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Release Notes

1.1.5_0.20.0 [2026-02-11]

Maintenance:

  • Added Claude Code integration for automated release note generation in GitLab CI pipeline
  • Updated flywheel-bids dependency constraint from ~=1.2 to >=1.2.29
  • Updated jsonschema dependency constraint from ~=4.0 to >=4.0,<5
  • Removed jupyter from development dependencies

1.1.4_0.20.0 [2026-01-12]

Enhancements:

  • Add HPC support

Maintenance:

  • Standardized Dockerfile build stage syntax by changing as to AS for better compatibility
  • Resolved security vulnerabilities in base image dependencies

1.1.3_0.20.0 [2025-08-20]

Enhancements:

  • Added HPC support with writable directory handling and directory linking functionality

Fixes:

  • Fixed FreeSurfer license installation to use writable directory when available
  • Corrected markdown link reference in CONTRIBUTING.md from Inputs to inputs

Maintenance:

  • Migrated from poetry to uv for dependency management with PEP 621 format
  • Updated .gitlab-ci.yml to reference flywheel-io/tools/etc/qa-ci instead of flywheel-io/scientific-solutions/etc/sse-qa-ci
  • Removed setuptools package to resolve HIGH security vulnerability
  • Updated pre-commit hooks to latest sse version with additional checks (pyproject_export, eolfix, hadolint, jsonlint, linkcheck, ruff_format, ruff_tests)
  • Enhanced Dockerfile with multi-stage build pattern (fw_base, build, bids_runner, dev, prod)
  • Added non-root user flywheel (UID/GID 31337) for production stage
  • Updated manifest configuration with show-job, uid, and gid fields
  • Added requirements-dev.txt to .dockerignore
  • Improved Dockerfile with better layer caching and --no-install-recommends flag for apt-get
  • Reformatted Python code with ruff formatter across all source and test files
  • Cleaned up trailing whitespace in markdown files
  • Removed alternative Dockerfile and deprecated .gitlab files
  • Removed legacy security scan configuration variables from .gitlab-ci.yml

Documentation:

  • Added section in README.md explaining how to update the BIDS algorithm version with step-by-step instructions

1.1.2_0.20.0 [2024-05-29]

Fixes:

  • Fixed parsing of command-line arguments containing equals signs in customize_bids_command() function

Maintenance:

  • Updated flywheel-bids dependency to use tag 1.2.14 instead of master branch
  • Changed package name from fw-gear-bids_qsiprep to fw-gear-bids-qsiprep in pyproject.toml
  • Changed gear builder image name from flywheel/bids_qsiprep to flywheel/bids-qsiprep in manifest.json
  • Changed api-key input from read-only to writable in manifest.json
  • Updated gear suite classification from "BIDS Apps" to "Image Processing"
  • Added detailed Flywheel classification metadata including function, modality, organ, species, and therapeutic area

Documentation:

  • Updated QSIPrep Docker image version from 0.16.1 to 0.20.0 in README.md
  • Added documentation link for BIDS app command usage
  • Clarified gear-dry-run configuration description to reference qsiprep command specifically
  • Expanded Outputs section with descriptions of output files: bids_tree.html, bids-qsiprep_qsiprep_{destination_container}.zip, qsiprep_log.txt, and job.log
  • Simplified Prerequisites section to reference Inputs section instead of generic template text
  • Enhanced Usage section with detailed workflow description and command-line argument handling
  • Added package description in pyproject.toml

1.1.0_0.20.0 [2024-03-06]

Enhancements:

  • Added .dockerignore to optimize Docker build context by excluding unnecessary files
  • Added .gitlab file for code ownership mapping
  • Added GitLab CI configuration with test coverage, security scans, and Docker publishing
  • Added pre-commit hooks for code quality enforcement including gearcheck, poetry_export, docker_build, markdownlint, yamllint, ruff, and pytest
  • Added comprehensive documentation including CONTRIBUTING.md with development guidelines
  • Added README.md with detailed gear usage instructions, workflow diagrams, and configuration options
  • Added FAQ.md for frequently asked questions
  • Added gear implementation for BIDS QSIPrep 0.20.0 with pennbbl/qsiprep Docker image
  • Added support for custom eddy configuration via eddy-config input file
  • Added support for reconstruction pipelines via recon-spec input file
  • Added support for archived runs to enable resuming previous analyses
  • Added output-resolution configuration option for specifying spatial resolution
  • Added FreeSurfer license file support
  • Added bidsignore file support for BIDS validation
  • Added gear-post-processing-only mode for metadata-only processing
  • Added gear-save-intermediate-output option to save work directory contents
  • Added multi-stage Dockerfile with isolated Flywheel and BIDS App dependencies
  • Added Python 3.10 virtual environment for Flywheel dependencies
  • Added main gear orchestration in run.py with BIDS App integration
  • Added parser module for configuration and input file handling
  • Added utilities for dry-run mode, eddy config validation, and setup validation
  • Added comprehensive test suite with fixtures and parametrized tests
  • Added alternative Dockerfile example for modern Python base images

Maintenance:

  • Configured GitLab CI with Python 3.10, test coverage threshold of 80%, and security scanning
  • Configured Docker build to use large runners with build-cluster-external tags
  • Installed build-essential, zip, nodejs, and tree system packages in Docker image
  • Installed Python 3.10.0 from source in BIDS App runner stage
  • Created Python virtual environment at /opt/flypy for Flywheel dependencies
  • Added flywheel-gear-toolkit ^0.6 dependency
  • Added flywheel-bids dependency from GitLab repository
  • Added jsonschema ^4.0 dependency
  • Added development dependencies: psutil, pytest, pytest-cov, pytest-mock, and jupyter
  • Configured ruff linter with line length 120 and specific ignore rules
  • Set notrack configuration default to true for privacy

Documentation:

  • Added LICENSE file with MIT license
  • Added development notes in docs/dev_notes.md about work directory configuration
  • Added docs/changelog.md placeholder for version history