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test_linux.yml
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name: test
on:
push:
branches: [main, "[0-9]+.[0-9]+.x"]
pull_request:
schedule:
- cron: "0 10 * * *" # runs at 10:00 UTC (03:00 PST) every day
workflow_dispatch:
concurrency:
group: ${{ github.workflow }}-${{ github.ref }}
cancel-in-progress: true
jobs:
test:
runs-on: ${{ matrix.os }}
defaults:
run:
shell: bash -e {0} # -e to fail on error
strategy:
fail-fast: false
matrix:
os: [ubuntu-latest]
python: ["3.10", "3.11", "3.12"]
name: integration
env:
OS: ${{ matrix.os }}
PYTHON: ${{ matrix.python }}
steps:
- uses: actions/checkout@v4
- uses: actions/setup-python@v5
with:
python-version: ${{ matrix.python }}
cache: "pip"
cache-dependency-path: "**/pyproject.toml"
- name: Install dependencies
run: |
python -m pip install --upgrade pip wheel uv
python -m uv pip install --system "scvi-tools[tests] @ ."
- name: Run pytest
env:
MPLBACKEND: agg
PLATFORM: ${{ matrix.os }}
DISPLAY: :42
COLUMNS: 120
run: |
coverage run -m pytest -v --color=yes
coverage report
- uses: codecov/codecov-action@v4
with:
token: ${{ secrets.CODECOV_TOKEN }}