refactor: split backend into harness (deerflow.*) and app (app.*) (#1131)

* refactor: extract shared utils to break harness→app cross-layer imports

Move _validate_skill_frontmatter to src/skills/validation.py and
CONVERTIBLE_EXTENSIONS + convert_file_to_markdown to src/utils/file_conversion.py.
This eliminates the two reverse dependencies from client.py (harness layer)
into gateway/routers/ (app layer), preparing for the harness/app package split.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

* refactor: split backend/src into harness (deerflow.*) and app (app.*)

Physically split the monolithic backend/src/ package into two layers:

- **Harness** (`packages/harness/deerflow/`): publishable agent framework
  package with import prefix `deerflow.*`. Contains agents, sandbox, tools,
  models, MCP, skills, config, and all core infrastructure.

- **App** (`app/`): unpublished application code with import prefix `app.*`.
  Contains gateway (FastAPI REST API) and channels (IM integrations).

Key changes:
- Move 13 harness modules to packages/harness/deerflow/ via git mv
- Move gateway + channels to app/ via git mv
- Rename all imports: src.* → deerflow.* (harness) / app.* (app layer)
- Set up uv workspace with deerflow-harness as workspace member
- Update langgraph.json, config.example.yaml, all scripts, Docker files
- Add build-system (hatchling) to harness pyproject.toml
- Add PYTHONPATH=. to gateway startup commands for app.* resolution
- Update ruff.toml with known-first-party for import sorting
- Update all documentation to reflect new directory structure

Boundary rule enforced: harness code never imports from app.
All 429 tests pass. Lint clean.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

* chore: add harness→app boundary check test and update docs

Add test_harness_boundary.py that scans all Python files in
packages/harness/deerflow/ and fails if any `from app.*` or
`import app.*` statement is found. This enforces the architectural
rule that the harness layer never depends on the app layer.

Update CLAUDE.md to document the harness/app split architecture,
import conventions, and the boundary enforcement test.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

* feat: add config versioning with auto-upgrade on startup

When config.example.yaml schema changes, developers' local config.yaml
files can silently become outdated. This adds a config_version field and
auto-upgrade mechanism so breaking changes (like src.* → deerflow.*
renames) are applied automatically before services start.

- Add config_version: 1 to config.example.yaml
- Add startup version check warning in AppConfig.from_file()
- Add scripts/config-upgrade.sh with migration registry for value replacements
- Add `make config-upgrade` target
- Auto-run config-upgrade in serve.sh and start-daemon.sh before starting services
- Add config error hints in service failure messages

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

* fix comments

* fix: update src.* import in test_sandbox_tools_security to deerflow.*

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

* fix: handle empty config and search parent dirs for config.example.yaml

Address Copilot review comments on PR #1131:
- Guard against yaml.safe_load() returning None for empty config files
- Search parent directories for config.example.yaml instead of only
  looking next to config.yaml, fixing detection in common setups

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

* fix: correct skills root path depth and config_version type coercion

- loader.py: fix get_skills_root_path() to use 5 parent levels (was 3)
  after harness split, file lives at packages/harness/deerflow/skills/
  so parent×3 resolved to backend/packages/harness/ instead of backend/
- app_config.py: coerce config_version to int() before comparison in
  _check_config_version() to prevent TypeError when YAML stores value
  as string (e.g. config_version: "1")
- tests: add regression tests for both fixes

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

* fix: update test imports from src.* to deerflow.*/app.* after harness refactor

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

---------

Co-authored-by: Claude Opus 4.6 <noreply@anthropic.com>
This commit is contained in:
DanielWalnut
2026-03-14 22:55:52 +08:00
committed by GitHub
parent 9b49a80dda
commit 76803b826f
198 changed files with 1786 additions and 941 deletions

