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@muhabalwan-aginx muhabalwan-aginx force-pushed the chore/pysdk-000-claude-doc-review branch from ca5d2d9 to c6c039d Compare November 10, 2025 13:01
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Claude finished @muhabalwan-aginx's task —— View job


Comprehensive PR Review - Complete ✅

I have thoroughly reviewed PR #252 against the Aignostics Python SDK standards as outlined in CLAUDE.md. This PR adds a new example module as a learning template, a Claude Code documentation review workflow, and GUI enhancements.


🚨 CRITICAL BLOCKING ISSUES

1. ❌ Missing Abstract Method Implementation (BLOCKING - CI Failure)

Location: src/aignostics/example/_service.py:8

Issue: The Service class inherits from BaseService but doesn't implement the required abstract methods health() and info(), causing all CI test jobs to fail with:

TypeError: Can't instantiate abstract class Service without an implementation 
for abstract methods 'health', 'info'

Impact:

  • All CI pipelines failing across all platforms (Ubuntu, macOS, Windows, ARM)
  • Cannot instantiate the service for any testing or usage
  • Blocks all other validation

Fix Required:

Add these methods to src/aignostics/example/_service.py:

from aignostics.utils import BaseService, Health, get_logger

class Service(BaseService):
    """Example service for demonstration purposes."""

    def __init__(self) -> None:
        """Initialize the example service."""
        super().__init__()
        logger.info("Example service initialized")

    def health(self) -> Health:
        """Check service health.
        
        Returns:
            Health: Service health status.
        """
        return Health(status=Health.Code.UP, details={"module": "example"})

    def info(self, mask_secrets: bool = True) -> dict[str, str]:
        """Get service information.
        
        Args:
            mask_secrets: Whether to mask sensitive information.
            
        Returns:
            dict[str, str]: Service information.
        """
        return {
            "module": "example",
            "version": "1.0.0",
            "purpose": "Learning template for SDK architecture",
            "description": "Demonstrates modulith pattern with Service + CLI + GUI",
        }

    @staticmethod
    def get_example_data() -> dict[str, str]:
        # ... existing code ...

Reference: See src/aignostics/qupath/_service.py:18-30 for working example.

Verification:

python -c "from aignostics.example import Service; s = Service(); print(s.health())"

2. ❌ Missing Test Coverage (BLOCKING)

Location: tests/aignostics/example/ (does not exist)

Issue: The new example module has ZERO tests, violating the 85% minimum coverage requirement stated in CLAUDE.md line 489.

Current State: No test directory exists for this module.

Fix Required:

Create comprehensive test suite following repository patterns:

File structure:

tests/aignostics/example/
├── __init__.py          # Empty file
├── service_test.py      # Service layer tests
├── cli_test.py          # CLI command tests
└── gui_test.py          # GUI tests (if nicegui available)

Example test implementation (tests/aignostics/example/service_test.py):

"""Tests for example module service."""

import pytest
from aignostics.example import Service
from aignostics.utils import Health

@pytest.mark.unit
def test_service_initialization(record_property) -> None:
    """Test example service can be initialized."""
    record_property("tested-item-id", "SPEC-EXAMPLE-SERVICE")
    service = Service()
    assert service is not None
    assert service.key() == "example"

@pytest.mark.unit
def test_service_health(record_property) -> None:
    """Test service health check returns UP status."""
    record_property("tested-item-id", "SPEC-EXAMPLE-SERVICE")
    service = Service()
    health = service.health()
    assert isinstance(health, Health)
    assert health.status == Health.Code.UP
    assert health.details["module"] == "example"

@pytest.mark.unit
def test_service_info(record_property) -> None:
    """Test service info returns expected structure."""
    record_property("tested-item-id", "SPEC-EXAMPLE-SERVICE")
    service = Service()
    info = service.info()
    assert isinstance(info, dict)
    assert "module" in info
    assert "version" in info
    assert "purpose" in info
    assert info["module"] == "example"

@pytest.mark.unit
def test_get_example_data(record_property) -> None:
    """Test get_example_data returns expected structure."""
    record_property("tested-item-id", "SPEC-EXAMPLE-SERVICE")
    data = Service.get_example_data()
    assert isinstance(data, dict)
    assert "message" in data
    assert "status" in data
    assert "module" in data
    assert data["status"] == "active"
    assert data["module"] == "example"

@pytest.mark.unit
def test_process_example(record_property) -> None:
    """Test process_example text transformation."""
    record_property("tested-item-id", "SPEC-EXAMPLE-SERVICE")
    input_text = "test input"
    result = Service.process_example(input_text)
    assert result == f"Processed: {input_text}"
    assert "test input" in result

CLI tests (tests/aignostics/example/cli_test.py):

"""Tests for example module CLI commands."""

import pytest
from typer.testing import CliRunner
from aignostics.example import cli

runner = CliRunner()

@pytest.mark.integration
def test_cli_hello_default(record_property) -> None:
    """Test hello command with default argument."""
    record_property("tested-item-id", "SPEC-EXAMPLE-CLI")
    result = runner.invoke(cli, ["hello"])
    assert result.exit_code == 0
    assert "World" in result.stdout

@pytest.mark.integration
def test_cli_hello_custom_name(record_property) -> None:
    """Test hello command with custom name."""
    record_property("tested-item-id", "SPEC-EXAMPLE-CLI")
    result = runner.invoke(cli, ["hello", "Alice"])
    assert result.exit_code == 0
    assert "Alice" in result.stdout

@pytest.mark.integration
def test_cli_data(record_property) -> None:
    """Test data command."""
    record_property("tested-item-id", "SPEC-EXAMPLE-CLI")
    result = runner.invoke(cli, ["data"])
    assert result.exit_code == 0
    assert "Example Data" in result.stdout

@pytest.mark.integration
def test_cli_process(record_property) -> None:
    """Test process command."""
    record_property("tested-item-id", "SPEC-EXAMPLE-CLI")
    result = runner.invoke(cli, ["process", "test text"])
    assert result.exit_code == 0
    assert "Processed: test text" in result.stdout

IMPORTANT: All tests MUST have markers (@pytest.mark.unit, @pytest.mark.integration, or @pytest.mark.e2e) as per CLAUDE.md line 725. Tests without markers will NOT run in CI.

Verification:

uv run pytest tests/aignostics/example/ -v
uv run coverage report --fail-under=85

3. ❌ Missing Module Documentation (BLOCKING)

Location: src/aignostics/example/CLAUDE.md (does not exist)

Issue: Root CLAUDE.md line 38 states: "Every module has detailed CLAUDE.md documentation." The example module violates this requirement.

Fix Required:

Create src/aignostics/example/CLAUDE.md following the pattern established in src/aignostics/qupath/CLAUDE.md.

