Merge pull request #14 from linkml/refactored-to-poetry

Refactored to use poetry. Updated registry entries

Makefile

@@ -1,90 +1,191 @@
-# All artifacts of the build should be preserved
+MAKEFLAGS += --warn-undefined-variables
+SHELL := bash
+.SHELLFLAGS := -eu -o pipefail -c
+.DEFAULT_GOAL := help
+.DELETE_ON_ERROR:
+.SUFFIXES:
 .SECONDARY:
 
-# ----------------------------------------
-# Model documentation and schema directory
-# ----------------------------------------
-SRC_DIR = src
-PKG_DIR = linkml_registry
-SCHEMA_DIR = $(SRC_DIR)/schema
-MODEL_DOCS_DIR = $(SRC_DIR)/docs
-SOURCE_FILES := $(shell find $(SCHEMA_DIR) -name '*.yaml')
-SRC = $(SCHEMA_DIR)/registry.yaml
-SCHEMA_NAMES = $(patsubst $(SCHEMA_DIR)/%.yaml, %, $(SOURCE_FILES))
-
-SCHEMA_NAME = registry
-SCHEMA_SRC = $(SCHEMA_DIR)/$(SCHEMA_NAME).yaml
-PKG_TGTS = python jsonld_context json_schema
-TGTS = docs python $(PKG_TGTS)
-
-# Targets by PKG_TGT
-PKG_T_GRAPHQL = $(PKG_DIR)/graphql
-PKG_T_JSON = $(PKG_DIR)/json
-PKG_T_JSONLD_CONTEXT = $(PKG_DIR)/jsonld
-PKG_T_JSON_SCHEMA = $(PKG_DIR)/jsonschema
-PKG_T_OWL = $(PKG_DIR)/owl
-PKG_T_RDF = $(PKG_DIR)/rdf
-PKG_T_SHEX = $(PKG_DIR)/shex
-PKG_T_SQLDDL = $(PKG_DIR)/sqlddl
-PKG_T_DOCS = $(MODEL_DOCS_DIR)
-PKG_T_PYTHON = $(PKG_DIR)
-PKG_T_MODEL = $(PKG_DIR)/model
-PKG_T_SCHEMA = $(PKG_T_MODEL)/schema
-
-# Global generation options
-GEN_OPTS = --log_level WARNING
-ENV = export PIPENV_VENV_IN_PROJECT=true && export PIPENV_PIPFILE=make-venv/Pipfile && export PIPENV_IGNORE_VIRTUALENVS=1
-RUN = pipenv run
-
-# ----------------------------------------
-# TOP LEVEL TARGETS
-# ----------------------------------------
-all: install gen
-index: models.yaml all
-
-# ---------------------------------------
-# We don't want to pollute the python environment with linkml tool specific packages.  For this reason,
-# we install an isolated instance of linkml in the pipenv-linkml directory
-# ---------------------------------------
-install: make-venv/env.lock
-
-make-venv/env.lock:
-	$(ENV) && pipenv install
-	touch make-venv/env.lock
-
-uninstall:
-	rm -f make-venv/env.lock
-	$(ENV) && pipenv --rm
-
-# ---------------------------------------
-# Test runner
-# ----------------------------------------
-test:
-	pipenv install --dev
-	pipenv run python -m unittest discover -p 'test_*.py'
-
-# ---------------------------------------
-# GEN: run generator for each target
-# ---------------------------------------
-#gen: $(patsubst %,gen-%,$(TGTS))
-
-gen:
-	$(RUN) gen-project -d . $(SRC)
-
-markdown:
-	$(RUN) gen-markdown -d target/docs/ -I index.md $(SRC)  && \
-	cp src/docs/*.md target/docs/
-
-linkml_registry/registry.py: registry.py 
-	cp $< $@
-
-
-
-# test docs locally.
-docserve:
-	$(RUN) mkdocs serve
-gh-deploy:
-	$(RUN) mkdocs gh-deploy
-
-models.yaml src/docs/registry.md: src/data/models.yaml
-	pipenv run python -m linkml_registry.cli eval -i $< --use-github-api -m src/docs/registry.md -o models.yaml
+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)
+
+
+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/linkml_common/schema/linkml_common.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 $< > $@/README.md
+.PHONY: examples/output
+
+# Test documentation locally
+serve: mkd-serve
+
+# Python datamodel
+$(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/linkml_common/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

README.md

@@ -18,7 +18,7 @@ Registry Schema:
 
 Make a Pull Request on:
 
- * [src/data/models.yaml](src/data/models.yaml)
+ * [src/linkml_registry/data/models.yaml](src/linkml_registry/data/models.yaml)
 
 You should also add the `linkml` tag on your repo so it shows up here: [https://github.com/topics/linkml](https://github.com/topics/linkml)