146
scripts/config-upgrade.sh Executable file
View File

@@ -0,0 +1,146 @@
#!/usr/bin/env bash
#
# config-upgrade.sh - Upgrade config.yaml to match config.example.yaml
#
# 1. Runs version-specific migrations (value replacements, renames, etc.)
# 2. Merges missing fields from the example into the user config
# 3. Backs up config.yaml to config.yaml.bak before modifying.
set -e
REPO_ROOT="$(cd "$(dirname "${BASH_SOURCE[0]}")/.." && pwd)"
EXAMPLE="$REPO_ROOT/config.example.yaml"
# Resolve config.yaml location: env var > backend/ > repo root
if [ -n "$DEER_FLOW_CONFIG_PATH" ] && [ -f "$DEER_FLOW_CONFIG_PATH" ]; then
CONFIG="$DEER_FLOW_CONFIG_PATH"
elif [ -f "$REPO_ROOT/backend/config.yaml" ]; then
CONFIG="$REPO_ROOT/backend/config.yaml"
elif [ -f "$REPO_ROOT/config.yaml" ]; then
CONFIG="$REPO_ROOT/config.yaml"
else
CONFIG=""
fi
if [ ! -f "$EXAMPLE" ]; then
echo "✗ config.example.yaml not found at $EXAMPLE"
exit 1
fi
if [ -z "$CONFIG" ]; then
echo "No config.yaml found — creating from example..."
cp "$EXAMPLE" "$REPO_ROOT/config.yaml"
echo "✓ config.yaml created. Please review and set your API keys."
exit 0
fi
# Use inline Python to do migrations + recursive merge with PyYAML
cd "$REPO_ROOT/backend" && uv run python3 -c "
import sys, shutil, copy, re
from pathlib import Path
import yaml
config_path = Path('$CONFIG')
example_path = Path('$EXAMPLE')
with open(config_path, encoding='utf-8') as f:
raw_text = f.read()
user = yaml.safe_load(raw_text) or {}
with open(example_path, encoding='utf-8') as f:
example = yaml.safe_load(f) or {}
user_version = user.get('config_version', 0)
example_version = example.get('config_version', 0)
if user_version >= example_version:
print(f'✓ config.yaml is already up to date (version {user_version}).')
sys.exit(0)
print(f'Upgrading config.yaml: version {user_version} → {example_version}')
print()
# ── Migrations ───────────────────────────────────────────────────────────
# Each migration targets a specific version upgrade.
# 'replacements': list of (old_string, new_string) applied to the raw YAML text.
# This handles value changes that a dict merge cannot catch.
MIGRATIONS = {
1: {
'description': 'Rename src.* module paths to deerflow.*',
'replacements': [
('src.community.', 'deerflow.community.'),
('src.sandbox.', 'deerflow.sandbox.'),
('src.models.', 'deerflow.models.'),
('src.tools.', 'deerflow.tools.'),
],
},
# Future migrations go here:
# 2: {
# 'description': '...',
# 'replacements': [('old', 'new')],
# },
}
# Apply migrations in order for versions (user_version, example_version]
migrated = []
for version in range(user_version + 1, example_version + 1):
migration = MIGRATIONS.get(version)
if not migration:
continue
desc = migration.get('description', f'Migration to v{version}')
for old, new in migration.get('replacements', []):
if old in raw_text:
raw_text = raw_text.replace(old, new)
migrated.append(f'{old} → {new}')
# Re-parse after text migrations
user = yaml.safe_load(raw_text) or {}
if migrated:
print(f'Applied {len(migrated)} migration(s):')
for m in migrated:
print(f' ~ {m}')
print()
# ── Merge missing fields ─────────────────────────────────────────────────
added = []
def merge(target, source, path=''):
\"\"\"Recursively merge source into target, adding missing keys only.\"\"\"
for key, value in source.items():
key_path = f'{path}.{key}' if path else key
if key not in target:
target[key] = copy.deepcopy(value)
added.append(key_path)
elif isinstance(value, dict) and isinstance(target[key], dict):
merge(target[key], value, key_path)
merge(user, example)
# Always update config_version
user['config_version'] = example_version
# ── Write ─────────────────────────────────────────────────────────────────
backup = config_path.with_suffix('.yaml.bak')
shutil.copy2(config_path, backup)
print(f'Backed up to {backup.name}')
with open(config_path, 'w', encoding='utf-8') as f:
yaml.dump(user, f, default_flow_style=False, allow_unicode=True, sort_keys=False)
if added:
print(f'Added {len(added)} new field(s):')
for a in added:
print(f' + {a}')
if not migrated and not added:
print('No changes needed (version bumped only).')
print()
print(f'✓ config.yaml upgraded to version {example_version}.')
print(' Please review the changes and set any new required values.')
"

