Disable Kubernetes on CI temporarily

DataBiosphere · Sep 13, 2023 · 33c850e · 33c850e
1 parent 9674239
commit 33c850e
Showing 1 changed file with 50 additions and 50 deletions.
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
@@ -9,7 +9,7 @@ variables:
   # Used to tell pytest which tests to be run by specifying markers,
   # Allows partitioning of tests to prevent duplicate running of tests in different jobs.
   # Currently specifies special tests that are not run by quick_test_offline.
-  MARKER: "tes or integrative or encryption or kubernetes or mesos or server_mode or fetchable_appliance or appliance or slow or docker or cwl or singularity or rsync3"
+  MARKER: "(tes or integrative or encryption or mesos or server_mode or fetchable_appliance or appliance or slow or docker or cwl or singularity or rsync3) and not kubernetes"
   TEST_THREADS: "3"
 before_script:
   # Log where we are running, in case some Kubernetes hosts are busted. IPs are assigned per host.
@@ -30,7 +30,7 @@ before_script:
     fi
   # Restart or start the Docker daemon
   - stopdocker || true
-  - sudo rm -f /var/run/docker.sock 
+  - sudo rm -f /var/run/docker.sock
   - startdocker || true
   - docker info
   - cat /etc/hosts
@@ -238,26 +238,26 @@ cwl_v1.1_kubernetes:
     - mkdir -p ${TOIL_WORKDIR}
     - make test threads="${TEST_THREADS}" tests="src/toil/test/cwl/cwlTest.py::CWLv11Test::test_kubernetes_cwl_conformance src/toil/test/cwl/cwlTest.py::CWLv11Test::test_kubernetes_cwl_conformance_with_caching"
 
-cwl_v1.2_kubernetes:
-  stage: main_tests
-  script:
-    - pwd
-    - ${MAIN_PYTHON_PKG} -m virtualenv venv && . venv/bin/activate && pip install -U pip wheel && make prepare && make develop extras=[cwl,aws,kubernetes]
-    - export TOIL_KUBERNETES_OWNER=toiltest
-    - export TOIL_AWS_SECRET_NAME=shared-s3-credentials
-    - export TOIL_KUBERNETES_HOST_PATH=/data/scratch
-    - export TOIL_WORKDIR=/var/lib/toil
-    - export SINGULARITY_CACHEDIR=/var/lib/toil/singularity-cache
-    - if [[ ! -z "${KUBERNETES_DOCKER_HUB_MIRROR}" ]] ; then export SINGULARITY_DOCKER_HUB_MIRROR="${KUBERNETES_DOCKER_HUB_MIRROR}" ; fi
-    - mkdir -p ${TOIL_WORKDIR}
-    - make test threads="${TEST_THREADS}" tests="src/toil/test/cwl/cwlTest.py::CWLv12Test::test_kubernetes_cwl_conformance src/toil/test/cwl/cwlTest.py::CWLv12Test::test_kubernetes_cwl_conformance_with_caching"
-  artifacts:
-    reports:
-      junit: "*.junit.xml"
-    paths:
-      - "*.junit.xml"
-    when: always
-    expire_in: 14 days
+#cwl_v1.2_kubernetes:
+#  stage: main_tests
+#  script:
+#    - pwd
+#    - ${MAIN_PYTHON_PKG} -m virtualenv venv && . venv/bin/activate && pip install -U pip wheel && make prepare && make develop extras=[cwl,aws,kubernetes]
+#    - export TOIL_KUBERNETES_OWNER=toiltest
+#    - export TOIL_AWS_SECRET_NAME=shared-s3-credentials
+#    - export TOIL_KUBERNETES_HOST_PATH=/data/scratch
+#    - export TOIL_WORKDIR=/var/lib/toil
+#    - export SINGULARITY_CACHEDIR=/var/lib/toil/singularity-cache
+#    - if [[ ! -z "${KUBERNETES_DOCKER_HUB_MIRROR}" ]] ; then export SINGULARITY_DOCKER_HUB_MIRROR="${KUBERNETES_DOCKER_HUB_MIRROR}" ; fi
+#    - mkdir -p ${TOIL_WORKDIR}
+#    - make test threads="${TEST_THREADS}" tests="src/toil/test/cwl/cwlTest.py::CWLv12Test::test_kubernetes_cwl_conformance src/toil/test/cwl/cwlTest.py::CWLv12Test::test_kubernetes_cwl_conformance_with_caching"
+#  artifacts:
+#    reports:
+#      junit: "*.junit.xml"
+#    paths:
+#      - "*.junit.xml"
+#    when: always
+#    expire_in: 14 days
 
 wdl:
   stage: main_tests
@@ -323,31 +323,31 @@ google_jobstore:
     - make test threads="${TEST_THREADS}" tests=src/toil/test/jobStores/jobStoreTest.py::GoogleJobStoreTest
 
