Proper deployment of hed-test submodule

Author: VisLab

.gitignore

@@ -136,7 +136,6 @@ hed_cache/
 spec_tests/hed-specification/tests
 spec_tests/hed-examples
 spec_tests/*.json
-spec_tests/hed-tests/json_test_data
 
 # GitHub Copilot instructions (project-specific)
 .github/copilot-instructions.md

.gitmodules

@@ -1,6 +1,6 @@
 [submodule "spec_tests/hed-tests"]
 	path = spec_tests/hed-tests
-	url = https://github.com/hed-standard/hed-tests/
+	url = https://github.com/hed-standard/hed-tests.git
 	branch = main
 
 [submodule "spec_tests/hed-examples"]

spec_tests/README.md

@@ -10,9 +10,8 @@ To run spec_tests locally, you need to have the following directory structure:
 
 ```
 spec_tests/
-├── hed-specification/
-│   └── tests/
-│       └── json_tests/          # JSON test files for error validation
+├── hed-tests/
+│   └── json_test_data/          # JSON test files from hed-tests repository
 ├── hed-examples/
 │   └── datasets/                # BIDS datasets for validation testing  
 ├── test_sidecar.json           # Already present
@@ -23,9 +22,24 @@ spec_tests/
 
 ## Setup Instructions
 
-1. **Copy Submodule Content**: 
-   - Copy the content of the `hed-specification` repository to `spec_tests/hed-specification/`
-   - Copy the content of the `hed-examples` repository to `spec_tests/hed-examples/`
+### Option 1: Using Git Submodules (Recommended)
+
+1. **Initialize Submodules**: 
+   ```powershell
+   git submodule update --init --recursive
+   ```
+   This will automatically clone the `hed-tests` and `hed-examples` repositories into the correct locations.
+
+2. **Update Submodules** (when needed):
+   ```powershell
+   git submodule update --remote
+   ```
+
+### Option 2: Manual Setup (Alternative)
+
+1. **Clone Required Repositories**: 
+   - Clone the `hed-tests` repository to `spec_tests/hed-tests/`
+   - Clone the `hed-examples` repository to `spec_tests/hed-examples/`
 
 2. **Verify Setup**: 
    - Run `python spec_tests/check_setup.py` to verify all required directories exist
@@ -60,7 +74,10 @@ python -m unittest spec_tests.test_hed_cache -v
 
 - The `test_hed_cache.py` tests should work immediately as they don't require the submodule content
 - The `test_errors.py` and `validate_bids.py` tests require the submodule content to be present
-- On GitHub Actions, the submodules are automatically checked out, but locally you need to copy the content manually
+- On GitHub Actions, the submodules are automatically checked out via the workflow configuration
+- Locally, initialize submodules using `git submodule update --init --recursive`
+- The `spec_tests/hed-tests/` directory is gitignored to prevent committing submodule content directly
+- Use `git submodule update --remote` to pull the latest changes from the submodule repositories
 
 ## Troubleshooting
 

spec_tests/check_setup.py

@@ -51,9 +51,8 @@ def main():
 
     # Required directories and their purposes
     required_dirs = [
-        ("hed-specification", "HED specification repository"),
-        ("hed-specification/tests", "HED specification test directory"),
-        ("hed-specification/tests/json_tests", "JSON test files for error testing"),
+        ("hed-tests", "HED tests repository"),
+        ("hed-tests/json_test_data", "JSON test data directory"),
         ("hed-examples", "HED examples repository"),
         ("hed-examples/datasets", "BIDS datasets for validation testing"),
     ]
@@ -87,9 +86,11 @@ def main():
         print("Tests that require missing content will be skipped gracefully.")
         print("\nCurrently available: test_hed_cache.py (works without submodules)")
         print("Currently skipped: test_errors.py, validate_bids.py (need submodule content)")
-        print("\nTo set up full spec_tests:")
-        print("1. Copy the hed-specification repository content to spec_tests/hed-specification/")
-        print("2. Copy the hed-examples repository content to spec_tests/hed-examples/")
+        print("\nTo set up full spec_tests using submodules:")
+        print("  git submodule update --init --recursive")
+        print("\nAlternatively, manually clone:")
+        print("1. Clone hed-tests repository to spec_tests/hed-tests/")
+        print("2. Clone hed-examples repository to spec_tests/hed-examples/")
 
     print("\nTo run available tests now:")
     print(f"  cd {os.path.dirname(spec_tests_dir)}")