Migration from Docker to Standalone Python Server (#73)

* Migration from docker to standalone server
Migration handling
Fixed tests
Use simpler in-memory storage
Support for concurrent logging to disk
Simplified direct connections to localhost

* Migration from docker / redis to standalone script
Updated tests
Updated run script
Fixed requirements
Use dotenv
Ask if user would like to install MCP in Claude Desktop once
Updated docs

* More cleanup and references to docker removed

* Cleanup

* Comments

* Fixed tests

* Fix GitHub Actions workflow for standalone Python architecture

- Install requirements-dev.txt for pytest and testing dependencies
- Remove Docker setup from simulation tests (now standalone)
- Simplify linting job to use requirements-dev.txt
- Update simulation tests to run directly without Docker

Fixes unit test failures in CI due to missing pytest dependency.

🤖 Generated with [Claude Code](https://claude.ai/code)

Co-Authored-By: Claude <noreply@anthropic.com>

* Remove simulation tests from GitHub Actions

- Removed simulation-tests job that makes real API calls
- Keep only unit tests (mocked, no API costs) and linting
- Simulation tests should be run manually with real API keys
- Reduces CI costs and complexity

GitHub Actions now only runs:
- Unit tests (569 tests, all mocked)
- Code quality checks (ruff, black)

🤖 Generated with [Claude Code](https://claude.ai/code)

