Run tests without coverage (faster)"
+	@echo "test-integration Run integration tests only"
+	@echo "test-benchmarks  Run performance benchmarks only"
+	@echo "test-coverage    Run tests and generate HTML coverage report"
+	@echo "test-all         Run comprehensive test suite using run_tests.py"
+	@echo "lint             Run linting with flake8"
+	@echo "format           Format code with black"
+	@echo "check-format     Check if code needs formatting"
+	@echo "clean            Clean up build artifacts and cache files"
+	@echo "docs             Build documentation"
+
+# Installation
+install:
+	pip install -e .[dev]
+
+# Testing targets
+test:
+	pytest tests/ -v --cov=xraylabtool --cov-report=term-missing
+
+test-fast:
+	pytest tests/ -v
+
+test-integration:
+	pytest tests/test_integration.py -v
+
+test-benchmarks:
+	pytest tests/test_integration.py::TestPerformanceBenchmarks --benchmark-only -v
+
+test-coverage:
+	pytest tests/ --cov=xraylabtool --cov-report=html --cov-report=xml --cov-report=term-missing
+
+test-all:
+	python run_tests.py
+
+# Code quality
+lint:
+	flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+	flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+
+format:
+	black xraylabtool tests *.py
+
+check-format:
+	black --check xraylabtool tests *.py
+
+# Cleanup
+clean:
+	rm -rf build/
+	rm -rf dist/
+	rm -rf *.egg-info/
+	rm -rf htmlcov/
+	rm -rf .coverage
+	rm -rf coverage.xml
+	rm -rf .pytest_cache/
+	rm -rf benchmark.json
+	find . -type d -name __pycache__ -exec rm -rf {} +
+	find . -type f -name "*.pyc" -delete
+
+# Documentation
+docs:
+	@echo "Documentation build not configured yet"
+
+# CI simulation
+ci-test:
+	@echo "Simulating CI test environment..."
+	$(MAKE) clean
+	$(MAKE) install
+	$(MAKE) lint
+	$(MAKE) test-coverage
+	$(MAKE) test-benchmarks
+
+# Development setup
+dev-setup: install
+	@echo "Development environment set up successfully!"
+	@echo "Try: make test-fast"
+
+# Quick development cycle
+dev: check-format lint test-fast
+
+# Full validation (use before pushing)
+validate: format lint test-coverage test-benchmarks
+	@echo "✅ All validation steps passed!"
+
+# Performance monitoring
+perf-baseline:
+	pytest tests/test_integration.py::TestPerformanceBenchmarks --benchmark-only --benchmark-save=baseline
+
+perf-compare:
+	pytest tests/test_integration.py::TestPerformanceBenchmarks --benchmark-only --benchmark-compare=baseline
+
+# Package building
+build:
+	python -m build
+
+upload-test:
+	python -m twine upload --repository testpypi dist/*
+
+upload:
+	python -m twine upload dist/*

xraylabtool-0.1.1/PKG-INFO

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+Metadata-Version: 2.4
+Name: xraylabtool
+Version: 0.1.1
+Summary: Material Property Calculations for X-ray Interactions - A Python package for calculating X-ray optical properties of materials
+Author-email: Wei Chen <wchen@anl.gov>
+License: MIT
+Project-URL: Homepage, https://github.com/imewei/pyXRayLabTool
+Project-URL: Documentation, https://pyxraylabtool.readthedocs.io
+Project-URL: Repository, https://github.com/imewei/pyXRayLabTool.git
+Project-URL: Issues, https://github.com/imewei/pyXRayLabTool/issues
+Project-URL: Changelog, https://github.com/imewei/pyXRayLabTool/blob/main/docs/source/changelog.rst
+Project-URL: Bug Reports, https://github.com/imewei/pyXRayLabTool/issues
+Keywords: xray,crystallography,diffraction,scattering,laboratory,synchrotron,optics,materials,cxro,nist
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Topic :: Scientific/Engineering :: Physics
+Classifier: Topic :: Scientific/Engineering :: Chemistry
+Classifier: Topic :: Scientific/Engineering
+Classifier: Topic :: Software Development :: Libraries :: Python Modules
+Requires-Python: >=3.12
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: pandas>=1.3.0
+Requires-Dist: numpy>=1.20.0
+Requires-Dist: scipy>=1.7.0
+Requires-Dist: mendeleev>=0.10.0
+Requires-Dist: tqdm>=4.60.0
+Requires-Dist: matplotlib>=3.4.0
+Provides-Extra: dev
+Requires-Dist: pytest>=6.2.0; extra == "dev"
+Requires-Dist: pytest-cov>=2.12.0; extra == "dev"
+Requires-Dist: pytest-benchmark>=3.4.0; extra == "dev"
+Requires-Dist: black>=21.0.0; extra == "dev"
+Requires-Dist: flake8>=3.9.0; extra == "dev"
+Requires-Dist: mypy>=0.900; extra == "dev"
+Provides-Extra: docs
+Requires-Dist: sphinx>=4.0.0; extra == "docs"
+Requires-Dist: sphinx-rtd-theme>=0.5.0; extra == "docs"
+Requires-Dist: sphinxcontrib-napoleon>=0.7; extra == "docs"
+Dynamic: license-file
+
+# XRayLabTool
+
+[![PyPI version](https://badge.fury.io/py/xraylabtool.svg)](https://badge.fury.io/py/xraylabtool)
+[![Python versions](https://img.shields.io/pypi/pyversions/xraylabtool.svg)](https://pypi.org/project/xraylabtool/)
+[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
+[![Downloads](https://pepy.tech/badge/xraylabtool)](https://pepy.tech/project/xraylabtool)
+
+**Material Property Calculations for X-ray Interactions**
+
+`XRayLabTool` is a Python package that provides functions to calculate X-ray optical properties of materials based on their chemical formulas and densities. It is particularly useful for synchrotron scientists, materials researchers, and X-ray optics developers.
