Changelog

Changes to XRayLabTool are documented in this file.

The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.

Version Categories

  • Added: New features

  • Changed: Changes in existing functionality

  • Deprecated: Soon-to-be removed features

  • Removed: Now removed features

  • Fixed: Bug fixes

  • Security: Vulnerability fixes

v0.4.4 (2026-06-25)

Added

  • Python 3.14 support: pyproject.toml classifier and CI matrix coverage (ubuntu/macOS/windows)

Fixed

  • parse_formula now rejects trailing/invalid characters (e.g. SiO2junk, Si-O2) instead of silently ignoring them

  • Complex energy inputs are rejected with a clear EnergyError rather than being coerced to their real part

  • Empty energy arrays now raise EnergyError instead of producing empty results

  • Batch processing disambiguates colliding result keys so no result is silently dropped

  • calculate_scattering_length_density reconciled with the pipeline kernel (SLD = 2π·δ/λ²; real part positive for δ > 0)

  • validate_energy_range defaults corrected to the supported 0.03–30 keV range

  • GUI: density spinbox range aligned with validate_density (0.001–30 g/cm³); non-numeric density cells are skipped instead of crashing

  • GUI “Save PNG” now exports the plot via pyqtgraph’s ImageExporter (the PyQtGraph widgets have no matplotlib figure, so the previous savefig path always errored)

  • xraylabtool batch no longer crashes on the default non-progress path, where the progress tracker yielded None

Changed

  • Removed unused EnhancedValidator / ErrorRecoveryManager machinery from the batch CLI path

  • Migrated class-scoped pytest fixtures to @classmethod for pytest 9 compatibility

v0.4.3 (2026-05-08)

Changed

  • Upgraded pip to >=26.1 in CI to resolve CVE-2026-6357

  • Expanded .gitignore with comprehensive uv/venv, CI, and tooling patterns

  • Updated Sphinx API docs to cover all public modules (calculators, gui, interfaces, utils)

  • Fixed Sphinx build output path in README development commands

Security

  • CI: pin pip>=26.1 in dependency-audit job to prevent CVE-2026-6357 false positives

v0.4.2 (2026-04-30)

Changed

  • UI/UX Pro Max upgrade applied to PySide6 interface

  • Upgraded form validation to use non-blocking toast notifications instead of blocking message boxes

  • Enhanced touch target sizes for all inputs and buttons

  • Standardized UI spacing and interactive states (loading buttons, disabled opacities)

v0.4.1 (2026-04-07)

Fixed

  • Version bump for patch release

v0.4.0 (2026-04-07)

Added

  • Backend abstraction layer (xraylabtool.backend) supporting NumPy and JAX backends

  • set_backend("jax") / set_backend("numpy") for runtime backend switching

  • InterpolationFactory for backend-agnostic PCHIP interpolation (scipy ↔ interpax)

  • PyQtGraph-based interactive plotting widgets (replaces matplotlib in GUI)

  • JAX float64 auto-configuration at package import time

  • 202 characterization tests with golden-value assertions for migration safety

  • Optional [jax] dependency group: pip install xraylabtool[jax]

  • Optional [plots] dependency group for matplotlib (publication plots)

  • Architecture Decision Records in docs/architecture/

  • Security scanning workflow and license compliance auditing

Changed

  • All core computation modules now use backend ops instead of direct NumPy

  • GUI plotting migrated from matplotlib to PyQtGraph for interactive performance

  • ColorPalette.mpl_cycle renamed to ColorPalette.plot_cycle

  • apply_matplotlib_theme() replaced with apply_pyqtgraph_theme()

  • scipy.constants eliminated from utils.py (uses constants.py directly)

  • matplotlib moved from required to optional dependency

  • ReadTheDocs migrated to uv-based builds on Ubuntu 24.04 / Python 3.13

  • CI updated to Python 3.13, latest GitHub Actions with SHA-pinned versions

Deprecated

  • optimization/vectorized_core.py manual SIMD heuristics (use JAX backend instead)

  • optimization/optimized_core.py monkey-patching (use set_backend('jax'))

Removed

  • ScalarFriendlyArray numpy subclass (replaced with plain numpy arrays)

  • Direct matplotlib dependency (now optional via [plots] extra)

  • Direct scipy.constants usage in computation path

v0.3.0 (2025-12-15)

Added

  • GUI modernization: dark mode toggle with persistent preferences

  • New theme engine supporting light and dark themes

Security

  • Replaced python-jose with PyJWT to address Minerva attack vulnerability

Fixed

  • Plot clipping issues with scrollbars

  • Single-point plot visibility in energy sweeps

  • Log path toggle contrast

  • GUI smoke test made non-blocking for CI reliability

Maintenance

  • Removed obsolete workflows (security.yml, performance-monitoring.yml, dependabot.yml)

  • Simplified lint job to use ruff only (removed isort/black)

  • Updated tool versions in CI

  • Added explicit permissions to all GitHub Actions workflows

v0.2.x (2025)

See the full history in CHANGELOG.md for detailed v0.2.0 through v0.2.7 release notes covering:

  • Enhanced CLI with shell completion support

  • Batch processing from CSV files

  • Performance benchmarking suite (150,000+ calculations/sec)

  • Cross-platform shell completion (bash, zsh, fish, PowerShell)

  • Mamba support and environment isolation

v0.1.0 (2024)

Added

  • Core X-ray optical properties calculations

  • Support for single materials and compounds

  • Complex refractive index calculations (delta, beta)

  • Critical angle and attenuation length calculations

  • Chemical formula parsing

  • Energy-wavelength conversions

  • Basic command-line interface

  • Atomic scattering factor data for 92 elements

Compatibility Matrix

Platform and Python Version Support

Version

Python 3.12

Python 3.13

Windows

macOS/Linux

v0.4.1

✅

✅

✅

✅

v0.4.0

✅

✅

✅

✅

v0.3.0

✅

✅

✅

✅

v0.2.x

✅

✅

✅

✅

v0.1.0

✅

❌

✅

✅

Migration Guides

For upgrading between versions, see: