Merge pull request #19 from jlab/dotplot #26

	name: integration tests & code style

	on:
	push:
	branches: [ master ]
	pull_request:
	branches: [ master ]

	jobs:
	build-linux:
	runs-on: ubuntu-latest

	steps:
	- name: Checkout Repo
	uses: actions/checkout@v3
	- name: Set up Python
	uses: actions/setup-python@v3
	- name: setup conda
	uses: conda-incubator/setup-miniconda@v2
	with:
	# This uses miniforge, rather than minicond. The primary difference
	# is that the defaults channel is not enabled at all
	miniforge-version: latest
	# These properties enable the use of mamba, which is much faster and far
	# less error prone than conda while being completely compatible with the
	# conda CLI
	use-mamba: true
	mamba-version: "*"
	environment-file: environment.yml
	python-version: "3.10"
	- name: Lint with flake8
	# Bash shells do not use ~/.profile or ~/.bashrc so these shells need to
	# be explicitely declared as shell: bash -el {0} on steps that need to be
	# properly activated (or use a default shell). This is because bash shells
	# are executed with bash --noprofile --norc -eo pipefail {0} thus ignoring
	# updated on bash profile files made by conda init bash. See Github
	# Actions Documentation and thread.
	shell: bash -el {0}
	run: \|
	flake8 phylofiller/
	- name: run python tests
	shell: bash -el {0}
	run: \|
	nosetests phylofiller --with-doctest --with-coverage
	- name: convert coverage
	shell: bash -el {0}
	run: \|
	coverage lcov
	- name: send coverage report
	uses: coverallsapp/github-action@master
	with:
	github-token: ${{ secrets.GITHUB_TOKEN }}
	path-to-lcov: "coverage.lcov"

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