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Makefile
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Makefile
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.DEFAULT_GOAL := default
include config.mk
SERVICES := auth batch ci monitoring website
SERVICES_PLUS_ADMIN_POD := $(SERVICES) admin-pod
SERVICES_IMAGES := $(patsubst %, %-image, $(SERVICES_PLUS_ADMIN_POD))
SERVICES_DATABASES := $(patsubst %, %-db, $(SERVICES))
SERVICES_MODULES := $(SERVICES) gear web_common
CHECK_SERVICES_MODULES := $(patsubst %, check-%, $(SERVICES_MODULES))
SPECIAL_IMAGES := hail-ubuntu batch-worker letsencrypt
HAILGENETICS_IMAGES = $(foreach img,hail vep-grch37-85 vep-grch38-95,hailgenetics-$(img))
CI_IMAGES = ci-utils hail-buildkit base hail-run
PRIVATE_REGISTRY_IMAGES = $(patsubst %, pushed-private-%-image, $(SPECIAL_IMAGES) $(SERVICES_PLUS_ADMIN_POD) $(CI_IMAGES) $(HAILGENETICS_IMAGES))
HAILTOP_VERSION := hail/python/hailtop/hail_version
SERVICES_IMAGE_DEPS = hail-ubuntu-image $(HAILTOP_VERSION) $(shell git ls-files hail/python/hailtop gear web_common)
EMPTY :=
SPACE := $(EMPTY) $(EMPTY)
EXTRA_PYTHONPATH := hail/python:$(subst $(SPACE),:,$(SERVICES_MODULES))
PYTHONPATH ?= ""
ifeq ($(PYTHONPATH), "")
PYTHONPATH := $(EXTRA_PYTHONPATH)
else
PYTHONPATH := $(PYTHONPATH):$(EXTRA_PYTHONPATH)
endif
PYTHON := PYTHONPATH="$(PYTHONPATH)" python3
default:
@echo Do not use this makefile to build hail, for information on how to \
build hail see: https://hail.is/docs/0.2/
@false
.PHONY: check-all
check-all: check-hail check-services
.PHONY: check-hail-fast
check-hail-fast:
ruff check hail
ruff format hail --diff
$(PYTHON) -m pyright hail/python/hailtop
ruff check hail/python/test/hailtop/batch
$(PYTHON) -m pyright hail/python/test/hailtop/batch
.PHONY: pylint-hailtop
pylint-hailtop:
# pylint on hail is still a work in progress
$(PYTHON) -m pylint --rcfile pylintrc hail/python/hailtop --score=n
.PHONY: check-hail
check-hail: check-hail-fast pylint-hailtop
cd hail && sh millw __.checkFormat + __.fix --check
.PHONY: check-services
check-services: $(CHECK_SERVICES_MODULES)
.PHONY: pylint-%
pylint-%:
$(PYTHON) -m pylint --rcfile pylintrc --recursive=y $* --score=n
.PHONY: check-%-fast
check-%-fast:
ruff check $*
ruff format $* --diff
$(PYTHON) -m pyright $*
curlylint $*
cd $* && bash ../check-sql.sh
.PHONY: check-%
$(CHECK_SERVICES_MODULES): check-%: check-%-fast pylint-%
.PHONY: isort-%
isort-%:
ruff check --select I --fix $*
.PHONY: check-pip-requirements
check-pip-requirements:
./check_pip_requirements.sh \
hail/python/hailtop \
hail/python \
hail/python/dev \
gear \
web_common \
batch \
ci
.PHONY: install-dev-requirements
install-dev-requirements:
python3 -m pip install \
-r hail/python/pinned-requirements.txt \
-r hail/python/dev/pinned-requirements.txt \
-r gear/pinned-requirements.txt \
-r web_common/pinned-requirements.txt \
-r batch/pinned-requirements.txt \
-r ci/pinned-requirements.txt
hail/python/hailtop/pinned-requirements.txt: hail/python/hailtop/requirements.txt
./generate-pip-lockfile.sh hail/python/hailtop
hail/python/pinned-requirements.txt: hail/python/hailtop/pinned-requirements.txt hail/python/requirements.txt
./generate-pip-lockfile.sh hail/python
