Objectify and improve structuring #227

	name: Anglerfish
	on: [push, pull_request]

	jobs:
	run_anglerfish:
	name: Anglerfish py-${{ matrix.python-version }}
	runs-on: ubuntu-latest
	strategy:
	matrix:
	python-version: [3.12]

	steps:
	# Checkout code and install miniconda + environment
	- uses: actions/checkout@v4
	- uses: mamba-org/setup-micromamba@v1
	with:
	init-shell: bash
	create-args: >-
	python=${{ matrix.python-version }}
	pip
	environment-file: environment.yml
	environment-name: anglerfish-dev

	# Install Anglerfish
	- shell: bash -l {0}
	name: Install Anglerfish
	run: \|
	python -m pip install .

	# Run anglerfish --help
	- shell: bash -l {0}
	name: Test anglerfish
	run: \|
	anglerfish --help

	# Run anglerfish using test data
	- shell: bash -l {0}
	name: Run anglerfish with test data
	run: \|
	anglerfish run -s testdata/samples.csv

	# Run anglerfish explore
	- shell: bash -l {0}
	name: Run anglerfish explore
	run: \|
	anglerfish explore -f testdata/BC18_P14351_1001.fastq.gz -o explore_output

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