Bump onecodex and scikit-bio versions #26

	name: test
	on:
	push:
	branches:
	- master
	pull_request:

	jobs:
	integration:
	runs-on: ubuntu-latest
	steps:
	- uses: actions/checkout@v3

	- name: Set up Python 3.11
	uses: actions/setup-python@v4
	with:
	python-version: 3.11

	- name: Install Python test dependencies in a venv
	run: \|
	python3 -m venv venv
	. venv/bin/activate
	pip install -q -U pip
	pip install --progress-bar=off pytest

	- name: Install diff-pdf
	run: \|
	sudo apt-get update
	sudo apt-get install -y --no-install-recommends \
	libpoppler-glib-dev \
	libwxgtk3.0-gtk3-dev

	git clone https://github.com/vslavik/diff-pdf.git
	# v0.5.1
	cd diff-pdf && git checkout 150de72f7eebf8c9d69ee79b3cd28d9e7d7793f5
	./bootstrap
	./configure
	make
	sudo mv diff-pdf /usr/bin/diff-pdf

	- name: Docker build
	run: \|
	docker build -t docker-onecodex-notebook .

	- name: Run lint checks & tests
	run: \|
	sudo chmod 777 -R .
	. venv/bin/activate
	py.test -vv test/

	- name: Upload Report PDFs
	if: always()
	uses: actions/upload-artifact@v2
	with:
	name: example reports
	path: diff.pdf

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