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Release Notes

1.1.1_6.0.6 [2025-09-23]

Documentation:

  • Updated CONTRIBUTING.md to reflect migration from poetry to uv for dependency management
  • Updated CONTRIBUTING.md with comprehensive pre-commit hooks documentation
  • Reformatted CONTRIBUTING.md to enforce 88-character line limit
  • Updated README.md with improved formatting and structure for inputs, configuration, and outputs sections
  • Updated manifest.json source URL to point to https://github.com/saslan-7/super-bet2
  • Removed docs/changelog.md file

1.1.0_6.0.6 [2025-08-21]

Enhancements:

  • Gear now runs as non-root user (flywheel:31337) for improved security

Maintenance:

  • Upgraded FSL from 5.0.11 to 6.0.6
  • Migrated from poetry to uv for package management
  • Updated base Docker image from debian:bullseye-slim to ubuntu:noble-20250529
  • Migrated to flywheel/fsl-base:6.0.6-focal for FSL installation
  • Updated Python dependency pins to address security vulnerabilities while maintaining numpy 1.26.4 compatibility with FSL 6.0.6
  • Updated flywheel-gear-toolkit from >=0.2 to >=0.6.22,<0.7
  • Updated CI configuration to reference flywheel-io/tools/etc/qa-ci
  • Configured CI to use larger GitLab runner for tests
  • Updated pre-commit hooks configuration
  • Updated MNI template path from avg152T1_brain.nii.gz to MNI152_T1_2mm_brain.nii.gz
  • Added requirements-dev.txt to .dockerignore

Documentation:

  • Updated FSL license URL in README

1.0.1_5.0.7 [2024-04-18]

Maintenance:

  • Upgraded python from 3.8 to 3.10
  • Replaced base image from neurodebian:xenial to debian:bullseye-slim
  • Updated FSL installation to use version 5.0.11 from official source
  • Added Miniconda for improved dependency management
  • Refactored package structure, renaming fw_gear_fsl_super_bet2 to fw_gear_fsl_superbet2 for consistency
  • Updated Docker build process to use pip installation of the package
  • Modified CI configuration to disable Poetry publishing (PUBLISH_POETRY: "false")
  • Updated input file handling to use dynamic path resolution from gear context
  • Fixed import paths and references throughout codebase to match new package name
  • Updated test suite to reflect new package structure and improved mocking

Documentation:

  • Removed outdated merge request template
  • Updated manifest.json with additional metadata fields including function, organ, species, and therapeutic_area
  • Corrected gear name from fsl-super-bet2 to fsl-superbet2 in manifest
  • Updated repository URLs to new location in Scientific Solutions namespace
  • Swapped source and url values in manifest for proper external links

1.0.0_5.0.7 [2024-03-13]

Enhancements:

  • Added initial implementation of FSL SuperBET2 gear for brain extraction from T1w MRI images
  • Added fractional_intensity_threshold configuration option to control brain outline estimation

Maintenance:

  • Added CI/CD pipeline configuration with .gitlab-ci.yml
  • Added pre-commit hooks for code quality enforcement including gearcheck, poetry_export, docker_build, markdownlint, yamllint, ruff, and pytest
  • Configured python 3.8 runtime environment in Dockerfile
  • Added flywheel-gear-toolkit ^0.2 dependency for gear infrastructure
  • Set test coverage requirement to 95% in .env
  • Added .dockerignore to optimize Docker build context
  • Added .gitignore for Python and IDE files

Documentation:

  • Added README.md with gear summary, inputs, configuration, and outputs
  • Added CONTRIBUTING.md with development setup and contribution guidelines
  • Added docs/release_notes.md for tracking release history
  • Added docs/changelog.md for informal design decisions
  • Added merge request template in .gitlab/merge_request_templates/default.md
  • Added LICENSE file with MIT license