Makefile

.PHONY: clean clean_env data lint environment serve_nb sync_data_to_s3 sync_data_from_s3 github_remote

#################################################################################
# GLOBALS                                                                       #
#################################################################################
SHELL := /bin/bash

PROJECT_DIR := $(shell dirname $(realpath $(lastword $(MAKEFILE_LIST))))
BUCKET = None
PACKAGE_NAME = biorepo
PYTHON_INTERPRETER = python3
CONDA_ENV_NAME = biorepo
CONDA_ROOT = $(shell conda info --root)
CONDA_ENV_DIR = $(CONDA_ROOT)/envs/$(CONDA_ENV_NAME)
CONDA_ENV_PY = $(CONDA_ENV_DIR)/bin/python

TEST_VENV=venv-test


ifeq (,$(shell which conda))
HAS_CONDA=False
else
HAS_CONDA=True
endif


ifeq (,$(shell which aria2c))
HAS_ARIA=False
else
HAS_ARIA=True
endif

ifeq (${CONDA_DEFAULT_ENV},$(CONDA_ENV_NAME))
PROJECT_CONDA_ACTIVE=True
else
PROJECT_CONDA_ACTIVE=False
endif

define BROWSER_PYSCRIPT
import os, webbrowser, sys
try:
	from urllib import pathname2url
except:
	from urllib.request import pathname2url

webbrowser.open("file://" + pathname2url(os.path.abspath(sys.argv[1])))
endef
export BROWSER_PYSCRIPT

BROWSER := python -c "$$BROWSER_PYSCRIPT"


#################################################################################
# COMMANDS                                                                      #
#################################################################################


## alias for show-help
help: show-help


## remove all build, test, coverage and Python artifacts
clean: clean-build clean-pyc clean-test


## remove build artifacts
clean-build:
	rm -fr build/
	rm -fr dist/
	rm -fr .eggs/
	find . -name '*.egg-info' -exec rm -fr {} +
	find . -name '*.egg' -exec rm -f {} +

## remove Python file artifacts
clean-pyc:
	find . -name '*.pyc' -exec rm -f {} +
	find . -name '*.pyo' -exec rm -f {} +
	find . -name '*~' -exec rm -f {} +
	find . -name '__pycache__' -exec rm -fr {} +

## remove test and coverage artifacts
clean-test:
	rm -fr .tox/
	rm -f .coverage
	rm -fr htmlcov/

## remove docs artifacts
clean-docs:
	$(MAKE) -C docs clean

## check style with flake8
lint:
	flake8 $(PACKAGE_NAME) tests

## run tests quickly with the default Python
test:
	py.test

## run tests on every Python version with tox
test-all:
	tox

## check code coverage quickly with the default Python
coverage:
	coverage run --source $(PACKAGE_NAME) -m pytest
	coverage report -m
	coverage html
	$(BROWSER) htmlcov/index.html

## generate Sphinx HTML documentation, including API docs
docs:
	rm -f docs/$(PACKAGE_NAME).rst
	rm -f docs/$(PACKAGE_NAME).*.rst
	rm -f docs/modules.rst
	$(MAKE) -C docs clean
	$(MAKE) -C docs html
	$(BROWSER) docs/_build/html/index.html

## compile the docs watching for changes
servedocs: docs
	watchmedo shell-command -p '*.rst' -c '$(MAKE) -C docs html' -R -D .

