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iskandr committed Jan 31, 2024
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53 changes: 53 additions & 0 deletions .github/workflows/tests.yml
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# 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

# TODO:
# - cache this directory $HOME/.cache/pyensembl/
# - update coveralls
name: Tests
on: [push, pull_request]

jobs:
build:
runs-on: ubuntu-latest
strategy:
fail-fast: true
matrix:
python-version: ["3.9", "3.10", "3.11"]

steps:
- name: Checkout repository
uses: actions/checkout@v3
- name: Set up Python ${{ matrix.python-version }}
uses: actions/setup-python@v3
with:
python-version: ${{ matrix.python-version }}
cache: "pip"
- name: Install dependencies
run: |
python -m pip install --upgrade pip
python -m pip install flake8 pytest pytest-cov coveralls
pip install -r requirements.txt
pip install .
- 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: Run default linting script
run: |
./lint.sh
- name: Install Ensembl data
run: |
echo "Before installing Ensembl releases" && df -h
pyensembl install --release 75 --species human --custom-mirror https://github.com/openvax/ensembl-data/releases/download/GRCh37.75/
pyensembl install --release 81 --species human --custom-mirror https://github.com/openvax/ensembl-data/releases/download/GRCh38.81/
pyensembl install --release 95 --species human --custom-mirror https://github.com/openvax/ensembl-data/releases/download/GRCh38.95/
pyensembl install --release 95 --species mouse --custom-mirror https://github.com/openvax/ensembl-data/releases/download/GRCm38.95/
echo "After installing Ensembl releases" && df -h
- name: Run unit tests
run: |
./test.sh
- name: Publish coverage to Coveralls
uses: coverallsapp/[email protected]
2 changes: 2 additions & 0 deletions README.md
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<!--
[![Build Status](https://travis-ci.org/iskandr/serializable.svg?branch=master)](https://travis-ci.org/iskandr/serializable)
-->

# serializable
Base class with serialization methods for user-defined Python objects
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