Update docs for v0.2.0: YAML config, pipeline steps, and QC#37
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Migrated documentation from Bash-based settings.sh to YAML-based config.yaml, reflecting the new configuration system and breaking changes in v0.2.0. Expanded and restructured configuration, installation, usage, and workflow documentation to cover the new pipeline step numbering, dedicated QC steps, SLURM job naming, and subject list enhancements. Updated examples, quick start, and migration instructions for improved clarity and onboarding.
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Pull request overview
This PR updates documentation for the v0.2.0 release, migrating from Bash-based settings.sh configuration to YAML-based config.yaml. The update reflects breaking changes including dedicated QC pipeline steps (steps 4-5) and renumbered fMRIPrep steps (steps 6-7), along with a unified SLURM job naming pattern. The documentation provides comprehensive migration guidance, updated configuration examples, and enhanced workflow descriptions to support the new architecture.
Key Changes
- Migrated all configuration examples from Bash to YAML format across installation, configuration, usage, and workflows documentation
- Restructured pipeline documentation to reflect seven sequential steps with dedicated QC steps (04-qc-metadata, 05-qc-volumes)
- Added comprehensive migration guide mapping old settings.sh variables to new config.yaml structure
Reviewed changes
Copilot reviewed 7 out of 7 changed files in this pull request and generated 2 comments.
Show a summary per file
| File | Description |
|---|---|
| docs/workflows.rst | Updated pipeline overview with 7-step structure, added detailed QC step documentation, converted configuration examples to YAML |
| docs/usage.rst | Updated step numbering, added SLURM job naming table, documented subject list comment filtering enhancement |
| docs/installation.rst | Converted setup instructions to YAML, added PyYAML dependency, included v0.1.x migration section |
| docs/index.rst | Updated project references to "fMRIPrep Workbench", added v0.2.0 breaking changes summary, updated quick start guide |
| docs/contributing.rst | Updated repository URLs and configuration file references |
| docs/configuration.rst | Complete rewrite with YAML examples, added comprehensive migration guide with mapping table |
| docs/conf.py | Updated version to 0.2.0 (release and version numbers) |
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Co-authored-by: Copilot <[email protected]>
Co-authored-by: Copilot <[email protected]>
Replaced Sphinx-based documentation (.rst, conf.py, Makefile, .readthedocs.yaml) with MkDocs-based Markdown files and configuration (mkdocs.yml). Updated .gitignore for MkDocs build artifacts. Added GitHub Actions workflow for deploying documentation to GitHub Pages. Documentation content and structure have been updated to use Markdown and Material for MkDocs features.
Introduced a main.html override to inject the Seline Analytics script into the site. Updated mkdocs.yml to use the custom overrides directory. Added comments regarding PDF plugin dependencies.
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Migrated documentation from Bash-based settings.sh to YAML-based config.yaml, reflecting the new configuration system and breaking changes in v0.2.0. Expanded and restructured configuration, installation, usage, and workflow documentation to cover the new pipeline step numbering, dedicated QC steps, SLURM job naming, and subject list enhancements. Updated examples, quick start, and migration instructions for improved clarity and onboarding.