Required structure:

# CLAUDE.md - Example Module

## Module Overview

The example module is a learning template that demonstrates the Aignostics SDK's modulith architecture pattern.

**Purpose**: Educational template showing best practices for:
- Service layer implementation with BaseService
- CLI command registration with Typer
- GUI page integration with NiceGUI
- Module auto-discovery via dependency injection

**User Interfaces**:
- **Service**: Core business logic (get_example_data, process_example)
- **CLI**: Three commands (hello, data, process)
- **GUI**: Interactive page at /example route

## Architecture & Design Patterns

### Service Layer
- Inherits from `BaseService`
- Implements required `health()` and `info()` methods
- Provides static utility methods for example operations
- No external dependencies beyond utils

### CLI Layer
- Uses Typer for command registration
- Three demonstration commands showing different patterns:
  - `hello`: Positional argument with default
  - `data`: No arguments, calls service layer
  - `process`: Required argument, processes input

### GUI Layer
- PageBuilder pattern for auto-discovery
- Interactive UI demonstrating service integration
- Accessible at `/example` route
- Shows cards with example data and text processing

## Development Guidelines

### Adding Features
1. Add business logic to `_service.py`
2. Add CLI commands to `_cli.py`
3. Update GUI in `_gui/_page_example.py` if needed
4. Write tests in `tests/aignostics/example/`

### Testing Strategy
- Unit tests for service methods
- Integration tests for CLI commands
- GUI tests if nicegui available (optional)
- Maintain 85%+ coverage

## Usage Examples

### Programmatic Usage
```python
from aignostics.example import Service

service = Service()
data = service.get_example_data()
processed = service.process_example("hello world")

CLI Usage

# Say hello
uv run aignostics example hello
uv run aignostics example hello "Alice"

# Get example data
uv run aignostics example data

# Process text
uv run aignostics example process "sample text"

GUI Access

# Launch GUI and navigate to /example
uv run aignostics gui

Dependencies

  • utils: Logging, BaseService, Health
  • Optional: nicegui (for GUI)

Key Files

  • _service.py: Core business logic (35 lines)
  • _cli.py: CLI commands (96 lines)
  • _gui/_page_builder.py: GUI registration (19 lines)
  • _gui/_page_example.py: GUI page (77 lines)

---

### 4. ❌ **Module Not Listed in Index** (BLOCKING)

**Location**: `src/aignostics/CLAUDE.md:7-18`

**Issue**: The new `example` module is not listed in the module index table or the module description list.

**Fix Required**:

1. **Add to module index table** (around line 7):

```markdown
| Module | Core Purpose | CLI | GUI | Service |
|--------|-------------|-----|-----|---------|
| **example** | Learning template module | ✅ | ✅ | ✅ |
| **platform** | Authentication & API client | ✅ | ❌ | ✅ |
...
  1. Add to module descriptions section (around line 20):
### 📚 example

**Learning template demonstrating SDK modulith architecture**

- **Core Features**: Service layer pattern, CLI/GUI integration, dependency injection demo
- **CLI**: Three demonstration commands (`hello`, `data`, `process`)
- **GUI**: Interactive example page with service integration
- **Dependencies**: `utils` only
- **Purpose**: Educational reference for creating new modules
  1. Add to root CLAUDE.md module documentation index (around line 40):
* [src/aignostics/example/CLAUDE.md](src/aignostics/example/CLAUDE.md) - Example learning module

5. ❌ Commit Message Convention Violations (BLOCKING)

Location: All 5 commits in this PR

Current commits:

c6c039d refine claude-code-doc-review 2.
3ecf712 refine claude-code-doc-review.
b4fce36 refine claude-code-doc-review.
09b182c add claude code new workflow
b57e344 Integrate new example module into using the same UI that is build for Python SDK

Issue: None follow conventional commit format required by CLAUDE.md line 1123: type(scope): description

Valid types: feat, fix, docs, refactor, test, chore, ci, perf, build

Fix Required:

On merge, squash all commits with a proper conventional commit message:

feat(example): add learning template module with CLI, GUI, and doc review workflow

- Add example module demonstrating SDK modulith architecture
  - Service layer with health() and info() implementations
  - CLI with three demonstration commands (hello, data, process)
  - GUI page with interactive examples at /example route
- Add Claude Code workflow for requirements/spec review
- Add link to example module from application homepage
- Comprehensive inline documentation for educational purposes

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

6. ⚠️ Pre-existing Unmarked Test (Not from this PR)

Location: tests/aignostics/platform/settings_test.py:198

Issue: Test function test_custom_env_file_location is missing required category marker.

Impact: This test does NOT run in CI because the pipeline filters by markers: pytest -m "unit or integration or e2e"

Current code:

def test_custom_env_file_location(reset_cached_settings, record_property) -> None:

Fix (recommend separate PR):

@pytest.mark.unit  # Uses mocked env, no external dependencies
def test_custom_env_file_location(reset_cached_settings, record_property) -> None:

Verification:

# Should return 0 tests (or 1 if this pre-existing issue not fixed)
uv run pytest -m "not unit and not integration and not e2e" --collect-only

✅ WHAT'S EXCELLENT

Code Quality: PASSING ✓

All static analysis passed before the runtime error:

  • Ruff format: All 157 files formatted correctly
  • Ruff lint: No linting violations
  • PyRight: 0 errors (basic mode)
  • MyPy: Success in strict mode (85 source files)

Architecture Compliance: EXCELLENT ✓

The example module correctly follows modulith architecture patterns:

  • ✅ Service layer inherits from BaseService (once abstract methods added)
  • ✅ CLI uses Typer with proper command registration
  • ✅ GUI uses PageBuilder pattern for auto-discovery
  • ✅ Conditional nicegui import (__init__.py:14)
  • ✅ No circular dependencies
  • ✅ CLI and GUI both depend only on Service layer (correct separation)
  • ✅ Uses relative imports within module (from ._service import Service)

Documentation Quality: GOLD STANDARD ✓

The CLI inline documentation (_cli.py:1-96) is exemplary:

  • Lines 1-12: Module-level docstring with concrete usage examples
  • Lines 32-52: Detailed explanation of Typer patterns with architectural reasoning
  • Lines 54-74: Service layer integration patterns documented
  • Lines 76-96: Real-world usage demonstrations

This is best-in-class educational code - perfect for onboarding new developers.

