Finalize Json interface, cleaning up the main branch.

.devcontainer/Dockerfile

@@ -52,9 +52,8 @@ RUN groupadd --gid $USER_GID $USERNAME \
     && mkdir -p /home/$USERNAME/.vscode-server /home/$USERNAME/.vscode-server-insiders \
     && chown ${USER_UID}:${USER_GID} /home/$USERNAME/.vscode-server*
 
-# Copy environment files (use lightweight env-codespace.yml for Codespaces)
+# Copy the Codespaces environment definition (CPU torch + Jupyter).
 COPY env-codespace.yml /tmp/env.yml
-COPY requirements.txt /tmp/requirements.txt
 
 # Create conda environment with mamba and aggressive cleanup to save space
 RUN mamba env create -f /tmp/env.yml && \

.devcontainer/README.md

@@ -20,51 +20,44 @@ This devcontainer provides a standardized development environment for the AutoQu
 
 ### Environment
 - **Python 3.10.13** with conda/mamba package management
-- **AutoQuake conda environment** with all dependencies from `env.yml`
+- **AutoQuake conda environment** built from `env-codespace.yml` (CPU-only PyTorch)
 - **Scientific computing stack**: NumPy, Pandas, SciPy, Matplotlib, ObsPy
-- **Machine Learning**: PyTorch, scikit-learn
-- **Seismology tools**: ObsPy, PyGMT, Pyrocko
-- **Development tools**: Black, isort, flake8, pre-commit
+- **Machine Learning**: PyTorch (CPU), scikit-learn, ONNX Runtime
+- **Seismology / geospatial tools**: ObsPy, PyGMT, Cartopy, pyproj
+- **Development tools**: Ruff, pre-commit
 
 ### VS Code Extensions
 - Python development suite (Python, Pylance, Jupyter)
-- Code formatting and linting (Black, Ruff, flake8)
+- Linting & formatting with Ruff
 - Git integration (GitLens, GitHub tools)
 - Documentation tools (Markdown, autodocstring)
-- Scientific computing support
 
 ### Development Tools
+- **Ruff** for linting and formatting (replaces black + isort + flake8)
 - **Pre-commit hooks** for code quality
 - **Jupyter Lab** ready to use
-- **Code formatting** with Black and isort
-- **Linting** with flake8 and Ruff
 
 ## 🛠️ Development Workflow
 
 ### Environment Activation
-The conda environment `AutoQuake_v0` is automatically activated. You can also use:
+The conda environment `AutoQuake_v0` is activated automatically in new terminals.
+To activate it manually:
 ```bash
-aq  # Quick alias to activate environment
+conda activate AutoQuake_v0
 ```
 
 ### Development Tools
 ```bash
-# You can create your own aliases if needed, such as:
-conda activate AutoQuake_v0    # Activate environment
-black . && isort .             # Format code
-flake8 .                       # Check code quality
-jupyter lab --ip=0.0.0.0 --port=8888 --no-browser --allow-root  # Start Jupyter
-```
-
-### Jupyter Development
-```bash
-aqjupyter   # Start Jupyter Lab on port 8888
+ruff check .                   # Lint
+ruff format .                  # Format (single quotes, 88 cols — see pyproject.toml)
+pytest tests/unit -m "not integration"   # Run the fast unit tests
+jupyter lab --ip=0.0.0.0 --port=8888 --no-browser  # Start Jupyter Lab
 ```
 
 ### Testing Your Setup
 ```bash
 conda activate AutoQuake_v0    # Ensure environment is active
-python -c "import autoquake; print('AutoQuake loaded successfully')"  # Test AutoQuake import
+python -c "import autoquake; print('AutoQuake loaded successfully')"  # Test import
 ```
 
 ## 📁 Project Structure
@@ -97,9 +90,8 @@ This environment is prepared for real-time seismic data processing with:
 ## 🔧 Customization
 
 ### Adding Dependencies
-1. Update `env.yml` for conda packages
-2. Update `requirements.txt` for pip packages
-3. Rebuild the container
+1. Add the package to `env.yml` (local/CI) **and** `env-codespace.yml` (Codespaces)
+2. Rebuild the container ("Dev Containers: Rebuild Container")
 
 ### VS Code Settings
 Modify `.devcontainer/devcontainer.json` to customize:
@@ -119,24 +111,24 @@ Add system packages in the Dockerfile under the apt-get install section.
 
 ### Python Environment Issues
 ```bash
-conda activate AutoQuake_v0  # Ensure environment is active
-python dev-utils.py          # Check environment status
+conda activate AutoQuake_v0   # Ensure environment is active
+conda env list                # Confirm AutoQuake_v0 exists
 ```
 
 ### Import Errors
-```bash
-pip install -e .  # Reinstall AutoQuake in development mode
-```
+The project runs from the repository root (pytest adds it to `sys.path` via
+`pyproject.toml`). If `import autoquake` fails, make sure your working directory
+is the repo root and the conda environment is active.
 
