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move to github actions
switch from travis as it creates issues.
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‎.github/workflows/docs.yml‎

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name: Documentation Checks
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on: [push]
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jobs:
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spell_check:
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strategy:
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max-parallel: 4
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matrix:
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os: [ubuntu-latest]
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runs-on: ${{ matrix.os }}
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steps:
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- name: Spell check install
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run: curl -L https://git.io/misspell | bash
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- name: Spell check docs
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run: bin/misspell -error docs/*
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code_docs:
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strategy:
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max-parallel: 4
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matrix:
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os: [ubuntu-latest]
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python-version: [3.7]
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runs-on: ${{ matrix.os }}
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steps:
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- uses: actions/checkout@v1
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v1
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with:
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python-version: ${{ matrix.python-version }}
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- name: Install dependencies
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run: |
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python -m pip install --upgrade pip
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pip install tox tox-gh-actions
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- name: Run docs tests
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run: tox -e docs
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‎.github/workflows/int.yml‎

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name: Integration Tests
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on: [pull_request]
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jobs:
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build:
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strategy:
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max-parallel: 4
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matrix:
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os: [ubuntu-latest]
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python-version: [3.7]
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runs-on: ${{ matrix.os }}
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name: Integration Tests
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steps:
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- uses: actions/checkout@v1
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v1
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with:
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python-version: ${{ matrix.python-version }}
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- name: Install requirements
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run: |
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wget https://github.com/openshift/source-to-image/releases/download/v1.2.0/source-to-image-v1.2.0-2a579ecd-linux-amd64.tar.gz
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tar -xvf source-to-image-v1.2.0-2a579ecd-linux-amd64.tar.gz
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sudo cp s2i /usr/local/bin
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pip install aiohttp
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pip install requests
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- name: Build image
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run: |
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s2i build . centos/python-36-centos7 cscfi/beacon-python
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- name: Start Services
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run: |
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pushd deploy/test
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docker-compose up -d
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sleep 10
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docker exec test_beacon_1 beacon_init data/ALL.chrMT.phase3_callmom-v0_4.20130502.genotypes.vcf.gz data/example_metadata.json
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docker exec test_beacon_1 beacon_init data/ALL.chrMT.phase3_callmom-v0_4.20130502.genotypes.vcf.gz /exdata/example_metadata_registered.json
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docker exec test_beacon_1 beacon_init data/ALL.chrMT.phase3_callmom-v0_4.20130502.genotypes.vcf.gz /exdata/example_metadata_controlled.json
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docker exec test_beacon_1 beacon_init data/ALL.chrMT.phase3_callmom-v0_4.20130502.genotypes.vcf.gz /exdata/example_metadata_controlled1.json
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- name: Run Integration test
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run: |
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pushd deploy/test
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python run_tests.py
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- name: Collect logs from docker
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if: ${{ failure() }}
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run: cd deploy && docker-compose logs --no-color -t > ../tests/dockerlogs || true
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- name: Persist log files
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if: ${{ failure() }}
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uses: actions/upload-artifact@v1
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with:
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name: test_debugging_help
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path: tests

‎.github/workflows/publish.yml‎

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name: Publish Docker image
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on:
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release:
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types: [published]
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push:
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branches: [master]
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jobs:
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push_to_registry:
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name: Push Beacon Docker image to Docker Hub
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v1
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- name: Login to DockerHub Registry
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run: echo ${{ secrets.DOCKER_PASSWORD }} | docker login -u ${{ secrets.DOCKER_USERNAME }} --password-stdin
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- name: Get the version
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id: vars
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run: echo ::set-output name=tag::$(echo ${GITHUB_REF:10})
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- name: Build the tagged Docker image
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run: docker build . --file Dockerfile --tag cscfi/beacon-python:${{steps.vars.outputs.tag}}
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- name: Push the tagged Docker image
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run: docker push cscfi/beacon-python:${{steps.vars.outputs.tag}}
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- name: Build the latest Docker image
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run: docker build . --file Dockerfile --tag cscfi/beacon-python:latest
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- name: Push the latest Docker image
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run: docker push cscfi/beacon-python:latest
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push_data_to_registry:
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name: Push Dataloader Docker image to Docker Hub
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v1
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- name: Login to DockerHub Registry
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run: echo ${{ secrets.DOCKER_PASSWORD }} | docker login -u ${{ secrets.DOCKER_USERNAME }} --password-stdin
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- name: Get the version
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id: vars
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run: echo ::set-output name=tag::$(echo ${GITHUB_REF:10})
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- name: Build the tagged Docker image
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run: |
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pushd deploy/test
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docker build . --file Dockerfile --tag cscfi/beacon-dataloader:${{steps.vars.outputs.tag}}
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- name: Push the tagged Docker image
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run: docker push cscfi/beacon-dataloader:${{steps.vars.outputs.tag}}
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- name: Build the latest Docker image
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run: |
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pushd deploy/test
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docker build . --file Dockerfile --tag cscfi/beacon-dataloader:latest
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- name: Push the latest Docker image
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run: docker push cscfi/beacon-dataloader:latest

