Commit 13104ddf authored by van den Berg's avatar van den Berg
Browse files

Update gitlab-ci tests

parent 2fb3b9f0
Pipeline #3612 failed with stages
in 2 minutes and 17 seconds
......@@ -3,8 +3,9 @@ variables:
.docker_before_script_anchor: &docker_before_script_anchor
before_script:
- pip install -r requirements.txt
- pip install -r requirements-dev.txt
- apt update -y && apt install python3-pip -y
- pip3 install -r requirements.txt
- pip3 install -r requirements-dev.txt
stages:
- sanity
......@@ -15,8 +16,8 @@ stages:
test_sanities:
<<: *docker_before_script_anchor
script:
- py.test --tag sanity
image: python:3.6-stretch
- pytest-3 --tag sanity
image: lumc/singularity-snakemake:3.5.2-5.9.1
tags:
- docker
stage: sanity
......@@ -24,35 +25,19 @@ test_sanities:
test_dry_run:
<<: *docker_before_script_anchor
script:
- py.test --tag dry-run
image: python:3.6-stretch
- pytest-3 --tag dry-run
image: lumc/singularity-snakemake:3.5.2-5.9.1
tags:
- docker
stage: dry-run
# this requires a priviliged docker container.
# most docker runners will not do this
test_integration_singularity:
before_script:
- apt update -y && apt install -y python3-pip
- pip3 install pyfaidx
- pip3 install -r requirements-dev.txt
script:
- py.test --tag singularity-integration
image: lumc/singularity-snakemake:3.0.3-5.4.0
tags:
- docker
stage: integration
test_integration:
before_script:
- export BASETEMP=$(mktemp -p ${RUN_BASE_DIR} -d)
script:
- source ${CONDA_SH}
- conda activate hutspot-pipeline
- export PATH=${PATH}:${CONDA_EXTRA_PATH}
- py.test --tag integration --basetemp ${BASETEMP} --keep-workflow-wd
- pytest-3 --tag integration --basetemp ${BASETEMP} --keep-workflow-wd
image: lumc/singularity-snakemake:3.5.2-5.9.1
tags:
- slurm
stage: integration
......@@ -61,10 +46,7 @@ test_functional:
before_script:
- export BASETEMP=$(mktemp -p ${RUN_BASE_DIR} -d)
script:
- source ${CONDA_SH}
- conda activate hutspot-pipeline
- export PATH=${PATH}:${CONDA_EXTRA_PATH}
- py.test --tag functional --basetemp ${BASETEMP} --keep-workflow-wd
- pytest-3 --tag functional --basetemp ${BASETEMP} --keep-workflow-wd
tags:
- slurm
stage: functional
......
pytest>=4.3.0
pytest-workflow>=1.1.0
\ No newline at end of file
pytest-workflow==1.2.3
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