Makefile

# STRING Database Science Skill - developer tasks
#
#   make test          offline unit tests (no network required)
#   make test-live     full suite including live STRING/UniProt integration tests
#   make lint          ruff static analysis
#   make regenerate-results   rebuild results/ from live STRING queries
#
# All targets use `uv run`, which resolves dependencies from pyproject.toml /
# the PEP 723 metadata in the CLI script.

CLI := skills/string_database/scripts/string_cli.py
GENE_FILE := sample_data/synthetic_cancer_genes.txt
TEST_RUNNER := uv run --with pytest --with polite-http pytest

.PHONY: test test-live test-valuesranks lint regenerate-results clean-results

test:
	RUN_LIVE_TESTS=0 $(TEST_RUNNER) tests/ -v

test-live:
	RUN_LIVE_TESTS=1 $(TEST_RUNNER) tests/ -v

test-valuesranks:
	RUN_LIVE_TESTS=1 RUN_LIVE_VALUESRANKS=1 $(TEST_RUNNER) tests/test_live_smoke.py -v -k valuesranks

lint:
	uv run --with ruff ruff check skills tests conftest.py

# Rebuild every committed artifact in results/ from live STRING queries so the
# checked-in dashboard is provably produced by the current code. Every step reads
# the same gene list; `@file` expands one identifier per line.
regenerate-results:
	uv run $(CLI) map -i @$(GENE_FILE) -s 9606 --limit_to_best -o results/mapped_genes.tsv
	uv run $(CLI) network -i @$(GENE_FILE) -s 9606 --required_score 400 --summary -o results/network_edges.tsv
	uv run $(CLI) ppi-enrichment -i @$(GENE_FILE) -s 9606 -o results/ppi_enrichment.tsv
	uv run $(CLI) enrichment -i @$(GENE_FILE) -s 9606 --fdr 0.05 --summary -o results/enrichment.tsv
	uv run $(CLI) dashboard \
		--title "Synthetic Cancer Gene Network & Pathway Analysis" \
		--map_file results/mapped_genes.tsv \
		--network_file results/network_edges.tsv \
		--ppi_file results/ppi_enrichment.tsv \
		--enrichment_file results/enrichment.tsv \
		-o results/dashboard.html

clean-results:
	rm -f results/mapped_genes.tsv results/network_edges.tsv results/ppi_enrichment.tsv \
	      results/enrichment.tsv results/dashboard.html