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Makefile
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.DEFAULT_GOAL := default
include config.mk
SERVICES := auth batch ci notebook monitoring website
SERVICES_PLUS_ADMIN_POD := $(SERVICES) admin-pod
SERVICES_IMAGES := $(patsubst %, %-image, $(SERVICES_PLUS_ADMIN_POD))
SERVICES_MODULES := $(SERVICES) gear web_common
CHECK_SERVICES_MODULES := $(patsubst %, check-%, $(SERVICES_MODULES))
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/python/hail
ruff check hail/python/hailtop
$(PYTHON) -m pyright hail/python/hailtop
.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
.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 $*
$(PYTHON) -m pyright $*
$(PYTHON) -m black $* --check --diff
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 \
auth \
batch \
ci
.PHONY: check-linux-pip-requirements
check-linux-pip-requirements:
./check_linux_pip_requirements.sh \
hail/python/hailtop \
hail/python \
hail/python/dev \
gear \
web_common \
auth \
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 auth/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-linux-pip-lockfile.sh hail/python/hailtop
hail/python/pinned-requirements.txt: hail/python/hailtop/pinned-requirements.txt hail/python/requirements.txt
./generate-linux-pip-lockfile.sh hail/python
hail/python/dev/pinned-requirements.txt: hail/python/pinned-requirements.txt hail/python/dev/requirements.txt
./generate-linux-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-linux-pip-lockfile.sh gear
web_common/pinned-requirements.txt: gear/pinned-requirements.txt web_common/requirements.txt
./generate-linux-pip-lockfile.sh web_common
auth/pinned-requirements.txt: web_common/pinned-requirements.txt auth/requirements.txt
./generate-linux-pip-lockfile.sh auth
batch/pinned-requirements.txt: web_common/pinned-requirements.txt batch/requirements.txt
./generate-linux-pip-lockfile.sh batch
ci/pinned-requirements.txt: web_common/pinned-requirements.txt ci/requirements.txt
./generate-linux-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: auth/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
hail-ubuntu-image: $(shell git ls-files docker/hail-ubuntu)
$(eval HAIL_UBUNTU_IMAGE := $(DOCKER_PREFIX)/hail-ubuntu:$(TOKEN))
python3 ci/jinja2_render.py '{"global":{"docker_prefix":"$(DOCKER_PREFIX)"}}' docker/hail-ubuntu/Dockerfile docker/hail-ubuntu/Dockerfile.out
./docker-build.sh docker/hail-ubuntu Dockerfile.out $(HAIL_UBUNTU_IMAGE)
echo $(HAIL_UBUNTU_IMAGE) > $@
base-image: hail-ubuntu-image docker/Dockerfile.base
$(eval BASE_IMAGE := $(DOCKER_PREFIX)/base:$(TOKEN))
python3 ci/jinja2_render.py '{"hail_ubuntu_image":{"image":"'$$(cat hail-ubuntu-image)'"}}' docker/Dockerfile.base docker/Dockerfile.base.out
./docker-build.sh . docker/Dockerfile.base.out $(BASE_IMAGE)
echo $(BASE_IMAGE) > $@
hail-run-image: base-image hail/Dockerfile.hail-run hail/python/pinned-requirements.txt hail/python/dev/pinned-requirements.txt docker/core-site.xml
$(eval BASE_IMAGE := $(DOCKER_PREFIX)/hail-run:$(TOKEN))
$(MAKE) -C hail wheel
python3 ci/jinja2_render.py '{"base_image":{"image":"'$$(cat base-image)'"}}' hail/Dockerfile.hail-run hail/Dockerfile.hail-run.out
./docker-build.sh . hail/Dockerfile.hail-run.out $(BASE_IMAGE)
echo $(BASE_IMAGE) > $@
private-repo-hailgenetics-hail-image: hail-ubuntu-image docker/hailgenetics/hail/Dockerfile $(shell git ls-files hail/src/main hail/python)
$(eval PRIVATE_REPO_HAILGENETICS_HAIL_IMAGE := $(DOCKER_PREFIX)/hailgenetics/hail:$(TOKEN))
$(MAKE) -C hail wheel
tar -cvf wheel-container.tar \
-C hail/build/deploy/dist \
hail-$$(cat hail/python/hail/hail_pip_version)-py3-none-any.whl
python3 ci/jinja2_render.py '{"hail_ubuntu_image":{"image":"'$$(cat hail-ubuntu-image)'"}}' docker/hailgenetics/hail/Dockerfile docker/hailgenetics/hail/Dockerfile.out
./docker-build.sh . docker/hailgenetics/hail/Dockerfile.out $(PRIVATE_REPO_HAILGENETICS_HAIL_IMAGE)
rm wheel-container.tar
echo $(PRIVATE_REPO_HAILGENETICS_HAIL_IMAGE) > $@
.PHONY: docs
docs:
$(MAKE) -C hail hail-docs-no-test batch-docs
gcloud storage cp gs://hail-common/builds/0.1/docs/hail-0.1-docs-5a6778710097.tar.gz .
