Commit fb0de71a authored by van den Berg's avatar van den Berg
Browse files

Fix tests and add caching

parent fb607603
Pipeline #5304 failed with stages
in 25 seconds
......@@ -38,29 +38,44 @@ jobs:
- integration-two-samples
- integration-target-baits
- integration-bed-coverage
- integration-restrict_BQSR
- integration-restrict-BQSR
- integration-targets-only
- integration-multisample
steps:
- uses: actions/checkout@v2
steps:
- uses: actions/checkout@v2
- uses: eWaterCycle/setup-singularity@v6
- name: Install singularity
uses: eWaterCycle/setup-singularity@v6
with:
singularity-version: 3.6.4
- uses: conda-incubator/setup-miniconda@v2.0.1
- name: Cache conda environment
uses: actions/cache@v2
env:
cache-name: cache-conda-environment
# Increase this value to reset the cache without changing
# environment.yml
cache-number: 0
with:
path: ~/conda_pkgs_dir
key: build-${{ env.cache-name }}-${{ env.cache-number }}-${{ hashFiles('environment.yml') }}
- name: Install miniconda
uses: conda-incubator/setup-miniconda@v2.0.1
# https://github.com/conda-incubator/setup-miniconda.
# https://github.com/marketplace/actions/setup-miniconda
with:
activate-environment: hutspot
environment-file: environment.yml
auto-activate-base: false
use-only-tar-bz2: true
- name: Run test in conda evironment
# Use --symlink to limit disk usage.
run: >-
pytest --keep-workflow-wd-on-fail --tag ${{ matrix.test }} --symlink tests/
pytest --keep-workflow-wd-on-fail --tag ${{ matrix.test }} tests/
- name: Check job stderr messages in case of failure
- name: Check pipeline stderr messages in case of failure
if: ${{ failure() }}
run: >-
bash -c '
......@@ -68,7 +83,7 @@ jobs:
echo $file; cat $file
done
'
- name: Check job stdout messages in case of failure
- name: Check pipeline stdout messages in case of failure
if: ${{ failure() }}
run: >-
bash -c '
......@@ -76,3 +91,11 @@ jobs:
echo $file; cat $file
done
'
- name: Check all job log files in case of failure
if: ${{ failure() }}
run: >-
bash -c '
for file in $(find /tmp/pytest_workflow_*/${{ matrix.test}}/log/ -type f); do
echo $file; cat $file
done
'
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