## package and upload a release
release: clean
	python setup.py sdist upload
	python setup.py bdist_wheel upload

## builds source and wheel package
dist: clean
	python setup.py sdist
	python setup.py bdist_wheel
	ls -l dist

error_if_active_conda_env:
ifeq (True,$(PROJECT_CONDA_ACTIVE))
	$(error "This project's conda env is active." )
endif

serve_nb:
	source activate $(CONDA_ENV_NAME); \
	jupyter notebook --notebook-dir notebooks

## installs virtual environments and requirements
install: install_python install_r

## uninstalls virtual environments and requirements
uninstall: error_if_active_conda_env uninstall_python


install_python:
ifeq ($(CONDA_ENV_PY), $(shell which python))
	@echo "Project conda env already installed."
else
	conda create -n $(CONDA_ENV_NAME) --file requirements.txt --yes  && \
	source activate $(CONDA_ENV_NAME) && \
	python -m ipykernel install --sys-prefix --name $(CONDA_ENV_NAME) --display-name "$(CONDA_ENV_NAME)" && \
	pip install -r requirements.pip.txt && \
	pip install -e .
endif


uninstall_python:
	source activate $(CONDA_ENV_NAME); \
	rm -rf $$(jupyter --data-dir)/kernels/$(CONDA_ENV_NAME); \
	rm -rf $(CONDA_ENV_DIR)




install_r:
	source activate $(CONDA_ENV_NAME) && \
	conda install --file requirements.r.txt --yes && \
	rm -rf $(CONDA_ENV_DIR)/share/jupyter/kernels/ir && \
	R -e "IRkernel::installspec(name = '$(CONDA_ENV_NAME)_R', displayname = '$(CONDA_ENV_NAME)_R')"

## Tests `python setup.py install` in a fresh venv
venv-test: venv-clean
	python3 -m venv --clear $(TEST_VENV) && \
	source $(TEST_VENV)/bin/activate && \
	pip install -e .

## Clean up after venv-test
venv-clean:
	rm -rf $(TEST_VENV)


## inits a local git repo, creates a repo on GitHub, pushes local to GitHub
github_remote:
	bash github/push_to_new_remote.sh


## Aquire the latest version of the  VIPER RNA-seq Pipeline if needed
get_viper_static_files:
ifeq (True,$(HAS_ARIA))
		@echo ">>> Detected aria2c, starting PARALLEL download."
		aria2c -d $(VIPER_STATIC_SYSTEM_DIR) -i .viper_static_urls


else
		@echo ">>> Did not detect aria2c, starting serial downloads with wget instead."
		wget -c  'https://www.dropbox.com/sh/8cqooj05i7rnyou/AADjyXpbADhHUCr_WAscP9MEa/hg19.tar.gz?dl=1'
		wget -c  'https://www.dropbox.com/sh/8cqooj05i7rnyou/AADUxqgzpcoVyjUcwYb5dhMBa/mm9.tar.gz?dl=1'
		wget -c  'https://www.dropbox.com/sh/8cqooj05i7rnyou/AABbSIjk9124KZh3IdV6ob31a/snpEff.tar.gz?dl=1'
endif




# install_viper: clean_viper get_viper_static_files
install_viper: clean_viper
	git clone https://bitbucket.org/cfce/viper.git
	patch -p0 < patches/viper/environment.yml.patch

	conda env create -f viper/envs/environment.yml -n $(CONDA_ENV_NAME_VIPER)
	ln -s $(VIPER_STATIC_SYSTEM_DIR) $(VIPER_STATIC_PROJ_DIR)
	ln -s $(VIPER_STATIC_PROJ_DIR) ref_files

	mkdir -p $(VIPER_CONFIGS_DIR)
	cp viper/config.yaml $(VIPER_CONFIGS_DIR)
	cp viper/metasheet.csv $(VIPER_CONFIGS_DIR)

clean_viper:
	rm -rf $$(jupyter --data-dir)/kernels/$(CONDA_ENV_NAME_VIPER)
	rm -rf $(CONDA_ENV_DIR_VIPER)
	rm -rf viper
	rm -rf data/external/viper_static_files
	rm -rf ref_files


## Install Python Dependencies
requirements: test_environment
	pip install -r requirements.txt

## Make Dataset
data:
	source activate $(CONDA_ENV_NAME); \
	python src/python/data/make_dataset.py

## Delete all compiled Python files
clean_bytecode:
	find . -name "__pycache__" -type d -exec rm -r {} \; ; \
	find . -name "*.pyc" -exec rm {} \;

lint:
	flake8 --exclude=lib/,bin/ .

