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Makefile
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init:
pip install -r requirements/main.txt
pip install -r requirements/dev.txt
pip install --editable .[dev]
update-deps:
# --allow-unsafe pins packages considered unsafe: distribute, pip, setuptools.
pip install --upgrade pip-tools pip setuptools
pip-compile --upgrade --build-isolation \
--allow-unsafe --resolver=backtracking --strip-extras \
--output-file requirements/main.txt \
requirements/main.in
pip-compile --allow-unsafe --upgrade --build-isolation \
--allow-unsafe --resolver=backtracking --strip-extras \
--output-file requirements/dev.txt \
requirements/dev.in
update: update-deps init
up-dev:
docker-compose up --build --force-recreate --detach --remove-orphans
dev-reset-db:
docker compose \
exec mongo /bin/bash -c "./app_tests/mongorestore-nmdc-testdb.sh"
up-test:
docker-compose --file docker-compose.test.yml \
up --build --force-recreate --detach --remove-orphans
test-build:
docker compose --file docker-compose.test.yml \
up test --build --force-recreate --detach --remove-orphans
test-dbinit:
docker compose --file docker-compose.test.yml \
exec mongo /bin/bash -c "/mongorestore-nmdc-testdb.sh"
test-run:
docker compose --file docker-compose.test.yml run test
test: test-build test-run
lint:
# Python syntax errors or undefined names
flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics --extend-ignore=F722
# exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 \
--statistics --extend-exclude="./build/" --extend-ignore=F722
down-dev:
docker-compose down
down-test:
docker-compose --file docker-compose.test.yml down
follow-fastapi:
docker-compose logs fastapi -f
fastapi-docker:
./docker-build.sh microbiomedata/nmdc-runtime-fastapi nmdc_runtime/fastapi.Dockerfile
fastapi-deploy-spin:
rancher kubectl rollout restart deployment/runtime-fastapi --namespace=nmdc-dev
dagster-docker:
./docker-build.sh microbiomedata/nmdc-runtime-dagster nmdc_runtime/dagster.Dockerfile
dagster-deploy-spin:
rancher kubectl rollout restart deployment/dagit --namespace=nmdc-dev
rancher kubectl rollout restart deployment/dagster-daemon --namespace=nmdc-dev
publish:
invoke publish
docs-dev:
mkdocs serve -a localhost:8080
nersc-sshproxy:
bash ~/nersc-sshproxy.sh # https://docs.nersc.gov/connect/mfa/#sshproxy
nersc-mongo-tunnels:
ssh -L27072:mongo-loadbalancer.nmdc.production.svc.spin.nersc.org:27017 \
-L28082:mongo-loadbalancer.nmdc-dev.development.svc.spin.nersc.org:27017 \
-L27092:mongo-loadbalancer.nmdc-dev.production.svc.spin.nersc.org:27017 \
-o ServerAliveInterval=60 \
dtn02.nersc.gov
mongorestore-nmdcdb-lite-archive:
wget https://portal.nersc.gov/project/m3408/meta/mongodumps/nmdcdb.lite.archive.gz
mongorestore --host localhost:27018 --username admin --password root --drop --gzip \
--archive=nmdcdb.lite.archive.gz
rm nmdcdb.lite.archive.gz
quick-blade:
python -c "from nmdc_runtime.api.core.idgen import generate_id; print(f'nmdc:nt-11-{generate_id(length=8, split_every=0)}')"
.PHONY: init update-deps update up-dev down-dev follow-fastapi \
fastapi-docker dagster-docker publish docs