Documentation: usage guides and architecture overview #20

New Issue

2026-04-12T16:53:41-04:00

aalexmmaldonado commented

2026-04-12 16:53:41 -04:00

(Migrated from github.com)

The docs site runs on MkDocs with the Material theme. Right now, index.md just includes README.md. As the project grows, contributors need an architecture map, and users need annotation-specific guides.

Scope

Write four pages.

An architecture overview (docs/architecture.md) explaining the data flow from PubChem API to AnnotationEntry to processor to DataFrame to Parquet. Include a diagram showing how Annotation, AnnotationProcessor, and ANNOTATION_REGISTRY connect.

A contributor guide for adding new annotations (docs/contributing/new-annotation.md). Walk through a hypothetical "Boiling Point" annotation from start to finish: enum member, processor class, registry entry, tests.

A per-annotation reference page starting with Dissociation Constants — output schema, example output, known parsing limitations, source-specific notes.

A development setup page (docs/development.md) covering clone, install with Pixi, run tests, and run linting.

Definition of done

Four pages that build and render correctly with mkdocs serve. Navigation configured in mkdocs.yml.

The docs site runs on MkDocs with the Material theme. Right now, `index.md` just includes `README.md`. As the project grows, contributors need an architecture map, and users need annotation-specific guides. ### Scope Write four pages. An architecture overview (`docs/architecture.md`) explaining the data flow from PubChem API to `AnnotationEntry` to processor to DataFrame to Parquet. Include a diagram showing how `Annotation`, `AnnotationProcessor`, and `ANNOTATION_REGISTRY` connect. A contributor guide for adding new annotations (`docs/contributing/new-annotation.md`). Walk through a hypothetical "Boiling Point" annotation from start to finish: enum member, processor class, registry entry, tests. A per-annotation reference page starting with Dissociation Constants — output schema, example output, known parsing limitations, source-specific notes. A development setup page (`docs/development.md`) covering clone, install with Pixi, run tests, and run linting. ### Definition of done Four pages that build and render correctly with `mkdocs serve`. Navigation configured in `mkdocs.yml`.

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Reference: data/pcdigitizer#20