Workflow Implementation: GOOD ✓

New Claude Code workflow (.github/workflows/claude-code-doc-review.yml):

  • ✅ Correct trigger: pull_request: [opened, synchronize, reopened]
  • ✅ Proper permissions: contents: read, pull-requests: write
  • ✅ Uses official anthropics/claude-code-action@v1
  • ✅ Clear, focused prompt for requirements/spec analysis
  • ✅ Appropriate model: claude-sonnet-4-5-20250929
  • ✅ Restricted tool access: Read,Glob,Grep,Bash(git:*)

Minor suggestion (non-blocking): Consider adding condition to exclude bot PRs:

if: ${{ !contains(github.actor, 'bot') }}

GUI Integration: CLEAN ✓

Application homepage changes (src/aignostics/application/_gui/_page_index.py:88-92):

  • ✅ Clear call-to-action linking to /example
  • ✅ Explains purpose of example module
  • ✅ Conditional on nicegui availability
  • ✅ Consistent styling with existing UI

Minor typo (non-blocking): "Hala walah" appears twice (lines 43, 47). If intentional, consider adding comment explaining the greeting.


📝 REQUIRED ACTIONS SUMMARY

IMMEDIATE (Fix CI - 15 minutes) ⚡

  1. Add abstract methods to Service class:
    • Add health() method returning Health object
    • Add info() method returning dict
    • Push changes to unblock CI

BEFORE MERGE (3 hours total)

  1. Create comprehensive test suite (~2 hours):

    • Create tests/aignostics/example/ directory structure
    • Add service_test.py with unit tests (use examples above)
    • Add cli_test.py with integration tests
    • Add gui_test.py if applicable
    • CRITICAL: All tests must have markers (@pytest.mark.unit, etc.)
    • Verify coverage: uv run coverage report --fail-under=85
  2. Add module documentation (~30 minutes):

    • Create src/aignostics/example/CLAUDE.md (use template above)
    • Update src/aignostics/CLAUDE.md module index
    • Add to module capabilities matrix
  3. Fix commit messages (~5 minutes):

    • Squash commits on merge with conventional commit format
    • Use suggested message above

OPTIONAL (Separate PR Recommended)

  1. Fix pre-existing unmarked test:
    • Add @pytest.mark.unit to test_custom_env_file_location
    • Location: tests/aignostics/platform/settings_test.py:198

🔧 VERIFICATION COMMANDS

After implementing fixes, run these commands to verify:

# 1. Verify Service can be instantiated
python -c "from aignostics.example import Service; s = Service(); print(s.health())"

# 2. Run example module tests
uv run pytest tests/aignostics/example/ -v

# 3. Check for unmarked tests (should find 0 or 1 pre-existing)
uv run pytest -m "not unit and not integration and not e2e" --collect-only

# 4. Verify coverage meets 85% threshold
make test
uv run coverage report --fail-under=85

# 5. Verify all linting passes
make lint

# 6. Test CLI commands work
uv run aignostics example hello
uv run aignostics example data
uv run aignostics example process "test"

💬 SUMMARY

Recommendation: ⛔ DO NOT MERGE - Critical blocking issues must be resolved.

Estimated Fix Time:

  • ⚡ Critical fix (abstract methods): 15 minutes
  • 📝 Full PR completion: ~3 hours total

Priority Order:

  1. Add health() and info() methods to unblock CI
  2. Create test suite to meet coverage requirements
  3. Add CLAUDE.md documentation
  4. Update module index in src/aignostics/CLAUDE.md
  5. Squash commits with proper message on merge

This is medical device software under FDA/MDR regulation. The high bar for testing and documentation is not optional - it's a compliance requirement. The code architecture and inline documentation are excellent; let's bring the supporting artifacts (tests, module docs) up to the same standard! 💪


Questions or need clarification? See:

  • BaseService pattern: src/aignostics/utils/_service.py:14-50
  • Working service example: src/aignostics/qupath/_service.py:18-30
  • Test patterns: tests/CLAUDE.md and tests/aignostics/platform/
  • Commit format: Root CLAUDE.md lines 1121-1145
  • Module documentation template: src/aignostics/qupath/CLAUDE.md

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Claude finished @muhabalwan-aginx's task —— View job


PR Review - Complete ✅

I've thoroughly reviewed PR #252 against the Aignostics Python SDK standards. This PR adds a new example module as a learning template, a Claude Code documentation review workflow, and GUI enhancements.

Review Summary

Blocking Issues Found: 3 critical issues preventing CI from passing
Architecture: Mostly compliant (good separation of concerns)
Documentation: Missing module CLAUDE.md and index updates


🚨 CRITICAL BLOCKING ISSUES

1. ❌ Import Error: get_logger Does Not Exist (BLOCKING - CI Failure)

Location: src/aignostics/example/_service.py:3 and src/aignostics/example/_cli.py:18

Issue: The example module attempts to import get_logger from aignostics.utils, but this function doesn't exist in the codebase. The repository uses loguru.logger directly instead.

Error in CI:

ImportError: cannot import name 'get_logger' from 'aignostics.utils'

Impact:

  • All CI test jobs failing with import errors
  • Module cannot be loaded or tested
  • Blocks all downstream tests that import the CLI

Fix Required:

File: src/aignostics/example/_service.py

Current (lines 3-5):

from aignostics.utils import BaseService, get_logger

logger = get_logger(__name__)

Should be:

from loguru import logger

from aignostics.utils import BaseService

File: src/aignostics/example/_cli.py

Current (lines 18-22):

from aignostics.utils import console, get_logger

from ._service import Service

logger = get_logger(__name__)

Should be:

from loguru import logger

from aignostics.utils import console

from ._service import Service

Reference: See src/aignostics/qupath/_service.py:24 for the correct pattern:

from loguru import logger

Verification:

# After fix, verify module imports without error
python -c "from aignostics.example import Service; print('OK')"
uv run pytest --collect-only 2>&1 | grep -i "import"

2. ❌ Missing Abstract Method Implementations (BLOCKING - Architecture Violation)

Location: src/aignostics/example/_service.py:8

Issue: The Service class inherits from BaseService but doesn't implement the two required abstract methods: health() and info(). This violates the modulith service pattern.

Impact:

  • Cannot instantiate the service
  • Will cause TypeError at runtime
  • Violates architecture requirements in CLAUDE.md

Fix Required:

Add these methods to src/aignostics/example/_service.py (insert after line 14, before line 16):

    def health(self) -> Health:
        """Check service health.
        
        Returns:
            Health: Service health status.
        """
        return Health(status=Health.Code.UP, details={"module": "example"})

    def info(self, mask_secrets: bool = True) -> dict[str, str]:
        """Get service information.
        
        Args:
            mask_secrets: Whether to mask sensitive information.
            
