Fix batch run dir #24

	# This workflow will install Python dependencies, run tests and lint with a single version of Python
	# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python

	name: CI testing

	on:
	pull_request:
	branches: [ "master", "dev" ]

	permissions:
	contents: read

	jobs:
	build:

	runs-on: ubuntu-latest
	defaults:
	run:
	shell: bash -el {0}
	steps:
	- uses: actions/checkout@v4
	- uses: conda-incubator/setup-miniconda@v3
	with:
	python-version: 3.8
	mamba-version: "*"
	channels: conda-forge,bioconda,defaults
	channel-priority: true

	- name: install dependancies
	run: \|
	wget https://raw.githubusercontent.com/jodyphelan/TBProfiler/dev/conda/linux-latest.txt
	conda create --name test --file linux-latest.txt


	- name: Install dependencies
	run: \|
	conda activate test
	pip install --force-reinstall git+https://github.com/jodyphelan/pathogen-profiler.git@dev
	pip install --force-reinstall .
	- name: Run tests
	run: \|
	cd tests
	mamba install pytest -y
	pytest -x .

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