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Add GH actions workflow to test on Cubed
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tomwhite committed Sep 2, 2024
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33 changes: 33 additions & 0 deletions .github/workflows/cubed.yml
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name: Cubed

on:
push:
pull_request:
# manual trigger
workflow_dispatch:

jobs:
build:
# This workflow only runs on the origin org
# if: github.repository_owner == 'sgkit-dev'
runs-on: ubuntu-latest
strategy:
matrix:
python-version: ["3.11"]

steps:
- uses: actions/checkout@v4
- name: Set up Python ${{ matrix.python-version }}
uses: actions/setup-python@v5
with:
python-version: ${{ matrix.python-version }}

- name: Install deps and sgkit
run: |
python -m pip install --upgrade pip
python -m pip install -r requirements.txt -r requirements-dev.txt
python -m pip install -U git+https://github.com/cubed-dev/cubed.git -U git+https://github.com/cubed-dev/cubed-xarray.git -U git+https://github.com/pydata/xarray.git
- name: Test with pytest
run: |
pytest -v sgkit/tests/test_aggregation.py -k "test_count_call_alleles" --use-cubed

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