Colton's Fixes

.gitignore

@@ -2,7 +2,8 @@
 __pycache__/
 *.py[cod]
 *$py.class
-.cache_status.yaml
+# Cache status file when initialized
+# Keep the initial false version in repo, ignore when it becomes true
 .DS_STORE
 
 # C extensions

.pre-commit-config.yaml

@@ -1,24 +1,34 @@
+exclude: 'pyreason/\.cache_status\.yaml'
 repos:
   - repo: local
     hooks:
-      # --- Unit tests ---
-      - id: pytest-unit-with-coverage
-        name: Run unit tests with coverage and open report
-        entry: bash -c 'pytest tests/unit/disable_jit --cov pyreason   --cov-report=html  && ( (command -v xdg-open >/dev/null && xdg-open htmlcov/index.html) || (command -v open >/dev/null && open htmlcov/index.html) || (command -v start >/dev/null && start htmlcov/index.html) )'
+      # --- COMMIT STAGE: Fast unit tests only ---
+      - id: pytest-unit-no-jit
+        name: Run JIT-disabled unit tests 
+        entry: .venv/bin/python -m pytest tests/unit/disable_jit -m "not slow" --tb=short -q
         language: system
         pass_filenames: false
+        stages: [pre-commit]
 
       - id: pytest-unit-jit
-        name: Run JIT-enabled unit tests
-        entry: bash -c 'pytest tests/unit/dont_disable_jit'
+        name: Run JIT-enabled unit tests 
+        entry: .venv/bin/python -m pytest tests/unit/dont_disable_jit -m "not slow" --tb=short -q
         language: system
         pass_filenames: false
+        stages: [pre-commit]
 
-      # --- Functional tests ---
-      - id: pytest-functional
-        name: Run functional tests
-        entry: bash -c 'pytest tests/functional'
+      # --- PUSH STAGE: Complete test suite ---
+
+      - id: pytest-unit-api
+        name: Run pyreason api unit tests 
+        entry: .venv/bin/python -m pytest tests/unit/api_tests --tb=short -q
+        language: system
+        pass_filenames: false
+        stages: [pre-push]
+
+      - id: pytest-functional-complete
+        name: Run functional test suite
+        entry: .venv/bin/python -m pytest tests/functional/ --tb=short
         language: system
         pass_filenames: false
-        # Only run manually, not on every commit
         stages: [pre-push]