Co-Authored-By: Claude <noreply@anthropic.com>

* Fixed tests

* Fixed tests

---------

Co-authored-by: Claude <noreply@anthropic.com>

.github/workflows/build_and_publish_docker.yml

@@ -1,197 +0,0 @@
-name: Build and Publish Docker Image to GHCR
-
-on:
-  push:
-    tags: [ 'v*' ]
-  repository_dispatch:
-    types: [docker-build]
-
-env:
-  REGISTRY: ghcr.io
-  IMAGE_NAME: beehiveinnovations/zen-mcp-server
-
-jobs:
-  build-and-push:
-    runs-on: ubuntu-latest
-    permissions:
-      contents: read
-      packages: write
-      id-token: write
-      attestations: write
-
-    steps:
-    - name: Checkout repository
-      uses: actions/checkout@v4
-      with:
-        token: ${{ secrets.PAT }}
-
-    - name: Set up Docker Buildx
-      uses: docker/setup-buildx-action@v3
-
-    - name: Log in to GitHub Container Registry
-      uses: docker/login-action@v3
-      with:
-        registry: ${{ env.REGISTRY }}
-        username: ${{ github.actor }}
-        password: ${{ secrets.GITHUB_TOKEN }}
-
-    - name: Extract metadata (tags, labels) for Docker
-      id: meta
-      uses: docker/metadata-action@v5
-      with:
-        images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
-        tags: |
-          type=ref,event=tag
-          type=raw,value=latest,enable=${{ github.ref_type == 'tag' }}
-          type=sha,prefix=main-,enable=${{ github.event_name == 'repository_dispatch' }}
-          type=raw,value=pr-${{ github.event.client_payload.pr_number }},enable=${{ github.event_name == 'repository_dispatch' && github.event.client_payload.pr_number != '' }}
-
-    - name: Build and push Docker image
-      id: build
-      uses: docker/build-push-action@v5
-      with:
-        context: .
-        platforms: linux/amd64,linux/arm64
-        push: true
-        tags: ${{ steps.meta.outputs.tags }}
-        labels: ${{ steps.meta.outputs.labels }}
-        cache-from: type=gha
-        cache-to: type=gha,mode=max
-
-    - name: Generate artifact attestation
-      uses: actions/attest-build-provenance@v1
-      with:
-        subject-name: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
-        subject-digest: ${{ steps.build.outputs.digest }}
-        push-to-registry: true
-
-    - name: Generate usage instructions
-      run: |
-        echo "## 🐳 Docker Image Published Successfully!" >> $GITHUB_STEP_SUMMARY
-        echo "" >> $GITHUB_STEP_SUMMARY
-        echo "**Image Registry:** GitHub Container Registry (GHCR)" >> $GITHUB_STEP_SUMMARY
-        echo "**Built Tags:** ${{ steps.meta.outputs.tags }}" >> $GITHUB_STEP_SUMMARY
-        echo "" >> $GITHUB_STEP_SUMMARY
-        
-        # Extract the first tag for the main pull command
-        MAIN_TAG=$(echo "${{ steps.meta.outputs.tags }}" | head -n1)
-        
-        echo "### 📥 Pull the Image" >> $GITHUB_STEP_SUMMARY
-        echo "\`\`\`bash" >> $GITHUB_STEP_SUMMARY
-        echo "docker pull $MAIN_TAG" >> $GITHUB_STEP_SUMMARY
-        echo "\`\`\`" >> $GITHUB_STEP_SUMMARY
-        echo "" >> $GITHUB_STEP_SUMMARY
-        
-        echo "### ⚙️ Claude Desktop Configuration" >> $GITHUB_STEP_SUMMARY
-        echo "\`\`\`json" >> $GITHUB_STEP_SUMMARY
-        echo "{" >> $GITHUB_STEP_SUMMARY
-        echo "  \"mcpServers\": {" >> $GITHUB_STEP_SUMMARY
-        echo "    \"gemini\": {" >> $GITHUB_STEP_SUMMARY
-        echo "      \"command\": \"docker\"," >> $GITHUB_STEP_SUMMARY
-        echo "      \"args\": [" >> $GITHUB_STEP_SUMMARY
-        echo "        \"run\", \"--rm\", \"-i\"," >> $GITHUB_STEP_SUMMARY
-        echo "        \"-e\", \"GEMINI_API_KEY\"," >> $GITHUB_STEP_SUMMARY
-        echo "        \"$MAIN_TAG\"" >> $GITHUB_STEP_SUMMARY
-        echo "      ]," >> $GITHUB_STEP_SUMMARY
-        echo "      \"env\": {" >> $GITHUB_STEP_SUMMARY
-        echo "        \"GEMINI_API_KEY\": \"your-gemini-api-key-here\"" >> $GITHUB_STEP_SUMMARY
-        echo "      }" >> $GITHUB_STEP_SUMMARY
-        echo "    }" >> $GITHUB_STEP_SUMMARY
-        echo "  }" >> $GITHUB_STEP_SUMMARY
-        echo "}" >> $GITHUB_STEP_SUMMARY
-        echo "\`\`\`" >> $GITHUB_STEP_SUMMARY
-        echo "" >> $GITHUB_STEP_SUMMARY
-        
-        echo "### 🏷️ All Available Tags" >> $GITHUB_STEP_SUMMARY
-        echo "Built and pushed the following tags:" >> $GITHUB_STEP_SUMMARY
-        echo "${{ steps.meta.outputs.tags }}" | sed 's/^/- `/' | sed 's/$/`/' >> $GITHUB_STEP_SUMMARY
-        echo "" >> $GITHUB_STEP_SUMMARY
-        
-        if [[ "${{ github.event_name }}" == "repository_dispatch" ]]; then
-          echo "**Note:** This is a development build triggered by PR #${{ github.event.client_payload.pr_number }}" >> $GITHUB_STEP_SUMMARY
-          echo "Use this image for testing the changes from that PR." >> $GITHUB_STEP_SUMMARY
-        elif [[ "${{ github.ref_type }}" == "tag" ]]; then
-          echo "**Note:** This is a release build from tag ${{ github.ref_name }}" >> $GITHUB_STEP_SUMMARY
-          echo "This image represents a stable release version." >> $GITHUB_STEP_SUMMARY
-        fi
-        
-        echo "" >> $GITHUB_STEP_SUMMARY
-        echo "### 📦 View in GitHub Container Registry" >> $GITHUB_STEP_SUMMARY
-        echo "[View all versions and tags →](https://github.com/${{ github.repository }}/pkgs/container/zen-mcp-server)" >> $GITHUB_STEP_SUMMARY
-
-    - name: Update README with latest image info
-      if: false # Temporarily disabled as agreed with repo author
-      # if: github.ref_type == 'tag' || (github.event_name == 'repository_dispatch' && github.event.client_payload.pr_number != '')
-      run: |
-        # Checkout main branch to avoid detached HEAD when pushing
-        git fetch origin main:main
-        git checkout main
-        # Extract the primary image tag for updating README
-        if [[ "${{ github.ref_type }}" == "tag" ]]; then
-          # For tag releases, use the version tag
-          LATEST_TAG="${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}:${{ github.ref_name }}"
-          UPDATE_TYPE="release"
-        elif [[ "${{ github.event_name }}" == "repository_dispatch" && "${{ github.event.client_payload.pr_number }}" != "" ]]; then
-          # For repository_dispatch (PR builds), use the PR tag
-          LATEST_TAG="${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}:pr-${{ github.event.client_payload.pr_number }}"
-          UPDATE_TYPE="development"
-        else
-          # For manual repository_dispatch without PR number, use latest tag
-          LATEST_TAG="${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}:latest"
-          UPDATE_TYPE="manual"
-        fi
-        
-        echo "Updating README.md with latest Docker image: $LATEST_TAG"
-        
-        # Update README.md with the latest image tag
-        sed -i.bak "s|ghcr\.io/[^/]*/zen-mcp-server:[a-zA-Z0-9\._-]*|$LATEST_TAG|g" README.md
-        
-        # Also update docs/user-guides/installation.md
-        sed -i.bak "s|ghcr\.io/[^/]*/zen-mcp-server:[a-zA-Z0-9\._-]*|$LATEST_TAG|g" docs/user-guides/installation.md
-        
-        # Also update docs/user-guides/configuration.md  
-        sed -i.bak "s|ghcr\.io/[^/]*/zen-mcp-server:[a-zA-Z0-9\._-]*|$LATEST_TAG|g" docs/user-guides/configuration.md
-        
-        # Check if there are any changes
-        if git diff --quiet README.md docs/user-guides/installation.md docs/user-guides/configuration.md; then
-          echo "No changes needed in documentation"
-        else
-          echo "Documentation updated with new image tag"
-          
-          # Configure git for automated commit
-          git config user.name "github-actions[bot]"
-          git config user.email "github-actions[bot]@users.noreply.github.com"
-          
-          # Add and commit changes
-          git add README.md docs/user-guides/installation.md docs/user-guides/configuration.md
-          
-          if [[ "$UPDATE_TYPE" == "release" ]]; then
-            git commit -m "docs: Update Docker image references to ${{ github.ref_name }}
-
-          Automated update after Docker image publish for release ${{ github.ref_name }}.
-          All documentation now references the latest stable image.
-
-          🤖 Automated by GitHub Actions"
-          elif [[ "$UPDATE_TYPE" == "development" ]]; then
-            git commit -m "docs: Update Docker image references for PR #${{ github.event.client_payload.pr_number }}
-
-          Automated update after Docker image publish for development build.
-          Documentation updated to reference the latest development image.
-
-          🤖 Automated by GitHub Actions"
-          else
-            git commit -m "docs: Update Docker image references to latest
-
-          Automated update after manual Docker image build.
-          Documentation updated to reference the latest image.
-
-          🤖 Automated by GitHub Actions"
-          fi
-          
-          # Push changes back to the repository
-          git push --set-upstream origin main
-          
-          echo "### 📝 Documentation Updated" >> $GITHUB_STEP_SUMMARY
-          echo "README.md and user guides have been automatically updated with the new Docker image tag: \`$LATEST_TAG\`" >> $GITHUB_STEP_SUMMARY
-        fi
-