        Returns:
            dict[str, str]: Service information.
        """
        return {
            "module": "example",
            "version": "1.0.0",
            "purpose": "Learning template for SDK architecture",
            "description": "Demonstrates modulith pattern with Service + CLI + GUI",
        }

Also update imports (line 3):

from aignostics.utils import BaseService, Health

Reference:

  • Abstract methods defined in src/aignostics/utils/_service.py:33-41
  • Working example in src/aignostics/qupath/_service.py:45-59

Verification:

python -c "from aignostics.example import Service; s = Service(); print(s.health())"

3. ❌ Missing Test Coverage (BLOCKING - Coverage Requirement)

Location: tests/aignostics/example/ (does not exist)

Issue: The new example module has ZERO tests, violating the 85% minimum coverage requirement stated in CLAUDE.md line 76.

Current State: No test directory exists for this module.

Impact:

  • SonarQube reports: 0.0% Coverage on New Code (required ≥ 80%)
  • Violates strict testing requirements for medical device software
  • Missing validation of service, CLI, and GUI functionality

Fix Required:

Create comprehensive test suite following repository patterns:

File structure:

tests/aignostics/example/
├── __init__.py          # Empty file
├── service_test.py      # Service layer tests
└── cli_test.py          # CLI command tests

Example test implementation (tests/aignostics/example/service_test.py):

"""Tests for example module service."""

import pytest

from aignostics.example import Service
from aignostics.utils import Health


@pytest.mark.unit
def test_service_initialization(record_property) -> None:
    """Test example service can be initialized."""
    record_property("tested-item-id", "SPEC-EXAMPLE-SERVICE")
    service = Service()
    assert service is not None
    assert service.key() == "example"


@pytest.mark.unit
def test_service_health(record_property) -> None:
    """Test service health check returns UP status."""
    record_property("tested-item-id", "SPEC-EXAMPLE-SERVICE")
    service = Service()
    health = service.health()
    assert isinstance(health, Health)
    assert health.status == Health.Code.UP
    assert health.details["module"] == "example"


@pytest.mark.unit
def test_service_info(record_property) -> None:
    """Test service info returns expected structure."""
    record_property("tested-item-id", "SPEC-EXAMPLE-SERVICE")
    service = Service()
    info = service.info()
    assert isinstance(info, dict)
    assert "module" in info
    assert "version" in info
    assert "purpose" in info
    assert info["module"] == "example"


@pytest.mark.unit
def test_get_example_data(record_property) -> None:
    """Test get_example_data returns expected structure."""
    record_property("tested-item-id", "SPEC-EXAMPLE-SERVICE")
    data = Service.get_example_data()
    assert isinstance(data, dict)
    assert "message" in data
    assert "status" in data
    assert "module" in data
    assert data["status"] == "active"
    assert data["module"] == "example"


@pytest.mark.unit
def test_process_example(record_property) -> None:
    """Test process_example text transformation."""
    record_property("tested-item-id", "SPEC-EXAMPLE-SERVICE")
    input_text = "test input"
    result = Service.process_example(input_text)
    assert result == f"Processed: {input_text}"
    assert "test input" in result

CLI tests (tests/aignostics/example/cli_test.py):

"""Tests for example module CLI commands."""

import pytest
from typer.testing import CliRunner

from aignostics.example import cli

runner = CliRunner()


@pytest.mark.integration
def test_cli_hello_default(record_property) -> None:
    """Test hello command with default argument."""
    record_property("tested-item-id", "SPEC-EXAMPLE-CLI")
    result = runner.invoke(cli, ["hello"])
    assert result.exit_code == 0
    assert "World" in result.stdout


@pytest.mark.integration
def test_cli_hello_custom_name(record_property) -> None:
    """Test hello command with custom name."""
    record_property("tested-item-id", "SPEC-EXAMPLE-CLI")
    result = runner.invoke(cli, ["hello", "Alice"])
    assert result.exit_code == 0
    assert "Alice" in result.stdout


@pytest.mark.integration
def test_cli_data(record_property) -> None:
    """Test data command."""
    record_property("tested-item-id", "SPEC-EXAMPLE-CLI")
    result = runner.invoke(cli, ["data"])
    assert result.exit_code == 0
    assert "Example Data" in result.stdout


@pytest.mark.integration
def test_cli_process(record_property) -> None:
    """Test process command."""
    record_property("tested-item-id", "SPEC-EXAMPLE-CLI")
    result = runner.invoke(cli, ["process", "test text"])
    assert result.exit_code == 0
    assert "Processed: test text" in result.stdout

IMPORTANT: All tests MUST have markers (@pytest.mark.unit, @pytest.mark.integration, or @pytest.mark.e2e) as per CLAUDE.md line 725. Tests without markers will NOT run in CI.

Verification:

# Run example module tests
uv run pytest tests/aignostics/example/ -v

# Check coverage
uv run coverage report --include="src/aignostics/example/*"

# Verify all tests have markers
uv run pytest tests/aignostics/example/ --collect-only

📋 REQUIRED DOCUMENTATION UPDATES

4. ⚠️ Missing Module Documentation (Required)

Location: src/aignostics/example/CLAUDE.md (does not exist)

Issue: Root CLAUDE.md line 38 states: "Every module has detailed CLAUDE.md documentation." The example module violates this requirement.

Fix Required:

Create src/aignostics/example/CLAUDE.md following the pattern in src/aignostics/qupath/CLAUDE.md:

# CLAUDE.md - Example Module

## Module Overview

The example module is a learning template that demonstrates the Aignostics SDK's modulith architecture pattern.

**Purpose**: Educational template showing best practices for:
- Service layer implementation with BaseService
- CLI command registration with Typer
- GUI page integration with NiceGUI
- Module auto-discovery via dependency injection

**User Interfaces**:
- **Service**: Core business logic (get_example_data, process_example)
- **CLI**: Three commands (hello, data, process)
- **GUI**: Interactive page at /example route

## Architecture & Design Patterns

### Service Layer
- Inherits from `BaseService`
- Implements required `health()` and `info()` methods
- Provides static utility methods for example operations
- No external dependencies beyond utils

### CLI Layer
- Uses Typer for command registration
- Three demonstration commands showing different patterns:
  - `hello`: Positional argument with default
  - `data`: No arguments, calls service layer
  - `process`: Required argument, processes input

### GUI Layer
- PageBuilder pattern for auto-discovery
- Interactive UI demonstrating service integration
- Accessible at `/example` route
- Shows cards with example data and text processing

## Development Guidelines

### Adding Features
1. Add business logic to `_service.py`
2. Add CLI commands to `_cli.py`
3. Update GUI in `_gui/_page_example.py` if needed
4. Write tests in `tests/aignostics/example/`

### Testing Strategy
- Unit tests for service methods
- Integration tests for CLI commands
- GUI tests if nicegui available (optional)
- Maintain 85%+ coverage

## Usage Examples

### Programmatic Usage
\`\`\`python
from aignostics.example import Service

service = Service()
data = service.get_example_data()
processed = service.process_example("hello world")
\`\`\`

### CLI Usage
\`\`\`bash
# Say hello
uv run aignostics example hello
uv run aignostics example hello "Alice"

# Get example data
uv run aignostics example data

# Process text
uv run aignostics example process "sample text"
\`\`\`

### GUI Access
\`\`\`bash
# Launch GUI and navigate to /example
uv run aignostics gui
\`\`\`

## Dependencies
- **utils**: Logging, BaseService, Health
- **Optional**: nicegui (for GUI)

## Key Files
- `_service.py`: Core business logic (35 lines)
- `_cli.py`: CLI commands (96 lines)
- `_gui/_page_builder.py`: GUI registration (19 lines)
- `_gui/_page_example.py`: GUI page (77 lines)

5. ⚠️ Module Not Listed in Index (Required)

Location: src/aignostics/CLAUDE.md:7-18

Issue: The new example module is not listed in the module index table or module descriptions.

