api-docs

API documentation

Applies Sun Lab conventions for generating API documentation HTML pages from source code docstrings using Sphinx, autodoc, Napoleon, and optionally Breathe/Doxygen for C++ code.

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Scope

Covers:

• Sphinx configuration (conf.py) for Python-only, C++-only, and hybrid projects
• RST file structure (index.rst, welcome.rst, api.rst)
• Doxygen configuration and Breathe integration for C++ code
• tox.ini [testenv:docs] build environment setup
• Makefile and make.bat wrappers
• Documentation hosting URL conventions
• Documentation dependency management via ataraxis-automation

Does not cover:

• MCP server modules or shared asset libraries — these are consumed by AI agents, not end-users, and MUST NOT be included in API documentation
• Writing Python docstrings or type annotations (see /python-style)
• README file conventions (see /readme-style)
• pyproject.toml dependency sections (see /pyproject-style)
• General project structure or architecture (see /explore-codebase)

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Documentation architecture

Project archetypes

Sun Lab projects follow one of three documentation archetypes based on language composition:

Archetype	Language	Extensions	Doxygen
Python-only	Pure Python	autodoc, napoleon, click, typehints, furo theme	No
C++-only	Pure C++	breathe, furo theme	Yes
Hybrid	Python + C++	All Python extensions + breathe	Yes

Directory structure

For the full project-level directory tree, invoke /project-layout. The documentation-specific layout within each project is:

project-root/
├── docs/
│   ├── Makefile              # Unix Sphinx wrapper (delegates to tox)
│   ├── make.bat              # Windows Sphinx wrapper
│   └── source/
│       ├── conf.py           # Sphinx configuration
│       ├── index.rst         # Main page with toctree
│       ├── welcome.rst       # Landing page content
│       └── api.rst           # API reference directives
├── Doxyfile                  # (C++ and hybrid projects only)
└── tox.ini                   # Contains [testenv:docs] build environment

C++ and hybrid projects additionally generate:

docs/source/doxygen/
└── xml/                      # Doxygen-generated XML consumed by Breathe

Extension stack

Python-only projects use these extensions in this exact order:

extensions = [
    'sphinx.ext.autodoc',
    'sphinx.ext.napoleon',
    'sphinx_click',
    'sphinx_autodoc_typehints',
]

C++-only projects use:

extensions = [
    'breathe',
]

Hybrid projects use all Python extensions plus breathe, inserted after sphinx_autodoc_typehints:

extensions = [
    'sphinx.ext.autodoc',
    'sphinx.ext.napoleon',
    'sphinx_click',
    'sphinx_autodoc_typehints',
    'breathe',
]

Ordering constraint: sphinx_click MUST appear before sphinx_autodoc_typehints. sphinx_autodoc_typehints imports the sphinx.ext.autodoc.mock submodule at load time, which shadows the mock function that sphinx_click needs. Loading sphinx_click first ensures it captures the correct function binding before the submodule shadowing occurs.

Documentation dependencies

All documentation dependencies are bundled as runtime dependencies of ataraxis-automation. Downstream projects include ataraxis-automation in their dev optional dependencies, which transitively provides all documentation tools. You MUST NOT add Sphinx or documentation dependencies directly to downstream project pyproject.toml files.

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Workflow

Creating documentation from scratch

1. Determine archetype: Identify whether the project is Python-only, C++-only, or hybrid based on the source code language composition.

2. Create directory structure: Create docs/source/ directory and the Makefile wrappers. Read rst-templates.md for Makefile and make.bat templates.

3. Generate conf.py: Read conf-py-templates.md and use the appropriate archetype template. Replace all placeholder values with project-specific information.

4. Generate RST files: Read rst-templates.md and create index.rst, welcome.rst, and api.rst using the templates. Populate api.rst with the correct directives for the project's modules.

5. Configure Doxygen (C++ and hybrid only): Read doxygen-reference.md and create a Doxyfile at the project root listing all C++ source files.

6. Configure tox build: Add the [testenv:docs] section to tox.ini following the appropriate pattern for the archetype.

7. Verify: Run through the verification checklist below.

Modifying existing documentation

1. Read existing files: Read docs/source/conf.py, docs/source/api.rst, and any other files you intend to modify before making changes.

2. Identify archetype: Check the extensions list in conf.py to determine the project archetype.

3. Apply changes: Follow the conventions in this skill and the reference files. Common modifications include:

   • Adding new Python modules to api.rst via automodule directives
   • Adding new Click CLI groups to api.rst via click directives
   • Adding new C++ source files to api.rst via doxygenfile directives (and to Doxyfile)
   • Updating project metadata in conf.py and welcome.rst

4. Verify: Run through the verification checklist below.

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Key conventions

conf.py rules

• Version extraction MUST use importlib_metadata.version() for Python and hybrid projects. C++-only projects hardcode the version string.
• Copyright format: 'YEAR, Sun (NeuroAI) lab' where YEAR is the current year.
• The templates_path and exclude_patterns fields are included but left at defaults (['_templates'] and [] respectively).
• Napoleon is configured for Google-style docstrings only (napoleon_numpy_docstring = False).
• All Napoleon and sphinx_autodoc_typehints settings MUST match the templates exactly. See conf-py-templates.md for the full settings.
• The HTML theme is always furo. Furo provides built-in light/dark mode toggling with no additional extensions required.

api.rst rules

• Each documented module or file gets its own RST section with an =-underlined heading.
• Python modules use automodule with :members:, :undoc-members:, and :show-inheritance:.
• Click CLI groups use click with :prog: set to the CLI entry point name and :nested: full.
• C++ files use doxygenfile with :project: set to the project name.
• Section headings MUST be descriptive names, not module paths (e.g., "Precision Timer" not "ataraxis_time.precision_timer.timer_class").
• You MUST NOT add automodule directives for MCP server modules or shared asset modules. These components are designed for consumption by AI agents, not end-users, and do not belong in API documentation.

