docs: Migrate thermocycler instruction manual to MkDocs (#19018)

# Overview

This migrates content from the Thermocycler GEN2 Instruction Manual to
markdown and mkdocs.

Most of the content is the same as the manual. Some new changes
particularly around the installation procedures and different lid types.
Remainder is largely the same.

RTC-780, RTC-710

## Test Plan and Hands on Testing

Please check for the usual writing and code stuff.

## Changelog

- Flex and OT-2 installation instructions now separate .md files.
- Updated lid info, including warnings about using rubber seals and PCR
lids at the same time.
- Adds information about the new shipping insert that replaces the
rubber seal.

## Review requests

I no longer have many of the original images. These may be in .indd
files. Any problems with images, pull originals from the InDesign files.
I do not have this software.

## Risk assessment

Docs changes, low risk.

---------

Co-authored-by: Ed Cormany <[email protected]>

Author: jwwojak

docs/mkdocs.yml

@@ -9,6 +9,7 @@ nav:
       - Modules home: modules/index.md
       - Flex Stacker: '!include stacker-manual/mkdocs.yml'
       - HEPA/UV Module: '!include hepa-uv/mkdocs.yml'
+      - Thermocycler Module: '!include thermocycler-manual/mkdocs.yml'
   - Python API: https://docs.opentrons.com/v2/
 
 plugins:

docs/shared/icons/opentrons/thermocycler.svg

@@ -115,3 +115,10 @@ figure.side-by-side img {
  .status-dot.yellow {
   background-color: #F09D20;
  }
+
+ /* Aligns status dots and text if needed*/
+.status-dot-container {
+  display: flex;
+  align-items: center;
+  gap: 5px;
+}

docs/shared/instruction-manuals.css

@@ -30,4 +30,12 @@ Opentrons hardware modules add features and capabilities to your robot.
 
     [:octicons-arrow-right-24: Instruction Manual](../hepa-uv/index.md)
 
+-   :opentrons-thermocycler:{ .xl .middle } __Thermocycler Module__
+
+    ---
+
+    An automated on-deck thermocycler in a 96-well plate format.
+
+    [:octicons-arrow-right-24: Instruction Manual](../thermocycler-manual/index.md)
+
 </div>

docs/shared/modules/index.md

@@ -11,9 +11,6 @@ theme:
   favicon: images/favicon.png
   logo: assets/logo.png
 
-extra_css:
-  - stylesheets/extra.css
-
 markdown_extensions:
   - md_in_html
   - toc:

