# Changelog

## [v1.1.3] - 2026-03-07

### Bug Fixes
- Fixed `umap_embedding` `NotFittedError` when fewer than two rows have nonzero variance
- Fixed flash response index label alignment with filtered response index ordering
- Fixed `EnsembleView` `FileNotFoundError` in example notebooks by using explicit `best_checkpoint_fn_kwargs`

### Documentation
- Added pretrained model download step to example notebooks
- Updated installation documentation

### Infrastructure
- Updated package configuration in `pyproject.toml`

[v1.1.3]: https://github.com/TuragaLab/flyvis/releases/tag/v1.1.3

## [v1.1.2] - 2024-12-09

### Infrastructure
- Migrated to importlib.resources for file path handling
  - Improved package installation reliability
  - Standardized default script path definitions
  - Removed unused PROJECT_ROOT constant
- Added colorama dependency
- Added warning system for unrecognized CLI arguments with colored output
- Improved virtual cluster output handling
  - Added proper output file handling for virtual cluster jobs
  - Added automatic output directory creation
  - Improved process management for local execution
  - Fixed job status tracking to use job_id

### Bug Fixes
- Fixed file exists error
- Fixed notebook compatibility issues

### Documentation
- Renamed package from 'flyvision' to 'flyvis' across all documentation, examples
- Updated CLI documentation and usage examples
- Added optional notebook output clearing step to building docs
- Removed pyright and version pin notes from contribute.md
- Cleaned up CLI help text formatting
- Updated file paths in examples to use relative paths
- Removed duplicate CLI documentation from mkdocs.yml

[v1.1.2]: https://github.com/TuragaLab/flyvis/releases/tag/v1.1.2

## [v1.1.1] - 2024-11-21

### Distribution
- Moved configuration files into package structure
- Switched to `importlib.resources` for resource management
- Removed MANIFEST.in in favor of pyproject.toml configuration
- Enhanced root directory resolution logic

### Infrastructure
- Improved cluster management with better dry-run and slurm support

### CLI
- Enhanced command-line interface error handling
- Improved argument parsing for multiple commands
- Added `init_config` for config-based customization of network and training

### Documentation
- Updated package metadata for PyPI
- Added project URLs to package configuration
- Removed broken badges from README
- Added explanations for hydra-config-based customization of network and training in `CLI Reference`

## [v1.1.0] - 2024-11-20

### Breaking
- Renamed package from `flyvision` to `flyvis` for better consistency

### Features
- Added Command Line Interface `flyvis` for scripts
- Improved test suite performance and coverage
- Relaxed Python version dependency and added multi-Python version testing

### Documentation
- Improved docs
- Updated project metadata for PyPI
- Removed broken badges from README

### Infrastructure
- Removed strict version pins for better compatibility (particularly removed UMAP constraints)
- Updated GitHub workflows
- Updated README badges
- Updated package-data handling

[v1.1.0]: https://github.com/TuragaLab/flyvis/releases/tag/v1.1.0
