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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 and this project adheres to Semantic Versioning.

[Unreleased]

[0.2.1] - 2026-04-18

Changed

  • GUI migrated from Streamlit to Dash — launch with python examples/gui_app.py
  • gui optional dependency updated: dash>=2.14.0 + dash-bootstrap-components>=1.5.0 (replaces streamlit)
  • launch_app.bat and stop_app.bat updated for Dash process management
  • Bumped black minimum from >=23.0.0 to >=24.3.0 in requirements.txt

Fixed

  • Removed stale streamlit dependency from requirements.txt and environment.yml
  • Corrected all remaining Streamlit references in docs to Dash (about.md, installation.md, contributing.md, tutorials/index.md)
  • Updated version number from 0.1.0 to 0.2.0 in docs/about.md (including BibTeX citation)
  • Fixed Python minimum version in docs/installation.md (3.8 → 3.9)
  • Updated author contact email to The-Schultz-Lab@users.noreply.github.com in docs/about.md
  • Replaced broken docs/ROADMAP.md and docs/PERFORMANCE_TESTING_GUIDE.md links in README.md and docs/contributing.md
  • Updated stale Streamlit cache reference in tests/test_performance.py
  • Fixed logo not rendering on PyPI by replacing relative logo.svg path with absolute raw GitHub URL

[0.2.0] - 2026-04-04

Added

  • Vibrational Mode Visualization - Complete system for visualizing molecular vibrations from quantum chemistry calculations
    • Three file format parsers: Gaussian (.log), ORCA (.out), Molden (.molden) with auto-detection
    • Three visualization modes:
      • Static displacement arrows using Plotly Cone traces
      • Animated vibrations with interactive controls (play/pause, frame slider)
      • Heatmap coloring by displacement magnitude
    • New vibrations.py module with comprehensive dataclasses and functions
    • Streamlit "Vibration Settings" section with file upload and interactive controls
    • 21 new tests achieving ~95% coverage of vibration module
    • Test fixtures for all three file formats (water molecule examples)
  • Exported vibration functions in __init__.py for public API access
  • Symbol-to-atomic-number mapping (symbol_to_number) in atomProperties.py
  • Conda environment (environment.yml) replacing venv-based setup
  • Security CI workflow: pip-audit dependency scanning + CodeQL static analysis
  • Dependabot configuration for automated dependency updates
  • Branch protection rules (required status checks, no force-push)
  • PyPI publishing checklist (docs/PYPI_PUBLISHING.md)

Changed

  • Aromatic bond rendering now uses ring-center geometry for correct dashed bond offset direction
  • Displacement arrows auto-scaled relative to molecular size for consistent visibility
  • Animation caching replaced @st.cache_data with session-state caching and live progress bar
  • Longer dashes (75% vs 60%) for aromatic bond rendering
  • Updated README installation instructions for conda workflow
  • Expanded test suite from 26 to 47 tests
  • Bumped requires-python from >=3.8 to >=3.9
  • Fixed repo URLs in pyproject.toml (now correctly point to The-Schultz-Lab org)

[0.1.0] - 2026-01-31

Added

  • Core 3D molecular visualization with Plotly and RDKit integration.
  • Input support for SMILES, XYZ, MOL/PDB, and cube files.
  • Streamlit GUI for interactive visualization.
  • Test suite and CI workflows.