[v2.0.0] Phase 3: Curate v2 Example and Input File Story

[Anselmoo]

Goal

Ship a supported, discoverable v2 example/input story for CLI, API, and notebook users.

Depends On

• [v2.0.0] Phase 1: Codebase Readiness Assessment #2084 (Phase 1: Codebase Readiness Assessment)
• [v2.0.0] Phase 2: Stabilize CI Baseline #2085 (Phase 2: Stabilize CI Baseline)

Background

The legacy Examples/ directory (~43 files) was removed in the v2 migration. Notebooks in docs/examples/ still fetch data from https://raw.githubusercontent.com/Anselmoo/spectrafit/main/Examples/data.csv (a URL that no longer resolves). Several docs pages still reference the deleted tree. spectrafit/generators/synthetic.py (SyntheticSpectrum + PeakDefinition) is the v2-safe foundation for reproducible examples.

Tasks

• TASK-009 — Create a curated root-level examples/ directory with v2-safe assets: README.md, JSON/TOML/YAML input files, small reference data, expected outputs; keep it clearly distinct from the deleted legacy Examples/ tree
• TASK-010 — Replace stale Examples/data.txt and Examples/data.csv references in README.md, docs/interface/usage.md, docs/interface/features.md, and docs/examples/example9_1.ipynb, example9_2.ipynb, example9_3.ipynb, example9_6.ipynb with supported v2 assets or generator-based examples
• TASK-011 — Remove or rewrite unsupported docs/example surfaces in docs/examples/index.md and mkdocs.yml tied to removed Mössbauer models (example10_1.ipynb), removed RIXS plugins (example9_4.ipynb), or removed autopeak configuration (example7.md)
• TASK-012 — Promote spectrafit/generators/synthetic.py and existing tests/conftest.py fixtures into the maintained example story

Acceptance Criteria

• Users can find at least one supported local-fit example and one supported multi-component/global-fit example from the repository root
• README.md and docs no longer point at deleted Examples/ assets
• Example navigation advertises only supported v2 workflows

Example Directory Structure (proposed)

examples/
├── README.md                  # overview and usage instructions
├── basic_fit/
│   ├── input.toml             # single-component v2-safe input
│   └── data.csv               # small reference spectrum (generated)
├── multi_peak_fit/
│   ├── input.toml
│   └── data.csv
└── global_fit/
    ├── input.toml
    └── data.csv

Constraints

• Do NOT reintroduce Mössbauer, RIXS-plugin, or legacy autopeak content
• Use SyntheticSpectrum / PeakDefinition from spectrafit/generators/synthetic.py for reproducible data generation
• Keep example files minimal and v2-safe

[Anselmoo]

🔶 Partial — spectrafit init landed; notebook template pending

Progress as part of #2094:

• ✅ spectrafit init command scaffolds a starter project (config files, directory structure)
• ✅ spectrafit jupyter command available for notebook-mode entry
• ⏳ Auto-generation of a reference .ipynb template (analogous to mcp-zen-of-languages onboarding) is not yet implemented — tracked as future work

Leaving open until the .ipynb reference template is shipped.

[stale]

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