Docs

Opentrons Docs: MkDocs Authoring Guide

The /docs project uses MkDocs with the Material theme, the monorepo plugin, mkdocstrings (Python), autorefs, and macros. Config lives in docs/mkdocs.yml. Extra CSS: opentrons-theme.css, instruction-manuals.css, python-api.css.

Directory Structure of /docs

The /docs directory is organized to support multiple documentation publications, site-global shared resources, and project build scripts.

Publication Directories (Multiple MkDocs Projects)

• Each major documentation set ("publication") exists in its own subdirectory, with its own mkdocs.yml and content:

  Publication Directory	Description
  docs/absorbance-plate-reader/	Absorbance Plate Reader Module manual
  docs/flex/	Opentrons Flex robot manual
  docs/heater-shaker/	Heater-Shaker Module manual
  docs/hepa-uv/	HEPA/UV Module manual
  docs/protocol-designer/	Protocol Designer application manual
  docs/python-api/	Python API reference and guides
  docs/stacker/	Flex Stacker Module manual
  docs/temperature-module/	Temperature Module manual
  docs/thermocycler/	Thermocycler Module manual

• Each publication is a self-contained MkDocs project, but shares a unified build/serve flow via the monorepo and the mkdocs-monorepo-plugin.
• New publications may be added for new (or newly documented) software or hardware products.
• Top-level /docs/mkdocs.yml aggregates all publications for the overall site, referencing their content via the monorepo plugin.

docs/shared/: Shared Content and Resources

• docs/shared/ holds assets, MDX-style includes, and support content used across multiple publications:
  • Images: docs/shared/images/ — interface elements used in multiple publications.
  • Icons: docs/shared/icons/ — custom Opentrons SVG icons.
  • Theme overrides: docs/shared/partials/ — HTML files used to modify the base Material theme.
  • CSS: Sitewide overrides in docs/shared/ (e.g., opentrons-theme.css, instruction-manuals.css).
• Refer to these resources in any publication via the monorepo plugin's path mapping.
• The only user-facing pages in shared/ are navigation pages, like docs/shared/modules/index.md.

3. Scripts and Ancillary Files

• Top-level /docs/ contains scripts and files for building, developing, and managing the documentation site:
  • mkdocs.yml — main config aggregating all sub-projects with the monorepo plugin.
  • Python setup: pyproject.toml specifies the uv setup, including the mkdocs package and required plugins.
  • Makefile: Contains commands for building the docs using the virtual environment.
• These files support the docs build but are not included as user-facing content.

Recommendation: Add your new publication as a subdirectory under /docs/, and place shared assets only in shared/. Scripts and configuration should remain at the top level unless specific to a publication.

File Conventions

• Filenames: Short, lowercase, hyphen-separated. Example: opentrons-app.md
• No H1 in markdown files. The page title comes from mkdocs.yml nav.
• title frontmatter: Required on every page. Controls the sticky title when scrolling and search results. Format: "Publication Name: Page Title". Omit repeated words.

---
title: "Opentrons Flex: Support and Contact Information"
---

• Hide TOC (cover pages only):

---
title: "HEPA/UV Module Instruction Manual"
hide: TOC
---

Header IDs

The autorefs plugin warns on duplicate headings across the entire site. Add unique IDs to disambiguate:

## Tips and tip racks { #tips-and-tip-racks-ot2 }
## Tips and tip racks { #tips-and-tip-racks-flex }
## Air gap { #air-gap-building-block }
## Air gap { #air-gap-complex }

Format: slug of header text + hyphen + short unique suffix. The # and spaces inside { } are required.

Images

• Vector illustrations: SVG preferred.
• Raster (screenshots, renders): PNG. High-DPI (2×) for screenshots. Resample large files to ≤1200px wide. Optimize with ImageOptim before committing.

Tables

Use Markdown tables by default:

| Specification | Description |
|:--------------|:------------|
| Module weight | 790 g       |

Switch to HTML tables when you need: rowspan/colspan, embedded lists, or CSS class attributes (e.g., .my-dot status icons).

Column widths (use sparingly — only when auto-widths are unusable):

| Setting {style="width: 25%;"} | Description |
|------|------|
| Flow rates | Set aspirate/dispense speed. |

Requires attr_list in markdown_extensions (already enabled globally).

Code Blocks

Always declare the language explicitly for syntax highlighting:

```python
foo = "bar"
```

Python API Docs (PAPI)

Version Notices

No special plugin — use italic text in its own paragraph:

*New in version 2.15*

*Changed in version 2.16:* The `mount` parameter is optional.

