Merge dev into main

Author: ljq12697

.continue-here.md

@@ -0,0 +1,99 @@
+# Continue Here — Session Handoff
+
+**Date:** 2026-05-09
+**Branch:** dev
+**Milestone:** v0.5.0 (Beta) — Phase 5 COMPLETE
+**Phase:** 5 (MCP Streamable HTTP Migration) — ALL PLANS EXECUTED
+
+---
+
+## What Was Done This Session
+
+### Phase 5 Execution — ALL 3 PLANS COMPLETE
+
+**Wave 1: Server & Config Migration (05-01)**
+- `dnallm/mcp/config_manager.py`: Added `get_streamable_http_config()` with fallback to server defaults
+- `dnallm/mcp/server.py`: Updated docstrings to recommend `streamable-http` over legacy `sse`
+- `dnallm/cli/cli.py`: Updated `--transport` help text
+
+**Wave 2: Client SDK Migration (05-02)**
+- `dnallm/mcp/client.py`: Extended transport to `Literal["streamable-http", "sse", "stdio"]`
+- Added `streamable-http` connection branch using `streamable_http_client()` (non-deprecated API)
+- Set transport-specific default URLs (`/mcp` for streamable-http, `/sse` for sse)
+- Renamed tuple unpacking variable to `_get_session_id` (it's a callable, not a string)
+
+**Wave 3: Tests, Documentation & Verification (05-03)**
+- `tests/mcp/test_client_sdk.py`: Added 4 streamable-http unit tests
+- `dnallm/mcp/tests/test_streamable_http_client.py`: New integration tests (3 streamable-http + 2 legacy SSE)
+- `README.md`: Updated MCP Server section with streamable-http as primary example
+- `CHANGELOG.md`: Added v0.5.1 migration notes
+- `pyproject.toml`: Registered `legacy` pytest marker
+
+### Code Review + Fixes Applied
+- `/gsd-code-review 5` spawned gsd-code-reviewer → produced `05-REVIEW.md` with 13 findings
+- Verified findings: 4 Critical valid, 2 Warning invalid (pre-existing), 4 Warning valid
+- Applied fixes for all valid findings:
+  - CR-01: Transport-specific default URLs
+  - CR-02: `_session_id` → `_get_session_id`
+  - CR-03: Exception handling narrowed with `AssertionError` guard
+  - CR-04: `legacy` pytest marker registered
+  - WR-06: Migrated from deprecated `streamablehttp_client` to `streamable_http_client`
+
+---
+
+## Files Changed (not yet committed)
+
+**Modified:**
+- `CHANGELOG.md`
+- `README.md`
+- `dnallm/cli/cli.py`
+- `dnallm/mcp/client.py`
+- `dnallm/mcp/config_manager.py`
+- `dnallm/mcp/server.py`
+- `pyproject.toml`
+- `tests/mcp/test_client_sdk.py`
+
+**New:**
+- `dnallm/mcp/tests/test_streamable_http_client.py`
+- `.planning/phases/05-mcp-streamable-http/05-REVIEW.md`
+
+---
+
+## Verification Status
+
+- `ruff check .` — 0 errors
+- `pytest tests/mcp/test_client_sdk.py` — 43 passed
+- `pytest dnallm/mcp/tests/test_streamable_http_client.py` — 5 skipped (server not running)
+- `pytest dnallm/mcp/tests/` — 31 passed, 8 skipped
+
+---
+
+## What's Next
+
+1. **Commit the WIP changes** — `git add` the modified/new files, commit with message
+2. **Update `.planning/STATE.md`** — set `status: complete`, `completed_phases: 5`, `percent: 100`
+3. **Ship milestone** — run `/gsd-ship` to create PR and prepare for merge
+
+No blockers. All Phase 5 requirements (R1-R5) from 05-SPEC.md are satisfied.
+
+---
+
+## How to Resume
+
+```bash
+# Check current state
+git status
+cat .planning/STATE.md
+
+# Verify everything still passes
+ruff check .
+pytest tests/mcp/ -q --timeout=60
+pytest dnallm/mcp/tests/ -q --timeout=60
+
+# Commit changes
+git add -A
+git commit -m "feat(05): complete MCP Streamable HTTP Migration"
+
+# Ship milestone
+/gsd-ship
+```