## Upload Data to S3
sync_data_to_s3:
	aws s3 sync data/ s3://$(BUCKET)/data/

## Download Data from S3
sync_data_from_s3:
	aws s3 sync s3://$(BUCKET)/data/ data/

## Set up python interpreter environment
create_environment:
ifeq (True,$(HAS_CONDA))
		@echo ">>> Detected conda, creating conda environment."
ifeq (3,$(findstring 3,$(PYTHON_INTERPRETER)))
	conda create --name $(CONDA_ENV_NAME) python=3.5
else
	conda create --name $(CONDA_ENV_NAME) python=2.7
endif
		@echo ">>> New conda env created. Activate with:\nsource activate $(CONDA_ENV_NAME)"
else
	@pip install -q virtualenv virtualenvwrapper
	@echo ">>> Installing virtualenvwrapper if not already intalled.\nMake sure the following lines are in shell startup file\n\
	export WORKON_HOME=$$HOME/.virtualenvs\nexport PROJECT_HOME=$$HOME/Devel\nsource /usr/local/bin/virtualenvwrapper.sh\n"
	@bash -c "source `which virtualenvwrapper.sh`;mkvirtualenv $(CONDA_ENV_NAME) --python=$(PYTHON_INTERPRETER)"
	@echo ">>> New virtualenv created. Activate with:\nworkon $(CONDA_ENV_NAME)"
endif

## Test python environment is setup correctly
test_environment:
	$(PYTHON_INTERPRETER) test_environment.py

#################################################################################
# Utils                                                                         #
#################################################################################
## patches the viper environment.yml
patch_viper_env_yml:
	diff -Naur viper/envs/environment.yml patches/viper/environment.yml > patches/viper/environment.yml.patch


#################################################################################
# PROJECT RULES                                                                 #
#################################################################################



#################################################################################
# Self Documenting Commands                                                     #
#################################################################################

.DEFAULT_GOAL := show-help

# Inspired by <http://marmelab.com/blog/2016/02/29/auto-documented-makefile.html>
# sed script explained:
# /^##/:
# 	* save line in hold space
# 	* purge line
# 	* Loop:
# 		* append newline + line to hold space
# 		* go to next line
# 		* if line starts with doc comment, strip comment character off and loop
# 	* remove target prerequisites
# 	* append hold space (+ newline) to line
# 	* replace newline plus comments by `---`
# 	* print line
# Separate expressions are necessary because labels cannot be delimited by
# semicolon; see <http://stackoverflow.com/a/11799865/1968>
.PHONY: show-help
## Show the available make targets
show-help:
	@echo "$$(tput bold)Available rules:$$(tput sgr0)"
	@echo
	@sed -n -e "/^## / { \
		h; \
		s/.*//; \
		:doc" \
		-e "H; \
		n; \
		s/^## //; \
		t doc" \
		-e "s/:.*//; \
		G; \
		s/\\n## /---/; \
		s/\\n/ /g; \
		p; \
	}" ${MAKEFILE_LIST} \
	| LC_ALL='C' sort --ignore-case \
	| awk -F '---' \
		-v ncol=$$(tput cols) \
		-v indent=19 \
		-v col_on="$$(tput setaf 6)" \
		-v col_off="$$(tput sgr0)" \
	'{ \
		printf "%s%*s%s ", col_on, -indent, $$1, col_off; \
		n = split($$2, words, " "); \
		line_length = ncol - indent; \
		for (i = 1; i <= n; i++) { \
			line_length -= length(words[i]) + 1; \
			if (line_length <= 0) { \
				line_length = ncol - indent - length(words[i]) - 1; \
				printf "\n%*s ", -indent, " "; \
			} \
			printf "%s ", words[i]; \
		} \
		printf "\n"; \
	}' \
	| more $(shell test $(shell uname) = Darwin && echo '--no-init --raw-control-chars')