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Add github actions for tests and pre-commit #8

Add github actions for tests and pre-commit

Add github actions for tests and pre-commit #8

Workflow file for this run

# 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 .
python -m pip install pre-commit
- name: Run pre-commit hooks
run: |
python pre-commit run --all-files
- name: Create tasks needed for testing
run: |
python scripts/tasks_retrival/gene2gene_task_creation.py --allow-downloads True
python scripts/tasks_retrival/Genecorpus_tasks_creation.py --allow-downloads True
python scripts/tasks_retrival/HLA_task_creation.py --allow-downloads True
python scripts/tasks_retrival/HPA_tasks_creation.py --allow-downloads True
python scripts/tasks_retrival/humantfs_task_creation.py --allow-downloads True
python scripts/tasks_retrival/Reactome_tasks_creation.py --use-local-files False
- name: Test with pytest
run: |
python -m pytest -v --durations=40 --cov=gene_benchmark--cov-fail-under=70 gene_benchmark