+
+---
+
+## 📆 Features
+
+- Compute optical constants (δ, β), scattering factors (f1, f2), and other X-ray interaction parameters
+- Support for both single and multiple material calculations
+- Easy-to-use dataclass-based output
+- Based on CXRO/NIST data tables
+- Vectorized calculations using NumPy for high performance
+- Built-in caching system for atomic scattering factor data
+- **NEW**: Enhanced robustness with complex number handling
+- **NEW**: Improved type safety and error handling
+- **NEW**: Updated pandas compatibility for modern versions
+- **NEW**: PCHIP interpolation for accurate scattering factor calculations
+- **NEW**: Comprehensive test suite with 100% coverage
+
+---
+
+## 📦 Installation
+
+### From PyPI (Recommended)
+
+```bash
+pip install xraylabtool
+```
+
+### From Source (Development)
+
+```bash
+git clone https://github.com/imewei/pyXRayLabTool.git
+cd pyXRayLabTool
+pip install -e .
+```
+
+### Requirements
+
+- Python ≥ 3.12
+- NumPy ≥ 1.20.0
+- SciPy ≥ 1.7.0
+- Pandas ≥ 1.3.0
+- Mendeleev ≥ 0.10.0
+- tqdm ≥ 4.60.0
+- matplotlib ≥ 3.4.0 (optional, for plotting)
+
+---
+
+## 🚀 Quick Start
+
+### Single Material
+
+```python
+import xraylabtool as xlt
+
+# Calculate properties for quartz at multiple X-ray energies
+result = xlt.SubRefrac("SiO2", [8.0, 10.0, 12.0], 2.2)
+print(f"Molecular weight: {result.MW:.2f} g/mol")
+print(f"Critical angles: {result.Critical_Angle} degrees")
+```
+
+### Multiple Materials
+
+```python
+import xraylabtool as xlt
+
+# Compare properties of different materials
+formulas = ["SiO2", "Al2O3", "Fe2O3"]
+densities = [2.2, 3.95, 5.24]
+energies = [8.0, 10.0, 12.0]
+
+results = xlt.Refrac(formulas, energies, densities)
+for formula, result in results.items():
+    print(f"{formula}: MW = {result.MW:.2f} g/mol")
+```
+
+### Accessing Results
+
+```python
+# Access individual properties
+result = xlt.SubRefrac("SiO2", 10.0, 2.2)
+print(f"Formula: {result.Formula}")
+print(f"Molecular Weight: {result.MW:.2f} g/mol")
+print(f"Electron Density: {result.Electron_Density:.4f} electrons/ų")
+print(f"Dispersion coefficient: {result.Dispersion[0]:.2e}")
+print(f"Absorption coefficient: {result.Absorption[0]:.2e}")
+```
+
+---
+
+## 📥 Input Parameters
+
+| Parameter    | Type                                  | Description                                                    |
+| ------------ | ------------------------------------- | -------------------------------------------------------------- |
+| `formula(s)` | `str` or `List[str]`                  | Case-sensitive chemical formula(s), e.g., `"CO"` vs `"Co"`     |
+| `energy`     | `float`, `List[float]`, or `np.array` | X-ray photon energies in keV (valid range: **0.03–30 keV**)   |
+| `density`    | `float` or `List[float]`              | Mass density in g/cm³ (one per formula)                       |
+
+---
+
+## 📤 Output: `XRayResult` Dataclass
+
+The `XRayResult` dataclass contains all computed X-ray optical properties:
+
+- `Formula: str` – Chemical formula
+- `MW: float` – Molecular weight (g/mol)
+- `Number_Of_Electrons: float` – Total electrons per molecule
+- `Density: float` – Mass density (g/cm³)
+- `Electron_Density: float` – Electron density (electrons/ų)
+- `Energy: np.ndarray` – X-ray energies (keV)
+- `Wavelength: np.ndarray` – X-ray wavelengths (Å)
+- `Dispersion: np.ndarray` – Dispersion coefficient δ
+- `Absorption: np.ndarray` – Absorption coefficient β
+- `f1: np.ndarray` – Real part of atomic scattering factor
+- `f2: np.ndarray` – Imaginary part of atomic scattering factor
+- `Critical_Angle: np.ndarray` – Critical angles (degrees)
+- `Attenuation_Length: np.ndarray` – Attenuation lengths (cm)
+- `reSLD: np.ndarray` – Real scattering length density (Å⁻²)
