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Release Notes

1.5.6_24.1.1 [2026-01-12]

Fixes:

  • Fixed broken documentation links in README.md for Freesurfer license instructions, data classification, and running gears as a batch

Maintenance:

  • Updated urllib3 to >=2.6.3 to address HIGH and CRITICAL security vulnerabilities
  • Removed hidden .gitlab file to enable security pipeline execution

1.5.5_24.1.1 [2025-07-22]

Enhancements:

  • Updated fmriprep from 23.2.1 to 24.1.1
  • Updated bids-client to 1.2.29

Fixes:

  • Fixed broken documentation links in README

Maintenance:

  • Added .gitlab file with code owners configuration

1.5.5_23.2.1 [2025-11-20]

Fixes:

  • Downgraded fmriprep from 24.1.1 to 23.2.1 to address compatibility issues
  • Removed vulnerable packages (busybox, sysstat, libexpat1, libicu72, libldap-2.5-0, libxml2) from base image
  • Fixed broken documentation links in README.md
  • Fixed markdown formatting in CONTRIBUTING.md for better readability

Maintenance:

  • Migrated from poetry to uv for dependency management
  • Updated flywheel-bids from 1.2.26 to 1.2.29
  • Removed .gitlab file to enable security pipelines

Documentation:

  • Updated Flywheel documentation URLs to reflect current site structure

1.5.4_24.1.1 [2025-02-04]

Enhancements:

  • Updated to work on HPC environments

Maintenance:

  • Updated BIDS Client to 1.2.26
  • Updated .gitlab-ci.yml reference to use main branch for QA CI tooling
  • Updated .pre-commit-config.yaml reference to use main branch for QA CI hooks
  • Disabled DEBUG mode in CI configuration (removed verbose command output)
  • Cleared PUBLISH_POETRY default value in CI configuration
  • Added conditional publish:poetry job that runs only when PUBLISH_POETRY is set and a tag exists
  • Removed always_run: true flag from gearcheck pre-commit hook
  • Updated gear builder image reference to flywheel/bids-fmriprep:1.5.4_24.1.1

1.5.3_24.1.1 [2025-01-31]

Maintenance:

  • Updated flywheel-bids from git reference to stable release version 1.2.26
  • Normalized string quote formatting in test fixtures and notebook scripts

1.5.2_24.1.1 [2025-01-29]

Enhancements:

  • Added autoupdate.py utility to automatically update gear Docker image and manifest versions
  • Added platform_test.py for automated testing of gear updates on Flywheel platform
  • Added support for .bidsignore file handling during BIDS validation
  • Added explicit FreeSurfer license path configuration via FS_LICENSE environment variable
  • Added addendum_clean_generated_bids_command() helper method to handle path formatting and spacing in BIDS commandline arguments

Fixes:

  • Fixed FreeSurfer license installation to use gear_context.writable_dir when available for HPC compatibility
  • Fixed path handling for commands containing spaces or system separators

Maintenance:

  • Updated base Docker image from python:3.10-slim to flywheel/python:3.12-debian
  • Updated fmriprep algorithm from 24.0.0 to 24.1.1
  • Updated Python version from 3.10 to 3.12 throughout Docker build process
  • Updated flywheel-bids dependency to commit 83c34dcedd37f5c08303199238ad207ef793f123
  • Updated .gitignore patterns from output/ and work/ to *output* and *work*
  • Migrated CI configuration from sse-qa-ci to etc/qa-ci project
  • Updated .pre-commit-config.yaml hooks reference to commit 4b12db22249808c61e7391e20d94e70567ebb7a7
  • Replaced docker_build pre-commit hook with hadolint, jsonlint, linkcheck, and markdownlint
  • Removed pytest from pre-commit hooks
  • Optimized Docker image build with --no-cache-dir flags and virtual environment --copies option
  • Added installed_packages.txt generation during Docker build for dependency tracking
  • Updated gear command path in manifest.json to use absolute path /flywheel/v0/run.py
  • Changed gear suite classification from BIDS Apps to Image Processing
  • Updated various documentation links to current Flywheel docs URLs
  • Added pytest configuration to ignore autoupdate.py during test runs
  • Updated Ruff linter configuration to ignore PLR0912 rule

Documentation:

  • Added comprehensive section on updating BIDS algorithm versions with step-by-step instructions
  • Updated FreeSurfer license documentation link
  • Converted markup from __bold__ to **bold** throughout CONTRIBUTING.md
  • Fixed broken links and updated formatting in README.md
  • Reformatted release notes with improved markdown structure

1.5.1_24.0.0 [2024-07-01]

Enhancements:

  • Added support for bids-filter-file input to allow custom BIDS input filters using PyBIDS
  • Added gear-intermediate-files and gear-intermediate-folders config options to selectively retain specific files or folders from intermediate work directory
  • Added gear-expose-all-outputs config option to keep all extra output files created during the run
  • Added gear-save-intermediate-output config option to save all intermediate output into fmriprep_work.zip
  • Added bidsignore input to provide custom .bidsignore file to bids-validator
  • Added derivatives input to provide previously calculated fMRIPrep output results as a zip file
  • Added fs-subject-dir input to provide existing FreeSurfer subject directories for reuse
  • Added gear-post-processing-only config option to skip BIDS algorithm and proceed directly to generating HTML reports and processing metadata
  • Added gear-keep-fsaverage config option to retain freesurfer/fsaverage* directories in output
  • Added bids_app_command config field to allow users to input fMRIPrep command as they would on CLI
  • Added pre-commit hooks for code quality including gearcheck, poetry_export, docker_build, yamllint, ruff, and pytest
  • Added comprehensive documentation including README.md, CONTRIBUTING.md, FAQ.md, and LICENSE
  • Added GitLab CI/CD configuration for automated testing and quality checks
  • Added integration tests and unit tests for parser, main, and helper functions
  • Added Jupyter notebooks for running bids-fmriprep and gathering resource usage data

Maintenance:

  • Upgraded base fMRIPrep version from previous releases to 24.0.0
  • Upgraded Python version to 3.10 in multi-stage Docker build
  • Migrated to flywheel-bids library for BIDS App toolkit functionality
  • Updated Docker build to use multi-stage builds isolating Flywheel dependencies from BIDS App image
  • Updated base Docker image to nipreps/fmriprep:24.0.0
  • Updated flywheel-gear-toolkit to ^0.6
  • Updated flywheel-sdk to 18.2.0
  • Added poetry for dependency management with pyproject.toml
  • Added .dockerignore to optimize Docker context build performance
  • Added .gitignore for Python, Mac, and editor-specific files
  • Configured CI pipeline with security scans, dependency scanning, license management, SAST, and secret detection
  • Added pytest coverage requirement of 80% minimum

Documentation:

  • Added detailed README.md with overview, usage instructions, workflow diagrams, prerequisite files and metadata requirements
  • Added CONTRIBUTING.md with instructions for dependency management, linting, testing, and merge request guidelines
  • Added FAQ.md for common questions and errors
  • Added release notes structure in docs/release_notes.md
  • Added changelog structure in docs/changelog.md