Fix Required:

  1. Add to module index table (line 7):
| Module | Core Purpose | CLI | GUI | Service |
|--------|-------------|-----|-----|---------|
| **example** | Learning template module ||||
| **platform** | Authentication & API client ||||
...
  1. Add to module descriptions section (after line 19):
### 📚 example

**Learning template demonstrating SDK modulith architecture**

- **Core Features**: Service layer pattern, CLI/GUI integration, dependency injection demo
- **CLI**: Three demonstration commands (`hello`, `data`, `process`)
- **GUI**: Interactive example page with service integration
- **Dependencies**: `utils` only
- **Purpose**: Educational reference for creating new modules
  1. Add to root CLAUDE.md module documentation index (around line 40):
* [src/aignostics/example/CLAUDE.md](src/aignostics/example/CLAUDE.md) - Example learning module

6. ⚠️ Commit Message Convention Violations (Required)

Location: All 6 commits in this PR

Current commits:

b53bd64 Merge branch 'main' into chore/pysdk-000-claude-doc-review
c6c039d refine claude-code-doc-review 2.
3ecf712 refine claude-code-doc-review.
b4fce36 refine claude-code-doc-review.
09b182c add claude code new workflow
b57e344 Integrate new example module into using the same UI that is build for Python SDK

Issue: None follow conventional commit format required by CLAUDE.md line 1123: type(scope): description

Valid types: feat, fix, docs, refactor, test, chore, ci, perf, build

Fix Required:

On merge, squash all commits with a proper conventional commit message:

feat(example): add learning template module with CLI, GUI, and doc review workflow

- Add example module demonstrating SDK modulith architecture
  - Service layer with health() and info() implementations
  - CLI with three demonstration commands (hello, data, process)
  - GUI page with interactive examples at /example route
- Add Claude Code workflow for requirements/spec review
- Add link to example module from application homepage
- Comprehensive inline documentation for educational purposes

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

✅ WHAT'S EXCELLENT

Code Quality: STRONG ✓

Static analysis components that ran successfully:

  • Ruff format: All files formatted correctly
  • Ruff lint: No linting violations (once imports fixed)
  • Architecture: Clean separation of CLI/GUI/Service layers

Architecture Compliance: GOOD ✓

The example module correctly follows modulith patterns:

  • ✅ Service layer pattern (once abstract methods added)
  • ✅ CLI uses Typer with proper command registration
  • ✅ GUI uses PageBuilder pattern for auto-discovery
  • ✅ Conditional nicegui import (__init__.py:14)
  • ✅ No circular dependencies
  • ✅ CLI and GUI both depend only on Service layer (correct separation)
  • ✅ Uses relative imports within module (from ._service import Service)

Documentation Quality: GOLD STANDARD ✓

The CLI inline documentation (_cli.py:1-96) is exemplary:

  • Lines 1-12: Module-level docstring with concrete usage examples
  • Lines 32-52: Detailed explanation of Typer patterns with architectural reasoning
  • Lines 54-74: Service layer integration patterns documented
  • Lines 76-96: Real-world usage demonstrations

This is best-in-class educational code - perfect for onboarding new developers. Once the technical issues are resolved, this will be an excellent learning resource.

Workflow Implementation: EXCELLENT ✓

New Claude Code workflow (.github/workflows/claude-code-doc-review.yml):

  • ✅ Correct trigger: pull_request: [opened, synchronize, reopened]
  • ✅ Proper permissions: contents: read, pull-requests: write
  • ✅ Uses official anthropics/claude-code-action@v1
  • ✅ Clear, focused prompt for requirements/spec analysis
  • ✅ Appropriate model: claude-sonnet-4-5-20250929
  • ✅ Restricted tool access: Read,Glob,Grep,Bash(git:*)
  • ✅ Well-formatted output template

This workflow is well-designed and follows GitHub Actions best practices.

GUI Integration: CLEAN ✓

Application homepage changes (src/aignostics/application/_gui/_page_index.py:85-88):

  • ✅ Clear call-to-action linking to /example
  • ✅ Explains purpose of example module
  • ✅ Conditional on nicegui availability
  • ✅ Consistent styling with existing UI

📝 REQUIRED ACTIONS SUMMARY

PRIORITY 1: Fix CI Blockers (30 minutes) ⚡

  1. Fix import errors (5 min):

    • Replace from aignostics.utils import get_logger with from loguru import logger in both _service.py and _cli.py
    • Add Health import to _service.py
  2. Add abstract methods (10 min):

    • Add health() method to Service class
    • Add info() method to Service class
  3. Verify CI unblocked (5 min):

    python -c "from aignostics.example import Service; s = Service(); print(s.health())"
    uv run pytest --collect-only 2>&1 | grep -i error

PRIORITY 2: Add Test Coverage (2-3 hours)

  1. Create test suite:
    • Create tests/aignostics/example/ directory structure
    • Add service_test.py with unit tests (use examples above)
    • Add cli_test.py with integration tests
    • CRITICAL: All tests must have markers (@pytest.mark.unit, etc.)
    • Verify coverage: uv run pytest tests/aignostics/example/ -v --cov=src/aignostics/example

PRIORITY 3: Add Documentation (30-45 minutes)

  1. Add module documentation:
    • Create src/aignostics/example/CLAUDE.md (use template above)
    • Update src/aignostics/CLAUDE.md module index table
    • Add module to descriptions section
    • Add to root CLAUDE.md module documentation list

PRIORITY 4: Fix Commit Message (5 minutes)

  1. Squash commits on merge with proper conventional commit format (use suggested message above)

🔧 VERIFICATION COMMANDS

After implementing fixes, run these commands to verify:

# 1. Verify Service can be instantiated
python -c "from aignostics.example import Service; s = Service(); print(s.health())"

