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CI #235

Workflow file for this run

name: CI
on:
schedule:
- cron: 00 00 * * 1 # run every Monday at 00:00
push:
branches: [main]
tags: [v*]
pull_request:
branches: [main]
jobs:
build:
runs-on: ${{ matrix.os }}
timeout-minutes: 10
strategy:
fail-fast: false
max-parallel: 4
matrix:
os: [ubuntu-latest, macos-latest]
python: ['3.8', '3.10', '3.11']
test_server: [false]
include:
- os: macos-latest
python: 3.9
env:
OS: ${{ matrix.os }}
PYTHON: ${{ matrix.python }}
steps:
- uses: actions/checkout@v3
with:
fetch-depth: 0
- name: Set up Python ${{ matrix.python }}
uses: actions/setup-python@v4
with:
python-version: ${{ matrix.python }}
- name: Get pip cache dir
id: pip-cache
run: |
echo "dir=$(pip cache dir)" >> $GITHUB_OUTPUT
- name: Cache pip
uses: actions/cache@v3
with:
path: ${{ steps.pip-cache.outputs.dir }}
key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }}
- name: Install dependencies
run: |
python -m pip install --upgrade pip
pip install tox tox-gh-actions codecov
- name: Install R
if: matrix.test_server
uses: r-lib/actions/setup-r@v1
with:
r-version: 4.0.3
- name: Get R cache dir
uses: actions/cache@v3
if: matrix.test_server
with:
path: ~/.local/share/renv
key: ${{ runner.os }}-renv-${{ hashFiles('**/renv.lock') }}
- name: Install OmnipathR
if: matrix.test_server
run: |
sudo apt-get install libcurl4-openssl-dev
sudo Rscript --vanilla -e "if (!(requireNamespace('BiocManager', quietly=TRUE))) { install.packages(c('BiocManager', 'curl'), repos='https://cloud.r-project.org/') }; BiocManager::install('OmnipathR')"
Rscript --vanilla -e "packageVersion('OmnipathR')"
- name: Test
env:
PLATFORM: ${{ matrix.platform }}
run: |
tox -vv
- name: Upload coverage to Codecov
if: success()
env:
CODECOV_NAME: ${{ matrix.python }}-${{ matrix.os }}
run: |
codecov --no-color --required --flags unittests
deploy:
if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags')
needs: build
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v3
with:
fetch-depth: 0
- name: Install dependencies
run: pip install build
- name: Build a binary wheel and a source tarball
run: python -m build --sdist --wheel --outdir dist/
- name: Publish package on PyPI
uses: pypa/gh-action-pypi-publish@release/v1
with:
user: __token__
password: ${{ secrets.PYPI_PASSWORD }}
skip_existing: true
verbose: true