 ### Port Conflicts
 The container forwards ports 8888, 8080, and 5000. Modify `devcontainer.json` if needed.
 
 ## 🤝 Contributing
 
-1. The environment automatically sets up pre-commit hooks
-2. Code is automatically formatted on save
-3. Run tests before committing: `aqtest`
-4. Follow the existing code style (Black formatting)
+1. The environment automatically sets up pre-commit hooks (commit + push)
+2. Code is automatically formatted on save by Ruff
+3. Run tests before committing: `pytest tests/unit -m "not integration"`
+4. Follow the existing code style (Ruff: single quotes, 88-column lines)
 
 ## 📝 Notes for Real-time Development
 
@@ -149,7 +141,7 @@ When implementing real-time features:
 ## 🆘 Getting Help
 
 - Check the main AutoQuake README for project-specific information
-- Run `python dev-utils.py` for environment diagnostics
+- Run `conda env list` and `conda list` to inspect the environment
 - Use the VS Code integrated terminal with all tools pre-configured
 
 Happy coding! 🎉

.devcontainer/devcontainer.json

@@ -11,67 +11,45 @@
 	"customizations": {
 		"vscode": {
 			"extensions": [
-				// Python Development
+				// Python (ruff is the single linter/formatter — matches pyproject.toml & CI)
 				"ms-python.python",
-				"ms-python.flake8",
-				"ms-python.pylint",
-				"ms-python.black-formatter",
+				"ms-python.vscode-pylance",
+				"ms-python.debugpy",
 				"charliermarsh.ruff",
-				"ms-python.isort",
+				"kevinrose.vsc-python-indent",
+				"njpwerner.autodocstring",
+
+				// Jupyter / scientific computing
 				"ms-toolsai.jupyter",
-				"ms-toolsai.vscode-jupyter-cell-tags",
-				"ms-toolsai.vscode-jupyter-slideshow",
-
-				// Scientific Computing & Data Science
 				"ms-toolsai.jupyter-keymap",
 				"ms-toolsai.jupyter-renderers",
-				"ms-python.vscode-pylance",
-				"njpwerner.autodocstring",
-				
-				// Git & Version Control
+				"ms-toolsai.vscode-jupyter-cell-tags",
+				"ms-toolsai.vscode-jupyter-slideshow",
+
+				// Git & GitHub
 				"eamodio.gitlens",
 				"github.vscode-pull-request-github",
 				"github.copilot",
 				"github.copilot-chat",
-				
-				// Documentation & Markdown
+
+				// Docs & config files
 				"yzhang.markdown-all-in-one",
 				"davidanson.vscode-markdownlint",
-				"ms-vscode.vscode-json",
-
-				// Development Tools
-				"ms-vscode.vscode-yaml",
-				"redhat.vscode-xml",
-				"ms-vscode.cmake-tools",
-				"ms-vscode.cpptools",
-
-				// Visualization & Plotting
-				"ms-python.debugpy",
-				"kevinrose.vsc-python-indent",
-				"donjayamanne.python-environment-manager",
-
-				// Remote Development
-				"ms-vscode-remote.remote-containers",
-				"ms-vscode-remote.remote-ssh",
-				"ms-vscode-remote.remote-wsl"
+				"redhat.vscode-yaml"
 			],
 			"settings": {
 				"python.defaultInterpreterPath": "/opt/conda/envs/AutoQuake_v0/bin/python",
 				"python.terminal.activateEnvironment": true,
 				"python.terminal.activateEnvInCurrentTerminal": true,
-				"python.linting.enabled": true,
-				"python.linting.pylintEnabled": false,
-				"python.linting.flake8Enabled": true,
-				"python.formatting.provider": "black",
-				"python.formatting.blackArgs": ["--line-length=88"],
-				"python.sortImports.args": ["--profile", "black"],
-				"ruff.args": ["--config", "pyproject.toml"],
 				"ruff.enable": true,
 				"ruff.organizeImports": true,
 				"editor.formatOnSave": true,
-				"editor.codeActionsOnSave": {
-					"source.organizeImports": "explicit",
-					"source.fixAll.ruff": "explicit"
+				"[python]": {
+					"editor.defaultFormatter": "charliermarsh.ruff",
+					"editor.codeActionsOnSave": {
+						"source.organizeImports.ruff": "explicit",
+						"source.fixAll.ruff": "explicit"
+					}
 				},
 				"files.trimTrailingWhitespace": true,
 				"files.insertFinalNewline": true,

.devcontainer/post-create.sh

@@ -1,4 +1,5 @@
 #!/bin/bash
+set -e
 
 echo "🚀 Setting up AutoQuake development environment..."
 
