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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

2.4.0 - 2025-10-16

Added

  • Track Builders Module (track_builders.py):

    • make_linear_track() - Create simple linear tracks
    • make_circular_track() - Create circular/annular tracks
    • make_tmaze_track() - Create T-maze tracks for alternation tasks
    • make_plus_maze_track() - Create plus/cross maze tracks
    • make_figure8_track() - Create figure-8 tracks
    • make_wtrack() - Create W-shaped tracks
    • make_rectangular_track() - Create rectangular perimeter tracks
    • make_ymaze_track() - Create Y-maze tracks with configurable angles
    • make_track_from_points() - Create tracks from manual point specification
    • make_track_from_image_interactive() - Interactive track builder from images (Jupyter-compatible)
    • _build_track_from_state() - Helper for retrieving interactive builder results in Jupyter

  • Validation & QC Module (validation.py):

    • check_track_graph_validity() - Validate track graph structure and attributes
    • get_projection_confidence() - Calculate confidence scores for position projections
    • detect_linearization_outliers() - Detect outliers using projection distance and jump detection
    • validate_linearization() - Comprehensive quality assessment with scoring and recommendations

  • Tutorial Notebooks:

    • track_linearization_tutorial.ipynb - Comprehensive pedagogical tutorial for basic usage
    • advanced_features_tutorial.ipynb - Tutorial covering track builders, validation, and interactive features

  • Core Functionality:

    • project_1d_to_2d() - Reverse mapping from 1D linear positions back to 2D coordinates
    • Numba-optimized Viterbi algorithm for HMM inference (when numba available)
    • Exposed project_1d_to_2d in package __init__.py

  • Infrastructure:

    • Pre-commit hooks configuration for automated code quality checks
    • Comprehensive CI/CD pipeline with quality, test, build, and publish jobs
    • Support for Python 3.13
    • PyPI Trusted Publishing (OIDC) support for secure releases
    • Automated GitHub release creation with changelog extraction
    • Notebook execution testing in CI
    • Modern dependency pinning with lower bounds following Scientific Python SPEC 0
    • Enhanced ruff configuration with numpy-specific and pandas-vet rules
    • Improved mypy configuration with test-specific overrides
    • pandas-stubs for better type checking
    • Comprehensive test suite for track builders and validation (117 tests total)

Changed

  • BREAKING: Dropped support for Python 3.9 (minimum version now 3.10)
  • Upgraded minimum dependency versions:
    • numpy >= 1.24 (was unpinned)
    • scipy >= 1.10 (was unpinned)
    • matplotlib >= 3.7 (was unpinned)
    • pandas >= 2.0 (was unpinned)
    • dask[array] >= 2023.5.0 (was unpinned, added array extra)
    • networkx >= 3.2.1 (explicit minimum for compatibility)
  • Replaced deprecated pandas .values with .to_numpy() in utils module
  • Updated CI workflow to test Python 3.10, 3.11, 3.12, and 3.13
  • Replaced old test_package_build.yml with modern release.yml workflow
  • Fixed non-breaking hyphen character in error message
  • Enhanced __init__.py with comprehensive module docstring
  • Improved README with new features section and tutorial links
  • Interactive track builder uses two-step workflow in Jupyter (non-blocking)
  • Outlier detection uses robust statistics (median + MAD) instead of mean + std

Fixed

  • Type Annotations & IDE Support: Improved type hints for better IDE autocomplete and type checking
    • edge_map now accepts both integer and string segment IDs (e.g., {0: "left_arm", 1: "right_arm"})
    • edge_spacing now accepts tuples, lists, and numpy arrays (previously only lists)
    • Achieved zero mypy errors in source code for improved code quality
  • Outlier detection false positives on uniform data (now uses robust statistics)
  • Interactive builder event loop blocking in Jupyter notebooks (non-blocking two-step workflow)

Infrastructure

  • New GitHub Actions workflow structure:
    • Separate quality, test, build, and publish jobs
    • Parallel testing across Python versions
    • Artifact management for distributions
    • Integration with Codecov for coverage reporting

2.3.2 - 2024-10-22

Changed

  • Revamped README with detailed usage and documentation
  • Fixed minor notebook formatting and output updates
  • Removed unused import from init.py
  • Refactored formatting for readability in core and tests

2.3.1 - 2024-10-16

Added

  • Support for merging edges in edge_map parameter

Changed

  • Improved track graph validation and documentation
  • Refactored type hints and added strict zip usage
  • Enhanced type hints and formatting for Python 3.10+

2.3.0 - 2024-09-24

Added

  • Comprehensive tests for core and utils modules
  • Fallback for version using importlib.metadata

Changed

  • Updated Python support matrix
  • Added development tooling configurations
  • Fixed edge_spacing error handling

2.2.0 - 2024-06-07

Changed

  • Added node ID to plot functionality
  • Various CI/CD improvements

2.1.0 - 2024-05-28

Changed

  • Updated version management
  • CI/CD workflow improvements

2.0.0 - 2023-08-21

Changed

  • Major refactoring and restructuring

1.0.0 - 2020-08-21

Added

  • Initial release with core linearization functionality
  • Track graph construction
  • HMM-based position classification
  • Visualization tools