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docker #162

Workflow file for this run

name: tests
on:
push:
branches: [ main ]
paths-ignore:
- '**.md'
- '**.ipynb'
- '**.bib'
- 'ms/*'
pull_request:
types: [opened, reopened, edited]
paths-ignore:
- '**.md'
- '**.ipynb'
- '**.bib'
- 'ms/*'
jobs:
create-env:
name: ${{ matrix.os }}
runs-on: ${{ matrix.os }}
defaults:
run:
shell: bash -l {0}
strategy:
fail-fast: false
matrix:
os: [ubuntu-latest, macos-latest]
steps:
- name: checkout repository
uses: actions/checkout@v3
with:
fetch-depth: 0
- name: create environment
uses: conda-incubator/setup-miniconda@v2
with:
python-version: 3.8
# mamba-version: "*"
channels: conda-forge,bioconda,defaults
auto-activate-base: false
activate-environment: tests_pynteny
environment-file: envs/pynteny-dev.yml
- name: Build & Install Pynteny
run: poetry build && pip install dist/pynteny*.whl
- name: Run tests and collect coverage
run: pynteny --help && coverage run --omit pynteny/wrappers.py,pynteny/cli.py,pynteny/subcommands.py,pynteny/utils.py -m unittest discover tests && coverage xml
- name: Upload coverage to Codecov
uses: codecov/codecov-action@v3
with:
version: "v0.1.15"