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.gitlab-ci.yml
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image: quay.io/vgteam/vg_ci_prebake:latest
# Note that we must run in a priviliged container for our internal Docker daemon to come up.
before_script:
- startdocker || true
- docker info
- cat /etc/hosts
- export PYTHONIOENCODING=utf-8
after_script:
# We need to clean up any files that Toil may have made via Docker that
# aren't deletable by the Gitlab user. If we don't do this, Gitlab will try
# and clean them up before running the next job on the runner, fail, and fail
# that next job.
- pwd
- sudo rm -rf tmp
- stopdocker || true
stages:
- main_tests
- test
- integration
# Python2.7
py2_batch_systems:
stage: test
script:
- pwd
- apt update && DEBIAN_FRONTEND=noninteractive apt install -y tzdata && apt install -y jq
- virtualenv -p python2.7 venv && . venv/bin/activate && make prepare && make develop extras=[all] && pip install htcondor awscli==1.16.272
# Get Kubernetes credentials
- mkdir -p ~/.kube
- cp "$GITLAB_SECRET_FILE_KUBE_CONFIG" ~/.kube/config
- mkdir -p ~/.aws
- cp "$GITLAB_SECRET_FILE_AWS_CREDENTIALS" ~/.aws/credentials
- python -m pytest -r s src/toil/test/batchSystems/batchSystemTest.py
- python -m pytest -r s src/toil/test/mesos/MesosDataStructuresTest.py
py2_cwl:
stage: test
script:
- pwd
- virtualenv -p python2.7 venv && . venv/bin/activate && make prepare && make develop extras=[all] && pip install htcondor
- python -m pytest src/toil/test/cwl/cwlTest.py
py2_wdl:
stage: test
script:
- pwd
- virtualenv -p python2.7 venv && . venv/bin/activate && make prepare && make develop extras=[all] && pip install htcondor
- python -m pytest src/toil/test/wdl/toilwdlTest.py
py2_jobstore_and_provisioning:
stage: test
script:
- pwd
- virtualenv -p python2.7 venv && . venv/bin/activate && make prepare && make develop extras=[all] && pip install htcondor
- python -m pytest src/toil/test/sort/sortTest.py
- python -m pytest src/toil/test/provisioners/aws/awsProvisionerTest.py
- python -m pytest src/toil/test/provisioners/clusterScalerTest.py
- python -m pytest src/toil/test/provisioners/gceProvisionerTest.py
py2_main:
stage: main_tests
script:
- pwd
- virtualenv -p python2.7 venv && . venv/bin/activate && make prepare && make develop extras=[all] && pip install htcondor
- python -m pytest src/toil/test/src
- python -m pytest src/toil/test/utils
py2_appliance_build:
stage: main_tests
script:
- pwd
- apt update && DEBIAN_FRONTEND=noninteractive apt install -y tzdata && apt install -y jq
- virtualenv -p python2.7 venv && . venv/bin/activate && make prepare && make develop extras=[all] && pip install htcondor awscli==1.16.272
# This reads GITLAB_SECRET_FILE_QUAY_CREDENTIALS
- python setup_gitlab_docker.py
- export TOIL_APPLIANCE_SELF=quay.io/ucsc_cgl/toil:$(python version_template.py dockerTag)
- echo $TOIL_APPLIANCE_SELF
- make push_docker
py2_integration_jobstore:
stage: integration
script:
- pwd
- apt update && DEBIAN_FRONTEND=noninteractive apt install -y tzdata && apt install -y jq
- virtualenv -p python2.7 venv && . venv/bin/activate && make prepare && make develop extras=[all] && pip install htcondor awscli==1.16.272
- export TOIL_TEST_INTEGRATIVE=True
- export TOIL_AWS_KEYNAME=id_rsa
- export TOIL_AWS_ZONE=us-west-2a
# This reads GITLAB_SECRET_FILE_SSH_KEYS
- python setup_gitlab_ssh.py
- mkdir -p ~/.aws
- cp "$GITLAB_SECRET_FILE_AWS_CREDENTIALS" ~/.aws/credentials
- python -m pytest src/toil/test/jobStores/jobStoreTest.py