hail/python/dev/pinned-requirements.txt: hail/python/pinned-requirements.txt hail/python/dev/requirements.txt
./generate-pip-lockfile.sh hail/python/dev
gear/pinned-requirements.txt: hail/python/pinned-requirements.txt hail/python/dev/pinned-requirements.txt hail/python/hailtop/pinned-requirements.txt gear/requirements.txt
./generate-pip-lockfile.sh gear
web_common/pinned-requirements.txt: gear/pinned-requirements.txt web_common/requirements.txt
./generate-pip-lockfile.sh web_common
batch/pinned-requirements.txt: web_common/pinned-requirements.txt batch/requirements.txt
./generate-pip-lockfile.sh batch
ci/pinned-requirements.txt: web_common/pinned-requirements.txt ci/requirements.txt
./generate-pip-lockfile.sh ci
.PHONY: generate-pip-lockfiles
generate-pip-lockfiles: hail/python/hailtop/pinned-requirements.txt
generate-pip-lockfiles: hail/python/pinned-requirements.txt
generate-pip-lockfiles: hail/python/dev/pinned-requirements.txt
generate-pip-lockfiles: gear/pinned-requirements.txt
generate-pip-lockfiles: web_common/pinned-requirements.txt
generate-pip-lockfiles: batch/pinned-requirements.txt
generate-pip-lockfiles: ci/pinned-requirements.txt
$(HAILTOP_VERSION):
$(MAKE) -C hail python/hailtop/hail_version
%-image: IMAGE_NAME = $(patsubst %-image,%,$@):$(TOKEN)
hailgenetics-%-image: IMAGE_NAME = hailgenetics/$(patsubst hailgenetics-%-image,%,$@):$(TOKEN)
hail-ubuntu-image: $(shell git ls-files docker/hail-ubuntu)
./docker-build.sh docker/hail-ubuntu Dockerfile $(IMAGE_NAME) --build-arg DOCKER_PREFIX=$(DOCKER_PREFIX)
echo $(IMAGE_NAME) > $@
base-image: hail-ubuntu-image docker/Dockerfile.base
./docker-build.sh . docker/Dockerfile.base $(IMAGE_NAME) --build-arg BASE_IMAGE=$(shell cat hail-ubuntu-image)
echo $(IMAGE_NAME) > $@
hail-run-image: base-image hail/Dockerfile.hail-run hail/python/pinned-requirements.txt hail/python/dev/pinned-requirements.txt docker/core-site.xml
$(MAKE) -C hail wheel
./docker-build.sh . hail/Dockerfile.hail-run $(IMAGE_NAME) --build-arg BASE_IMAGE=$(shell cat base-image)
echo $(IMAGE_NAME) > $@
hailgenetics-hail-image: hail-ubuntu-image docker/hailgenetics/hail/Dockerfile $(shell git ls-files hail/src/main hail/python)
$(MAKE) HAIL_RELEASE_MODE=1 -C hail wheel
./docker-build.sh . docker/hailgenetics/hail/Dockerfile $(IMAGE_NAME) \
--build-arg BASE_IMAGE=$(shell cat hail-ubuntu-image)
echo $(IMAGE_NAME) > $@
hail-dev-image: hailgenetics-hail-image hail/python/dev/pinned-requirements.txt
./docker-build.sh . docker/Dockerfile.hail-dev $(IMAGE_NAME) \
--build-arg HAIL_IMAGE=$(shell cat $<)
echo $(IMAGE_NAME) > $@
hail-0.1-docs-5a6778710097.tar.gz:
gcloud storage cp gs://hail-common/builds/0.1/docs/$@ .
hail/build/www: hail-0.1-docs-5a6778710097.tar.gz $(shell git ls-files hail)
@echo !!! This target does not render the notebooks because it takes a long time !!!
$(MAKE) -C hail hail-docs-do-not-render-notebooks batch-docs
mkdir -p hail/build/www/docs/0.1
tar -xvf hail-0.1-docs-5a6778710097.tar.gz -C hail/build/www/docs/0.1 --strip-components 2
touch $@ # Copying into the dir does not necessarily touch it
website/website/docs: hail/build/www
cp -r hail/build/www/docs website/website/
touch $@ # Copying into the dir does not necessarily touch it
docs.tar.gz: hail/build/www
tar czf docs.tar.gz -C hail/build/www .
