Makefile

MAKEFLAGS += --warn-undefined-variables
SHELL := bash
.SHELLFLAGS := -eu -o pipefail -c
.DEFAULT_GOAL := help
.DELETE_ON_ERROR:
.SUFFIXES:
.SECONDARY:

# environment variables
.EXPORT_ALL_VARIABLES:
ifdef LINKML_ENVIRONMENT_FILENAME
include ${LINKML_ENVIRONMENT_FILENAME}
else
include config.public.mk
endif

RUN = uv run
SCHEMA_NAME = $(LINKML_SCHEMA_NAME)
SOURCE_SCHEMA_PATH = $(LINKML_SCHEMA_SOURCE_PATH)
SOURCE_SCHEMA_DIR = $(dir $(SOURCE_SCHEMA_PATH))
SRC = src
DEST = project
PYMODEL = $(SRC)/$(SCHEMA_NAME)/datamodel
DOCDIR = docs
DOCTEMPLATES = $(SRC)/docs/doc-templates

# Use += to append variables from the variables file
CONFIG_YAML =
ifdef LINKML_GENERATORS_CONFIG_YAML
CONFIG_YAML += "--config-file"
CONFIG_YAML += ${LINKML_GENERATORS_CONFIG_YAML}
endif

GEN_DOC_ARGS =
ifdef LINKML_GENERATORS_DOC_ARGS
GEN_DOC_ARGS += ${LINKML_GENERATORS_DOC_ARGS}
endif


# basename of a YAML file in model/
.PHONY: all clean setup gen-project gendoc new-rig validate-rigs

# note: "help" MUST be the first target in the file,
# when the user types "make" they should get help info
help: status
	@echo ""
	@echo "make install -- install dependencies"
	@echo "make test -- runs tests"
	@echo "make lint -- perform linting"
	@echo "make testdoc -- builds docs and runs local test server"
	@echo "make new-rig -- create a new RIG from template (requires INFORES and NAME)"
	@echo "make validate-rigs -- validate all RIG files against the schema"
	@echo "make help -- show this help"
	@echo ""

# install any dependencies required for building
install:
	uv sync --extra dev
.PHONY: install

all: site
site: gen-project gendoc
%.yaml: gen-project
deploy: all mkd-gh-deploy

# generates all project files
gen-project: $(PYMODEL)
	$(RUN) gen-project ${CONFIG_YAML} -d $(DEST) $(SOURCE_SCHEMA_PATH) && mv $(DEST)/*.py $(PYMODEL)


test: test-schema test-python validate-rigs gendoc

test-schema:
	$(RUN) gen-project ${CONFIG_YAML} -d tmp $(SOURCE_SCHEMA_PATH)

test-python:
	$(RUN) python -m pytest

lint:
	$(RUN) linkml-lint $(SOURCE_SCHEMA_PATH)

# Test documentation locally
serve: mkd-serve

# Python datamodel
$(PYMODEL):
	mkdir -p $@

$(DOCDIR):
	mkdir -p $@

gendoc: $(DOCDIR)
	cp $(SOURCE_SCHEMA_PATH) $(DOCDIR) ; \
	cp $(SRC)/docs/files/*.md $(DOCDIR) ; \
	if ls $(SRC)/docs/files/*.yaml 1> /dev/null 2>&1; then cp $(SRC)/docs/files/*.yaml $(DOCDIR); fi ; \
	cp -r $(SRC)/docs/images $(DOCDIR)/images ; \
	$(RUN) python $(SRC)/scripts/rig_to_markdown.py --input-dir $(SRC)/docs/rigs --output-dir $(DOCDIR) ; \
	$(RUN) python $(SRC)/scripts/generate_rig_index.py --rig-dir $(SRC)/docs/rigs --template-dir $(DOCTEMPLATES) --input-file $(SRC)/docs/files/rig_index.md --output-file $(DOCDIR)/rig_index.md ; \
	if ls $(SRC)/docs/rigs/*.yaml 1> /dev/null 2>&1; then cp $(SRC)/docs/rigs/*.yaml $(DOCDIR)/; fi ; \
	$(RUN) gen-doc ${GEN_DOC_ARGS} -d $(DOCDIR) --template-directory $(DOCTEMPLATES) $(SOURCE_SCHEMA_PATH)

testdoc: gendoc serve

MKDOCS = $(RUN) mkdocs
mkd-%:
	$(MKDOCS) $*

# only necessary if setting up via cookiecutter
.cruft.json:
	echo "creating a stub for .cruft.json. IMPORTANT: setup via cruft not cookiecutter recommended!" ; \
	touch $@

# Create a new RIG from template
# Usage: make new-rig INFORES=infores:ctd NAME="CTD Chemical-Disease Associations"
new-rig:
ifndef INFORES
	$(error INFORES is required. Usage: make new-rig INFORES=infores:example NAME="Example RIG")
endif
ifndef NAME
	$(error NAME is required. Usage: make new-rig INFORES=infores:example NAME="Example RIG")
endif
	$(RUN) python $(SRC)/scripts/create_rig.py --infores "$(INFORES)" --name "$(NAME)"

# Validate all RIG files against the schema
validate-rigs:
	@echo "Validating RIG files against schema..."
	@for rig_file in $(SRC)/docs/rigs/*.yaml; do \
		if [ -f "$$rig_file" ]; then \
			echo "Validating $$rig_file"; \
			$(RUN) linkml-validate --schema $(SOURCE_SCHEMA_PATH) "$$rig_file"; \
		fi; \
	done
	@echo "✓ All RIG files validated successfully"

clean:
	rm -rf $(DEST)
	rm -rf tmp
	rm -fr $(DOCDIR)/*
	rm -fr $(PYMODEL)/*

include project.Makefile