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build.yaml
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build.yaml
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steps:
- kind: createNamespace
name: default_ns
namespaceName: default
public: true
secrets:
- hail-vdc-sa-key
- gcr-pull-key
- hail-ci-0-1-github-oauth-token
- test-gsa-key
- auth-oauth2-client-secret
- scorecard-github-access-token
- zulip-config
- kind: deploy
name: deploy_batch_sa
namespace:
valueFrom: default_ns.name
config: batch/service-account.yaml
dependsOn:
- default_ns
- kind: createNamespace
name: batch_pods_ns
namespaceName: batch-pods
public: false
secrets:
- gcr-push-service-account-key
- test-gsa-key
- hail-ci-0-1-service-account-key
dependsOn:
- default_ns
- deploy_batch_sa
- kind: deploy
name: deploy_batch_sa_batch_pods
namespace:
valueFrom: batch_pods_ns.name
config: batch/service-account-batch-pods.yaml
dependsOn:
- default_ns
- batch_pods_ns
- deploy_batch_sa
- kind: deploy
name: deploy_default_admin_admin
namespace:
valueFrom: batch_pods_ns.name
config: ci/default-admin-admin.yaml
dependsOn:
- default_ns
- batch_pods_ns
- kind: deploy
name: deploy_ci_agent
namespace:
valueFrom: batch_pods_ns.name
config: ci/ci-agent.yaml
dependsOn:
- batch_pods_ns
- kind: deploy
name: deploy_ci_agent_default
namespace:
valueFrom: default_ns.name
config: ci/ci-agent-default.yaml
dependsOn:
- default_ns
- batch_pods_ns
- kind: deploy
name: deploy_test_batch_sa
namespace:
valueFrom: batch_pods_ns.name
config: batch/test-sa.yaml
dependsOn:
- batch_pods_ns
- kind: buildImage
name: base_image
dockerFile: docker/Dockerfile.base
contextPath: .
publishAs: base
- kind: buildImage
name: service_base_image
dockerFile: docker/Dockerfile.service-base
contextPath: .
publishAs: service-base
dependsOn:
- base_image
- kind: runImage
name: copy_files
image:
valueFrom: base_image.image
script: |
set -ex
cd /io
mkdir repo
cd repo
{{ code.checkout_script }}
make -C hail python/hail/hail_version python/hail/hail_pip_version
git rev-parse HEAD > git_version
outputs:
- from: /io/repo/auth/sql
to: /repo/auth/
- from: /io/repo/ci/sql
to: /repo/ci/
- from: /io/repo/batch/sql
to: /repo/batch/
- from: /io/repo/batch/test
to: /repo/batch/
- from: /io/repo/notebook/sql
to: /repo/notebook/
- from: /io/repo/hail/python/hailtop
to: /repo/hailtop/
- from: /io/repo/hail/python/test
to: /repo/test/
- from: /io/repo/hail/python/cluster-tests/
to: /repo/hail/python/cluster-tests
- from: /io/repo/hail/python/hail/hail_version
to: /hail_version
- from: /io/repo/hail/python/hail/hail_pip_version
to: /hail_pip_version
- from: /io/repo/git_version
to: /git_version
dependsOn:
- base_image
- kind: runImage
name: check_gear
image:
valueFrom: service_base_image.image
script: |
set -ex
python3 -m flake8 gear
python3 -m pylint --rcfile pylintrc gear
python3 -m flake8 web_common
python3 -m pylint --rcfile pylintrc web_common
dependsOn:
- service_base_image
- kind: createDatabase
name: test_database_instance
databaseName: test-instance
migrations: []
namespace:
valueFrom: default_ns.name
scopes:
- test
dependsOn:
- default_ns
- kind: runImage
name: create_database_server_config
image:
valueFrom: base_image.image
script: |
kubectl -n {{ default_ns.name }} get -o json --export secret {{ test_database_instance.admin_secret_name }} | jq '.metadata.name = "database-server-config"' | kubectl -n {{ default_ns.name }} apply -f -
serviceAccount:
name: admin
namespace:
valueFrom: default_ns.name
scopes:
- test
dependsOn:
- default_ns
- base_image
- test_database_instance
- kind: runImage
