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Merge pull request #11 from apriltuesday/EVA-3330 #45

Merge pull request #11 from apriltuesday/EVA-3330

Merge pull request #11 from apriltuesday/EVA-3330 #45

# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
name: Python package
on:
push:
branches: [ main ]
pull_request:
branches: [ main ]
jobs:
build:
runs-on: ubuntu-latest
strategy:
matrix:
python-version: [3.8, 3.9]
nextflow-version: [21.10.5, 22.10.7]
java-version: [11]
steps:
- uses: actions/checkout@v2
- name: Set up Java ${{ matrix.java-version }}
uses: actions/setup-java@v2
with:
distribution: 'temurin'
java-version: ${{ matrix.java-version }}
- uses: actions/checkout@v2
- name: Set up Python ${{ matrix.python-version }}
uses: actions/setup-python@v2
with:
python-version: ${{ matrix.python-version }}
- name: Install dependencies
run: |
python -m pip install --upgrade pip
pip install flake8 pytest
if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
python setup.py install
# Install Nextflow
mkdir /tmp/nextflow && cd /tmp/nextflow
wget -qO- https://github.com/nextflow-io/nextflow/releases/download/v${{ matrix.nextflow-version }}/nextflow-${{ matrix.nextflow-version }}-all | bash
echo "/tmp/nextflow" >> $GITHUB_PATH
cd -
# Build java dependencies
tests/nextflow-tests/build_tests.sh
- name: Lint with flake8
run: |
# stop the build if there are Python syntax errors or undefined names
flake8 . --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: Test with pytest
run: |
# reduce the default SSL security level to get around a misconfiguration in the Ensembl server
# https://github.com/Ensembl/ensembl-rest/issues/427
# See https://askubuntu.com/a/1233456
sed 's/DEFAULT@SECLEVEL=2/DEFAULT@SECLEVEL=1/' /usr/lib/ssl/openssl.cnf > openssl_sec1.cnf
export OPENSSL_CONF=openssl_sec1.cnf
PYTHONPATH=. pytest tests
- name: Test nextflow workflow
run: |
# Run nextflow tests
export NXF_DEFAULT_DSL=2
tests/nextflow-tests/run_tests.sh