remove `defaults` from `conda` envs (#52) #92

	name: Run tests

	on:
	push:
	branches:
	- main
	pull_request:
	branches:
	- main

	jobs:
	test:
	name: Run tests
	runs-on: ubuntu-latest
	timeout-minutes: 60
	steps:
	- name: checkout
	uses: actions/checkout@v4
	with:
	lfs: true

	- name: build conda environment
	uses: conda-incubator/setup-miniconda@v3
	with:
	activate-environment: seqneut-pipeline
	environment-file: environment.yml
	auto-activate-base: false
	auto-update-conda: true
	channel-priority: strict

	- name: lint with ruff
	# NOTE: must specify the shell so that conda init updates bashrc see:
	# https://github.com/conda-incubator/setup-miniconda#IMPORTANT
	shell: bash -el {0}
	run: ruff check .

	- name: check code format with black
	shell: bash -el {0}
	run: black --check .

	- name: check snakemake files format with snakefmt
	shell: bash -el {0}
	run: snakefmt --check .

	- name: lint snakemake files with snakemake --lint
	shell: bash -el {0}
	run: cd test_example && snakemake --lint && cd ..

	- name: run pipeline on test example
	shell: bash -el {0}
	run: >
	rm -rf docs
	&& cd test_example
	&& rm -rf results
	&& snakemake --software-deployment-method conda -j 2
	&& cd ..

	- name: test titers as expected
	shell: bash -el {0}
	run: cd test_example && python test_titers_as_expected.py && cd ..

	- name: upload results in case of error
	uses: actions/upload-artifact@v4
	if: failure()
	with:
	name: results
	path: test_example/results
	retention-days: 7

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