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Update to version 4.1.1 #996

Update to version 4.1.1

Update to version 4.1.1 #996

Workflow file for this run

name: pVACtools tests
on:
push:
branches: [ master, staging, hotfix ]
pull_request:
types: [opened, synchronize, edited, reopened]
branches: [ master, staging, hotfix]
jobs:
run_tests:
name: "Test pVACtools in various Python versions"
runs-on: ubuntu-latest
strategy:
matrix:
python-version: ['3.7', '3.8', '3.9', '3.10', '3.11']
steps:
- name: Maximize build space
uses: AdityaGarg8/remove-unwanted-software@v2
with:
remove-android: 'true'
remove-dotnet: 'true'
remove-haskell: 'true'
remove-codeql: 'true'
- uses: actions/checkout@v2
- name: Set up Python ${{ matrix.python-version }}
uses: actions/setup-python@v2
with:
python-version: ${{ matrix.python-version }}
- name: Install system dependencies
run: |
sudo apt-get -qq update
sudo apt-get install -y ghostscript
sudo apt-get install -y gcc
sudo apt-get install -y pandoc
pip install pypandoc==1.7.2
pip install coverage
pip install coveralls
- name: Install Python dependencies
run: |
pip install polars==0.16.18
pip install pypandoc==1.7.2
pip install "tensorflow<2.16"
pip install git+https://github.com/griffithlab/bigmhc.git#egg=bigmhc
pip install git+https://github.com/griffithlab/deepimmuno.git#egg=deepimmuno
pip install -e .
mhcflurry-downloads fetch
- name: List installed packages
run: |
pip list
- name: Run tests
env:
TEST_FLAG: 1
run: coverage run --source=pvactools.lib,pvactools.tools -m unittest discover -v -s tests
- name: Coveralls
env:
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
run: coveralls --service=github