‎.github/workflows/style.yml‎

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name: Python style check
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on: [push]
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jobs:
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style_check:
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strategy:
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max-parallel: 4
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matrix:
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os: [ubuntu-latest]
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python-version: [3.6, 3.7]
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runs-on: ${{ matrix.os }}
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steps:
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- uses: actions/checkout@v1
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v1
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with:
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python-version: ${{ matrix.python-version }}
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- name: Install dependencies
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run: |
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python -m pip install --upgrade pip
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pip install tox tox-gh-actions
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- name: Test flake8 syntax with tox
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run: tox -e flake8
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- name: Do bandit static check with tox
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run: tox -e bandit

‎.github/workflows/unit.yml‎

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name: Python Unit Tests
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on: [push]
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jobs:
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unit_test:
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strategy:
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max-parallel: 4
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matrix:
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os: [ubuntu-latest]
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python-version: [3.6, 3.7]
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runs-on: ${{ matrix.os }}
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steps:
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- uses: actions/checkout@v1
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v1
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with:
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python-version: ${{ matrix.python-version }}
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- name: Install libcurl-devel
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run: sudo apt-get install libcurl4-openssl-dev
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- name: Install dependencies
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run: |
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python -m pip install --upgrade pip
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pip install tox tox-gh-actions
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- name: Run unit tests
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env:
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COVERALLS_REPO_TOKEN: ${{ secrets.COVERALLS_REPO_TOKEN }}
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run: tox -e unit_tests

‎.travis.yml‎

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‎README.md‎

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## beacon-python - Python-based Beacon API Web Server
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[![Build Status](https://travis-ci.org/CSCfi/beacon-python.svg?branch=master)](https://travis-ci.org/CSCfi/beacon-python)
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[![Coverage Status](https://coveralls.io/repos/github/CSCfi/beacon-python/badge.svg?branch=master)](https://coveralls.io/github/CSCfi/beacon-python?branch=master)
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![Integration Tests](https://github.com/CSCfi/beacon-python/workflows/Integration%20Tests/badge.svg)
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![Python Unit Tests](https://github.com/CSCfi/beacon-python/workflows/Python%20Unit%20Tests/badge.svg)
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[![Coverage Status](https://coveralls.io/repos/github/CSCfi/beacon-python/badge.svg?branch=HEAD)](https://coveralls.io/github/CSCfi/beacon-python?branch=HEAD)
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[![Documentation Status](https://readthedocs.org/projects/beacon-python/badge/?version=latest)](https://beacon-python.readthedocs.io/en/latest/?badge=latest)
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[![Docker Image](https://images.microbadger.com/badges/image/cscfi/beacon-python.svg)](https://microbadger.com/images/cscfi/beacon-python)
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Documentation: https://beacon-python.readthedocs.io
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‎tests/coveralls.py‎

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# Solution provided by https://stackoverflow.com/questions/32757765/conditional-commands-in-tox-tox-travis-ci-and-coveralls
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if __name__ == '__main__':
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if 'TRAVIS' in os.environ:
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if 'COVERALLS_REPO_TOKEN' in os.environ:
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rc = call('coveralls')
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sys.stdout.write("Coveralls report from TRAVIS CI.\n")
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# raise SystemExit(rc)

‎tox.ini‎

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flake8-docstrings
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commands = flake8 .
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[testenv]
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[testenv:unit_tests]
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setenv =
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CONFIG_FILE = {toxinidir}/tests/test.ini
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passenv = TRAVIS TRAVIS_*
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passenv =
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TRAVIS TRAVIS_*
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COVERALLS_REPO_TOKEN
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deps =
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.[test]
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-rrequirements.txt
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# Stop after first failure
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commands = py.test -x --cov=beacon_api tests/ --cov-fail-under=80
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python {toxinidir}/tests/coveralls.py
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[travis]
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unignore_outcomes = True
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[gh-actions]
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python =
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3.6: py36
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3.7: py37
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3.6: flake8, unit_tests, docs, bandit
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3.7: flake8, unit_tests, docs, bandit

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