ci: all conda deps also explicitely listed in GHA #37

	name: Test and Doc

	on:
	push:
	pull_request:

	defaults:
	run:
	shell: bash -l {0}

	permissions:
	contents: write

	jobs:

	Test:
	strategy:
	fail-fast: false
	matrix:
	os: [ubuntu-latest]
	python-version: [ "3.9", "3.10", "3.11" ]
	include:
	- os: ubuntu-latest
	# - os: windows-latest
	# - os: macos-latest
	runs-on: ${{ matrix.os }}

	steps:

	- name: 🧾 Checkout repository
	uses: actions/checkout@v4

	- name: 🛠️ Install Python ${{ matrix.python-version }} and deps with micromamba
	uses: mamba-org/setup-micromamba@v1
	with:
	init-shell: bash
	cache-environment: false
	post-cleanup: 'none'
	generate-run-shell: true
	condarc: \|
	channels:
	- conda-forge
	- bioconda
	- nodefaults
	create-args: >-
	python=${{ matrix.python-version }}
	gcc
	zlib
	bowtie2
	bwa
	samtools
	prodigal
	hmmer
	openjdk

	- name: 📦 Install package
	run: \|
	pip install .[test]
	shell: micromamba-shell {0}

	- name: ✅ Check that package functions work
	run: \|
	metator --help
	metator --version
	$(python -c "from metator import LOUVAIN_PATH; print(LOUVAIN_PATH)")/louvain -h
	java -cp $(python -c "from metator import LEIDEN_PATH; print(LEIDEN_PATH)") -h
	shell: micromamba-shell {0}

	- name: 🧪 Run tests with Python ${{ matrix.python-version }}
	run: \|
	ruff check . --select=E9,F63,F7,F82
	pytest --cov --cov-report=xml
	codecov
	shell: micromamba-shell {0}

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