name: delete_auth_tables
image:
valueFrom: service_base_image.image
script: |
set -ex
mysql --defaults-extra-file=/sql-config/sql-config.cnf < /io/sql/delete-auth-tables.sql
inputs:
- from: /repo/auth/sql
to: /io/
secrets:
- name: database-server-config
namespace:
valueFrom: default_ns.name
mountPath: /sql-config
runIfRequested: true
scopes:
- dev
dependsOn:
- default_ns
- service_base_image
- copy_files
- kind: createDatabase
name: auth_database
databaseName: auth
migrations:
- name: initial
script: /io/sql/initial.sql
inputs:
- from: /repo/auth/sql
to: /io/
namespace:
valueFrom: default_ns.name
shutdowns:
- kind: Deployment
namespace:
valueFrom: default_ns.name
name: auth
dependsOn:
- default_ns
- copy_files
- delete_auth_tables
- kind: runImage
name: create_deploy_config
image:
valueFrom: base_image.image
script: |
set -ex
# k8s deploy config
cat > deploy-config.json <<EOF
{"location":"k8s","default_namespace":"{{ default_ns.name }}","service_namespace":{}}
EOF
kubectl -n {{ default_ns.name }} delete --ignore-not-found secret deploy-config
kubectl -n {{ default_ns.name }} create secret generic deploy-config --from-file=./deploy-config.json
if [ {{ default_ns.name }} != {{ batch_pods_ns.name }} ]; then
kubectl -n {{ batch_pods_ns.name }} delete --ignore-not-found secret deploy-config
kubectl -n {{ batch_pods_ns.name }} create secret generic deploy-config --from-file=./deploy-config.json
fi
# gce deploy config
cat > deploy-config.json <<EOF
{"location":"gce","default_namespace":"{{ default_ns.name }}","service_namespace":{}}
EOF
kubectl -n {{ default_ns.name }} delete --ignore-not-found secret gce-deploy-config
kubectl -n {{ default_ns.name }} create secret generic gce-deploy-config --from-file=./deploy-config.json
serviceAccount:
name: admin
namespace:
valueFrom: default_ns.name
dependsOn:
- default_ns
- batch_pods_ns
- base_image
- deploy_default_admin_admin
- kind: deploy
name: deploy_admin_pod
namespace:
valueFrom: default_ns.name
config: admin-pod/admin-pod.yaml
scopes:
- deploy
- dev
dependsOn:
- default_ns
- service_base_image
- create_deploy_config
- kind: runImage
name: create_session_key
image:
valueFrom: base_image.image
script: |
set -ex
# create session keys
N=$(kubectl -n {{ default_ns.name }} get secret --ignore-not-found=true --no-headers session-secret-key | wc -l | tr -d '[:space:]')
if [[ $N != 0 ]]; then
exit
fi
mkdir /session-secret-key
cat > generate-session-key.py <<EOF
import base64
from cryptography import fernet
with open('/session-secret-key/session-secret-key', 'wb') as f:
f.write(base64.urlsafe_b64decode(fernet.Fernet.generate_key()))
EOF
python3 generate-session-key.py
kubectl -n {{ default_ns.name }} create secret generic session-secret-key --from-file=/session-secret-key/session-secret-key
serviceAccount:
name: admin
namespace:
valueFrom: default_ns.name
dependsOn:
- default_ns
- base_image
- kind: runImage
name: create_accounts
image:
valueFrom: service_base_image.image
script: |
set -ex
export HAIL_DEPLOY_CONFIG_FILE=/deploy-config/deploy-config.json
# create accounts
mkdir /user-tokens
cat > create-session.py <<EOF
import sys
import json
import asyncio
from hailtop.config import get_deploy_config
from hailtop.auth import get_tokens
from hailtop.utils import async_to_blocking
from gear import create_database_pool, insert_user, create_session
async def main():
dbpool = await create_database_pool()
tokens = get_tokens()
user_spec = json.loads(sys.argv[1])
user_id = await insert_user(dbpool, user_spec)
deploy_config = get_deploy_config()
auth_ns = deploy_config.service_ns('auth')
