tests

docker #164

	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"

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