py2_integration_sort:
stage: integration
script:
- pwd
- apt update && DEBIAN_FRONTEND=noninteractive apt install -y tzdata && apt install -y jq
- virtualenv -p python2.7 venv && . venv/bin/activate && make prepare && make develop extras=[all] && pip install htcondor awscli==1.16.272
- export TOIL_TEST_INTEGRATIVE=True
- export TOIL_AWS_KEYNAME=id_rsa
- export TOIL_AWS_ZONE=us-west-2a
# This reads GITLAB_SECRET_FILE_SSH_KEYS
- python setup_gitlab_ssh.py
- mkdir -p ~/.aws
- cp "$GITLAB_SECRET_FILE_AWS_CREDENTIALS" ~/.aws/credentials
- python -m pytest src/toil/test/sort/sortTest.py
- python -m pytest src/toil/test/provisioners/clusterScalerTest.py
#py2_integration_provisioner:
# stage: integration
# script:
# - pwd
# - apt update && DEBIAN_FRONTEND=noninteractive apt install -y tzdata && apt install -y jq
# - virtualenv -p python2.7 venv && . venv/bin/activate && make prepare && make develop extras=[all] && pip install htcondor awscli==1.16.272
# - export TOIL_TEST_INTEGRATIVE=True
# - export TOIL_AWS_KEYNAME=id_rsa
# - export TOIL_AWS_ZONE=us-west-2a
# # This reads GITLAB_SECRET_FILE_SSH_KEYS
# - python setup_gitlab_ssh.py
# - mkdir -p ~/.aws
# - cp "$GITLAB_SECRET_FILE_AWS_CREDENTIALS" ~/.aws/credentials
# - python -m pytest src/toil/test/provisioners/aws/awsProvisionerTest.py
# Python3.6
py3_batch_systems:
stage: test
script:
- pwd
- apt update && DEBIAN_FRONTEND=noninteractive apt install -y tzdata && apt install -y jq
- virtualenv -p python3.6 venv && . venv/bin/activate && make prepare && make develop extras=[all] && pip install htcondor awscli==1.16.272
- python -m pytest -r s src/toil/test/batchSystems/batchSystemTest.py
- python -m pytest -r s src/toil/test/mesos/MesosDataStructuresTest.py
py3_cwl:
stage: test
script:
- pwd
- virtualenv -p python3.6 venv && . venv/bin/activate && make prepare && make develop extras=[all] && pip install htcondor
- python -m pytest src/toil/test/cwl/cwlTest.py
py3_wdl:
stage: test
script:
- pwd
- virtualenv -p python3.6 venv && . venv/bin/activate && make prepare && make develop extras=[all] && pip install htcondor
- python -m pytest src/toil/test/wdl/toilwdlTest.py
py3_jobstore_and_provisioning:
stage: test
script:
- pwd
- virtualenv -p python3.6 venv && . venv/bin/activate && make prepare && make develop extras=[all] && pip install htcondor
- python -m pytest src/toil/test/jobStores/jobStoreTest.py
- python -m pytest src/toil/test/sort/sortTest.py
- python -m pytest src/toil/test/provisioners/aws/awsProvisionerTest.py
- python -m pytest src/toil/test/provisioners/clusterScalerTest.py
- python -m pytest src/toil/test/provisioners/gceProvisionerTest.py
py3_main:
stage: main_tests
script:
- pwd
- virtualenv -p python3.6 venv && . venv/bin/activate && make prepare && make develop extras=[all] && pip install htcondor
- python -m pytest src/toil/test/src
- python -m pytest src/toil/test/utils
#py3_integration:
# stage: integration
# script:
# - pwd
# - apt update && DEBIAN_FRONTEND=noninteractive apt install -y tzdata && apt install -y jq
# - virtualenv -p python3.6 venv && . venv/bin/activate && make prepare && make develop extras=[all] && pip install htcondor awscli==1.16.272
# - export TOIL_TEST_INTEGRATIVE=True
# - export TOIL_AWS_KEYNAME=id_rsa
# - export TOIL_AWS_ZONE=us-west-2a
# # This reads GITLAB_SECRET_FILE_SSH_KEYS
# - python setup_gitlab_ssh.py
# - mkdir -p ~/.aws
# - cp "$GITLAB_SECRET_FILE_AWS_CREDENTIALS" ~/.aws/credentials
# - python -m pytest src/toil/test/jobStores/jobStoreTest.py