tokens[auth_ns] = await create_session(dbpool, user_id)
tokens.write()
async_to_blocking(main())
EOF
# batch, auth gsa keys
kubectl -n {{ default_ns.name }} get -o json --export secret test-gsa-key | jq '.metadata.name = "auth-gsa-key"' | kubectl -n {{ default_ns.name }} apply -f -
kubectl -n {{ default_ns.name }} get -o json --export secret test-gsa-key | jq '.metadata.name = "batch-gsa-key"' | kubectl -n {{ default_ns.name }} apply -f -
# create ci
N=$(kubectl -n {{ default_ns.name }} get secret --ignore-not-found=true --no-headers ci-tokens | wc -l | tr -d '[:space:]')
if [[ $N = 0 ]]; then
rm -f /user-tokens/tokens.json
kubectl -n {{ default_ns.name }} get -o json --export secret test-gsa-key | jq '.metadata.name = "ci-gsa-key"' | kubectl -n {{ default_ns.name }} apply -f -
kubectl -n {{ default_ns.name }} get -o json --export secret test-gsa-key | jq '.metadata.name = "ci-gsa-key"' | kubectl -n {{ batch_pods_ns.name }} apply -f -
python3 create-session.py '{"state":"active","username":"ci","is_service_account":1,"gsa_email":"[email protected]","bucket_name":"hail-test-dmk9z","gsa_key_secret_name":"ci-gsa-key","tokens_secret_name":"ci-tokens"}'
kubectl -n {{ default_ns.name }} create secret generic ci-tokens --from-file=/user-tokens/tokens.json
fi
# created ci
# create test
N=$(kubectl -n {{ default_ns.name }} get secret --ignore-not-found=true --no-headers test-tokens | wc -l | tr -d '[:space:]')
if [[ $N = 0 ]]; then
# if test-tokens does not exist
rm -f /user-tokens/tokens.json
python3 create-session.py '{"state":"active","username":"test","gsa_email":"[email protected]","bucket_name":"hail-test-dmk9z","gsa_key_secret_name":"test-gsa-key","tokens_secret_name":"test-tokens"}'
kubectl -n {{ batch_pods_ns.name }} create secret generic test-tokens --from-file=/user-tokens/tokens.json
fi
# created test
# create test-dev
N=$(kubectl -n {{ default_ns.name }} get secret --ignore-not-found=true --no-headers test-dev-tokens | wc -l | tr -d '[:space:]')
if [[ $N = 0 ]]; then
# if test-dev-tokens does not exist
rm -f /user-tokens/tokens.json
python3 create-session.py '{"state":"active","username":"test-dev","gsa_email":"[email protected]","bucket_name":"hail-test-dmk9z","gsa_key_secret_name":"test-gsa-key","tokens_secret_name":"test-dev-tokens","is_developer":1}'
kubectl -n {{ batch_pods_ns.name }} create secret generic test-dev-tokens --from-file=/user-tokens/tokens.json
fi
# created test-dev
scopes:
- test
- dev
serviceAccount:
name: admin
namespace:
valueFrom: default_ns.name
secrets:
- name:
valueFrom: auth_database.user_secret_name
namespace:
valueFrom: default_ns.name
mountPath: /sql-config
- name: gce-deploy-config
namespace:
valueFrom: default_ns.name
mountPath: /deploy-config
dependsOn:
- default_ns
- batch_pods_ns
- deploy_test_batch_sa
- deploy_default_admin_admin
- auth_database
- service_base_image
- create_deploy_config
- kind: buildImage
name: hail_build_image
dockerFile: hail/Dockerfile.hail-build
contextPath: hail
publishAs: hail-build
dependsOn:
- base_image
- kind: buildImage
name: hail_run_image
dockerFile: hail/Dockerfile.hail-run
contextPath: hail
publishAs: hail-run
dependsOn:
- service_base_image
- kind: buildImage
name: scorecard_image
dockerFile: scorecard/Dockerfile
contextPath: .
publishAs: scorecard
dependsOn:
- service_base_image
- kind: runImage
name: check_scorecard
image:
valueFrom: scorecard_image.image
script: |
set -ex
python3 -m flake8 scorecard
python3 -m pylint --rcfile pylintrc scorecard
dependsOn:
- scorecard_image
- kind: buildImage
name: auth_image
dockerFile: auth/Dockerfile
contextPath: .
