[Epic] Comprehensive Documentation and Architecture Overview for SPIMquant

[akhanf]

Epic: Comprehensive SPIMquant Documentation (MkDocs)

This epic is to create in-depth user and developer documentation for SPIMquant, describing in detail what the pipeline does under the hood. The goal is to help both users and contributors understand the tools, workflows, outputs, and how to reproduce/extend figures. Documentation should include illustrative diagrams (using DAG outputs from snakemake as mermaid diagrams), rule-by-rule breakdown by .smk file, and explanations of processing steps and output products.

Project Scope

• Overview of SPIMquant's workflow, processing steps, and outputs
• Illustrative Documents & Figures
  • DAG outputs (run on tests/bids_ds) split into smaller, understandable pieces with mermaid diagrams.
  • Explanations for each major workflow/component.
  • Figures/documentation for the types of rules in each .smk file (e.g. split by file: what each does)
  • Generated figures include code/instructions for regeneration for use in CI.
• mkdocs-based Documentation Root
  • Use zarrnii as an example for structure if helpful.
  • Create a new docs/ documentation root using mkdocs.

Deliverables

• Modular documentation pages (overview, specific workflows, outputs, rule breakdown by .smk file, figures)
• Version-controlled code/scripts to generate every included figure or diagram
• Example output shown from processing tests/bids_ds

Acceptance

• All docs live in new docs/ root, structured for mkdocs site
• All generated diagrams/figures are reproducible with included scripts
• Can be extended with future workflow/scientific additions

Sub-issues

See below for sub-tasks to be filed as separate issues/PRs.