.github/workflows/docker-test.yml

@@ -1,32 +0,0 @@
-name: Docker Build Test
-
-on:
-  pull_request:
-    branches: [ main ]
-
-jobs:
-  docker-build-test:
-    runs-on: ubuntu-latest
-    
-    steps:
-    - name: Checkout repository
-      uses: actions/checkout@v4
-
-    - name: Set up Docker Buildx
-      uses: docker/setup-buildx-action@v3
-
-    - name: Test Docker build
-      uses: docker/build-push-action@v5
-      with:
-        context: .
-        push: false
-        tags: test:latest
-        cache-from: type=gha
-        cache-to: type=gha,mode=max
-
-    - name: Build test summary
-      run: |
-        echo "### ✅ Docker Build Test Passed" >> $GITHUB_STEP_SUMMARY
-        echo "" >> $GITHUB_STEP_SUMMARY
-        echo "Docker image builds successfully and is ready for production." >> $GITHUB_STEP_SUMMARY
-

.github/workflows/test.yml

@@ -25,6 +25,7 @@ jobs:
       run: |
         python -m pip install --upgrade pip
         pip install -r requirements.txt
+        pip install -r requirements-dev.txt
     
     - name: Run unit tests
       run: |
@@ -49,7 +50,7 @@ jobs:
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install ruff black
+        pip install -r requirements-dev.txt
     
     - name: Run black formatter check
       run: black --check .
@@ -57,61 +58,3 @@ jobs:
     - name: Run ruff linter
       run: ruff check .
 
-  simulation-tests:
-    runs-on: ubuntu-latest
-    # Only run simulation tests on main branch pushes (requires manual API key setup)
-    if: github.event_name == 'push' && github.ref == 'refs/heads/main'
-    steps:
-    - uses: actions/checkout@v4
-    
-    - name: Set up Python
-      uses: actions/setup-python@v4
-      with:
-        python-version: "3.11"
-    
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        pip install -r requirements.txt
-    
-    - name: Check API key availability
-      id: check-key
-      run: |
-        has_key=false
-        if [ -n "${{ secrets.GEMINI_API_KEY }}" ] || [ -n "${{ secrets.OPENAI_API_KEY }}" ]; then
-          has_key=true
-          echo "✅ API key(s) found - running simulation tests"
-        else
-          echo "⚠️ No API keys configured - skipping simulation tests"
-        fi
-        echo "api_key_available=$has_key" >> $GITHUB_OUTPUT
-    
-    - name: Set up Docker
-      if: steps.check-key.outputs.api_key_available == 'true'
-      uses: docker/setup-buildx-action@v3
-    
-    - name: Build Docker image
-      if: steps.check-key.outputs.api_key_available == 'true'
-      run: |
-        docker compose build
-    
-    - name: Run simulation tests
-      if: steps.check-key.outputs.api_key_available == 'true'
-      run: |
-        # Start services
-        docker compose up -d
-        
-        # Wait for services to be ready
-        sleep 10
-        
-        # Run communication simulator tests
-        python communication_simulator_test.py --skip-docker
-      env:
-        GEMINI_API_KEY: ${{ secrets.GEMINI_API_KEY }}
-        OPENAI_API_KEY: ${{ secrets.OPENAI_API_KEY }}
-    
-    - name: Skip simulation tests
-      if: steps.check-key.outputs.api_key_available == 'false'
-      run: |
-        echo "🔒 Simulation tests skipped (no API keys configured)"
-        echo "To enable simulation tests, add GEMINI_API_KEY and/or OPENAI_API_KEY as repository secrets"