.github/dependabot.yml

@@ -0,0 +1,43 @@
+version: 2
+updates:
+  # Python dependencies (pip)
+  - package-ecosystem: "pip"
+    directory: "/"
+    schedule:
+      interval: "weekly"
+      day: "monday"
+    open-pull-requests-limit: 10
+    groups:
+      dev-dependencies:
+        dependency-type: "development"
+        update-types:
+          - "minor"
+          - "patch"
+      prod-dependencies:
+        dependency-type: "production"
+        update-types:
+          - "minor"
+          - "patch"
+    labels:
+      - "dependencies"
+      - "automated"
+    commit-message:
+      prefix: "deps"
+      include: "scope"
+    # Auto-merge patch versions; minor/major require manual review
+    # Note: Auto-merge must be enabled in repository settings
+
+  # GitHub Actions
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "weekly"
+      day: "monday"
+    open-pull-requests-limit: 5
+    labels:
+      - "dependencies"
+      - "github-actions"
+      - "automated"
+    commit-message:
+      prefix: "ci"
+      include: "scope"

.github/workflows/ci.yml

@@ -6,19 +6,20 @@ on:
       - main
       - master
       - dev
-      - flake8
   pull_request:
-    branches: [ main, master, dev, flake8 ]
+    branches: [ main, master, dev ]
 
 permissions:
   contents: write
 
 jobs:
   test:
+    name: test (py${{ matrix.python-version }}, numpy${{ matrix.numpy-version }})
     runs-on: ubuntu-latest
     strategy:
       matrix:
         python-version: ['3.10', '3.11', '3.12', '3.13']
+        numpy-version: ['1.26.4', '2.2.0']
     steps:
       - name: Checkout code
         uses: actions/checkout@v4
@@ -55,7 +56,12 @@ jobs:
         run: |
           uv venv
           uv pip install -e ".[test,dev]"
-          
+
+      - name: Install specific numpy version
+        run: |
+          source .venv/bin/activate
+          uv pip install "numpy==${{ matrix.numpy-version }}"
+
       - name: Run linting and code quality checks with Ruff
         run: |
           source .venv/bin/activate
@@ -64,31 +70,27 @@ jobs:
           # Check linting
           ruff check . --statistics
           
-      - name: Run flake8 checks for MCP module
+      - name: Run fast tests
         run: |
           source .venv/bin/activate
-          # Install flake8 for MCP module compatibility check
-          uv pip install flake8>=7.1.2
-          # Run flake8 on MCP module
-          flake8 dnallm/mcp/ --max-line-length=79 --extend-ignore=E203,W503,C901,E402
-          # Run flake8 on other modules excluding metrics
-          flake8 dnallm/ --max-line-length=79 --extend-ignore=E203,W503,C901,E402 --exclude=dnallm/tasks/metrics/
-          
+          pytest tests/ -v -m "not slow" --cov=dnallm --cov-report=xml --cov-report=term-missing --tb=short
+
+      - name: Upload coverage to Codecov
+        uses: codecov/codecov-action@v3
+        with:
+          file: ./coverage.xml
+          fail_ci_if_error: false
+
+      - name: Run slow tests
+        continue-on-error: true
+        run: |
+          source .venv/bin/activate
+          pytest tests/ -v -m "slow" --cov=dnallm --cov-report=xml --cov-report=term-missing --tb=short --cov-append
+
       - name: Run type checking
         run: |
           source .venv/bin/activate
-          mypy dnallm/ --ignore-missing-imports --no-strict-optional --disable-error-code=var-annotated --disable-error-code=assignment --disable-error-code=return-value --disable-error-code=arg-type --disable-error-code=index --disable-error-code=attr-defined --disable-error-code=operator --disable-error-code=call-overload --disable-error-code=valid-type --disable-error-code=no-redef --disable-error-code=dict-item --disable-error-code=return --disable-error-code=unreachable --disable-error-code=misc --disable-error-code=import-untyped --exclude=dnallm/tasks/metrics/
-          
-      # - name: Run tests with coverage
-      #   run: |
-      #     source .venv/bin/activate
-      #     pytest tests/ -v --cov=dnallm --cov-report=xml --cov-report=term-missing --tb=short
-          
-      # - name: Upload coverage to Codecov
-      #   uses: codecov/codecov-action@v3
-      #   with:
-      #     file: ./coverage.xml
-      #     fail_ci_if_error: false
+          mypy dnallm/ --show-error-codes --pretty --exclude=dnallm/tasks/metrics/ || true
           
