BioGraphRAG/Makefile at main · collaborativebioinformatics/BioGraphRAG · GitHub

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PYTHON ?= python3
VENV ?= .venv
ACTIVATE = source $(VENV)/bin/activate

.PHONY: help setup data prime_to_neptune pkg_to_neptune load_prime load_pkg embed qa api ui teardown lint test

help:
	@echo "Available targets: setup, data, prime_to_neptune, pkg_to_neptune, load_prime, load_pkg, embed, qa, api, ui, teardown, lint, test"

setup:
	@test -d $(VENV) || python3 -m venv $(VENV)
	$(ACTIVATE) && pip install --upgrade pip
	$(ACTIVATE) && pip install -r requirements.txt

data:
	$(ACTIVATE) && $(PYTHON) -m src.data.pubmedkg --config configs/default.yaml

prime_to_neptune:
	$(ACTIVATE) && $(PYTHON) -m src.ingest.prime_to_neptune --config configs/ingest_prime.yaml

pkg_to_neptune:
	$(ACTIVATE) && $(PYTHON) -m src.ingest.pkg_to_neptune --config configs/ingest_pkg.yaml

load_prime:
	$(ACTIVATE) && $(PYTHON) -m src.ingest.neptune_loader --config configs/default.yaml --prefix graph/prime/

load_pkg:
	$(ACTIVATE) && $(PYTHON) -m src.ingest.neptune_loader --config configs/default.yaml --prefix graph/pkg/

embed:
	$(ACTIVATE) && $(PYTHON) -m src.embeddings.text_embed --config configs/default.yaml
	$(ACTIVATE) && $(PYTHON) -m src.embeddings.node_embed --config configs/default.yaml
	$(ACTIVATE) && $(PYTHON) -m src.retrieval.vector_store --config configs/default.yaml

qa:
	$(ACTIVATE) && $(PYTHON) -m src.qa.answer --config configs/default.yaml --question-file configs/demo_questions.yaml

api:
	$(ACTIVATE) && uvicorn src.api.app:app --reload

ui:
	$(ACTIVATE) && streamlit run src/ui/app.py --server.port=8501

teardown:
	$(ACTIVATE) && $(PYTHON) -m src.utils.aws --teardown --config configs/default.yaml

lint:
	$(ACTIVATE) && ruff check src tests

test:
	$(ACTIVATE) && pytest -q