Makefile

@@ -0,0 +1,179 @@
+# PyReason Test Suite Makefile
+# Provides convenient shortcuts for running different test configurations
+
+.PHONY: help test test-all test-fast test-api test-jit test-no-jit test-consistency \
+        test-parallel test-no-coverage coverage-report coverage-html coverage-xml \
+        clean clean-coverage clean-reports install-deps lint check-deps
+
+# Default target
+.DEFAULT_GOAL := help
+
+# Variables
+PYTHON := python3
+RUN_TESTS := $(PYTHON) run_tests.py
+PIP := $(PYTHON) -m pip
+
+# Auto-detect python if python3 doesn't work
+PYTHON_CHECK := $(shell $(PYTHON) --version 2>/dev/null || echo "failed")
+ifeq ($(PYTHON_CHECK),failed)
+    PYTHON := python
+    RUN_TESTS := $(PYTHON) run_tests.py
+    PIP := $(PYTHON) -m pip
+endif
+
+# Colors for output
+BLUE := \033[34m
+GREEN := \033[32m
+YELLOW := \033[33m
+RED := \033[31m
+BOLD := \033[1m
+RESET := \033[0m
+
+# Help target
+help: ## Show this help message
+	@echo "$(BOLD)PyReason Test Suite$(RESET)"
+	@echo "$(BLUE)Available targets:$(RESET)"
+	@echo ""
+	@awk 'BEGIN {FS = ":.*?## "} /^[a-zA-Z_-]+:.*?## / {printf "  $(GREEN)%-20s$(RESET) %s\n", $$1, $$2}' $(MAKEFILE_LIST)
+	@echo ""
+	@echo "$(BLUE)Examples:$(RESET)"
+	@echo "  make test                 # Run all test suites with coverage and open report"
+	@echo "  make test-fast            # Run only fast test suites"
+	@echo "  make test-api             # Run only API tests"
+	@echo "  make test-parallel        # Run tests in parallel where possible"
+	@echo "  make coverage-html        # Generate HTML coverage report"
+
+# Main test targets
+test: ## Run all test suites with coverage and open report
+	@echo "$(BOLD)$(BLUE)Running all test suites...$(RESET)"
+	$(RUN_TESTS)
+	@echo "$(BOLD)$(GREEN)Opening coverage report in browser...$(RESET)"
+	@if [ -f test_reports/htmlcov/index.html ]; then \
+		open test_reports/htmlcov/index.html 2>/dev/null || \
+		xdg-open test_reports/htmlcov/index.html 2>/dev/null || \
+		echo "$(GREEN)HTML report available at: test_reports/htmlcov/index.html$(RESET)"; \
+	else \
+		echo "$(YELLOW)No HTML coverage report found$(RESET)"; \
+	fi
+
+test-all: test ## Alias for 'test' target
+
+test-only: ## Run all test suites with coverage (no browser)
+	@echo "$(BOLD)$(BLUE)Running all test suites...$(RESET)"
+	$(RUN_TESTS)
+
+test-fast: ## Run only fast test suites (api_tests, dont_disable_jit)
+	@echo "$(BOLD)$(BLUE)Running fast test suites...$(RESET)"
+	$(RUN_TESTS) --fast
+
+test-parallel: ## Run test suites in parallel where possible
+	@echo "$(BOLD)$(BLUE)Running test suites in parallel...$(RESET)"
+	$(RUN_TESTS) --parallel
+
+test-no-coverage: ## Run all tests without coverage collection
+	@echo "$(BOLD)$(BLUE)Running tests without coverage...$(RESET)"
+	$(RUN_TESTS) --no-coverage
+
+# Individual test suite targets
+test-api: ## Run only API tests (tests/unit/api_tests)
+	@echo "$(BOLD)$(BLUE)Running API tests...$(RESET)"
+	$(RUN_TESTS) --suite api_tests
+
+test-jit: ## Run only JIT-disabled tests (tests/unit/disable_jit)
+	@echo "$(BOLD)$(BLUE)Running JIT-disabled tests...$(RESET)"
+	$(RUN_TESTS) --suite don_disable_jit
+
+test-no-jit: ## Run only JIT-enabled tests (tests/unit/dont_disable_jit)
+	@echo "$(BOLD)$(BLUE)Running JIT-enabled tests...$(RESET)"
+	$(RUN_TESTS) --suite disable_jit
+
+test-consistency: ## Run numba consistency tests
+	@echo "$(BOLD)$(BLUE)Running consistency tests...$(RESET)"
+	$(PYTHON) -m pytest tests/unit/dont_disable_jit/test_numba_consistency.py -v
+
+test-functional: ## Run functional/end-to-end tests
+	@echo "$(BOLD)$(BLUE)Running functional tests...$(RESET)"
+	$(RUN_TESTS) --suite functional
+
+
+test-all-suites: ## Run all test suites including functional tests