publishAs: auth
dependsOn:
- service_base_image
- kind: runImage
name: check_auth
image:
valueFrom: auth_image.image
script: |
set -ex
python3 -m flake8 auth
python3 -m pylint --rcfile pylintrc auth
dependsOn:
- auth_image
- kind: buildImage
name: site_image
dockerFile: site/Dockerfile
contextPath: site
publishAs: site
dependsOn:
- base_image
- kind: buildImage
name: router_image
dockerFile: router/Dockerfile
contextPath: router
publishAs: router
dependsOn:
- base_image
- kind: buildImage
name: batch_image
dockerFile: batch/Dockerfile
contextPath: .
publishAs: batch
dependsOn:
- service_base_image
- kind: buildImage
name: batch_worker_image
dockerFile: batch/Dockerfile.worker
contextPath: .
publishAs: batch-worker
- kind: runImage
name: check_batch
image:
valueFrom: batch_image.image
script: |
set -ex
python3 -m flake8 batch
python3 -m pylint --rcfile pylintrc batch
dependsOn:
- batch_image
- kind: buildImage
name: test_ci_image
dockerFile: ci/Dockerfile.test
contextPath: .
publishAs: test-ci
scopes:
- test
- dev
dependsOn:
- base_image
- kind: buildImage
name: image_fetcher_image
dockerFile: image-fetcher/Dockerfile
contextPath: image-fetcher
publishAs: image-fetcher
- kind: buildImage
name: ci_image
dockerFile: ci/Dockerfile
contextPath: .
publishAs: ci
dependsOn:
- service_base_image
- kind: runImage
name: check_ci
image:
valueFrom: ci_image.image
script: |
set -ex
python3 -m flake8 ci
python3 -m pylint --rcfile pylintrc ci
dependsOn:
- ci_image
- kind: buildImage
name: ci_utils_image
dockerFile: ci/Dockerfile.ci-utils
contextPath: ci
publishAs: ci-utils
dependsOn:
- service_base_image
- kind: runImage
name: build_hail
image:
valueFrom: hail_build_image.image
resources:
memory: "7.5G"
cpu: "4"
script: |
set -ex
cd /io
rm -rf repo
mkdir repo
cd repo
{{ code.checkout_script }}
cd hail
time make jars python-version-info wheel
time (cd python && zip -r hail.zip hail hailtop)
time tar czf test.tar.gz -C python test
time tar czf resources.tar.gz -C src/test resources
time tar czf data.tar.gz -C python/hail/docs data
time tar czf www-src.tar.gz www
time tar czf cluster-tests.tar.gz python/cluster-tests
(cd build/deploy/dist/ && tar -cvf wheel-container.tar hail-*-py3-none-any.whl)
outputs:
- from: /io/repo/hail/build/libs/hail-all-spark.jar
to: /hail.jar
- from: /io/repo/hail/build/libs/hail-all-spark-test.jar
to: /hail-test.jar
- from: /io/repo/hail/testng-build.xml
to: /testng-build.xml
- from: /io/repo/hail/testng-cpp-codegen.xml
to: /testng-cpp-codegen.xml
- from: /io/repo/hail/python/hail.zip
to: /hail.zip
- from: /io/repo/hail/build/deploy/dist/wheel-container.tar
to: /wheel-container.tar
- from: /io/repo/hail/test.tar.gz
to: /test.tar.gz
- from: /io/repo/hail/resources.tar.gz
to: /resources.tar.gz
- from: /io/repo/hail/data.tar.gz
to: /data.tar.gz
- from: /io/repo/hail/www-src.tar.gz
to: /www-src.tar.gz
- from: /io/repo/hail/cluster-tests.tar.gz
to: /cluster-tests.tar.gz
dependsOn:
- hail_build_image
- kind: buildImage
name: query_image
dockerFile: query/Dockerfile
contextPath: .
