.gitlab-ci.yml 1.14 KB
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variables:
  GIT_SUBMODULE_STRATEGY: recursive

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.docker_before_script_anchor: &docker_before_script_anchor
  before_script:
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    - apt update -y && apt install python3-pip -y
    - pip3 install -r requirements.txt
    - pip3 install -r requirements-dev.txt
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stages:
  - sanity
  - dry-run
  - integration
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  - functional
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test_sanities:
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  <<: *docker_before_script_anchor
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  script:
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    - pytest-3 --tag sanity
  image: lumc/singularity-snakemake:3.5.2-5.9.1
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  tags:
    - docker
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  stage: sanity
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test_dry_run:
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  <<: *docker_before_script_anchor
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  script:
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    - pytest-3 --tag dry-run
  image: lumc/singularity-snakemake:3.5.2-5.9.1
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  tags:
    - docker
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  stage: dry-run

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test_integration:
  before_script:
    - export BASETEMP=$(mktemp -p ${RUN_BASE_DIR} -d)
  script:
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    - pytest-3 --tag integration --basetemp ${BASETEMP} --keep-workflow-wd
  image: lumc/singularity-snakemake:3.5.2-5.9.1
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  tags:
    - slurm
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  stage: integration
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test_functional:
  before_script:
    - export BASETEMP=$(mktemp -p ${RUN_BASE_DIR} -d)
  script:
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    - pytest-3 --tag functional --basetemp ${BASETEMP} --keep-workflow-wd
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  tags:
    - slurm
  stage: functional
  only:
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    - schedules