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
rm hail-0.1-docs-5a6778710097.tar.gz
tar czf docs.tar.gz -C hail/build/www .
website-image: docs
$(SERVICES_IMAGES): %-image: $(SERVICES_IMAGE_DEPS) $(shell git ls-files $$*)
$(eval IMAGE := $(DOCKER_PREFIX)/$*:$(TOKEN))
python3 ci/jinja2_render.py '{"hail_ubuntu_image":{"image":"'$$(cat hail-ubuntu-image)'"}}' $*/Dockerfile $*/Dockerfile.out
./docker-build.sh . $*/Dockerfile.out $(IMAGE)
echo $(IMAGE) > $@
ci-utils-image: base-image $(SERVICES_IMAGE_DEPS) $(shell git ls-files ci)
$(eval CI_UTILS_IMAGE := $(DOCKER_PREFIX)/ci-utils:$(TOKEN))
python3 ci/jinja2_render.py '{"base_image":{"image":"'$$(cat base-image)'"}}' ci/Dockerfile.ci-utils ci/Dockerfile.ci-utils.out
./docker-build.sh . ci/Dockerfile.ci-utils.out $(CI_UTILS_IMAGE)
echo $(CI_UTILS_IMAGE) > $@
hail-buildkit-image: ci/buildkit/Dockerfile
$(eval HAIL_BUILDKIT_IMAGE := $(DOCKER_PREFIX)/hail-buildkit:$(TOKEN))
python3 ci/jinja2_render.py '{"global":{"docker_prefix":"$(DOCKER_PREFIX)"}}' ci/buildkit/Dockerfile ci/buildkit/Dockerfile.out
./docker-build.sh ci buildkit/Dockerfile.out $(HAIL_BUILDKIT_IMAGE)
echo $(HAIL_BUILDKIT_IMAGE) > $@
batch/jvm-entryway/build/libs/jvm-entryway.jar: $(shell git ls-files batch/jvm-entryway)
cd batch/jvm-entryway && ./gradlew shadowJar
batch-worker-image: batch/jvm-entryway/build/libs/jvm-entryway.jar $(SERVICES_IMAGE_DEPS) $(shell git ls-files batch)
$(eval BATCH_WORKER_IMAGE := $(DOCKER_PREFIX)/batch-worker:$(TOKEN))
python3 ci/jinja2_render.py '{"hail_ubuntu_image":{"image":"'$$(cat hail-ubuntu-image)'"},"global":{"cloud":"$(CLOUD)"}}' batch/Dockerfile.worker batch/Dockerfile.worker.out
./docker-build.sh . batch/Dockerfile.worker.out $(BATCH_WORKER_IMAGE)
echo $(BATCH_WORKER_IMAGE) > $@
vep-grch37-image: hail-ubuntu-image
$(eval VEP_GRCH37_IMAGE := $(DOCKER_PREFIX)/hailgenetics/vep-grch37-85:$(TOKEN))
python3 ci/jinja2_render.py '{"hail_ubuntu_image":{"image":"'$$(cat hail-ubuntu-image)'"}}' vep/grch37/85/Dockerfile vep/grch37/85/Dockerfile.out
./docker-build.sh docker/vep/grch37/85/Dockerfile.out $(VEP_GRCH37_IMAGE)
echo $(VEP_GRCH37_IMAGE) > $@
vep-grch38-image: hail-ubuntu-image
$(eval VEP_GRCH38_IMAGE := $(DOCKER_PREFIX)/hailgenetics/vep-grch38-95:$(TOKEN))
python3 ci/jinja2_render.py '{"hail_ubuntu_image":{"image":"'$$(cat hail-ubuntu-image)'"}}' vep/grch38/95/Dockerfile vep/grch38/95/Dockerfile.out
./docker-build.sh docker/vep/grch38/95/Dockerfile.out $(VEP_GRCH38_IMAGE)
echo $(VEP_GRCH38_IMAGE) > $@