chore: remove legacy non-Snakemake script and align docs #146

	name: MutationScan CI

	on:
	push:
	branches: [ main, master ]
	pull_request:
	branches: [ main, master ]

	jobs:
	build-and-test:
	runs-on: ubuntu-latest

	# Crucial: forces every step to use the Conda environment
	defaults:
	run:
	shell: bash -el {0}

	steps:
	- name: Checkout Code
	uses: actions/checkout@v3

	- name: Set up Conda Environment
	uses: conda-incubator/setup-miniconda@v3
	with:
	activate-environment: mutationscan
	environment-file: environment.yml
	auto-activate: true
	miniforge-variant: Miniforge3
	use-mamba: true

	- name: Install Package
	run: \|
	# Installs MutationScan so the core logic is importable by pytest
	pip install -e .

	- name: Run Core Unit Tests
	run: \|
	# Using python -m pytest ensures it uses the Conda environment's pytest
	python -m pytest tests/unit/ -v

	- name: Validate Snakemake DAG (Dry-Run)
	run: \|
	# Override the input_csv requirement by forcing the local_genomes route.
	# This proves the DAG compiles without needing actual biological data files.
	snakemake -n --cores 1 --config local_genomes="data/genomes"

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