publishAs: query
inputs:
- from: /hail.jar
to: /query/hail.jar
dependsOn:
- service_base_image
- build_hail
- kind: runImage
name: check_query
image:
valueFrom: query_image.image
script: |
set -ex
python3 -m flake8 query
python3 -m pylint --rcfile pylintrc query
dependsOn:
- query_image
- kind: deploy
name: deploy_query_sa
namespace:
valueFrom: default_ns.name
config: query/service-account.yaml
dependsOn:
- default_ns
- kind: deploy
name: deploy_query_sa_batch_pods
namespace:
valueFrom: batch_pods_ns.name
config: query/service-account-batch-pods.yaml
dependsOn:
- default_ns
- batch_pods_ns
- deploy_query_sa
- kind: deploy
name: deploy_query
namespace:
valueFrom: default_ns.name
config: query/deployment.yaml
wait:
- kind: Service
name: query
for: alive
dependsOn:
- default_ns
- batch_pods_ns
- query_image
- deploy_query_sa
- deploy_query_sa_batch_pods
- kind: buildImage
name: hail_repl_image
dockerFile: hail/Dockerfile.hail-repl
contextPath: hail
publishAs: hail-run
inputs:
- from: /wheel-container.tar
to: /wheel-container.tar
dependsOn:
- base_image
- build_hail
- kind: deploy
name: deploy_hail_repl
runIfRequested: true
scopes:
- dev
namespace:
valueFrom: default_ns.name
config: hail/hail_repl.yaml
dependsOn:
- default_ns
- hail_repl_image
- kind: runImage
name: test_hail_java
image:
valueFrom: hail_run_image.image
resources:
memory: "7.5G"
cpu: "2"
script: |
set -ex
cd /io
mkdir -p src/test
tar xzf resources.tar.gz -C src/test
gcloud -q auth activate-service-account --key-file=/test-gsa-key/key.json
gsutil -m cp -r src/test/resources/fs gs://hail-test-dmk9z/{{ token }}/test/resources/
HAIL_TEST_SKIP_R=1 HAIL_GS_FS_TEST_RESOURCES=gs://hail-test-dmk9z/{{ token }}/test/resources/fs java -cp hail-test.jar:$SPARK_HOME/jars/* org.testng.TestNG -listener is.hail.LogTestListener testng-build.xml
inputs:
- from: /resources.tar.gz
to: /io/resources.tar.gz
- from: /hail-test.jar
to: /io/hail-test.jar
- from: /testng-build.xml
to: /io/testng-build.xml
outputs:
- from: /io/test-output
to: /test-output
secrets:
- name: test-gsa-key
namespace:
valueFrom: batch_pods_ns.name
mountPath: /test-gsa-key
dependsOn:
- batch_pods_ns
- hail_run_image
- build_hail
- kind: buildImage
name: hail_base_image
dockerFile: hail/Dockerfile.hail-base
contextPath: .
publishAs: hail-base
dependsOn:
- hail_run_image
- build_hail
inputs:
- from: /hail.jar
to: /hail.jar
- from: /hail.zip
to: /hail.zip
- kind: runImage
name: check_hailtop
image:
valueFrom: hail_base_image.image
script: |
set -ex
python3 -m flake8 hailtop
python3 -m pylint --rcfile pylintrc hailtop
dependsOn:
- hail_base_image
- kind: buildImage
name: notebook_image
dockerFile: notebook/Dockerfile
contextPath: .
publishAs: notebook
dependsOn:
- service_base_image
- kind: runImage
name: check_notebook
image:
valueFrom: notebook_image.image
script: |
set -ex
python3 -m flake8 notebook
python3 -m pylint --rcfile pylintrc notebook
dependsOn:
- notebook_image
- kind: runImage
name: test_hail_python_0
image:
valueFrom: hail_run_image.image
resources:
memory: "7.5G"
cpu: "2"
script: |
set -ex
cd /io
tar xzf test.tar.gz
tar xzf resources.tar.gz
tar xzf data.tar.gz
tar xvf wheel-container.tar
python3 -m pip install --no-dependencies hail-*-py3-none-any.whl
export HAIL_TEST_RESOURCES_DIR=./resources
export HAIL_DOCTEST_DATA_DIR=./data
export PYSPARK_SUBMIT_ARGS="--driver-memory 6g pyspark-shell"
export PYTEST_SPLITS=5
export PYTEST_SPLIT_INDEX=0
