CI/CD

feat: amino acid translation by nextclade #36

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

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

	jobs:
	build:
	runs-on: ubuntu-latest
	strategy:
	fail-fast: true
	matrix:
	python-version: ["3.10"]
	poetry-version: ["1.8.3"]

	steps:
	- name: Checkout Code
	uses: actions/checkout@v4
	with:
	fetch-depth: 0

	- name: Set up Conda
	uses: conda-incubator/setup-miniconda@v2
	with:
	auto-update-conda: true
	python-version: ${{ matrix.python-version }}
	environment-file: environment.yml
	activate-environment: myenv

	- name: Install Poetry
	uses: snok/install-poetry@v1
	with:
	virtualenvs-create: true
	virtualenvs-in-project: true
	version: ${{ matrix.poetry-version }}

	- name: Cache dependencies
	id: cache-deps
	uses: actions/cache@v2
	with:
	path: .venv
	key: pydeps-${{ hashFiles('**/poetry.lock') }}

	- name: Activate Conda environment
	shell: bash -l {0}
	run: \|
	source $(conda info --base)/etc/profile.d/conda.sh
	conda activate myenv

	- name: Set Python version for Poetry
	run: poetry env use $(which python)

	- name: Install the dependencies
	run: poetry install --no-interaction --no-root --with dev
	if: steps.cache-deps.outputs.cache-hit != 'true'

	- name: Install the module
	run: poetry install --with dev --no-interaction

	- name: Run unit tests
	run: poetry run pytest

	- name: Run Ruff
	run: poetry run ruff check .

	- name: Run interrogate
	run: poetry run interrogate src

	- name: Run Pyright (type checking)
	run: poetry run pyright

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