MAKEFLAGS += --warn-undefined-variables SHELL := bash .SHELLFLAGS := -eu -o pipefail -c .DEFAULT_GOAL := help .DELETE_ON_ERROR: .SUFFIXES: .SECONDARY: RUN = poetry run # get values from about.yaml file SCHEMA_NAME = $(shell ${SHELL} ./utils/get-value.sh name) SOURCE_SCHEMA_PATH = $(shell ${SHELL} ./utils/get-value.sh source_schema_path) SOURCE_SCHEMA_DIR = $(dir $(SOURCE_SCHEMA_PATH)) SRC = src DEST = project PYMODEL = $(SRC)/$(SCHEMA_NAME)/datamodel DOCDIR = docs EXAMPLEDIR = examples SHEET_MODULE = personinfo_enums SHEET_ID = $(shell ${SHELL} ./utils/get-value.sh google_sheet_id) SHEET_TABS = $(shell ${SHELL} ./utils/get-value.sh google_sheet_tabs) SHEET_MODULE_PATH = $(SOURCE_SCHEMA_DIR)/$(SHEET_MODULE).yaml # environment variables include config.env GEN_PARGS = ifdef LINKML_GENERATORS_PROJECT_ARGS GEN_PARGS = ${LINKML_GENERATORS_PROJECT_ARGS} endif GEN_DARGS = ifdef LINKML_GENERATORS_MARKDOWN_ARGS GEN_DARGS = ${LINKML_GENERATORS_MARKDOWN_ARGS} endif # basename of a YAML file in model/ .PHONY: all clean # 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 setup -- initial setup (run this first)" @echo "make site -- makes site locally" @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 deploy -- deploys site" @echo "make update -- updates linkml version" @echo "make help -- show this help" @echo "" status: check-config @echo "Project: $(SCHEMA_NAME)" @echo "Source: $(SOURCE_SCHEMA_PATH)" # generate products and add everything to github setup: install gen-project gen-examples gendoc git-init-add # install any dependencies required for building install: git init poetry install .PHONY: install # --- # Project Synchronization # --- # # check we are up to date check: cruft-check cruft-check: cruft check cruft-diff: cruft diff update: update-template update-linkml update-template: cruft update # todo: consider pinning to template update-linkml: poetry add -D linkml@latest # EXPERIMENTAL create-data-harmonizer: npm init data-harmonizer $(SOURCE_SCHEMA_PATH) all: site site: gen-project gendoc %.yaml: gen-project deploy: all mkd-gh-deploy compile-sheets: $(RUN) sheets2linkml --gsheet-id $(SHEET_ID) $(SHEET_TABS) > $(SHEET_MODULE_PATH).tmp && mv $(SHEET_MODULE_PATH).tmp $(SHEET_MODULE_PATH) # In future this will be done by conversion gen-examples: cp src/data/examples/* $(EXAMPLEDIR) # generates all project files gen-project: $(PYMODEL) $(RUN) gen-project ${GEN_PARGS} -d $(DEST) $(SOURCE_SCHEMA_PATH) && mv $(DEST)/*.py $(PYMODEL) gen-pydantic: $(PYMODEL) $(RUN) gen-pydantic $(SOURCE_SCHEMA_PATH) --pydantic_version 1 > $(PYMODEL)/nwb_schema_pydantic.py $(RUN) run_patches --phase post_generation_pydantic gen-pydantic-test: $(PYMODEL) $(RUN) gen-pydantic src/nwb_schema_language/schema/test_multival.yml --pydantic_version 1 > $(PYMODEL)/test_multival_pydantic.py # $(RUN) run_patches --phase post_generation test: test-schema test-python test-examples test-schema: $(RUN) gen-project ${GEN_PARGS} -d tmp $(SOURCE_SCHEMA_PATH) test-python: $(RUN) python -m unittest discover lint: $(RUN) linkml-lint $(SOURCE_SCHEMA_PATH) check-config: @(grep my-datamodel about.yaml > /dev/null && printf "\n**Project not configured**:\n\n - Remember to edit 'about.yaml'\n\n" || exit 0) convert-examples-to-%: $(patsubst %, $(RUN) linkml-convert % -s $(SOURCE_SCHEMA_PATH) -C Person, $(shell ${SHELL} find src/data/examples -name "*.yaml")) examples/%.yaml: src/data/examples/%.yaml $(RUN) linkml-convert -s $(SOURCE_SCHEMA_PATH) -C Person $< -o $@ examples/%.json: src/data/examples/%.yaml $(RUN) linkml-convert -s $(SOURCE_SCHEMA_PATH) -C Person $< -o $@ examples/%.ttl: src/data/examples/%.yaml $(RUN) linkml-convert -P EXAMPLE=http://example.org/ -s $(SOURCE_SCHEMA_PATH) -C Person $< -o $@ test-examples: examples/output examples/output: src/nwb_schema_language/schema/nwb_schema_language.yaml mkdir -p $@ $(RUN) linkml-run-examples \ --output-formats json \ --output-formats yaml \ --counter-example-input-directory src/data/examples/invalid \ --input-directory src/data/examples/valid \ --output-directory $@ \ --schema $< > $@/README.md # Test documentation locally serve: mkd-serve # Python datamodel $(PYMODEL): mkdir -p $@ $(DOCDIR): mkdir -p $@ gendoc: $(DOCDIR) cp $(SRC)/docs/*md $(DOCDIR) ; \ $(RUN) gen-doc ${GEN_DARGS} -d $(DOCDIR) $(SOURCE_SCHEMA_PATH) testdoc: gendoc serve MKDOCS = $(RUN) mkdocs mkd-%: $(MKDOCS) $* PROJECT_FOLDERS = sqlschema shex shacl protobuf prefixmap owl jsonschema jsonld graphql excel git-init-add: git-init git-add git-commit git-status git-init: git init git-add: .cruft.json git add .gitignore .github .cruft.json Makefile LICENSE *.md examples utils about.yaml mkdocs.yml poetry.lock project.Makefile pyproject.toml src/nwb_schema_language/schema/*yaml src/*/datamodel/*py src/data src/docs tests src/*/_version.py git add $(patsubst %, project/%, $(PROJECT_FOLDERS)) git-commit: git commit -m 'chore: initial commit' -a git-status: git status # only necessary if setting up via cookiecutter .cruft.json: echo "creating a stub for .cruft.json. IMPORTANT: setup via cruft not cookiecutter recommended!" ; \ touch $@ clean: rm -rf $(DEST) rm -rf tmp rm -fr docs/* rm -fr $(PYMODEL)/* include project.Makefile