docs/stacker-manual/docs/stylesheets/extra.css

@@ -0,0 +1,141 @@
+---
+title: "Thermocycler Module: Safety and Compliance"
+---
+
+# Safety Information and Regulatory Compliance
+
+Opentrons recommends that you follow the safe use specifications in this section and throughout this manual.
+
+## Safe Use Specifications
+
+### Input and Output Connections
+
+The Thermocycler requires the following power input, met by the included power supply.
+
+!!!warning
+    Do not replace the power supply cable unless directed by Opentrons Support.
+
+### Power supply (AC)
+
+- **Voltage**: 100–240 V
+- **Frequency**: 50/60 Hz
+- **Current**: 8.5–5 A
+- **Overvoltage**: Category II
+
+### Environmental Conditions { #thermocycler-environmental-conditions }
+
+The Thermocycler should only be used indoors on a sturdy, dry, flat horizontal surface. Install this module in a low-vibration environment with stable ambient conditions. Keep it away from direct sunlight or HVAC systems that may cause significant temperature or humidity changes.
+
+!!!note
+    The Thermocycler should not be powered on or used in conditions outside of the acceptable operating conditions.
+
+The following table defines the environmental standards for recommended use, acceptable use, and storage of your Thermocycler.
+
+| Environmental Conditions | Recommended | Acceptable | Storage and Transportation |
+|----|----|----|----|
+| Ambient Temperatures | +20 to +25 °C | +2 to +40 °C | –10 to +60 °C |
+| Relative Humidity | 30–80%, non-condensing | 30–80%, non-condensing (below 30 °C) | 10–85%, non-condensing (below 30 °C) |
+| Altitude | Approximately 500 m above sea level | Up to 2000 m above sea level | Up to 2000 m above sea level |
+
+The following table lists and defines standards for recommended use, acceptable use, and storage.
+
+| Operating Conditions | Description |
+|----|----|
+| Recommended | Opentrons has validated the Thermocycler’s performance in the conditions recommended for system operation. Operating the Thermocycler in these conditions helps provide optimal results. |
+| Acceptable | The Thermocycler is safe to use in conditions acceptable for system operation, but results may vary. |
+| Storage | Storage and transportation conditions only apply when the device is completely disconnected from power and other equipment. |
+
+### Low Temperature Condensation
+
+Holding the Thermocycler below ambient temperature for extended periods can cause condensation to develop in and on the device.
+
+!!!warning
+    Do not set the plate temperature below the ambient temperature for over two hours: condensation could affect performance or damage the module.
+
+### Software Requirements
+
+The Thermocycler requires version 6.2.0 (or higher) of the Opentrons App and robot software. You can download the Opentrons App for Mac, Windows, or Linux at <https://opentrons.com/ot-app>.
+
+### Labware Compatibility
+
+The Thermocycler is compatible with full-skirted, 96-well PCR plates. Performance specifications are based on use with Opentrons Tough PCR Plates, available from the [Tips and Labware section](https://opentrons.com/products/categories/tips-&-labware) of the Opentrons website.
+
+## Module Safety Warnings
+
+Warning symbols posted on the Opentrons Thermocycler and in this manual warn you about sources of potential injury or harm. The following table defines these safety warning symbols.
+
+<table>
+  <thead>
+    <tr>
+      <th>Symbol</th>
+      <th>Description</th>
+    </tr>
+  </thead>
+  <tbody> <tr>
+      <td><img src="../images/caution-yellow.svg" alt="Exclamation mark caution symbol"></td>
+      <td><strong>CAUTION: Injury or damage.</strong><br>
+          Operating the Opentrons Thermocycler before reading this manual poses a risk of personal injury or instrument damage. Only qualified laboratory personnel should operate this equipment.
+      </td>
+    </tr>
+    <tr>
+      <td><img src="../images/electric-shock-yellow.svg" alt="Electric shock caution symbol"></td>
+      <td><strong>CAUTION: Electrical shock.</strong><br>
+          Do not attempt to repair or remove the outer case of the Opentrons Thermocycler or its power supply unless directed by Opentrons Support. Attempting to do so puts you at risk of electrical shock.
+      </td>
+    </tr>
+    <tr>
+      <td><img src="../images/hot-surface-yellow.svg" alt="Hot surface caution symbol"></td>
+      <td><strong>CAUTION: Hot surface.</strong><br>
+          The Opentrons Thermocycler generates enough heat to cause serious burns. Wear safety goggles or other eye protection at all times during operation. Always ensure the sample block returns to idle temperature before opening the lid and removing samples. Allow maximum clearance to avoid accidental burns. The lid seal can also be hot when opened. Unplug the unit after use, if possible.
+      </td>
+    </tr>
+    <tr>
+      <td><img src="../images/pinch-yellow.svg" alt="Pinch point caution symbol"></td>
+      <td><strong>CAUTION: Pinch point.</strong><br>
+          The lid on the Opentrons Thermocycler presents a pinch point hazard. Keep hands and fingers away from the module while the lid is opening or closing.
+      </td>
+    </tr>
+    <tr>
+      <td><img src="../images/explosive-yellow.svg" alt="Explosion warning symbol"></td>
+      <td><strong>CAUTION: Risk of explosion.</strong><br>
+          Do not operate the Opentrons Thermocycler in areas used for working with explosive substances. Do not process explosive or highly reactive materials in the module or use it with substances that could generate explosive gases.
+      </td>
+    </tr>
+  </tbody>
+</table>
+
+## Standards Compliance
+
+The Thermocycler has been tested and found to be in compliance with all applicable requirements of the following safety and electromagnetic standards.
+
+### Safety
+
+- IEC/UL/CSA 61010-1 Safety­ Requirements­ for­ Electrical Equipment­ for Measurement­ Control­ and­ Laboratory Use–­Part­ 1:­ General Requirements
+- IEC/UL/CSA­ 61010-2-010­ Particular­ Requirements­ for Laboratory­ Equipment for­ the Heating­ of­ Materials
+
+### Electromagnetic Compatibility
+
+- EN/BSI 61326-1­ Electrical ­ Equipment­ for Measurement Control­ and­ Laboratory­ Use­–EMC Requirements–Part­ 1: General­ Requirements
+- EN 55011 Industrial, Scientific and Medical Equipment–Radio Frequency­ Disturbance Characteristics–Limits­ and­ Methods of­ Measurement
+- FCC 47CFR Part 15 Subpart B Class A: Unintentional Radiators
+- IC ICES-003 Spectrum Management and Telecommunications Interference Causing Equipment Standard–Information Technology Equipment (Including Digital Apparatus)
+
+### FCC Warnings and Notes
+
+**Warning:** Changes or modifications to this unit not expressly approved by Opentrons could void the user’s authority to operate the equipment. This device complies with part 15 of the FCC Rules. Operation is subject to the following two conditions:
+
+- This device may not cause harmful interference.
+- This device must accept any interference received, including interference that may cause undesired operation.
+
+**Note:** This equipment has been tested and found to comply with the limits for a Class A digital device, pursuant to part 15 of the FCC rules. These limits are designed to provide a reasonable protection against harmful interference when the equipment is operated in a commercial environment. This equipment generates, uses, and can radiate radio frequency energy and, if not installed and used in accordance with the instruction manual, may cause harmful interference to radio communications. Operation of this equipment in a residential area is likely to cause harmful interference in which case the user will be required to correct the interference at their own expense.
+
+### Canada ISED
+
+Canada ICES-003(A)/NMB-003(A)
+This­ product­ meets­ the­ applicable­ Innovation,­ Science­ and Economic Development Canada technical specifications.
+
+Le présent produit est conforme aux spécifications techniques applicables d’Innovation, Sciences et Développement économique Canada.
+
+### CISPR 11 Class A
+
+**Caution:** This equipment is not intended for use in residential environments and may not provide adequate protection to radio reception in such environments.

