Infrastructure Documentation

Documentation Module

Figure management, image handling, and documentation integration for research manuscripts.

FigureManager (figure_manager.py)

Automatic figure numbering, cross-referencing, and metadata tracking:

from infrastructure.documentation import FigureManager, FigureMetadata

manager = FigureManager()

# Register a figure (label auto-generated from filename if omitted)
manager.register_figure(
    filename="results.png",
    caption="Experimental results showing...",
    label="fig:results",
    section="Results",
)

# Get figure metadata by label
meta = manager.get_figure("fig:results")  # Returns FigureMetadata | None

ImageManager (image_manager.py)

Image file management and processing:

from pathlib import Path
from infrastructure.documentation import ImageManager, FigureManager

img_manager = ImageManager(FigureManager())

# Insert a registered figure into a markdown file under a section
img_manager.insert_figure(Path("manuscript/01_intro.md"), "fig:results", section="Results")

# Validate that referenced figures exist and labels are registered
errors = img_manager.validate_figures(Path("manuscript/01_intro.md"))  # list[(label, error)]

MarkdownIntegration (markdown_integration.py)

Auto-insertion of figures and content into markdown manuscripts:

from pathlib import Path
from infrastructure.documentation import MarkdownIntegration, FigureManager

integrator = MarkdownIntegration(Path("manuscript"), FigureManager())

# Insert a figure into a named section of a markdown file
integrator.insert_figure_in_section(Path("manuscript/01_intro.md"), "fig:results", "Results")

Glossary & API Documentation (glossary_gen.py)

Generate API documentation and glossaries from source code:

from infrastructure.documentation import build_api_index, generate_markdown_table, ApiEntry
from infrastructure.documentation.glossary_gen import inject_between_markers

# Build API index from source
api_entries = build_api_index(source_dir)

# Generate markdown table
table = generate_markdown_table(api_entries)

# Inject between markers in a markdown file (operates on text, not a file path)
updated_text = inject_between_markers(
    text=original_text,
    begin_marker="",
    end_marker="",
    content=table,
)

CLI:

# Positional args: SRC_DIR GLOSSARY_MD (no --project flag)
uv run python -m infrastructure.documentation.generate_glossary_cli \
  projects/{name}/src projects/{name}/manuscript/98_symbols_glossary.md

# With no args, defaults to /project/src and /project/manuscript/98_symbols_glossary.md

Source & license

This open-source skill is cataloged on AgentStack and links to its original source — we do not rehost the code.

• Author: docxology
• Source: docxology/template
• License: Apache-2.0
• Homepage: https://doi.org/10.5281/zenodo.19139090

Install and usage instructions live in the source repository linked above.