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WIP: test with apptainer #186

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27 changes: 11 additions & 16 deletions .github/workflows/ci-tests.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -10,6 +10,9 @@ concurrency:
group: build-${{ github.event.pull_request.number || github.ref }}
cancel-in-progress: true

env:
apptainer_version: 1.1.8

jobs:

tox:
Expand All @@ -34,9 +37,9 @@ jobs:

- name: Set up Singularity
if: ${{ matrix.step == 'unit' || matrix.step == 'mypy' }}
run: |
wget --no-verbose https://github.com/sylabs/singularity/releases/download/v3.10.4/singularity-ce_3.10.4-focal_amd64.deb
sudo apt-get install -y ./singularity-ce_3.10.4-focal_amd64.deb
uses: eWaterCycle/setup-apptainer@v2
with:
apptainer-version: ${{ env.apptainer_version }}

- name: Set up Python
uses: actions/setup-python@v4
Expand Down Expand Up @@ -108,24 +111,16 @@ jobs:

release_test:
name: cwl-utils release test

runs-on: ubuntu-22.04

steps:
- uses: actions/checkout@v3

- name: Set up Singularity
run: |
wget --no-verbose https://github.com/sylabs/singularity/releases/download/v3.10.4/singularity-ce_3.10.4-jammy_amd64.deb
sudo apt-get install -y ./singularity-ce_3.10.4-jammy_amd64.deb

- name: pull some containers
run: |
export CWL_SINGULARITY_CACHE=$(echo $GITHUB_WORKSPACE)/singularity_cache
mkdir -p ${CWL_SINGULARITY_CACHE}
singularity pull --name ${CWL_SINGULARITY_CACHE}/node_alpine.sif docker://docker.io/node:alpine
ls -lh ${CWL_SINGULARITY_CACHE}
echo ${CWL_SINGULARITY_CACHE}
echo "CWL_SINGULARITY_CACHE=${CWL_SINGULARITY_CACHE}" >> $GITHUB_ENV
- name: Set up Apptainer
uses: eWaterCycle/setup-apptainer@2
with:
apptainer-version: ${{ env.apptainer_version }}

- name: Set up Python
uses: actions/setup-python@v4
Expand Down
8 changes: 4 additions & 4 deletions .github/workflows/tag_to_publish.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -9,7 +9,7 @@ concurrency:
cancel-in-progress: true

env:
singularity_version: 3.6.4
apptainer_version: 1.1.8

jobs:
release_to_pypi:
Expand All @@ -20,10 +20,10 @@ jobs:
steps:
- uses: actions/checkout@v3

- name: Set up Singularity
uses: eWaterCycle/setup-singularity@v7
- name: Set up Apptainer
uses: eWaterCycle/setup-apptainer@v2
with:
singularity-version: ${{ env.singularity_version }}
apptainer-version: ${{ env.apptainer_version }}

- name: Set up Python
uses: actions/setup-python@v4
Expand Down