seqforge/mkdocs.yml at main · liuhlab/seqforge · GitHub

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site_name: seqforge
site_description: A compiler from FASTQ + unstructured metadata to a validated manifest and a runnable pipeline.
site_url: https://liuhlab.github.io/seqforge/
repo_url: https://github.com/liuhlab/seqforge
repo_name: liuhlab/seqforge
edit_uri: edit/main/docs/

theme:
  name: material
  # White silhouette of the mark — its internal gaps (flames, DNA rungs, anvil) read as negative
  # space against the teal header. The favicon stays full-colour: browser tabs are not teal.
  logo: assets/logo.png
  favicon: assets/favicon.png
  features:
    - navigation.sections
    - content.code.copy
    - content.code.annotate
    - content.action.edit
    - content.tabs.link
    - toc.follow
  palette:
    - media: "(prefers-color-scheme: light)"
      scheme: default
      primary: teal
      accent: teal
      toggle:
        icon: material/brightness-7
        name: Switch to dark mode
    - media: "(prefers-color-scheme: dark)"
      scheme: slate
      primary: teal
      accent: teal
      toggle:
        icon: material/brightness-4
        name: Switch to light mode
  icon:
    repo: fontawesome/brands/github

extra_css:
  - stylesheets/extra.css

plugins:
  - search

# Concepts sits last on purpose: it is the "why it is shaped this way" layer, and a first-time
# reader should reach the commands before the reasoning.
nav:
  - Home: index.md
  - Getting started: getting-started.md
  - Tutorials:
      - Compiling with Claude: tutorials/with-claude.md
      - Compiling Step-by-step: tutorials/step-by-step.md
      - Adding a technology: tutorials/adding-a-technology.md
  - Concepts:
      - The two artifacts: concepts/artifacts.md
      - How a dataset is identified: concepts/identifying.md
      - When it refuses: concepts/refusal.md
  # "Supported assays" is nested one level under the section on purpose: with `navigation.sections`
  # only the TOP level renders expanded, so the assay list stays folded behind a collapsible toggle
  # and the sidebar does not grow a long flat list.
  - Knowledge base:
      - Overview: kb/index.md
      - Supported assays:
          - 10x Chromium 3' v3 & v3.1: kb/10x-3p-gex-v3.md
          - 10x Chromium 3' v2: kb/10x-3p-gex-v2.md
          - BD Rhapsody WTA: kb/bd-rhapsody-wta.md
          - SPLiT-seq: kb/splitseq.md
          - Bulk RNA-seq: kb/bulk-rnaseq.md

# Three trees stay in the repo and OUT of the site, deliberately; this site is the human layer on top
# of them. The argument is ADR-0045 — cited by number, because a record moves between directories
# and its number does not.
#
# A new file under either needs no change here — the directory entries below cover it — but a NEW
# agent-facing tree does, and must be added to `ignores` in .markdownlint-cli2.yaml in the same
# commit. They are one list, and test_docs.py fails when they drift.
exclude_docs: |
  adr/
  agents/
  research/

markdown_extensions:
  - admonition
  - attr_list
  - md_in_html
  - pymdownx.details
  - pymdownx.highlight:
      anchor_linenums: true
  - pymdownx.inlinehilite
  # base_path "." is the repo root (mkdocs runs there), so a KB page can pull in the canonical
  # README that lives beside its spec.yaml — one source, rendered in two places. check_paths turns a
  # broken include into a hard `--strict` failure instead of a silently empty page.
  - pymdownx.snippets:
      base_path: ["."]
      check_paths: true
  # mermaid ships inside mkdocs-material — no extra dependency, just the fence wiring. This is the
  # one place seqforge extends the sibling repos' shared extension block rather than copying it.
  - pymdownx.superfences:
      custom_fences:
        - name: mermaid
          class: mermaid
          format: !!python/name:pymdownx.superfences.fence_code_format
  - pymdownx.tabbed:
      alternate_style: true
  - toc:
      permalink: true

# Google Analytics 4 — shared Liu Lab org property. The same tag is used
# across every liuhlab GitHub Pages site so traffic lands in one GA4
# property, separated by page path. gtag.js is GFW-blocked, so
# mainland-China readers are counted host-side (Tencent Cloud) instead.
extra:
  analytics:
    provider: google
    property: G-6M1CJF9WXY