Add GC content std.dev. limit and coverage std. dev. limit Binning metrics

Makefile

@@ -1,23 +1,155 @@
-hello:
-	@echo "Please inspect Makefile for list of commands"
+.PHONY: clean black create_environment install image docs clean unit_test unit_test_data unit_test_data_download unit_test_data_build unit_test_wip unit_test_entrypoints
 
+#################################################################################
+# GLOBALS                                                                       #
+#################################################################################
+
+PROJECT_DIR := $(shell dirname $(realpath $(lastword $(MAKEFILE_LIST))))
+PROJECT_NAME = autometa
+PYTHON_INTERPRETER = python3
+# This was retrieved from https://drive.google.com/file/d/1bSlPldaq3C6Cf9Y5Rm7iwtUDcjxAaeEk/view?usp=sharing
+TEST_DATA_FILEID = 1bSlPldaq3C6Cf9Y5Rm7iwtUDcjxAaeEk
+
+ifeq (,$(shell which conda))
+HAS_CONDA=False
+else
+HAS_CONDA=True
+endif
+
+#################################################################################
+# COMMANDS                                                                      #
+#################################################################################
+
+## Delete all compiled Python files
+clean:
+	find . -type f -name "*.py[co]" -delete
+	find . -type d -name "__pycache__" -delete
+	find . -type d -name "htmlcov" -delete
+	find . -type d -name "Autometa.egg-info" -delete
+	find . -type d -name "dist" -delete
+	find . -type d -name "build" -delete
+
+## Apply black formatting
+black:
+	black --exclude autometa/validation autometa
+
+## Set up python interpreter environment
+create_environment: requirements.txt
+ifeq (True,$(HAS_CONDA))
+		@echo ">>> Detected conda, creating conda environment."
+ifeq (3,$(findstring 3,$(PYTHON_INTERPRETER)))
+	conda create --name $(PROJECT_NAME) python=3 --file=requirements.txt
+else
+	conda create --name $(PROJECT_NAME) python=2.7 --file=requirements.txt
+endif
+	@echo ">>> New conda env created. Activate with:\nsource activate $(PROJECT_NAME)"
+else
+	$(PYTHON_INTERPRETER) -m pip install -q virtualenv virtualenvwrapper
+	@echo ">>> Installing virtualenvwrapper if not already installed.\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 $(PROJECT_NAME) --python=$(PYTHON_INTERPRETER)"
+	@echo ">>> New virtualenv created. Activate with:\nworkon $(PROJECT_NAME)"
+endif
+
+#################################################################################
+# PROJECT RULES                                                                 #
+#################################################################################
+
+## Install autometa from source
 install:
-	python setup.py install
+	$(PYTHON_INTERPRETER) setup.py install
+
+## Install dependencies for test environment
+test_environment: tests/requirements.txt
+	$(PYTHON_INTERPRETER) -m pip install --requirement=tests/requirements.txt
 
+## Build docker image from Dockerfile (auto-taggged as jason-c-kwan/autometa:<current-branch>)
+image: Dockerfile
+	docker build . -t jason-c-kwan/autometa:`git branch --show-current`
+
+## Build documentation for autometa.readthedocs.io
 docs:
-	make clean html -C docs && open docs/build/html/index.html
+	make clean html -C docs
+	@echo "docs built. Open docs/build/html/index.html to view"
 
-clean:
-	@echo "Removing everything under 'htmlcov'..."
-	@rm -rf htmlcov && make clean -C docs
+## Download test_data.json for unit testing
+unit_test_data_download:
+	gdown --id $(TEST_DATA_FILEID) -O tests/data/test_data.json
+
+## Build test_data.json file for unit testing (requires all files from https://drive.google.com/open?id=189C6do0Xw-X813gspsafR9r8m-YfbhTS be downloaded into tests/data/)
+unit_test_data_build: tests/data/records.fna
+	$(PYTHON_INTERPRETER) make_test_data.py
+
+## Run all unit tests
+unit_test: tests/data/test_data.json test_environment
+	$(PYTHON_INTERPRETER) -m pytest --durations=0 --cov=autometa --emoji --cov-report=html tests
+
+## Run unit tests marked with WIP
+unit_test_wip: tests/data/test_data.json test_environment
+	$(PYTHON_INTERPRETER) -m pytest -m "wip" --durations=0 --cov=autometa --emoji --cov-report=html tests
+
+## Run unit tests marked with entrypoint
+unit_test_entrypoints: tests/data/test_data.json test_environment
+	$(PYTHON_INTERPRETER) -m pytest -m "entrypoint" --durations=0 --cov=autometa --emoji --cov-report=html tests
 
-test: tests/data/test_data.json
-	python -m pytest --durations=0 --cov=autometa --emoji --cov-report html
 
-test-wip: tests/data/test_data.json
-	python -m pytest -m "wip" --durations=0 --cov=autometa --emoji --cov-report html
+#################################################################################
+# Self Documenting Commands                                                     #
+#################################################################################
 
-test-entrypoints: tests/data/test_data.json
-	python -m pytest -m "entrypoint" --durations=0 --cov=autometa --emoji --cov-report html
+.DEFAULT_GOAL := help
 
-.PHONY: hello docs clean test test-wip test-entrypoints
+# 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: help
+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')