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49 changes: 26 additions & 23 deletions .github/workflows/python-package-conda.yml
Original file line number Diff line number Diff line change
@@ -1,42 +1,45 @@
name: Test MWE with Python 3.9-3.13
name: CI

on:
push:
paths:
- 'scxmatch/**'
- 'tests/**'
- 'pyproject.toml'
- '.github/workflows/**'
pull_request:
paths:
- 'scxmatch/**'
- 'tests/**'
- 'pyproject.toml'
- '.github/workflows/**'


jobs:
test-bioconda-install:
test:
runs-on: ubuntu-latest

strategy:
fail-fast: false
matrix:
python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]

steps:
- name: Checkout repo
uses: actions/checkout@v2
- uses: actions/checkout@v4

- name: Set up Miniconda
uses: conda-incubator/setup-miniconda@v2
- name: Set up Micromamba
uses: mamba-org/setup-micromamba@v2
with:
miniconda-version: 'latest'
channels: conda-forge, bioconda
auto-activate-base: true
environment-name: test-env
create-args: >-
python=${{ matrix.python-version }}
graph-tool
channels: conda-forge
cache-environment: true

- name: Install package with test dependencies
shell: bash -el {0}
run: pip install -e ".[test]"

- name: Install dependencies and run test
shell: bash -l {0}
run: |
conda create -n test-environment -y \
python=${{ matrix.python-version }} \
pip

conda install -n test-environment -y -c conda-forge graph-tool

conda run -n test-environment python -m pip install --upgrade pip
conda run -n test-environment python -m pip install .

conda run -n test-environment python tests/test_mwe.py
- name: Run tests
shell: bash -el {0}
run: pytest -m "not slow"
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