Moving monarch-py into monarch-app (#189)

- Merge monarch-py and monarch-api into backend of monarch-app
- Combine and update documentation
- api is now an optional extra and comes with its own command:
    - `cd <monarch-app>`
    - `poetry -C backend install -E api`
    - `monarch-api`
- add option to download specific version of solr kg
- bump minor version
- update testing a bit, disabled a couple until we can get a decent mock
solr implementation
- they still run locally though, so before each commit/pr we should
absolutely spin up a local solr and run `make test-backend` for now (not
ideal, but. where we're at)

.github/workflows/test-backend.yaml

@@ -34,7 +34,7 @@ jobs:
       #    install your root project, if required
       #----------------------------------------------
       - name: Install library
-        run: poetry -C backend install --no-interaction
+        run: poetry -C backend install --no-interaction -E api 
 
       #----------------------------------------------
       #              run pytest

Makefile

@@ -1,6 +1,7 @@
-RUN = poetry -C backend/ run
-VERSION = $(shell cd backend && poetry version -s)
+RUN = poetry -C backend run
+VERSION = $(shell poetry -C backend version -s)
 ROOTDIR = $(shell pwd)
+SCHEMADIR = $(ROOTDIR)/backend/src/monarch_py/datamodels
 
 ### Help ###
 .PHONY: help
@@ -62,7 +63,7 @@ install: install-backend install-frontend
 .PHONY: install-backend
 install-backend:
 	cd backend && \
-		poetry install
+		poetry install -E api --with dev
 
 
 .PHONY: install-frontend
@@ -73,24 +74,21 @@ install-frontend:
 
 
 .PHONY: model
-model: schema/
-	$(RUN) monarch schema > schema/model.yaml
-	$(RUN) gen-pydantic schema/model.yaml > backend/src/monarch_api/model.py
-	$(RUN) gen-typescript schema/model.yaml > frontend/src/api/model.ts
-	$(RUN) black backend/src/monarch_api/model.py
+model: install-backend	
+	$(RUN) gen-pydantic $(SCHEMADIR)/model.yaml > $(SCHEMADIR)/model.py
+	$(RUN) gen-typescript $(SCHEMADIR)/model.yaml > frontend/src/api/model.ts
+	$(RUN) black backend/src/monarch_py/datamodels/model.py
 
 
-.PHONY: fixtures
-fixtures: install-backend
-	@echo "Generating fixtures..."
-	@echo "This requires a running instance of Monarch Solr."
-	$(RUN) python scripts/generate_fixtures.py
-	$(RUN) black backend/tests/fixtures/
+### Documentation ###
+
+docs/Data-Model:
+	mkdir -p $@
 
-# Documentation
 .PHONY: docs
-docs: install-backend model
-	$(RUN) gen-doc -d $(ROOTDIR)/docs/Data-Model/ $(ROOTDIR)/schema/model.yaml
+docs: install-backend docs/Data-Model
+	$(RUN) gen-doc -d $(ROOTDIR)/docs/Data-Model/ $(SCHEMADIR)/model.yaml
+	$(RUN) typer backend/src/monarch_py/cli.py utils docs --name monarch --output docs/Usage/CLI.md
 	$(RUN) mkdocs build
 
 
@@ -101,16 +99,25 @@ test: test-backend test-frontend
 
 
 .PHONY: test-backend
-test-backend: install-backend model
+test-backend: 
 	$(RUN) pytest backend/tests
 
 
 .PHONY: test-frontend
-test-frontend: install-frontend model
+test-frontend: 
 	cd frontend && \
 		yarn test
 
 
+.PHONY: fixtures
+fixtures: 
+	@echo "Generating fixtures..."
+	@echo "This requires a running instance of Monarch Solr."
+	$(RUN) python scripts/generate_fixtures.py
+	$(RUN) black backend/tests/fixtures/
+	cd frontend && \
+		yarn lint 
+
 ### Development ###
 
 .PHONY: dev-frontend
@@ -119,10 +126,10 @@ dev-frontend: frontend/src/api/model.ts
 		yarn dev
 
 
-.PHONY: dev-backend
-dev-backend: backend/src/monarch_api/model.py
+.PHONY: dev-api
+dev-api: 
 	cd backend && \
-		poetry run uvicorn src.monarch_api.main:app --reload
+		poetry run uvicorn src.monarch_py.api.main:app --reload
 
 
 ### Docker ###
@@ -151,34 +158,34 @@ clean:
 
 .PHONY: clobber
 clobber:
-	rm -f schema/monarch-py.yaml \
-		backend/src/monarch_api/model.py \
+	rm -f schema/model.yaml \
+		backend/src/monarch_py/datamodels/model.py \
 		frontend/src/api/model.ts
 
 
 .PHONY: lint
-lint: install lint-frontend lint-backend
+lint: lint-frontend lint-backend
 
 
 .PHONY: lint-frontend
-lint-frontend: install-frontend
+lint-frontend: 
 	cd frontend && \
 		yarn test:lint
 
 
 .PHONY: lint-backend
-lint-backend: install-backend
+lint-backend: 
 	$(RUN) flake8 --exit-zero --max-line-length 120 backend/src backend/tests
 	$(RUN) isort --check-only --diff backend/src backend/tests
-	$(RUN) black --check --diff backend/src backend/tests
+	$(RUN) black --check --diff -l 120 backend/src backend/tests
 
 
 .PHONY: format
 format: format-frontend format-backend
 
 
 .PHONY: format-backend
-format-backend: install-backend
+format-backend: 
 	$(RUN) autoflake \
 		--recursive \
 		--remove-all-unused-imports \
@@ -187,10 +194,10 @@ format-backend: install-backend
 		--in-place \
 		backend/src backend/tests
 	$(RUN) isort backend/src backend/tests
-	$(RUN) black backend/src backend/tests
+	$(RUN) black -l 120 backend/src backend/tests
 
 
 .PHONY: format-frontend
-format-frontend: install-frontend
+format-frontend:
 	cd frontend && \
 		yarn lint

backend/.gitignore

@@ -0,0 +1,145 @@
+model/biolink-model.yaml
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+pip-wheel-metadata/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+.python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+*-env/
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# data input and ouptut
+data/
+output/
+test-output/
+
+#IDE stuff
+.idea/
+
+#MacOS DS Store
+.DS_STORE
+
+# Transform logs
+logs/

backend/Dockerfile

@@ -29,7 +29,7 @@ RUN apt-get update -y && \
 
 # copy project requirement files here to ensure they will be cached.
 WORKDIR $PYSETUP_PATH
-COPY . /opt/monarch-api
+COPY . /opt/monarch-app
 
 # install runtime deps - uses $POETRY_VIRTUALENVS_IN_PROJECT internally
 RUN curl -sSL https://install.python-poetry.org | python3 && \
@@ -41,11 +41,11 @@ RUN curl -sSL https://install.python-poetry.org | python3 && \
 
 FROM builder-base as production
 ENV SKLEARN_ALLOW_DEPRECATED_SKLEARN_PACKAGE_INSTALL=True
-WORKDIR /opt/monarch-api/backend
+WORKDIR /opt/monarch-app/backend
 
-RUN poetry install
+RUN poetry install -E api
 
-CMD ["/opt/poetry/bin/poetry", "run", "uvicorn", "src.monarch_api.main:app", "--host", "0.0.0.0", "--port", "8000"]
+CMD ["/opt/poetry/bin/poetry", "run", "uvicorn", "src.monarch_py.api.main:app", "--host", "0.0.0.0", "--port", "8000"]
 
 ### Image URLs for reference ###
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