@@ -7,50 +8,29 @@ source /opt/conda/etc/profile.d/conda.sh
 
 # Activate the AutoQuake environment
 conda activate AutoQuake_v0
-
-# Verify environment activation
 echo "📦 Active conda environment: $CONDA_DEFAULT_ENV"
 
-# Install development dependencies (ipykernel and jupyterlab already in env-codespace.yml)
-echo "🔧 Installing development tools..."
-pip install --no-cache-dir \
-    black \
-    isort \
-    flake8 \
-    pre-commit
-
-# Install the AutoQuake package in development mode
-echo "📥 Installing AutoQuake in development mode..."
-pip install -e .
+# Dev-only tooling (kept out of the conda env so it stays lean).
+# Ruff replaces black + isort + flake8; pre-commit runs it on every commit.
+echo "🔧 Installing development tools (ruff, pre-commit)..."
+pip install --no-cache-dir ruff pre-commit
 
-# Initialize git submodules if they exist
+# Initialize git submodules (EQNet, GaMMA) so the full pipeline can import them.
 if [ -f ".gitmodules" ]; then
     echo "🔗 Initializing git submodules..."
     git submodule update --init --recursive
 fi
 
-# Set up pre-commit hooks for code quality
+# Install pre-commit hooks for code quality (commit + push stages).
 echo "🎯 Setting up pre-commit hooks..."
 pre-commit install
+pre-commit install --hook-type pre-push
 
-# Create Jupyter kernel for the environment
+# Register a Jupyter kernel for the environment.
 echo "📓 Setting up Jupyter kernel..."
 python -m ipykernel install --user --name=AutoQuake_v0 --display-name="AutoQuake v0.1"
 
-# Create commonly used directories
-mkdir -p data
-mkdir -p outputs
-mkdir -p logs
-
-# Set up git configuration helper
-echo "🔧 Setting up git configuration..."
-echo '#!/bin/bash
-echo "Quick setup for git configuration:"
-echo "git config --global user.name \"Your Name\""
-echo "git config --global user.email \"your.email@example.com\""
-' > setup-git.sh
-chmod +x setup-git.sh
-
-echo "✨ AutoQuake development environment setup completed!"
+echo "✨ AutoQuake development environment ready!"
 echo ""
-echo "🚀 Ready for AutoQuake development!"
+echo "   Run the test suite with:  pytest tests/unit -m \"not integration\""
+echo "   Run the full pipeline with:  python predict.py <config.json>"

.github/workflows/submodule-check.yml

@@ -0,0 +1,83 @@
+name: Submodule Compatibility Check
+
+on:
+  # Manual trigger
+  workflow_dispatch:
+
+  # Weekly check on Sunday at 00:00 UTC
+  schedule:
+    - cron: '0 0 * * 0'
+
+env:
+  PYTHON_VERSION: "3.10"
+
+jobs:
+  check-submodules:
+    name: Check Submodule Compatibility
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+        with:
+          submodules: recursive
+          fetch-depth: 0
+
+      - name: Fetch latest submodule commits
+        run: |
+          git submodule foreach 'git fetch origin'
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ env.PYTHON_VERSION }}
+
+      - name: Install dependencies
+        run: |
+          pip install pytest pandas pydantic numpy pyproj
+
+      - name: Run compatibility check
+        run: python scripts/check-submodule-compat.py
+
+      - name: Run tests with current submodules
+        run: pytest tests/ -v --tb=short
+        continue-on-error: true
+
+      - name: Create issue if tests fail
+        if: failure()
+        uses: actions/github-script@v7
+        with:
+          script: |
+            const title = 'Submodule Compatibility Issue Detected';
+            const body = `
+            ## Submodule Compatibility Check Failed
+
+            The weekly submodule compatibility check has detected potential issues.
+
+            **Workflow Run:** [View Details](${process.env.GITHUB_SERVER_URL}/${process.env.GITHUB_REPOSITORY}/actions/runs/${process.env.GITHUB_RUN_ID})
+
+            Please review the workflow logs and address any compatibility issues before updating submodules.
+
+            ### Next Steps
+            1. Review the compatibility report in the workflow logs
+            2. Check for API changes in submodules
+            3. Update code if necessary
+            4. Run \`python scripts/check-submodule-compat.py\` locally to verify fixes
+            `;
+
+            // Check if issue already exists
+            const issues = await github.rest.issues.listForRepo({
+              owner: context.repo.owner,
+              repo: context.repo.repo,
+              state: 'open',
+              labels: 'submodule-compat'
+            });
+
+            if (issues.data.length === 0) {
+              await github.rest.issues.create({
+                owner: context.repo.owner,
+                repo: context.repo.repo,
+                title: title,
+                body: body,
+                labels: ['submodule-compat', 'automated']
+              });
+            }