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push-pr_workflow.yml
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name: Python CI
on: [push, pull_request]
jobs:
Changelog:
name: CHANGELOG.md updated
runs-on: ubuntu-latest
if: github.event_name == 'pull_request'
steps:
- name: Checkout code
uses: actions/checkout@v4
with:
fetch-depth: 0 # Checkout the whole history, in case the target is way far behind
- name: Check if target branch has been merged
run: |
if git merge-base --is-ancestor ${{ github.event.pull_request.base.sha }} ${{ github.sha }}; then
echo "Target branch has been merged into the source branch."
else
echo "Target branch has not been merged into the source branch. Please merge in target first."
exit 1
fi
- name: Check that CHANGELOG has been updated
run: |
# If this step fails, this means you haven't updated the CHANGELOG.md file with notes on your contribution.
if git diff --name-only ${{ github.event.pull_request.base.sha }} ${{ github.sha }} | grep -q '^CHANGELOG.md$'; then
echo "Thanks for helping keep our CHANGELOG up-to-date!"
else
echo "Please update the CHANGELOG.md file with notes on your contribution."
exit 1
fi
Lint:
runs-on: ubuntu-latest
env:
MAX_LINE_LENGTH: 127
MAX_COMPLEXITY: 15
steps:
- uses: actions/checkout@v4
- name: Set up Python
uses: actions/setup-python@v5
with:
python-version: '3.x'
- name: Check cache
uses: actions/cache@v4
with:
path: ~/.cache/pip
key: ${{ hashFiles('requirements/release.txt') }}-${{ hashFiles('requirements/dev.txt') }}
- name: Install dependencies
run: |
python3 -m pip install --upgrade pip
if [ -f requirements.txt ]; then pip install --upgrade -r requirements.txt; fi
pip3 install --upgrade -r requirements/dev.txt
- 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 --max-complexity=$MAX_COMPLEXITY --statistics --max-line-length=$MAX_LINE_LENGTH
- name: Lint with isort
run: |
python3 -m isort --check --line-length $MAX_LINE_LENGTH merlin
python3 -m isort --check --line-length $MAX_LINE_LENGTH tests
python3 -m isort --check --line-length $MAX_LINE_LENGTH *.py
- name: Lint with Black
run: |
python3 -m black --check --line-length $MAX_LINE_LENGTH --target-version py38 merlin
python3 -m black --check --line-length $MAX_LINE_LENGTH --target-version py38 tests
python3 -m black --check --line-length $MAX_LINE_LENGTH --target-version py38 *.py
- name: Lint with PyLint
run: |
python3 -m pylint merlin --rcfile=setup.cfg --exit-zero
python3 -m pylint tests --rcfile=setup.cfg --exit-zero
Local-test-suite:
runs-on: ubuntu-latest
env:
GO_VERSION: 1.18.1
SINGULARITY_VERSION: 3.9.9
OS: linux
ARCH: amd64
strategy:
matrix:
python-version: ['3.7', '3.8', '3.9', '3.10', '3.11']
steps:
- uses: actions/checkout@v4
- name: Set up Python ${{ matrix.python-version }}
uses: actions/setup-python@v5
with:
python-version: ${{ matrix.python-version }}
- name: Check cache
uses: actions/cache@v4
with:
path: ${{ env.pythonLocation }}
key: ${{ env.pythonLocation }}-${{ hashFiles('requirements/release.txt') }}-${{ hashFiles('requirements/dev.txt') }}
- name: Install dependencies
run: |
python3 -m pip install --upgrade pip
if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
pip3 install -r requirements/dev.txt
- name: Install singularity
run: |
sudo apt-get update && sudo apt-get install -y \
build-essential \
libssl-dev \
uuid-dev \
libgpgme11-dev \
squashfs-tools \
libseccomp-dev \
pkg-config
wget https://go.dev/dl/go$GO_VERSION.$OS-$ARCH.tar.gz
sudo tar -C /usr/local -xzf go$GO_VERSION.$OS-$ARCH.tar.gz
rm go$GO_VERSION.$OS-$ARCH.tar.gz
export PATH=$PATH:/usr/local/go/bin
wget https://github.com/sylabs/singularity/releases/download/v$SINGULARITY_VERSION/singularity-ce-$SINGULARITY_VERSION.tar.gz
tar -xzf singularity-ce-$SINGULARITY_VERSION.tar.gz
cd singularity-ce-$SINGULARITY_VERSION
./mconfig && \
make -C ./builddir && \
sudo make -C ./builddir install
- name: Install merlin to run unit tests
run: |
pip3 install -e .