# 2. Verify no import errors in tests
uv run pytest --collect-only 2>&1 | grep -i "import"

# 3. Run example module tests
uv run pytest tests/aignostics/example/ -v

# 4. Check coverage
uv run pytest tests/aignostics/example/ --cov=src/aignostics/example --cov-report=term-missing

# 5. Verify all tests have markers (should collect tests, not error)
uv run pytest tests/aignostics/example/ --collect-only -v

# 6. Run full test suite
make test_unit

# 7. Verify all linting passes
make lint

# 8. Test CLI commands work
uv run aignostics example hello
uv run aignostics example data
uv run aignostics example process "test"

💬 FINAL RECOMMENDATION

Status: ⛔ DO NOT MERGE - Critical blocking issues must be resolved

Estimated Fix Time:

  • ⚡ Critical fixes (imports + abstract methods): 30 minutes
  • 📝 Full PR completion (tests + docs): ~3-4 hours total

Priority Order:

  1. Fix import errors (unblock CI)
  2. Add abstract methods (complete service contract)
  3. Create test suite (meet coverage requirements)
  4. Add CLAUDE.md documentation
  5. Update module indexes
  6. Squash commits with proper message on merge

This is medical device software under FDA/MDR regulation. The high bar for testing and documentation is not optional - it's a compliance requirement.

The good news: The architecture is solid, the inline documentation is excellent, and the workflow implementation is professional. These issues are straightforward to fix. Once resolved, this will be a valuable addition to the SDK! 💪


Questions or need clarification on any issue? See:

  • BaseService pattern: src/aignostics/utils/_service.py:14-50
  • Working service example: src/aignostics/qupath/_service.py:24-59
  • Logger usage pattern: src/aignostics/qupath/_service.py:24
  • Test patterns: tests/aignostics/platform/ for examples
  • Commit format: Root CLAUDE.md lines 1121-1145
  • Module documentation template: src/aignostics/qupath/CLAUDE.md

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github-actions bot commented Dec 3, 2025

Claude finished @muhabalwan-aginx's task —— View job


Comprehensive PR Review - PR #252

I've conducted a thorough review of this PR against the Aignostics Python SDK standards as documented in CLAUDE.md. This PR adds a new example module as a learning template, along with a Claude Code documentation review workflow.


🚨 CRITICAL BLOCKING ISSUES

These issues MUST be resolved before merge. They are causing CI failures and violating core architecture requirements.

1. ❌ Import Error: get_logger Does Not Exist (BLOCKING)

Locations:

  • src/aignostics/example/_service.py:3
  • src/aignostics/example/_cli.py:18
  • src/aignostics/example/_gui/_page_example.py:7

Issue: The example module imports get_logger from aignostics.utils, but this function does not exist in the codebase. The SDK uses loguru.logger directly.

Evidence:

$ grep -r "get_logger" src/aignostics/utils/
# Returns no matches

Current Code:

from aignostics.utils import BaseService, get_logger
logger = get_logger(__name__)

Should Be:

from loguru import logger
from aignostics.utils import BaseService

Reference: src/aignostics/qupath/_service.py:24 shows the correct pattern:

from loguru import logger

Fix Required:

  1. In _service.py line 3: Replace from aignostics.utils import BaseService, get_logger with from loguru import logger and from aignostics.utils import BaseService on separate lines
  2. In _cli.py line 18: Replace from aignostics.utils import console, get_logger with from loguru import logger and from aignostics.utils import console
  3. In _gui/_page_example.py line 7: Replace from aignostics.utils import get_logger with from loguru import logger

2. ❌ Missing Abstract Method Implementations (BLOCKING)

Location: src/aignostics/example/_service.py:8-35

Issue: The Service class inherits from BaseService but does not implement the two required abstract methods: health() and info().

From BaseService (src/aignostics/utils/_service.py:33-50):

@abstractmethod
def health(self) -> Health:
    """Get health of this service. Override in subclass."""

@abstractmethod
def info(self, mask_secrets: bool = True) -> dict[str, Any]:
    """Get info of this service. Override in subclass."""

Fix Required:

Add these methods to _service.py (after line 14, before line 16). Also update imports to include Health:

from loguru import logger

from aignostics.utils import BaseService, Health


class Service(BaseService):
    """Example service for demonstration purposes."""

    def __init__(self) -> None:
        """Initialize the example service."""
        super().__init__()
        logger.info("Example service initialized")

    def health(self) -> Health:
        """Check service health.
        
        Returns:
            Health: Service health status.
        """
        return Health(status=Health.Code.UP, details={"module": "example"})

    def info(self, mask_secrets: bool = True) -> dict[str, str]:
        """Get service information.
        
        Args:
            mask_secrets: Whether to mask sensitive information.
            
        Returns:
            dict[str, str]: Service information.
        """
        return {
            "module": "example",
            "version": "1.0.0",
            "purpose": "Learning template for SDK architecture",
            "description": "Demonstrates modulith pattern with Service + CLI + GUI",
        }

    @staticmethod
    def get_example_data() -> dict[str, str]:
        # ... existing code

Reference: See src/aignostics/qupath/_service.py:211-238 for a working implementation.

Verification:

python -c "from aignostics.example import Service; s = Service(); print(s.health())"

3. ❌ Zero Test Coverage (BLOCKING)

Location: tests/aignostics/example/ (does not exist)

Issue: The new example module has ZERO tests. This violates:

  • 85% minimum coverage requirement (CLAUDE.md:77)
  • SonarQube report shows: "0.0% Coverage on New Code (required ≥ 80%)"

Impact:

  • Medical device software requires comprehensive testing
  • Violates FDA/MDR compliance requirements
  • No validation of service, CLI, or GUI functionality

Fix Required:

Create test suite with this structure:

tests/aignostics/example/
├── __init__.py          # Empty file
├── service_test.py      # Service layer tests
└── cli_test.py          # CLI command tests

Example Implementation (tests/aignostics/example/service_test.py):

"""Tests for example module service."""

import pytest

from aignostics.example import Service
from aignostics.utils import Health


@pytest.mark.unit
def test_service_initialization(record_property) -> None:
    """Test example service can be initialized."""
    record_property("tested-item-id", "SPEC-EXAMPLE-SERVICE")
    service = Service()
    assert service is not None
    assert service.key() == "example"


@pytest.mark.unit
def test_service_health(record_property) -> None:
    """Test service health check returns UP status."""
    record_property("tested-item-id", "SPEC-EXAMPLE-SERVICE")
    service = Service()
    health = service.health()
    assert isinstance(health, Health)
    assert health.status == Health.Code.UP
    assert health.details["module"] == "example"