website-image: docs.tar.gz
$(SERVICES_IMAGES): %-image: $(SERVICES_IMAGE_DEPS) $(shell git ls-files $$* ':!:**/deployment.yaml')
./docker-build.sh . $*/Dockerfile $(IMAGE_NAME) --build-arg BASE_IMAGE=$(shell cat hail-ubuntu-image)
echo $(IMAGE_NAME) > $@
ci-utils-image: base-image $(SERVICES_IMAGE_DEPS) $(shell git ls-files ci)
./docker-build.sh . ci/Dockerfile.ci-utils $(IMAGE_NAME) --build-arg BASE_IMAGE=$(shell cat base-image)
echo $(IMAGE_NAME) > $@
hail-buildkit-image: ci/buildkit/Dockerfile
./docker-build.sh ci buildkit/Dockerfile $(IMAGE_NAME) --build-arg DOCKER_PREFIX=$(DOCKER_PREFIX)
echo $(IMAGE_NAME) > $@
batch/jvm-entryway/build/libs/jvm-entryway.jar: $(shell git ls-files batch/jvm-entryway)
cd batch/jvm-entryway && ./gradlew shadowJar
batch-worker-image: batch/jvm-entryway/build/libs/jvm-entryway.jar $(SERVICES_IMAGE_DEPS) $(shell git ls-files batch)
python3 ci/jinja2_render.py '{"hail_ubuntu_image":{"image":"'$$(cat hail-ubuntu-image)'"},"global":{"cloud":"$(CLOUD)"}}' batch/Dockerfile.worker batch/Dockerfile.worker.out
./docker-build.sh . batch/Dockerfile.worker.out $(IMAGE_NAME)
echo $(IMAGE_NAME) > $@
hailgenetics-vep-grch37-85-image: hail-ubuntu-image
./docker-build.sh docker/vep docker/vep/grch37/85/Dockerfile $(IMAGE_NAME) \
--build-arg BASE_IMAGE=$(shell cat hail-ubuntu-image)
echo $(IMAGE_NAME) > $@
hailgenetics-vep-grch38-95-image: hail-ubuntu-image
./docker-build.sh docker/vep docker/vep/grch38/95/Dockerfile $(IMAGE_NAME) \
--build-arg BASE_IMAGE=$(shell cat hail-ubuntu-image)
echo $(IMAGE_NAME) > $@
terra-batch-image: batch-image
./docker-build.sh . batch/terra-chart/Dockerfile.batch $(IMAGE_NAME) \
--build-arg BASE_IMAGE=$(shell cat batch-image)
echo $(IMAGE_NAME) > $@
terra-batch-worker-image: batch-worker-image
$(MAKE) -C hail shadowJar HAIL_RELEASE_MODE=1
./docker-build.sh . batch/terra-chart/Dockerfile.worker $(IMAGE_NAME) \
--build-arg BASE_IMAGE=$(shell cat batch-worker-image)
echo $(IMAGE_NAME) > $@
letsencrypt-image:
./docker-build.sh letsencrypt Dockerfile $(IMAGE_NAME)
echo $(IMAGE_NAME) > $@
$(PRIVATE_REGISTRY_IMAGES): pushed-private-%-image: %-image
! [ -z $(NAMESPACE) ] # call this like: make ... NAMESPACE=default
[ $(DOCKER_PREFIX) != docker.io ] # DOCKER_PREFIX should be an internal private registry
! [ -z $(DOCKER_PREFIX) ] # DOCKER_PREFIX must not be empty
docker tag $(shell cat $*-image) $(DOCKER_PREFIX)/$(shell cat $*-image)
docker push $(DOCKER_PREFIX)/$(shell cat $*-image)
echo $(DOCKER_PREFIX)/$(shell cat $*-image) > $@
.PHONY: local-mysql
local-mysql:
cd docker/mysql && docker compose up -d
.PHONY: $(SERVICES_DATABASES)
$(SERVICES_DATABASES): %-db: local-mysql
ifdef DROP
$(SERVICES_DATABASES): %-db:
MYSQL_PWD=pw mysql -h 127.0.0.1 -u root -e 'DROP DATABASE `local-$*`'
else
$(SERVICES_DATABASES): %-db:
python3 ci/create_local_database.py $* local-$*
endif
.PHONY: sass-compile-watch
sass-compile-watch:
cd web_common/web_common && sass --watch -I styles --style=compressed styles:static/css
.PHONY: run-dev-proxy
run-dev-proxy:
SERVICE=$(SERVICE) adev runserver --root . devbin/dev_proxy.py
.PHONY: devserver
devserver:
$(MAKE) -j 2 sass-compile-watch run-dev-proxy
.PHONY: benchmark
benchmark: hail-dev-image
$(MAKE) -C hail HAIL_DEV_IMAGE="$(shell cat $<)" benchmark