Bump pypa/gh-action-pypi-publish from 1.8.12 to 1.9.0 #112

	name: Python package

	on: [ push , pull_request]

	jobs:
	build:

	runs-on: ubuntu-latest
	strategy:
	matrix:
	python-version: ["3.8", "3.9", "3.10", "3.11"]

	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 dependencies
	run: \|
	python -m pip install --upgrade pip
	pip install flake8 pytest
	pip install .
	- name: Lint with flake8
	run: \|
	# stop the build if there are Python syntax errors or undefined names
	flake8 . --exit-zero --count --select=E9,F63,F7,F82 --show-source --statistics
	# exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
	flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
	- name: Download test omamer db file
	run: \|
	wget -O Homininae.h5 'https://omabrowser.org/All/Homininae.h5'
	- name: Download sample fasta file
	run: \|
	wget -O human_sample.fa 'https://rest.uniprot.org/uniprotkb/search?format=fasta&query=%28%28proteome%3AUP000005640%29%29&size=200'
	head -n 10 human_sample.fa
	- name: Test
	run: \|
	ls -l
	omamer search --db Homininae.h5 --query human_sample.fa --out human_sample.omamer
	cat human_sample.omamer

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