feat(spatialomics): integrate SpatialOmics module with root project

- Add SpatialOmics to root Makefile MODULES list
- Add SpatialOmics tests to format target
- Update generate-python-classes.yml workflow
- Update main.yaml workflow for Synapse schema generation
- Add SpatialOmics documentation to main README.md
- Follows CONTRIBUTING.md Step 7, 8, and 9 requirements

Author: aditigopalan

.github/workflows/generate-python-classes.yml

@@ -21,7 +21,7 @@ on:
   workflow_dispatch:
     inputs:
       modules:
-        description: 'Modules to regenerate (comma-separated: biospecimen,clinical,wes,sequencing,imaging,scrna-seq,digitalpathology,multiplexmicroscopy,all). Leave empty or "all" to generate all modules.'
+        description: 'Modules to regenerate (comma-separated: biospecimen,clinical,wes,sequencing,imaging,scrna-seq,digitalpathology,multiplexmicroscopy,spatialomics,all). Leave empty or "all" to generate all modules.'
         required: false
         default: 'all'
         type: choice
@@ -35,6 +35,7 @@ on:
           - scrna-seq
           - digitalpathology
           - multiplexmicroscopy
+          - spatialomics
           - biospecimen,clinical
           - biospecimen,wes
           - clinical,wes
@@ -212,6 +213,19 @@ jobs:
           echo "⏭️ Skipping MultiplexMicroscopy (not in selected modules)"
         fi
     
+    - name: Generate Python Classes for SpatialOmics
+        if: steps.set-modules.outputs.modules != 'all'
+        run: |
+          MODULES="${{ steps.set-modules.outputs.modules }}"
+          if echo "$MODULES" | grep -q "spatialomics"; then
+            echo "🔄 Generating Python classes for SpatialOmics module..."
+            cd modules/SpatialOmics
+            make gen-schema
+            echo "✅ SpatialOmics Python classes generated"
+          else
+            echo "⏭️ Skipping SpatialOmics (not in selected modules)"
+          fi
+    
     - name: Run Tests
       id: run-tests
       continue-on-error: true

.github/workflows/main.yaml

@@ -45,7 +45,7 @@ jobs:
       - name: Generate Synapse-compatible JSON schemas
         run: |
           export PATH="$HOME/.local/bin:$PATH"
-          for module in Clinical WES Biospecimen Sequencing Imaging scRNA-seq DigitalPathology MultiplexMicroscopy; do
+          for module in Clinical WES Biospecimen Sequencing Imaging scRNA-seq DigitalPathology MultiplexMicroscopy SpatialOmics; do
             if [ -f modules/$module/Makefile ] && grep -q "^gen-synapse-schema:" modules/$module/Makefile; then
               echo "Generating Synapse schema for $module module..."
               make -C modules/$module gen-synapse-schema

Makefile

@@ -23,7 +23,7 @@ SOURCE_SCHEMA_PATH = modules/Clinical/domains/clinical.yaml
 GEN_DOC_ARGS = --no-mergeimports
 
 # List of modules (add new modules here)
-MODULES = Clinical WES CoreFile Biospecimen Sequencing Imaging scRNA-seq DigitalPathology MultiplexMicroscopy
+MODULES = Clinical WES CoreFile Biospecimen Sequencing Imaging scRNA-seq DigitalPathology MultiplexMicroscopy SpatialOmics
 
 .PHONY: all clean setup gen-project gendoc git-init-add git-init git-add git-commit git-status help install test modules-gen modules-test format
 
@@ -101,6 +101,7 @@ format:
 		modules/scRNA-seq/tests/ \
 		modules/DigitalPathology/tests/ \
 		modules/MultiplexMicroscopy/tests/ \
+		modules/SpatialOmics/tests/ \
 		modules/*/src/
 
 # ---

README.md

@@ -2,8 +2,6 @@
 
 ---
 
-## ⚠️ **DO NOT USE – UNDER DEVELOPMENT** ⚠️  
-
 This data model is in **active development**. It builds on **HTAN Phase 1** and incorporates input from the **Cancer Data Standards (CDS)** initiative. Expect frequent changes until a stable version is released.
 
 ---
@@ -77,6 +75,12 @@ The diagram above illustrates the separation between **Record-Based Modules** (C
 - **Structure**: Three data levels (Level 2: imaging + channel metadata, Level 3: segmentation masks, Level 4: cell-by-feature tables)
 - **Features**: Channel metadata, image dimensions, multiplex assay types, CRDC alignment
 
+### **Spatial Omics Module**
+- **Purpose**: Sequencing-based and sequence-hybridization spatial omics assays (Visium, Xenium, CosMx, STOmics, etc.)
+- **Location**: `modules/SpatialOmics/`
+- **Structure**: Four data levels (Level 1: raw data bundle optional, Level 3: processed bundle required, Level 4: interoperable file optional, Panel: panel information)
+- **Features**: Platform flexibility, bundle-level metadata, panel information, QC metrics, conditional requirements
+
 ## 📁 Project Structure
 
 ```
@@ -90,7 +94,8 @@ htan2-data-model/
 │   ├── WES/                   # Whole Exome Sequencing
 │   ├── scRNA-seq/             # Single-cell RNA sequencing
 │   ├── DigitalPathology/      # Digital Pathology imaging
-│   └── MultiplexMicroscopy/   # Multiplex Microscopy imaging
+│   ├── MultiplexMicroscopy/   # Multiplex Microscopy imaging
+│   └── SpatialOmics/          # Spatial Omics assays
 ├── config/                    # LinkML configuration
 ├── scripts/                   # Utility scripts
 ├── tests/                     # Root-level tests
@@ -156,6 +161,7 @@ Each module contains detailed documentation:
 - **scRNA-seq Module**: See `modules/scRNA-seq/README.md` for single-cell RNA sequencing levels
 - **Digital Pathology Module**: See `modules/DigitalPathology/README.md` for digital pathology imaging
 - **Multiplex Microscopy Module**: See `modules/MultiplexMicroscopy/README.md` for multiplex microscopy imaging
+- **Spatial Omics Module**: See `modules/SpatialOmics/README.md` for spatial omics assays
 
 ## 🤝 Contributing