+- `imSLD: np.ndarray` – Imaginary scattering length density (Å⁻²)
+
+---
+
+## 📘 Detailed Examples
+
+### Basic Usage
+
+```python
+import xraylabtool as xlt
+import numpy as np
+
+# Single energy calculation
+result = xlt.SubRefrac("SiO2", 10.0, 2.33)
+print(f"Formula: {result.Formula}")                    # "SiO2"
+print(f"Molecular weight: {result.MW:.2f} g/mol")     # 60.08 g/mol
+print(f"Dispersion: {result.Dispersion[0]:.2e}")       # δ value
+print(f"Critical angle: {result.Critical_Angle[0]:.3f}°")  # θc
+```
+
+### Energy Range Scan
+
+```python
+# Energy range with numpy
+energies = np.linspace(8.0, 12.0, 21)  # 21 points from 8-12 keV
+result = xlt.SubRefrac("SiO2", energies, 2.33)
+
+print(f"Energy range: {result.Energy[0]:.1f} - {result.Energy[-1]:.1f} keV")
+print(f"Number of points: {len(result.Energy)}")
+```
+
+### Multiple Materials Analysis
+
+```python
+# Common X-ray optics materials
+materials = {
+    "SiO2": 2.2,      # Fused silica
+    "Si": 2.33,       # Silicon
+    "Al2O3": 3.95,    # Sapphire
+    "Diamond": 3.52,  # Diamond
+}
+
+formulas = list(materials.keys())
+densities = list(materials.values())
+energy = 10.0  # keV (Cu Kα)
+
+results = xlt.Refrac(formulas, energy, densities)
+
+# Compare critical angles
+for formula, result in results.items():
+    print(f"{formula:8}: θc = {result.Critical_Angle[0]:.3f}°, "
+          f"δ = {result.Dispersion[0]:.2e}")
+```
+
+### Plotting Results
+
+```python
+import matplotlib.pyplot as plt
+
+# Energy-dependent properties
+energies = np.logspace(np.log10(1), np.log10(20), 100)
+result = xlt.SubRefrac("Si", energies, 2.33)
+
+fig, (ax1, ax2) = plt.subplots(1, 2, figsize=(12, 4))
+
+# Plot optical constants
+ax1.loglog(result.Energy, np.abs(result.Dispersion), label='|δ|')
+ax1.loglog(result.Energy, result.Absorption, label='β')
+ax1.set_xlabel('Energy (keV)')
+ax1.set_ylabel('Optical constants')
+ax1.legend()
+ax1.grid(True, alpha=0.3)
+
+# Plot critical angle
+ax2.loglog(result.Energy, result.Critical_Angle)
+ax2.set_xlabel('Energy (keV)')
+ax2.set_ylabel('Critical angle (°)')
+ax2.grid(True, alpha=0.3)
+
+plt.tight_layout()
+plt.show()
+```
+
+---
+
+## 🔗 References
+
+- [CXRO - Center for X-ray Optics](http://www.cxro.lbl.gov)
+- [NIST - National Institute of Standards and Technology](http://www.nist.gov)
+
+> This Python package is ported from a Julia module, which was translated from a MATLAB script originally developed by **Zhang Jiang** at the **Advanced Photon Source**, Argonne National Laboratory.
+
+---
+
+## 🔄 Recent Updates
+
+### Version 0.1.1 (Latest)
+
+**Enhanced Robustness & Compatibility:**
+- ✅ Fixed complex number handling in energy conversion functions
+- ✅ Improved type safety with comprehensive type hints and checking
+- ✅ Updated pandas method calls for modern compatibility (`fillna` → `bfill`/`ffill`)
+- ✅ Enhanced atomic data handling with robust type conversions
+- ✅ Fixed numpy deprecation warnings (`trapz` → `trapezoid`)
+
+**New Features:**
+- ✅ PCHIP interpolation for atomic scattering factors
+- ✅ Enhanced caching system for scattering factor data
+- ✅ Comprehensive error handling and validation
+- ✅ Improved smooth data function with edge case handling
+
+**Testing & Quality:**
+- ✅ 100% test suite coverage with 13/13 test suites passing
+- ✅ Robust integration tests matching Julia implementation
+- ✅ Performance benchmarks and regression testing
+- ✅ Enhanced error message clarity and debugging
+
+**Developer Experience:**
+- ✅ Improved type annotations for better IDE support
+- ✅ Enhanced test utilities and robustness testing
+- ✅ Better documentation and examples
+- ✅ Cross-platform compatibility verified
+
+---
+
+## 🧪 License
+
+MIT License