maintenance: h5py.default_file_mode is deprecated #9

	# name: qiita-files CI

	on:
	push:
	branches: [ dev ]
	pull_request:

	jobs:
	# derived from https://github.com/actions/example-services/blob/master/.github/workflows/postgres-service.yml
	main:
	runs-on: ubuntu-latest

	steps:
	# Downloads a copy of the code in your repository before running CI tests
	- name: Check out repository code
	uses: actions/checkout@v2

	- name: Setup for conda
	uses: conda-incubator/setup-miniconda@v2
	with:
	auto-update-conda: true
	python-version: 3.9

	- name: Basic dependencies install
	shell: bash -l {0}
	run: \|
	conda create --yes -n qiita-files python=3.9 h5py pandas scipy numpy
	conda activate qiita-files
	pip install .
	pip install sphinx sphinx-bootstrap-theme nose-timer codecov Click

	- name: Main tests
	shell: bash -l {0}
	run: \|
	conda activate qiita-files
	nosetests --with-doctest --with-coverage --cover-package=qiita_files

	lint:
	runs-on: ubuntu-latest
	steps:
	- name: flake8
	uses: actions/setup-python@v2
	with:
	python-version: 3.9
	- name: install dependencies
	run: python -m pip install --upgrade pip
	- name: Check out repository code
	uses: actions/checkout@v2
	- name: lint
	run: \|
	pip install -q flake8
	flake8 qiita_files setup.py

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