+	@echo "$(BOLD)$(BLUE)Running all test suites including functional...$(RESET)"
+	$(RUN_TESTS)
+
+# Coverage targets
+coverage-report: ## Show coverage report in terminal
+	@echo "$(BOLD)$(BLUE)Generating coverage report...$(RESET)"
+	@if [ -f test_reports/coverage.xml ]; then \
+		coverage report --rcfile=test_reports/.coveragerc 2>/dev/null || \
+		echo "$(YELLOW)Run 'make test' first to generate coverage data$(RESET)"; \
+	else \
+		echo "$(YELLOW)No coverage data found. Run 'make test' first$(RESET)"; \
+	fi
+
+coverage-html: ## Generate HTML coverage report
+	@echo "$(BOLD)$(BLUE)Opening HTML coverage report...$(RESET)"
+	@if [ -f test_reports/htmlcov/index.html ]; then \
+		open test_reports/htmlcov/index.html 2>/dev/null || \
+		xdg-open test_reports/htmlcov/index.html 2>/dev/null || \
+		echo "$(GREEN)HTML report available at: test_reports/htmlcov/index.html$(RESET)"; \
+	else \
+		echo "$(YELLOW)No HTML coverage report found. Run 'make test' first$(RESET)"; \
+	fi
+
+coverage-xml: ## Show path to XML coverage report
+	@echo "$(BOLD)$(BLUE)XML Coverage Report:$(RESET)"
+	@if [ -f test_reports/coverage.xml ]; then \
+		echo "$(GREEN)XML report available at: test_reports/coverage.xml$(RESET)"; \
+	else \
+		echo "$(YELLOW)No XML coverage report found. Run 'make test' first$(RESET)"; \
+	fi
+
+# Development targets
+lint: ## Run linting checks
+	@echo "$(BOLD)$(BLUE)Running linting checks...$(RESET)"
+	@echo "$(YELLOW)Note: Add your preferred linter commands here$(RESET)"
+	# Example: flake8 pyreason tests
+	# Example: black --check pyreason tests
+	# Example: mypy pyreason
+
+check-deps: ## Check if required dependencies are installed
+	@echo "$(BOLD)$(BLUE)Checking dependencies...$(RESET)"
+	@$(PYTHON) -c "import pytest; print('✓ pytest installed')" 2>/dev/null || \
+		(echo "$(RED)✗ pytest not installed$(RESET)" && exit 1)
+	@$(PYTHON) -c "import coverage; print('✓ coverage installed')" 2>/dev/null || \
+		(echo "$(RED)✗ coverage not installed$(RESET)" && exit 1)
+	@$(PYTHON) -c "import pyreason; print('✓ pyreason importable')" 2>/dev/null || \
+		(echo "$(YELLOW)⚠ pyreason not importable (may need installation)$(RESET)")
+	@echo "$(GREEN)Dependencies check complete$(RESET)"
+
+install-deps: ## Install testing dependencies
+	@echo "$(BOLD)$(BLUE)Installing testing dependencies...$(RESET)"
+	$(PIP) install pytest coverage pytest-cov pytest-timeout
+	@echo "$(GREEN)Testing dependencies installed$(RESET)"
+
+# Cleanup targets
+clean: clean-coverage clean-reports ## Clean all generated files
+	@echo "$(BOLD)$(BLUE)Cleaning all generated files...$(RESET)"
+	@find . -name "*.pyc" -delete 2>/dev/null || true
+	@find . -name "__pycache__" -type d -exec rm -rf {} + 2>/dev/null || true
+	@find . -name ".pytest_cache" -type d -exec rm -rf {} + 2>/dev/null || true
+	@echo "$(GREEN)Cleanup complete$(RESET)"
+
+clean-coverage: ## Clean coverage files
+	@echo "$(BOLD)$(BLUE)Cleaning coverage files...$(RESET)"
+	@rm -f .coverage .coverage.* 2>/dev/null || true
+	@rm -rf test_reports/htmlcov 2>/dev/null || true
+	@rm -f test_reports/coverage.xml 2>/dev/null || true
+
+clean-reports: ## Clean test report files
+	@echo "$(BOLD)$(BLUE)Cleaning test reports...$(RESET)"
+	@rm -rf test_reports 2>/dev/null || true
+
+# Version and info
+info: ## Show project and tool versions
+	@echo "$(BOLD)$(BLUE)Project Information:$(RESET)"
+	@echo "Python: $$($(PYTHON) --version)"
+	@echo "Pytest: $$($(PYTHON) -c 'import pytest; print(pytest.__version__)' 2>/dev/null || echo 'Not installed')"
+	@echo "Coverage: $$($(PYTHON) -c 'import coverage; print(coverage.__version__)' 2>/dev/null || echo 'Not installed')"
+	@echo "Working Directory: $$(pwd)"
+	@echo "Test Runner: $$(ls -la run_tests.py 2>/dev/null || echo 'Not found')"

