Release Notes

2.1.3_24.0.2 [2024-10-18]

Enhancements:

Added HPC (High Performance Computing) capabilities with directory linking and writability checks
Added setup directory to .dockerignore for improved Docker build context

Fixes:

Fixed FreeSurfer license installation to use writable directory when available for HPC environments
Fixed test assertion methods to use assert_called_once() instead of called_once property

Maintenance:

Updated flywheel-bids dependency from git reference to versioned package ^1.2.25
Removed override of test:gear that used larger runner in .gitlab-ci.yml
Reorganized Dockerfile stages with improved reprozip installation placement
Updated Dockerfile base image stage naming and comments for clarity
Consolidated apt-get operations in base image for better layer efficiency

Documentation:

Converted CONTRIBUTING.md formatting from HTML-style bold/italic to markdown (__text__ → **text**, *text* → _text_)
Standardized list markers from * to - throughout CONTRIBUTING.md and README.md
Fixed indentation and formatting inconsistencies in README.md
Added missing blank line in FAQ.md for proper markdown formatting
Improved code block formatting and removed trailing spaces in documentation

Enhancements:

Added autoupdate.py module for automated Dockerfile and manifest synchronization
Added platform test script for automated gear testing on Flywheel instance

Maintenance:

Upgraded python from 3.9 to 3.12 in CI pipeline and Docker image
Updated base Docker image to flywheel/python:3.12-debian
Updated nipreps/mriqc from 24.0.0 to 24.0.2
Updated flywheel-bids to use latest from master branch
Upgraded pytest from ^6.1.2 to ^7.0
Upgraded pytest-cov from ^3.0.0 to ^4.0
Upgraded pytest-mock to ^3.11
Removed pyzmq version constraint workaround
Added linux-libc-dev security upgrade to Dockerfile
Updated environment variables: added MAMBA_ROOT_PREFIX, NUMEXPR_MAX_THREADS, TEMPLATEFLOW_HOME, and UV_USE_IO_URING
Updated LD_LIBRARY_PATH and PATH environment variables for new Python version
Migrated Ruff configuration to new lint.* prefix format

Enhancements:

Fixes:

Fixed FSL license documentation link from fsldownloads_registration to fsl/docs/#/license

Maintenance:

Migrated CI configuration from sse-qa-ci to qa-ci project
Updated .gitlab-ci.yml to use gear-specific CI template with medium runner
Updated .pre-commit-config.yaml hooks including hadolint, jsonlint, linkcheck, markdownlint, and yamllint
Added --no-cache-dir flag to pip install commands in Dockerfile
Updated Python symlink in Dockerfile to use /usr/local/bin/python3.9
Updated flywheel-bids from git source to version 1.2.17
Added development dependencies: packaging, ordered-set, more_itertools, importlib_resources, importlib_metadata, tomli, wheel, platformdirs

Documentation:

Enhancements:

Added gear-FREESURFER_LICENSE configuration option to accept FreeSurfer license text as space-separated input
Added gear-expose-all-outputs configuration option to retain all extra output files created during the run
Added gear-intermediate-files configuration option to specify individual files to retain from intermediate work directory
Added gear-intermediate-folders configuration option to specify folders to retain from intermediate work directory
Added gear-save-intermediate-output configuration option to save all intermediate output as {{bids_app_binary}}_work.zip
Added validation pipeline to check gear-dependent configuration options before downloading BIDS data or running algorithms
Added support for parsing input files from manifest to make filepaths available for BIDS app commands
Added automatic copying of .bidsignore file from input directory to BIDS directory for validator runs

Fixes:

Fixed argument parsing to split --equals=sign x format into separate arguments instead of keeping them combined
Added pyzmq<26.0.0 version constraint to avoid broken builds in 26.0.1 and 26.0.2

Maintenance:

Updated flywheel-gear-toolkit from git reference to version ^0.6
Updated flywheel-bids from git reference to tag 1.2.14
Changed bids-app-modalities to bids-app-data-types throughout codebase
Added ruff_format pre-commit hook for code formatting
Updated Flywheel classification with function, modality, organ, species, and therapeutic area metadata
Changed gear suite from "BIDS Apps" to "Quality Assurance"
Updated PATH environment variable to prioritize /opt/ants and /opt/afni before conda
Added PWD environment variable set to /flywheel/v0
Changed api-key input from read-only to read-write
Refactored setup_bids_env to accept app_context as parameter instead of returning it
Applied code formatting improvements throughout codebase using ruff_format
Updated CI configuration from ci/default.yml to ci/large-default.yml
Added CI variables: APT_INSTALL, PUBLISH_POETRY, and CACHE_CLEAR
Cleared DEBUG variable default value in CI configuration

Enhancements:

Added BIDS MRIQC gear for automatic prediction of quality and visual reporting of MRI scans
Added support for extracting no-reference Image Quality Metrics (IQMs) from T1w, T2w, and BOLD images
Added metadata storage of IQMs under file.info.derived.IQM field for analyzed files
Added HTML quality report generation for individual scans and group-level analyses
Added support for project, subject, session, and acquisition level analyses
Added group-level TSV summary file generation
Added anonymized quality metrics submission to MRIQC repository (opt-out available via no-sub config)
Added post-processing-only mode to regenerate reports from archived results
Added archived runs input support for reprocessing previous analyses

Maintenance:

Integrated MRIQC 23.1.0 algorithm from nipreps
Added flywheel-gear-toolkit and flywheel-bids dependencies
Added CI/CD pipeline with .gitlab-ci.yml configuration
Added pre-commit hooks for gearcheck, poetry_export, docker_build, ruff, and pytest
Set up testing framework with pytest, pytest-cov, and pytest-mock
Added python 3.9 support
Added multi-stage Dockerfile to isolate Flywheel dependencies from BIDS App image
Added .dockerignore to optimize Docker build context

Documentation: