Update performance tables scripts (#39) #201

	# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
	# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python

	name: Python package

	on:
	push:
	branches: [ "main" ]
	pull_request:
	branches: [ "main" ]

	jobs:
	build:

	runs-on: ubuntu-latest
	strategy:
	fail-fast: false
	matrix:
	python-version: ["3.10", "3.11", "3.12"]

	steps:
	- uses: actions/checkout@v4
	- name: Set up Python ${{ matrix.python-version }}
	uses: actions/setup-python@v3
	with:
	python-version: ${{ matrix.python-version }}
	- name: Install packagge
	run: \|
	python -m pip install --upgrade pip pytest pytest-cov
	python -m pip install -e .

	- name: Create tasks needed for testing
	run: \|
	python scripts/tasks_retrieval/gene2gene_task_creation.py --allow-downloads True
	python scripts/tasks_retrieval/Genecorpus_tasks_creation.py --allow-downloads True
	python scripts/tasks_retrieval/HLA_task_creation.py --allow-downloads True
	python scripts/tasks_retrieval/HPA_tasks_creation.py --allow-downloads True
	python scripts/tasks_retrieval/humantfs_task_creation.py --allow-downloads True
	python scripts/tasks_retrieval/Reactome_tasks_creation.py --allow-downloads True
	python scripts/tasks_retrieval/uniprot_keyword_tasks_creation.py --allow-downloads True

	- name: Test with pytest
	run: \|
	python -m pytest -v --durations=40 --cov=gene_benchmark--cov-fail-under=70 gene_benchmark

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