python3 -m pytest --ignore=test/hailtop/batch/ --log-cli-level=INFO -s -vv --instafail --durations=50 test
inputs:
- from: /wheel-container.tar
to: /io/wheel-container.tar
- from: /test.tar.gz
to: /io/test.tar.gz
- from: /resources.tar.gz
to: /io/resources.tar.gz
- from: /data.tar.gz
to: /io/data.tar.gz
dependsOn:
- hail_run_image
- build_hail
- kind: runImage
name: test_hail_python_1
image:
valueFrom: hail_run_image.image
resources:
memory: "7.5G"
cpu: "2"
script: |
set -ex
cd /io
tar xzf test.tar.gz
tar xzf resources.tar.gz
tar xzf data.tar.gz
tar xvf wheel-container.tar
python3 -m pip install --no-dependencies hail-*-py3-none-any.whl
export HAIL_TEST_RESOURCES_DIR=./resources
export HAIL_DOCTEST_DATA_DIR=./data
export PYSPARK_SUBMIT_ARGS="--driver-memory 6g pyspark-shell"
export PYTEST_SPLITS=5
export PYTEST_SPLIT_INDEX=1
python3 -m pytest --ignore=test/hailtop/batch/ --log-cli-level=INFO -s -vv --instafail --durations=50 test
inputs:
- from: /wheel-container.tar
to: /io/wheel-container.tar
- from: /test.tar.gz
to: /io/test.tar.gz
- from: /resources.tar.gz
to: /io/resources.tar.gz
- from: /data.tar.gz
to: /io/data.tar.gz
dependsOn:
- hail_run_image
- build_hail
- kind: runImage
name: test_hail_python_2
image:
valueFrom: hail_run_image.image
resources:
memory: "7.5G"
cpu: "2"
script: |
set -ex
cd /io
tar xzf test.tar.gz
tar xzf resources.tar.gz
tar xzf data.tar.gz
tar xvf wheel-container.tar
python3 -m pip install --no-dependencies hail-*-py3-none-any.whl
export HAIL_TEST_RESOURCES_DIR=./resources
export HAIL_DOCTEST_DATA_DIR=./data
export PYSPARK_SUBMIT_ARGS="--driver-memory 6g pyspark-shell"
export PYTEST_SPLITS=5
export PYTEST_SPLIT_INDEX=2
python3 -m pytest --ignore=test/hailtop/batch/ --log-cli-level=INFO -s -vv --instafail --durations=50 test
inputs:
- from: /wheel-container.tar
to: /io/wheel-container.tar
- from: /test.tar.gz
to: /io/test.tar.gz
- from: /resources.tar.gz
to: /io/resources.tar.gz
- from: /data.tar.gz
to: /io/data.tar.gz
dependsOn:
- hail_run_image
- build_hail
- kind: runImage
name: test_hail_python_3
image:
valueFrom: hail_run_image.image
resources:
memory: "7.5G"
cpu: "2"
script: |
set -ex
cd /io
tar xzf test.tar.gz
tar xzf resources.tar.gz
tar xzf data.tar.gz
tar xvf wheel-container.tar
python3 -m pip install --no-dependencies hail-*-py3-none-any.whl
export HAIL_TEST_RESOURCES_DIR=./resources
export HAIL_DOCTEST_DATA_DIR=./data
export PYSPARK_SUBMIT_ARGS="--driver-memory 6g pyspark-shell"
export PYTEST_SPLITS=5
export PYTEST_SPLIT_INDEX=3
python3 -m pytest --ignore=test/hailtop/batch/ --log-cli-level=INFO -s -vv --instafail --durations=50 test
inputs:
- from: /wheel-container.tar
to: /io/wheel-container.tar
- from: /test.tar.gz
to: /io/test.tar.gz
- from: /resources.tar.gz
to: /io/resources.tar.gz
- from: /data.tar.gz
to: /io/data.tar.gz
dependsOn:
- hail_run_image
- build_hail
- kind: runImage
name: test_hail_python_4
image:
valueFrom: hail_run_image.image
resources:
memory: "7.5G"
cpu: "2"
script: |
set -ex
cd /io
tar xzf test.tar.gz
tar xzf resources.tar.gz
tar xzf data.tar.gz
tar xvf wheel-container.tar
python3 -m pip install --no-dependencies hail-*-py3-none-any.whl
export HAIL_TEST_RESOURCES_DIR=./resources
export HAIL_DOCTEST_DATA_DIR=./data
export PYSPARK_SUBMIT_ARGS="--driver-memory 6g pyspark-shell"
export PYTEST_SPLITS=5
export PYTEST_SPLIT_INDEX=4
python3 -m pytest --ignore=test/hailtop/batch/ --log-cli-level=INFO -s -vv --instafail --durations=50 test
inputs:
- from: /wheel-container.tar
to: /io/wheel-container.tar
