adds comments to makefile

Makefile

@@ -1,107 +1,132 @@
+# List of phony targets (targets that don't represent files)
 .PHONY: all clean venv run format format-check lint mypy test dist reformat dev
 
+# Define Python and pip executables inside virtual environment
 PYTHON := venv/bin/python
 PIP := venv/bin/pip
 
+# Default target that runs the application
 all: run
 
+# Remove all generated files and directories
 clean:
-	rm -rf venv build dist .pytest_cache .mypy_cache *.egg-info
+    rm -rf venv build dist .pytest_cache .mypy_cache *.egg-info
 
-DB_PATH=scipaperloader/papers# Backup the database
+# Define database path
+DB_PATH=scipaperloader/papers.db
+
+# Backup the database with timestamp
 backup-db:
     @mkdir -p backups
     @timestamp=$$(date +%Y%m%d_%H%M%S); \
     cp $(DB_PATH) backups/papers_$$timestamp.db && \
     echo "Database backed up to backups/papers_$$timestamp.db"
 
-# Create sample test data
+# Create sample test data for development and testing
 sample-data: venv
     $(PYTHON) scipaperloader/scripts/create_sample_data.py
 
-# Export database as SQL
+# Export database as SQL script with timestamp
 export-db: venv
     @mkdir -p exports
     @timestamp=$$(date +%Y%m%d_%H%M%S); \
     $(PYTHON) -c "import sqlite3; conn = sqlite3.connect('$(DB_PATH)'); with open('exports/papers_$$timestamp.sql', 'w') as f: f.write(''.join(conn.iterdump()));" && \
-    echo "Database exported to exports/papers_$$timestamp.sql"	# Run with production settings
+    echo "Database exported to exports/papers_$$timestamp.sql"
-	run-prod: venv
-		FLASK_ENV=production venv/bin/flask --app scipaperloader run --host=0.0.0.0
 
-# Check for security vulnerabilities
+# Run the application with production settings
+run-prod: venv
+    FLASK_ENV=production venv/bin/flask --app scipaperloader run --host=0.0.0.0
+
+# Check for security vulnerabilities in dependencies
 security-check: venv
-$(PIP) install safety
+    $(PIP) install safety
-venv/bin/safety check
+    venv/bin/safety check
 
-# Run specific migration commands
+# Create a new database migration with provided message
 db-migrate: venv
-	venv/bin/flask --app scipaperloader db migrate -m "$(message)"
+    venv/bin/flask --app scipaperloader db migrate -m "$(message)"
 
+# Apply pending database migrations
 db-upgrade: venv
-	venv/bin/flask --app scipaperloader db upgrade
+    venv/bin/flask --app scipaperloader db upgrade
 
+# Revert the last database migration
 db-downgrade: venv
-	venv/bin/flask --app scipaperloader db downgrade		# Generate API documentation using sphinx
+    venv/bin/flask --app scipaperloader db downgrade
-	
+
+# Generate API documentation using Sphinx
 docs: venv
-	$(PIP) install sphinx sphinx_rtd_theme
+    $(PIP) install sphinx sphinx_rtd_theme
-	cd docs && venv/bin/sphinx-build -b html source build
+    cd docs && venv/bin/sphinx-build -b html source build
 
-# Create a code coverage report
+# Create a code coverage report for the test suite
 coverage: venv
-	$(PYTHON) -m pytest --cov=scipaperloader --cov-report=html
+    $(PYTHON) -m pytest --cov=scipaperloader --cov-report=html
-	@echo "Coverage report generated in htmlcov/"
+    @echo "Coverage report generated in htmlcov/"
 
-# Generate a requirements.txt file
+# Generate a requirements.txt file from current environment
 requirements: venv
-	$(PIP) freeze > requirements.txt
+    $(PIP) freeze > requirements.txt
-	@echo "Requirements file updated"			# Show project stats
+    @echo "Requirements file updated"
-	stats:
-		@echo "Lines of Python code:"
-		@find scipaperloader -name "*.py" | xargs wc -l | sort -nr
-		@echo "Number of routes:"
-		@grep -r "@bp.route" scipaperloader | wc -l
-		@echo "Database file size:"
-		@du -h $(DB_PATH) 2>/dev/null || echo "Database file not found"
-		
-	# Show TODOs in code
-	todos:
-		@grep -r "TODO\|FIXME" scipaperloader || echo "No TODOs found".db
 
+# Show project statistics (code lines, routes, database size)
+stats:
+    @echo "Lines of Python code:"
+    @find scipaperloader -name "*.py" | xargs wc -l | sort -nr
+    @echo "Number of routes:"
+    @grep -r "@bp.route" scipaperloader | wc -l
+    @echo "Database file size:"
+    @du -h $(DB_PATH) 2>/dev/null || echo "Database file not found"
+
+# Show TODOs and FIXMEs in code
+todos:
+    @grep -r "TODO\|FIXME" scipaperloader || echo "No TODOs found"
+
+# Reset the database: delete, initialize, and migrate
 reset-db:
-	rm -f $(DB_PATH)
+    rm -f $(DB_PATH)
-	flask db init || true
+    flask db init || true
-	flask db migrate -m "Initial migration"
+    flask db migrate -m "Initial migration"
-	flask db upgrade
+    flask db upgrade
 
+# Create and set up virtual environment
 venv:
-	python3 -m venv venv && \
+    python3 -m venv venv && \
-		$(PIP) install --upgrade pip setuptools && \
+        $(PIP) install --upgrade pip setuptools && \
-		$(PIP) install --editable ".[dev]"
+        $(PIP) install --editable ".[dev]"
 
+# Run the application in debug mode
 run: venv
-	venv/bin/flask --app scipaperloader --debug run
+    venv/bin/flask --app scipaperloader --debug run
 
+# Format code using Black and isort
 format:
-	venv/bin/black .
+    venv/bin/black .
-	venv/bin/isort .
+    venv/bin/isort .
 
+# Check if code meets formatting standards
 format-check:
-	venv/bin/black --check .
+    venv/bin/black --check .
-	venv/bin/isort --check .
+    venv/bin/isort --check .
 
+# Reformat and lint code
 reformat: format lint
 
+# Check code for style issues using flake8
 lint:
-	venv/bin/flake8 .
+    venv/bin/flake8 .
 
+# Run static type checking with mypy
 mypy:
-	venv/bin/mypy scipaperloader
+    venv/bin/mypy scipaperloader
 
+# Run the test suite
 test:
-	venv/bin/pytest
+    venv/bin/pytest
 
+# Build distribution package after running checks
 dist: format-check lint mypy test
-	$(PIP) wheel --wheel-dir dist --no-deps .
+    $(PIP) wheel --wheel-dir dist --no-deps .
 
+# Set up complete development environment
 dev: clean venv