## 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