Fix mehari cli flags to get consistent transcript annotation. #41

	name: CI

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

	jobs:
	cancel-previous:
	runs-on: ubuntu-latest
	if: github.ref != 'refs/heads/main'
	steps:
	- uses: khan/[email protected]
	with:
	workflows: "main.yml"
	env:
	GITHUB_TOKEN: '${{ secrets.GITHUB_TOKEN }}'

	testing-R:
	runs-on: ubuntu-latest
	strategy:
	matrix:
	python-version:
	- "3.12"
	steps:
	- name: Checkout repository
	uses: actions/checkout@v4

	- name: Set up Miniforge
	uses: conda-incubator/setup-miniconda@v3
	with:
	activate-environment: stemcnv-check-general-R
	channels: conda-forge,bioconda
	environment-file: stemcnv_check/envs/general-R.yaml
	miniforge-version: latest
	auto-activate-base: false
	- name: Run tests
	shell: bash -l {0}
	run: Rscript -e "testthat::test_local()"
	# env:
	# DIFF_MAIN: ${{ github.event_name == 'pull_request' }}
	# DIFF_LAST_COMMIT: ${{ github.ref == 'refs/heads/main' }}

	testing-py:
	runs-on: ubuntu-latest
	strategy:
	matrix:
	python-version:
	- "3.12"
	steps:
	- name: Checkout repository
	uses: actions/checkout@v4

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

	- name: Install dependencies
	run: pip install .[test]

	- run: pytest

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