welcome.rst rules

• Title format: Welcome to PROJECT_NAME API documentation page with matching = underline.
• First paragraph: the bare project description — the same sentence used in all other canonical description locations for the project archetype (e.g., pyproject.toml, __init__.py, README.md, or library.json). No language or project name prefix.
• Second paragraph: for Ataraxis projects, standard Ataraxis project attribution with links to the Ataraxis <https://github.com/Sun-Lab-NBB/ataraxis>_ repository and the Sun (NeuroAI) lab. For non-Ataraxis projects, this paragraph is optional or may contain other project-relevant context. May include additional context (e.g., companion libraries) after the attribution when appropriate.
• Third paragraph: standard disclaimer that the site contains API docs only, with link to GitHub repository.
• Footer: explicit RST link targets for the GitHub repo and Sun lab URLs.

tox.ini docs environment

For the complete tox.ini conventions and all other environment definitions, invoke /tox-config. /tox-config is the authoritative source; if any pattern here conflicts, /tox-config takes precedence. The docs-specific patterns are summarized here for convenience.

Python-only projects (no external Doxygen dependency):

[testenv:docs]
description =
    Builds the API documentation from source code docstrings using Sphinx. The result can be
    viewed by loading 'docs/build/html/index.html'.
depends = uninstall
commands =
    sphinx-build -b html -d docs/build/doctrees docs/source docs/build/html -j auto -v

C++ and hybrid projects add Doxygen before Sphinx:

[testenv:docs]
description =
    Builds the API documentation from source code docstrings using Doxygen, Breathe and Sphinx.
    The result can be viewed by loading 'docs/build/html/index.html'.
deps = ataraxis-automation==VERSION
depends = uninstall
allowlist_externals = doxygen
commands =
    doxygen Doxyfile
    sphinx-build -b html -d docs/build/doctrees docs/source docs/build/html -j auto -v

Rules:

• The depends = uninstall ensures a clean environment state before building.
• Downstream projects pin deps = ataraxis-automation==VERSION to the current release. The ataraxis-automation project itself omits this field since it IS ataraxis-automation.
• The Sphinx build command MUST use -j auto for parallel building and -v for verbose output.
• C++ and hybrid projects MUST add allowlist_externals = doxygen and run doxygen Doxyfile before the Sphinx build command.
• C++-only projects use skip_install = true since there is no Python package to install. See doxygen-reference.md for the full tox pattern.

Hosting convention

Documentation is hosted on Netlify with standardized URLs:

https://PROJECT_NAME-api-docs.netlify.app/

This URL is declared in pyproject.toml under [project.urls] as the Documentation key.

Makefile and make.bat

These are standard Sphinx wrapper files. They are rarely used directly since builds are invoked via tox (tox -e docs). Use the exact templates from rst-templates.md when creating new projects.

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Related skills

Skill	Relationship
/python-style	Defines docstring and type annotation conventions consumed by autodoc
/cpp-style	Defines Doxygen comment conventions consumed by Breathe
/readme-style	Defines README conventions; README links to hosted API docs
/pyproject-style	Defines pyproject.toml conventions including documentation URL
/project-layout	Provides full project directory trees; this skill owns docs/ internals
/tox-config	Owns full tox.ini conventions; this skill summarizes docs env patterns
/commit	Should be invoked after completing documentation changes
/explore-codebase	Provides project context needed to identify modules for api.rst

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Proactive behavior

You should proactively offer to invoke this skill when:

• Creating a new Sun Lab project that needs API documentation
• Adding new Python modules or Click CLI commands that should appear in API docs
• Adding C++ source files to a hybrid or C++ project
• The user asks about Sphinx, autodoc, Breathe, Doxygen, or documentation generation

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Verification checklist

You MUST verify your work against this checklist before submitting any documentation changes.

API Documentation Compliance:
- [ ] Documentation archetype correctly identified (Python-only, C++-only, or hybrid)
- [ ] Directory structure matches convention (docs/source/ with conf.py, index.rst, welcome.rst, api.rst)
- [ ] conf.py uses correct extension stack for the archetype
- [ ] conf.py uses correct extension ordering
- [ ] Version extracted via importlib_metadata (Python/hybrid) or hardcoded (C++-only)
- [ ] Copyright uses current year and 'Sun (NeuroAI) lab' format
- [ ] Napoleon configured for Google-style only (numpy disabled)
- [ ] All sphinx_autodoc_typehints settings present and correct (Python/hybrid)
- [ ] Breathe configuration present and correct (C++/hybrid)
- [ ] html_theme set to 'furo'
- [ ] index.rst includes welcome.rst and has toctree with api
- [ ] welcome.rst follows template with correct project name and description
- [ ] welcome.rst includes Sun lab and GitHub repository links
- [ ] api.rst uses automodule with :members:, :undoc-members:, :show-inheritance: (Python)
- [ ] api.rst uses click directive with :prog: and :nested: full (Click CLIs)
- [ ] api.rst uses doxygenfile with :project: (C++ files)
- [ ] api.rst section headings are descriptive, not module paths
- [ ] No MCP server or shared asset modules included in api.rst
- [ ] Doxyfile present at project root (C++/hybrid only)
- [ ] Doxyfile outputs to docs/source/doxygen with XML generation enabled
- [ ] tox.ini [testenv:docs] follows correct pattern for archetype
- [ ] tox.ini docs command uses -j auto -v flags
- [ ] Makefile and make.bat present in docs/
- [ ] No Sphinx dependencies added directly to downstream pyproject.toml
- [ ] Documentation URL follows https://PROJECT-api-docs.netlify.app/ convention