Makefile

# ======================================================================
#  _____  __   __  _  __   __         __  __          _
# |  __ \ \ \ / / (_)\ \ / /         |  \/  |        | |
# | |__) | \ V /   _  \ V /   _____  | \  / |  __ _  | | __  ___  _ __
# |  _  /   > <   | |  > <   |_____| | |\/| | / _` | | |/ / / _ \| '__|
# | | \ \  / . \  | | / . \          | |  | || (_| | |   < |  __/| |
# |_|  \_\/_/ \_\ |_|/_/ \_\         |_|  |_| \__,_| |_|\_\ \___||_|
#
# ======================================================================
# Automated Scientific Article Generation and Publishing System
#
# 🆕 RECOMMENDED: Use the modern rxiv CLI for the best experience:
#   pip install rxiv-maker
#   rxiv init my-paper && cd my-paper && rxiv pdf
#
# 🚀 LEGACY MAKEFILE INTERFACE (maintained for backward compatibility):
#   make setup        # Install Python dependencies
#   make pdf          # Generate PDF (requires LaTeX)
#   make help         # Show all available commands
#
# Author: Rxiv-Maker Project
# Documentation: See README.md
# ======================================================================

# ======================================================================
# ⚙️  CONFIGURATION VARIABLES
# ======================================================================

# Export all variables but handle MANUSCRIPT_PATH specially
export
.EXPORT_ALL_VARIABLES:

# ======================================================================
# 🌐 CROSS-PLATFORM COMPATIBILITY
# ======================================================================

# Streamlined OS detection
ifdef MAKEFILE_FORCE_UNIX
    DETECTED_OS := GitHub-Actions-Unix
    SHELL_NULL := /dev/null
    VENV_PYTHON := .venv/bin/python
else ifeq ($(OS),Windows_NT)
    DETECTED_OS := Windows
    SHELL_NULL := nul
    VENV_PYTHON := .venv\Scripts\python.exe
else
    UNAME_S := $(shell uname -s)
    DETECTED_OS := $(if $(findstring Linux,$(UNAME_S)),Linux,$(if $(findstring Darwin,$(UNAME_S)),macOS,Unix))
    SHELL_NULL := /dev/null
    VENV_PYTHON := .venv/bin/python
endif

# Simplified cross-platform Python command selection
ifeq ($(OS),Windows_NT)
    PYTHON_EXEC := $(shell where uv >nul 2>&1 && echo uv run python || (if exist "$(VENV_PYTHON)" (echo $(VENV_PYTHON)) else (echo python)))
else
    PYTHON_EXEC := $(shell command -v uv >$(SHELL_NULL) 2>&1 && echo "uv run python" || (test -f "$(VENV_PYTHON)" && echo "$(VENV_PYTHON)" || echo python3))
endif

# ======================================================================
# 💻 LOCAL ENGINE CONFIGURATION
# ======================================================================

# Engine mode: LOCAL only (Docker/Podman engines deprecated)
# For containerized execution, use docker-rxiv-maker repository
RXIV_ENGINE := LOCAL

# Always use local Python execution
PYTHON_CMD = $(PYTHON_EXEC)
ENGINE_STATUS = 💻 Local

# Simplified rxiv CLI helper - no more complex fallback logic
# The unified rxiv CLI handles all path resolution and environment variables
RXIV_CLI = MANUSCRIPT_PATH="$(MANUSCRIPT_PATH)" rxiv

# Error handling helper for validation failures
define VALIDATION_ERROR
	echo ""; \
	echo "❌ Validation failed! Please fix the issues above before building PDF."; \
	echo "💡 Run 'make validate' for detailed error analysis"; \
	echo "💡 Use 'make pdf-no-validate' to skip validation and build anyway."; \
	exit 1
endef

OUTPUT_DIR := output

# Simple MANUSCRIPT_PATH handling: command line > environment > .env file > default
-include .env
MANUSCRIPT_PATH ?= MANUSCRIPT
export MANUSCRIPT_PATH

ARTICLE_DIR = $(MANUSCRIPT_PATH)
FIGURES_DIR = $(ARTICLE_DIR)/FIGURES
STYLE_DIR := src/tex/style
PYTHON_SCRIPT := src/py/commands/generate_preprint.py
FIGURE_SCRIPT := src/py/commands/generate_figures.py

# Testing configuration
TEMPLATE_FILE := src/tex/template.tex
ARTICLE_MD = $(ARTICLE_DIR)/01_MAIN.md
MANUSCRIPT_CONFIG = $(ARTICLE_DIR)/00_CONFIG.yml
SUPPLEMENTARY_MD = $(ARTICLE_DIR)/02_SUPPLEMENTARY_INFO.md
REFERENCES_BIB = $(ARTICLE_DIR)/03_REFERENCES.bib

# Output file names based on manuscript path
MANUSCRIPT_NAME = $(notdir $(MANUSCRIPT_PATH))
OUTPUT_TEX = $(MANUSCRIPT_NAME).tex
OUTPUT_PDF = $(MANUSCRIPT_NAME).pdf

# ======================================================================
# 📌 DEFAULT AND CONVENIENCE TARGETS
# ======================================================================

# Default target
.PHONY: all
all: pdf

# ======================================================================
# 🚀 QUICK START COMMANDS
# ======================================================================
# Main user-facing commands with simple names

# Install Python dependencies only (cross-platform)
.PHONY: setup
setup:
	@echo "⚙️  Setting up Python environment..."
	$(PYTHON_CMD) -m pip install -e .

# Reinstall Python dependencies (removes .venv and creates new one) - cross-platform
.PHONY: setup-reinstall
setup-reinstall:
	@$(RXIV_CLI) setup --reinstall

# Test platform detection
.PHONY: test-platform
test-platform:
	@echo "Host machine: $(UNAME_M)"

# Install system dependencies (LaTeX, Node.js, R, etc.)
.PHONY: install-deps
install-deps:
	@echo "🔧 Installing system dependencies..."
	$(RXIV_CLI) setup --mode system-only

# Install system dependencies in minimal mode
.PHONY: install-deps-minimal
install-deps-minimal:
	@echo "🔧 Installing system dependencies (minimal mode)..."
	$(RXIV_CLI) setup --mode minimal

# Check system dependencies
.PHONY: check-deps
check-deps:
	@echo "🔍 Checking system dependencies..."
	$(RXIV_CLI) setup --check-only

# Check system dependencies (verbose)
.PHONY: check-deps-verbose
check-deps-verbose:
	@echo "🔍 Checking system dependencies (verbose)..."
	$(RXIV_CLI) setup --check-only --verbose

# Generate PDF with validation (requires LaTeX installation)
.PHONY: pdf
pdf:
	@echo "📄 Generating PDF: $(MANUSCRIPT_PATH) → $(OUTPUT_DIR)"
	$(RXIV_CLI) pdf "$(MANUSCRIPT_PATH)" --output-dir $(OUTPUT_DIR) $(if $(FORCE_FIGURES),--force-figures)

# Generate PDF without validation (for debugging)
.PHONY: pdf-no-validate
pdf-no-validate:
	@echo "📄 Generating PDF (no validation): $(MANUSCRIPT_PATH) → $(OUTPUT_DIR)"
	$(RXIV_CLI) pdf "$(MANUSCRIPT_PATH)" --output-dir $(OUTPUT_DIR) --skip-validation $(if $(FORCE_FIGURES),--force-figures)

# Generate PDF with change tracking against a git tag
.PHONY: pdf-track-changes
pdf-track-changes:
ifndef TAG
	$(error TAG is required. Usage: make pdf-track-changes TAG=v1.0.0)
endif
	@echo "🔍 Generating PDF with change tracking against tag: $(TAG)"
	$(RXIV_CLI) track-changes "$(MANUSCRIPT_PATH)" $(TAG) --output-dir $(OUTPUT_DIR)

# Prepare arXiv submission package
.PHONY: arxiv
arxiv: pdf
	@echo "📦 Preparing arXiv submission package..."
	$(RXIV_CLI) arxiv "$(MANUSCRIPT_PATH)" --output-dir $(OUTPUT_DIR)

# ======================================================================
# 🔍 VALIDATION COMMANDS
# ======================================================================

# Validate manuscript structure and content (with detailed report)
.PHONY: validate
validate:
	@echo "🔍 Running manuscript validation..."
	$(RXIV_CLI) validate "$(MANUSCRIPT_PATH)" --detailed || { $(VALIDATION_ERROR); }
	@echo "✅ Validation passed!"

# Internal validation target for PDF build (quiet mode)
.PHONY: _validate_quiet
_validate_quiet:
	@echo "🔍 Validating manuscript: $(MANUSCRIPT_PATH)"
	$(RXIV_CLI) validate "$(MANUSCRIPT_PATH)" || { $(VALIDATION_ERROR); }

# ======================================================================
# 🧪 TESTING AND CODE QUALITY
# ======================================================================

# Run all tests
.PHONY: test
test:
	@echo "🧪 Running all tests..."
	@$(PYTHON_CMD) -m pytest tests/ -v

# Repository integrity and safeguard validation
# Note: validate-repo, test-safeguards, and test-submodule-guardrails targets removed
# as submodules are no longer used for distribution

.PHONY: validate-all
validate-all: validate
	@echo "✅ All validation checks completed successfully!"

# Run unit tests only
.PHONY: test-unit
test-unit:
	@echo "🧪 Running unit tests..."
	@$(PYTHON_CMD) -m pytest tests/unit/ -v

# Run integration tests only
.PHONY: test-integration
test-integration:
	@echo "🧪 Running integration tests..."
	@$(PYTHON_CMD) -m pytest tests/integration/ -v

# Lint code
.PHONY: lint
lint:
	@echo "🔍 Linting code..."
	@$(PYTHON_CMD) -m ruff check src/

# Format code
.PHONY: format
format:
	@echo "🎨 Formatting code..."
	@$(PYTHON_CMD) -m ruff format src/

# Type checking
.PHONY: typecheck
typecheck:
	@echo "🔍 Running type checking..."
	@$(PYTHON_CMD) -m mypy src/

# Run all code quality checks
.PHONY: check
check: lint typecheck
	@echo "✅ All code quality checks passed!"

# ======================================================================
# �📚 BIBLIOGRAPHY MANAGEMENT
# ======================================================================

# Fix bibliography issues automatically by searching CrossRef
.PHONY: fix-bibliography
fix-bibliography:
	@echo "🔧 Attempting to fix bibliography issues..."
	$(RXIV_CLI) bibliography fix "$(MANUSCRIPT_PATH)" || { \
		echo "❌ Bibliography fixing failed!"; \
		echo "💡 Run with --dry-run to see potential fixes first"; \
		echo "💡 Use --verbose for detailed logging"; exit 1; }

# Preview bibliography fixes without applying them
.PHONY: fix-bibliography-dry-run
fix-bibliography-dry-run:
	@echo "🔍 Checking potential bibliography fixes..."
	$(RXIV_CLI) bibliography fix "$(MANUSCRIPT_PATH)" --dry-run

# Add bibliography entries from DOI
.PHONY: add-bibliography
add-bibliography:
	@# Extract DOI arguments from command line
	@DOI_ARGS=""; \
	for arg in $(MAKECMDGOALS); do \
		if echo "$$arg" | grep -E '^10\.[0-9]{4}.*' >/dev/null 2>&1; then \
			DOI_ARGS="$$DOI_ARGS $$arg"; \
		fi; \
	done; \
	if [ -z "$$DOI_ARGS" ]; then \
		echo "❌ Error: No DOI(s) provided"; \
		echo "💡 Usage: make add-bibliography 10.1000/example"; \
		echo "💡 Multiple: make add-bibliography 10.1000/ex1 10.1000/ex2"; \
		exit 1; \
	fi; \
	echo "📚 Adding bibliography entries from DOI(s):$$DOI_ARGS"; \
	$(RXIV_CLI) bibliography add "$(MANUSCRIPT_PATH)" $$DOI_ARGS $(if $(OVERWRITE),--overwrite)

# Allow DOI patterns as pseudo-targets
.PHONY: $(shell echo 10.*)
10.%: ;
	@# DOI patterns are handled by add-bibliography target

# ======================================================================
# 🔨 INTERNAL BUILD TARGETS (Deprecated - now handled by Python)
# ======================================================================
# These targets are kept for compatibility but delegate to Python commands

# ======================================================================
# 🧹 MAINTENANCE
# ======================================================================

# Consolidated cleaning targets using simplified CLI
# Clean output directory (cross-platform)
.PHONY: clean
clean:
	@echo "🧹 Cleaning: $(MANUSCRIPT_PATH) → $(OUTPUT_DIR)"
	$(RXIV_CLI) clean "$(MANUSCRIPT_PATH)" --output-dir $(OUTPUT_DIR)

# Specialized cleaning targets
.PHONY: clean-output clean-figures clean-arxiv clean-temp clean-cache
clean-output:
	$(RXIV_CLI) clean --output-only --output-dir $(OUTPUT_DIR)

clean-figures:
	$(RXIV_CLI) clean "$(MANUSCRIPT_PATH)" --figures-only

clean-arxiv:
	$(RXIV_CLI) clean --arxiv-only

clean-temp:
	$(RXIV_CLI) clean --temp-only

clean-cache:
	$(RXIV_CLI) clean --cache-only

# ======================================================================
# 📖 HELP AND DOCUMENTATION
# ======================================================================

# Show comprehensive help
.PHONY: help
help:
	@VERSION=$$(PYTHONPATH="$(PWD)/src" $(PYTHON_CMD) -c "from rxiv_maker import __version__; print(__version__)" 2>/dev/null || echo "unknown"); \
	echo "🚀 Rxiv-Maker v$$VERSION ($(DETECTED_OS)) - $(ENGINE_STATUS)"; \
	echo ""; \
	echo "📋 Essential Commands:"; \
	echo "  make setup        - Install Python dependencies"; \
	echo "  make install-deps - Install system dependencies (LaTeX, etc.)"; \
	echo "  make pdf          - Generate PDF with validation"; \
	echo "  make validate     - Check manuscript for issues"; \
	echo "  make clean        - Remove output files"; \
	echo "  make arxiv        - Prepare arXiv submission"; \
	echo ""; \
	echo "💻 Engine Mode:"; \
	echo "  LOCAL only - Uses local installations"; \
	echo "  For containers: use docker-rxiv-maker repository"; \
	echo ""; \
	echo "⚙️  Common Options:"; \
	echo "  FORCE_FIGURES=true           - Force figure regeneration"; \
	echo "  MANUSCRIPT_PATH=MY_PAPER     - Use custom manuscript"; \
	echo ""; \
	echo "📁 Current: $(MANUSCRIPT_PATH)/ → $(OUTPUT_DIR)/"; \
	echo "⚡ Quick Start: make setup && make pdf"