docs/stacker-manual/mkdocs.yml

@@ -0,0 +1,66 @@
+---
+title: "Thermocycler Module: Flex Attachment Steps"
+---
+
+# Flex Attachment Steps
+
+Setting up the Thermocycler on your robot includes attaching it to the deck and running a first-time calibration process. The instructions here and on the touchscreen will help you get started. The tools you need are included in the User Kit that came with your Flex.
+
+## Attaching the Thermocycler
+
+<div class="instruction-list" markdown>
+
+1. Use a 2.5 mm hex screwdriver to remove the A1 expansion slot plate and the A1 and B1 deck slot plates.
+
+2. Using both hands, lift the module carefully and insert it into its caddy. Make sure the module's exhaust port faces the exhaust duct on the caddy.
+
+3. Use a 2.5 mm hex screwdriver to turn the anchor screws clockwise to tighten the anchors. The module is secure when it doesn't move while gently pulling on it and rocking it from side to side.
+
+4. Connect the USB cable to the module and route the remaining cable through the cable management bracket.
+
+5. Connect the power connector to the module by pressing it firmly into place. Route the remaining cable through the cable management bracket.
+
+6. Insert the caddy, exhaust duct first, into the open deck slot. Route the USB and power cables through the removable side covers as you lower the caddy into position.
+
+7. Connect the USB cable to a USB port on the Flex.
+
+8. Connect the power cable from the module to the external power supply unit. Manually tighten the locking ring to secure it to the power supply.
+
+9. Connect the power supply to a wall outlet and turn on the power supply. If you see a white light on the Thermocycler, it is powered on. 
+
+10. Press the illuminated button on the Thermocycler to open the lid.
+
+11. Remove and discard the shipping insert after opening the module's lid. The insert consists of a pad attached to a PCR plate.
+
+    ![Thermocycler shipping insert](images/shipping-insert.svg)
+
+</div>
+
+When successfully connected, the module appears in the Pipettes and Modules section on your robot's device detail page in the Opentrons App.
+
+Next, you'll calibrate the module.
+
+## Calibrating the Thermocycler
+
+You need to calibrate the Thermocycler after attaching it for the first time. To calibrate the Thermocycler, turn on the power supply. This starts the calibration workflow process on the touchscreen. Instructions on the touchscreen will take you through a guided workflow process, which is also outlined below.
+
+!!!warning
+    The gantry and pipette move during calibration. Keep your hands clear of the working area before tapping an action button on the touchscreen.
+
+<div class="instruction-list" markdown>
+
+1. Tap **Start setup** on the touchscreen. The robot checks the module's firmware and updates it automatically, if required.
+
+2. Attach the module's calibration adapter and tap **Confirm placement**.
+
+3. Attach the calibration probe to the indicated pipette.
+
+4. Tap **Begin calibration**.
+
+5. After the calibration process is complete, remove the calibration block from the module and remove the calibration probe from the pipette.
+
+6. Click **Exit**.
+
+</div>
+
+Your module is now calibrated. You will not have to recalibrate the same module if you remove and reattach it to the same Flex.