test other conda setup #17

	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
	# - name: Install conda packages
	# # The `-l` is needed so conda environment activation works correctly
	# shell: bash -l {0}
	# run: \|
	# mamba install --file environment.yml

	# - name: Install dependencies
	# run: \|
	# # $CONDA is an environment variable pointing to the root of the miniconda directory
	# $CONDA/bin/conda env update --file environment.yml --name base
	- name: Lint with flake8
	run: \|
	$CONDA/bin/flake8 phylofiller/
	- name: run python tests
	run: \|
	$CONDA/bin/nosetests phylofiller --with-doctest --with-coverage
	- name: convert coverage
	run: \|
	$CONDA/bin/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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