Makefile

.PHONY: clean doc doc-clean tests check test install pipeline-docs


install:
	@which pip > /dev/null
	@pip freeze|grep 'pbsmrtpipe=='>/dev/null \
      && pip uninstall -y pbsmrtpipe \
      || echo -n ''
	@pip install ./
	@echo "Installed version pbsmrtpipe $(shell pbsmrtpipe --version)"

clean: doc-clean clean-testkit
	rm -rf build/;\
	find . -name "*.egg-info" | xargs rm -rf;\
	rm -rf dist/;\
	find . -name "*.pyc" | xargs rm -f;
	rm -f nosetests.xml

doc:
	sphinx-apidoc -o docs/ pbsmrtpipe/ && cd docs/ && make html

doc-clean:
	rm -rf docs/pbsmrtpipe.*.rst
	rm -rf docs/modules.rst
	cd docs && make clean

unit-test:
	nosetests --verbose --logging-conf nose.cfg pbsmrtpipe/pb_tasks/tests/*.py pbsmrtpipe/tests/test_*.py

clean-testkit:
	find testkit-data -name "job_output" | xargs rm -rf;
	find testkit-data -name "0.stdout" | xargs rm -rf;
	find testkit-data -name "0.stderr" | xargs rm -rf;

test-pylint:
	pylint --errors-only pbsmrtpipe

test-dev: clean-testkit
	cd testkit-data && pbtestkit-multirunner --debug --nworkers 8 dev.fofn

test-unit:
	nosetests --verbose --with-xunit --logging-conf nose.cfg pbsmrtpipe/pb_tasks/tests/*.py pbsmrtpipe/tests/test_*.py

test-pipelines:
	nosetests --verbose --logging-conf nose.cfg pbsmrtpipe/tests/test_pb_pipelines_sanity.py

# This should probably go away
test-tasks:
	nosetests --verbose --logging-conf nose.cfg pbsmrtpipe/pb_tasks/tests/test_*.py

test-loader:
	python -c "import pbsmrtpipe.loader as L; L.load_all()"

test-contracts:
	python -c "import pbsmrtpipe.loader as L; L.load_all()"

test-chunk-operators:
	python -c "import pbsmrtpipe.loader as L; L.load_and_validate_chunk_operators()"

test-sanity: test-contracts test-pipelines test-chunk-operators test-loader write-pipeline-templates

test-suite: test-sanity test-unit test-dev write-pipeline-templates

test-clean-suite: install test-suite

clean-all: clean clean-testkit
	find . -name "*.pyc" | xargs rm -rf;\
	rm -rf report_unittests.log

build-java-classes:
	avro-tools compile schema pbsmrtpipe/schemas java-classes/

write-pipeline-templates-avro:
	mkdir -p extras/pipeline-templates-avro
	pbsmrtpipe show-templates --output-templates-avro extras/pipeline-templates-avro

write-pipeline-templates-json:
	mkdir -p extras/pipeline-templates-json
	pbsmrtpipe show-templates --output-templates-json extras/pipeline-templates-json

write-pipeline-templates: write-pipeline-templates-avro write-pipeline-templates-json

test-chunk:
	nosetests --verbose --logging-conf nose.cfg pbsmrtpipe/tests/test_tools_dev_tasks.py


emit-dev-tool-contracts:
	python -m pbsmrtpipe.pb_tasks.dev emit-tool-contracts -o pbsmrtpipe/registered_tool_contracts

show-pipelines:
	pbsmrtpipe show-templates

show-templates: show-pipelines


reinstall-pb-repos:
	pip uninstall -y pbcommand
	pip uninstall -y pbcore
	pip uninstall -y pbcoretools
	pip install -r PB_REQUIREMENTS.txt

repl:
	ipython -i -c "import pbsmrtpipe.loader as L; rx_tasks, rx_files, rx_operators, rx_pipelines = L.load_all()"

pipeline-docs:
	pbsmrtpipe show-templates --output-templates-json extras/pipeline-templates-json
	python -m pbsmrtpipe.tools.resources_to_rst extras/pipeline-templates-json -o pipeline-docs

show-workflow-options:
	pbsmrtpipe show-workflow-options | grep "^Option" | sed 's/.*:\ *//; s/.*\.//;' > extras/workflow_options.txt