Linking to the API Reference

Combines mkdocstrings (unique IDs = fully qualified object names) with autorefs (cross-page links):

[`InstrumentContext.aspirate()`][opentrons.protocol_api.InstrumentContext.aspirate]
[`aspirate()`][opentrons.protocol_api.InstrumentContext.aspirate]
When [aspirating][opentrons.protocol_api.InstrumentContext.aspirate], you should…

[`well_bottom_clearance`][opentrons.protocol_api.InstrumentContext.well_bottom_clearance]
Adjust the [bottom clearance][opentrons.protocol_api.InstrumentContext.well_bottom_clearance] to…

Rules:

• Python object names → monospace (backticks)
• Descriptive link text → regular font
• Methods get trailing (), other objects do not

mkdocstrings Reference Pages

Pull an entire class's public docstrings:

::: opentrons.protocol_api.Liquid

Exclude additional members (must restate global filters):

::: opentrons.protocol_api.Well
    options:
      filters:
        - "!^__"
        - "!estimate_liquid_height_after_pipetting"

Include only specific members (rare):

::: opentrons.protocol_api.LiquidClass
    options:
      filters:
        - "get_for"

Docstring Format

Google-style docstrings (configured globally in mkdocs.yml):

"""
Blow an extra amount of air through a pipette's tip to clear it.

Args:
    location:
        The blowout location.
        If no location is specified, the pipette will blow out from its current
        position.

        *Changed in version 2.16*: Accepts `TrashBin` and `WasteChute` values.

Raises:
    RuntimeError: If no location is specified and the location cache is `None`.

Returns:
    InstrumentContext: This instance.
"""

The @requires_version decorator auto-populates the minimum API version in the reference header — no extra markup needed.

Macros (Text Substitutions)

Two global substitutions defined in mkdocs.yml under extra::

extra:
  apiLevel: 2.27
  robot_stack_version: 8.8.0

Use with double braces and a space inside:

requirements = {"robotType": "Flex", "apiLevel": "{{ apiLevel }}"}

Substitutions are active in all content including code blocks. Update mkdocs.yml whenever the API level or robot stack version is bumped.

CSS Patterns

All custom CSS lives in the extra_css files. The patterns below are already defined in the shared theme; use the class names as shown.

Parts Lists (Image Grids)

Flex grid: 2–4 figures per row depending on window size. Used in hardware manuals.

<div class="parts-list" markdown>

<figure markdown> ![Opentrons Flex robot](images/parts-list/flex-robot.svg "Opentrons Flex robot") <figcaption>(1) Opentrons Flex robot</figcaption> </figure>

<figure markdown> ![USB cable](images/parts-list/usb-cable.svg "USB cable") <figcaption>(1) USB cable</figcaption> </figure>

</div>

Screenshots with Borders

White-background screenshots need a border to stand out:

<figure class="screenshot" markdown>
![Alt text describing screenshot.](images/my-screen.png "Screen title")
</figure>

Side-by-Side Figures

Exactly two images side by side (compare/contrast):

<figure class="side-by-side" markdown>
![Green run completed screen.](images/run-completed.png "Run completed")
![Red run failed screen.](images/run-failed.png "Run failed")
</figure>

For three or more images, use the parts-list pattern instead.

Instruction Lists (Circular Numbered Bullets)

For unboxing/setup steps — numbered items with large blue circular bullets. Close and reopen the div when a header interrupts the list (numbering continues with sane_lists):

<div class="instruction-list" markdown>

1. Unlock the eight latches holding the top to the sides.

   ![Crate latches.](images/unboxing/1-crate-latches.svg "Unboxing step 1")

2. Remove the top panel.

</div>

### Part 2: Release the Flex

<div class="instruction-list" markdown>

3. Continue with next numbered step…

</div>

Material Icons

Insert icons inline using shortcodes (don't overuse for decoration):

Click the :octicons-x-circle-fill-16: on a fixture to remove it.

Custom Opentrons Icons

1. Put in docs/shared/icons/opentrons/. Rename with lowercase-hyphens and .svg extension (e.g., protocol-designer.svg).
2. Use shortcode: :opentrons-protocol-designer:
3. Run mkdocs build — new icons don't appear under mkdocs serve until a full build.

Use only outline variants for consistency.

Round Colored Status Dots

For LED color/pattern tables (modules like Stacker):

<td><span class="my-dot green"></span> Green</td>
<td><span class="my-dot blue"></span> Blue</td>

Available colors: white, green, blue, red, yellow. Other colors can be added in CSS file as needed.

Table Header Color

Table <th> cells are automatically styled blue (#D0E6FE) by the theme CSS. To highlight cells outside the first row, use an HTML table with explicit <th> placement (e.g., a horizontal header column).

Fonts & Colors

• Proportional: Public Sans
• Monospace: Reddit Mono
• Primary blue: #006CFA
• Accent orange: #F09D20

These are set globally in opentrons-theme.css. Do not override them in page-level CSS.