merlin config
- name: Install CLI task dependencies generated from the 'feature demo' workflow
run: |
merlin example feature_demo
pip3 install -r feature_demo/requirements.txt
- name: Run pytest over unit test suite
run: |
python3 -m pytest -v --order-scope=module tests/unit/
- name: Run integration test suite for local tests
run: |
python3 tests/integration/run_tests.py --verbose --local
Integration-tests:
runs-on: ubuntu-latest
env:
GO_VERSION: 1.18.1
SINGULARITY_VERSION: 3.9.9
OS: linux
ARCH: amd64
strategy:
matrix:
python-version: ['3.7', '3.8', '3.9', '3.10', '3.11']
steps:
- uses: actions/checkout@v4
- name: Set up Python ${{ matrix.python-version }}
uses: actions/setup-python@v5
with:
python-version: ${{ matrix.python-version }}
- name: Check cache
uses: actions/cache@v4
with:
path: ${{ env.pythonLocation }}
key: ${{ env.pythonLocation }}-${{ hashFiles('requirements/release.txt') }}-${{ hashFiles('requirements/dev.txt') }}
- name: Install dependencies
run: |
python3 -m pip install --upgrade pip
if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
pip3 install -r requirements/dev.txt
- name: Install merlin
run: |
pip3 install -e .
merlin config
- name: Install singularity
run: |
sudo apt-get update && sudo apt-get install -y \
build-essential \
libssl-dev \
uuid-dev \
libgpgme11-dev \
squashfs-tools \
libseccomp-dev \
pkg-config
wget https://go.dev/dl/go$GO_VERSION.$OS-$ARCH.tar.gz
sudo tar -C /usr/local -xzf go$GO_VERSION.$OS-$ARCH.tar.gz
rm go$GO_VERSION.$OS-$ARCH.tar.gz
export PATH=$PATH:/usr/local/go/bin
wget https://github.com/sylabs/singularity/releases/download/v$SINGULARITY_VERSION/singularity-ce-$SINGULARITY_VERSION.tar.gz
tar -xzf singularity-ce-$SINGULARITY_VERSION.tar.gz
cd singularity-ce-$SINGULARITY_VERSION
./mconfig && \
make -C ./builddir && \
sudo make -C ./builddir install
- name: Install CLI task dependencies generated from the 'feature demo' workflow
run: |
merlin example feature_demo
pip3 install -r feature_demo/requirements.txt
# TODO remove the --ignore statement once those tests are fixed
- name: Run integration test suite for distributed tests
run: |
pytest --ignore tests/integration/test_celeryadapter.py tests/integration/
Distributed-test-suite:
runs-on: ubuntu-latest
services:
# rabbitmq:
# image: rabbitmq:latest
# ports:
# - 5672:5672
# options: --health-cmd "rabbitmqctl node_health_check" --health-interval 10s --health-timeout 5s --health-retries 5
# Label used to access the service container
redis:
# Docker Hub image
image: redis
# Set health checks to wait until redis has started
options: >-
--health-cmd "redis-cli ping"
--health-interval 10s
--health-timeout 5s
--health-retries 5
ports:
- 6379:6379
strategy:
matrix:
python-version: ['3.7', '3.8', '3.9', '3.10', '3.11']
steps:
- uses: actions/checkout@v2
- name: Set up Python ${{ matrix.python-version }}
uses: actions/setup-python@v2
with:
python-version: ${{ matrix.python-version }}
- name: Check cache
uses: actions/cache@v2
with:
path: ${{ env.pythonLocation }}
key: ${{ env.pythonLocation }}-${{ hashFiles('requirements/release.txt') }}-${{ hashFiles('requirements/dev.txt') }}
- name: Install dependencies
run: |
python3 -m pip install --upgrade pip
if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
pip3 install -r requirements/dev.txt
- name: Install merlin and setup redis as the broker
run: |
pip3 install -e .
merlin config --broker redis
- name: Install CLI task dependencies generated from the 'feature demo' workflow
run: |
merlin example feature_demo
pip3 install -r feature_demo/requirements.txt
- name: Run integration test suite for distributed tests
env:
REDIS_HOST: redis
REDIS_PORT: 6379
run: |
python3 tests/integration/run_tests.py --verbose --distributed
# - name: Setup rabbitmq config
# run: |
# merlin config --test rabbitmq
# - name: Run integration test suite for rabbitmq
# env:
# AMQP_URL: amqp://localhost:${{ job.services.rabbitmq.ports[5672] }}
# RABBITMQ_USER: Jimmy_Space
# RABBITMQ_PASS: Alexander_Rules
# ports:
# - ${{ job.services.rabbitmq.ports['5672'] }}
# run: |
# python3 tests/integration/run_tests.py --verbose --ids 31 32