contributing.md

@@ -30,18 +30,118 @@ this command to view linting results:
 ruff check .
 ```
 
-## Running Tests Manually
+## Running Tests
 
-The automated hooks cover most scenarios, but you can invoke the test suites
-directly:
+### Enhanced Test Suite
+
+PyReason uses a unified test runner that handles multiple test configurations automatically. The test suite is organized into four directories:
+
+- **`tests/unit/api_tests/`** - Tests for main pyreason.py API functions (JIT enabled, real pyreason)
+- **`tests/unit/disable_jit/`** - Tests for internal interpretation logic (JIT disabled, stubbed environment)
+- **`tests/unit/dont_disable_jit/`** - Tests for components that benefit from JIT (JIT enabled, lightweight stubs)
+- **`tests/functional/`** - End-to-end functional tests (JIT enabled, real pyreason, longer running)
+
+### Quick Start
+
+```bash
+# Install testing dependencies
+make install-deps
+
+# Run all test suites with unified coverage
+make test
+
+# Run only fast test suites
+make test-fast
+
+# Generate HTML coverage report
+make coverage-html
+```
+
+### Individual Test Suites
+
+```bash
+# API tests (real pyreason, JIT enabled)
+make test-api
+
+# JIT disabled tests (stubbed environment)
+make test-jit
+
+# JIT enabled tests (lightweight stubs)
+make test-no-jit
+
+# Consistency tests
+make test-consistency
+
+# Functional/end-to-end tests
+make test-functional
+```
+
+### Advanced Options
+
+```bash
+# Run with parallel execution where possible
+make test-parallel
+
+# Run without coverage collection (faster)
+python run_tests.py --no-coverage
+
+# Run specific suites
+python run_tests.py --suite api_tests --suite dont_disable_jit
+
+# Run functional tests (multiple options)
+make test-functional          # Using test runner
+pytest tests/functional       # Traditional approach
+```
+
+### Traditional Pytest (Per Suite)
+
+You can still run pytest directly on individual directories:
 
 ```bash
-pytest tests/unit
+# API tests
+pytest tests/unit/api_tests/ -v
+
+# JIT disabled tests
+NUMBA_DISABLE_JIT=1 pytest tests/unit/disable_jit/ -v
+
+# JIT enabled tests
+pytest tests/unit/dont_disable_jit/ -v
+
+# Functional tests
+pytest tests/functional/ -v
 ```
 
+### Coverage Reports
+
+The test runner automatically combines coverage from all suites:
+
+- **Terminal Report:** Summary shown after test execution
+- **HTML Report:** `test_reports/htmlcov/index.html`
+- **XML Report:** `test_reports/coverage.xml`
+
+### Troubleshooting
+
 ```bash
-pytest tests/functional
+# Check system status and dependencies
+make info
+make check-deps
+
+# Validate test runner setup
+python test_runner_validation.py
+
+# Test pytest configuration
+python -c "import configparser; c=configparser.ConfigParser(); c.read('pytest.ini'); print('pytest.ini is valid')"
+
+# Run a single functional test
+pytest tests/functional/test_hello_world.py -v
+
+# Clean up generated files
+make clean
 ```
 
-Running tests locally before committing or pushing helps catch issues early and
-speeds up code review.
+**Common Issues:**
+- **Functional tests fail with warnings**: The pytest.ini has been updated to ignore expected warnings from numba and networkx
+- **Tests time out**: Functional tests have longer timeouts (600s) and global timeout is disabled
+- **Import errors**: Ensure pytest and dependencies are installed with `make install-deps`
+
+Running tests locally before committing or pushing helps catch issues early and speeds up code review. The unified test runner ensures consistent behavior across different development environments.

pyproject.toml

@@ -1,8 +1,3 @@
 [build-system]
 requires = ['setuptools>=42']
 build-backend = 'setuptools.build_meta'
-
-[tool.pytest.ini_options]
-pythonpath = [
-  "."
-]

pyreason/pyreason.py

@@ -509,8 +509,9 @@ def reset_rules():
     """
     Resets rules to none
     """
-    global __rules
+    global __rules, __annotation_functions
     __rules = None
+    __annotation_functions = []
     if __program is not None:
         __program.reset_rules()
 

pyreason/scripts/components/world.py

@@ -51,4 +51,4 @@ def __str__(self):
         for label in self._world.keys():
             result = result + label.get_value() + ',' + self._world[label].to_str() + '\n'
 
-        return result
+        return result