tests

Add check for amplicon size too small. #262

	name: tests

	on:
	push:
	branches:
	- "**"
	tags:
	- "!**"
	workflow_call:

	env:
	POETRY_VERSION: 1.8.2

	jobs:
	Tests:
	runs-on: ubuntu-latest
	strategy:
	matrix:
	PYTHON_VERSION: ["3.11", "3.12"]
	steps:
	- uses: actions/checkout@v4

	- name: Set up Python ${{ matrix.PYTHON_VERSION }}
	uses: actions/setup-python@v5
	with:
	python-version: ${{ matrix.PYTHON_VERSION }}

	- name: Install and configure Poetry
	uses: snok/install-poetry@v1
	with:
	version: ${{env.POETRY_VERSION}}
	installer-parallel: true

	- name: Set up miniconda
	uses: conda-incubator/setup-miniconda@v3
	with:
	miniforge-version: latest
	channels: bioconda,conda-forge
	activate-environment: prymer
	environment-file: prymer.yml
	channel-priority: true
	auto-update-conda: true
	auto-activate-base: false
	python-version: ${{ matrix.PYTHON_VERSION }}

	- name: Install the project's dependencies
	shell: bash -el {0}
	run: poetry install

	- name: Test the codebase
	shell: bash -el {0}
	run: poetry run pytest

	- name: Upload coverage reports to Codecov
	uses: codecov/[email protected]
	with:
	token: ${{ secrets.CODECOV_TOKEN }}

	- name: Test building the documentation
	shell: bash -el {0}
	run: poetry run mkdocs build --strict

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