refactor: env and secrets + test: front-to-end #124

	# This pipeline checks whether the package
	# installs properly, passes unit tests and whether
	# the code formatting is right.
	name: CI/CD (Poetry + Conda)

	on:
	push:
	branches: [ main ] # Or your main branch name
	pull_request:
	branches: [ main ]

	jobs:
	build:
	runs-on: ubuntu-latest

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

	- name: Run black formatting check
	uses: psf/black@stable

	- name: Set up Conda
	uses: conda-incubator/setup-miniconda@v2
	with:
	auto-update-conda: true
	channels: conda-forge, bioconda
	environment-file: environment.yml
	activate-environment: sr2silo

	- name: Install Poetry
	run: \|
	source $(conda info --base)/etc/profile.d/conda.sh
	conda activate sr2silo
	conda install -c conda-forge poetry

	- name: Install the module
	run: \|
	source $(conda info --base)/etc/profile.d/conda.sh
	conda activate sr2silo
	poetry install --with dev --no-interaction

	- name: Run unit tests
	run: \|
	source $(conda info --base)/etc/profile.d/conda.sh
	conda activate sr2silo
	poetry run pytest

	- name: Run Ruff
	run: \|
	source $(conda info --base)/etc/profile.d/conda.sh
	conda activate sr2silo
	poetry run ruff check .

	- name: Run interrogate
	run: \|
	source $(conda info --base)/etc/profile.d/conda.sh
	conda activate sr2silo
	poetry run interrogate src

	- name: Run Pyright
	run: \|
	source $(conda info --base)/etc/profile.d/conda.sh
	conda activate sr2silo
	poetry run pyright

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