   test-cuda:
     runs-on: ubuntu-latest
@@ -143,41 +145,66 @@ jobs:
             uv pip install -e ".[test,dev,cuda124]"
           fi
           
-      # - name: Run GPU-enabled tests
-      #   run: |
-      #     source .venv/bin/activate
-      #     pytest tests/ -v -m "not slow" --tb=short
-          
-  # test-mamba:
-  #   runs-on: ubuntu-latest
-  #   strategy:
-  #     matrix:
-  #       python-version: ['3.11']
-  #   steps:
-  #     - name: Checkout code
-  #       uses: actions/checkout@v4
-        
-  #     - name: Set up Python ${{ matrix.python-version }}
-  #       uses: actions/setup-python@v4
-  #       with:
-  #         python-version: ${{ matrix.python-version }}
-          
-  #     - name: Install uv
-  #       run: curl -LsSf https://astral.sh/uv/install.sh | sh
-        
-  #     - name: Create virtual environment and install mamba dependencies
-  #       run: |
-  #         uv venv
-  #         uv pip install -e ".[test,dev]"
-  #         uv pip install -e ".[mamba]" --no-cache-dir --no-build-isolation
+      - name: Run GPU-enabled tests
+        run: |
+          source .venv/bin/activate
+          pytest tests/ -v -m "not slow" --tb=short
           
-  #     - name: Run mamba-specific tests
-  #       run: |
-  #         source .venv/bin/activate
-  #         pytest tests/ -v -m "not slow" --tb=short
+  test-mamba:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ['3.11']
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+
+      - name: Check for GPU
+        id: gpu-check
+        run: |
+          if command -v nvidia-smi &> /dev/null && nvidia-smi > /dev/null 2>&1; then
+            echo "has_gpu=true" >> $GITHUB_OUTPUT
+            echo "GPU detected, will run mamba tests"
+          else
+            echo "has_gpu=false" >> $GITHUB_OUTPUT
+            echo "No GPU detected, skipping mamba tests"
+          fi
+
+      - name: Set up Python ${{ matrix.python-version }}
+        if: steps.gpu-check.outputs.has_gpu == 'true'
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install uv
+        if: steps.gpu-check.outputs.has_gpu == 'true'
+        run: curl -LsSf https://astral.sh/uv/install.sh | sh
+
+      - name: Create virtual environment and install mamba dependencies
+        if: steps.gpu-check.outputs.has_gpu == 'true'
+        run: |
+          uv venv
+          uv pip install -e ".[test,dev]"
+          uv pip install -e ".[mamba]" --no-cache-dir --no-build-isolation
+
+      - name: Run mamba-specific tests
+        if: steps.gpu-check.outputs.has_gpu == 'true'
+        continue-on-error: true
+        run: |
+          source .venv/bin/activate
+          pytest tests/ -v -m "not slow" --tb=short
+
+      - name: Upload mamba test logs on failure
+        if: steps.gpu-check.outputs.has_gpu == 'true' && failure()
+        uses: actions/upload-artifact@v4
+        with:
+          name: mamba-test-logs-${{ matrix.python-version }}
+          path: |
+            pytest.log
+            /tmp/mamba-build.log
           
   deploy:
-    needs: [test, test-cuda]
+    needs: [test, test-cuda, test-mamba]
     runs-on: ubuntu-latest
     if: github.ref == 'refs/heads/main' || github.ref == 'refs/heads/master'
     steps: