A Makefile is like a lab protocol, just like a lab protocol outlines the steps to prepare a sample, a makefile lists the steps to build your project. This enables scientists to automate these steps efficiently, allowing them to focus more on the science. Much like following a protocol ensures reproducibility in an experiment, using a Makefile ensures the reproducibility of your project development process.
Here's when and when not to use Makefiles:
Simplifying Repetitive Tasks: Makefiles are ideal for automating routine tasks such as building code projects, running tests, generating documentation and deploying applications.
Efficiency and Reproducibility: By defining dependencies and commands in a Makefile, researchers can automate tasks efficiently, saving time and reducing manual errors. This also ensures that development process is reproducible across different environments, like on MacOs, Linux, or even Windows.
Small to Medium-Sized Projects: Makefiles are well-suited for smaller projects where dependencies are straightforward. Keep it simple and avoid overcomplicating the Makefile.
Complex Projects: For such complex data analysis pipelines with intricate dependencies or dynamic outputs, tools like Nextflow or Snakemake are more suitable.
Large-Scale Projects: As projects grow in size and complexity, Makefiles can become cumbersome. They may struggle to scale efficiently with the computational resources required to run them, especially when managing large-scale data processing pipelines.
In summary, Makefiles are best for automating simple development tasks, while for complex data analysis tasks, consider more advanced tools.
When you think Makefiles is the right fit for your project, let's dive in and explore how to set them up!
First get Make installed on your system.
# Debian/Ubuntu
sudo apt install make
# macOS
brew install make
# Windows
choco install make
⚠️ Please ensure proper tab indentation for the Makefile since Make requires tabs, not spaces for indentation.
🚨 Using spaces instead of tabs can lead to errors when running the Makefile, so configure your editor to use tabs for indentation.
Here's a basic template to get you started:
.DEFAULT_GOAL := help
.PHONY: deploy
deploy: test docs build ## Deploy to production
@echo "Deploying to production..."
# Add your deployment commands here
.PHONY: test
test: ## Run tests
@echo "Running tests..."
# Add your test commands here
.PHONY: docs
docs: ## Generate documentation
@echo "Generating documentation...."
# Add your documentation commands here
.PHONY: build
build: ## Build the project
@echo "Building the project..."
# Add your build commands here
.PHONY: help
help:
@grep -E '^[a-zA-Z_-]+:.*?## .*$$' $(MAKEFILE_LIST) | sort | awk 'BEGIN {FS = ":.*?## "}; {printf "\033[36m%-16s\033[0m %s\n", $$1, $$2}'
help target is set as the default. This means running make without any arguments will run the help target.$ make
build Build the project
deploy Deploy to production
docs Generate documentation
test Run tests
test are action commands, not files.
These targets do not depend on whether files have been changed, they simply execute the commands.help target generates a help message with descriptions of each target.make deploy, it will run these targets in sequence:
first test, then docs, followed by build, and finally it will execute the deploy command.Makefiles are an underrated gem in the scientific world, offering powerful automation capabilities that take care of the boring tasks 🤖, while ensuring efficiency and reproducibility of your development process.
By automating the boring, Makefiles let you focus on what matters most—the science itself 🔬.