Makefile

# This Makefile provides shortcut commands to facilitate local development.

# Common variables
PACKAGE_NAME = winnow

# LAST_COMMIT returns the current HEAD commit
LAST_COMMIT = $(shell git rev-parse --short HEAD)

# VERSION represents a clear statement of which tag based version of the repository you're actually running.
# If you run a tag based version, it returns the according HEAD tag, otherwise it returns:
# * `LAST_COMMIT-staging` if no tags exist
# * `BASED_TAG-SHORT_SHA_COMMIT-staging` if a previous tag exist
VERSION := $(shell git describe --always --exact-match --abbrev=0 --tags $(LAST_COMMIT) 2> /dev/null)
ifndef VERSION
	BASED_VERSION := $(shell git describe --always --abbrev=3 --tags $(git rev-list --tags --max-count=1))
	ifndef BASED_VERSION
	VERSION = $(LAST_COMMIT)-staging
	else
	VERSION = $(BASED_VERSION)-staging
	endif
endif

# Docker variables
DOCKER_HOME_DIRECTORY = "/app"
DOCKER_RUNS_DIRECTORY = "/runs"

DOCKERFILE := Dockerfile

DOCKER_IMAGE_NAME = winnow
DOCKER_IMAGE_TAG = $(VERSION)
DOCKER_IMAGE = $(DOCKER_IMAGE_NAME):$(DOCKER_IMAGE_TAG)

DOCKER_RUN_FLAGS = --rm --gpus all --ipc=host --ulimit memlock=-1 --ulimit stack=67108864 --shm-size='1gb'
DOCKER_RUN_FLAGS_VOLUME_MOUNT_HOME = $(DOCKER_RUN_FLAGS) --volume $(PWD):$(DOCKER_HOME_DIRECTORY)
DOCKER_RUN_FLAGS_VOLUME_MOUNT_RUNS = $(DOCKER_RUN_FLAGS) --volume $(PWD)/runs:$(DOCKER_RUNS_DIRECTORY)
DOCKER_RUN = docker run $(DOCKER_RUN_FLAGS) $(DOCKER_IMAGE_NAME)

PYTEST = uv run pytest tests --verbose --cov=winnow --cov-report xml:coverage.xml --cov-report term-missing --junitxml=pytest.xml --cov-fail-under=0

#################################################################################
## Docker build commands																#
#################################################################################

.PHONY: build build-arm

define docker_buildx_template
	docker buildx build --platform=$(1) --progress=plain . \
		-f $(DOCKERFILE) -t $(2) --build-arg GID=$(shell id -g) \
		--build-arg UID=$(shell id -u)  --build-arg LAST_COMMIT=$(LAST_COMMIT) \
		--build-arg VERSION=$(VERSION) --build-arg HOME_DIRECTORY=$(DOCKER_HOME_DIRECTORY) \
		--build-arg RUNS_DIRECTORY=$(DOCKER_RUNS_DIRECTORY)
endef

## Build Docker image for winnow on AMD64
build:
	$(call docker_buildx_template,linux/amd64,$(DOCKER_IMAGE))

## Build Docker image for winnow on ARM64
build-arm:
	$(call docker_buildx_template,linux/arm64,$(DOCKER_IMAGE))

#################################################################################
## Install packages commands													#
#################################################################################

.PHONY: install install-frozen install-dev

## Install project dependencies (may resolve and update lockfile if needed)
# Note that uv includes the `dev` group by default, so we need to exclude it with `--no-dev`
install:
	uv sync --no-dev

## Install development tools (testing, linting, etc.)
install-dev:
	uv sync

## Install project dependencies exactly as specified in lockfile (fast, no resolution)
install-frozen:
	uv sync --frozen

## Install all dependencies
install-all:
	uv sync --all-extras

#################################################################################
## Development commands														 	#
#################################################################################

.PHONY: tests clean-coverage test-docker bash build-package clean-build clean-workspace test-build clean-all-build test-cli-isolated test-cli-config set-gcp-credentials

## Run all tests
tests:
	$(PYTEST)

## Clean coverage reports
clean-coverage:
	rm -rf htmlcov/ .coverage coverage.xml pytest.xml

## Run all tests in the Docker Image
test-docker:
	docker run $(DOCKER_RUN_FLAGS) $(DOCKER_IMAGE) $(PYTEST)

## Open a bash shell in the Docker image
bash:
	docker run -it $(DOCKER_RUN_FLAGS) $(DOCKER_IMAGE) /bin/bash

## Build the winnow-fdr package (creates wheel and sdist in dist/)
build-package:
	uv build

## Clean all build artifacts (dist/, build/, *.egg-info/)
clean-build:
	rm -rf dist/ build/ *.egg-info/ winnow_fdr.egg-info/

## Build the package and then clean up (safe test build)
test-build: build-package clean-build

## Set the GCP credentials
set-gcp-credentials:
	uv run python scripts/set_gcp_credentials.py
	gcloud auth activate-service-account dtu-denovo-sa@ext-dtu-denovo-sequencing-gcp.iam.gserviceaccount.com --key-file=ext-dtu-denovo-sequencing-gcp.json --project=ext-dtu-denovo-sequencing-gcp

#################################################################################
## Sample data and CLI commands													#
#################################################################################

.PHONY: train-sample predict-sample clean clean-all

## Run winnow train with sample data
train-sample:
	uv run winnow train \
	dataset.spectrum_path_or_directory=examples/example_data/spectra.mgf \
	dataset.predictions_path=examples/example_data/predictions.csv \
	model_output_dir=models/new_model \
	dataset_output_path=results/calibrated_dataset.csv \
	calibrator.features.retention_time_feature.train_fraction=0.3 \
	calibrator.features.retention_time_feature.min_train_points=2 \
	calibrator.hidden_layer_sizes="[32, 16]" \
	calibrator.early_stopping=false \
	calibrator.max_iter=100

## Run winnow predict with sample data (uses locally trained model from models/new_model)
predict-sample:
	uv run winnow predict \
	calibrator.pretrained_model_name_or_path=models/new_model \
	fdr_control.fdr_threshold=1.0 \
	dataset.spectrum_path_or_directory=examples/example_data/spectra.mgf \
	dataset.predictions_path=examples/example_data/predictions.csv

## Clean output directories (does not delete sample data)
clean:
	rm -rf models/ results/