@pytest.mark.unit
def test_service_info(record_property) -> None:
    """Test service info returns expected structure."""
    record_property("tested-item-id", "SPEC-EXAMPLE-SERVICE")
    service = Service()
    info = service.info()
    assert isinstance(info, dict)
    assert "module" in info
    assert "version" in info
    assert info["module"] == "example"


@pytest.mark.unit
def test_get_example_data(record_property) -> None:
    """Test get_example_data returns expected structure."""
    record_property("tested-item-id", "SPEC-EXAMPLE-SERVICE")
    data = Service.get_example_data()
    assert isinstance(data, dict)
    assert "message" in data
    assert "status" in data
    assert data["status"] == "active"


@pytest.mark.unit
def test_process_example(record_property) -> None:
    """Test process_example text transformation."""
    record_property("tested-item-id", "SPEC-EXAMPLE-SERVICE")
    result = Service.process_example("test input")
    assert result == "Processed: test input"

CLI Tests (tests/aignostics/example/cli_test.py):

"""Tests for example module CLI commands."""

import pytest
from typer.testing import CliRunner

from aignostics.example import cli

runner = CliRunner()


@pytest.mark.integration
def test_cli_hello_default(record_property) -> None:
    """Test hello command with default argument."""
    record_property("tested-item-id", "SPEC-EXAMPLE-CLI")
    result = runner.invoke(cli, ["hello"])
    assert result.exit_code == 0
    assert "World" in result.stdout


@pytest.mark.integration
def test_cli_hello_custom_name(record_property) -> None:
    """Test hello command with custom name."""
    record_property("tested-item-id", "SPEC-EXAMPLE-CLI")
    result = runner.invoke(cli, ["hello", "Alice"])
    assert result.exit_code == 0
    assert "Alice" in result.stdout


@pytest.mark.integration
def test_cli_data(record_property) -> None:
    """Test data command."""
    record_property("tested-item-id", "SPEC-EXAMPLE-CLI")
    result = runner.invoke(cli, ["data"])
    assert result.exit_code == 0
    assert "Example Data" in result.stdout


@pytest.mark.integration
def test_cli_process(record_property) -> None:
    """Test process command."""
    record_property("tested-item-id", "SPEC-EXAMPLE-CLI")
    result = runner.invoke(cli, ["process", "test text"])
    assert result.exit_code == 0
    assert "Processed: test text" in result.stdout

CRITICAL: Every test MUST have a marker (@pytest.mark.unit, @pytest.mark.integration, or @pytest.mark.e2e). Tests without markers will NOT run in CI because the pipeline explicitly filters by markers.

Verification:

uv run pytest tests/aignostics/example/ -v
uv run coverage report --include="src/aignostics/example/*"

📋 REQUIRED DOCUMENTATION UPDATES

4. ⚠️ Missing Module CLAUDE.md (Required)

Location: src/aignostics/example/CLAUDE.md (does not exist)

Issue: Root CLAUDE.md line 39 states: "Every module has detailed CLAUDE.md documentation." The example module violates this requirement.

Fix Required:

Create src/aignostics/example/CLAUDE.md with this content:

# CLAUDE.md - Example Module

## Module Overview

The example module is a learning template that demonstrates the Aignostics SDK's modulith architecture pattern.

**Purpose**: Educational template showing best practices for:
- Service layer implementation with BaseService
- CLI command registration with Typer
- GUI page integration with NiceGUI
- Module auto-discovery via dependency injection

**User Interfaces**:
- **Service**: Core business logic (get_example_data, process_example)
- **CLI**: Three commands (hello, data, process)
- **GUI**: Interactive page at /example route

## Architecture & Design Patterns

### Service Layer
- Inherits from `BaseService`
- Implements required `health()` and `info()` methods
- Provides static utility methods for example operations
- No external dependencies beyond utils

### CLI Layer
- Uses Typer for command registration
- Three demonstration commands:
  - `hello`: Positional argument with default value
  - `data`: No arguments, calls service layer
  - `process`: Required argument, processes input text

### GUI Layer
- PageBuilder pattern for auto-discovery
- Interactive UI at `/example` route
- Demonstrates service integration patterns
- Shows cards with example data and text processing

## Usage Examples

### Programmatic Usage
\`\`\`python
from aignostics.example import Service

service = Service()
data = service.get_example_data()
processed = service.process_example("hello world")
\`\`\`

### CLI Usage
\`\`\`bash
# Say hello
uv run aignostics example hello
uv run aignostics example hello "Alice"

# Get example data
uv run aignostics example data

# Process text
uv run aignostics example process "sample text"
\`\`\`

### GUI Access
\`\`\`bash
# Launch GUI and navigate to /example
uv run aignostics gui
\`\`\`

## Dependencies
- **utils**: BaseService, Health, console, logger
- **Optional**: nicegui (for GUI)

## Testing Strategy
- Unit tests for service methods
- Integration tests for CLI commands
- Maintain 85%+ coverage

## Key Files
- `_service.py`: Core business logic (35 lines)
- `_cli.py`: CLI commands (96 lines)
- `_gui/_page_builder.py`: GUI registration (19 lines)
- `_gui/_page_example.py`: GUI page (77 lines)

5. ⚠️ Module Not Listed in Index (Required)

Location: src/aignostics/CLAUDE.md

Issue: The new example module is not listed in the module index table or module descriptions.

Fix Required:

1. Add to module index table (line 7):

| Module | Core Purpose | CLI | GUI | Service |
|--------|-------------|-----|-----|---------|
| **example** | Learning template module ||||
| **platform** | Authentication & API client ||||
...

2. Add module description section (after line 19, before platform section):

### 📚 example

**Learning template demonstrating SDK modulith architecture**

- **Core Features**: Service layer pattern, CLI/GUI integration, dependency injection demo
- **CLI**: Three demonstration commands (`hello`, `data`, `process`)
- **GUI**: Interactive example page with service integration at `/example` route
- **Dependencies**: `utils` only
- **Purpose**: Educational reference for creating new modules following SDK patterns

3. Add to root CLAUDE.md module documentation index (line ~40):

* [src/aignostics/example/CLAUDE.md](src/aignostics/example/CLAUDE.md) - Example learning module

6. ⚠️ Commit Message Convention Violations (Required)

Location: All commits in this branch

Relevant commits from this PR:

c6c039d refine claude-code-doc-review 2.
3ecf712 refine claude-code-doc-review.
b4fce36 refine claude-code-doc-review.
09b182c add claude code new workflow
b57e344 Integrate new example module into using the same UI that is build for Python SDK

Issue: None follow the conventional commit format required by CLAUDE.md line 1123: type(scope): description

Valid types: feat, fix, docs, refactor, test, chore, ci, perf, build

Fix Required:

On merge, squash all commits with a proper conventional commit message:

feat(example): add learning template module with CLI, GUI, and doc review workflow

