Makefile

SHELL := /bin/bash
.SHELLFLAGS := -eu -o pipefail -c
.DELETE_ON_ERROR:
.ONESHELL:

include config.mk
-include config.local.mk

.PHONY: help check dirs clean print-config all
.DEFAULT_GOAL := help

help: ## Show targets
	@echo "Usage: make <target>"
	@grep -E '^[a-zA-Z0-9_/.-]+:.*?## ' $(MAKEFILE_LIST) | sort | \
	awk 'BEGIN{FS=":.*?## "}{printf "  %-22s %s\n", $$1, $$2}'

print-config: ## Show config
	@echo "=== CONFIG ($$(date)) ==="
	@echo "FASTA   = $(FASTA)"
	@echo "OUT     = $(OUT)"
	@echo "DATASET = $(DATASET)"
	@echo "IQTREE  = $(IQTREE)"
	@echo "MPTP    = $(MPTP)"
	@echo "PYTHON  = $(PYTHON)"

check: ## Verify core tools
	@for t in "$(PYTHON)"; do command -v $$t >/dev/null || { echo "Missing: $$t"; exit 1; }; done
	@echo "[OK] core tools present"

dirs: ## Create output folders
	@mkdir -p $(OUT)/{logs,trees,spart,tmp}

clean: ## Remove outputs
	@rm -rf $(OUT)

# Snapshot config
$(LOGDIR)/run_config.txt: | dirs
	@$(MAKE) -s print-config >"$@"

# ===== QC =====
$(OUT)/tmp/fasta.qc.ok: $(FASTA) | dirs ## FASTA sanity check
	bin/qc_fasta.sh "$<" >"$(LOGDIR)/qc_fasta.log" 2>&1
	@touch "$@"

# ===== IQ-TREE (ML tree) =====
$(OUT)/trees/ml.treefile: $(FASTA) $(OUT)/tmp/fasta.qc.ok | dirs ## ML tree
	"$(IQTREE)" -s "$<" -m $(IQTREE_MODEL) -bb $(IQTREE_BB) -nt AUTO -seed $(SEED) -pre "$(OUT)/trees/coi" -redo \
	  >"$(LOGDIR)/iqtree.stdout.log" 2>"$(LOGDIR)/iqtree.stderr.log" || { echo "[IQTREE] failed"; exit 1; }
	cp "$(OUT)/trees/coi.treefile" "$@"

# ===== mPTP (MCMC) → SPART =====
$(OUT)/spart/mptp.spart: $(OUT)/trees/ml.treefile | dirs ## mPTP partition from ML tree
	bin/run_mptp.sh "$<" "$(OUT)/tmp/mptp.tsv" $(MPTP_ITERS) $(MPTP_BURNIN) $(MPTP_THIN) $(MPTP_SEED) \
	  >"$(LOGDIR)/mptp.log" 2>&1
	"$(PYTHON)" bin/mptp_tsv_to_spart.py --tsv "$(OUT)/tmp/mptp.tsv" --dataset "$(DATASET)" --out "$@"

# ===== Top-level (core only for now) =====
all: $(LOGDIR)/run_config.txt $(OUT)/trees/ml.treefile $(OUT)/spart/mptp.spart ## Build core (IQ-TREE→mPTP)


# ===== ASAP → SPART =====
$(OUT)/spart/asap.spart: $(FASTA) | dirs ## ASAP partition
	bin/run_asap.sh "$(ASAP)" "$<" "$@" "$(ASAP_DIST)" "$(ASAP_REPS)" "$(SEED)" "$(OUT)/tmp/asap"

.PHONY: fast
fast: ## Quick test profile (cheap settings)
	$(MAKE) -B out/spart/asap.spart ASAP_DIST=K2P ASAP_REPS=100 SEED=42
	$(MAKE) -B out/spart/mptp.spart MPTP_ITERS=100000 MPTP_BURNIN=10000 MPTP_THIN=100 SEED=42