View File

@@ -124,7 +124,7 @@ detect_sandbox_mode() {
}
' "$DEER_FLOW_CONFIG_PATH")
if [[ "$sandbox_use" == *"src.community.aio_sandbox:AioSandboxProvider"* ]]; then
if [[ "$sandbox_use" == *"deerflow.community.aio_sandbox:AioSandboxProvider"* ]]; then
if [ -n "$provisioner_url" ]; then
echo "provisioner"
else

View File

@@ -47,9 +47,9 @@ detect_sandbox_mode() {
}
' "$config_file")
if [[ "$sandbox_use" == *"src.sandbox.local:LocalSandboxProvider"* ]]; then
if [[ "$sandbox_use" == *"deerflow.sandbox.local:LocalSandboxProvider"* ]]; then
echo "local"
elif [[ "$sandbox_use" == *"src.community.aio_sandbox:AioSandboxProvider"* ]]; then
elif [[ "$sandbox_use" == *"deerflow.community.aio_sandbox:AioSandboxProvider"* ]]; then
if [ -n "$provisioner_url" ]; then
echo "provisioner"
else

View File

@@ -30,7 +30,7 @@ fi
echo "Stopping existing services if any..."
pkill -f "langgraph dev" 2>/dev/null || true
pkill -f "uvicorn src.gateway.app:app" 2>/dev/null || true
pkill -f "uvicorn app.gateway.app:app" 2>/dev/null || true
pkill -f "next dev" 2>/dev/null || true
pkill -f "next-server" 2>/dev/null || true
nginx -c "$REPO_ROOT/docker/nginx/nginx.local.conf" -p "$REPO_ROOT" -s quit 2>/dev/null || true
@@ -78,6 +78,10 @@ if ! { \
exit 1
fi
# ── Auto-upgrade config ──────────────────────────────────────────────────
"$REPO_ROOT/scripts/config-upgrade.sh"
# ── Cleanup trap ─────────────────────────────────────────────────────────────
cleanup() {
@@ -85,7 +89,7 @@ cleanup() {
echo ""
echo "Shutting down services..."
pkill -f "langgraph dev" 2>/dev/null || true
pkill -f "uvicorn src.gateway.app:app" 2>/dev/null || true
pkill -f "uvicorn app.gateway.app:app" 2>/dev/null || true
pkill -f "next dev" 2>/dev/null || true
pkill -f "next start" 2>/dev/null || true
# Kill nginx using the captured PID first (most reliable),
@@ -121,18 +125,24 @@ echo "Starting LangGraph server..."
./scripts/wait-for-port.sh 2024 60 "LangGraph" || {
echo " See logs/langgraph.log for details"
tail -20 logs/langgraph.log
if grep -qE "config_version|outdated|Environment variable .* not found|KeyError|ValidationError|config\.yaml" logs/langgraph.log 2>/dev/null; then
echo ""
echo " Hint: This may be a configuration issue. Try running 'make config-upgrade' to update your config.yaml."
fi
cleanup
}
echo "✓ LangGraph server started on localhost:2024"
echo "Starting Gateway API..."
(cd backend && uv run uvicorn src.gateway.app:app --host 0.0.0.0 --port 8001 $GATEWAY_EXTRA_FLAGS > ../logs/gateway.log 2>&1) &
(cd backend && PYTHONPATH=. uv run uvicorn app.gateway.app:app --host 0.0.0.0 --port 8001 $GATEWAY_EXTRA_FLAGS > ../logs/gateway.log 2>&1) &
./scripts/wait-for-port.sh 8001 30 "Gateway API" || {
echo "✗ Gateway API failed to start. Last log output:"
tail -60 logs/gateway.log
echo ""
echo "Likely configuration errors:"
grep -E "Failed to load configuration|Environment variable .* not found|config\.yaml.*not found" logs/gateway.log | tail -5 || true
echo ""
echo " Hint: Try running 'make config-upgrade' to update your config.yaml with the latest fields."
cleanup
}
echo "✓ Gateway API started on localhost:8001"