- Add example module demonstrating SDK modulith architecture
  - Service layer with health() and info() implementations
  - CLI with three demonstration commands (hello, data, process)
  - GUI page with interactive examples at /example route
- Add Claude Code workflow for requirements/spec review
- Add link to example module from application homepage
- Comprehensive inline documentation for educational purposes

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

✅ WHAT'S EXCELLENT

Despite the blocking issues, there are several outstanding aspects of this PR:

Code Quality: STRONG ✓

The code that exists shows good quality:

  • ✅ Clean architecture with proper separation of concerns (CLI/GUI/Service)
  • ✅ No circular dependencies detected
  • ✅ Conditional nicegui import pattern correct (__init__.py:14)
  • ✅ Proper use of relative imports within module

Documentation: GOLD STANDARD ✓

The inline documentation in _cli.py is exemplary:

  • Lines 1-12: Module-level docstring with concrete usage examples
  • Lines 32-52: Detailed explanation of Typer patterns with architectural reasoning
  • Lines 54-74: Service layer integration patterns documented
  • Lines 76-96: Real-world usage demonstrations

This is best-in-class educational code - once the technical issues are resolved, this will be an excellent learning resource for SDK contributors.

Architecture Compliance: GOOD ✓

The module correctly follows modulith patterns:

  • ✅ Service layer inherits from BaseService (once abstract methods added)
  • ✅ CLI uses Typer with proper command registration pattern
  • ✅ GUI uses PageBuilder pattern for auto-discovery
  • ✅ CLI and GUI both depend only on Service layer (correct separation)
  • ✅ No module coupling violations

Workflow Implementation: EXCELLENT ✓

New Claude Code workflow (.github/workflows/claude-code-doc-review.yml):

  • ✅ Correct trigger: pull_request: [opened, synchronize, reopened]
  • ✅ Proper permissions: contents: read, pull-requests: write
  • ✅ Uses official anthropics/claude-code-action@v1
  • ✅ Clear, focused prompt for requirements/spec analysis
  • ✅ Appropriate model: claude-sonnet-4-5-20250929
  • ✅ Restricted tool access: Read,Glob,Grep,Bash(git:*)
  • ✅ Well-formatted output template

This workflow is well-designed and follows GitHub Actions best practices.

GUI Integration: CLEAN ✓

Application homepage changes (src/aignostics/application/_gui/_page_index.py:85-88):

  • ✅ Clear call-to-action linking to /example
  • ✅ Explains purpose: "understand the SDK architecture"
  • ✅ Conditional on nicegui availability
  • ✅ Consistent styling with existing UI

📝 ACTION PLAN

PRIORITY 1: Fix Critical Blockers (30-45 minutes) ⚡

1. Fix import errors (10 min):

  • Replace get_logger imports with from loguru import logger in:
    • src/aignostics/example/_service.py:3
    • src/aignostics/example/_cli.py:18
    • src/aignostics/example/_gui/_page_example.py:7
  • Add Health import to _service.py

2. Add abstract methods (10 min):

  • Add health() method to Service class (see fix above)
  • Add info() method to Service class (see fix above)

3. Verify fixes work (5 min):

python -c "from aignostics.example import Service; s = Service(); print(s.health())"
uv run pytest --collect-only 2>&1 | grep -i error

PRIORITY 2: Add Test Coverage (2-3 hours)

4. Create comprehensive test suite:

  • Create tests/aignostics/example/ directory
  • Add __init__.py (empty file)
  • Add service_test.py with 5 unit tests (see examples above)
  • Add cli_test.py with 4 integration tests (see examples above)
  • CRITICAL: All tests must have markers
  • Verify: uv run pytest tests/aignostics/example/ -v --cov=src/aignostics/example

PRIORITY 3: Add Documentation (30-45 minutes)

5. Create module documentation:

  • Create src/aignostics/example/CLAUDE.md (use template above)
  • Update src/aignostics/CLAUDE.md:
    • Add to module index table
    • Add module description section
  • Add to root CLAUDE.md module list (line ~40)

PRIORITY 4: Fix Commit Message (5 minutes)

6. Squash commits on merge with proper conventional commit format (use suggested message above)


🔧 VERIFICATION COMMANDS

After implementing all fixes, run these commands to verify:

# 1. Verify imports work
python -c "from aignostics.example import Service; s = Service(); print('OK')"

# 2. Verify abstract methods implemented
python -c "from aignostics.example import Service; s = Service(); print(s.health()); print(s.info())"

# 3. Run example module tests
uv run pytest tests/aignostics/example/ -v

# 4. Check coverage for example module only
uv run pytest tests/aignostics/example/ --cov=src/aignostics/example --cov-report=term-missing

# 5. Verify all tests have markers
uv run pytest tests/aignostics/example/ --collect-only -v

# 6. Test CLI commands work
uv run aignostics example hello
uv run aignostics example data
uv run aignostics example process "test"

# 7. Run full unit test suite (should pass)
make test_unit

# 8. Verify linting passes (after import fixes)
make lint

💬 FINAL RECOMMENDATION

Status: ⛔ DO NOT MERGE - Critical blocking issues must be resolved

Estimated Fix Time:

  • ⚡ Critical blockers (imports + abstract methods): 30-45 minutes
  • 📝 Full PR completion (tests + docs): ~4-5 hours total

Priority Order:

  1. Fix import errors (unblock module loading)
  2. Add abstract methods (complete BaseService contract)
  3. Create test suite (meet 85% coverage requirement)
  4. Add CLAUDE.md documentation
  5. Update module indexes in src/aignostics/CLAUDE.md
  6. Squash commits with proper conventional commit message

Context: This is medical device software under FDA/MDR regulation. The high bar for testing and documentation is not optional - it's a compliance requirement mandated by regulatory bodies.

The good news: The architecture is solid, the inline documentation is exemplary, and the workflow implementation is professional. These are straightforward issues to fix. Once resolved, this will be a valuable educational resource for the SDK! 💪


📚 REFERENCES

For implementing fixes, refer to:

  • BaseService pattern: src/aignostics/utils/_service.py:14-50
  • Working service example: src/aignostics/qupath/_service.py:211-238
  • Logger usage: src/aignostics/qupath/_service.py:24
  • Test patterns: tests/aignostics/platform/ for examples
  • Test markers: .github/CLAUDE.md:100-150
  • Commit format: Root CLAUDE.md:1121-1145
  • Module docs template: src/aignostics/qupath/CLAUDE.md

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sonarqubecloud bot commented Dec 7, 2025

Quality Gate Failed Quality Gate failed

Failed conditions
1 Security Hotspot
0.0% Coverage on New Code (required ≥ 80%)

See analysis details on SonarQube Cloud

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