- from: /test.tar.gz
to: /io/test.tar.gz
- from: /resources.tar.gz
to: /io/resources.tar.gz
- from: /data.tar.gz
to: /io/data.tar.gz
dependsOn:
- hail_run_image
- build_hail
- kind: runImage
name: test_python_docs
image:
valueFrom: hail_base_image.image
script: |
set -ex
cd /hail/python/hail
python3 -m pytest --instafail \
--doctest-modules \
--doctest-glob='*.rst' \
--ignore=docs/conf.py \
--ignore=docs/doctest_write_data.py
dependsOn:
- hail_base_image
- kind: runImage
name: make_docs
image:
valueFrom: hail_base_image.image
script: |
set -ex
export HAIL_SHORT_VERSION='0.2'
export SPHINXOPTS='-tchecktutorial'
mkdir -p {{ token }}/python
cd {{ token }}
unzip -q -d python /io/hail.zip
tar xzf /io/www-src.tar.gz
sed -E "s/\(hail\#([0-9]+)\)/(\[#\1](https:\/\/github.com\/hail-is\/hail\/pull\/\1))/g" \
< python/hail/docs/change_log.md \
| pandoc -o python/hail/docs/change_log.rst
make -C www
make -C python/hail/docs BUILDDIR=_build clean html
make -C python/hailtop/batch/docs BUILDDIR=_build clean html
mkdir -p www/docs
rm -f www/*.md
mv python/hail/docs/_build/html www/docs/0.2
mv python/hailtop/batch/docs/_build/html www/docs/batch
HAIL_CACHE_VERSION=$(cat python/hail/hail_version)
find www -iname *.html -type f -exec sed -i -e "s/\.css/\.css\?v\=$HAIL_CACHE_VERSION/" {} +;
tar czf /io/www.tar.gz www
resources:
memory: "7.5G"
cpu: "2"
inputs:
- from: /hail.zip
to: /io/hail.zip
- from: /www-src.tar.gz
to: /io/www-src.tar.gz
outputs:
- from: /io/www.tar.gz
to: /www.tar.gz
dependsOn:
- hail_base_image
- build_hail
- kind: deploy
name: deploy_router
namespace:
valueFrom: default_ns.name
config: router/deployment.yaml
wait:
- kind: Service
name: router
for: alive
link:
- www
- notebook
- ci
dependsOn:
- default_ns
- router_image
- kind: deploy
name: deploy_site
namespace:
valueFrom: default_ns.name
config: site/deployment.yaml
wait:
- kind: Service
name: site
for: alive
dependsOn:
- default_ns
- site_image
- deploy_router
- kind: deploy
name: deploy_scorecard
namespace:
valueFrom: default_ns.name
config: scorecard/deployment.yaml
scopes:
- deploy
- dev
dependsOn:
- default_ns
- scorecard_image
- deploy_router
- kind: runImage
name: create_dummy_oauth2_client_secret
image:
valueFrom: base_image.image
script: |
set -ex
kubectl -n {{ default_ns.name }} create secret generic auth-oauth2-client-secret || true
scopes:
- test
- dev
dependsOn:
- default_ns
- base_image
- kind: deploy
name: deploy_auth
namespace:
valueFrom: default_ns.name
config: auth/deployment.yaml
wait:
- kind: Service
name: auth
for: alive
dependsOn:
- default_ns
- batch_pods_ns
- create_deploy_config
- create_session_key
- deploy_router
- auth_database
- auth_image
- create_dummy_oauth2_client_secret
- kind: runImage
name: delete_batch_tables
image:
valueFrom: service_base_image.image
script: |
set -ex
mysql --defaults-extra-file=/sql-config/sql-config.cnf < /io/sql/delete-batch-tables.sql
inputs:
- from: /repo/batch/sql
to: /io/
secrets:
- name: database-server-config
namespace:
valueFrom: default_ns.name
mountPath: /sql-config
runIfRequested: true
scopes:
- dev
dependsOn:
- default_ns
- service_base_image
- copy_files
- kind: runImage
name: delete_ci_tables
image:
valueFrom: service_base_image.image
script: |
set -ex
mysql --defaults-extra-file=/sql-config/sql-config.cnf < /io/sql/delete-ci-tables.sql
inputs:
- from: /repo/ci/sql
to: /io/
secrets:
- name: database-server-config
namespace:
valueFrom: default_ns.name
mountPath: /sql-config
runIfRequested: true