View File

@@ -16,7 +16,7 @@ cd "$REPO_ROOT"
echo "Stopping existing services if any..."
pkill -f "langgraph dev" 2>/dev/null || true
pkill -f "uvicorn src.gateway.app:app" 2>/dev/null || true
pkill -f "uvicorn app.gateway.app:app" 2>/dev/null || true
pkill -f "next dev" 2>/dev/null || true
nginx -c "$REPO_ROOT/docker/nginx/nginx.local.conf" -p "$REPO_ROOT" -s quit 2>/dev/null || true
sleep 1
@@ -49,12 +49,16 @@ if ! { \
exit 1
fi
# ── Auto-upgrade config ──────────────────────────────────────────────────
"$REPO_ROOT/scripts/config-upgrade.sh"
# ── Cleanup on failure ───────────────────────────────────────────────────────
cleanup_on_failure() {
echo "Failed to start services, cleaning up..."
pkill -f "langgraph dev" 2>/dev/null || true
pkill -f "uvicorn src.gateway.app:app" 2>/dev/null || true
pkill -f "uvicorn app.gateway.app:app" 2>/dev/null || true
pkill -f "next dev" 2>/dev/null || true
nginx -c "$REPO_ROOT/docker/nginx/nginx.local.conf" -p "$REPO_ROOT" -s quit 2>/dev/null || true
sleep 1
@@ -73,16 +77,22 @@ nohup sh -c 'cd backend && NO_COLOR=1 uv run langgraph dev --no-browser --allow-
./scripts/wait-for-port.sh 2024 60 "LangGraph" || {
echo "✗ LangGraph failed to start. Last log output:"
tail -60 logs/langgraph.log
if grep -qE "config_version|outdated|Environment variable .* not found|KeyError|ValidationError|config\.yaml" logs/langgraph.log 2>/dev/null; then
echo ""
echo " Hint: This may be a configuration issue. Try running 'make config-upgrade' to update your config.yaml."
fi
cleanup_on_failure
exit 1
}
echo "✓ LangGraph server started on localhost:2024"
echo "Starting Gateway API..."
nohup sh -c 'cd backend && uv run uvicorn src.gateway.app:app --host 0.0.0.0 --port 8001 > ../logs/gateway.log 2>&1' &
nohup sh -c 'cd backend && PYTHONPATH=. uv run uvicorn app.gateway.app:app --host 0.0.0.0 --port 8001 > ../logs/gateway.log 2>&1' &
./scripts/wait-for-port.sh 8001 30 "Gateway API" || {
echo "✗ Gateway API failed to start. Last log output:"
tail -60 logs/gateway.log
echo ""
echo " Hint: Try running 'make config-upgrade' to update your config.yaml with the latest fields."
cleanup_on_failure
exit 1
}

View File

@@ -35,14 +35,14 @@ from requests.exceptions import SSLError
from langchain.agents.middleware import AgentMiddleware
from langchain_core.messages import ToolMessage
from src.agents.lead_agent.agent import _build_middlewares
from src.config import get_app_config
from src.sandbox.middleware import SandboxMiddleware
from deerflow.agents.lead_agent.agent import _build_middlewares
from deerflow.config import get_app_config
from deerflow.sandbox.middleware import SandboxMiddleware
from src.agents.middlewares.thread_data_middleware import ThreadDataMiddleware
from deerflow.agents.middlewares.thread_data_middleware import ThreadDataMiddleware
HANDSHAKE_ERROR = "[SSL: UNEXPECTED_EOF_WHILE_READING] EOF occurred in violation of protocol (_ssl.c:1000)"
logging.getLogger("src.agents.middlewares.tool_error_handling_middleware").setLevel(logging.CRITICAL)
logging.getLogger("deerflow.agents.middlewares.tool_error_handling_middleware").setLevel(logging.CRITICAL)
def _make_ssl_error():
@@ -150,7 +150,7 @@ def _validate_outputs(label, outputs):
def _build_sub_middlewares():
try:
from src.agents.middlewares.tool_error_handling_middleware import build_subagent_runtime_middlewares
from deerflow.agents.middlewares.tool_error_handling_middleware import build_subagent_runtime_middlewares
except Exception:
return [
ThreadDataMiddleware(lazy_init=True),