# SciencePlots Toolkit Index

High-signal entry points and documentation for AI agents.

## Core Agent Instruction

- [AGENTS.md](AGENTS.md): Root-level mandates and operational procedures
- [.agents/skills/scienceplots-viz/SKILL.md](.agents/skills/scienceplots-viz/SKILL.md): Primary plotting skill - ALWAYS use for Python/plotting tasks
- [CHANGELOG.md](CHANGELOG.md): Version history and structural changes
- [CONTRIBUTING.md](CONTRIBUTING.md): Development standards and workflows

## Capabilities & Workflows

- [.agents/skills/](.agents/skills/): Agent skills and domain expertise
  - [scienceplots-viz/SKILL.md](.agents/skills/scienceplots-viz/SKILL.md): Scientific visualization with Matplotlib and SciencePlots
  - Skill includes: Path handling, plotting standards, implementation workflows, verification

## Templates

- [docs/templates/PLAN.md](docs/templates/PLAN.md): Implementation plan template with intent classification
- [docs/templates/SPEC.md](docs/templates/SPEC.md): Feature specification template
- [docs/templates/SKILL.md](docs/templates/SKILL.md): Skill identity and mandate template (2 layouts)

## Project Documentation

- [README.md](README.md): Human-centric project overview and quick start
- [docs/ARCHITECTURE.md](docs/ARCHITECTURE.md): System design and component mapping
- [docs/PYTHON_STANDARDS.md](docs/PYTHON_STANDARDS.md): Source of truth for Python coding rules
- [docs/API_DESIGN.md](docs/API_DESIGN.md): API design principles and visibility rules
- [docs/PHILOSOPHY.md](docs/PHILOSOPHY.md): Engineering principles and philosophy
- [GIT_WORKFLOW.md](GIT_WORKFLOW.md): Git operations and branching strategy

## Source Code

- [src/scienceplots_toolkit/](src/scienceplots_toolkit/): Core package
  - [__init__.py](src/scienceplots_toolkit/__init__.py): Public API exports
  - [style.py](src/scienceplots_toolkit/style.py): configure_matplotlib_style(), get_figsize()
  - [utils.py](src/scienceplots_toolkit/utils.py): save_plot(), configure_24h_axis(), add_stats_box()
  - [analysis.py](src/scienceplots_toolkit/analysis.py): plot_profile_with_quantiles(), generate_profile_grid()
  - [latex.py](src/scienceplots_toolkit/latex.py): PreambleManager for LaTeX configuration
  - [cli.py](src/scienceplots_toolkit/cli.py): CLI orchestrator and @plot_function decorator

## Examples

- [examples/](examples/): Working example scripts
  - [example_basic.py](examples/example_basic.py): Basic plotting demonstrations
  - [example_energy.py](examples/example_energy.py): Energy-specific profile plots
  - [example_readme.py](examples/example_readme.py): README documentation plots
  - [example_orchestrator.py](examples/example_orchestrator.py): Batch orchestration examples

## Testing

- [tests/](tests/): Test suite
  - [test_style.py](tests/test_style.py): Style configuration tests
  - [test_utils.py](tests/test_utils.py): Utility function tests
  - [test_analysis.py](tests/test_analysis.py): Analysis module tests
  - [test_visual_baselines.py](tests/test_visual_baselines.py): Visual regression tests
  - [baseline/](tests/baseline/): Visual baseline reference images

## Agent Tools

- [tools/agent/](tools/agent/): Agent utilities and validation
  - [validate_standards.py](tools/agent/validate_standards.py): Repository structure validation
  - [validate_skill.py](tools/agent/validate_skill.py): SKILL.md structural validation
  - [eval_skill.py](tools/agent/eval_skill.py): Skill quality evaluation

## Output

- [output/](output/): Generated plots (PNG + PDF)
  - Created by scripts, excluded from git (see .aiignore)

## Configuration

- [pyproject.toml](pyproject.toml): Project configuration and dependencies
- [.pre-commit-config.yaml](.pre-commit-config.yaml): Pre-commit hooks configuration
- [.aiignore](.aiignore): AI agent session data exclusion

## Related Files

- [PUBLICATION_PLAN.md](PUBLICATION_PLAN.md): PyPI publication workflow
- [RELEASE.md](RELEASE.md): Release process and versioning