 # Cactus-on-Kubernetes integration (as a script and not a pytest test)
-cactus_integration:
-  stage: integration
-  script:
-    - set -e
-    - ${MAIN_PYTHON_PKG} -m virtualenv --system-site-packages venv
-    - . venv/bin/activate
-    - pip install -U pip wheel
-    - pip install .[aws,kubernetes]
-    - export TOIL_KUBERNETES_OWNER=toiltest
-    - export TOIL_AWS_SECRET_NAME=shared-s3-credentials
-    - export TOIL_KUBERNETES_HOST_PATH=/data/scratch
-    - export TOIL_WORKDIR=/var/lib/toil
-    - export SINGULARITY_CACHEDIR=/var/lib/toil/singularity-cache
-    - mkdir -p ${TOIL_WORKDIR}
-    - BUCKET_NAME=toil-test-$RANDOM-$RANDOM-$RANDOM
-    - cd
-    - git clone https://github.com/ComparativeGenomicsToolkit/cactus.git --recursive
-    - cd cactus
-    - git fetch origin
-    - git checkout f5adf4013326322ae58ef1eccb8409b71d761583
-    - git submodule update --init --recursive
-    # We can't use setuptools 66 on Ubuntu due to https://github.com/pypa/setuptools/issues/3772
-    - pip install --upgrade 'setuptools<66' pip
-    - pip install --upgrade .
-    - pip install --upgrade numpy psutil # Cactus installs an old psutil that Toil isn't compatible with. TODO: Do we really need Numpy?
-    - if [[ ! -z "${KUBERNETES_DOCKER_HUB_MIRROR}" ]] ; then export SINGULARITY_DOCKER_HUB_MIRROR="${KUBERNETES_DOCKER_HUB_MIRROR}" ; fi
-    - toil clean aws:us-west-2:${BUCKET_NAME}
-    - time cactus --setEnv SINGULARITY_DOCKER_HUB_MIRROR --batchSystem kubernetes --retryCount=3 --consCores 2 --binariesMode singularity --clean always aws:us-west-2:${BUCKET_NAME} examples/evolverMammals.txt examples/evolverMammals.hal --root mr --defaultDisk "8G" --logDebug
+#cactus_integration:
+#  stage: integration
+#  script:
+#    - set -e
+#    - ${MAIN_PYTHON_PKG} -m virtualenv --system-site-packages venv
+#    - . venv/bin/activate
+#    - pip install -U pip wheel
+#    - pip install .[aws]
+#    - export TOIL_KUBERNETES_OWNER=toiltest
+#    - export TOIL_AWS_SECRET_NAME=shared-s3-credentials
+#    - export TOIL_KUBERNETES_HOST_PATH=/data/scratch
+#    - export TOIL_WORKDIR=/var/lib/toil
+#    - export SINGULARITY_CACHEDIR=/var/lib/toil/singularity-cache
+#    - mkdir -p ${TOIL_WORKDIR}
+#    - BUCKET_NAME=toil-test-$RANDOM-$RANDOM-$RANDOM
+#    - cd
+#    - git clone https://github.com/ComparativeGenomicsToolkit/cactus.git --recursive
+#    - cd cactus
+#    - git fetch origin
+#    - git checkout f5adf4013326322ae58ef1eccb8409b71d761583
+#    - git submodule update --init --recursive
+#    # We can't use setuptools 66 on Ubuntu due to https://github.com/pypa/setuptools/issues/3772
+#    - pip install --upgrade 'setuptools<66' pip
+#    - pip install --upgrade .
+#    - pip install --upgrade numpy psutil # Cactus installs an old psutil that Toil isn't compatible with. TODO: Do we really need Numpy?
+#    - if [[ ! -z "${KUBERNETES_DOCKER_HUB_MIRROR}" ]] ; then export SINGULARITY_DOCKER_HUB_MIRROR="${KUBERNETES_DOCKER_HUB_MIRROR}" ; fi
+#    - toil clean aws:us-west-2:${BUCKET_NAME}
+#    - time cactus --setEnv SINGULARITY_DOCKER_HUB_MIRROR --batchSystem kubernetes --retryCount=3 --consCores 2 --binariesMode singularity --clean always aws:us-west-2:${BUCKET_NAME} examples/evolverMammals.txt examples/evolverMammals.hal --root mr --defaultDisk "8G" --logDebug