--- a
+++ b/makefile
@@ -0,0 +1,89 @@
+## makefile automates the build and deployment for python projects
+
+
+## Build system
+#
+PROJ_TYPE =		python
+PROJ_MODULES =		git python-resources python-cli python-doc python-doc-deploy markdown
+PY_DEP_POST_DEPS +=	modeldeps
+PY_CLI_ARGS +=		--config test-resources/config/default.conf
+ADD_CLEAN +=		medcat.log
+CLEAN_DEPS +=		pycleancache cleanexample
+
+## Project
+#
+ENTRY_BIN =		./mednlp
+TEST_SENT =		"John Smith was diagnosed with liver disease while in Chicago."
+
+
+## Includes
+#
+include ./zenbuild/main.mk
+
+
+## Targets
+#
+# install models and their dependencies instead of letting the app do it
+.PHONY:			modeldeps
+modeldeps:
+			$(PIP_BIN) install $(PIP_ARGS) -r \
+				resources/requirements/model.txt --no-deps
+
+# try to reinstall the `nmslib` python package
+.PHONY:			reinstallnmslib
+reinstallnmslib:
+			@echo "reinstall no binary nmslib for speed and warnings"
+			pip uninstall -y nmslib || true
+			pip install --no-binary :all: nmslib
+
+# test scispacy entity link db
+.PHONY:			testentlink
+testentlink:
+			make PY_SRC_TEST=test/entlink test
+
+# test parsing
+.PHONY:			testparse
+testparse:
+			@$(ENTRY_BIN) show $(PY_CLI_ARGS) $(TEST_SENT) | \
+				diff - test-resources/integration/parse.txt || \
+				exit 1
+
+# not CUIs/results are after defaulting to notebook only MedCAT model
+.PHONY:			testfeatures
+testfeatures:
+			@$(ENTRY_BIN) features $(PY_CLI_ARGS) \
+				--ids pref_name_,loc --medonly $(TEST_SENT) | \
+				diff - test-resources/integration/features.csv || \
+				exit 1
+
+# test CTS (UMLS terminology service)
+.PHONY:			testclinicaltuis
+testclinicaltuis:
+			@$(ENTRY_BIN) group byname $(PY_CLI_ARGS) -q \
+				Anatomy,Devices,Disorders,Drugs,Genes,Living,Objects,Occupations,Phenomena,Physiology,Procedures | \
+				diff - test-resources/integration/tuis.txt || \
+				exit 1
+
+# integration tests
+.PHONY:			testint
+testint:
+			@example/features/features.py show | \
+				diff - test-resources/integration/ex-features.txt || \
+				exit 1
+			@example/cui2vec/cui2vec.py similarity -t heart 2>&1 | \
+				grep -v RuntimeWarning | \
+				grep -v 'dists = dot' | \
+				diff - test-resources/integration/cui2vec.txt || \
+				exit 1
+			@example/uts/uts.py | \
+				diff - test-resources/integration/uts.txt || \
+				exit 1
+
+# unit and integration tests
+.PHONY:			testall
+testall:		test testentlink testparse testfeatures testclinicaltuis testint
+
+# remove cached files created by the examples
+.PHONY:			cleanexample
+cleanexample:
+			rm -fr example/cache