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Test

Test #19

Workflow file for this run

name: Test
on:
push:
branches: [master]
pull_request:
branches: [master]
schedule:
- cron: "0 5 1,15 * *"
concurrency:
group: ${{ github.workflow }}-${{ github.ref }}
cancel-in-progress: true
jobs:
test:
runs-on: ${{ matrix.os }}
defaults:
run:
shell: bash -l {0} # -e to fail on error
strategy:
fail-fast: false
matrix:
os: [ubuntu-latest, macos-13]
python: ["3.7", "3.8", "3.9", "3.10", "3.11"]
name: ${{ matrix.name }} Python ${{ matrix.python }}
env:
OS: ${{ matrix.os }}
PYTHON: ${{ matrix.python }}
steps:
- uses: actions/checkout@v3
# - name: Set up Python ${{ matrix.python }}
# uses: actions/setup-python@v4
# with:
# python-version: ${{ matrix.python }}
# cache: "pip"
# cache-dependency-path: "**/pyproject.toml"
- uses: conda-incubator/setup-miniconda@v3
with:
mamba-version: "*"
auto-update-conda: true
auto-activate-base: false
python-version: ${{ matrix.python }}
channels: conda-forge, bioconda, defaults
activate-environment: test_dbcan
environment-file: envs/test.yml
- name: export test_dbcan environment
run: mamba env export
# - name: Install test dependencies
# run: |
# python -m pip install --upgrade pip wheel
# - name: create run_dbcan environment
# run: conda create -n run_dbcan python=${{ matrix.python }}
# - name: activate run_dbcan environment
# run: conda activate run_dbcan
- name: Install dependencies
run: |
pip install ${{ matrix.pip-flags }} ".[dev,test]"
# - name: Add conda to PATH
# run: |
# echo ::add-path::$CONDA/bin
- name: Build dbCAN Database
run: |
dbcan_build --cpus 1 --db-dir db --clean
# conda install -y -c bioconda -c conda-forge hmmer diamond blast prodigal
- name: Test
env:
MPLBACKEND: agg
PLATFORM: ${{ matrix.os }}
DISPLAY: :42
run: |
coverage run -m pytest -v --color=yes