Refactor hub.smk and create_hub.py to use "method" instead of "pileup… #764

	name: Python package

	on: [push]

	jobs:
	Build_and_Test:

	runs-on: ubuntu-latest
	strategy:
	matrix:
	python-version: ["3.12"]

	steps:
	- uses: actions/checkout@v2
	- uses: eWaterCycle/setup-apptainer@v2
	with:
	apptainer-version: 1.1.2
	- name: Add singularity hub remote
	run: \|
	apptainer remote add --no-login SylabsCloud cloud.sylabs.io
	apptainer remote use SylabsCloud
	- name: Set up Python ${{ matrix.python-version }}
	uses: actions/setup-python@v2
	with:
	python-version: ${{ matrix.python-version }}
	- name: Set up conda using miniforge
	uses: conda-incubator/setup-miniconda@v3
	with:
	environment-file: environment_minimal.yml
	miniforge-version: latest
	miniforge-variant: Mambaforge
	python-version: ${{ matrix.python-version }}
	use-mamba: true
	- name: Install package dependencies
	run: \|
	mamba env update -n test -f environment_minimal.yml
	shell: bash -l {0}
	- name: Install testing dependencies
	run: \|
	mamba env update -n test -f testing.yml
	shell: bash -l {0}
	- name: Install the package
	shell: bash -l {0}
	run: \|
	pip install .
	- name: Conda list
	shell: pwsh
	run: mamba list
	- name: Test design works
	shell: pwsh
	run: \|
	seqnado-design chip tests/data/fastq/CTCF*.fastq.gz
	- name: Test with pytest
	shell: pwsh
	run: \|
	pytest -vv -s --cov=./ --cov-report=xml --cores 4
	- name: Upload coverage reports to Codecov
	uses: codecov/[email protected]
	with:
	token: ${{ secrets.CODECOV_TOKEN }}
	slug: alsmith151/SeqNado

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